bluuebunny/crossref_metadata_2025_split huggingface dataset:
Establishment of open-source semi-automated behavioral analysis system and quantification of the difference of sexual motivation between laboratory and wild strains
Authors: Tomihara Soma , Oka Yoshitaka , Kanda Shinji 
Published: May 2021

AbstractBehavioral analysis plays an important role in wide variety of biological studies, but behavioral recordings often tend to be laborious and are associated with inevitable human-errors. It also takes much time to perform manual behavioral analyses while replaying the videos. On the other hand, presently available automated recording/analysis systems are often specialized for certain types of behavior of specific animals. Here, we established an open-source behavioral recording system using Raspberry Pi, which automatically performs video-recording and systematic file-sorting, and the behavioral recording can be performed more efficiently, without unintentional human operational errors. We also developed an Excel macro that enables us to easily perform behavioral annotation with simple manipulation. Thus, we succeeded in developing an analysis suite that mitigates human tasks and thus reduces human errors. By using this suite, we analyzed the sexual behavior of a laboratory and a wild medaka strain and found a difference in sexual motivation presumably resulting from domestication.
A case–control study investigating food addiction in Parkinson patients
Authors: de Chazeron Ingrid , Durif F. , Lambert C. , Chereau-Boudet I. , Fantini M. L. , Marques A. , Derost P. , Debilly B. , Brousse G. , Boirie Y. , Llorca P. M. 
Published: May 2021

AbstractEating disorders (EDs) in patients with Parkinson’s disease (PD) are mainly described through impulse control disorders but represent one end of the spectrum of food addiction (FA). Although not formally recognized by DSM-5, FA is well described in the literature on animal models and humans, but data on prevalence and risk factors compared with healthy controls (HCs) are lacking. We conducted a cross-sectional study including 200 patients with PD and 200 age- and gender-matched HCs. Characteristics including clinical data (features of PD/current medication) were collected. FA was rated using DSM-5 criteria and the Questionnaire on Eating and Weight Patterns-Revised (QEWP-R). Patients with PD had more EDs compared to HCs (27.0% vs. 13.0%, respectively, p < 0.001). They mainly had FA (24.5% vs. 12.0%, p = 0.001) and night eating syndrome (7.0% vs. 2.5% p = 0.03). In PD patients, FA was associated with female gender (p = 0.04) and impulsivity (higher attentional non-planning factor) but not with the dose or class of dopaminergic therapy. Vigilance is necessary, especially for PD women and in patients with specific impulsive personality traits. Counterintuitively, agonist dopaminergic treatment should not be used as an indication for screening FA in patients with PD.
A reliable set of reference genes to normalize oxygen-dependent cytoglobin gene expression levels in melanoma
Authors: De Backer Joey , Maric Darko , Bosman Matthias , Dewilde Sylvia , Hoogewijs David 
Published: May 2021

AbstractCytoglobin (CYGB) is a ubiquitously expressed protein with a protective role against oxidative stress, fibrosis and tumor growth, shown to be transcriptionally regulated under hypoxic conditions. Hypoxia-inducible CYGB expression is observed in several cancer cell lines and particularly in various melanoma-derived cell lines. However, reliable detection of hypoxia-inducible mRNA levels by qPCR depends on the critical choice of suitable reference genes for accurate normalization. Limited evidence exists to support selection of the commonly used reference genes in hypoxic models of melanoma. This study aimed to select the optimal reference genes to study CYGB expression levels in melanoma cell lines exposed to hypoxic conditions (0.2% O2) and to the HIF prolyl hydroxylase inhibitor roxadustat (FG-4592). The expression levels of candidate genes were assessed by qPCR and the stability of genes was evaluated using the geNorm and NormFinder algorithms. Our results display that B2M and YWHAZ represent the most optimal reference genes to reliably quantify hypoxia-inducible CYGB expression in melanoma cell lines. We further validate hypoxia-inducible CYGB expression on protein level and by using CYGB promoter-driven luciferase reporter assays in melanoma cell lines.
Positive Epstein–Barr virus detection in coronavirus disease 2019 (COVID-19) patients
Authors: Chen Ting , Song Jiayi , Liu Hongli , Zheng Hongmei , Chen Changzheng 
Published: May 2021

