bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antibiotic consumption at community pharmacies: A multicenter repeated prevalence surveillance using WHO methodology
Authors: Saleem Zikria , Faller Erwin Martinez , Godman Brian , Malik Muhammad Sajeel Ahmed , Iftikhar Aqsa , Iqbal Sonia , Akbar Aroosa , Hashim Mahnoor , Amin Aneeqa , Javeed Sidra , Amir Afreenish , Zafar Alia , Sabih Farah , Hashmi Furqan Khurshid , Hassali Mohamed Azmi 
Published: December 2021

Background: Antibiotics are losing their effectiveness because of the rapid emergence of resistant bacteria. Unnecessary antimicrobial use increases antimicrobial resistance (AMR). There are currently no published data on antibiotic consumption in Pakistan at the community level. This is a concern given high levels of self-purchasing of antibiotics in Pakistan and variable knowledge regarding antibiotics and AMR among physicians and pharmacists. Objective: The objective of this repeated prevalence survey was to assess the pattern of antibiotic consumption data among different community pharmacies to provide a baseline for developing future pertinent initiatives. Methods: A multicenter repeated prevalence survey conducted among community pharmacies in Lahore, a metropolitan city with a population of approximately 10 million people, from October to December 2017 using the World Health Organization (WHO) methodology for a global program on surveillance of antimicrobial consumption. Results: The total number of defined daily doses (DDDs) dispensed per patient ranged from 0.1 to 50.0. In most cases, two DDDs per patient were dispensed from pharmacies. Co-amoxiclav was the most commonly dispensed antibiotic with a total number of DDDs at 1018.15. Co-amoxiclav was followed by ciprofloxacin with a total number of 486.6 DDDs and azithromycin with a total number of 472.66 DDDs. The least consumed antibiotics were cefadroxil, cefotaxime, amikacin, and ofloxacin, with overall consumption highest in December. Conclusion: The study indicated high antibiotic usage among community pharmacies in Lahore, Pakistan particularly broad-spectrum antibiotics, which were mostly dispensed inappropriately. The National action plan of Pakistan on AMR should be implemented by policymakers including restrictions on the dispensing of antimicrobials.
Utility of the Modified and High‐Sensitivity Modified Glasgow Prognostic Scores for Hypopharyngeal Squamous Cell Carcinoma
Authors: Iuchi Hiroyuki , Ohori Junichiro , Matsuzaki Hisahiro , Kiyama Satoshi , Yamashita Masaru 
Published: December 2021

ObjectiveTo determine whether the modified Glasgow prognostic score (mGPS) and high‐sensitivity mGPS (HS‐mGPS) could predict outcomes among patients with hypopharyngeal squamous cell carcinoma (HSCC).Study DesignRetrospective cohort study.SettingAffiliated university hospital.MethodsWe reviewed the records of 115 patients with histologically confirmed HSCC between March 2007 and December 2019. Univariate and multivariable Cox proportional hazard analyses were performed for overall survival (OS) and disease‐free survival (DFS).ResultsThe 5‐year OS rates were 84.0% for the mGPS0 group, 47.8% for the mGPS1 group, and 17.9% for the mGPS2 group (P <. 0001), while the 5‐year OS rates were 86.7% for the HS‐mGPS0 group, 69.0% for the HS‐mGPS1 group, and 22.2% for the HS‐mGPS2 group (P <. 001). The mGPS and HS‐mGPS were both associated with OS in the univariate analyses, although only the HS‐mGPS was independently associated with OS (hazard ratio, 2.68 [95% CI, 1.19‐6.05]; P <. 05). The 5‐year DFS rates were 75.8% for the mGPS0 group, 53.0% for the mGPS1 group, and 13.8% for the mGPS2 group (P <. 001), while the 5‐year DFS rates were 79.8% for the HS‐mGPS0 group, 56.8% for the HS‐mGPS1 group, and 11.6% for the HS‐mGPS2 group (P <. 001). The mGPS and HS‐mGPS were both associated with DFS in the univariate analyses, although only the HS‐mGPS was independently associated with DFS (hazard ratio, 2.35 [95% CI, 1.03‐5.37]; P <. 05).ConclusionOur study suggests that the HS‐mGPS is useful as prognostic factor in HSCC.
The impact of implementation climate on community mental health clinicians’ attitudes toward exposure: An evaluation of the effects of training and consultation
Authors: Woodard Grace S. , Triplett Noah S. , Frank Hannah E. , Harrison Julie P. , Robinson Sophia , Dorsey Shannon 
Published: December 2021

