bluuebunny/crossref_metadata_2025_split huggingface dataset:
Religion and Revolution in Europe
Authors: Banks Bryan A. , Johnson Edwards Erica 
Published: December 2021

Abstract
The French Revolution and Napoleonic Empire altered the religious landscape of France, Europe, and the wider world. Revolutionaries reduced religion to a matter of opinion in the 10th Article of the Declaration of the Rights of Man and Citizen (1789), legitimizing their seizure of Catholic lands and disavowal of the religious and political hierarchy of Old Regime France and its empire in the process. This in turn ignited a dechristianization campaign, local conflicts between Catholics, Protestants, and Jewish communities, and counter-revolutionary war in France. The violence reverberated well beyond France’s borders, both throughout Europe and in imperial and non-imperial spaces. From Prussia to Portugal to Port-au-Prince, revolutionaries inspired violence against and in defence of religion, drove les religieux across borders and into the borderlands, and sparked debates over secularization (laïcization, in France) and the rights of individuals and collective, religious bodies for generations.
Religion and Nationality in Europe
Authors: Grosby Steven 
Published: December 2021

Abstract
Throughout European history, the relationship between religion and nationality has been varied and complex. Numerous times religion has been a bearer of national traditions and a nation has been a bearer of religious traditions, as can be seen in the Church’s conciliarism and the use of the Biblical image of Israel in Christian Hebraism. However, there have also existed sharp tensions between religion and nationality, as can be seen in how the New Testament has been understood and in Canon law. These variations must be accounted for. Why and how has religion both contributed to the consolidation and continued existence of a nation, and been disruptive of that consolidation and continued existence? When pursuing answers posed by these questions, a more accurate understanding of culture, religion, and nationality will be necessary by taking into account the distinction between unity and uniformity.
Deproblematizing the Federal–Unitary Dichotomy: Insights from a Public Opinion Survey about Approaches to Designing a Political System in Afghanistan
Authors: Mobasher Mohammad Bashir , Qadam Shah Mohammad 
Published: December 2021

AbstractThis study draws on results of an opinion survey about public views in Afghanistan regarding concepts related to federalism. We argue that concepts such as unitarism, federalism, centralization, and decentralization are highly politicized and often misunderstood when they enter the public discourse. As the survey results indicate, the association of ethnic groups with different systems of governance, although popular in Afghanistan, is misleading. A concurrent majority of ethnic groups takes a more nuanced approach of favoring central authorities on some issues, local authorities on others, and shared or divided authorities on the rest. The findings are helpful in contributing to a better understanding of how Afghans view federalism, and also by providing guidance to constitution-makers in designing institutional arrangements and distributions of power that address society’s needs.
Lockdown on Peace? COVID-19’s Impact on Women Peacebuilders
Authors: Santos Agnieszka Fal-Dutra , Salamat Nikou , Bölükoğlu Sena , Baron B Kathryn , Choi Christine , Gasperetti Heidi M 
Published: December 2021

Abstract
COVID-19 threatens to slow progress on the implementation of peace agreements, and reverse hard-won gains of women peacebuilders’ work towards holistic, gender-equal peace, rooted in human security. Through an analysis of in-depth interviews from a purposive sample of women peacebuilders in Colombia, South Sudan, the Philippines, and Ukraine, this article contributes to a greater understanding of the pandemic’s impact on women’s peace activism, as these peacebuilders adapted to emerging realities and became first responders. We argue that the pandemic has deepened the marginalization of women peacebuilders from formal peace processes, possibly to detriment of both immediate recovery and long-term peacebuilding.
The Homodigital Propeller Flap: A New Tool for Fingertip Reconstruction. Surgical Technique, Anatomical Study, and Clinical Relevance
Authors: Roulet Steven , Delgove Anaïs , Chirez Pierre , Chaput Benoit , Casoli Vincent , Pelissier Philippe , Pinsolle Vincent , Lepivert Jean-Christophe 
Published: December 2021

Background:
An ideal flap for fingertip injuries should cover a significant loss of substance and avoid joint flexion to prevent later contracture and joint stiffness. In this study, the authors describe a modified homodigital island flap—the homodigital propeller flap—to better meet these requirements.

