bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cardiopulmonary Bypass Duration and the Incidence of Pressure Injuries in Patients Undergoing Cardiovascular Surgery
Authors: Chen Xiaomei , Liao Haitao , Gao Wen , Chen Yunchao , Huang Jiegang , Wei Yiping 
Published: July 2020

PURPOSE:
The purpose of our study was to investigate the association between cardiopulmonary bypass (CPB) duration and the incidence of pressure injuries (PIs) in patients undergoing cardiovascular surgery.

DESIGN:
Retrospective chart review.

SUBJECTS AND SETTING:
Two hundred and eighty-eight patients who underwent cardiovascular surgery with CPB from January 2016 through December 2016 in a 2000-bed general hospital, which integrates medical service, education, and research and in which 300 to 350 cardiovascular surgical procedures with CPB are performed each year.

METHODS:
We retrospectively collected data from patients' medical records. Univariate analysis and multivariate logistic regression analysis were performed to identify the independent risk factors for the development of PI. In addition, a simple linear regression model was conducted to assess the relationship between CPB duration and PI development.

RESULTS:
Of the 288 patients, 56 developed 80 PIs, with an incidence of 19.4% (95% confidence interval, 14.9%-24.3%). Multivariate logistic regression analysis showed that CPB duration, use of vasoactive drugs, and diabetes mellitus were independent risk factors for the development of PIs in patients receiving cardiovascular surgery. Median CPB duration was significantly longer in the group with PIs compared with the group without PIs (144 [range 48-415] minutes compared with 102.5 [range 16-678] minutes, P = .000). This result was consistent in the subgroup analysis of pediatric and adult patients. Pressure injuries also increased proportionally with CPB duration, from 12.2% at 60 minutes or shorter to 45.5% at more than 300 minutes (P = .002, R
2 = 0.936).

CONCLUSIONS:
The CPB duration, use of vasoactive drugs, and presence of diabetes mellitus are independent risk factors for the development of PIs in patients undergoing cardiovascular surgery with CPB. Our findings indicated that PI incidence increased incrementally with the duration of CPB. We recommend implementing measures to prevent PIs in cardiovascular surgical patients, especially those undergoing prolonged CPB, receiving vasoactive drugs, and diagnosed with diabetes.
Foot Health Assessment and Problem Identification in a Dominican Batey Community
Authors: O'Connor Jennifer J. , Enriquez Maithe , Wipke-Tevis Deidre D. 
Published: July 2020

PURPOSE:
Foot problems can adversely impact foot function and quality of life. Foot problems are often overlooked, particularly in populations with limited health care access. Little is known about the foot health of Haitian immigrants who live and work in the bateyes (rural sugarcane villages) of the Dominican Republic. These immigrant workers may experience foot problems that could affect foot function and the ability to work and provide for their families.

DESIGN:
Cross-sectional, exploratory, descriptive study design.

SUBJECTS AND SETTING:
A convenience sample of adults was recruited from an ongoing community-based participatory research project evaluating a mobile hypertension screening and treatment clinic program in 11 Dominican batey communities.

METHODS:
Foot health was assessed using the Foot Problems Checklist, a 24-item survey instrument developed for this study based on a review of the literature and foot clinician expertise. A certified foot care nurse recorded foot health data on the Foot Problems Checklist via visual and physical inspection.

RESULTS:
Study participants were 25 females and 16 males, aged 18 to 90 years, and all had at least one foot health problem. The most common foot problems were calluses (78%), dry skin (76%), thick nails (59%), jagged nails (29%), long/overgrown nails (17%), and skin fissures (12%).

