Sarcoidosis and Mediastinal Tuberculous Lymphadenitis (MTLA) are two granulomatous diseases. Differentiation between these two diseases is dependent on clinical presentation, microbiological investigation, and cytopathological examination. In endemic regions, differential diagnosis of MTLA and sarcoidosis might be difficult. Endobronchial ultrasound guided Transbronchial Needle Aspiration (EBUS-TBNA) is a new diagnostic procedure for the diagnosis of mediastinal lymphadenopathy. EBUS not only enables the sampling of Lymph Nodes (LN), but also visualization of sonographic features of them. We hypothesized that the sonographic features of LN may help to differentiate MTLA from sarcoidosis.This is a retrospective analysis of patients with intrathoracic lymphadenopathy who underwent EBUS-TBNA and were finally diagnosed as sarcoidosis or MTLA. Size, shape, margin, echogenicity, and coagulation necrosis were compared between the groups.A total of 257 LNs  were examined in 101 patients. A heterogeneous echotexture of lymph nodes was significantly more common (P <0.0001) in MTLA (69%) than sarcoidosis (36.2%). Also, necrosis was statistically significantly higher in MTLA compared to sarcoidosis (P<0.0001). The vascular pattern was similar in both groups (P=0.9050). Nearly half of the patients had grade 1 vascular pattern in both groups. The odds for diagnosis of MTLA were significantly higher in the presence of heterogeneous echotexture  or necrosis sign .Vascular patterns of two diseases were similar. Heterogeneous echotexture and necrosis sign in the LNs on EBUS are specific for MTLA. Combination of these findings with a positive tuberculin skin test, favors the diagnosis of MTLA over sarcoidosis. Mycobacterium tuberculosis (M. tuberculosis), Tuberculin Skin Test (TST) and cytopathological features of granulomas  are two granulomatous diseases. Differentiation between these diseases is dependent on clinical presentation, microbiological investigation for anulomas , 2.Conventional Transbronchial Needle Aspiration (TBNA) has long been the available diagnostic procedure –5. RecenIn endemic regions, differential diagnosis of MTLA and sarcoidosis might be difficult. The microbiological investigation is highly specific. However, its sensitivity is low. In some situations, stains fail to identify the bacilli. In theory, cytopathological features of sarcoid and tuberculous granulomas are different. The presence of necrosis in granulomas is diagnostic for MTLA. However, sarcoid granulomas might occasionally be necrotizing and tuberculous granulomas non-necrotizing .Studies revealed that EBUS sonographic features of LNs such as round shape, distinct margin, heterogeneous echogenicity, the absence of Central Hilar Structure (CHS) or the presence of necrosis may help to differentiate metastatic LNs from non-metastasic LNs –17.In this study, we hypothesized that the sonographic features of EBUS may help to differentiate MTLA from sarcoidosis.In this retrospective study, we enrolled patients with a final diagnosis of MTLA or sarcoidosis among the patients who underwent EBUS-TBNA between 2011 and 2015. Size, shape, margin, echogenicity, presence or absence of a central hilar structure or coagulation necrosis were compared between the two groupsM. tuberculosis either with Acid-Fast Bacilli staining (AFB) and/or culture and clinical and radiological response after treatment or spontaneous remission.The diagnosis of sarcoidosis was made on the presence of consistent clinical and radiological presentation; demonstration of granulomatous inflammation on EBUS without detection of M. tuberculosis; a positive Nucleic Acid Amplification (NAA) test result with high clinical suspicion of histological changes consistent with tuberculosis (granulomatous inflammation with or without necrosis); or supportive histological changes (granulomatous inflammation without necrosis) with high clinical suspicion and a response to anti-tuberculosis treatment.Patients were diagnosed as MTLA if there was necrotizing granulomatous inflammation or culture and/or AFB of sampled LNs were positive for All procedures were performed by the same bronchoscopist through the oral route under local anesthesia and conscious sedation with an EBUS-guided TBNA bronchoscope . Each LN was punctured at least twice, and tissue core specimens were obtained with a 22-gauge needle. The aspirate was then blown on to a glass slide and also cell blocks were obtained. If no tissue core specimen was obtainable from the initial two aspirations, three or more aspirations of the LN were performed until enough tissue core was obtained.The aspirate was smeared onto glass slides and stained with Hematoxylin and Eosin (HE). Additionally, cell block was prepared . Rapid On-Site cytological Examination (ROSE) was not available.mL of Middlebrook 7H9 medium and vortexed. Then, the suspensions were digested and decontaminated by using a commercial decontamination kit; Mycoprosafe . Mycobacterial cultivation was performed by MGIT 960 system  according to the recommendations of the manufacturer as described elsewhere  Assay on the basis of BD ProbeTec ET system , which utilizes homogenous Strand Displacement Amplification (SDA) technology and fluorescent Energy Transfer (ET). Real-Time PCR was used for molecular detection. The NAA test was performed and evaluated according to the recommendations of the manufacturers.NAA tests were used for detection of cm or ≥ 1 cm,Size; short –axis dimension< 1 Shape; oval or round Echogenicity; homogeneous or heterogeneous Presence or absence of necrosis EBUS images of LNs were classified according to previous studies , 20.SizGrade 0: no blood flowGrade 1: few vesselsGrade 2: few flow signals and/or few small vesselsGrade 3: rich flow, more than four vessels with different diameters and twist helical flow signal.EBUS doppler – mode image characteristics of LNs Vascular pattern characteristics of LNs were categorized based on the study by Nakajima et al. :Grade 0http://www.statsdirect.com). Data were expressed as the mean±standard deviation (SD) or number with a percentage. Differences between continuous variables in the 2 groups were evaluated with Mann-Whitney U test; differences between categorical data were compared using the x2 test or the Fisher exact test. Multivariate logistic regression analysis was performed to define factors predicting the diagnosis of tuberculosis.Statistical analysis was performed using the commercial statistical package StatsDirect  were examined. Subcarinal LNs were the most sampled station. Patients with sarcoidosis were significantly younger compared to MTLA. The short axis of the LNs on EBUS ranged from 4 to 34 s of LNs .The percentage of conglomerate LNs was significantly higher in the sarcoidosis group. In both groups, most of the LNs had distinct margin. The percentage of heterogeneous echotexture was 69% in the MTLA group and 36.2% in the sarcoidosis group. The difference was statistically significant (P<0.0001). Also, necrosis was statistically significantly higher in the MTLA group (42.9%) compared to sarcoidosis (2.3%) (P<0.0001). The vascular pattern was similar in both groups (P=0.9050). Nearly half of the patients had grade 1 vascular pattern in both groups . Presencmm. This difference was statistically significant (P=0.001).The odds for diagnosis of MTLA were significantly higher in the presence of heterogeneous echotexture  or necrosis sign (OR 131.2) . In the On multivariate analysis, the presence of heterogeneous echotexture and the necrosis signs were significant predictors of the diagnosis of MTLA. A combination of a positive TST with either heterogeneous echotexture or necrosis sign had a specificity of 91% for a diagnosis of MTLA .In this study, we compared the EBUS sonographic characteristics of LNs in patients with sarcoidosis and MTLA. The results of this study suggest that heterogeneous echotexture and necrosis in the LNs on EBUS favor a diagnosis of MTLA over sarcoidosis.A few studies described the ultrasonographic features of LNs in sarcoidosis and MTLA –24. ImaiResearchers have compared the ultrasonographic features of sarcoidosis and tuberculous lymphadenitis. Dhooria et al. reported that heterogeneous echotexture or necrosis was specific for tuberculosis . Rana etIn our study, there wasn’t any statistically significant difference between sarcoidosis and MTLA regarding size and margins of LNs. As previously stated , a distimm as positive in order to provide a comparison point for our results with previous studies. The percentage of patients with a TST≥10 mm was significantly higher in the MTLA group. However, TST cut-off differs according to the underlying disease. For example, in patients with underlying immunosuppression, TST is positive if ≥5 mm or TST≥10 mm in patients with the end-stage renal disease. Furthermore, TST can be false positive in patients who were vaccinated with Bacille Calmette–Guerin (BCG)  .Previous studies , 26 haveOur study has some limitations. First, it’s a retrospective, single-center study with a limited number of patients, especially in the MTLA group. In addition, we did not follow any numeric criterion for defining the shape.In conclusion, the sonographic features of LNs may be reassuring for the final diagnosis. Heterogeneous echotexture and necrosis in LNs on EBUS are specific for MTLA.


