bluuebunny/crossref_metadata_2025_split huggingface dataset:
Planning Face, Hand, and Leg Movements: Anatomical Constraints on Preparatory Inhibition
Authors: Labruna Ludovica , Tischler Claudia , Cazares Cristian , Greenhouse Ian , Duque Julie , Lebon Florent , Ivry Richard B. 
Published: January 2019

AbstractMotor-evoked potentials (MEPs), elicited by Transcranial Magnetic Stimulation (TMS) over the motor cortex, are reduced during the preparatory period in delayed response tasks. Here we examine how MEP suppression varies as a function of the anatomical organization of the motor cortex. MEPs were recorded from a left index muscle while participants prepared a hand or leg movement in Experiment 1, or prepared an eye or mouth movement in Experiment 2. In this manner, we assessed if the level of MEP suppression in a hand muscle varied as a function of the anatomical distance between the agonist for the forthcoming movement and the muscle targeted by TMS. MEPs suppression was attenuated when the cued effector was anatomically distant from the hand (e.g., leg or facial movement compared to finger movement). A similar effect was observed in Experiment 3 in which MEPs were recorded from a muscle in the leg and the forthcoming movement involved the upper limb or face. These results demonstrate an important constraint on preparatory inhibition: It is sufficiently broad to be manifest in a muscle that is not involved in the task, but is not global, showing a marked attenuation when the agonist muscle belongs to a different segment of the body.New & NoteworthyUsing TMS, we examine changes in corticospinal excitability as people prepare to move. Consistent with previous work, we observe a reduction in excitability during the preparatory period, an effect observed in both task relevant and task irrelevant muscles. However, this preparatory inhibition is anatomically constrained, attenuated in muscles belonging to a different body segment than the agonist of the forthcoming movement.
Spatial sorting enables comprehensive characterization of liver zonation
Authors: Ben-Moshe Shani , Shapira Yonatan , Moor Andreas E. , Halpern Keren Bahar , Itzkovitz Shalev 
Published: January 2019

AbstractThe mammalian liver is composed of repeating hexagonal units termed lobules. Spatially-resolved single-cell transcriptomics revealed that about half of hepatocyte genes are differentially expressed across the lobule. Technical limitations impede reconstructing similar global spatial maps of other hepatocyte features. Here, we used zonated surface markers to sort hepatocytes from defined lobule zones with high spatial resolution. We applied transcriptomics, microRNA array measurements and Mass-spectrometry proteomics to reconstruct spatial atlases of multiple zonated hepatocyte features. We found that protein zonation largely overlapped mRNA zonation. We identified zonation of key microRNAs such as miR-122, and inverse zonation of microRNAs and their hepatocyte gene targets, implying potential regulation through zonated mRNA degradation. These targets included the pericentral Wnt receptors Fzd7 and Fzd8 and the periportal Wnt inhibitors Tcf7l1 and Ctnnbip1. Our approach facilitates reconstruction of spatial atlases of multiple cellular features in the liver and in other structured tissues.
Genomic analysis of the four ecologically distinct cactus host populations ofDrosophila mojavensis
Authors: Allan Carson W. , Matzkin Luciano M. 
Published: January 2019

AbstractBackgroundRelationships between an organism and its environment can be fundamental in the understanding how populations change over time and species arise. Local ecological conditions can shape variation at multiple levels, among these are the evolutionary history and trajectories of coding genes. This study examines the rate of molecular evolution at protein-coding genes throughout the genome in response to host adaptation in the cactophilicDrosophila mojavensis. These insects are intimately associated with cactus necroses, developing as larvae and feeding as adults in these necrotic tissues.Drosophila mojavensisis composed of four isolated populations across the deserts of western North America and each population has adapted to utilize different cacti that are chemically, nutritionally, and structurally distinct.ResultsHigh coverage Illumina sequencing was performed on three previously unsequenced populations ofD. mojavensis. Genomes were assembled using the previously sequenced genome ofD. mojavensisfrom Santa Catalina Island (USA) as a template. Protein coding genes were aligned across all four populations and rates of protein evolution were determined for all loci using a several approaches.ConclusionsLoci that exhibited elevated rates of molecular evolution tended to be shorter, have fewer exons, low expression, be transcriptionally responsive to cactus host use and have fixed expression differences across the four cactus host populations. Fast evolving genes were involved with metabolism, detoxification, chemosensory reception, reproduction and behavior. Results of this study gives insight into the process and the genomic consequences of local ecological adaptation.
A unified framework for inferring the multi-scale organization of chromatin domains from Hi-C
Authors: Bak Ji Hyun , Kim Min Hyeok , Liu Lei , Hyeon Changbong 
Published: January 2019

