bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adar-mediated A-to-I editing is required for embryonic patterning and innate immune response regulation in zebrafish
Authors: Niescierowicz Katarzyna , Pryszcz Leszek , Navarrete Cristina , Tralle Eugeniusz , Sulej Agata , Abu Nahia Karim , Kasprzyk Marta Elżbieta , Misztal Katarzyna , Pateria Abhishek , Pakuła Adrianna , Bochtler Matthias , Winata Cecilia 
Published: September 2022

AbstractAdenosine deaminases (ADARs) catalyze the deamination of adenosine to inosine, also known as A-to-I editing, in RNA. Although A-to-I editing occurs widely across animals and is well studied, new biological roles are still being discovered. Here, we study the role of A-to-I editing in early zebrafish development. We demonstrate that Adar, the zebrafish orthologue of mammalian ADAR1, is essential for establishing the antero-posterior and dorso-ventral axes and patterning. Genome-wide editing discovery reveals pervasive editing in maternal and the earliest zygotic transcripts, the majority of which occurred in the 3’-UTR. Interestingly, transcripts implicated in gastrulation as well as dorso-ventral and antero-posterior patterning are found to contain multiple editing sites. Adar knockdown or overexpression affect gene expression by 12 hpf. Analysis ofadar-/- zygotic mutants further reveals that the previously described role of Adar in mammals in regulating the innate immune response is conserved in zebrafish. Our study therefore establishes distinct maternal and zygotic functions of RNA editing by Adar in embryonic patterning along the zebrafish antero-posterior and dorso-ventral axes, and in the regulation of the innate immune response, respectively.
Amyloidogenesis via interfacial shear in a containerless biochemical reactor aboard the International Space Station
Authors: McMackin Patrick , Adam Joe , Griffin Shannon , Hirsa Amir 
Published: September 2022

AbstractFluid interfaces significantly influence the dynamics of protein solutions, effects that can be isolated by performing experiments in microgravity, greatly reducing the amount of solid boundaries present, allowing air-liquid interfaces to become dominant. This investigation examined the effects of protein concentration on interfacial shear-induced fibrillization of insulin in microgravity within a containerless biochemical reactor, the ring-sheared drop (RSD), aboard the international space station (ISS). Human insulin was used as a model amyloidogenic protein for studying protein kinetics with applications to in situ pharmaceutical production, tissue engineering, and diseases such as Alzheimer’s, Parkinson’s, infectious prions, and type 2 diabetes. Experiments investigated three main stages of amyloidogenesis: nucleation studied by seeding native solutions with fibril aggregates, fibrillization quantified using intrinsic fibrillization rate after fitting measured solution intensity to a sigmoidal function, and gelation observed by detection of solidification fronts. Results demonstrated that in surface-dominated amyloidogenic protein solutions: seeding with fibrils induces fibrillization of native protein, intrinsic fibrillization rate is independent of concentration, and that there is a minimum fibril concentration for gelation with gelation rate and rapidity of onset increasing monotonically with increasing protein concentration. These findings matched well with results of previous studies within ground-based analogs.
Comparing the performance of Kernel PCA Mix Chart with PCA Mix Chart for monitoring mixed quality characteristics
Authors: Ahsan Muhammad , Mashuri Muhammad , Khusna Hidayatul 
Published: September 2022

AbstractAlong with the development of information and technology, the quality characteristics of a product cannot be monitored separately in the different types of control charts. In the past, conventional control charts were developed to monitor only one type of quality characteristic. The variable control charts are used to observe the variable or metric quality characteristics. Meanwhile, in monitoring non-metric characteristics or categorical data, attribute control charts are employed. To accommodate these two types of data, the PCA Mix control chart is suggested to simultaneously monitor these two types of data in one chart. However, some drawbacks occur when this chart is applied to monitor non-metric data which has an imbalanced proportion. Therefore, the Kernel PCA Mix control chart is created to overcome the gaps that occurred in the PCA Mix chart. Similar to the previous chart, this chart is also constructed using Hotelling’sT2statistics with Kernel Density Estimation control limit. Several simulations are used to evaluate the performance of the proposed control charts. The simulation results show that the proposed chart has a better result than the previous control chart, especially for a small mean shift with an imbalanced proportion of non-metric data. However, the PCA Mix chart has a similar performance to the proposed chart when it is applied to monitor the balanced proportion of categorical data with a large mean shift. The application with simulated data with various scenarios and the real-world case also shows that the Kernel PCA Mix chart performs better compared to the performance of the PCA Mix chart.
Adaptive SIR model with vaccination: simultaneous identification of rates and functions illustrated with COVID-19
Authors: Marinov Tchavdar T. , Marinova Rossitza S. 
Published: September 2022

