bluuebunny/crossref_metadata_2025_split huggingface dataset:
Monitoring priority substances in biota under the Water Framework Directive: how effective is a tiered approach based on caged invertebrates? A proof-of-concept study targeting PFOS in French rivers
Authors: Babut Marc , Ferrari Benoit J. D. , Jame Patrick , Assoumani Azziz , Lestremau François , Hette-Tronquart Nicolas , Miege Cécile , Perceval Olivier 
Published: October 2020

Abstract
Background
This study aims to describe and test a tiered approach for assessing compliance to Environmental Quality standards (EQSs) for priority substances in biota in line with the European Water Framework Directive. This approach is based on caged gammarids and trophic magnification factors (TMFs) at the first tier, with fish analyzed at the second tier at sites predicted to exceed the EQS at the first tier. A dataset was implemented by monitoring perfluorooctane sulfonate (PFOS) in caged gammarids exposed at 15 sites in French rivers, and in fish muscle and rest-of-body from the same sites. Isotopic ratios (δ13C and δ15 N) were also measured in gammarids and fish. Two scenarios were developed to compare measured PFOS concentrations in fish against predicted concentrations based on measures in caged gammarids and TMFs. Scenario (1) compared measured PFOS concentrations in fish fillets with predicted PFOS concentrations based on measured concentrations in caged gammarids and δ15 N. Scenario (2) tested whether or not EQS exceedance was correctly predicted based on measured concentrations in caged gammarids and trophic levels (TLs) from wild fish and gammarid populations.

Results
δ13C and δ15 N variations showed that caged gammarids used local food resources during exposure in the field. PFOS concentrations in gammarids were fairly variable through time at each site. In fish, concentrations ranged from < 1 to 250 ng g−1 (wet weight). After adjustment to the TL at which the EQS is set, 12 sites were above the EQS for PFOS. In scenario (1), predicted concentrations were almost correct at 7 sites out of 15. Most incorrect predictions were overestimations that were slightly improved by applying a lower (neutral) TMF. In scenario (2) we tested several variants for parameters involved in the predictions. The most efficient combination yielded two wrong predictions out of 15. This result was obtained with a higher (more conservative) TMF value, mean concentrations in gammarids from several field exposures during a year, and a TL for gammarids at the median of the distribution in French rivers.

Conclusion
The proposed tiered approach was thus efficient. However, the number of sites was relatively limited, and the dataset was biased towards EQS exceedance. The tiered approach warrants further validation.
Cockle shell-derived aragonite calcium carbonate nanoparticle for targeting cancer and breast cancer stem cells
Authors: Ibiyeye Kehinde Muibat , Idris Sherifat Banke , Zuki Abu Bakar Zakaria 
Published: October 2020

AbstractCockle shell-derived aragonite calcium carbonate nanoparticles (CACNP) have demonstrated prospect as nano-sized drug carriers for targeting cancer cells. CACNP is biocompatible, biodegradable and its biomaterial is readily available and is of low cost. In addition, CACNP is highly porous, has a large surface area which confer a high loading capacity. The pH-dependent release properties as well as its potential for surface functionalization with targeting agents make CACNP useful in passive and active targeting of cancer cells and cancer stem cells. In this article, we reviewed the current state of CACNP as nano-sized drug carrier for targeting cancer cells, cancer stem cells and its biocompatibility.
AllCoPol: inferring allele co-ancestry in polyploids
Authors: Lautenschlager Ulrich , Wagner Florian , Oberprieler Christoph 
Published: October 2020

Abstract
Background
Inferring phylogenetic relationships of polyploid species and their diploid ancestors (leading to reticulate phylogenies in the case of an allopolyploid origin) based on multi-locus sequence data is complicated by the unknown assignment of alleles found in polyploids to diploid subgenomes. A parsimony-based approach to this problem has been proposed by Oberprieler et al. (Methods Ecol Evol 8:835–849, 2017), however, its implementation is of limited practical value. In addition to previously identified shortcomings, it has been found that in some cases, the obtained results barely satisfy the applied criterion. To be of better use to other researchers, a reimplementation with methodological refinement appears to be indispensable.

Results
We present the AllCoPol package, which provides a heuristic method for assigning alleles from polyploids to diploid subgenomes based on the Minimizing Deep Coalescences (MDC) criterion in multi-locus sequence datasets. An additional consensus approach further allows to assess the confidence of phylogenetic reconstructions. Simulations of tetra- and hexaploids show that under simplifying assumptions such as completely disomic inheritance, the topological errors of reconstructed phylogenies are similar to those of MDC species trees based on the true allele partition.

