bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hyperglycemia minimally alters primary self-renewing human colonic epithelial cells while TNFα-promotes severe intestinal epithelial dysfunction
Authors: Dutton Johanna S , Hinman Samuel S , Kim Raehyun , Attayek Peter J , Maurer Mallory , Sims Christopher S , Allbritton Nancy L 
Published: May 2021

Abstract
Hyperglycemia is thought to increase production of inflammatory cytokines and permeability of the large intestine. Resulting intestinal inflammation is then often characterized by excess secretion of tumor necrosis factor alpha (TNFα). Thus, hyperglycemia in hospitalized patients suffering from severe trauma or disease is frequently accompanied by TNFα secretion, and the combined impact of these insults on the intestinal epithelium is poorly understood. This study utilized a simple yet elegant model of the intestinal epithelium, comprised of primary human intestinal stem cells and their differentiated progeny, to investigate the impact of hyperglycemia and inflammatory factors on the colonic epithelium. When compared to epithelium cultured under conditions of physiologic glucose, cells under hyperglycemic conditions displayed decreased mucin-2 (MUC2), as well as diminished alkaline phosphatase (ALP) activity. Conditions of 60 mM glucose potentiated secretion of the cytokine IL-8 suggesting that cytokine secretion during hyperglycemia may be a source of tissue inflammation. TNFα measurably increased secretion of IL-8 and IL-1β, which was enhanced at 60 mM glucose. Surprisingly, intestinal permeability and paracellular transport were not altered by even extreme levels of hyperglycemia. The presence of TNFα increased MUC2 presence, decreased ALP activity, and negatively impacted monolayer barrier function. When TNFα hyperglycemia and ≤30 mM glucose and were combined, MUC2 and ALP activity remained similar to that of TNFα alone, although synergistic effects were seen at 60 mM glucose. An automated image analysis pipeline was developed to assay changes in properties of the zonula occludens-1 (ZO-1)-demarcated cell boundaries. While hyperglycemia alone had little impact on cell shape and size, cell morphologic properties were extraordinarily sensitive to soluble TNFα. These results suggest that TNFα acted as the dominant modulator of the epithelium relative to glucose, and that control of inflammation rather than glucose may be key to maintaining intestinal homeostasis.
Automated production of research data marts from a canonical fast healthcare interoperability resource data repository: applications to COVID-19 research
Authors: Lenert Leslie A , Ilatovskiy Andrey V , Agnew James , Rudisill Patricia , Jacobs Jeff , Weatherston Duncan , Deans Jr Kenneth R 
Published: May 2021

Abstract

Objective
The rapidly evolving COVID-19 pandemic has created a need for timely data from the healthcare systems for research. To meet this need, several large new data consortia have been developed that require frequent updating and sharing of electronic health record (EHR) data in different common data models (CDMs) to create multi-institutional databases for research. Traditionally, each CDM has had a custom pipeline for extract, transform, and load operations for production and incremental updates of data feeds to the networks from raw EHR data. However, the demands of COVID-19 research for timely data are far higher, and the requirements for updating faster than previous collaborative research using national data networks have increased. New approaches need to be developed to address these demands.

Methods
In this article, we describe the use of the Fast Healthcare Interoperability Resource (FHIR) data model as a canonical data model and the automated transformation of clinical data to the Patient-Centered Outcomes Research Network (PCORnet) and Observational Medical Outcomes Partnership (OMOP) CDMs for data sharing and research collaboration on COVID-19.

Results
FHIR data resources could be transformed to operational PCORnet and OMOP CDMs with minimal production delays through a combination of real-time and postprocessing steps, leveraging the FHIR data subscription feature.

