bluuebunny/crossref_metadata_2025_split huggingface dataset:
Context-dependent limb movement encoding in neuronal populations of motor cortex
Authors: Omlor Wolfgang , Wahl Anna-Sophia , Sipilä Pia , Lütcke Henry , Laurenczy Balazs , Chen I-Wen , Sumanovski Lazar T. , van ’t Hoff Marcel , Bethge Philipp , Voigt Fabian F. , Schwab Martin E. , Helmchen Fritjof 
Published: October 2019

AbstractNeuronal networks of the mammalian motor cortex (M1) are important for dexterous control of limb joints. Yet it remains unclear how encoding of joint movement in M1 depends on varying environmental contexts. Using calcium imaging we measured neuronal activity in layer 2/3 of the M1 forelimb region while mice grasped regularly or irregularly spaced ladder rungs during locomotion. We found that population coding of forelimb joint movements is sparse and varies according to the flexibility demanded from individual joints in the regular and irregular context, even for equivalent grasping actions across conditions. This context-dependence of M1 encoding emerged during task learning, fostering higher precision of grasping actions, but broke apart upon silencing of projections from secondary motor cortex (M2). These findings suggest that M1 exploits information from M2 to adapt encoding of joint movements to the flexibility demands of distinct familiar contexts, thereby increasing the accuracy of motor output.
The global diversity of Haemonchus contortus is shaped by human intervention and climate
Authors: Sallé G. , Doyle S. R. , Cortet J. , Cabaret J. , Berriman M. , Holroyd N. , Cotton J. A. 
Published: October 2019

AbstractHaemonchus contortus is a haematophagous parasitic nematode of veterinary interest. We have performed a survey of its genome-wide diversity using single-worm whole genome sequencing of 223 individuals sampled from 19 isolates spanning five continents. We find an African origin for the species, together with evidence for parasites spreading during the transatlantic slave trade and colonisation of Australia. Strong selective sweeps surrounding the β-tubulin locus, a target of benzimidazole anthelmintic drug, are identified in independent populations. These sweeps are further supported by signals of diversifying selection enriched in genes involved in response to drugs and other anthelmintic-associated biological functions. We also identify some candidate genes that may play a role in ivermectin resistance. Finally, genetic signatures of climate-driven adaptation are described, revealing a gene acting as an epigenetic regulator and components of the dauer pathway. These results begin to define genetic adaptation to climate in a parasitic nematode.
Nanoscale deformation mechanics reveal resilience in nacre of Pinna nobilis shell
Authors: Gim Jiseok , Schnitzer Noah , Otter Laura M. , Cui Yuchi , Motreuil Sébastien , Marin Frédéric , Wolf Stephan E. , Jacob Dorrit E. , Misra Amit , Hovden Robert 
Published: October 2019

AbstractThe combination of soft nanoscale organic components with inorganic nanograins hierarchically designed by natural organisms results in highly ductile structural materials that can withstand mechanical impact and exhibit high resilience on the macro- and nano-scale. Our investigation of nacre deformation reveals the underlying nanomechanics that govern the structural resilience and absorption of mechanical energy. Using high-resolution scanning/transmission electron microscopy (S/TEM) combined with in situ indentation, we observe nanoscale recovery of heavily deformed nacre that restores its mechanical strength on external stimuli up to 80% of its yield strength. Under compression, nacre undergoes deformation of nanograins and non-destructive locking across organic interfaces such that adjacent inorganic tablets structurally join. The locked tablets respond to strain as a continuous material, yet the organic boundaries between them still restrict crack propagation. Remarkably, the completely locked interface recovers its original morphology without any noticeable deformation after compressive contact stresses as large as 1.2 GPa.
Sub-nanomolar sensitive GZnP3 reveals TRPML1-mediated neuronal Zn2+ signals
Authors: Minckley Taylor F. , Zhang Chen , Fudge Dylan H. , Dischler Anna M. , LeJeune Kate D. , Xu Haoxing , Qin Yan 
Published: October 2019

