bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila
Authors: Rech Gabriel E. , Radío Santiago , Guirao-Rico Sara , Aguilera Laura , Horvath Vivien , Green Llewellyn , Lindstadt Hannah , Jamilloux Véronique , Quesneville Hadi , González Josefa 
Published: April 2022

AbstractHigh quality reference genomes are crucial to understanding genome function, structure and evolution. The availability of reference genomes has allowed us to start inferring the role of genetic variation in biology, disease, and biodiversity conservation. However, analyses across organisms demonstrate that a single reference genome is not enough to capture the global genetic diversity present in populations. In this work, we generate 32 high-quality reference genomes for the well-known model species D. melanogaster and focus on the identification and analysis of transposable element variation as they are the most common type of structural variant. We show that integrating the genetic variation across natural populations from five climatic regions increases the number of detected insertions by 58%. Moreover, 26% to 57% of the insertions identified using long-reads were missed by short-reads methods. We also identify hundreds of transposable elements associated with gene expression variation and new TE variants likely to contribute to adaptive evolution in this species. Our results highlight the importance of incorporating the genetic variation present in natural populations to genomic studies, which is essential if we are to understand how genomes function and evolve.
Distinct molecular and immune hallmarks of inflammatory arthritis induced by immune checkpoint inhibitors for cancer therapy
Authors: Kim Sang T. , Chu Yanshuo , Misoi Mercy , Suarez-Almazor Maria E. , Tayar Jean H. , Lu Huifang , Buni Maryam , Kramer Jordan , Rodriguez Emma , Hussain Zulekha , Neelapu Sattva S. , Wang Jennifer , Shah Amishi Y. , Tannir Nizar M. , Campbell Matthew T. , Gibbons Don L. , Cascone Tina , Lu Charles , Blumenschein George R. , Altan Mehmet , Lim Bora , Valero Vincente , Loghin Monica E. , Tu Janet , Westin Shannon N. , Naing Aung , Garcia-Manero Guillermo , Abdel-Wahab Noha , Tawbi Hussein A. , Hwu Patrick , Oliva Isabella C. Glitza , Davies Michael A. , Patel Sapna P. , Zou Jun , Futreal Andrew , Diab Adi , Wang Linghua , Nurieva Roza 
Published: April 2022

AbstractImmune checkpoint inhibitors are associated with immune-related adverse events (irAEs), including arthritis (arthritis-irAE). Management of arthritis-irAE is challenging because immunomodulatory therapy for arthritis should not impede antitumor immunity. Understanding of the mechanisms of arthritis-irAE is critical to overcome this challenge, but the pathophysiology remains unknown. Here, we comprehensively analyze peripheral blood and/or synovial fluid samples from 20 patients with arthritis-irAE, and unmask a prominent Th1-CD8+ T cell axis in both blood and inflamed joints. CX3CR1hi CD8+ T cells in blood and CXCR3hi CD8+ T cells in synovial fluid, the most clonally expanded T cells, significantly share TCR repertoires. The migration of blood CX3CR1hi CD8+ T cells into joints is possibly mediated by CXCL9/10/11/16 expressed by myeloid cells. Furthermore, arthritis after combined CTLA-4 and PD-1 inhibitor therapy preferentially has enhanced Th17 and transient Th1/Th17 cell signatures. Our data provide insights into the mechanisms, predictive biomarkers, and therapeutic targets for arthritis-irAE.
Pace of passive margin tectonism revealed by U-Pb dating of fracture-filling calcite
Authors: Amidon William H. , Kylander-Clark Andrew R. C. , Barr Matthew N. , Graf Samuel F. I. , West David P. 
Published: April 2022

AbstractA growing body of evidence demonstrates that Atlantic-style passive margins have experienced episodes of uplift and volcanism in response to changes in mantle circulation long after cessation of rifting. Passive margins are thus an attractive archive from which to retrieve records of mantle circulation and lithospheric alteration. However, this archive remains under-utilized due to difficulty in deciphering the surficial records of passive margin tectonism and linking them to seismic velocity structure. Here we present a new approach to unraveling the tectonic history of passive margins using U-Pb dating of calcite in faults and fractures along the eastern North American margin. These ages show a 40 Myr long period of continuous fracturing and faulting from ~115 to 75 Ma followed by another episode in Mio-Pliocene time. We argue that the former event represents a response to Cretaceous lithospheric alteration whereas the latter records development of modern relief in the northern Appalachians.
In situ dual doping for constructing efficient CO2-to-methanol electrocatalysts
Authors: Li Pengsong , Bi Jiahui , Liu Jiyuan , Zhu Qinggong , Chen Chunjun , Sun Xiaofu , Zhang Jianling , Han Buxing 
Published: April 2022

