bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolic and cardiovascular outcomes of bariatric surgery
Authors: Iqbal Zohaib , Adam Safwaan , Ho Jan H. , Syed Akheel A. , Ammori Basil J. , Malik Rayaz A. , Soran Handrean 
Published: July 2020

Purpose of review
Bariatric surgery is an effective therapy for morbid obesity that also improves weight-related metabolic parameters and reduces morbidity and mortality. The purpose of this review is to consolidate our current understanding of metabolic, macrovascular and microvascular benefits of bariatric surgery and to provide an update.

Recent findings
Early resolution of insulin resistance and type 2 diabetes mellitus (T2DM) varies by type of bariatric surgery and appears to be mediated by changes in secretion of gut hormones, metabolism of bile acids, expression of glucose transporters and the gut microbiome. Dyslipidaemia, atherosclerosis, microvascular complications of obesity and diabetes, systemic and tissue-level inflammation show evidence of regression and hypertension improves significantly after bariatric surgery.

Summary
Bariatric surgery leads to improvements in obesity-related metabolic comorbidities such as dyslipidaemia, HDL functionality, hypertension, T2DM, insulin resistance and inflammation. It slows the atherosclerotic process and reduces cardiovascular and all-cause mortality. Recent data have demonstrated regression of the microvascular complications of obesity and diabetes including the regeneration of small nerve fibres. The magnitude of change in short-term metabolic effects depends on the surgical procedure whilst longer term effects are related to the amount of sustained excess weight loss.
Metabolic pathway analysis in the presence of biological constraints
Authors: Dague Philippe 
Published: July 2020

AbstractMetabolic pathway analysis is a key method to study a metabolism in its steady state and the concept of elementary fluxes (EFs) plays a major role in the analysis of a network in terms of non-decomposable pathways. The supports of theEFscontain in particular those of the elementary flux modes (EFMs), which are the support-minimal pathways, andEFscoincide withEFMswhen the only flux constraints are given by the irreversibility of certain reactions. Practical use of bothEFMsandEFshas been hampered by the combinatorial explosion of their number in large, genomescale, systems. TheEFsgive the possible pathways in a steady state but the real pathways are limited by biological constraints, such as thermodynamic or, more generally, kinetic constraints and regulatory constraints from the genetic network. We provide results on the mathematical structure and geometrical characterization of the solution space in the presence of such biological constraints and revisit the concept ofEFMsandEFsin this framework. We show that most of the results depend only on very general properties of compatibility of constraints with the sign function: either signinvariance for regulatory constraints or sign-monotonicity (a stronger property) for thermodynamic and kinetic constraints. We show in particular thatEFsfor sign-monotone constraints are just those of the originalEFsthat satisfy the constraint and we show how to integrate their computation efficiently in the double description method, the most widely used method in the tools dedicated to EFMs computation.
Sample pooling on triplets to speed up SARS-CoV-2 diagnosis using CDC FDA EUA RT-qPCR kit
Authors: Freire-Paspuel Byron , Vega-Mariño Patricio , Velez Alberto , Cruz Marilyn , Garcia-Bereguiain Miguel Angel 
Published: July 2020

AbstractThe CDC designed “FDA Emergeny Use Autorization” 2019-nCoV CDC RT-qPCR kit uses 3 different FAM probes for SARS-CoV-2 diagnosis so 3 reactions per sample are needed. We herein describe a sample pooling protocol: 3 RNA extractions are combined into a single PCR reaction. The sensitivity for this protocol is 100% as no shift on Ct values for N1 or N2 probes were observed. For a typical 96-well plate, triplet assay allows 96 samples processing, speeding up diagnosis.
Predicting Adverse Drug Reactions of Two-drug Combinations using Structural and Transcriptomic Drug Representations to Train a Artificial Neural Network
Authors: Shankar Susmitha , Bhandari Ishita , Okou David T. , Srinivasa Gowri , Athri Prashanth 
Published: July 2020