AbstractIdentifying chromatin domains (CDs) from high-throughput chromosome conformation capture (Hi-C) data is currently a central problem in genome research. Here we present a unified algorithm, Multi-CD, which infers CDs at various genomic scales by leveraging the information from Hi-C. By integrating a model of the chromosome from polymer physics, statistical physics-based clustering analysis, and Bayesian inference, Multi-CD identifies the CDs that best represent the global pattern of correlation manifested in Hi-C. The multi-scale intra-chromosomal structures compared across different cell types allow us to glean the principles of chromatin organization: (i) Sub-TADs, TADs, and meta-TADs constitute a robust hierarchical structure. (ii) The assemblies of compartments and TAD-based domains are governed by different organizational principles. (iii) Sub-TADs are the common building blocks of chromosome architecture. CDs obtained from Multi-CD applied to Hi-C data enable a quantitative and comparative analysis of chromosome organization in different cell types, providing glimpses into structure-function relationship in genome.
Short-range interactions govern cellular dynamics in microbial multi-genotype systems
Authors: Co A. Dal , van Vliet S. , Kiviet D. J. , Schlegel S. , Ackermann M. 
Published: January 2019

AbstractEcosystem processes result from interaction between organisms. When interactions are local, the spatial organization of organisms defines their network of interactions, and thus influences the system’s functioning. This can be especially relevant for microbial systems, which often consist of spatially structured communities of cells connected by a dense interaction network. Here we measured the spatial interaction network between cells in microbial systems and identify the factors that determine it. Combining quantitative single-cell analysis of synthetic bacterial communities with mathematical modeling, we find that cells only interact with other cells in their immediate neighbourhood. This short interaction range impacts the functioning of the whole system by reducing its ability to perform metabolic processes collectively. Our experiments and models demonstrate that the spatial scale of cell-to-cell interaction plays a fundamental role in understanding and controlling natural communities, and in engineering microbial systems for specific purposes.Significance StatementCommunities of interacting microbes perform fundamental processes on earth. We do not understand well how these processes emerge from the interactions between individual microbial cells. Our work investigates how strongly individual cells interact and how the strength of the interaction depends on the distance between cells. The discovery that individual cells ‘live in a small world’, i.e. they only interact with a small number of cells around them, changes our understanding of how cells in natural microbial communities are metabolically coupled and how their spatial arrangement determines emergent properties at the community level. Our quantitative single-cell approach allows to address central questions on systems composed of interacting genotypes and to increase our understanding and ability to control microbial communities.
Using environmental DNA for the detection of Schistosoma mansoni: toward improved environmental surveillance of schistosomiasis
Authors: Sengupta Mita Eva , Hellström Micaela , Kariuki Henry Curtis , Olsen Annette , Thomsen Philip Francis , Mejer Helena , Willerslev Eske , Mwanje Mariam , Madsen Henry , Kristensen Thomas Krogsgaard , Stensgaard Anna-Sofie , Vennervald Birgitte Jyding 
Published: January 2019

