bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of Short-Term Patient Outcomes Following Overlapping Orthopaedic Surgery at a Large Academic Medical Center
Authors: Glauser Gregory , Osiemo Benjamin , Goodrich Stephen , McClintock Scott D. , Weber Kristy L. , Levin L. Scott , Malhotra Neil R. 
Published: February 2020

Background:
Overlapping surgery is a long-standing practice that has not been well studied. The aim of this study was to assess whether overlapping surgery is associated with untoward outcomes for orthopaedic patients.

Methods:
Coarsened exact matching was used to assess the impact of overlap on outcomes among elective orthopaedic surgical interventions (n = 18,316) over 2 years (2014 and 2015) at 1 health-care system. Overlap was categorized as any overlap, and subcategories of exclusively beginning overlap and exclusively end overlap. Study subjects were matched on the Charlson comorbidity index score, duration of surgery, surgical costs, body mass index, length of stay, payer, and race, among others. Serious unanticipated events were studied.

Results:
A total of 3,395 patients had any overlap and were matched (a match rate of 90.8% of 3,738). For beginning and end overlap, matched groups were created, with a match rate of 95.2% of 1043 and 94.7% of 863, respectively. Among matched patients, any overlap did not predict an unanticipated return to surgery at 30 days (8.2% for any overlap and 8.3% for no overlap; p = 0.922) or 90 days (14.1% and 14.1%, respectively; p = 1.000). Patients who had surgery with any overlap demonstrated no difference compared with controls with respect to reoperation, readmission, or emergency room (ER) visits at 30 or 90 days (a reoperation rate of 3.1% and 3.2%, respectively [p = 0.884] at 30 days and 4.2% and 3.5% [p = 0.173] at 90 days; a readmission rate of 10.3% and 11.0% [p = 0.352] at 30 days and 5.5% and 5.2% [p = 0.570] at 90 days; and an ER visit rate of 5.2% and 4.6% [p = 0.276] at 30 days and 4.8% and 4.3% [p = 0.304] at 90 days). Patients with surgical overlap showed reduced mortality compared with controls during follow-up (1.8% and 2.6%, respectively; p = 0.029). Patients with beginning and/or end overlap had a similar lack of association with serious unanticipated events; however, patients with end overlap showed an increased unexpected rate of return to the operating room after reoperation at 90 days (13.3% versus 9.7%; p = 0.015).

Conclusions:
Nonconcurrent overlapping surgery was not associated with adverse outcomes in a large, matched orthopaedic surgery population across 1 academic health system.

Level of Evidence:
Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.
Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes
Authors: Treiber Michelle L. , Taft Diana H. , Korf Ian , Mills David A. , Lemay Danielle G. 
Published: February 2020

Abstract
Background
Shotgun metagenomes are often assembled prior to annotation of genes which biases the functional capacity of a community towards its most abundant members. For an unbiased assessment of community function, short reads need to be mapped directly to a gene or protein database. The ability to detect genes in short read sequences is dependent on pre- and post-sequencing decisions. The objective of the current study was to determine how library size selection, read length and format, protein database, e-value threshold, and sequencing depth impact gene-centric analysis of human fecal microbiomes when using DIAMOND, an alignment tool that is up to 20,000 times faster than BLASTX.
Results
Using metagenomes simulated from a database of experimentally verified protein sequences, we find that read length, e-value threshold, and the choice of protein database dramatically impact detection of a known target, with best performance achieved with longer reads, stricter e-value thresholds, and a custom database. Using publicly available metagenomes, we evaluated library size selection, paired end read strategy, and sequencing depth. Longer read lengths were acheivable by merging paired ends when the sequencing library was size-selected to enable overlaps. When paired ends could not be merged, a congruent strategy in which both ends are independently mapped was acceptable. Sequencing depths of 5 million merged reads minimized the error of abundance estimates of specific target genes, including an antimicrobial resistance gene.
Conclusions
Shotgun metagenomes of DNA extracted from human fecal samples sequenced using the Illumina platform should be size-selected to enable merging of paired end reads and should be sequenced in the PE150 format with a minimum sequencing depth of 5 million merge-able reads to enable detection of specific target genes. Expecting the merged reads to be 180-250bp in length, the appropriate e-value threshold for DIAMOND would then need to be more strict than the default. Accurate and interpretable results for specific hypotheses will be best obtained using small databases customized for the research question.
Compliance with spectacle use in children with refractive errors- a systematic review and meta-analysis
Authors: Dhirar Nonita , Dudeja Sankalp , Duggal Mona , Gupta Parul Chawla , Jaiswal Nishant , Singh Meenu , Ram Jagat 
Published: February 2020

