bluuebunny/crossref_metadata_2025_split huggingface dataset:
SneakySnake: a fast and accurate universal genome pre-alignment filter for CPUs, GPUs and FPGAs
Authors: Alser Mohammed , Shahroodi Taha , Gómez-Luna Juan , Alkan Can , Mutlu Onur 
Published: November 2020

Abstract

Motivation
We introduce SneakySnake, a highly parallel and highly accurate pre-alignment filter that remarkably reduces the need for computationally costly sequence alignment. The key idea of SneakySnake is to reduce the approximate string matching (ASM) problem to the single net routing (SNR) problem in VLSI chip layout. In the SNR problem, we are interested in finding the optimal path that connects two terminals with the least routing cost on a special grid layout that contains obstacles. The SneakySnake algorithm quickly solves the SNR problem and uses the found optimal path to decide whether or not performing sequence alignment is necessary. Reducing the ASM problem into SNR also makes SneakySnake efficient to implement on CPUs, GPUs and FPGAs.

Results
SneakySnake significantly improves the accuracy of pre-alignment filtering by up to four orders of magnitude compared to the state-of-the-art pre-alignment filters, Shouji, GateKeeper and SHD. For short sequences, SneakySnake accelerates Edlib (state-of-the-art implementation of Myers’s bit-vector algorithm) and Parasail (state-of-the-art sequence aligner with a configurable scoring function), by up to 37.7× and 43.9× (&gt;12× on average), respectively, with its CPU implementation, and by up to 413× and 689× (&gt;400× on average), respectively, with FPGA and GPU acceleration. For long sequences, the CPU implementation of SneakySnake accelerates Parasail and KSW2 (sequence aligner of minimap2) by up to 979× (276.9× on average) and 91.7× (31.7× on average), respectively. As SneakySnake does not replace sequence alignment, users can still obtain all capabilities (e.g. configurable scoring functions) of the aligner of their choice, unlike existing acceleration efforts that sacrifice some aligner capabilities.

Availabilityand implementation
https://github.com/CMU-SAFARI/SneakySnake.

Supplementary information
Supplementary data are available at Bioinformatics online.
Liftoff: accurate mapping of gene annotations
Authors: Shumate Alaina , Salzberg Steven L 
Published: November 2020

Abstract

Motivation
Improvements in DNA sequencing technology and computational methods have led to a substantial increase in the creation of high-quality genome assemblies of many species. To understand the biology of these genomes, annotation of gene features and other functional elements is essential; however, for most species, only the reference genome is well-annotated.

Results
One strategy to annotate new or improved genome assemblies is to map or ‘lift over’ the genes from a previously annotated reference genome. Here, we describe Liftoff, a new genome annotation lift-over tool capable of mapping genes between two assemblies of the same or closely related species. Liftoff aligns genes from a reference genome to a target genome and finds the mapping that maximizes sequence identity while preserving the structure of each exon, transcript and gene. We show that Liftoff can accurately map 99.9% of genes between two versions of the human reference genome with an average sequence identity &gt;99.9%. We also show that Liftoff can map genes across species by successfully lifting over 98.3% of human protein-coding genes to a chimpanzee genome assembly with 98.2% sequence identity.

Availability and implementation
Liftoff can be installed via bioconda and PyPI. In addition, the source code for Liftoff is available at https://github.com/agshumate/Liftoff.

Supplementary information
Supplementary data are available at Bioinformatics online.
MorphOT: transport-based interpolation between EM maps with UCSF ChimeraX
Authors: Ecoffet Arthur , Poitevin Frédéric , Dao Duc Khanh 
Published: November 2020

Abstract

Motivation
Cryogenic electron microscopy (cryo-EM) offers the unique potential to capture conformational heterogeneity, by solving multiple three-dimensional classes that co-exist within a single cryo-EM image dataset. To investigate the extent and implications of such heterogeneity, we propose to use an optimal-transport-based metric to interpolate barycenters between EM maps and produce morphing trajectories.

Results
While standard linear interpolation mostly fails to produce realistic transitions, our method yields continuous trajectories that displace densities to morph one map into the other, instead of blending them.

Availability and implementation
Our method is implemented as a plug-in for ChimeraX called MorphOT, which allows the use of both CPU or GPU resources. The code is publicly available on GitHub (https://github.com/kdd-ubc/MorphOT.git), with documentation containing tutorial and datasets.

