bluuebunny/crossref_metadata_2025_split huggingface dataset:
Robust temporal map of human in vitro myelopoiesis using single-cell genomics
Authors: Alsinet Clara , Primo Maria , Lorenzi Valentina , Knights Andrew J , Sancho-Serra Carmen , Park Jong-Eun , Wyspianska Beata S , Tough David F , Alvarez-Errico Damiana , Gaffney Daniel J , Vento-Tormo Roser 
Published: November 2021

SummaryMyeloid cells have a central role in homeostasis and tissue defence. Characterising the current in vitro protocols of myelopoiesis is imperative for their use in research and immunotherapy as well as for understanding the early stages of myeloid differentiation in humans. Here, we profiled the transcriptome of more than 400k cells and generated a robust molecular map of the differentiation of human induced pluripotent stem cells (iPSC) into macrophages. By integrating our in vitro datasets with in vivo single-cell developmental atlases, we found that in vitro macrophage differentiation recapitulates features of in vivo yolk sac hematopoiesis, which happens prior to the appearance of definitive hematopoietic stem cells (HSC). During in vitro myelopoiesis, a wide range of myeloid cells are generated, including erythrocytes, mast cells and monocytes, suggesting that, during early human development, the HSC-independent immune wave gives rise to multiple myeloid cell lineages. We leveraged this model to characterize the transition of hemogenic endothelium into myeloid cells, uncovering poorly described myeloid progenitors and regulatory programs. Taking advantage of the variety of myeloid cells produced, we developed a new protocol to produce type 2 conventional dendritic cells (cDC2) in vitro. We found that the underlying regulatory networks coding for myeloid identity are conserved in vivo and in vitro. Using genetic engineering techniques, we validated the effects of key transcription factors important for cDC2 and macrophage identity and ontogeny. This roadmap of early myeloid differentiation will serve as an important resource for investigating the initial stages of hematopoiesis, which are largely unexplored in humans, and will open up new therapeutic opportunities.
The natural adaptation and human selection history of African sheep genomes
Authors: Ahbara Abulgasim M. , Robert Christelle , Kebede Adebabay , Abeba Ayelle , Latairish Suliman , Agoub Mukhtar Omar , Musa Hassan H. , Wiener Pam , Clark Emily , Hanotte Olivier , Mwacharo Joram M. 
Published: November 2021

AbstractAfrican sheep manifest diverse but distinct physio-anatomical traits which are the outcomes of natural- and human-driven selection. Here, we generated 34.8 million variants from 150 indigenous African sheep genomes sequenced at an average depth of ∼54x for 130 samples (Ethiopia, Libya) and ∼10x for 20 samples (Sudan), representing sheep from diverse environments, tail morphology and post-Neolithic introductions to Africa. Phylogenetic and model-based admixture analysis provided evidence of four genetic groups that correspond to altitudinal geographic origins and tail morphotypes. Comparative genomic analysis identified targets of selection spanning conserved haplotype structures overlapping genes and gene families relating to hypoxia responses, caudal vertebrae and tail skeleton length, ear morphology, and tail fat-depot structure. Our findings provide novel insights underpinning variation and response to human selection and environmental adaptation, and possible pleiotropic gene interactions in indigenous African sheep genomes, which guaranteed the successful establishment of the species on the continent.
Monophyly of Diverse Bigyromonadea and their Impact on Phylogenomic Relationships Within Stramenopiles
Authors: Cho Anna , Tikhonenkov Denis V. , Hehenberger Elisabeth , Karnkowska Anna , Mylnikov Alexander P. , Keeling Patrick J. 
Published: November 2021