AbstractThe objective of this study was to detect the Epstein–Barr virus (EBV) coinfection in coronavirus disease 2019 (COVID-19). In this retrospective single-center study, we included 67 COVID-19 patients with onset time within 2 weeks in Renmin Hospital of Wuhan University from January 9 to February 29, 2020. Patients were divided into EBV/SARS-CoV-2 coinfection group and SARS-CoV-2 infection alone group according to the serological results of EBV, and the characteristics differences between the two groups were compared. The median age was 37 years, with 35 (52.2%) females. Among these COVID-19 patients, thirty-seven (55.2%) patients were seropositive for EBV viral capsid antigen (VCA) IgM antibody. EBV/SARS-CoV-2 coinfection patients had a 3.09-fold risk of having a fever symptom than SARS-CoV-2 infection alone patients (95% CI 1.11–8.56; P = 0.03). C-reactive protein (CRP) (P = 0.02) and the aspartate aminotransferase (AST) (P = 0.04) in EBV/SARS-CoV-2 coinfection patients were higher than that in SARS-CoV-2 infection alone patients. EBV/SARS-CoV-2 coinfection patients had a higher portion of corticosteroid use than the SARS-CoV-2 infection alone patients (P = 0.03). We find a high incidence of EBV coinfection in COVID-19 patients. EBV/SARS-CoV-2 coinfection was associated with fever and increased inflammation. EBV reactivation may associated with the severity of COVID-19.
The association between hepatitis C virus infection and renal cell cancer, prostate cancer, and bladder cancer: a systematic review and meta-analysis
Authors: Ma Yucheng , Huang Zhongli , Jian Zhongyu , Wei Xin 
Published: May 2021

AbstractTo update the current evidence on whether hepatitis C virus (HCV) infection represents a possible risk factor for renal cell cancer (RCC), prostate cancer (PCa), and bladder cancer (BC). We searched the literature on Pubmed, Web of Science, and Embases before April 2021. A systematic review and meta-analysis were performed. Finally, we extracted 12 studies based on the eligible criteria. Across 11 studies for HCV and RCC, the incorporated RR was 1.28 (95% CI 1.05–1.55), which meant that participants with HCV infection were associated with higher RCC risk. The pooled RR in hazard ratio (HR) subgroup (HR 1.59, 95% CI 1.22–2.08), cohort studies subgroup (RR 1.47, 95% CI 1.18–1.82), and North America subgroup (RR 1.71, 95% CI 1.40–2.09) detected a stronger association between HCV and RCC risk. Although an inverse association was seen for PCa (RR 0.75, 95% CI 0.54–1.03) across seven studies, it was not statistically significant (P = 0.075). There was no significant association between HCV and BC with an incorporated RR of 0.92 (95% CI, 0.82–1.03) across five studies. Our study demonstrated that HCV infection was significantly associated with increased RCC risk. There appeared to be an inverse association for HCV in PCa risk but not statistically significant. No significant association was found between HCV and BC risk. Prospective, large-scale, and well-designed cohort studies are required to validate the association between HCV and RCC, and to investigate the role of HCV on PCa.
The dynamics of evolutionary rescue from a novel pathogen threat in a host metapopulation
Authors: Jiao Jing , Fefferman Nina 
Published: May 2021

