bluuebunny/crossref_metadata_2025_split huggingface dataset:
Defining the molecular correlate of arteriolar hyalinosis in kidney disease progression by integration of single cell transcriptomic analysis and pathology scoring
Authors: Menon Rajasree , Otto Edgar A. , Barisoni Laura , Melo Ferreira Ricardo , Limonte Christine P. , Godfrey Bradley , Eichinger Felix , Nair Viji , Naik Abhijit S. , Subramanian Lalita , D’Agati Vivette , Henderson Joel M. , Herlitz Leal , Kiryluk Krzysztof , Moledina Dennis G. , Moeckel Gilbert W. , Palevsky Paul M. , Parikh Chirag R. , Randhawa Parmjeet , Rosas Sylvia E. , Rosenberg Avi Z. , Stillman Isaac , Toto Robert , Torrealba Jose , Vazquez Miguel A. , Waikar Sushrut S. , Alpers Charles E. , Nelson Robert G. , Eadon Michael T. , Kretzler Matthias , Hodgin Jeffrey B. ,   Kidney Precision Medicine Project (KPMP),   Nephrotic Syndrome Study Network (NEPTUNE)
Published: June 2023

ABSTRACTArteriolar hyalinosis in kidneys is an independent predictor of cardiovascular disease, the main cause of mortality in chronic kidney disease (CKD). The underlying molecular mechanisms of protein accumulation in the subendothelial space are not well understood. Using single cell transcriptomic data and whole slide images from kidney biopsies of patients with CKD and acute kidney injury in the Kidney Precision Medicine Project, the molecular signals associated with arteriolar hyalinosis were evaluated. Co-expression network analysis of the endothelial genes yielded three gene set modules as significantly associated with arteriolar hyalinosis. Pathway analysis of these modules showed enrichment of transforming growth factor beta / bone morphogenetic protein (TGFβ / BMP) and vascular endothelial growth factor (VEGF) signaling pathways in the endothelial cell signatures. Ligand-receptor analysis identified multiple integrins and cell adhesion receptors as over-expressed in arteriolar hyalinosis, suggesting a potential role of integrin-mediated TGFβ signaling. Further analysis of arteriolar hyalinosis associated endothelial module genes identified focal segmental glomerular sclerosis as an enriched term. On validation in gene expression profiles from the Nephrotic Syndrome Study Network cohort, one of the three modules was significantly associated with the composite endpoint (> 40% reduction in estimated glomerular filtration rate (eGFR) or kidney failure) independent of age, sex, race, and baseline eGFR, suggesting poor prognosis with elevated expression of genes in this module. Thus, integration of structural and single cell molecular features yielded biologically relevant gene sets, signaling pathways and ligand-receptor interactions, underlying arteriolar hyalinosis and putative targets for therapeutic intervention.
Decoding Phase Separation of Prion-Like Domains through Data-Driven Scaling Laws
Authors: Maristany M. Julia , Aguirre Gonzalez Anne , Espinosa Jorge R. , Huertas Jan , Collepardo-Guevara Rosana , Joseph Jerelle A. 
Published: June 2023

AbstractProteins containing prion-like low complexity domains (PLDs) are common drivers of the formation of biomolecular condensates and are prone to misregulation due to amino acid mutations. Here, we exploit the accuracy of our residue-resolution coarse-grained model, Mpipi, to quantify the impact of amino acid mutations on the stability of 140 PLD mutants from six proteins (hnRNPA1, TDP43, FUS, EWSR1, RBM14, and TIA1). Our simulations reveal the existence of scaling laws that quantify the range of change in the critical solution temperature of PLDs as a function of the number and type of amino acid sequence mutations. These rules are consistent with the physicochemical properties of the mutations and extend across the entire family tested, suggesting that scaling laws can be used as tools to predict changes in the stability of PLD condensates. Our work offers a quantitative lens into how the emergent behavior of PLD solutions varies in response to physicochemical changes of single PLD molecules.
Fluorochrome-dependent specific changes in spectral profiles using different compensation beads or human cells in full spectrum cytometry
Authors: Shevchenko Yaroslava , Lurje Isabella , Tacke Frank , Hammerich Linda 
Published: June 2023