AbstractStramenopiles are a diverse but relatively well-studied eukaryotic supergroup with considerable genomic information available (Sibbald and Archibald, 2017). Nevertheless, the relationships between major stramenopile subgroups remain unresolved, in part due to a lack of data from small nanoflagellates that make up a lot of the genetic diversity of the group. This is most obvious in Bigyromonadea, which is one of four major stramenopile subgroups but represented by a single transcriptome. To examine the diversity of Bigyromonadea and how the lack of data affects the tree, we generated transcriptomes from seven novel bigyromonada species described in this study: Develocauda condao, Develocanicus komovi, Develocanicus vyazemskyi, Cubaremonas variflagellatum, Pirsonia chemainus, Feodosia pseudopoda, and Koktebelia satura. Both maximum likelihood and Bayesian phylogenomic trees based on a 247 gene-matrix recovered a monophyletic Bigyromonadea that includes two diverse subgroups, Developea and Pirsoniales, that were not previously related based on single gene trees. Maximum likelihood analyses show Bigyromonadea related to oomycetes, whereas Bayesian analyses and topology testing were inconclusive. We observed similarities between the novel bigyromonad species and motile zoospores of oomycetes in morphology and the ability to self- aggregate. Rare formation of pseudopods and fused cells were also observed, traits that are also found in members of labyrinthulomycetes, another osmotrophic stramenopiles. Furthermore, we report the first case of eukaryovory in the flagellated stages of Pirsoniales. These analyses reveal new diversity of Bigyromonadea, and altogether suggest their monophyly with oomycetes, collectively known as Pseudofungi, is the most likely topology of the stramenopile tree.
LiveCellMiner: A New Tool to Analyze Mitotic Progression
Authors: Moreno-Andrés Daniel , Bhattacharyya Anuk , Scheufen Anja , Stegmaier Johannes 
Published: November 2021

AbstractLive-cell imaging has become state of the art to accurately identify the nature of mitotic and cell cycle defects. Low- and high-throughput microscopy setups have yield huge data amounts of cells recorded in different experimental and pathological conditions. Tailored semi-automated and automated image analysis approaches allow the analysis of high-content screening data sets, saving time and avoiding bias. However, they were mostly designed for very specific experimental setups, which restricts their flexibility and usability. The general need for dedicated experiment-specific user-annotated training sets and experiment-specific user-defined segmentation parameters remains a major bottleneck for fully automating the analysis process. In this work we present LiveCellMiner, a highly flexible open-source software tool to automatically extract, analyze and visualize both aggregated and time-resolved image features with potential biological relevance. The software tool allows analysis across high-content data sets obtained in different platforms, in a quantitative and unbiased manner. As proof of principle application, we analyze here the dynamic chromatin and tubulin cytoskeleton features in human cells passing through mitosis highlighting the versatile and flexible potential of this tool set.
Coronary Artery Disease (CAD) - risk factors and causes: In Libyan patients
Authors: Bheleel Osama , Abdulhamid Alaa , Alhadi Ibtisam , Grash Hanaa , almuaket Hajer , Mohamed Abdelhamid Mohamed Hadi 
Published: November 2021

AbstractAimsCoronary artery disease (CAD) is the leading cause of death worldwide in both men and women. Accordingly, we retrospectively reviewed the effects of various risk factors on coronary angiographic outcomes.Methods and ResultsData were collected from the catheter lab through Tripoli university hospital records, whereas the team reviewed clinical data and coronary artery diagrams for one year from 01/04/2019 to 31/03/2020. In our study, the total number of cases was 666; 401 male and 265 female, ranging in age between 27 and 91 years. Considering the data, a significantly increased incidence of coronary artery disease (CAD) among the male who smokes, and who were less than 60 years of age. Furthermore, in the present study, the total number of normal patients was predominantly female. The most common risk factors for women were diabetes mellitus (DM), hypertension (HTN) (12%,13% respectively). While the men share the significant effects of smoking on coronary angiography (C. Angio) findings (40.52%), and most of them underwent a percutaneous coronary intervention (PCI).ConclusionsIn our study, there was evidence that CAD is a prevalent disease among the middle-aged populations with male gender preference. The risk factors including diabetes, hypertension, and smoking are the most contributing factors for the developing CAD in Libya.
Uptake of Covid-19 vaccines among frontline workers in California state prisons
Authors: Prince Lea , Long Elizabeth , Studdert David M. , Leidner David , Chin Elizabeth T. , Andrews Jason R. , Salomon Joshua A. , Goldhaber-Fiebert Jeremy D. 
Published: November 2021

