bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pain-related behavior is associated with increased joint innervation, ipsilateral dorsal horn gliosis, and dorsal root ganglia activating transcription factor 3 expression in a rat ankle joint model of osteoarthritis
Authors: Bourassa Valerie , Deamond Haley , Yousefpour Noosha , Fitzcharles Mary-Ann , Ribeiro-da-Silva Alfredo 
Published: March 2021

Abstract

Introduction:
Osteoarthritis (OA)-associated pain is often poorly managed, as our understanding of the underlying pain mechanisms remains limited. The known variability from patient to patient in pain control could be a consequence of a neuropathic component in OA.

Methods:
We used a rat monoiodoacetate model of the ankle joint to study the time-course of the development of pain-related behavior and pathological changes in the joint, dorsal root ganglia (DRG), and spinal cord, and to investigate drug treatments effects.

Results:
Mechanical hypersensitivity and loss of mobility (as assessed by treadmill) were detected from 4 weeks after monoiodoacetate. Cold allodynia was detected from 5 weeks. Using histology and x-ray microtomography, we confirmed significant cartilage and bone degeneration at 5 and 10 weeks. We detected increased nociceptive peptidergic and sympathetic fiber innervation in the subchondral bone and synovium at 5 and 10 weeks. Sympathetic blockade at 5 weeks reduced pain-related behavior. At 5 weeks, we observed, ipsilaterally only, DRG neurons expressing anti-activating transcription factor 3, a neuronal stress marker. In the spinal cord, there was microgliosis at 5 and 10 weeks, and astrocytosis at 10 weeks only. Inhibition of glia at 5 weeks with minocycline and fluorocitrate alleviated mechanical allodynia.

Conclusion:
Besides a detailed time-course of pathology in this OA model, we show evidence of contributions of the sympathetic nervous system and dorsal horn glia to pain mechanisms. In addition, late activating transcription factor 3 expression in the DRG that coincides with these changes provides evidence in support of a neuropathic component in OA pain.
Micro-mechanical fracture dynamics and damage modelling in brittle materials
Authors: Gomez Q. , Ionescu I. R. 
Published: March 2021

This study explores the interplay between wave propagation and damage in brittle materials. The damage models, based on micro-mechanical fracture dynamics, capture any possible unstable growth of micro-cracks, introducing a macroscopic loss of stability. After stating the non-dimensional mathematical problem describing the wave propagation with damage, we introduce a non-dimensional number, called the microscopic evolution index, which links the micro and macro scales and discriminates the microscopic scale behaviour. For large values of microscopic evolution index, corresponding to a microscopic quasi-static process coupled with a macroscopic dynamic one, the macroscopic dynamic system could lose its hyperbolicity or become very stiff and generate shock waves. A semi-analytical solution to the one-dimensional wave propagation problem with damage, which could be very useful in the accuracy evaluation of the numerical schemes, was constructed. Concerning the asymptotic behaviour of the dynamic exact solution on the microscopic evolution index (or on the strain rate), an important strain rate sensitivity was found: the pulse loses its amplitude for decreasing strain rate and, starting with a critical value, the micro-scale model is rate independent. A possible regularization technique to smooth the shock waves at low and moderate strain rates is discussed. Finally, some numerical results analyse the role played by the the friction on the micro-cracks in the damage modelling of blast wave propagation.
This article is part of the theme issue ‘Fracture dynamics of solid materials: from particles to the globe’.
Thermal jet drilling of granite rock: a numerical 3D finite-element study
Authors: Saksala Timo , Kouhia Reijo , Mardoukhi Ahmad , Hokka Mikko 
Published: March 2021