The effects of deposition time and annealing temperature on the quality of SnS2 films was investigated in detail. By optimizing the preparation conditions, the SnS2 array film exhibited efficient photoelectric detection performance under sunlight. Furthermore, in order to improve the performance of the photodetector based on SnS2 nanosheets film, a transparent graphene film was introduced as the hole-transport layer by wet-chemical method directly transferring techniques. Graphene/SnS2 nanosheets array film heterojunction photodetectors exhibit enhanced photoresponsivity. The light on/off ratio of the photodetector based on graphene/SnS2 was 1.53, about 1.4 times higher than that of the pristine SnS2 array films. The improved photoresponse performance suggested that the effective heterojunction between vertical SnS2 nanosheets array film and graphene suppresses the recombination of photogenerated carriers. The results indicate that the graphene/SnS2 heterojunction photodetectors have great potential in photodetection devices.Two-dimensional (2D) metal dichalcogenides have attracted considerable attention for use in photoelectric devices due to their unique layer structure and strong light-matter interaction. In this paper, vertically grown SnS GraphenD materiae sheets . As a ree sheets ,5, photoe sheets ,7,8, trae sheets ,10, batte sheets , photovoe sheets , photocae sheets ,14, and e sheets ,16 and te sheets , environe sheets , and opte sheets ,20, Howee sheets .2 is an n-type semiconductor with a layered cadmium iodide (CdI2) structure. Each layer is covalently bonded by three atomic planes and separated by weak van der Waals interaction. SnS2 exhibits a high optical absorption coefficient and strong photoconductive properties in visible regions and this has given rise to increased interest due to its particular structure, suitable band gap (~2.2 eV), good chemical stability, low-cost and environmental friendliness [2 thin film for location-selective synthesis, and the response time and quantum efficiency of the fabricated photodetector was ~5 microseconds and 11.3%, respectively. Tao et al. [2 self-assembled microsphere film by double-sided tape. The device shows a good photoresponse in the region of UV (300 nm) though to NIR (830 nm) light. However, vertical SnS2 nanosheets array film combined with transparent graphene film for photodetector application has rarely been investigated.Recently, the combination of graphene with various two-dimensional (2D) layered materials has proven to be an effective strategy to achieve the unique electronic and optoelectronic applications of 2D materials ,23,24. Andliness . Therefondliness ,27, solandliness ,29, photndliness ,31, fielndliness ,33, photndliness ,35,36, endliness  used cheo et al.  studied 2 film vertically grown on conductive fluorine-doped tin oxide (FTO) glass substrate was fabricated by the low-temperature CBD method. The optimal fabrication conditions for pure SnS2 array film was investigated. After annealing treatment at 300 °C in nitrogen atmosphere, the crystalline of SnS2 showed an obvious improvement. A highly transparent graphene thin film was deposited onto n-type SnS2 array film to form a Schottky junction. The graphene/SnS2 heterojunction was constructed by the direct wet-chemical transfer method. Graphene, as a hole-transport layer, promotes the charge transfer at the interface of the heterojunction. The corresponding photodetector based on graphene/SnS2 composite film shows enhanced and stable photoelectric performance. In this work, SnS2. The cleaned substrates were further treated by plasma for 5 min. SnS2 nanosheets array film was synthesized by the CBD method, similar to that previously reported in [2 film is shown in 4·5H2O  was dissolved in 240 mL anhydrous ethanol. The mixture was stirred for 15 min under ambient conditions before 0.15 mol thioacetamide  was added. Then, the mixture was placed in a beaker of 50 mL volume. Finally, a piece of cleaned FTO substrate was placed at an angle against the wall of the beaker with the conductive side facing down. The CBD process was carried out at 60 °C in a water bath kettle for 0.5 h, 1 h and 1.5 h, respectively. When the kettle was cooled down to room temperature, the FTO substrates were removed and thoroughly rinsed with deionized water. Finally, the samples were dried in an oven at 80 °C for 6 h. To further remove any impurities on the sample surface and improve the crystallinity, the samples were annealed at 250 °C, 300 °C and 350 °C for 1 h in nitrogen (N2) atmosphere [All chemicals in the experiment were of the highest purity available and were used without further purification. In this experiment, the resistivity of distilled water was 18.0 M Ω cm. FTO substrates were ultrasonically cleaned successively with acetone, isopropanol, and ethanol, followed by rinsing with deionized water and drying in the flow of Norted in . The synmosphere . The pre2 heterojunction was constructed by the wet-chemical transfer method [2 film. The large area of graphene films on Cu foil substrates were purchased from the Graphene Technology Corporation, China. Firstly, graphene film was delaminated from the Cu foil by the conventional polymethyl methacrylate  assisted transfer method  solution for 6 h to etch the Cu foil completely. The floating PMMA/graphene films were fished out and rinsed several times in deionized water. Finally, the PMMA/graphene film was picked up by FTO substrates with SnS2 nanosheets grown and dried in a flow of N2, as shown in 2 heterojunction films were then used for photodetector fabrication. Graphene/SnSr method ,43, wher2 and graphene/SnS2 thin films was investigated by an electrochemical workstation . The CHI electrochemical workstation was used to measure dark and illuminated current at a scan rate of 10 mV/s. The bias voltage was 3 V. The active area of samples was kept at 1 cm2 by a mask. A 500W xenon lamp was used to simulate sunlight. . The morphology and microstructure of the samples were characterized by field emission scanning electron microscope (SEM) ). The composition of the crystal structure was identified by X-ray diffractometer  using Cu Kα radiation (λ = 1.5418Å). UV-vis absorption was recorded with Cary 5000 UV-Vis-NIR spectrophotometer  in the range of 350 nm to 800 nm. In order to investigate the photoelectric performance of the samples, Au electrodes were deposited on the samples with a shadow mask by a thermal evaporation method. The photoelectric performance of the photodetector based on the pristine SnS2 array films on FTO substrate were prepared by a simple CBD method . We investigated the density change of SnS2 nanosheets by changing the reaction time to obtain the optimal condition. The reaction temperature of all the samples was 60 °C. Altering the reaction time from 1 h to 1.5 h barely changed the morphology of the nanocrystalline, but the thickness of the single SnS2 nanosheets film increased from 534 nm to 1120 nm, as shown in 2 nanocrystals with non-overlapping structures were interlaced and interconnected with each other. With the extension of the reaction time, the density of ordered SnS2 gradually increased when the CBD time was between 0.5 h and 1 h. The top-view SEM image of pristine SnS2 film on FTO prepared at 60 °C for 0.5 h is shown in 2 and graphene/ SnS2 thin film on FTO prepared at 60 °C for 1 h and the AFM results are presented in 2, the average surface roughness of graphene/SnS2 thin film decreased from 70 nm to 45.7 nm. The results show that the sample with lower surface roughness and better compactness is prepared under this condition. In our experiment, an orange film started to peel off from the FTO substrate when the reaction time was longer than 1.5 h. The reason for the dissolution/partial peel-off might be explained by considering the reaction kinetics [The vertically grown SnS2 array films was characterized by X-ray diffraction. 2 atmosphere. The red curves in 2 ; a = 0.3638 nm, c = 0.588 nm). The XRD diffraction peaks at 14.83°, 28.45°, 32.14° correspond to the (001), (100), (002) planes of the samples. No other peaks were observed in the XRD spectra at other angles, which suggests the high purity of the SnS2 films. The investigation also showed that no phase transition occurs during the calcining process. In addition, we used the Scherrer equation to estimate the thickness of the individual sheets that are standing up perpendicular to the substrate in the XRD data. For example, the full width at half maximum (FHWM) of the prepared samples fabricated at 60 °C for a CBD time of 1 h are 0.6217, 0.6827, 0.7382 degrees, which correspond to the XRD diffraction peaks at 14.83°, 28.45°, 32.14°, respectively. According to the Scherrer equation, the average grain thickness is 12.89 nm. Similarly, the average grain thickness of samples for 1.5 h is 14.13 nm. The data shows that the average thickness increases with the increasing reaction time. By increasing annealed temperature , the photocurrent increases (decreases) sharply. It was also observed that under illumination of multiple cycles, the photocurrent and dark current did not change significantly, indicating that the performance was stable. The time response was also used to calculate the rise and decay time, which is closely related to the charge trapping/detrapping and recombination processes. The dark current of the device was large, which is probably due to the large free charge caused by the defects [on/Ioff) is 1.1 and the response time (rise time/decay time) are 5.4 s and 5.1 s, respectively. This efficient photoresponse indicates that the photogenerated electrons are easily transferred from the SnS2 film electrodes to FTO and the as-prepared SnS2 film has potential application in photodetector.The crystallinity of SnSperature a–c, it it 350 °C d, which  defects ,47. Acco2 array film  of graphene/SnS2 heterojunction is 1.53, higher than that of pure SnS2 film with 1.1. The results show that the high off current and low on-off current ratio may be due to the low contact resistance between graphene and SnS2 layers; further improvement could be made by modifying the device configuration in the future. Furthermore, the response time (rise time/decay time) of the hybrid graphene/SnS2 film is 5 s/4.9 s, which is superior to that of the pure SnS2 array film (5.4 s/5.1 s). Under a high power light illumination, due to the abundance of photogenerated electron-hole pairs, the photogenerated carriers pass through the electrode for a long time, the current slowly rises to the optimal value, and the response time is long. The enhanced photoelectric performance is because graphene as a hole transporting layer was introduced by a simple transfer method to form a Schottky junction photodetector with vertical SnS2 array film. As already known, graphene has a zero-band gap characteristic resulting from its valence bands exhibiting linear dispersion degeneration near Dirac point energy. Nevertheless, under a built-in electric field formed at the interface between graphene and SnS2 array film, graphene can be tuned to display p-type behavior, as shown in 2 nanosheets array film, electron–hole pairs are predominantly produced in the depletion layer. The photo-generated holes transfer swiftly to the graphene and are collected by Au electrodes. The Schottky junction is beneficial for effective charge carrier separation. Consequently, the recombination of the photogenerated electrons and holes are effectively inhibited, leading to improved photoresponse performance. Moreover, since the graphene/SnS2 interface has charge trap states in ambient conditions, it reduces the dark current. We repeated the measurement in the vacuum environment , and the current was measured by Keithley 2636B . The results are shown in Wet chemical transfer techniques were used to deposit the highly transparent graphene film on the n-type SnStructure ,49. As t2/graphene composites film has been fabricated in situ on FTO by using low-temperature CBD and then the direct wet-chemical transfer method. The hybrid graphene/SnS2 film exhibits superior photoelectric performance compared to pristine SnS2 nanosheets array film. The light on/off ratio for SnS2 nanosheets is 1.1, whereas for the graphene/SnS2 composite, it is 1.53. The successful demonstration of the photoelectric enhancement based on 2D graphene/SnS2 array film opens up new opportunities for the application of other low-temperature soluble transition metal sulfide combined with graphene in photodetectors.In summary, 2D SnS


MUC5B) and telomerase reverse transcriptase (TERT) polymorphisms and telomere length (TL) with honeycombing extent and survival in a Chinese IPF cohort. Seventy-nine patients diagnosed with IPF were enrolled. The honeycombing extents in high resolution CT scan (HRCT) were quantitatively scored and defined as mild (<10%), moderate (10–50%), and severe (>50%) upon the honeycombing extents involving the total lung. We tested five single-nucleotide polymorphisms [rs35705950, rs868903 in MUC5B, rs2736100, rs2853676 in TERT and rs1881984 in Telomerase RNA Gene (TERC) and TLs in peripheral blood leucocytes, and evaluated their associations with radiographic extent and survival in IPF. The minor allele frequencies (MAF) were significantly greater for MUC5B rs868903 (P = 0.042) and TERT rs2853676 (P = 0.041) in IPF than those in healthy controls. CT/CC genotype of MUC5B rs868903 (p = 0.045) and short TLs (p = 0.035) were correlated with the more extensive honeycombing opacities in HRCT. After adjustment for age, sex, and smoking status, MUC5B rs868903 polymorphism was the significant gene risk factors for reduced survival (p = 0.044) in IPF. MUC5B promoter rs868903 polymorphism and TLs were associated with radiographic extent and survival in a Chinese IPF cohort. These findings suggested a genetic clue for exploring the underlying molecular basis and pathogenesis of IPF.Genetic factors were identified to be associated with the development of idiopathic pulmonary fibrosis (IPF). We aimed to investigate associations between mucin 5B ( Two new agents, pirfenidone and nintedanib, have been recommended for the treatment. However, these treatments could only slow disease progression and could not halt or reverse the fibrotic process2. According to the 2018 guideline, usual interstitial pneumonias (UIP) pattern with the presence of honeycombing in high resolution CT scan (HRCT) of the chest is critical for making a definite diagnosis of IPF1. The extent of honeycombing in HRCT is a predictive factor of mortality in IPF3.Idiopathic pulmonary fibrosis (IPF) is a fatal interstitial pneumonia with unknown causes and a median survival of about 3 years4. Prior studies indicated that the mucin 5B (MUC5B) promoter, telomerase