bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predictive Factors Influencing Functional Results After Proximal Hamstring Tendon Avulsion Surgery: A Patient-Reported Outcome Study After 227 Operations From a Single Center
Authors: Best Raymond , Meister Anorte , Meier Malin , Huth Jochen , Becker Ulrich 
Published: October 2021

Background: Although debilitating, proximal hamstring tendon avulsion injuries are rare and often overlooked or misdiagnosed. Consequently, delayed diagnosis and surgical treatment may result in poor outcomes. Studies investigating a correlation between postoperative functional outcomes and this delay in surgical treatment or other concomitant factors in large cohorts have not yet been performed to our knowledge. Purpose/Hypothesis: The purpose of this study was to conduct an investigation in a large patient group regarding factors that could influence a patient’s functional outcome after hamstring surgery. We hypothesized that this outcome would significantly correlate to the time between trauma and surgery. Study Design: Case series; Level of evidence, 4. Methods: Patients who received surgical treatment of proximal hamstring tendon avulsion injuries in our institution between the years 2010 and 2020 were asked to complete a validated, injury-specific outcome measurement, the Perth Hamstring Assessment Tool (PHAT; 0-100 points). In addition to calculating these outcomes, we evaluated the association of the obtained results with possible predictive factors such as age, sex, stump retraction shown on magnetic resonance imaging (MRI), and timing and duration of surgery. Results: A total of 226 patients (227 operations) were eligible for the study, and 204 cases of hamstring tendon avulsion injury met our inclusion criteria. The return rate for the PHAT questionnaire was 85.3%. The mean PHAT score revealed good results (79.8 ± 19.1). Irrespective of concomitant factors, the scores of male patients were significantly higher compared with those of female patients (83.8 ± 16.9 vs 75.8 ± 20.6 respectively; P = .004). The mean time to surgery was 5.7 weeks after trauma, and more delayed surgery correlated significantly with lower PHAT scores ( P = .003; r = –0.228). The mean degree of stump retraction on MRI (5 cm) did not significantly influence PHAT scores ( P = .525; r = –0.06). Conclusion: Delay of surgery and female sex were disadvantageous in terms of a good functional outcome measure (PHAT score) after hamstring tendon refixation surgery. By contrast, patient age as well as the retraction of the tendon stump on preoperative MRI did not influence PHAT scores in the present study.
“The Heart is a House”: A Heuristic for Generating Cardiac Differential Diagnoses
Authors: Sengupta Malavika Pia , Crawford Timothy N , Leeds Frederic Stuart 
Published: October 2021

BACKGROUND Differential diagnosis (DDx) is a core clinical reasoning skill that all medical students and physicians must acquire and develop. Metamemory techniques (MMTs), including mnemonic devices and other heuristics, are frequently taught to students as a means of enhancing DDx generation. The Heart is A House (HIAH) , an MMT that works by prompting students to think about cardiac disease in terms of four structural subsystems, can be used to facilitate the generation of cardiac differentials, but its efficacy has not been studied. METHODS In a 3-hour DDx workshop, second-year medical students were given a brief case vignette of a patient with chest pain and dyspnea and asked to generate initial differential diagnoses before and after learning HIAH. Descriptive statistics and paired T-tests were used to compare the sizes of cardiac-only and total differentials pre-/post-HIAH. Cardiac diagnoses were classified according to the structural categories described by HIAH, and Simpson's Diversity Index (SDI) was used to evaluate the effect of HIAH on the variety of cardiac diagnoses produced. RESULTS All students in the course ( N = 111) submitted pre-post differential lists. The mean number of diagnoses included in their differentials did not change significantly after exposure to HIAH (7.98 vs. 8.71, P = .09). However, the number of potentially correct cardiac diagnoses increased from 1.79 to 4.75 ( P < .0001), and the variety of structure/function cardiac categories considered by students increased more than twofold (from an SDI of 0.16 to 0.4, P < .0001). These increases were accompanied by a small increase in incorrect diagnoses ( + 2.47%, P = .0003) and a larger decrease in potentially correct noncardiac diagnoses (−41.88%, P < .0001). CONCLUSION The use of HIAH was associated with an increase in the size and variety of cardiac differentials. This increase may have come at the cost of a reduced noncardiac differential. Educators may find HIAH useful for guiding students as they reason through cases involving potential cardiac etiologies. As with all heuristics, care must be exercised to avoid introducing unwanted bias.
GFICLEE: ultrafast tree-based phylogenetic profile method inferring gene function at the genomic-wide level
Authors: Fang Yang , Li Menglong , Li Xufeng , Yang Yi 
Published: October 2021