Supplementary information
Supplementary data are available at Bioinformatics online.
New computational model for miRNA-mediated repression reveals novel regulatory roles of miRNA bindings inside the coding region
Authors: Bergman Shaked , Diament Alon , Tuller Tamir 
Published: November 2020

Abstract

Motivation
MicroRNAs (miRNAs) are short (∼24nt), non-coding RNAs, which downregulate gene expression in many species and physiological processes. Many details regarding the mechanism which governs miRNA-mediated repression continue to elude researchers.

Results
We elucidate the interplay between the coding sequence and the 3′UTR, by using elastic net regularization and incorporating translation-related features to predict miRNA-mediated repression. We find that miRNA binding sites at the end of the coding sequence contribute to repression, and that weak binding sites are linked to effective de-repression, possibly as a result of competing with stronger binding sites. Furthermore, we propose a recycling model for miRNAs dissociated from the open reading frame (ORF) by traversing ribosomes, explaining the observed link between increased ribosome density/traversal speed and increased repression. We uncover a novel layer of interaction between the coding sequence and the 3′UTR (untranslated region) and suggest the ORF has a larger role than previously thought in the mechanism of miRNA-mediated repression.

Availability and implementation
The code is freely available at https://github.com/aescrdni/miRNA_model.

Supplementary information
Supplementary data are available at Bioinformatics online.
Practical cardiovascular imaging approach to diagnose immune checkpoint inhibitor myocarditis
Authors: Kondapalli Lavanya , Medina Theresa , Groves Daniel W 
Published: November 2020

Abstract
Immuno-oncology employs various therapeutic strategies that harness a patient’s own immune system to fight disease and has been a promising new strategy for cancer therapy over the last decade. Immune checkpoint inhibitors (ICI), are monoclonal antibodies, that increase antitumor immunity by blocking intrinsic down-regulators of immunity, such as cytotoxic T-lymphocyte antigen 4 (CTLA-4) and programmed cell death 1 (PD-1) or its ligand, programmed cell death ligand 1 (PD-L1). Seven ICIs are currently approved by the Food and Drug Administration and have increased the overall survival for patients with various cancer subtypes. These are used either as single agents or in combination with other checkpoint inhibitors, small molecular kinase inhibitors or cytotoxic chemotherapies. There are also many other immune modifying agents including other checkpoint inhibitor antibodies that are under investigation in clinical trials.
Right ventricular function and outcome in patients undergoing transcatheter aortic valve replacement
Authors: Koschutnik Matthias , Dannenberg Varius , Nitsche Christian , Donà Carolina , Siller-Matula Jolanta M , Winter Max-Paul , Andreas Martin , Zafar Amna , Bartko Philipp E , Beitzke Dietrich , Loewe Christian , Aschauer Stefan , Anvari-Pirsch Anahit , Goliasch Georg , Hengstenberg Christian , Kammerlander Andreas A , Mascherbauer Julia 
Published: November 2020

Abstract

Aims
Right ventricular dysfunction (RVD) on echocardiography has been shown to predict outcomes in patients undergoing transcatheter aortic valve replacement (TAVR). However, a comparison with the gold standard, RV ejection fraction (EF) on cardiovascular magnetic resonance (CMR), has never been performed.

Methods and results
Consecutive patients scheduled for TAVR underwent echocardiography and CMR. RV fractional area change (FAC), tricuspid annular plane systolic excursion, RV free-lateral-wall tissue Doppler (S’), and strain were assessed on echocardiography, and RVEF on CMR. Patients were prospectively followed. Adjusted regression analyses were used to report the strength of association per 1-SD decline for each RV function parameter with (i) N-terminal prohormone of brain natriuretic peptide (NT-proBNP) levels, (ii) prolonged in-hospital stay (&gt;14 days), and (iii) a composite of heart failure hospitalization and death. Two hundred and four patients (80.9 ± 6.6 y/o; 51% female; EuroSCORE-II: 6.3 ± 5.1%) were included. At a cross-sectional level, all RV function parameters were associated with NT-proBNP levels, but only FAC and RVEF were significantly associated with a prolonged in-hospital stay [adjusted odds ratio 1.86, 95% confidence interval (CI) 1.07–3.21; P = 0.027 and 2.29, 95% CI 1.43–3.67; P = 0.001, respectively]. A total of 56 events occurred during follow-up (mean 13.7 ± 9.5 months). After adjustment for the EuroSCORE-II, only RVEF was significantly associated with the composite endpoint (adjusted hazard ratio 1.70, 95% CI 1.32–2.20; P &lt; 0.001).