reverse transcriptase (TERT) polymorphisms and Telomerase RNA Gene (TERC) contributed to disease susceptibility and prognosis in patients with IPF7, while most these studies were conducted in western countries, data in Asian populations were limited11. Furthermore, most studies focused on rs35705950 in MUC5B promoter polymorphism that was reported rare among Asian Ancestries8, while few studies investigated the associations in MUC5B rs868903 at chromosome 11p15. The association between MUC5B rs868903 and IPF was observed in an allelic testing and it was reported as a highly associated SNP in Genome-Wide Association Study (GWAS) discovery12.The pathogenesis of IPF remains unclear and a detailed understanding of the molecular risk factors for IPF is urgently required. Genetic factors were identified to be associated with the development of IPF14. Telomerase gene mutations, which could result in telomere shortening, were considered as genetic risk factors in family pulmonary fibrosis. Shorter telomere lengths (TL) were attributed to the increased susceptibility and independently associated with reduced survival in IPF15. However, few studies evaluated the associations between gene risk factors and honeycombing extent in HRCT. Jonathan K. Alder et al. compared alveolar and lymphocyte telomere lengths from the same individuals and found that peripheral blood telomere may reflect alveolar epithelium telomere length16. Thus, we chose five SNPs, including MUC5B SNPs , TERT SNPs  and TERC SNP (rs1881984) after searching the literature12, tested these SNPs and TLs in peripheral blood leucocytes, and investigated their associations with the radiographic extent of honeycombing in HRCT and survival in a Chinese cohort.IPF was also reported as the most frequent manifestation of telomerase-associated diseaseIn total, 93 patients diagnosed with IPF and 200 age- and sex-matched healthy controls from center of Health Examination of Nanjing Drum Hospital were identified from January 2014 to October 2017. Among IPF patients, 14 of them missing clinical data were excluded, 79 patients with complete clinical and radiographic information were enrolled. They were 68 (86.08%) males and 11 (13.92%) females with mean age of 64.19 ± 8.86 years (range from 37 to 81 years old). 42 (53.16%) patients had a history of smoking. All patients denied a family history or special occupational exposures. After reviewing HRCT appearances, 13 (16.46%) patients had a mild (<10%) extent of honeycombing proportion in HRCT, 34 patients (43.04%) had a moderate (10–50%) proportion and 32 (40.51%) patients had a severe (>50%) proportion. After admission, 21 (26.58%) patients received pirfenidone therapy, 15 (18.99%) patients received N-acetylcysteine (NAC) therapy alone, 26 (32.91%) received a combination of glucocorticoids and N-acetylcysteine therapy, one patient (1.27%) received nintedanib therapy. No treatment was performed in 16 patients (20.25%). Most of the patients who received glucocorticoids were initially given these therapies before definite diagnosis and glucocorticoids were stopped gradually after definite diagnosis. None patient in this cohort was performed lung transplantation because of the patients’ refusal.The age- and sex-matched healthy controls included 200 self-reported healthy employees at the Center of Physical Examination of our hospital. This study was approved by Ethics Committee of Nanjing Drum Tower Hospital.MUC5B rs868903 in IPF cohort was 55.06% which was significantly higher than those in control group . The A allele frequency of TERT rs2853676 in IPF cohort was 12.05%, which was lower than that in control group . MUC5B and TERT genotypes were similar between IPF cohort and control group  between healthy controls and patients was tested with the goodness-of-fit Chi-square Test. The C allele frequency of The mean TL in IPF patients was significantly shorter than that in healthy controls . When we stratified the patients according to the honeycombing extents in HRCT, the mean TL in mild extent of honeycombing group was 2.226 ± 0.644, the moderate group was 1.936 ± 0.638 and severe group was 1.647 ± 0.748. After adjustment of age and sex, short TLs were significantly correlated with the extent of radiological honeycombing in HRCT .A multivariate ordinal logistic regression analysis was performed to assess whether gene polymorphisms were independently associated with extent of honeycombing. After adjustment for age, sex and smoking status, CT/CC types of MUC5B rs868903 had significantly shorter OS than those with TT after adjustment for age, sex, and smoking status  patients died during follow-up. Overall survival was defined as the time from the date of diagnosis of IPF when they were identified to the date of death from any cause. Mean overall survival (OS) was 23.66 months. Patients with CT and CC genotypes of MUC5B rs868903 polymorphisms and TLs, and the radiological extents in a Chinese IPF cohort. The current study showed that both MUC5B promoter rs868903 polymorphisms and TLs in peripheral blood leucocytes were significantly associated with radiological features on the extent of honeycombing in HRCT. Moreover, our study firstly reported that MUC5B promoter rs868903 polymorphisms were associated with the reduced survival in a Chinese IPF cohort.To our knowledge, it is the first study to investigate associations between MUC5B might play a critical role in the pathogenesis of IPF10. In 2011, a large genome-wide linkage study evaluated the role of MUC5B promoter rs35705950 in the risk of IPF. Their results showed that the minor allele resulted in the increasing expression of MUC5B in the lung10. Meanwhile, genetic variants of MUC5B had also been identified in both Pittsburgh and Chicago cohorts10. These studies also suggested that dysregulated MUC5B expression in the lung might be involved in the pathogenesis of IPF. After that, a three-stage genome-wide association study (GWAS) have replicated the previously identified association between rs35705950 and IPF in European-American patients17. Carmel et al. also reported that MUC5B polymorphism rs35705950 was significantly associated with increased susceptibility to IPF in a UK population11. However, prior studies mainly focused on the associations between MUC5B rs35705950 and IPF. Few studies investigated another important SNP in MUC5B promoter (rs868903), which had been considered as one of the most strongly associated SNPs both in IPF and in IIP12. Moreover, prior studies just included patients from western countries. Data on these associations in East-Asia populations remained limited.A series of studies had demonstrated that MUC5B rs868903 polymorphism was associated with the extent of honeycombing opacities in HRCT and mortality in Chinese patients with IPF. Of note, no significant correlations between MUC5B promoter rs35705950 and IPF were observed, likely due to the small sample size and racial differences. Similarly, Peljto and co-authors found that MUC5B promoter rs35705950 polymorphism was very rare in Asian population8. According to the guideline1, honeycombing was a distinguishing feature of UIP pattern in HRCT which was the key appearance for the definite diagnosis of IPF. Pathologically, honeycombing in HRCT represented the abnormal tissue repair and progressive lung scaring formations following repetitive alveolar injury18. Our study provided a clue that MUC5B polymorphism may play a significant molecular factor in the disease development and outcome of IPF19. Further studies are needed to investigate the underlying mechanisms of MUC5B in the pathogenesis of IPF.The current study, for the first time, demonstrated that 14. Telomerase gene polymorphisms have been reported to be associated with IPF in recent studies17. Previous work on the genetic basis of IPF showed that families with mutant telomerase genes displayed genetic anticipation and telomerase gene mutations were the commonest inherent risk factors of familial pulmonary fibrosis21. Our previous study also showed that telomerase gene mutations were associated with TL shortening and telomere shortening increased susceptibility and had valuable for predicting survival for patients with IPF13. In this study, we found that MAF of rs2853676 in TERT was significantly different between patients with IPF and healthy controls. Although no association was found between telomerase gene polymorphisms with IPF probably due to the small size sample, we observed that TL was associated with the extent of honeycombing in patients with IPF. These interesting findings argued that TL could participate the pathology of IPF. Ongoing investigations should be carried out to dissect the molecular mechanisms of telomere shortening in IPF.The field of telomere research had revealed that IPF was the most common manifestation of telomere-mediated diseasesCO) had been reported to provide accurate prognostic information23. In the genetic and molecular level, previous studies reported that TL was an independent risk factor of survival in patients with IPF15. MUC5B rs35705950 promoter was also reported to be strongly associated with the reduced survival of IPF10. In addition, several plasma proteins such as matrix metalloproteinase-7 (MMP-7), intercellular adhesion molecule-1 (ICAM-1), interleukin-8, and vascular cell adhesion molecule-1 (VCAM-1) had been evaluated as a tool for prognosis determination24. However, there was not a perfect predictive system generally acceptable so far. In this study, we firstly showed that MUC5B promoter rs868903 was associated with the radiographic fibrosis extent in HRCT and reduced survival in a Chinese IPF cohort. Taken together, our study provided a clue that an ideal predicting model should consider a combination of clinical, radiographic and genetic information, which enable better risk stratification and following personal treatment in future clinical trials.The clinical course of IPF was highly heterogeneous and evaluation of the progression and mortality remained a great challenging. Traditional physiologic changes of lung function parameters in six months including forced vital capacity (FVC), forced expired volume in 1 second (FEV1), diffusion capacity for carbon monoxide of lung  exclusion of other known causes of ILD  and either; (ii) the presence of UIP HRCT pattern not subjected to surgical lung biopsy; (iii) specific combinations of HRCT patterns and histopathology patterns in patients subjected to lung tissue sampling. Based on the criteria, patients who had typical UIP pattern on HRCT were included in the study. Patients who had known causes of pulmonary fibrosis were excluded.The diagnosis of IPF was established in accordance with the criterion recommended by the 2018 international guidelineVenous blood samples of all patients were collected at diagnosis with informed consent. The healthy controls were from center of Health Examination of Nanjing Drum Hospital. Genomic DNAs of IPF patients and healthy controls were extracted and purified from circulating leukocytes by using TIANamp Blood DNA Kit  and Genomic DNA Purification Kit . Sequencing reactions were induced by using a BigDye Terminator Cycle Sequencing Ready Reaction Kit . DNA samples were genotyped to identify SNPs associated with IPF by polymerase chain reaction (PCR). PCR conditions were available according to the requirements. Primers were designed by software PRIMER3 and were as the following: rs868903—forward, TGCAACACCAGCTCACCAT; reverse, GTCCACAGCAGCATCACT; rs1881984—forward, ATAATGAGAGTTCAGGGGA; reverse, ACAAAGCTAAAAGACAAGG; rs2736100—forward, AACATTGCTACCCTTGTCC; reverse, CTCCTCGTGAGTCTCCACA; rs2853676—forward, GTTCTCTGTGCCCTGAAGG; reverse, TGAAAGTGGCTGATGTTGA; rs35705950—forward, CCGCCCCTTTGTCTCCACT; reverse, ACTTTGCCCTCGTCCCTCC.15. The standard curve was established by continuously diluting a reference DNA with deionized water into eight kinds of concentrations ranging from 1.875 to 240 ng/μL. Telomere/single copy numbers (T/S) ratio represented the relative telomere length of genomic DNA26.Quantitative polymerase chain reaction (qPCR) was used to identify the relative repeat copy number of telomere and single gene (36B4a) with Power SYBR Green PCR Master Mix . Each reaction was performed in triplicate. The primer sequences were designed as the following: telomere—forward, ACACTAAGGTTTGGGTTTGGGTTTGGGTTTGGGTTAGTGT; reverse, TGTTAGGTATCCCTATCCCTATCCCTATCCCTATCCCTAACA; single gene (36B4a)—forward, CAGCAAGTGGGAAGGTGTAATCC; reverse, CCCATTCTATCATCAACGGGTACAA27, two dedicated chest radiologists (K.Z. and X.X.) reviewed the HRCT appearances respectively and quantitatively scored the extent of honeycombing involving as the percentage of total lung. The extent of honeycombing was defined as mild when it involved as <10% of total lung, moderate when involved 10–50% of total lung and severe when the honeycombing opacities involved >50% of the total lung. The variability of score by the two radiologists was evaluated and determined to be satisfactory for consistency27. Both radiologists were blinded to clinical and other demographic information.Chest HRCT scans of all patients were performed at end inspiration when they were enrolled. Based on prior studyAll patients were regularly followed up every three to six months from the diagnosis. The evaluation in follow up included re-examination of chest HRCT and pulmonary function test. The primary endpoint was lung transplant or death of all causes. None of patients in this cohort received lung transplant. Survival time was defined as the interval from the date of diagnosis to death. Survival status was obtained from telephone interviews and the medical records. The follow-up time was censored at October 31, 2017.MUC5B after adjusting for age, sex and smoking status. Association between TLs and extent of honeycombing in HRCT was evaluated by one-way ANOVA and General Linear Model adjusted by sex and age. All of the statistical analyses were performed by IBM SPSS Statistics (version 22.0J) and Graph Pad Prism 7.0. P value less than 0.05 was considered statistically significant for all tests.Minor allele frequency (MAF) and genotype frequency of SNPs were calculated and compared with Chi-square Test and Multiple Regression Analysis adjusted by age and sex. Associations between genotype polymorphisms and radiographic extent of honeycombing were assessed by multivariate logistic regression. The model was used to estimate odds ratios (ORs) and corresponding 95% confidence intervals (CIs) of rs868903 in This study was approved by Ethics Committee of Nanjing Drum Tower Hospital. Written informed consents were obtained from all participants and all research was performed in accordance with the relevant guidelines/regulations.


