B is identifiedfor a Jahn–Teller reconstructed V1(5–9) monovacancyin freestanding graphene. For graphene with stable ripples inducedby a compressive strain of 5%, a bond reconstruction produces a V1(55–66) structure for the monovacancy, which is localizedat the saddle points of the ripple. The sizeable local distortioninduced by reconstruction modifies both the geometric and electronicproperties of rippled graphene and quenches the magnetic moment ofthe vacancy due to the sp3 hybridization of the centralatom. The nonmagnetic V1(55–66) structure is foundto be stable on rippled structures, with the formation energy ∼2.3eV lower than that of the metastable distorted V1(5–9)structures localized at sites other than the saddle points. The electronicground state of distorted V1(5–9) corresponds toa wide range of fractional magnetic moments (0.50–1.25 μB). The computed relative stabilities and the electronic andmagnetic properties of the V1(5–9) structures arefound to be closely related to their local distortions. This analysisof the fundamental properties of defective graphene under compressionsuggests a number of strategies for generating regular defect patternswith tuneable magnetic and electronic properties and may, therefore,be used as a novel technique to achieve more precise control of grapheneelectronic structure for various application scenarios such as transistors,strain sensors, and directed chemisorption.The electronic and spintronic properties of the monovacanciesinfreestanding and isotopically compressed graphene are investigatedusing hybrid exchange density functional perturbation theory. Whenthe effects of electronic self-interaction are taken into account,an integer magnetic moment of 2 μ By locally breaking the bipartite symmetryof the graphene lattice, defects may facilitate a precise tuning ofthe electronic and spintronic functionalities of graphene.12Graphene is well knownfor its high carrier mobility,16 and theoretically.20 The monovacancy is generated by removing a carbon atom from thepristine graphene lattice via irradiation of focused electron or protonbeams.16 Following the generation of the monovacancy withthree dangling bonds and C3 symmetry,a symmetry breaking Jahn–Teller reconstruction (JTR) is observed,15 leading to a pentagon-distorted nonagon V1(5–9) structure with C2 symmetry. The monovacancy disrupts the delocalized π bandand may lead to unpaired electron density that potentially resultsin a net magnetization of graphene,19 making ita potential candidate for use in spintronic devices. However, thereare debates over the exact magnetic moment of monovacancy,25 and Rodrigo et al.25 arguedthat it is an artifact that originates from the finite-size effectsin periodic calculations. Although the overall magnetization is usuallyregarded as zero when multiple monovacancies exist in graphene,23 the ferromagnetic hysteresis of proton irradiated graphite is observedat room temperature when an external field is applied.26As the simplest vacancy defect, monovacancy has been widelystudiedboth experimentally29 Strain effectivelytunes the electronic properties of a graphene sheet by changing bothits overall and local geometries. Particularly, large in-plane compressivestrain, which is beyond the Euler-type buckling limit (−0.7to −0.8%),30 can open an electronicband gap by inducing periodic out-of-plane bending, or ripples.29 Strains beyond this limit are experimentallyachieved by confining graphene monolayers in a polymer matrix or adiamond anvil cell.31 However, previous theoreticalstudies have found difficulties that the prediction of ripple wavelengthsis predetermined by the choice of periodic simulation cell.37 The nature of the interplay between monovacancies and strain-inducedripples remains an open question. Some preliminary results have beenobtained by either applying tensile strains25 or under the assumption that the strained graphene sheet is ideallyflat.21 The most noticeable finding isthe strain-induced bond reconstruction of monovacancies, indicatingthe probable existence of novel strain-tuneable properties. The restorationof the pre-JTR structure with three dangling bonds25 and a second-order JTR22 have both beenpredicted to be stable under tensile strains. For compressive strains,Santos et al.36 used density functionaltheory in the generalized gradient approximation [GGA–densityfunctional theory (DFT)] calculations to discover a new bond reconstructionof monovacancies in rippled graphene, which quenches the spin polarizationand suggests that it is possible to switch on/off the magnetizationof graphene by bond reconstruction.Considering its two-dimensional (2D) nature,the lattice mismatchbetween graphene and its substrates, on which it is grown or supported,results in non-negligible strains in practice.40 The distribution of monovacancyformation energies across the rippled sheet is then investigated tolocate the thermodynamically favorable sites of the monovacancy. Themost stable nonmagnetic V1(55–66) structure is identifiedand studied, while the magnetic properties of monovacancies at otherpositions are discussed. This investigation clarifies the origin ofthe inconsistent magnetic moments of a freestanding monovacancy reportedin the previous literature.25 It re-confirms the existence and the essential stabilizing effectof the V1(55–66) bond reconstruction, previouslyreported by Santos et al.,36 now usinga more rigorous a priori approach that determines the ripple configurationsbefore adding the defects. The relationship between the local geometryof monovacancies and the magnetic moment of the system is also exploredin detail. This relationship may offer a practical way to switch on/offthe magnetism of defective graphene by strain engineering. It is alsofound that novel monovacancy patterns can be engineered by applyingcompressive strains, enabling the more precise tailoring of graphenetransistors.In the current work, thetuneable magnetization of monovacanciesin compressed graphene is investigated. Properties of the monovacancyin freestanding graphene are first investigated as a reference. Afterward,the ground state periodic rippled structure of a sheet compressedby 5% in-plane isotropic strain is obtained based on the density functionalperturbation theory (DFPT).243 The HSE06 finite range hybrid exchange functional44 is used to minimize the significant self-interactionerrors inherent in local and gradient corrected functionals in thebroken magnetic symmetry of monovacancy graphene.49 A modified Gaussian basis set for condensed matter calculation 6-21G*,with an optimized exponent (0.26 Bohr–2) of theouter sp-type shell and a d-type shell,50 is adopted. All-electron DFT calculations are performed, so no shapeassumption is made to ionic potential or electron charge density.A 2D periodic boundary condition with an open boundary in the thirddirection (z) is used to model the graphene sheet.The 2D first Brillouin zone of the graphene primitive cell is sampledwith a 24 × 24 k-point mesh generated by theMonkhorst–Pack method.51 This meshexplicitly includes the Dirac point. The sizes of the k-mesh for supercell calculations are scaled to achieve consistent k-point sampling. Mulliken charge analysis is performedto estimate the atomic charge and spin populations. Owing to the semi-metallicnature of graphene, finite temperature Mermin smearing of the Fermisurface is used,52 with a width of 10–4 Hartree. The convergence threshold of the total energyin electronic minimization is 10–8 Hartree per cell.In geometry optimization using the BFGS algorithm, the convergencecriteria are 3 × 10–4 Hartree Bohr–1 for forces and 1.2 × 10–3 Bohr for displacements.The optimized lattice constant is 2.45 Å, which agrees well withthat deduced from X-ray diffraction (2.46 Å).53The calculationsreported here are based on DFT and DFPT as implementedin CRYSTAL17.15 Therefore, the formation energy Ef of a monovacancy is defined as followsThe monovacancy defect studied in this paper is assumedto be chargeneutral, consistent with the experimental observation.Edefect and Epristine are, respectively, thetotal energies of the defectiveand pristine graphene; μC is the chemical potentialper carbon atom in the pristine graphene lattice.z-coordinate in a hexagonallattice, which is summed up to the second nearest neighbors of a givenatomic position 54To quantifythe local curvature of strain-induced ripples, theLaplacian of the atomic ai is the vector pointingfrom the central carbon atom at ith secondnearest neighbor; z coordinates of the central atom and its ith secondnearest neighbor.56 POAV is defined as the specific vector that makes the three angles,θσπ, between the three σ bonds around the central atom and the vector itself equal. The averagehybridization n̅ of σ-orbitals, thatis, 56As a result of its nonplanar configuration,the orbital hybridizationof carbon atoms in rippled graphene is nonuniformly changed acrossthe sheet and depends on the local geometry. The π orbital axisvector (POAV) analysis is a straightforward parameter to characterizethe hybridization of nonplanar conjugated carbon atoms.33.124 In 1(5–9) structure with a remainingdangling bond and a stretched C–C bond of 1.85 Å (plottedin gray). The freestanding defective graphene sheet generally maintainsits original flat configuration. The elongated reconstructed bondof the pentagon introduces significant local tensile strain that dissipatesslowly along the zigzag direction, as indicated by the orange andyellow bonds in The structural, electronic,and magnetic properties of a monovacancy defect in a freestanding6 × 6 graphene supercell, which corresponds to a defect concentrationof 1.4%, are investigated in this section to discuss the origin ofits long-debated fractional magnetic moment. The computed formationenergy of this monovacancy in freestanding graphene is 8.32 eV, whichagrees well with the previous DFT studies on both periodic and isolatedsystems (7.3–8.58 eV).B, which comprises one unpaired electron from the dangling sp2 bond and 1/3 of an electron from each 2pz orbital of the 3 neighbors of the monovacancy.23 The computed magnetic moments of a monovacancyin periodic systems have frequently been reported as fractional valuesbetween 1 and 2 μB in previous studies.57 This was considered to originate from the finite size effects inperiodic calculations and Rodrigo et al.25 suggested that the magnetic moment of an isolated monovacancy convergesto 2 μB using large-scale DFT up to 30 × 30supercell. However, the current study suggests that an alternativeexplanation for the inconsistency lies in the well-known electronself-interaction error of DFT, which is significant for the previouslyused (semi-)local functionals based on local spin density approximation(LSDA) and GGA.58 The consequences of this error have been widely documented in stronglycorrelated systems resulting from the electron confinement that occursin dangling bonds or n-doped systems.62 Pisani et al.45 estimated a significantHubbard U parameter of ∼3.25 eV for grapheneribbons with the GGA–PBE functional, indicating the large self-interactionthat exists in the nonbonding localized orbitals when the πband of graphene is disrupted. For the current system, LSDA and GGAfunctionals may provide a spuriously delocalized charge distribution,leading to incorrect electronic and magnetic ground states. With therange-separated HSE06 functional, the description of the strong on-siteCoulomb interactions is improved,63 andthe magnetic moment of the monovacancy converges to 2 μB within a relatively small supercell. Therefore, it can beconcluded that the self-interaction correction of HSE06 reproducesthe same fundamental descriptions, as those provided by global hybrids47 and more recently developed hyper-GGA functionals.58The monovacancy is spin-polarized due to the danglingbond. Thecalculated magnetic moment of the monovacancy is 2 μ25 with the discrepancy due to the correction for electronic self-interactionincluded here. The monovacancy and resultant magnetic ordering breakthe symmetry of graphene, opening a band gap of 0.31 eV for majorityspin states (spin-up) and 0.06 eV for minority spin states (spin-down).From this, it is clear that if the spins of the monovacancies arealigned, the sheet will be a narrow band gap semiconductor with stronglyspin-dependent transport. In the presence of magnetic defect states,the self-doping of the filled valance band upshifts the Dirac pointin the spin-down band structure by 0.41 eV. Electrons move from theinitially occupied spin-down states near the Fermi surface to thespin-up defect π states.The computed band structure and densityof states (DOS) of themonovacancy are plotted in 64 Results suggest that all the spin-up electrons contributeto the bonding states and are beneath the Fermi level, while all thespin-down electrons contribute to the antibonding states and are abovethe Fermi level. Spin-up states, therefore, stabilize the reconstructedbond. It further supports the conclusion that spin-down π statesdo not