bluuebunny/crossref_metadata_2025_split huggingface dataset:
LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilities
Authors: Zhang He , Zhang Liang , Mathews David H , Huang Liang 
Published: July 2020

Abstract

Motivation
RNA secondary structure prediction is widely used to understand RNA function. Recently, there has been a shift away from the classical minimum free energy methods to partition function-based methods that account for folding ensembles and can therefore estimate structure and base pair probabilities. However, the classical partition function algorithm scales cubically with sequence length, and is therefore prohibitively slow for long sequences. This slowness is even more severe than cubic-time free energy minimization due to a substantially larger constant factor in runtime.

Results
Inspired by the success of our recent LinearFold algorithm that predicts the approximate minimum free energy structure in linear time, we design a similar linear-time heuristic algorithm, LinearPartition, to approximate the partition function and base-pairing probabilities, which is shown to be orders of magnitude faster than Vienna RNAfold and CONTRAfold (e.g. 2.5 days versus 1.3 min on a sequence with length 32 753 nt). More interestingly, the resulting base-pairing probabilities are even better correlated with the ground-truth structures. LinearPartition also leads to a small accuracy improvement when used for downstream structure prediction on families with the longest length sequences (16S and 23S rRNAs), as well as a substantial improvement on long-distance base pairs (500+ nt apart).

Availability and implementation
Code: http://github.com/LinearFold/LinearPartition; Server: http://linearfold.org/partition.

Supplementary information
Supplementary data are available at Bioinformatics online.
Predicting mechanism of action of cellular perturbations with pathway activity signatures
Authors: Ren Yan , Sivaganesan Siva , Clark Nicholas A , Zhang Lixia , Biesiada Jacek , Niu Wen , Plas David R , Medvedovic Mario 
Published: July 2020

Abstract

Motivation
Misregulation of signaling pathway activity is etiologic for many human diseases, and modulating activity of signaling pathways is often the preferred therapeutic strategy. Understanding the mechanism of action (MOA) of bioactive chemicals in terms of targeted signaling pathways is the essential first step in evaluating their therapeutic potential. Changes in signaling pathway activity are often not reflected in changes in expression of pathway genes which makes MOA inferences from transcriptional signatures (TSeses) a difficult problem.

Results
We developed a new computational method for implicating pathway targets of bioactive chemicals and other cellular perturbations by integrated analysis of pathway network topology, the Library of Integrated Network-based Cellular Signature TSes of genetic perturbations of pathway genes and the TS of the perturbation. Our methodology accurately predicts signaling pathways targeted by the perturbation when current pathway analysis approaches utilizing only the TS of the perturbation fail.

Availability and implementation
Open source R package paslincs is available at https://github.com/uc-bd2k/paslincs.

Supplementary information
Supplementary data are available at Bioinformatics online.
Automatic classification of single-molecule force spectroscopy traces from heterogeneous samples
Authors: Ilieva Nina I , Galvanetto Nicola , Allegra Michele , Brucale Marco , Laio Alessandro 
Published: July 2020

AbstractMotivationSingle-molecule force spectroscopy (SMFS) experiments pose the challenge of analysing protein unfolding data (traces) coming from preparations with heterogeneous composition (e.g. where different proteins are present in the sample). An automatic procedure able to distinguish the unfolding patterns of the proteins is needed. Here, we introduce a data analysis pipeline able to recognize in such datasets traces with recurrent patterns (clusters).ResultsWe illustrate the performance of our method on two prototypical datasets: ∼50 000 traces from a sample containing tandem GB1 and ∼400 000 traces from a native rod membrane. Despite a daunting signal-to-noise ratio in the data, we are able to identify several unfolding clusters. This work demonstrates how an automatic pattern classification can extract relevant information from SMFS traces from heterogeneous samples without prior knowledge of the sample composition.Availability and implementationhttps://github.com/ninailieva/SMFS_clustering.Supplementary informationSupplementary data are available at Bioinformatics online.
Adaptive multiorientation resolution analysis of complex filamentous network images
Authors: Kittisopikul Mark , Vahabikashi Amir , Shimi Takeshi , Goldman Robert D , Jaqaman Khuloud 
Published: July 2020

Abstract

Motivation
Microscopy images of cytoskeletal, nucleoskeletal and other structures contain complex junctions of overlapping filaments with arbitrary geometry. Yet, state-of-the-art algorithms generally perform single orientation analysis to segment these structures, resulting in gaps near junctions, or assume particular junction geometries to detect them.