LY56, LE58, and LN66 in the first hot spot of PD-L1 are important for PD-L1-antibodies and small-inhibitors in common, while LM115 is important for small-inhibitors. Therefore, the 3D-SPIEs-based map would provide valuable information for designing new small-molecule inhibitors to inhibit PPI of PD-1/PD-L1 and the FMO/3D-SPIEs method provides an effectual tool to understand PPI and integrate PPI and small-ligand interactions at a quantum mechanical level.Inhibitors to interfere protein-protein interactions (PPI) between programmed cell death 1 (PD-1) and programmed death ligand-1 (PD-L1) block evasion of cancers from immune surveillance. Analyzing hot spot residues in PPI is important for small-molecule drug development. In order to find out hot spots on PPI interface in PD-1/PD-L1 complex, we analyzed PPI in PD-1/PD-L1 with a new analysis method, 3-dimensional scattered pair interactions energies (3D-SPIEs), which assorts significant interactions with fragment molecular orbital (FMO) method. By additionally analyzing PPI in PD-1/antibody and PD-L1/antibody complexes, and small-ligand interactions in PD-L1/peptide and PD-L1/small-molecule complexes, we narrowed down the hot spot region with 3D-SPIEs-based interaction map, which integrates PPI and small-ligand interactions. Based on the map, there are two hot spot regions in PPI of PD-1/PD-L1 and the first hot spot region is important for inhibitors. In particular,  PD-1 is transcriptionally expressed on activated T cells, B cells and myeloid cells5. An activated T cell expresses PD-1 on its surface and produces interferons which can induce many tissues to express programmed death ligand-1 (PD-L1)7. PD-1 binds to its ligand to deliver negative or co-inhibitory signals8, and results in the activation of inhibitory kinases related with proliferation and adhesion of T cells1. The PD-1/PD-L1 pathway downregulates immune responses and preserves tolerance to self-antigens by curbing improper autoimmune responses under normal physiological conditions9. PD-1 ligands are commonly upregulated in different tumor types, where they are used to evade immune responses7. Blocking the PD-1/PD-L1 interactions can reanimate exhausted T cell phenotype and result in normalization of antitumor response10. The success in clinical studies, where anti-PD-1 agents reduced the remote metastasis of melanoma cells or colon cancer cells, improved the knowledge of PD-1/PD-L1 as an important anticancer target in human beings8. Although several nonpeptidic small-molecule inhibitors of the PD-1/PD-L1 interaction are reported11, it still has been challenges to develop small molecular inhibitors targeting PD-1 and PD-L1 due to their flat and large interface. The lack of information about protein-protein interactions (PPI) between PD-1 and PD-L1 has hindered the anti-PD-1-targeted, or anti-PD-L1-targeted, small molecular drug development in cancer therapies.Programmed cell death protein 1 (PD-1) is a type I transmembrane receptor belonging to the CD28 family12. However, PPI-targeted small molecular drug development seemed intractable due to relatively flatter and featureless interfaces of PPI, compared to traditional pharmacophore based targets13. Encouraged by successful assistances of the computational methods in drug discovery, there have been many attempts to develop PPI-targeted drugs by using in silico approaches based on the molecular mechanics (MM) methods15. Nonetheless, a direct application of the present MM to PPI has limits, because MM methods depend on predetermined parameters optimized to reproduce average values and classical mechanics could not describe the molecular system precisely. The use of quantum mechanics (QM) comes to the fore, because QM could overcome the limitations of MM. Although QM could not be easily applied to the large biological systems, such as PPI, due to huge computational cost15, it provides the analysis of the components of molecular interaction in post Hartree-Fock level with energy decomposition analysis (EDA) method, developed by Morokuma et al.16. The EDA in QM can describe the important dispersion interactions and non-classical interactions, including CH-π, cation-π, and so on in PPI, which were not easy for MM to describe.Protein-protein interactions (PPI) play a crucial role in the regulation of many biological processes and a functional disorder of PPI strongly results in a variety of diseases including cancerset al. developed fragment molecular orbital (FMO) method for large molecules and molecular systems in 199917, and pair interaction energy decomposition analysis (PIEDA) in 200718. It has advantages of drastically reducing the computing time without compromising the accuracy of the results compared with traditional QM method, and of providing PIEDA as a practical application of EDA. Recent progress in method development and applications was well summarized in review articles of Fedorov et al.20 It has been successfully applied to investigate the protein-ligand interactions based on PIEDA qualitatively and quantitatively22. In case of PPI as a large molecular system, there have been a few cases to apply FMO method, where a partner protein was defined as a fragment for facilitating PPI analysis and it required huge computational cost23.As a practical application of EDA, Kitaura In this work, we applied FMO method to investigate PPI between PD-1 and PD-L1. In order to find hot spot residues in PD-1/PD-L1 complex, we performed FMO calculation of wild type complex. For analyzing PPI with computational cost being low by using a-fragment-per-a-residue fragmentation scheme, we devised a 3-dimensional scattered pair interaction energies (3D-SPIEs) analysis tool. The 3D-SPIEs method sorts pair interaction energy (PIE) out by using distance between fragments and energy value information, so it provides a 3-dimensional scatter plot and important interactions in PPI. To narrow down hot spot region in PD-1/PD-L1, we performed FMO calculations of PD-1/antibody complexes, PD-L1/antibody complexes, PD-L1/peptide complexes, and PD-L1/small-molecule complexes. For integrating PPI in the antibody complexes and the small-ligand interactions in small-ligand complexes, we made 3D-SPIEs-based interaction map in PD-1/PD-L1. In order to validate PPI predictability of the FMO results, we compared them with the reported site-directed mutagenesis results. Finally, we summarized FMO/3D-SPIEs results as an interaction map, by integrating the information from PPI and small-ligand interactions, and found the hot spot region in PD-1/PD-L1 at a quantum-mechanical level.All X-ray structures in this work are summarized in Table 24, we used polarizable continuum model (PCM) for solvent screening effects and introduced distance information to sort out the meaningful PIEs from overestimated PIEs. As for distance information, we selected only PIEs within a specific distance (5.4 Å) between two fragments, which reflected the distance used for the approximate of electrostatic potential in FMO method25. The brief scheme of 3-dimensional scattered pair interaction energies (3D-SPIEs) method is shown in Fig. Analyzing protein-protein interactions (PPI) between a target protein and a partner protein can be correlated with analyzing pair interaction energy (PIE) in FMO calculations with a-fragment-per-a-residue fragmentation scheme. Because the calculated PIE often show unphysically large values primarily due to electrostatic interactionset al.7 13 PPI: Y68:LD122, Q75:LD26, Q75:LR125, A132:LQ66, I134:LY56, I134:LE58, I134:LY123, E136:LR113, E136:LY123, E136:LR125, N66:LD122, Q75:LI126, and K78:LT20, and 3 water-bridge-interactions: I134:HOH202:LY56, I134:HOH202:LE58, and N66:HOH203:LA121.In order to find out amino acids on PPI interface that form hot spots in wild type PD-1/PD-L1 complex, we performed FMO calculation of the wild-type complex and analyzed it with 3D-SPIEs method. It detected 28 PPI between PD-1 and PD-L1, which are summarized in Supplementary Table et al. reported three hot spots on the PPI interface between PD-L1 and PD-17 the first hot spot was LY56, LE58, LR113, LM115, and LY123; the second was LM115, LA121, and LY123; and the third was from LD122 to LR125. PPI in PD-1/PD-L1 complex analyzed with FMO method are delineated in Fig. et al.7, only E136:LY123 were strong, which can belong to the third hot spot. Therefore, we rearranged the reported three hot spot regions into two hot spot regions in PD-1/PD-L1 complex based on the FMO results. , V111 , R112 , A113 , and R114  in PD-1, N58A mutation would change intra-protein interactions in β-sheet 2 (V64) and β-sheet 4 (Q99). Because N-glucan on N58 and N58 interacted with E61 , V64 , P83 , Q99 , and P101 , N49A mutation would change intra-protein interactions in the loop. Because N74 interacted with P72  and N116 interacted with S118 , the N74A and N116A mutations would change intra-protein interactions in β-turn and α-helix 9, respectively.The FMO results can provide not only PPI, but also intra-protein interactions (non-PPI) in the single protein. It was reported that there were four potential N-linked glycosylation sites in PD-1 et al.27 and 10 PPI of the traditional quantum chemistry results28. 14 PPI: E61:LCY57, N66:HCR102, Q75:HCT30, T76:HCY101, D77:HCS54, D77:HCN55, K78:HCY33, K78:HCY101, D85:HCR99, R86:LCD97, Q88:HCN59, E61:LCY34, S62:LCY57, and Q88:HCY35, and 10 PPI: V64:HCF103, N66:HCF103, Y68:HCR102, K78:HCR102, K78:HCF103, D85:HCR102, Q88:LCY33, P89:LCY35, I126:HCR102, and I134:HCR102.In PD-1/pembrolizumab complex, the FMO results detected 37 PPI, which are summarized in Supplementary Table In order to investigate the common hot spot regions among two PD-1-antibodies and PD-L1, we illustrate the FMO results in Fig. In order to narrow down hot spot regions in PD-1/PD-L1 complex, we performed FMO calculations of five antibody complexes in complex with PD-L1 and analyzed them with 3D-SPIEs method. There were the reported five antibody complexes in complex with PD-L1: BMS-936559, Avelumab, KN035, Atezolizumab, and Durvalumb.et al.29LD49:HCG105, LD49:LCY32, LY56:HCH59, LE58:HCK57, and LH69:HCS106.In PD-L1/BMS-936559 complex, the FMO results detected 17 PPI, which are summarized in Supplementary Table et al.30LE58:HCY52, LE58:HCV104, LE60:LCY34, LD61:HCV104, LD61:HCT105, LD61:HCT106, LY56:HCG55 and LN63:HCT103.In PD-L1/Avelumab complex, the FMO results detected 33 PPI, which are summarized in Supplementary Table In PD-L1/KN035 complex, the FMO results detected 25 PPI, which are summarized in Supplementary Table 32. The FMO results showed 21 PPI related with the mutagenesis data, where the mutations on LY56, LE58, LD61, LN63, LQ66, LR113, LM115, LY123, and LR125 in PD-L1 made the lower binding affinity to KN035. In particular, it was reported that I54A in PD-L1 decreased binding affinity between PD-L1 and KN035. The FMO results showed 4 intra-protein interactions with LI54 in PD-L1: LI54:LL50, LI54:LH69, LI54:LG70, and LI54:LY118. Because LI54 in β-sheet 4 may stabilize the structure of PD-L1 by interacting with LL50 in loop, LH69 next to β-sheet 5, LG70 next to β-sheet 6, and LY118 next to β-sheet 3, I54A