bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accelerated Bayesian inference of population size history from recombining sequence data
Authors: Terhorst Jonathan 
Published: March 2024

AbstractI presentphlash, a new Bayesian method for inferring population history from whole genome sequence data.phlashispopulationhistorylearning byaveragingsampledhistories: it works by drawing random, low-dimensional projections of the coalescent intensity function from the posterior distribution of apsmc-like model, and averaging them together to form an accurate and adaptive size history estimator. On simulated data,phlashtends to be faster and have lower error than several competing methods includingsmc++,msmc2, and FitCoal. Moreover, it provides a full posterior distribution over population size history, leading to automatic uncertainty quantification of the point estimates, as well to new Bayesian testing procedures for detecting population structure and ancient bottlenecks. On the technical side, the key advance is a novel algorithm for computing the score function (gradient of the log-likelihood) of a coalescent hidden Markov model: when there areMhidden states, the algorithm requires. 𝒪(M2) time and. 𝒪(1) memory per decoded position, the same cost as evaluating the log-likelihood itself using the naïve forward algorithm. This algorithm is combined with a hand-tuned implementation that fully leverages the power of modern GPU hardware, and the entire method has been released as an easy-to-use Python software package.
Metabolic Disease and The Risk of Post-COVID Conditions: A Retrospective Cohort Study
Authors: Xie Wubin , Hsu Heather E. , Shafer Paul R. , Podolsky Meghan I. , Stokes Andrew C. 
Published: March 2024

ABSTRACTObjectiveTo examine the influence of having a baseline metabolic disorder (diabetes, hypertension, and/or obesity) on the risk of developing new clinical sequelae potentially related to SARS-CoV-2 in a large sample of commercially insured adults in the US.Design, setting, and participantsDeidentified data were collected from the IBM/Watson MarketScan Commercial Claims and Encounters (CCAE) Databases and Medicare Supplemental and Coordination of Benefits (MDCR) Databases from 2019 to 2021. A total of 839,344 adults aged 18 and above with continuous enrollment in the health plan were included in the analyses. Participants were grouped into four categories based on their COVID-19 diagnosis and whether they had at least one of the three common metabolic disorders at baseline (diabetes, obesity, or hypertension).Measures and methodsICD-10-CM codes were used to determine new symptoms and conditions after the acute phase of SARS-CoV-2 infection, defined as ending 21 days after initial diagnosis date, or index period for those who did not have a COVID-19 diagnosis. Propensity score matching (PSM) was used to create comparable reference groups. Cox proportional hazard models were conducted to estimate hazard ratios and 95% confidence intervals.ResultsAmong the 772,377 individuals included in the analyses, 36,742 (4.8%) without and 20,912 (2.7%) with a baseline metabolic disorder were diagnosed with COVID-19. On average, COVID-19 patients with baseline metabolic disorders had more 2.4 more baseline comorbidities compared to those without baseline metabolic disorders. Compared to adults with no baseline metabolic condition, the risks of developing new clinical sequelae were highest among COVID-19 patients with a baseline metabolic condition (HRs ranging from 1.51 to 3.33), followed by those who had a baseline metabolic condition but with no COVID-19 infection (HRs ranging from 1.33 to 2.35), and those who had COVID-19 but no baseline metabolic condition (HRs ranging from 1.34 to 2.85).ConclusionsIn a large national cohort of commercially insured adults, COVID-19 patients with a baseline metabolic condition had the highest risk of developing new clinical sequelae post-acute infection phase, followed by those who had baseline metabolic condition but no COVID-19 infection and those who had COVID-19 but no baseline metabolic disorder.
Anorexia nervosa is associated with higher brain mu-opioid receptor availability
Authors: Pak Kyoungjune , Tuisku Jouni , Karlsson Henry K. , Hirvonen Jussi , Rebelos Eleni , Pekkarinen Laura , Sun Lihua , Latva-Rasku Aino , Helin Semi , Rajander Johan , Karukivi Max , Nuutila Pirjo , Nummenmaa Lauri 
Published: March 2024

