syedzayyan/paper_mill_benchmark huggingface dataset:
Bridging or Bonding: An Organizational Framework for Studying Social Capital in Kindergartens.

The article develops our understanding of social capital by analyzing social capital as an organizational phenomenon.The analysis is based on qualitative data consisting of interviews and documents obtained from six different kindergartens in norway.Kindergartens are used as a "prism" through which we can understand how social capital is formed-and the mechanisms that shape the development of various forms of networks within welfare organizations.More specifically we look at drop-in kindergartens.The specific purpose of these kindergartens is to provide open and inclusive arenas that promote integration and community.We find that the kindergartens vary in the degree to which they succeed in building bridging forms of networks and communities.Using concepts from organizational theory and wenger's (1998) theory of communities of practice, we find that formal organizational factors such as ownership, organizational goals, profiling, location, and educational content impact the formation of bridging forms of social capital.The composition of the user groups and the user groups' motivation for participating most clearly affect the conditions for community formation.The composition of the user groups is the result of a number of organizational factors and organizational mechanisms.Kindergartens that have a heterogeneous user group, and a user group with a community orientation (morse 2006), are more successful at creating bridging types of social networks.

Journal: International journal of environmental research and public health (2021)
Publication types: Journal Article
Association between Influenza Vaccination and Positive SARS-CoV-2 IgG and IgM Tests in the General Population of Katowice Region, Poland.

The explanation of the potential interaction between the influenza vaccine and sars-co v-2 infection is urgently needed in the public health.The objective of the study is to compare the occurrence of positive sars-co v-2 ig g and ig m tests in subjects with and without recent (last year) seasonal influenza vaccinations.In a cross-sectional study located in three large towns of silesian voivodeship (poland), we studied 5479 subjects in which 1253 (22.9%) had a positive anti-sars-co v-2 ig g test and 400 (7.3%) had a positive anti-sars-co v-2 ig m test.Seasonal influenza vaccination remains an independent factor protecting against positive ig g tests (or = 0.68; 0.55-0.83).The effect is not apparent with ig m antibodies.The obtained results confirmed that the serological status of sars-co v-2 infection depends on vaccination against seasonal influenza.

Journal: Vaccines (2021)
Publication types: Journal Article
Cloning and Molecular Characterization of the Recombinant CVB4E2 Immunogenic Viral Protein (rVP1), as a Potential Subunit Protein for Vaccine and Immunodiagnostic Reagent Candidate.

The aim of the present study was, first, to clone the vp1 gene of the human coxsackievirus b4 strain e2 (cvb4e2) in the prokaryotic p uc19 plasmid expression vector then to compare it with the structural capsid proteins of the same strain using bioinformatic tools.Pcr colony amplification followed through a restriction digestion analysis and sequencing process which affirmed the success of the cloning process.Sds-page and western blotting were used to characterize the purified recombinant viral protein expressed in bacteria cells.The blastn tool revealed that the nucleotide sequence of the recombinant vp1 (r vp1) expressed by p uc19 highly matched the target nucleotide sequence of the diabetogenic cvb4e2 strain.Secondary structure and three-dimension structure prediction suggested that r vp1, such as wild-type vp1, is chiefly composed of random coils and a high percentage of exposed amino acids.Linear b-cell epitope prediction showed that several antigenic epitopes are likely present in r vp1 and cvb4e2 vp1 capsid protein.Additionally, phosphorylation site prediction revealed that both proteins may affect the signal transduction of host cells and can be involved in virus virulence.The present work highlights the usefulness of cloning and bioinformatics characterizations for gene investigation.Furthermore, the collected data are helpful for future experimental research related to the development of immunodiagnostic reagents and subunit vaccines based on the expression of immunogenic viral capsid proteins.

Journal: Microorganisms (2023)
Publication types: Journal Article
Effect of Methionine Deficiency on the Growth Performance, Serum Amino Acids Concentrations, Gut Microbiota and Subsequent Laying Performance of Layer Chicks.