Background Most evidence-based treatments (EBTs) for posttraumatic stress disorder (PTSD) and anxiety disorders include exposure; however, in community settings, the implementation of exposure lags behind other EBT components. Clinician-level determinants have been consistently implicated as barriers to exposure implementation, but few organizational determinants have been studied. The current study examines an organization-level determinant, implementation climate, and clinician-level determinants, clinician demographic and background factors, as predictors of attitudes toward exposure and changes in attitudes following training. Method Clinicians ( n = 197) completed a 3-day training with 6 months of twice-monthly consultation. Clinicians were trained in cognitive behavioral therapy (CBT) for anxiety, depression, behavior problems, and trauma-focused CBT (TF-CBT). Demographic and background information, implementation climate, and attitudes toward exposure were assessed in a pre-training survey; attitudes were reassessed at post-consultation. Implementation climate was measured at the aggregated/group-level and clinician-level. Results Attitudes toward exposure significantly improved from pre-training to post-consultation ( t(193) = 9.9, p < .001; d = 0.71). Clinician-level implementation climate scores did not predict more positive attitudes at pre-training ( p > .05) but did predict more positive attitudes at post-consultation (ß = −2.46; p < .05) and greater changes in those attitudes (ß = 2.28; p < .05). Group-level implementation climate scores did not predict attitudes at pre-training, post-consultation, or changes in attitudes (all ps > .05). Higher frequency of self-reported CBT use was associated with more positive attitudes at pre-training (ß = −0.81; p < .05), but no other clinician demographic or background determinants were associated with attitudes at post-consultation (all p > .05) or with changes in attitudes (all p > .05). Conclusions Clinician perceptions of implementation climate predicted greater improvement of attitudes toward exposure following EBT training and consultation. Findings suggest that organizational determinants outside of training impact changes in clinicians’ attitudes. Training in four EBTs, only two of which include exposure as a component, resulted in positive changes in clinicians’ attitudes toward exposure, which suggests non-specialty trainings can be effective at changing attitudes, which may enable scale-up.
Nasopharyngeal metatranscriptome profiles of infants with bronchiolitis and risk of childhood asthma: a multicentre prospective study
Authors: Raita Yoshihiko , Pérez-Losada Marcos , Freishtat Robert J. , Hahn Andrea , Castro-Nallar Eduardo , Ramos-Tapia Ignacio , Stearrett Nathaniel , Bochkov Yury A. , Gern James E. , Mansbach Jonathan M. , Zhu Zhaozhong , Camargo Carlos A. , Hasegawa Kohei 
Published: December 2021

BackgroundBronchiolitis is not only the leading cause of hospitalisation in US infants but also a major risk factor for asthma development. Growing evidence supports clinical heterogeneity within bronchiolitis. Our objectives were to identify metatranscriptome profiles of infant bronchiolitis, and to examine their relationship with the host transcriptome and subsequent asthma development.MethodsAs part of a multicentre prospective cohort study of infants (age <1 year) hospitalised for bronchiolitis, we integrated virus and nasopharyngeal metatranscriptome (species-level taxonomy and function) data measured at hospitalisation. We applied network-based clustering approaches to identify metatranscriptome profiles. We then examined their association with the host transcriptome at hospitalisation and risk for developing asthma.ResultsWe identified five metatranscriptome profiles of bronchiolitis (n=244): profile A: virusRSVmicrobiomecommensals; profile B: virusRSV/RV-AmicrobiomeH.influenzae; profile C: virusRSVmicrobiomeS.pneumoniae; profile D: virusRSVmicrobiomeM.nonliquefaciens; and profile E: virusRSV/RV-CmicrobiomeM.catarrhalis. Compared with profile A, profile B infants were characterised by a high proportion of eczema,Haemophilus influenzaeabundance and enriched virulence related to antibiotic resistance. These profile B infants also had upregulated T-helper 17 and downregulated type I interferon pathways (false discovery rate (FDR) <0.005), and significantly higher risk for developing asthma (17.9%versus38.9%; adjusted OR 2.81, 95% CI 1.11–7.26). Likewise, profile C infants were characterised by a high proportion of parental asthma,Streptococcus pneumoniaedominance, and enriched glycerolipid and glycerophospholipid metabolism of the microbiome. These profile C infants had an upregulated RAGE signalling pathway (FDR <0.005) and higher risk of asthma (17.9%versus35.6%; adjusted OR 2.49, 95% CI 1.10–5.87).ConclusionsMetatranscriptome and clustering analysis identified biologically distinct metatranscriptome profiles that have differential risks of asthma.
Association between depression and sleep apnoea: a Mendelian randomisation study
Authors: Chen Gui , Xie Junyang , Liu Weixing , Liang Tianhao , Liao Xiao , Liao Wenjing , Song Lijuan , Zhang Xiaowen 
Published: December 2021

