bluuebunny/crossref_metadata_2025_split huggingface dataset:
A hybrid framework to predict ski jumping forces by combining data‐driven pose estimation and model‐based force calculation
Authors: Nam Yunhyoung , Do Youngkyung , Kim Jaehoon , Lee Heonyong , Kim Do‐Nyun 
Published: January 2022

ABSTRACTThe aim of this paper is to propose a hybrid framework that combines a data‐driven pose estimation with model‐based force calculation in order to predict the ski jumping force from a recorded motion video. A skeletal model consisting of five joints (ear, hip, knee, ankle, and toe) and four rigid segments (head/arm/trunk or HAT, thigh, shank, and foot) connecting each joint is developed. The joint forces are calculated from the dynamic equilibrium equations, which requires the time history of joint coordinates. They are estimated from a recorded motion video using a deep neural network for pose estimation trained with human motion data. Joint coordinates can be obtained by the proposed deep neural network directly from images of jumping motion without using any markers. The validity and usefulness of the proposed method are confirmed in lab experiments. Further, our method is practically applicable to the study in a real competition environment because it is not required to attach any sensor or marker to athletes.Highlights
A method to predict the ski jumping force from a recorded motion video is proposed.
It combines a data‐driven pose estimation with a model‐based force calculation.
The proposed method does not require any markers and sensors to be attached to athletes.
In a laboratory environment, the relative error in the maximum jumping force is less than 7%.
The method can be easily applied to a field study in a real competition environment.
Spatiotemporal dynamic of environmental indices of watershed sustainability in connection with land-use change
Authors: Mirchooli Fahimeh , Sadeghi Seyed Hamidreza , Khaledi Darvishan Abdulvahed 
Published: January 2022

ABSTRACT
Exploring spatial and temporal land-use changes is valuable for local governments to address issues of sustainability and planning policy where urbanization and industrialization are taking place. Besides anthropogenic effects, natural driving forces like climate change may also affect sustainability. However, such relationships have not been studied minutely. Hence, this study first investigates the land-use changes and their relationship with land surface temperature (LST) for the Shazand Watershed, Iran, in 1986, 1998, 2008, and 2016 coincided with supplementary industrialization stages. Furthermore, the relations among LST and other biophysical parameters, including Normalized Difference Vegetation Index (NDVI), Normalized Difference Buildup Index (NDBI), and Normalized Difference Water Index (NDWI), were analyzed, and corresponding variations were explored. The results indicated that the mean LST of the study watershed has an increasing trend from 1986 to 2008 due to land-use change and drought intensification. Later, LST decreased in 2016. Lower LST was associated with irrigation farming and orchard, and higher LST was related to sparse oak forest areas. There was also a negative correlation between LST and NDVI. As a result, it was inferred that greenery declined LST. Conversely, a positive correlation was found between LST and NDBI resulting from the built-up areas. Since LST could influence biological, physical, chemical processes, it can therefore be supported as an effective index for environmental sustainability assessment.
In situ quantification of NO synthesis in a warm air glow discharge by WMS-based Mid-IR QCL absorption spectroscopy
Authors: WANG Chuanqi , QIAO Junjie , SONG Yijia , YANG Qi , WANG Dazhi , ZHANG Qingyuan , SHU Zhan , XIONG Qing 
Published: January 2022

Abstract
Nitric oxide (NO) is one of the most crucial products in the plasma-based nitrogen fixation process. In this work, in situ measurements were performed for quantifying the NO synthesis spatially in a warm air glow discharge, through the method of Mid-infrared quantum cascade laser absorption spectroscopy (QCL-AS). Two ro-vibrational transitions at 1900.076 cm−1 and 1900.517 cm−1 of the ground-state NO(X) were probed sensitively by the help of the wavelength modulation spectroscopy (WMS) approach to increase the signal/noise (S/N) level. The results show a decline trend of NO synthesis rate along the discharge channel from the cathode to the anode. However, from the point of energy efficiency, the cathode region is of significantly low energy efficiency of NO production. Severe disproportionality was found for the high energy consumption but low NO production in the region of cathode area, compared to that in the positive column zone. Further analysis demonstrates the high energy cost of NO production in the cathode region, is ascribed to the extremely high reduced electric field

