bluuebunny/crossref_metadata_2025_split huggingface dataset:
ScaleQC: a scalable lossy to lossless solution for NGS data compression
Authors: Yu Rongshan , Yang Wenxian 
Published: May 2020

Abstract

Motivation
Per-base quality values in Next Generation Sequencing data take a significant portion of storage even after compression. Lossy compression technologies could further reduce the space used by quality values. However, in many applications, lossless compression is still desired. Hence, sequencing data in multiple file formats have to be prepared for different applications.

Results
We developed a scalable lossy to lossless compression solution for quality values named ScaleQC (Scalable Quality value Compression). ScaleQC is able to provide the so-called bit-stream level scalability that the losslessly compressed bit-stream by ScaleQC can be further truncated to lower data rates without incurring an expensive transcoding operation. Despite its scalability, ScaleQC still achieves comparable compression performance at both lossless and lossy data rates compared to the existing lossless or lossy compressors.

Availability and implementation
ScaleQC has been integrated with SAMtools as a special quality value encoding mode for CRAM. Its source codes can be obtained from our integrated SAMtools (https://github.com/xmuyulab/samtools) with dependency on integrated HTSlib (https://github.com/xmuyulab/htslib).

Supplementary information
Supplementary data are available at Bioinformatics online.
Anti-Müllerian hormone production in the ovary: a comparative study in bovine and porcine granulosa cells†
Authors: Estienne Anthony , Jarrier Peggy , Staub Christophe , Venturi Eric , Le Vern Yves , Clemente Nathalie , Monniaux Danielle , Monget Philippe 
Published: May 2020

AbstractIn this study, we aimed to determine the origin of the difference, in terms of anti-Müllerian hormone production, existing between the bovine and porcine ovaries. We first confirmed by quantitative real-time-Polymerase-Chain Reaction, ELISA assay and immunohistochemistry that anti-Müllerian hormone mRNA and protein production are very low in porcine ovarian growing follicles compared to bovine ones. We then have transfected porcine and bovine granulosa cells with vectors containing the luciferase gene driven by the porcine or the bovine anti-Müllerian hormone promoter. These transfection experiments showed that the porcine anti-Müllerian hormone promoter is less active and less responsive to bone morphogenetic protein stimulations than the bovine promoter in both porcine and bovine cells. Moreover, bovine but not porcine granulosa cells were responsive to bone morphogenetic protein stimulation after transfection of a plasmidic construction including a strong response element to the bone morphogenetic proteins (12 repetitions of the GCCG sequence) upstream of the luciferase reporter gene. We also showed that SMAD6, an inhibitor of the SMAD1-5-8 pathway, is strongly expressed in porcine compared to the bovine granulosa cells. Overall, these results suggest that the low expression of anti-Müllerian hormone in porcine growing follicles is due to both a lack of activity/sensitivity of the porcine anti-Müllerian hormone promoter, and to the lack of responsiveness of porcine granulosa cells to bone morphogenetic protein signaling, potentially due to an overexpression of SMAD6 compared to bovine granulosa cells. We propose that the low levels of anti-Müllerian hormone in the pig would explain the poly-ovulatory phenotype in this species.
Connecting Hydroxychloroquine In Vitro Antiviral Activity to In Vivo Concentration for Prediction of Antiviral Effect: A Critical Step in Treating Patients With Coronavirus Disease 2019
Authors: Fan Jianghong , Zhang Xinyuan , Liu Jiang , Yang Yuching , Zheng Nan , Liu Qi , Bergman Kimberly , Reynolds Kellie , Huang Shiew-Mei , Zhu Hao , Wang Yaning 
Published: May 2020

Abstract
Translation of in vitro antiviral activity to the in vivo setting is crucial to identify potentially effective dosing regimens of hydroxychloroquine. In vitro 50%/90% maximal effective concentration values for hydroxychloroquine should be compared to the in vivo free extracellular tissue concentration, which is similar to the free plasma hydroxychloroquine concentration.
Molecular and Serological Assays for SARS-CoV-2: Insights from Genome and Clinical Characteristics
Authors: Shi Jiping , Han Dongsheng , Zhang Runling , Li Jinming , Zhang Rui 
Published: May 2020

Abstract

Background
The ongoing outbreak of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed a challenge for worldwide public health. A reliable laboratory assay is essential both to confirm suspected patients and to exclude patients infected with other respiratory viruses, thereby facilitating the control of global outbreak scenarios.

