bluuebunny/crossref_metadata_2025_split huggingface dataset:
Failed despots and the equitable distribution of fitness in a subsidized species
Authors: Brunk Kristin M , West Elena H , Peery M Zachariah , Pidgeon Anna 
Published: July 2022

AbstractTerritorial species are often predicted to adhere to an ideal despotic distribution and under-match local food resources, meaning that individuals in high-quality habitat achieve higher fitness than those in low-quality habitat. However, conditions such as high density, territory compression, and frequent territorial disputes in high-quality habitat are expected to cause habitat quality to decline as population density increases and, instead, promote resource matching. We studied a highly human-subsidized and under-matched population of Steller’s jays (Cyanocitta stelleri) to determine how under-matching is maintained despite high densities, compressed territories, and frequent agonistic behaviors, which should promote resource matching. We examined the distribution of fitness among individuals in high-quality, subsidized habitat, by categorizing jays into dominance classes and characterizing individual consumption of human food, body condition, fecundity, and core area size and spatial distribution. Individuals of all dominance classes consumed similar amounts of human food and had similar body condition and fecundity. However, the most dominant individuals maintained smaller core areas that had greater overlap with subsidized habitat than those of subordinates. Thus, we found that (1) jays attain high densities in subsidized areas because dominant individuals do not exclude subordinates from human food subsidies and (2) jay densities do not reach the level necessary to facilitate resource matching because dominant individuals monopolize space in subsidized areas. Our results suggest that human-modified landscapes may decouple dominance from fitness and that incomplete exclusion of subordinates may be a common mechanism underpinning high densities and creating source populations of synanthropic species in subsidized environments.
HiC-TE: a computational pipeline for Hi-C data analysis to study the role of repeat family interactions in the genome 3D organization
Authors: Lexa Matej , Cechova Monika , Nguyen Son Hoang , Jedlicka Pavel , Tokan Viktor , Kubat Zdenek , Hobza Roman , Kejnovsky Eduard 
Published: July 2022

AbstractMotivationThe role of repetitive DNA in the 3D organization of the interphase nucleus is a subject of intensive study. In studies of 3D nucleus organization, mutual contacts of various loci can be identified by Hi-C sequencing. Typical analyses use binning of read pairs by location to reduce noise. We use binning by repeat families instead to make similar conclusions about repeat regions.ResultsTo achieve this, we combined Hi-C data, reference genome data and tools for repeat analysis into a Nextflow pipeline identifying and quantifying the contacts of specific repeat families. As an output, our pipeline produces heatmaps showing contact frequency and circular diagrams visualizing repeat contact localization. Using our pipeline with tomato data, we revealed the preferential homotypic interactions of ribosomal DNA, centromeric satellites and some LTR retrotransposon families and, as expected, little contact between organellar and nuclear DNA elements. While the pipeline can be applied to any eukaryotic genome, results in plants provide better coverage, since the built-in TE-greedy-nester software only detects tandems and LTR retrotransposons. Other repeats can be fed via GFF3 files. This pipeline represents a novel and reproducible way to analyze the role of repetitive elements in the 3D organization of genomes.Availability and implementationhttps://gitlab.fi.muni.cz/lexa/hic-te/.Supplementary informationSupplementary data are available at Bioinformatics online.
Inhibition of lysosomal acid β-glucosidase induces cell apoptosis via impairing mitochondrial clearance in pancreatic cancer
Authors: Yanagaki Mitsuru , Shirai Yoshihiro , Shimada Yohta , Hamura Ryoga , Taniai Tomohiko , Horiuchi Takashi , Takada Naoki , Haruki Koichiro , Furukawa Kenei , Uwagawa Tadashi , Kobayashi Hiroshi , Ikegami Toru 
Published: July 2022