mutation may make β-sheet flexible and the stability unstable.The FMO results were in agreement with the published site-directed mutagenesis studieset al.:32LA52:LCY93, LY56:HCW50, LE58:HCY54, LE58:HCG55, LE58:HCS57, LD61:HCG55, LN63:HCS57, LQ66:HCS57, LY123:HCW101, LR125:HCS30, LR125:HCD31, and LR125:HCY54.In PD-L1/Atezolizumab complex, the FMO results detected 40 PPI, which are summarized in Supplementary Table 32. The FMO results showed 19 PPI related with the mutagenesis data, where the mutations of I54A, Y56A, E58A, N63A, Q66A, R113A, M115A, Y123A, and R125A in PD-L1 reduced the binding affinity between PD-L1 and atezolizumab. The mutations except I54A and M115A were correlated well with the FMO results. The FMO results showed three and four intra-protein interactions with I54 and M115 in PD-L1, respectively: three non-PPI in LI54: LI54:LL50, LI54:LV68, and LI54:LY118: and four non-PPI in LM115: LM115: LW57, LM115: LR113, LM115: LY123, and LM115: LK124. Because LI54 stabilizes PD-L1 by interacting with the end of β-sheets (LV68 and LY118) and loop (LL50), I54A mutation may make PD-L1 unstable. Because LM115 stabilizes the hot spot regions of PD-L1, M115A mutation may make the hot regions of PD-L1 flexible.The FMO results were in agreement with with the sited-directed mutagenesis studieset al.33LD26:LCR28, LE58:HCK52, LV111:HCE105, LR113:HCE57, LK124:LCS94, LK124:LCW97, LR125:HCG104, and LR125:LCG93.In PD-L1/Durvalumab complex, the FMO results detected 26 PPI, which are summarized in Supplementary Table LY56 and LE58 in common, while four of them had PPI with LD61, LQ66, LR113, LY123, and LR125 in PD-L1. In the wild-type complex, LD61 had no PPI between PD-1 and PD-L1, but had intra-protein interactions with LR113 , which may contribute to the stability in the first hot spot in PD-L1. Some antibodies had PPI with LE60, LH69, and LD122. The FMO results showed that most PPI between PD-L1-antibodies and PD-L1 focused on the PPI on the first hot spot between PD-1 and PD-L1.In order to investigate the common hot spot regions among five PD-L1-antibodies and PD-1, we illustrated the FMO results in Fig. In order to narrow down hot spot regions in PD-1/PD-L1 complex, we performed FMO calculations of two peptide complexes in complex with PD-L1 and four small-molecule complexes in complex with two PD-L1 proteins, and analyzed them with 3D-SPIEs method in case of peptide inhibitors and traditional bar graph method in case of small-molecule inhibitors.LY56, LE58, LN63, LQ66, LE71, LE72, LD73, LR113, and LM115 are summarized in Supplementary Table 34. 57W8:LY56, 57W8:LQ66, 57W10:LR113 and 57W10:LM115.In PD-L1/peptide-57 complex, the FMO results detected 9 strong interactions between peptide-57 and PD-L1 with 9 residues and 6 water-bridge interactions: 9 residues: LV55, LY56, LE58, LD61, LK62, LN63, LQ66, LR113, LM115, and LY123 are summarized in Supplementary Table 71Y11:LE58, 71Y11:LR113, 71F1:LY56, 71F1:LE58, 71F1:LQ66, 71NMePhe7(MEA7):LV55, MEA7:LM115, MEA2:LQ6, and 71NMeNle3(9KK3):LQ6. In the mutagenesis data, the exchange of the central 71Y11 to alanine, lack of 71F1 and 71NMePhe7, and methylation on 71NMePhe2 and 71NMeNle3 caused the lower binding affinity34.In PD-L1/peptide-71 complex, the FMO results detected 10 strong interactions between peptide-71 and PD-L1 with 10 residues and 4 water-bridge interactions: 10 residues: There were the reported four nonpeptidic small-molecule inhibitors in complex with two PD-L1 proteins by Bristol-Myers-Squibb . Because it was reported that these compounds made dimerization of two PD-L1 proteins, we used superscripts ‘A’ and ‘B’ to annotate protein molecules depending on the chain arrangement in the crystal structures.LY56A, LE58A, LQ66A, LM115A, LD122A, LY56B, LM115B, LS117B, and LD122B: and one water molecule: HOH206. In BMS-37/PD-L1 complex, the FMO results detected 10 strong interactions with PD-L1 with 9 residues and one water molecule: 9 residues: LT20A, LY56A, LM115A, LD122A, LY56B, LE58B, LQ66B, LM115B, and LD122B: and one water molecule: HOH227. In BMS-200/PD-L1 complex, the FMO results detected 16 strong interactions with PD-L1 with 12 residues and four water molecules: 12 residues: LT20A, LY56A, LM115A, LS117A, LD122A, LY56B, LE58B, LQ66B, LM115B, LA121B, LD122B, and LY123B: and four water molecules: HOH229, HOH250, HOH306, and HOH316. In BMS-202/PD-L1 complex, the FMO results detected 13 strong interactions with PD-L1 with 10 residues and three water molecule: 10 residues: LT20A, LY56A, LM115A, LS117A, LD122A, LY56B, LE58B, LQ66B, LD73B, LM115B, and LD122B: and three water molecules: HOH301, HOH316, and HOH325.The FMO results of BMS compounds and two PD-L1 proteins are illustrated in Fig. LY56, LE58, and LQ66. In the second hot spot, most of PD-L1-antibodies had interactions with LD122 and LR125, while most of peptides and small-molecule inhibitors had interactions with LD122. According to the map, the first hot spot might be the most important hot spot on PPI interface in the PD-1/PD-L1 complex. Notably, LM115, located between the first and the second hot spot regions on PPI interface, had significant interactions with all of peptides and small-molecule inhibitors, while there was no PPI in wild-type complex, while two of the five PD-L1-antibodies had PPI with LM115. In intra-protein interactions in PD-L1 of the wild-type, LM115 interacted with LW57 , LY123 , and LK124 . It indicated that LM115 may be also important for maintenance of the first hot spot region in PD-L1 and play a role of pivot, connecting the first and the second hot spots, for small ligands.To integrate information between PPI and small-molecule-protein interactions, we made 3D-SPIEs-based interaction map. see Figs . In the Given the successful prospects in clinical studies of monoclonal antibodies targeting the PD-1/PD-L1 axis, several agents to block the PD-1/PD-L1 axis have been developed. The understanding of PPI between PD-1 and PD-L1 is vital for successful structure-based drug design. Even though the crystal structures of PD-1/PD-L1 complex were solved, it has been still a challenge to find small-molecule inhibitors. Visual inspection or traditional molecular mechanic approaches do not always give a clear answer, especially in protein-protein interactions. In the present study, we made the 3D-SPIEs-based interaction map in PD-1/PD-L1, which integrated PPI and small-molecule-protein interactions at a quantum-mechanical level. In the map, it indicated that the first hot spot region is important for inhibiting PPI in PD-1/PD-L1, which all antibodies and small-ligands focused on. The integrated information can be used in the design of new compounds in hit-to-lead or lead optimization stages for targeting PD-1/PD-L1 in drug discovery.35. Here, we analyzed water molecules which were resolved in the crystal structures. Using the FMO method to analyze the water-bridge interactions in protein-protein system can allow us to identify water molecules which are energetically favorable or unfavorable. And this information can be used to design several agents that can interact with certain water molecules or displace the interactions. However, identification and verification of water molecules depends on the resolution of X-ray crystal structures. The FMO method is suitable for analyzing the roles of already predicted, or identified, water molecules which have been determined by other computational methods15.Water molecules play a crucial role in the protein-protein interactions, though they can be quickly exchanged with bulk solvent19. The information from the FMO/PIEDA method allows us to distinguish whether the interactions are strong, moderate, weak or not, and whether they are attractive or repulsive between the ligand and its neighboring residues. Furthermore, it can be used as an efficient ab initio tool for design, assessment and filtering of new compounds, which may reduce the effort and the cost of chemical synthesis in drug discovery.FMO/PIEDA method has been a practical tool for rational structure-based drug design, because it offers a precise and comprehensive information on the protein-ligand interactions36, it has not been generally employed in other PPI cases. Although the analysis scheme, summing all PIEs over all residues of a partner protein, facilitated the analysis of PPI with a bar graph, it required the huge computational cost. Here, we introduced the 3D scattered pair interaction energies (3D-SPIEs) to sort and analyze PIEs between fragments, which provided two advantages. Firstly, it allowed the FMO method to be applied easily to protein-protein systems due to lower computational cost from a-fragment-per-a-residue scheme. It would provide a protocol to analyze PPI, which can be applied to protein-RNA and protein-DNA complexes in future. Secondly, most protein-protein interactions, detected by the FMO/3D-SPIEs, method were in agreement with the published reports and mutagenesis data. Not only providing the reported PPI, it had additional advantage of distinguishing inter-protein (PPI) and intra-protein (non-PPI) interactions. In some cases, the alanine scanning experiments could be inconclusive, because the mutations could affect the binding free energy by a mechanism unrelated with PPI37. Some mutations might destabilize the unbound state of protein and alter its conformation, so hot spots identified by alanine scanning experiments could be false positives37. It indicated that the application of FMO method to PPI can predict site-directed mutagenesis study results, and furthermore provide intra-protein interactions affecting stability. It would provide the starting points to modify proteins and nucleic-acids as a powerful tool in protein-engineering and nucleic-acid-engineering for the higher binding affinity.Even though the FMO method was successfully applied to the protein-protein interaction of influenza hemagglutininIn summary, the outcome of this study provided three points. Firstly, as a protocol, the FMO/3D-SPIEs method can be applied to analyze hot spot region of PPI. Secondly, in analyzing case-by-case PPI, the FMO/3D-SPIEs results had a qualitative correlation with site-directed mutagenesis results, and additionally provided intra-protein interactions for stability. Thirdly, the integrated information with PPI and small-ligand interactions in PD-1/PD-L1, the FMO/3D-SPIEs results provided valuable information for hot spot regions in PD-1/PD-L1, and designing new potential small-molecule targeting PD-1/PD-L1. Therefore, the FMO/3D-SPIEs method allowed the FMO method to be used to understand not only the nature of protein-ligand complexes, but also protein-protein complexes. The FMO method can be hereby used to analyze hot spots in PPI, protein-RNA, and protein-DNA, and provide new direction to hit-to-lead, lead optimization, protein engineering, and nucleic-acid engineering in future.Maestro program39. Hydrogen atoms were added to the crystal structures at physiological pH (7.4) and their positions were optimized with the PROPKA implemented in Maestro program40. Then the restrained energy minimization was performed on PD-1/mAb and PD-L1/mAb crystal structures with