Content
In this review, we focus on the genomic, transmission, and clinical characteristics of SARS-CoV-2, and comprehensively summarize the principles and related details of assays for SARS-CoV-2. We also explore the quality assurance measures for these assays.

Summary
SARS-CoV-2 has some unique gene sequences and specific transmission and clinical features that can inform the conduct of molecular and serological assays in many aspects, including the design of primers, the selection of specimens, and testing strategies at different disease stages. Appropriate quality assurance measures for molecular and serological assays are needed to maintain testing proficiency. Because serological assays have the potential to identify later stages of the infection and to confirm highly suspected cases with negative molecular assay results, a combination of these two assays is needed to achieve a reliable capacity to detect SARS-CoV-2.
Microbial enrichment, functional characterization and isolation from a cold seep yield piezotolerant obligate hydrocarbon degraders
Authors: Van Landuyt Josefien , Cimmino Lorenzo , Dumolin Charles , Chatzigiannidou Ioanna , Taveirne Felix , Mattelin Valérie , Zhang Yu , Vandamme Peter , Scoma Alberto , Williamson Adam , Boon Nico 
Published: May 2020

ABSTRACTDeep-sea environments can become contaminated with petroleum hydrocarbons. The effects of hydrostatic pressure (HP) in the deep sea on microbial oil degradation are poorly understood. Here, we performed long-term enrichments (100 days) from a natural cold seep while providing optimal conditions to sustain high hydrocarbon degradation rates. Through enrichments performed at increased HP and ambient pressure (AP) and by using control enrichments with marine broth, we demonstrated that both pressure and carbon source can have a big impact on the community structure. In contrast to previous studies, hydrocarbonoclastic operational taxonomic units (OTUs) remained dominant at both AP and increased HP, suggesting piezotolerance of these OTUs over the tested pressure range. Twenty-three isolates were obtained after isolation and dereplication. After recultivation at increased HP, an Alcanivorax sp. showed promising piezotolerance in axenic culture. Furthermore, preliminary co-cultivation tests indicated synergistic growth between some isolates, which shows promise for future synthetic community construction. Overall, more insights into the effect of increased HP on oil-degrading communities were obtained as well as several interesting isolates, e.g. a piezotolerant hydrocarbonoclastic bacterium for future deep-sea bioaugmentation investigation.
Four decades of soil water stress history together with host genotype constrain the response of the wheat microbiome to soil moisture
Authors: Azarbad Hamed , Tremblay Julien , Giard-Laliberté Charlotte , Bainard Luke D , Yergeau Etienne 
Published: May 2020

ABSTRACT
There is little understanding about how soil water stress history and host genotype influence the response of wheat-associated microbiome under short-term decreases in soil moisture. To address this, we investigated how plant breeding history (four wheat genotypes; two with recognized drought resistance and two without) and soil water stress history (same wheat field soil from Saskatchewan with contrasting long-term irrigation) independently or interactively influenced the response of the rhizosphere, root and leaf bacterial and fungal microbiota to short-term decreases in soil water content (SWC). We used amplicon sequencing (16S rRNA gene for bacteria and ITS region for fungi) to characterize the wheat microbiome. Fungal and bacterial communities responses to short-term decreases in SWC were mainly constrained by soil water stress history, with some smaller, but significant influence of plant genotype. One exception was the leaf-associated fungal communities, for which the largest constraint was genotype, resulting in a clear differentiation of the communities based on the genotype's sensitivity to water stress. Our results clearly indicate that soil legacy does not only affect the response to water stress of the microbes inhabiting the soil, but also of the microorganisms more closely associated with the plant tissues, and even of the plant itself.
The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health
Authors: De Filippis Francesca , Pasolli Edoardo , Ercolini Danilo 
Published: May 2020

