bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cerebellar glutamatergic system impacts spontaneous motor recovery by regulating Gria1 expression
Authors: Asthana Pallavi , Kumar Gajendra , Milanowski Lukasz M. , Au Ngan Pan Bennett , Chan Siu Chung , Huang Jianpan , Feng Hemin , Kwan Kin Ming , He Jufang , Chan Kannie Wai Yan , Wszolek Zbigniew K. , Ma Chi Him Eddie 
Published: September 2022

AbstractPeripheral nerve injury (PNI) often results in spontaneous motor recovery; however, how disrupted cerebellar circuitry affects PNI-associated motor recovery is unknown. Here, we demonstrated disrupted cerebellar circuitry and poor motor recovery in ataxia mice after PNI. This effect was mimicked by deep cerebellar nuclei (DCN) lesion, but not by damaging non-motor area hippocampus. By restoring cerebellar circuitry through DCN stimulation, and reversal of neurotransmitter imbalance using baclofen, ataxia mice achieve full motor recovery after PNI. Mechanistically, elevated glutamate-glutamine level was detected in DCN of ataxia mice by magnetic resonance spectroscopy. Transcriptomic study revealed that Gria1, an ionotropic glutamate receptor, was upregulated in DCN of control mice but failed to be upregulated in ataxia mice after sciatic nerve crush. AAV-mediated overexpression of Gria1 in DCN rescued motor deficits of ataxia mice after PNI. Finally, we found a correlative decrease in human GRIA1 mRNA expression in the cerebellum of patients with ataxia-telangiectasia and spinocerebellar ataxia type 6 patient iPSC-derived Purkinje cells, pointing to the clinical relevance of glutamatergic system. By conducting a large-scale analysis of 9,655,320 patients with ataxia, they failed to recover from carpal tunnel decompression surgery and tibial neuropathy, while aged-match non-ataxia patients fully recovered. Our results provide insight into cerebellar disorders and motor deficits after PNI.
Automated reconstruction of whole-embryo cell lineages by learning from sparse annotations
Authors: Malin-Mayor Caroline , Hirsch Peter , Guignard Leo , McDole Katie , Wan Yinan , Lemon William C. , Kainmueller Dagmar , Keller Philipp J. , Preibisch Stephan , Funke Jan 
Published: September 2022

AbstractWe present a method to automatically identify and track nuclei in time-lapse microscopy recordings of entire developing embryos. The method combines deep learning and global optimization. On a mouse dataset, it reconstructs 75.8% of cell lineages spanning 1 h, as compared to 31.8% for the competing method. Our approach improves understanding of where and when cell fate decisions are made in developing embryos, tissues, and organs.
A harmonized dataset of sediment diatoms from hundreds of lakes in the northeastern United States
Authors: Potapova Marina G. , Lee Sylvia S. , Spaulding Sarah A. , Schulte Nicholas O. 
Published: September 2022

AbstractSediment diatoms are widely used to track environmental histories of lakes and their watersheds, but merging datasets generated by different researchers for further large-scale studies is challenging because of taxonomic discrepancies caused by rapidly evolving diatom nomenclature and taxonomic concepts. We collated five datasets of lake sediment diatoms from the Northeastern USA using a harmonization process which included updating synonyms, tracking the identity of inconsistently identified taxa, and grouping those that could not be resolved taxonomically. Each harmonization step led to an increase in variation explained by environmental variables and a parallel reduction of variation attributable to taxonomic inconsistency. To maximize future use of the data and underlying specimens we provide the original and harmonized counts for 1327 core samples from 607 lakes, name translation schemes, sample metadata, specimen museum locations, and the Northeast Lakes Voucher Flora, which is a set of light microscope images grouped into 1154 morphological operational taxonomic units. Post-hoc harmonization enables data quality control when other approaches (e.g., upfront management of taxonomic consistency) are not possible.
Learning to predict synchronization of coupled oscillators on randomly generated graphs
Authors: Bassi Hardeep , Yim Richard P. , Vendrow Joshua , Koduluka Rohith , Zhu Cherlin , Lyu Hanbaek 
Published: September 2022

