Antimicrobial resistance (AMR) is a crucial multifactorial and complex global problem and Bangladesh poses a regional and global threat with a high degree of antibiotic resistance. Although the routine application of antimicrobials in the livestock industry has largely contributed to the health and productivity, it correspondingly plays a significant role in the evolution of different pathogenic bacterial strains having multidrug resistance (MDR) properties. Bangladesh is implementing the National Action Plan (NAP) for containing AMR in human, animal, and environment sectors through “One Health” approach where the Department of Livestock Services (DLS) is the mandated body to implement NAP strategies in the animal health sector of the country. This review presents a “snapshot” of the predisposing factors, and current situations of AMR along with the weakness and strength of DLS to contain the problem in animal farming practices in Bangladesh. In the present review, resistance monitoring data and risk assessment identified several direct and/or indirect predisposing factors to be potentially associated with AMR development in the animal health sector of Bangladesh. The predisposing factors are inadequate veterinary healthcare, monitoring and regulatory services, intervention of excessive informal animal health service providers, and farmers’ knowledge gap on drugs, and AMR which have resulted in the misuse and overuse of antibiotics, ultimate in the evolution of antibiotic-resistant bacteria and genes in all types of animal farming settings of Bangladesh. MDR bacteria with extreme resistance against antibiotics recommended to use in both animals and humans have been reported and been being a potential public health hazard in Bangladesh. Execution of extensive AMR surveillance in veterinary practices and awareness-building programs for stakeholders along with the strengthening of the capacity of DLS are recommended for effective containment of AMR emergence and dissemination in the animal health sector of Bangladesh. Microorganisms are among the man’s best friends and also worst foes. Antimicrobial agents have been extremely important cornerstones of modern medicine in food animal production since the last half of the previous century. Antimicrobials have contributed considerably to the prevention and treatment of infectious diseases in livestock, and some of them have played a very important role in the promotion of animal growth and feed efficiency ,2. AntimTerrestrial and aquatic food-animal production industries are expanding rapidly to meet the increasing demand for animal-source nutrition worldwide. This expansion is comparatively greater in low-and middle-income countries (LMICs) than in high-income countries. Rising demand for animal-source nutrition in LMICs is working as driving force for shifting of the small-scale animal farming systems to intensive, large-scale, and specialized commercialization. Non-therapeutic use of antimicrobials for prevention and control of disease or as antimicrobial growth promoters (AGP) are common practices in intensive farm-animal production systems . Use of Bangladesh is a developing country in the Southeast Asian region. The livestock sector of Bangladesh is endowed with 403 million terrestrial animals, which shares about 1.47% of the gross domestic product to the national economy. This sector is also providing full-time and part-time employment to 20% and 50% people of the country, respectively . Both poThe World Health Organization (WHO) endorsed a Global Action Plan (GAP) in 2015 based on “One Health” approach for combatting the emerging global threat from AMR . In aligGoogle and retrieved from the relevant institutional websites. Studies conducted on the AMR situation in humans, agriculture, aquaculture, or the environment were excluded considering irrelevant to the present study. The articles directly assessed husbandry and medication practices along with antibiotic-resistant bacteria or genes in food-producing or non food-producing animals of Bangladesh were included for general review. The literatures described “in place” institutional and policy structures of DLS to combat AMR burden in Bangladesh were also considered.To prepare this review, we conducted a literature review on the AMR situation in the animal health sector of Bangladesh and across the globe from Google Scholar, PubMed, ResearchGate, and Crossref databases. First, we focused the introductory section on the background of AMR situation worldwide, its impacts on livestock and public health sectors, the possible source of AMR in livestock, and current trends in antibiotic usage in Bangladesh. The databases were searched using the term “AMR situation in Bangladesh” with alternative terms “AMR pathogens in animal sector of Bangladesh;” “AMR bacteria in animal sector of Bangladesh;” “AMR bacteria in poultry sector of Bangladesh;” and “AMR bacteria in farm animals of Bangladesh.” “Antibiotic-resistant” or “antimicrobial-resistant” terms were also used as alternative to “AMR.” Searches were filtered for research or review articles published in the English language from January 2011 to June 2020. Grey materials/unpublished documents were searched using The key findings  related to this study were retrieved from the articles. Extracted data were analyzed at 95% confidence level using IBM SPSS Statistics 20 software. To find out the associations and level of significance among different variables, we used Pearson Chi-square test.We identified a total of 44 peer-reviewed articles that contained information relevant to the present study. Of these, five articles  reportedIn rural Bangladesh, 57.7% of households own livestock, including large animals , small ruminants (sheep and goats), and poultry . Government veterinary healthcare providers rarely (9.7%) visit these households. In the absence of adequate veterinary healthcare service, animal owners in rural areas avail low-cost animal health care from pharmacies and unlicensed village doctors (82.5%). In addition to feed additives, animal owners use antibiotics, largely at suboptimal doses on suggestions of the informal animal healthcare providers . The preMedication practices in poultry sector of Bangladesh are very complex. In commercial poultry farms, especially in small and medium-scale settings the poultry and feed dealers are the main influencers on antibiotic usage. The poultry and feed dealers provide financial support and farming related technical information to the farmers to initiate and operate their farms. Thereby, the farmers become obliged to buy poultry chicks, feed, and medicine from the dealers. Sales representatives of the pharmaceutical companies are another influencing group in poultry farming systems. In addition to providing product information, sales representatives also provide treatment advice directly to the farmers. Recently, qualified veterinary doctors appointed by the hatcheries, feed companies and pharmaceutical companies are providing poultry management and treatment services to the farmers .The study revealed that the incidence of active infections, high mortality rates, and an aspiration to prevent disease were the major drivers of antimicrobials use in poultry farms. Broiler farmers use antibiotics for therapeutic purposes, for prophylaxis, and also for growth promotion. The majority of the farmers (>60%) use antibiotics without any prescription from veterinary doctors . Layer fThe small and medium-scale poultry farmers apply multiple antibiotics, even banned antibiotics to poultry throughout the production cycle following the suggestions of the poultry dealers . As manyEscherichia coli was identified in different types of birds from both conventional and unconventional farming systems in different areas of Bangladesh. Newly hatched broiler and layer chicks in hatcheries of Gazipur district experienced navel infection with ABR E. coli with a higher degree of resistance against ampicillin (80-100%), amoxicillin (60-100%), and kanamycin (80%) [E. coli isolates recovered from dead, sick, and apparently healthy broilers of Gazipur, Mymensingh, and Chattogram districts showed a varying magnitude of resistance against tetracycline (45.5-100%), ampicillin (100%), trimethoprim-sulfamethoxazole (26.7-94.59%), nalidixic acid (25.7-91.89%), ampicillin (25.7%), streptomycin (20.8%), and ciprofloxacin [E. coli from all the broiler sources developed resistance. All E. coli isolates from apparently healthy broilers of LBMs in Chattogram city carried blaTEM, tetA, and Sul2 multidrug-resistant genes. Likewise, MDR E. coli was also reported in layer chickens with resistance against the same type of antibiotics as in broiler from different areas of Bangladesh [E. coli with resistance against tetracycline (100%), fluoroquinolone (85%), sulfamethoxazole-trimethoprim (85%), aminoglycosides (71%), and nitrofurantoin (21%) was identified in backyard poultry of Bangladesh. These extended-spectrum β-lactamases (ESBL) producing E. coli from backyard poultry carried mcr-1 plasmid and resistant genes blaCTX-M-group-1, blaTEM-1 (ESBL), qnrB (fluoroquinolone), and rmtB (aminoglycoside) [E. coli was also found prevalent in ducks, geese, quails, and pigeons from unconventional commercial farms and LBMs [E. coli isolates from the birds of unconventional farms were resistant against tetracycline (90%), amoxicillin (70%), sulfamethoxazole (90%), and other antibiotics commonly used in broiler and layer farms. Besides the farming settings, alarmingly MDR and XDR E. coli with resistance against oxytetracycline (93%), amoxicillin (91.9%), ampicillin (89.5%), trimethoprim–sulfamethoxazole (88.4%), tetracycline (84.9%), and carbapenems (89.6%) were reported in frozen chicken meats from various parts of Bangladesh. ESBL genes blaTEM, blaSHV, and blaCTX-M-2 were prevalent in these MDR and XDR E. coli [A total of eight ABR bacterial species were reported in layer, broiler, backyard poultry, ducks, pigeons, and quails in nine different districts of Bangladesh  8,15,16,27-44. Afloxacin -30. Of tngladesh . Ubiquitand LBMs -33. The  E. coli .Salmonella species were reported from various types of birds reared in different farming systems. Day-old chicks, dead, sick, and even apparently healthy layer birds harbored MDR Salmonella with resistance against penicillin-G (90-100%), ampicillin (100%), amoxicillin (98-100%), tetracycline (93%), nitrofurantoin (78%), sulfamethoxazole (60%), gentamycin (46%), and ciprofloxacin (20-40%) [Salmonella spp. was also identified in cloacal swabs, litter, and feed samples of broiler farms with resistance against a range of antibiotics and the antibiotic resistance was carried by tetA (97.14%), floR, blaTEM-1, and aadA1 (77.14%) genes [Salmonella in unconventional farming systems. Apparently healthy quails and pigeons were found to carry MDR Salmonella with resistance against amoxicillin (90%), ampicillin (80%), erythromycin (80%), tetracycline (60%), chloramphenicol (40%), kanamycin (40%), gentamicin (40%), nalidixic acid (40%), sulfamethoxazole (30%), and ciprofloxacin (20%) [Salmonella with the highest resistance to imipenem (83.33%) [Salmonella from all of the poultry-associated sources has already developed resistance against a broad range of antibiotics, including ampicillin, amoxicillin, tetracycline, and gentamycin (Multidrug-resistant (MDR) icillin 9-100%, te20-40%) ,38,40. M% ,38,40.