cross the Fermi level. Otherwise, electrons will occupy theantibonding states near the Fermi level, leading to a fractional magneticmoment and reducing the stability of the reconstructed system.To characterize the interactionstrength of the JTR bond, the spin-polarizedCOHP curves projected on the two atoms connected by it are plottedin 23 have revealed that the ferromagneticcoupling between the spin localized at the vacancies originates fromthe regular arrangement of monovacancies in the same sublattice. Anantiferromagnetic coupling is generated if monovacancies are accommodatedin the opposite sublattices.In 23 Experimentally, monovacancieshave been generated in graphite using proton irradiation and alignedin an external field with some ferromagnetic hysteresis observed atroom temperature.26 This is consistentwith the high Curie temperatures predicted for idealized theoreticalmodels of the ferromagnetic phases.23Typically, monovacancies in graphenewill distribute randomly betweenthe two sublattices and therefore the net macroscopic magnetizationwill be zero.3.240 is used to compute the harmonicvibrations of the sheet and, thus, to predict the wavelengths of thelow energy strain-induced ripples at 5% isotropic compressive strain.In what follows, positive values denote compressive strains, unlessstated otherwise. The wavelength of strain-induced ripples λcan be predicted by the wavevector k corresponding to the minimum frequency of the soft phonon modesfollowing the relationship of λ = 2π/|k|.40 The wavevector k =  is found to be nearthe minimum frequency (Supporting Information) computed and thus the predicted stable ripples are commensuratewith a 6 × 6 supercell of the primitive graphene cell. Withinthis cell, the harmonic ripple can be induced and then the internalcoordinates optimized to find representations of the stable ripples.Larger ripple wavelengths are predicted under smaller strains . To ensure the overall reliabilityof the current study while keeping the simulation cost feasible, thecase of the 6 × 6 supercell compressed by 5% strain is investigatedin detail, since similar geometries and behaviors are predicted underlower strains with longer wavelengths.40In order to understand the interplay betweenripple formation and monovacancies, we first consider the structureof the low energy ripples. DFPT40 Strain-generated ripple patterns show asixfold symmetry, consistent with the graphene lattice; see Theoptimized geometry is illustrated in 16 the formation energies before and after bond reconstructionare computed. In this way, the energy surfaces, respectively, characterizingthe kinetics ,is shown in the inset. The central atom in red is sp3 hybridized,leading to a slightly flattened tetrahedron and the long sp3 bonds with four neighboring atoms. V1(55–66) issignificantly distorted due to the compressive strain, as characterizedby its local curvature. The twisting angle between the opposite pentagonsis 52.23°, while the angle between opposite hexagons is 54.40°.The dihedral angles of the neighboring pentagons and hexagons arearound 139.66∼139.95°.A detailed analysis of the reconstructed monovacancy at the saddlepoint marked by the dotted magenta circle in 1(55–66) monovacancyis generated,hexagons at saddle points bear the largest local strain (1(55–66), which results in the elongation of some bondsalong this direction. Similar strain relief is not observed alongthe pentagon–pentagon direction, which is vertical to the displacement.Therefore, among the original saddle points, only those along thepentagon–pentagon direction continue to be the regions of strainconcentration. The connection between strain distribution and theformation energy of a site indicates the possibility of mediatingthe monovacancy patterns in the sheet via strains.Before the Vl strain 2. By com1 and an unstrained defectivegraphene sheet .16 Meanwhile, influences of the defect are observed.Partially localized defect states are observed, which is not as evidentas in the case of V1(5–9). In contrast to 1(55–66),owing to the bond reconstruction.The changein local geometry is accompanied by a change in theelectronic structure. The band structure and DOS of the ground stateconfiguration shown in ne sheet 1b. The s1(55–66).Its second nearest atoms from pentagons transfer the most charge toits nearest neighbors, where the largest distortion is observed. Thisphenomenon might be caused by the strong σ-orbital couplingoriginating from the short bonds of pentagons. The charge depletionregion is not as obvious, but more extended, along the hexagon–hexagondirection.The atomic charge populationdistribution is illustrated in 1(55–66), are plotted. Thelargest values are reported at the nearest neighbors of the centralatom due to local distortions, indicating a greater contribution ofsp3 hybridization. n̅ of other atomssurrounding V1(55–66) also exhibit a moderate increase.Atoms in rippled regions have much smaller values when compared withthose around V1(55–66), while atoms at inflexionpoints maintain the pure sp2 hybridization.In 1(55–66) is bonded withfour neighbors; in this case, a pure sp3 hybridizationshould be expected; however, there is a degree of sp2 hybridization,considering the asymmetry of the tetrahedron, as shown in pz orbital, which differs from the curves of the other orbitals,especially in the ±1.5 eV region around the Fermi level. Interestingly,compared with those of px and py orbitals, thePDOS curve of s orbital shows more patterns similar to that of pz orbital, including the absence of peaksin energy ranges of −1.5 to −1 eV and 2 to 2.5 eV, andthe peaks at ∼1.2 eV, which indicates the more significantmixing between s and pz orbitals.The centralatom of Vpz orbitals.33 The partialcharge density projected on the VBM of graphene is shown in 1(55–66)due to its σ-bonded pz orbital. However, the inset shows an almost negligible chargedistribution around it, verifying the conclusion that sp2 hybridization also has a slight contribution. Meanwhile, an enhancedπ-orbital coupling region is observed around the central atom,corresponding to the charge accumulation region in In the flat graphene, the states at VBM are occupiedby electronsfrom the delocalized π-bonded 3.31(5–9)structure, which is metastable when the removed atom is not at a saddlepoint, except for 2 asymmetric V1(55–66) cases (1(5–9) structures are found to be metastable with various distortions,they provide ideal cases for discussing the properties of compressivestrain-mediated V1(5–9) defect. Magnetic momentsvary between 0.50 μB and 1.25 μB for distorted V1(5–9) sites across the 6 ×6 supercell. To understand the origin of these fractional magneticmoments and the stability of distorted V1(5–9) onrippled graphene, a statistical analysis of their local geometriesis conducted. θ is defined as the dihedral angle between thepentagon and the plane of atoms b1, b2 and d. l® is the average length between d and b1, b2 (rS) are calculated betweenlocal geometry parameters and magnetic moments of the distorted V1(5–9), as shown in The JTR leads to a pentagon-distorted nonagon V6) cases 2d. Sinced b1, b2 5a inset.2zrm does not strongly correlate to the magnetic moments.Parameters describing the unsaturated atom d showstronger correlations, which is reasonable considering that the atom d contributes to the unpaired electron. The parameters θand l̅ exhibit strong correspondence  on the overall spin distribution is alsorecently observed in 2D covalent organic frameworks, which is provento be robust at a finite temperature.65 Even though the monovacancy formation energy Ef is not monotonically correlated to the local geometry parametersor the magnetic moment of the distorted V1(5–9), 1(5–9) monovacancies with similar structural parameterstend to possess similar magnetic moments and formation energies.1(5–9)in the same color-shaded region are assumed to possess similar electronicand spintronic properties. To better understand the influences ofdifferent local geometries on the electronic structures and stabilitiesof V1(5–9), three cases, respectively, from theblue , green, and red regions areselected.Considering the similarities mentioned above, V1(5–9) with variousdistortions. PDOS curves  structureand reduces the probability of reconstruction, which is counterintuitivesince V1(5–9) with increased distortion has a lowermagnetic moment and seems to be closer to the reconstructed V1(55–66). However, it is noteworthy that the distortionalso disperses the bond strains across the sheet , while the confined geometry and severe straincondition at saddle points probably limit the displacements and keepthe strains concentrating at the saddle point, which leads to theV1(55–66) reconstruction. Similarly, V1(55–66) deviating from saddle points increases due to the stronger sp3 hybridization of theunsaturated atom. The curve of the most distorted V1(55–66)with medium Ef shows a reverse spin distributionfrom the third nearest neighbor, which originates from the reversedspin orientations of the 2 atoms connected by the JTR bond .The damped fluctuation patterns illustrated in 41(5–9) monovacancy is predictedto have a spin asymmetric conductivity and localized strong ferromagneticcoupling, with a magnetic moment of 2 μB when theelectron self-interaction error is corrected. A periodic “eggbox”ripple pattern generated by 5% in-plane isotropic compressive strainis predicted to minimize the finite size effects inherent in ad hocchoices of supercells. This study finds that the reconstructed V1(55–66) at saddle points of the ripples is the moststable configuration, which forms sp3 bonds and quenchesthe local magnetic moment, with respect to the distorted V1(5–9) observed at the other sites across the rippled sheet.Correlations among local distortions, electronic, and spintronic properties,and stabilities of distorted V1(5–9) are discussed.It is found that more distorted V1(5–9) defectstend to be more stable and have smaller magnetic moments. Accordingto the current study, the switching between spin-polarized and non-spin-polarizedstates of graphene is achievable by the V1(55–66)reconstruction. It can be estimated that this reconstruction doesnot strongly depend on defect density, since only the local distortionsaround a monovacancy determine its stability.The strain-tuneablemagnetism of defect graphene is achieved bythe crucial interplay between monovacancies and strain-induced ripples.The unstrained V1(5–9) or a thermodynamically stable V1(55–66)structure can be obtained. Considering that the substrates are commonlyused to generate isotropic strains in graphene, the practical implementationof this mechanism will depend on finding suitable substrates withmoderate coupling with graphene, upon which the graphene can be strainedwhile being free from the graphene–substrate interactions thatmight interfere in the formation of monovacancies or quench magneticstates. As reported by Zhang et al.,66 structural and spintronic properties of V1(5–9)on the rotationally misaligned topmost layer of chemical vapor depositedgraphite is well preserved and might be a potential candidate forexperimental investigations.In general, bycontrolling the local distortion of a monovacancyvia compressive strains, either a kinetically stable V15 and the influences of thermal fluctuation on ripple configurations.However, it is still noteworthy that the significant stabilizing effect(∼2.3 eV lower in formation energy) of the V1(55–66)reconstruction makes it thermodynamically favorable for a V1(5–9) to diffuse toward a saddle point and to get reconstructedat room temperature if the switching mechanism is followed as usuallyassumed in theoretical studies.67 The hopping barrier decreases as the compressive bond strain increases,57 probably making the diffusivity of V1(5–9) commensurate with the rippled geometry of compressedgraphene. This probably leads to a patterned monovacancy distributionwith long-range periodicity tuned by compressive strains, allowingfor even further modifications of graphene-based electronics.Besides, the stability and diffusionof the generated monovacancyat finite temperatures are still unclear due to the complicated monovacancymigration mechanisms observed in experiment1(55–66)exhibit the predominant increase of the frontier  electrondensity (1(55–66) defects. Thismight enable patterned adsorbate self-assembly and functionalizationat the molecular level, which is important for the controlled engineeringof the configuration and properties of graphene.40Meanwhile, it is also probable for multiple monovacancies to coalescearound the saddle points, where the strain concentrates, leading tothe expansion of the vacancy and the failure of the sheet. On theother hand, neighbors around the central atom of Vdensity 4b,whichIn conclusion, via the interplay between ripple andmonovacancy,the electronic and spintronic properties of graphene can be effectivelytuned to achieve more precise control of graphene, making it a potentialoption for application in various scenarios.