Methods:
An anatomical model of fingertip loss is used to analyze the advancement achieved without flexion of the finger. Twenty-four fresh-frozen fingers were dissected. Wires were inserted to maintain joints in extension. The skin paddle was similar in location to a homodigital island flap. The neurovascular bundle was dissected without exceeding the proximal interphalangeal joint and was released from the proximal half of the paddle. Then, the homodigital propeller flap was rotated 180 degrees to cover the defect. A mixture of India ink and barium sulfate was injected into the pedicle artery after the release of the proximal half of the flap from the neurovascular pedicle to assess residual flap vascularization. India ink highlights the residual subcutaneous vascularization network of the cutaneous paddle. A radiographic study of the flap was then performed to visualize the subcutaneous vascular network of the cutaneous paddle.

Results:
The homodigital propeller flap achieved an average cutaneous advancement of 18 mm (range, 15 to 22 mm) and allowed full coverage of cutaneous defects for all fingers while maintaining the proximal interphalangeal joint in strict extension.

Conclusions:
The homodigital propeller flap is a refinement of the classic homodigital island flap. It allows efficient coverage of fingertip defects because of a large advancement without flexion of the finger, reducing the risk of stiffness.
Utility of Dermal Wound Matrices Compared with Local-Tissue Rearrangement and Free Flap Reconstruction for Oncologic Scalp Wounds: A Multidisciplinary Dual Matched-Pair Analysis
Authors: Othman Sammy , Shakir Sameer , Azoury Saïd C. , Lukowiak Tess , Shin Thuzar M. , Sobanko Joseph F. , Miller Christopher J. , Etzkorn Jeremy R. , Fischer John P. , Kovach Stephen J. 
Published: December 2021

Background:Local tissue rearrangement, free flap reconstruction, and Bilayer Wound Matrix represent reconstructive modalities for coverage of scalp defects; however, preferred indications are less clear. The authors aimed to evaluate the efficacy of these interventions.Methods:A retrospective review (2008 to 2019) was performed of subjects requiring soft-tissue reconstruction of oncologic scalp wounds. Subjects were dual matched into two comparative cohorts: (1) local tissue rearrangement versus Bilayer Wound Matrix, and (2) free flap reconstruction versus Bilayer Wound Matrix. Ninety-day wound coverage, hospital length of stay, operative time, and wound complications were compared.Results:In total, 361 subjects were included. Following matching, 126 subjects constituted the local tissue rearrangement versus Bilayer Wound Matrix cohort, and 56 constituted the free flap reconstruction versus Bilayer Wound Matrix cohort. Local tissue rearrangement/Bilayer Wound Matrix median defect size was 35 ± 42.5 cm2. Local tissue rearrangement provided significantly better wound coverage at 90 days (95.2 percent) compared to Bilayer Wound Matrix (84.1 percent) (p< 0.040). Median defect size in the free flap reconstruction/Bilayer Wound Matrix cohort was 100 ± 101.1 cm2. Ninety-day success (free flap reconstruction, 92.9 percent; Bilayer Wound Matrix, 96.4 percent;p< 1.00) and reoperation rates (14.3 percent versus 3.6 percent;p< 0.352) were similar. However, free flap reconstruction had significantly greater operative times (418 minutes versus 100 minutes;p< 0.001).Conclusions:Local tissue rearrangement may be more reliable for smaller wounds (<100 cm2) compared to Bilayer Wound Matrix. Bilayer Wound Matrix may have comparable efficacy to free flap reconstruction for larger defects (150 to 250 cm2), and may be more cost-effective, given greater operative time and length of stay associated with free flap reconstruction.CLINICAL QUESTION/LEVEL OF EVIDENCE:Therapeutic, III.
Risk Factors Associated With an Impaired Antibody Response in Kidney Transplant Recipients Following 2 Doses of the SARS-CoV-2 mRNA Vaccine
Authors: Yi Stephanie G. , Moore Linda W. , Eagar Todd , Graviss Edward A. , Nguyen Duc T. , Ibrahim Hassan , Huang Howard J. , Hobeika Mark , McMillan Robert , Saharia Ashish , Mobley Constance , Podder Hemangshu , Drews Ashley , Ghobrial R. Mark , Gaber A. Osama , Knight Richard J. 
Published: December 2021

Background.
Data about vaccine efficacy in solid organ transplant patients are limited. We previously reported our initial observation of a 6.2% immunogenicity rate in kidney transplant recipients (KTRs) after administration of 1 dose of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mRNA vaccine. We sought to report our observations of anti-SARS-CoV-2 antibody in KTRs after 2 doses of the SARS-CoV-2 mRNA vaccine.

Methods.
We identified 105 KTRs who received 2 doses of the Pfizer-BioNTech or Moderna mRNA-1273 vaccine per availability and had anti-SARS-CoV-2 labs obtained at least 2 wk following administration of the second dose. Antibody testing was performed using 3 clinically validated qualitative and semiquantitative assays.