AbstractSuppose we are given a system of coupled oscillators on an unknown graph along with the trajectory of the system during some period. Can we predict whether the system will eventually synchronize? Even with a known underlying graph structure, this is an important yet analytically intractable question in general. In this work, we take an alternative approach to the synchronization prediction problem by viewing it as a classification problem based on the fact that any given system will eventually synchronize or converge to a non-synchronizing limit cycle. By only using some basic statistics of the underlying graphs such as edge density and diameter, our method can achieve perfect accuracy when there is a significant difference in the topology of the underlying graphs between the synchronizing and the non-synchronizing examples. However, in the problem setting where these graph statistics cannot distinguish the two classes very well (e.g., when the graphs are generated from the same random graph model), we find that pairing a few iterations of the initial dynamics along with the graph statistics as the input to our classification algorithms can lead to significant improvement in accuracy; far exceeding what is known by the classical oscillator theory. More surprisingly, we find that in almost all such settings, dropping out the basic graph statistics and training our algorithms with only initial dynamics achieves nearly the same accuracy. We demonstrate our method on three models of continuous and discrete coupled oscillators—the Kuramoto model, Firefly Cellular Automata, and Greenberg-Hastings model. Finally, we also propose an “ensemble prediction” algorithm that successfully scales our method to large graphs by training on dynamics observed from multiple random subgraphs.
Gut permeability may be associated with periprosthetic joint infection after total hip and knee arthroplasty
Authors: Chisari Emanuele , Cho Jeongeun , Wouthuyzen-Bakker Marjan , Parvizi Javad 
Published: September 2022

AbstractA growing number of recent investigations on the human genome, gut microbiome, and proteomics suggests that the loss of mucosal barrier function, particularly in the gastrointestinal tract, may substantially affect antigen trafficking, ultimately influencing the close bidirectional interaction between the gut microbiome and the immune system. This cross-talk is highly influential in shaping the host immune system function and ultimately affecting the outcome of interventions. We hypothesized that the loss of mucosal barrier in the gut may be associatedto acute and chronic periprosthetic joint infections (PJI). Zonulin, soluble CD14 (sCD14), and lipopolysaccharide (LPS) were tested in plasma as part of a prospective cohort study of patients undergoing primary arthroplasty or revision arthroplasty because of an aseptic failure or PJI (as defined by the 2018 criteria). All blood samples were collected before antibiotic administration. Samples were tested using commercially available enzyme-linked immunosorbent assays as markers for gut permeability. A total of 134 patients were included in the study of which 44 patients had PJI (30 chronic and 14 acute), and the remaining 90 patients were categorized as non-infected that included 64 patients revised for aseptic failure, and 26 patients undergoing primary total joint arthroplasty. Both Zonulin (7.642 ± 6.077 ng/mL vs 4.560 ± 3.833 ng/mL; p < 0.001) and sCD14 levels (555.721 ± 216.659 ng/mL vs 396.872 ± 247.920 ng/mL; p = 0.003) were significantly elevated in the PJI group compared to non-infected cases. Higher levels of Zonulin were found in acute infections compared to chronic PJI (11.595 ± 6.722 ng/mL vs. 5.798 ± 4.841 ng/mL; p = 0.005). This prospective study reveals a possible link between gut permeability and the ‘gut-immune-joint axis’ in PJI. If this association continues to be borne out with a larger cohort and more in-depth analysis, it will have a clinically significant implication in managing patients with PJI. It may be that in addition to the administration of antimicrobials, patients with PJI and other orthopaedic infections may benefit from administration of gastrointestinal modulators such as pro and prebiotics.
Quantifying collective identity online from self-defining hashtags
Authors: Barron Alexander T. J. , Bollen Johan 
Published: September 2022

AbstractMass communication over social media can drive rapid changes in our sense of collective identity. Hashtags in particular have acted as powerful social coordinators, playing a key role in organizing social movements like the Gezi park protests, Occupy Wall Street,#metoo, and#blacklivesmatter. Here we quantify collective identity from the use of hashtags as self-labels in over 85,000 actively-maintained Twitter user profiles spanning 2017–2019. Collective identities emerge from a graph model of individuals’ overlapping self-labels, producing a hierarchy of graph clusters. Each cluster is bound together and characterized semantically by specific hashtags key to its formation. We define and apply two information-theoretic measures to quantify the strength of identities in the hierarchy. First we measure collective identity coherence to determine how integrated any identity is from local to global scales. Second, we consider the conspicuousness of any identity given its vocabulary versus the global identity map. Our work reveals a rich landscape of online identity emerging from the hierarchical alignment of uncoordinated self-labeling actions.
Applying Mendelian randomization to appraise causality in relationships between smoking, depression and inflammation
Authors: Galan D. , Perry B. I. , Warrier V. , Davidson C. C. , Stupart O. , Easton D. , Khandaker G. M. , Murray G. K. 
Published: September 2022

