bluuebunny/crossref_metadata_2025_split huggingface dataset:
Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger
Authors: Cheng Shi-Ping , Jia Kai-Hua , Liu Hui , Zhang Ren-Gang , Li Zhi-Chao , Zhou Shan-Shan , Shi Tian-Le , Ma Ai-Chu , Yu Cong-Wen , Gao Chan , Cao Guang-Lei , Zhao Wei , Nie Shuai , Guo Jing-Fang , Jiao Si-Qian , Tian Xue-Chan , Yan Xue-Mei , Bao Yu-Tao , Yun Quan-Zheng , Wang Xin-Zhu , Porth Ilga , El-Kassaby Yousry A , Wang Xiao-Ru , Li Zhen , Van de Peer Yves , Mao Jian-Feng 
Published: August 2021

Abstract
Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.
Disrupting the LINC complex by AAV mediated gene transduction prevents progression of Lamin induced cardiomyopathy
Authors: Chai Ruth Jinfen , Werner Hendrikje , Li Peter Yiqing , Lee Yin Loon , Nyein Khaing Thet , Solovei Irina , Luu Tuan Danh Anh , Sharma Bhavya , Navasankari Raju , Maric Martina , Sim Lois Yu En , Loh Ying Jie , Aliwarga Edita , Cheong Jason Wen Long , Chojnowski Alexandre , Autio Matias Ilmari , Haiyang Yu , Boon Tan Kenneth Kian , Keng Choong Tat , Ng Shi Ling , Chew Wei Leong , Ferenczi Michael , Burke Brian , Foo Roger Sik Yin , Stewart Colin L. 
Published: August 2021

AbstractMutations in the LaminA gene are a common cause of monogenic dilated cardiomyopathy. Here we show that mice with a cardiomyocyte-specific Lmna deletion develop cardiac failure and die within 3–4 weeks after inducing the mutation. When the same Lmna mutations are induced in mice genetically deficient in the LINC complex protein SUN1, life is extended to more than one year. Disruption of SUN1’s function is also accomplished by transducing and expressing a dominant-negative SUN1 miniprotein in Lmna deficient cardiomyocytes, using the cardiotrophic Adeno Associated Viral Vector 9. The SUN1 miniprotein disrupts binding between the endogenous LINC complex SUN and KASH domains, displacing the cardiomyocyte KASH complexes from the nuclear periphery, resulting in at least a fivefold extension in lifespan. Cardiomyocyte-specific expression of the SUN1 miniprotein prevents cardiomyopathy progression, potentially avoiding the necessity of developing a specific therapeutic tailored to treating each different LMNA cardiomyopathy-inducing mutation of which there are more than 450.
The middle lipin domain adopts a membrane-binding dimeric protein fold
Authors: Gu Weijing , Gao Shujuan , Wang Huan , Fleming Kaelin D. , Hoffmann Reece M. , Yang Jong Won , Patel Nimi M. , Choi Yong Mi , Burke John E. , Reue Karen , Airola Michael V. 
Published: August 2021

AbstractPhospholipid synthesis and fat storage as triglycerides are regulated by lipin phosphatidic acid phosphatases (PAPs), whose enzymatic PAP function requires association with cellular membranes. Using hydrogen deuterium exchange mass spectrometry, we find mouse lipin 1 binds membranes through an N-terminal amphipathic helix, the Ig-like domain and HAD phosphatase catalytic core, and a middle lipin (M-Lip) domain that is conserved in mammalian and mammalian-like lipins. Crystal structures of the M-Lip domain reveal a previously unrecognized protein fold that dimerizes. The isolated M-Lip domain binds membranes both in vitro and in cells through conserved basic and hydrophobic residues. Deletion of the M-Lip domain in lipin 1 reduces PAP activity, membrane association, and oligomerization, alters subcellular localization, diminishes acceleration of adipocyte differentiation, but does not affect transcriptional co-activation. This establishes the M-Lip domain as a dimeric protein fold that binds membranes and is critical for full functionality of mammalian lipins.
A self-healing ferroelectric liquid crystal electro-optic shutter based on vertical surface-relief grating alignment
Authors: Wyatt Peter J. M. , Bailey James , Nagaraj Mamatha , Jones J. Cliff 
Published: August 2021