AbstractAdverse drug reactions (ADRs) are pharmacological events triggered by drug interactions with various sources of origin including drug-drug interactions. While there are many computational studies that explore models to predict ADRs originating from single drugs, only a few of them explore models that predict ADRs from drug combinations. Further, as far as we know, none of them have developed models using transcriptomic data, specifically the LINCS L1000 drug induced gene expression data to predict ADRs for drug combinations. In this study we use the TWOSIDES database as a source of ADRs originating from two-drug combinations. 34,549 common drug pairs between these two databases were used to train an artificial neural network (ANN), to predict 243 ADRs that were induced by at least 10% of the drug pairs. Our model predicts the occurrence of these ADRs with an average accuracy of 82% across a multi fold cross validation.Source Code and input dataset used in this study can be found at:https://bitbucket.org/ishita98/prediction-of-adr/src/master/
Hyperosmotic stress induces downstream-of-gene transcription and alters the RNA Polymerase II interactome despite widespread transcriptional repression
Authors: Rosa-Mercado Nicolle A. , Zimmer Joshua T. , Apostolidi Maria , Rinehart Jesse , Simon Matthew D. , Steitz Joan A. 
Published: July 2020

SummaryStress-induced readthrough transcription results in the synthesis of thousands of downstream-of-gene (DoG) containing transcripts. The mechanisms underlying DoG formation during cellular stress remain unknown. Nascent transcription profiles during DoG induction in human cell lines using TT-TimeLapse-seq revealed that hyperosmotic stress induces widespread transcriptional repression. Yet, DoGs are produced regardless of the transcriptional level of their upstream genes. ChIP-seq confirmed that the stress-induced redistribution of RNA Polymerase (Pol) II correlates with the transcriptional output of genes. Stress-induced alterations in the Pol II interactome are observed by mass spectrometry. While subunits of the cleavage and polyadenylation machinery remained Pol II-associated, Integrator complex subunits dissociated from Pol II under stress conditions. Depleting the catalytic subunit of the Integrator complex, Int11, using siRNAs induces hundreds of readthrough transcripts, whose parental genes partially overlap those of stress-induced DoGs. Our results provide insights into the mechanisms underlying DoG production and how Integrator activity influences DoG transcription.In briefRosa-Mercado et al. report that hyperosmotic stress causes widespread transcriptional repression in human cells, yet DoGs arise regardless of the transcriptional response of their upstream genes. They find that the interaction between Pol II and Integrator is disrupted by hypertonicity and that knocking down the Integrator nuclease leads to DoG production.HighlightsHyperosmotic stress triggers transcriptional repression of many genes.DoG RNAs arise independent of the transcriptional level of their upstream gene.The interaction between Pol II and Integrator subunits decreases after salt stress.Depletion of the Int11 nuclease subunit induces the production of hundreds of DoGs.
Important effect of the X chromosome in genomic evaluations of reproductive traits in beef cattle
Authors: Solar Diaz Iara Del Pilar , de Camargo Gregório Miguel Ferreira , da Cruz Valdecy Aparecida Rocha , Costa Hermisdorff Isis da , Damasceno Carvalho Caio Victor , de Albuquerque Lucia Galvão , Costa Raphael Bermal 
Published: July 2020

AbstractThe aim of this study was to evaluate the efficiency of inclusion and the prediction ability of the X chromosome for reproductive (occurrence of early pregnancy – P16 and age at first calving - AFC) and andrological traits (scrotal circumference -SC) in a herd of Nellore beef cattle herd. 3,263 genotypes of females and males were used. Genomic prediction for SC, AFC and P16 was carried out considering two scenarios: 1) only autosomal markers or 2) autosomal + X chromosome markers. To evaluate the effect of inclusion of the X chromosome on selection, the responses to the selection performed were compared including or not the X chromosome in the evaluation of the traits. Higher heritability estimates were obtained for SC (0.40 and 0.31), AFC (0.11 and 0.09) and P16 (0.43 and 0.38) for the analyses including the X chromosome compared to those without. The percent reduction on mean genomic breeding values when selection was based on the results of analysis that did not include the X chromosome to 1, 5 and 10% of the top males, was for SC slightly more than 7% of the mean genomic breeding value of the selected animals. For P16, the loss can reach more than 4%, while this loss does not seem to be as important for AFC. Average predictive correlation of 0.79, 0.98 and 0.84 for SC, AFC and P16 was obtained, respectively. These estimates demonstrate that inclusion of the X chromosome in the analysis can improve the prediction of genomic breeding values, especially for SC.
DIRT/3D: 3D root phenotyping for field grown maize (Zea mays)
Authors: Liu Suxing , Barrow Carlos Sherard , Hanlon Meredith , Lynch Jonathan P. , Bucksch Alexander 
Published: July 2020