AbstractSmoking, inflammation and depression commonly co-occur and may be mechanistically linked. However, key questions remain around the direction of association and the influence of residual confounding. We aimed to characterize the association between lifetime smoking and depression, as well as to assess the role that genetically-predicted C-reactive protein (CRP) level, (an archetypal generalized inflammatory marker) and/or IL-6 activity, as a potential explanation for this association. We performed inverse variance weighted Mendelian randomization (MR) analyses using recently published summary-level GWAS data for lifetime smoking index, CRP levels, and depression. A subset of inflammatory-related genetic variants from the lifetime smoking GWAS were also used to assess the potential inflammatory causal pathways between smoking and depression. The analysis indicated reciprocal relationships of lifetime smoking with depression (ORSmk–Dep = 2.01, 95% CI 1.71–2.37, p < 0.001; ORDep–Smk = 1.09, 95% CI 1.06–1.13, p < 0.001), CRP levels and IL-6 activity (ORSmk–CRP = 1.40, 95% CI 1.21–1.55, p < 0.001; ORCRP–Smk = 1.03, 95% CI 1.02–1.05, p < 0.001, ORIL-6/CRP–Smk = 1.06 (1.03–1.09), p < 0.001). These associations were also supported by the majority of the robust MR methods performed. We did not find evidence for a reciprocal relationship between CRP levels (using > 500 genetic instruments for CRP) and depression (ORCRP–Dep = 1.01, 95% CI 0.99–1.04; ORDep–CRP = 1.03, 95% CI 0.99–1.07). We observed little variation in the IVW estimates between smoking and depression when we limited the genetic variants assessed to those related to measures of generalized inflammation, but we found evidence for an attenuation of the smoking-depression association in multivariable mendelian randomization when adjusting for IL-6 activity, suggesting that the IL-6 pathway may be at least in part responsible for the association of smoking and depression. Our study supports potential bidirectional causal associations between lifetime smoking and depression which may be at least in part explained by the IL-6 signalling pathway. The IL-6 pathway may represent a putative therapeutic target for smoking and to mitigate the effects of smoking on depression.
Study of curling mechanism by precision kinematic measurements of curling stone’s motion
Authors: Murata Jiro 
Published: September 2022

AbstractWhy do curling stones curl? That is a question physicists are often asked, yet no answer has been established. Stones rotating clockwise curl right, contrary to our naive expectations. After a century of debate between contradicting hypotheses, this paper provides a possible answer based on experimental evidence. A digital image analysis technique was used to perform precision kinematic measurements of a curling stone’s motion to identify the curling mechanism. We observed a significant left–right asymmetric friction due to velocity dependence on the friction coefficient. Combined with the discrete point-like nature of the friction between ice and stone, swinging around slow-side friction points has been concluded as the dominant origin of the curling. Many new angular momentum transfer phenomena have been found, supporting this conclusion.
An ab initio study on resistance switching in hexagonal boron nitride
Authors: Ducry Fabian , Waldhoer Dominic , Knobloch Theresia , Csontos Miklos , Jimenez Olalla Nadia , Leuthold Juerg , Grasser Tibor , Luisier Mathieu 
Published: September 2022