OPLS3 in Maestro program with 0.3 Å RMSD (root mean square deviation)41. Water molecules in the crystal structures were included in FMO calculations to explore their roles in protein-protein interactions.X-ray crystal structures were collected from the Protein Data Bank (PDB), a wild-type PD-1/PD-L1 complex (PDB ID: 4ZQK): two crystal structures of PD-1/mAb complexes: nivolumab (PDB ID: 5WT9) and pembrolizumab (PDB ID: 5B8C), five crystal structures of PD-L1/mAb complexes: BMS-936559 (PDB ID: 5GGT), avelumab (PDB ID: 5GRJ), KN035 (PDB ID: 5JDS), atezolizumab (PDB ID: 5XXY), and durvalumab (PDB ID: 5X8M), two crystal structures of the PD-L1/peptide complexes: peptide-71 (PDB ID: 5O45) and peptide-57 (PDB ID: 5O4Y), and four crystal structures of small molecule inhibitor in complex with two PD-L1 molecules: BMS-8 (PDB ID: 5J8O), BMS-37 (PDB ID: 5N2D), BMS-200 (PDB ID: 5N2F), and BMS-202 (PDB ID: 5J89). All the missing side chains and loops of the crystal structures were filled using Prime implemented in 42. Two-body FMO method was applied to PD-1/PD-L1, PD-1/mAb, PD-L1/mAb, and PD-L1/small-ligand complexes to investigate key interactions at the second order Møller-Plesset perturbation (MP2)43 and polarizable continuum model (PCM)44 with 6-31G** basis set (FMO-MP2/6-31G**/PCM level). The implicit solvation model (PCM) was employed with explicitly expressed water molecules present in the X-ray crystal structures. In FMO calculations of PD-1/mAb and PD-L1/mAb, only Fv domains of mAb and crystallographic water molecules around the region were included. All inputs files were prepared with an in-house code in compliance with the hybrid orbital projection (HOP)45 scheme fragmentation. Each residue and water molecule was defined as a fragment and two cysteine residues forming the disulfide bridge were defined as a fragment (a-fragment-per-a-residue fragmentation scheme).All FMO calculations were performed with the version Aug 18, 2016 in GAMESS15.(i)46. In FMO calculations, all the residues in protein are divided at the sp3 bond of Cα position, not peptide bond, based on the hybrid orbital projection (HOP)45 scheme, where the fragmentation is performed at an atom, not midway of bond47 in Fig. 47.Fragmentation is a starting point for FMO method. In a-fragment-per-a-residue fragmentation scheme, each residue of protein, ligand and water molecule can be defined as a fragment except two cysteine residues forming disulfide bond. It should be noted that each fragment, representing amino acid residues, is different from the normal assignment for the amino acid residues(ii)48 theory in the whole electrostatic field and all the electron densities are self-consistently solved through self-consistent-charge (SCC) iterations24.All the MOs on each fragment (monomer) are optimized by self-consistent-field (SCF)(iii)24. Dimer fragments are made of two monomer fragments. The difference between the third step (dimer) and the second step (monomer) is that the Hamiltonian operator of dimer includes the electrostatic potential generated by surrounding N-2 monomers and that of monomer includes it generated by surrounding N-1 monomers, where N means the number of fragments.Schrödinger equations for fragment pair (dimer) are self-consistently solved in the same way as for the second step, independently(iv)i and j, indicates a sum of four energies including the electrostatic 18. Solvation energy In total property evaluation step, all MO calculations for monomer and dimer are pieced together to generate whole picture of the system. FMO provides the pair interaction energies (PIEs) between fragments. In pair interaction energy decomposition analysis (PIEDA), PIE or mentclass2pt{minimTwo body FMO calculation consists of four sequential steps on (i) fragmentation, (ii) fragment (monomer) self-consistent field (SCF) calculation, (iii) fragment pair (dimer) SCF calculation, and iv) total property, including energy and gradient, evaluation36, because name of ligand fragment can be omitted in protein-ligand system. However, names of residue fragments in PPI cannot be omitted because they include crucial information. For facilitating analysis of PPI and representing the results with two-dimensional bar graphs, a partner protein can be defined as a fragment, which requires huge computational cost. In order to reduce computational cost and obtain interaction information of all residue pairs in PPI system, we used a-fragment-per-a-residue fragmentation scheme and devised 3-dimensional scattered pair interaction energies (3D-SPIEs) analysis method. , z axis indicates the distance between two fragments, and the dots have color according to their PIEs values. And then, PIEDA information is shown when dots are hovered.The main advantage of FMO is that it can account for the energy and structural fitness that stabilizes the complex by calculating the interaction energy (PIE) between the fragments, which make up the protein-protein or protein-ligand complexes. Therefore, it is necessary to sort and analyze the information obtained from the FMO calculations in an easy-to-understand way. The FMO results consist of three-dimensional data, whose elements are pair interaction energies and names of two fragments. In traditional and powerful way, the FMO results can be analyzed with two-dimensional bar graphssee Fig.  In 3D-SPSupporting Information


The generated high-quality graphene consists of few-layer sheets with a uniform size of less than 1 μm. The obtained graphene was uniformly dispersed and tightly integrated into a polyamide 66 (PA66) matrix to create high-performance multifunctional polymer nanocomposites. The tensile strength and thermal conductivity of 0.3 and 0.5 wt% EG/PA66 composites were found to be ~32.6% and ~28.8% greater than the corresponding values calculated for pure PA66, respectively. This confirms that the new protocol of liquid phase exfoliation of graphite has excellent potential for use in the industrial-scale production of high-quality graphene for numerous applications.In this paper, the sodium salt of styrene-maleic anhydride copolymer (SMA) was used as a stabilizer in the process of graphite exfoliation to few-layer graphene using the technique of microfluidization in water. This method is simple, scalable, and cost-effective, and it produces graphene at concentrations as high as 0.522 mg mL C[−1 K−1) ,9,10,11,Recently, liquid phase exfoliation (LPE) of graphite powder to few-layer graphene has attracted the interest of many researchers ,13,14. T−1). This shows that more effective low-cost stabilizers need to be developed for use in large-scale graphene preparation procedures.To enhance the yield and quality of the graphene produced by LPE or microfluidization methods, stabilizers, such as aqueous surfactants and polymers, are used. However, most of the currently used stabilizers, such as sodium dodecyl benzene sulfonate (SDBS) , sodium Styrene-maleic anhydride (SMA) copolymer is a polymer dispersant that is widely used in the fields of biology, medicine, optics, electronics, among others . The funThis study constitutes the first reported investigation of the efficiency of SMA in facilitating graphite exfoliation via microfluidization in an aqueous system. The effects of SMA concentration, microfluidization cycle number, and chamber pressure on the effectiveness of graphene production are systematically analyzed, and an exfoliation mechanism is proposed. The exfoliated graphene is used to prepare graphene/polyamide 66 (PA66) composites and graphene films by melt blending injection and vacuum filtration, respectively, and the mechanical, thermal, and electrical properties of these materials are analyzed.Pristine graphite  was provided by Qingdao Tengshengda Carbon Machinery Co., Ltd., in China. Meanwhile, the emulsion of SMA sodium salt  and the polyamide 66 (EPR27) pellets were purchased from Shanghai Leather Chemical Factory and Pingdingshan Shenma Co., Ltd., in China, respectively. SDBS was provided by Shanghai Aladding Chemical Reagent Co., Ltd., China.−1 graphite solutions at concentrations of 5, 10, and 15 mg mL−1. The 500 mL SMA/graphite mixtures were stirred for 30 min to ensure homogeneity, then they were exfoliated using a lab-scale pressure homogenized microfluidizer . The chamber pressure was varied between 80 and 120 MPa, and the number of cycles completed through the interaction chamber (cycle number) was set to 5, 10, 20, or 30. Upon the termination of the microfluidization process, the graphite suspensions were centrifuged at 3000 rpm for 30 min to remove un-exfoliated graphite sheets, and the topmost part (80%) was collected. Then, the exfoliated graphene (EG) dispersions were subsequently vacuum filtrated through a 0.22-μm pore size membrane, and then freeze dried to obtain EG powder. The chemical transformations implicated in graphite exfoliation by SMA-assisted microfluidization in water are illustrated in The SMA stabilizer was added to 10 mg mLMicrofluidization is a homogenization technique that uses high pressure to pass fluids through a narrow channel (<100 μm). Typically, graphite exfoliation is achieved using either normal or lateral mechanical forces. In microfluidization, the two mechanisms are combined to attain high exfoliation efficiency. The process is characterized by three main phenomena: cavitation, shear, and collision . CavitatSMA assists in the exfoliation process by incorporating itself between the carbon sheets in such a way that it minimizes the interactions between them. The stabilizer is composed of long chain molecules that bind to the surface of graphene sheets via non-covalent π–π interactions. The interacted SMA forms a coating layer with repulsive tails that prevent interactions with other graphene sheets. The process of SMA-assisted liquid phase exfoliation of graphite is illustrated in The exfoliated graphene powder was dispersed in commercially bought PA66 pellets by mechanical mixing for 3 h. The mixtures containing 0.1, 0.2, 0.3, 0.4, and 0.5 wt% EG were subsequently fed into a twin-screw extruder  operated at a melting temperature of around 280 °C and rotation speed of 100 rpm. The extrudates were pelletized, dried, and then molded to tensile specimens using an injection molding machine .