AbstractThe development of crops with deeper roots holds substantial promise to mitigate the consequences of climate change. Deeper roots are an essential factor to improve water uptake as a way to enhance crop resilience to drought, to increase nitrogen capture, to reduce fertilizer inputs and, to increase carbon sequestration from the atmosphere to improve soil organic fertility. A major bottleneck to achieving these improvements is high-throughput phenotyping to quantify root phenotypes of field-grown roots. We address this bottleneck with DIRT/3D, a newly developed image-based 3D root phenotyping platform, which measures 18 architecture traits from mature field-grown maize root crowns excavated with the Shovelomics technique. DIRT/3D reliably computed all 18 traits, including distance between whorls and the number, angles, and diameters of nodal roots, on a test panel of 12 contrasting maize genotypes. The computed results were validated through comparison with manual measurements. Overall, we observed a coefficient of determination ofr2>0.84 and a high broad-sense heritability offor all but one trait. The average values of the 18 traits and a newly developed descriptor to characterize a complete root architecture distinguished all genotypes. DIRT/3D is a step towards automated quantification of highly occluded maize root crowns. Therefore, DIRT/3D supports breeders and root biologists in improving carbon sequestration and food security in the face of the adverse effects of climate change.
Androgen Receptor promotes renal cell carcinoma (RCC) vasculogenic mimicry (VM)viaaltering TWIST1 nonsense-mediated decay through lncRNA-TANAR
Authors: You Bosen , Sun Yin , Liu Qing , Wang Keliang , Fang Ruizhe , Liu Bingmei , Chou Fuju , Luo Jie , Wang Ronghao , Meng Jialin , Huang Chi-Ping , Yeh Shuyuan , Xu Wanhai , Chang Chawnshang 
Published: July 2020

AbstractWhile the androgen receptor (AR) may influence the progression of clear cell renal cell carcinoma (ccRCC), its role to impact vasculogenic mimicry (VM) to alter the ccRCC progression and metastasis remains obscure. Here we demonstrated that elevated AR expression was positively correlated with tumor-originated vasculogenesis in ccRCC patients. Consistently,in vitroresearch revealed AR promoted VM formation in ccRCC cell linesviamodulating lncRNA-TANAR/TWIST1 signals. Mechanism dissection showed that AR could increase lncRNA-TANAR (TANAR) expression through binding to the androgen response elements (AREs) located on its promoter region. Moreover, we found that TANAR could impede nonsense-mediated mRNA decay (NMD) of TWIST1 mRNA by direct interaction with TWIST1 5’UTR. A preclinical study usingin vivomouse model with orthotopic xenografts of ccRCC cells further confirmed thein vitrodata. Together, these results illustrated that AR-mediated lnc-TANAR signals might play a crucial role in ccRCC VM formation and metastasis, and targeting this newly identified AR/lncRNA-TANAR/TWIST1 signaling may help in the development of a novel anti-angiogenesis therapy to better suppress the ccRCC progression.
Mimicry drives convergence in structural and light transmission features of transparent wings in Lepidoptera
Authors: Pinna Charline , Vilbert Maëlle , Borensztajn Stephan , de Marcillac Willy Daney , Piron-Prunier Florence , Pomerantz Aaron F. , Patel Nipam , Berthier Serge , Andraud Christine , Gomez Doris , Elias Marianne 
Published: July 2020

AbstractMüllerian mimicry is a positive interspecific interaction, whereby co-occurring defended prey species share a common aposematic signal. In Lepidoptera, aposematic species typically harbour conspicuous opaque wing colour patterns with convergent optical properties among co-mimetic species. Surprisingly, some aposematic mimetic species have partially transparent wings, raising the questions of whether optical properties of transparent patches are also convergent, and of how transparency is achieved. Here we conducted a comparative study of wing optics, micro and nanostructures in neotropical mimetic clearwing Lepidoptera, using spectrophotometry and microscopy imaging. We show that transparency, as perceived by predators, is convergent among co-mimics. Underlying micro- and nanostructures are also convergent despite a large structural diversity. We reveal that while transparency is primarily produced by microstructure modifications, nanostructures largely influence light transmission, maybe enabling additional fine-tuning in transmission properties. This study shows that transparency might not only enable camouflage but can also be part of aposematic signals.
Chronic Pb2+exposure causes theta-band hypersynchrony disrupting sensory motor gating and exacerbating absence seizures
Authors: Schultheiss Nathan W. , McGlothan Jennifer L. , Guilarte Tomás R. , Allen Timothy A. 
Published: July 2020