AbstractFerroelectric liquid crystals remain of interest for display and spatial light modulators because they exhibit significantly faster optical response times than nematics. However, smectic layers are sensitive to shock-induced flow and are usually permanently displaced once a well-aligned sample is disrupted, rendering such devices inoperable. We introduce a vertical alignment geometry combined with a surface-relief grating to control both the smectic layer and director orientations. This mode undergoes “self-healing” of the smectic layers after disruption by shock-induced flow. Sub-millisecond switching between optically distinct states is demonstrated using in-plane electric fields. Self-healing occurs within a second after being disrupted by shock, wherein both the layer and director realign without additional external stimulus. The route to material improvements for optimised devices is discussed, promising faster spatial light modulators for high-speed adaptive optics, micro-displays for virtual/augmented reality and telecommunications with inherent shock stability.
Microchannelled alkylated chitosan sponge to treat noncompressible hemorrhages and facilitate wound healing
Authors: Du Xinchen , Wu Le , Yan Hongyu , Jiang Zhuyan , Li Shilin , Li Wen , Bai Yanli , Wang Hongjun , Cheng Zhaojun , Kong Deling , Wang Lianyong , Zhu Meifeng 
Published: August 2021

AbstractDeveloping an anti-infective shape-memory hemostatic sponge able to guide in situ tissue regeneration for noncompressible hemorrhages in civilian and battlefield settings remains a challenge. Here we engineer hemostatic chitosan sponges with highly interconnective microchannels by combining 3D printed microfiber leaching, freeze-drying, and superficial active modification. We demonstrate that the microchannelled alkylated chitosan sponge (MACS) exhibits the capacity for water and blood absorption, as well as rapid shape recovery. We show that compared to clinically used gauze, gelatin sponge, CELOX™, and CELOX™-gauze, the MACS provides higher pro-coagulant and hemostatic capacities in lethally normal and heparinized rat and pig liver perforation wound models. We demonstrate its anti-infective activity against S. aureus and E. coli and its promotion of liver parenchymal cell infiltration, vascularization, and tissue integration in a rat liver defect model. Overall, the MACS demonstrates promising clinical translational potential in treating lethal noncompressible hemorrhage and facilitating wound healing.
Nearest centroid classification on a trapped ion quantum computer
Authors: Johri Sonika , Debnath Shantanu , Mocherla Avinash , SINGK Alexandros , Prakash Anupam , Kim Jungsang , Kerenidis Iordanis 
Published: August 2021

AbstractQuantum machine learning has seen considerable theoretical and practical developments in recent years and has become a promising area for finding real world applications of quantum computers. In pursuit of this goal, here we combine state-of-the-art algorithms and quantum hardware to provide an experimental demonstration of a quantum machine learning application with provable guarantees for its performance and efficiency. In particular, we design a quantum Nearest Centroid classifier, using techniques for efficiently loading classical data into quantum states and performing distance estimations, and experimentally demonstrate it on a 11-qubit trapped-ion quantum machine, matching the accuracy of classical nearest centroid classifiers for the MNIST handwritten digits dataset and achieving up to 100% accuracy for 8-dimensional synthetic data.
Long-range supercurrents through a chiral non-collinear antiferromagnet in lateral Josephson junctions
Authors: Jeon Kun-Rok , Hazra Binoy Krishna , Cho Kyungjune , Chakraborty Anirban , Jeon Jae-Chun , Han Hyeon , Meyerheim Holger L. , Kontos Takis , Parkin Stuart S. P. 
Published: August 2021

AbstractThe proximity-coupling of a chiral non-collinear antiferromagnet (AFM)1–5 with a singlet superconductor allows spin-unpolarized singlet Cooper pairs to be converted into spin-polarized triplet pairs6–8, thereby enabling non-dissipative, long-range spin correlations9–14. The mechanism of this conversion derives from fictitious magnetic fields that are created by a non-zero Berry phase15 in AFMs with non-collinear atomic-scale spin arrangements1–5. Here we report long-ranged lateral Josephson supercurrents through an epitaxial thin film of the triangular chiral AFM Mn3Ge (refs. 3–5). The Josephson supercurrents in this chiral AFM decay by approximately one to two orders of magnitude slower than would be expected for singlet pair correlations9–14 and their response to an external magnetic field reflects a clear spatial quantum interference. Given the long-range supercurrents present in both single- and mixed-phase Mn3Ge, but absent in a collinear AFM IrMn16, our results pave a way for the topological generation of spin-polarized triplet pairs6–8 via Berry phase engineering15 of the chiral AFMs.
Quantum chemical calculations of lithium-ion battery electrolyte and interphase species
Authors: Spotte-Smith Evan Walter Clark , Blau Samuel M. , Xie Xiaowei , Patel Hetal D. , Wen Mingjian , Wood Brandon , Dwaraknath Shyam , Persson Kristin Aslaug 
Published: August 2021