CONCLUSIONS:
While the foot problems we observed were not considered serious, they could become progressively debilitating and be prevented with proper self-management guided by appropriate knowledge and skills and available supplies. We recommend the development and testing of foot care self-management interventions deliverable via mobile clinics to increase access and improve foot health outcomes.
Sequential MAVS- and MyD88/TRIF-signaling triggers anti-viral responses of tick-borne encephalitis virus-infected murine astrocytes
Authors: Ghita Luca , Breitkopf Veronika , Mulenge Felix , Pavlou Andreas , Gern Olivia Luise , Durán Verónica , Prajeeth Chittappen Kandiyil , Kohls Moritz , Jung Klaus , Stangel Martin , Steffen Imke , Kalinke Ulrich 
Published: July 2020

AbstractTick-borne encephalitis virus (TBEV), a member of theFlaviviridaefamily, is typically transmitted upon tick bite and can cause meningitis and encephalitis in humans. In TBEV infected mice,mitochondrial antiviral signaling protein(MAVS), the downstream adaptor ofretinoic acid inducible gene I-like receptor(RLR)-signaling, is needed to induce early type I interferon (IFN) responses and to confer protection. To identify the brain resident cell subset that produces protective IFN-β in TBEV infected mice, we isolated neurons, astrocytes and microglia and exposed these cells to TBEVin vitro. Under such conditions, neurons showed the highest percentage of infected cells, whereas astrocytes and microglia were infected to a lesser extent. In the supernatant (SN) of infected neurons, IFN-β was not detectable, while infected astrocytes showed very high and microglia low IFN-β production. Transcriptome analyses of astrocytes implied that MAVS-signaling was needed early after TBEV infection. Accordingly, MAVS-deficient astrocytes showed enhanced TBEV infection and significantly reduced early IFN-β responses. At later time points, moderate amounts of IFN-β were detected in the SN of infected MAVS-deficient astrocytes. Transcriptome analyses indicated that MAVS-deficiency negatively affected the induction of early anti-viral responses, which resulted in significantly increased TBEV replication. Treatment with MyD88 and TRIF inhibiting peptides reduced late IFN-β responses of TBEV infected WT astrocytes and entirely blocked IFN-β responses of infected MAVS-deficient astrocytes. Thus, upon TBEV exposure of brain-resident cells, astrocytes are important IFN-β producers that show biphasic IFN-β induction that initially depends on MAVS- and later on MyD88/TRIF-signaling.
Single-cell analysis of developing B cells reveals dynamic gene expression networks that govern B cell development and transformation
Authors: Lee Robin D. , Munro Sarah A. , Knutson Todd P. , LaRue Rebecca S. , Heltemes-Harris Lynn M. , Farrar Michael A. 
Published: July 2020

SummaryIntegration of external signals and B-lymphoid transcription factor activities orchestrate B cell lineage commitment through alternating cycles of proliferation and differentiation, producing a diverse repertoire of mature B cells. We used single-cell transcriptomics and proteomics to characterize B cell development. Our analysis revealed unique transcriptional signatures that refine the pre-B cell expansion stages into novel pre-BCR-dependent and pre-BCR-independent proliferative phases. These changes correlate with unexpected dynamic and reciprocal changes in expression of the transcription factor EBF1 and the RNA binding protein YBX3, that are defining features of the pre-BCR-dependent stage. Using pseudotime analysis, we further characterize the expression kinetics of different biological modalities across B cell development, including transcription factors, cytokines, chemokines, and their associated receptors. Our findings reveal the underlying heterogeneity of developing B cells and point to key developmental nodes linked to B cell transformation.
Recurrent training rejuvenates and enhances transcriptome and methylome responses in young and older human muscle
Authors: Blocquiaux Sara , Ramaekers Monique , Van Thienen Ruud , Nielens Henri , Delecluse Christophe , De Bock Katrien , Thomis Martine 
Published: July 2020