E
/
N

therein not selectively preferable for the processes of vibrational excitation or dissociation of N2 and O2 molecules. This drags down the overall energy efficiency of NO synthesis by this typical warm air glow discharge, particularly for the ones with short electrode gaps. Limitations of further improving the energy cost of NO synthesis by variations of the discharge operation conditions, such as discharge current or airflow rate, imply other effective manners able to tune the energy delivery selectively to the NO formation process, are sorely needed.
MS-Decipher: a user-friendly proteome database search software with an emphasis on deciphering the spectra of O-linked glycopeptides
Authors: Mao Jiawei , Zhu He , Liu Luyao , Fang Zheng , Dong Mingming , Qin Hongqiang , Ye Mingliang 
Published: January 2022

Abstract

Motivation
The interpretation of mass spectrometry (MS) data is a crucial step in proteomics analysis, and the identification of post-translational modifications (PTMs) is vital for the understanding of the regulation mechanism of the living system. Among various PTMs, glycosylation is one of the most diverse ones. Though many search engines have been developed to decipher proteomic data, some of them are difficult to operate and have poor performance on glycoproteomic datasets compared to advanced glycoproteomic software.

Results
To simplify the analysis of proteomic datasets, especially O-glycoproteomic datasets, here, we present a user-friendly proteomic database search platform, MS-Decipher, for the identification of peptides from MS data. Two scoring schemes can be chosen for peptide-spectra matching. It was found that MS-Decipher had the same sensitivity and confidence in peptide identification compared to traditional database searching software. In addition, a special search mode, O-Search, is integrated into MS-Decipher to identify O-glycopeptides for O-glycoproteomic analysis. Compared with Mascot, MetaMorpheus and MSFragger, MS-Decipher can obtain about 139.9%, 48.8% and 6.9% more O-glycopeptide-spectrum matches. A useful tool is provided in MS-Decipher for the visualization of O-glycopeptide-spectra matches. MS-Decipher has a user-friendly graphical user interface, making it easier to operate. Several file formats are available in the searching and validation steps. MS-Decipher is implemented with Java, and can be used cross-platform.

Availability and implementation
MS-Decipher is freely available at https://github.com/DICP-1809/MS-Decipher for academic use. For detailed implementation steps, please see the user guide.

Supplementary information
Supplementary data are available at Bioinformatics online.
ProteinBERT: a universal deep-learning model of protein sequence and function
Authors: Brandes Nadav , Ofer Dan , Peleg Yam , Rappoport Nadav , Linial Michal 
Published: January 2022

Abstract

Summary
Self-supervised deep language modeling has shown unprecedented success across natural language tasks, and has recently been repurposed to biological sequences. However, existing models and pretraining methods are designed and optimized for text analysis. We introduce ProteinBERT, a deep language model specifically designed for proteins. Our pretraining scheme combines language modeling with a novel task of Gene Ontology (GO) annotation prediction. We introduce novel architectural elements that make the model highly efficient and flexible to long sequences. The architecture of ProteinBERT consists of both local and global representations, allowing end-to-end processing of these types of inputs and outputs. ProteinBERT obtains near state-of-the-art performance, and sometimes exceeds it, on multiple benchmarks covering diverse protein properties (including protein structure, post-translational modifications and biophysical attributes), despite using a far smaller and faster model than competing deep-learning methods. Overall, ProteinBERT provides an efficient framework for rapidly training protein predictors, even with limited labeled data.

Availability and implementation
Code and pretrained model weights are available at https://github.com/nadavbra/protein_bert.

Supplementary information
Supplementary data are available at Bioinformatics online.
Benchmarking the empirical accuracy of short-read sequencing across theM. tuberculosisgenome
Authors: Marin Maximillian , Vargas Roger , Harris Michael , Jeffrey Brendan , Epperson L Elaine , Durbin David , Strong Michael , Salfinger Max , Iqbal Zamin , Akhundova Irada , Vashakidze Sergo , Crudu Valeriu , Rosenthal Alex , Farhat Maha Reda 
Published: January 2022