AbstractWhen a novel disease strikes a naïve host population, there is evidence that the most immediate response can involve host evolution while the pathogen remains relatively unchanged. When hosts also live in metapopulations, there may be critical differences in the dynamics that emerge from the synergy among evolutionary, ecological, and epidemiological factors. Here we used a Susceptible-Infected-Recovery model to explore how spatial and temporal ecological factors may drive the epidemiological and rapid-evolutionary dynamics of host metapopulations. For simplicity, we assumed two host genotypes: wild type, which has a positive intrinsic growth rate in the absence of disease, and robust type, which is less likely to catch the infection given exposure but has a lower intrinsic growth rate in the absence of infection. We found that the robust-type host would be strongly selected for in the presence of disease when transmission differences between the two types is large. The growth rate of the wild type had dual but opposite effects on host composition: a smaller increase in wild-type growth increased wild-type competition and lead to periodical disease outbreaks over the first generations after pathogen introduction, while larger growth increased disease by providing more susceptibles, which increased robust host density but decreased periodical outbreaks. Increased migration had a similar impact as the increased differential susceptibility, both of which led to an increase in robust hosts and a decrease in periodical outbreaks. Our study provided a comprehensive understanding of the combined effects among migration, disease epidemiology, and host demography on host evolution with an unchanging pathogen. The findings have important implications for wildlife conservation and zoonotic disease control.
Extracting neuronal activity signals from microscopy recordings of contractile tissue using B-spline Explicit Active Surfaces (BEAS) cell tracking
Authors: Kazwiny Youcef , Pedrosa João , Zhang Zhiqing , Boesmans Werend , D’hooge Jan , Vanden Berghe Pieter 
Published: May 2021

AbstractCa2+ imaging is a widely used microscopy technique to simultaneously study cellular activity in multiple cells. The desired information consists of cell-specific time series of pixel intensity values, in which the fluorescence intensity represents cellular activity. For static scenes, cellular signal extraction is straightforward, however multiple analysis challenges are present in recordings of contractile tissues, like those of the enteric nervous system (ENS). This layer of critical neurons, embedded within the muscle layers of the gut wall, shows optical overlap between neighboring neurons, intensity changes due to cell activity, and constant movement. These challenges reduce the applicability of classical segmentation techniques and traditional stack alignment and regions-of-interest (ROIs) selection workflows. Therefore, a signal extraction method capable of dealing with moving cells and is insensitive to large intensity changes in consecutive frames is needed. Here we propose a b-spline active contour method to delineate and track neuronal cell bodies based on local and global energy terms. We develop both a single as well as a double-contour approach. The latter takes advantage of the appearance of GCaMP expressing cells, and tracks the nucleus’ boundaries together with the cytoplasmic contour, providing a stable delineation of neighboring, overlapping cells despite movement and intensity changes. The tracked contours can also serve as landmarks to relocate additional and manually-selected ROIs. This improves the total yield of efficacious cell tracking and allows signal extraction from other cell compartments like neuronal processes. Compared to manual delineation and other segmentation methods, the proposed method can track cells during large tissue deformations and high-intensity changes such as during neuronal firing events, while preserving the shape of the extracted Ca2+ signal. The analysis package represents a significant improvement to available Ca2+ imaging analysis workflows for ENS recordings and other systems where movement challenges traditional Ca2+ signal extraction workflows.
Single channel properties of mitochondrial large conductance potassium channel formed by BK-VEDEC splice variant
Authors: Gałecka Shur , Kulawiak Bogusz , Bednarczyk Piotr , Singh Harpreet , Szewczyk Adam 
Published: May 2021

AbstractThe activation of mitochondrial large conductance calcium-activated potassium (mitoBKCa) channels increases cell survival during ischemia/reperfusion injury of cardiac cells. The basic biophysical and pharmacological properties of mitoBKCacorrespond to the properties of the BKCachannels from the plasma membrane. It has been suggested that the VEDEC splice variant of theKCNMA1gene product encoding plasma membrane BKCais targeted toward mitochondria. However there has been no direct evidence that this protein forms a functional channel in mitochondria. In our study, we used HEK293T cells to express the VEDEC splice variant and observed channel activity in mitochondria using the mitoplast patch-clamp technique. For the first time, we found that transient expression with the VEDEC isoform resulted in channel activity with the conductance of 290 ± 3 pS. The channel was voltage-dependent and activated by calcium ions. Moreover, the activity of the channel was stimulated by the potassium channel opener NS11021 and inhibited by hemin and paxilline, which are known BKCachannel blockers. Immunofluorescence experiments confirmed the partial colocalization of the channel within the mitochondria. From these results, we conclude that the VEDEC isoform of the BKCachannel forms a functional channel in the inner mitochondrial membrane. Additionally, our data show that HEK293T cells are a promising experimental model for expression and electrophysiological studies of mitochondrial potassium channels.
IMP3 protein is an independent prognostic factor of clinical stage II rectal cancer
Authors: Bevanda Glibo Daniela , Bevanda Danijel , Vukojević Katarina , Tomić Snježana 
Published: May 2021