−1. Meanwhile, the crystallinity of the investigated material was analyzed using an X-ray diffractometer  operated in the range of 10–60° (2θ) and/or a differential scanning calorimeter  scanning between −30 °C and 300 °C at the rate of 10 °C min−1 under a nitrogen atmosphere. The surface morphologies and mechanical properties of pure PA66 and EG/PA66 composites were analyzed using a field-emission scanning electron microscope  and a universal tensile machine , respectively. For strength testing, dried dumbbell specimens were prepared, and their mechanical properties were evaluated at a tensile speed of 50 mm min−1. The tests were repeated five times, and only the average values are reported. The thermal conductivities of pure PA66 and its EG-modified composites were also assessed at 25 °C using an analyzer .The graphene dispersion was analyzed by UV-visible spectroscopy  in the range of 200–800 nm, using a quartz cell with an optical path of 1 cm. All dispersions were diluted 10 times for UV-Vis analysis. The morphology of as-prepared graphene was observed by transmission electron microscopy  at 100 kV, whereas the thickness of the material was determined using atomic force microscopy  in tapping mode. The structures of SMA, graphite, and graphene were evaluated using a Raman spectrometer  equipped with a 532 nm excitation laser, as well as a Fourier-transform infrared (FTIR) spectrometer  scanning in the range of 4000–400 cmCG) was calculated using the Lambert–Beer law [A is the absorbance value at 660 nm, measured using UV-Vis spectroscopy, α is the absorption coefficient, C is the concentration of graphene, and l is the optical path length (l = 1 cm). The value of α was determined based on the absorbance of graphene dispersions whose concentrations (CG) are known. For this purpose, samples of EG suspensions were analyzed by UV-Vis spectroscopy then vacuum filtrated through a 0.22-μm pore size membrane. The collected solid was thoroughly washed by water to eliminate excess SMA, then it was dried and weighed to determine the mass of graphene, which was used to calculate CG. Finally, α was estimated based on the slope of the linear fit between A and CG. As shown in α for the SMA-stabilized graphene dispersions prepared in this study is 1308 mL·mg−1·m−1. Henceforth, the concentrations of EG dispersions are determined using this value.The concentration of graphene in the prepared EG dispersions (Beer law A = α·C·−1) on CG was assessed under a microfluidization pressure of 120 MPa. The results presented in CG are attained at CSMA = 10 mg·mL−1, irrespective of the number of microfluidization cycles. A higher concentration of SMA will not promote further increase in CG because of the graphene surface that becomes saturated with adsorbed SMA molecules [The influence of SMA concentration  is recorded at 120 MPa and 30 cycles. Pressures beyond 120 MPa were not investigated, because the pressure is adjusted by the gap valve. In fact, pressures higher than this value result in agglomeration and blockage during the microfluidization process. To compare the exfoliation effect between SMA and the conventional surfactant, SDBS was also used to assisted the microfluidization exfoliation. Under the same condition of microfluidization process , the resulted graphene concentration assisted by SDBS was as low as 0.328 mg·mL−1, which indicates that SMA is a relatively efficient stabilizer for the synthesis of graphene.The effects of pressure and number of cycles are also analyzed, as shown in CG offer additional evidence of the successful exfoliation of graphite to graphene. As shown in CG data, greater absorbance is observed at higher numbers of microfluidization cycles, indicating an improved exfoliation effect. The UV-Vis spectra recorded in this study are similar to those reported by Phiri [The UV-Vis spectra used to calculate by Phiri  and Pu eby Phiri .The effect of the number of microfluidization cycles on graphene structure was analyzed using TEM . Figure The thickness of the graphene produced after 30 cycles of microfluidization was measured by AFM a, and th−1 (2D). The degree of defect in EG is determined based on the ratio of ID/IG; a lower ratio signifies a higher quality of the graphene flake. Based on the Raman spectrum depicted in ID/IG ratio increases from 0.07 for pristine graphite to 0.38 for as-prepared graphene because of the structural defects generated during the exfoliation process. Nevertheless, the ID/IG ratio obtained in this study using SMA-assisted microfluidization (0.38) is comparable with those achieved using other LPE methods (0.2–0.5) [The Raman spectrum of the prepared graphene was recorded and compared to that of graphite after 30 cycles of microfluidization under 120 MPa. The data illustrated in 0.2–0.5) ,27,28, w−1), typical to graphite. By contrast, three fitting curves are clearly observed in the spectra of the graphene products, as shown in −1) belongs to the monolayer or bilayer graphene sheets. However, the second peak (2676 cm−1) and the third peak (2714 cm−1) are attributed to few-layer and multilayer graphene sheets in products [The 2D-band of pristine graphite and the as-prepared graphene film was fitted using the non-linear least square fit program (Gauss–Lorentzian). After deconvolution, the objective results with high correlation are shown in products . The exfproducts . Furtherproducts .The crystallization of EG was analyzed using XRD and compared to the crystal formation in pristine graphite. As shown in −1 are significantly shifted  in the EG sample. This suggests that the IR peaks observed in the graphene spectrum are mainly due to SMA molecules that are non-covalently bound to the material via π–π interactions [FTIR spectra of graphite, SMA, and graphene confirm the existence of π–π interactions between the stabilizer and the carbon sheets. As shown in ractions .−1, which is greater than the values determined for the same material produced by sonication-based LPE methods (6000–6500 S m−1) [The electrical conductivity of graphene films prepared by vacuum filtration was measured using the four-point probe technique. Before testing, the films were dried overnight in a vacuum oven set at 50 °C. As shown in 0 S m−1) ,31.The results presented thus far prove that high-quality graphene may be generated in relatively large concentrations via SMA-assisted microfluidization in water. This green approach is characterized by high efficiency and low cost, which renders it useful for the fabrication of graphene-based polymer composites, particularly when compared to the alternative CVD and GO (graphene oxide) reduction methods. Polyamide 66 (PA66) is an engineering plastic that is widely used because of its good processability and excellent mechanical properties . HoweverThe effect of EG content on the mechanical properties of PA66 is illustrated in It is well-known that the mechanical properties of composites are enhanced by good dispersibility and strong interfacial adhesion between the modifier and the matrix. Therefore, we used SEM to characterize these properties in the EG/PA66 composites. The SEM micrographs in Tm) of the investigated composites are practically the same, irrespective of the EG content. This indicates that the samples possess analogous lamellae thicknesses and spherulite sizes [Tc) compared to pure PA66, which signifies that EG acts as an effective heterogeneous nucleating agent that promotes crystallization [Xc = 36.6%) is achieved using 0.3 wt% EG, leading to the highest tensile strength of the composites. Excessive EG (>0.3 wt%) results in unavoidable reaggregation, which may impede the movement of molecular chains, thereby reducing the crystallinity [In addition to dispersibility, crystallinity is another factor that influences the mechanical properties of EG/PA66 composites . In thiste sizes . Moreovelization ,37. The allinity . These r−1·K−1) is 28.8% greater than that of the pure PA66 (0.2657 W·m−1·K−1). Previously, it has been shown that the incorporation of 0.25 wt% graphene in silicone foams increases thermal conductivity by only 6% [ only 6% . Therefo only 6% , leading−1 and a uniform lateral size of less than 1 μm. Compared to graphene oxide and reduced graphene oxide, the EG synthesized in this study is of high quality (ID/IG = 0.38) and has good electrical conductivity (7500 S m−1). Furthermore, the process of exfoliation is fast and waste-free, which renders it suitable for large-scale production. When combined with polymers such as PA66, SMA-stabilized EG shows good dispersion and interface compatibility, which significantly reinforces the EG/PA66 composites. Overall, this study presents a green and facile approach to produce high-quality graphene and paves the way for the fabrication of high-performance multi-functional graphene/polymer composites.In summary, we report a new and green method for the exfoliation of graphite to few-layer graphene, based on the technique of SMA-assisted microfluidization in water. This method yields graphene concentrations as high as 0.522 mg mL


Graphene is a very attractive material for broadband photodetection in hyperspectral imaging and sensing systems. However, its potential use has been hindered by tradeoffs between the responsivity, bandwidth, and operation speed of existing graphene photodetectors. Here, we present engineered photoconductive nanostructures based on gold-patched graphene nano-stripes, which enable simultaneous broadband and ultrafast photodetection with high responsivity. These nanostructures merge the advantages of broadband optical absorption, ultrafast photocarrier transport, and carrier multiplication within graphene nano-stripes with the ultrafast transport of photocarriers to gold patches before recombination. Through this approach, high-responsivity operation is realized without the use of bandwidth-limiting and speed-limiting quantum dots, defect states, or tunneling barriers. We demonstrate high-responsivity photodetection from the visible to infrared regime (0.6 A/W at 0.8 μm and 11.5 A/W at 20 μm), with operation speeds exceeding 50 GHz. Our results demonstrate improvement of the response times by more than seven orders of magnitude and an increase in bandwidths of one order of magnitude compared to those of higher-responsivity graphene photodetectors based on quantum dots and tunneling barriers. Scientists have made graphene nano-stripes that could lead to photodetector technologies with greater bandwidth, ultrafast speed, and high  responsivity for use in imaging and sensing systems. Graphene has become an attractive material for use in broadband photodetection technologies owing to its unique electronic and optical properties, such as its high electrical conductivity and ability to absorb a broad spectral range of light. However, its potential has been hindered by tradeoffs between the responsivity, bandwidth and speed of existing graphene photodetectors. Now, Mona Jarrahi and colleagues from the University of California Los Angeles, in America, have fabricated gold-patched graphene nano-stripes that offer broadband, ultrafast, and highly responsive photodetection. The work has led to photodetectors with response times more than seven orders of magnitude, and bandwidths of one order of magnitude greater than currently available. These characteristics stem from the unique band structure of graphene, which enables carrier generation via optical absorption over an extremely broad spectral range from the ultraviolet to microwave regime. Moreover, the high electron/hole mobility and weak scattering in graphene enables an ultrafast temporal response in graphene photodetectors. Additionally, the two-dimensional nature of graphene enables multiple electron/hole pairs to be generated for a single absorbed photon5. Furthermore, the compatibility of graphene photodetectors with silicon-based fabrication platforms enables integration with low-cost and high-performance complementary metal oxide semiconductor read-out and post-processing circuits.Graphene has rapidly