bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intraindividual Consistency of Iodine Concentration in Dual-Energy Computed Tomography of the Chest and Abdomen
Authors: Zopfs David , Reimer Robert Peter , Sonnabend Kristina , Rinneburger Miriam , Hentschke Clemens M. , Persigehl Thorsten , Lennartz Simon , Große Hokamp Nils 
Published: September 2020

Objectives
Dual-energy computed tomography (DECT)–derived quantification of iodine concentration (IC) is increasingly used in oncologic imaging to characterize lesions and evaluate treatment response. However, only limited data are available on intraindividual consistency of IC and its variation. This study investigates the longitudinal reproducibility of IC in organs, vessels, and lymph nodes in a large cohort of healthy patients who underwent repetitive DECT imaging.

Materials and Methods
A total of 159 patients, who underwent a total of 469 repetitive (range, 2–4), clinically indicated portal-venous phase DECT examinations of the chest and abdomen, were retrospectively included. At time of imaging, macroscopic tumor burden was excluded by follow-up imaging (≥3 months). Iodine concentration was measured region of interest-based (N = 43) in parenchymatous organs, vessels, lymph nodes, and connective tissue. Normalization of IC to the aorta and to the trigger delay as obtained from bolus tracking was performed. For statistical analysis, intraclass correlation coefficient and modified variation coefficient (MVC) were used to assess intraindividual agreement of IC and its variation between different time points, respectively. Furthermore, t tests and analysis of variance with Tukey-Kramer post hoc test were used.

Results
The mean intraclass correlation coefficient over all regions of interest was good to excellent (0.642–0.936), irrespective of application of normalization or the normalization technique. Overall, MVC ranged from 1.8% to 25.4%, with significantly lower MVC in data normalized to the aorta (5.8% [1.8%–15.8%]) in comparison with the MVC of not normalized data and data normalized to the trigger delay (P < 0.01 and P = 0.04, respectively).

Conclusions
Our study confirms intraindividual, longitudinal variation of DECT-derived IC, which varies among vessels, lymph nodes, organs, and connective tissue, following different perfusion characteristics; normalizing to the aorta seems to improve reproducibility when using a constant contrast media injection protocol.
Alternatives to Gadolinium-Based Contrast Agents
Authors: Tweedle Michael F. 
Published: September 2020

Abstract
Gadolinium-based contrast agents have been used in hundreds of millions of patients in the past 30 years, with an exemplary safety record. However, assumptions made at their inception have been recently challenged, rekindling innovation efforts. This critical review outlines the motivations, technical obstacles, problems, and the most recent published progress toward the creation of alternatives to the existing gadolinium-based contrast agent.
Ambroxol Hydrochloride Inhibits the Interaction between Severe Acute Respiratory Syndrome Coronavirus 2 Spike Protein’s Receptor Binding Domain and Recombinant Human ACE2
Authors: Olaleye Omonike A. , Kaur Manvir , Onyenaka Collins C. 
Published: September 2020

AbstractSevere Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), enters the host cells through two main pathways, both involving key interactions between viral envelope-anchored spike glycoprotein of the novel coronavirus and the host receptor, angiotensin-converting enzyme 2 (ACE2). To date, SARS-CoV-2 has infected up to 26 million people worldwide; yet, there is no clinically approved drug or vaccine available. Therefore, a rapid and coordinated effort to re-purpose clinically approved drugs that prevent or disrupt these critical entry pathways of SARS-CoV-2 spike glycoprotein interaction with human ACE2, could potentially accelerate the identification and clinical advancement of prophylactic and/or treatment options against COVID-19, thus providing possible countermeasures against viral entry, pathogenesis and survival. Herein, we discovered that Ambroxol hydrochloride (AMB), and its progenitor, Bromhexine hydrochloride (BHH), both clinically approved drugs are potent effective modulators of the key interaction between the receptor binding domain (RBD) of SARS-CoV-2 spike protein and human ACE2. We also found that both compounds inhibited SARS-CoV-2 infection-induced cytopathic effect at micromolar concentrations. Therefore, in addition to the known TMPRSS2 activity of BHH; we report for the first time that the BHH and AMB pharmacophore has the capacity to target and modulate yet another key protein-protein interaction essential for the two known SARS-CoV-2 entry pathways into host cells. Altogether, the potent efficacy, excellent safety and pharmacologic profile of both drugs along with their affordability and availability, makes them promising candidates for drug repurposing as possible prophylactic and/or treatment options against SARS-CoV-2 infection.
Perceptions and Attitudes of Prison Staff towards ADHD – double jeopardy for inmates affected
Authors: Buadze Anna , Friedl Nadine , Schleifer Roman , Young Susan , Schneeberger Andres , Liebrenz Michael 
Published: September 2020

