bluuebunny/crossref_metadata_2025_split huggingface dataset:
HiC4D: forecasting spatiotemporal Hi-C data with residual ConvLSTM
Authors: Liu Tong , Wang Zheng 
Published: July 2023

Abstract
The Hi-C experiments have been extensively used for the studies of genomic structures. In the last few years, spatiotemporal Hi-C has largely contributed to the investigation of genome dynamic reorganization. However, computationally modeling and forecasting spatiotemporal Hi-C data still have not been seen in the literature. We present HiC4D for dealing with the problem of forecasting spatiotemporal Hi-C data. We designed and benchmarked a novel network and named it residual ConvLSTM (ResConvLSTM), which is a combination of residual network and convolutional long short-term memory (ConvLSTM). We evaluated our new ResConvLSTM networks and compared them with the other five methods, including a naïve network (NaiveNet) that we designed as a baseline method and four outstanding video-prediction methods from the literature: ConvLSTM, spatiotemporal LSTM (ST-LSTM), self-attention LSTM (SA-LSTM) and simple video prediction (SimVP). We used eight different spatiotemporal Hi-C datasets for the blind test, including two from mouse embryogenesis, one from somatic cell nuclear transfer (SCNT) embryos, three embryogenesis datasets from different species and two non-embryogenesis datasets. Our evaluation results indicate that our ResConvLSTM networks almost always outperform the other methods on the eight blind-test datasets in terms of accurately predicting the Hi-C contact matrices at future time-steps. Our benchmarks also indicate that all of the methods that we benchmarked can successfully recover the boundaries of topologically associating domains called on the experimental Hi-C contact matrices. Taken together, our benchmarks suggest that HiC4D is an effective tool for predicting spatiotemporal Hi-C data. HiC4D is publicly available at both http://dna.cs.miami.edu/HiC4D/ and https://github.com/zwang-bioinformatics/HiC4D/.
The comparable tumour microenvironment in sporadic andNF2-related schwannomatosis vestibular schwannoma
Authors: Gregory Grace E , Jones Adam Paul , Haley Michael J , Hoyle Christopher , Zeef Leo A H , Lin I-Hsuan , Coope David J , King Andrew T , Evans D Gareth , Paszek Pawel , Couper Kevin N , Brough David , Pathmanaban Omar N 
Published: July 2023

AbstractBilateral vestibular schwannoma is the hallmark of NF2-related schwannomatosis, a rare tumour predisposition syndrome associated with a lifetime of surgical interventions, radiotherapy and off-label use of the anti-angiogenic drug bevacizumab. Unilateral vestibular schwannoma develops sporadically in non-NF2-related schwannomatosis patients for which there are no drug treatment options available. Tumour-infiltrating immune cells such as macrophages and T-cells correlate with increased vestibular schwannoma growth, which is suggested to be similar in sporadic and NF2-related schwannomatosis tumours. However, differences between NF2-related schwannomatosis and the more common sporadic disease include NF2-related schwannomatosis patients presenting an increased number of tumours, multiple tumour types and younger age at diagnosis. A comparison of the tumour microenvironment in sporadic and NF2-related schwannomatosis tumours is therefore required to underpin the development of immunotherapeutic targets, identify the possibility of extrapolating ex vivo data from sporadic vestibular schwannoma to NF2-related schwannomatosis and help inform clinical trial design with the feasibility of co-recruiting sporadic and NF2-related schwannomatosis patients. This study drew together bulk transcriptomic data from three published Affymetrix microarray datasets to compare the gene expression profiles of sporadic and NF2-related schwannomatosis vestibular schwannoma and subsequently deconvolved to predict the abundances of distinct tumour immune microenvironment populations. Data were validated using quantitative PCR and Hyperion imaging mass cytometry. Comparative bioinformatic analyses revealed close similarities in NF2-related schwannomatosis and sporadic vestibular schwannoma tumours across the three datasets. Significant inflammatory markers and signalling pathways were closely matched in NF2-related schwannomatosis and sporadic vestibular schwannoma, relating to the proliferation of macrophages, angiogenesis and inflammation. Bulk transcriptomic and imaging mass cytometry data identified macrophages as the most abundant immune population in vestibular schwannoma, comprising one-third of the cell mass in both NF2-related schwannomatosis and sporadic tumours. Importantly, there were no robust significant differences in signalling pathways, gene expression, cell type abundance or imaging mass cytometry staining between NF2-related schwannomatosis and sporadic vestibular schwannoma. These data indicate strong similarities in the tumour immune microenvironment of NF2-related schwannomatosis and sporadic vestibular schwannoma.
Annuloplasty effect of transcatheter edge-to-edge repair with MitraClip system on multiple degenerative mitral regurgitations
Authors: Fukutomi Motoki , Onishi Takayuki , Sasaki Haruka , Tobaru Tetsuya 
Published: July 2023