AbstractBackgroundPrisons are high-risk environments for Covid-19. Vaccination levels among prison staff remain troublingly low - lower than levels among residents and members of the surrounding community. The situation is troubling because prison staff are a key vector for Covid-19 transmission.ObjectiveTo assess patterns and timing of staff vaccination in California state prisons and identify individual- and community-level factors associated with being unvaccinated.DesignWe calculated fractions of prison staff and incarcerated residents in California state prisons who remained unvaccinated. Adjusted analyses identified demographic, community, and peer factors associated with vaccination uptake among staff.SettingCalifornia Department of Corrections and Rehabilitation prisons.ParticipantsCustody and healthcare staff who worked in direct contact with residents.Main Outcomes and MeasuresRemaining unvaccinated through June 30, 2021.ResultsA total of 26% of custody staff and 52% of healthcare staff took ≥1 dose in the first two months of vaccine offer; uptake stagnated thereafter. By June 30, 2021, 61% of custody and 37% of healthcare staff remained unvaccinated. Remaining unvaccinated was positively associated with younger age, prior Covid-19, residing in a community with relatively low vaccination rates, and sharing shifts with co-workers who had relatively low vaccination rates.Conclusions and RelevanceVaccine uptake among prison staff in California in regular contact with incarcerated residents has plateaued at levels that pose ongoing risks—both of further outbreaks in the prisons and transmission into surrounding communities. Staff decisions to forego vaccination appear to be complex and multifactorial. Achieving safe levels of vaccine protection among frontline staff may necessitate requiring vaccination as condition of employment.
Optimizing one-dose and two-dose cholera vaccine allocation in outbreak settings: A modeling study
Authors: Leung Tiffany , Eaton Julia , Matrajt Laura 
Published: November 2021

AbstractBackgroundA global stockpile of oral cholera vaccine (OCV) was established in 2013 for use in outbreak response and are licensed as two-dose regimens. Vaccine availability, however, remains limited. Previous studies have found that a single dose of OCV may provide substantial protection against cholera.MethodsUsing a mathematical model with two age groups paired with optimization algorithms, we determine the optimal vaccination strategy with one and two doses of vaccine to minimize cumulative overall infections, symptomatic infections, and deaths. We explore counterfactual vaccination scenarios in three distinct settings: Maela, the largest refugee camp in Thailand, with high in- and out-migration; N’Djamena, Chad, a densely populated region; and Haiti, where departments are connected by rivers and roads.ResultsOver the short term under limited vaccine supply, the optimal strategies for all objectives prioritize one dose to the older age group (over five years old), irrespective of setting and level of vaccination coverage. As more vaccine becomes available, it is optimal to administer a second dose for long-term protection. With enough vaccine to cover the whole population with one dose, the optimal strategies can avert up to 30% to 90% of deaths and 36% to 92% of symptomatic infections across the three settings over one year. The one-dose optimal strategies can avert 1.2 to 1.8 times as many cases and deaths as a two-dose pro-rata strategy.ConclusionsIn an outbreak setting, speedy vaccination campaigns with a single dose of OCV may avert more cases and deaths than a two-dose pro-rata campaign under a limited vaccine supply.
Effectiveness of digital contact tracing for COVID-19 in New South Wales, Australia
Authors: Vogt Florian , Haire Bridget , Selvey Linda , Kaldor John 
Published: November 2021

ABSTRACTBackgroundDigital proximity tracing applications were rolled out early in the COVID-19 pandemic in many countries to complement conventional contact tracing. Empirical evidence about their benefits for pandemic response remains scarce. We evaluated the effectiveness and usefulness of ‘COVIDSafe’, Australia’s national smartphone-based proximity tracing application for COVID-19.MethodsIn this prospective study, conducted in New South Wales, Australia between May and November 2020, we calculated the positive predictive value and sensitivity of COVIDSafe, its additional contact yield, and the number of averted public exposure events. Semi-structured interviews with public health staff were conducted to assess the application’s usefulness.ResultsThere were 619 confirmed COVID-19 cases and over 25,300 close contacts during the study period. COVIDSafe was used by 137 (22%) cases and detected 79 (0·3%) close contacts. It had a positive predictive value of 39% and a sensitivity of 15%, and detected 17 (0·07%) additional close contacts that were not identified by conventional contact tracing. The application generated a substantial additional workload for public health staff and was not considered useful.ConclusionsCOVIDSafe was not sufficiently effective to make a meaningful contribution to the COVID-19 response in Australia’s most populous state over a 6-month period. This contrasts optimistic projections from modelling studies about the added value of digitally supported contact tracing. We found no evidence that it adds value to conventional contact tracing, and recommend that their implementation should always include comprehensive effectiveness evaluations.
Vitronectin acts as a key regulator of adhesion and migration in human umbilical cord-derived MSCs under different stress conditions
Authors: Sen Ankita , Ta Malancha 
Published: November 2021