AbstractBackgroundAttention deficit hyperactivity disorder (ADHD) is a neurodevelopmental disorder that is associated with risk-taking behaviors, poor self-control and interpersonal difficulties. Affected individuals have an increased probability of involvement in the criminal justice system, contributing to a higher rate of arrest and imprisonment compared with the general population. Current data on the prevalence of ADHD among prisoners reports rates of 26%, but finds them inadequately treated.AimsBecause prison staff play a central role in the identification of inmates with mental disorders, they could well be key to improving provision of care. There is however little knowledge of the conceptions, perceptions and attitudes of prison staff towards ADHD. Such information could help to identify starting points for awareness training and to further implementation of specific ADHD treatment.MethodsTo bridge this gap, we employed a qualitatively driven mixed methods design combining qualitative data collection in the form of narrative interviews with 19 prison staff from a Swiss correctional facility with quantitative data collection in the form of a survey that included the Attitudes Toward Prisoners scale. The interviews were analyzed with QSR NVIVO 11 and a qualitative content analysis approach was used to evaluate findings.ResultsPrison staff were generally aware of ADHD and its symptomology, believed it to a be “real”, but “fashionable” disorder and favored hereditary-genetic or biological explanatory models for its development. They viewed inmates with ADHD rather negatively, as complicating correctional efforts, perceived them as sticking out, as tying up more resources and as frequently being involved in confrontations. Our findings suggest that difficulties in pragmatic aspects of communication and language comprehension may be perceived “as not listening or following instructions” creating additional tensions. Consequently, inmates with ADHD are more often exposed to disciplinary sanctions, such as solitary confinement - an intervention deemed “necessary” by staff. Therefore, staff training on ADHD might need to cover evidence on adverse effects. Non-pharmacological interventions for treatment were preferred and considered to be highly efficacious. Skepticism towards pharmacological treatment prevailed, even when benefits from stimulant medication were described. Acceptance of multimodal treatment among prison staff may require customized strategies.
Comorbidities and Susceptibility to COVID-19: A Generalized Gene Set Meta-Analysis Approach
Authors: Beckman MF , Igba CK , Mougeot FB , Mougeot J-LC 
Published: September 2020

ABSTRACTBackgroundThe COVID-19 pandemic has led to over 820,000 deaths for almost 24 million confirmed cases worldwide, as of August 27th, 2020, per WHO report. Risk factors include pre-existing conditions such as cancer, cardiovascular disease, diabetes, obesity, and cancer. There are currently no effective treatments. Our objective was to complete a meta-analysis to identify comorbidity-associated single nucleotide polymorphisms (SNPs), potentially conferring increased susceptibility to SARS-CoV-2 infection using a computational approach.ResultsSNP datasets were downloaded from publicly available GWAS catalog for 141 of 258 candidate COVID-19 comorbidities. Gene-level SNP analysis was performed to identify significant pathways by using MAGMA program. SNP annotation program was used to analyze MAGMA-identified genes. COVID-19 comorbidities from six disease categories were found to have significant associated pathways, which were validated by Q-Q plots (p<0.05). The top 250 human mRNA gene expressions for SNP-affected pathways, extracted from publicly accessible gene expression profiles, were evaluated for significant pathways. Protein-protein interactions of identified differentially expressed genes, visualized with STRING program, were significant (p<0.05). Gene interaction networks were found to be relevant to SARS and influenza pathogenesis.ConclusionPathways potentially affected by or affecting SARS-CoV-2 infection were identified in underlying medical conditions likely to confer susceptibility and/or severity to COVID-19. Our findings have implications in COVID-19 treatment development.
Mathematical Modelling of the Spread of the Coronavirus under Social Restrictions
Authors: Al-arydah Mo’tassem , Berhe Hailay Weldegiorgis , Dib Khalid , Madhu Kalyanasundaram 
Published: September 2020