ABSTRACTBackgroundThe interaction between the muscle methylome and transcriptome is understudied during ageing and periods of resistance training in young, but especially older adults. In addition, more information is needed on the role of retained methylome training adaptations in muscle memory to understand muscle phenotypical and molecular restoration after inactivity or disuse.MethodsWe measured CpG methylation (microarray) and RNA expression (RNA sequencing) in young (n = 5; age = 22 ± 2 yrs) and older (n = 6; age = 65 ± 5 yrs) vastus lateralis muscle samples, taken at baseline, after 12 weeks of resistance training, after training interruption (2 weeks of leg immobilization in young men, 12 weeks of detraining in older men) and after 12 weeks of retraining to identify muscle memory-related adaptations and rejuvenating effects of training.ResultsWe report that of the 427 differentially expressed genes with advanced age, 71 % contained differentially methylated (dm)CpGs in older versus young muscle. The more dmCpGs within a gene, the clearer the inverse methylation-expression relationship. Around 73 % of the age-related dmCpGs approached younger methylation levels when older muscle was trained for 12 weeks. A second resistance training period after training cessation increased the number of hypomethylated CpGs and upregulated genes in both young and older muscle. We found indication for an epi-memory within pro-proliferatingAMOTL1in young muscle and mechanosensing-relatedVCLin older muscle. For the first time, we integrate muscle methylome and transcriptome data in relation to both ageing and training/inactivity-induced responses and identify focal adhesion as an important pathway herein.ConclusionPreviously trained muscle is more responsive to training than untrained muscle at methylome and transcriptome level and recurrent resistance training can partially restore ageing-induced methylome alterations.
Phylogeny inference under the general Markov model using MST-backbone
Authors: Kalaghatgi Prabhav 
Published: July 2020

AbstractMotivationPhylogeny inference via maximum likelihood is NP-hard. Current methods make simplifying assumptions such as stationarity, homogeneity, and time-reversibility for computational ease. The stationarity assumption is violated by empirical observations of GC content evolution, and might systematically bias phylogeny inference. The general Markov model (GM) is a suitable alternative to stationary models because it allows for the evolution of GC content. Related work on the GM model has predominantly focused on inferring unrooted trees using either the log-det distance or phylogenetic invariants.MethodsWe adapted the structural EM framework to perform tree search under the GM model (SEM-GM). Additionally, we implemented a minimum spanning tree framework called MST-backbone to improve the scalability of SEM-GM by constraining search through tree space. MST-backbone(SEM-GM) was used to infer unrooted trees, which are subsequently rooted under the GM model; the latter procedure is called rSEM-GM. We compared our method with RAxML-NG, IQ-TREE, and FastTree on simulated data. We validated our methods on six empirical datasets.ResultsEstimated experimental phylogenies are rooted with high accuracy under the GM model (recall ranging from 80% to 94%). However, virus phylogenies are not realistically rooted, suggesting that the GM model may be overtrained on some empirical datasets. The comparative analysis of simulated data suggests that MST-backbone(SEM-GM) and FastTree scale linearly whereas rSEM-GM, RAxML-NG, and IQ-TREE scale quadratically. The results on empirical data suggest that it is not necessary to use the general time-reversible model for computational ease.Availabilityhttps://github.com/prabhavk/mst-backbone-sem-gmContactprabhav.kalaghatgi@molgen.mpg.deSupplementary informationSupplementary data are available online
Bi-channel Image Registration and Deep-learning Segmentation (BIRDS) for efficient, versatile 3D mapping of mouse brain
Authors: Wang Xuechun , Zeng Weilin , Yang Xiaodan , Fang Chunyu , Han Yunyun , Fei Peng 
Published: July 2020

AbstractWe have developed an open-source software called BIRDS (bi-channel image registration and deep-learning segmentation) for the mapping and analysis of 3D microscopy data of mouse brain. BIRDS features a graphical user interface that is used to submit jobs, monitor their progress, and display results. It implements a full pipeline including image pre-processing, bi-channel registration, automatic annotation, creation of 3D digital frame, high-resolution visualization, and expandable quantitative analysis (via link with Imaris). The new bi-channel registration algorithm is adaptive to various types of whole brain data from different microscopy platforms and shows obviously improved registration accuracy. Also, the attraction of combing registration with neural network lies in that the registration procedure can readily provide training data for network, while the network can efficiently segment incomplete/defective brain data that are otherwise difficult for registration. Our software is thus optimized to enable either minute-timescale registration-based segmentation of cross-modality whole-brain datasets, or real-time inference-based image segmentation for various brain region of interests. Jobs can be easily implemented on Fiji plugin that can be adapted for most computing environments.
Next-generation diagnostics: virus capture facilitates a sensitive viral diagnosis for epizootic and zoonotic pathogens including SARS-CoV-2
Authors: Wylezich Claudia , Calvelage Sten , Schlottau Kore , Ziegler Ute , Pohlmann Anne , Höper Dirk , Beer Martin 
Published: July 2020