AbstractMotivationShort-read whole-genome sequencing (WGS) is a vital tool for clinical applications and basic research. Genetic divergence from the reference genome, repetitive sequences and sequencing bias reduces the performance of variant calling using short-read alignment, but the loss in recall and specificity has not been adequately characterized. To benchmark short-read variant calling, we used 36 diverse clinical Mycobacterium tuberculosis (Mtb) isolates dually sequenced with Illumina short-reads and PacBio long-reads. We systematically studied the short-read variant calling accuracy and the influence of sequence uniqueness, reference bias and GC content.ResultsReference-based Illumina variant calling demonstrated a maximum recall of 89.0% and minimum precision of 98.5% across parameters evaluated. The approach that maximized variant recall while still maintaining high precision (&lt;99%) was tuning the mapping quality filtering threshold, i.e. confidence of the read mapping (recall = 85.8%, precision = 99.1%, MQ ≥ 40). Additional masking of repetitive sequence content is an alternative conservative approach to variant calling that increases precision at cost to recall (recall = 70.2%, precision = 99.6%, MQ ≥ 40). Of the genomic positions typically excluded for Mtb, 68% are accurately called using Illumina WGS including 52/168 PE/PPE genes (34.5%). From these results, we present a refined list of low confidence regions across the Mtb genome, which we found to frequently overlap with regions with structural variation, low sequence uniqueness and low sequencing coverage. Our benchmarking results have broad implications for the use of WGS in the study of Mtb biology, inference of transmission in public health surveillance systems and more generally for WGS applications in other organisms.Availability and implementationAll relevant code is available at https://github.com/farhat-lab/mtb-illumina-wgs-evaluation.Supplementary informationSupplementary data are available at Bioinformatics online.
Sirt1 attenuates astrocyte activation via modulating Dnajb1 and chaperone-mediated autophagy after closed head injury
Authors: Zhang Zhuo , Zhang Xu , Wu Xin , Zhang Yan , Lu Jie , Li Dan 
Published: January 2022

Abstract
Our previous study indicates that Silent information regulator 1 (Sirt1) is involved in macroautophagy by upregulating light chain 3 (LC3) expression in astrocyte to exert a neuroprotective effect. Chaperon-mediated autophagy (CMA), another form of autophagy, is also upregulated after brain injury. However, little is known about the role of Sirt1 in regulation of the CMA. In the present study, an in vivo model of closed head injury (CHI) and an in vitro model of primary cortical astrocyte stimulated with interleukin-1β were employed to mimic the astrocyte activation induced by traumatic brain injury. Lentivirus carrying target complementary DNA (cDNA) or short hairpin RNA (shRNA) sequence was used to overexpress Sirt1 or knockdown DnaJ heat shock protein family member B1 (Dnajb1) (a molecular chaperone). We found that Sirt1 overexpression ameliorated neurological deficits, reduced tissue loss, and attenuated astrocyte activation after CHI, which was reversed by Dnajb1-shRNA administration. The upregulation of CMA activity induced by CHI in vivo and in vitro was inhibited after Dnajb1 knockdown. Sirt1 potently promoted CMA activity via upregulating Dnajb1 expression. Mechanically, Sirt1 could interact with Dnajb1 and modulate the deacetylation and ubiquitination of Dnajb1. These findings collectively suggest that Sirt1 plays a protective role against astrocyte activation, which may be associated with the regulation of the CMA activity via modulating the deacetylation and ubiquitination of Dnajb1 after CHI.
Impact of Biannual Mass Azithromycin Treatment on Enteropathogen Carriage in Children &lt;5 Years Old in Niger
Authors: Platts-Mills James A , Ayoub Elias G , Zhang Jixian , McQuade Elizabeth T Rogawski , Arzika Ahmed M , Maliki Ramatou , Abdou Amza , Keenan Jeremy D , Lietman Thomas M , Liu Jie , Houpt Eric R 
Published: January 2022

Abstract
We analyzed samples obtained at baseline and 24 months in a mass azithromycin administration trial in Niger using quantitative polymerase chain reaction. In villages randomized to azithromycin, Shigella was the only pathogen reduced at 24 months (prevalence ratio, 0.36 [95% confidence interval: .17–.79]; difference in log quantity, −.42 [−.75 to −.10]).
Detailed Transcriptional Landscape of Peripheral Blood Points to Increased Neutrophil Activation in Treatment-Naïve Inflammatory Bowel Disease
Authors: Juzenas Simonas , Hübenthal Matthias , Lindqvist Carl Mårten , Kruse Robert , Steiert Tim Alexander , Degenhardt Frauke , Schulte Dominik , Nikolaus Susanna , Zeissig Sebastian , Bergemalm Daniel , Almer Sven , Hjortswang Henrik , Bresso Francesca ,   SIC IBD Working Group, Strüning Nina , Kupcinskas Juozas , Keller Andreas , Lieb Wolfgang , Rosenstiel Philip , Schreiber Stefan , D’Amato Mauro , Halfvarson Jonas , Hemmrich-Stanisak Georg , Franke Andre 
Published: January 2022