AbstractBackgroundCOVID-19 has affected most countries and declared as pandemic. Most countries have implemented some social restrictions to control it. In this work we will use mathematical modelling to assess the current social restrictions in controlling the spread of the disease.MethodsWe formulate a simple susceptible-infectious-recovery (SIR) model to describe the spread of the coronavirus under social restrictions. The transmission rate in this model is considered variable to catch social restrictions impact. We analyze this model, then fit the model to 160 days induced death data in Italy, Iran, USA, Germany, France, India, Spain and China. we estimate some factors that help in understanding not only the spread of the disease but also assess the current social restriction in controlling this disease.ResultsWe find a formula for the basic reproduction function (R(t)) and the maximum number of daily infected people. Then estimate the model’s parameters with 95% confidence intervals in these countries. We notice that the model has excellent fit to the disease death data in all considered countries except Iran. The percentage of disease death estimated by the model in Germany and France are 3.8% and 1.2% respectively, which are close to reported percentages values. Finally, we estimate the time, after first reported death, spent under social restrictions to reduce the basic reproduction function (R(t)) to one unit. The times to do that in Italy, USA, Germany, France, Spain and China are 40, 50, 34,58, 31, and 15 days respectively. However, the Indian social restrictions in the 160 days were not enough to reach R(t) = 1.ConclusionThe transmission rate is between 0.1035–1.6076 and recovery rate is between 0–0.2456. The disease death rates calculated for Germany and France are more realistic than others with average value 0.0023. Extending the same social restrictions for enough time could control the disease in Italy, USA, Germany, France, India, Spain and China. While, more social restrictions are needed to control the disease in India.
COVID-19 Mortality in Cancer Patients: A Report from a Tertiary Cancer Centre in India
Authors: Mehta Anurag , Vasudevan Smreti , Parkash Anuj , Sharma Anurag , Vashist Tanu , Krishna Vidya 
Published: September 2020

AbstractBackgroundCancer patients, especially those receiving cytotoxic therapy are assumed to have a higher probability of death from COVID-19. We have conducted this study to identify the Case Fatality Rate (CFR) in cancer patients with COVID-19 and have explored the relationship of various clinical factors to mortality in our patient cohort.MethodsAll active cancer cases presented to the hospital from 8th June to 24 August 2020, and developed symptoms/ radiological features suspicious of COVID-19 were tested by Real-time polymerase chain reaction assay and/or cartridge-based nucleic acid amplification test from a combination of naso-oropharyngeal swab for SARS-CoV-2. Clinical data, treatment details, and outcomes were assessed from the medical records.ResultsOf the total 3101 cancer patients admitted to the hospital, 1088 patients were tested and 186 patients were positive for SARS-CoV-2. The CFR in the cohort was 27/186 (14.5%). Univariate analysis showed that the risk of death was significantly associated with the presence of comorbidities [OR: 2.68; (95%CI: 1.13–6.32); P = 0.02], multiple comorbidities [OR: 3.01; (95%CI: 1.02–9.07); P = 0.046 for multiple vs. single], and the severity of COVID-19 presentation [OR: 27.48; (95%CI: 5.34–141.49); P = 0.0001 for severe vs. not severe]. Among all comorbidities, diabetes [OR: 3.3; (95%CI: 1.35–8.09); P = 0.008] and cardiovascular diseases [OR: 3.77; (95%CI: 1.02–13.91); P = 0.045] were significant risk factors for death. The receipt of anticancer treatments including chemotherapy, surgery, radiotherapy, targeted therapy, and immunotherapy within a month before the onset of COVID-19 symptoms had no significant effect on the mortality of cancer patients.ConclusionTo the best of our knowledge, this is the first study from India reporting the CFR, clinical associations, and risk factors for mortality in SARS-CoV-2 infected cancer patients. Our study shows that the frequency of COVID-19 in cancer patients is high, and the CFR is 7.6 times more than the national average. Anticancer therapies did not increase the risk of death. Pre-existing comorbidities specially diabetes, multiple comorbidities, and severity of COVID-19 presenting symptoms are significantly linked with COVID-19 related death in the cohort.
Self-reassurance reduces neural and self-report reactivity to negative life events
Authors: Kim Jeffrey J. , Cunnington Ross , Kirby James N. 
Published: September 2020