ABSTRACTLactic acid bacteria (LAB) are present in foods, the environment and the animal gut, although fermented foods (FFs) are recognized as the primary niche of LAB activity. Several LAB strains have been studied for their health-promoting properties and are employed as probiotics. FFs are recognized for their potential beneficial effects, which we review in this article. They are also an important source of LAB, which are ingested daily upon FF consumption. In this review, we describe the diversity of LAB and their occurrence in food as well as the gut microbiome. We discuss the opportunities to study LAB diversity and functional properties by considering the availability of both genomic and metagenomic data in public repositories, as well as the different latest computational tools for data analysis. In addition, we discuss the role of LAB as potential probiotics by reporting the prevalence of key genomic features in public genomes and by surveying the outcomes of LAB use in clinical trials involving human subjects. Finally, we highlight the need for further studies aimed at improving our knowledge of the link between LAB-fermented foods and the human gut from the perspective of health promotion.
Thoracoscopic left S1 + 2 segmentectomy as a good resolution for preserving pulmonary function
Authors: Tane Shinya , Nishio Wataru , Fujibayashi Yusuke , Nishikubo Megumi , Nishioka Yuki , Ogawa Hiroyuki , Kitamura Yoshitaka , Takenaka Daisuke , Yoshimura Masahiro 
Published: May 2020

Abstract

OBJECTIVES
Segmentectomies such as S1 + 2, S1 + 2+3 and S4 + 5 segmentectomy are used to treat patients with non-small-cell lung cancer (NSCLC) in the left upper lobe. However, the preservable lung volume and changes after such segmentectomies remain unknown. We compared the residual pulmonary function after thoracoscopic segmentectomy or lobectomy in the left upper lobe and examined the efficacy of S1 + 2 segmentectomy regarding postoperative pulmonary function.

METHODS
Patients with left upper lobe NSCLC who underwent thoracoscopic segmentectomy or lobectomy were included. Spirometry and computed tomography were performed before and 6 months after resection, and the ipsilateral preserved lobe volume was calculated using 3-dimensional computer tomography. The percentage of postoperative/preoperative forced expiratory volume in 1 s and actual/predicted regional forced expiratory volume in 1 s (preservation rate) in the residual lobe were compared.

RESULTS
Eighty-eight patients underwent lobectomy and 70 patients underwent segmentectomy (23 S1 + 2, 35 S1 + 2+3 and 12 S4 + 5 segmentectomies). The percentage of postoperative/preoperative forced expiratory volume in 1 s was 97 in S1 + 2, 82 in S1 + 2+3, 86 in S4 + 5 segmentectomy and 73 in left upper lobectomy, indicating that segmentectomy could be a meaningful approach to preserve pulmonary function. The preservation rate was 83% in S1 + 2 and 62% in S1 + 2+3 segmentectomy and was significantly higher in S1 + 2 than in S1 + 2+3 segmentectomy (P &lt; 0.001).

CONCLUSIONS
Postoperative pulmonary function and the preservable lung volume of the residual lobe after thoracoscopic S1 + 2 segmentectomy were well-preserved among other segmentectomies and lobectomy. Thoracoscopic S1 + 2 segmentectomy is a good alternative for preserving postoperative function.
Variational regularization of inverse problems for manifold-valued data
Authors: Storath Martin , Weinmann Andreas 
Published: May 2020

Abstract
In this paper, we consider the variational regularization of manifold-valued data in the inverse problems setting. In particular, we consider total variation and total generalized variation regularization for manifold-valued data with indirect measurement operators. We provide results on the well-posedness and present algorithms for a numerical realization of these models in the manifold setup. Further, we provide experimental results for synthetic and real data to show the potential of the proposed schemes for applications.
Risk prediction of delirium in hospitalized patients using machine learning: An implementation and prospective evaluation study
Authors: Jauk Stefanie , Kramer Diether , Großauer Birgit , Rienmüller Susanne , Avian Alexander , Berghold Andrea , Leodolter Werner , Schulz Stefan 
Published: May 2020

Abstract

Objective
Machine learning models trained on electronic health records have achieved high prognostic accuracy in test datasets, but little is known about their embedding into clinical workflows. We implemented a random forest–based algorithm to identify hospitalized patients at high risk for delirium, and evaluated its performance in a clinical setting.

Materials and Methods
Delirium was predicted at admission and recalculated on the evening of admission. The defined prediction outcome was a delirium coded for the recent hospital stay. During 7 months of prospective evaluation, 5530 predictions were analyzed. In addition, 119 predictions for internal medicine patients were compared with ratings of clinical experts in a blinded and nonblinded setting.