Abstract
Background
Phylogenetic profiling is widely used to predict novel members of large protein complexes and biological pathways. Although methods combined with phylogenetic trees have significantly improved prediction accuracy, computational efficiency is still an issue that limits its genome-wise application.

Results
Here we introduce a new tree-based phylogenetic profiling algorithm named GFICLEE, which infers common single and continuous loss (SCL) events in the evolutionary patterns. We validated our algorithm with human pathways from three databases and compared the computational efficiency with current tree-based with 10 different scales genome dataset. Our algorithm has a better predictive performance with high computational efficiency.

Conclusions
The GFICLEE is a new method to infers genome-wide gene function. The accuracy and computational efficiency of GFICLEE make it possible to explore gene functions at the genome-wide level on a personal computer.
The resistance of peanut to soil-borne pathogens improved by rhizosphere probiotics under calcium treatment
Authors: Zhang Wei , Zhang Bo-wen , Deng Jie-fu , Li Lin , Yi Tu-yong , Hong Yan-yun 
Published: October 2021

Abstract
Background
Peanut (Arachis hypogaea L.) is an important oil and economic crop. Calcium modulates plants in response to abiotic stresses and improves plant resistance to pathogens. Enrichment of beneficial microorganisms in the rhizosphere is associated with plant disease resistance and soil development. The purpose of this study was to analyze the differences in peanut rhizosphere microbial community structure between the calcium treatment and the control during two growth stages and to explain why calcium application could improve the resistance of peanuts to soil-borne pathogens.

Results
The 16S rDNA amplicon sequencing of rhizosphere microbiome showed that calcium application significantly enriched Serratia marcescens and other three dominant strains at the seedling stage. At the pod filling stage, ten dominant stains such as Sphingomonas changbaiensis and Novosphingobium panipatense were enriched by calcium. Serratia marcescens aseptic fermentation filtrate was mixed with PDA medium and inoculated with the main soil-borne pathogens in the seedling stage, which could inhibit the growth of Fusarium solani and Aspergillus flavus. The aseptic fermentation filtrate of Novosphingobium panipatense was mixed with PDA medium and inoculated with the main soil-borne pathogens in the pod filling stage, which could inhibit the growth of Sclerotium rolfsii and Leptosphaerulina arachidicola.

Conclusions
Calcium application increases the resistance of peanuts to soil-borne pathogens by enriching them with specific dominant bacteria.
Technical challenges regarding the use of formalin-fixed paraffin embedded (FFPE) tissue specimens for the detection of bacterial alterations in colorectal cancer
Authors: Lam Suk Yee , Ioannou Athanasia , Konstanti Prokopis , Visseren Thijmen , Doukas Michail , Peppelenbosch Maikel Petrus , Belzer Clara , Fuhler Gwenny Manel 
Published: October 2021

Abstract
Background
Formalin-fixed paraffin embedded (FFPE) tissues may provide an exciting resource to study microbial associations in human disease, but the use of these low biomass specimens remains challenging. We aimed to reduce unintentional bacterial interference in molecular analysis of FFPE tissues and investigated the feasibility of conducting quantitative polymerase chain reaction (qPCR) and 16S rRNA amplicon sequencing using 14 colorectal cancer, 14 normal adjacent and 13 healthy control tissues.