Abstract

Background Primary objective of this review was to measure compliance with spectacle use in children with refractive errors. Secondary objective was to understand the reasons for non-compliance.Methods The databases searched were Ovid, EMBASE, CINAHL and Pubmed. All studies up to March, 2018 were included. The search terms were- ((((((Compliance [Title/Abstract]) OR Adherence[Title/Abstract]) OR Compliant[Title/Abstract]) OR Adherent[Title/Abstract])) AND (((Spectacle[Title/Abstract]) OR Spectacles[Title/Abstract]) OR Eye Glasses[Title/Abstract])) AND ((((Child[Title/Abstract]) OR Children[Title/Abstract]) OR Adolescent[Title/Abstract]) OR Adolescents[Title/Abstract]). Two researchers independently searched the databases and initial screening obtained 33 articles. The PRISMA guidelines were followed for conducting and writing the systematic review. Two reviewers assessed data quality independently using the Quality Assessment tool for systematic reviews of observational studies (QATSO). Poor quality studies were those, which had a score of less than 33% on the QATSO tool. Sensitivity analysis was done to determine if poor quality studies effected compliance. Galbraith plot was used to investigate statistical heterogeneity amongst studies. A random effects model was used to pool compliance.Results Twenty-three studies were included in the review, of which 20 were included in the quantitative analysis. All the studies were cross sectional. The overall compliance with spectacle use was 40.14% (95% CI- 32.78-47.50). The compliance varied from 9.84% (95% CI=2.36-17.31) to 78.57% (95% CI=68.96-88.18). The compliance derived in sensitivity analysis was 40.09%. Reasons for non-compliance were broken/lost spectacles, forgetfulness, and parental disapproval.Conclusion Appropriate remedial measures such as health education and strengthening vision care services will be required to address poor compliance with spectacle use among children.
Evolution of PHAS Loci in the Young Spike of Allohexaploid Wheat
Authors: Zhang Rongzhi , Huang Siyuan , Li Shiming , Song Guoqi , Li Yulian , Li Wei , Li Jihu , Gao Jie , Gu Tiantian , Li Dandan , Zhang Shujuan , Li Genying 
Published: February 2020

Abstract

Background: PhasiRNAs (phased secondary siRNAs) play important regulatory roles in the development processes and biotic or abiotic stresses in plants. Some of phasiRNAs involve in the reproductive development in grasses, which include two categories, 21-nt (nucleotide) and 24-nt phasiRNAs. They are triggered by miR2118 and miR2275 respectively, in premeiotic and meiotic anthers of rice, maize and other grass species. Wheat ( Triticum aestivum ) with three closely related subgenomes (subA, subB and subD), is a model of allopolyploid in plants. Knowledge about the role of phasiRNAs in the inflorescence development of wheat is absent until now, and the evolution of PHAS loci in polyploid plants is also unavailable. Results : Using 261 small RNA expression datasets from various tissues, a batch of PHAS (phasiRNA precursors) loci were identified in the young spike of wheat, most of which were regulated by miR2118 and miR2275 in their target site regions. Dissection of PHAS and their trigger miRNAs among the diploid (AA and DD), tetraploid (AABB) and hexaploid (AABBDD) genomes of Triticum indicated that distribution of PHAS loci were dominant randomly in local chromosomes, while miR2118 was dominant only in the subB genome. The diversity of PHAS loci in the three subgenomes of wheat and their progenitor genomes (AA, DD and AABB) suggested that they originated or diverged at least before the occurrence of the tetraploid AABB genome. The positive correlation between the PHAS loci or the trigger miRNAs and the ploidy of genome indicated the expansion of genome was the major drive force for the increase of PHAS loci and their trigger miRNAs in Triticum . In addition, the expression profiles of the PHAS transcripts suggested they responded to abiotic stresses such as cold stress in wheat. Conclusions: Altogether, non-coding phasiRNAs are conserved transcriptional regulators that display quick plasticity in Triticum genome. They may be involved in reproductive development and abiotic stress in wheat. It could be referred to molecular research on male reproductive development in Triticum .
Long-Lasting Insecticidal Nets retain bio-efficacy after five years of storage: implications for malaria control programmes
Authors: Musa Jeremiah John , Moore Sarah , Moore Jason , Mbuba Emmanuel , Mbeyela Edgar , Kobe Dickson , Swai Johnson K. , Odufuwa Olukayode G. 
Published: February 2020