ABSTRACTAnorexia nervosa (AN) is a severe psychiatric disorder, characterized by restricted eating, fear to gain weight, and a distorted body image. Mu-opioid receptor (MOR) functions as a part of complex opioid system and supports both homeostatic and hedonic control of eating behavior. Thirteen patients with AN and thirteen healthy controls (HC) were included in this study. We measured 1) MOR availability with [11C]carfentanil positron emission tomography (PET), 2) brain glucose uptake (BGU) with 2-deoxy-2[18F]fluoro-D-glucose ([18F]FDG) PET during hyperinsulinemic-euglycemic clamp and 3) blood-oxygen-level-dependent signal with functional magnetic resonance imaging. All subjects underwent a screening visit consisting of physical examination, anthropometric measurements, fasting blood samples, an oral glucose tolerance test, psychiatric assessment, and an inquiry regarding medical history. Body fat mass (%) was measured and M value was calculated. MOR availability from caudate and putamen was higher in patients with AN and those from nucleus accumbens (NAcc) and thalamus showed the higher trend in patients with AN. There was no area where MOR availability was lower in patients with AN. BGU was not different between AN and HC. MOR availability and BGU were negatively correlated in caudate, NAcc and thalamus and showed the trend of negative association in putamen. In conclusion, AN is associated with higher MOR availability in the brain regions implicated in reward processing, while BGU remains unaltered. Therefore, the endogenous opioid system might be one of the key components underlying AN. This better understanding of AN could support the development of new treatments for AN.
Comparative Analysis of DNA Structural Parameters and the Corresponding Computational Tools to Differentiate Regulatory DNA Motifs and Promoters
Authors: Manivelan Vasumathi , Kavyashree Basavaraju , Sadanandan Bindu , Vaidya Sravanti , Acharya Kshitish K 
Published: March 2024

ABSTRACTAnalyzing and distinguishing functionally distinct DNA regions is crucial for various applications, including predicting DNA motifs and promoters, and exploring the mechanisms of gene expression regulation in disease conditions. Our understanding of mammalian promoters, particularly those associated with differentially expressed genes (DEGs), particularly remains limited. However, existing methods for such analysis require refinement. Despite the value of DNA Structural Parameters (DSPs), users often struggle to objectively select parameters and tools, especially given the limited options available. This study addresses this challenge by thoroughly investigating DSP-tool combinations – particularly the local structural parameters that can be analyzed via web-interfaces, with a goal to discern human DNA motifs and promoters. What sets this study apart are the following aspects: a) examination of disease-associated promoters; b) attention to regulatory specific DNA motifs; c) compilation and comparison of all publicly available online tools and parameters for analyzing DNA structures, and test all available DSP-tool combinations. Through the execution of over half a million queries, the study identified DSP-tool combinations that consistently outperformed others in differentiating DNA sequences across various types of analyses. Notably, the ‘propeller twist’ emerged as a standout DSP, while DNAshape, complemented by DNAshapeR scripts, demonstrated exceptional performance among the tools across four distinct types of analyses: testing motifs, sequences post motif insertion, comparing promoters with control sequences, and analyzing promoters of genes either up- or down-regulated under disease conditions. Significant alterations were observed in the values of multiple DSPs for 100-nucleotide-long promoter and control sequences following the insertion of single motifs such as triplex target sites (TTS), quadruplex-forming structural motifs (QSFM), and transcription factor binding sites (TFBS). However, no single combination proved universally successful. For instance, when analyzing promoters associated with differential gene expression, different combinations proved effective across various human diseases. These findings provide valuable insights for making informed selections among available options for sequence-based queries.
TFIIS is required for reproductive development and thermal adaptation in barley
Authors: Ahmad Imtiaz , András Kis , Verma Radhika , Szádeczky-Kardoss István , Szaker Henrik Mihály , Pettkó-Szandtner Aladár , Silhavy Dániel , Havelda Zoltán , Csorba Tibor 
Published: March 2024

AbstractRegulation of transcriptional machinery and its adaptive role under different stress conditions are studied extensively in the dicot model plantArabidopsis, but our knowledge on monocot species remains elusive. TFIIS is an RNA polymerase II associated transcription elongation co-factor. Previously it was shown that TFIIS ensures efficient transcription elongation that is necessary for heat stress survival inA. thaliana. However, the function of TFIIS has not been analysed in monocots. In the present work, we have generated and studied independenttfIIscrisprmutant barley lines. We show that, TFIIS is needed for reproductive development and heat stress survival in barley. The molecular basis of HS-sensitivity oftfIIsmutants is the retarded expression of heat stress protein transcripts, that leads to late accumulation of HSP chaperones, enhanced proteotoxicity and ultimately to lethality. We also show that TFIIS is induced and autoregulated in response to heat, supporting a conserved adaptive function of these control elements for plant thermal adaptation. In sum, our results are a step forward for the better understanding of transcriptional machinery regulation in monocot crops.
A Novel 3D Imaging Approach for Quantification of GLUT4 Levels across the Intact Myocardium
Authors: Geiser Angéline , Currie Susan , Al-Hasani Hadi , Chadt Alexandra , McConnell Gail , Gould Gwyn W. 
Published: March 2024