Results
Bacterial contaminants from the laboratory environment and the co-extraction of human DNA can affect bacterial analysis. The application of undiluted template improves bacterial DNA amplification, allowing the detection of specific bacterial markers (Escherichia coli and Faecalibacterium prausnitzii) by qPCR. Nested and non-nested PCR-based 16S rRNA amplicon sequencing approaches were employed, showing that bacterial communities of tissues and paired paraffin controls cluster separately at genus level on weighted Unifrac in both non-nested (R2 = 0.045; Pr(> F) = 0.053) and nested (R2 = 0.299; Pr(> F) = 0.001) PCR datasets. Nevertheless, considerable overlap of bacterial genera within tissues was seen with paraffin, DNA extraction negatives (non-nested PCR) or PCR negatives (nested PCR). Following mathematical decontamination, no differences in α- and β diversity were found between tumor, normal adjacent and control tissues.

Conclusions
Bacterial marker analysis by qPCR seems feasible using non-normalized template, but 16S rRNA amplicon sequencing remains challenging. Critical evaluation of laboratory procedures and incorporation of positive and negative controls for bacterial analysis of FFPE tissues are essential for quality control and to account for bacterial contaminants.
Genomic convergence between Akkermansia muciniphila in different mammalian hosts
Authors: Geerlings Sharon Y. , Ouwerkerk Janneke P. , Koehorst Jasper J. , Ritari Jarmo , Aalvink Steven , Stecher Bärbel , Schaap Peter J. , Paulin Lars , de Vos Willem M. , Belzer Clara 
Published: October 2021

Abstract
Background
Akkermansia muciniphila is a member of the human gut microbiota where it resides in the mucus layer and uses mucin as the sole carbon, nitrogen and energy source. A. muciniphila is the only representative of the Verrucomicrobia phylum in the human gut. However, A. muciniphila 16S rRNA gene sequences have also been found in the intestines of many vertebrates.

Results
We detected A. muciniphila-like bacteria in the intestines of animals belonging to 15 out of 16 mammalian orders. In addition, other species belonging to the Verrucomicrobia phylum were detected in fecal samples. We isolated 10 new A. muciniphila strains from the feces of chimpanzee, siamang, mouse, pig, reindeer, horse and elephant. The physiology and genome of these strains were highly similar in comparison to the type strain A. muciniphila MucT. Overall, the genomes of the new strains showed high average nucleotide identity (93.9 to 99.7%). In these genomes, we detected considerable conservation of at least 75 of the 78 mucin degradation genes that were previously detected in the genome of the type strain MucT.

Conclusions
The low genomic divergence observed in the new strains may indicate that A. muciniphila favors mucosal colonization independent of the differences in hosts. In addition, the conserved mucus degradation capability points towards a similar beneficial role of the new strains in regulating host metabolic health.
Exploration of the anti-insomnia mechanism of Ganoderma by central-peripheral multi-level interaction network analysis
Authors: Qiu Yu , Mao Zhu-Jun , Ruan Ye-Ping , Zhang Xin 
Published: October 2021

AbstractBackgroundGanoderma(Lingzhiin Chinese) has shown good clinical outcomes in the treatment of insomnia, restlessness, and palpitation. However, the mechanism by whichGanodermaameliorates insomnia is unclear. We explored the mechanism of the anti-insomnia effect ofGanodermausing systems pharmacology from the perspective of central-peripheral multi-level interaction network analysis.MethodsThe active components and central active components ofGanodermawere obtained from the TCMIP and TCMSP databases, then screened to determine their pharmacokinetic properties. The potential target genes of these components were identified using the Swiss Target Prediction and TCMSP databases. The results were matched with the insomnia target genes obtained from the GeneCards, OMIM, DisGeNET, and TCMIP databases. Overlapping targets were subjected to multi-level interaction network analysis and enrichment analysis using the STRING, Metascape, and BioGPS databases. The networks analysed were protein-protein interaction (PPI), drug-component-target gene, component-target gene-organ, and target gene-extended disease; we also performed gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses.ResultsIn total, 34 sedative-hypnotic components (including 5 central active components) were identified, corresponding to 51 target genes. Multi-level interaction network analysis and enrichment analysis demonstrated thatGanodermaexerted an anti-insomnia effect via multiple central-peripheral mechanisms simultaneously, mainly by regulating cell apoptosis/survival and cytokine expression through core target genes such as TNF, CASP3, JUN, and HSP90αA1; it also affected immune regulation and apoptosis. Therefore,Ganodermahas potential as an adjuvant therapy for insomnia-related complications.ConclusionGanodermaexerts an anti-insomnia effect via complex central-peripheral multi-level interaction networks.
Workplace violence and influencing factors among paramedic pre hospital paramedic personnel (city and road) in Iran: a quality content analysis
Authors: Hadian Marziye , Jabbari Alireza , Sheikhbardsiri Hojjat 
Published: October 2021