Conclusions
AllCoPol is a Python package for phylogenetic reconstructions of polyploids offering enhanced functionality as well as improved usability. The included methods are supplied as command line tools without the need for prior programming knowledge.
GeneSetCluster: a tool for summarizing and integrating gene-set analysis results
Authors: Ewing Ewoud , Planell-Picola Nuria , Jagodic Maja , Gomez-Cabrero David 
Published: October 2020

Abstract
Background
Gene-set analysis tools, which make use of curated sets of molecules grouped based on their shared functions, aim to identify which gene-sets are over-represented in the set of features that have been associated with a given trait of interest. Such tools are frequently used in gene-centric approaches derived from RNA-sequencing or microarrays such as Ingenuity or GSEA, but they have also been adapted for interval-based analysis derived from DNA methylation or ChIP/ATAC-sequencing. Gene-set analysis tools return, as a result, a list of significant gene-sets. However, while these results are useful for the researcher in the identification of major biological insights, they may be complex to interpret because many gene-sets have largely overlapping gene contents. Additionally, in many cases the result of gene-set analysis consists of a large number of gene-sets making it complicated to identify the major biological insights.

Results
We present GeneSetCluster, a novel approach which allows clustering of identified gene-sets, from one or multiple experiments and/or tools, based on shared genes. GeneSetCluster calculates a distance score based on overlapping gene content, which is then used to cluster them together and as a result, GeneSetCluster identifies groups of gene-sets with similar gene-set definitions (i.e. gene content). These groups of gene-sets can aid the researcher to focus on such groups for biological interpretations.

Conclusions
GeneSetCluster is a novel approach for grouping together post gene-set analysis results based on overlapping gene content. GeneSetCluster is implemented as a package in R. The package and the vignette can be downloaded at https://github.com/TranslationalBioinformaticsUnit
ESCRT machinery plays a role in microautophagy in yeast
Authors: Morshed Shamsul , Tasnin Most Naoshia , Ushimaru Takashi 
Published: October 2020

Abstract
Background
Microautophagy, which degrades cargos by direct lysosomal/vacuolar engulfment of cytoplasmic cargos, is promoted after nutrient starvation and the inactivation of target of rapamycin complex 1 (TORC1) protein kinase. In budding yeast, microautophagy has been commonly assessed using processing assays with green fluorescent protein (GFP)-tagged vacuolar membrane proteins, such as Vph1 and Pho8. The endosomal sorting complex required for transport (ESCRT) system is proposed to be required for microautophagy, because degradation of vacuolar membrane protein Vph1 was compromised in ESCRT-defective mutants. However, ESCRT is also critical for the vacuolar sorting of most vacuolar proteins, and hence reexamination of the involvement of ESCRT in microautophagic processes is required.

Results
Here, we show that the Vph1-GFP processing assay is unsuitable for estimating the involvement of ESCRT in microautophagy, because Vph1-GFP accumulated highly in the prevacuolar class E compartment in ESCRT mutants. In contrast, GFP-Pho8 and Sna4-GFP destined for vacuolar membranes via an alternative adaptor protein-3 (AP-3) pathway, were properly localized on vacuolar membranes in ESCRT-deficient cells. Nevertheless, microautophagic degradation of GFP-Pho8 and Sna4-GFP after TORC1 inactivation was hindered in ESCRT mutants, indicating that ESCRT is indeed required for microautophagy after nutrient starvation and TORC1 inactivation.

Conclusions
These findings provide evidence for the direct role of ESCRT in microautophagy induction.
Symbiotic microbiome Staphylococcus aureus from human nasal mucus modulates IL-33-mediated type 2 immune responses in allergic nasal mucosa
Authors: Jeon Yung Jin , Gil Chan Hee , Won Jina , Jo Ara , Kim Hyun Jik 
Published: October 2020

Abstract
Background
The host-microbial commensalism can shape the innate immune responses in respiratory mucosa and nasal microbiome also modulates front-line immune mechanism in the nasal mucosa. Inhaled allergens encounter the host immune system first in the nasal mucosa, and microbial characteristics of nasal mucus directly impact the mechanisms of initial allergic responses in nasal epithelium. However, the roles of the nasal microbiome in allergic nasal mucosa remain uncertain. We sought to determine the distribution of nasal microbiomes in allergic nasal mucosa and elucidate the interplay between nasal microbiome Staphylococcus species and Th2 cytokines in allergic rhinitis (AR) models.