AbstractAlthough numerous fluorescent Zn2+ sensors have been reported, it is unclear whether and how Zn2+ can be released from the intracellular compartments into the cytosol due to a lack of probes that can detect physiological dynamics of cytosolic Zn2+. Here, we create a genetically encoded sensor, GZnP3, which demonstrates unprecedented sensitivity for Zn2+ at sub-nanomolar concentrations. Using GZnP3 as well as GZnP3-derived vesicular targeted probes, we provide the first direct evidence that Zn2+ can be released from endolysosomal vesicles to the cytosol in primary hippocampal neurons through the TRPML1 channel. Such TRPML1-mediated Zn2+ signals are distinct from Ca2+ in that they are selectively present in neurons, sustain longer, and are significantly higher in neurites as compared to the soma. Together, our work not only creates highly sensitive probes for investigating sub-nanomolar Zn2+ dynamics, but also reveals new pools of Zn2+ signals that can play critical roles in neuronal function.
Large scale and integrated platform for digital mass culture of anchorage dependent cells
Authors: Cho Kyoung Won , Kim Seok Joo , Kim Jaemin , Song Seuk Young , Lee Wang Hee , Wang Liu , Soh Min , Lu Nanshu , Hyeon Taeghwan , Kim Byung-Soo , Kim Dae-Hyeong 
Published: October 2019

AbstractIndustrial applications of anchorage-dependent cells require large-scale cell culture with multifunctional monitoring of culture conditions and control of cell behaviour. Here, we introduce a large-scale, integrated, and smart cell-culture platform (LISCCP) that facilitates digital mass culture of anchorage-dependent cells. LISCCP is devised through large-scale integration of ultrathin sensors and stimulator arrays in multiple layers. LISCCP provides real-time, 3D, and multimodal monitoring and localized control of the cultured cells, which thereby allows minimizing operation labour and maximizing cell culture performance. Wireless integration of multiple LISCCPs across multiple incubators further amplifies the culture scale and enables digital monitoring and local control of numerous culture layers, making the large-scale culture more efficient. Thus, LISCCP can transform conventional labour-intensive and high-cost cell cultures into efficient digital mass cell cultures. This platform could be useful for industrial applications of cell cultures such as in vitro toxicity testing of drugs and cosmetics and clinical scale production of cells for cell therapy.
Extracellular pyridine nucleotides trigger plant systemic immunity through a lectin receptor kinase/BAK1 complex
Authors: Wang Chenggang , Huang Xiaoen , Li Qi , Zhang Yanping , Li Jian-Liang , Mou Zhonglin 
Published: October 2019

AbstractSystemic acquired resistance (SAR) is a long-lasting broad-spectrum plant immunity induced by mobile signals produced in the local leaves where the initial infection occurs. Although multiple structurally unrelated signals have been proposed, the mechanisms responsible for perception of these signals in the systemic leaves are unknown. Here, we show that exogenously applied nicotinamide adenine dinucleotide (NAD+) moves systemically and induces systemic immunity. We demonstrate that the lectin receptor kinase (LecRK), LecRK-VI.2, is a potential receptor for extracellular NAD+(eNAD+) and NAD+phosphate (eNADP+) and plays a central role in biological induction of SAR. LecRK-VI.2 constitutively associates with BRASSINOSTEROID INSENSITIVE1-ASSOCIATED KINASE1 (BAK1) in vivo. Furthermore, BAK1 and its homolog BAK1-LIKE1 are required for eNAD(P)+signaling and SAR, and the kinase activities of LecR-VI.2 and BAK1 are indispensable to their function in SAR. Our results indicate that eNAD+is a putative mobile signal, which triggers SAR through its receptor complex LecRK-VI.2/BAK1 inArabidopsis thaliana.
Oncolytic adenovirus programmed by synthetic gene circuit for cancer immunotherapy
Authors: Huang Huiya , Liu Yiqi , Liao Weixi , Cao Yubing , Liu Qiang , Guo Yakun , Lu Yinying , Xie Zhen 
Published: October 2019

AbstractImproving efficacy of oncolytic virotherapy remains challenging due to difficulty increasing specificity and immune responses against cancer and limited understanding of its population dynamics. Here, we construct programmable and modular synthetic gene circuits to control adenoviral replication and release of immune effectors selectively in hepatocellular carcinoma cells in response to multiple promoter and microRNA inputs. By performing mouse model experiments and computational simulations, we find that replicable adenovirus has a superior tumor-killing efficacy than non-replicable adenovirus. We observe a synergistic effect on promoting local lymphocyte cytotoxicity and systematic vaccination in immunocompetent mouse models by combining tumor lysis and secretion of immunomodulators. Furthermore, our computational simulations show that oncolytic virus which encodes immunomodulators can exert a more robust therapeutic efficacy than combinatorial treatment with oncolytic virus and immune effector. Our results provide an effective strategy to engineer oncolytic adenovirus, which may lead to innovative immunotherapies for a variety of cancers.
Self-sensing, tunable monolayer MoS2 nanoelectromechanical resonators
Authors: Manzeli Sajedeh , Dumcenco Dumitru , Migliato Marega Guilherme , Kis Andras 
Published: October 2019

