bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intronic ATTTC repeat expansions in STARD7 in familial adult myoclonic epilepsy linked to chromosome 2
Authors: Corbett Mark A. , Kroes Thessa , Veneziano Liana , Bennett Mark F. , Florian Rahel , Schneider Amy L. , Coppola Antonietta , Licchetta Laura , Franceschetti Silvana , Suppa Antonio , Wenger Aaron , Mei Davide , Pendziwiat Manuela , Kaya Sabine , Delledonne Massimo , Straussberg Rachel , Xumerle Luciano , Regan Brigid , Crompton Douglas , van Rootselaar Anne-Fleur , Correll Anthony , Catford Rachael , Bisulli Francesca , Chakraborty Shreyasee , Baldassari Sara , Tinuper Paolo , Barton Kirston , Carswell Shaun , Smith Martin , Berardelli Alfredo , Carroll Renee , Gardner Alison , Friend Kathryn L. , Blatt Ilan , Iacomino Michele , Di Bonaventura Carlo , Striano Salvatore , Buratti Julien , Keren Boris , Nava Caroline , Forlani Sylvie , Rudolf Gabrielle , Hirsch Edouard , Leguern Eric , Labauge Pierre , Balestrini Simona , Sander Josemir W. , Afawi Zaid , Helbig Ingo , Ishiura Hiroyuki , Tsuji Shoji , Sisodiya Sanjay M. , Casari Giorgio , Sadleir Lynette G. , van Coller Riaan , Tijssen Marina A. J. , Klein Karl Martin , van den Maagdenberg Arn M. J. M. , Zara Federico , Guerrini Renzo , Berkovic Samuel F. , Pippucci Tommaso , Canafoglia Laura , Bahlo Melanie , Striano Pasquale , Scheffer Ingrid E. , Brancati Francesco , Depienne Christel , Gecz Jozef 
Published: October 2019

AbstractFamilial Adult Myoclonic Epilepsy (FAME) is characterised by cortical myoclonic tremor usually from the second decade of life and overt myoclonic or generalised tonic-clonic seizures. Four independent loci have been implicated in FAME on chromosomes (chr) 2, 3, 5 and 8. Using whole genome sequencing and repeat primed PCR, we provide evidence that chr2-linked FAME (FAME2) is caused by an expansion of an ATTTC pentamer within the first intron of STARD7. The ATTTC expansions segregate in 158/158 individuals typically affected by FAME from 22 pedigrees including 16 previously reported families recruited worldwide. RNA sequencing from patient derived fibroblasts shows no accumulation of the AUUUU or AUUUC repeat sequences and STARD7 gene expression is not affected. These data, in combination with other genes bearing similar mutations that have been implicated in FAME, suggest ATTTC expansions may cause this disorder, irrespective of the genomic locus involved.
Cryo-EM structure and polymorphism of Aβ amyloid fibrils purified from Alzheimer’s brain tissue
Authors: Kollmer Marius , Close William , Funk Leonie , Rasmussen Jay , Bsoul Aref , Schierhorn Angelika , Schmidt Matthias , Sigurdson Christina J. , Jucker Mathias , Fändrich Marcus 
Published: October 2019

AbstractThe formation of Aβ amyloid fibrils is a neuropathological hallmark of Alzheimer’s disease and cerebral amyloid angiopathy. However, the structure of Aβ amyloid fibrils from brain tissue is poorly understood. Here we report the purification of Aβ amyloid fibrils from meningeal Alzheimer’s brain tissue and their structural analysis with cryo-electron microscopy. We show that these fibrils are polymorphic but consist of similarly structured protofilaments. Brain derived Aβ amyloid fibrils are right-hand twisted and their peptide fold differs sharply from previously analyzed Aβ fibrils that were formed in vitro. These data underscore the importance to use patient-derived amyloid fibrils when investigating the structural basis of the disease.
TAF1 plays a critical role in AML1-ETO driven leukemogenesis
Authors: Xu Ye , Man Na , Karl Daniel , Martinez Concepcion , Liu Fan , Sun Jun , Martinez Camilo Jose , Martin Gloria Mas , Beckedorff Felipe , Lai Fan , Yue Jingyin , Roisman Alejandro , Greenblatt Sarah , Duffort Stephanie , Wang Lan , Sun Xiaojian , Figueroa Maria , Shiekhattar Ramin , Nimer Stephen 
Published: October 2019