AbstractBackgroundThe detection of pathogens in clinical and environmental samples using high-throughput sequencing (HTS) is often hampered by large amounts of background information, which is especially true for viruses with small genomes. Enormous sequencing depth can be necessary to compile sufficient information for identification of a certain pathogen. Generic HTS combining with in-solution capture enrichment can markedly increase the sensitivity for virus detection in complex diagnostic samples.MethodsA virus panel based on the principle of biotinylated RNA-baits was developed for specific capture enrichment of epizootic and zoonotic viruses (VirBaits). The VirBaits set was supplemented by a SARS-CoV-2 predesigned bait set for testing recent SARS-CoV-2 positive samples. Libraries generated from complex samples were sequenced via generic HTS and afterwards enriched with the VirBaits set. For validation, an internal proficiency test for emerging epizootic and zoonotic viruses (African swine fever virus, Ebolavirus, Marburgvirus, Nipah henipavirus, Rift Valley fever virus) was conducted.ResultsThe VirBaits set consists of 177,471 RNA-baits (80-mer) based on about 18,800 complete viral genomes targeting 35 epizootic and zoonotic viruses. In all tested samples, viruses with both DNA and RNA genomes were clearly enriched ranging from about 10-fold to 10,000-fold for viruses including distantly related viruses with at least 72% overall identity to viruses represented in the bait set. Viruses showing a lower overall identity (38% and 46%) to them were not enriched but could nonetheless be detected based on capturing conserved genome regions. The internal proficiency test supports the improved virus detection using the combination of HTS plus targeted enrichment but also point to the risk of carryover between samples.ConclusionsThe VirBaits approach showed a high diagnostic performance, also for distantly related viruses. The bait set is modular and expandable according to the favored diagnostics, health sector or research question. The risk of carryover needs to be taken into consideration. The application of the RNA-baits principle turned out to be user-friendly, and even non-experts (without sophisticated bioinformatics skills) can easily use the VirBait workflow. The rapid extension of the established VirBaits set adapted to actual outbreak events is possible without any problems as shown for SARS-CoV-2.
ROX Index Predicts Intubation in Patients with COVID-19 Pneumonia and Moderate to Severe Hypoxemic Respiratory Failure Receiving High Flow Nasal Therapy
Authors: Patel Maulin , Chowdhury Junad , Mills Nicole , Marron Robert , Gangemi Andrew , Dorey-Stein Zachariah , Yousef Ibraheem , Zheng Matthew , Tragesser Lauren , Giurintano Julie , Gupta Rohit , Rali Parth , D’Alonzo Gilbert , Zhao Huaqing , Patlakh Nicole , Marchetti Nathaniel , Criner Gerard J. , Gordon Matthew ,   for the Temple University COVID-19 Research Group
Published: July 2020