AbstractExcellent mechanical properties and the presence of piezoresistivity make single layers of transition metal dichalcogenides (TMDCs) viable candidates for integration in nanoelectromechanical systems (NEMS). We report on the realization of electromechanical resonators based on single-layer MoS2with both piezoresistive and capacitive transduction schemes. Operating in the ultimate limit of membrane thickness, the resonant frequency of MoS2resonators is primarily defined by the built-in mechanical tension and is in the very high frequency range. Using electrostatic interaction with a gate electrode, we tune the resonant frequency, allowing for the extraction of resonator parameters such as mass density and built-in strain. Furthermore, we study the origins of nonlinear dynamic response at high driving force. The results shed light on the potential of TMDC-based NEMS for the investigation of nanoscale mechanical effects at the limits of vertical downscaling and applications such as resonators for RF-communications, force and mass sensors.
Deciphering nanoconfinement effects on molecular orientation and reaction intermediate by single molecule imaging
Authors: Dong Bin , Pei Yuchen , Mansour Nourhan , Lu Xuemei , Yang Kai , Huang Wenyu , Fang Ning 
Published: October 2019

AbstractNanoconfinement could dramatically change molecular transport and reaction kinetics in heterogeneous catalysis. Here we specifically design a core-shell nanocatalyst with aligned linear nanopores for single-molecule studies of the nanoconfinement effects. The quantitative single-molecule measurements reveal unusual lower adsorption strength and higher catalytic activity on the confined metal reaction centres within the nanoporous structure. More surprisingly, the nanoconfinement effects on enhanced catalytic activity are larger for catalysts with longer and narrower nanopores. Experimental evidences, including molecular orientation, activation energy, and intermediate reactive species, have been gathered to provide a molecular level explanation on how the nanoconfinement effects enhance the catalyst activity, which is essential for the rational design of highly-efficient catalysts.
Hierarchical organization of urban mobility and its connection with city livability
Authors: Bassolas Aleix , Barbosa-Filho Hugo , Dickinson Brian , Dotiwalla Xerxes , Eastham Paul , Gallotti Riccardo , Ghoshal Gourab , Gipson Bryant , Hazarie Surendra A. , Kautz Henry , Kucuktunc Onur , Lieber Allison , Sadilek Adam , Ramasco José J. 
Published: October 2019

AbstractThe recent trend of rapid urbanization makes it imperative to understand urban characteristics such as infrastructure, population distribution, jobs, and services that play a key role in urban livability and sustainability. A healthy debate exists on what constitutes optimal structure regarding livability in cities, interpolating, for instance, between mono- and poly-centric organization. Here anonymous and aggregated flows generated from three hundred million users, opted-in to Location History, are used to extract global Intra-urban trips. We develop a metric that allows us to classify cities and to establish a connection between mobility organization and key urban indicators. We demonstrate that cities with strong hierarchical mobility structure display an extensive use of public transport, higher levels of walkability, lower pollutant emissions per capita and better health indicators. Our framework outperforms previous metrics, is highly scalable and can be deployed with little cost, even in areas without resources for traditional data collection.
Vastly extended drug release from poly(pro-17β-estradiol) materials facilitates in vitro neurotrophism and neuroprotection
Authors: D’Amato Anthony R. , Puhl Devan L. , Ellman Samuel A. T. , Balouch Bailey , Gilbert Ryan J. , Palermo Edmund F. 
Published: October 2019