AbstractAn Adaptive Susceptible-Infected-Removed-Vaccinated (A-SIRV) epidemic model with time-dependent transmission and removal rates is constructed for investigating the dynamics of an epidemic disease such as the COVID-19 pandemic. Real data of COVID-19 spread is used for the simultaneous identification of the unknown time-dependent rates and functions participating in the A-SIRV system. The inverse problem is formulated and solved numerically using the Method of Variational Imbedding, which reduces the inverse problem to a problem for minimizing a properly constructed functional for obtaining the sought values. To illustrate and validate the proposed solution approach, the present study used available public data for several countries with diverse population and vaccination dynamics—the World, Israel, The United States of America, and Japan.
Construction of a trio-based structural variation panel utilizing activated T lymphocytes and long-read sequencing technology
Authors: Otsuki Akihito , Okamura Yasunobu , Ishida Noriko , Tadaka Shu , Takayama Jun , Kumada Kazuki , Kawashima Junko , Taguchi Keiko , Minegishi Naoko , Kuriyama Shinichi , Tamiya Gen , Kinoshita Kengo , Katsuoka Fumiki , Yamamoto Masayuki 
Published: September 2022

AbstractLong-read sequencing technology enable better characterization of structural variants (SVs). To adapt the technology to population-scale analyses, one critical issue is to obtain sufficient amount of high-molecular-weight genomic DNA. Here, we propose utilizing activated T lymphocytes, which can be established efficiently in a biobank to stably supply high-grade genomic DNA sufficiently. We conducted nanopore sequencing of 333 individuals constituting 111 trios with high-coverage long-read sequencing data (depth 22.2x, N50 of 25.8 kb) and identified 74,201 SVs. Our trio-based analysis revealed that more than 95% of the SVs were concordant with Mendelian inheritance. We also identified SVs associated with clinical phenotypes, all of which appear to be stably transmitted from parents to offspring. Our data provide a catalog of SVs in the general Japanese population, and the applied approach using the activated T-lymphocyte resource will contribute to biobank-based human genetic studies focusing on SVs at the population scale.
The Association between Breast Cancer Related Lymphedema and Area Deprivation Index
Authors: Chiang Sarah N. , Finnan Michael J. , Varagur Kaamya , Skolnick Gary B. , Sacks Justin M. , Christensen Joani M. 
Published: September 2022

Abstract
Background Lymphedema affects up to 34% of patients after breast cancer treatment but remains underdiagnosed and undertreated. Here, we use area deprivation index (ADI), a measure of neighborhood socioeconomic disadvantage, to determine how socioeconomic status may affect risk for and diagnosis of breast cancer-related lymphedema.
Methods Records of patients who underwent surgical treatment of breast cancer between 2017–2020 were examined. Patients' nine-digit ZIP codes were utilized to determine their deprivation level as a national ADI percentile, and those fitting into the most and least deprived quartiles were compared with evaluate lymphedema risk factors and incidence.
Results A total of 1,333 breast cancer patients were included, 812 (61%) of whom resided within the most disadvantaged ADI quartile nationally, and 521 within the least disadvantaged quartile. The most deprived group had higher rates of diabetes, obesity, and regional breast cancer, and received more extensive surgeries (7.5% modified radical mastectomy vs 1.9%, p < 0.001) and chemotherapy compared with the least disadvantaged quartile. The most disadvantaged cohort were more often at extreme risk of lymphedema utilizing the Risk Assessment Tool Evaluating Lymphedema Risk (9.1% versus 2.5%, p < 0.001); however, the incidence of lymphedema diagnoses was not significantly higher (13% vs 12%, p > 0.9). Logistic regression showed that the most deprived ADI quartile had 44% lower odds of a lymphedema diagnosis in comparison to the least deprived quartile.
Conclusion Residing in more socioeconomically disadvantaged neighborhoods is associated with lower odds of a lymphedema diagnosis, despite higher rates of risk factors for lymphedema, suggesting significant underdiagnosis in this population.
Campsiandra laurifolia Reduces Oxidative Stress and Inflammation in Rats with Ulcerative Colitis
Authors: da Fonseca Sandielly Rebeca Benitez , de Souza Lucas Petitemberte , Fillmann Henrique Sarubbi , Hartmann Renata Minuzzo , Colares Josieli Raskopf , Schemitt Elizângela Gonçalves , Brasil Marilda da Silva , Suyenaga Edna Sayuri , Marroni Norma Anair Possa 
Published: September 2022