Abstract

Background: Long Lasting Insecticidal Nets (LLINs) are the most sustainable and effective malaria control tool currently available. Global targets are for 80% of the population living in malaria endemic areas to have access to (own) and use a LLIN. However, current access to LLINs in endemic areas is 56% due to system inefficiencies and budget limitations. Thus, cost-effective approaches to maximize access to effective LLINs in endemic areas are required. This study evaluated whether LLINs that had been stored for five years under manufacturer’s recommended conditions may be optimally effective against Anopheles mosquitoes, to inform malaria control programmes and governments on the periods over which LLINs may be stored between distributions, in an effort to maximise use of available LLINs. Methods: Standard World Health Organization (WHO) bioassays (cone and tunnel test) were used to evaluate the bio-efficacy and wash resistance of Olyset ® and DawaPlus ® 2.0 (rebranded Tsara ® Soft) LLINs after five years of storage at 25°C - 33.4°C and 40% - 100% relative humidity. In addition, a small scale Ifakara Ambient Chamber test (I-ACT) was conducted to compare the bio-efficacy of one long stored LLINs to one new LLIN of the same brand, washed or unwashed. LLINs were evaluated using laboratory reared fully susceptible Anopheles gambiae s.s (Ifakara strain) and pyrethroid resistant Anopheles arabiensis (Kingani strain). Results: After five years of storage, both unwashed and washed, Olyset ® and DawaPlus ® 2.0 (Tsara ® Soft) LLINs passed WHO bio-efficacy criteria on knockdown (KD60) ≥95%, 24-hour mortality ≥80% and ≥90% blood-feeding inhibition in WHO assays against susceptible An. gambiae s.s. DawaPlus ® 2.0 LLINs also passed combined WHO bioassay criteria against resistant An. arabiensis. Confirmatory I-ACT tests using whole nets demonstrated that long-stored LLINs showed higher efficacy than new LLINs on both feeding inhibition and mortality endpoints against resistant strains. Conclusions: Even after long-term storage of around 5 years, both Olyset ® and DawaPlus ® 2.0 LLINs remain efficacious against susceptible Anopheles mosquitoes at optimal storage range of 25°C - 33.4°C for temperature and 40% - 100% relative humidity measured by standard WHO methods. DawaPlus ® 2.0 (Tsara ® Soft) remained efficacious against resistant strain.
Incidence, Clinical Profile, and Risk Factors for Serious Bacterial Infections in Children Hospitalized With Fever in Ujjain, India
Authors: Pathak Ashish , Upadhayay Radika , Mathur Aditya , Rathi Sunil , Lundborg Cecilia Stålsby 
Published: February 2020