Results
We developed a fully automated image analysis approach to address the challenge of determining the number of orientations and their values at each point in space to detect both lines and their junctions. Our approach does not assume any fixed number of orientations or any particular geometry in the case of multiple coincident orientations. It is based on analytically resolving coincident orientations revealed by steerable ridge filtering in an adaptive manner that balances orientation resolution and spatial localization. Combining this multiorientation resolution information with a generalization of the concept of non-maximum suppression allowed us to then identify the centers of lines and their junctions in an image. We validated our approach using a wide array of synthetic junctions and by comparison to manual segmentation. We also applied it to light microscopy images of cytoskeletal and nucleoskeletal networks.

Availability and implementation
https://github.com/mkitti/AdaptiveResolutionOrientationSpace.

Supplementary information
Supplementary information is available at Bioinformatics online.
In Their Own Words: Gene E. Likens
Authors: Verdier James M 
Published: July 2020

Abstract
In Their Own Words chronicles the stories of scientists who have made great contributions to their fields, particularly within the biological sciences. These short oral histories provide our readers a way to learn from and share their experiences. Each month, we will publish in the pages of BioScience and on our podcast, BioScience Talks (http://bioscienceaibs.libsyn.com), the results of these conversations. This oral history is with Dr. Gene E. Likens, emeritus president of the Cary Institute of Ecosystem Studies and a distinguished professor at the University of Connecticut. He also served as president of the American Institute of Biological Sciences.
Note: Both the text and audio versions have been edited for clarity and length.
An International Prospective Cohort Study To Validate 2 Prediction Rules for Infections Caused by Third-generation Cephalosporin-resistant Enterobacterales
Authors: Deelen J W Timotëus , Rottier Wouter C , Giron Ortega José A , Rodriguez-Baño Jesús , Harbarth Stephan , Tacconelli Evelina , Jacobsson Gunnar , Zahar Jean-Ralph , van Werkhoven Cornelis H , Bonten Marc J M ,   ESBL-PREDICT Study Team
Published: July 2020

Abstract

Background
The possibility of bloodstream infections caused by third-generation cephalosporin-resistant Enterobacterales (3GC-R-BSI) leads to a trade-off between empiric inappropriate treatment (IAT) and unnecessary carbapenem use (UCU). Accurately predicting 3GC-R-BSI could reduce IAT and UCU. We externally validate 2 previously derived prediction rules for community-onset (CO) and hospital-onset (HO) suspected bloodstream infections.

Methods
In 33 hospitals in 13 countries we prospectively enrolled 200 patients per hospital in whom blood cultures were obtained and intravenous antibiotics with coverage for Enterobacterales were empirically started. Cases were defined as 3GC-R-BSI or 3GC-R gram-negative infection (3GC-R-GNI) (analysis 2); all other outcomes served as a comparator. Model discrimination and calibration were assessed. Impact on carbapenem use was assessed at several cutoff points.

Results
4650 CO infection episodes were included and the prevalence of 3GC-R-BSI was 2.1% (n = 97). IAT occurred in 69 of 97 (71.1%) 3GC-R-BSI and UCU in 398 of 4553 non–3GC-R-BSI patients (8.7%). Model calibration was good, and the AUC was .79 (95% CI, .75–.83) for 3GC-R-BSI. The prediction rule potentially reduced IAT to 62% (60/97) while keeping UCU comparable at 8.4% or could reduce UCU to 6.3% (287/4553) while keeping IAT equal. IAT and UCU in all 3GC-R-GNIs (analysis 2) improved at similar percentages. 1683 HO infection episodes were included and the prevalence of 3GC-R-BSI was 4.9% (n = 83). Here model calibration was insufficient.

