bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring the functional composition of the human microbiome using a hand-curated microbial trait database
Authors: Weissman J L , Dogra Sonia , Javadi Keyan , Bolten Samantha , Flint Rachel , Davati Cyrus , Beattie Jess , Dixit Keshav , Peesay Tejasvi , Awan Shehar , Thielen Peter , Breitwieser Florian , Johnson Philip L. F. , Karig David , Fagan William F. , Bewick Sharon 
Published: June 2021

AbstractBackgroundEven when microbial communities vary wildly in their taxonomic composition, their functional composition is often surprisingly stable. This suggests that a functional perspective could provide much deeper insight into the principles governing microbiome assembly. Much work to date analyzing the functional composition of microbial communities, however, relies heavily on inference from genomic features. Unfortunately, output from these methods can be hard to interpret and often suffers from relatively high error rates.ResultsWe built and analyzed a domain-specific microbial trait database from known microbe-trait pairs recorded in the literature to better understand the functional composition of the human microbiome. Using a combination of phylogentically conscious machine learning tools and a network science approach, we were able to link particular traits to areas of the human body, discover traits that determine the range of body areas a microbe can inhabit, and uncover drivers of metabolic breadth.ConclusionsDomain-specific trait databases are an effective compromise between noisy methods to infer complex traits from genomic data and exhaustive, expensive attempts at database curation from the literature that do not focus on any one subset of taxa. They provide an accurate account of microbial traits and, by limiting the number of taxa considered, are feasible to build within a reasonable time-frame. We present a database specific for the human microbiome, in the hopes that this will prove useful for research into the functional composition of human-associated microbial communities.
WeFaceNano: a user-friendly pipeline for complete ONT sequence assembly and detection of antibiotic resistance in multi-plasmid bacterial isolates
Authors: Heikema Astrid P. , Jansen Rick , Hiltemann Saskia D. , Hays John P. , Stubbs Andrew P. 
Published: June 2021

Abstract
Background
Bacterial plasmids often carry antibiotic resistance genes and are a significant factor in the spread of antibiotic resistance. The ability to completely assemble plasmid sequences would facilitate the localization of antibiotic resistance genes, the identification of genes that promote plasmid transmission and the accurate tracking of plasmid mobility. However, the complete assembly of plasmid sequences using the currently most widely used sequencing platform (Illumina-based sequencing) is restricted due to the generation of short sequence lengths. The long-read Oxford Nanopore Technologies (ONT) sequencing platform overcomes this limitation. Still, the assembly of plasmid sequence data remains challenging due to software incompatibility with long-reads and the error rate generated using ONT sequencing. Bioinformatics pipelines have been developed for ONT-generated sequencing but require computational skills that frequently are beyond the abilities of scientific researchers. To overcome this challenge, the authors developed ‘WeFaceNano’, a user-friendly Web interFace for rapid assembly and analysis of plasmid DNA sequences generated using the ONT platform. WeFaceNano includes: a read statistics report; two assemblers (Miniasm and Flye); BLAST searching; the detection of antibiotic resistance- and replicon genes and several plasmid visualizations. A user-friendly interface displays the main features of WeFaceNano and gives access to the analysis tools.

Results
Publicly available ONT sequence data of 21 plasmids were used to validate WeFaceNano, with plasmid assemblages and anti-microbial resistance gene detection being concordant with the published results. Interestingly, the “Flye” assembler with “meta” settings generated the most complete plasmids.

Conclusions
WeFaceNano is a user-friendly open-source software pipeline suitable for accurate plasmid assembly and the detection of anti-microbial resistance genes in (clinical) samples where multiple plasmids can be present.
Infection related catheter complications in patients undergoing prone positioning for acute respiratory distress syndrome: an exposed/unexposed study
Authors: Louis Guillaume , Belveyre Thibaut , Jacquot Audrey , Hochard Hélène , Aissa Nejla , Kimmoun Antoine , Goetz Christophe , Levy Bruno , Novy Emmanuel 
Published: June 2021

Abstract
Background
Prone positioning (PP) is a standard of care for patients with moderate–severe acute respiratory distress syndrome (ARDS). While adverse events associated with PP are well-documented in the literature, research examining the effect of PP on the risk of infectious complications of intravascular catheters is lacking.

Method
All consecutive ARDS patients treated with PP were recruited retrospectively over a two-year period and formed the exposed group. Intensive care unit (ICU) patients during the same period without ARDS for whom PP was not conducted but who had an equivalent disease severity were matched 1:1 to the exposed group based on age, sex, centre, length of ICU stay and SAPS II (unexposed group). Infection-related catheter complications were defined by a composite criterion, including catheter tip colonization or intravascular catheter-related infection.