Due to the chaos and confusion caused by the sudden transition from face-to-face teaching to online and remote teaching in early 2020, numerous language teachers had no choice but to rely on online communities on social networking sites. The current study therefore examined how some language teachers were utilising online communities on Facebook during the COVID-19 pandemic. Employing a mixed-methods approach, data were mainly collected through: (1) an eight-month observation of a technology-focused language teacher community on Facebook to identify different types of posts generated by its members before and during the COVID-19 pandemic (n = 340); (2) a questionnaire to understand the community members’ backgrounds and experiences of being in the community (n = 51); (3) semi-structured interviews with some of the questionnaire participants (n = 13); and (4) a post-interview questionnaire (n = 12) to get a better understanding of their responses. A content analysis of online posts and community members’ responses suggest that language teacher communities on Facebook were supporting teachers during the stressful periods of the pandemic professionally and emotionally. The main findings are discussed in terms of the benefits and drawbacks of using online language teacher communities for professional purposes. The overall goal of the study is to offer much-needed answers on how pre-existing communities can be used to assist language teachers in times of a crisis. Many language teachers around the world, including those who were once reluctant to use technology for teaching purposes, were forced to temporarily teach online because of the COVID-19 pandemic , which include SNSs  and semi-structured interviews with some of its members (n = 14), Yildirim  found thWhilst these studies demonstrate that online teacher communities on SNSs bring about various benefits to teachers’ professional lives, the negative aspects should also be noted. Not the least of these is the difficult aspect of sustaining a successful online community, as indicated in a recent study conducted by Nilimarkka et al.  who examAs illustrated in the preceding section, there have been an increasing number of studies investigating the general use of online teacher communities in non-language teaching contexts. However, since language teachers have specific needs in that they need to continuously enhance their professional knowledge, including subject knowledge about a language  and pedagogical knowledge of how to teach language skill areas to learners with different backgrounds using a wide variety of tools and materials, throughout their careers  were about sharing information or resources and 94 posts (27.6%) were about asking for assistance. A content analysis of the 246 posts about sharing information or resources resulted in 11 main categories, which are summarised in Table As shown in Table In three different time periods before the pandemic , the start of the pandemic , and during the pandemic (June 2020–August 2020), both types of posts about asking for assistance and sharing information or resources were found, though the breakdown of the subcategories differed  indicated that they had been using technology in some way in their classes before the pandemic. Out of the 50 questionnaire respondents who claimed that they were using technology in their classes, 44 respondents (88%) stated that the ways in which they used technology changed due to the pandemic. Most of the respondents reported that they used video conferencing tools , Learning Management Systems (LMSs) , or both to teach online. Two of the respondents claimed that the pandemic did not affect their teaching as they had already been teaching online prior to the pandemic.Following the initial questionnaire, semi-structured interviews were conducted with 13 of the community members. It was found that all the interviewees were in two or more language teacher communities at the time of the interview. From the interviewees’ responses, the perceived positive and negative aspects of being in language teacher communities on Facebook during a pandemic were identified.We, as teachers, want to read, we want to learn, we want to expand our knowledge base, but we don’t often have the time to do that. I think, being part of groups like this helps to streamline information a lot better, so if I only have a five-minute break between my classes, I hop on to Facebook and something pops up about something interesting going on in the tech world then that’s my five-minute knowledge boost for the day.Firstly, a few interviewees commented on the convenient and accessible aspect of the online communities. For instance, the following comment shows how language teachers can easily learn through reading the posts shared in the communities in their spare time:.” Some of the interviewees seemed to find the online communities to be particularly important during the pandemic, as indicated in the following comment made by a language teacher who joined a language teacher community on Facebook at the beginning of the pandemic:In the beginning [of the pandemic], it [the online community] was kind of like counselling because everybody else was freaking out and stressed, because they had the pressure of learning new technology themselves… We all relate to each other, so in the beginning it was more like a counselling kind of thing with helping each other, and that was useful.More than a third of the interviewees also indicated that they viewed the online communities as a virtual space to get professional or emotional support. One interviewee explained how she turned to the observed community if she had a question since she believed that “it’s almost guaranteed that someone can help youDeveloping an online course takes a very long time, but we were asked to do it in a matter of weeks with no training… So, I was looking to get insights from not only people who had done this before but also who were in the same situation that I was in.The majority of the interviewees (n = 12) reported that they were suddenly told that they needed to teach online despite not having any experience in teaching online prior to the pandemic. Several interviewees indicated that they joined language teacher communities on Facebook at the beginning of the pandemic. One interviewee claimed that she joined the observed community in April 2020 to connect with language teachers who had prior experience in teaching online as well as those dealing with similar problems:I don’t like getting drawn into these online discussions and debates because it just doesn’t seem like it’s worth anyone’s time, so that’s probably why I don’t actually post much.Although many interviewees reported on the positive aspects of being in language teacher communities on Facebook, a few did express some concerns. Several interviewees reported that they had occasionally witnessed or personally received harsh comments in the communities. One interviewee claimed that she disliked how a member from the online language teacher communities made rude comments to her when she posted a question in the community. In addition, a different interviewee indicated that he was reluctant to post in the language teacher communities on Facebook as he wanted to avoid arguments:Looking on the bright side, one interviewee even claimed that through her experience of being in language teacher communities on Facebook, it has made her realise the importance of online etiquette and safety and tries to teach her students about the importance of how they present themselves online.I have been able to source more tools, techniques and insights from online communities and implemented it into my lesson.In the post-interview questionnaire, which was distributed after the interviews, the interviewees were asked some questions to clarify the information obtained from the interviews. In response to the question asking whether or not their teaching practice had changed as a result of participating in the online communities, nine out of 12 interviewees indicated “yes.” As indicated in the following comment, the interviewee explained how she was able to incorporate what she had learnt from the online communities into her actual lessons:I’ve learned more about online teaching and made use of some of the recommendations that I found in the groups.In a similar vein, an interviewee who did not have much experience in teaching online before the pandemic claimed that participating in the online communities enabled her to learn more about online teaching and directly benefited on what she had learned from the communities:I ended up mostly troubleshooting things on my own. It’s not that I was disappointed in the community I found online, only that I utilized it less than I thought I would when I joined.On the other hand, it should also be noted that a small number of interviewees (n = 3) indicated that their teaching practice had not changed as a result of participating in the online communities. All three interviewees commonly reported in the questionnaire that they were “very confident” in using technology for teaching purposes, and one of them commented that he did not rely much on the online communities during the pandemic because he was able to fix most of his problems alone:From his response, it is evident that not all online community members were heavily making use of the online communities for professional learning purposes.As the primary objective of the study was to uncover how language teachers were utilising technology-focused online language teacher communities on Facebook during the pandemic, in the current section, the ways in which language teachers in the study were affected by the pandemic situation are first described, and subsequently, the main benefits and challenges of using online language teacher communities during the pandemic are outlined.Echoing the findings from the study conducted by MacIntyre et al.  which shThe study’s findings clearly indicated that technology-focused language teacher communities on Facebook brought about numerous professional benefits to language teachers who were suddenly forced to teach online during the pandemic. In line with relevant literature , semi-structured interviews (n = 13), and post-interview questionnaire (n = 12). As lurkers  are a common feature of online communities (Popover & Fullwood, The current longitudinal study provides some insights into the realities of a language teacher community on Facebook during a pandemic. Language teachers in different regions of Japan were providing each other with professional and emotional support in the observed technology-focused language teacher community on Facebook: In particular, when in-person interactions were limited, they were able to support each other through sharing information, resources, and words of comfort and asking teaching-related questions. Without the help from their peers in the communities on Facebook, teachers with no or little experience in using technology for teaching purposes would have struggled even more. Even those who were experienced in using technology benefited from the social aspects of the communities as they were able to socialise with each other in the online social gatherings and related events, which, in turn, helped them overcome their feeling of loneliness and isolation. Although the past two years have witnessed a proliferation of research in crisis management in education (e.g., Back et al., Although it is unclear how language teachers will use the online communities once the pandemic ends completely, they are likely to continuously play an important role in assisting teachers who use digital tools for teaching purposes even in the post-pandemic era. Of course, technology-focused language teacher communities on Facebook will not be a panacea for combatting all the problems that language teachers encounter when they use technology, but it is undeniable that they provide valuable support for teachers, especially when institutional support is lacking.