AbstractCentral nervous system (CNS) injuries persist for years, and currently there are no therapeutics that can address the complex injury cascade that develops over this time-scale. 17β-estradiol (E2) has broad tropism within the CNS, targeting and inducing beneficial phenotypic changes in myriad cells following injury. To address the unmet need for vastly prolonged E2 release, we report first-generation poly(pro-E2) biomaterial scaffolds that release E2 at nanomolar concentrations over the course of 1–10 years via slow hydrolysis in vitro. As a result of their finely tuned properties, these scaffolds demonstrate the ability to promote and guide neurite extension ex vivo and protect neurons from oxidative stress in vitro. The design and testing of these materials reported herein demonstrate the first step towards next-generation implantable biomaterials with prolonged release and excellent regenerative potential.
A database for using machine learning and data mining techniques for coronary artery disease diagnosis
Authors: Alizadehsani R. , Roshanzamir M. , Abdar M. , Beykikhoshk A. , Khosravi A. , Panahiazar M. , Koohestani A. , Khozeimeh F. , Nahavandi S. , Sarrafzadegan N. 
Published: October 2019

AbstractWe present the coronary artery disease (CAD) database, a comprehensive resource, comprising 126 papers and 68 datasets relevant to CAD diagnosis, extracted from the scientific literature from 1992 and 2018. These data were collected to help advance research on CAD-related machine learning and data mining algorithms, and hopefully to ultimately advance clinical diagnosis and early treatment. To aid users, we have also built a web application that presents the database through various reports.
Chromosome-level genome assembly of golden pompano (Trachinotus ovatus) in the family Carangidae
Authors: Zhang Dian-Chang , Guo Liang , Guo Hua-Yang , Zhu Ke-Cheng , Li Shang-Qi , Zhang Yan , Zhang Nan , Liu Bao-Suo , Jiang Shi-Gui , Li Jiong-Tang 
Published: October 2019

AbstractGolden pompano (Trachinotus ovatus), a marine fish in the Carangidae family, has a wide geographical distribution and adapts to severe environmental rigours. It is also an economically valuable aquaculture fish. To understand the genetic mechanism of adaption to environmental rigours and improve the production in aquaculture, we assembled its genome. By combination of Illumina and Pacbio reads, the obtained genome sequence is 647.5 Mb with the contig N50 of 1.80 Mb and the scaffold N50 of 5.05 Mb. The assembly covers 98.9% of the estimated genome size (655 Mb). Based on Hi-C data, 99.4% of the assembled bases are anchored into 24 pseudo-chromosomes. The annotation includes 21,915 protein-coding genes, in which 95.7% of 2,586 BUSCO vertebrate conserved genes are complete. This genome is expected to contribute to the comparative analysis of the Carangidae family.
Multiple-data-based monthly geopotential model set LDCmgm90
Authors: Chen Wei , Luo Jiesi , Ray Jim , Yu Nan , Li Jian Cheng 
Published: October 2019

AbstractWhile the GRACE (Gravity Recovery and Climate Experiment) satellite mission is of great significance in understanding various branches of Earth sciences, the quality of GRACE monthly products can be unsatisfactory due to strong longitudinal stripe-pattern errors and other flaws. Based on corrected GRACE Mascon (mass concentration) gridded mass transport time series and updated LDCgam (Least Difference Combination global angular momenta) data, we present a new set of monthly gravity models called LDCmgm90, in the form of Stokes coefficients with order and degree both up to 90. The LDCgam inputs are developed by assimilating degree-2 Stokes coefficients from various versions of GRACE (including Mascon products) and SLR (Satellite Laser Ranging) monthly gravity data into combinations of outputs from various global atmospheric, oceanic, and hydrological circulation models, under the constraints of accurately measured Earth orientation parameters in the Least Difference Combination (LDC) scheme. Taking advantages of the relative strengths of the various input solutions, the LDCmgm90 is free of stripes and some other flaws of classical GRACE products.
Distributed radiomics as a signature validation study using the Personal Health Train infrastructure
Authors: Shi Zhenwei , Zhovannik Ivan , Traverso Alberto , Dankers Frank J. W. M. , Deist Timo M. , Kalendralis Petros , Monshouwer René , Bussink Johan , Fijten Rianne , Aerts Hugo J. W. L. , Dekker Andre , Wee Leonard 
Published: October 2019