BackgroundStudies have reported a close relationship between depression and sleep apnoea, yet it is unknown whether these are causally related. Thus, we aimed to determine whether depression is associated with the aetiology of sleep apnoea.MethodsWe used publicly available genetic summary data from two large consortia: the Psychiatric Genomics Consortium, with data from 36 single-nucleotide polymorphisms (SNPs) closely associated with major depressive disorder (MDD), and the UK Biobank, including 456 736 patients with sleep apnoea and 766 964 controls. For Mendelian randomisation (MR) analysis, we used the inverse-variance weighted method, weighted median method, MR-Egger regression, MR pleiotropy residual sum and outlier test to retrieve summary data. Analyses were performed using the “TwoSampleMR” package in R.ResultsOut of the 36 SNPs associated with MDD, we found statistically significant evidence of a potential causal effect of MDD on the risk of sleep apnoea (OR 1.004, 95% CI 1.001–1.006; p=0.001). Similar results were obtained using the MR-Egger and weighted median methods. Additionally, we found no heterogeneity or pleiotropy.ConclusionsOur findings suggest that depression slightly increases the risk of sleep apnoea. Further investigation of the potential biological mechanisms is necessary.
Respiratory symptoms and radiological findings in post-acute COVID-19 syndrome
Authors: Jutant Etienne-Marie , Meyrignac Olivier , Beurnier Antoine , Jaïs Xavier , Pham Tai , Morin Luc , Boucly Athénaïs , Bulifon Sophie , Figueiredo Samy , Harrois Anatole , Jevnikar Mitja , Noël Nicolas , Pichon Jérémie , Roche Anne , Seferian Andrei , Soliman Samer , Duranteau Jacques , Becquemont Laurent , Monnet Xavier , Sitbon Olivier , Bellin Marie-France , Humbert Marc , Savale Laurent , Montani David 
Published: December 2021

RationaleThe characteristics of patients with respiratory complaints and/or lung radiologic abnormalities after hospitalisation for coronavirus disease 2019 (COVID-19) are unknown. The objectives were to determine their characteristics and the relationships between dyspnoea, radiologic abnormalities and functional impairment.MethodsIn the COMEBAC (Consultation Multi-Expertise de Bicêtre Après COVID-19) cohort study, 478 hospital survivors were evaluated by telephone 4 months after hospital discharge, and 177 who had been hospitalised in an intensive care unit (ICU) or presented relevant symptoms underwent an ambulatory evaluation. New-onset dyspnoea and cough were evaluated, and the results of pulmonary function tests and high-resolution computed tomography of the chest were collected.ResultsAmong the 478 patients, 78 (16.3%) reported new-onset dyspnoea, and 23 (4.8%) new-onset cough. The patients with new-onset dyspnoea were younger (56.1±12.3versus61.9±16.6 years), had more severe COVID-19 (ICU admission 56.4%versus24.5%) and more frequent pulmonary embolism (18.0%versus6.8%) (all p≤0.001) than patients without dyspnoea. Among the patients reassessed at the ambulatory care visit, the prevalence of fibrotic lung lesions was 19.3%, with extent <25% in 97% of the patients. The patients with fibrotic lesions were older (61±11versus56±14 years, p=0.03), more frequently managed in an ICU (87.9versus47.4%, p<0.001), had lower total lung capacity (74.1±13.7versus84.9±14.8% pred, p<0.001) and diffusing capacity of the lung for carbon monoxide (DLCO) (73.3±17.9versus89.7±22.8% pred, p<0.001). The combination of new-onset dyspnoea, fibrotic lesions andDLCO<70% pred was observed in eight out of 478 patients.ConclusionsNew-onset dyspnoea and mild fibrotic lesions were frequent at 4 months, but the association of new-onset dyspnoea, fibrotic lesions and lowDLCOwas rare.
GENPPI: standalone software for creating protein interaction networks from genomes
Authors: Anjos William F. , Lanes Gabriel C. , Azevedo Vasco A. , Santos Anderson R. 
Published: December 2021