AbstractMethanol is a highly desirable product of CO2 electroreduction due to its wide array of industrial applications. However, the development of CO2-to-methanol electrocatalysts with high performance is still challenging. Here we report an operationally simple in situ dual doping strategy to construct efficient CO2-to-methanol electrocatalysts. In particular, when using Ag,S-Cu2O/Cu as electrocatalyst, the methanol Faradaic efficiency (FE) could reach 67.4% with a current density as high as 122.7 mA cm−2 in an H-type cell using 1-butyl-3-methylimidazolium tetrafluoroborate/H2O as the electrolyte, while the current density was below 50 mA cm−2 when the FE was greater than 50% over the reported catalysts. Experimental and theoretical studies suggest that the anion S can effectively adjust the electronic structure and morphology of the catalysts in favor of the methanol pathway, whereas the cation Ag suppresses the hydrogen evolution reaction. Their synergistic interactions with host material enhance the selectivity and current density for methanol formation. This work opens a way for designing efficient catalysts for CO2 electroreduction to methanol.
Multi-animal pose estimation, identification and tracking with DeepLabCut
Authors: Lauer Jessy , Zhou Mu , Ye Shaokai , Menegas William , Schneider Steffen , Nath Tanmay , Rahman Mohammed Mostafizur , Di Santo Valentina , Soberanes Daniel , Feng Guoping , Murthy Venkatesh N. , Lauder George , Dulac Catherine , Mathis Mackenzie Weygandt , Mathis Alexander 
Published: April 2022

AbstractEstimating the pose of multiple animals is a challenging computer vision problem: frequent interactions cause occlusions and complicate the association of detected keypoints to the correct individuals, as well as having highly similar looking animals that interact more closely than in typical multi-human scenarios. To take up this challenge, we build on DeepLabCut, an open-source pose estimation toolbox, and provide high-performance animal assembly and tracking—features required for multi-animal scenarios. Furthermore, we integrate the ability to predict an animal’s identity to assist tracking (in case of occlusions). We illustrate the power of this framework with four datasets varying in complexity, which we release to serve as a benchmark for future algorithm development.
Urban growth modelling and social vulnerability assessment for a hazardous Kathmandu Valley
Authors: Mesta Carlos , Cremen Gemma , Galasso Carmine 
Published: April 2022

AbstractIn our rapidly urbanizing world, many hazard-prone regions face significant challenges regarding risk-informed urban development. This study addresses this issue by investigating evolving spatial interactions between natural hazards, ever-increasing urban areas, and social vulnerability in Kathmandu Valley, Nepal. The methodology considers: (1) the characterization of flood hazard and liquefaction susceptibility using pre-existing global models; (2) the simulation of future urban built-up areas using the cellular-automata SLEUTH model; and (3) the assessment of social vulnerability, using a composite index tailored for the case-study area. Results show that built-up areas in Kathmandu Valley will increase to 352 km2by 2050, effectively doubling the equivalent 2018 figure. The most socially vulnerable villages will account for 29% of built-up areas in 2050, 11% more than current levels. Built-up areas in the 100-year and 1000-year return period floodplains will respectively increase from 38 km2and 49 km2today to 83 km2and 108 km2in 2050. Additionally, built-up areas in liquefaction-susceptible zones will expand by 13 km2to 47 km2. This study illustrates how, where, and to which extent risks from natural hazards can evolve in socially vulnerable regions. Ultimately, it emphasizes an urgent need to implement effective policy measures for reducing tomorrow's natural-hazard risks.
Experimental evolution of active Brownian grains driven by quantum effects in superfluid helium
Authors: Petrov Oleg F. , Boltnev Roman E. , Vasiliev Mikhail M. 
Published: April 2022