become an attractive candidate material for broadband and ultrafast photodetection because of its distinct optical and electronic characteristics6. Various techniques have been explored to address these challenges and to enhance the responsivity of graphene photodetectors. Despite the significant advantages of these techniques for offering high photodetection responsivities, the scope and potential use of existing graphene photodetectors remain limited by tradeoffs between high responsivity, an ultrafast temporal response, and broadband operation.Most graphene photodetectors utilize graphene–metal junctions or graphene p–n junctions to spatially separate and extract photogenerated carriers. The low optical absorption inside the effective junction regions (~100−200 nm) and short photocarrier lifetime of graphene (~1 ps) represent the two major challenges for the development of high-responsivity graphene photodetectors10. However, the response times for these graphene photodetectors have been limited by long carrier trapping times due to the introduced defect and edge states. Hybrid graphene–quantum dot photodetectors offer a powerful alternative for enhancing the photodetection responsivity by increasing light absorption and introducing large carrier multiplication factors14. However, the bandwidth and response time for this type of graphene photodetector are restricted by the narrow spectral bandwidth and long carrier trapping times of the quantum dots. Photodetectors based on two graphene layers separated by a thin tunnel barrier have also led to enhanced broadband responsivity via separation of the photogenerated electrons and holes through quantum tunneling and minimization of their recombination15. However, the response times for this type of graphene photodetector have been limited by the long carrier trapping times in the tunneling barriers utilized. Waveguide-integrated graphene photodetectors have been considered to be another promising alternative and offer enhanced ultrafast responsivity by increasing the interaction length of light within graphene19. These graphene photodetectors have the additional advantage of process compatibility with standard photonic integrated circuits. However, their spectral bandwidth has been restricted by the bandwidth limitations of the waveguides utilized. Moreover, microcavities, plasmonic structures, and optical antennae have all been integrated with graphene to achieve high responsivities by increasing the interaction length of light within graphene32. However, the bandwidth of these types of graphene photodetectors has been limited by the resonant nature of the structures utilized.For example, responsivity-enhanced photodetection in graphene from the visible to mid-infrared wavelengths has been achieved by increasing the photocarrier lifetime through band-structure engineering and defect engineering. For this purpose, carrier trapping mechanisms and patterned graphene nanostructures have been utilized to introduce bandgap and midgap defect states in grapheneIn this work, we use engineered photoconductive nanostructures based on gold-patched graphene nano-stripes, which have unique electrical and optical characteristics that enable simultaneous broadband and ultrafast photodetection with high responsivity. The key novelty that enables the superior performance of these photoconductive nanostructures is the confinement of most of the photocarrier generation and conduction to the graphene nano-stripes and gold patches, respectively. Therefore, such nanostructures benefit from the broadband optical absorption and photocarrier multiplication capabilities of graphene and avoid the negative effects of the short photocarrier lifetime of graphene.2 layer. The gold patches are then patterned by electron beam lithography and formed by 5/45 nm Ti/Au deposition and liftoff. The graphene nano-stripes are then patterned by another electron beam lithography step and formed by oxygen plasma etching. Next, the bias lines and output pads are patterned by optical lithography and formed by 20/200 nm Ti/Au deposition and liftoff. Finally, gate pads are patterned by optical lithography and formed by SiO2 plasma etching, followed by 20/200 nm Ti/Au deposition and liftoff.Commercially available chemical vapor deposition (CVD)-grown graphene is first transferred to a high-resistivity silicon wafer covered with a 130-nm-thick thermally grown SiO2). The responsivity values are calculated from the photocurrent measured using a source measure unit , and the optical power measured using a calibrated near-infrared photodetector . A Globar light source  combined with different infrared bandpass filters is used to measure the photodetector responsivity in the infrared range (3–20 μm wavelength range). A list of the filters used, including their spectral characteristics, is given in Supplementary Table A supercontinuum laser  is used to measure the photodetector responsivity in the visible/near-infrared regime (0.8–1.8 μm wavelength range). The fiber-coupled output of the supercontinuum laser is placed very close to the device to ensure that all of the output power is incident on the device active area  are carried out to demonstrate the unique capability of the designed gold patches to efficiently concentrate the incident optical beam onto the graphene nano-stripes over a broad optical wavelength range. Figure 5. Such carrier multiplication factors have not been previously exploited in monolayer graphene photodetectors without the use of quantum dots because of the short photocarrier lifetime in graphene14. However, carrier multiplication can be used to boost the photoconductive gain of the gold-patched graphene nano-stripes at lower wavelengths because of the fast photocarrier transport time to the gold patches. Since the use of any defect states and/or quantum dots is avoided, the gold-patched graphene nano-stripes enable high responsivity photodetection without sacrificing the ultrafast broadband operation.Gold-patched graphene nano-stripes can exploit the enhanced carrier multiexcitation generation that occurs at higher photon energy levels to compensate for the lower optical absorption at lower wavelengths2. This figure also shows a scanning electron microscopy image of the gold patches . A supercontinuum laser and Globar light source combined with bandpass filters are used to measure the photodetector responsivity in the visible/near-infrared and infrared regimes, respectively . The responsivity spectrum for the fabricated photodetector at an optical power of 2.5 μW, gate voltage of 25 V, and bias voltage of 20 mV is shown in Fig. Fig. The photoconductive gain of the fabricated photodetector is calculated from the measured responsivity and estimated optical absorption in graphene, as shown in Fig. Fig. 35. The variation in the band-bending slopes leads to an increase in the induced photocurrent when the gate voltage decreases. This trend changes for gate voltages of <22 V, with a small decrease in the induced photocurrent observed for a further decrease of the gate voltage. The small reduction in the photocurrent at gate voltages <22 V can be explained by the decreased carrier mobility at high carrier densities due to the increase in carrier scattering38. The highest responsivity level is obtained at a gate voltage of 22 V. The photodetector responsivity decreases at higher optical powers . However, because interband optical transitions are only allowed when ħω≤2Ef, the photodetector responsivity is substantially reduced by Pauli blocking at lower photon energies when the gate voltage is lowered from 65 to 22 V and −20 V.Figure Figure f noise current with respect to the Johnson Nyquist and shot-noise currents, which is similar to the operation of commercially available room-temperature infrared detectors40. Under this operation condition, the photodetector noise current, which is dominated by Johnson Nyquist and shot-noise sources, is extracted from the measured photocurrent and resistance data  of the fabricated photodetector is calculated to assess the noise performance. For this calculation, we assume an optical chopping frequency above 1 kHz and lock-in the detection of the output signal to significantly reduce the 1/1/2 Fig. , demonstRg, and SiO2 capacitance, Cox, are measured to be 70 Ω and 5.2 pF, respectively. Additionally, the gold-patch capacitance, Cg, and substrate resistance, Rsub, are estimated to be 12.9 fF and 5 MΩ, respectively. As can be observed from the device electrical model, the use of a high-resistivity silicon substrate leads to a large resistance, Rsub, in series with the SiO2 capacitance, Cox, eliminating the negative impact of this capacitance on the ultrafast photodetection speed. Therefore, the photodetector frequency response predicted by this electrical model is dominated by the parasitic resistance of the graphene nano-stripes and parasitic capacitance of the gold patches, leading to a predicted photoresponse cutoff frequency of 425 GHz.A unique attribute of the graphene photodetector is that its superior bandwidth/responsivity performance is accompanied by an ultrafast photodetection speed. This ultrafast speed is made possible through the special design of the utilized gold-patched graphene nano-stripes, which offers broadband optical absorption in graphene and subpicosecond photocarrier transport times to the gold patches while maintaining low capacitive/resistive parasitics. A high-frequency electrical model of the graphene photodetector is shown in Fig. The high-frequency operation of the fabricated photodetector is characterized using two fiber-coupled, wavelength-tunable, distributed-feedback (DFB) lasers with 783 and 785 nm center wavelengths (TOPTICA #LD-0783-0080-DFB and #LD-0785-0080-DFB), as illustrated in Fig. 42. The presented graphene photodetector shows responsivity levels that are more than two orders of magnitude higher compared to previously reported high-speed graphene photodetectors19. The photodetector also shows response times that are more than seven orders of magnitude faster and bandwidths that are one order of magnitude broader compared to higher-responsivity graphene photodetectors based on quantum dots14 and tunneling barriers15. We expect the unique combination of broadband and ultrafast photodetection with high responsivity enabled by the gold-patched graphene nano-stripes will have a significant impact on future hyperspectral imaging and sensing systems. To further enhance the device performance, the symmetric gold patches can be replaced with asymmetric metal patches, which will lead to symmetry breaking for the electrical potential inside the graphene nano-stripes, enabling bias-free, low-dark-current device operation43.In this work, we present the unique electrical and optical characteristics of gold-patched graphene nano-stripes, which enable simultaneous broadband and ultrafast photodetection with high responsivity. We demonstrate high-responsivity photodetection from the visible to the infrared regime (0.6 A/W at 0.8 μm and 11.5 A/W at 20 μm), with operation speeds exceeding 50 GHz. Fig. Supplementary Material