Conclusion
RVD as defined by echocardiography is associated with an advanced disease state but fails to predict outcomes after adjustment for pre-existing clinical risk factors in TAVR patients. In contrast, RVEF on CMR is independently associated with heart failure hospitalization and death.
How to initiate eHealth in congenital heart disease patients?
Authors: Schuuring Mark J , Kauw Dirkjan 
Published: November 2020

Abstract
Patients with congenital heart disease (CHD) are a vulnerable subgroup of cardiac patients. These patients have a high morbidity and high mortality rate. As the number of patients with CHD keeps growing, while also getting older, new tools for the care and follow-up of these vulnerable patients are warranted. eHealth has an enormous potential to revolutionize health care, and particularly for CHD patients, by expanding care beyond hospital walls and even moving some of the provided care to the comfort of home. As new eHealth tools continue to grow in number, such as invasive eHealth tools, health care delivered through eHealth continues to evolve. This teaching series summarizes current insights and discusses challenges yet to be overcome. Importantly, none of them are insurmountable. This all lays ground for a promising future for eHealth in the care of patients with CHD.
Prices of Peers: Identifying Endogenous Price Effects in the Housing Market
Authors: Szumilo Nikodem 
Published: November 2020

Abstract
The paper identifies neighbourhood price spillovers in the housing market. Although this concept has attracted some theoretical research and is strongly supported by practitioners, it has proven very difficult to show in empirical data. By using the linear-in-means model, which is routinely applied to identify endogenous effects in groups of peers, the study summarises all threats to identification and demonstrates how they can be addressed by exploiting information asymmetry between buyers of different houses and delays in revealing transaction prices. The results show that a 1% increase in the price of a house increases the house price of its neighbour by up to 0.3%.
Three-dimensional changes of the upper airway in patients with Class II malocclusion treated with functional appliances: a systematic review and meta-analysis
Authors: Li Jie , Ge Xiaolei , Guan Huibo , Zhang Shilong , Qiao Xing , Chang Weiwei , Ma Wensheng 
Published: November 2020

Summary

Background/objective
To evaluate the three-dimensional (3D) changes of the upper airway in patients with Class II malocclusion treated with functional appliances (FAs).

Search methods and eligibility criteria
A comprehensive search of seven electronic databases was conducted from the date of inception to 12 July 2020. Manual search was also performed in relevant Chinese and English periodicals. Prospective and retrospective studies evaluating the 3D airway changes after FAs applied on growing patients with skeletal Class II malocclusion were included.

Data collection and analysis
Risk of bias assessment of each included study was performed referring to ROBINS-I. The effects of FAs on upper airway were evaluated by meta-analysis using STATA software. The outcome variables were the changes of oropharyngeal airway volumes (OAVs), nasopharyngeal airway volumes (NAVs), minimum cross-sectional area (MCA) and antero-posterior position of hyoid bone (HB). The overall quality of evidence for each outcome was rated based on Grading of Recommendations Assessment, Development and Evaluation recommendations.

Results
Nine studies were ultimately included in the systematic review and five were included and analyzed in meta-analysis. The results indicated that the pooled mean differences among these studies were 2162.80 [95 per cent confidence interval (CI): 1264.97, 3060.62), 382.20 (95 per cent CI: 140.95, 623.44), 59.91 (95 per cent CI: 41.45, 78.38), and 0.63 (95 per cent CI: −1.97, 3.23) for changes of OAVs, NAVs, MCA, and antero-posterior position of HB, respectively.

Conclusion
Weak evidence suggests that FAs can increase OAVs, NAVs, and MCA in growing patients with Class II malocclusion. Weak evidence also suggests that antero-posterior position of HB cannot be affected by FAs. Further studies are necessary to assess the stability of its effect on the upper airway in the long term.