This paper presents a numerical study on thermal jet drilling of granite rock that is based on a thermal spallation phenomenon. For this end, a numerical method based on finite elements and a damage–viscoplasticity model are developed for solving the underlying coupled thermo-mechanical problem. An explicit time-stepping scheme is applied in solving the global problem, which in the present case is amenable to extreme mass scaling. Rock heterogeneity is accounted for as random clusters of finite elements representing rock constituent minerals. The numerical approach is validated based on experiments on thermal shock weakening effect of granite in a dynamic Brazilian disc test. The validated model is applied in three-dimensional simulations of thermal jet drilling with a short duration (0.2 s) and high intensity (approx. 3 MW m−2) thermal flux. The present numerical approach predicts the spalling as highly (tensile) damaged rock. Finally, it was shown that thermal drilling exploiting heating-forced cooling cycles is a viable method when drilling in hot rock mass.This article is part of the theme issue ‘Fracture dynamics of solid materials: from particles to the globe’.
Novel biomarkers of habitual alcohol intake and associations with risk of pancreatic and liver cancers and liver disease mortality
Authors: Loftfield Erikka , Stepien Magdalena , Viallon Vivian , Trijsburg Laura , Rothwell Joseph , Robinot Nivonirina , Biessy Carine , Bergdahl Ingvar A. , Bodén Stina , Schulze Matthias B. , Bergman Manuela , Weiderpass Elisabete , Schmidt Julie A. , Zamora-Ros Raul , Nøst Therese H. , Sandanger Torkjel M , Sonestedt Emily , Ohlsson Bodil , Katzke Verena , Kaaks Rudolf , Ricceri Fulvio , Tjønneland Anne , Dahm Christina C. , Sánchez Maria-Jose , Trichopoulou Antonia , Tumino Rosario , Chirlaque María-Dolores , Masala Giovanna , Ardanaz Eva , Vermeulen Roel , Brennan Paul , Albanes Demetrius , Weinstein Stephanie J. , Scalbert Augustin , Freedman Neal D. , Gunter Marc J. , Jenab Mazda , Sinha Rashmi , Keski-Rahkonen Pekka , Ferrari Pietro 
Published: March 2021

AbstractBackgroundAlcohol is an established risk factor for several cancers, but modest alcohol-cancer associations may be missed due to measurement error in self-reported assessments. The identification of biomarkers of habitual alcohol intake may enhance evidence on the role of alcohol in cancer onset.MethodsUntargeted metabolomics was used to identify metabolites correlated with habitual alcohol intake in a discovery dataset from the European Prospective Investigation into Cancer and Nutrition (EPIC; n=454). Significant correlations were replicated in independent datasets of controls from case-control studies nested within EPIC (n=281) and the Alpha-Tocopherol, Beta-Carotene Cancer Prevention (ATBC; n=438) study. Conditional logistic regression was used to estimate odds ratios (OR) and 95% confidence intervals for associations of alcohol-associated metabolites and self-reported alcohol intake with risk of pancreatic cancer, hepatocellular carcinoma (HCC), liver cancer, and liver disease mortality in the contributing studies.ResultsTwo metabolites displayed a dose-response association with alcohol intake: 2-hydroxy-3-methylbutyric acid and an unidentified compound (m/z(+):231.0839). A 1-SD increase in log2-transformed levels of 2-hydroxy-3-methylbutyric acid was associated with risk of HCC (OR=2.14; 1.39-3.31) and pancreatic cancer (OR=1.65; 1.17-2.32) in EPIC and liver cancer (OR=2.00; 1.44-2.77) and liver disease mortality (OR=2.16; 1.63-2.86) in ATBC. Conversely, a 1-SD increase in log2-transformed questionnaire-derived alcohol intake was not associated with HCC or pancreatic cancer in EPIC or liver cancer in ATBC but was associated with liver disease mortality (OR=2.19; 1.60-2.98) in ATBC.Conclusions2-Hydroxy-3-methylbutyric acid is a candidate biomarker of habitual alcohol intake that may advance the study of alcohol and cancer risk in population-based studies.
A meta-analysis of single visit pollination effectiveness
Authors: Page M.L. , Nicholson C.C. , Brennan R.M. , Britzman A.T. , Greer J. , Hemberger J. , Kahl H. , Müller U. , Peng Y. , Rosenberger N.M. , Stuligross C. , Wang L. , Yang L.H. , Williams N.M. 
Published: March 2021