AbstractBackground and AimsInflammatory bowel disease [IBD] is a chronic relapsing disorder of the gastrointestinal tract, which generally manifests as Crohn’s disease [CD] or ulcerative colitis [UC]. These subtypes are heterogeneous in terms of disease location and histological features, while sharing common clinical presentation, genetic associations and, thus, common immune regulatory pathways.MethodsUsing miRNA and mRNA coupled transcriptome profiling and systems biology approaches, we report a comprehensive analysis of blood transcriptomes from treatment-naïve [n = 110] and treatment-exposed [n = 177] IBD patients as well as symptomatic [n = 65] and healthy controls [n = 95].ResultsBroadly, the peripheral blood transcriptomes of CD and UC patients were similar. However, there was an extensive gene deregulation in the blood of IBD patients, while only a slight deregulation in symptomatic controls, when compared with healthy controls. The deregulated mRNAs and miRNAs are mainly involved in the innate immunity and are especially enriched in neutrophil activation-related pathways. Oxidative phosphorylation and neutrophil activation-related modules were found to be differentially co-expressed among treatment-naïve IBD as compared to healthy controls. In the deregulated neutrophil activation-related co-expression module, IL1B was identified as the central gene. Levels of co-expression among IL1B and chemosensing receptor [CXCR1/2 and FPR1/2] genes were reduced in the blood of IBD patients when compared with healthy controls.ConclusionsImmune dysregulation seen in peripheral blood transcriptomes of treatment-naïve IBD patients is mainly driven by neutrophil activation.
IL-23 Blockade in Anti-TNF Refractory IBD: From Mechanisms to Clinical Reality
Authors: Atreya Raja , Neurath Markus F 
Published: January 2022

Abstract
Increasing insights into the immunopathogenesis of inflammatory bowel diseases [IBD] have led to the advent of targeted therapies that inhibit crucial mediators of the inflammatory process, thereby widening our available therapeutic armamentarium. Anti-tumour necrosis factor [anti-TNF] agents are still a mainstay of our therapeutic endeavours and the introduction of corresponding biosimilars has further widened their use. Nevertheless, only a subgroup of treated patients benefit from the initiated treatment and there is secondary non-response in the course of therapy. Initiation of subsequent therapy often poses a challenge to the treating physician, as non-response to primary anti-TNF treatment generally characterizes a patient group that is more treatment-resistant, which may be due to the immunological impregnation by prior anti-TNF exposure. At present, there is currently no guidance for the most appropriate second-line therapy after anti-TNF failure. Here, we review the efficacy of secondary biological therapy in anti-TNF-treated patients. We focus on and assess available clinical trial data of the emerging substance class of IL-23p19 inhibitors, which have demonstrated remarkable efficacy not only in anti-TNF-naïve but also refractory patients. We present molecular mechanisms that drive IL-23-mediated resistance to ongoing anti-TNF therapy and discuss the dynamic fluidity of the mucosal cytokine network in the course of therapy that perpetuates the mucosal inflammatory reaction. Translation of these findings into clinical practice might finally lead to initiation of the most appropriate therapy at the right time of the individual disease course, which would have important implications for the patient’s probability of response to treatment.
Comparative Insecticide Application Techniques (Micro-Sprinkler) Against Drosophila suzukii Matsumura (Diptera: Drosophilidae) in Highbush Blueberry
Authors: Mermer Serhan , Tait Gabriella , Pfab Ferdinand , Mirandola Enrico , Bozaric Aleksandar , Thomas Canessa D , Moeller Maxwell , Oppenheimer Katherine G , Xue Lan , Wang Lu , Walton Vaughn M 
Published: January 2022