AbstractComplex structures, consisting of a large number of interacting subsystems, have the ability to self-organize and evolve, when the scattering of energy coming from the outside ensures the maintenance of stationary ordered structures with an entropy less than the equilibrium entropy. One of the fundamental problems here is the role of quantum phenomena in the evolution of macroscopic objects. We provide experimental evidence for the active Brownian motion and evolution of structures driven by quantum effects for micron-sized grains levitating in superfluid helium. The active Brownian motion of grains was induced by quantum turbulence during the absorption of laser irradiation by grains. The intensity of Brownian motion associated with quantum vortices increased by 6–7 orders of magnitude compared to the values from the Einstein formula. We observed the grain structures in a state far from thermodynamic equilibrium and their evolution to more complex organized structures with lower entropy due to the quantum mechanism of exceedingly high entropy loss in superfluid helium.
Systemic bis-phosphinic acid derivative restores chloride transport in Cystic Fibrosis mice
Authors: da Cunha Mélanie Faria , Pranke Iwona , Sassi Ali , Schreiweis Christiane , Moriceau Stéphanie , Vidovic Dragana , Hatton Aurélie , Carlon Mariane Sylvia , Creste Geordie , Berhal Farouk , Prestat Guillaume , Freund Romain , Odolczyk Norbert , Jais Jean Philippe , Gravier-Pelletier Christine , Zielenkiewicz Piotr , Jullien Vincent , Hinzpeter Alexandre , Oury Franck , Edelman Aleksander , Sermet-Gaudelus Isabelle 
Published: April 2022

AbstractMutations in the Cystic Fibrosis Transmembrane Conductance Regulator gene (CFTR) are responsible for Cystic Fibrosis (CF). The most common CF-causing mutation is the deletion of the 508th amino-acid of CFTR (F508del), leading to dysregulation of the epithelial fluid transport in the airway’s epithelium and the production of a thickened mucus favoring chronic bacterial colonization, sustained inflammation and ultimately respiratory failure. c407 is a bis-phosphinic acid derivative which corrects CFTR dysfunction in epithelial cells carrying the F508del mutation. This study aimed to investigate c407 in vivo activity in the F508del Cftrtm1Eur murine model of CF. Using nasal potential difference measurement, we showed that in vivo administration of c407 by topical, short-term intraperitoneal and long-term subcutaneous route significantly increased the CFTR dependent chloride (Cl−) conductance in F508del Cftrtm1Eur mice. This functional improvement was correlated with a relocalization of F508del-cftr to the apical membrane in nasal epithelial cells. Importantly, c407 long-term administration was well tolerated and in vitro ADME toxicologic studies did not evidence any obvious issue. Our data provide the first in vivo preclinical evidence of c407 efficacy and absence of toxicity after systemic administration for the treatment of Cystic Fibrosis.
Stress pulmonary circulation parameters assessed by a cardiovascular magnetic resonance in patients after a heart transplant
Authors: Opatřil Lukáš , Panovsky Roman , Mojica-Pisciotti Mary , Máchal Jan , Krejčí Jan , Holeček Tomáš , Masárová Lucia , Feitová Věra , Godava Július , Kincl Vladimír , Kepák Tomáš , Závodná Gabriela , Špinarová Lenka 
Published: April 2022

AbstractRest pulmonary circulation parameters such as pulmonary transit time (PTT), heart rate corrected PTT (PTTc) and pulmonary transit beats (PTB) can be evaluated using several methods, including the first-pass perfusion from cardiovascular magnetic resonance. As previously published, up to 58% of patients after HTx have diastolic dysfunction detectable only in stress conditions. By using adenosine stress perfusion images, stress analogues of the mentioned parameters can be assessed. By dividing stress to rest biomarkers, potential new ratio parameters (PTT ratio and PTTc ratio) can be obtained. The objectives were to (1) provide more evidence about stress pulmonary circulation biomarkers, (2) present stress to rest ratio parameters, and (3) assess these biomarkers in patients with presumed diastolic dysfunction after heart transplant (HTx) and in childhood cancer survivors (CCS) without any signs of diastolic dysfunction. In this retrospective study, 48 patients after HTx, divided into subgroups based on echocardiographic signs of diastolic dysfunction (41 without, 7 with) and 39 CCS were enrolled. PTT was defined as the difference between the onset time of the signal intensity increase in the left and the right ventricle. PTT in rest conditions were without significant differences when comparing the CCS and HTx subgroup without diastolic dysfunction (4.96 ± 0.93 s vs. 5.51 ± 1.14 s, p = 0.063) or with diastolic dysfunction (4.96 ± 0.93 s vs. 6.04 ± 1.13 s, p = 0.13). However, in stress conditions, both PTT and PTTc were significantly lower in the CCS group than in the HTx subgroups, (PTT: 3.76 ± 0.78 s vs. 4.82 ± 1.03 s, p < 0.001; 5.52 ± 1.56 s, p = 0.002). PTT ratio and PTTc ratio were below 1 in all groups. In conclusion, stress pulmonary circulation parameters obtained from CMR showed prolonged PTT and PTTc in HTx groups compared to CCS, which corresponds with the presumption of underlying diastolic dysfunction. The ratio parameters were less than 1.
Laminin matrix regulates beta-cell FGFR5 expression to enhance glucose-stimulated metabolism
Authors: Pal Vidhant , Wang Yufeng , Regeenes Romario , Kilkenny Dawn M. , Rocheleau Jonathan V. 
Published: April 2022