AbstractSchistosomiasis is a waterborne, infectious disease with high morbidity and significant economic burdens affecting more than 250 million people globally. Disease control has, with notable success, for decades focused on drug treatment of infected human populations, but a recent paradigm shift now entails moving from control to elimination. To achieve this ambitious goal more sensitive diagnostic tools are needed to monitor progress towards transmission interruption in the environment, especially in low-intensity infection areas. We report on the development of an environmental DNA (eDNA) based tool to efficiently detect DNA traces of the parasite Schistosoma mansoni directly in the aquatic environment, where the non-human part of the parasite life cycle occurs. To our knowledge, this is the first report of the successful detection of S. mansoni in freshwater samples using aquatic eDNA. True eDNA was detected in as few as 10 cercariae/L water in laboratory experiments. The field applicability of the method was tested at known transmission sites in Kenya, where comparison of schistosome detection by conventional snail surveys (snail collection and cercariae shedding) with eDNA (water samples) showed 71% agreement between the methods. The eDNA method furthermore detected schistosome presence at two additional sites where snail shedding failed, demonstrating a higher sensitivity of eDNA sampling. We conclude that eDNA provides a promising new tool to significantly improve the environmental surveillance of S. mansoni. Given the proper method and guideline development, eDNA could become an essential future component of the schistosomiasis control tool box needed to achieve the goal of elimination.SignificanceAccurate detection and delineation of schistosomiasis transmission sites will be vital in on-going efforts to control and ultimately eliminate one of the most neglected tropical parasitic diseases affecting more than 250 million people worldwide. Conventional methods to detect parasites in the environment are cumbersome and have low sensitivity. We therefore developed an environmental DNA (eDNA) based method for schistosome detection in aquatic environments. Aquatic eDNA showed higher sensitivity than conventional snail surveys. We conclude that eDNA is a promising non-invasive and sensitive tool for environmental surveillance of schistosomiasis transmission. As the efforts and aims to control the disease are transitioning towards complete transmission interruption, this could be the robust and cost-effective surveillance tool needed in the “end game” of schistosomiasis.
Modelling structural constraints on protein evolution via side-chain conformational states
Authors: Perron Umberto , Kozlov Alexey M. , Stamatakis Alexandros , Goldman Nick , Moal Iain H. 
Published: January 2019

AbstractFew models of sequence evolution incorporate parameters describing protein structure, despite its high conservation, essential functional role and increasing availability. We present a structurally-aware empirical substitution model for amino acid sequence evolution in which proteins are expressed using an expanded alphabet that relays both amino acid identity and structural information. Each character specifies an amino acid as well a rotamer state: the discrete geometric pattern of permitted side-chain atomic positions. By assigning rotamer states in 251,194 protein structures and identifying 4,508,390 substitutions between closely related sequences, we generate a 55-state model that shows that the evolutionary properties of amino acids depend strongly upon side-chain geometry. The model performs as well as or better than traditional 20-state models for divergence time estimation, tree inference and ancestral state reconstruction. We conclude that the concomitant evolution of sequence and structure is a valuable source of phylogenetic information.
A nucleotide resolution map of Top2-linked DNA breaks in the yeast and human genome
Authors: Gittens William , Johnson Dominic J. , Allison Rachal M. , Cooper Tim J. , Thomas Holly , Neale Matthew J 
Published: January 2019

AbstractDNA topoisomerases are required to resolve DNA topological stress. Despite this essential role, abortive topoisomerase activity generates aberrant protein-linked DNA breaks, jeopardising genome stability. Here, to understand the genomic distribution and mechanisms underpinning topoisomerase-induced DNA breaks, we map Top2 DNA cleavage with strand-specific nucleotide resolution across theS. cerevisiaeand human genomes—and use the meiotic Spo11 protein to validate the broad applicability of this method to explore the role of diverse topoisomerase family members. Our data characterises Mre11-dependent repair in yeast, and defines two strikingly different fractions of Top2 activity in humans: tightly localised CTCF-proximal, and broadly distributed transcription-proximal, the latter correlated with gene length and expression. Moreover, single nucleotide accuracy enables us to reveal the influence primary DNA sequence has upon Top2 cleavage—distinguishing canonical DNA double-strand breaks (DSBs) from a major population of DNA single-strand breaks (SSBs) induced by etoposide (VP16)in vivo.
Estimating virulence from relative survival
Authors: Agnew Philip 
Published: January 2019