Results
During clinical application, the algorithm achieved a sensitivity of 74.1% and a specificity of 82.2%. Discrimination on prospective data (area under the receiver-operating characteristic curve = 0.86) was as good as in the test dataset, but calibration was poor. The predictions correlated strongly with delirium risk perceived by experts in the blinded (r = 0.81) and nonblinded (r = 0.62) settings. A major advantage of our setting was the timely prediction without additional data entry.

Discussion
The implemented machine learning algorithm achieved a stable performance predicting delirium in high agreement with expert ratings, but improvement of calibration is needed. Future research should evaluate the acceptance of implemented machine learning algorithms by health professionals.

Conclusions
Our study provides new insights into the implementation process of a machine learning algorithm into a clinical workflow and demonstrates its predictive power for delirium.
Evaluation of the GENE-UP ® E. coli O157:H7 Method for the Detection of E. coli O157:H7 in Select Foods: Collaborative Study, 2019.03
Authors: Johnson Ronald , Mills John , Pittet Jean-Louis , Rannou Maryse , Bird Patrick , Nelson Maria 
Published: May 2020

Abstract

Background
The GENE-UP® E. coli O157:H7 2 (ECO 2) assay (Performance Tested MethodSM 121805) incorporates Fluorescence Resonance Energy Transfer hybridization probes into its proprietary PCR technology for the rapid detection of E. coli O157:H7 in select foods.

Objective
The purpose of this validation was to evaluate the method’s interlaboratory performance and submit the result to AOAC INTERNATIONAL for adoption as First Action Official MethodSM for the detection of E. coli O157:H7 in select foods.

Method
The GENE-UP® method was evaluated in a multi-laboratory study as part of the MicroVal validation process using unpaired test portions for one food matrix, raw milk cheese (Comté, 34% fat, 0.8% salt). The candidate method was compared to the ISO 16654:2001 reference method. Fourteen participants from 13 laboratories throughout the European Union participated. Three levels of contamination were evaluated: a non-inoculated control level (0 colony-forming units (CFU)/test portion), a low contamination level (∼5 CFU/test portion), and a high contamination level (∼10 CFU/test portion). Data from that study were analyzed according to the Probability of Detection (POD) statistical model as presented in the AOAC validation guidelines. The difference in laboratory POD (dLPODC) values with 95% confidence interval across collaborators was calculated for each level between the candidate and reference method results, and between the candidate presumptive and confirmed results.

Results
The dLPODC values with 95% confidence interval were; 0.00 (–0.04, 0.04), 0.27 (0.04, 0.49), and 0.17 (0.01, 0.33) for the non-inoculated, low and high contamination levels respectively.

Conclusions
The dLPODC results indicate a significant difference between the candidate method and the reference method for both the low and high contamination levels, with the candidate method producing higher recovery of the target organism at both levels.

Highlights
The GENE-UP E. coli O157:H7 assay provides industry with a rapid, accurate detection method for E. coli O157:H7 in a broad range of foods.
Colonic lavage in treatment of refractory Clostridium difficile infection: an adaptation of the Pittsburgh protocol
Authors: Morgan Maura , Farrell Timothy , Ndubizu Gordian U , Farrell Timothy J 
Published: May 2020

Abstract
Clostridium difficile infection (CDI) is a common nosocomial sequela in patients treated with antibiotics. Surgical intervention is indicated in fulminant cases. However, the mortality associated with total colectomy and end ileostomy is high. Previous reports have indicated that surgical intervention for severe complicated CDI with formation of a loop ileostomy leading to the diversion of fecal stream followed by colonic lavage can be beneficial in treating severe CDI. This procedure is known as the Pittsburgh protocol and has been reported to decrease the mortality and the need for a total colectomy in patients with severe complicated CDI. In this case, we present a 75-year-old female with refractory CDI. In her treatment, we adapted the Pittsburgh protocol and utilized a 20-French MIC gastrostomy tube to recreate the ileocecal valve and control the colonic lavage without retrograde flow.
Disc and wind in black hole X-ray binary MAXI J1820+070 observed through polarized light during its 2018 outburst
Authors: Kosenkov Ilia A , Veledina Alexandra , Berdyugin Andrei V , Kravtsov Vadim , Piirola Vilppu , Berdyugina Svetlana V , Sakanoi Takeshi , Kagitani Masato , Poutanen Juri 
Published: May 2020