Conclusions
The approach leverages evolving standards for the availability of EHR data developed to facilitate data exchange under the 21st Century Cures Act and could greatly enhance the availability of standardized datasets for research.
Application and evaluation of a K-Medoids-based shape clustering method for an articulated design space
Authors: Yousif Shermeen , Yan Wei 
Published: May 2021

AbstractResearch on articulating the design space in computational generative systems is ongoing, to overcome the issue of possible overwhelming multiplicity and redundancy of emerging design options. The article contributes to this line of research of design space articulation, in order to facilitate designers’ successful exploration in computational design. We have recently developed a method for shape clustering using K-Medoids, a machine learning-based strategy. The method performs clustering of similar design shapes and retrieves a representative shape for each cluster in 2D grid-based representation. In this paper, we present a progress in our project where the method has been applied to a new test case, and empirically verified using clustering evaluation methods. Our clustering evaluation results show comparable accuracy when assessed against an external study and provide insight into the evaluation criteria for machine learning methods, as presented in the paper.
Comparison of Artificial Diets and Natural Prey for Mass Rearing of Orius strigicollis (Hemiptera: Anthocoridae) Using Demographic Characteristics to Optimize Cost-Efficiency
Authors: Hung Yi-Ting , Yang Chin-Cheng Scotty , Saska Pavel , Tuan Shu-Jen 
Published: May 2021

Abstract
Orius strigicollis (Poppius) has been commonly released to control minute pests due to its remarkable foraging and predation ability. Despite decades long history of mass-rearing using eggs of Cadra cautella Walker (Lepidoptera: Pyralidae) as food, the cost of this food impeded the predator’s marketing potential. Finding cost-effective artificial diets for mass rearing programs is, therefore, the key to promote the use of this generalist predator in practice. The aim of this study was to explore suitability of alternative diets for mass rearing of this predator, using the age-stage, two-sex life table. Eight recipes of artificial diets were initially screened, and the candidate diets were subsequently evaluated using the population parameters of O. strigicollis. The highest intrinsic rate of increase was found in the O. strigicollis fed on the meridic combined Diet 1, where nymphs and adults were fed different diets. However, the intensive period of oviposition by females reared on oligidic Diet O3 contributed to the shorter rearing period (42 d) and lower rearing cost than that on combined Diet 1 (60 d). Besides, with the harvest rate of 0.919, the minimal population size of 10,774 individuals with a stable age-stage distribution was needed for daily harvesting 1,000 third instars of O. strigicollis reared on Diet O3 at the rearing cost of 0.295 NTD (new Taiwanese dollar) per nymph. Thus, Diet O3 was determined to be the most cost-effective recipe for the mass-rearing of O. strigicollis among those used in this study.
Intraday Trades Profile Estimation: An Intensity Approach
Authors: Sancetta Alessio 
Published: May 2021

Abstract
The intraday trades profile is the expected intensity of a counting process where the counts measure the number of trades over an interval. It needs to capture the salient features of the trading activity, its spikes, and periods of relative quietness. This calls for an estimator with a time varying resolution that allows us to identify jumps. The problem can be recast as a regression one, using a fused Lasso penalty. The framework allows us to identify jumps within possibly thousands different locations within a day when the number of trading days at disposal is in the order of hundreds. This can be done without imposing any conditions on the counting process except for certain regularity conditions on the expected intensity. The empirical results suggest that much of the trading activity in some liquid futures can be captured by a deterministic seasonal component in the trade arrival process.
How US Private Foundations Change Payouts Based on Financial Shocks: Revealed Publicness or Revealed Privateness?
Authors: Calabrese Thad D , Ely Todd L 
Published: May 2021

AbstractThis article asks what distribution behavior of private foundations in the United States reveals about their motivations and strategy. Do private foundations intentionally distribute additional money to grantees to help them manage through business cycles and maintain services during economic downturns? Such behavior would be consistent with revealed publicness with respect to distributions. Do they retrench during difficult economic times to protect their endowments? Or do they simply distribute money independent from the larger economy? The current study considers these conflicting expectations, and empirically tests whether private foundation distributions vary with endowment returns and the larger economy as suggested by competing theories. Using administrative data filed with the Internal Revenue Service, fixed effects regression models indicate that private foundations change distributions in a manner consistent with retrenchment or independently from the larger economy, depending on the sample used. The results do not support the notion that private foundations act with prosocial-countercyclical motivations about distributions—in which more money is distributed during economic downturns—despite their receiving significant public subsidies.
p-Coumaric acid mitigates lipopolysaccharide induced brain damage via alleviating oxidative stress, inflammation and apoptosis
Authors: Daroi Pratibha Atul , Dhage Shrikant Ninaji , Juvekar Archana Ramesh 
Published: May 2021