Abstract
Drosophila suzukii (Matsumura), spotted-wing drosophila, is a major pest in small fruit crops including highbush blueberry. Controlling D. suzukii is challenging and chemical control is the main method to manage D. suzukii populations. Growers have expressed interest in using micro-sprinklers as an alternative method to apply insecticides. The current study aimed to evaluate if insecticide applications using micro-sprinklers can be used as an alternative method to protect the fruit from D. suzukii egg-laying. Modeling was used as an additional tool to parameterize the relative insecticide efficacy on oviposition. Field measurements of different treatments were conducted over periods of eleven days on commercial-standard highbush blueberry. Cyantraniliprole and spinetoram were applied using both a micro-sprinkler and a backpack sprayer. Treatments of Chromobacterium subtsugae and zeta-cypermethrin were only applied using a backpack sprayer. Both cyantraniliprole and spinetoram treatments resulted in moderate suppression of D. suzukii egg-laying. No statistical significance was found between micro-sprinkler and backpack sprayer applications for these two insecticides. Zeta-cypermethrin treatments using a backpack sprayer resulted in the most significant suppression of D. suzukii egg-laying over eleven days, while C. subtsugae was less effective at preventing D. suzukii egg-laying. Modeling simulations estimate the impact of the control methods on D. suzukii populations dynamics and simulation outputs indicated that backpack sprayers reduced D. suzukii populations at more pronounced levels compared to micro-sprinkler applications. The present study indicates that there is an underlying value of micro-sprinkler systems as an alternative and rapid spray application technique to help suppress D. suzukii pest populations during high-pressure periods in highbush blueberry production.
SGLT-2 inhibitors and cardiovascular outcomes in patients with and without a history of heart failure: a systematic review and meta-analysis
Authors: Razuk Victor , Chiarito Mauro , Cao Davide , Nicolas Johny , Pivato Carlo A , Camaj Anton , Power David , Beerkens Frans , Jones Davis , Alter Aviv , Mathew Alvin , Spirito Alessandro , Contreras Johanna P , Dangas George D , Mehran Roxana 
Published: January 2022

Abstract

Aims
Sodium–glucose cotransporter 2 (SGLT-2) inhibitors have cardiovascular (CV) benefits in patients with heart failure with reduced ejection fraction (HFrEF). Whether these medications improve CV outcomes irrespective of heart failure history or left ventricular ejection fraction (LVEF) in HFrEF remains unknown.

Methods and results
All randomized, placebo-controlled trials of SGLT-2 inhibitors reporting similar CV outcomes were searched in PubMed from 1 January 2010 to 1 October 2021. The primary outcome was the composite of hospitalization for heart failure or CV death. Secondary outcomes included all-cause mortality. Pooled hazard ratios (HRs) and 95% confidence intervals (CIs) were used as effect estimates and calculated with a random-effects model. Data from 11 trials and a total of 66 957 patients (n = 36 758 SGLT-2 group, n = 30 199 placebo group) were included. SGLT-2 inhibitors reduced the risk of hospitalization for heart failure or CV death in patients with (HR 0.76, 95% CI 0.71–0.80) and without (HR 0.76, 95% CI 0.68–0.86; Pinteraction = 0.69) heart failure. Patients with (HR 0.87, 95% CI 0.80–0.95) and without (HR 0.84, 95% CI 0.73–0.95; Pinteraction = 0.67) heart failure treated with SGLT-2 inhibitors had a reduction in all-cause mortality. Reduction in the primary outcome was consistently observed in HFrEF patients with (HR 0.68, 95% CI 0.59–0.78) and without (HR 0.84, 95% CI 0.71–0.99; Pinteraction = 0.13) severely reduced LVEF, and in heart failure with preserved ejection fraction patients (HR 0.80, 95% CI 0.70–0.92; Pinteraction = 0.65).

Conclusion
SGLT-2 inhibitors improved CV outcomes irrespective of heart failure history or type, and severity of LVEF reduction.
Transitional Inequality Offset: Educational Expansion and Inequality of Educational Opportunity in European Countries between 2000 and 2018
Authors: Katrňák Tomáš , Hubatková Barbora 
Published: January 2022

Abstract
Educational expansion has been taking place in European countries since 2000. We address the relationship between this educational expansion and the inequality of educational opportunity (IEO) by educational origin. We analyse the European Social Survey data from 20 European countries over five rounds (2002, 2006, 2010, 2014, and 2018). Our analysis is restricted to the 25–34 age groups. We use a multilevel sequential logit (MLSL) model for three hierarchical educational transitions (sequences), delimited by four International Standard Classification of Education (ISCED97) categories. We apply the MLSL model to decompose IEO in completed education into the educational origin effects on passing transitions and the structural effects (weights) connected with transitions. Our results show that educational expansion slightly weakens IEO in completed education, but this is far from being a situation in which IEO does not exist. IEO is maintained in educational transitions by transitional inequality offset. The effect of the weight of each transition takes over the educational origin effect on passing transitions and vice versa over educational expansion. Both these effects are maintained in balance; educational expansion changes primarily their ratio. This holds true until one of the transitions becomes mostly universal. After that, its contribution (weighted origin effect) to IEO in completed education begins to diminish.