%) genes . Two stuin (20%) ,39. In L(83.33%) ,36. Salmntamycin .Enterobacter spp. were documented in layer poultry with resistance against a range of antibiotics used in both animals and humans [Citrobacter portucalensis from layer poultry also showed resistance against a wide range of antibiotics mediated by eight AMR genes in its genome [Pasteurella, Bacillus, and Staphylococcus species isolated from apparently healthy Japanese quails and newly hatched broiler and layer chicks showed resistance against commonly used antibiotics  which is recommended to use in humans only [E. coli with resistance against ampicillin (100%), amoxicillin (30-100%), and streptomycin (70-100%) [E. coli, milk of mastitis-affected cows was also a source of antibiotic-resistant Bacillus, Streptococcus, Staphylococcus, Klebsiella, Enterobacter, and Shigella spp. which developed resistance against several antibiotics (S. aureus isolates showed the highest resistance to oxytetracycline (74.5%), followed by oxacillin (55.9%), ciprofloxacin (49.6%), amoxicillin (42.0%), trimethoprim/sulfamethoxazole (30.0%), and to a less extent to gentamicin (17.9%), penicillin (11.0%), and erythromycin (8.2%) [Different species of ABR bacteria have been documented from dairy, goat, and wild animal sources in different areas of Bangladesh. MDR ironment . Along wans only . Milk of70-100%) ,45. Besiibiotics  [17-19,4n (8.2%) . The disSalmonella spp. carrying tetA and SHV resistance genes were reported from cow dung, milk, milkers’ hand, and dairy farm environment with resistance against a number of antibiotics such as erythromycin (87.5%), tetracycline (86.76%), oxytetracycline (75.73%), and ertapenem (50%) [Salmonella spp. even in wild Irrawaddy squirrels was identified. The wild Irrawaddy squirrels also harbored ABR E. coli, Staphylococcus, and Yersinia spp. All the antibiotic-resistant bacteria isolated from wild Irrawaddy squirrels showed resistance against amoxicillin, tetracycline, colistin sulfate, sulfamethoxazole-trimethoprim, and cephalexin [MDR foodborne zoonotic pathogen em (50%) . Dissemiphalexin .Contamination of the animal originated food products by antibiotic-resistant bacteria with resistance against tetracycline (100%), nalidixic acid (100%), oxacillin (100%), erythromycin (53.33%), ciprofloxacin (40%), doxycycline (26.66%), and ampicillin (6.67%) was also reported .The state veterinary service of Bangladesh is provided through the DLS, Government of Bangladesh. DLS is providing veterinary service to the field level through its eight divisional, 64 district and 488 sub-district (Upazila) livestock offices. The veterinary hospital network of the country includes one central veterinary hospital, 64 district and 488 sub-district (Upazila) veterinary hospitals. In addition, there are nine metro veterinary hospitals to provide services in city areas. One to two registered veterinarians along with other supportive sub-technical personnel are deployed in each district, sub-district (Upazila) or metro veterinary hospitals . The regThe Bangladesh government enacted “Fish Feed and Animal Feed Act, 2010” and “Animal Feed Rule, 2013” which prohibited the use of antibiotics in animal feed and restricted the use of colistin as a critically important antibiotic. These regulations empowered DLS to designate competent personnel for enforcing activities such as investigation, arrest, search, and seizure, prosecutions to prevent use of antibiotics in animal feed. Bangladesh is implementing the NAP for containing AMR in human, animal, and environment sectors through “One Health” approach where a coordinated effort from all implementing partners with strong commitment and participation are necessary for combating AMR in Bangladesh as well as to ensure one health. The NAP has assigned DLS to execute all necessary activities to achieve strategic objectives for containing AMR problems in veterinary practices. Although such activities are being performed by the DLS, there are still some policy gaps, including an explicit financing modality, specifications for antimicrobial stewardship in the veterinary sector, and rigorous operational, monitoring, and evaluation frameworks .The animal health system of Bangladesh is explicitly “pluralistic” involving unqualified healthcare providers and different influential groups at different stages ,23. The The aforesaid risk factors have resulted in the emergence of distinguished AMR bacteria in different animal farming settings of Bangladesh Tables- and 2. TE. coli was the most abundant and Salmonella was the second most  between poultry and dairy farming settings with respect to AMR pathogen emergence deciphers that both types of farms are equally contributing to the emergence of AMR burden in Bangladesh. Of the AMR pathogens, MDR t Tables-. The und studies . High pr Ecuador . Other th Tables-., E. coli, Salmonella, Enterobacter, Staphylococcus, and Campylobacter spp. are potential zoonotic pathogens creating direct human health hazards [Among the MDR pathogens hazards . Unhygie hazards ,58. More hazards ,18,44,54E. coli, Salmonella, and Enterobacter isolated from both poultry and dairy also showed resistance against imipenem, azithromycin, and colistin sulfate recommended for human use only and strictly prohibited to use in animal health [mcr-1 gene in ARB is alarming considering their potentiality to reduce the efficacy of last-resort antibiotics [The reported MDR pathogens developed resistance against number of antibiotics commonly recommended to use in animal health ,24 Tabl and 2. Tl health ,22,41. Tibiotics ,34.Although the DLS, Bangladesh has sufficiently extended its institutional establishments  throughout the country, these institutions are deficient in manpower, disease diagnostic facilities, and logistics. The veterinarians deployed in each of these hospitals are vested in providing service to a large jurisdiction which is practically impossible. Less availability of the state veterinary service often becomes a cause of “dissatisfaction” among the farmers . MoreoveThere is no alternative to formulating and executing an extensive and pragmatic surveillance program to unveil the real picture of the AMR situation in veterinary practices of Bangladesh. Scientific research to improve understanding of the risk factors for the emergence and spread of AMR is required to design evidence-based appropriate interventions. This review study revealed the AMR situation of a small area of the country and the inclusion of statistically significant number of districts in the surveillance program is recommended. Moreover, the surveillance program should include a survey on the type and amount of the antimicrobials used in different animal farming practices in Bangladesh. To explicit the emergence and distribution of the AMR pathogens in veterinary practices, laboratory-based AMR assessment in significant sample size from different farming settings is crucial. Research should address veterinary and human drug use, social, and economic influences on prescribing and drug-dispensing practices, traditional beliefs and local cultures, and environmental factors that promote the development of drug-resistant pathogens. The drug administration of Bangladesh should consider categorization of antimicrobials and preserve some items as prescription-only medicines. This will avoid availability or misuse of antimicrobial agents because pre-authorization or their use under supervision of infection experts will be required.For effective monitoring, surveillance, AMR stewardship activities and awareness building on AMU and AMR, qualified manpower along with adequate funding is a prerequisite. Capacity building of veterinary hospitals and laboratories of the DLS with adequate manpower, training, logistics, and fund mobilization are crucial for successful containment of AMR in the veterinary sector of Bangladesh. However, we conclusively recommend the following measures for effective mitigation of AMR problems in veterinary practices of Bangladesh – (1) cross-sectorial policy commitment and coordination for the implementation of NAP; (2) development of the annual action plan, including national surveillance of AMR, awareness campaigns, and assessment of knowledge about AMR; (3) increasing regulatory role or law enforcement capacities of the implementing organizations; and (4) research on understanding the risk factors for the emergence and spread of AMR.AMR is considered one of the most important global health issues and Bangladesh is assessed as having a high risk of AMR. The emergence and zoonotic spread of ABR bacteria or associated-resistant genes is crucial because of their existence in animal farming environment, including soil, and water, animal products and by-products. AMR is a “One Health” problem, and its rational containment warrants inclusion of the veterinary sector. Thus, the present review study was envisaged to explicit the current situation, and knowledge gaps of AMR burden in the veterinary sector of Bangladesh. In this comprehensive review of the AMR situation in veterinary practices of Bangladesh, we tried to retrieve maximum available information. Nevertheless, due to limited open data sharing policy by some of the journals and restricted access to some of the databases, the search may not be exhaustive. Therefore, this review is limited by the inclusion of a small number of articles, even though sufficiently elucidated the underlying causes of AMR emergence, current situation of AMR in veterinary practices of Bangladesh along with the weaknesses and strength of DLS to contain the problem. Hence, this review article could be used as a reference work for formulation, adoption, and implementation of a rational and pragmatic future AMR containment program in veterinary practices in Bangladesh.MAA: Conceptualized and designed the review. MAA and MNH: Collected the literature. MAA: Analyzed the data. MAA and MNH: Drafted the manuscript. AZS, SS, and MMK: Edited and finalized the manuscript. MMK: Acquisition of funds. All the authors read and approved the manuscript.


