bluuebunny/crossref_metadata_2025_split huggingface dataset:
Eddy current measurement in hollow conducting tube in electromagnetic forming process
Authors: Choudhary H. , Kolge T. , Kapoor R. , Sharma A. 
Published: June 2022

Abstract
Electromagnetic forming (EMF) is a high strain rate metal
deformation process that utilizes Lorentz force to expand or
compress the conducting tube. Stored electrostatic energy of
capacitor bank is discharged through solenoid coil which surrounds
the conducting tube. Capacitor bank and solenoid coil form a series
R-L-C circuit during current discharge through the coil and hence,
the coil current is damped sinusoidal. Coil current produces time
varying magnetic field which induces eddy current in conducting
tube. Interaction of eddy current in the tube and magnetic field in
air gap between tube and coil causes Lorentz force to expand or
compress the conducting tube. The eddy current is a vital parameter
in electromagnetic forming study and its measurement is almost
unfeasible owing to very few mm gap between coil and conducting
tube. Here we establish a novel method to determine the eddy current
in a cylindrical tube, using a superposition theorem, when a damped
sinusoidal current is passed through a finite solenoid coil. The
present study uses a Al-Mg alloy tube to demonstrate this method of
eddy current determination.
Cold neutron triple-axis spectrometer (Cold TAS) at HANARO
Authors: Hiraka H. , Ji S. 
Published: June 2022

Abstract
A cold neutron triple-axis spectrometer (Cold TAS) has been
installed in HANARO at the Korea Atomic Energy Research Institute,
South Korea. It has been designed for high-resolution
inelastic-neutron-scattering (INS) measurements of spin and lattice
dynamics using a neutron velocity selector (NVS) for incident cold
neutrons. We evaluated the wavelength resolution and harmonics
filtration of the NVS and verified the vertical focusing effects of
the pyrolytic-graphite crystal monochromator. The beam flux at the
sample position and the spectrometer resolution, which are key
factors in INS experiments, attained the typical TAS specification.
Finally, we exemplified INS spectra to show the current performance
of the high-resolution mode and magnetic-excitation measurements.
Data-driven quantification of nitrogen enrichment impact on Northern Hemisphere plant biomass
Authors: Liu Yongwen , Piao Shilong , Makowski David , Ciais Philippe , Gasser Thomas , Song Jian , Wan Shiqiang , Peñuelas Josep , Janssens Ivan A 
Published: June 2022

Abstract
The production of anthropogenic reactive nitrogen (N) has grown so much in the last century that quantifying the effect of N enrichment on plant growth has become a central question for carbon (C) cycle research. Numerous field experiments generally found that N enrichment increased site-scale plant biomass, although the magnitude of the response and sign varied across experiments. We quantified the response of terrestrial natural vegetation biomass to N enrichment in the Northern Hemisphere (>30° N) by scaling up data from 773 field observations (142 sites) of the response of biomass to N enrichment using machine-learning algorithms. N enrichment had a significant and nonlinear effect on aboveground biomass (AGB), but a marginal effect on belowground biomass. The most influential variables on the AGB response were the amount of N applied, mean biomass before the experiment, the treatment duration and soil phosphorus availability. From the machine learning models, we found that N enrichment due to increased atmospheric N deposition during 1993–2010 has enhanced total biomass by 1.1 ± 0.3 Pg C, in absence of losses from harvest and disturbances. The largest effect of N enrichment on plant growth occurred in northeastern Asia, where N deposition markedly increased. These estimates were similar to the range of values provided by state-of-the-art C–N ecosystem process models. This work provides data-driven insights into hemisphere-scale N enrichment effect on plant biomass growth, which allows to constrain the terrestrial ecosystem process model used to predict future terrestrial C storage.
Ruling Party Patronage, Brokerage, and Contestations at Urban Markets in Harare
Authors: Oosterom Marjoke , Gukurume Simbarashe 
Published: June 2022

