bluuebunny/crossref_metadata_2025_split huggingface dataset:
Untangling Sequences: Behavior vs. External Causes
Authors: Ahmad Subutai , Hawkins Jeff 
Published: September 2017

ABSTRACTThere are two fundamental reasons why sensory inputs to the brain change over time. Sensory inputs can change due to external factors or they can change due to our own behavior. Interpreting behavior-generated changes requires knowledge of how the body is moving, whereas interpreting externally-generated changes relies solely on the temporal sequence of input patterns. The sensory signals entering the neocortex change due to a mixture of both behavior and external factors. The neocortex must disentangle them but the mechanisms are unknown. In this paper, we show that a single neural mechanism can learn and recognize both types of sequences. In the model, cells are driven by feedforward sensory input and are modulated by contextual input. If the contextual input includes information derived from efference motor copies, the cells learn sensorimotor sequences. If the contextual input consists of nearby cellular activity, the cells learn temporal sequences. Through simulation we show that a network containing both types of contextual input automatically separates and learns both types of input patterns. We review experimental data that suggests the upper layers of cortical regions contain the anatomical structure required to support this mechanism.
Superiorab initioIdentification, Annotation and Characterisation of TEs and Segmental Duplications from Genome Assemblies
Authors: Zeng Lu , Kortschak R. Daniel , Raison Joy M. , Bertozzi Terry , Adelson David L. 
Published: September 2017

AbstractTransposable Elements (TEs) are mobile DNA sequences that make up significant fractions of amniote genomes. However, they are difficult to detect and annotateab initiobecause of their variable features, lengths and clade-specific variants. We have addressed this problem by refining and developing a Comprehensiveab initioRepeat Pipeline (CARP) to identify and cluster TEs and other repetitive sequences in genome assemblies. The pipeline begins with a pairwise alignment using krishna, a custom aligner. Single linkage clustering is then carried out to produce families of repetitive elements. Consensus sequences are then filtered for protein coding genes and then annotated using Repbase and a custom library of retrovirus and reverse transcriptase sequences. This process yields three types of family: fully annotated, partially annotated and unannotated. Fully annotated families reflect recently diverged/young known TEs present in Repbase. The remaining two types of families contain a mixture of novel TEs and segmental duplications. These can be resolved by aligning these consensus sequences back to the genome to assess copy number vs. length distribution. Our pipeline has three significant advantages compared to other methods forab initiorepeat identification: 1) we generate not only consensus sequences, but keep the genomic intervals for the original aligned sequences, allowing straightforward analysis of evolutionary dynamics, 2) consensus sequences represent low-divergence, recently/currently active TE families, 3) segmental duplications are annotated as a useful by-product. We have compared ourab initiorepeat annotations for 7 genome assemblies (1 unpublished) to other methods and demonstrate that CARP compares favourably with RepeatModeler, the most widely used repeat annotation package.Author summaryTransposable elements (TEs) are interspersed repetitive DNA sequences, also known as ‘jumping genes’, because of their ability to replicate in to new genomic locations. TEs account for a significant proportion of all eukaryotic genomes. Previous studies have found that TE insertions have contributed to new genes, coding sequences and regulatory regions. They also play an important role in genome evolution. Therefore, we developed a novel,ab initioapproach for identifying and annotating repetitive elements. The idea is simple: define a “repeat” as any sequence that occurs at least twice in the genome. Ourab initiomethod is able to identify species-specific TEs with high sensitivity and accuracy including both TEs and segmental duplications. Because of the high degree of sequence identity used in our method, the TEs we find are less diverged and may still be active. We also retain all the information that links identified repeat consensus sequences to their genome intervals, permiting direct evolutionary analysis of the TE families we identify.
The partial duplication of an E3-ligase gene inTriticeaespecies mediates resistance to powdery mildew fungi
Authors: Rajaraman Jeyaraman , Douchkov Dimitar , Lück Stefanie , Hensel Götz , Nowara Daniela , Pogoda Maria , Rutten Twan , Meitzel Tobias , Höfle Caroline , Hückelhoven Ralph , Klinkenberg Jörn , Trujillo Marco , Bauer Eva , Schmutzer Thomas , Himmelbach Axel , Mascher Martin , Lazzari Barbara , Stein Nils , Kumlehn Jochen , Schweizer Patrick 
Published: September 2017