This study was conducted to investigate the effect of methionine (met) deficiency in the rearing period on the growth performance, amino acids metabolism, intestinal development and gut microbiome of egg-laying chicks and the continuous effects on the performance, egg quality, and serum amino acids metabolism of the subsequent development process.Three hundred sixty one-day-old chicks were randomly divided into two groups and fed on a basal diet (nc group, met 0.46%) and met deficiency diet (met- group, met 0.27%).Each group included six replicates with 30 chicks per replicate.The trial lasted 6 weeks (0-6 weeks), both groups were fed the same basal diet which met the needs of met during the observation period (7-24 weeks).Results showed that met deficiency significantly decreased (p< 0.05) body weight (bw), average daily weight gain (adg), average daily feed intake (adfi) and tibia length (tl) compared to the nc group during the trial period (0-6 weeks).Also, met deficiency dramatically increased (p< 0.05) feed conversion ratio (fcr) during the trial and observation period (7-24 weeks).In addition, during the observation period, the bw and adg were decreased (p< 0.05) in the met- group.Moreover, met- group decreased (p< 0.05) villi height and villi height/crypt depth ratio in jejunum at 6th weeks.In addition, the concentrations of serum main free amino acids (faa) in the met- group were significantly increased (p< 0.05) at 6th weeks, while were decreased at 16th weeks.Based on the α-diversity and pco a analysis in β-diversity, there were no significant differences in the cecal microbial composition between nc and met- groups.However, the lef se analysis revealed that differential genera were enriched in the nc or met- groups.The haugh unit, shell thickness and egg production in the met- group were significantly lower (p< 0.05) than in the nc group.In conclusion, these results revealed that dietary supplementation of appropriate met could substantially improve the growth performance, host amino acid metabolism and intestinal development and continuously improve the laying performance and thus boost the health of growing hens.

Journal: Frontiers in veterinary science (2022)
Publication types: Journal Article
Perception of COVID-19 Testing in the Entire Population.

In the slovak republic, a mass testing of the entire population was performed.Estimates show that this testing cost more than 400 million eur and thousands of euros were paid for one positively identified case.Thus, it is possible to state a high cost for such a project, which has been criticized by many parties.On the other hand, from a public health point of view, mass testing has helped fight the pandemic.Both the health and economic perspectives are important in assessing the success of a pandemic strategy, but the social perspective is equally important.In fact, the situation is perceived from the position of public leaders who make decisions, but also from the position of the society that bears individual political decisions.It is not appropriate to forget about the society that is most affected by restrictions, testing, health status, but also the burden on the state budget.The objective of the presented research was to examine the perception of testing for coronavirus disease 2019 (covid-19) in the slovak population.Non-parametric difference tests and correspondence analysis were used for statistical processing.The research sample consisted of 806 respondents and data collection took place in february 2021.The main findings include significant differences in perceptions between the first and the last participation in testing in terms of gender, age, testing experience, and time aspect.The last participation in testing showed lower rates of positive aspects related to the internal motivation to test compared to the first participation.In contrast, external stimulation by government regulations related to restrictions in the absence of a negative result was higher in the last participation in testing.There were also differences between the first and the last test in the level of doubts about the accuracy of the test result, while a higher level was found at the last testing participation.It can be concluded that the frequency of testing and its requirements need to be approached very carefully over time, as it is likely that the positive perceptions may deteriorate.The recommendations include clear and timely government communication, trust building and health education.

Journal: Frontiers in public health (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Molecular testing for H. pylori clarithromycin and quinolone resistance: a prospective Chinese study.

In china, there is a high prevalence of antibiotic-resistant helicobacter pylori infections in the population.The aim of the study was to assess a new arms-pcr test for detection of h.Pylori clarithromycin resistance (cr) and quinolone resistance (qr) mutations and evaluate the spectrum of antibiotic resistance in patients from three chinese provinces.Sanger sequencing and multiplex arms-pcr were used to detect h.Pylori cr and qr bacteria in gastric biopsy samples.Among the 1,182 patients enrolled with gastritis, 643 (54.4%) were positive for h.Pylori.Of these, 371 (57.7%) had antibiotic-resistant strains, comprising 236 (63.6%) with a single drug antibiotic-resistant strain and 135 (36.4%) with multiple drug-resistant strains.Following sanger sequencing analysis of 23s r rna and gyr a gene for mutations (antibiotic resistance markers), rates of cr, qr, and multidrug resistance (cr and qr) were 19.9, 12.0, and 25.8%, respectively.The 23s r rna cr mutation a2143g (286, 96.9%) and the gyr a qr mutations c261a (85, 31.5%) and g271a (71, 26.3%) were common.Benchmarking against sanger sequencing results, multiplex arms-pcr test had a high diagnostic sensitivity and specificity for detection of cr (96 and 93%), qr (95 and 92%) and multidrug resistance (95 and 95%).Based on our findings, the high incidence of single and multiple antibiotic resistance requires the routine checking of antibiotic resistance in all patients with suspected h.Pylori infections.Multiplex arms-pcr is a simple and rapid test that can be now used for more efficient treatment of h.Pylori infections and reduces the misuse of antibiotics.

