bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical phenotyping and genetic diagnosis of a large cohort of Sudanese families with hereditary spinocerebellar degenerations
Authors: Yahia Ashraf , Hamed Ahlam A. A. , Mohamed Inaam N. , Elseed Maha A. , Salih Mustafa A. , El-sadig Sarah M. , Siddig Hassab Elrasoul , Nasreldien Ali Elsir Musa , Abdullah Mohamed Ahmed , Elzubair Maha , Omer Farouk Yassen , Bakhiet Aisha Motwakil , Abubaker Rayan , Abozar Fatima , Adil Rawaa , Emad Sara , Musallam Mhammed Alhassan , Eltazi Isra Z. M. , Omer Zulfa , Malik Hiba , Mohamed Mayada O. E. , Elhassan Ali A. , Mohamed Eman O. E. , Ahmed Ahmed K. M. A. , Ahmed Elhami A. A. , Eltaraifee Esraa , Hussein Bidour K. , Abd Allah Amal S. I. , Salah Lina , Nimir Mohamed , Tag Elseed Omnia M. , Elhassan Tasneem E. A. , Elbashier Abubakr , Alfadul Esraa S. A. , Fadul Moneeb , Ali Khalil F. , Taha Shaimaa Omer M. A. , Bushara Elfatih E. , Amin Mutaz , Koko Mahmoud , Ibrahim Muntaser E. , Ahmed Ammar E. , Elsayed Liena E. O. , Stevanin Giovanni 
Published: April 2023

AbstractHereditary spinocerebellar degenerations (SCDs) is an umbrella term that covers a group of monogenic conditions that share common pathogenic mechanisms and include hereditary spastic paraplegia (HSP), cerebellar ataxia, and spinocerebellar ataxia. They are often complicated with axonal neuropathy and/or intellectual impairment and overlap with many neurological conditions, including neurodevelopmental disorders. More than 200 genes and loci inherited through all modes of Mendelian inheritance are known. Autosomal recessive inheritance predominates in consanguineous communities; however, autosomal dominant and X-linked inheritance can also occur. Sudan is inhabited by genetically diverse populations, yet it has high consanguinity rates. We used next-generation sequencing, genotyping, bioinformatics analysis, and candidate gene approaches to study 90 affected patients from 38 unrelated Sudanese families segregating multiple forms of SCDs. The age-at-onset in our cohort ranged from birth to 35 years; however, most patients manifested childhood-onset diseases (the mean and median ages at onset were 7.5 and 3 years, respectively). We reached the genetic diagnosis in 63% and possibly up to 73% of the studied families when considering variants of unknown significance. Combining the present data with our previous analysis of 25 Sudanese HSP families, the success rate reached 52–59% (31–35/59 families). In this article we report candidate variants in genes previously known to be associated with SCDs or other phenotypically related monogenic disorders. We also highlight the genetic and clinical heterogeneity of SCDs in Sudan, as we did not identify a major causative gene in our cohort, and the potential for discovering novel SCD genes in this population.
Retinoic acid signaling modulation guides in vitro specification of human heart field-specific progenitor pools
Authors: Zawada Dorota , Kornherr Jessica , Meier Anna B. , Santamaria Gianluca , Dorn Tatjana , Nowak-Imialek Monika , Ortmann Daniel , Zhang Fangfang , Lachmann Mark , Dreßen Martina , Ortiz Mariaestela , Mascetti Victoria L. , Harmer Stephen C. , Nobles Muriel , Tinker Andrew , De Angelis Maria Teresa , Pedersen Roger A. , Grote Phillip , Laugwitz Karl-Ludwig , Moretti Alessandra , Goedel Alexander 
Published: April 2023

AbstractCardiogenesis relies on the precise spatiotemporal coordination of multiple progenitor populations. Understanding the specification and differentiation of these distinct progenitor pools during human embryonic development is crucial for advancing our knowledge of congenital cardiac malformations and designing new regenerative therapies. By combining genetic labelling, single-cell transcriptomics, and ex vivo human-mouse embryonic chimeras we uncovered that modulation of retinoic acid signaling instructs human pluripotent stem cells to form heart field-specific progenitors with distinct fate potentials. In addition to the classical first and second heart fields, we observed the appearance of juxta-cardiac field progenitors giving rise to both myocardial and epicardial cells. Applying these findings to stem-cell based disease modelling we identified specific transcriptional dysregulation in first and second heart field progenitors derived from stem cells of patients with hypoplastic left heart syndrome. This highlights the suitability of our in vitro differentiation platform for studying human cardiac development and disease.
Structure and mechanism of oxalate transporter OxlT in an oxalate-degrading bacterium in the gut microbiota
Authors: Jaunet-Lahary Titouan , Shimamura Tatsuro , Hayashi Masahiro , Nomura Norimichi , Hirasawa Kouta , Shimizu Tetsuya , Yamashita Masao , Tsutsumi Naotaka , Suehiro Yuta , Kojima Keiichi , Sudo Yuki , Tamura Takashi , Iwanari Hiroko , Hamakubo Takao , Iwata So , Okazaki Kei-ichi , Hirai Teruhisa , Yamashita Atsuko 
Published: April 2023