AbstractFull spectrum flow cytometry is a powerful tool for immune monitoring on a single-cell level and with currently available machines, panels of 40 or more markers per sample are possible. However, with an increased panel size, spectral unmixing issues arise, and appropriate single stain reference controls are required for accurate experimental results and to avoid unmixing errors. In contrast to conventional flow cytometry, full spectrum flow cytometry takes into account even minor differences in spectral signatures and requires the full spectrum of each fluorochrome to be identical in the reference control and the fully stained sample to ensure accurate and reliable results. In general, using the cells of interest is considered optimal, but certain markers may not be expressed at sufficient levels to generate a reliable positive control. In this case, compensation beads show some significant advantages as they bind a consistent amount of antibody independent of its specificity. In this study, we evaluated two types of manufactured compensation beads for use as reference controls for full spectrum cytometry and compared them to human and murine primary leukocytes. While most fluorochromes show the same spectral profile on beads and cells, we demonstrate that specific fluorochromes show a significantly different spectral profile depending on which type of compensation beads is used, and some fluorochromes should be used on cells exclusively. Finally, we provide a list of appropriate reference controls for 30 of the most commonly used and commercially available fluorochromes.
Genital microbiota in infertile couples
Authors: Baud David , Peric Adriana , Vidal A. , Weiss JM. , Engel Philipp , Das Sudip , Stojanov Milos 
Published: June 2023

AbstractBacteria colonise most of the human body and the genital tract is not an exception. While it has been known for decades that a vaginal microbiota exists, other genital sites have traditionally been viewed as sterile environments, with bacterial presence associated only with pathological conditions. However, recent studies identified specific patterns of bacterial colonisation in most genital sites. Shifts in the bacterial colonisation of the female genital tract have been linked to impairment of reproduction and adverse pregnancy outcomes, such as preterm birth.The goal of this project is to understand the association between the genital microbiota of couples seeking assisted procreation aid and the outcome of this treatment. Male and female partners will be studied as a unit (“couple microbiota”) and the interaction between their microbiota will be evaluated.We have characterised microbial samples coming from vaginal and penile swabs, as well as follicular fluid and semen, using next generation sequencing (16S rRNA profiling). The results were linked to clinical data of the patients included in the study and particularly to the results of the fertility treatment process. With this project, we aim to gain a better understanding of how the male genital microbiota could influence the lower (vagina) and upper (follicular fluid) female genital tracts.
A sparse code for natural sound context in auditory cortex
Authors: Espejo Mateo López , David Stephen V. 
Published: June 2023

AbstractAccurate sound perception can require integrating information over hundreds of milliseconds or even seconds. Spectro-temporal models of sound coding by single neurons in auditory cortex indicate that the majority of sound-evoked activity can be attributed to stimuli with a few tens of milliseconds. It remains uncertain how the auditory system integrates information about sensory context on a longer timescale. Here we characterized long-lasting contextual effects in auditory cortex (AC) using a diverse set of natural sound stimuli. We measured context effects as the difference in a neuron’s response to a single probe sound following two different context sounds. Many AC neurons showed context effects lasting longer than the temporal window of a traditional spectro-temporal receptive field. The duration and magnitude of context effects varied substantially across neurons and stimuli. This diversity of context effects formed a sparse code across the neural population that encoded a wider range of contexts than any constituent neuron. Encoding model analysis indicates that context effects can be explained by activity in the local neural population, suggesting that recurrent local circuits support a long-lasting representation of sensory context in auditory cortex.
The influence ofGC-biased gene conversion on nonadaptive sequence evolution in short introns ofDrosophila melanogaster
Authors: Yıldırım Burçin , Vogl Claus 
Published: June 2023