ABSTRACTCellular heterogeneity is a well-accepted feature of tissues, and both transcriptional and metabolic diversity have been revealed by numerous approaches, including optical imaging. However, the high magnification objective lenses needed for high-resolution imaging provides information from only small layers of tissue, which can result in poor cell statistics. There is therefore an unmet need for an imaging modality that can provide detailed molecular and cellular insight within intact tissue samples in 3D. Using GFP-tagged GLUT4 as proof of concept, we present here a novel optical mesoscopy approach that allows precise measurement of the spatial location of GLUT4 within specific anatomical structures across the myocardium in ultrathick sections (5 mm x 5 mm x 3 mm) of intact mouse heart. We reveal distinct GLUT4 distribution patterns across cardiac walls and highlight specific changes in GLUT4 expression levels in response to high fat diet-feeding, and we identify gender-dependent differences in expression patterns. This method is applicable to any target that can be labelled for light microscopy, and to other complex tissues when organ structure needs to be considered simultaneously with cellular detail.SUMMARY STATEMENTHere we present a novel 3D optical mesoscopy approach that allows the study of both GLUT4 protein expression levels and structural distribution within ultrathick sections of intact murine hearts, in response to high fat diet-feeding.
Fibroblasts enhance the growth and survival of adult feline small intestinal organoids
Authors: Hryckowian Nicole D , Studener Katelyn , Knoll Laura J 
Published: March 2024

AbstractIntestinal organoids are important cell culture models that complement live animal studies of intestinal biology. Adult feline small intestinal organoids are needed for infectious disease research but are difficult to work with due to slow growth and rapid senescence. We introduce a method of co-culturing adult feline small intestinal organoids with growth inhibited human foreskin fibroblast feeder cells to enhance organoid proliferation and survival. With feeder cells, feline jejunal and ileal organoids survived at least nine months in culture until cryopreservation. Fibroblast supplementation also increased the maximum size of cat and mouse intestinal organoids, making them easier for microinjection. The increased proliferation, longevity, and size make fibroblast-supplementation of feline small intestinal organoids a significant improvement on current methods. These methods have high potential to reduce the number of cats used for research and may be applicable for intestinal cells from other animals that are difficult to culture.
Unravelling open innovation determinants and firm performance relationships in CEE and SEE countries
Authors: Abazi-Alili Hyrije , Hashi Iraj , Rexhepi Gadaf , Ramadani Veland , Kallmuenzer Andreas 
Published: March 2024

Purpose Open innovation (OI), by now one of the major concepts for the analysis of innovation, is seen as a methodology for collaboratively designing and implementing solutions by engaging stakeholders in an iterative and inclusive service design process. This paper aims to empirically investigate OI capacities, defined as a cooperative, knowledge-sharing innovation ecosystem, and to explore how it can lead to improved performance of firms in Central and Eastern European (CEE) and Southeastern European (SEE) countries.Design/methodology/approach The study builds on the World Bank/European Bank for Reconstruction and Development (EBRD’s) Business Environment Enterprise Performance Survey (BEEPS) dataset for 2009, 2013 and 2019. Primarily, the research model was estimated using log-transformed ordinary least squares (OLS). Taking into consideration that this method might produce substantial bias, yielding misleading inferences, this study is fitting Poisson pseudo maximum likelihood estimators with robust standard errors and instrumental variable/generalized method of moments estimation (IV/GMM) approach for comparative results. Secondarily, the research model was tested using structural equation modelling (SEM) to investigate the relationship between five OI capacities and firm performance.Findings The findings indicate that there is a significant positive relationship between most OI capacities and firm performance, except for innovation, which did not show a statistically significant relationship with firm performance. Specifically, research and development (R&D), knowledge and coopetition are statistically significant and positively associated with firm performance, whereas transformation is statistically significant but negatively associated with firm performance. The IV/GMM estimations’ findings support the view that the firm performance is significantly affected by OI capacities, together with some control variables such as size, age, foreign ownership and year dummy to have a significant impact on firm performance.Originality/value This paper fills an identified gap in the literature by investigating the impact of OI on firm performance executed in the specific CEE and SEE country context.
Evaluating spatial inequity in last-mile delivery: a national analysis
Authors: Fried Travis , Goodchild Anne Victoria , Sanchez-Diaz Ivan , Browne Michael 
Published: March 2024

PurposeDespite large bodies of research related to the impacts of e-commerce on last-mile logistics and sustainability, there has been limited effort to evaluate urban freight using an equity lens. Therefore, this study proposes a modeling framework that enables researchers and planners to estimate the baseline equity performance of a major e-commerce platform and evaluate equity impacts of possible urban freight management strategies. The study also analyzes the sensitivity of various operational decisions to mitigate bias in the analysis.Design/methodology/approachThe model adapts empirical methodologies from activity-based modeling, transport equity evaluation, and residential freight trip generation (RFTG) to estimate person- and household-level delivery demand and cargo van traffic exposure in 41 U.S. Metropolitan Statistical Areas (MSAs).FindingsEvaluating 12 measurements across varying population segments and spatial units, the study finds robust evidence for racial and socio-economic inequities in last-mile delivery for low-income and, especially, populations of color (POC). By the most conservative measurement, POC are exposed to roughly 35% more cargo van traffic than white populations on average, despite ordering less than half as many packages. The study explores the model’s utility by evaluating a simple scenario that finds marginal equity gains for urban freight management strategies that prioritize line-haul efficiency improvements over those improving intra-neighborhood circulations.Originality/valuePresents a first effort in building a modeling framework for more equitable decision-making in last-mile delivery operations and broader city planning.
Is the proliferation of private standards acting as a non-tariff trade barrier in agrifood trade? Evidence from Chilean grape exports
Authors: Anríquez Gustavo , Gajardo José Tomás , Henry de Frahan Bruno 
Published: March 2024