Abstract

Background
Previous reports have shown a mitral annuloplasty-like effect after MitraClip, i.e. a shortening of the anterior-posterior diameter of mitral valve annulus. However, the clinical benefit of this phenomenon is unclear.

Case summary
An 87-year-old woman with multiple degenerative mitral regurgitation (MR) jets, including a central-medial jet and a lateral jet, underwent MitraClip procedure. After a single clip implantation, anterior-posterior diameter of mitral annulus was shortened and both MR jets were significantly reduced.

Discussion
Even in the case of multiple MR jets, a single clip deployment with the MitraClip system may provide an acceptable MR reduction if the clip shows the mitral annuloplasty effect.
The eukaryome of African children is influenced by geographic location, gut biogeography, and nutritional status
Authors: Vonaesch Pascale , Billy Vincent , Mann Allison E , Morien Evan , Habib Azimdine , Collard Jean-Marc , Dédé Michel , Kapel Nathalie , Sansonetti Philippe J , Parfrey Laura Wegener ,   for the Afribiota Investigators, Barbot-Trystram Laurence , Barouki Robert , Bastaraud Alexandra , Collard Jean-Marc , Doria Maria , Duffy Darragh , Finlay B Brett , Djorie Serge Ghislain , Giles-Vernick Tamara , Hasan Milena , Godje Bolmbaye Privat , Gody Jean-Chrysostome , Hunald Francis Allen , Kapel Nathalie , Lombart Jean-Pierre , Manirakiza Alexandre , Nigatoloum Synthia Nazita , Parfrey Laura Wegener , Raharimalala Lisette , Rakotondrainipiana Maheninasy , Randremanana Rindra , Randriamizao Harifetra Mamy Richard , Randrianirina Frédérique , Robinson Annick , Rubbo Pierre-Alain , Sansonetti Philippe , Schaeffer Laura , Gouandjika-Vassilache Ionela , Vonaesch Pascale , Vondo Sonia Sandrine , Vigan-Womas Inès 
Published: July 2023

AbstractEukaryotes have historically been studied as parasites, but recent evidence suggests they may be indicators of a healthy gut ecosystem. Here, we describe the eukaryome along the gastrointestinal tract of children aged 2–5 years and test for associations with clinical factors such as anaemia, intestinal inflammation, chronic undernutrition, and age. Children were enrolled from December 2016 to May 2018 in Bangui, Central African Republic and Antananarivo, Madagascar. We analyzed a total of 1104 samples representing 212 gastric, 187 duodenal, and 705 fecal samples using a metabarcoding approach targeting the full ITS2 region for fungi, and the V4 hypervariable region of the 18S rRNA gene for the overall eukaryome. Roughly, half of all fecal samples showed microeukaryotic reads. We find high intersubject variability, only a handful of taxa that are likely residents of the gastrointestinal tract, and frequent co-occurrence of eukaryotes within an individual. We also find that the eukaryome differs between the stomach, duodenum, and feces and is strongly influenced by country of origin. Our data show trends towards higher levels of Fusarium equiseti, a mycotoxin producing fungus, and lower levels of the protist Blastocystis in stunted children compared to nonstunted controls. Overall, the eukaryome is poorly correlated with clinical variables. Our study is of one of the largest cohorts analyzing the human intestinal eukaryome to date and the first to compare the eukaryome across different compartments of the gastrointestinal tract. Our results highlight the importance of studying populations across the world to uncover common features of the eukaryome in health.
Comparative transcriptomics and gene expression divergence associated with homoploid hybrid speciation in Argyranthemum
Authors: White Oliver W , Reyes-Betancort Alfredo , Carine Mark A , Chapman Mark A 
Published: July 2023