ABSTRACTChronic lead (Pb2+) exposure from childhood contributes to an array of cognitive and behavioral dysfunctions including impaired attention and intellectual ability, learning and memory deficits, and delinquency. It is also an environmental risk factor for adult psychopathologies, most notably schizophrenia and epilepsy. Pb2+is a potent N-methyl-D-aspartate receptor (NMDAR) antagonist and exposure during early life elicits a cascade of cellular neurotoxic effects that alter the developmental trajectory leading to a loss of parvalbumin-expressing interneurons in hippocampus and altered synaptic transmission. Little is known, however, about the impact of chronic Pb2+exposure on hippocampal network dynamics which serve as a link between cellular-molecular effects and cognitive-behavioral consequences of Pb2+neurotoxicity. Here, we tested the effects of chronic Pb2+exposure on the hippocampal local field potential (LFP) of freely-behaving rats. Pb2+exposure caused striking theta rhythmic hypersynchrony and heightened behavioral modulation of theta during locomotor behavior. Pb2+exposure also markedly exacerbated absence seizures appearing in the LFP as spike-wave discharges with a theta-band fundamental frequency and strong theta-harmonic synchronization. Mechanisms of theta rhythmogenesis have been implicated in impairments of prepulse inhibition of the acoustic startle reflex (PPI), so we tested the effect of Pb2+exposure on PPI in male and female rats at different developmental timepoints. We found that adult males (PN50 and 120), but neither females nor juvenile males showed reduced PPI independent of changes in the startle reflex. This pattern recapitulates sex- and age-dependencies of PPI disruption in schizophrenic patients. Overall, these results are consistent with the hypothesis that Pb2+is an environmental risk factor for psychopathology in adulthood, especially those symptoms related to cognitive and sensory-motor gating processes that depend on rhythmic coordination of network activity in the hippocampus.
Prevalence and experience of fatigue in survivors of critical illness: A mixed-methods systematic review
Authors: Bench Suzanne , Stayt Louise , Shah Akshay , Dhiman Paula , Czuber-Dochan Wladyslawa 
Published: July 2020

ABSTRACTObjectiveTo investigate the prevalence, experience and management of fatigue in adult survivors of critical illness.Data sourcesAn electronic search was performed on seven databases: CINAHL, Medline, EMBASE, PsycINFO, Emcare, British Nursing Index, and Web of Science.Study selection and data extractionSeventy-six peer-reviewed, English language studies that investigated fatigue or vitality in adult patients admitted to an Intensive Care Unit (ICU) and followed up for any period were included. Extracted data were split into three datasets for analysis: data from vitality domain of SF-36 (dataset A); other quantitative data (dataset B); and qualitative data (dataset C). Methodological quality was assessed using the critical appraisal skills programme (CASP) tools.Data synthesisWe adopted a segregated approach to mixed-methods synthesis. We merged all datasets, attributing all results to one of four qualitative themes: prevalence and severity; contributing factors; impacts on quality of life; assessment and management.ResultsThe prevalence of fatigue ranged from 13.8 to 80.9%; fatigue severity reached its nadir at approximately one-month post-ICU discharge, improved over time but seldom reached reference population scores. Various biological, disease-related and psychological factors associated with fatigue were identified including age, poor pre-morbid status and sleep disturbance. No critical illness specific tool to assess fatigue in ICU survivors was identified. A paucity of evidence-based interventions for management of fatigue in ICU survivors were identified despite fatigue negatively impacting on survivors’ quality of life.ConclusionsThis mixed method review shows that fatigue is highly prevalent in ICU survivors, negatively impacting their recovery. To date, no ICU specific fatigue assessment tool or targeted intervention has been designed to manage this symptom. Our review has identified factors, which may increase or mitigate against fatigue, along with potential management strategies, which should be used to inform future research and practice.
Orthogonal Functions for Evaluating Social Distancing Impact on CoVID-19 Spread
Authors: Eng Genghmun 
Published: July 2020