PurposeThe purpose of this paper is to describe and analyze the impacts that the recent proliferation of private and overlapping standards is having in the trade of agricultural products from developing countries.Design/methodology/approachIn a first stage industry experts in the Chilean fresh fruit trading industry were interviewed to understand the perceived impact that private standards are imposing in the industry. These interviews allowed to identify the market case study, table grapes, the landscape of private standards and their prevalence in different countries. In a second stage, a gravity trade model for trade in table grapes was estimated, with a focus on the more stringent countries identified by experts in the first stage.FindingsWe show evidence that the proliferation of private standards required by large European retailers has diverted trade away from more stringent countries that require more certifications (and into less stringent European markets). We also show that the costs of these additional certifications have been shared by trading partners, via an increase in direct sales, as opposed to consignment (the traditional marketing mode), which is associated with higher prices.Research limitations/implicationsThe impacts of the recent proliferation of private and overlapping standards in international trade needs to be better understood both by the legal and economic literature. While the use of private standards has been growing since the 1990s, there is a recent trend of large European retailers imposing their own and overlapping standards that needs to be better understood to inform policy.Originality/valueWhile there is a thin literature on the impact of private standards on trade, most of this has studied the effects of the now de facto mandatory GlobalGAP certification. However, there is a recent trend by large European retailers of demanding their own private certifications, together with other already existing overlapping private standards. This study describes and analyzes the impacts of this rather new trend.
The power of good corporate governance in activating the impact of internal information quality on tax savings
Authors: Saragih Arfah Habib 
Published: March 2024

PurposeThis paper examines the moderating effect of good corporate governance on the association between internal information quality and tax savings.Design/methodology/approachThis study uses a quantitative approach. It employs an Australian sample of analysis composed of 1,295 firm-year observations from the period 2017 to 2021. Data relating to corporate governance are hand-collected from the annual reports.FindingsBased on the result of the analysis, this study demonstrates that the interaction between corporate governance and quality of internal information is positively associated with tax savings. Superior corporate governance is critical in activating the effect of internal information quality on tax savings. This finding is robust to a battery of robustness checks and additional tests.Research limitations/implicationsThis examination utilizes only publicly traded companies from one developed country.Practical implicationsFor the company management, an effective governance structure must be at the top because it will determine the development of all other areas. This study emphasizes the need to continuously improve the effectiveness of corporate governance practices. For long-term investors, an important indicator that can be considered in assessing the “safety” of a company’s tax strategy is its corporate governance aspects. For regulators, this study is expected to assist regulators in creating a more adequate corporate governance implementation and disclosure package to be implemented by corporations in the future.Originality/valueThis study provides new evidence on a crucial construct that can strengthen the relationship between internal information quality and tax savings.
Green marketing strategy, technology implementation and corporate performance: the role of green creative behaviour and institutional isomorphism
Authors: Nyamekye Michael Boadi , Martey Edward Markwei , Agbemabiese George Cudjoe , Preko Alexander Kofi , Gyepi-Garbrah Theophilus , Appah Emmanuel 
Published: March 2024

PurposeThis paper aimed to test a proposed framework highlighting strategic green marketing initiatives and how they drive new technology implementation towards green corporate performance, underpinned by institutional isomorphism.Design/methodology/approachThe study used a quantitative method and convenience sampling approach in gathering data using adapted questionnaires to solicit first-hand information from 225 employees of small and medium-sized enterprises (SMEs) in the tourism and hospitality sector underpinned by the theory of institutional isomorphism.FindingsThe study shows that green communication and green strategy alignment have significant predictive effects on new technology implementation. Cultural isomorphism significantly moderated the effects of implementing new technology (i.e. green communication and strategy alignment). In addition, “new technology implementation had a significant predictive effect on green corporate performance”. Meanwhile, the moderation effect of “green creative behaviour on the new technology-green corporate performance dyad was positive but insignificant.”Originality/valueThe study’s novel framework confirms how green communication strategy and green strategy alignment complement cultural isomorphism to explain the impact of new technology implementation on green corporate performance, underpinned by institutional isomorphism.