AbstractAML1-ETO (AE) is a fusion transcription factor, generated by the t(8;21) translocation, that functions as a leukemia promoting oncogene. Here, we demonstrate that TATA-Box Binding Protein Associated Factor 1 (TAF1) associates with K43 acetylated AE and this association plays a pivotal role in the proliferation of AE-expressing acute myeloid leukemia (AML) cells. ChIP-sequencing indicates significant overlap of the TAF1 and AE binding sites. Knockdown of TAF1 alters the association of AE with chromatin, affecting of the expression of genes that are activated or repressed by AE. Furthermore, TAF1 is required for leukemic cell self-renewal and its reduction promotes the differentiation and apoptosis of AE+ AML cells, thereby impairing AE driven leukemogenesis. Together, our findings reveal a role of TAF1 in leukemogenesis and identify TAF1 as a potential therapeutic target for AE-expressing leukemia.
Offshore transport of particulate organic carbon in the California Current System by mesoscale eddies
Authors: Amos Caitlin M. , Castelao Renato M. , Medeiros Patricia M. 
Published: October 2019

AbstractThe California Current System is characterized by upwelling and rich mesoscale eddy activity. Cyclonic eddies generally pinch off from meanders in the California Current, potentially trapping upwelled water along the coast and transporting it offshore. Here, we use satellite-derived measurements of particulate organic carbon (POC) as a tracer of coastal water to show that cyclones located offshore that were generated near the coast contain higher carbon concentrations in their interior than cyclones of the same amplitude generated offshore. This indicates that eddies are in fact trapping and transporting coastal water offshore, resulting in an offshore POC enrichment of 20.9 ± 11 Gg year−1. This POC enrichment due to the coastally-generated eddies extends for 1000 km from shore. This analysis provides large-scale observational-based evidence that eddies play a quantitatively important role in the offshore transport of coastal water, substantially widening the area influenced by highly productive upwelled waters in the California Current System.
The rapid electrochemical activation of MoTe2 for the hydrogen evolution reaction
Authors: McGlynn Jessica C. , Dankwort Torben , Kienle Lorenz , Bandeira Nuno A. G. , Fraser James P. , Gibson Emma K. , Cascallana-Matías Irene , Kamarás Katalin , Symes Mark D. , Miras Haralampos N. , Ganin Alexey Y. 
Published: October 2019

AbstractThe electrochemical generation of hydrogen is a key enabling technology for the production of sustainable fuels. Transition metal chalcogenides show considerable promise as catalysts for this reaction, but to date there are very few reports of tellurides in this context, and none of these transition metal telluride catalysts are especially active. Here, we show that the catalytic performance of metallic 1T′-MoTe2 is improved dramatically when the electrode is held at cathodic bias. As a result, the overpotential required to maintain a current density of 10 mA cm−2 decreases from 320 mV to just 178 mV. We show that this rapid and reversible activation process has its origins in adsorption of H onto Te sites on the surface of 1T′-MoTe2. This activation process highlights the importance of subtle changes in the electronic structure of an electrode material and how these can influence the subsequent electrocatalytic activity that is displayed.
Constraining the rise of oxygen with oxygen isotopes
Authors: Killingsworth B. A. , Sansjofre P. , Philippot P. , Cartigny P. , Thomazo C. , Lalonde S. V. 
Published: October 2019

AbstractAfter permanent atmospheric oxygenation, anomalous sulfur isotope compositions were lost from sedimentary rocks, demonstrating that atmospheric chemistry ceded its control of Earth’s surficial sulfur cycle to weathering. However, mixed signals of anoxia and oxygenation in the sulfur isotope record between 2.5 to 2.3 billion years (Ga) ago require independent clarification, for example via oxygen isotopes in sulfate. Here we show <2.31 Ga sedimentary barium sulfates (barites) from the Turee Creek Basin, W. Australia with positive sulfur isotope anomalies of ∆33S up to + 1.55‰ and low δ18O down to −19.5‰. The unequivocal origin of this combination of signals is sulfide oxidation in meteoric water. Geochemical and sedimentary evidence suggests that these S-isotope anomalies were transferred from the paleo-continent under an oxygenated atmosphere. Our findings indicate that incipient oxidative continental weathering, ca. 2.8–2.5 Ga or earlier, may be diagnosed with such a combination of low δ18O and high ∆33S in sulfates.
Rapid identification of pathogenic bacteria using Raman spectroscopy and deep learning
Authors: Ho Chi-Sing , Jean Neal , Hogan Catherine A. , Blackmon Lena , Jeffrey Stefanie S. , Holodniy Mark , Banaei Niaz , Saleh Amr A. E. , Ermon Stefano , Dionne Jennifer 
Published: October 2019