AbstractMesenchymal stem cell (MSC)-based therapy gets compromised as adverse microenvironmental conditions like nutrient deprivation, ischemia, hypoxia at the target site affect migration, engraftment and viability, of MSCs post transplantation. To improve the treatment efficacy, it is critical to identify factors involved in regulating migration and adhesion of MSCs under such microenvironmental stress conditions. In our study, we observed that human Wharton’s jelly-derived MSCs (WJ-MSCs) exhibited increase in cell spread area and adhesion, with reduction in cellular migration under serum starvation stress. The changes in adhesion and migration characteristics were accompanied by formation of large number of super mature focal adhesions along with extensive stress fibres and altered ECM gene expression with notable induction in vitronectin (VTN) expression. NF-κβ was found to be a positive regulator of VTN expression while ERK pathway regulated it negatively. Molecular and phenotypic comparison studies with inhibition of these signalling pathways or knocking down of VTN under serum starvation established the correlation between increase in VTN expression and increased cellular adhesion with corresponding reduction in cell migration. VTN knockdown also resulted in reduction of super mature focal adhesions and extensive stress fibres, which were formed under serum starvation. Additionally, VTN induction was not detected in hypoxia-treated WJ-MSCs, and the MSCs showed no significant change in the adhesion or migration properties under hypoxia. However, when VTN expression was induced under hypoxia by ERK pathway inhibition, similar increase in cell spread area and adhesion were observed. Our study thus highlights VTN as a key player which is induced under serum starvation stress and possibly regulates the adhesion and migration properties of WJ-MSCs via focal adhesion signalling.
Common variation in EDN1 regulatory regions highlights the role of PPARγ as a key regulator of Endothelin in vitro
Authors: Lago-Docampo Mauro , Solarat Carlos , Méndez-Martínez Luis , Baloira Adolfo , Valverde Diana 
Published: November 2021

AbstractPulmonary Arterial Hypertension (PAH) is a rare disease caused by the obliteration of the pulmonary arterioles, increasing pulmonary vascular resistance and eventually causing right heart failure. Endothelin-1 is a vasoconstrictor peptide whose levels are indicators of disease progression and its pathway is one of the commonest targeted by current treatments.We sequenced the EDN1 untranslated regions of a small subset of PAH patients, predicted the effect in silico, and used a luciferase assay with the different genotypes to analyze its influence on gene expression. Finally, we used siRNAs against the major transcription factors predicted for these regions (PPARγ, KLF4, and VDR) to assess Endothelin-1 expression in cell culture and validate the binding sites.First, we detected a SNP in the 5’UTR (rs397751713) and another in the 3’regulatory region (rs2859338) that increased luciferase activity in vitro depending on their genotype. We determined in silico that KLF4/PPARγ could be binding in the rs397751713 and VDR in rs2859338. By using siRNAs and luciferase, we determined that PPARγ binds differentially in rs397751713. PPARγ and VDR Knock-Down, increased EDN1 mRNA levels and Endothelin-1 production in PAECs, while PPARγ and KLF4 Knock-Down increased the Endothelin-1 production in HeLa.In conclusion, common variants in EDN1 regulatory regions could alter Endothelin-1 levels. We were able to validate that PPARγ binds in rs397751713 and is key to regulate Endothelin-1. Also, KLF4 and VDR regulate Endothelin-1 production in a cell-dependent manner, but for VDR this interaction does not happen by binding directly to the regions we studied.
Methylglyoxal Induces Endothelial Dysfunction via Stunning-like Phenotype
Authors: Fleming Thomas , von Nettelbladt Bastian , Morgenstern Jakob , Campos Marta , Le Marois Maxime , Bartosova Maria , Hausser Ingrid , Schwab Constantin , Fischer Andreas , Nawroth Peter P. , Szendroedi Julia , Herzig Stefan 
Published: November 2021