Journal: European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology (2021)
Publication types: Journal Article
Practice Patterns Among Hand Surgeons According to Primary Residency Training: A National Surgical Quality Improvement Project Study.

Introduction hand surgery fellowships accept applicants from 3 different residencies: general surgery, orthopedic surgery, and plastic surgery.Although all of these specialties culminate into a board-certified hand surgeon, each specialty receives drastically different training in residency, which can have effects on which procedures these surgeons feel comfortable performing in their own practices.This study aims to compare practice patterns and complication rates among hand surgeons by residency training.Methods the national surgical quality improvement program database was queried between the years of 2014 and 2018 for all current procedural terminology codes pertaining to upper-extremity surgical procedures performed below the elbow.Procedures not performed by a general, orthopedic, or plastic surgeon were excluded, as well as polytraumas.Procedures were then stratified by anatomic region, tissue type, and primary specialty of the attending surgeon.Data collected included the number of each procedure, patient complexity, and complications.Statistical analysis consisted of a t test for continuous variables, χ2 analysis for categorical variables, and linear regression analysis to compare complications rates between specialties.Results a total of 76,980 unique cases were included in our analysis: 4979 (6.4%) at the elbow, 43,680 (56.7%) at the forearm/wrist, 23,284 (30.2%) at the hand, 1421 (1.8%) flaps/grafts, 285 (0.4%) vascular, and 3331 (4.3%) neurological.Orthopedics performed most (79.5%) of the procedures, whereas plastic surgeons and general surgeons performed 17.3% and 3.1%, respectively.There were also significant differences by anatomic location/type of procedure, with orthopedic surgeons performing 99.2% of procedures at the elbow but only 67.7% of procedures at the hand.Linear regression analysis showed general surgeons had the lowest complication rates.Conclusions our data show significant differences in the number of upper-extremity surgeries performed by surgeons from each specialty at different anatomic locations.this could be due to differences in training during residency or proportionately more orthopedic surgeons being "full-time" hand surgeons.These data could affect hiring patterns in hospitals seeking hand surgeons depending on the variety of pathology encountered at that particular institution.

Journal: Annals of plastic surgery (2021)
Publication types: Journal Article
Physicochemical and Microstructural Analyses of Pepsin-Soluble Collagens Derived from Lizardfish (Saurida tumbilBloch, 1795) Skin, Bone and Scales.

Reducing food waste is critical for sustainability.In the case of fish processing, more than sixty percent of by-products are generated as waste.Lizardfish (saurida tumbil bloch, 1795) is an economically important species for surimi production.To address waste disposal and maximize income, an effective utilization of fish by-products is essential.This study aims to isolate and characterize pepsin-soluble collagens from the skin, bone and scales of lizardfish.Significant differences (p 70%) in acidic conditions (particularly at p h 4.0) and at low sodium chloride concentrations (0−30 g/l).Microstructural analysis depicted that all extracted collagens were multi-layered, irregular, dense, sheet-like films linked by random coiled filaments.Overall, pepsin-soluble collagens from lizardfish skin, bone and scales could serve as potential alternative sources of collagens.

Journal: Gels (Basel, Switzerland) (2022)
Publication types: Journal Article
Recombinant human platelet-derived growth factor improves root coverage of a collagen matrix for multiple adjacent gingival recessions: A triple-blinded, randomized, placebo-controlled trial.