Abstract
Background
The goal of every emergency department is to provide the highest quality services in the shortest time using limited resources. However, occupational violence is so prevalent among pre-hospital paramedic personnel that some experts claim that it is impossible to find pre-hospital personnel without an experience of violence in the workplace. Therefore, it seems necessary to investigate the causes of violence among this population group and find ways to control it.

Aim
The present study aimed to investigate the Violence and influencing factors among paramedic pre-hospital personnel.

Method
This qualitative study was conducted to explore the views of a group of pre-hospital paramedic personnel (n = 45) selected through purposive sampling. The data was collected through in-depth and semi-structured interviews and analyzed using Graneheim and Lundman’s conventional content analysis methods. The trial version of MAXQDA 16 software was used to manage the coding process.

Results
Based on the results of the analysis of data collected from prehospital paramedic personnel, three main categories including: human factors, organizational factors, and environmental factors and 20 subcategories were detected.

Conclusion
If authorities neglect violence in the workplace and do not take serious actions to prevent it, violence and, more importantly, “hostility” will gradually prevail in the workplace. It also increases the stress and anxiety of staff and consequently severely deteriorates their job performance. Hence, authorities are strongly recommended not to ignore this issue and, instead, take measures, for instance hold workshops, to train personnel about the techniques of anger and violence control.
Surgical Outcomes of LigaSure Hemorrhoidectomy in the Elderly Population: A retrospective cohort study
Authors: Chen Chuang-Wei , Lu Tzung-Ju , Hsiao Koung-Hung 
Published: October 2021

Abstract
Background
This study aims to assess the association between age and outcomes in patients undergoing hemorrhoidectomy.

Methods
This is a population-based cohort study. A retrospectively collected database with consecutive patients whose symptomatic prolapsed hemorrhoids managed by the LigaSure hemorrhoidectomy between Jan. 2015 and May 2017 was reviewed. Among 1238 patients, 1075 were under 65 years old (group 1), and 163 were 65 years old or older (group 2). Both groups were compared regarding baseline characteristics and surgical outcomes.

Results
All patients tolerated the whole course of the operation in the prone jackknife position without anesthetic-associated complications. There was no significant difference between these two groups regarding sex, hemorrhoids grade, operation time, duration of hospital stays, postoperative pain score, analgesic consumption, total postoperative complications, re-admission rate, reoperation rate and follow-up times. The multivariate logistic regression analysis that may contribute to postoperative complications revealed no significant difference for all complications between both groups.

Conclusion
The LigaSure hemorrhoidectomy for elderly patients is safe and effective without significant difference in short-term operative outcomes and all complication rates, compared with younger patients.
Incidence and determinants of adverse outcomes among women who were managed for eclampsia in the University of Gondar Comprehensive Specialized Hospital, Northwest Ethiopia
Authors: Getaneh Yisfa , Fekadu Elfalet , Jemere Adamu Takele , Mengistu Zelalem , Tarekegn Gebrekidan Ewnetu , Oumer Mohammed 
Published: October 2021

Abstract
Background
The incidence of eclampsia and its adverse maternal outcomes are very high in developing countries, particularly in Subsaharan African Countries. Identifying predictors for adverse maternal outcomes of eclampsia has paramount importance for helping health care providers to optimize their management outcomes. Therefore, this study aimed to assess the incidence of adverse maternal outcomes of eclampsia and its determinant factors.