AbstractAn oxalate-degrading bacterium in the gut microbiota absorbs food-derived oxalate to use this as a carbon and energy source, thereby reducing the risk of kidney stone formation in host animals. The bacterial oxalate transporter OxlT selectively uptakes oxalate from the gut to bacterial cells with a strict discrimination from other nutrient carboxylates. Here, we present crystal structures of oxalate-bound and ligand-free OxlT in two distinct conformations, occluded and outward-facing states. The ligand-binding pocket contains basic residues that form salt bridges with oxalate while preventing the conformational switch to the occluded state without an acidic substrate. The occluded pocket can accommodate oxalate but not larger dicarboxylates, such as metabolic intermediates. The permeation pathways from the pocket are completely blocked by extensive interdomain interactions, which can be opened solely by a flip of a single side chain neighbouring the substrate. This study shows the structural basis underlying metabolic interactions enabling favourable symbiosis.
Nanoscale thermodynamics needs the concept of a disjoining chemical potential
Authors: Dong W. 
Published: April 2023

AbstractDisjoining pressure was discovered by Derjaguin in 1930’s, which describes the difference between the pressure of a strongly confined fluid and the corresponding one in a bulk phase. It has been revealed recently that the disjoining pressure is at the origin of distinct differential and integral surface tensions for strongly confined fluids. Here we show how the twin concept, disjoining chemical potential, arises in a reminiscent way although it comes out eighty years later. This twin concept advances our understanding of nanoscale thermodynamics. Ensemble-dependence (or environment-dependence) is one hallmark of thermodynamics of small systems. We show that integral surface tension is ensemble-dependent while differential surface tension is not. Moreover, two generalized Gibbs-Duhem equations involving integral surface tensions are derived, as well as two additional adsorption equations relating surface tensions to adsorption-induced strains. All the results obtained in this work further evidence that an approach alternative of Hill’s nanothermodynamics is possible, by extending Gibbs surface thermodynamics instead of resorting to Hill’s replica trick. Moreover, we find a compression-expansion hysteresis without any underlying phase transition.
Cellular differentiation into hyphae and spores in halophilic archaea
Authors: Tang Shu-Kun , Zhi Xiao-Yang , Zhang Yao , Makarova Kira S. , Liu Bing-Bing , Zheng Guo-Song , Zhang Zhen-Peng , Zheng Hua-Jun , Wolf Yuri I. , Zhao Yu-Rong , Jiang Song-Hao , Chen Xi-Ming , Li En-Yuan , Zhang Tao , Chen Pei-Ru , Feng Yu-Zhou , Xiang Ming-Xian , Lin Zhi-Qian , Shi Jia-Hui , Chang Cheng , Zhang Xue , Li Rui , Lou Kai , Wang Yun , Chang Lei , Yin Min , Yang Ling-Ling , Gao Hui-Ying , Zhang Zhong-Kai , Tao Tian-Shen , Guan Tong-Wei , He Fu-Chu , Lu Yin-Hua , Cui Heng-Lin , Koonin Eugene V. , Zhao Guo-Ping , Xu Ping 
Published: April 2023

AbstractSeveral groups of bacteria have complex life cycles involving cellular differentiation and multicellular structures. For example, actinobacteria of the genus Streptomyces form multicellular vegetative hyphae, aerial hyphae, and spores. However, similar life cycles have not yet been described for archaea. Here, we show that several haloarchaea of the family Halobacteriaceae display a life cycle resembling that of Streptomyces bacteria. Strain YIM 93972 (isolated from a salt marsh) undergoes cellular differentiation into mycelia and spores. Other closely related strains are also able to form mycelia, and comparative genomic analyses point to gene signatures (apparent gain or loss of certain genes) that are shared by members of this clade within the Halobacteriaceae. Genomic, transcriptomic and proteomic analyses of non-differentiating mutants suggest that a Cdc48-family ATPase might be involved in cellular differentiation in strain YIM 93972. Additionally, a gene encoding a putative oligopeptide transporter from YIM 93972 can restore the ability to form hyphae in a Streptomyces coelicolor mutant that carries a deletion in a homologous gene cluster (bldKA-bldKE), suggesting functional equivalence. We propose strain YIM 93972 as representative of a new species in a new genus within the family Halobacteriaceae, for which the name Actinoarchaeum halophilum gen. nov., sp. nov. is herewith proposed. Our demonstration of a complex life cycle in a group of haloarchaea adds a new dimension to our understanding of the biological diversity and environmental adaptation of archaea.
Cellcano: supervised cell type identification for single cell ATAC-seq data
Authors: Ma Wenjing , Lu Jiaying , Wu Hao 
Published: April 2023