Abstract
Sphingolipid metabolism plays an important role in the formation of cellular membranes and is associated with malignant potential and chemosensitivity of cancer cells. Sphingolipid degradation depends on multiple lysosomal glucosidases. We focused on acid β-glucosidase (GBA), a lysosomal enzyme the deficiency of which is related to mitochondrial dysfunction. We analyzed the function of GBA in pancreatic ductal adenocarcinoma (PDAC). Human PDAC cell lines (PANC-1, BxPC-3 and AsPC-1) were examined under conditions of GBA knockdown via the short interfering RNA (siRNA) method. We assessed the morphological changes, GBA enzyme activity, GBA protein expression, cell viability, reactive oxygen species (ROS) generation, mitochondrial membrane potential (MMP) and mitophagy flux of PDAC cells. The GBA protein level and enzyme activity differed among cell lines. GBA knockdown suppressed cell proliferation and induced apoptosis, especially in PANC-1 and BxPC-3 cells, with low GBA enzyme activity. GBA knockdown also decreased the MMP and impaired mitochondrial clearance. This impaired mitochondrial clearance further induced dysfunctional mitochondria accumulation and ROS generation in PDAC cells, inducing apoptosis. The antiproliferative effects of the combination of GBA suppression and gemcitabine were higher than those of gemcitabine alone. These results showed that GBA suppression exerts a significant antitumor effect and may have therapeutic potential in the clinical treatment of PDAC.
Excessive risk and poor outcome of hospital-acquired peritoneal dialysis-related peritonitis
Authors: Szeto Cheuk-Chun , Ng Jack Kit-Chung , Fung Winston Wing-Shing , Chan Gordon Chun-Kau , Cheng Phyllis Mei-Shan , Law Man-Ching , Pang Wing-Fai , Li Philip Kam-Tao , Leung Chi-Bon , Chow Kai-Ming 
Published: July 2022

ABSTRACT

Background
Peritoneal dialysis (PD) is a home-based renal replacement therapy. Since hospital staff are not often familiar with PD and its complications, PD patients may have an excess risk of developing PD-related peritonitis during hospital admission for unrelated reasons, and the outcome may be affected.

Methods
We reviewed 371 episodes of hospital-acquired PD peritonitis in our center from 2000 to 2019. Their clinical characteristics and outcomes were compared with 825 episodes that required hospital admission and 1964 episodes that were treated as outpatient.

Results
Hospitalized PD patients had a significantly higher risk of developing peritonitis than outpatients [incident rate ratio 4.41 (95% confidence interval 3.95–4.91]. Hospital-acquired peritonitis episodes were more commonly culture negative. Bacterial isolates from the hospital-acquired episodes were more likely resistant to ceftazidime (P &lt; .0001) than the other groups. The primary response rate, complete cure rate and overall mortality of the hospital-acquired episodes were 66.6%, 62.0%, and 23.2%, respectively, all worse than episodes that developed outside the hospital (P &lt; .0001 for all).

Conclusion
PD patients admitted to the hospital had a 4-fold increase in the risk of developing peritonitis. Hospital-acquired peritonitis episodes were more likely culture negative and resistant to antibiotics. They also had a lower primary response rate, a lower complete cure rate and higher mortality than episodes that developed outside the hospital.
Can fisheries bioenergetics modelling refine spatially explicit assessments of climate change vulnerability?
Authors: Troia Matthew J , Perkin Joshuah S 
Published: July 2022