AbstractElevated levels of methylglyoxal (MG) and its associated post-translational modifications have been reported to be associated with progression and development of numerous pathological conditions. Despite such extensive evidence, it still remains unclear what the specific effects of MG are other than that induction of cytotoxicity. Here we evaluated the effects of MG in cardiac endothelial cells in vitro. We found that MG leads to a non-proliferative state and endothelial dysfunction, which is reversible as MG-H1, a major post-translational modification induced by MG, is turned over by lysosomal degradation. MG-induced cellular stunning/paralysis describes a new hallmark for cellular dysfunction which could lead to alterations in tissue homeostasis as well as cell-to-cell interactions, thereby contributing to the pathogenesis of diseases.
Structural basis for Cas9 off-target activity
Authors: Pacesa Martin , Lin Chun-Han , Cléry Antoine , Saha Aakash , Arantes Pablo R. , Bargsten Katja , Irby Matthew J. , Allain Frédéric H.T. , Palermo Giulia , Cameron Peter , Donohoue Paul D. , Jinek Martin 
Published: November 2021

ABSTRACTThe target DNA specificity of the CRISPR-associated genome editor nuclease Cas9 is determined by complementarity to a 20-nucleotide segment in its guide RNA. However, Cas9 can bind and cleave partially complementary off-target sequences, which raises safety concerns for its use in clinical applications. Here we report crystallographic structures of Cas9 bound tobona fideoff-target substrates, revealing that off-target binding is enabled by a range of non-canonical base pairing interactions within the guide–off-target heteroduplex. Off-target sites containing single-nucleotide deletions relative to the guide RNA are accommodated by base skipping or multiple non-canonical base pairs rather than RNA bulge formation. Additionally, PAM-distal mismatches result in duplex unpairing and induce a conformational change of the Cas9 REC lobe that perturbs its conformational activation. Together, these insights provide a structural rationale for the off-target activity of Cas9 and contribute to the improved rational design of guide RNAs and off-target prediction algorithms.
A novel enhancer that regulates Bdnf expression in developing neurons
Authors: Brookes Emily , Alan Au Ho Yu , Varsally Wazeer , Barrington Christopher , Hadjur Suzana , Riccio Antonella 
Published: November 2021

SummaryBrain derived neurotrophic factor (BDNF) is a critical secreted peptide that promotes neuronal differentiation and survival, and its downregulation is implicated in many neurological disorders. Here, we investigated the regulation of the mouse Bdnf gene in cortical neurons and identified a novel enhancer that promotes the expression of many Bdnf transcript variants during differentiation, increasing total Bdnf mRNA levels. Enhancer activity contributes to Bdnf-mediated effects on neuronal clustering and activity-dependent dendritogenesis. During Bdnf activation, enhancer-promoter contacts increase, and the region moves away from the repressive nuclear periphery. Our findings suggest that changes in nuclear structure may contribute to the expression of essential growth factors during neuronal development.
Transgenic tools for targeted chromosome rearrangements allow construction of balancer chromosomes in non-melanogaster Drosophila species
Authors: Stern David L. 
Published: November 2021

AbstractPerhaps the most valuable single set of resources for genetic studies of Drosophila melanogaster is the collection of multiply-inverted chromosomes commonly known as balancer chromosomes. Balancers prevent the recovery of recombination exchange products within genomic regions included in inversions and allow perpetual maintenance of deleterious alleles in living stocks and the execution of complex genetic crosses. Balancer chromosomes have been generated traditionally by exposing animals to ionizing radiation and screening for altered chromosome structure or for unusual marker segregation patterns. These approaches are tedious and unpredictable, and have failed to produce the desired products in some species. Here I describe transgenic tools that allow targeted chromosome rearrangements in Drosophila species. The key new resources are engineered reporter genes containing introns with yeast recombination sites and enhancers that drive fluorescent reporter genes in multiple body regions. These tools were used to generate a doubly-inverted chromosome 3R in D. simulans that serves as an effective balancer chromosome.