Results
Staphylococcus aureus (AR-SA) and S. epidermidis (AR-SE) were isolated from the nasal mucosa of patients with AR. The influence of nasal microbiome Staphylococcus species on allergic nasal mucosa was also tested with in vitro and in vivo AR models. Pyrosequencing data showed that colonization by S. epidermidis and S. aureus was more dominant in nasal mucus of AR subjects. The mRNA and protein levels of IL-33 and TSLP were significantly higher in AR nasal epithelial (ARNE) cells which were cultured from nasal mucosa of AR subjects, and exposure of ARNE cells to AR-SA reduced IL-33 mRNA and secreted protein levels. Particularly, ovalbumin-driven AR mice inoculated with AR-SA by intranasal delivery exhibited significantly reduced IL-33 in their nasal mucosa. In the context of these results, allergic symptoms and Th2 cytokine levels were significantly downregulated after intranasal inoculation of AR-SA in vivo AR mice.

Conclusion
Colonization by Staphylococcus species was more dominant in allergic nasal mucosa, and nasal commensal S. aureus from subjects with AR mediates anti-allergic effects by modulating IL-33-dependent Th2 inflammation. The results demonstrate the role of host-bacterial commensalism in shaping human allergic inflammation.
Genome-wide characterization, evolution and expression profiling of UDP-glycosyltransferase family in pomelo (Citrus grandis) fruit
Authors: Wu Boping , Liu Xiaohong , Xu Kai , Zhang Bo 
Published: October 2020

Abstract
Background
Pomelo is one of the three major species of citrus. The fruit accumulates a variety of abundant secondary metabolites that affect the flavor. UDP-glycosyltransferases (UGTs) are involved in the glycosylation of secondary metabolites.

Results
In the present study, we performed a genome-wide analysis of pomelo UGT family, a total of 145 UGTs was identified based on the conserved plant secondary product glycosyltransferase (PSPG) motif. These UGT genes were clustered into 16 major groups through phylogenetic analysis of these genes with other plant UGTs (A-P). Pomelo UGTs were distributed unevenly among the chromosomes. At least 10 intron insertion events were observed in these UGT genome sequences, and I-5 was identified to be the highest conserved one. The expression profile analysis of pomelo UGT genes in different fruit tissues during development and ripening was carried out by RNA-seq.

Conclusions
We identified 145 UGTs in pomelo fruit through transcriptome data and citrus genome database. Our research provides available information on UGTs studies in pomelo, and provides an important research foundation for screening and identification of functional UGT genes.
Impact of low skeletal muscle mass index and perioperative blood transfusion on the prognosis for HCC following curative resection
Authors: Bekki Tomoaki , Abe Tomoyuki , Amano Hironobu , Hattori Minoru , Kobayashi Tsuyoshi , Nakahara Masahiro , Ohdan Hideki , Noriyuki Toshio 
Published: October 2020

Abstract
Background
This study aimed to assess the prognostic factors including low skeletal muscle mass index (SMI) and perioperative blood transfusion for patients with hepatocellular carcinoma (HCC) following curative surgery.

Methods
This study included 139 patients with HCC who underwent hepatectomy between 2005 and 2016. Univariate and multivariate analyses were performed to identify variables associated with overall survival (OS) and recurrence-free survival (RFS).

Results
Low SMI was significantly related with poor OS, while blood transfusion had a strong impact on RFS. The male ratio and body mass index in the low SMI group were significantly higher than those in the high SMI group. There were no significant differences in age, virus etiology, laboratory data, liver function, tumor makers, and operative variables between the groups. Tumor factors such as tumor diameter, tumor number, poor differentiation, and intrahepatic metastasis (IM) did not significantly differ between the two groups. Operation time, intraoperative blood loss volume, and recurrence ratio were significantly higher in the blood transfusion group than in the non-transfusion group. IM was associated with poor OS and RFS.