AbstractComputational cell type identification is a fundamental step in single-cell omics data analysis. Supervised celltyping methods have gained increasing popularity in single-cell RNA-seq data because of the superior performance and the availability of high-quality reference datasets. Recent technological advances in profiling chromatin accessibility at single-cell resolution (scATAC-seq) have brought new insights to the understanding of epigenetic heterogeneity. With continuous accumulation of scATAC-seq datasets, supervised celltyping method specifically designed for scATAC-seq is in urgent need. Here we develop Cellcano, a computational method based on a two-round supervised learning algorithm to identify cell types from scATAC-seq data. The method alleviates the distributional shift between reference and target data and improves the prediction performance. After systematically benchmarking Cellcano on 50 well-designed celltyping tasks from various datasets, we show that Cellcano is accurate, robust, and computationally efficient. Cellcano is well-documented and freely available at https://marvinquiet.github.io/Cellcano/.
MAIT cell inhibition promotes liver fibrosis regression via macrophage phenotype reprogramming
Authors: Mabire Morgane , Hegde Pushpa , Hammoutene Adel , Wan Jinghong , Caër Charles , Sayegh Rola Al , Cadoux Mathilde , Allaire Manon , Weiss Emmanuel , Thibault-Sogorb Tristan , Lantz Olivier , Goodhardt Michèle , Paradis Valérie , de la Grange Pierre , Gilgenkrantz Hélène , Lotersztajn Sophie 
Published: April 2023

AbstractRecent data have shown that liver fibrosis can regress even at later stages of cirrhosis and shifting the immune response from pro-inflammatory towards a resolutive profile is considered as a promising option. The immune regulatory networks that govern the shift of the inflammatory phenotype and thus potential reversal of liver fibrosis are lesser known. Here we show that in precision-cut human liver slices obtained from patients with end-stage fibrosis and in mouse models, inhibiting Mucosal-Associated Invariant T (MAIT) cells using pharmacological or antibody-driven approaches, limits fibrosis progression and even regresses fibrosis, following chronic toxic- or non-alcoholic steatohepatitis (NASH)-induced liver injury. Mechanistic studies, combining RNA sequencing, in vivo functional studies (performed in male mice) and co-culture experiments indicate that disruption of the MAIT cell-monocyte/macrophage interaction results in resolution of fibrosis both by increasing the frequency of restorative Ly6Clo at the expenses of pro-fibrogenic Ly6Chi monocyte-derived macrophages and promoting an autophagic phenotype in both subsets. Thus, our data show that MAIT cell activation and the consequential phenotype shift of liver macrophages are important pathogenic features of liver fibrosis and could be targeted by anti-fibrogenic therapy.
Parabacteroides distasonis ameliorates hepatic fibrosis potentially via modulating intestinal bile acid metabolism and hepatocyte pyroptosis in male mice
Authors: Zhao Qi , Dai Man-Yun , Huang Ruo-Yue , Duan Jing-Yi , Zhang Ting , Bao Wei-Min , Zhang Jing-Yi , Gui Shao-Qiang , Xia Shu-Min , Dai Cong-Ting , Tang Ying-Mei , Gonzalez Frank J. , Li Fei 
Published: April 2023

AbstractParabacteroides distasonis (P. distasonis) plays an important role in human health, including diabetes, colorectal cancer and inflammatory bowel disease. Here, we show that P. distasonis is decreased in patients with hepatic fibrosis, and that administration of P. distasonis to male mice improves thioacetamide (TAA)- and methionine and choline-deficient (MCD) diet-induced hepatic fibrosis. Administration of P. distasonis also leads to increased bile salt hydrolase (BSH) activity, inhibition of intestinal farnesoid X receptor (FXR) signaling and decreased taurochenodeoxycholic acid (TCDCA) levels in liver. TCDCA produces toxicity in mouse primary hepatic cells (HSCs) and induces mitochondrial permeability transition (MPT) and Caspase-11 pyroptosis in mice. The decrease of TCDCA by P. distasonis improves activation of HSCs through decreasing MPT-Caspase-11 pyroptosis in hepatocytes. Celastrol, a compound reported to increase P. distasonis abundance in mice, promotes the growth of P. distasonis with concomitant enhancement of bile acid excretion and improvement of hepatic fibrosis in male mice. These data suggest that supplementation of P. distasonis may be a promising means to ameliorate hepatic fibrosis.
Single-shot polarimetry of vector beams by supervised learning
Authors: Pierangeli Davide , Conti Claudio 
Published: April 2023