AbstractUse of high flow nasal therapy (HFNT) to treat COVID-19 pneumonia has been greatly debated around the world due to concern for increased healthcare worker transmission and delays in invasive mechanical Ventilation (IMV).MethodsA retrospective analysis of consecutive patients admitted to Temple University Hospital in Philadelphia, Pennsylvania, from March 10, 2020, to May 17, 2020 with moderate to severe respiratory failure treated with High Flow nasal therapy (HFNT). HFNT patients were divided into two groups: HFNT only and HFNT progressed to IMV. The primary outcome was the ability of the ROX index to predict the need of IMV.ResultsOf the 837 patients with COVID-19, 129 met inclusion criteria. The mean age was 60.8 (±13.6) years, BMI 32.6 (±8), 58 (45 %) were female, 72 (55.8%) were African American, 40 (31%) Hispanic. 48 (37.2%) were smokers. Mean time to intubation was 2.5 days (± 3.3). ROX index of less than 5 at HFNT initiation was predictive of progression to IMV (OR = 2.137, p = 0,052). Any decrease in ROX index after HFNT initiation was predictive of intubation (OR= 14.67, p <0.0001). ΔROX (<=0 versus >0), peak D-dimer >4000 and admission GFR < 60 ml/min were very strongly predictive of need for IMV (ROC = 0.86, p=). Mortality was 11.2% in HFNT only group versus 47.5% in the HFNT progressed to IMV group (p,0.0001). Mortality and need for pulmonary vasodilators were higher in the HNFT progressed to IMV group.ConclusionROX index is a valuable, noninvasive tool to evaluate patients with moderate to severe hypoxemic respiratory failure in COVID-19 treated with HFNT. ROX helps predicts need for IMV and thus limiting morbidity and mortality associated with IMV.
Scale-free structure of cancer networks and their vulnerability to hub-directed combination therapy
Authors: Chen Andrew X. , Zopf Christopher J. , Mettetal Jerome , Shyu Wen Chyi , Bolen Joseph , Chakravarty Arijit , Palani Santhosh 
Published: July 2020

AbstractBackgroundThe effectiveness of many targeted therapies is limited by toxicity and the rise of drug resistance. A growing appreciation of the inherent redundancies of cancer signaling has led to a rise in the number of combination therapies under development, but a better understanding of the overall cancer network topology would provide a conceptual framework for choosing effective combination partners. In this work, we explore the scale-free nature of cancer protein-protein interaction networks in 14 indications. Scale-free networks, characterized by a power-law degree distribution, are known to be resilient to random attack on their nodes, yet vulnerable to directed attacks on their hubs (their most highly connected nodes).ResultsConsistent with the properties of scale-free networks, we find that lethal genes are associated with ∼5-fold higher protein connectivity partners than non-lethal genes. This provides a biological rationale for a hub-centered combination attack. Our simulations show that combinations targeting hubs can efficiently disrupt 50% of network integrity by inhibiting less than 1% of the connected proteins, whereas a random attack can require inhibition of more than 30% of the connected proteins.ConclusionsWe find that the scale-free nature of cancer networks makes them vulnerable to focused attack on their highly connected protein hubs. Thus, we propose a new strategy for designing combination therapies by targeting hubs in cancer networks that are not associated with relevant toxicity networks.
Building a tRNA thermometer to access the world’s biochemical diversity
Authors: Cimen Emre , Jensen Sarah E. , Buckler Edward S. 
Published: July 2020

ABSTRACTBecause ambient temperature affects biochemical reactions, organisms living in extreme temperature conditions adapt protein composition and structure to maintain biochemical functions. While it is not feasible to experimentally determine optimal growth temperature (OGT) for every known microbial species, organisms adapted to different temperatures have measurable differences in DNA, RNA, and protein composition that allow OGT prediction from genome sequence alone. In this study, we built a model using tRNA sequence to predict OGT. We used tRNA sequences from 100 archaea and 683 bacteria species as input to train two Convolutional Neural Network models. The first pairs individual tRNA sequences from different species to predict which comes from a more thermophilic organism, with accuracy ranging from 0.538 to 0.992. The second uses the complete set of tRNAs in a species to predict optimal growth temperature, achieving a maximumr2of 0.86; comparable with other prediction accuracies in the literature despite a significant reduction in the quantity of input data. This model improves on previous OGT prediction models by providing a model with minimum input data requirements, removing laborious feature extraction and data preprocessing steps, and widening the scope of valid downstream analyses.