Cognitive dysfunction, particularly attentional impairment, is a core feature of many psychiatric disorders, yet is inadequately addressed by current treatments. Development of targeted therapeutics for the remediation of attentional deficits requires knowledge of underlying neurocircuit, cellular, and molecular mechanisms that cannot be directly assayed in the clinic. This level of detail can only be acquired by testing animals in cross-species translatable attentional paradigms, in combination with preclinical neuroscience techniques. The 5-choice continuous performance test (5C-CPT) and rodent continuous performance test (rCPT) represent the current state of the art of preclinical assessment of the most commonly studied subtype of attention: sustained attention, or vigilance. These tasks present animals with continuous streams of target stimuli to which they must respond (attention), in addition to non-target stimuli from which they must withhold responses . The 5C-CPT and rCPT utilize the same measures as gold-standard clinical continuous performance tests and predict clinical efficacy of known pro-attentional drugs. They also engage common brain regions across species, although efforts to definitively establish neurophysiological construct validity are ongoing. The validity of these tasks as translational vigilance assessments enables their use in characterizing the neuropathology underlying attentional deficits of animal models of psychiatric disease, and in determining therapeutic potential of drugs ahead of clinical testing. Here, we briefly review the development and validation of such tests of attentional functioning, as well as the data they have generated pertaining to inattention, disinhibition, and impulsivity in psychiatric disorders. Psychiatric disorders affect roughly one in every four people worldwide. Cognitive system dysfunction is a critical factor across diseases, either defining a given condition or closely correlating with functional outcome. Impaired attention is common across many such disorders, including attention deficit hyperactivity disorder (ADHD), schizophrenia, and bipolar disorder (BD) ,2. The lNumerous tests have been developed to assess attention in rodents over the last four decades ,6,7. TheThis limitation of the 5CSRT was partly addressed by the Sustained Attention Task  in mice lacking functional neurokinin-1 receptor (NK1R) ,45, a moTACR1 .O-methyltransferase inhibitor tolcapone, the α7 nicotinic acetylcholine receptor (α7-nAChR) agonist encenicline, and a selective dopamine D4 receptor (DRD4) agonist [TACR1 polymorphisms, the 5C-CPT demonstrates considerable utility in the context of preclinical ADHD research.Other research has utilized the inter-individual heterogeneity of rodent attention to assess the effects of frontline and novel ADHD medications on rats of high and low baseline inattention and impulsivity. This strategy generates cohorts of rats that model the three subtypes of adult ADHD  that demonstrate high levels of pharmacological predictive validity when assessed in the 5C-CPT. Specifically, traditional ADHD therapeutics improved accuracy and overall vigilance in ‘low-attentive' rats and normalized motoric impulsivity and/or response disinhibition  in ‘hig agonist ,53. The  agonist ,51, tolc agonist . Meanwhi agonist ,56, and  agonist . Finally agonist . While fN-methyl-D-aspartate receptor (NMDAR) antagonism rat model of schizophrenia [Pharmacological, genetic, and developmental animal models of schizophrenia have also been assessed in the 5C-CPT. Consistent with patient CPT performance ,58, the ophrenia  reliablyophrenia . Namely,ophrenia , as wellophrenia ,61. Thisophrenia ,30, indiophrenia  aligns wophrenia . Other sophrenia   and ophrenia  (a propoophrenia ). While ophrenia ) or putaophrenia ) schizopenhanced in DAT KD mice [The neural substrates of specifically BD-associated inattention were investigated by assessing patients in the 5C-CPT during manic and euthymic states alongside dopamine transporter knock-down (DAT KD) mice . DAT KD  KD mice . Taken w KD mice . Additio KD mice .In summary, the 5C-CPT is a well-validated, clinically sensitive assay that has already proven useful in: (1) delineating neural mechanisms underlying vigilance; (2) characterizing animal models of clinical populations; and (3) identifying potential therapeutics that can be tested in patients.The rCPT  is a recDespite its reduced capacity to assess response inhibition, the rCPT nevertheless demonstrates validity as an assay of vigilance and impulsivity/disinhibition. Lesion studies have illustrated cross-species convergence in neural substrates underlying response inhibition in the rCPT and the clinic ,83; nameAs with the 5C-CPT, the construct and predictive validity of the rCPT enables its use in the context of preclinical psychiatric research. To date, three studies have utilized the rCPT to characterize the attentional profiles of neurodevelopmental models of schizophrenia and ADHD. Rats exposed to the neurotoxin methylazoxymethanol acetate (MAM) during gestation — a model of schizophrenia-relevant neurological abnormalities and behavioral and cognitive deficits ,91 — demHere, we provided a brief history of the use of rodent behavioral tests developed to explicitly assess sustained attention. It is important to note that while all behavioral tasks require attention to a certain degree , we argue that, without outcome measures specifically designed to assay attention or validation for human testing, the translatability of their findings to human-relevant attention must be questioned. Even the well-validated 5C-CPT and rCPT have limitations. For example, the training time required often precludes the testing of juveniles and adolescents, thus limiting the ability to assess animal models relevant to childhood ADHD, juvenile onset disorders, and prodromal and first-break schizophrenia. Some protocols  may expThe 5C-CPT and rCPT can be readily applied to the study of neuropsychiatric conditions beyond those described above. For example, the underlying mechanisms of Alzheimer's disease and delirium, in which inattention is consistently identified by clinical CPTs ,104 and In summary, current cross-species attention assessments owe a great deal to earlier operant tasks, such as the 5CSRT and SAT; however, while these older tasks remain useful, the data generated by the more recent CPT-like paradigms appear to have greater translatability to humans. The 5C-CPT is well-validated as a cross-species vigilance assay, and is also clinically sensitive and compatible with EEG and fMRI. The rCPT, though yet to be validated in this depth, offers a flexibility in testing that will enable assessment of more aspects of attention. The preliminary neurophysiological construct validity of the 5C-CPT and rCPT represents great promise for future rodent vigilance testing, with the potential for incorporating modern neuroscientific techniques to determine underlying circuit networks and neurotransmitter activity. These tasks, in combination with improved psychiatry-relevant manipulations in rodents, will ultimately facilitate discovery of targeted therapeutics for attentional enhancement.Attentional dysfunction is a critical aspect of many psychiatric conditions, yet few pharmacotherapies exist for the specific remediation of such deficits.Cross-species translatable cognitive assays enable study of the neural substrates underlying attention in humans and rodents at a higher level of resolution than is possible with clinical techniques.The 5-choice continuous performance test (5C-CPT) and rodent continuous performance test (rCPT) measure sustained attention in rodents in a manner consistent with benchmark clinical assessments, and engage similar brain regions across species.The 5C-CPT and rCPT are sensitive to similar pharmacological and parametric manipulations as analogous clinical tasks, and animal models of psychiatric disease tested in these paradigms demonstrate attentional deficits consistent with those observed in clinical populations.The 5C-CPT and rCPT enable identification of novel therapeutic targets and pharmacological interventions for the remediation of attentional deficits.


Single Cell Implementation to Find Expressed Retrotransposons (SCIFER). SCIFER aligns scRNA-Seq reads uniquely to the genome and extracts alignments from single cells by cell-specific barcodes. In contrast to the alignment performed using default parameters, this alignment strategy increases accuracy of L1 locus identification by retaining only reads that are uniquely mapped to individual L1 loci. L1 loci expressed in single cells are unambiguously identified using a list of L1 loci manually validated to be expressed in bulk RNA-Seq datasets generated from the same cell line or organ.Endogenous expression of L1 mRNA is the first step in an L1-initiated mutagenesis event. However, the contribution of individual cell types to patterns of organ-specific L1 mRNA expression remains poorly understood, especially at single-locus resolution. We introduce a method to quantify expression of mobile elements at the single-locus resolution in scRNA-Seq datasets called Validation of SCIFER using MCF7 cells determined technical parameters needed for optimal detection of L1 expression in single cells. We show that unsupervised analysis of L1 expression in single cells exponentially inflates both the levels of L1 expression and the number of expressed L1 loci. Application of SCIFER to analysis of scRNA-Seq datasets generated from mouse and human testes identified that mouse Round Spermatids and human Spermatogonia, Spermatocytes, and Round Spermatids express the highest levels of L1 mRNA. Our analysis also determined that similar to mice, human testes from unrelated individuals share as much as 80% of expressed L1 loci. Additionally, SCIFER determined that individual mouse cells co-express different L1 sub-families and different families of transposable elements, experimentally validating their co-existence in the same cell.SCIFER detects mRNA expression of individual L1 loci in single cells. It is compatible with scRNA-Seq datasets prepared using traditional sequencing methods. Validated using a human cancer cell line, SCIFER analysis of mouse and human testes identified key cell types supporting L1 expression in these species. This will further our understanding of differences and similarities in endogenous L1 mRNA expression patterns in mice and humans.The online version contains supplementary material available at 10.1186/s13100-022-00276-0. Long INterspersed Element-1 (LINE-1 or L1) mRNA has multiple negative consequences for genome stability. L1 mRNA expression can lead to retrotransposition of L1 transcripts or trans-retrotransposition of transcripts from other mobile elements, such as Alu or SVA [Expression of u or SVA . Additiou or SVA –7. Experu or SVA , 9. Prevu or SVA –14, but L1 sequences are abundant in the human genome, which contains 500,000 truncated and full-length copies, as well as in the mouse genome, which harbors 600,000 truncated and full-length copies –17. A crWe developed a method to rigorously analyze L1 mRNA expression at a single-locus resolution by filtering out truncated and passively transcribed L1 sequences , 20, 30.Methods to quantify transposable element expression in single cells, such as the study by Shao, et al,.  