Methods
A retrospective follow-up study design was applied. The data were extracted from patient charts using a structured, pre-tested, questionnaire. Descriptive analyses (frequencies, means, and standard deviation) were calculated, and bi-variable and multivariable logistic regression models were used to testing the association between independent variables and an outcome variable. After the data were coded and entered into Epi-Info Version 7.2 Software, the data were analyzed using STATA Version 14 Statistical Software.

Results
The magnitude of eclampsia was 5.36 per 1000 pregnancies (95% CI: 4.72, 6.10). The incidence of adverse maternal outcomes in eclamptic mothers was 53.7% (95% CI: 47.02, 60.24%). After adjusting for covariates maternal age 30–34, AOR 5.4 [95% CI = 1.02, 28.6]; age above 34, AOR 10.5 [95% CI = 1.3, 88.6]; gravidity 2–4, AOR 0.3 [95% CI = 0.1, 0.9]; 10 or more convulsions, AOR 4.6 [95% CI = 1.4, 14.9]; mild pyrexia, AOR 20.4 [95% CI = 3.7, 112.7]; moderate pyrexia, AOR 14.6 [95% CI = 1.7125.1]; platelet count below 50,000 cells/mm3, AOR 34.9 [95% CI = 3.6, 336.2]; platelet count between 50,000 and 99,000 cells/mm3, AOR 24.5 [95%CI = 5.4111.6]; and stillbirth of the current pregnancy, AOR 23.2 [95%CI = 2.1257.5] were strong predictors of adverse maternal outcomes in eclamptic mothers.

Conclusions
The incidence of adverse maternal outcomes of eclampsia was found to be high compared to similar studies discussed in this study. This study recommends early identification of patients with the risk factors (having many convulsions, high body temperature, low platelet count, patient age above 30 years, and 2–4 pregnancies), strengthening the referral system, and advocation of research on the area of adverse maternal outcomes and thereby encourage evidence-based medicine.
Association between sitting time at work and the onset of major depressive episode: a 1-year prospective cohort study using the Bayesian regression
Authors: Watanabe Kazuhiro , Kawakami Norito 
Published: October 2021

AbstractBackgroundAlthough sedentary behavior is associated with the onset of major depressive disorder, it remains unclear whether sedentary behavior at work increases the risk of depression. The present study used the Bayesian approach to investigate the association between sitting time at work and the onset of major depressive episode (MDE).MethodsA 1-year prospective cohort study was conducted among 233 Japanese workers without MDE (response rate: 4.3%). MDE onset was assessed using the self-reported WHO Composite International Diagnostic Interview version 3.0. A Bayesian Cox proportional hazard model was used to estimate the hazard ratio (HR) between long sitting time at work and MDE onset.ResultsA total of 231 workers were included in the analysis. During the follow-up, 1621 person-months were observed, and six participants experienced MDE onset. Incident rates per months were 0.34, 0.11, and 1.02% in short (< 7.2 h per day), medium (7.2–9.5 h), and long (9.5+ h) sitting time at work, respectively. The estimated median posterior probability distribution of the HR of long sitting time was 3.00 (95% highest density interval [HDI]: 0.73–12.03). The estimated median remained positive after adjustment for physical activity level and other covariates (HR = 2.11, 95% HDI: 0.42–10.22). The 10-base Bayesian factor for H1 (HR = 1.00) compared with the alternatives (H0, HR = 1.00) was 0.68 in the adjusted model. The analysis, which treated sitting time at work as a continuous variable, estimated that the median of the posterior probability distribution of the HR of sitting time was 0.79 (95% HDI: 0.58–1.07. The 10-base Bayesian factor was 2.73 in the linear association.ConclusionsLong sitting time at work (9.5+ h per day) might be associated with MDE onset among workers. However, the linear association indicated conflicting results. Non-linear associations between sitting time and MDE onset might explain this inconsistency. The evidence for an adverse association between sitting time at work and MDE onset remains inconclusive.