ABSTRACTIn plant-pathogen interactions, components of the plant ubiquitination machinery are preferred targets of pathogen-encoded effectors suppressing defense responses or co-opting host cellular functions for accommodation. Here, we employed transient and stable gene silencing-and over-expression systems inHordeum vulgare(barley) to study the function ofHvARM1(forH. vulgare Armadillo 1), a partial gene duplicate of the U-box/armadillo-repeat E3 ligase HvPUB15(forH. vulgare Plant U-Box 15). The partialARM1gene was derived from an ancient gene-duplication event in a common ancestor of theTriticeaetribe of grasses comprising the major crop speciesH. vulgare,Triticum aestivumandSecale cereale. The barley geneHvARM1contributed to quantitative host as well as nonhost resistance to the biotrophic powdery mildew fungusBlumeria graminis, and allelic variants were found to be associated with powdery mildew-disease severity. Both HvPUB15 and HvARM1 proteins interacted in yeast and plant cells with the susceptibility-related, plastid-localized barley homologs of THF1 (for Thylakoid formation 1) and of ClpS1 (for Clp-protease adaptor S1) ofArabidopsis thaliana. The results suggest a neo-functionalizationHvARM1to increase resistance against powdery mildew and provide a link to plastid function in susceptibility to biotrophic pathogen attack.
Cryo-EM reconstruction of AlfA fromBacillus subtilisreveals the structure of a simplified actin-like filament at 3.4 Å resolution
Authors: Szewczak-Harris Andrzej , Löwe Jan 
Published: September 2017

AbstractLow copy-number plasmid pLS32 ofBacillus subtilissubsp.nattocontains a partitioning system that ensures segregation of plasmid copies during cell division. The partitioning locus comprises actin-like protein AlfA, adaptor protein AlfB and the centromeric sequenceparN. Similar to the ParMRC partitioning system fromE. coliplasmid R1, AlfA filaments form actin-like double helical filaments that arrange into an antiparallel bipolar spindle, which attaches its growing ends to sister plasmids, through interactions with AlfB andparN. Since, compared with ParM and other actin-like proteins, AlfA is highly diverged in sequence, we determined the atomic structure of non-bundling AlfA filaments to 3.4 Å resolution by cryo-EM. The structure reveals how the deletion of subdomain IIB of the canonical actin-fold has been accommodated by unique longitudinal and lateral contacts, whilst still enabling formation of left-handed, double helical, polar and staggered filaments that are architecturally similar to ParM. Through cryo-EM reconstruction of bundling AlfA filaments we obtained a pseudo-atomic model of AlfA doublets: the assembly of two filaments. The filaments are antiparallel, as required by the segregation mechanism, and exactly anti-phasic with 8-fold integer helical symmetry, to enable efficient doublet formation. The structure of AlfA filaments and doublets shows, in atomic detail, signs of the strong evolutionary pressure for simplicity, placed on plasmids: deletion of an entire domain of the actin fold is compensated by changes to all interfaces so that the required properties of polymerisation, nucleotide hydrolysis and antiparallel doublet formation are retained to fulfil the system's biological raison d'être.Significance StatementProtein filaments perform a vast array of functions inside almost all living cells. Actin-like proteins in archaea and bacteria have previously been found to form a surprising diversity of filament architectures, reflecting their divergent cellular roles. Actin-like AlfA is unique in that it is much smaller than all other filament forming actin-like proteins. With an atomic structure of the AlfA filament, obtained by high-resolution electron cryo-microscopy, we have revealed—at atomic level of detail—how AlfA filaments form dynamic filaments capable of transporting plasmid DNA in cells and how these filaments arrange into antiparallel bundles required for the segregation mechanism.
Precopulatory behavior and sexual conflict in the desert locust
Authors: Golov Y. , Harari A. , Rillich J. , Ayali A. 
Published: September 2017