Abstract

Objectives
Systemic administration of lipopolysaccharide induces neuroinflammation leading to cognitive deficit and memory impairment. Herein, we investigated the effects of p-Coumaric acid (PCA) in LPS induced neuroinflammation in mice. PCA is reported to possess free radicle scavenging and neuroprotective action.

Methods
Mice received treatment with PCA (80 mg/kg, and 100 mg/kg, p.o.) for 28 days. LPS (0.25 mg/kg) was administered intraperitoneally from Day 15 to 21, to all groups. Memory impairment and cognitive deficit were assessed by MWM and Y maze test, followed by estimation of ROS, TNF-α, IL-6, caspase-3 and c-Jun in the brain homogenate by ELISA. Histopathological changes were investigated using Nissl and H&E staining.

Key findings
PCA attenuated increased oxidative stress, significantly increasing SOD, GSH levels and decreasing MDA level and AChE activity in mice brain, lowered the levels of TNF-α and IL-6 indicating protection against neuroinflammatory reaction. PCA also suppressed neuronal apoptosis, as indicated by decreased levels of caspase-3 and c-Jun. Further, histopathological findings revealed that PCA attenuated neuronal loss and pathological abnormalities in the hippocampus.

Conclusions
Our findings give compulsive evidence suggesting a protective effect of PCA in neuroinflammation, cognitive impairment and neuronal apoptosis induced by LPS, through its antioxidant, AChE inhibitory, anti-inflammatory and antiapoptotic activity determined by behavioural, biochemical and histopathological measures.
Reactive oxygen species and organellar signaling
Authors: Phua Su Yin , De Smet Barbara , Remacle Claire , Chan Kai Xun , Van Breusegem Frank 
Published: May 2021

Abstract
The evolution of photosynthesis and its associated metabolic pathways has been crucial to the successful establishment of plants, but has also challenged plant cells in the form of production of reactive oxygen species (ROS). Intriguingly, multiple forms of ROS are generated in virtually every plant cell compartment through diverse pathways. As a result, a sophisticated network of ROS detoxification and signaling that is simultaneously tailored to individual organelles and safeguards the entire cell is necessary. Here we take an organelle-centric view on the principal sources and sinks of ROS across the plant cell and provide insights into the ROS-induced organelle to nucleus retrograde signaling pathways needed for operational readjustments during environmental stresses.
Parsec-scale properties of eight Fanaroff–Riley type 0 radio galaxies
Authors: Cheng Xiaopeng , An Tao , Sohn Bong Won , Hong Xiaoyu , Wang Ailing 
Published: May 2021

ABSTRACT
We report the high-resolution radio observations of eight Fanaroff–Riley type 0 radio galaxies (FR 0s), selected from the published FR 0 sample. These observations were carried out with the Very Long Baseline Array (VLBA) and European VLBI Network (EVN) at frequencies of 5 and 8 GHz with a highest resolution of ∼0.6 milliarcsec. All eight sources show compact structures on projected physical sizes of 0.3–10 parsec. Six sources show a two-sided structure and two sources show a one-sided jet structure. J1025+1022 shows an X-shaped jet structure, which could result from a reorientation of the jet axis due to a restart of the central engine or a projection of a highly curved inner jet. However, more studies are needed to examine these scenarios. Proper motions for 22 jet components of the eight sources are determined to be between $-0.08\, c$ and $0.51\, c$. Although most of the sources exhibit flat spectra, other observed characteristics, such as low-amplitude flux density variations, low jet proper motion speeds and symmetric two-sided jet structures, tend to support the fact that the parsec-scale FR 0 jets are mildly relativistic with lower bulk Lorentz factors and larger viewing angles.
The spatial power spectrum and derived turbulent properties of isolated galaxies
Authors: Körtgen Bastian , Pingel Nickolas , Killerby-Smith Nicholas 
Published: May 2021