Results.
KTRs had a 36.2% antibody response rate, whereas an age ≥68 years and a longer time from transplant were factors associated with antibody response.

Conclusions.
The low antibody response in KTRs may be associated with the immunosuppressive state. More data are needed to evaluate if KTRs may require higher vaccine doses or an additional booster dose to increase their ability to mount an immune response to the SARS-CoV-2 vaccine.
A large, curated, open-source stroke neuroimaging dataset to improve lesion segmentation algorithms
Authors: Liew Sook-Lei , Lo Bethany , Donnelly Miranda R. , Zavaliangos-Petropulu Artemis , Jeong Jessica N. , Barisano Giuseppe , Hutton Alexandre , Simon Julia P. , Juliano Julia M. , Suri Anisha , Ard Tyler , Banaj Nerisa , Borich Michael R. , Boyd Lara A. , Brodtmann Amy , Buetefisch Cathrin M. , Cao Lei , Cassidy Jessica M. , Ciullo Valentina , Conforto Adriana B. , Cramer Steven C. , Dacosta-Aguayo Rosalia , Rosa Ezequiel de la , Domin Martin , Dula Adrienne N. , Feng Wuwei , Franco Alexandre R. , Geranmayeh Fatemeh , Gramfort Alexandre , Gregory Chris M. , Hanlon Colleen A. , Hordacre Brenton G. , Kautz Steven A. , Khlif Mohamed Salah , Kim Hosung , Kirschke Jan S. , Liu Jingchun , Lotze Martin , MacIntosh Bradley J. , Mataró Maria , Mohamed Feroze B. , Nordvik Jan E. , Park Gilsoon , Pienta Amy , Piras Fabrizio , Redman Shane M. , Revill Kate P. , Reyes Mauricio , Robertson Andrew D. , Seo Na Jin , Soekadar Surjo R. , Spalletta Gianfranco , Sweet Alison , Telenczuk Maria , Thielman Gregory , Westlye Lars T. , Winstein Carolee J. , Wittenberg George F. , Wong Kristin A. , Yu Chunshui 
Published: December 2021

AbstractAccurate lesion segmentation is critical in stroke rehabilitation research for the quantification of lesion burden and accurate image processing. Current automated lesion segmentation methods for T1-weighted (T1w) MRIs, commonly used in rehabilitation research, lack accuracy and reliability. Manual segmentation remains the gold standard, but it is time-consuming, subjective, and requires significant neuroanatomical expertise. We previously released a large, open-source dataset of stroke T1w MRIs and manually segmented lesion masks (ATLAS v1.2, N=304) to encourage the development of better algorithms. However, many methods developed with ATLAS v1.2 report low accuracy, are not publicly accessible or are improperly validated, limiting their utility to the field. Here we present ATLAS v2.0 (N=955), a larger dataset of T1w stroke MRIs and manually segmented lesion masks that includes both training (public) and test (hidden) data. Algorithm development using this larger sample should lead to more robust solutions, and the hidden test data allows for unbiased performance evaluation via segmentation challenges. We anticipate that ATLAS v2.0 will lead to improved algorithms, facilitating large-scale stroke rehabilitation research.
Analysis of single-cell RNA-sequencing data to identify quiescent and proliferating neural cell populations in Glioblastoma
Authors: Vikram Rajeev , Chou Wen□Cheng , Wu Pei-Ei , Chen Wei-Ting , Shen Chen-Yang 
Published: December 2021