Conclusions
Low SMI and blood transfusion were independently related with long-term prognosis in patients with HCC following curative surgery.
Three-tube method and covered metallic stent for the treatment of anastomotic leakage after esophagectomy
Authors: Bi Yonghua , Wu Zhengyang , Yi Mengfei , Han Xinwei , Ren Jianzhuang 
Published: October 2020

Abstract
Background
Anastomotic leakage is common and life-threatening complication after esophagectomy. The management of esophageal anastomotic leakage remains challenging. We aimed to determine the safety, feasibility and efficacy of three-tube method and covered metallic stent placement for the management of anastomotic leakage.

Methods
Twenty-six consecutive patients with anastomotic leakage were treated using three-tube method and covered metallic stent and the medical records were retrospectively assessed. All patients received placement of abscess drainage tube, jejunal feeding tube and gastrointestinal decompression tube as well as esophageal covered stent, followed by continue abscess drainage, nutritional support and anti-inflammatory treatment. Tubes and esophageal stents will be removed once anastomotic leakage heals.

Results
The procedure was technically successful in 23 patients (95.8%). A total of 31 covered stents were used. Esophageal stents and abscess drainage tubes were successfully removed from 14 patients. The median retention duration was 2.3 months and 2.6 months for stent and abscess drainage tubes, respectively. No perioperative death, esophageal rupture, massive hemorrhage, or other severe complications were observed during procedures. The abscess cavity had markedly decreased in 8 patients or disappeared in 16 cases. During follow-up, 8 patients died of cancer recurrence and 2 patients died of severe pulmonary infection. The 1-, 3-, 5-year survival rates were 60.1, 51.5 and 51.5%, respectively.

Conclusion
Three-tube method and covered metallic stent placement is safe, feasible and efficacious for treatment of anastomotic leakage after esophagectomy.
Challenges of transferring rural adults with chronic HCV infection for further HCV RNA confirmation and free DAAs treatment: a success story of the interdisciplinary collaboration approach
Authors: Li Wei , Chang Te-Sheng , Chang Shu-Zhi , Chen Ching-Hwa , Chen Mei-Yen 
Published: October 2020

Abstract
Background
Chronic hepatitis C virus (HCV), which is a concern in many countries, is the leading cause of liver cancer around the world. Since Taiwan launched its national health insurance system in 1995, it has managed to extend health coverage to 99% of the Taiwanese population, providing free but limited antiviral treatment each year since 2017. However, many people in rural areas are unaware that they have chronic HCV; nor do they realize that new drugs with high cure rates could drastically reduce their health burden. The aim of this study is to explore the implementation facilitators of and barriers to inviting potentially infected patients in rural areas to be transferred for HCV ribonucleic acid (RNA) confirmation and new drug treatment.

Methods
A descriptive and prospective study design with an interdisciplinary collaboration approach was implemented. After five elements of referral were developed, telephone counseling was conducted between August 2018 and May 2019 in Yunlin, Taiwan. The elements of referral developed by the research team were: (1) forming and coordinating physicians’ schedules, (2) recruiting and training volunteers, (3) training the nursing staff, (4) raising funds or resources, and (5) connecting with village leaders. Thereafter, we collaborated with two district health centers, a private local hospital, and health clinics. Based on the medical records provided by these agencies, community adults that were HCV antibody (anti-HCV) positive were invited to join the program.

Results
Of the 1795 adults who were serum anti-HCV positive, 1149 (64%) accepted transfer to a qualified hospital; of these, 623 (54.2%) had an HCV infection. 552 (88.6%) of those infected started receiving direct-acting antivirals (DAAs) treatment. The top four barriers to accepting transfer were: (1) they perceived themselves to be healthy (n = 98, 32.3%); (2) mistrust of treatment/healthcare (n = 60, 20.2%); (3) limited transportation to the hospital (n = 52, 17.5%); and (4) work conflict (n = 30, 10.1%).

Conclusion
An interdisciplinary collaboration approach significantly contributed to the invitation of CHC patients, as well as their acceptance of HCV RNA confirmation and free DAAs treatment. Using anti-HCV data from previous medical records for case-finding and collaborating with a hospital and health clinics proved to be an efficient strategy.
Chest palpitations in a teenager as an unusual presentation of Lyme disease: case report
Authors: Myers Faith , Mishra Pooja E. , Cortez Daniel , Schleiss Mark R. 
Published: October 2020

Abstract
Background
The incidence of Lyme disease (LD) in North America has increased substantially in the past two decades. Concomitant with the increased incidence of infection has been an enhancement in the recognition of LD complications. Here, we report a case of Lyme carditis complicated by heart block in a pediatric patient admitted to our children’s hospital. What is unique about this case is that the complaint of chest palpitations is an infrequent presentation of LD, and what it adds to the scientific literature is an improved understanding of LD in the pediatric population.