AbstractPopulation genetic inference of selection on the nucleotide sequence level often proceeds by comparison to a reference sequence evolving only under mutation and population demography. Among the few candidates for such a reference sequence is the 5’ part of short introns (5SI) inDrosophila. In addition to mutation and population demography, however, there is evidence for a weak force favoringGCbases, likely due toGC-biased gene conversion (gBGC), and for the effect of linked selection. Here, we use polymorphism and divergence data ofDrosophila melanogasterto detect and describe the forces affecting the evolution of the 5SI. We separately analyze mutation classes, compare them between chromosomes, and relate them to recombination rate frequencies.GC-conservative mutations seem to be mainly influenced by mutation and drift, with linked selection mostly causing differences between the central and the peripheral (i.e., telomeric and centromeric) regions of the chromosome arms. ComparingGC-conservative mutation patterns between autosomes and the X chromosome, showed differences in mutation rates, rather than linked selection, in the central chromosomal regions after accounting for differences in effective populations sizes. On the other hand,GC-changing mutations show asymmetric site frequency spectra, indicating the presence of gBGC, varying among mutation classes and in intensity along chromosomes, but approximately equal in strength in autosomes and the X chromosome.
Autonomic regions of the brainstem show a sex-specific inflammatory response to systemic neonatal lipopolysaccharide
Authors: Hedley Kateleen E , Cuskelly Annalisa , Callister Robert J , Horvat Jay C , Hodgson Deborah M , Tadros Melissa A 
Published: June 2023

AbstractEarly life inflammation has been linked to long-term deficits in the central nervous system in relation to behavioural disorders, but it is now becoming more apparent it can also lead to autonomic dysfunction. The brainstem contains all critical control centres for autonomic homeostasis, so we used the well-established model of neonatal lipopolysaccharide (LPS) exposure to examine the immediate and long-term impacts of systemic inflammation on the autonomic regions of the brainstem. Wistar rats were injected with LPS or saline on postnatal days 3 and 5, with sacrifices made on postnatal days 7 and 90. At both timepoints inflammatory mediators were assessed in the brainstem via RT-qPCR and microglia were characterised by immunofluorescence in the autonomic regions of the brainstem. In the brainstem there was a distinct sex-specific response of all measured inflammatory mediators at both ages, as well as significant neonatal sex differences in inflammatory mediators at baseline. AT both ages, microglial morphology had a significant change to branch length and soma size in a sex-specific manner, which strongly indicate a significant effect of neonatal immune activation. This data not only highlights the strong sex-specific response of neonates to LPS administration, but also the significant impact on the brainstem in adulthood.
Confinement by liquid-liquid interface replicatesin vivoneutrophil deformations and elicits bleb based migration
Authors: Schrope Jonathan H. , Horn Adam , Lazorchak Kaitlyn , Tinnen Clyde W. , Stevens Jack J , Farooqui Mehtab , Robertson Tanner , Li Jiayi , Bennin David , Juang Terry , Ahmed Adeel , Li Chao , Huttenlocher Anna , Beebe David J 
Published: June 2023

AbstractLeukocytes navigate through interstitial spaces resulting in deformation of both the motile leukocytes and surrounding cells. Creating anin vitrosystem that models the deformable cellular environment encounteredin vivohas been challenging. Here, we engineer microchannels with a liquid-liquid interface that exerts confining pressures (200-3000 Pa) similar to cells in tissues, and, thus, is deformable by cell generated forces. Consequently, the balance between migratory cell-generated and interfacial pressures determines the degree of confinement. Pioneer cells that first contact the interfacial barrier require greater deformation forces to forge a path for migration, and as a result migrate slower than trailing cells. Critically, resistive pressures are tunable by controlling the curvature of the liquid interface, which regulates motility. By granting cells autonomy in determining their confinement, and tuning environmental resistance, interfacial deformations are made to match those of surrounding cellsin vivoduring interstitial neutrophil migration in a larval zebrafish model. We discover that, in this context, neutrophils employ a bleb-based mechanism of force generation to deform a barrier exerting cell-scale confining pressures.Significance StatementImmune cells sense physical forces provided by surrounding cellular tissues to regulate their motility. Here, we introduce the use of liquid-liquid interfaces to model forces exerted by surrounding cells during interstitial motilityin vivo. Neutrophils interacting with the interface employ a bleb-based mechanism of force generation to induce interfacial deformation. This work furthers our understanding of the mechanisms employed by immune cells to traverse through deformable barriers akin to cells in the body, and introduces a pioneering technology enabling the study of cell interaction with soft materials.
Serological evidence of high pathogenicity virus infection inEidolon helvumfruit bats in Nigeria
Authors: Cantoni Diego , Mayora-Neto Martin , Auld Bethany , Costa Kelly Da , Rosario Joanne Del , Ameh Veronica O. , Sabeta Claude T. , Derveni Mariliza , Hamlet Arran , Wright Edward , Scott Simon , Giotis Efstathios S. , Banyard Ashley , Temperton Nigel 
Published: June 2023