ABSTRACT
The turbulent dynamics of nearby and extragalactic gas structures can be studied with the column density power spectrum that is often described by a broken power law. In an extragalactic context, the breaks in the power spectra have been interpreted to constrain the disc scale height, which marks a transition from 2D disc-like to 3D motion. However, this interpretation has recently been questioned when accounting for instrumental effects. We use numerical simulations to study the spatial power spectra of isolated galaxies and investigate the origins of the break scale. We split the gas into various phases and analyse the time evolution of the power spectrum characteristics, such as the slope(s) and the break scale. We find that the break scale is phase dependent. The physics traced by the break scale also differ: in the warm gas it marks the transition from 2D (disc-like) to 3D (isotropic) turbulence. In the cold gas, the break scale traces the typical size of molecular clouds. We further show that the break scale almost never traces the disc scale height. We study turbulent properties of the interstellar medium (ISM) to show that, in the case where the break scale traces a transition to isotropic turbulence, the fraction of required accretion energy to sustain turbulent motions in the ISM increases significantly. Lastly, we demonstrate through simulated observations that it is crucial to account for observational effects, such as the beam and instrumental noise, in order to accurately recover the break scale in real observations.
Collisional excitation of deuterated hydroxyl (OD) by molecular hydrogen
Authors: Dagdigian Paul J 
Published: May 2021

ABSTRACT
Cross sections and rate coefficients for transitions between hyperfine levels associated with the 14 lowest rotational/fine-structure levels of OD induced by collisions with ortho-H2 and para-H2 are presented. These collisional parameters have been computed in time-independent close-coupling quantum-scattering calculations with a potential energy surface (PES) describing the OD–H2 interaction, which was obtained by transformation of the OH–H2 PES. Rate coefficients have been computed for temperatures from 5 to 200 K. Cross sections for OD transitions between rotational/fine-structure levels are found to be significantly larger than the corresponding transitions in OH, mainly because of the reduced energy gaps in OD. The hyperfine-resolved rate coefficients were employed in simple radiative transfer calculations for OD and compared with analogous calculations for OH.
The influence of the size of ice–dust particles on the amplitude of the change in the brightness of a comet caused by an outburst
Authors: Wesołowski M 
Published: May 2021

ABSTRACTThis paper presents a new approach to analysing the brightness change of a Jupiter family comet. We assume that the coma contains particles composed of water ice, carbonaceous, and silicate dust. Different sizes of dust particles were taken into account following the adopted size distribution. From an analysis of modern space missions, it is clear that the sizes of the dominant coma particles at the time of the outburst are in the order of micrometres to centimetres. However, most of these particles have dimensions that are comparable to the wavelength of electromagnetic radiation coming from the Sun. In the case of dust particles, four groups were distinguished depending on their dimensions. The performed calculations show that the particle size significantly influences the change of the cometary brightness, i.e. the scattering efficiency of the incident sunlight that occurs on the particle. The conducted numerical simulations show that the changes in the brightness of the comet oscillate approximately from −8 to −1 mag. This means that we can talk about outbursts, the amplitudes of which are most often observed.
The Evolution Pathway of Ammonia-Oxidizing Archaea Shaped by Major Geological Events
Authors: Yang Yiyan , Zhang Chuanlun , Lenton Timothy M , Yan Xinmiao , Zhu Maoyan , Zhou Mengdi , Tao Jianchang , Phelps Tommy J , Cao Zhiwei 
Published: May 2021