AbstractMany animals provide essential ecosystem services in the form of plant pollination. A rich literature documents considerable variation in the single visit pollination effectiveness of different plant visitors, but this literature has yet to be comprehensively synthesized. We conducted a hierarchical meta-analysis of 193 studies and extracted 1716 single visit effectiveness (SVE) comparisons for 252 plant species. We paired SVE data with visitation frequency data for 75 of these studies. Given the global dominance of honeybees in pollinator communities, we used these data to ask: 1) Do honeybees (Apis mellifera) and other floral visitors vary in their SVE?; 2) To what extent do plant and pollinator attributes predict the difference in SVE between honeybees and other visitors?; and 3) Is there a correlation between floral visitation frequency and SVE? We found that honeybees were significantly less effective than the most effective non-honeybee pollinator. Although not significantly different, honeybees also tended to be less effective than the mean community effectiveness. Honeybees were less effective as pollinators of crop plants and when compared to birds and other bees. Visitation frequency and pollination effectiveness were positively correlated, but this trend was largely driven by data from communities where honeybees were absent, suggesting that honeybees generally combine high visitation frequency and lower SVE. Our study demonstrates that non-honeybee floral visitors are highly effective pollinators of many crop and non-crop plants. While the high visitation frequency typically displayed by honeybees undoubtably makes them important pollinators, we show that honeybees are slightly less effective than the average pollinator and rarely the most effective pollinator of the plants they visit. As such, honeybees may be imperfect substitutes for the loss of wild pollinators and safeguarding global crop production will benefit from conservation of non-honeybee taxa.Open Research Statement:Although we are fully committed to data transparency, we are also aware of different research teams working on related meta-analyses. As such, we prefer to wait until our paper is accepted to make data publicly available but are happy to share data upon request. Data will be permanently archived on Figshare following acceptance.
Embryo Lethality Assay for Evaluating Virulence of Isolates from Bacterial Chondronecrosis with Osteomyelitis in Broilers
Authors: Ekesi Nnamdi S. , Hasan Amer , Parveen Alia , Shwani Abdulkarim , Rhoads Douglas D. 
Published: March 2021

AbstractWe used an embryo lethality assay (ELA) to assess virulence for different isolates from cases of bacterial chondronecrosis with osteomyelitis (BCO) in broilers. ELA has been used to measure virulence and lethal dosage of Enterococcus faecalis and Enterococcus cecorum. We hypothesized that ELA could substitute for more laborious and costly assessments of BCO isolate pathogenicity using live birds. We evaluated two different levels of bacteria injected into eggs from layer and commercial broiler embryos. Significant findings include a) Escherichia coli from neighboring farms operated by the same integrator had very different embryo lethality, b) isolate Staphylococcus agnetis 908 had low virulence in ELA, even though this isolate can induce more than 50% BCO lameness, c) Enterococcus cecorum 1415 also had low pathogenicity; even though it was recovered from severe bilateral tibial dyschondroplasia, d) human and chicken isolates of S. aureus had significant pathogenicity, e) virulence for some isolates was highly variable possibly corresponding with quality of the embryos/fertile eggs used, and f) ELA pathogenicity was much lower for our BCO isolates than previous reports which may reflect maternal environment. Overall, ELA virulence and BCO virulence are not always concordant indicating that that ELA may not be an effective measure for assessing virulence with respect to BCO.ImportanceLameness is among the most significant animal welfare issues in the poultry industry. Bacterial infections are a major cause of lameness and different bacterial species have been obtained from lame broilers. Reliable lab-based assays are required to assess relative virulence of bacteria obtained from lame broilers. Embryo Lethality Assays have been used to compare virulence. Our results suggest that this assay may not be an effective measure of virulence related to lameness.
Impact of School Reopening on Pandemic Spread: A Case Study using an Agent-Based Model for COVID-19
Authors: Tatapudi Hanisha , Das Tapas K. 
Published: March 2021

ABSTRACTThis article examines the impact of partial/full reopening of school/college campuses on the spread of a pandemic using COVID-19 as a case study. The study uses an agent-based simulation model that replicates community spread in an urban region of U.S.A. via daily social mixing of susceptible and infected individuals. Data representing population demographics, SARS-CoV-2 epidemiology, and social interventions guides the model’s behavior, which is calibrated and validated using data reported by the government. The model indicates a modest but significant increase (8.15 %) in the total number of reported cases in the region for a complete (100%) reopening compared to keeping schools and colleges fully virtual. For partial returns of 75% and 50%, the percent increases in the number of reported cases are shown to be small (2.87% and 1.26%, respectively) and statistically insignificant. The AB model also predicts that relaxing the stringency of the school safety protocol for sanitizing, use of mask, social distancing, testing, and quarantining and thus allowing the school transmission coefficient to double may result in a small increase in the number of reported infected cases (2.14%). Hence for pandemic outbreaks from viruses with similar characteristics as for SARS-CoV-2, keeping the schools and colleges open with a modest campus safety protocol and in-person attendance below a certain threshold may be advisable.
Hepatitis B infection is causally associated with extrahepatic cancers: a Mendelian randomization study
Authors: Kamiza Abram Bunya , Fatumo Segun , Singini Mwiza Gideon , Yeh Chih-Ching , Chikowore Tinashe 
Published: March 2021