Conclusions
A prediction rule for CO 3GC-R infection was validated in an international cohort and could improve empirical antibiotic use. Validation of the HO rule yielded suboptimal performance.
From micro- to macroevolution: brood parasitism as a driver of phenotypic diversity in birds
Authors: Medina Iliana , Kilner Rebecca M , Langmore Naomi E 
Published: July 2020

AbstractA fundamental question in biology is how diversity evolves and why some clades are more diverse than others. Phenotypic diversity has often been shown to result from morphological adaptation to different habitats. The role of behavioral interactions as a driver of broadscale phenotypic diversity has received comparatively less attention. Behavioral interactions, however, are a key agent of natural selection. Antagonistic behavioral interactions with predators or with parasites can have significant fitness consequences, and hence act as strong evolutionary forces on the phenotype of species, ultimately generating diversity between species of both victims and exploiters. Avian obligate brood parasites lay their eggs in the nests of other species, their hosts, and this behavioral interaction between hosts and parasites is often considered one of the best examples of coevolution in the natural world. In this review, we use the coevolution between brood parasites and their hosts to illustrate the potential of behavioral interactions to drive evolution of phenotypic diversity at different taxonomic scales. We provide a bridge between behavioral ecology and macroevolution by describing how this interaction has increased avian phenotypic diversity not only in the brood parasitic clades but also in their hosts.
Case report of an isolated myocarditis due to COVID-19 infection in a paediatric patient
Authors: Fischer Quentin , Brillat-Savarin Nina , Ducrocq Grégory , Ou Phalla 
Published: July 2020

Abstract

Background
Cardiovascular complications of COVID-19 have been reported in the adult population including myocarditis. However, less is known about the myocardial involvement in paediatric patients.

Case summary
A 15-year-old boy was admitted to our intensive cardiac care unit with COVID-19 and an isolated acute myocarditis, confirmed on cardiac magnetic resonance imaging. No pulmonary lesion was observed on the chest CT scan. We report here the initial presentation, medical care, and clinical course of this patient.

Discussion
In the context of the acute COVID-19 outbreak, screening for COVID-19 infection should be performed in children presenting with myocardial injury in an inflammatory context.
Cost-utility of ticagrelor plus aspirin in diabetic patients with stable coronary artery disease
Authors: Wu Bin , Shi Lizheng 
Published: July 2020

Abstract

Aims
Ticagrelor plus aspirin could reduce the risks of major adverse cardiac events in diabetic patients with stable coronary artery disease (SCD), and yet it also increases bleeding risk. This study would compare the cost and effectiveness of aspirin and ticagrelor plus aspirin therapies in diabetic patients with SCD from a US healthcare sector perspective.

Methods and results
A state-transition Markov model was developed to project probabilities of myocardial infarction, ischaemic stroke, bleeding, and death with and without ticagrelor among all diabetic patients with SCD as the overall population, and those with a history of previous percutaneous coronary intervention (PCI) as a sub-population. Model inputs were extracted from published sources. Lifetime costs and quality-adjusted life-years (QALYs) were measured. The clinical benefits and bleeding risk of ticagrelor added to aspirin were translated into additional 0.08 QALYs at incremental costs of $19 580 in the overall population, yielding an incremental cost-utility ratio (ICUR) of $260 032/QALY. In the sub-population with an additional 0.43 QALYs at an incremental cost of $20 189, the ICUR was $46 426/QALY. Two-way sensitivity showed the clinical benefits of ticagrelor plus aspirin was counterbalanced by its risk of major bleeding. One-way sensitivity and probabilistic sensitivity analysis demonstrated that the results were generally robust except the all-cause death reduction.

Conclusion
The results indicated that ticagrelor plus aspirin is likely to be a cost-effective option in the diabetic patients with a history of PCI. Diabetes management can be improved by carefully prescribing ticagrelor to individuals with low risk of bleeding and high risk of ischaemic events.
Anatomical feasibility of a new off-the-shelf inner branch stent graft (E-nside) for endovascular treatment of thoraco-abdominal aneurysms
Authors: Bilman Victor , Cambiaghi Tommaso , Grandi Alessandro , Carta Niccolò , Melissano Germano , Chiesa Roberto , Bertoglio Luca 
Published: July 2020

Abstract

OBJECTIVES

The aim of this study was to evaluate the proportion of thoraco-abdominal aortic aneurysms (TAAAs) that could theoretically be treated with the JOTEC® E-nside® Thoracoabdominal Branch Endoprosthesis off-the-shelf multibranched endograft.