AbstractPrediction modelling with radiomics is a rapidly developing research topic that requires access to vast amounts of imaging data. Methods that work on decentralized data are urgently needed, because of concerns about patient privacy. Previously published computed tomography medical image sets with gross tumour volume (GTV) outlines for non-small cell lung cancer have been updated with extended follow-up. In a previous study, these were referred to as Lung1 (n = 421) and Lung2 (n = 221). The Lung1 dataset is made publicly accessible via The Cancer Imaging Archive (TCIA; https://www.cancerimagingarchive.net). We performed a decentralized multi-centre study to develop a radiomic signature (hereafter “ZS2019”) in one institution and validated the performance in an independent institution, without the need for data exchange and compared this to an analysis where all data was centralized. The performance of ZS2019 for 2-year overall survival validated in distributed radiomics was not statistically different from the centralized validation (AUC 0.61 vs 0.61; p = 0.52). Although slightly different in terms of data and methods, no statistically significant difference in performance was observed between the new signature and previous work (c-index 0.58 vs 0.65; p = 0.37). Our objective was not the development of a new signature with the best performance, but to suggest an approach for distributed radiomics. Therefore, we used a similar method as an earlier study. We foresee that the Lung1 dataset can be further re-used for testing radiomic models and investigating feature reproducibility.
Dynamics of beneficial epidemics
Authors: Berdahl Andrew , Brelsford Christa , Bacco Caterina De , Dumas Marion , Ferdinand Vanessa , Grochow Joshua A. , Hébert-Dufresne Laurent , Kallus Yoav , Kempes Christopher P. , Kolchinsky Artemy , Larremore Daniel B. , Libby Eric , Power Eleanor A. , Stern Caitlin A. , Tracey Brendan D. 
Published: October 2019

AbstractPathogens can spread epidemically through populations. Beneficial contagions, such as viruses that enhance host survival or technological innovations that improve quality of life, also have the potential to spread epidemically. How do the dynamics of beneficial biological and social epidemics differ from those of detrimental epidemics? We investigate this question using a breadth-first modeling approach involving three distinct theoretical models. First, in the context of population genetics, we show that a horizontally-transmissible element that increases fitness, such as viral DNA, spreads superexponentially through a population, more quickly than a beneficial mutation. Second, in the context of behavioral epidemiology, we show that infections that cause increased connectivity lead to superexponential fixation in the population. Third, in the context of dynamic social networks, we find that preferences for increased global infection accelerate spread and produce superexponential fixation, but preferences for local assortativity halt epidemics by disconnecting the infected from the susceptible. We conclude that the dynamics of beneficial biological and social epidemics are characterized by the rapid spread of beneficial elements, which is facilitated in biological systems by horizontal transmission and in social systems by active spreading behavior of infected individuals.
Electronic structure of MAPbI3 and MAPbCl3: importance of band alignment
Authors: Caputo Marco , Cefarin Nicola , Radivo Andrea , Demitri Nicola , Gigli Lara , Plaisier Jasper R. , Panighel Mirco , Di Santo Giovanni , Moretti Sacha , Giglia Angelo , Polentarutti Maurizio , De Angelis Filippo , Mosconi Edoardo , Umari Paolo , Tormen Massimo , Goldoni Andrea 
Published: October 2019

AbstractSince their first appearance, organic-inorganic perovskite absorbers have been capturing the attention of the scientific community. While high efficiency devices highlight the importance of band level alignment, very little is known on the origin of the strong n-doping character observed in the perovskite. Here, by means of a highly accurate photoemission study, we shed light on the energy alignment in perovskite-based devices. Our results suggest that the interaction with the substrate may be the driver for the observed doping in the perovskite samples.
Modeling cancer drug response through drug-specific informative genes
Authors: Parca Luca , Pepe Gerardo , Pietrosanto Marco , Galvan Giulio , Galli Leonardo , Palmeri Antonio , Sciandrone Marco , Ferrè Fabrizio , Ausiello Gabriele , Helmer-Citterich Manuela 
Published: October 2019

AbstractRecent advances in pharmacogenomics have generated a wealth of data of different types whose analysis have helped in the identification of signatures of different cellular sensitivity/resistance responses to hundreds of chemical compounds. Among the different data types, gene expression has proven to be the more successful for the inference of drug response in cancer cell lines. Although effective, the whole transcriptome can introduce noise in the predictive models, since specific mechanisms are required for different drugs and these realistically involve only part of the proteins encoded in the genome. We analyzed the pharmacogenomics data of 961 cell lines tested with 265 anti-cancer drugs and developed different machine learning approaches for dissecting the genome systematically and predict drug responses using both drug-unspecific and drug-specific genes. These methodologies reach better response predictions for the vast majority of the screened drugs using tens to few hundreds genes specific to each drug instead of the whole genome, thus allowing a better understanding and interpretation of drug-specific response mechanisms which are not necessarily restricted to the drug known targets.