Abstract
BackGround
Bacterial genomes are being deposited into online databases at an increasing rate. Genome annotation represents one of the first efforts to understand organisms and their diseases. Some evolutionary relationships capable of being annotated only from genomes are conserved gene neighbourhoods (CNs), phylogenetic profiles (PPs), and gene fusions. At present, there is no standalone software that enables networks of interactions among proteins to be created using these three evolutionary characteristics with efficient and effective results.

Results
We developed GENPPI software for the ab initio prediction of interaction networks using predicted proteins from a genome. In our case study, we employed 50 genomes of the genus Corynebacterium. Based on the PP relationship, GENPPI differentiated genomes between the ovis and equi biovars of the species Corynebacterium pseudotuberculosis and created groups among the other species analysed. If we inspected only the CN relationship, we could not entirely separate biovars, only species. Our software GENPPI was determined to be efficient because, for example, it creates interaction networks from the central genomes of 50 species/lineages with an average size of 2200 genes in less than 40 min on a conventional computer. Moreover, the interaction networks that our software creates reflect correct evolutionary relationships between species, which we confirmed with average nucleotide identity analyses. Additionally, this software enables the user to define how he or she intends to explore the PP and CN characteristics through various parameters, enabling the creation of customized interaction networks. For instance, users can set parameters regarding the genus, metagenome, or pangenome. In addition to the parameterization of GENPPI, it is also the user’s choice regarding which set of genomes they are going to study.

Conclusions
GENPPI can help fill the gap concerning the considerable number of novel genomes assembled monthly and our ability to process interaction networks considering the noncore genes for all completed genome versions. With GENPPI, a user dictates how many and how evolutionarily correlated the genomes answer a scientific query.
Asymptomatic Bacteriuria, antimicrobial susceptibility pattern and associated risk factors among pregnant women attending antenatal care in Assosa General Hospital, Western Ethiopia
Authors: Abu Duresa , Abula Teferra , Zewdu Tesfu , Berhanu Muluken , Sahilu Tamiru 
Published: December 2021

Abstract
Background
Asymptomatic bacteriuria is a common problem in pregnant women and about 40% of women with untreated asymptomatic bacteriuria during pregnancy develop pyelonephritis, which might lead to low birth weight, premature rupture of membranes, and preterm labour. Therefore, this study aimed to assess the prevalence of asymptomatic bacteriuria, antimicrobial susceptibility pattern of the isolates among pregnant women attending the antenatal care of Assosa general hospital, western Ethiopia.

Methods
A facility-based cross-sectional study was conducted from January to February 2019. Two hundred and eighty-three pregnant women with no symptoms of urinary tract infections participated in the study. Bacterial isolates were identified as per the standard bacteriological procedure using colony characteristics, Gram-staining, and series of biochemical tests. Antimicrobial susceptibility test was carried out by Kirby- Bauer disk diffusion technique on Muller-Hinton agar medium and the diameter of zone of inhibition was interpreted according to Clinical Laboratory Standard Institute guidelines.

Results
The overall prevalence of asymptomatic bacteriuria among pregnant women in this study was 13.78% (i.e. 39 out of 283 urine samples were positive for bacterial isolates). E. coli was the most predominant isolate (53.8%) followed by K. pneumoniae (17.95%), S. aureus (15.4%), and coagulase-negative staphylococci (12.8%). Gram-negative bacteria were highly resistant to tetracycline (96.4%), and ampicillin (90.5%).

Conclusion
Significant bacteriuria was observed in asymptomatic pregnant women. A large number of the bacterial isolates were resistant to the commonly used antimicrobial drugs.
Sex differences in treatment strategy and adverse outcomes among patients 75 and older with atrial fibrillation in the MarketScan database
Authors: Subramanya Vinita , Claxton J’Neka S. , Lutsey Pamela L. , MacLehose Richard F. , Chen Lin Y. , Chamberlain Alanna M. , Norby Faye L. , Alonso Alvaro 
Published: December 2021

Abstract
Background
Women with atrial fibrillation (AF) experience greater symptomatology, worse quality of life, and have a higher risk of stroke as compared to men, but are less likely to receive rhythm control treatment. Whether these differences exist in elderly patients with AF, and whether sex modifies the effectiveness of rhythm versus rate control therapy has not been assessed.