METHODS
Preoperative computed tomography scans of patients with atherosclerotic TAAA treated between 2007 and 2019 were reviewed, and the anatomical feasibility of the E-nside graft was verified by a retrospective study (clinicaltrials.gov: NCT03959670) based on the investigational manufacturer instructions for use. The anatomical factors determining overall feasibility were divided into vascular access (AC) feasibility, aortic (AO) feasibility and visceral vessels (VV) feasibility.

RESULTS
Two hundred sixty-eight patients with thoraco-abdominal aneurysms were analysed: the overall treatment feasibility was 43%. AC feasibility was 78%, AO feasibility 60% and VV feasibility 79%. An iliac diameter &lt;8.5 mm excluded 21% of the patients. Aortic feasibility was limited by infrarenal aortic diameter (16%) and size of aortic lumen at the level of visceral vessels (14%). Visceral vessels feasibility was mainly limited by inadequate number (8%) or diameter (12%) of target vessels. Height and orientation of target vessels were adequate in 97% of the cases. Overall feasibility was negatively influenced by female gender (Odds ratio: 3.89; 95% confidence interval 2.03–7.44; P &lt; 0.001): the limiting factors in this subgroup being iliac diameter, infrarenal aortic diameter and visceral vessels diameter.

CONCLUSIONS
The E-nside off-the-shelf stent graft can be theoretically employed in almost half of the cases from an all-comers cohort of patients with TAAA. Improvement of device profile and creation of a dedicated infrarenal component are warranted to increase overall feasibility. Female gender significantly affects the overall feasibility.

Clinicaltrials.gov
NCT03959670.
Differences in substrate use linked to divergent carbon flow during litter decomposition
Authors: Albright Michaeline B N , Thompson Jaron , Kroeger Marie E , Johansen Renee , Ulrich Danielle E M , Gallegos-Graves La Verne , Munsky Brian , Dunbar John 
Published: July 2020

ABSTRACT
Discovering widespread microbial processes that create variation in soil carbon (C) cycling within ecosystems may improve soil C modeling. Toward this end, we screened 206 soil communities decomposing plant litter in a common garden microcosm environment and examined features linked to divergent patterns of C flow. C flow was measured as carbon dioxide (CO2) and dissolved organic carbon (DOC) from 44-days of litter decomposition. Two large groups of microbial communities representing ‘high’ and ‘low’ DOC phenotypes from original soil and 44-day microcosm samples were down-selected for fungal and bacterial profiling. Metatranscriptomes were also sequenced from a smaller subset of communities in each group. The two groups exhibited differences in average rate of CO2 production, demonstrating that the divergent patterns of C flow arose from innate functional constraints on C metabolism, not a time-dependent artefact. To infer functional constraints, we identified features – traits at the organism, pathway or gene level – linked to the high and low DOC phenotypes using RNA-Seq approaches and machine learning approaches. Substrate use differed across the high and low DOC phenotypes. Additional features suggested that divergent patterns of C flow may be driven in part by differences in organism interactions that affect DOC abundance directly or indirectly by controlling community structure.
Liver microRNA-29b-3p positively correlates with relative enhancement values of magnetic resonance imaging and represses liver fibrosis
Authors: Gong Xijun , Wang Xiaolin , Zhou Fangfang 
Published: July 2020