AbstractUlcerative colitis (UC) affects the mucosa and submucosa of the large intestine. One of the mechanisms involved in its etiology is oxidative stress (OS), directly involved in the inflammatory process characteristic of UC. The Campsiandra laurifolia, known as acapurana, was described as possessing antioxidant properties. We used 24 male Wistar rats, divided into control (CO), control + acapurana (CO + A), colitis (CL), and colitis + acapurana (CL + A) groups. This study performed histological analysis, measuring anal sphincter pressure (ASP) and lipoperoxidation (LPO). The activity of the antioxidant enzyme superoxide dismutase (SOD) and glutathione (GSH) levels were evaluated. The expression of the nuclear factor kappa B (NFκB) and inducible nitric oxide synthase (iNOS) was analyzed by immunohistochemistry. The statistical analysis used was the one-way analysis of variance (ANOVA), followed by the Student-Newman-Keuls test; values were expressed as mean ± standard error, and the significance level was p < 0.05. In the animals of the CL group, we observed the destruction of the crypts and the presence of mucosal ulcers, edema, and submucosal inflammatory infiltrate, as well as increased damage to the intestinal mucosa, reduced ASP, increased LPO and SOD activity, reduced GSH levels, and increased expression of NFκB and iNOS. The administration of C. laurifolia in the CL + A group was shown to cause regeneration of crypts, reduction of inflammatory infiltrate, reduction of damage to the intestinal mucosa, increase in ASP, and reduction in LPO with the restoration of SOD activity and GSH levels. The immunohistochemistry of NFκB and iNOS was significantly reduced. Therefore, the C. laurifolia aqueous extract appears to exert an antioxidant and anti-inflammatory effect in rats with AA-induced colitis.
Correlation between Central Obesity and Liver Function in Young Adults—A Cross-Sectional Study
Authors: Alvin John , KM Damodara Gowda 
Published: September 2022

Abstract:
Background Visceral fat is a more accurate predictor of metabolic and cardiovascular disease risk than body fat alone. Although the liver function is associated with waist-to-hip ratio (WHR) in studies, this correlation is not well established in young central obese individuals. In this study, we examined the correlation between liver function parameters and central obesity in young obese subjects.
Methods Subjects with central obesity among the student and staff community between 18 and 40 years were recruited for the study after their written and informed consent. Male subjects whose WHR is above 0.90 and females above 0.85 were included. The liver function was assessed by estimating alanine transaminase (ALT), aspartate transaminase (AST), albumin, globulin, albumin:globulin ratio (A:G ratio), total bilirubin, direct bilirubin, and Gamma-glutamyl transferase (GGT). The data were analyzed using Pearson correlation to find the statistical significance between lung function parameters in centrally obese individuals with their WHR using SPSS version-16. A p-value less than 0.05 was considered the level of significance.
Results The results showed an insignificant correlation between the liver function parameters (p > 0.05) and WHR except for serum albumin (p < 0.021). The level of AST, ALT, total protein, globulin, A:G ratio, GGT, total Bilirubin, and direct bilirubin in young male and female central obese subjects have not deviated from the normal physiological range.
Conclusion The serum albumin level estimation will be considered an early indicator of metabolic disorder due to central obesity.
Clinical Score Application for Abdominopelvic Computed Tomography Used in the Diagnosis of Renal Colic Patients
Authors: Gönüllü Gizem , Selvi Fatih , Bedel Cihan 
Published: September 2022