Results
A total of 101 exposed patients were included in the study. Most had direct ARDS (pneumonia). The median [Q1–Q3] PP session number was 2 [1–4]. These patients were matched with 101 unexposed patients. The mortality rates of the exposed and unexposed groups were 31 and 30%, respectively. The incidence of the composite criterion was 14.2/1000 in the exposed group compared with 8.2/1000 days in the control group (p = 0.09). Multivariate analysis identified PP as a factor related to catheter colonization or infection (p = 0.04).

Conclusion
Our data suggest that PP is associated with a higher risk of CVC infectious complications.
Klebsiella spp. cause severe and fatal disease in Mozambican children: antimicrobial resistance profile and molecular characterization
Authors: Massinga Arsénia J. , Garrine Marcelino , Messa Augusto , Nobela Nélio A. , Boisen Nadia , Massora Sergio , Cossa Anélsio , Varo Rosauro , Sitoe António , Hurtado Juan Carlos , Ordi Jaume , Mucavele Hélio , Nhampossa Tacilta , Breiman Robert F. , Whitney Cynthia G. , Blau Dianna M. , Bassat Quique , Mandomando Inácio 
Published: June 2021

Abstract
Background
Klebsiella spp. are important pathogens associated with bacteremia among admitted children and is among the leading cause of death in children < 5 years in postmortem studies, supporting a larger role than previously considered in childhood mortality. Herein, we compared the antimicrobial susceptibility, mechanisms of resistance, and the virulence profile of Klebsiella spp. from admitted and postmortem children.

Methods
Antimicrobial susceptibility and virulence factors of Klebsiella spp. recovered from blood samples collected upon admission to the hospital (n = 88) and postmortem blood (n = 23) from children < 5 years were assessed by disk diffusion and multiplex PCR.

Results
Klebsiella isolates from postmortem blood were likely to be ceftriaxone resistant (69.6%, 16/23 vs. 48.9%, 43/88, p = 0.045) or extended-spectrum β-lactamase (ESBL) producers (60.9%, 14/23 vs. 25%, 22/88, p = 0.001) compared to those from admitted children. blaCTX-M-15 was the most frequent ESBL gene: 65.3%, 9/14 in postmortem isolates and 22.7% (5/22) from admitted children. We found higher frequency of genes associated with hypermucoviscosity phenotype and invasin in postmortem isolates than those from admitted children: rmpA (30.4%; 7/23 vs. 9.1%, 8/88, p = 0.011), wzi-K1 (34.7%; 8/23 vs. 8%; 7/88, p = 0.002) and traT (60.8%; 14/23 vs. 10.2%; 9/88, p < 0.0001), respectively. Additionally, serine protease auto-transporters of Enterobacteriaceae were detected from 1.8% (pic) to 12.6% (pet) among all isolates. Klebsiella case fatality rate was 30.7% (23/75).

Conclusion
Multidrug resistant Klebsiella spp. harboring genes associated with hypermucoviscosity phenotype has emerged in Mozambique causing invasive fatal disease in children; highlighting the urgent need for prompt diagnosis, appropriate treatment and effective preventive measures for infection control.
Neonatal hypoxic-ischemic encephalopathy diagnosis and treatment: a National Survey in China
Authors: Wang Zheng , Zhang Peng , Zhou Wenhao , Xia Shiwen , Zhou Wei , Zhou Xiaoyu , Cheng Xiuyong , Shi Yuan , Lin Zhenlang , Song Dongli , Cheng Guoqiang 
Published: June 2021

Abstract
Background
Neonatal hypoxic-ischemic encephalopathy (HIE) affects as many as 100,000 infants each year in China. Therapeutic hypothermia reduces HIE related mortality and long-term neurodevelopmental disabilities. National guidelines for HIE management were published a decade ago. This study aimed to investigate the current status of HIE diagnosis and treatment in China.

Method
This prospective cross-sectional national survey used a questionnaire evaluating practices related to HIE management. Descriptive statistics and Chi-square or Fisher’s exact test were used, and a p-value of < 0.05 was considered significant.