AbstractBackgroundWhilst research has shown how self-criticism may increase both neural and self-report markers of negative emotion, less well known is how self-reassurance - a compassionately-motivated cognitive self-relating style - may regulate negative emotion.MethodUsing fMRI, we invited participants to engage in self-criticism and self-reassurance toward written descriptions of negative life events (mistakes, setbacks, failures).ResultsOur results identify that neural markers of negative emotion and self-report markers of trial intensity during fMRI are suppressed under conditions of self-reassurance, relative to self-criticism.LimitationsFuture work to control for autobiographical memory during this fMRI task is needed, to explore how memory can contribute to self-reassurance and self-criticism.ConclusionsEngagement in self-reassurance can reduce the ‘sting’ of negative life-events, both neural and self-report, which holds important implications for therapy.
The DNA Damage-Sensing NER Repair Factor XPC-RAD23B Does Not Recognize Bulky DNA Lesions with a Missing Nucleotide Opposite the Lesion
Authors: Feher Katie M. , Kolbanovskiy Alexander , Durandin Alexander , Shim Yoonjung , Min Jung-Hyun , Lee Yuan Cho , Shafirovich Vladimir , Mu Hong , Broyde Suse , Geacintov Nicholas E. 
Published: September 2020

AbstractThe Nucleotide Excision Repair (NER) mechanism removes a wide spectrum of structurally different lesions that critically depend on the binding of the DNA damage sensing NER factor XPC-RAD23B (XPC) to the lesions. The bulky mutagenic benzo[a]pyrene diol epoxide metabolite-derivedcis- andtrans-B[a]P-dG lesions (G*) adopt base-displaced intercalative (cis) or minor groove (trans)conformations in fully paired DNA duplexes with the canonical C opposite G* (G*:C duplexes). While XPC has a high affinity for binding to these DNA lesions in fully complementary double-stranded DNA, we show here that deleting only the C in the complementary strand opposite the lesion G* embedded in 50-mer duplexes, fully abrogates XPC binding. Accurate values of XPC dissociation constants (KD) were determined by employing an excess of unmodified DNA as a competitor; this approach eliminated the binding and accumulation of multiple XPC molecules to the same DNA duplexes, a phenomenon that prevented the accurate estimation of XPC binding affinities in previous studies. Surprisingly, a detailed comparison of XPC dissociation constantsKDof unmodified and lesion-containing G*:Del complexes, showed that theKDvalues were ∼ 2.5 – 3.6 times greater in the case of G*:Del than in the unmodified G:Del and fully base-paired G:C duplexes. The origins of this unexpected XPC lesion avoidance effect is attributed to the intercalation of the bulky, planar B[a]P aromatic ring system between adjacent DNA bases that thermodynamically stabilize the G*:Del duplexes. The strong lesion-base stacking interactions associated with the absence of the partner base, prevent the DNA structural distortions needed for the binding of the BHD2 and BHD3 β–hairpins of XPC to the deletion duplexes, thus accounting for the loss of XPC binding and the known NER-resistance of G*:Del duplexes.
A Linear Time Solution to the Labeled Robinson-Foulds Distance Problem
Authors: Briand Samuel , Dessimoz Christophe , El-Mabrouk Nadia , Nevers Yannis 
Published: September 2020

AbstractMotivationComparing trees is a basic task for many purposes, and especially in phylogeny where different tree reconstruction tools may lead to different trees, likely representing contradictory evolutionary information. While a large variety of pairwise measures of similarity or dissimilarity have been developed for comparing trees with no information on internal nodes, very few address the case of inner node-labeled trees. Yet such trees are common; for instance reconciled gene trees have inner nodes labeled with the type of event giving rise to them, typically speciation or duplication. Recently, we proposed a formulation of the Labeled Robinson Foulds edit distance with edge extensions, edge contractions between identically labeled nodes, and node label flips. However, this distance proved difficult to compute, in particular because shortest edit paths can require contracting “good” edges, i.e. edges present in the two trees.ResultsHere, we report on a different formulation of the Labeled Robinson Foulds edit distance — based on node insertion, deletion and label substitution — which we show can be computed in linear time. The new formulation also maintains other desirable properties: being a metric, reducing to Robinson Foulds for unlabeled trees and maintaining an intuitive interpretation. The new distance is computable for an arbitrary number of label types, thus making it useful for applications involving not only speciations and duplications, but also horizontal gene transfers and further events associated with the internal nodes of the tree. To illustrate the utility of the new distance, we use it to study the impact of taxon sampling on labeled gene tree inference, and conclude that denser taxon sampling yields better trees.
1RS.1BL molecular resolution provides novel contributions to wheat improvement
Authors: Ru Zhengang , Juhasz Angela , Li Danping , Deng Pingchuan , Zhao Jing , Gao Lifeng , Wang Kai , Keeble-Gagnere Gabriel , Yang Zujun , Li Guangrong , Wang Daowen , Bose Utpal , Colgrave Michelle , Kong Chuizheng , Zhao Guangyao , Zhang Xueyong , Liu Xu , Cui Guoqing , Wang Yuquan , Niu Zhipeng , Wu Liang , Cui Dangqun , Jia Jizeng , Appels Rudi , Kong Xiuying 
Published: September 2020