AbstractLithium-ion batteries (LIBs) represent the state of the art in high-density energy storage. To further advance LIB technology, a fundamental understanding of the underlying chemical processes is required. In particular, the decomposition of electrolyte species and associated formation of the solid electrolyte interphase (SEI) is critical for LIB performance. However, SEI formation is poorly understood, in part due to insufficient exploration of the vast reactive space. The Lithium-Ion Battery Electrolyte (LIBE) dataset reported here aims to provide accurate first-principles data to improve the understanding of SEI species and associated reactions. The dataset was generated by fragmenting a set of principal molecules, including solvents, salts, and SEI products, and then selectively recombining a subset of the fragments. All candidate molecules were analyzed at the ωB97X-V/def2-TZVPPD/SMD level of theory at various charges and spin multiplicities. In total, LIBE contains structural, thermodynamic, and vibrational information on over 17,000 unique species. In addition to studies of reactivity in LIBs, this dataset may prove useful for machine learning of molecular and reaction properties.
Associations between the thyroid panel and serum protein concentrations across pregnancy
Authors: Lisowska-Myjak Barbara , Strawa Agnieszka , Zborowska Hanna , Jakimiuk Artur , Skarżyńska Ewa 
Published: August 2021

AbstractEstablishing any characteristic associations between the serum parameters of thyroid function and serum proteins in pregnancy may aid in elucidating the role of the thyroid gland in the regulation of pregnancy-specific metabolic processes and in selecting candidate biomarkers for use in their clinical assessment. Concentrations of thyroid stimulating hormone (TSH), free tri-iodothyronine (fT3) and free thyroxine (fT4), six electrophoretically separated protein fractions (albumin, alpha-1-, alpha2-, beta-1-, beta-2- and gamma-globulins), representative proteins—albumin (ALB), transferrin (TRF), alpha-2-macroglobulin (AMG) and ceruloplasmin (CER) were measured in 136 serum samples from 65 women in their consecutive trimesters of pregnancy. The concentrations of TSH, fT4 and fT3 were significantly correlated (p < 0.05) with the concentrations of the albumin, alpha-2- and beta-1 globulin fractions. Significant correlations (p < 0.05) which were positive between fT4 and ALB and negative between fT4 and TRF were established throughout pregnancy. Significant negative correlations (p < 0.05) were demonstrated for fT3 with alpha-2-globulin, AMG and CER. Changes in the serum concentrations of thyroid hormones seen between the trimesters were found to correlate with the concentrations of high-abundance serum proteins. Opposite directions of correlations between fT4 and ALB and fT4 and TRF observed throughout pregnancy may indicate the shared biological role of these parameters in maintaining maternal homeostasis and they suggest their potential use in the clinic as a simple biomarker panel. A negative correlation of fT3 with CER in the second trimester possibly reflects their involvement in the active regulation of metabolic processes.
Assessment and modeling using machine learning of resistance to scald (Rhynchosporium commune) in two specific barley genetic resources subsets
Authors: Hiddar Houda , Rehman Sajid , Lakew Berhane , Verma Ramesh Pal Singh , Al-Jaboobi Muamar , Moulakat Adil , Kehel Zakaria , Filali-Maltouf Abdelkarim , Baum Michael , Amri Ahmed 
Published: August 2021