Since the C–F bond is the most polar in organic chemistry, the orientation of fluorine substituents originating from the rotation around C–C(F) bonds should affect the polarity and, consequently, the physicochemical and biological properties of fluorine-containing agrochemicals. Accordingly, this study aims to determine the most likely conformers of some fluorine-containing agrochemicals and to correlate their molecular dipole moments with the respective  Whilst in the last years the agrochemical industry has encountered a period of downturn affected by new regulations, low crop prices, biochemical resistance, among other variables, recent events have shown signs of recovery . CurrentFluorination is a common strategy employed as part of the optimization process during the design of new chemical compounds, which includes the modulation of a variety of properties such as lipophilicity, biological half-life, and biosorption –4. This From a conformational analysis point of view, the fluorine atom presents minimal steric effects; on the other hand, due to its high electronegativity, the C–F bond is highly polarized, which characterizes it as a site for electrostatic and hyperconjugative interactions . AdditioAlthough the stereochemical effects of fluorination, responsible for specific interactions and conformational preferences of several groups of compounds, have become increasingly well understood , their dI, Igg, Iag and Iga , the conformational analysis started with a Monte Carlo conformational search at the ωB97X-D/6-31G [Iag . To evaluate the other possible conformations along the 1,2-disubstituted ethane motif, the C–C(F) bond was rotated to additionally obtain conformers Igg and Iga, and the corresponding geometries were then optimized. The resulting geometries and relative conformational energies are summarized in Given the high degree of freedom in the chemical structure of penoxsulam  –17 level31G ,18, resu,p) [Iag . This coIga, where the gauche fluorine atom points to the opposite direction of the amine group, the triazole ring was farther away from the 1,2-disubstituted ethane moiety. Note that the gas-phase relative conformational energy ΔE increases, i.e., becomes less stabilizing, in the order Iag < Iga < Igg. The difference in energy between Iag and Iga is somehow small , and these conformers are equally stable according to the relative Gibbs free energy ΔG . The inclusion of an implicit polar solvent (e.g. water), however, decreases the difference in energy among conformers and Igg becomes the most stable conformer in solution, i.e., a double gauche effect takes place (see data in parentheses in Igg has the highest dipole moment (data shown in the next section) and is naturally more stabilized by polar solvents. Therefore, further analysis will consider the gas phase, since in this way we are accounting for the intrinsic intramolecular interactions without the influence of solvent as an external factor.At first, we observe that the overall geometry is quite similar among the three conformers. Only for Iag keeping other geometrical parameters fixed. In this way, we can specifically investigate the intramolecular interactions governing conformational preferences in the 1,2–disubstituted ethane motif. Furthermore, we decomposed the conformational energy along rotation around the C–C(F) bond within the framework of the natural bond orbital (NBO) analysis [EL, which accounts for classical interactions) and non-Lewis  contributions  bond is rotated from conformer analysis  into theibutions . Note thIgg is the most stabilized by the ΔENL term, which can be attributed to the stabilizing interactions featured in the gauche effect [gauche arrangement along the two F–C–C–O pathways. The charge transfer from the filled σCH orbital to the empty σ*CF or σ*CO orbitals amounts to 4.6/4.5 and 3.3 kcal mol−1, respectively, which are more stabilizing than the corresponding σCF/CO → σ*CO/CF and nF/O → σ*CO/CF in the anti-orientation , and classical electrostatic and steric interactions are the main factors governing conformational preferences of penoxsulam (I).From e effect ,20, due entation . Note th Notario , and O’H Notario . Besidesreferred , while trmations . TherefoP, since this physicochemical property does not depend on the geometry of penoxsulam inside a biological receptor.It is worth mentioning that the structure of penoxsulam in the biological environment is already known in the literature  and, accn-octanol/water partition coefficient – log P, through molecular dipole moment (μ). The molecular dipole moment, μ is a relatively simple parameter that can inform on subtle intramolecular interactions that favor one structural arrangement over another, as previously mentioned. Therefore, by using a weighted average μ over the most likely conformations to correlate with experimental log P, one can assess the dependence of log P with molecular conformation.Herein, we aim at evaluating the correlation of molecular conformation with lipophilicity, described in terms of the P data was selected from a single database [I), pyroxsulam (II), cloransulam-methyl (III), flumioxazin (IV), fluroxypyr-1-methylheptyl ester (V), ethalfluralin (VI), and trifluralin (VII). The data set contains compounds without rotatable C–C(F) bonds (III–V), with a rotatable C–C(F) bond that does not generate different conformers , and with a rotatable C–C(F) bond that generates different conformers (I). The μ values for all herbicides were computed through theoretical calculations  and are presented in P data.Accordingly, a consistent set of fluorine-containing agrochemicals  with expdatabase , which cI) has a rotatable C–C(F) bond  and, consequently, has the dependence of the molecular dipole moment μ with the rotation around this bond. It is well-known that μ is influenced by two main factors: the molecular dimensions and the electron distribution [I and a weighted average μ was obtained from the calculated μ of the three conformers Igg, Iag, and Iga. Then, the calculated μ values were plotted against the experimental log P (2) was 0.86, which can be considered a suitable correlation coefficient. A hypothesis test for the significance of the observed correlation, based on the p-value , was also carried out. A p-value of 0.00264 was obtained, which is much smaller than the critical value of 0.05. Therefore, the null hypothesis (that considers the correlation coefficient as 0) is rejected, which reinforces the dependence of lipophilicity on the total molecular polarity.Penoxsulam  exhibits a considerably higher discrepancy than that correlation obtained from μ when compared to the optimal value of 1. A linear regression of experimental log P against calculated log P values obtained from another source (the ChemSketch module of the ACD/Labs program) yields a similar result  for estimating log ics tool  to prediP prediction are usually available.Nevertheless, a reservation should be considered for small organofluorine compounds, for which well-parameterized models for log Regarding the use of calculated molecular dipole moments as a descriptor of lipophilicity for small molecules, a more detailed analysis is required. Accordingly, a series of structurally simpler organofluorine compounds were retrieved , all fro7, 9, and 10 have the dependence of the molecular dipole moment μ with the rotation around the C–C bond. The correlation plots between the experimental log P of compounds 1–11 and a) dipole moment and b) predicted log P are shown in Compounds 2 value of 0.53, which indicates a rough correlation between μ and log P. However, when applying the same hypothesis test, as for the first data set, a p-value of 0.0115 was obtained, which suggests that, although smaller than the first correlation, there is also a dependence between the calculated dipole moment and lipophilicity for small molecules. The considerably lower correlation may be explained by the fact that, in a small molecule, subtle structural changes strongly influence the overall molecular dipole and, sometimes, the introduction of a polar bond in a molecule decreases the overall molecular dipole moment. For instance, carbon tetrafluoride has four polar bonds, but it is apolar, while the other fluorinated methanes are all polar. Thus, the use of calculated molecular dipole moments as descriptors for lipophilicity in these small organofluorines should be used with caution. On the other hand, P, which reinforces that for simple molecules there are well-parameterized models for log P prediction, in spite of the remarkable systematic error.From In summary, the overall molecular polarity is influenced not only by the nature of the substituent group (as considered by additive techniques of prediction), but also by the orientation of the neat molecular dipole moment vector. In this sense, methods that ignore such influences result in reduced accuracy when predicting physicochemical properties of complex structures, such as the herbicides presented herein. Taking into account the correlation between lipophilicity and molecular conformation contributes to rationalize the effect of fluorine introduction on lipophilicity. Furthermore, the use of the molecular dipole moment that considers information on the molecular conformation, as presented herein, is a simple and straightforward parameter that can be valuable as a descriptor in quantitative structure–property relationships (QSPR). This could contribute significantly in studies involving organofluorine agrochemicals, for example, towards modeling herbicidal activity, and/or for environmental risk assessment.I–VII was performed at the ωB97X-D/6-31G [1–11 were calculated at the same level, which has been successfully applied to predict the conformational energies of other fluorine-containing compounds [P was calculated using the Molinspiration Cheminformatics tool [The conformational search of agrochemicals 31G –17 level31G . The low31G ,18, in tompounds –34. Freqompounds . Insightompounds ,36. The ics tool  and moleics tool .File 1I–VII and compounds 1–11 analyzed herein.Additional linear correlation, main conformers from the Monte Carlo conformational search, Cartesian coordinates and energies of the conformers of agrochemicals


P = 0.049). The total injection volume for HA-Ks was significantly lower than that for HA-Mc . However, no significant difference in these items was observed between HA-Mc and HA-Ks-80%. HA-Mc and HA-Ks were considered to be almost the same. Nonetheless, HA-Ks exhibited higher viscosity and SIM performance than HA-Mc. HA-Ks-80% had almost the same performance as HA-Mc. Thus, understanding SIM performance and characteristics requires a focus on the viscosity of SIMs.In Japan, two 0.4% sodium hyaluronate (HA)-based submucosal injection materials (SIMs) are currently used in endoscopic submucosal dissection (ESD): MucoUp (HA-Mc) and Ksmart (HA-Ks). HA-Mc and HA-Ks have the same concentration and are, thus, construed by most endoscopists to have no difference. Nevertheless, visual observation conveys the impression that HA-Ks have a higher viscosity than HA-Mc, suggesting that HA-Ks performs better than HA-Mc. This study aimed to examine the differences between HA-Mc and HA-Ks. HA-Ks exhibited higher viscosity due to greater weight-average molecular weight compared with HA-Mc. HA-Ks had significantly greater submucosal elevation height (SEH) than HA-Mc; the SEH of HA-Ks-80% (80% dilution of HA-Ks) was the same as that of HA-Mc. The ESD procedure time was significantly shorter with HA-Ks than with HA-Mc (15.2 ± 4.1 vs. 19.5 ± 5.9;  The use of high-performance submucosal injection materials (SIMs) can strongly support the realization of rapid and safe endoscopic treatments9. High-performance SIMs currently used in endoscopic treatments are viscous solutions, and recent studies have described the viscoelastic properties of solutions suitable for high-performance SIMs11.Endoscopic submucosal dissection (ESD) is performed for gastrointestinal cancer or polyp in several medical institutions, and the number of endoscopic treatments is increasing year by year14. MucoUp  and Ksmart  are the two HAs currently marketed and used in Japan, and both have the same HA concentration of 0.4%. HA-Ks (Ksmart) began to be used in 2019—that is, more than 10 years after the launch of HA-Mc (MucoUp). As HA-Mc and HA-Ks have the same HA concentration, most endoscopists construe that HA-Mc practically does not differ from HA-Ks with respect to viscosity, ease of injection, and SIM performance. Therefore, both HA-Mc and HA-Ks are being used and