Abstract
Background To develop risk scoring for the use of computed tomography (CT) imaging using the visual analog scale (VAS), physical examination, and laboratory findings of renal colic patients admitted to the emergency department (ED).
Materials and Methods This is prospective observational study. Among the patients who presented to the ED with abdominal or flank pain, patients who were scheduled for CT imaging for urolithiasis were included in the study. The mean VAS pain scores, physical examination findings, laboratory parameters, and macroscopic and microscopic values in urinalysis were compared between the two groups with and without stones on CT.
Results Of the 196 urolithiasis patients included in the study, 165 had ureteral stones, 76 had renal stones, and 45 had renal and ureteral stones. While the difference between the urine erythrocyte averages of the two groups was borderline significant (p = 0.04), there was a high difference between the urinary hemoglobin amounts (p < 0.001). In patients with urinary system stone disease, hydronephrosis, and ureteral dilatation, hemoglobin ++ and above were more significant (p < 0.001). For ureteral stones, pain intensity increased as the size increased (r = 0.34 p < 0.001). White blood cells > 10,000 103/mL, and C-reactive protein (CRP) ≤ 5 mg/L were more significant in patients with acute renal colic.
Conclusions Although we cannot develop a clinical scoring system for renal colic patients, the meaningful results we found for urinary stone disease can be used in a newly developed scoring system. It can be used in new scoring systems in the ED using a high VAS score, presence and amount of urine hemoglobin, CRP) ≤ 5 mg/L, and creatinine value.
A connectivity-based approach to evaluating port importance in the global container shipping network
Authors: Jarumaneeroj Pisit , Ramudhin Amar , Barnett Lawton Jorge 
Published: September 2022

AbstractThis paper proposes a framework for evaluating the strategic importance of container ports based on their connectivity. The Container Port Connectivity Index is computed and decomposed into components according to the Liner Shipping Connectivity Index—each reflecting its contribution to the overall port importance score. The framework produces separate scores for each component, thus allowing port stakeholders to better comprehend why a particular port has become important, and for what reasons. The decomposition approach also allows more detailed analyses, and explanations of the impacts of major economic phenomena—i.e., the expansion of Panama Canal or the crumbling of Hanjin shipping—on the relative importance of ports within the Global Container Shipping Network, as more explanatory variables become available. Our computational results indicate that, while the connectivity of ports related to these events is impacted, changes on connectivity rankings could be adequately explained by the proposed decomposition scheme. The inbound connectivity of New York, for example, was slightly improved after the Panama Canal expansion—from the 29th place in Q1/2016 to the 24th place in Q2/2016—due mainly to the rise in the larger capacity of ships calling. However, in Q3/2016, its inbound rank returned to the 29th place, which was mainly due to the decline in the number of liner services available, number of liner companies, and number of ships calling. The effects of Hanjin’s bankruptcy, on the contrary, were more localized and relatively brief.
Translaboration
Authors: Zwischenberger Cornelia , Alfer Alexa 
Published: September 2022

Abstract
Translaboration, a concept derived from blending ‘translation’ and ‘collaboration,’ has the concept of labour at its core. This paper investigates the dimension of labour in online collaborative translation, relates translational labour to Arendt’s categories of work and action, and proceeds to broaden the discussion to the labour involved in translation more generally. It also considers what effect the application of these concepts has on the interests of translators and other stakeholders. Probing the labour of translation has a profound bearing on framings of both voluntary and professional translation practices and potentially reshapes discussions of the translation concept as such. Rather than pitting ‘work’ and ‘labour’ as competing concepts, this paper shows that labour, work, and action all apply to translation and can be brought into productive dialogue in the translaborative space.
Exposure to animal feeding operations including concentrated animal feeding operations (CAFOs) and environmental justice in Iowa, USA
Authors: Son Ji-Young , Bell Michelle L 
Published: September 2022