AbstractBarley production worldwide is limited by several abiotic and biotic stresses and breeding of highly productive and adapted varieties is key to overcome these challenges. Leaf scald, caused byRhynchosporium communeis a major disease of barley that requires the identification of novel sources of resistance. In this study two subsets of genebank accessions were used: one extracted from the Reference set developed within the Generation Challenge Program (GCP) with 191 accessions, and the other with 101 accessions selected using the filtering approach of the Focused Identification of Germplasm Strategy (FIGS). These subsets were evaluated for resistance to scald at the seedling stage under controlled conditions using two Moroccan isolates, and at the adult plant stage in Ethiopia and Morocco. The results showed that both GCP and FIGS subsets were able to identify sources of resistance to leaf scald at both plant growth stages. In addition, the test of independence and goodness of fit showed that FIGS filtering approach was able to capture higher percentages of resistant accessions compared to GCP subset at the seedling stage against two Moroccan scald isolates, and at the adult plant stage against four field populations of Morocco and Ethiopia, with the exception of Holetta nursery 2017. Furthermore, four machine learning models were tuned on training sets to predict scald reactions on the test sets based on diverse metrics (accuracy, specificity, and Kappa). All models efficiently identified resistant accessions with specificities higher than 0.88 but showed different performances between isolates at the seedling and to field populations at the adult plant stage. The findings of our study will help in fine-tuning FIGS approach using machine learning for the selection of best-bet subsets for resistance to scald disease from the large number of genebank accessions.
Modeling photosynthetic resource allocation connects physiology with evolutionary environments
Authors: Sundermann Esther M. , Lercher Martin J. , Heckmann David 
Published: August 2021

AbstractThe regulation of resource allocation in biological systems observed today is the cumulative result of natural selection in ancestral and recent environments. To what extent are observed resource allocation patterns in different photosynthetic types optimally adapted to current conditions, and to what extent do they reflect ancestral environments? Here, we explore these questions for C3, C4, and C3–C4 intermediate plants of the model genus Flaveria. We developed a detailed mathematical model of carbon fixation, which accounts for various environmental parameters and for energy and nitrogen partitioning across photosynthetic components. This allows us to assess environment-dependent plant physiology and performance as a function of resource allocation patterns. Models of C4 plants optimized for conditions experienced by evolutionary ancestors perform better than models accounting for experimental growth conditions, indicating low phenotypic plasticity. Supporting this interpretation, the model predicts that C4 species need to re-allocate more nitrogen between photosynthetic components than C3 species to adapt to new environments. We thus hypothesize that observed resource distribution patterns in C4 plants still reflect optimality in ancestral environments, allowing the quantitative inference of these environments from today’s plants. Our work allows us to quantify environmental effects on photosynthetic resource allocation and performance in the light of evolutionary history.
In vivo imaging of mGlu5 receptor expression in humans with Fragile X Syndrome towards development of a potential biomarker
Authors: Mody Maria , Petibon Yoann , Han Paul , Kuruppu Darshini , Ma Chao , Yokell Daniel , Neelamegam Ramesh , Normandin Marc D. , Fakhri Georges El , Brownell Anna-Liisa 
Published: August 2021

AbstractFragile X Syndrome (FXS) is a neurodevelopmental disorder caused by silencing of the Fragile X Mental Retardation (FMR1) gene. The resulting loss of Fragile X Mental Retardation Protein (FMRP) leads to excessive glutamate signaling via metabotropic glutamate subtype 5 receptors (mGluR5) which has been implicated in the pathogenesis of the disorder. In the present study we used the radioligand 3-[18F]fluoro-5-(2-pyridinylethynyl)benzonitrile ([18F]FPEB) in simultaneous PET-MR imaging of males with FXS and age- and gender-matched controls to assess the availability of mGlu5 receptors in relevant brain areas. Patients with FXS showed lower [18F]FPEB binding potential (p <  0.01), reflecting reduced mGluR5 availability, than the healthy controls throughout the brain, with significant group differences in insula, anterior cingulate, parahippocampal, inferior temporal and olfactory cortices, regions associated with deficits in inhibition, memory, and visuospatial processes characteristic of the disorder. The results are among the first to provide in vivo evidence of decreased availability of mGluR5 in the brain in individuals with FXS than in healthy controls. The consistent results across the subjects, despite the tremendous challenges with neuroimaging this population, highlight the robustness of the protocol and support for its use in drug occupancy studies; extending our radiotracer development and application efforts from mice to humans.
The relationship between the characteristics of burst suppression pattern and different etiologies in epilepsy
Authors: Yang Haipo , Gong Pan , Jiao Xianru , Zhou Qiujun , Zhang Yuehua , Jiang Yuwu , Yang Zhixian 
Published: August 2021