To evaluate the efficacy of recombinant human platelet-derived growth factor (rh pdgf)-bb combined with a cross-linked collagen matrix (ccm) for the treatment of multiple adjacent gingival recession type 1 defects (magrs) in combination with the coronally advanced flap (caf).Materials and methods thirty patients were enrolled in this triple-blind, randomized, placebo-controlled trial and treated with either caf + ccm + rh pdgf, or caf + ccm + saline.The primary outcome was mean root coverage (m rc) at 6 months.Complete root coverage, gain in gingival thickness (gt), keratinized tissue width, volumetric and ultrasonographic changes, and patient-reported outcome measures were also assessed.Mixed-modelling regression analyses were used for statistical comparisons.Results at 6 months, the m rc of the ccm + rh pdgf and ccm alone groups were 88.25% and 77.72%, respectively (p = .02).A significant gain in gt was consistently observed for both treatment arms, and more so for the patients receiving the matrix containing rh pdgf through time (0.51 vs.0.80 mm, on average, p = .01).The rh pdgf + ccm treated patients presented greater volume gain, higher soft tissue thickness, and a superior aesthetic score.Conclusion rh pdgf enhances the clinical, volumetric, and aesthetic outcomes of magrs above the results achieved with caf + ccm alone (clinical trials.gov nct04462237).

Journal: Journal of clinical periodontology (2022)
Publication types: Journal Article;Randomized Controlled Trial;Research Support, Non-U.S. Gov't
Recirculation of reject water in deep-dewatering process to influent of wastewater treatment plant and dewaterability of sludge conditioned with Fe2+/H2O2, Fe2+/Ca(ClO)2, and Fe2+/Na2S2O8: From bench to pilot-scale study.

Deep dewatering of sewage sludge pretreated with advanced oxidation processes (aops) is a strategy for efficient sludge reduction and subsequent disposal.The pretreatment and dewatering performance of sludge conditioned with three types of aops (fe2+/h2o2, fe2+/ca(cl o)2, and fe2+/na2s2o8), compared with sludge conditioned with traditional conditioner (fe3+/ca o), were investigated in both bench and pilot-scale tests.All of those conditioner systems could reduce the water content of dewatered sludge cake to below 60 wt% in bench-scale (about 16 kg raw sludge per round) and pilot-scale (approximate 800 kg raw sludge per round) diaphragm filter press dewatering.Compared with raw sludge, the deep-dewatering filtrate after different conditioning and dewatering processes had higher ammonia nitrogen (nh4+-n) and chemical oxygen demand (cod) contents due to the degradation of organic matter, and much lower total phosphorus (tp) content due to the formation of iron phosphate precipitate.A better biodegradability (i.e.Higher bod5/cod ratio) was found in the deep-dewatering filtrate of sludge conditioned with fe2+/h2o2(25.2 %) and fe2+/ca(cl o)2(17.4 %).Most of the heavy metals (cr, cu, ni, and pb) (>79 wt%) have remained in the dewatered sludge cake, and most of the cl element (>90 wt%) in the sludge pretreated by fe2+/ca(cl o)2and fe3+/ca o was kept in the filtrate, rather than the dewatered sludge cake.Based on the pilot-scale experimental results, if all the filtrate in the deep-dewatering process returned to the influent of wwtp, the loading ratios of tp, nh4+-n, cod in the four conditioner systems were less than 3 wt%.The above results proved that the aops conditioned sludge could achieve deep-dewatering in pilot-scale and the direct recirculation of deep-dewatering filtrate to the influent of wastewater treatment plant was feasible.

Journal: Environmental research (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Investigation of the Mechanism of Traditional Chinese Medicines in Angiogenesis through Network Pharmacology and Data Mining.