Registration
The review protocol was not registered prior to the study.
Timing of Food Intake Drives the Circadian Rhythm of Blood Pressure
Authors: Zhang Dingguo , Colson Jackson C , Jin Chunhua , Becker Bryan K , Rhoads Megan K , Pati Paramita , Neder Thomas H , King McKenzi A , Valcin Jennifer A , Tao Binli , Kasztan Malgorzata , Paul Jodi R , Bailey Shannon M , Pollock Jennifer S , Gamble Karen L , Pollock David M 
Published: November 2020

AbstractTiming of food intake has become a critical factor in determining overall cardiometabolic health. We hypothesized that timing of food intake entrains circadian rhythms of blood pressure (BP) and renal excretion in mice. Male C57BL/6J mice were fed ad libitum or reverse feeding (RF) where food was available at all times of day or only available during the 12-h lights-on period, respectively. Mice eating ad libitum had a significantly higher mean arterial pressure (MAP) during lights-off compared to lights-on (113 ± 2 mmHg vs 100 ± 2 mmHg, respectively; P &lt; 0.0001); however, RF for 6 days inverted the diurnal rhythm of MAP (99 ± 3 vs 110 ± 3 mmHg, respectively; P &lt; 0.0001). In contrast to MAP, diurnal rhythms of urine volume and sodium excretion remained intact after RF. Male Bmal1 knockout mice (Bmal1KO) underwent the same feeding protocol. As previously reported, Bmal1KO mice did not exhibit a diurnal MAP rhythm during ad libitum feeding (95 ± 1 mmHg vs 92 ± 3 mmHg, lights-off vs lights-on; P &gt; 0.05); however, RF induced a diurnal rhythm of MAP (79 ± 3 mmHg vs 95 ± 2 mmHg, lights-off vs lights-on phase; P &lt; 0.01). Transgenic PERIOD2::LUCIFERASE knock-in mice were used to assess the rhythm of the clock protein PERIOD2 in ex vivo tissue cultures. The timing of the PER2::LUC rhythm in the renal cortex and suprachiasmatic nucleus was not affected by RF; however, RF induced significant phase shifts in the liver, renal inner medulla, and adrenal gland. In conclusion, the timing of food intake controls BP rhythms in mice independent of Bmal1, urine volume, or sodium excretion.
Prevalence of Self-reported Cognitive Impairment Among Arab American Immigrants in the United States
Authors: Dallo Florence J , Kindratt Tiffany B , Zahodne Laura 
Published: November 2020

Abstract

Background and Objectives
Studies evaluating self-reported cognitive impairment among Arab American immigrants have not been conducted. Our objective was 2-fold: (a) to estimate and compare the age- and sex-adjusted prevalence of self-reported cognitive impairment between Arab American immigrants and U.S.- and immigrant non-Hispanic Whites, non-Hispanic Blacks, Hispanics and non-Hispanic Asians and (b) to examine associations between race, ethnicity, nativity status, and cognitive impairment among Arab American immigrants and non-Hispanic Whites (U.S.- and foreign-born) after controlling for explanatory factors.

Research Design and Methods
We used 18 years (2000–2017) of National Health Interview Survey data (n = 228 985; ages ≥ 45 years). Weighted percentages, prevalence estimates, and multivariable logistic regression models were calculated.

Results
The age- and sex-adjusted prevalence of self-reported cognitive impairment was significantly higher among Arab American immigrants (9.7%) compared to U.S.-born and non-Hispanic White immigrants (~7.4%).

Discussion and Implications
This is the first study to indicate that ethnic disparities in self-reported cognitive impairment may extend to Arab American immigrants. Additional studies need to be conducted to better understand the prevalence of cognitive impairment.
Optimal plant defence under competition for light and nutrients: an evolutionary modelling approach
Authors: de Vries Jorad , Evers Jochem B , Poelman Erik H , Anten Niels P R 
Published: November 2020