AbstractStudies of mating and reproductive behavior have contributed much to our understanding of various animals’ ecological success. The desert locust,Schistocerca gregaria, is an important agricultural pest. However, knowledge of locust courtship and precopulatory behavior is surprisingly limited. Here we provide a comprehensive study of the precopulatory behavior of both sexes of the desert locust in the gregarious phase, with particular emphasis on the conflict between the sexes. Detailed HD-video monitoring of courtship and mating of 20 locust pairs, in a controlled environment, enabled both qualitative and quantitative descriptions of the behavior. A comprehensive list of behavioral elements was used to generate an eight-step ethogram, depicting from first encounter between the sexes to actual copulation. Further analyses included the probability of each element occurring, and a kinematic diagram based on a transitional matrix. Eleven novel behavioral elements are described in this study, and two potential points of conflict between the sexes are identified. Locust sexual interaction was characterized by the dominance of the males during the pre-mounting stage, and an overall stereotypic male courtship behavior. In contrast, females displayed no clear courtship-related behavior and an overall less organized behavioral sequence. Central elements in the sexual behavior of the females were low-amplitude hind-leg vibration, as well as rejecting males by jumping and kicking. Intricate reciprocal interactions between the sexes were evident mostly at the mounting stage. The reported findings contribute important insights to our knowledge of locust mating and reproductive behavior, and may assist in confronting this devastating agricultural pest.
Retrosplenial cortex and its role in spatial cognition
Authors: Mitchell Anna , Czajkowksi Rafal , Zhang Ningyu , Jeffery Kate , Nelson Andrew 
Published: September 2017

AbstractRetrosplenial cortex (RSC) is a region within the posterior neocortical system, heavily interconnected with an array of brain networks, both cortical and subcortical, that is engaged by a myriad of cognitive tasks. Although there is no consensus as to its precise function, evidence from both human and animal studies clearly points to a role in spatial cognition. However, the spatial processing impairments that follow RSC damage are not straightforward to characterise, leading to difficulties in defining the exact nature of its role. In the present article we review this literature and classify the types of ideas that have been put forward into three broad, somewhat overlapping classes: (i) Learning of landmark location, stability and permanence; (ii) Integration between spatial reference frames, and (iii) Consolidation and retrieval of spatial knowledge (“schemas”). We evaluate these models and suggest ways to test them, before briefly discussing whether the spatial function may be a subset of a more general function in episodic memory.
Genetic differences in the behavioral organization of binge eating, conditioned food reward, and compulsive-like eating in C57BL/6J and DBA/2J strains
Authors: Babbs Richard K. , Kelliher Julia C. , Scotellaro Julia L. , Luttik Kimberly P. , Mulligan Megan K. , Bryant Camron D. 
Published: September 2017

ABSTRACTBinge eating (BE) is a heritable symptom of eating disorders associated with anxiety, depression, malnutrition, and obesity. Genetic analysis of BE could facilitate therapeutic discovery. We used an intermittent, limited access BE paradigm involving sweetened palatable food (PF) to examine genetic differences in BE, conditioned food reward, and compulsive-like eating between C57BL/6J (B6J) and DBA/2J (D2J) inbred mouse strains. D2J mice showed a robust escalation in intake and conditioned place preference for the PF-paired side. D2J mice also showed a unique style of compulsive-like eating in the light/dark conflict test where they rapidly hoarded and consumed PF in the preferred unlit environment. BE and compulsive-like eating exhibited narrow-sense heritability estimates between 56 and 73 percent. To gain insight into the genetic basis, we phenotyped and genotyped a small cohort of 133 B6J × D2J-F2mice at the peak location of three quantitative trait loci (QTL) previously identified in F2mice for sweet taste (chromosome 4: 156 Mb), bitter taste (chromosome 6: 133 Mb) and behavioral sensitivity to drugs of abuse (chromosome 11: 50 Mb). The D2J allele on chromosome 6 was associated with greater PF intake on training days and greater compulsive-like PF intake, but only in males, suggesting that decreased bitter taste may increase BE in males. The D2J allele on chromosome 11 was associated with an increase in final PF intake and slope of escalation across days. Future studies employing larger crosses and genetic reference panels comprising B6J and D2J alleles will identify causal genes and neurobiological mechanisms.
Decoupling of the nuclear division cycle and cell size control in the coenocytic cycle of the ichthyosporeanSphaeroforma arctica
Authors: Ondracka Andrej , Ruiz-Trillo Iñaki 
Published: September 2017