implemenSingle Cell Implementation for Finding Expressed Retrotransposons (SCIFER). SCIFER extracts scRNA-Seq reads generated from traditional 10X Chromium Single Cell 3′ Genomics sequencing along with their barcodes and realigns them to the reference genome using Bowtie [Here, we report a new bioinformatics tool designed for analysis of L1 mRNA expression quantification from individual L1 loci in single cells called g Bowtie  with unig Bowtie , 20, 30.g Bowtie , 20, 30.Single Cell Implementation to Find Expressed Retrotransposons) is a method to quantify L1 mRNA expression at the locus-specific level in scRNA-Seq datasets. SCIFER aligns data from a standard 10X Chromium Single Cell 3′ RNA-Seq dataset to the reference genome using procedures optimized to deal with the very high genomic copy number of L1 elements  by cross referencing the list of L1 loci that were assigned same-sense RNA-Seq alignments in the scRNA-Seq dataset with a list of full-length L1 loci validated to be expressed in MCF7 cells from a previous study  were down sampled in 10% intervals and the average number of expressed L1 loci detected in each resulting interval sample was compared Fig. A. This aP < 0.0001, comparing Fig. To determine limitations imposed by lower sequencing coverage, we performed SCIFER analysis on a low coverage MCF7 scRNA-Seq dataset with 10-fold less sequencing coverage and 5-fold more sequenced cells compared to the High coverage MCF7 scRNA-Seq dataset Fig.  B. The cr = 0.55, P < 0.0001 Additional file P < 0.0001). The positive L1 FPKM-RPM correlation and high percent of shared expressed loci detected between Low coverage scRNA-Seq and bulk RNA-Seq establishes that L1 expression detection, averaged across a population of cells, is not dramatically impacted by reduced sequencing depth. However, the number of expressed L1 loci per cell and their levels of expression are underestimated when a low coverage dataset is used. Additionally, similar to the High coverage scRNA-Seq dataset, L1 loci expressed in bulk RNA-Seq but missed by SCIFER in lower sequencing coverage scRNA-Seq datasets are those L1 loci that have low expression levels.We next compared the total L1 expression levels detected by SCIFER in the Low coverage MCF7 dataset with L1 expression levels detected in the bulk RNA-seq dataset. Despite reduced sensitivity of detection of L1 expression per cell in the Low coverage dataset, RPM per expressed L1 locus in the Low coverage dataset was positively correlated with bulk RNA-Seq L1 FPKM  to determine the extent of variation in L1 expression between individual cells Fig. C. This aWe also detect expression of housekeeping genes (HKGs) in cells with read numbers downsampled in 10% increments, the same three cells used in Fig. P < 0.0001, Additional file P < 0.0001, Additional file P < 0.0001, Additional file Previously, our comprehensive analysis of locus-specific L1 mRNA expression in mouse organs determined that testes express the highest levels of L1 mRNA compared to other mouse organs, including male and female brains, male and female lungs, ovaries, and uteri . To deteP < 0.0001, P < 0.0001, P < 0.0001, respectively, Fig. P = 4.39E-99, P = 1.20E-28, P = 3.89E-94, respectively, Additional file P < 0.0001, P < 0.0001, P < 0.0001, respectively, Fig. SCIFER analysis was performed on the scRNA-Seq mouse testis samples to discover the levels and patterns of L1 mRNA expression in different cell types using a list of L1 loci validated to be expressed in mouse testes from a previous publication . SCIFER To understand potential changes in L1 expression during spermatogenesis, we compared the identity of L1 loci expressed in different sperm cell types identified in our single cell pool. Comparison of L1 loci expressed in different sperm cell types determined that in the Mouse 1 dataset, Spermatocytes, Round Spermatids, Elongating Spermatids, and Condensing Spermatids share only 2% 5 of 212) of L1 loci expressed in testes, with 157 L1 loci being detected to be expressed only in Round Spermatids alone Fig. D. In the of 212 or = 0.51, P < 0.0001, Fig. r = 0.72, P < 0.0001, Fig. P < 0.0001, Fig. Previously we found that in MCF7 cells SCIFER detects 88–93% of expressed L1 loci detected in bulk RNA-Seq and the L1 FPKM-RPM levels of expressed L1s are positively correlated between SCIFER-detected L1 loci expression in single cells and bulk RNA-Seq  that were manually validated to be expressed in bulk RNA-Seq were analyzed in scRNA-Seq datasets  and Spermatocytes 0.029) compared to Spermatogonia (0.025), Elongated Spermatids 0.28), and Condensing Spermatids (0.007)  (P < 0.0001) , which allows unique mapping of scRNA-Seq reads to the genome while retaining cell-specific barcodes. SCIFER analysis also includes validating L1 expression detected in scRNA-Seq with the analysis of L1 expression in bulk RNA-Seq from a matching tissue sample using our existing approach for identifying expressed L1 mRNAs from individual sites, while eliminating those that are passively expressed [Using RNA-Seq to measure the expression of L1 elements derived from their own promoter is technically challenging, both because of difficulties properly aligning short-read sequences to a single, specific locus and the high levels of passive inclusion of L1 sequences in other transcripts that create high levels of background , 20–22. xpressed , 20, 30.We validated SCIFER as a method for measuring L1 expression in single cells by analyzing a scRNA-Seq dataset generated from a pooled sample of MCF7 and HEK293 cells to determine whether our method was sensitive enough to detect the same loci as seen in the bulk RNA-Seq studies .These findings have important implications for experimental design and comparative analysis of L1 expression in single cells. For example, comparisons between scRNA-Seq with significantly different average sequencing depth per cell are likely to produce artifacts regarding the number of expressed L1 loci per cell and the number of cells expressing specific L1 loci. However, both High and Low coverage datasets can be used for organ-derived studies to identify relative contribution of different cell types to L1 expression and the diversity and cell type specificity of expressed L1 loci in a specific organ Fig. .Our single-cell analysis also provides evidence that SCIFER can be adapted for detection of other repetitive sequences and assist in answering outstanding questions regarding mobile element biology. It has been proposed that L1 promoter evolution is driven in part by co-expression of different L1 subfamilies, which leads to their competition for cellular transcription factors and other transcriptional machinery –65. UsinWe also performed SCIFER analysis on human testes to observe whether L1 expression patterns in testes are conserved between mice and humans. Bulk RNA-Seq of human testes from two unrelated 20 yo donors showed a high level of similarity in the L1 loci expressed  of origin of L1 expression in different organs and species. Additionally, SCIFER has the ability to uncover evolutionary niches occupied by different classes of TEs or TE subfamilies, as well as to understand L1 impact on function and genome stability of single cells.MCF7 (ATCC HTB-22) and HEK293-FRT-LacZeo cells were maintained in DMEM with high glucose (Gibco) supplemented with 10% fetal bovine serum (Gibco), sodium pyruvate, essential and nonessential amino acids, and L-glutamine. Cells at 100% confluency were detached using accutase (Innovative Cell Technologies) and resuspended in DPBS. MCF7 and HEK293-FRT-LacZeo cells were combined at a 9:1 ratio with 180 MCF7 and 20 HEK293 cells per uL. The single cell suspension was confirmed to be 84.4–83.1% viable prior to RNA preparation and sequencing.Human testis bulk RNA samples from two 20-year-old (yo) donors were obtained from AMSBIO (product codes: CR562159 and CR562389). RNA was then poly-A selected prior to stranded, paired-end RNA sequencing using an Illumina NextSeq 2000 in the Tulane NextGen sequencing core.Single-cell RNA sequencing was carried out on individual cells using the 10X Genomics Chromium™ Single Cell 3′ Library & Gel Bead Kit v3 and 150 cycle kit by the Tulane NextGen sequencing core. Eight hundred fifty-three cells were sequenced and barcoded. Sequencing was carried out on an Illumina NextSeq 2000. Pooled MCF7 and HEK293-FRT-LacZeo cells were separated by aligning reads to an FRT-LacZeo genome. Cell barcodes with reads aligning to the FRT-LacZeo locus were classified as HEK293-FRT-LacZeo cells.The shallow sequenced MCF7 scRNA-Seq dataset and mouse and human testes scRNA-Seq datasets were obtained from NCBI SRA. The shallow sequenced MCF7 scRNA-Seq dataset is listed under SRR10018060. The mouse testes datasets are listed under SRR6129050 (Mouse 1) and SRR6129051 (Mouse 2). The human testes datasets are listed under SRR6860521 (24 yo) and SRR6860523 (25 yo).The strategy for detection of L1 mRNA used here has been described previously . BrieflyBioinformatic Analysis for bulk RNA-Seq , resulting in unambiguous assignment of reads to their best genomic location , as previously reported , 30. ForThe described formula for RPM is shown below:10X Chromium Single Cell 3′ Genomics data was demultiplexed and converted into fastq format using cellranger v3.1.0 mkfastq tool. The cellranger v3.1.0 count program was then used to analyze scRNA-Seq reads and alignment of reads to the appropriate reference genome to generate a gene expression matrix. The total number of L1 UMIs from SCIFER analysis were loaded into the gene expression matrix and analyzed using Seurat v4.0.5. The datasets were normalized  and L1 expression was compared between cell clusters and cell types (FindAllMarkers).n = 2) were made using the normalized gene expression levels downloaded from the Seurat object and Welch’s t-tests.Seurat v4.0.5 was used to compare gene expression levels between clusters and cell types . Cells wt-test with Welch’s correction when making comparisons between two groups and by one-way ANOVA with multiple comparisons and “two-stage” Benjamini, Krieger, & Yekutiel for controlling the false discovery rate when making comparison within a n > 2 group. To measure linear correlation between two variables and determine the r value, a two-tailed Pearson correlation test was performed. Data presented from Seurat was analyzed using a non-parametric Wilcoxon rank-sum test with Bonferroni correction and the adjusted P-values from Bonferroni correction are plotted. Statistical analysis was performed with GraphPad Prism and Seurat v4.0.5.Bar graphs are presented with the mean and standard deviation bars. Data were analyzed by two-tailed Student’s Additional file 1. Single cell RNA-Seq reads align to the 3′ end of genes and L1 loci. A. Alignment of scRNA-Seq reads (top), bulk RNA-Seq reads (middle), and DNA-Seq reads (bottom) to the L1 consensus sequence using Bowtie v0.12.8. The sequencing read scale is indicated in the bottom left corners. B. Alignment of MCF7 