Abstract
Health consequences of intensive livestock industry and implications for environmental justice are of great concern in Iowa, USA, which has an extensive history of animal feeding operations (AFOs). We examined disparities in exposure to AFOs including concentrated AFOs (CAFOs) with several environmental justice metrics and considered exposure intensity based on animal units (AUs). Using data on permitted AFOs from the Iowa Department of Natural Resources, we evaluated environmental disparities by multiple environmental justice metrics (e.g. race/ethnicity, socio-economic status (SES), income inequality (Gini index), racial isolation, and educational isolation) using 2010 Census tract-level variables. We used an exposure metric incorporating the density and intensity as the sum of AUs within each Census tract. We investigated exposure disparities by comparing distributions of environmental justice metrics based on operation type (e.g. confinement, open feedlot, large CAFOs), animal type, and Census tract-level AFOs exposure intensity categories (i.e. from low exposure (quartile 1) to high exposure (quartile 4)). AFOs in Iowa were located in areas with lower percentages of racial/ethnic minority persons and high SES communities. For example, the percent of the population that is non-Hispanic Black was over 9 times higher in Census tracts without AFOs than tracts with AFOs (5.14% vs. 0.55%). However, when we considered AFO exposure intensity within the areas having AFO exposure, areas with higher AFO exposure had higher percentages of racial/ethnic minority persons (e.g. Hispanic) and low SES communities (e.g. higher educational isolation) compared to areas with lower AFO exposure. Findings by AFO type (e.g. large CAFO, medium CAFO) showed similar patterns of the distribution of environmental justice metrics as the findings for AFOs overall. We identified complex disparities with higher exposure to non-disadvantaged subpopulations when considering areas with versus without AFOs, but higher exposure to disadvantaged communities within areas with AFOs.
MERRIN: MEtabolic regulation rule INference from time series data
Authors: Thuillier Kerian , Baroukh Caroline , Bockmayr Alexander , Cottret Ludovic , Paulevé Loïc , Siegel Anne 
Published: September 2022

AbstractMotivationMany techniques have been developed to infer Boolean regulations from a prior knowledge network (PKN) and experimental data. Existing methods are able to reverse-engineer Boolean regulations for transcriptional and signaling networks, but they fail to infer regulations that control metabolic networks.ResultsWe present a novel approach to infer Boolean rules for metabolic regulation from time-series data and a PKN. Our method is based on a combination of answer set programming and linear programming. By solving both combinatorial and linear arithmetic constraints, we generate candidate Boolean regulations that can reproduce the given data when coupled to the metabolic network. We evaluate our approach on a core regulated metabolic network and show how the quality of the predictions depends on the available kinetic, fluxomics or transcriptomics time-series data.Availability and implementationSoftware available at https://github.com/bioasp/merrin.Supplementary informationSupplementary data are available at https://doi.org/10.5281/zenodo.6670164.
Design centering enables robustness screening of pattern formation models
Authors: Solomatina Anastasia , Cezanne Alice , Kalaidzidis Yannis , Zerial Marino , Sbalzarini Ivo F 
Published: September 2022

AbstractMotivationAccess to unprecedented amounts of quantitative biological data allows us to build and test biochemically accurate reaction–diffusion models of intracellular processes. However, any increase in model complexity increases the number of unknown parameters and, thus, the computational cost of model analysis. To efficiently characterize the behavior and robustness of models with many unknown parameters remains, therefore, a key challenge in systems biology.ResultsWe propose a novel computational framework for efficient high-dimensional parameter space characterization of reaction–diffusion models in systems biology. The method leverages the Lp-Adaptation algorithm, an adaptive-proposal statistical method for approximate design centering and robustness estimation. Our approach is based on an oracle function, which predicts for any given point in parameter space whether the model fulfills given specifications. We propose specific oracles to efficiently predict four characteristics of Turing-type reaction–diffusion models: bistability, instability, capability of spontaneous pattern formation and capability of pattern maintenance. We benchmark the method and demonstrate that it enables global exploration of a model’s ability to undergo pattern-forming instabilities and to quantify robustness for model selection in polynomial time with dimensionality. We present an application of the framework to pattern formation on the endosomal membrane by the small GTPase Rab5 and its effectors, and we propose molecular mechanisms underlying this system.Availability and implementationOur code is implemented in MATLAB and is available as open source under https://git.mpi-cbg.de/mosaic/software/black-box-optimization/rd-parameter-space-screening.Supplementary informationSupplementary data are available at Bioinformatics online.