AbstractImmunohistochemical level of IMP3-protein in patients with rectal cancer in clinical stage II (141), were correlated with sociodemographic, pathohistological and clinical indicators and duration of overall-survival and progression-free-survival. Vascular invasion was associated with IMP3-positive immunostaining (p < 0.001). Vascular invasion ratio in the group of poorly-differentiated-tumors was 21 times higher than in the group of well-differentiated-tumors. IMP3-positive patients lived 2.2 times shorter than negative (p < 0.001). Patients with well-differentiated-tumors lived 1.7 times longer than the subjects with poorly-differentiated-tumors (p < 0.001). Patients without vascular invasion lived 2.7 times longer than the subjects with vascular invasion (p < 0.001). The risk of mortality was 2.3 times higher for IMP3 positive patients (p = 0.027) and 10.4 higher for the patients with vascular invasion (p < 0.001). IMP3-negative participants had 2.3 times longer free interval without disease (p < 0.001). The free interval without disease was 3.6 times longer in the group without vascular invasion (p < 0.001). The risk of disease relapse in the IMP3 positive group was 5.3 times higher (p < 0.001) and with vascular invasion was 8 times longer (p < 0.001). The risk of disease relapse was 6.8 times higher in the group with vascular invasion (p < 0.001). Patients with rectal cancer and high IMP3-protein level will have a shorter overall survival relative to patients without or with low levels of IMP3. The analysis of IMP3 expression by immunohistochemistry pointed IMP3 as an independent prognostic factor of clinical stage II rectal cancer.
Multi Locus View: an extensible web-based tool for the analysis of genomic data.
Authors: Sergeant Martin J. , Hughes Jim R. , Hentges Lance , Lunter Gerton , Downes Damien J. , Taylor Stephen 
Published: May 2021

AbstractTracking and understanding data quality, analysis and reproducibility are critical concerns in the biological sciences. This is especially true in genomics where next generation sequencing (NGS) based technologies such as ChIP-seq, RNA-seq and ATAC-seq are generating a flood of genome-scale data. However, such data are usually processed with automated tools and pipelines, generating tabular outputs and static visualisations. Interpretation is normally made at a high level without the ability to visualise the underlying data in detail. Conventional genome browsers are limited to browsing single locations and do not allow for interactions with the dataset as a whole. Multi Locus View (MLV), a web-based tool, has been developed to allow users to fluidly interact with genomics datasets at multiple scales. The user is able to browse the raw data, cluster, and combine the data with other analysis and annotate the data. User datasets can then be shared with other users or made public for quick assessment from the academic community. MLV is publically available athttps://mlv.molbiol.ox.ac.uk.
A combined approach for single-cell mRNA and intracellular protein expression analysis
Authors: Reimegård Johan , Tarbier Marcel , Danielsson Marcus , Schuster Jens , Baskaran Sathishkumar , Panagiotou Styliani , Dahl Niklas , Friedländer Marc R. , Gallant Caroline J. 
Published: May 2021

AbstractCombined measurements of mRNA and protein expression in single cells enable in-depth analysis of cellular states. We present SPARC, an approach that combines single-cell RNA-sequencing with proximity extension essays to simultaneously measure global mRNA and 89 intracellular proteins in individual cells. We show that mRNA expression fails to accurately reflect protein abundance at the time of measurement, although the direction of changes is in agreement during neuronal differentiation. Moreover, protein levels of transcription factors better predict their downstream effects than do their corresponding transcripts. Finally, we highlight that protein expression variation is overall lower than mRNA variation, but relative protein variation does not reflect the mRNA level. Our results demonstrate that mRNA and protein measurements in single cells provide different and complementary information regarding cell states. SPARC presents a state-of-the-art co-profiling method that overcomes current limitations in throughput and protein localization, including removing the need for cell fixation.
Microscale tracking of coral-vibrio interactions
Authors: Gavish Assaf R , Shapiro Orr H , Kramarsky-Winter Esti , Vardi Assaf 
Published: May 2021