bulk RNA-Seq and MCF7 scRNA-Seq reads to the actin (ACTB) gene locus (top) and an L1 locus (bottom). Images were taken from IGV and the visible tracks include, from top to bottom, chromosome location indicated by the red line, scale in base pairs, mappability from a DNA-Seq samples aligned with the same bowtie settings used for RNA-Seq , RNA molecules per cell (middle), and percent of mitochondrial reads per cell (right) for each MCF7 cell cluster. C. The number of expressed L1 loci per cell for all High coverage MCF7 cell clusters is shown in the individual value plot . D. The L1 mRNA expression level per cell for all MCF7 clusters is shown in the individual value plot . E. The normalized expression levels for MCF7 Clusters 1, 3, and 4 from Seurat analysis are shown . F. The number of reads per HKG averaged between 3 MCF7 cells downsampled in 10% intervals is shown. G. The average number of expressed HKGs detected in 3 MCF7 cells is shown with decreasing read depth . The black bars have significantly higher numbers of detected HKGs compared to the gray bars . The lightest gray bar (10%) indicates detection of less than half of expressed HKGs detected with 100% of reads. H. A correlation matrix of HKGs expressed in 10 MCF7 cells. The HKGs are listed at the top of the matrix and the 10 cells are listed along the left side. Filled boxes indicate that the HKG was expressed in the corresponding cell.Additional file 3. Low depth sequencing reduces sensitivity of L1 mRNA expression detection in MCF7 single cells. A. A t-SNE plot of the Low coverage MCF7 scRNA-Seq dataset. Cell clusters are indicated in the figure legend. B. The number of million mapped reads per cell in each cluster is shown in the individual value plot. C. L1 mRNA expression quantified by RPM for each cell is shown in the individual value plot. D. The number of expressed L1 loci per cell in each cluster is shown in the individual value plot E. The L1 FPKM values for bulk RNA-Seq (left y-axis) and L1 RPM values for Low coverage MCF7 scRNA-Seq (right y-axis) are shown in the dot-plot. Orange circles indicate L1 loci with detected expression in the bulk dataset that were not detected to be expressed in scRNA-Seq. The nested Venn diagram shows the number of shared expressed L1 loci from the bulk and scRNA-Seq datasets. The violin plot shows the FPKM values for expressed L1 loci unique to the bulk dataset and those shared between bulk and scRNA-Seq .Additional file 4. Expression patterns of genes involved in spermatogenesis in mouse testes. Cell types are abbreviated as follows: Spermatocytes (Spcyt), Round Spermatids (RS), Elongating Spermatids (ES), Condensing Spermatids (CS), Sertoli (Ser), Leydig (Ley). A. Mouse 1 gene expression patterns for TATA-Box Binding Protein Like-1 (TBPL1) (A1), Protamine (PRM1) (A2), and Transition Protein 1 (TNP1) (A3). B. Mouse 2 gene expression patterns for TBPL1 (B1), PRM1 (B2), and TNP1 (B3). C. The heat map shows the normalized expression patterns for each cell type and gene in Mouse 1 (top) and Mouse 2 (bottom). The asterisks indicate a significant change in gene expression in the cell type compared to the preceding cell type in the row (P < 0.0001). D. The normalized expression levels for Mouse 1 testis cell types from Seurat analysis are shown .Additional file 5. SCIFER analysis of L1 mRNA expression in mouse testis biological replicates. A. The number of million mapped reads per cell for each testis cell type is shown for Mouse 1 . B. The number of million mapped reads per cell for each testis cell type is shown for Mouse 2 ANOVA,, ***, < 0.0005, ****,< 0.0001). C. L1 mRNA expression measured by RPM per cell for all testis cell types is shown in the scatter plot for Mouse 1 . D. L1 mRNA expression measured by RPM per cell for all testis cells types is shown in the scatter plot for Mouse 2 . E. The number of expressed L1 loci per cell for each testis cell type is shown in the scatter plot for Mouse 1 . F. The number of expressed L1 loci per cell for each testis cell type is shown in the scatter plot for Mouse 2 . G. The L1 RPM values for L1 loci indicated on the X-axis are shown for each sperm cell type in Mouse 2. The Venn Diagram shows the number of expressed L1 loci shared by the sperm cell types with the percentage of shared expressed L1 loci indicated above the diagram. H. L1 mRNA expression compared between Mouse 1 and Mouse 2 for Spermatocytes (SC) (H1), Round Spermatids (RS) (H2), Elongating Spermatids (ES) (H3), and Condensing Spermatids (CS) (H4).Additional file 6. Expression patterns of genes involved in limiting L1 expression and integration in mice. Cell types are abbreviated as follows: Spermatocytes (Spcyt), Round Spermatids (RS), Elongating Spermatids (ES), Condensing Spermatids (CS), Sertoli (Ser), Leydig (Ley). A. Mouse 1 gene expression patterns for Phospholipase D Family Member 6 (PLD6) (A1), Heat Shock Protein 90 Alpha Family Class A Member 1 (HSP90AA1) (A2), and Ubiquitin Like with PHD And Ring Finger Domains 1 (UHRF1) (A3). B. Mouse 2 gene expression patterns for PLD6 (B1), HSP90AA1 (B2), and UHRF1 (B3). C. The heat map shows the normalized expression patterns for each cell type and gene in Mouse 1 (top) and Mouse 2 (bottom). The asterisks indicate a significant change in gene expression in the cell type compared to the preceding cell type in the row (P < 0.0001).Additional file 7. Expression of LTRs and L1 subfamilies is non uniform across single cells in mouse testis. A. The number of expressed L1 loci per L1 subfamily is shown for Mouse 1. The L1 subfamilies are indicated in the legend. B. The number of Round Spermatids expressing L1 loci from each mouse L1 subfamily is shown in the Venn diagram. C. The number of reads per LTR locus is shown for bulk RNA-Seq, Mouse 1 Single Cells, and Mouse 2 Single Cells. The Venn diagram shows the number of expressed LTR loci shared between the three datasets. D. Cells expressing at least one LTR loci are shown for each cell type in Mouse 1 (D1) and Mouse 2 (D2). LTR expression is indicated with purple and L1 co-expression is indicated with teal.Additional file 8 Expression patterns of genes involved in spermatogenesis in human testes. Cell types are abbreviated as follows: Spermatogonial Stem Cells (SSCs), Differentiating Spermatogonia (Diff Spg), Spermatocytes (Spcyt), Round Spermatids (RS), Elongating Spermatids (ES), Condensing Spermatids (CS), Macrophages (Macro), Endothelial (Endo), Myoid (Myo), and Sertoli (Ser). A. 24 yo Human Testis gene expression patterns for PRM1 (A1), SPAG6 (A2), TNP1 (A3), and TNP2 (A4). B. 25 yo Human Testis gene expression patterns for PRM1 (B1), SPAG6 (B2), TNP1 (B3), and TNP2 (B4). C. The heat map shows the normalized expression patterns for each cell type and gene in 24 yo Testis (top) and 25 yo Testis (bottom). The asterisks indicate a significant change in gene expression in the cell type compared to the preceding cell type in the row (P < 0.0001). D. The normalized expression levels for 24 yo testis cell types from Seurat analysis are shown .Additional file 9. Analysis of L1 mRNA expression in human testes with bulk RNA-Seq and scRNA-Seq. A. The L1 FPKM values for L1 loci listed on the X-axis are shown for two 20 yo human testis bulk RNA-Seq samples. The number of expressed L1 loci shared between the two replicates is shown in the Venn diagram with the percentage of shared expressed loci indicated above the diagram. B. The L1 RPM values for L1 loci listed on the X-axis are shown for a 24 yo and a 25 yo human testis scRNA-Seq sample. The number of expressed L1 loci shared between the two replicates is shown in the Venn diagram with the percentage of shared expressed loci indicated above the diagram. C. The million mapped reads per cell for all cell types in the 24 yo scRNA-Seq dataset is shown in the scatter plot. Statistics are shown for sperm cells and sperm progenitor cell types only. D. The L1 mRNA expression level per cell for all 24 yo testis cell types is shown in the scatter plot. E. The number of expressed L1 loci per cell for all 24 yo testis cell types is shown in the scatter plot. F. The million mapped reads per cell for all cell types in the 24 yo scRNA-Seq dataset is shown in the scatter plot. Statistics are shown for sperm cells and sperm progenitor cell types only. G. The L1 mRNA expression level per cell for all 25 yo testis cell types is shown in the scatter plot. H. The number of expressed L1 loci per cell for all 25 yo testis cell types is shown in the scatter plot. I. The L1 RPM values for L1 loci indicated on the X-axis are shown for each sperm cell type in the 25 yo human testis sample. The Venn Diagram shows the number of expressed L1 loci shared by the sperm cell types with the percentage of shared expressed L1 loci indicated above the diagram. J. The L1 FPKM values for bulk RNA-Seq (left y-axis) and L1 RPM values for scRNA-Seq (right y-axis) of human testis are shown in the dot-plot. Orange circles indicate L1 loci with detected expression in the bulk dataset that were not detected to be expressed in scRNA-Seq. The nested Venn diagram shows the number of shared expressed L1 loci from the bulk and scRNA-Seq datasets. K. The violin plot shows the FPKM values for expressed L1 loci unique to the bulk dataset and those shared between bulk and scRNA-Seq .Additional file 10. Expression patterns of genes involved in limiting L1 expression and integration in humans. Cell types are abbreviated as follows: Spermatogonial Stem Cells (SSCs), Differentiating Spermatogonia (Diff Spg), Spermatocytes (Spcyt), Round Spermatids (RS), Elongating Spermatids (ES), Condensing Spermatids (CS), Macrophages (Macro), Endothelial (Endo), Myoid (Myo), and Sertoli (Ser). A. 24 yo Human Testis gene expression patterns for DNMT1 (A1), MECP2 (A2), KDM1A (A3), TP53 (A4), TRIM28 (A5), ERCC4 (A6), MOV10 (A7), and RNASEH2B (A8). B. 25 yo Human Testis gene expression patterns for DNMT1 (B1), MECP2 (B2), KDM1A (B3), TP53 (B4), TRIM28 (B5), ERCC4 (B6), MOV10 (B7), and RNASEH2B (B8). C. The heat map shows the normalized expression patterns for each cell type and gene in 24 yo Testis (top) and 25 yo Testis (bottom). The asterisks indicate a significant change in gene expression in the cell type compared to the preceding cell type in the row (P < 0.05).Additional file 11. Directions for running Single Cell Implementation to Find Expressed Retrotransposons (SCIFER).Additional file 12. Coordinates of L1 loci identified to be expressed in bulk RNA-Seq of MCF7 cells and included in SCIFER analysis.Additional file 13. Coordinates of LTR loci identified to be expressed in bulk RNA-Seq of 2 mo mouse testes and included in SCIFER analysis.Additional file 14. Coordinates of L1 loci identified to be expressed in bulk RNA-Seq of 2 mo mouse testes and included in SCIFER analysis.Additional file 15. Coordinates and FPKM of L1 loci identified to be expressed in bulk RNA-Seq of 20 yo human testes and included in SCIFER analysis.Additional file 16. Results of comparing gene expression values in mouse testes using unpaired t-test with Welch’s correction.Additional file 17. Results of comparing gene expression values in human testes using unpaired t-test with Welch’s correction.