ABSTRACT
This study contributes to debates on varieties of clientelism through an analysis of brokerage and ruling party patronage at urban markets in Harare, Zimbabwe. Urban markets are sites of contestation between the opposition-dominated city council and actors aligned with the ruling party, the Zimbabwe African National Union—Patriotic Front (ZANU-PF). Based on qualitative case study research at two designated markets, the article demonstrates how ruling party brokers are central to organizing patronage and political mobilization, thus sustaining authoritarian politics. While ruling party patronage is a deliberate strategy to control urban spaces, the article demonstrates how it is being negotiated. Factionalism within ZANU-PF shifted the power of brokers, and the lockdown enforced in response to the coronavirus disease 2019 pandemic in 2020 caused a rupture, offering the city council and opposition-aligned youth the opportunity to (re)claim control over vending spaces. This article contributes to debates on clientelism in authoritarian regime settings, by showing the imbrication of coercion and patronage in the role of the broker and demonstrating how patronage is organized vertically through brokerage. This study extends the study of clientelism beyond electoral politics, since brokers are not always politicians, but nonetheless are part of the systems of ruling party patronage.
Effects of sublethal single, simultaneous and sequential abiotic stresses on phenotypic traits of Arabidopsis thaliana
Authors: Morales Alejandro , de Boer Hugo J , Douma Jacob C , Elsen Saskia , Engels Sophie , Glimmerveen Tobias , Sajeev Nikita , Huber Martina , Luimes Mathijs , Luitjens Emma , Raatjes Kevin , Hsieh Chenyun , Teapal Juliane , Wildenbeest Tessa , Jiang Zhang , Pareek Ashwani , Singla-Pareek Sneh , Yin Xinyou , Evers Jochem , Anten Niels P R , van Zanten Martijn , Sasidharan Rashmi 
Published: June 2022

Abstract
Plant responses to abiotic stresses are complex and dynamic, and involve changes in different traits, either as the direct consequence of the stress, or as an active acclimatory response. Abiotic stresses frequently occur simultaneously or in succession, rather than in isolation. Despite this, most studies have focused on a single stress and single or few plant traits. To address this gap, our study comprehensively and categorically quantified the individual and combined effects of three major abiotic stresses associated with climate change (flooding, progressive drought and high temperature) on 12 phenotypic traits related to morphology, development, growth and fitness, at different developmental stages in four Arabidopsis thaliana accessions. Combined sublethal stresses were applied either simultaneously (high temperature and drought) or sequentially (flooding followed by drought). In total, we analysed the phenotypic responses of 1782 individuals across these stresses and different developmental stages. Overall, abiotic stresses and their combinations resulted in distinct patterns of effects across the traits analysed, with both quantitative and qualitative differences across accessions. Stress combinations had additive effects on some traits, whereas clear positive and negative interactions were observed for other traits: 9 out of 12 traits for high temperature and drought, 6 out of 12 traits for post-submergence and drought showed significant interactions. In many cases where the stresses interacted, the strength of interactions varied across accessions. Hence, our results indicated a general pattern of response in most phenotypic traits to the different stresses and stress combinations, but it also indicated a natural genetic variation in the strength of these responses. This includes novel results regarding the lack of a response to drought after submergence and a decoupling between leaf number and flowering time after submergence. Overall, our study provides a rich characterization of trait responses of Arabidopsis plants to sublethal abiotic stresses at the phenotypic level and can serve as starting point for further in-depth physiological research and plant modelling efforts.
riboCleaner: a pipeline to identify and quantify rRNA read contamination from RNA-seq data in plants
Authors: Huang Pu , Davis Erin , Cao Xia , Cameron Hunter J 
Published: June 2022

AbstractMotivationAnalysis of gene expression data can be crucial for elucidating biological relationships within living organisms. However, accurate quantification of gene expression relies directly upon the accuracy of the reference genome or transcriptome to which the expression data are mapped. Errors in gene annotation can lead to errors in the quantification of gene expression. One source of gene annotation error in eukaryotes arises from incorrect predictions of messenger RNA gene models within ribosomal DNA (rDNA) regions.ResultsHere, we provide examples of how the presence of false gene models in rDNA regions can result in a handful of genes appearing to contribute to &gt;50% of the total transcripts per million values of entire RNA-seq datasets. To this end, we have created riboCleaner, a bioinformatics pipeline designed to identify misannotated gene models in rDNA regions and quantify rRNA-derived reads in RNA-seq data. We also show the applicability of riboCleaner in several plant genome assemblies.Availability and implementationWe have implemented riboCleaner as a containerized Snakemake workflow. The workflow, instructions for building the container and other documentation are available at https://github.com/basf. The data underlying this article are available in GitHub at https://github.com/basf/riboCleaner. For convenience, a prebuilt Docker image containing riboCleaner is available at https://hub.docker.com/u/basfcontainers.Supplementary informationSupplementary data are available at Bioinformatics online.
Identifying interactions in omics data for clinical biomarker discovery using symbolic regression
Authors: Christensen Niels Johan , Demharter Samuel , Machado Meera , Pedersen Lykke , Salvatore Marco , Stentoft-Hansen Valdemar , Iglesias Miquel Triana 
Published: June 2022