AbstractWe previously showed that pancreatic beta-cells plated on laminin matrix express reduced levels of FGFR1, a receptor linked to beta-cell metabolism and differentiation. Due to recent evidence that adult beta-cells also express FGFR5, a co-receptor for FGFR1, we now aim to determine the effect of laminin on FGFR5 expression and consequent effects on beta-cell metabolism. Using a genetically encoded sensor for NADPH/NADP+ redox state (Apollo-NADP+), we show overexpression of FGFR5 enhances glucose-stimulated NADPH metabolism in beta-cell lines as well as mouse and human beta-cells. This enhanced response was accompanied by increased insulin secretion as well as increased expression of transcripts for glycolytic enzymes (Glucokinase/GCK, PKM2) and the functional maturity marker Urocortin 3 (UCN3). Culturing beta-cells on laminin matrix also stimulated upregulation of endogenous FGFR5 expression, and similarly enhanced beta-cell glucose-stimulated NADPH-metabolism as well as GCK and PKM2 transcript expression. The metabolism and transcript responses triggered by laminin were disrupted by R5ΔC, a truncated receptor isoform that inhibits the FGFR5/FGFR1 signaling complex. Collectively these data reveal that beta-cells respond to laminin by increasing FGFR5 expression to enhance beta-cell glucose metabolism.
Behavioural and neural indices of perceptual decision-making in autistic children during visual motion tasks
Authors: Manning Catherine , Hassall Cameron D. , Hunt Laurence T. , Norcia Anthony M. , Wagenmakers Eric-Jan , Evans Nathan J. , Scerif Gaia 
Published: April 2022

AbstractMany studies report atypical responses to sensory information in autistic individuals, yet it is not clear which stages of processing are affected, with little consideration given to decision-making processes. We combined diffusion modelling with high-density EEG to identify which processing stages differ between 50 autistic and 50 typically developing children aged 6–14 years during two visual motion tasks. Our pre-registered hypotheses were that autistic children would show task-dependent differences in sensory evidence accumulation, alongside a more cautious decision-making style and longer non-decision time across tasks. We tested these hypotheses using hierarchical Bayesian diffusion models with a rigorous blind modelling approach, finding no conclusive evidence for our hypotheses. Using a data-driven method, we identified a response-locked centro-parietal component previously linked to the decision-making process. The build-up in this component did not consistently relate to evidence accumulation in autistic children. This suggests that the relationship between the EEG measure and diffusion-modelling is not straightforward in autistic children. Compared to a related study of children with dyslexia, motion processing differences appear less pronounced in autistic children. Exploratory analyses also suggest weak evidence that ADHD symptoms moderate perceptual decision-making in autistic children.
The Polyscore of autonomic parameters predicts mortality and identifies low-risk individuals among diabetic survivors of acute myocardial infarction
Authors: Steger Alexander , Dommasch Michael , Müller Alexander , Barthel Petra , Sinnecker Daniel , Wieg Larissa , Hapfelmeier Alexander , Heidegger Helene Hildegard , Huster Katharina Maria , Martens Eimo , Laugwitz Karl-Ludwig , Schmidt Georg , Dirschinger Ralf 
Published: April 2022