regarded as the same SIM in actual endoscopic treatment.SIMs based on sodium hyaluronate (HA) were developed in around 2000 and are currently widely used in endoscopic treatments owing to their superior performance and low tissue toxicity17. Hence, consistent with this visual observation, it is quite possible that HA-Mc differs from HA-Ks with respect to viscosity. Our previous studies showed that a SIM with higher viscosity has higher performance, as viscosity is strongly positively correlated to performance11. Based on these findings, HA-Ks is expected to have higher SIM performance than HA-Mc.Visual observation conveys the impression that there exists a clear difference in viscosity between HA-Mc and HA-Ks. Specifically, the flow speed of the solution and the disappearance speed of bubbles generated in the solution are clearly lower in HA-Ks than in HA-Mc Video , indicat19. Utilizing these methods, we precisely evaluated the viscosity and SIM performance of HA-Mc and HA-Ks. Furthermore, the weight-average molecular weights of HA in HA-Mc and HA-Ks were compared.Through detailed evaluations, the present study aimed to examine the differences between HA-Mc and HA-Ks and to demonstrate that understanding SIM performance and characteristics requires a focus on the components, concentrations, and viscosity of SIMs. We developed original methods for the accurate measurements of viscosity, submucosal elevation height (SEH), and injection pressure (IP) of SIMs−1) and, to a slight extent, the characteristics of a pseudoplastic fluid  at high shear rates (1–100 s−1). HA-Ks showed a greater decrease in viscosity with increasing shear rate than HA-Mc, indicating stronger pseudoplastic properties. The viscosity of HA-Ks was higher than that of HA-Mc at all shear rates  at low shear rates 0.01–1 s–1 s−1 an−1 most significantly affected the SIM performance , and viscosity at a shear rate of 1000 s−1 most significantly affected the ease of injection . Therefore, viscosity evaluation was performed with emphasis on these two values. At a shear rate of 1 s−1, the viscosity of HA-Ks was significantly higher than that of HA-Mc , and the viscosities of HA-Ks-80% and HA-Mc were almost the same . This result indicated that HA-Ks had higher SIM performance than HA-Mc and that HA-Ks-80% and HA-Mc had almost the same SIM performance. At a shear rate of 1000 s−1, the viscosity of HA-Ks was slightly higher than that of HA-Mc , whereas the viscosity of HA-Ks-80% was slightly lower than that of HA-Mc , suggesting that HA-Mc had a slightly lower IP than HA-Ks but a slightly higher IP than HA-Ks-80% , and molecular weight distribution curves were created. The comparison of molecular weight distributions between HA-Mc and HA-Ks revealed that HA-Ks had higher molecular weight than HA-Mc. Furthermore, the weight-average molecular weight, which has the strongest correlation with physical properties , was approximately 1.3 times higher in HA-Ks than in HA-Mc Fig. .Figure 2First, each SIM was injected into the submucosa at the center of the specimens tested, and the SEH was measured over time. The SEHs of HA-Mc, HA-Ks, and HA-Ks-80% were greater than those of saline. Furthermore, the SEHs of HA-Ks were all greater than those of HA-Mc, and the SEHs of HA-Ks-80% and HA-Mc were almost the same Fig. A.Figure Next, saline, HA-Mc, HA-Ks, and HA-Ks-80% were injected at the edge of specimens. The obtained SEH values were lower than the magnitudes measured after injection into the center of specimens; nevertheless, similar trends were observed Fig. B.P < 0.05; Fig. Finally, the SEHs of HA-Mc and HA-Ks were compared. When HA-Mc was injected into the submucosa at the center of specimens, the SEH was 5.60 ± 0.13 mm immediately after injection and 2.69 ± 0.10 mm after 30 min. When HA-Ks was injected, the SEH was 5.83 ± 0.13 mm immediately after injection and 2.91 ± 0.11 mm after 30 min. At all post-injection times , the SEHs of HA-Ks were significantly greater than those of HA-Mc . The total injection volume was significantly lower for HA-Ks than for HA-Mc . The total number of submucosal HA-Ks injections per treatment was considerably smaller than the total number of submucosal HA-Mc injections . No significant difference in visual analog scale (VAS) measurements in ESD  was observed between ESD using HA-Ks and ESD using HA-Mc. Furthermore, there were no significant differences between HA-Mc and HA-Ks-80% with respect to ESD procedure time, total volume of injected SIM, and VAS measurements in ESD.ESD was performed with HA-Mc, HA-Ks, or HA-Ks-80% in an ex vivo porcine stomach model, and the outcomes were compared Table . The ESD17. Therefore, focusing on the constituent components and concentrations of SIMs and directly measuring and comparing the viscosities of SIMs are extremely important to understand the differences in SIM characteristics.As HA-Mc and HA-Ks are HA solutions of the same concentration (0.4%), both SIMs have been considered to have almost identical characteristics: viscosity, ease of local injection , and SIM performance . However, HA solutions with different weight-average molecular weights may have different viscosities even if the HA concentration is the same, and the HA solution with higher weight-average molecular weight generally tends to have higher viscosity11; hence, it was expected that HA-Ks had higher SEH and IP than HA-Mc. In actual measurements, the SEH and IP of HA-Ks were significantly higher than those of HA-Mc, suggesting that HA-Ks exhibited higher performance than HA-Mc.The viscosity analysis showed that the viscosity of HA-Ks was higher than that of HA-Mc at all shear rates. Furthermore, the evaluation of molecular weight distribution by SEC revealed that HA-Ks contained HA with higher weight-average molecular weight than HA-Mc. These results indicated that HA-Ks had higher viscosity due to greater weight-average molecular weight than HA-Mc. The difference in weight-average molecular weight between HA-Mc and HA-Ks is expected to be due to differences in the manufacturing process of sodium hyaluronate between the two agents. In addition, previous studies reported a strong positive correlation between SIM viscosity and SEH/IP3 s−1 and IP and between viscosity at a shear rate of 100 s−1 and SEH11. The results of this study indicate that pseudoplastic fluid-based SIMs  are estimated to have higher performance than Newtonian fluid-based SIMs  when both types of SIMs have the same ease of injection21. The viscosity analysis revealed that the viscosities of HA-Ks and HA-Ks-80% tended to decrease at high shear rates, as compared to the viscosity of HA-Mc, and that HA-Ks and HA-Ks-80% exhibited stronger pseudoplastic fluid characteristics than HA-Mc. Therefore, the result of this analysis suggests that HA-Ks and HA-Ks-80% have more suitable viscosity characteristics as high-performance SIMs than HA-Mc. In fact, the viscosity at a shear rate of 100 s−1 and SEH of HA-Ks-80% were almost the same as those of HA-Mc, and the viscosity at a shear rate of 103 s−1 and IP of HA-Ks-80% were lower than those of HA-Mc. In other words, HA-Ks-80% has the same SIM performance as HA-Mc and is easier to inject than HA-Mc.In our previous study, the strongest correlations were observed between viscosity at a shear rate of 10In order to evaluate the SIM performance in actual endoscopic treatment, we conducted a trial using an ex vivo model of ESD to compare the results of ESD treatment with HA-Mc, HA-Ks, and HA-Ks-80%. The ESD procedure time was significantly shorter with HA-Ks than with HA-Mc, and the total injection volume was significantly lower for HA-Ks than for HA-Mc. We speculate that significantly higher SEHs of HA-Ks can reduce ESD procedure time. In the evaluation of procedure difficulty by endoscopists using VAS, no significant difference between these two SIMs was identified. These results suggest that the difference in procedure difficulty was not so great that the endoscopists could not clearly perceive it. In fact, the difference remained unnoticed by endoscopists who had used these SIMs from the time that the two SIMs were launched until the present. However, these results also indicate that HA-Ks is certainly a better SIM with higher performance than HA-Mc, and the change from HA-Mc to HA-Ks may improve the ESD outcomes. Furthermore, no significant differences in the ESD procedure time and total volume of injected SIM were noted between HA-Mc and HA-Ks-80%. These results suggest that HA-Ks-80% has almost the same SIM performance as HA-Mc. Because HA-Ks-80% has a lower infusion pressure than HA-Mc and is easier to inject than HA-Mc, considering all factors, HA-Ks-80% may be concluded to be slightly superior to HA-Mc.From the above, our study findings suggest that changing the SIM used for ESD from HA-Mc to HA-Ks may lead to improvements in ESD outcomes. Nonetheless, the present study has some limitations that need to be underlined. This study is a basic research using an ex vivo model of ESD, and SIM performance is not the only determinant of ESD outcomes. Considering these limitations, future clinical studies are required to confirm whether the results of this study can be applied to actual ESD.23. As HA-Ks-80% is 80% dilution of HA-Ks, the content of HA-Ks-80% is increased from 20 to 25 mL at the same drug price. This is synonymous with a 20% drop in the drug price, which suggests that the use of HA-Ks-80% may reduce medical costs without deteriorating the ESD outcomes.Furthermore, this study suggested that HA-Ks-80% had almost the same performance as HA-Mc and could be used for ESD instead of HA-Mc. Both HA-Mc and HA-Ks have almost the same drug price (approximately 72 USD) and the same content (20 mL)Thus, the results of this study demonstrate that understanding SIM performance and characteristics requires a focus on the components, concentrations, and viscosity of SIMs. These results are applicable not only to HA but also to all viscous SIMs used worldwide and will considerably contribute to advancements in endoscopic treatments for gastrointestinal tumors via the identification of the optimal SIMs for these treatments.In conclusion, although HA-Mc and HA-Ks were considered to be almost the same, the detailed viscosity analysis and SIM performance evaluation revealed that HA-Ks exhibited higher viscosity and SIM performance than HA-Mc. Furthermore, our study showed that HA-Ks-80% had almost the same performance as HA-Mc and could be used as an alternative to HA-Mc for ESD. Our study findings suggest that changing the SIM used for ESD from HA-Mc to HA-Ks may lead to improvements in ESD outcomes and that the use of HA-Ks-80% may reduce medical costs without deteriorating the ESD outcomes.Otsuka Normal Saline  was used as 0.9% (w/v) sodium chloride solution , whereas MucoUp and Ksmart were used as HA-Mc and HA-Ks, respectively. Additionally, Ksmart was diluted to a concentration of 90%, 80%, or 75% in saline and used as HA-Ks-90%, HA-Ks-80%, or HA-Ks-75%, respectively.25. The viscosity of SIMs was measured at 25 °C using a DHR-1 controlled-stress rheometer  with a 60-mm cone-plate geometry (1°). A solvent trap containing distilled water prevented sample dehydration during measurement. Each SIM (1.5 mL) was loaded onto the rheometer and left for 5 min to enable relaxation to the original gel structure. Steady-flow viscosity was measured in the flow-sweep mode (steady-flow measurement) and calculated as shear stress divided by shear rate. Steady-flow viscosity  and shear stress  were determined using the TRIOS software version 4.4.0.41651 (TA Instruments) for a range of shear rates .Viscosity analysis was performed using a rheometer29. Briefly, 4.9 mL of 0.1 M aqueous sodium chloride solution was added as a solvent to 0.1 mL of the measurement sample. The mixture was gently stirred at 25 °C, and filtration was subsequently performed using a 0.5-μm filter. SEC was carried out using a differential refractive index detector  and TSKgel GMPWXL column . Monodisperse pullulan  was used as a standard sample. Data processing was performed using a data processing system for gel permeation chromatography , and molecular weight distribution curves for both samples were prepared from the measured values. The molecular weight was a relative value based on pullulan.Molecular weight distributions of HA-Mc and HA-Ks were measured using SEC, and the average molecular weights were compared. The method for measuring molecular weight distributions by SEC is described belowFrom these measured data, the average molecular weight was determined using the following