AbstractTheEidolon helvumfruit bat is the most widely distributed fruit bat in Africa and is known to be a reservoir for several pathogenic viruses that can cause disease in humans. To assess the risk of zoonotic spillover, we conducted a serological survey of 304 serum samples fromE. helvumbats that were captured for human consumption in Makurdi, Nigeria. Using pseudotyped viruses, we screened the samples for neutralising antibodies against viruses from theCoronaviridae, Filoviridae, OrthomyxoviridaeandParamyxoviridaefamilies. We report the presence of neutralising antibodies against henipavirus lineage GH-M74a virus (odds ratio 6.23; p<0.001), Nipah virus (odds ratio 4.04; p=0.00031), bat influenza H17N10 virus (odds ratio 7.25; p<0.001) and no significant association with Ebola virus (odds ratio 0.56; p=0.375) in the bat cohort. The data suggest a potential risk of zoonotic spillover including the possible circulation of highly pathogenic viruses inE. helvumpopulations. These findings highlight the importance of maintaining sero-surveillance ofE. helvumto monitor changes in virus prevalence and distribution over time and across different geographic locations.Article summary lineThe detection of neutralizing antibodies against henipavirus GH-M74a virus, Nipah virus, and H17N10 virus inEidolon helvumbat sera from Nigeria using pseudotyped viruses suggests a potential risk of zoonotic spillover.
Adaptive framing of sustainability in CEO letters
Authors: Arvidsson Susanne , Sabelfeld Svetlana 
Published: June 2023

PurposeThis study provides insights into the external powers that can influence business leaders' communication on sustainability. It shows how the socio-political context manifested in national and transnational policies, regulations and other socio-political events can influence the CEO talk about sustainability.Design/methodology/approachThis study adopts an interpretative and qualitative method of analysis using the lenses of the theoretical concepts of framing and legitimacy, analysing CEOs’ letters from 10 multinational industrial companies based in Sweden, over the period of 2008–2019.FindingsThe results show that various discourses of sustainability, emerging from policies and regulatory initiatives, socio-political events and civil society activism, are reflected in the ways CEOs frame sustainability over time. This article reveals that CEOs not only lead the discourse of profitable sustainability, but they also slowly adapt their sustainability talk to other discourses led by the policymakers, regulators and civil society. This pattern of a slow adaptation is especially visible in a period characterised by increased discourses of climate urgency and regulations related to social and environmental sustainability.Research limitations/implicationsThe theoretical frame is built by integrating the concepts of legitimacy and framing. Appreciating dynamic notions of legitimacy and framing, the study suggests a novel view of reporting as a film series, presenting many frames of sustainability over time. It helps the study to conceptualise CEO framing of sustainability as adaptive framing. This study suggests using a dynamic notion of adaptive framing in future longitudinal studies of corporate- and accounting communication.Practical implicationsThe results show that policymakers, regulators and civil society, through their initiatives, influence the CEOs' framing of sustainability. It is thus important for regulators to substantiate sustainability-related discourses and develop conceptual tools and language of social and environmental sustainability that can lead CEO framing more effectively.Originality/valueThe study engages with Goffman's notion of dynamic framing. Dynamic framing suggests a novel view of reporting as a film series, presenting many frames of sustainability over time and conceptualises CEO framing of sustainability as adaptive framing.
The use of multiplex ARMS-PCR for mutational analysis of beta-globin gene in consanguineous population of KP Pakistan
Authors: Ghalib Ayesha , Khan Valeed , Shams Sumaira , Pervaiz Ruqiya 
Published: June 2023