AbstractRaman optical spectroscopy promises label-free bacterial detection, identification, and antibiotic susceptibility testing in a single step. However, achieving clinically relevant speeds and accuracies remains challenging due to weak Raman signal from bacterial cells and numerous bacterial species and phenotypes. Here we generate an extensive dataset of bacterial Raman spectra and apply deep learning approaches to accurately identify 30 common bacterial pathogens. Even on low signal-to-noise spectra, we achieve average isolate-level accuracies exceeding 82% and antibiotic treatment identification accuracies of 97.0±0.3%. We also show that this approach distinguishes between methicillin-resistant and -susceptible isolates of Staphylococcus aureus (MRSA and MSSA) with 89±0.1% accuracy. We validate our results on clinical isolates from 50 patients. Using just 10 bacterial spectra from each patient isolate, we achieve treatment identification accuracies of 99.7%. Our approach has potential for culture-free pathogen identification and antibiotic susceptibility testing, and could be readily extended for diagnostics on blood, urine, and sputum.
Thermotolerance in the pathogen Cryptococcus neoformans is linked to antigen masking via mRNA decay-dependent reprogramming
Authors: Bloom Amanda L. M. , Jin Richard M. , Leipheimer Jay , Bard Jonathan E. , Yergeau Donald , Wohlfert Elizabeth A. , Panepinto John C. 
Published: October 2019

AbstractA common feature shared by systemic fungal pathogens of environmental origin, such as Cryptococcus neoformans, is their ability to adapt to mammalian core body temperature. In C. neoformans, this adaptation is accompanied by Ccr4-mediated decay of ribosomal protein mRNAs. Here we use the related, but thermo-intolerant species Cryptococcus amylolentus to demonstrate that this response contributes to host-temperature adaptation and pathogenicity of cryptococci. In a C. neoformans ccr4Δ mutant, stabilized ribosomal protein mRNAs are retained in the translating pool, and stress-induced transcriptomic changes are reduced in comparison with the wild type strain, likely due to ineffective translation of transcription factors. In addition, the mutant displays increased exposure of cell wall glucans, and recognition by Dectin-1 results in increased phagocytosis by lung macrophages, linking mRNA decay to adaptation and immune evasion.
The oomycete Lagenisma coscinodisci hijacks host alkaloid synthesis during infection of a marine diatom
Authors: Vallet Marine , Baumeister Tim U. H. , Kaftan Filip , Grabe Veit , Buaya Anthony , Thines Marco , Svatoš Aleš , Pohnert Georg 
Published: October 2019

AbstractFlagellated oomycetes frequently infect unicellular algae, thus limiting their proliferation. Here we show that the marine oomycete Lagenisma coscinodisci rewires the metabolome of the bloom-forming diatom Coscinodiscus granii, thereby promoting infection success. The algal alkaloids β-carboline and 2,3,4,9-tetrahydro-1H-β-carboline-3-carboxylic acid are induced during infection. Single-cell profiling with AP-MALDI-MS and confocal laser scanning microscopy reveals that algal carbolines accumulate in the reproductive form of the parasite. The compounds arrest the algal cell division, increase the infection rate and induce plasmolysis in the host. Our results indicate that the oomycete manipulates the host metabolome to support its own multiplication.
Structural insights of human mitofusin-2 into mitochondrial fusion and CMT2A onset
Authors: Li Yu-Jie , Cao Yu-Lu , Feng Jian-Xiong , Qi Yuanbo , Meng Shuxia , Yang Jie-Feng , Zhong Ya-Ting , Kang Sisi , Chen Xiaoxue , Lan Lan , Luo Li , Yu Bing , Chen Shoudeng , Chan David C. , Hu Junjie , Gao Song 
Published: October 2019

AbstractMitofusin-2 (MFN2) is a dynamin-like GTPase that plays a central role in regulating mitochondrial fusion and cell metabolism. Mutations in MFN2 cause the neurodegenerative disease Charcot-Marie-Tooth type 2A (CMT2A). The molecular basis underlying the physiological and pathological relevance of MFN2 is unclear. Here, we present crystal structures of truncated human MFN2 in different nucleotide-loading states. Unlike other dynamin superfamily members including MFN1, MFN2 forms sustained dimers even after GTP hydrolysis via the GTPase domain (G) interface, which accounts for its high membrane-tethering efficiency. The biochemical discrepancy between human MFN2 and MFN1 largely derives from a primate-only single amino acid variance. MFN2 and MFN1 can form heterodimers via the G interface in a nucleotide-dependent manner. CMT2A-related mutations, mapping to different functional zones of MFN2, lead to changes in GTP hydrolysis and homo/hetero-association ability. Our study provides fundamental insight into how mitofusins mediate mitochondrial fusion and the ways their disruptions cause disease.
A deep learning framework to predict binding preference of RNA constituents on protein surface
Authors: Lam Jordy Homing , Li Yu , Zhu Lizhe , Umarov Ramzan , Jiang Hanlun , Héliou Amélie , Sheong Fu Kit , Liu Tianyun , Long Yongkang , Li Yunfei , Fang Liang , Altman Russ B. , Chen Wei , Huang Xuhui , Gao Xin 
Published: October 2019