AbstractMotivationThe identification of predictive biomarker signatures from omics and multi-omics data for clinical applications is an active area of research. Recent developments in assay technologies and machine learning (ML) methods have led to significant improvements in predictive performance. However, most high-performing ML methods suffer from complex architectures and lack interpretability.ResultsWe present the application of a novel symbolic-regression-based algorithm, the QLattice, on a selection of clinical omics datasets. This approach generates parsimonious high-performing models that can both predict disease outcomes and reveal putative disease mechanisms, demonstrating the importance of selecting maximally relevant and minimally redundant features in omics-based machine-learning applications. The simplicity and high-predictive power of these biomarker signatures make them attractive tools for high-stakes applications in areas such as primary care, clinical decision-making and patient stratification.Availability and implementationThe QLattice is available as part of a python package (feyn), which is available at the Python Package Index (https://pypi.org/project/feyn/) and can be installed via pip. The documentation provides guides, tutorials and the API reference (https://docs.abzu.ai/). All code and data used to generate the models and plots discussed in this work can be found in https://github.com/abzu-ai/QLattice-clinical-omics.Supplementary informationSupplementary material is available at Bioinformatics online.
Functional characterization of co-phosphorylation networks
Authors: Ayati Marzieh , Yılmaz Serhan , Chance Mark R , Koyuturk Mehmet 
Published: June 2022

AbstractMotivationProtein phosphorylation is a ubiquitous regulatory mechanism that plays a central role in cellular signaling. According to recent estimates, up to 70% of human proteins can be phosphorylated. Therefore, the characterization of phosphorylation dynamics is critical for understanding a broad range of biological and biochemical processes. Technologies based on mass spectrometry are rapidly advancing to meet the needs for high-throughput screening of phosphorylation. These technologies enable untargeted quantification of thousands of phosphorylation sites in a given sample. Many labs are already utilizing these technologies to comprehensively characterize signaling landscapes by examining perturbations with drugs and knockdown approaches, or by assessing diverse phenotypes in cancers, neuro-degerenational diseases, infectious diseases and normal development.ResultsWe comprehensively investigate the concept of ‘co-phosphorylation’ (Co-P), defined as the correlated phosphorylation of a pair of phosphosites across various biological states. We integrate nine publicly available phosphoproteomics datasets for various diseases (including breast cancer, ovarian cancer and Alzheimer’s disease) and utilize functional data related to sequence, evolutionary histories, kinase annotations and pathway annotations to investigate the functional relevance of Co-P. Our results across a broad range of studies consistently show that functionally associated sites tend to exhibit significant positive or negative Co-P. Specifically, we show that Co-P can be used to predict with high precision the sites that are on the same pathway or that are targeted by the same kinase. Overall, these results establish Co-P as a useful resource for analyzing phosphoproteins in a network context, which can help extend our knowledge on cellular signaling and its dysregulation.Availability and implementationgithub.com/msayati/Cophosphorylation. This research used the publicly available datasets published by other researchers as cited in the manuscript.Supplementary informationSupplementary data are available at Bioinformatics online.
FMRP-dependent production of large dosage-sensitive proteins is highly conserved
Authors: Flanagan Keegan , Baradaran-Heravi Alireza , Yin Qi , Dao Duc Khanh , Spradling Allan C , Greenblatt Ethan J 
Published: June 2022