Abstract
Background Fever is a cause for concern for both parents and the treating pediatrician and a common reason for antibiotic overuse. However, the proportion of children hospitalized for fever with serious bacterial infection (SBI) is uncertain. We aimed to evaluate the epidemiological, clinical, hematological, and biochemical risks for SBI among the children admitted with fever. Method This prospective study was conducted in a rural teaching hospital in India on consecutive children, aged 3 months–12 years, presenting with fever 100°F (37.7°C) or higher. The presence of SBI was confirmed with one of the following criteria: (a) a positive blood culture; (b) roentgenographically confirmed pneumonia with high titres of C-reactive protein; (c) a culture-confirmed urinary tract infection; (d) enteric fever diagnosed clinically in addition to either a positive blood culture or high Widal titers; and (e) meningitis diagnosed clinically in addition to either a positive blood culture or cerebrospinal fluid culture. A predefined questionnaire was filled. Results A total of 302 children were included in the study, out of which 47% (95% CI 41.4%-52.7%) presented with SBI. The factors associated with confirmed SBI in bivariate analysis were history of previous hospitalization, history of chronic illness, history of medication in the previous one week, a partially immunized child, history of common cold, moderate-grade fever, toxic look, significant lymphadenopathy, absence of BCG scar, delayed development, irritability, breathlessness, respiratory distress, poor feeding, significant weight loss, suspected urinary tract infection, hyponatremia, hypokalemia, and abnormal leucocyte count. The final generalized logistic regression model revealed partially immunized child (RR 4.26), breathlessness (RR 1.80), weight loss (RR 2.28), and suspected urinary tract infection (RR 1.95) as risk factors for the increased risk of SBI. Conclusion The study identified multiple risk factors for SBI. Pediatricians can be made aware of these risk factors. Further studies are warranted to identify age-specific risk factors for SBI because most clinicians depend on clinical signs and symptoms to identify SBI.
Camelina sativa meal hydrolysate as sustainable biomass for the production of carotenoids by Rhodosporidium toruloides
Authors: Bertacchi Stefano , Bettiga Maurizio , Porro Danilo , Branduardi Paola 
Published: February 2020

Abstract
Background: As the circular economy advocates a near total waste reduction, the industry has shown an increased interest towards the exploitation of various residual biomasses. The origin and availability of biomass used as feedstock strongly affects the sustainability of biorefineries, where it is converted in energy and chemicals. Here, we explored the valorization of Camelina meal, the leftover residue from Camelina sativa oil extraction. In fact, in addition to Camelina meal use as animal feed, there is an increasing interest in further valorizing its macromolecular content or its nutritional value. Results: Camelina meal hydrolysates were used as nutrient and energy source for the fermentation of the carotenoid-producing yeast Rhodosporidium toruloides in shake flasks. Total acid hydrolysis revealed that carbohydrates accounted for a maximum of 31 ± 1.0% of Camelina meal. However, because acid hydrolysis is not optimal for subsequent microbial fermentation, an enzymatic hydrolysis protocol was assessed, yielding a maximum sugar recovery of 53.3%. Separate Hydrolysis and Fermentation, Simultaneous Saccharification and Fermentation, and SSF preceded by presaccharification of Camelina meal hydrolysate produced 5 ± 0.7, 16 ± 1.9, and 13 ± 2.6 mg/L of carotenoids, respectively. Importantly, the presence of water-insoluble solids, which normally inhibit microbial growth, correlated with a higher titer of carotenoids, suggesting that the latter could act as scavengers. Conclusions: This study paves the way for the exploitation of Camelina meal as feedstock in biorefinery processes. The process under development provides an example of how different final products can be obtained from this side stream, such as pure carotenoids and carotenoid-enriched Camelina meal can potentially increase the initial value of the source material. The obtained data will help assess the feasibility of using Camelina meal to generate high value-added products.
Association between subthreshold depression and self-care behaviours in people with type 2 diabetes: a systematic review of observational studies
Authors: Shrestha Monika , Ng Ashley , Al-Ghareeb Amal , Alenazi Fatimah , Gray Richard 
Published: February 2020

Abstract
Background: Self-care behaviours in people living with type 2 diabetes are important to achieving optimal glycemic control. Major depression in type 2 diabetes is associated with decreased adherence to self-care behaviours. The association between subthreshold depression and self-care behaviours, however, has not previously been systematically reviewed. The objective of this review is to determine the association between subthreshold depression and self-care behaviours. Methods: A systematic search was performed in five electronic databases that included MEDLINE, EMBASE, PsycINFO, Emcare, and CINAHL. Any observational studies in adults with type 2 diabetes, investigating the association between subthreshold depression and any self-care behaviours were included in the review. Qualitative studies, review articles and grey literature were excluded. Two reviewers independently completed title and abstract and full-text screening, appraised study quality, and extracted the data. A third reviewer resolved any discrepancies between the reviewers if needed. Included articles were critically appraised using the Joanna Briggs Institute (JBI) Critical Appraisal Checklist. Meta-analyses were not conducted, because criteria for conducting such analyses were not met. Results: A total of 6,408 articles were identified through the database searching. After the abstract and full-text review, two articles met the inclusion criteria. One of the included study was cross-sectional while the other was a longitudinal study. Both studies showed inconsistent findings in the association between subthreshold depression and self-care behaviours. Important risks of bias were identified in the included studies. Discussion: The evidence from the two included studies on a possible association between subthreshold depression and self-care behaviours in adults with type 2 diabetes was not consistent and potentially biased. Our review established a gap in knowledge and suggests that further high-quality studies are needed to examine the association between subthreshold depression and self-care behaviours in people with type 2 diabetes. Systematic review registration: PROSPERO CRD42018116373
Antimicrobial resistance among pathogens that infect the bloodstream: a multicenter surveillance report for 1998–2017
Authors: tian lei , zhang zhen , sun ziyong 
Published: February 2020