Results
The 273 hospitals that completed the survey were located in 31 of the 34 provincial districts in China. Eighty-eight percent of the hospitals were Level III hospitals, and 74% treated 10 or more HIE cases annually. Awareness rates of the national guidelines for HIE diagnosis, HIE treatment, and therapeutic hypothermia protocol were 85, 63, and 78%, respectively. Neurological manifestations and blood gas were used as HIE diagnostic criteria by 96% (263/273) and 68% (186/273) of the hospitals, respectively. Therapeutic hypothermia was used in 54% (147/273) of hospitals. The percentage of general hospitals that implemented therapeutic hypothermia (43%, 71/165) was significantly lower than that in maternity and infant hospitals (67%, 49/73) (χ2 = 11.752, p = 0.001) and children’s hospitals (77%, 27/35) (χ2 = 13.446, p < 0.001). Reasons for not providing therapeutic hypothermia included reduction of HIE cases in recent years (39%), high cost of cooling devices and treatment (31%), lack of training (26%), and safety concerns (4%). Among the hospitals that provided therapeutic hypothermia, 27% (39/147) were in full compliance with the recommended protocol. Eighty-one percent (222/273) of the hospitals treated HIE infants with putative neuroprotective agents alone or in combination with cooling. Ninety-one percent of the hospitals had long-term neurodevelopmental follow-up programs for infants with HIE.

Conclusions
There is significant heterogeneity in HIE diagnosis and treatment in China. Therapeutic hypothermia has not become a standard of care for neonatal HIE nationwide. Unproven agents are widely used for HIE treatment. Nationwide standardization of HIE management and dissemination of therapeutic hypothermia represent the opportunities to reduce mortality and improve long-term neurodevelopmental outcomes of children affected by HIE.
Prevalence of symptoms of body dysmorphic disorder (BDD) and associated features in Swiss military recruits: a self-report survey
Authors: Drüge Marie , Rafique Gabriela , Jäger Anne , Watzke Birgit 
Published: June 2021

Abstract
Background
Body dysmorphic disorder (BDD), defined as the obsessive idea that some aspect of one’s own body or appearance is severely flawed/deformed, is relatively common in the general population and has been shown to have strong associations with mood and anxiety disorders and substance abuse disorders. Furthermore, a previous study on symptoms of BDD among people in the military showed that muscles are an important area of preoccupation. Hence, this study aimed to 1. assess the prevalence of BDD symptoms in Swiss military recruits, 2. specify the areas of preoccupation, and 3. analyze associated features (depression and alcohol/drug abuse).

Method
A total of 126 Swiss male military recruits (age: M = 20.12, SD = 1.09, range: 18–24) were examined using self-report measurements to assess symptoms of BDD, depression, alcohol/drug abuse.

Results
The results showed that symptoms of BDD were relatively common (9.5% reached the cutoff value for probable BDD, 84% reported some symptoms), with the muscles as the most common area of preoccupation. A positive correlation (r = .38, p < .001) between depressive symptoms and symptoms of BDD was found, thus no correlation between alcohol/drug abuse and symptoms of BDD.

Conclusion
The results indicate a need to develop and implement measures for prevention (e.g. raising awareness among the military) and intervention in this specific population.
Determinants of adverse birth outcome in Sub-Saharan Africa: analysis of recent demographic and health surveys
Authors: Tamirat Koku Sisay , Sisay Malede Mequanent , Tesema Getayeneh Antehunegn , Tessema Zemenu Tadesse 
Published: June 2021

Abstract
Background
More than 75% of neonatal deaths occurred in the first weeks of life as a result of adverse birth outcomes. Low birth weight, preterm births are associated with a variety of acute and long-term complications. In Sub-Saharan Africa, there is insufficient evidence of adverse birth outcomes. Hence, this study aimed to determine the pooled prevalence and determinants of adverse birth outcomes in Sub-Saharan Africa.

Method
Data of this study were obtained from a cross-sectional survey of the most recent Demographic and Health Surveys (DHS) of ten Sub-African (SSA) countries. A total of 76,853 children born five years preceding the survey were included in the final analysis. A Generalized Linear Mixed Models (GLMM) were fitted and an adjusted odds ratio (AOR) with a 95% Confidence Interval (CI) was computed to declare statistically significant determinants of adverse birth outcomes.

Result
The pooled prevalence of adverse birth outcomes were 29.7% (95% CI: 29.4 to 30.03). Female child (AOR = 0.94, 95%CI: 0.91 0.97), women attended secondary level of education (AOR = 0.87, 95%CI: 0.82 0.92), middle (AOR = 0.94,95%CI: 0.90 0.98) and rich socioeconomic status (AOR = 0.94, 95%CI: 0.90 0.99), intimate-partner physical violence (beating) (AOR = 1.18, 95%CI: 1.14 1.22), big problems of long-distance travel (AOR = 1.08, 95%CI: 1.04 1.11), antenatal care follow-ups (AOR = 0.86, 95%CI: 0.83 0.86), multiparty (AOR = 0.88, 95%CI: 0.84 0.91), twin births (AOR = 2.89, 95%CI: 2.67 3.14), and lack of women involvement in healthcare decision-making process (AOR = 1.10, 95%CI: 1.06 1.13) were determinants of adverse birth outcomes.