AbstractRising water temperature under climate change is affecting the physiology, population dynamics and geographic distribution of freshwater taxa. We propose a novel application of individual-based bioenergetics modelling (BEM) to assess the physiological impacts of warming on freshwater fishes across broad spatial extents. We test this approach using the Guadalupe bass (Micropterus treculii), a species of conservation and recreational significance that is endemic to central TX, USA. We projected historical-to-future changes (middle 20th century to end of 21st century) in daily bioenergetics of individual fish across 7872 stream reaches and compared this output to changes in reach occupancy derived from traditional species distribution modelling (SDM). SDMs project an 8.7% to 52.1% decrease in reach occupancy, depending on model parameterizations and climate change scenarios. Persistence is projected in the central Edwards Plateau region, whereas extirpations are projected for the warmer southeastern region. BEM projected a median 79.3% and 143.2% increase in somatic growth of age-1 Guadalupe bass across historically occupied reaches under moderate and severe climate change scenarios, respectively. Higher end-of-year body size under future climate was caused by a longer growing season. Future scenarios exploring suppressed or enhanced prey consumption suggest that small changes in prey availability will have relatively greater effects on growth than forecasted changes in temperature. Projected growth was geographically discordant with SDM-based habitat suitability, suggesting that SDMs do not accurately reflect fundamental thermal niche dimensions. Our assessment suggests that for locations where the species persists, Guadalupe bass may benefit from warming, although realized consumption gains will depend on seasonal, spatially varying changes in prey availability and other biotic and abiotic factors. More generally, we demonstrate that uniting species-specific BEM with spatially explicit climate change projections can elucidate the physiological impacts of climate change—including seasonal variation—on freshwater fishes across broad geographic extents to complement traditional SDM.
Using transcriptomics to predict and visualize disease status in bighorn sheep (Ovis canadensis)
Authors: Bowen Lizabeth , Manlove Kezia , Roug Annette , Waters Shannon , LaHue Nate , Wolff Peregrine 
Published: July 2022

Abstract
Increasing risk of pathogen spillover coupled with overall declines in wildlife population abundance in the Anthropocene make infectious disease a relevant concern for species conservation worldwide. While emerging molecular tools could improve our diagnostic capabilities and give insight into mechanisms underlying wildlife disease risk, they have rarely been applied in practice. Here, employing a previously reported gene transcription panel of common immune markers to track physiological changes, we present a detailed analysis over the course of both acute and chronic infection in one wildlife species where disease plays a critical role in conservation, bighorn sheep (Ovis canadensis). Differential gene transcription patterns distinguished between infection statuses over the course of acute infection and differential correlation (DC) analyses identified clear changes in gene co-transcription patterns over the early stages of infection, with transcription of four genes—TGFb, AHR, IL1b and MX1—continuing to increase even as transcription of other immune-associated genes waned. In a separate analysis, we considered the capacity of the same gene transcription panel to aid in differentiating between chronically infected animals and animals in other disease states outside of acute disease events (an immediate priority for wildlife management in this system). We found that this transcription panel was capable of accurately identifying chronically infected animals in the test dataset, though additional data will be required to determine how far this ability extends. Taken together, our results showcase the successful proof of concept and breadth of potential utilities that gene transcription might provide to wildlife disease management, from direct insight into mechanisms associated with differential disease response to improved diagnostic capacity in the field.
Mathematical models of message discrepancy: previous models and a modified psychological discounting model
Authors: Chung Sungeun , Fink Edward L 
Published: July 2022

Abstract
Formal modeling is rare in communication studies. Still, several mathematical models have been proposed regarding the persuasive effects of message discrepancy, the difference between a message’s advocated position and a message recipient’s initial position. With numerical simulations, we analyzed four formal models to identify their strengths and weaknesses. Based on analyses of previous models, we proposed a modified psychological discounting model by solving a differential equation regarding the rate of change of the probability of message acceptance with respect to psychological discrepancy. Whereas previous models predicted nonmonotonic relationships between message discrepancy and belief change, the new model predicts that as message discrepancy increases, belief change monotonically increases unless facilitating factors change due to extremely discrepant messages. We discuss differences between the previous models and the new model, and their significance and implications for theories of persuasion as well as the limitations of the new model.
Sex recognition does not modulate aggression toward nest intruders in a paper wasp
Authors: de Souza André Rodrigues , Franca Wilson , Prato Amanda , Nascimento Fábio Santos do 
Published: July 2022