ABSTRACTBackgroundDiffuse Glioblastoma (GBM) has high mortality and remains one of the most challenging type of cancer to treat. Identifying and characterizing the cells populations driving tumor growth and therapy resistance has been particularly difficult owing to marked inter and intra tumoral heterogeneity observed in these tumors. These tumorigenic populations contain long lived cells associated with latency, immune evasion and metastasis.MethodsHere, we analyzed the single-cell RNA-sequencing data of high grade glioblastomas from four different studies using integrated analysis of gene expression patterns, cell cycle stages and copy number variation to identify gene expression signatures associated with quiescent and cycling neuronal tumorigenic cells.ResultsThe results show that while cycling and quiescent cells are present in GBM of all age groups, they exist in a much larger proportion in pediatric glioblastomas. These cells show similarities in their expression patterns of a number of pluripotency and proliferation related genes. Upon unbiased clustering, these cells explicitly clustered on their cell cycle stage. Quiescent cells in both the groups specifically overexpressed a number of genes for ribosomal protein, while the cycling cells were enriched in the expression of high-mobility group and heterogeneous nuclear ribonucleoprotein group genes. A number of well-known markers of quiescence and proliferation in neurogenesis showed preferential expression in the quiescent and cycling populations identified in our analysis. Through our analysis, we identify ribosomal proteins as key constituents of quiescence in glioblastoma stem cells.ConclusionsThis study identifies gene signatures common to adult and pediatric glioblastoma quiescent and cycling stem cell niches. Further research elucidating their role in controlling quiescence and proliferation in tumorigenic cells in high grade glioblastoma will open avenues in more effective treatment strategies for glioblastoma patients.
Sub-communities of the vaginal microbiota in pregnant and non-pregnant women
Authors: Symul Laura , Jeganathan Pratheepa , Costello Elizabeth K. , France Michael , Bloom Seth M. , Kwon Douglas S. , Ravel Jacques , Relman David A. , Holmes Susan 
Published: December 2021

AbstractDiverse and non-Lactobacillus-dominated vaginal microbial communities are associated with adverse health outcomes such as preterm birth and the acquisition of sexually transmitted infections. Despite the importance of recognizing and understanding the key risk-associated features of these communities, their heterogeneous structure and properties remain ill-defined. Clustering approaches are commonly used to characterize vaginal communities, but they lack sensitivity and robustness in resolving substructures and revealing transitions between potential sub-communities. Here, we address this need with an approach based on mixed membership topic models, using longitudinal data from cohorts of pregnant and non-pregnant study participants. We identify several non-Lactobacillus-dominated sub-communities common to both cohorts and independent of reproductive status. In non-pregnant individuals, we find that the menstrual cycle modulates transitions between and within sub-communities. In addition, a specific non-Lactobacillus-dominated sub-community, which was associated with preterm delivery in pregnant participants, was also more common during menses, a time of elevated vaginal inflammation in non-pregnant participants. Overall, our analyses based on mixed membership models reveal substructures of vaginal ecosystems which may have important clinical and biological associations.
Language Models for the Prediction of SARS-CoV-2 Inhibitors
Authors: Blanchard Andrew E , Gounley John , Bhowmik Debsindhu , Shekar Mayanka Chandra , Lyngaas Isaac , Gao Shang , Yin Junqi , Tsaris Aristeidis , Wang Feiyi , Glaser Jens 
Published: December 2021

ABSTRACTThe COVID-19 pandemic highlights the need for computational tools to automate and accelerate drug design for novel protein targets. We leverage deep learning language models to generate and score drug candidates based on predicted protein binding affinity. We pre-trained a deep learning language model (BERT) on ∼9.6 billion molecules and achieved peak performance of 603 petaflops in mixed precision. Our work reduces pre-training time from days to hours, compared to previous efforts with this architecture, while also increasing the dataset size by nearly an order of magnitude. For scoring, we fine-tuned the language model using an assembled set of thousands of protein targets with binding affinity data and searched for inhibitors of specific protein targets, SARS-CoV-2 Mpro and PLpro. We utilized a genetic algorithm approach for finding optimal candidates using the generation and scoring capabilities of the language model. Our generalizable models accelerate the identification of inhibitors for emerging therapeutic targets.
Syntaxin 5 determines Weibel-Palade body size and Von Willebrand factor secretion by controlling Golgi architecture
Authors: Kat Marije , Karampini Ellie , Hoogendijk Arie Johan , Bürgisser Petra , Mulder Aat A. , van Alphen Floris , Olins Jenny , Geerts Dirk , van den Biggelaar Maartje , Margadant Coert , Voorberg Jan , Bierings Ruben 
Published: December 2021