Abstract
Mutations in FMR1 are the most common heritable cause of autism spectrum disorder. FMR1 encodes an RNA-binding protein, FMRP, which binds to long, autism-relevant transcripts and is essential for normal neuronal and ovarian development. In contrast to the prevailing model that FMRP acts to block translation elongation, we previously found that FMRP activates the translation initiation of large proteins in Drosophila oocytes. We now provide evidence that FMRP-dependent translation is conserved and occurs in the mammalian brain. Our comparisons of the mammalian cortex and Drosophila oocyte ribosome profiling data show that translation of FMRP-bound mRNAs decreases to a similar magnitude in FMRP-deficient tissues from both species. The steady-state levels of several FMRP targets were reduced in the Fmr1 KO mouse cortex, including a ∼50% reduction of Auts2, a gene implicated in an autosomal dominant autism spectrum disorder. To distinguish between effects on elongation and initiation, we used a novel metric to detect the rate-limiting ribosome stalling. We found no evidence that FMRP target protein production is governed by translation elongation rates. FMRP translational activation of large proteins may be critical for normal human development, as more than 20 FMRP targets including Auts2 are dosage sensitive and are associated with neurodevelopmental disorders caused by haploinsufficiency.
Range Expansion of Native and Invasive Ticks: A Looming Public Health Threat
Authors: Molaei Goudarz , Eisen Lars M , Price Keith J , Eisen Rebecca J 
Published: June 2022

Abstract
Native and invasive tick species pose a serious public health concern in the United States. Range expansion of several medically important tick species has resulted in an increasing number of communities at risk for exposure to ticks and tick-borne pathogens.
Evaluation of Recombinant Live-Attenuated Respiratory Syncytial Virus (RSV) Vaccines RSV/ΔNS2/Δ1313/I1314L and RSV/276 in RSV-Seronegative Children
Authors: Cunningham Coleen K , Karron Ruth A , Muresan Petronella , Kelly Matthew S , McFarland Elizabeth J , Perlowski Charlotte , Libous Jennifer , Oliva Jennifer , Jean-Philippe Patrick , Moye Jack , Schappell Elizabeth , Barr Emily , Rexroad Vivian , Johnston Benjamin , Chadwick Ellen G , Cielo Mikhaela , Paul Mary , Deville Jaime G , Aziz Mariam , Yang Lijuan , Luongo Cindy , Collins Peter L , Buchholz Ursula J ,   the International Maternal Pediatric Adolescent AIDS Clinical Trials (IMPAACT) 2018 Study Team
Published: June 2022

Abstract

Background
This United States-based study compared 2 candidate vaccines: RSV/ΔNS2/Δ1313/I1314L, attenuated by NS2 gene-deletion and temperature-sensitivity mutation in the polymerase gene; and RSV/276, attenuated by M2-2 deletion.

Methods
RSV-seronegative children aged 6–24 months received RSV/ΔNS2/Δ1313/I1314L (106 plaque-forming units [PFU]), RSV/276 (105 PFU), or placebo intranasally. Participants were monitored for vaccine shedding, reactogenicity, and RSV serum antibodies, and followed over the subsequent RSV season.

Results
Enrollment occurred September 2017 to October 2019. During 28 days postinoculation, upper respiratory illness and/or fever occurred in 64% of RSV/ΔNS2/Δ1313/I1314L, 84% of RSV/276, and 58% of placebo recipients. Symptoms were generally mild. Cough was more common in RSV/276 recipients than RSV/ΔNS2/Δ1313/I1314L (48% vs 12%; P = .012) or placebo recipients (17%; P = .084). There were no lower respiratory illness or serious adverse events. Eighty-eight and 96% of RSV/ΔNS2/Δ1313/I1314L and RSV/276 recipients were infected with vaccine (shed vaccine and/or had ≥4-fold rises in RSV antibodies). Serum RSV-neutralizing titers and anti-RSV F IgG titers increased ≥4-fold in 60% and 92% of RSV/ΔNS2/Δ1313/I1314L and RSV/276 vaccinees, respectively. Exposure to community RSV during the subsequent winter was associated with strong anamnestic RSV-antibody responses.

Conclusions
Both vaccines had excellent infectivity and were well tolerated. RSV/276 induced an excess of mild cough. Both vaccines were immunogenic and primed for strong anamnestic responses.