AbstractTwo-dimensional materials have been widely investigated to implement memristive devices for data storage or neuromorphic computing applications because of their ultra-scaled thicknesses and clean interfaces. For example, resistance switching in hexagonal boron nitride (h-BN) has been demonstrated. This mechanism is most of the time attributed to the movement of metallic ions. It has however also been reported when h-BN is contacted with two inert electrodes such as graphene or Pt. We suggest here that the switching mechanism of the latter devices, which has not yet been clearly established, relies on locals change of the electronic structure of h-BN as caused by atomic defects, e.g., multi-vacancies. This class of intrinsic h-BN defects can create electrically controllable interlayer bridges. We use a combination of hybrid density functional theory and the Non-equilibrium Green’s function formalism to show that a single interlayer bridge resulting from the presence of a trivacancy in a graphene/h-BN/graphene stack leads to a switching voltage of ~5 V and a high-to-low resistance ratio >100. Both values lie within the reported experimental range and thus confirm the likelihood that intrinsic defects play a key role in the resistance switching of h-BN in contact with inert electrodes.
An integrated magneto-optic modulator for cryogenic applications
Authors: Pintus Paolo , Ranzani Leonardo , Pinna Sergio , Huang Duanni , Gustafsson Martin V. , Karinou Fotini , Casula Giovanni Andrea , Shoji Yuya , Takamura Yota , Mizumoto Tetsuya , Soltani Mohammad , Bowers John E. 
Published: September 2022

AbstractSuperconducting circuits can operate at higher energy efficiencies than their room-temperature counterparts and have the potential to enable large-scale control and readout of quantum computers. However, the required interface with room-temperature electronics creates difficulties in scaling up such cryogenic systems. One option is to use optical fibres as a medium in conjunction with fast optical modulators that can be efficiently driven by electrical signals at low temperatures. However, as superconducting circuits are current operated with low impedances, they interface poorly with conventional electro-optical modulators. Here we report an integrated current-driven modulator that is based on the magneto-optic effect and can operate at temperatures as low as 4 K. The device combines a magneto-optic garnet crystal with a silicon waveguide resonator and integrates an electromagnet to modulate the refractive index of the garnet. The modulator offers data rates of up to 2 Gbps with an energy consumption below 4 pJ per bit of transferred information, which could be reduced to less than 50 fJ per bit by replacing dissipative electrodes with superconductors and optimizing the geometric parameters.
Ectopic JAK–STAT activation enables the transition to a stem-like and multilineage state conferring AR-targeted therapy resistance
Authors: Deng Su , Wang Choushi , Wang Yunguan , Xu Yaru , Li Xiaoling , Johnson Nickolas A. , Mukherji Atreyi , Lo U-Ging , Xu Lingfan , Gonzalez Julisa , Metang Lauren A. , Ye Jianfeng , Tirado Carla Rodriguez , Rodarte Kathia , Zhou Yinglu , Xie Zhiqun , Arana Carlos , Annamalai Valli , Liu Xihui , Vander Griend Donald J. , Strand Douglas , Hsieh Jer-Tsong , Li Bo , Raj Ganesh , Wang Tao , Mu Ping 
Published: September 2022

AbstractEmerging evidence indicates that various cancers can gain resistance to targeted therapies by acquiring lineage plasticity. Although various genomic and transcriptomic aberrations correlate with lineage plasticity, the molecular mechanisms enabling the acquisition of lineage plasticity have not been fully elucidated. We reveal that Janus kinase (JAK)–signal transducer and activator of transcription (STAT) signaling is a crucial executor in promoting lineage plasticity-driven androgen receptor (AR)-targeted therapy resistance in prostate cancer. Importantly, ectopic JAK–STAT activation is specifically required for the resistance of stem-like subclones expressing multilineage transcriptional programs but not subclones exclusively expressing the neuroendocrine-like lineage program. Both genetic and pharmaceutical inhibition of JAK–STAT signaling resensitizes resistant tumors to AR-targeted therapy. Together, these results suggest that JAK–STAT are compelling therapeutic targets for overcoming lineage plasticity-driven AR-targeted therapy resistance.
Acetábulo de metal trabeculado customizado na revisão de artroplastia total do quadril
Authors: Queiroz Roberto Dantas , Fingerhut David Jeronimo Peres , Saito Luiz Henrique 
Published: September 2022

ResumoO seguinte relato de caso tem como objetivo demonstrar uma cirurgia de revisão de artroplastia total do quadril (RATQ) com o uso de componente acetabular customizado de metal trabeculado para correção de defeito acetabular severo. Atualmente, na literatura existem poucas descrições completas do planejamento e procedimentos cirúrgicos envolvendo próteses customizadas, tanto pela dificuldade técnica, inerente ao ato cirúrgico, quanto devido aos altos custos relacionados ao planejamento e materiais.
A Narrative Review on Fanconi Anemia: Genetic and Diagnostic Considerations
Authors: Sharma Preksha , Sharma Neha , Sharma Dhruva 
Published: September 2022