AbstractThis study aims to identify potential microRNAs (miRNAs) contribute to liver fibrosis progression and investigate how the miRNA is involved. We recruited totally 58 patients. Magnetic resonance imaging was employed to detect fibrosis. Classification of liver fibrosis was carried out by Ishak scoring system. Cell viability was tested using cell counting kit-8. Measurements of mRNA and protein expressions were conducted using real-time quantitative polymerase chain reaction and western blotting. Luciferase reporter assay was recruited for determination of miR-29b-3p targets. We found that relative enhancement (RE) values were reduced with the increases in fibrosis stages and was negatively associated with Ishak scores. In comparison with patients without liver fibrosis, miR-29b-3p level was remarkably reduced in those with liver fibrosis. Its level was found to be positively associated with RE values. Transforming growth factor beta 1 (TGF-β1)-induced hepatic stellate cell (HSC) activation significantly decreased miR-29b-3p expression. However, miR-29b-3p overexpression repressed TGF-β1-induced collagen I protein and alpha-smooth muscle actin (α-SMA) expression. As expected, its overexpression also reduced cell viability. We found that miR-29b-3p directly bind to signal transducer and activator of transcription 3 (STAT3) and suppressed its expression. Our study demonstrates that low expression of miR-29b-3p may contribute to the progression of liver fibrosis by suppressing STAT3.
In Times of Trouble: A Framework for Understanding Consumers’ Responses to Threats
Authors: Campbell Margaret C , Inman J Jeffrey , Kirmani Amna , Price Linda L 
Published: July 2020

AbstractThe COVID-19 pandemic and the accompanying economic downturn have dramatically impacted the lives of consumers around the world. From a conceptual perspective, such health and economic threats can severely disrupt consumers’ sense of ontological security and elicit adaptive responses by both consumers and marketers. Given the opportune timing, this issue of the Journal of Consumer Research is focused on articles that address questions of consumers’ responses to external threats. The purpose of this introduction is to provide an organizing “conceptual tapestry” to connect the articles appearing in the issue. This framework is provided as a tool to help researchers structure their particular projects within the broader landscape of consumer threat response and to present some potential directions for future research. In conjunction with these articles, we hope that this conceptual framework will provide a point of departure for researchers seeking to enhance the understanding of how consumers and markets collectively respond over the short term and long term to threats that disrupt consumers’ routines, lives, or even the fabric of society.
Sharpening the Precision of Pest Management Decisions: Assessing Variability Inherent in Catch Number and Absolute Density Estimates Derived from Pheromone-Baited Traps Monitoring Insects Moving Randomly
Authors: Miller James R 
Published: July 2020

Abstract
During a trapping study interval, each target insect is either caught or not caught. Therefore, the current analysis treats trapping as a binomial process. Data from a binomial calculator, along with computer simulations of random walkers, documented that the inherent variance associated with estimates of absolute population density generated by a single catch number in a pheromone-baited monitoring trap becomes very high when catch probability averaged across the trap’s sampling area falls below 0.02, as is the case for most insect trapping systems operating in the open field. The imprecision associated with interpretations of single catch numbers renders many current pest management decisions risky and unsatisfactory. Here we reinforce how single-trap, multiple-release experiments can and should be used to measure catch probability, plume reach, and trap sampling area. When catch probability lies in the danger zone below 0.02, steps are suggested for how multiple traps might be deployed to raise composite catch probability to a level where estimates of absolute pest density become reliable. Heat transfer is offered as an appropriate conceptual model for the mechanics of trapping. A call is made for a radical rethinking in the designs of insect monitoring traps in light of their significant current deficits highlighted by this study.
Modeling endodermal organ development and diseases using human pluripotent stem cell-derived organoids
Authors: Pan Fong Cheng , Evans Todd , Chen Shuibing 
Published: July 2020

AbstractRecent advances in development of protocols for directed differentiation from human pluripotent stem cells (hPSCs) to defined lineages, in combination with 3D organoid technology, have facilitated the generation of various endoderm-derived organoids for in vitro modeling of human gastrointestinal development and associated diseases. In this review, we discuss current state-of-the-art strategies for generating hPSC-derived endodermal organoids including stomach, liver, pancreatic, small intestine, and colonic organoids. We also review the advantages of using this system to model various human diseases and evaluate the shortcomings of this technology. Finally, we emphasize how other technologies, such as genome editing and bioengineering, can be incorporated into the 3D hPSC-organoid models to generate even more robust and powerful platforms for understanding human organ development and disease modeling.