AbstractA pathogen’s virulence is a key parameter in the mathematical models on which most epidemiological theory is based. In these models virulence generally has a very specific definition where it is the increased per capita rate of mortality of infected hosts due to infection. Empirical studies involving the experimental infection of hosts often estimate virulence with the aim of comparing these estimates to values or patterns predicted in the theoretical literature. However most empirical studies do not estimate virulence as it is defined in the theoretical literature, thus potentially confounding comparisons between the two approaches. Here the analysis of relative survival is applied to the type of data routinely generated in empirical studies to estimate virulence as it is defined in the theoretical literature. The theoretical grounds for approach are outlined, followed by worked examples estimating the virulence of different pathogens with data from published studies. Code allowing virulence to be estimated by maximum likelihood withRis provided.
Antero-posterior versus lateral vestibular input processing in human visual cortex
Authors: Aedo-Jury Felipe , Cottereau Benoit R. , Celebrini Simona , Cauquil Alexandra Séverac 
Published: January 2019

AbstractVisuo-vestibular integration is crucial for locomotion, yet cortical mechanisms involved remain poorly understood. We combined binaural monopolar galvanic vestibular stimulation (GVS) and functional magnetic resonance imaging (fMRI) to characterize the cortical networks activated during antero-posterior and lateral stimulations in humans. We focused on functional areas that selectively respond to egomotion-consistent optic flow patterns: the human middle temporal complex (hMT+), V6, the ventral intraparietal (VIP) area, the cingulate sulcus visual (CSv) area and the posterior insular cortex (PIC). Areas hMT+, CSv, and PIC were equivalently responsive during lateral and antero-posterior GVS while areas VIP and V6 were highly activated during antero-posterior GVS but remained silent during lateral GVS. Using psychophysiological interaction (PPI) analyses, we confirmed that a cortical network including areas V6 and VIP is engaged during antero-posterior GVS. Our results suggest that V6 and VIP play a specific role in processing multisensory signals specific to locomotion during navigation.
Earliest-known intentionally deformed human cranial fossil from Asia and the initiation of hereditary hierarchy in the early Holocene
Authors: Ni Xijun , Li Qiang , Stidham Thomas A. , Yang Yangheshan , Ji Qiang , Jin Changzhu , Samiullah Khizar 
Published: January 2019

AbstractHereditary hierarchy is one of the major features of complex societies. Without a written record, prehistoric evidence for hereditary hierarchy is rare. Intentional cranial deformation (ICD) is a cross-generational cultural practice that embodies social identity and culture beliefs in adults through the behavior of altering infant head shape. Therefore, ICD is usually regarded as an archeological clue for the occurrence of hereditary hierarchy. With a calibrated radiocarbon age of 11245-11200 years BP, a fossil skull of an adult male displaying ICD discovered in Northeastern China is among the oldest-known ICD practices in the world. Along with the other earliest global occurrences of ICD, this discovery points to the early initiation of complex societies among the non-agricultural local societies in Northeastern Asia in the early Holocene. A population increase among previously more isolated terminal Pleistocene/early Holocene hunter-gatherer groups likely increased their interactions, possibly fueling the formation of the first complex societies.
Tracing the evolution of the plastome and mitogenome in the Chloropicophyceae uncovered convergent tRNA gene losses and a variant plastid genetic code
Authors: Turmel Monique , Santos Adriana Lopes dos , Otis Christian , Sergerie Roxanne , Lemieux Claude 
Published: January 2019