AbstractDuring social interactions, the behavior of an individual often depends on the sex of its social partner. Many animal societies have males and females that play very different behavioral roles, although they coexist and interact non-sexually. At specific phases of the colony cycle, social wasp females and males are contemporaries within a nest, they often interact, although mating occurs mostly off the nest, therefore providing an opportunity to test sex discrimination in contexts other than classical sexual ones. We performed a lure presentation experiment to test if Mischocyttarus metathoracicus discriminate between conspecifics of the 2 sexes during on-nest social interactions. Female wasps discriminated conspecific sex during experimentally simulated nest intrusions. Visual and chemical cues may account for this sex discrimination. Despite sex discrimination (evidenced by differential inspective behavior from the nest females toward the female and the male lures), female wasps were as aggressive toward lures of both sexes. In the female-dominated hymenopteran societies, males are often subordinate and not aggressive on nest, resulting in females directing less aggression to them compared to other females. Instead, M. metathoracicus males and females are both aggressive toward nestmates, so they might be perceived as similar threat during on-nest social interactions.
Prognostic impact of examined mediastinal lymph node count in clinical N0 non-small cell lung cancer
Authors: Kamigaichi Atsushi , Aokage Keiju , Katsumata Shinya , Ishii Genichiro , Wakabayashi Masashi , Miyoshi Tomohiro , Tane Kenta , Samejima Joji , Tsuboi Masahiro 
Published: July 2022

Abstract

OBJECTIVES
The number of examined mediastinal lymph nodes (mLNs) could represent the quality of mediastinal lymphadenectomy for non-small cell lung cancer (NSCLC). This study aimed to evaluate the prognostic impact of the number of examined individual mLNs in patients with resectable NSCLC.

METHODS
We retrospectively evaluated 1420 patients with clinical stage IA–IIB, N0 NSCLC who underwent complete resection by lobectomy, which involved hilar and mLN dissection, between 2008 and 2016. We investigated the threshold number of examined mLNs that had prognostic significance and evaluated their effects on the risk of mLN recurrence.

RESULTS
In a respective multivariable analysis according to the number of examined mLNs, examining ≥3 mLNs [reference (ref.) mLNs ≤2] achieved statistical significance and had the best prognosis (hazard ratio, 0.68; P = 0.013). In the multivariable analyses for each pathological N (pN) stage, ≥3 examined mLNs (ref. mLNs ≤2) were an independent prognostic factor in pN1 disease (hazard ratio, 0.32, P = 0.002), but not in pN0 or pN2 disease. The cumulative incidence of mLN recurrence was significantly lower in patients with ≥3 examined mLNs (ref. mLNs ≤2, hazard ratio, 0.27; P = 0.008) in pN1 disease. Patients with ≥3 examined mLNs had higher upstaging rates to pN2 than those with ≤2 examined mLNs.

CONCLUSIONS
Examining ≥3 mLNs contributed to a favourable prognosis and low mLN recurrence risk in patients with clinical stage I–II, N0 NSCLC. Our findings can serve as a benchmark for the number of required mLNs to be examined.
Histological and structural effects of biodegradable polydioxanone stents in the rabbit trachea
Authors: Morante-Valverde Rocío , Usategui Alicia , López María , Grau Montserrat , Luna-Paredes Ma Carmen , Albi Salomé , Alonso-Riaño Marina , Pablos José L , Antón-Pacheco Juan L 
Published: July 2022

Abstract

OBJECTIVES
The aim of this study was to evaluate the potential biologic effects caused by the successive placement of biodegradable polydioxanone (PDO) stents in the rabbit trachea. PDO stents could eventually induce a fibroproliferative reaction in the submucosa that could be beneficial in the treatment of malacia due to an increase in its consistency without impairing the tracheal lumen.

METHODS
Sixteen adult NZ rabbits were distributed into 3 groups with different survival times according to the number of stents placed: 1 stent (14 weeks), 2 stents (28 weeks) and 3 stents (42 weeks). Stent insertion was performed endoscopically in the cervical trachea of the animal. Histopathological studies included Masson’s trichrome staining for submucosal fibrosis and Safranin O to assess the structural integrity of cartilage. Potential inflammatory changes were analysed by means of immunohistochemistry determining the number of CD45-positive cells.