Abstract
Ecological isolation is increasingly thought to play an important role in speciation, especially for the origin and reproductive isolation of homoploid hybrid species. However, the extent to which divergent and/or transgressive gene expression changes are involved in speciation is not well studied. In this study, we employ comparative transcriptomics to investigate gene expression changes associated with the origin and evolution of two homoploid hybrid plant species, Argyranthemum sundingii and A. lemsii (Asteraceae). As there is no standard methodology for comparative transcriptomics, we examined five different pipelines for data assembly and analysing gene expression across the four species (two hybrid and two parental). We note biases and problems with all pipelines, and the approach used affected the biological interpretation of the data. Using the approach that we found to be optimal, we identify transcripts showing DE between the parental taxa and between the homoploid hybrid species and their parents; in several cases, putative functions of these DE transcripts have a plausible role in ecological adaptation and could be the cause or consequence of ecological speciation. Although independently derived, the homoploid hybrid species have converged on similar expression phenotypes, likely due to adaptation to similar habitats.
Association between SARS-CoV-2 Symptoms, Ct Values, and Serological Response in Vaccinated and Unvaccinated Healthcare Personnel
Authors: Farnsworth Christopher W , O’Neil Caroline A , Dalton Claire , McDonald David , Vogt Lucy , Hock Karl , Arter Olivia , Wallace Meghan A , Muenks Carol , Amor Mostafa , Alvarado Kelly , Peacock Kate , Jolani Kevin , Fraser Victoria J , Burnham Carey-Ann D , Babcock Hilary M , Budge Phillip J , Kwon Jennie H 
Published: July 2023

Abstract

Background
SARS-CoV-2 vaccines are effective at reducing symptomatic and asymptomatic COVID-19. Limited studies have compared symptoms, threshold cycle (Ct) values from reverse transcription (RT)-PCR testing, and serological testing results between previously vaccinated vs unvaccinated populations with SARS-CoV-2 infection.

Methods
Healthcare personnel (HCP) with a positive SARS-CoV-2 RT-PCR test within the previous 14 to 28 days completed surveys including questions about demographics, medical conditions, social factors, and symptoms of COVID-19. Ct values were observed, and serological testing was performed for anti-nucleocapsid (anti-N) and anti-Spike (anti-S) antibodies at enrollment and 40 to 90 days later. Serological results were compared to HCP with no known SARS-CoV-2 infection and negative anti-N testing.

Results
There were 104 unvaccinated/not fully vaccinated and 77 vaccinated HCP with 2 doses of an mRNA vaccine at time of infection. No differences in type or duration of symptoms were reported (P = 0.45). The median (interquartile range [IQR]) Ct was 21.4 (17.6–24.6) and 21.5 (18.1–24.6) for the unvaccinated and vaccinated HCP, respectively. Higher anti-N IgG was observed in unvaccinated HCP (5.08 S/CO, 3.08–6.92) than vaccinated (3.61 signal to cutoff ratio [S/CO], 2.16–5.05). Anti-S IgG was highest among vaccinated HCP with infection (34 285 aribitrary units [AU]/mL, 17 672–61 775), followed by vaccinated HCP with no prior infection (1452 AU/mL, 791–2943), then unvaccinated HCP with infection (829 AU/mL, 290–1555). Anti-S IgG decreased 1.56% (0.9%–1.79%) per day in unvaccinated and 0.38% (0.03%–0.94%) in vaccinated HCP.