SUMMARYWheat-rye 1RS.1BL translocation has a significant impact on wheat yield and hence food production globally. However, the genomic basis of its contributions to wheat improvement is undetermined. Here, we generated a high-quality assembly of 1RS.1BL translocation comprising 748,715,293 bp with 4,996 predicted protein-coding genes. We found the size of 1RS is larger than 1BS with the active centromere domains shifted to the 1RS side instead of the 1BL side in Aikang58 (AK58). The gene alignment showed excellent synteny with 1BS from wheat and genes from 1RS were expressed well in wheat especially for 1RS where expression was higher than that of 1BS for the grain-20DPA stage associated with greater grain weight and negative flour quality attributes. A formin-like-domain protein FH14 (TraesAK58CH1B01G010700) was important in regulating cell division. Two PPR genes were most likely the genes for the multi fertility restoration locusRfmulti. Our data not only provide the high-resolution structure and gene complement for the 1RS.1BL translocation, but also defined targets for enhancing grain yield, biotic and abiotic stress, and fertility restoration in wheat.
The effect of E-liquid exposure onCaenorhabditis elegans
Authors: Wang Ying , Ingram Thomas L , Marshall Sophie , Shephard Freya , Chakrabarti Lisa 
Published: September 2020

AbstractE-cigarettes are being promoted as a less harmful alternative to smoking tobacco. However, vaping is a new phenomenon and safety profiles have not been fully established. Model organisms can be used to examine the cellular processes that may be changed by exposure to the E-liquids used for vaping. Mitochondria are essential in eukaryotic cells for production of ATP, protein biogenesis, metabolic pathways, cellular signalling, stress responses and apoptosis. Mitochondrial health can be used as a proxy for many aspects of healthy cellular physiology. Mutations in the PINK1 gene can lead to mitochondria-specific autophagy deficiency. We exposed two strains ofCaenorhabditis elegans, CB5600 control and CC46 pink1, with 10% concentrations of nine different flavoured E liquids. We measured lifespan, movement, body size, brood size, and we examined their mitochondrial networks to investigate the effect of the E-liquids. We show that the CC46 (pink1) strain is affected by the E-liquids, even the flavours without nicotine, and that they have reduced lifespan, movement ability and mitochondrial organisation. We found that some E-liquids can dramatically shorten lifespan in this strain. Our data emphasise a need to carefully ascertain the potential harm that may be caused by the use of E-liquids.
FUS-ALS mutants alter FMRP phase separation equilibrium and impair protein translation
Authors: Birsa N. , Ule A.M. , Garone M.G. , Tsang B. , Mattedi F. , Chong P.A. , Humphrey J. , Jarvis S. , Pisiren M. , Wilkins O.G. , Nosella M. , Devoy A. , Bodo C. , Fernandez de la Fuente R. , Fisher E.M.C. , Rosa A. , Viero G. , Forman-Kay J.D. , Schiavo G. , Fratta P. 
Published: September 2020

SummaryMutations in the RNA binding protein (RBP) FUS cause amyotrophic lateral sclerosis (ALS) and result in its nuclear depletion and cytoplasmic mislocalisation, with cytoplasmic gain of function thought to be crucial in pathogenesis. Here, we show that expression of mutant FUS at physiological levels drives translation inhibition in both mouse and human motor neurons. Rather than acting directly on the translation machinery, we find that mutant FUS forms cytoplasmic condensates that promote the phase separation of FMRP, another RBP associated with neurodegeneration and robustly involved in translation regulation. FUS and FMRP co-partition and repress translationin vitro. In ourin vivomodel, FMRP RNA targets are depleted from ribosomes. Our results identify a novel paradigm by which FUS mutations favour the condensed state of other RBPs, impacting on crucial biological functions, such as protein translation.