Purposeß-thalassemia is a hereditary disorder due to mutation in the ß-globin gene on chromosome 11. Out of 200 known ß-globin gene chain mutations recognized, it is better to identify the most common mutation in specific regions and ethnicity for cost-effective molecular diagnosis of this disorder. Therefore, this study aims to practice multiplex-amplification refractory mutation system (ARMS) PCR on patients with thalassemia in Khyber Pakhtunkhwa (KP) to investigate the most common mutations in the ß-globin chain gene.Design/methodology/approachTwenty-two individuals (patients, their parents and non-affected siblings) with signed consent were studied from six consanguineous families of ß-thalassemia. Blood samples were collected for DNA isolation. For the detection of mutations in the ß-globin gene, ARMS-PCR was used. The amplicon was visualized through 2% Agarose Gel.FindingsThe most common mutations among different ethnic groups in the study area residents were Fr 8-9 (+G) and IVS 1-5 (G> C). The prominent enhancing factors for ß-thalassemia are inter-family marriages and lack of awareness.Practical implicationsMultiplex ARMS_PCR is the most valuable technique for assessing multiple mutations in a single reaction tube.Social implicationsDue to extensively found ethnic and regional variations and a high rate of consanguinity, the Pashtun population has a great risk of mutations in their genome. Therefore, ARMS-PCR is a cost-effective mutational diagnostic strategy that can help to control disease burden.Originality/valueLimited studies using ARMS-PCR for mutational analysis in the ß-globin gene are conducted. This study is unique as it targeted consanguineous families of KP Pakistan.
Causal modelling of testing and assessment ethics among proctors of public examinations in Oyo state
Authors: Jinadu Afeez Tunde 
Published: June 2023

PurposeUpholding assessment ethics are common concerns during annual public examination performance appraisal. Previous studies have focused more on examination stakeholder: testees outside proctors however, assessment ethics cannot be studied excluding proctors variables therefore, the study investigated consistency of a structural equation modelling of security, environment, professionalism, testing and assessment ethics.Design/methodology/approachEx-post facto design was adopted. Simple random sampling technique was employed to choose 90 proctors drawn from 45 colleges. Proctors Examination Ethics Questionnaire (reliability = 0.86) was used to collect data for the study. Data collected were analysed using path analysis at 0.05 significant levels.FindingsOut of the six hypothesised paths significantly explaining the consistency of the causal model. Test security, environment and professionalism accounted for both direct and indirect effects on assessment ethics. All model fit indices were established to explain testing and assessment model.Research limitations/implicationsFew proctor variables were studied, therefore assessment ethics may not be explained other than through proctor variables considered in this study.Practical implicationsAssessment ethics may not be violated if test security, testing environment and professionalism are not cared for during test administration as shown in the study.Social implicationsIt added to knowledge base in ethical areas of assessment, a 21st-century proctors in upholding testing and assessment ethics, security, environment and professionalism are to be considered.Originality/valueThere was a positive causal effect of security, environment and professionalism on testing and assessment ethics among proctors in public examinations.
Business network and balanced scorecard: an analysis of small and medium enterprises in Malaysia
Authors: Abdul Rahman Abdul Aziz , Chong Poh Ling , Ong Tze San , Teh Boon Heng , Ong Tze Chin 
Published: June 2023

PurposeThe aim of this paper is to characterise the association between business network and the balanced scorecard used by Malaysian small and medium enterprises (SMEs) as a method for assessing firm efficiency. The business network takes into account both the dimensions of stability and efficiency. The business network can help SMEs, with fewer resources to remain competitive. By having a secure business network, the performance of SMEs in Malaysia can be further improved. A business network can facilitate swift coordination amongst distant geographies to create new competitive advantages by accessing market segments, resources as well as building strategic business alliances.Design/methodology/approachA total of 404 sets of data collected by using stratified random sampling and structured questionnaire as an instrument. The list of SMEs collected from the Malaysia Foreign Trade Growth Corporate Directory (MATRADE) directories. Structural equation modelling (SEM) was utilised to analyse the data.FindingsThe findings show that the business network plays a role in the balanced scorecard (BSC) outcomes of Malaysian SMEs.Originality/valueThis article provides the owners and managers with an awareness to rapidly achieve the company's efficiency. Finally, the new article often has some consequences for decision-makers and regulators.