AbstractCoenocytes (multinucleated cells formed by sequential nuclear divisions without cytokinesis) are commonly found across the eukaryotic kingdom, including in animals, plants and several lineages of unicellular eukaryotes. Despite their commonality, little is known about how cell growth, nuclear divisions and cell divisions are coordinated in coenocytes. Among the unicellular eukaryotes that form coenocytes are ichthyosporeans, a lineage of unicellular holozoans that are of significant interest due to their phylogenetic placement as one of the closest relatives to animals. Here, we characterize the coenocytic cell division cycle in the ichthyosporeanSphaeroforma arctica. In laboratory conditions, we observed thatS. arcticacells undergo a highly regular periodic coenocytic cell cycle. Nuclear division cycles occur synchronously within the coenocyte and in regular time intervals (~11 hours per nuclear cycle) until reaching 64-128 nuclei and releasing daughter cells. The duration of the nuclear division cycles is constant across a wide range of nutrient concentration. In contrast, the volume of the coenocytes increase more slowly in lower nutrient concentration, which also results in smaller newborn daughter cells. This suggests thatS. arcticacells are capable to adapt the cell growth rate to nutrient concentration while maintaining the timing of nuclear division cycles, suggesting that in ichthyosporeans the mechanisms regulating highly periodic nuclear division cycles operate independently from mechanisms sensing the cell size.
Genome-scale transcriptional regulatory network models of psychiatric and neurodegenerative disorders
Authors: Pearl Jocelynn R. , Bergey Dani E. , Funk Cory C. , Basu Bijoya , Oshone Rediet , Shannon Paul , Hood Leroy , Price Nathan D. , Colantuoni Carlo , Ament Seth A. 
Published: September 2017

AbstractGenetic and genomic studies suggest an important role for transcriptional regulatory changes in brain diseases, but roles for specific transcription factors (TFs) remain poorly understood. We integrated human brain-specific DNase I footprinting and TF-gene co-expression to reconstruct a transcriptional regulatory network (TRN) model for the human brain, predicting the brain-specific binding sites and target genes for 741 TFs. We used this model to predict core TFs involved in psychiatric and neurodegenerative diseases. Our results suggest that disease-related transcriptomic and genetic changes converge on small sets of disease-specific regulators, with distinct networks underlying neurodegenerative vs. psychiatric diseases. Core TFs were frequently implicated in a disease through multiple mechanisms, including differential expression of their target genes, disruption of their binding sites by disease-associated SNPs, and associations of the genetic loci encoding these TFs with disease risk. We validated our model’s predictions through systematic comparison to publicly available ChIP-seq and TF perturbation studies and through experimental studies in primary human neural stem cells. Combined genetic and transcriptional evidence supports roles for neuronal and microglia-enriched, MEF2C-regulated networks in Alzheimer’s disease; an oligodendrocyte-enriched, SREBF1-regulated network in schizophrenia; and a neural stem cell and astrocyte-enriched, POU3F2-regulated network in bipolar disorder. We provide our models of brain-specific TF binding sites and target genes as a resource for network analysis of brain diseases.
Microglia remodel synapses by presynaptic trogocytosis and spine head filopodia induction
Authors: Weinhard Laetitia , Neniskyte Urte , Bartolomei Giulia di , Bolasco Giulia , Machado Pedro , Schieber Nicole L. , Exiga Melanie , Vadisiute Auguste , Raggioli Angelo , Schertel Andreas , Schwab Yannick , Gross Cornelius T. 
Published: September 2017