ABSTRACT
We describe the first complete polarimetric data set of the entire outburst of a low-mass black hole X-ray binary system and discuss the constraints for geometry and radiative mechanisms it imposes. During the decaying hard state, when the optical flux is dominated by the non-thermal component, the observed polarization is consistent with the interstellar values in all filters. During the soft state, the intrinsic polarization of the source is small, ∼0.15 per cent in B and V filters, and is likely produced in the irradiated disc. A much higher polarization, reaching ∼0.5 per cent in V and R filters, at a position angle of ∼25○ observed in the rising hard state coincides in time with the detection of winds in the system. This angle coincides with the position angle of the jet. The detected optical polarization is best explained by scattering of the non-thermal (hot flow or jet base) radiation in an equatorial wind.
膳食纤维和全谷物的定义、法规现状及前沿研究
Authors: Korczak Renee , Slavin Joanne L 
Published: May 2020

Abstract
本文目的是回顾全球膳食纤维和全谷物(whole grain, WG)的定 义和法规现状，并讨论居民达到相应推荐摄入量的影响因素 膳食指 南中普遍推荐富含膳食纤维的植物性食物，如全谷物，但全谷物和膳 食纤维的推荐摄入量取决于定义和法规规定 美国和加拿大官方对 膳食纤维的推荐摄入量是采用医学研究所的膳食参考摄入量(dietary reference intakes, DRIs)所规定的 膳食纤维的适宜摄入量(adequate intake, AI)是依据前瞻性队列研究所得出的膳食纤维摄入对心血管疾 病风险影响而确定的 研究发现每1000 kcal 能量的食物中含14 g 膳食 纤维即对心血管疾病(cardiovascular disease, CVD)有保护作用 因此，当根据能量建立推荐膳食摄入量时，这一数值(14 g/1000 Kcal)是整 个生命周期膳食纤维适宜摄入量的基础 然而，膳食纤维实际摄入量 约为推荐摄入量的一半 全谷物推荐摄入量的制定和全谷物食品的定 义具有同样的挑战性，因为全谷物推荐摄入量需要依据全谷物的定义 来制定 2005 年《美国居民膳食指南》建议，全谷物食品应占所有谷 类食品的一半，但每天实际摄入量一般少于一份，而远没有达到推荐 的三份 制定全谷物推荐摄入量的科学依据是基于相同的前瞻性队列 研究结果和指南中已知的膳食纤维的心血管疾病保护作用 因此，膳 食纤维是北美和世界各国膳食指南推荐摄入的营养素，全谷物则是相 应推荐的膳食模式 实现膳食纤维和全谷物推荐摄入量的挑战包括低 碳水化合物饮食、低谷物蛋白饮食和避免加工食品的公共卫生学建议
Which Patients Discharged to Home-Based Outpatient Parenteral Antimicrobial Therapy Are at High Risk of Adverse Outcomes?
Authors: Keller Sara C , Wang Nae-Yuh , Salinas Alejandra , Williams Deborah , Townsend Jennifer , Cosgrove Sara E 
Published: May 2020

Abstract

Background
Patients increasingly receive home-based outpatient parenteral antimicrobial therapy (OPAT). Understanding which patients might be at higher risk of complications is critical in effectively triaging resources upon and after hospital discharge.

Methods
A prospective cohort of patients discharged from 1 of 2 academic medical centers in Baltimore, Maryland, between March 2015 and December 2018 were consented and randomly divided into derivation and validation cohorts for development of a risk score for adverse OPAT outcomes. Data from the derivation cohort with the primary outcome of a serious adverse outcome (infection relapse, serious adverse drug event, serious catheter complication, readmission, or death) were analyzed to derive the risk score equation using logistic regression, which was then validated in the validation cohort for performance of predicting a serious adverse outcome.

Results
Of 664 patients in the total cohort, half (332) experienced a serious adverse outcome. The model predicting having a serious adverse outcome included type of catheter, time on OPAT, using a catheter for chemotherapy, using a catheter for home parenteral nutrition, being treated for septic arthritis, being on vancomycin, being treated for Enterococcus, being treated for a fungal infection, and being treated empirically. A score ≥2 on the serious adverse outcome score had a 94.0% and 90.9% sensitivity for having a serious adverse outcome in the derivation and validation cohorts, respectively.

Conclusions
A risk score can be implemented to detect who may be at high risk of serious adverse outcomes, but all patients on OPAT may require monitoring to prevent or detect adverse events.