Although traditional chinese medicine is effective and safe for the treatment of angiogenesis, thein vivointervention mechanism is diverse, complex, and largely unknown.Therefore, we aimed to explore the active ingredients of traditional chinese medicine and their mechanisms of action against angiogenesis.Data on angiogenesis-related targets were collected from gene cards, therapeutic target database, online mendelian inheritance in man, drug bank, and dis ge net.These were matched to related molecular compounds and ingredients in the traditional chinese medicine system pharmacology platform.The data were integrated and based on the condition of degree > 1, and relevant literature, target-compound, compound-medicine, and target-compound-medicine networks were constructed using cytoscape.Molecular docking was used to predict the predominant binding combination of core targets and components.We obtained 79 targets for angiogenesis; 41 targets were matched to 3839 compounds, of which 110 compounds were selected owing to their high correlation with angiogenesis.Fifty-five combinations in the network were obtained by molecular docking, among which ptgs2-astragalin (-9.18 kcal/mol), kdr-astragalin (-7.94 kcal/mol), ptgs2-quercetin (-7.41 kcal/mol), and ptgs2-myricetin (-7.21 kcal/mol) were top.These results indicated that the selected potential core compounds have good binding activity with the core targets.Eighty new combinations were obtained from the network, and the top combinations based on affinity were kdr-beta-carotene (-10.13 kcal/mol), mmp9-beta-sitosterol (-8.04 kcal/mol), mmp9-astragalin (-7.82 kcal/mol), and mmp9-diosgenin (-7.51 kcal/mol).The core targets included ptgs2, kdr, vegfa, and mmp9.The essential components identified were astragalin, kaempferol, myricetin, quercetin, andβ-sitosterol.The crucial chinese medicines identified included polygoni cuspidati rhizoma et radix,morus alba root bark, and forsythiae fructus.By systematically analysing the ingredients of traditional chinese medicine and their targets, it is possible to determine their potential mechanisms of action against pathological angiogenesis.Our study provides a basis for further research and the development of new therapeutics for angiogenesis.

Journal: Evidence-based complementary and alternative medicine : eCAM (2021)
Publication types: Journal Article
Epstein-Barr Virus Epitope-Major Histocompatibility Complex Interaction Combined with Convergent Recombination Drives Selection of Diverse T Cell Receptor α and β Repertoires.

Recognition modes of individual t cell receptors (tcrs) are well studied, but factors driving the selection of tcr repertoires from primary through persistent human virus infections are less well understood.Using deep sequencing, we demonstrate a high degree of diversity of epstein-barr virus (ebv)-specific clonotypes in acute infectious mononucleosis (aim).Only 9% of unique clonotypes detected in aim persisted into convalescence; the majority (91%) of unique clonotypes detected in aim were not detected in convalescence and were seeming replaced by equally diverse "de novo" clonotypes.The persistent clonotypes had a greater probability of being generated than nonpersistent clonotypes due to convergence recombination of multiple nucleotide sequences to encode the same amino acid sequence, as well as the use of shorter complementarity-determining regions 3 (cdr3s) with fewer nucleotide additions (i.e., sequences closer to germ line).Moreover, the two most immunodominant hla-a2-restricted ebv epitopes, brlf1109and bmlf1280, show highly distinct antigen-specific public (i.e., shared between individuals) features.In fact, tcrα cdr3 motifs played a dominant role, while tcrβ played a minimal role, in the selection of tcr repertoire to an immunodominant ebv epitope, brlf1.This contrasts with the majority of previously reported repertoires, which appear to be selected either on tcrβ cdr3 interactions with peptide/major histocompatibility complex (mhc) or in combination with tcrα cdr3.Understanding of how tcr-peptide-mhc complex interactions drive repertoire selection can be used to develop optimal strategies for vaccine design or generation of appropriate adoptive immunotherapies for viral infections in transplant settings or for cancer.importanceseveral lines of evidence suggest that tcrα and tcrβ repertoires play a role in disease outcomes and treatment strategies during viral infections in transplant patients and in cancer and autoimmune disease therapy.Our data suggest that it is essential that we understand the basic principles of how to drive optimum repertoires for both tcr chains, α and β.We address this important issue by characterizing the cd8 tcr repertoire to a common persistent human viral infection (ebv), which is controlled by appropriate cd8 t cell responses.The ultimate goal would be to determine if the individuals who are infected asymptomatically develop a different tcr repertoire than those that develop the immunopathology of aim.Here, we begin by doing an in-depth characterization of both cd8 t cell tcrα and tcrβ repertoires to two immunodominant ebv epitopes over the course of aim, identifying potential factors that may be driving their selection.

Journal: mBio (2020)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, U.S. Gov't, Non-P.H.S.