equations:In the abovementioned equations, Mi represents the molecular weight at each elution position; Ni, the number of molecules; Mw, the weight-average molecular weight; Mn, the number average molecular weight; and Mz, the Z‐average molecular weight. The weight-average molecular weight (Mw) has the strongest correlation with physical properties. The number average molecular weight (Mn) is the average molecular weight associated with the low-molecular-weight component, whereas the Z‐average molecular weight (Mz) is the average molecular weight associated with the high-molecular-weight component.20. In the present study, the same ex vivo model was used to evaluate SIM performance. Specifically, gastric specimens were cut into 5 × 5 cm squares and immediately stored at − 30 °C. To ensure uniform conditions, all frozen gastric specimens were thawed just before the analysis procedure. Thawed specimens were stretched flat on a rubber board, and a constant tension (1.5 N) was applied by stretching both ends of the specimens with a clip.We previously developed a new ex vivo model that could accurately measure the SEH after SIM injectionTo evaluate the performance of various SIMs, the magnitudes of SEH were measured at specific time intervals. With a 2.5-mL syringe and 23-gauge needle, 2.5 mL of each solution was horizontally injected into the submucosa at the center and edge of specimens to produce submucosal elevation. SEH was precisely measured using a digital height gauge  at 0, 2.5, 5, 7.5, 10, 12.5, 15, 17.5, 20, 30, 45, and 60 min after injection.Injection into the submucosal layer at the edge of specimens reproduced the conditions of submucosal injection during endoscopic treatments after mucosal incision . Five independent measurements were performed, and the obtained results were expressed as means and standard deviations.11. To evaluate the IP of each SIM, a 21-, 23-, or 25-gauge endoscopic injection needle , digital pressure gauge , and syringe with a solution were connected to a three-way stopcock . The digital pressure gauge was connected to the three-way stopcock via an infusion extension tube. When the pressure value was stable for 3 s, the magnitudes of IP were measured using a syringe pump  that could set the injection speed and syringe type. A 20-mL or 10-mL syringe (Terumo) was used, and the injection speed was set at a rate of 0.1, 0.2, 0.3, 0.4, or 0.5 mL/s. Three independent IP measurements were performed for each SIM, and the obtained results were expressed as means and standard deviations.We previously established a method for accurate IP measurement33. For this ex vivo model of ESD, stomachs obtained from 6-month-old domestic hybrid female pigs were immediately frozen after harvesting and thawed at 25 °C for 6 h before each experiment. The pyloric side of the stomach was fixed to an overtube . As the upper third of the porcine stomach is similar to the human stomach, a pseudolesion was created on the upper stomach.To examine the performance of HA-Mc, HA-Ks, and HA-Ks-80%, blinded head‐to‐head comparisons of two off‐label SIMs were performed using an ex vivo porcine stomach model of ESDESD was conducted on a 2.5‐cm‐diameter pseudolesion in the ex vivo porcine stomach model by an endoscopist  with experience in performing around 50–100 gastrointestinal ESD procedures. All pseudolesions were created in the upper body of the porcine stomach, where good operability of the scope was ensured. The SIM used for each procedure was randomized, and the endoscopist was blinded to the SIM used; three ESD procedures per SIM were performed. The primary outcome was the total ESD procedure time. The secondary outcomes were the total volume of injected SIM, total number of SIM injections, and ease of dissection, as assessed using a 100‐mm VAS, with the highest and lowest scores indicating “extremely difficult” and “extremely easy,” respectively.ESD was performed as follows. For this study, a gastrointestinal endoscope  with a transparent hood was used, and the Endosaber  was utilized to create pseudolesions on the mucosa of the stomach model. To create a safe submucosal elevation, an appropriate amount of SIM was injected into the submucosal layer using a 25-gauge endoscopic injection needle . Subsequently, the mucosa around the pseudolesions was circumferentially incised using the Endosaber and VIO 3 electrosurgical generator . Finally, the connective tissue of the submucosal layer was dissected using a Flush knife with a swift coagulation current  . The procedure time, total volume of injected SIM, total number of SIM injection, and ease of dissection were evaluated for each ESD.Finally, histologic sections were made from each resected block and were stained with hematoxylin and eosin. The specimen was then microscopically evaluated, and confirmed that both the ESD specimens resected using HA-Mc and HA-Ks had the submucosal layer properly dissected.The above-described protocols using porcine gastrointestinal tracts were conducted in accordance with the animal care guidelines of Kyoto Prefectural University of Medicine. All methods in this study were performed in compliance with the ARRIVE guidelines and the other relevant guidelines and regulations.t-test. All reported P values were two-sided, and magnitudes with P < 0.05 were considered statistically significant.For all repeated experiments, the data obtained were presented as means and standard deviations and analyzed using the GraphPad Prism 7 software . Continuous variables were analyzed using Student’s Supplementary information.Supplementary video.


With the development of biomolecular modeling and simulation, especially implicit solvent modeling, higher requirements are set for the stability, efficiency and mesh quality of molecular mesh generation software. In this review, we summarize the recent works in biomolecular mesh generation and molecular visualization. First, we introduce various definitions of molecular surface and corresponding meshing software. Second, as the mesh quality significantly influences biomolecular simulation, we investigate some remeshing methods in the fields of computer graphics and molecular modeling. Then, we show the application of biomolecular mesh in the boundary element method (BEM) and the finite element method (FEM). Finally, to conveniently visualize the numerical results based on the mesh, we present two types of molecular visualization systems. With the development of biophysics and computational sciences, numerical simulation methods are widely applied in the biomolecular field, such as the transport processes within ion channels and the electrostatic interactions of proteins. The typically used methods include molecular dynamics –3, BrownA number of numerical methods have been used to solve the continuous model, including the finite element method (FEM) , 13–16, Visual analysis is important in scientific computations. So far, there have been many tools for molecular visualization. The visual molecular tool can lead to biophysical development. For instance, the visualization of protein-ligand complex is critical in elaborating protein-ligand interactions and aiding novel drug design. Visualizing three-dimensional (3D) molecular structures of biopolymers has become a routine in the life sciences, e.g., ligand-binding pockets or other details in macromolecular assemblies help to elucidate the relationship between protein structure and function.This paper aims to summarize the various definitions of molecular surfaces, review the state-of-the-art methods for molecular surface remeshing, including our recent work, and introduce their applications in implicit solvent modeling and simulation. In addition, applications of molecular remeshing and molecular visualization tools are also explored. The remainder of this paper is structured as follows. In “The molecular surface is defined in various senses. The most widely used molecular surfaces include the van der Waals surface (VDWs) , the solThe VDWs is defined as the surface of the union of the spherical atomic surfaces with the VDW radius of each atom within the molecule. Using the VDWs makes it convenient to calculate the molecular surface area and the surface normal, but it contains many pores that cannot contain water molecules.The solvent accessible surface , also knIn contrast to the VDWs, the SES contains less cracks and surface dimples. The SAS and SES are represented by the trajectory of the center and the inter-boundary of a rolling probe on the VDWs, respectively. Figure The skin surface is defined by a set of weighted points representing the atoms and a scalar called the shrink factor controlling the hyperboloidal connections between neighboring spheres. The skin surface is smoother than the VDWs and its tangent is continuous . For theS is the hypersurface function.The MMS  is definUnlike the definitions above, the Gaussian surface  is defind is positive and controls the decay speed of the kernel functions; xiand ri are the location and radius of atom i, respectively; canddare usually set as 1 and 0.5, respectively. Compared with other definitions of molecular surface, the Gaussian surface is smooth and more suitable to represent the electron density of a molecule [c and d can be chosen such that the Gaussian surface approximates the SES, SAS and VDWs well [The Gaussian surface is smoother.The Gaussian surface provides a realistic representation of the electron density of a molecule compared to other molecular surface definitions .The Gaussian surface is well established –40 and hThe parameter molecule . These tDWs well , 36. ComWith the various definitions of molecular surface proposed, numerous works have been devoted to the computation of molecular surfaces. The biomolecular surface mesh substantiates that it is indeed a discrete representation of the biomolecular surfaces, which has a wide range of applications in the visualization, geometric calculation and solution of the implicit solvent model. The development of mathematical modeling and numerical simulation of biomolecular systems, especially the solution of implicit solvent model, proposes new requirements for the biomolecular surface mesh, such as high quality, efficiency and stability.In recent years, as a variety of molecular surfaces definitions have been put forward, many kinds of algorithms for calculating the molecular surface meshes are constantly emerging, as described below. In 1983, Connolly , 46, proIn 2015, MSMS, Molsurf, NanoShaper, EDTsurf, TMSmesh and GAMer were compared and discussed by Liu et al. . These mThe reasons that TMSmesh 2.0  is at leSecond, a more efficient and much sharper bound estimator of the summation of Gaussian kernels in a cube is adopted as shown in Fig. Third, trilinear polynomials are used to approximate the surface, which reduces the computation cost significantly. For a trilinear surface see Fig. , the surA mesh is a discretization of a geometric domain into small and simple units or elements , where tVarious approaches in surface remeshing have their own targeted goals and objectives. However, the following challenges are mostly considered for analysis of the applicability and validity of a specific approach , 67.Mi to the output mesh Mf, as calculated by Eq. is the Euclidean distance between two points p and q in a 3D space. The distance from point p to surface M is defined as the shortest distance between p and the nearest point in M, as given in Eq.  ≠ dh. The two-sided Hausdorff distance is given in Eq.  is an important goal in surface remeshing. Typically regular vertices are preferred. Short edges and triangles with small or large angles are avoided to improve the efficiency of numerical simulations . SimilarThe output mesh should be valid. The validity of mesh ensures that the mesh is closed and a simple manifold . The mesPrior to surface remeshing, the mesh is generated with any suitable method for a given application. In order to ensure a better approximation, the mesh is generated with high complexity, e.g., with 3D scanners . SimilarAt is the area of the triangle t, ptis its half-perimeter, and ht is the length of its longest edge [Qmin and Qavg are used for analysis of the meshing results. Similarly, θmin and θmax, are also used for comparison. In addition, a, b, and care the lengths of the triangle’s edges and S = (a + b + c)/2 .The main objective of quality meshing is to improve different quality parameters. The parameters used for meshing quality measurements in previous papers , 66, 73 est edge . Typicalications . Similarications . The imphttp://lsec.cc.ac.cn/~lubz/Meshing.html), which was used in the previous TMSmesh tests. In the PQR format, the occupancy and temperature factor columns of a PDB file is replaced with charge Q and radius R, respectively. These files are compatible with several popular computational biology tools [A benchmark for molecular structures in the PDB (protein data bank) and PQR formats can be found in the following website:  is the parameter to control the rate of smoothing, Nirepresents the number of vertices in one ring and qj represent the jth adjacent vertex in the one-ring of the ith vertex. The results of SMOPT show a significant improvement in the mesh quality. However, there still exist very small angles that destroy the quality of triangles. In our recent paper [In the field of molecular modeling, Decherchi and Rocchia  triangulnt paper , we usedWe tested the meshes in boundary element calculations of the Poisson-Boltzmann electrostatics. The BEM software used is a publicly available PB solver, i.e., AFMPB. As a representative molecular system, we chose the structure Connexin. The initial coordinates for Connexin are obtained from the PDB (code GJB2 ). The suOver the past decades, little research has been conducted on the volume mesh generation of molecules in biophysics. In 2014, Tu et al.  built a The triangulated molecular surface can be generated by some surface mesh generators as shown in “For transmembrane proteins, the mesh needs to add membrane information, as shown in Fig. Currently, parallel computers enable us to solve a problem with a mesh containing tens of millions of vertices. However, CPU time and memory limitations still challenge the generation of a large high-quality mesh on a single machine. Obviously, a parallel environment significantly reduces the amount of time required for large-scale mesh generation.In 2016, Xie et al.  proposedThe meshes in Fig. http://www.pymol.org), VMD [To date, dozens of visualization tools are available for molecular visualization. PyMOL (rg), VMD  and Chimrg), VMD  are amonrg), VMD , is usedDue to the requirement nature of three-dimensional (3D) graphics, most molecular viewers are desktop applications. The need to install specialized applications, and occasionally, the restriction of software licenses, results in hurdles to the sharing of molecular data. Unlike a desktop application, a standards-based client-side web application comes pre-installed with every computer and mobile device with a modern web browser and can be seamlessly integrated into online environments for accessing and analyzing molecular data. Subsequently, web browsers need to display 3D content with additional plug-ins. Next we will discuss a few applications for molecular visualization.Jmol  is implehttp://web.chemdoodle.com) benefit from GPU acceleration. PV [http://threejs.org) framework for interfacing with WebGL. It features an experimental version of surface construction based on the EDTSurf algorithm. However, GLmol lacks a full featured API and the use of the Three.js library leads to performance inefficiencies as well. In 2015, Alexander et al. [www.xyzgate.com).In contrast, WebGL visualizers such as ChemDoodle Web Components , the solvent accessible surface (SAS), the solvent excluded surface (SES), the minimal molecular surface (MMS), the molecular skin surface and the Gaussian surface.Then, we presented a comprehensive review of the molecular surface remeshing techniques. We also presented the applications of molecular surface remeshing. In addition, our recent work about membrane-channel protein system and volume mesh generation were also summarized. Furthermore, few commonly used tools for surface remeshing and molecular visualization have also been discussed.There are few directions of further work in molecular surface remeshing and related research. The surface remeshing methods are dependent on the input meshes, as described in “The mesh generated with TMSmesh has a number of small angles and short edges which are difficult for further improvement (see Fig.


CFI) that cause low systemic levels of the protein (FI) have been reported as a strong risk factor for advanced age-related macular degeneration (AMD). This study set out to replicate these findings.Rare genetic variants in complement factor I (FI levels were measured by sandwich ELISA in an independent cohort of 276 patients with AMD and 205 elderly controls. Single-nucleotide polymorphism genotyping and Sanger sequencing were used to assess genetic variability.CFI variant (28.3 µg/mL) compared to those with AMD without a rare CFI variant  or the control population with  or without  a rare CFI variant. Thirty-six percent of patients with AMD with a rare CFI variant had levels below the fifth percentile, compared to 6% in controls with CFI variants. Multiple regression analyses revealed a decreased FI level associated with a rare CFI variant was a risk factor for AMD . Additionally, measurement of FI in aqueous humor revealed a large FI concentration gradient between systemic circulation and the eye (∼286-fold).The median FI level was significantly lower in those individuals with AMD and a rare CFI causing low systemic FI levels are strongly associated with AMD. The impermeability of the Bruch's membrane to FI will have implications for therapeutic replacement of FI in individuals with CFI variants and low FI levels at risk of AMD.Rare genetic variants in  Studies over the past decade or so have implicated the complement system, and more specifically the AP,CFI gene on ch4q25, is a serine protease and an endogenous inhibitor of the complement pathway.,,,,FI, which is encoded by the Complete deficiency of FI in humans results in unchecked turnover of the AP, a consumptive C3 deficiency, and predisposition to infection with encapsulated organisms .CFI variants in AMD,,CFI causing low levels (type I variants) are the predominant driver of AMD risk (OR 13.6).Association studies first identified common single-nucleotide polymorphisms (SNPs) associated with AMD risk, suggesting a role for ,In addition to genetic studies linking impaired complement regulation by FI to AMD, amyloid β, a constituent of drusen deposits in AMD, has been suggested to interact with FI, impairing its function in both AMD and Alzheimer disease.CFI variants causing low plasma FI levels as a strong risk factor for AMD (OR 12).These genetic and in vitro studies suggest a role for impaired regulation of the complement system through FI in AMD. In this study, we replicate, in an independent cohort, the association of rare The Southampton AMD cohort contains 577 patients with AMD and 651 elderly controls. Cases and controls were examined and diagnosed by AJL as previously described,Aqueous fluid was extracted, along with corresponding serum, from patients in a distinct cohort of 16 cases and 14 controls by AJL during cataract surgery and stored at –80°C before FI levels were measured.2SO4) was added and the plates were immediately read at 450nm absorbance using a Floustar Optima plate reader (BMG Labtech). FI levels of patients were measured using the ELISA described, and results were read on the plate reader, which had integrated interpolation software for immediate results given from the computer-generated standard curve. Calculated intraplate and interplate percent coefficient of variation were 3.18 and 14.87, respectively, for a normal control patient across all 25 plates in triplicate. The fifth percentile plasma FI cutoff of 23.69 µg/mL was calculated using the levels of the 205 control patients that were measured. For measurements of aqueous fluid, the standard curve was extended from 8 to 10 1:2 dilutions, with an average lower limit of detection of 0.54 ng/mL and lower limit of quantification (LLOQ) of 0.87 ng/µL, as calculated by interpolation of the blank + SD of two blank replicates per plate multiplied by 3 and 10, respectively. Serum samples were diluted 1:1000, while aqueous fluid was diluted 1:80 in order to fit the detectable range; the concentration of the lowest test sample was never below the LLOQ for an individual plate.Ninety-six well-plates  were coated with 2 µg/mL capture antibody  in a sodium bicarbonate buffer and incubated overnight at 4°C. The plates were then washed three times with PBST  before 50 µL of blocking buffer solution (1% BSA in PBST) was added to each well. Again, the plates were washed before 50 µL of sample and standard was added to wells in triplicate and duplicate, respectively. The standard was made up of 8 1:2 serial dilutions from 1 µg/mL purified FI . The plates were incubated for 1 hour at room temperature before further stages of washing, addition of 50 µL detection antibody (Ab) , washing with PBST, and addition of 50 µL tertiary Horseradish Peroxidase (HRP)-conjugated donkey anti-mouse secondary Ab  (1/2000 in blocking buffer). A final wash step was performed before 100µL tetramethylbenzidine solution was added to each well. After incubation for 5 minutes, 100µL of stop solution (1 M HSNP-chip genotyping of the Southampton AMD case-control cohort was performed as part of the sequencing of the AMD-European Union-Johns Hopkins University (EU-JHU) cohort by the procedures outlined in the study by the AMD Gene Consortium.U test  scale in order to normalize the distributions. Significance was defined as *P < 0.05, **P < 0.01, ***P < 0.001, and ****P < 0.0001.All standard statistical tests, apart from those in U test  and DunnU test , and theents see  and S3. P = 0.0034). A low plasma FI cutoff point was established by taking the lower fifth percentile cutoff points in the control cohort (23.69 µg/mL), as shown in The FI plasma level was measured in 276 patients with AMD and 205 elderly controls. The median FI level was lower in cases compared to controls .Genetic analysis of the cohort revealed 23 distinct rare The relationship between FI level and two common SNPs was analyzed in this cohort, rs11726949 and rs9998151  and S2. CFI genotype. The median FI level was significantly lower in those individuals with AMD and a rare CFI variant (28.3 µg/mL) compared to those with AMD without a rare CFI variant  or the control population with  or without  a rare CFI variant . K441R was identified in four cases and two controls but did not reach a level of significant association with AMD in the cohort. K441R was associated with low levels , and both of these low FI level K441R carriers had early AMD. The variants P553S and G261D were found in more controls than cases, although not significantly so , which were greatly amplified if the patient had a rare CFI variant . In fact, only risk of early AMD was significantly affected by low FI levels alone. To consolidate this, it was further calculated that in any AMD and late AMD groups, the ORs produced by the models were in fact statistically significantly increased by having a rare genetic CFI variant . This clearly illustrates the deleterious nature of type I CFI variants, with patients far more likely to develop disease with a lower FI level and a CFI variant.Finally, multiple regression analyses were performed using available patient data, and statistical models were created to calculate ORs for any, early, and late AMD manifestation in patients per decrease in FI level by one unit on the log (ln) scale  in patients with no rare CFI variant and that being male was linked with a patient having a lower FI level (P = 0.047). We also found that having a rare, nonsynonymous CFI variant was greatly associated with having a lower FI level in all individuals (P < 0.0001).In addition to the FI level analyses, it was also elucidated that high CRP levels were associated with late, but not early, AMD risk  and 14 control patients. In this small cohort, there was little difference in the mean FI serum levels in dry (62.08 µg/mL), wet (57.98 µg/mL), or control (48.58 µg/mL) patients. Likewise, there were no differences in mean aqueous FI levels between dry (0.24 µg/mL), wet (0.24 µg/mL), or control (0.26 µg/mL) patients . HoweverCFI resulting in low FI plasma levels are a strong risk factor for AMD. The median FI plasma level in patients with AMD was significantly lower than in the control population, but this was largely driven by rare genetic variants in the CFI gene, with a significantly lower median level identified in those patients with AMD with variants compared to those without. Further, 36% of patients with AMD with a rare CFI variant had low levels compared to 6% of the control population with a rare CFI variant, remarkably similar figures to those described in Kavanagh et