Abstract
Background Bloodstream infections (BSIs) are a common consequence of infectious diseases and cause high morbidity and mortality. Appropriate antibiotic use is critical for patients’ treatment and prognosis. Long-term monitoring and analyzing of bacterial resistance are important for guiding physicians in choosing the appropriate antibiotics and understanding the changes in bacterial resistance and infection control. Here, we report a retrospective study on antimicrobial resistance in BSI-associated pathogens.Methods Data from the Hubei Province Antimicrobial Resistance Surveillance System (HBARSS) from 1998–2017 were retrospectively analyzed using WHONET 5.6 software. Results Data from HBARSS (1998–2017) revealed that 40,518 Gram-positive bacteria and 26,568 Gram-negative bacteria caused BSIs, the most common of which were Staphylococcus aureus and Escherichia coli. Drug susceptibility data showed that the resistance rates of E. coli and Klebsiella pneumoniae to cefotaxime were significantly higher than those to ceftazidime. Carbapenem-resistant (CR) E. coli and K. pneumoniae have also emerged. In 2013–2017, K. pneumoniae showed resistance levels reaching 15.8% and 17.5% to imipenem and meropenem, respectively, and Acinetobacter baumannii showed high resistance rates ranging from 60–80% to common antibiotics. Control of methicillin-resistant Staphylococcus aureus (MRSA) remains a major challenge, and in 2009–2017, the MRSA detection rate was 40–50%. Conclusions Prevalence of CR K. pneumoniae has increased significantly in recent years. Resistance rates of A. baumannii to common antimicrobial agents have increased exponentially, reaching high levels. MRSA remains a challenge to control.
Construction of immune human library and screening of neutralizing antibodies specific to glycoprotein of severe fever with thrombocytopenia syndrome virus
Authors: zhang wenshuai , Guo Xiling , Chi Ying , Jiao Yongjun 
Published: February 2020

Abstract
Background Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease circulated in eastern Asian countries including China, Japan and South Korea. Currently, there are no effective prophylactic or therapeutic measurements available in the clinical settings. Antibody-mediated prevention and treatment can be an effective complement to the clinical supporting strategies. Glycoprotein N (Gn) and Glycoprotein C (Gc) are two of the highly antigenic envelope proteins on the SFTS virus (SFTSV) surface and contain neutralizing epitopes that can induce neutralizing antibodies. Methods To obtain the neutralizing antibodies specific to glycoprotein of SFTSV, we used phage display technology to generate a human phage antibody library with ScFv format from the peripheral lymphocytes of 8 patients who had recovered from SFTS. The library was bio-panned against recombinant Gn and Gc proteins for four rounds to find their specific antibody clones. Finally, the selected clones were characterized by binding activity test, virus neutralization and Competitive ELISA.Results An immune human ScFv antibody library against SFTSV with high capacity and diversity was constructed. After 4 rounds of panning, 6 distinct clones were found. Of them, 5 were specific to Gn, whereas only 1 was specific to Gc. The immunofluorescence assay showed only three clones with Gn specificity called MAb 4A6, MAb 2B6 and MAb 1F2, respectively, could bind nature virion. All these clones showed broad neutralization activity against the SFTSV, and had different antigenic epitopes from MAb 4-5, a previous identified antibody clone. Conclusions Three new monoclonal antibodies described in our study could be used as potential agents in immunotherapy against SFTSV infection.