Abstract
Primordial nitrification processes have been studied extensively using geochemical approaches, but the biological origination of nitrification remains unclear. Ammonia-oxidizing archaea (AOA) are widely distributed nitrifiers and implement the rate-limiting step in nitrification. They are hypothesized to have been important players in the global nitrogen cycle in Earth’s early history. We performed systematic phylogenomic and marker gene analyses to elucidate the diversification timeline of AOA evolution. Our results suggested that the AOA ancestor experienced terrestrial geothermal environments at ∼1,165 Ma (1,928–880 Ma), and gradually evolved into mesophilic soil at ∼652 Ma (767–554 Ma) before diversifying into marine settings at ∼509 Ma (629–412 Ma) and later into shallow and deep oceans, respectively. Corroborated by geochemical evidence and modeling, the timing of key diversification nodes can be linked to the global magmatism and glaciation associated with the assembly and breakup of the supercontinent Rodinia, and the later oxygenation of the deep ocean. Results of this integrated study shed light on the geological forces that may have shaped the evolutionary pathways of the AOA, which played an important role in the ancient global nitrogen cycle.
IUPred3: prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation
Authors: Erdős Gábor , Pajkos Mátyás , Dosztányi Zsuzsanna 
Published: May 2021

AbstractIntrinsically disordered proteins and protein regions (IDPs/IDRs) exist without a single well-defined conformation. They carry out important biological functions with multifaceted roles which is also reflected in their evolutionary behavior. Computational methods play important roles in the characterization of IDRs. One of the commonly used disorder prediction methods is IUPred, which relies on an energy estimation approach. The IUPred web server takes an amino acid sequence or a Uniprot ID/accession as an input and predicts the tendency for each amino acid to be in a disordered region with an option to also predict context-dependent disordered regions. In this new iteration of IUPred, we added multiple novel features to enhance the prediction capabilities of the server. First, learning from the latest evaluation of disorder prediction methods we introduced multiple new smoothing functions to the prediction that decreases noise and increases the performance of the predictions. We constructed a dataset consisting of experimentally verified ordered/disordered regions with unambiguous annotations which were added to the prediction. We also introduced a novel tool that enables the exploration of the evolutionary conservation of protein disorder coupled to sequence conservation in model organisms. The web server is freely available to users and accessible at https://iupred3.elte.hu.
Quantifying splice-site usage: a simple yet powerful approach to analyze splicing
Authors: Dent Craig I , Singh Shilpi , Mukherjee Sourav , Mishra Shikhar , Sarwade Rucha D , Shamaya Nawar , Loo Kok Ping , Harrison Paul , Sureshkumar Sridevi , Powell David , Balasubramanian Sureshkumar 
Published: May 2021

AbstractRNA splicing, and variations in this process referred to as alternative splicing, are critical aspects of gene regulation in eukaryotes. From environmental responses in plants to being a primary link between genetic variation and disease in humans, splicing differences confer extensive phenotypic changes across diverse organisms (1–3). Regulation of splicing occurs through differential selection of splice sites in a splicing reaction, which results in variation in the abundance of isoforms and/or splicing events. However, genomic determinants that influence splice-site selection remain largely unknown. While traditional approaches for analyzing splicing rely on quantifying variant transcripts (i.e. isoforms) or splicing events (i.e. intron retention, exon skipping etc.) (4), recent approaches focus on analyzing complex/mutually exclusive splicing patterns (5–8). However, none of these approaches explicitly measure individual splice-site usage, which can provide valuable information about splice-site choice and its regulation. Here, we present a simple approach to quantify the empirical usage of individual splice sites reflecting their strength, which determines their selection in a splicing reaction. Splice-site strength/usage, as a quantitative phenotype, allows us to directly link genetic variation with usage of individual splice-sites. We demonstrate the power of this approach in defining the genomic determinants of splice-site choice through GWAS. Our pilot analysis with more than a thousand splice sites hints that sequence divergence in cis rather than trans is associated with variations in splicing among accessions of Arabidopsis thaliana. This approach allows deciphering principles of splicing and has broad implications from agriculture to medicine.