Conclusions
Vaccinated HCP infected with SARS-CoV-2 reported comparable symptoms and had similar Ct values relative to unvaccinated. However, vaccinated HCP had increased and prolonged anti-S and decreased anti-N response relative to unvaccinated.
Chromatographic Techniques for Assessment of Bisoprolol Fumarate and Perindopril Arginine in Solid Formulations under Various Stress Conditions and Application to Six Sigma, Content Uniformity, and Comparative Dissolution Approaches
Authors: Mahmoud Osama A , Omran Ahmed A , Binsaleh Ammena Y , Almalki Manal A , Mohamed Mahmoud A 
Published: July 2023

Abstract

Background
Antihypertensives bisoprolol fumarate (BIS) and perindopril arginine (PER) were simultaneously determined in their pure, bulk, and combined tablet dosage form.

Objective
This study develops a novel, reproducible, and accurate Reversed phase high-performance liquid chromatography (RP-HPLC) and Reversed phase ultra-performance liquid chromatography (RP-UPLC) with photodiode array detection techniques, which were then applied to in vitro dissolution studies.

Methods
The first RP-HPLC method relied on isocratic elution using a mobile phase of methanol–0.05 M phosphate buffer pH 2.6 (1 + 1, by volume), and separation was performed using a Thermo Hypersil C8 column (150 mm × 4.6 mm, 5 μm). Ion-pair UPLC was the second method. An acceptable resolution was achieved using an RP-C18 chromatographic column, Agilent Eclipse (100 × 2.1 mm, 1.7 μm), with a mobile phase containing 0.005 M sodium 1-heptane sulfonate–triethylamine (64 + 1 + 35, by volume), adjusted with phosphoric acid to a pH of 2.0. RP-HPLC used a 1.0 mL/min flow rate, while UPLC used 0.5 mL/min, and the two methods used detection at 210 nm.

Results
Calibration curves of BIS and PER were linear for RP-HPLC and RP-UPLC methods at 0.5-15 and 0.5-40 μg/mL, respectively. BIS and PER had RP-UPLC LODs of 0.22 and 0.10 μg/mL, respectively, and LOQs of 0.68 and 0.31 μg/mL, respectively. As a result, the approach has been effectively applied to in vitro dissolution testing for drugs in generic and reference products, showing that the two products are comparable. The Six Sigma approach was implemented to compare the recommended and United States Pharmacopeia (USP) procedures, which both exhibited process capability index (Cpk) &gt;1.33. A content uniformity test demonstrated that the drugs in their dosage form met the acceptance limit (85–115%). The degradation products were reliably distinguished from pure drugs for a range of retention times.

Conclusion
In their commercial drug product, the proposed method could be used in QC laboratories for concurrent testing, content uniformity, and in vitro dissolution investigations of BIS and PER. The methods were successfully validated per International Council for Harmonisation (ICH) guidelines.

Highlights
This study is innovative since it is the first to establish and validate specific and reproducible UPLC and HPLC methods for the concurrent quantitation of the studied drugs in their binary mixture and application to lean Six Sigma, content uniformity, and comparative dissolution approaches.
From the Universal Declaration of Human Rights to a Pandemic Treaty: Will a Right to Medicines Forever be ‘Under Construction’?
Authors: Forman Lisa 
Published: July 2023

Abstract
Global disparities in access to COVID-19 vaccines have illuminated long-standing tensions between intellectual property rights and the right to health. Debates over solutions to these disparities have focused on a waiver to the TRIPS Agreement and a prospective pandemic treaty which will attempt to regulate the impact of intellectual property rights on access to essential pandemic health goods. These disparities and debates underscore the imperative for effective legal solutions capable of addressing the restrictive impact of intellectual property rights on the affordability and production of essential health products. Yet from a legal perspective, a claim for affordable medicines is at its essence a fundamental human right, especially that of the right to health. While the right to health has long been entrenched within international human rights law, the legal and political force of a right to medicines is less clear. Accordingly, this article broadly analyses the legal and political state of play of a right to medicines in international law. It proceeds in the following ways: (1) it explores how health fits into the conceptual foundations of human rights; (2) it considers evidence from international law and policy of the legal and political emergence of a right to medicines as part of rights to health and science; (3) it considers the implications of the TRIPS waiver and of a prospective pandemic treaty for the development of this right; (4) it concludes with thoughts about what these developments imply for the legal and political force of a right to medicines in international law.
Investigation of neurophysiologic and functional connectivity changes following glioma resection using magnetoencephalography
Authors: Samuel Nardin , Harmsen Irene E , Ding Mandy Yi Rong , Sarica Can , Vetkas Artur , Wong Christine , Lawton Vanessa , Yang Andrew , Rowland Nathan C , Kalia Suneil K , Valiante Taufik , Wennberg Richard , Zadeh Gelareh , Kongkham Paul , Kalyvas Aristotelis , Lozano Andres M 
Published: July 2023