RESULTS
Stent placement was successful in every case. Histological studies did not show a statistically significant increase in tracheal wall collagen area and cartilage structure was not modified in those rabbits with 1 or more PDO stents inserted compared to non-stented tracheal sections. Furthermore, no statistically significant changes in the number of CD45+ cells were observed in stented tracheal segments compared to normal tracheal tissues.

CONCLUSIONS
According to our data, successive PDO stenting caused mild inflammatory changes in the tracheal wall and no increase in the collagen matrix, and the cartilaginous support was not modified during a long follow-up period (up to 42 weeks). These findings suggest that they may be safe and show good biocompatibility in the long term.
General practitioners’ role in improving health care in care homes: a realist review
Authors: Chadborn Neil H , Devi Reena , Goodman Claire , Williams Christopher D , Sartain Kate , Gordon Adam L 
Published: July 2022

Abstract

Background
Despite recent focus on improving health care in care homes, it is unclear what role general practitioners (GPs) should play. To provide evidence for future practice we set out to explore how GPs have been involved in such improvements.

Methods
Realist review incorporated theory-driven literature searches and stakeholder interviews, supplemented by focussed searches on GP-led medication reviews and end-of-life care. Medline, Embase, CINAHL, PsycInfo, Web of Science, and the Cochrane library were searched. Grey literature was identified through internet searches and professional networks. Studies were included based upon relevance. Data were coded to develop and test contexts, mechanisms, and outcomes for improvements involving GPs.

Results
Evidence was synthesized from 30 articles. Programme theories described: (i) “negotiated working with GPs,” where other professionals led improvement and GPs provided expertise; and (ii) “GP involvement in national/regional improvement programmes.” The expertise of GPs was vital to many improvement programmes, with their medical expertise or role as coordinators of primary care proving pivotal. GPs had limited training in quality improvement (QI) and care home improvement work had to be negotiated in the context of wider primary care commitments.

Conclusions
GPs are central to QI in health care in care homes. Their contributions relate to their specialist expertise and recognition as leaders of primary care but are challenged by available time and resources to develop this role.
Interspecific Differences in the Flow Regimes and Drag of North Pacific Skate Egg Cases
Authors: Hall Kayla C , Elcock Jaida N , Hoff Gerald R , Stevenson Duane E , Summers Adam P , Donatelli Cassandra M 
Published: July 2022

Synopsis
Skates are a diverse group of dorso-ventrally compressed cartilaginous fish found primarily in high-latitude seas. These slow-growing oviparous fish deposit their fertilized eggs into cases, which then rest on the seafloor. Developing skates remain in their cases for 1–4 years after they are deposited, meaning the abiotic characteristics of the deposition sites, such as current and substrate type, must interact with the capsule in a way to promote long residency. Egg cases are morphologically variable and can be identified to species. Both the gross morphology and the microstructures of the egg case interact with substrate to determine how well a case stays in place on a current-swept seafloor. Our study investigated the egg case hydrodynamics of eight North Pacific skate species to understand how their morphology affects their ability to stay in place. We used a flume to measure maximum current velocity, or “break-away velocity,” each egg case could withstand before being swept off the substrate and a tilt table to measure the coefficient of static friction between each case and the substrate. We also used the programing software R to calculate theoretical drag on the egg cases of each species. For all flume trials, we found the morphology of egg cases and their orientation to flow to be significantly correlated with break-away velocity. In certain species, the morphology of the egg case was correlated with flow rate required to dislodge a case from the substrate in addition to the drag experienced in both the theoretical and flume experiments. These results effectively measure how well the egg cases of different species remain stationary in a similar habitat. Parsing out attachment biases and discrepancies in flow regimes of egg cases allows us to identify where we are likely to find other elusive species nursery sites. These results will aid predictive models for locating new nursery habitats and protective policies for avoiding the destruction of these nursery sites.