AbstractProtein-RNA interaction plays important roles in post-transcriptional regulation. However, the task of predicting these interactions given a protein structure is difficult. Here we show that, by leveraging a deep learning model NucleicNet, attributes such as binding preference of RNA backbone constituents and different bases can be predicted from local physicochemical characteristics of protein structure surface. On a diverse set of challenging RNA-binding proteins, including Fem-3-binding-factor 2, Argonaute 2 and Ribonuclease III, NucleicNet can accurately recover interaction modes discovered by structural biology experiments. Furthermore, we show that, without seeing any in vitro or in vivo assay data, NucleicNet can still achieve consistency with experiments, including RNAcompete, Immunoprecipitation Assay, and siRNA Knockdown Benchmark. NucleicNet can thus serve to provide quantitative fitness of RNA sequences for given binding pockets or to predict potential binding pockets and binding RNAs for previously unknown RNA binding proteins.
Tuning wettability of molten lithium via a chemical strategy for lithium metal anodes
Authors: Wang Shu-Hua , Yue Junpei , Dong Wei , Zuo Tong-Tong , Li Jin-Yi , Liu Xiaolong , Zhang Xu-Dong , Liu Lin , Shi Ji-Lei , Yin Ya-Xia , Guo Yu-Guo 
Published: October 2019

AbstractMetallic lithium affords the highest theoretical capacity and lowest electrochemical potential and is viewed as a leading contender as an anode for high-energy-density rechargeable batteries. However, the poor wettability of molten lithium does not allow it to spread across the surface of lithiophobic substrates, hindering the production and application of this anode. Here we report a general chemical strategy to overcome this dilemma by reacting molten lithium with functional organic coatings or elemental additives. The Gibbs formation energy and newly formed chemical bonds are found to be the governing factor for the wetting behavior. As a result of the improved wettability, a series of ultrathin lithium of 10–20 μm thick is obtained together with impressive electrochemical performance in lithium metal batteries. These findings provide an overall guide for tuning the wettability of molten lithium and offer an affordable strategy for the large-scale production of ultrathin lithium, and could be further extended to other alkali metals, such as sodium and potassium.
Structure of a cyanobacterial photosystem I tetramer revealed by cryo-electron microscopy
Authors: Kato Koji , Nagao Ryo , Jiang Tian-Yi , Ueno Yoshifumi , Yokono Makio , Chan Siu Kit , Watanabe Mai , Ikeuchi Masahiko , Shen Jian-Ren , Akimoto Seiji , Miyazaki Naoyuki , Akita Fusamichi 
Published: October 2019

AbstractPhotosystem I (PSI) functions to harvest light energy for conversion into chemical energy. The organisation of PSI is variable depending on the species of organism. Here we report the structure of a tetrameric PSI core isolated from a cyanobacterium, Anabaena sp. PCC 7120, analysed by single-particle cryo-electron microscopy (cryo-EM) at 3.3 Å resolution. The PSI tetramer has a C2 symmetry and is organised in a dimer of dimers form. The structure reveals interactions at the dimer-dimer interface and the existence of characteristic pigment orientations and inter-pigment distances within the dimer units that are important for unique excitation energy transfer. In particular, characteristic residues of PsaL are identified to be responsible for the formation of the tetramer. Time-resolved fluorescence analyses showed that the PSI tetramer has an enhanced excitation-energy quenching. These structural and spectroscopic findings provide insights into the physiological significance of the PSI tetramer and evolutionary changes of the PSI organisations.
Diamond growth from organic compounds in hydrous fluids deep within the Earth
Authors: Frezzotti Maria Luce 
Published: October 2019