Conclusion
This study showed that the magnitude of adverse birth outcomes was high, abnormal baby size and preterm births were the most common adverse birth outcomes. This finding suggests that encouraging antenatal care follow-ups and socio-economic conditions of women are essential. Moreover, special attention should be given to multiple pregnancies, improving healthcare accessibilities to rural areas, and women’s involvement in healthcare decision-making.
Spatio-temporal epidemiology of the tuberculosis incidence rate in Iran 2008 to 2018
Authors: Kiani Behzad , Raouf Rahmati Amene , Bergquist Robert , Hashtarkhani Soheil , Firouraghi Neda , Bagheri Nasser , Moghaddas Elham , Mohammadi Alireza 
Published: June 2021

Abstract
Background
Effective reduction of tuberculosis (TB) requires information on the distribution of TB incidence rate across time and location. This study aims to identify the spatio-temporal pattern of TB incidence rate in Iran between 2008 and 2018.

Methods
This cross-sectional study was conducted on aggregated TB data (50,500 patients) at the provincial level provided by the Ministry of Health in Iran between 2008 and 2018. The Anselin Local Moran’s I and Getis-Ord Gi* were performed to identify the spatial variations of the disease. Furthermore, spatial scan statistic was employed for purely temporal and spatio-temporal analyses. In all instances, the null hypothesis of no clusters was rejected at p ≤ 0.05.

Results
The overall incidence rate of TB decreased from 13.46 per 100,000 (95% CI: 13.19–13.73) in 2008 to 10.88 per 100,000 (95% CI: 10.65–11.11) in 2018. The highest incidence rate of TB was observed in southeast and northeast of Iran for the whole study period. Additionally, spatial cluster analysis discovered Khuzestan Province, in the West of the country, having significantly higher rates than neighbouring provinces in terms of both total TB and smear-positive pulmonary TB (SPPTB). Purely temporal analysis showed that high-rate and low-rate clusters were predominantly distributed in the time periods 2010–2014 and 2017–2018. Spatio-temporal results showed that the statistically significant clusters were mainly distributed from centre to the east during the study period. Some high-trend TB and SPPTB statistically significant clusters were found.

Conclusion
The results provided an overview of the latest TB spatio-temporal status In Iran and identified decreasing trends of TB in the 2008–2018 period. Despite the decreasing incidence rate, there is still need for screening, and targeting of preventive interventions, especially in high-risk areas. Knowledge of the spatio-temporal pattern of TB can be useful for policy development as the information regarding the high-risk areas would contribute to the selection of areas needed to be targeted for the expansion of health facilities.
Association between body mass index and patient-reported-outcome questionnaire scores (CAT™, ACT™, mMRC dyspnoea scale, IPAQ) in Ukraine, Kazakhstan and Azerbaijan: results of the CORE study
Authors: Nugmanova D. , Feshchenko Y. , Iashyna L. , Polianska M. , Malynovska K. , Stafeyeva I. , Makarova J. , Vasylyev A. 
Published: June 2021

Abstract
Background
The overweight/obese population (evaluated by a body mass index, BMI) represents a global health problem and contributes to the development of various chronic diseases. In this epidemiological study we evaluated this relationship by analyzing patient-reported questionnaires related to respiratory function, physical activity and BMI.

Methods
In 2013–2015, adult residents of selected cities were enrolled to this study in: Ukraine (M/F: 403/561), Kazakhstan (M/F = 348/597) and Azerbaijan (M/F: 389/544). Height was measured using a vertical measuring board, and body weight was measured by using portable digital scales. All participants were interviewed using CAT™, mMRC scale and IPAQ; respondents who also reported wheezing or whistling chest sounds during the previous 12 months additionally ACT™.