Based on coupled-mode theory (CMT) and the finite-difference time-domain (FDTD) approach, we propose a graphene metasurface-based and multifunctional polarization beam splitter that is dynamically tunable. The structure, comprising two graphene strips at the top and bottom and four triangular graphene blocks in the center layer, can achieve triple plasma-induced transparency (PIT). In a single polarization state, the computational results reveal that synchronous or asynchronous six-mode electro-optical switching modulation may be performed by modifying the Fermi levels of graphene, with a maximum modulation degree of amplitude (MDA) of 97.6% at 5.148 THz. In addition, by varying the polarization angle, a polarization-sensitive, tunable polarization beam splitter (PBS) with an extinction ratio and insertion loss of 19.6 dB and 0.35 dB at 6.143 THz, respectively, and a frequency modulation degree of 25.2% was realized. Combining PIT with polarization sensitivity provides a viable platform and concept for developing graphene metasurface-based multifunctional and tunable polarization devices. Polarization, along with amplitude and phase, is an essential property of electromagnetic wave propagation. A polarization beam splitter (PBS) is a crucial polarization modulation device that can separate two orthogonal polarization modes in electromagnetic waves and can be used in single-polarization devices within various parts of an integrated system so that subsequent chip signal processing can be performed independently. Consequently, it has significant applications in optical storage, optical communication, and integrated optical circuits ,2,3, andMany scientists prefer graphene because it exhibits less major losses in metamaterials than conventional metallic materials. Metamaterials made of graphene also benefit from dynamic modulation, which modifies the graphene’s Fermi levels by varying the externally supplied bias voltage to induce various visual phenomena. In optical devices, including electro-optical switches ,12,13,14However, the majority of these devices only work in one polarization state. PBSs have become a popular area of research because integrated systems require a polarization control mechanism to maintain a single polarization state across the system. Due to their low process needs and straightforward design, most PBSs are currently constructed using the directional coupling design approach. For instance, Tian et al., developed a portable ultra-wideband PBS , while BThis work proposes a triple-layer metamaterial made up of two graphene strips and four graphene blocks. Finite-difference time-domain (FDTD) simulations were performed , and couachieved . Xia et achieved . The extachieved  and becoy-polarized light, and transmission spectra as shown in y-direction is present alone. The graphene strip in the x-direction is not instantly activated by the incident light when it exists independently. Instead, it belongs to a dark mode, as indicated by the black line in The top view structural unit of the graphene metamaterials is shown in As shown by the green line in A representing Bright Mode 1, resonant cavity B representing Bright Mode 2, and resonant cavity C representing Dark Mode. As a result, incoming light can stimulate it twice, making it a bright mode (Bright Mode 2). Triple PIT is produced at Peak 1, Peak 2, and Peak 3 when the three structures are combined. Furthermore, when the three-layer graphene structure is present, Bright Mode 1 influences the interstitial coupling between the graphene blocks, which results in some deviation of Peak 2 from the resonance point at 8.034 THz and transmission spectra of the entire structure, as shown by the red line in A, B, and C can be expressed by the following equation [A, B, and C, and is related to the thickness of the dielectric films A, B, and C are the amplitudes of the three modes, “in/out” are the input or output waves, and “Based on the schematic diagram, the relationship between resonant cavities equation .(1)y-polarized state, as depicted in Firstly, we analyze the results in the As shown in The performance of the electro-optical switch can be expressed by the modulation degree of amplitude (MDA) :(13)MDA=Firstly, the polarization angle of the incident light is varied from 0° to 90°, as shown in x-polarized state. Due to the different pinch distances of the graphene blocks in the x and y directions, the distance between the two resonance points increases. Still, x-polarization does not couple with the Dark Mode to generate the PIT. These are the primary reasons for the polarization sensitivity of this structure. The polarization sensitivity we analyzed coincides with Zhang’s theory that the PIT of metamaterials is destroyed when the polarization angle changes [As shown in  changes .y-polarization is selected, and the x-polarization is filtered out. Instead, the x-polarization is filtered out at 3.201 THz, and the y-polarization is filtered out at 7.062 THz. These enable the realization of a multi-frequency polarizer. When combined with the polar coordinates in The four frequency points’ specific modulation positions and implementation mechanism are denoted in x-polarization and 0.42, 0.04, 0.09, and 0.4 for y-polarization, respectively. As mentioned in some articles, the transmittance is considered to be in a normal operating state when it is greater than 0.8 [x-polarization wave is reflected with a reflectivity of up to 86% and almost no absorption, so we can assume it is entirely reflected back. At this frequency point, the orthogonal polarizations are spatially separated, creating an excellent polarization beam splitter. As shown in x-polarized light is reflected, and y-polarized light is transmitted directly. In addition, the performance of a PBS is typically determined by the polarization extinction ratio (PER) and insertion loss (IL), as shown in the following equations [x- and y-polarization were synchronously blue-shifted.As shown in than 0.8 . Only atquations :(14)PER=This PBS can be dynamically modulated by changing the Fermi levels of graphene. The modulation degree of frequency is typically used to describe the frequency modulation effect, as shown in the following equation:In conclusion, we simulated a three-layer metamaterial structure of two graphene bands and four graphene blocks. Based on plasma-induced transparency, a six-mode dynamically tunable synchronous and asynchronous electro-optical switch was achieved by tuning the Fermi levels of graphene; its MDA is 80.1%, 97.6%, 67.8%, 80.2%, 80%, and 84.9 % at 3.021 THz, 5.148 THz, 6.248 THz, 7.062 THz, 7.745 THz, and 9.458 THz, respectively. Moreover, we explored the impact of polarization angle variation on graphene metamaterials. The results demonstrate that a change in the polarization angle disrupts the PIT formed by the structure, resulting in polarization sensitivity. Consequently, a polarization beam splitter was constructed with PER and IL values of 19.6 dB and 0.36 dB, respectively. In addition, based on the dynamic tunability of graphene, the operating frequency point of the polarization beam splitter is adjustable with an MDF up to 25.2%. This research lays the groundwork for the future construction of graphene-based multifunctional optoelectronic devices and configurable polarization beam splitters. The findings provide a theoretical basis for designing and implementing graphene-based, multifunctional, fully transmittable metasurface beam splitters for on-chip integration.


Plasmon coupling and hybridization in 2D materials plays a significant role for controlling light–matter interaction at the nanoscale. We present a near-field radiation heat transfer (NFRHT) between vertically separated graphene and black phosphorene sheets at different temperatures in nanoscale separations. Radiation exchange from the theory of fluctuation electrodynamics is modulated by the carrier density of graphene and phosphorene. Direct comparison of NFRHT black phosphorene–graphene to symmetric graphene–graphene radiation exchange can be as much as 4 times higher for the selected doping range in both armchair (AC) and zigzag (ZZ) orientations of BP. The strong NFRHT enhancement of the specific optical properties of the heterogenous 2D material is due to the strong coupling of propagating surface plasmon polaritons as demonstrated by the distribution of the heat transfer coefficient. We also demonstrate that the magnitude of the near-field radiation enhancement is found to acutely depend on the vacuum gap of the graphene and BP pair. Interestingly, for separation distances below 200 nm, the total near-field heat transfer between black phosphorene and graphene exceeds that between graphene and graphene by 5 times. The radiation enhancement can be further tuned based on the orientation, AC, and ZZ of black phosphorene. These results prominently enable dynamic control of the total NFRHT relying on tunable anisotropic characteristics of BP irrespective of graphene's optical conductivity. Furthermore, the heterogeneous pairs of 2D materials potentially provide alternative platforms to achieve beyond super-Planckian radiation. Plasmon coupling and hybridization in 2D materials plays a significant role for controlling light–matter interaction at the nanoscale. Control of NFRHT has been covered in several structural arrangements and materials;11–17 however, a challenge arises in enhancing NFRHT due to the large number of independent parameters, and more importantly, lack of degree of freedom for active tunability.Near-field radiative heat transfer (NFRHT) between two bodies separated by a distance much smaller than or comparable to the thermal wavelength can break the blackbody (BB) limit.2 and, very recently, black phosphorene.18–21 Graphene exhibits highly tunable optical properties via voltage-gating,18,22 good thermal stability,23 and high carrier mobility.18 Moreover, graphene supports strongly confined surface plasmons with a frequency that varies with the wave number.24–26 Theoretically predicted tuning and coupling of surface mode plasmon of a graphene sheet with a nearby body, resulting in a significant increase of the NFRHT,27–30 has been confirmed experimentally.31 In addition, the near-field active thermal radiation response of graphene in subwavelength geometries, graphene ribbon,32,33 periodic nanoribbon,34 or nanodisks35–37 has demonstrated enhanced radiation. Most recently, Black phosphorus (BP) is also reported to have a layer dependent tunable direct bandgap,38 thermal stability,39 high carrier mobility,20,21 and remarkable in-plane anisotropic electrical and optical properties.40 In contrast to graphene, BP shows polarization dependency in the anisotropic surface plasmon response due to an order of magnitude difference in the in-plane effective electron masses along the two crystal axes results.41,42 These plasmon properties allow for the realization of novel 2D polarization dependent and tunable NFRHT.33,43–45 Another interesting approach to study is the NFRHT between heterogenous 2D material, shown to be possible using a graphene sheet and a MoS2 sheet.46 However, both graphene and MoS2 are nearly isotropic materials. This makes the graphene and MoS2 orientation indiscriminate in light matter interaction. Recently, the NFRHT of the graphene (GR) heterogenous (GR–BP) in contact with bulk substrate SiC has shown anisotropic effects in near field radiation heat transfer.47 However, SiC supports hyperbolic phonon polariton modes in the midinfrared range. In hybrid structures composed of 2D material, graphene/SiC or BP/SiC, SPPs can couple with hyperbolic phonon polariton.47 The hybrid modes move from the substrate and introduce a change in the propagation, and evanescent waves either greatly improve or reduce the NFRHT by creating a new channel. Therefore, it is important to understand the NFRHT and tuning capability graphene and BP heterogeneous system without dispersive hyperbolic layer.In this context, a breakthrough for active tuning mechanics has been effectively achieved in two-dimensional (2D) semiconductors: prominently graphene or MoS48 the near-field radiation transfers energy between the BP and the graphene, which are compared to two identical suspended graphene sheets by analysing the distribution of the heat transfer coefficient of the emitter and the receiver 2D layers. The NFRHT model shows that BP–GR has a more selective optical modulation compared to the graphene–graphene system. Furthermore, the NFRHT differences between these two systems are explored, considering the inherent BP optical anisotropy nature. The effect of the reorientation of BP is found to be significant in modulating the NFRHT, perhaps creating possible conditions roughly equivalent to or greater than graphene. The hybrid modes, which evolve from low to high parallel wave vectors in the infrared range, controlled by graphene and BP optical parameters determine the tunnelling probability. We also discuss the total radiation, enhancement in the 2D structure relative to the value of separation distance, offering potential routes toward passive or active control of NFRHT. In particular, we examined the ratio of total heat transfer of