AbstractPlants compete with their neighbours for limiting resources such as light and nitrogen, which can promote competitive ability at the expense of other functions such as chemical defence against insect herbivory. This trade-off is strongly influenced by dynamic interactions with biotic and abiotic factors. Yet, understanding how these interactions influence the balance between growth and defence remains one of the key challenges in the field of plant evolutionary ecology. In this study, we investigated how resource availability, competition pressure and insect herbivore pressure drive selection on the balance between the acquisition and protection of resources. To this end, we developed a novel simulation model that combines a functional-structural plant (FSP) model of plant growth in a 3D light climate with a model of natural selection. This mechanistic modelling approach simulates plant growth, competition for above- and below-ground resources, and natural selection to investigate selection pressures on traits related to growth and defence as imposed by different levels of plant density, nitrogen availability and herbivory. The model presented in this study was able to recreate the functional equilibria predicted by principal ecological theories on the effects of resource availability and resource-driven trade-offs. This illustrates the potential of mechanistic modelling approaches such as the one presented here for future research on plant responses to dynamic and variable environments. Our results further showed a three-way interaction between plant competition for light, competition for nitrogen and herbivory that determined the optimal balance between the acquisition and protection of resources. This shows that the value of investing in the acquisition or the protection of resources is a dynamic problem that is influenced by multiple ecological interactions, trade-offs and tragedies of the commons, and therefore requires an eco-evolutionary context to be fully understood.
Middleware for providing activity-driven assistance in cyber-physical production systems☆
Authors: Dhiman Hitesh , Röcker Carsten 
Published: November 2020

AbstractAssistance is becoming increasingly relevant in carrying out industrial work in the context of cyber-physical production systems (CPPSs) and Industry 4.0. While assistance in a single task via a single interaction modality has been explored previously, crossdevice interaction could improve the quality of assistance, especially given the concurrent and distributed nature of work in CPPSs. In this paper, we present the theoretical foundations and implementation of MiWSICx (Middleware for Work Support in Industrial Contexts), a middleware that showcases how multiple interactive computing devices such as tablets, smartphones, augmented/virtual reality glasses, and wearables could be combined to provide crossdevice industrial assistance. Based on activity theory, MiWSICx models human work as activities combining multiple users, artifacts, and cyber-physical objects. MiWSICx is developed using the actor model for deployment on a variety of hardware alongside a CPPS to provide multiuser, crossdevice, multiactivity assistance.
Social Security, Labor Supply, and Health of Older Workers: Quasi-Experimental Evidence from a Large Reform
Authors: Saporta-Eksten Itay , Shurtz Ity , Weisburd Sarit 
Published: November 2020

AbstractWe study the effects of public pension systems on the retirement timing of older workers and, in turn, the health consequences of delaying retirement by those workers. Causal inference relies on a social security reform in Israel that shifted payments from husbands to their (nonworking) wives, thereby substantially reducing the implied tax on the husband's employment while keeping overall household wealth constant. Using administrative social security data, we estimate extensive-margin labor supply elasticities with respect to the average net-of-tax rate of about 0.43 for men over 65. Using the reform to instrument for employment, we find that working an additional full year at old age decreases longevity. This mortality effect occurs after age 75 and is driven by workers holding blue-collar jobs. Finally, we evaluate the effect of the reform on earnings. The results imply a small value for an additional year of life, suggesting that workers underestimate the health cost of employment at older ages. (JEL: J10, J26, J22, H31)
SARS-CoV-2 spike protein binds to bacterial lipopolysaccharide and boosts proinflammatory activity
Authors: Petruk Ganna , Puthia Manoj , Petrlova Jitka , Samsudin Firdaus , Strömdahl Ann-Charlotte , Cerps Samuel , Uller Lena , Kjellström Sven , Bond Peter J , Schmidtchen and Artur 
Published: November 2020

AbstractThere is a link between high lipopolysaccharide (LPS) levels in the blood and the metabolic syndrome, and metabolic syndrome predisposes patients to severe COVID-19. Here, we define an interaction between SARS-CoV-2 spike (S) protein and LPS, leading to aggravated inflammation in vitro and in vivo. Native gel electrophoresis demonstrated that SARS-CoV-2 S protein binds to LPS. Microscale thermophoresis yielded a KD of ∼47 nM for the interaction. Computational modeling and all-atom molecular dynamics simulations further substantiated the experimental results, identifying a main LPS-binding site in SARS-CoV-2 S protein. S protein, when combined with low levels of LPS, boosted nuclear factor-kappa B (NF-κB) activation in monocytic THP-1 cells and cytokine responses in human blood and peripheral blood mononuclear cells, respectively. The in vitro inflammatory response was further validated by employing NF-κB reporter mice and in vivo bioimaging. Dynamic light scattering, transmission electron microscopy, and LPS-FITC analyses demonstrated that S protein modulated the aggregation state of LPS, providing a molecular explanation for the observed boosting effect. Taken together, our results provide an interesting molecular link between excessive inflammation during infection with SARS-CoV-2 and comorbidities involving increased levels of bacterial endotoxins.