Results
45.4% of respondents in Ukraine, 47.6% in Kazakhstan and 54.9% of respondents in Azerbaijan were found to be overweight/obese (BMI ≥ 25 kg/m2). The mean CAT™ total score among this population versus those respondents with a normal weight was 5.2 versus 3.6 (Ukraine, p < 0.001), 4.2 versus 2.9 (Kazakhstan, p < 0.001) and 5.9 versus 4.3 (Azerbaijan, p < 0.001). The number of respondents without airflow limitations (mMRC score 0) among overweight/obese respondents versus normal weight respondents was 298 (68.2%) versus 456 (86.7%) in Ukraine, 261 (58.1%) versus 387 (78.2%) in Kazakhstan and 343 (67.1%) versus 345 (82.3%) in Azerbaijan. The ACT™ total score between overweight/obese respondents and normal weight respondents was not statistically different. IPAQ showed a tendency towards a higher proportion of “low activity” results (compared to “moderate” and “high”) in the overweight/obese subgroup (24.7% vs. 23.8% in Kazakhstan, 18.5% vs. 14.6% in Azerbaijan), and in Ukraine this difference was significant (12.4% vs. 5.2%, p < 0.001).

Conclusion
CAT™ and mMRC are widely used tools for respiratory function assessment. Despite CAT™ scores being close to a normal value (< 5), the relationship of both CAT™ and mMRC scores with being overweight/obese was demonstrated in the general adult population of three CIS countries. IPAQ may also be a useful instrument for measuring activity level however, more objective studies are required to evaluate the relationship between BMI and physical activity.
Orthotic treatment of idiopathic toe walking with a lower leg orthosis with circular subtalar blocking
Authors: Berger N. , Bauer M. , Hapfelmeier A. , Salzmann M. , Prodinger P. M. 
Published: June 2021

Abstract
Background
There is no universally accepted treatment standard for idiopathic toe walking patients (ITW) in the current literature. None of the established methods provide homogenous satisfying results. In our department we treat ITW patients with lower leg orthoses with a circular foot unit for a total of 16 weeks. In this study we reviewed our database to evaluate the success of our treatment protocol for a 24 months follow up period.

Results
Twenty-two patients were included in this study. Age at the beginning of treatment was 7.0 years +/− 2.9 (range 2.5-13.1). Percentage of ITW at the beginning of treatment according to the perception of the parents was 89% +/− 22.2 (range 50-100). Immediately after the treatment with our device, percentage of ITW dropped to 11% +/− 13.2 (range 0-50). After 12 months, 73% of the patients (16/22) walked completely normal or showed ITW less than 10% of the day. After 24 months, 64% of the patients kept a normal gait (14/22).

Conclusion
This study provides evidence that the treatment of idiopathic toe walking with lower leg orthoses with a circular foot unit results in satisfying long-term results in two thirds of the patients.
Bias estimation in study design: a meta-epidemiological analysis of transcatheter versus surgical aortic valve replacement
Authors: Youn Saerom , Wong Shannon Avery , Chrystoja Caitlin , Tomlinson George , Wijeysundera Harindra C. , Bell Chaim M. , Gagliardi Anna R. , Baxter Nancy N. , Takata Julie , Sandhu Lakhbir , Urbach David Robert 
Published: June 2021

Abstract
Background
Paucity of RCTs of non-drug technologies lead to widespread dependence on non-randomized studies. Relationship between nonrandomized study design attributes and biased estimates of treatment effects are poorly understood. Our purpose was to estimate the bias associated with specific nonrandomized study attributes among studies comparing transcatheter aortic valve implantation with surgical aortic valve replacement for the treatment of severe aortic stenosis.

Results
We included 6 RCTs and 87 nonrandomized studies. Surgical risk scores were similar for comparison groups in RCTs, but were higher for patients having transcatheter aortic valve implantation in nonrandomized studies. Nonrandomized studies underestimated the benefit of transcatheter aortic valve implantation compared with RCTs. For example, nonrandomized studies without adjustment estimated a higher risk of postoperative mortality for transcatheter aortic valve implantation compared with surgical aortic valve replacement (OR 1.43 [95% CI 1.26 to 1.62]) than high quality RCTs (OR 0.78 [95% CI 0.54 to 1.11). Nonrandomized studies using propensity score matching (OR 1.13 [95% CI 0.85 to 1.52]) and regression modelling (OR 0.68 [95% CI 0.57 to 0.81]) to adjust results estimated treatment effects closer to high quality RCTs. Nonrandomized studies describing losses to follow-up estimated treatment effects that were significantly closer to high quality RCT than nonrandomized studies that did not.

Conclusion
Studies with different attributes produce different estimates of treatment effects. Study design attributes related to the completeness of follow-up may explain biased treatment estimates in nonrandomized studies, as in the case of aortic valve replacement where high-risk patients were preferentially selected for the newer (transcatheter) procedure.