BP–GR and GR–GR, and its dependence on the anisotropy, doping, and spacing.Through numerical and analytic solutions based on the transfer matrix method combined with fluctuation electrodynamics,σg(ω), is modelled with a 2D sheet conductivity that includes the contribution of an intraband transition term σD , and interband transitions term, σI, where σg(ω) = σD(ω) + σI(ω).49G(x) = sinh[x/kBT]/[cosh(μ/kBT) + cosh(x/kBT)], e is the electron charge, ℏ is the reduced Planck constant, kB is the Boltzmann constant, μ is the chemical potential, T is temperature, ω is the angular frequency, and τ is the relaxation scattering time, which we have fixed to the value τ = 10−13 s.50The optical conductivity in graphene, σjj, of BP is given by a simple semiclassical Drude model in the infrared regime,40j represents AC and ZZ-direction η describes the relaxation rate and is chosen to be 10 meV40 which is within the range obtained from ab-simulation51 and Di = πne2/mj is the anisotropic Drude weight, n is the electron doping, and mj represents the layer dependent effective mass of electrons along the j, (AC or ZZ) direction. In this work we use monolayer BP with arm-chair, mx = 0.15m0, and zigzag, my = 0.7m0, direction masses, where m0 is the free electron mass.40The anisotropic layer dependent surface conductivity, σij, consisting of transverse conductivities, longitudinal conductivities, and crossed conductivity components, which lies in the xy-plane. We obtain the Fresnel coefficients solving Maxwell's electromagnetic equation imposing the appropriate electromagnetic field boundary condition and representing the 2D conducting sheet surface current (Js) from Ohm's law. We assume that the electric field Ei in medium i, and Ej in medium j, i and j indicated medium above and below the 2D layer, with dielectric permittivity εi = εj = 1.0. The corresponding magnetic field components, Hi and Hj, can be found using Maxwell's equation. The boundary conditions of the parallel and perpendicular gives n̂ × (Ei − Ej) = 0, n̂ × (Hi − Hj) = Js. The unit vector normal to the 2D layer is n̂ = −ẑ, and Js = σijE. Solving the boundary conditions, the Fresnel coefficients of reflection for s, p and the cross-polarization term expressions are52,53rppij, rssij and rspij are the Fresnel coefficients between the medium i and j for s, p and the mixture sp polarization. The z-component wavevector for s and p-polarization along each region is , , and ε0 is the vacuum permittivity, μ0 is the vacuum permeability and β is the wave vector parallel to the surfaces of the 2D layers. This work studies BP AC orientation aligned with x-direction and ZZ along y-axis and vice versa. The incident polarization direction is collinear to one of the principal BP directions so that the crossed conductivity effect, σxy = 0, results in the cross-polarization rps = 0. A similar method has been followed recently by Xiao-Jie Yi et al.47 A rotated BP from the optical axis does change the momentum vector of along x and y and hence the expression of the reflection spectra.54Before setting the model of radiation heat transfer, we examined the light–matter interaction for the suspended isotropic 2D materials. As shown in TE) and the thermally cold (TR) surfaces can be formulated following the framework of fluctuational electrodynamics as:55q(ω) is the net spectral heat flux, Θ = ωℏ/(exp(ωℏ/kBT) − 1)is the average energy of Planck's oscillator, and ξs(p) is the energy transmission coefficient that depends on the frequency and wave vector corresponding to s(p)-polarization of light. The energy transmission coefficient considering polarization coupling and contribution of evanescent modes, β > k0, and propagating modes, β < k0, is given by56k0z is the normal wavevector component in vacuum of BP and graphene, Im takes the imaginary part of a complex quantity, and d is the distance of the vacuum gap.Now the NFRHT initiated by the coupling of the propagating surface modes meditated between the thermally hot  and σR (receiver), respectively, are brought into proximity with a vacuum gap separation d. The temperatures of the emitter and the receiver are labeled TE = 300 K and TR = 290 K, (TE > TR), respectively. We represent gate modulation or applied voltage bias effect in terms of changing the carrier density n, of graphene and BP. This indirect relation of gate-modulation of BP and graphene can be controlled independently leading to more degrees of freedom. The carrier density potential of graphene can be described also in terms of chemical potential, ng = μ2/(ℏvf)2π, where vF = 106 ms−1 is the Fermi velocity. The values of ng used in this work ranges from 0.74 × 1012 cm−2 to 4.7 × 1013 cm−2, with an equivalent range of μ = 0.1 eV to 0.9 eV, and nb = 2.0 × 1012 cm−2 to 9.0 × 1013 cm−2 in order to get optimum NFRHT.Throughout the paper, we consider the configuration in x-direction and ZZ is in the y-direction. The separation distance d between graphene and BP is 10 nm. The figure shows the spectral heat flux (SHF) calculated from ng = 0.74 × 1012 cm−2, 6.6 × 1012 cm−2 and high doped 2.65 × 1013 cm−2, which corresponds to a chemical potential of μ = 0.1 eV, 0.3 and 0.6 eV, respectively, and BP varying the doping-level, nb = 0.5 × 1013 cm−2, 1.0 × 1013 cm−2, 5.0 × 1012 cm−2.First, we consider the scenario in TE = 300 K and TR = 290 K. We selected identical gate voltage for the emitter and receiver graphene, ngE = ngR = ng since the latter case shows strong spectral heat flux.38 Therefore, low gate modulated NFRHT between identical graphene shows enhanced radiative energy transport than between low and highly gate modulated graphene. Further support of this conclusion is provided in the ESI Fig. 1 (a) and (b).ng = 0.74 × 1012 cm−2 and decreases more than ten times when the doping is 2.65 × 1013 cm−2. In addition, at higher graphene carrier density, ng = 2.65 × 1013 cm−2, SRH becomes broader due to weakening of interband effect.27,29,38 In the case of BPE–GRR, increasing number density nb from 0.2 × 1013 cm−2 to 5.0 × 1013 cm−2 has a dramatic effect on the SHF at low carrier density, ng = 0.74 × 1012 cm−2, n. Compared to BPE–GRR for all ng and nb, GRE–GRR is higher than BPE–GRR at ng = 2.65 × 1013 cm−2. The role of the dependency of ng and nb on the SHF is further evaluated for 6.6 × 1012 cm−2 and 2.65 × 1013 cm−2, ng = 4 × 1012 cm−2 SHF for BPE–GRR is higher than the that of GRE–GRR from moderate to high doping, ng = 6.6 × 1012 cm−2 the SHF of BPE–GRR is smaller than GRE–GRR and larger by a factor of two for nb = 5.0 × 1012 cm−2 and 5.0 × 1013 cm−2. This indicates in BPE–GRR there is a critical nb value between 5.0 × 1012 cm−2 and 1.0 × 1013 cm−2 making the transition of enhanced SHF than GRE–GRR, in ng = 2.65 × 1013 cm−2, we observe that BPE–GRR 2D system outperforms identical graphene sheets, within the whole range of nb, having two times higher SHF for ng = 1.0 × 1013 cm−2 and 5.0 × 1013 cm−2.In all figures of x-axis and AC direction is along the y-axis. For this purpose, we show in nb is close to 1.0 × 1013 cm−2 for ng = 0.74 × 1012 cm−2, reaches a minimum or a comparable density to GRE–GRR system. In the ZZ direction the SHF can be tuned by a factor of 2 to 4 between nb = 0.5 × 1013 cm−2 and nb = 1.0 × 1013 cm−2.So far, we have discussed the case of doping effect of BPE–GRR in AC orientation. However, besides electrostatic tuning of graphene and BP, effective mass of BP is readily different in the AC and ZZ direction, as shown in the optical conductivity 12 cm−2, a consistent result of AC orientation  in ξ of the BPE–GRR system, similar to the case in nb = 0.5 × 1013 cm−2, 1.0 × 1013 cm−2 and 5.0 × 1013 cm−2 and ng = 0.74 × 1012 cm−2 and 6.6 × 1012 cm−2 at separation distance, d = 10 nm.To explain the different phenomena observed in 27,28 Here one mode is originated from the BPE side and a second from the GRR; they are labelled SPB and SPG, respectively. The band are characteristics reflections of the SPPs dispersion band and an indication of electromagnetic coupling process of BP and graphene. The strength of the two bright band colors indicates a high transmission coefficient and the coupling strength of the SPPs of black phosphorene and graphene. Therefore, they are the major contributors to the SHF between black phosphorene and graphene. In nb = 0.5 × 1013 cm−2 and for ng = 0.74 × 1012 cm−2. The upper branch is BP like, and lower branch is graphene like. Short momentum and frequency spanning in the lower branch are due to the interband transition damping, specifically at energies ħω < 2μ.26,28,34The contours show two bright bands covering a wide range of frequencies and momentum. These bright bands correspond to the symmetric (lower frequencies) and anti-symmetric (higher frequencies) branches of the coupled SPPs between 2D materials.nb, indicating mismatch between the hybrid SPPs modes of the BP emitter and the graphene receiver, ng = 6.6 × 1012 cm−2, nb similarly increases movement of the bright band and shifts towards higher ω and a lower β. The rise in strong offsets of the branches lead to the overall reduction of the NFRHT observed at a large ng GB/QGG, as an efficiency factor to gain better insight into the performance of BP and graphene, where QGB is the BPE–GRR system total heat flux and QGG is the GRE–GRR system total heat flux.The strong modulation of the NFRHT between GR and BP is shown to be quite generic, and it appears to be influenced by a wide range of parameters. We test this concept by exploring the total radiation, Q, is computed for a range of BP and graphene carrier densities for extremely narrow separation d = 10 nm, intermediate d = 100 nm, and a larger separation d = 750 nm, which are displayed in d = 10 nm to d = 500 and 750 nm, the monotonic decrease of both maximum and minimum total heat flux is obvious because of the weaker SPPs coupling at a larger gap distance. In addition, this reduction is a result of weak near-field coupling and short propagation distance of the evanescence field, which decreases the available of plasmonically-activated modes. The heat flux ratio reaches up to the maximum scale 1.5, at d = 10 nm in both AC and ZZ orientation, η, diminishes for nb of BP and for all ng in AC orientation, while in ZZ orientation of BP leads to a greater η. From this theoretical analysis, we can conclude that BP–GR system shows superiorities compared to GR–GR in designing super Plank radiation heat transfer. As the separation increases further, efficiency of η > 1 is still sustained for the selected doping range, ng from 0.74 × 1012 cm−2 to 4.7 × 1013 cm−2 and nb from 2.0 × 1012 cm−2 to 9.0 × 1013 cm−2, there is a linear bright region that shows efficiency η > 1. Specifically, for ng < 1.18 × 1013 cm−2 and nb above 2.0 × 1012 cm−2 in ZZ orientation and from 0.1 eV to 0.8 eV and BP doping level up to nb = 5.0 × 1012 cm−2 AC orientation. Away from this BP and graphene carrier density range, the ratio is less than 1 irrespective of the BP orientation, which is an undesirable case for NFRHT enhancement of the heterogeneous 2D BP–GR system. However, this theoretical result suggests an alternate solution of realizing enhanced and reduced near-field radiation heat transfer mechanism. In particular, we can freely control the functionality of this heterogeneous system enhancing and reducing heat transfer by changing the orientation of BP and doping of both BP and graphene. Furthermore, our results demonstrate the superiority of this heterogeneous 2D material pair, which give rise to the anisotropic thermal emission by physical reorientation of BP in addition to gate-modulation of graphene and doping of BP.The total heat flux, 12 cm−2). However, in the BPE–GRR system, the NFRHT critical value is significantly enhanced when a gate (>3.0 × 1012 cm−2) is applied to graphene and BP for selective doping. By choosing appropriate parameters of doping level of BP and graphene, a NFRHT 4 times higher can be achieved in BPE–GRR than GRE–GRR. This enhanced NFRHT effect is also realized in the total heat flux BP–GR pairs leading to more than 5 times higher than GR–GR system at d < 100 nm. In addition, by varying the relative orientation of the BP layer, one can switch from amplified NFRHT to reduced or vice versa. The NFRHT in 2D heterogeneous system resulting from preferential orientation would be dependent on the combination of gate-voltage (carrier density). Thus, for a given carrier density of BP and graphene, the heat tunnelling should be adjusted to obtain the desired radiation transfer either enhanced or reduced. We believe that our work contributes to the active pursuit in the field of SPPs supporting hybrid nonidentical 2D structures both made from atomically thin (few layers) materials. This study can further motivate future studies of hybrid surface plasmon induced NFRHT between new discovered anisotropic 2D ReS2 and ReSe2.57,58Our work explores NFRHT originated from SPPs assisted photon transmission for a pair coupled graphene and BP heterogeneous 2D materials. We found that the radiation beyond the Plank limit and enhanced photon tunnelling is favourable in a homogenous graphene–graphene system for low-gate modulation (<3.0 × 10The authors declare no conflict of interest.RA-009-C9RA04695J-s001