Abstract

Background
In patients with glioma, clinical manifestations of neural network disruption include behavioral changes, cognitive decline, and seizures. However, the extent of network recovery following surgery remains unclear. The aim of this study was to characterize the neurophysiologic and functional connectivity changes following glioma surgery using magnetoencephalography (MEG).

Methods
Ten patients with newly diagnosed intra-axial brain tumors undergoing surgical resection were enrolled in the study and completed at least two MEG recordings (pre-operative and immediate post-operative). An additional post-operative recording 6–8 weeks following surgery was obtained for six patients. Resting-state MEG recordings from 28 healthy controls were used for network-based comparisons. MEG data processing involved artifact suppression, high-pass filtering, and source localization. Functional connectivity between parcellated brain regions was estimated using coherence values from 116 virtual channels. Statistical analysis involved standard parametric tests.

Results
Distinct alterations in spectral power following tumor resection were observed, with at least three frequency bands affected across all study subjects. Tumor location-related changes were observed in specific frequency bands unique to each patient. Recovery of regional functional connectivity occurred following glioma resection, as determined by local coherence normalization. Changes in inter-regional functional connectivity were mapped across the brain, with comparable changes in low to mid gamma-associated functional connectivity noted in four patients.

Conclusion
Our findings provide a framework for future studies to examine other network changes in glioma patients. We demonstrate an intrinsic capacity for neural network regeneration in the post-operative setting. Further work should be aimed at correlating neurophysiologic changes with individual patients’ clinical outcomes.
Renewable energy and industrial development in pioneering and lagging regions: the offshore wind industry in southern Denmark and Normandy
Authors: Jolly Suyash , Steen Markus , Hansen Teis , Afewerki Samson 
Published: July 2023

Abstract
The increasing deployment of renewable energy (RE) hinges on the development and upscaling of manufacturing and logistics capacities, offering industrial development opportunities for regions and countries. In this paper, we analyse how contextual factors pertaining to pre-existing regional assets and multi-scalar institutional environments influence RE-related industrial development at the regional scale. To this avail, we purposefully selected two contrasting regional case studies of offshore wind energy-related industry developments in Southern Denmark (a pioneering region) and Normandy (France, a latecomer region) and discuss developments until 2020. Our qualitative analysis is informed by theoretical and empirical insights from the economic geography and sustainability transitions research fields. The identified contrasting regional path creation processes reflect substantial differences in context conditions, providing insights into how regions can capture value in the ongoing energy transitions.
Consequences of workplace bullying on hotel employees: a three-wave longitudinal approach
Authors: Singh Anupriya , Srivastava Shalini 
Published: July 2023

Purpose
Workplace bullying has appalling fallouts for organizations and employees. While the association between bullying and employees’ exit intentions has been sufficiently established in research, the underlying conditions remain overlooked. Using the affective events and conservation of resources theories as the theoretical lens, the purpose of this study is to probe work alienation and emotional exhaustion as sequential mediators in the association between bullying and employees’ exit intentions.

Design/methodology/approach
A sequential mediation model was examined using three-wave longitudinal data gathered from 406 employees working with hotels situated in tourist destinations of India.

Findings
Work alienation serves as a significant mediator between bullying and emotional exhaustion. More importantly, work alienation and emotional exhaustion emerged as sequential mediators in the association between bullying and exit intentions.

Originality/value
Research on workplace bullying is often cross-sectional, and researchers have called for time-lagged and/or longitudinal examination. While responding to the frequent calls made by researchers to examine underlying conditions, this three-wave longitudinal study advocates for holistic cognizance, i.e., how workplace bullying results in employees’ exit.