AbstractOverwhelming evidence suggests that chronic hepatitis infection is associated with extrahepatic cancers. However, uncertainties exist about this association as much of the current evidence evolve from observational studies which are susceptible to confounding. We performed two-sample Mendelian randomization (MR) to explore the causal associations between chronic hepatitis infection and extrahepatic cancers. Genetic variants associated with chronic hepatitis B virus (HBV) infection and chronic hepatitis C virus (HCV) infection were identified from a large genome-wide association study. Summary level data for cancer of the biliary tract, cervix, colorectum, endometrium, esophagus, gastric, liver, lung, ovary and pancreas were obtained from the Biobank Japan. Using the inverse variance weighted method, we found chronic HBV infection to be causally associated with gastric cancer (odds ratio [OR] = 1.19 and 95% confidence interval [CI] = 1.13-1.25, P-value = 0.001) and lung cancer (OR = 1.21, 95% CI = 1.14-1.28, P-value = 0.001). Moreover, chronic HBV infection (OR = 1.34, 95% CI = 1.17-1.53, P-value = 0.007) and chronic HCV infection (OR = 2.75, 95% CI = 2.21-3.42, P-value = 0.0008) were all causally associated with liver cancer, supporting a well-established association between chronic hepatitis infection and liver cancer. In conclusions, our MR findings revealed that chronic HBV infection is causally associated with extrahepatic cancers including gastric and lung cancers.
Hydroxyl-radical scavenging activity of hydrogen does not significantly contribute to its biological function
Authors: Li Qinjian , Xie Fei , Yi Yang , Zhao Pengxiang , Zhang Xin , Zhang Xiaokang , Zhang Xujuan , Ma Xuemei 
Published: March 2021

AbstractSince Ohsawa et al. reported a biological antioxidant function of hydrogen in 2007, researchers have now shown it to exert protective effects in a wide range of human and animal disease models. Clinical observations and scientific arguments suggest that a selective scavenging property of H2cannot adequately explain the beneficial effects of hydrogen. However, there is no experiment challenging the original published data, which suggested that molecular hydrogen dissolved in solution reacts with hydroxyl radicals in cell-free systems. Here we report that a hydrogen-saturated solution (0.6 mM) did not significantly reduce hydroxyl radicals in the Fenton system using 1 mM H2O2. We replicated the same condition as Ohsawa’s study (i.e. 5 μM H2O2), and observed a decrease in•OH radicals in both the H2-rich and N2-rich solutions, which may be caused by a decreased dissolved oxygen concentration. Finally, we determined the effect of hydrogen on a high-valence iron enzyme, horseradish peroxidase (HRP), and found that hydrogen could directly increase HRP activity in a dose-dependent manner. Overall, these results indicate that although H2and•OH can react, the reaction rate is too low to have physiological function. The target of hydrogen is more complex, and its interaction with enzymes or other macro-molecules deserve more attention and in-depth study.
Subcellular architecture and metabolic connection in the planktonic photosymbiosis between Collodaria (radiolarians) and their microalgae
Authors: Decelle Johan , Veronesi Giulia , LeKieffre Charlotte , Gallet Benoit , Chevalier Fabien , Stryhanyuk Hryhoriy , Marro Sophie , Ravanel Stéphane , Tucoulou Rémi , Schieber Nicole , Finazzi Giovanni , Schwab Yannick , Musat Niculina 
Published: March 2021