AbstractSurvivors of an acute myocardial infarction with diabetes mellitus retain an increased mortality risk. Reliable assessment of individual risk is required for effective and cost-efficient medical care in these patients. The Polyscore is a previously established risk predictor consisting of seven autonomic tests derived from electrocardiogram, blood pressure, and respiration. The Polyscore allows classification of survivors of myocardial infarction in groups at low, intermediate and high mortality risk. The aim of this study was to investigate the prognostic value of the Polyscore in diabetic survivors of acute myocardial infarction, which may be impaired by the presence of diabetic autonomic neuropathy. Survivors of an acute myocardial infarction were included in a prospective cohort study during hospitalisation due to the index event at two university hospitals in Munich, Germany. The Polyscore was determined from simultaneous non-invasive 30-min recordings of electrocardiogram, continuous arterial blood pressure, and respiration which were performed in all participants. Patients were followed for 5 years. The primary and secondary outcomes were all-cause mortality and cardiac mortality. 184 of 941 enrolled patients (19.6%) suffered from diabetes mellitus. 5-year-mortality was higher in diabetic patients (15.2%) compared to non-diabetic patients (5.8%). A multivariable Cox regression model confirmed the Polyscore as a strong predictor of mortality in diabetic post-MI patients (intermediate risk: HR 6.56, 95% CI 1.61–26.78, p = 0.004, mortality 22.8%; high risk: HR 18.76, 95% CI 4.35–80.98, p < 0.001, mortality 68.8%). There was no interaction between diabetes mellitus and the Polyscore regarding mortality prediction (p = 0.775). Interestingly, in contrast to the groups at intermediate and high risk (73 patients, 39.7%), the Polyscore identified a majority of diabetic patients (111, 60.3%) with a low mortality risk, comparable to that of low-risk non-diabetic patients (3.6% and 2.1%, respectively, p = 0.339). Consistent results were observed for cardiac mortality. This analysis shows that the Polyscore predicts all-cause and cardiac mortality in diabetic survivors of acute myocardial infarction. Within these patients it identifies a large population not affected by the excess mortality associated with diabetes in this setting. Thus, the Polyscore may facilitate risk-adapted follow-up strategies in diabetic survivors of myocardial infarction.
Substrate effect on hydrogen evolution reaction in two-dimensional Mo2C monolayers
Authors: Lee Sujin , Min Byungjoon , Bang Junhyeok 
Published: April 2022

AbstractThe physical and chemical properties of atomically thin two-dimensional (2D) materials can be modified by the substrates. In this study, the substrate effect on the electrocatalytic hydrogen evolution reaction (HER) in 2D Mo2C monolayers was investigated using first principles calculations. The isolated Mo2C monolayer shows large variation in HER activity depending on hydrogen coverage: it has relatively low activity at low hydrogen coverage but high activity at high hydrogen coverage. Among Ag, Au, Cu, and graphene substrates, the HER activity is improved on the Ag and Cu substrates especially at low hydrogen coverage, while the effects of the Au and graphene substrates on the HER activity are insignificant. The improvement is caused by the charge redistribution in the Mo2C layer on the substrate, and therefore the HER activity becomes high for any hydrogen coverage on the Ag and Cu substrates. Our results suggest that, in two-dimensional electrocatalysis, the substrate has a degree of freedom to tune the catalytic activity.
Mapping riparian zone macro litter abundance using combination of optical and thermal sensor
Authors: Ramdani Fatwa , Sianturi Riswan Septriayadi , Furqon Muhammad Tanzil , Ananta Mahardeka Tri 
Published: April 2022

AbstractA significant increase in the world's population will lead to an increase in consumption and, therefore, an increase in global waste. Various attempts have been made to monitor and map waste, but the proposed approaches are difficult and complicated, and they incur high costs. In this study, to overcome limitations in monitoring and mapping plastic waste, using combined optical and thermal sensors installed on drones is proposed. The study area is the riparian zone, or the zone around the river, where the accumulation of plastic waste at the mouth of the river eventually reaches the sea. The image data obtained were processed using machine learning methods to produce high accuracy and precision. To determine the effectiveness of the proposed method, an accuracy assessment was conducted. The results of this study indicate that the combination of optical and thermal sensors provides the best accuracy compared to using only single optical or thermal image data.