Case presentation
The patient was a 16-year-old male who presented with the main concerns of acute onset of palpitations and chest pain. An important clinical finding was Erythema migrans (EM) on physical exam. The primary diagnoses were LD with associated Lyme carditis, based on the finding of 1st degree atrioventricular heart block (AVB) and positive IgM and IgG antibodies to Borrelia burgdorferi. Interventions included echocardiography, electrocardiography (EKG), and intravenous antibiotics. The hospital course was further remarkable for transition to 2nd degree heart block and transient episodes of complete heart block. A normal sinus rhythm and PR interval were restored after antibiotic therapy and the primary outcome was that of an uneventful recovery.

Conclusions
Lyme carditis occurs in < 5% of LD cases, but the “take-away” lesson of this case is that carditis can be the presenting manifestation of B. burgdorferi infection in pediatric patients. Any patient with suspected Lyme carditis manifesting cardiac symptoms such as syncope, chest pain, or EKG changes should be admitted for parenteral antibiotic therapy and cardiac monitoring. The most common manifestation of Lyme carditis is AVB. AVB may manifest as first-degree block, or may present as high-grade second or third-degree block. Other manifestations of Lyme carditis may include myopericarditis, left ventricular dysfunction, and cardiomegaly. Resolution of carditis is typically achieved through antibiotic administration, although pacemaker placement should be considered if the PR interval fails to normalize or if higher degrees of heart block, with accompanying symptoms, are encountered. With the rising incidence of LD, providers must maintain a high level of suspicion in order to promptly diagnose and treat Lyme carditis.
Retrospective analysis of the etiology, clinical characteristics and outcomes of community-acquired bacterial meningitis in the University Infectious Diseases Centre in Lithuania
Authors: Matulyte E. , Kiveryte S. , Paulauskiene R. , Liukpetryte E. , Vaikutyte R. , Matulionyte R. 
Published: October 2020

Abstract
Background
The morbidity and mortality in community-acquired bacterial meningitis (CABM) remain substantial, and the etiology, clinical characteristics, treatment outcomes and predictors of poor prognosis must be assessed regularly. The aim of this study was to identify the distribution of etiological agents and their relationship with clinical characteristics, treatment and outcomes in this cohort of patients with CABM.

Methods
Our retrospective chart review analyzed the causative microorganisms, clinical characteristics, laboratory findings, treatment and outcomes of 159 adults with CABM hospitalized in the Infectious Diseases Centre of Vilnius University Hospital from January 1, 2009 to December 31, 2016. A Glasgow Outcome Scale (GOS) score ≤ 3 was defined as unfavorable outcome. Predictors of an unfavorable outcome were identified through logistic regression analysis.

Results
The median patient age was 36 (IQR 24–56), and 51.6% were male. Microbiologically confirmed causative agents were identified in 80 (50.3%) patients: N. meningitidis in 55 (34.6%) patients with serotype B accounting for 85% of cases, S. pneumoniae in 15 (9.4%), L. monocytogenes in 5 (3.1%) and other in 5 (3.1%). The clinical triad of fever, neck stiffness and a change in mental status was present in 59.1% of patients. Coexisting conditions and comorbidities were similar in all groups stratified by etiology. Initial antimicrobial treatment consisted of penicillin in 78 patients (49.1%) and ceftriaxone in 72 patients (45.3%). The median time in which antibiotic treatment was started was 40 min (IQR 30.0–90.0). The outcome was unfavorable in 15.7% of episodes and death occurred in 5.7% of cases and did not differ according to the causative agent. Risk factors for an unfavorable outcome were age > 65 years, coexisting pneumonia and a platelet count <150x10e9/l.

Conclusions
The most common causative agent of CABM was N. meningitidis, with serotype B clearly dominant. Causative agents did not influence the disease outcome. The strongest risk factors for an unfavorable outcome were older age, pneumonia and a low platelet count. Since the introduction of routine vaccination against meningococcus B for infants in Lithuania in 2018, the national vaccination policy may hopefully contribute to a decrease in the incidence of serogroup B meningococcal disease in the Lithuanian population.