AbstractStates of light encoding multiple polarizations - vector beams - offer unique capabilities in metrology and communication. However, their practical application is limited by the lack of methods for measuring many polarizations in a scalable and compact way. Here we demonstrate polarimetry of vector beams in a single shot without any polarization optics. We map the beam polarization content into a spatial intensity distribution through light scattering and exploit supervised learning for single-shot measurements of multiple polarizations. We characterize structured light encoding up to nine polarizations with accuracy beyond 95% on each Stokes parameter. The method also allows us to classify beams with an unknown number of polarization modes, a functionality missing in conventional techniques. Our findings enable a fast and compact polarimeter for polarization-structured light, a general tool that may radically impact optical devices for sensing, imaging, and computing.
Mapping the pathways of photo-induced ion migration in organic-inorganic hybrid halide perovskites
Authors: Kim Taeyong , Park Soyeon , Iyer Vasudevan , Shaheen Basamat , Choudhry Usama , Jiang Qi , Eichman Gage , Gnabasik Ryan , Kelley Kyle , Lawrie Benjamin , Zhu Kai , Liao Bolin 
Published: April 2023

AbstractOrganic-inorganic hybrid perovskites exhibiting exceptional photovoltaic and optoelectronic properties are of fundamental and practical interest, owing to their tunability and low manufacturing cost. For practical applications, however, challenges such as material instability and the photocurrent hysteresis occurring in perovskite solar cells under light exposure need to be understood and addressed. While extensive investigations have suggested that ion migration is a plausible origin of these detrimental effects, detailed understanding of the ion migration pathways remains elusive. Here, we report the characterization of photo-induced ion migration in perovskites using in situ laser illumination inside a scanning electron microscope, coupled with secondary electron imaging, energy-dispersive X-ray spectroscopy and cathodoluminescence with varying primary electron energies. Using methylammonium lead iodide and formamidinium lead iodide as model systems, we observed photo-induced long-range migration of halide ions over hundreds of micrometers and elucidated the transport pathways of various ions both near the surface and inside the bulk of the samples, including a surprising finding of the vertical migration of lead ions. Our study provides insights into ion migration processes in perovskites that can aid perovskite material design and processing in future applications.
Macroscopic transition metal dichalcogenides monolayers with uniformly high optical quality
Authors: Li Qiuyang , Alfrey Adam , Hu Jiaqi , Lydick Nathanial , Paik Eunice , Liu Bin , Sun Haiping , Lu Yang , Wang Ruoyu , Forrest Stephen , Deng Hui 
Published: April 2023

AbstractThe unique optical properties of transition metal dichalcogenide (TMD) monolayers have attracted significant attention for both photonics applications and fundamental studies of low-dimensional systems. TMD monolayers of high optical quality, however, have been limited to micron-sized flakes produced by low-throughput and labour-intensive processes, whereas large-area films are often affected by surface defects and large inhomogeneity. Here we report a rapid and reliable method to synthesize macroscopic-scale TMD monolayers of uniform, high optical quality. Using 1-dodecanol encapsulation combined with gold-tape-assisted exfoliation, we obtain monolayers with lateral size > 1 mm, exhibiting exciton energy, linewidth, and quantum yield uniform over the whole area and close to those of high-quality micron-sized flakes. We tentatively associate the role of the two molecular encapsulating layers as isolating the TMD from the substrate and passivating the chalcogen vacancies, respectively. We demonstrate the utility of our encapsulated monolayers by scalable integration with an array of photonic crystal cavities, creating polariton arrays with enhanced light-matter coupling strength. This work provides a pathway to achieving high-quality two-dimensional materials over large areas, enabling research and technology development beyond individual micron-sized devices.
Major proliferation of transposable elements shaped the genome of the soybean rust pathogen Phakopsora pachyrhizi
Authors: Gupta Yogesh K. , Marcelino-Guimarães Francismar C. , Lorrain Cécile , Farmer Andrew , Haridas Sajeet , Ferreira Everton Geraldo Capote , Lopes-Caitar Valéria S. , Oliveira Liliane Santana , Morin Emmanuelle , Widdison Stephanie , Cameron Connor , Inoue Yoshihiro , Thor Kathrin , Robinson Kelly , Drula Elodie , Henrissat Bernard , LaButti Kurt , Bini Aline Mara Rudsit , Paget Eric , Singan Vasanth , Daum Christopher , Dorme Cécile , van Hoek Milan , Janssen Antoine , Chandat Lucie , Tarriotte Yannick , Richardson Jake , Melo Bernardo do Vale Araújo , Wittenberg Alexander H. J. , Schneiders Harrie , Peyrard Stephane , Zanardo Larissa Goulart , Holtman Valéria Cristina , Coulombier-Chauvel Flavie , Link Tobias I. , Balmer Dirk , Müller André N. , Kind Sabine , Bohnert Stefan , Wirtz Louisa , Chen Cindy , Yan Mi , Ng Vivian , Gautier Pierrick , Meyer Maurício Conrado , Voegele Ralf Thomas , Liu Qingli , Grigoriev Igor V. , Conrath Uwe , Brommonschenkel Sérgio H. , Loehrer Marco , Schaffrath Ulrich , Sirven Catherine , Scalliet Gabriel , Duplessis Sébastien , van Esse H. Peter 
Published: April 2023