Abstract
To improve our understanding of coral infection and disease, it is important to study host-pathogen interactions at relevant spatio-temporal scales. Here, we provide a dynamic microscopic view of the interaction between a coral pathogen, Vibrio coralliilyticus and its coral host Pocillopora damicornis. This was achieved using a microfluidics-based system facilitating control over flow, light and temperature conditions. Combined with time-resolved biochemical and microbial analyses of the system exudates, this approach provides novel insights into the early phases of a coral infection at unprecedented spatio-temporal resolution. We provide evidence that infection may occur through ingestion of the pathogen by the coral polyps, or following pathogen colonization of small tissue lesions on the coral surface. Pathogen ingestion invariably induced the release of pathogen-laden mucus from the gastrovascular cavity. Despite the high bacterial load used in our experiments, approximately one-third of coral fragments tested did not develop further symptoms. In the remaining two-thirds, mucus spewing was followed by the severing of calicoblastic connective tissues (coenosarc) and subsequently necrosis of most polyps. Despite extensive damage to symptomatic colonies, we frequently observed survival of individual polyps, often accompanied by polyp bail-out. Biochemical and microbial analyses of exudates over the course of symptomatic infections revealed that severing of the coenosarc was followed by an increase in matrix metaloprotease activity, and subsequent increase in both pathogen and total bacterial counts. Combined, these observations provide a detailed description of a coral infection, bringing us a step closer to elucidating the complex interactions underlying coral disease.
Task-Specific Iconic Gesturing During Spoken Discourse in Aphasia
Authors: Stark Brielle C. , Cofoid Caroline 
Published: May 2021

Purpose:
In persons living with aphasia, we will explore the relationship between iconic gesture production during spontaneous speech and discourse task, spoken language, and demographic information.

Method:
Employing the AphasiaBank database, we coded iconic gestures in 75 speakers with aphasia during two spoken discourse tasks: a procedural narrative, which involved participants telling the experimenter how to make a sandwich (“Sandwich”), and a picture sequence narrative, which had participants describe the picture sequence to the experimenter (“Window”). Forty-three produced a gesture during both tasks, and we further evaluate data from this subgroup as a more direct comparison between tasks.

Results:
More iconic gestures, at a higher rate, were produced during the procedural narrative. For both tasks, there was a relationship between iconic gesture rate, modeled as iconic gestures per word, and metrics of language dysfluency extracted from the discourse task as well as a metric of fluency extracted from a standardized battery. Iconic gesture production was correlated with aphasia duration, which was driven by performance during only a single task (Window), but not with other demographic metrics, such as aphasia severity or age. We also provide preliminary evidence for task differences shown through the lens of two types of iconic gestures.

Conclusions:
While speech-language pathologists have utilized gesture in therapy for poststroke aphasia, due to its possible facilitatory role in spoken language, there has been considerably less work in understanding how gesture differs across naturalistic tasks and how we can best utilize this information to better assess gesture in aphasia and improve multimodal treatment for aphasia. Furthermore, our results contribute to gesture theory, particularly, about the role of gesture across naturalistic tasks and its relationship with spoken language.

Supplemental Material

https://doi.org/10.23641/asha.14614941
Raman analysis of chemisorbed tribofilm for metal‐on‐polyethylene hip joint prostheses
Authors: Rufaqua Risha , Vrbka Martin , Hemzal Dušan , Choudhury Dipankar , Rebenda David , Křupka Ivan , Hartl Martin 
Published: May 2021

AbstractThe biochemical reaction during the formation of lubricant film the in case of a cobalt‐chromium ball on an ultrahigh‐molecular weight polyethylene cup was studied. Three types of model synovial fluids and hyaluronic acid (HA) at physiologic concentrations were used in the experiment. The coefficient of friction was measured using a pendulum hip simulator, and Raman spectroscopy was used to perceive chemical reactions between the synovial fluid and implant material. Raman spectra evidenced that the three model fluids and HA chemisorbed onto the cobalt‐chromium surface. An α‐helix structure of the model fluid components was detected on the surface of the prosthesis.