Methods
We studied 135,850 men and 139,767 women aged ≥ 75 years diagnosed with AF in the MarketScan Medicare database between 2007 and 2015. Anticoagulant use was defined as use of warfarin or a direct oral anticoagulant. Rate control was defined as use of rate control medication or atrioventricular node ablation. Rhythm control was defined by use of anti-arrhythmic medication, catheter ablation or cardioversion. We used multivariable Poisson and Cox regression models to estimate the association of sex with treatment strategy and to determine whether the association of treatment strategy with adverse outcomes (bleeding, heart failure and stroke) differed by sex.

Results
At the time of AF, women were on average (SD) 83.8 (5.6) years old and men 82.5 (5.2) years, respectively. Compared to men, women were less likely to receive an anticoagulant or rhythm control treatment. Rhythm control (vs. rate) was associated with a greater risk for heart failure with a significantly stronger association in women (HR women = 1.41, 95% CI 1.34–1.49; HR men = 1.21, 95% CI 1.15–1.28, p < 0.0001 for interaction). No sex differences were observed for the association of treatment strategy with the risk of bleeding or stroke.

Conclusion
Sex differences exist in the treatment of AF among patients aged 75 years and older. Women are less likely to receive an anticoagulant and rhythm control treatment. Women were also at a greater risk of experiencing heart failure as compared to men, when treated with rhythm control strategies for AF. Efforts are needed to enhance use AF therapies among women. Future studies will need to delve into the mechanisms underlying these differences.
Sweet’s syndrome and mucosal prolapse polyps in a male patient with ulcerative colitis
Authors: Zhao Xixian , Jiang Si , Chen Yanan , Liu Jialong , Liu Jing , Shi Xianyan 
Published: December 2021

Abstract
Background
Sweet’s syndrome (SS), also known as acute febrile neutrophilic dermatosis, is a rare neutrophilic dermatitis characterized by pyrexia, neutrophilia and painful papulonodular lesions with a neutrophilic dermal infiltrate.

Case presentation
We presented a case report of classical SS associated with ulcerative colitis (UC) and mucosal prolapse polyps (MPPs) in a male patient.

Conclusions
The particularity of this case is the occurrence of MPPs in a male patient with UC and classical SS. We also discussed whether this patient with concurrent Epstein–Barr virus infection could be treated with corticosteroids.
The microbiological diagnostic performance of metagenomic next-generation sequencing in patients with sepsis
Authors: Ren Di , Ren Chao , Yao Renqi , Zhang Lin , Liang Xiaomin , Li Guiyun , Wang Jiaze , Meng Xinke , Liu Jia , Ye Yu , Li Haoli , Wen Sha , Chen Yanhong , Zhou Dan , He Xisi , Li Xiaohong , Lai Kai , Li Ying , Gui Shuiqing 
Published: December 2021

Abstract
Background
In this study, we aimed to perform a comprehensive analysis on the metagenomic next-generation sequencing for the etiological diagnosis of septic patients, and further to establish optimal read values for detecting common pathogens.

Methods

In this single-center retrospective study, septic patients who underwent pathogen detection by both microbial culture and metagenomic next-generation sequencing in the intensive care unit of the Second People’s Hospital of Shenzhen from June 24, 2015, to October 20, 2019, were included.

Results
A total of 193 patients with 305 detected specimens were included in the final analysis. The results of metagenomic next-generation sequencing showed significantly higher positive rates in samples from disparate loci, including blood, bronchoalveolar lavage fluid, and cerebrospinal fluid, as well as in the determination of various pathogens. The optimal diagnostic reads were 2893, 1825.5, and 892.5 for Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae, respectively.

Conclusions
The metagenomic next-generation sequencing is capable of identifying multiple pathogens in specimens from septic patients, and shows significantly higher positive rates than culture-based diagnostics. The optimal diagnostic reads for frequently detected microbes might be useful for the clinical application of metagenomic next-generation sequencing in terms of timely and accurately determining etiological pathogens for suspected and confirmed cases of sepsis due to well-performed data interpretation.