AbstractThe tiny green algae belonging to the Chloropicophyceae play a key role in marine phytoplankton communities; this newly erected class of prasinophytes comprises two genera (ChloropiconandChloroparvula) containing each several species. We sequenced the plastomes and mitogenomes of eightChloropiconand fiveChloroparvulaspecies to better delineate the phylogenetic affinities of these taxa and to infer the suite of changes that their organelle genomes sustained during evolution. The relationships resolved in organelle-based phylogenomic trees were essentially congruent with previously reported rRNA trees, and similar evolutionary trends but distinct dynamics were identified for the plastome and mitogenome. Although the plastome sustained considerable changes in gene content and order at the time the two genera split, subsequently it remained stable and maintained a very small size. The mitogenome, however, was remodeled more gradually and showed more fluctuation in size, mainly as a result of expansions/contractions of intergenic regions. Remarkably, the plastome and mitogenome lost a common set of three tRNA genes, with thetrnI(cau) andtrnL(uaa) losses being accompanied with important variations in codon usage. Unexpectedly, despite the disappearance oftrnI(cau) from the plastome in theChloroparvulalineage, AUA codons (the codons recognized by this gene product) were detected in certain plastid genes. By comparing the sequences of plastid protein-coding genes from chloropicophycean and phylogenetically diverse chlorophyte algae with those of the corresponding predicted proteins, we discovered that the AUA codon was reassigned from isoleucine to methionine inChloroparvula. This noncanonical genetic code has not previously been uncovered in plastids.
Ecological niche differentiation in soil cyanobacterial communities across the globe
Authors: Cano-Díaz Concha , Maestre Fernando T. , Eldridge David J. , Singh Brajesh K. , Bardgett Richard D. , Fierer Noah , Delgado-Baquerizo Manuel 
Published: January 2019

AbstractCyanobacteria are key organisms in the evolution of life on Earth, but their distribution and environmental preferences in terrestrial ecosystems remain poorly understood. This lack of knowledge is particularly evident for two recently discovered non-photosynthetic cyanobacterial classes, Melainabacteria and Sericytochromatia, limiting our capacity to predict how these organisms and the important ecosystem functions they perform will respond to ongoing global change. Here, we conducted a global field survey covering a wide range of vegetation types and climatic conditions to identify the environmental factors associated with the distribution of soil cyanobacterial communities. Network analyses revealed three major clusters of cyanobacterial phylotypes, each one dominated by members of one of the extant classes of Cyanobacteria (Oxyphotobacteria, Melainabacteria and Sericytochromatia), suggesting that species within these taxonomic groups share similar environmental preferences. Melainabacteria appear mostly in acidic and humid ecosystems, especially forests, Oxyphotobacteria are prevalent in arid and semiarid areas, and Sericytochromatia are common in hyperarid oligotrophic environments. We used this information to construct a global atlas of soil cyanobacteria. Our results provide novel insights into the ecology and biogeography of soil cyanobacteria and highlight how their global distribution could change in response to increased aridity, a landmark feature of climate change in terrestrial ecosystems worldwide.Significance statementCyanobacteria have shaped the history of life on Earth and can be important photosynthesizers and nitrogen fixers in terrestrial ecosystems worldwide. The recent discovery of two non-photosynthetic classes has advanced our understanding of their evolution, but their distribution and environmental preferences remain poorly described. Using a global survey conducted across 237 locations on six continents, we identified three main groups of soil cyanobacteria with contrasting environmental preferences: acidic and humid ecosystems, arid and semiarid areas, and hyperarid oligotrophic ecosystems. We then constructed the first global atlas of soil cyanobacteria, an important advance in our understanding of the ecology and biogeography of these functionally important organisms.
Identification of Anonymous DNA Using Genealogical Triangulation
Authors: Ellenbogen Paul , Narayanan Arvind 
Published: January 2019

AbstractConsumer genetics databases hold dense genotypes of millions of people, and the number is growing quickly [1] [2]. In 2018, law enforcement agencies began using such databases to identify anonymous DNA via long-range familial searches. We show that this technique is far more powerful if combined with a genealogical database of the type collected by online ancestry services. We present a “genealogical triangulation” algorithm and study its effectiveness on simulated datasets. We show that for over 50% of targets, their anonymous DNA can be identified (matched to the correct individual or same-sex sibling) when the genetic database includes just 1% of the population. We also show the effectiveness of “snowball identification” in which a successful identification adds to the genetic genealogical database, increasing the identification accuracy for future instances. We discuss our technique’s potential to enhance law enforcement capabilities as well as its privacy risks.