AbstractPhotosymbiosis is widespread and ecologically important in the oceanic plankton but remains poorly studied. Here, we used multimodal subcellular imaging to investigate the photosymbiosis between colonial Collodaria and their microalga dinoflagellate (Brandtodinium) collected in surface seawaters. We showed that this symbiosis is a very dynamic system whereby symbionts interact with different host cells via extracellular vesicles within the “greenhouse-like” colony. 3D electron microscopy revealed that the volume of the photosynthetic apparatus (plastid and pyrenoid) of the microalgae increased in symbiosis compared to free-living while the mitochondria volume was similar. Stable isotope probing coupled with NanoSIMS showed that carbon and nitrogen were assimilated and stored in the symbiotic microalga in starch granules and purine crystals, respectively. Nitrogen was also allocated to the algal nucleus (nucleolus). After 3 hours, low13C and15N transfer was detected in the host Golgi. Metal mapping revealed that intracellular iron concentration was similar in free-living and symbiotic microalgae (ca 40 ppm) and two-fold higher in the host, whereas copper concentration increased in symbiotic microalgae (up to 6900 ppm) and was detected in the host cell and extracellular vesicles. Sulfur mapping also pinpointed the importance of this nutrient for the algal metabolism. This study, which revealed subcellular changes of the morphology and nutrient homeostasis in symbiotic microalgae, improves our understanding on the metabolism of this widespread and abundant oceanic symbiosis and paves the way for more studies to investigate the metabolites exchanged.
A Creb3-Like Transcription Factor Coordinates ER Function upon Food Intake to Regulate Lipid Metabolism
Authors: Khan Haris A. , Toh Ming , Schauer Tamás , Beresford Rory J. , Ortega-Prieto Paula , Postic Catherine , Margulies Carla E. 
Published: March 2021

SUMMARYIngestion of nutrients elicits essential physiological responses, including absorption, digestion, cessation of feeding and nutrient storage. The endoplasmic reticulum (ER) is central to this nutritional homeostasis, since it regulates intracellular organelle function, drives intercellular communication and promotes metabolite distribution. We identified theDrosophilaCreb3L-family transcription factor, CrebA, as the key metabolic regulator of ER function, thereby affecting lipid metabolism and feeding behavior. In response to feeding, CrebA activity is rapidly and transiently activated. CrebA directly drives the expression of the ER protein sorting machinery. We demonstrate that CrebA levels regulate lipid metabolism through lipoprotein secretion into the hemolymph and suppress feeding behavior. Further, CrebA mouse homologs are also upregulated in the liver following feeding and drive the transcriptional activation of ER protein sorting machinery genes in mammals. Our results reveal an evolutionarily conserved transcription switch which is turned on in response to food ingestion and orchestrates a negative feedback loop that promotes satiety by regulating ER function and protein secretion.
Accurate analysis of short read sequencing in complex genomes: A case study using QTL-seq to target blanchability in peanut (Arachis hypogaea)
Authors: Korani Walid , O’Connor Dan , Chu Ye , Chavarro Carolina , Ballen Carolina , Ozias-Akins Peggy , Wright Graeme , Clevenger Josh 
Published: March 2021

AbstractNext Generation sequencing was a step change for molecular genetics and genomics. Illumina sequencing in particular still provides substantial value to animal and plant genomics. A simple yet powerful technique, referred to as QTL sequencing (QTL-seq) is susceptible to high levels of noise due to ambiguity of alignment of short reads in complex regions of the genome. This noise is particularly high when working with polyploid and/or outcrossing crop species, which impairs the efficacy of QTL-seq in identifying functional variation. By filtering loci based on the optimal alignment of short reads, we have developed a pipeline, named Khufu, that substantially improves the accuracy of QTL-seq analysis in complex genomes, allowingde novovariant discovery directly from bulk sequence. We first demonstrate the pipeline by identifying and validating loci contributing to blanching percentage in peanut using lines from multiple related populations. Using other published datasets in peanut,Brassica rapa, Hordeum volgare, Lactua satvia, andFelis catus, we demonstrate that Khufu produces more accurate results straight from bulk sequence. Khufu works across species, genome ploidy level, and data types. In cases where identified QTL were fine mapped, the fine mapped region corresponds to the top of the peak identified by Khufu. The accuracy of Khufu allows the analysis of population sequencing at very low coverage (<3x), greatly decreasing the amount of sequence needed to genotype even the most complex genomes.