AbstractVon Willebrand factor (VWF) is a multimeric hemostatic protein primarily synthesized in endothelial cells (ECs). VWF is stored in endothelial storage organelles, the Weibel-Palade bodies (WPBs), whose biogenesis strongly depends on VWF anterograde trafficking and Golgi architecture. Elongated WPB morphology is correlated to longer VWF strings with better adhesive properties. We previously identified the SNARE SEC22B, which is involved in anterograde ER-to-Golgi transport, as a novel regulator of WPB elongation. To elucidate novel determinants of WPB morphology we explored endothelial SEC22B interaction partners in a mass spectrometrybased approach, identifying the Golgi SNARE Syntaxin 5 (STX5). We established STX5 knockdown in ECs using shRNA-dependent silencing and analyzed WPB and Golgi morphology, using confocal and electron microscopy. STX5-depleted ECs exhibited extensive Golgi fragmentation and decreased WPB length, which was associated with reduced intracellular VWF levels, and impaired stimulated VWF secretion. However, the secretion-incompetent organelles in shSTX5 cells maintained WPB markers such as Angiopoietin 2, P-selectin, Rab27A, and CD63. Taken together, our study has identified SNARE protein STX5 as a novel regulator of WPB biogenesis.
Mutations on RBD of SARS-CoV-2 Omicron variant result in stronger binding to human ACE2 receptor
Authors: Lupala Cecylia S. , Ye Yongjin , Chen Hong , Su Xiao-Dong , Liu Haiguang 
Published: December 2021

AbstractThe COVID-19 pandemic caused by the SARS-CoV-2 virus has led to more than 270 million infections and 5.3 million of deaths worldwide. Several major variants of SARS-CoV-2 have emerged and posed challenges in controlling the pandemic. The recently occurred Omicron variant raised serious concerns about reducing the efficacy of vaccines and neutralization antibodies due to its vast mutations. We have modelled the complex structure of the human ACE2 protein and the receptor binding domain (RBD) of Omicron Spike protein (S-protein), and conducted atomistic molecular dynamics simulations to study the binding interactions. The analysis shows that the Omicron RBD binds more strongly to the human ACE2 protein than the original strain. The mutations at the ACE2-RBD interface enhance the tight binding by increasing hydrogen bonding interaction and enlarging buried solvent accessible surface area.
De novo apical domain formation inside the Drosophila adult midgut epithelium
Authors: Chen Jia , St Johnston Daniel 
Published: December 2021

AbstractIn the adult Drosophila midgut, basal intestinal stem cells give rise to enteroblasts that integrate into the epithelium as they differentiate into enterocytes. Integrating enteroblasts must generate a new apical domain and break through the septate junctions between neighbouring enterocytes, while maintaining barrier function. We observe that enteroblasts form an apical membrane initiation site when they reach the septate junction between the overlying enterocytes. A space appears above the enteroblast as Cadherin clears from its apical surface. New septate junctions then form laterally with neighbouring enterocytes and the AMIS develops into pre-apical compartment with a fully-formed brush border. Finally, the overlying septate junction dissolves and the pre-enterocyte reaches the gut lumen. Enteroblasts therefore form an apical domain before they have a free apical surface. The process of enteroblast integration resembles lumen formation in mammalian epithelial cysts, highlighting the similarities between the fly midgut and mammalian epithelia.
Transcriptomic heterogeneity of Sox2-expressing pituitary cells
Authors: Fletcher Patrick A. , Prévide Rafael M. , Smiljanic Kosara , Sherman Arthur , Coon Steven L. , Stojilkovic Stanko S. 
Published: December 2021

AbstractThe mammalian pituitary gland is a complex organ consisting of hormone-producing cells (HPC), nonhormonal folliculostellate cells (FSC) and pituicytes, vascular pericytes and endothelial cells, and putative Sox2-expressing stem cells. Here, we used scRNAseq analysis of adult female rat pituitary cells to study the heterogeneity of pituitary cells with a focus on evaluating the transcriptomic profile of the Sox2-expressing population. Samples containing whole pituitary and separated anterior and posterior lobe cells allowed the identification of all expected pituitary resident cell types and lobe-specific subpopulations of vascular cells. Sox2 was expressed uniformly in all FSC, pituicytes, and a fraction of HPC. FSC comprised two subclusters; FSC1 contained more cells but expressed less genetic diversity compared to FSC2. The latter contained proliferative cells, expressed genes consistent with stem cell niche formation, including tight junctions, and shared genes with HPC. The FSC2 transcriptome profile was also consistent with the activity of pathways regulating cell proliferation and stem cell pluripotency, including the Hippo and Wnt pathways. The expression of other stem cell marker genes was common for FSC and pituicytes (Sox9, Cd9, Hes1, Vim, S100b) or cell type-specific (FSC: Prop1, Prrx1, Pitx1, Pitx2, Lhx3; pituicytes: Fgf10, Tbx3, Lhx2, Nkx2-1, Rax). FSC and pituicytes also expressed other astroglial marker genes, some common and other distinct, consistent with their identities as astroglial cells of the pituitary. These data suggest functional heterogeneity of FSC, with a larger fraction representing classical FSC, and a smaller fraction containing active stem-like cells and HPC-committed progenitors.