AbstractEarly CoVID-19 growth often obeys: , with Ko = [(ln 2)/(tdbl)], where tdbl is the pandemic doubling time, prior to society-wide Social Distancing. Previously, we modeled Social Distancing with tdbl as a linear function of time, where N [t] 1 ≈ exp[+KAt/ (1+,γot)] is used here. Additional parameters besides {Ko, γo} are needed to better model different ρ[t] = dN [t]/dt shapes. Thus, a new Orthogonal Function Model [OFM] is developed here using these orthogonal function series:

where N (Z) and Z[t] form an implicit N [t] N (Z[t]) function, giving:

with Lm(Z) being the Laguerre Polynomials. At large MF values, nearly arbitrary functions for N [t] and ρ [t] = dN [t]/dt can be accommodated. How to determine {KA, γo} and the {gm; m = (0, +MF)} constants from any given N (Z) dataset is derived, with ρ [t] set by:
The bing com USA CoVID-19 data was analyzed using MF = (0, 1, 2) in the OFM. All results agreed to within about 10 percent, showing model robustness. Averaging over all these predictions gives the following overall estimates for the number of USA CoVID-19 cases at the pandemic end:

which compares the pre- and post-early May bing com revisions. The CoVID-19 pandemic in Italy was examined next. The MF = 2 limit was inadequate to model the Italy ρ [t] pandemic tail. Thus, regions with a quick CoVID-19 pandemic shutoff may have additional Social Distancing factors operating, beyond what can be easily modeled by just progressively lengthening pandemic doubling times (with 13 Figures).
ASSOCIATIONS OF AGE, BODY MASS INDEX, AND BIOCHEMICAL PARAMETERS WITH BRAIN MORPHOLOGY IN PATIENTS WITH ANOREXIA NERVOSA
Authors: Bang Lasse , Tamnes Christian K. , Norbom Linn B. , Thomassen Rut A. , Holm Jill S. , Skotte Laila H. , Juliusson Petur B. , Mejlænder-Evjensvold Magnus , Rø Øyvind 
Published: July 2020

ABSTRACTINTRODUCTIONAccumulating evidence shows that patients with anorexia nervosa (AN) have globally reduced brain mass, including lower cortical volume and thickness, which largely normalizes following weight restoration. The dynamic underlying mechanisms for these processes are unknown, and how age and severity of emaciation are associated with brain morphology in AN is poorly understood. We investigated associations of age, body mass index (BMI) and biochemical parameters with brain morphology in a large sample of patients in treatment. METHODS: We included 85 patients (94% female) aged 12-48 (mean = 23) years with clinical and quality controlled magnetic resonance imaging (MRI) data. T1-weighted MRI images, clinical characteristics, and biochemical parameters were retrospectively collected from hospital records. Brain morphology was measured using FreeSurfer, and associations were investigated using regression models and correlations. RESULTS: Controlling for BMI, age showed significant associations with brain morphology generally concordant with known typical brain developmental patterns. Controlling for age, BMI showed significant positive associations with cortical volume and thickness. There were no significant interaction effects between age and BMI. None of the biochemical parameters correlated significantly with brain morphology.DISCUSSIONOur findings suggest the presence of normal neurodevelopmental patterns in AN and highlight the value of considering age-related effects on brain morphology. Importantly, we showed that severity of emaciation is related to brain morphology reductions, underscoring the importance of weight restoration. More studies are needed to shed light on potential biochemical mechanisms associated with brain alterations in AN.
Stealth fluorescence labeling for live microscopy imaging of mRNA delivery
Authors: Baladi Tom , Nilsson Jesper R. , Gallud Audrey , Celauro Emanuele , Gasse Cécile , Levi-Acobas Fabienne , Sarac Ivo , Hollenstein Marcel , Dahlén Anders , Esbjörner Elin K. , Wilhelmsson L. Marcus 
Published: July 2020

AbstractMethods for tracking of RNA molecules inside living cells are critical to probe their dynamics and biological functions, but also to monitor delivery of therapeutic RNA. We here describe a method for fluorescence labeling of RNAs of any length, via the enzymatic incorporation of the minimally perturbing and intrinsically fluorescent tricyclic cytosine analogue tCO. Using this approach, we demonstrate incorporation of tCOin up to 100% of all natural cytosine positions of a 1.2 kb mRNA encoding for the histone H2B fused to GFP (H2B:GFP). The resulting transcript is fully compatible with both in vitro transcription and subsequent in cell translation. Spectroscopic characterization of the in vitro transcribed mRNA, shows that the incorporation rate of tCOis on par with cytosine, facilitating efficient labeling and controlled tuning of labeling ratios for different applications. Using live cell confocal microscopy and flow cytometry, we show that the tCO-labeled mRNA is efficiently and correctly translated into H2B:GFP upon electroporation as well as lipid-mediated transfection of human Huh-7 cells; correct translation was further confirmed in cell-free systems. Importantly, the spectral properties of the tCO-modified transcripts and their translation product, in this case H2B:GFP, allow for their straightforward and simultaneous visualization in live cells.