AbstractTo analyze the relationship between the characteristics of burst suppression (BS) pattern and different etiologies in epilepsy. Patients with a BS pattern who were younger than 6 months old were screened from our electroencephalogram (EEG) database. The synchronized and symmetric BS patterns under different etiologies in epilepsy were analyzed. A total of 32 patients had a BS pattern on EEG. The etiologies included genetic disorders (37.5%), cortical malformations (28.1%), inborn errors of metabolism (12.5%), and unknown (21.9%). Twenty-five patients were diagnosed with Ohtahara syndrome, one as early myoclonic encephalopathy, and one as epilepsy of infancy with migrating focal seizure. Five cases could not be classified into any epileptic syndrome. Asynchronous BS pattern was identified in 18 cases, of which 13 (72%) patients had genetic and/or metabolic etiologies. Synchronous BS pattern was identified in 14 cases, of which 8 (57%) patients had structural etiologies. Twenty-three patients had symmetric BS patterns, of which 15 (65%) patients had genetic etiologies. Nine patients had asymmetric BS patterns, of which 8 (89%) patients had structural etiologies. Patients with genetic epilepsies tended to have asynchronous and symmetric BS patterns, whereas those with structural epilepsies were more likely to have synchronous and asymmetric BS patterns.
Abnormal [18F]FDG PET/MRI findings in paraspinal structures of patients with suspected cerebrospinal fluid leak
Authors: Yoon Daehyun , Cipriano Peter William , Penticuff Ryan , Castillo Jessa Ballesteros , Xu Yingding , Carroll Ian Richard , Biswal Sandip 
Published: August 2021

AbstractA combination of magnetic resonance imaging (MRI), computed tomography (CT), and radionuclide cisternography are typically used to locate a cerebrospinal fluid (CSF) leak. However, the site of leakage cannot be determined, making treatment more difficult. Therefore, more sensitive imaging tools are needed. A whole-body [18F]fluorodeoxyglucose (FDG) positron emission tomography (PET)/MRI was conducted on six patients with suspected CSF leak and the resulting images were reviewed in comparison with those from six healthy controls. Paraspinal regions of focally increased uptake of [18F]FDG were quantified using maximum standardized uptake values (SUVmax) and compared to the SUVmax of corresponding regions in the healthy controls. All six patients with suspected CSF leak showed paraspinal regions of significantly greater [18F]FDG uptake compared to the corresponding areas in controls (P < 0.05). Two patients treated with local injections (epidural blood patches and/or epidural fibrin patches) on the site of abnormal PET/MRI findings reported temporary but significant improvement in symptoms. Our results suggest [18F]FDG PET/MRI is sensitive to abnormalities potentially due to suspected CSF leak, which are not necessarily visible on conventional MRI alone or by the standard-of-care imaging methods.
Yippee like 4 (Ypel4) is essential for normal mouse red blood cell membrane integrity
Authors: Mattebo Alexander , Sen Taha , Jassinskaja Maria , Pimková Kristýna , Prieto González-Albo Isabel , Alattar Abdul Ghani , Ramakrishnan Ramprasad , Lang Stefan , Järås Marcus , Hansson Jenny , Soneji Shamit , Singbrant Sofie , van den Akker Emile , Flygare Johan 
Published: August 2021

AbstractThe YPEL family genes are highly conserved across a diverse range of eukaryotic organisms and thus potentially involved in essential cellular processes. Ypel4, one of five YPEL family gene orthologs in mouse and human, is highly and specifically expressed in late terminal erythroid differentiation (TED). In this study, we investigated the role of Ypel4 in murine erythropoiesis, providing for the first time an in-depth description of a Ypel4-null phenotype in vivo. We demonstrated that the Ypel4-null mice displayed a secondary polycythemia with macro- and reticulocytosis. While lack of Ypel4 did not affect steady-state TED in the bone marrow or spleen, the anemia-recovering capacity of Ypel4-null cells was diminished. Furthermore, Ypel4-null red blood cells (RBC) were cleared from the circulation at an increased rate, demonstrating an intrinsic defect of RBCs. Scanning electron micrographs revealed an ovalocytic morphology of Ypel4-null RBCs and functional testing confirmed reduced deformability. Even though Band 3 protein levels were shown to be reduced in Ypel4-null RBC membranes, we could not find support for a physical interaction between YPEL4 and the Band 3 protein. In conclusion, our findings provide crucial insights into the role of Ypel4 in preserving normal red cell membrane integrity.