Clinical Trials Registration
NCT03227029 and NCT03422237.
Mobile Burn Disaster Response Teams: A Scoping Review
Authors: Fuchko Danielle , King-Shier Kathryn , Gabriel Vincent 
Published: June 2022

AbstractThe resources needed to deliver modern burn care may be overwhelmed by mass casualty disasters. In 2021, the World Health Organization (WHO) recommended that countries prepare teams of deployable burn experts to assist with responding to a mass casualty disaster. The aim of this scoping review was to identify existing literature regarding burn mobile response team organization, describe the reported effectiveness of these teams, identify challenges in adopting the WHO recommendations, and consider how the recommendations may be reconsidered. We conducted a scoping review of all literature types published up to January 2022. Searches of MEDLINE, EMBASE, Scopus, and CINAHL databases were conducted to identify reports informing or reporting the use of mobile burn care specialty teams that respond to events resulting in multiple burn-injured victims, including pediatric victims and military response to civilian events. Of 6132 identified reports, 26 publications were reviewed. Three types of mobile burn response teams were identified: (1) teams organized by burn care networks, (2) government-organized medical disaster teams with burn-specific experts, and (3) the U.S. Army Burn Flight Team. Teams have responded to events such as terrorist attacks by providing specialized burn supplies and personnel. These teams have demonstrated expert triage and stabilization advantages but are limited by the number of deployable specialists. Although the WHO recommends increasing the number of mobile burn response teams available around the world, few countries have implemented this recommendation. A hybrid model where responders on scene communicate with burn center experts to manage triage may address these challenges.
The Transposition Rate Has Little Influence on the Plateauing Level of the P-element
Authors: Kofler Robert , Nolte Viola , Schlötterer Christian 
Published: June 2022

AbstractThe popular trap model assumes that the invasions of transposable elements (TEs) in mammals and invertebrates are stopped by piRNAs that emerge after insertion of the TE into a piRNA cluster. It remains, however, still unclear which factors influence the dynamics of TE invasions. The activity of the TE (i.e., transposition rate) is one frequently discussed key factor. Here we take advantage of the temperature-dependent activity of the P-element, a widely studied eukaryotic TE, to test how TE activity affects the dynamics of a TE invasion. We monitored P-element invasion dynamics in experimental Drosophila simulans populations at hot and cold culture conditions. Despite marked differences in transposition rates, the P-element reached very similar copy numbers at both temperatures. The reduction of the insertion rate upon approaching the copy number plateau was accompanied by similar amounts of piRNAs against the P-element at both temperatures. Nevertheless, we also observed fewer P-element insertions in piRNA clusters than expected, which is not compatible with a simple trap model. The ping-pong cycle, which degrades TE transcripts, becomes typically active after the copy number plateaued. We generated a model, with few parameters, that largely captures the observed invasion dynamics. We conclude that the transposition rate has at the most only a minor influence on TE abundance, but other factors, such as paramutations or selection against TE insertions are shaping the TE composition.
Cellular-level distribution of manganese in Macadamia integrifolia, M. ternifolia, and M. tetraphylla from Australia
Authors: Abubakari Farida , Fernando Denise R , Nkrumah Philip Nti , Harris Hugh H , Erskine Peter D , van der Ent Antony 
Published: June 2022

Abstract
Macadamia integrifolia and M. tetraphylla, unlike M. ternifolia, are known for their edible nuts. All three species over-accumulate the trace metal nutrient manganese (Mn) in their shoots. This study seeks to examine tissue- and cellular-level distribution of Mn and other plant nutrients in the three Macadamia species. The distribution of Mn, calcium, iron, and potassium were investigated in whole leaves and cross-sections of roots, petioles, and leaves using synchrotron-based X-ray fluorescence microscopy (XFM) in M. integrifolia, M. tetraphylla, and M. ternifolia. The results show Mn sequestration primarily in the leaf and midrib palisade mesophyll cells of all three species. Leaf interveinal regions, root cortical cells, and phloem cells were also found to be Mn loaded. The current study confirms earlier findings but further reveals that Mn is concentrated in the vacuoles of mesophyll cells owing to the exceptional resolution of the synchrotron XFM data, and the fact that fresh hydrated samples were used. New insights gained here into Mn compartmentalization in these highly Mn-tolerant Macadamias expand knowledge about potentially toxic over-accumulation of an essential micronutrient, which ultimately stands to inform strategies around farming edible species in particular.