AbstractMicroglia are highly motile glial cells that are proposed to mediate synaptic pruning during neuronal circuit formation. Disruption of signaling between microglia and neurons leads to an excess of immature synaptic connections, thought to be the result of impaired phagocytosis of synapses by microglia. However, until now the direct phagocytosis of synapses by microglia has not been reported and fundamental questions remain about the precise synaptic structures and phagocytic mechanisms involved. Here we used light sheet fluorescence microscopy to follow microglia-synapse interactions in developing organotypic hippocampal cultures, complemented by three-dimensional ultrastructural characterization using correlative light and electron microscopy (CLEM). Our findings define a set of dynamic microglia-synapse interactions, including the selective partial phagocytosis, or trogocytosis (trogo-: nibble), of presynaptic structures and the induction of postsynaptic spine head filopodia by microglia. These findings allow us to propose a mechanism for the facilitatory role of microglia in synaptic circuits remodeling and maturation.
C. elegansDBL-1/BMP Regulates Lipid Accumulation via Interaction with Insulin Signaling
Authors: Clark JF , Meade M , Ranepura G , Hall DH , Savage-Dunn C 
Published: September 2017

AbstractMetabolic homeostasis is coordinately controlled by diverse inputs, which must be understood to combat metabolic disorders. Here we introduce DBL-1, theC. elegansBMP2/4 homolog, as a significant regulator of lipid homeostasis. We used neutral lipid staining and a lipid droplet marker to demonstrate that both increases and decreases in DBL-1/BMP signaling result in reduced lipid stores and lipid droplet count. We find that lipid droplet size, however, correlates positively with the level of DBL 1/BMP signaling. Regulation of lipid accumulation in the intestine occurs through non-cell-autonomous signaling, since expression of SMA-3, a Smad signal transducer, in the epidermis (hypodermis) is sufficient to rescue the loss of lipid accumulation. Finally, genetic evidence indicates that DBL-1/BMP functions upstream of Insulin/IGF-1 Signaling (IIS) in lipid metabolism. We conclude that BMP signaling regulates lipid metabolism inC. elegansthrough inter-organ signaling to IIS, shedding light on a less well-studied regulatory mechanism for metabolic homeostasis.
Open for business? An integrative framework and empirical assessment for business model innovation in the gastronomic sector
Authors: Bogers Marcel , Jensen Jørgen Dejgård 
Published: September 2017

Purpose
The purpose of this paper is to identify and explore different business models that are active in the gastronomic industry and assess where there may be opportunities and limitations for innovation.

Design/methodology/approach
The authors develop a conceptualization of the business model concept and some of its main components – considering an internal and external orientation – and how they can be applied to the gastronomic sector. On this basis, the authors propose, develop and test an empirical framework for the economic sustainability of gastronomic enterprises. Based on data from a publicly available database of the Danish hospitality sector, the authors conduct hierarchical cluster analysis to identify different business models for the Danish gastronomic sector.

Findings
Given the diversity of the gastronomic sector, there can be a multitude of alternative business models and characteristics, which may enable the sector to create value through, for example, product differentiation, market segmentation, and so on. The analysis revealed nine different clusters, which represent different business models in terms of value creation, segmentation, and resource utilization – highlighting either more closed or open business models. These business models offer a basis for considering the opportunities and barriers for business model innovation – for both startups and incumbent firms – within gastronomy and agri-food more generally.

Originality/value
The gastronomic sector is diverse and heterogeneous with a multitude of possible alternative business models. This paper provides a basis for considering the key enablers of business model development in this sector. The integrative framework and empirical assessment provides a basis for further exploring business model innovation in the gastronomic sector in particular and the agri-food sector more generally.