AbstractFanconi anemia (FA) is an autosomal recessive disorder, both genetically and phenotypically. It is characterized by chromosomal instability, progressive bone marrow failure, susceptibility to cancer, and various other congenital abnormalities. It involves all the three cell lines of blood. So far, biallelic mutations in 21 genes and one x-linked gene have been detected and found to be associated with FA phenotype. Signs and symptoms start setting in by the age of 4 to 7 years, mainly hematological symptoms. This includes pancytopenia, that is, a reduction in the number of white blood cells (WBCs), red blood cells (RBCs), and platelets. Therefore, the main criteria for diagnosis of FA include skeletal malformations, pancytopenia, hyperpigmentation, short stature, urogenital abnormalities, central nervous system, auditory, renal, ocular, and familial occurrence. Patients showing signs and symptoms of FA should be thoroughly evaluated. A complete blood count will reveal a reduced number of RBC, WBC, and platelets, that is, pancytopenia. Chromosomal breakage study/stress cytogenetics should be done in patients with severe pancytopenia. Momentousness timely diagnosis of current disease, prenatal diagnosis, and genetic counseling should be emphasized.
Evolving Knowledge on Primary and Secondary Prevention of Venous Thromboembolism in Carriers of Hereditary Thrombophilia: A Narrative Review
Authors: Campello Elena , Prandoni Paolo 
Published: September 2022

AbstractThe association between heritability of venous thromboembolism (VTE) and thrombophilia was first reported clinically in 1956, later followed by the first description of a congenital cause of hypercoagulability—antithrombin deficiency—in 1965. Since then, our knowledge of hereditary causes of hypercoagulability, which may predispose carriers to VTE has improved greatly. Novel genetic defects responsible for severe thrombophilia have been recently identified and we have learned that a wide range of interactions between thrombophilia and other genetic and acquired risk factors are important determinants of the overall individual risk of developing VTE. Furthermore, therapeutic strategies in thrombophilic patients have benefited significantly from the introduction of direct oral anticoagulants. The present review is an overview of the current knowledge on the mechanisms underlying inherited thrombophilia, with a particular focus on the latest achievements in anticoagulation protocols and prevention strategies for thrombosis in carriers of this prothrombotic condition.
Bilateral trade and politico-administrative border relations in Africa: an analysis of the case of Nigeria and Benin Republic
Authors: Omeh Paul Hezekiah , Abada Ifeanyichukwu Michael , Onah Celestine Chijioke , Anozie Ngozika Josephine , Amujiri Benjamin 
Published: September 2022

SUMMARY
Bilateral formal trade relations between Nigeria and the Republic of Benin have increased significantly in the last 10 years. There has also been an increase in the smuggling of contraband goods due to the porous borders. This briefing explores the nexus between bilateral trade and politico-administrative border relations between the two countries. It interrogates the character of the border relations and consequences for the political economy of trade. The briefing highlights that border politics drive formal and informal trade relations. It also highlights other drivers of illegal activities in the border areas, including the cultural affinity between inhabitants living within the contiguous borders, and compromised government officials.
First-principles study on high-pressure phases and compression properties of gold-bearing intermetallic compounds
Authors: Li Bingtan , Liu Hanyu , Liu Guangtao , Chen Kaiguo 
Published: September 2022

Abstract
Compared to elemental gold (Au), Au-based alloys have attracted wide attention for their economy and superior performance stemming from their distinctive physicochemical properties. The study of the structural characterization for alloy materials remains one of the fundamental issues associated with their future applications essentially. In this work, we theoretically explore some typical intermetallic compounds of Au-based alloys under high pressure, which has been an effective means to generate intriguing crystal configurations with unexpected behaviors. Our ab initio simulations find that Fd-3m-AuRb, Fd-3m-AuBa, and Fd-3m-AuLa become stable above ∼10 GPa, and Pmmn-AuAl becomes stable above ∼20 GPa. Further investigations of their compression behaviors reveal that the bulk moduli of Au-based alloys can be greatly reduced by combining alkali and alkaline earth metals. The present results have unraveled the high-pressure phases of Au-bearing compounds and provide insights for exploring their important compressibility that is strongly relevant to the containing non-Au elements.