AbstractAt subduction zones, most diamonds form by carbon saturation in hydrous fluids released from lithospheric plates on equilibration with mantle rocks. Although organic molecules are predicted among dissolved species which are the source for carbon in diamonds, their occurrence is not demonstrated in nature, and the physical model for crustal diamond formation is debated. Here, using Raman microspectroscopy, I determine the structure of carbon-based phases inside fluid inclusions in diamond-bearing rocks from the Alps. The results provide direct evidence that diamond surfaces are coated by sp2-, and sp3-bonded amorphous carbon and functional groups of carboxylic acids (e.g., carboxyl, carboxylate, methyl, and methylene), indicating the geosynthesis of organic compounds in deep hydrous fluids. Moreover, this study suggests diamond nucleation via metastable molecular precursors. As a possible scenario, with carbon saturation by reduction of carboxylate groups, I consider tetrahedral H-terminated C groups as templates for the growth of sp3-structured carbon.
An updated and unified earthquake catalog from 1787 to 2018 for seismic hazard assessment studies in Mexico
Authors: Sawires Rashad , Santoyo Miguel A. , Peláez José A. , Corona Fernández Raúl Daniel 
Published: October 2019

AbstractHere we present a new updated and unified Poissonian earthquake catalog for Mexico. The details about the catalog compilation, the removal of duplicate events, unifying the magnitude scales, removal of dependent events through the declustering process and its completeness analysis are presented. Earthquake and focal mechanism data have been compiled from various local, regional and international sources. Large earthquake events (MW ≥ 6.5) have been carefully revised for their epicentral locations and magnitudes from trusted publications. Different magnitude-conversion relationships, compatible with available local and regional ones, has been established to obtain unified moment magnitude estimates for the whole catalog. Completeness periods for the declustered catalog were estimated for the definition of appropriate seismic source models for the whole territory. The final unified Poissonian earthquake catalog spans from 1787 to 2018, covering a spatial extent of 13° to 33°N and 91° to 117°W. This catalog is compatible with other published catalogs providing basis for new analysis related to seismicity, seismotectonics and seismic hazard assessment in Mexico.
Prenatal hypoxia-induced epigenomic and transcriptomic reprogramming in rat fetal and adult offspring hearts
Authors: Chen Xin , Zhang Lubo , Wang Charles 
Published: October 2019

AbstractThe molecular mechanism of antenatal hypoxia impacting on fetal heart development and elevated risk of heart disease of adult offspring is poorly understood. We present a dataset integrating DNA methylome and transcriptome analyses of antenatal hypoxia affecting rat fetal and adult offspring hearts to understand hypoxia-mediated epigenomic reprogramming of the heart development. We showed that antenatal hypoxia not only induced DNA methylomic and transcriptomic changes in the fetal hearts, but also had a delayed and lasting effect on the adult offspring hearts. Of interest, antenatal hypoxia induced opposite changes in DNA methylation patterns in fetal and adult hearts, with a hypermethylation in the fetus and a hypomethylation in the adult. An extensive preprocessing, quality assessment, and downstream data analyses were performed on the genomic dataset so that the research community may take advantage of the public resource. These dataset could be exploited as a comprehensive resource for understanding fetal hypoxia-mediated epigenetic reprogramming in the heart development and further developmental programming of heart vulnerability to disease later in life.Figshare doi: https://doi.org/10.6084/m9.figshare.9948572
7 Tesla MRI of the ex vivo human brain at 100 micron resolution
Authors: Edlow Brian L. , Mareyam Azma , Horn Andreas , Polimeni Jonathan R. , Witzel Thomas , Tisdall M. Dylan , Augustinack Jean C. , Stockmann Jason P. , Diamond Bram R. , Stevens Allison , Tirrell Lee S. , Folkerth Rebecca D. , Wald Lawrence L. , Fischl Bruce , van der Kouwe Andre 
Published: October 2019

AbstractWe present an ultra-high resolution MRI dataset of an ex vivo human brain specimen. The brain specimen was donated by a 58-year-old woman who had no history of neurological disease and died of non-neurological causes. After fixation in 10% formalin, the specimen was imaged on a 7 Tesla MRI scanner at 100 µm isotropic resolution using a custom-built 31-channel receive array coil. Single-echo multi-flip Fast Low-Angle SHot (FLASH) data were acquired over 100 hours of scan time (25 hours per flip angle), allowing derivation of synthesized FLASH volumes. This dataset provides an unprecedented view of the three-dimensional neuroanatomy of the human brain. To optimize the utility of this resource, we warped the dataset into standard stereotactic space. We now distribute the dataset in both native space and stereotactic space to the academic community via multiple platforms. We envision that this dataset will have a broad range of investigational, educational, and clinical applications that will advance understanding of human brain anatomy in health and disease.