al.This study validates, in an independent cohort, the findings of Kavanagh et al.,P = 0.01) and a decrease in FI level  in patients with no CFI variant, whereas there was a trend toward significance in the any AMD group . Statistical models that combined a decrease in FI level and a rare CFI variant all showed significant AMD ORs—any AMD (OR 12), early AMD (OR 30.3), and late AMD (OR 10.6)—and these ORs for any and late AMD were significantly higher than those in the respective models without CFI variants. These data suggest that a low FI level associated with a rare CFI variant is a strong risk factor for AMD. This is in keeping with the findings of Kavanagh et al.,CFI variant and low FI level, which would best compare with the late AMD OR of 10.6 in this study, albeit that a different modeling was used for calculation of the affect.Multiple regression analyses demonstrated a significant association between early AMD . Previous studies have shown an association between high CRP levels and AMD.CFI variant or early or any AMD without a CFI variant).Regression analysis also demonstrated that a higher CRP level is significantly associated with late AMD in patients without rare –Nine separate variants were seen in association with low FI levels: G119R, G162D, R187*, N245S, A258T, I340T, G362A, V412M, and K441R. Five of these variants have previously been associated with low levels of FI in either aHUS ,,CFI variants and AMD, physiologic variation can mask a type I mutation. N245S is to date an entirely novel rare CFI variant, which was detected by Sanger sequencing and observed associated with a very low FI level in a patient with AMD in the cohort. V412M, which has been reported recently in familial AMD with severe phenotype,In our study, the patient with P50A had normal levels of FI, and although it has also been identified in patients with aHUS with normal FI levels,CFI variants, 10.3% had low FI levels compared to 4.6% in the control population. Although it is possible that other genetic factors determining FI expression were not examined in our study, it maybe that sequestration of FI at sites of complement activation may account for these low levels. It has been noted in Systemic Lupus Erythematosus (SLE) that factor I serum levels are lower during SLE active phases compared to recessive phases in patients, suggesting possible complement-mediated FI consumption during disease.In our study, we also noted that in patients with AMD without rare CFI, we were able to sample serum and aqueous humor simultaneously. FI levels identified in the aqueous humor were similar to those in previously published work by Schick et al.CFH risk genotype was associated with AMD but not donor CFH genotype, suggesting the role of intraocular complement activation.CFI is more highly expressed in the macular RPE compared to the neural retina or cells of the peripheral retina, whereas measurements of other alternative pathway proteins showed no region-specific distribution differences. Together, these data suggest an important role for complement inhibition within the inner and outer macular, lending particular credence to a role in AMD, and show that cells of the eye have the ability to express and secrete the majority of complement components and regulators, including CFI, to varying degrees. We therefore hypothesize that being heterozygous for a type I CFI variant would lead to haploinsufficiency in the microenvironment of the eye, resulting in higher levels of alternative pathway activity. These data suggest that patients with type I CFI variants may benefit from complement inhibitory therapy, but the impermeability of the eye to FI suggests that intraocular administration may be required.In a small subgroup of patients with AMD and controls without rare genetic mutations in CFI variants causing low FI levels are a substantial risk factor for AMD and identify several individual rare, type I CFI variants in patients with AMD with low FI levels. This replicates the findings of Kavanagh et al.In summary, we demonstrate that rare genetic


Health policy and systems research (HPSR) is an inherently cross-disciplinary field of investigation. However, conflicting conceptualisations about inter-, multi- and transdisciplinary research have contributed to confusion about the characteristics of cross-disciplinary approaches in HPSR. This review was conducted to (1) define the characteristic features of context–mechanism–outcome (CMO) configurations in cross-disciplinary HPSR, (2) develop criteria for evaluating cross-disciplinarity and (3) synthesise emerging challenges of the approach.The paper is a critical realist synthesis conducted in three phases, as follows: (1) scoping the literature, (2) searching for and screening the evidence, and (3) extracting and synthesising the evidence. Five databases, namely the International Bibliography of the Social Sciences and Web of Science, PubMed central, Embase and CINHAL, and reference lists of studies that qualified for inclusion in the review were searched. The search covered peer-reviewed original research, reviews, commentary papers, and institutional or government reports published in English between January 1998 and January 2020.A total of 7792 titles were identified in the online search and 137 publications, comprising pilot studies as well as anecdotal and empirical literature were selected for the final review. The review draws attention to the fact that cross-disciplinary HPSR is not defined by individual characteristics but by the combination of a particular type of research question and setting (context), a specific way of researchers working together (mechanism), and research output (outcome) that is superior to what could be achieved under a monodisciplinary approach. This CMO framework also informs the criteria for assessing whether a given HPSR is truly cross-disciplinary. The challenges of cross-disciplinary HPSR and their accompanying coping mechanisms were also found to be context driven, originating mainly from conceptual disagreements, institutional restrictions, communication and information management challenges, coordination problems, and resource limitations.These findings have important implications. First, the CMO framework of cross-disciplinary HPSR can provide guidance for researchers engaging in new projects and for policy-makers using their findings. Second, the proposed criteria for evaluating theory and practice of cross-disciplinary HPSR may inform the systematic development of new research projects and the structured assessment of existing ones. Third, a better understanding of the challenges of cross-disciplinary HPSR and potential response mechanisms may help researchers to avoid these problems in the future. Since the early 2000s, there have been growing calls for the application of cross-disciplinary approaches to health policy and systems research (HPSR) from both governance and research circles , 2. PoliThe aim of multiple disciplinary research, subsequently referred to as CDR, is to draw together relevant conceptual, theoretical and methodological frameworks from various disciplines to enable scientific assessments of complex social problems that are more comprehensive and more relevant than what monodisciplinary approaches would achieve –16. HoweWithout a shared understanding of the characteristics of cross-disciplinarity in HPSR, there is a risk that traditional disciplinary approaches simply persist in disguise. In addition, how to evaluate whether a given study or publication is, in fact, based on CDR has not been thoroughly investigated. These ambiguities within the literature can lead to conceptual misapplication and confusion in theory development, hence inhibiting the fundamental aims of CDR in the field. Besides these fundamental conceptual ambiguities, there are a multitude of practical challenges of cross-disciplinary HPSR , 23–25 tAs the literature on the characteristic features of cross-disciplinarity in HPSR remains mixed, fragmented and conflicting, it provides limited guidance on why and how the approach works or does not work when applied in different contexts through different mechanisms. We believe that part of the problem is complexity. First, in health policy and systems settings, social problems are becoming increasingly complex and multifactorial just like the interventions deployed to address them –28. SecoIn this paper, we draw on the experiences and accounts of researchers to develop a critical synthesis of the configurations linking contexts and mechanisms with outcomes in cross-disciplinary HPSR. We aimed to critically explore the contexts in which different mechanisms of cross-disciplinarity may produce certain research outcomes. We also synthesised practical lessons on the contexts of emerging challenges and response mechanisms in this area. More specifically, the review aimed at (1) defining the characteristic features of CMO configurations in cross-disciplinary HPSR; (2) developing a framework for evaluating cross-disciplinarity in HPSR; and (3) synthesising emerging challenges of the approach that shape its contexts, mechanisms and outcomes.research on the policies, organizations, programmes and people that make up health systems, as well as how the interactions amongst these elements, and the broader influences over decision- making practices within the health system, influence system performance”  AND [“Health policy and systems research”]. Following this initial review, we revised our review aims to focus on CMO configurations in cross-disciplinary HPSR and the contexts of emerging challenges and coping mechanisms.During the design of the review, we had considered using narrative synthesis. However, based on our scoping review, we identified that the review aims could not be achieved using narrative synthesis and traditional forms of systematic reviews –39. We fCritical realism incorporates insights from the interpretivist approach of causal explanation of interfaces among components in theory construction –47. CentBoth realist and interpretive syntheses focus on identifying theories, which can provide guidance to the available literature , 43. In Guided by the scoping review, the final list of search terms included: [“Cross disciplin” OR “Cross-disciplin” OR “Team science” OR “Multidisciplin” OR “Multi-disciplin” OR “Interdisciplin” OR “Inter-disciplin” OR “Transdisciplin” OR “Trans-disciplin”] AND [“Medical research” OR “Clinical research” OR “Public Health Research” OR “Health policy and systems research” OR “Health policy research” OR “Health system research” OR “Health policy and systems analysis” OR “Health policy and systems evaluation” OR “Health policy and systems assessment” OR “Health services research” OR “Health sciences research”].Two reviewers first independently searched two cross-disciplinary databases – International Bibliography of the Social Sciences and Web of Science Platform – between June 20 and July 22, 2018. A date range of January 1998 to June 2018 was set. Three reviewers conducted additional searches in January 2020 in the International Bibliography of the Social Sciences, Web of Science Platform and three health-focused databases, namely PubMed Central, Embase or CINHAL. In this second search, we set the date range of January 1998 to January 2020. Our search targeted publications that were peer-reviewed original, review or commentary articles as well as institutional or government reports published in English. All forms of study designs were considered. Eligible citations were exported into EndNote X7 reference management software for screening. After removal of duplicates, the remaining citations were further screened according to the criteria set out below.In step one, in view of the large number of materials remaining after removal of duplicates Fig. , three rAs set out in the inclusion/exclusion criteria above, the selection of studies was based on their potential to adequately address the research aims. In line with Pawson’s appraisal criterion, the quality check was based on two questions. First, ‘Does the research address the theory under test?’  and secoIn view of the study’s aims, a three-step qualitative synthesis was adopted, inspired by Turner’s methodology of evidence synthesis , consistIn the final step of synthesis, we drew on the emergent themes to develop theoretical insights on two aspects of the cross-disciplinary HPSR literature. The first aspect is based on the theme that the diverse concepts of cross-disciplinary HPSR reflect a CMO configuration, a dimension that has not