AbstractWith >7000 species the order of rust fungi has a disproportionately large impact on agriculture, horticulture, forestry and foreign ecosystems. The infectious spores are typically dikaryotic, a feature unique to fungi in which two haploid nuclei reside in the same cell. A key example is Phakopsora pachyrhizi, the causal agent of Asian soybean rust disease, one of the world’s most economically damaging agricultural diseases. Despite P. pachyrhizi’s impact, the exceptional size and complexity of its genome prevented generation of an accurate genome assembly. Here, we sequence three independent P. pachyrhizi genomes and uncover a genome up to 1.25 Gb comprising two haplotypes with a transposable element (TE) content of ~93%. We study the incursion and dominant impact of these TEs on the genome and show how they have a key impact on various processes such as host range adaptation, stress responses and genetic plasticity.
Sterol methyltransferases in uncultured bacteria complicate eukaryotic biomarker interpretations
Authors: Brown Malory O. , Olagunju Babatunde O. , Giner José-Luis , Welander Paula V. 
Published: April 2023

AbstractSterane molecular fossils are broadly interpreted as eukaryotic biomarkers, although diverse bacteria also produce sterols. Steranes with side-chain methylations can act as more specific biomarkers if their sterol precursors are limited to particular eukaryotes and are absent in bacteria. One such sterane, 24-isopropylcholestane, has been attributed to demosponges and potentially represents the earliest evidence for animals on Earth, but enzymes that methylate sterols to give the 24-isopropyl side-chain remain undiscovered. Here, we show that sterol methyltransferases from both sponges and yet-uncultured bacteria function in vitro and identify three methyltransferases from symbiotic bacteria each capable of sequential methylations resulting in the 24-isopropyl sterol side-chain. We demonstrate that bacteria have the genomic capacity to synthesize side-chain alkylated sterols, and that bacterial symbionts may contribute to 24-isopropyl sterol biosynthesis in demosponges. Together, our results suggest bacteria should not be dismissed as potential contributing sources of side-chain alkylated sterane biomarkers in the rock record.
Experimental cheat-sensitive quantum weak coin flipping
Authors: Neves Simon , Yacoub Verena , Chabaud Ulysse , Bozzio Mathieu , Kerenidis Iordanis , Diamanti Eleni 
Published: April 2023

AbstractAs in modern communication networks, the security of quantum networks will rely on complex cryptographic tasks that are based on a handful of fundamental primitives. Weak coin flipping (WCF) is a significant such primitive which allows two mistrustful parties to agree on a random bit while they favor opposite outcomes. Remarkably, perfect information-theoretic security can be achieved in principle for quantum WCF. Here, we overcome conceptual and practical issues that have prevented the experimental demonstration of this primitive to date, and demonstrate how quantum resources can provide cheat sensitivity, whereby each party can detect a cheating opponent, and an honest party is never sanctioned. Such a property is not known to be classically achievable with information-theoretic security. Our experiment implements a refined, loss-tolerant version of a recently proposed theoretical protocol and exploits heralded single photons generated by spontaneous parametric down conversion, a carefully optimized linear optical interferometer including beam splitters with variable reflectivities and a fast optical switch for the verification step. High values of our protocol benchmarks are maintained for attenuation corresponding to several kilometers of telecom optical fiber.