been critically explored in the literature. In the second instance, we go beyond populating the challenges of cross-disciplinarity, as the present literature does, to illustrate the contexts and various mechanisms for responding to diverse challenges of the approach. In doing so, we aim to enable researchers to develop pragmatic coping mechanisms for addressing challenges that are likely to emerge in cross-disciplinary collaborations. We continued reviewing selected articles until we reached a point of theoretical saturation, where no new data were identified to complement the developed theory.Box 1 Concepts of cross-disciplinary researchCross-disciplinary research: a general term for research that involves two or more disciplines to address a topic/problem that is beyond the scope of a single discipline [scipline , 32, 33.Multidisciplinary research: different disciplines working discretely on different aspects of a problem to achieve a broadly gauged analysis [analysis , 33, 34.Interdisciplinary research: robust integration of concepts, methods and perspectives from two or more disciplines to address a problem [ problem , 34.Transdisciplinary research: a much more integrative approach involving team members from different disciplines working together and using shared concepts, methods and theories that transcend their respective disciplinary perspectives [pectives , 35.A total of 7792 titles were identified in the online search. After removing duplicates, 5794 records were screened based on titles and abstracts and 5475 records that did not explicitly or implicitly mention any of the CDR terminologies used in our search were further removed. After conducting full-text assessment of the remaining 319 materials, 188 were excluded for various reasons detailed in Fig. Across the selected studies, CDR is also regularly termed as team science , collaboThe included publications generally focused on three main aspects of cross-disciplinarity, namely building understanding of the different cross-disciplinary approaches to HPSR, generating interest in the use of cross-disciplinary approaches to HPSR, and opportunities and constraints that characterize cross-disciplinarity. Generally, all studies selected for review discussed the potentials and emerging challenges of CDR in health policy and systems fields. All the selected studies also discussed some distinguishing features of cross-disciplinary HPSR. One study  examinedIn general, the selected studies highlight that cross-disciplinary HPSR involves the integration of multiple disciplines and methods and is characterised by a uniquely collaborative sociocultural and institutional environment. Within the selected publications, we found that cross-institutional collaboration is an (emerging) essential aspect of cross-disciplinarity. Many studies broadly consider cross-disciplinary collaborations to include both disciplinary and institutional crossing , 61, 62,However, taken in isolation, none of these features clearly distinguishes cross-disciplinary from monodisciplinary approaches. For instance, a mixed methodology is largely used in monodisciplinary research too. Participation of multiple stakeholders is also common in monodisciplinary studies. Our synthesis shows that the most distinguishing characteristic feature of cross-disciplinary HPSR is the configuration of particular contexts, and specific ways of working together (mechanism) to result in certain outputs of cross-disciplinarity (outcome). As illustrated in Fig. As presented in Fig. There is strong controversy in the literature about whether MDR, IDR and TDR are distinct forms of cross-disciplinary HPSR. While some scholars use the three terms/forms interchangeably or argue against their distinction –21, manyThe literature agrees that problems addressed by all forms (notions) of CDR should be beyond the scope of monodisciplinary approaches. However, depending on the degree of cross-disciplinary integration, the research questions may differ across the involved disciplines ), may be shared between disciplines or have been mutually agreed upon  and transdisciplinary health policy and systems research (TDHPSR)). Some of the articles argue that combinations of findings from different monodisciplinary studies about a common health problem, which were not conducted in a predetermined coordinated manner, are enough to provide cross-disciplinary understanding and solutions , 23, 70.Based on the different concepts discussed in the literature, cross-disciplinary HPSR can be characterised as a continuum, ranging from MDR, to IDR and to TDR. The continuum reflects three degrees of cross-disciplinary integration, that is, additivity (MDHPSR), interactivity (IDHPSR) and iterativity (TDHPSR). In MDHPSR, cross-disciplinary output is obtained by summarizing (adding) the findings of individual discipline-specific studies, each providing a monodisciplinary viewpoint on the problem in question , 70, 73.Based on our CMO framework Fig.  and a br‘Context’ generally defines the suitability or appropriateness of a CDR approach to the question or problem at hand. Cross-disciplinarity is not necessarily applicable in every HPSR project. Therefore, in evaluating cross-disciplinarity, it is important to establish whether (1) the nature of the problem and expected outcomes, 2) the accompanying research question and purpose of investigation, and (3) the setting are beyond the scope of monodisciplinary approaches. We found eight specific indicators for evaluating whether these conditions are fulfilled in a given study  communication, all highlighting commitment to a common language throughout the project, such as whether they have developed common vocabulary, and refined their terminology through an iterative process. Finally, a fourth appraisal criterion is about the process for addressing potential conflicts, which can be evaluated using two indicators – first, whether and how the researchers have explained and addressed their own dilemmas and biases, and second, an explicit indication of cross-disciplinary/institutional ethics.The review further identified two appraisal criteria and six indicators for assessing the ‘outcome’ of cross-disciplinarity in HPSR. The first three indicators assess the validity of the study’s cross-disciplinarity claims by focussing on whether (1) the cross-disciplinary purpose was achieved, (2) the planned cross-disciplinary balance was maintained, and (3) a common vocabulary was adhered to. The remaining three indicators focus on establishing that the study produces additional scientific value and novel results in addressing the targeted health problem compared to what monodisciplinary approaches could have achieved.Generally, all the articles reviewed highlighted several challenges of cross-disciplinary HPSR, which can be classified under five main inter-related themes, namely conceptual challenges, institutional challenges, challenges related to communication and information management, coordination challenges, and resource challenges. However, the literature reveals numerous interactions among these challenges, which were often multifactorial and required delicate negotiations to be overcome. In this section, a description is given of the practical mechanisms for responding to these challenges , a specific way of researchers working together (mechanism), and a certain research output (outcome) that is superior to what could be achieved under a monodisciplinary approach. Existing analysis of integration in CDR have not clearly illustrated the unique influence of CMO configurations in the integration process , 103. OuWhile the criteria do not claim to evaluate research quality as several studies in the broader CDR literature have provided significant guidance in that regard , 34, 104In other words, drawing upon the broader team science literature , 35, 104Cross-disciplinary HPSR is widely acknowledged as a very challenging endeavour. This review shows that challenges in the field relate to conceptual, institutional, communication and information management, coordination and resources. While similar findings have been established in studies outside HPSR settings , 99, 104Previous attempts at characterising cross-disciplinary HPSR have overly focused on comparing different concepts of cross-disciplinarity , often claiming superiority of one over the other. Others have looked at cross-disciplinarity in the limited context of mixed-methodology. For instance, O’Cathain et al.  and De AThere are many examples of evaluation frameworks in the cross-disciplinary literature. However, we find that they are overly generic , 105 or The challenges and potential solutions for cross-disciplinary HPSR synthesised in this review may also provide guidance in the design and implementation of future research projects. As challenges vary across contexts, developing a context-driven research management plan may help to avoid these from the outset of new projects , 55, 57.Going forward, two main areas need priority attention in future research; first, developing methodological guidance on how to perform cross-disciplinary HPSR should attract priority attention to assure further advancement of the field. We acknowledge that some important efforts in that regard have emerged , 26. HowFirst, despite the extensive literature search conducted, as cross-disciplinary HPSR is noted to generally be an emerging approach, our search may have excluded studies that did not use the CDR terminologies applied in our search. We also recognise that articles that are cross-disciplinary may not have (explicitly or implicitly) described themselves as such in their titles/abstracts. However, based on our scoping review, the terminologies applied in our search are the most commonly used in both classic and recent literature , 32. In Second, the review was also limited to articles published in English and much of the literature is anecdotal or based on description of pilot projects, raising concerns about the generalisation of our framework. Despite these limitations, given the wide similarities across studies captured in this review, we believe that our findings adequately synthesise the most important themes in the existing literature. In addition, although our selection of the most important challenges was subjective but based on available literature, there was wide agreement across studies about emerging challenges of the approach in the HPSR field. We recognise that this review should be taken as a starting point for a broader discussion about the concept, theory and evaluation of cross-disciplinary HPSR, which may ultimately lead to the development of quality assessment and reporting guidelines similar to those offered by the EQUATOR network  conceptualising the CMO configuration of cross-disciplinary health policy and systems research; (2) developing criteria for evaluating cross-disciplinarity; and (3) synthesising potential response mechanisms to emerging challenges of the approach.These contributions have important implications for researchers and decision-makers. First, a better understanding of the characteristic features of cross-disciplinary HPSR  is essential for researchers to conduct high quality investigations and for policy-makers to engage with researchers in ways that engender translational research outcomes. Second, given the increasing complexity of the cross-disciplinary knowledge field, we have presented criteria for evaluating both theory and practice of cross-disciplinary HPSR. Policy-makers and researchers can use the criteria for the systematic development of new CDR projects and for a structured assessment of existing ones, ultimately contributing to better quality of future HPSR projects. Third, deeper understanding of the challenges of cross-disciplinary HPSR and potential response mechanisms may help (early career) researchers to manage similar situations, thus avoiding common deficiencies.The only way we can make sense of the world is to see the connections between things” [Further advancement of cross-disciplinary HPSR will require creativity and innovation to effectively navigate the growing complexity of cross-disciplinarity itself and the health and social problems targeted for investigation. The CMO framework of cross-disciplinary HPSR signals opportunities for developing understanding of whether/how different elements of cross-disciplinarity interact to produce greater and innovative impact on policy and practice. As Tannen notes, “ things” .Additional file 1. Summary of characteristics of studies included in the review.