bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sleep-Dependent Memory Consolidation and Incremental Sentence Comprehension: Computational Dependencies during Language Learning as Revealed by Neuronal Oscillations
Authors: Cross Zachariah R. , Kohler Mark J. , Schlesewsky Matthias , Gaskell M. Gareth , Bornkessel-Schlesewsky Ina 
Published: November 2017

AbstractWe hypothesise a beneficial influence of sleep on the consolidation of the combinatorial mechanisms underlying incremental sentence comprehension. These predictions are grounded in recent work examining the effect of sleep on the consolidation of linguistic information, which demonstrate that sleep-dependent neurophysiological activity consolidates the meaning of novel words and simple grammatical rules. However, the sleep-dependent consolidation of sentence-level combinatorics has not been studied to date. Here, we propose that dissociable aspects of sleep neurophysiology consolidate two different types of combinatory mechanisms in human language: sequence-based (order-sensitive) and dependency-based (order-insensitive) combinatorics. The distinction between the two types of combinatorics is motivated both by cross-linguistic considerations and the neurobiological underpinnings of human language. Unifying this perspective with principles of sleep-dependent memory consolidation, we posit that a function of sleep is to optimise the consolidation of sequence-based knowledge (the when) and the establishment of semantic schemas of unordered items (the what) that underpin cross-linguistic variations in sentence comprehension. This hypothesis builds on the proposal that sleep is involved in the construction of predictive codes, a unified principle of brain function that supports incremental sentence comprehension. Finally, we discuss neurophysiological measures (EEG/MEG) that could be used to test these claims, such as the quantification of neuronal oscillations, which reflect basic mechanisms of information processing in the brain.
Covalent linkage of the DNA repair template to the CRISPR/Cas9 complex enhances homology-directed repair
Authors: Savic Natasa , Ringnalda Femke , Bargsten Katja , Li Yizhou , Berk Christian , Hall Jonathan , Neri Dario , Jinek Martin , Schwank Gerald 
Published: November 2017

AbstractThe CRISPR/Cas9 targeted nuclease technology allows the insertion of genetic modifications with single base-pair precision. The preference of mammalian cells to repair Cas9-induced DNA double-strand breaks via non-homologous end joining (NHEJ) rather than via homology-directed repair (HDR) however leads to relatively low rates of correctly edited loci. Here we demonstrate that covalently linking the DNA repair template to Cas9 increases the ratio of HDR over NHEJ up to 23-fold, and therefore provides advantages for clinical applications where high-fidelity repair is needed.
MCO: towards an ontology and unified vocabulary for a framework-based annotation of microbial growth conditions
Authors: Tierrafría VH , Mejía-Almonte C , Camacho-Zaragoza JM , Salgado H , Alquicira K , Gama-Castro S , Collado-Vides J. 
Published: November 2017

AbstractMotivationA major component in our understanding of the biology of an organism is the mapping of its genotypic potential into the repertoire of its phenotypic expression profiles. This genotypic to phenotypic mapping is executed by the machinery of gene regulation that turns genes on and off, which in microorganisms is essentially studied by changes in growth conditions and genetic modifications. Although many efforts have been made to systematize the annotation of experimental conditions in microbiology, the available annotation is not based on a consistent and controlled vocabulary for the unambiguous description of growth conditions, making difficult the identification of biologically meaningful comparisons of knowledge generated in different experiments or laboratories, a task urgently needed given the massive amounts of data generated by high throughput (HT) technologies.ResultsWe curated terms related to experimental conditions that affect gene expression inE. coliK-12. Since this is the best studied microorganism, the collected terms are the seed for the first version of the Microbial Conditions Ontology (MCO), a controlled and structured vocabulary that can be expanded to annotate microbial conditions in general. Moreover, we developed an annotation framework using the MCO terms to describe experimental conditions, providing the foundation to identify regulatory networks that operate under a particular condition. MCO supports comparisons of HT-derived data from different repositories. In this sense, we started to map common RegulonDB terms and Colombos bacterial expression compendia terms to MCO.Availability and ImplementationAs far as we know, MCO is the first ontology for growth conditions of any bacterial organism and it is available athttp://regulondb.ccg.unam.mx/. Furthermore, we will disseminate MCO throughout the Open Biomedical Ontology (OBO) Foundry in order to set a standard for the annotation of gene expression data derived from conventional as well as HT experiments inE. coliand other microbial organisms. This will enable the comparison of data from diverse data sources.Contactsgama@ccg.unam.mx,collado@ccg.unam.mx
The effect of macromolecular crowding on single-round transcription by E. coli RNA polymerase
Authors: Chung SangYoon , Lerner Eitan , Jin Yan , Kim Soohong , Alhadid Yazan , Grimaud Logan Wilson , Zhang Irina X. , Knobler Charles M. , Gelbart William M. , Weiss Shimon 
Published: November 2017

ABSTRACTBiological reactions in the cellular environment differ physicochemically from those performed in dilute buffer solutions due to, in part, slower diffusion of various components in the cellular milieu, increase in their chemical activities, and modulation of their binding affinities and conformational stabilities.In vivotranscription is therefore expected to be strongly influenced by the ‘crowdedness’ of the cell. Previous studies of transcription under macromolecular crowding conditions have focused mainly on multiple cycles of RNAP-Promoter associations, assuming that the association is the rate-determining step of the entire transcription process. However, recent reports demonstrated that late initiation and promoter escape could be the rate-determining steps for some promoter DNA sequences. The investigation of crowding effects on these steps undersingle-roundconditions is therefore crucial for better understanding of transcription initiationin vivo. Here, we have implemented anin vitrotranscription quenched-kinetics single-molecule assay to investigate the dependence of transcription reaction rates on the sizes and concentrations of crowders. Our results demonstrate an expected slowdown of transcription kinetics due to increased viscosity, and an unexpected enhancement in transcription kinetics by large crowding agents (at a given viscosity). More importantly, the enhancement’s dependence on crowder size significantly deviates from hard-sphere model (scaled-particle theory) predictions, commonly used for description of crowding effects. Our findings shed new light on how enzymatic reactions are affected by crowding conditions in the cellular milieu.
Is dopamine D1 receptor availability related to social behavior? A positron emission tomography replication study
Authors: Plavén-Sigray Pontus , Matheson Granville J. , Gustavsson Petter , Stenkrona Per , Halldin Christer , Farde Lars , Cervenka Simon 
Published: November 2017

BackgroundAssociations between dopamine receptor levels and pro- and antisocial behavior have previously been demonstrated in human subjects using positron emission tomography (PET) and self-rated measures of personality traits. So far, only one study has focused on the D1-dopamine receptor (D1-R), ﬁnding a positive correlation with the trait social desirability, which is characterized by low dominant and high afﬁliative behavior, while physical aggression showed a negative correlation. The aim of the present study was to replicate these previous ﬁndings using a new independent sample of subjects.MethodsTwenty-six healthy males were examined with the radioligand [11C]SCH-23390, and completed the Swedish universities Scales of Personality (SSP) which includes measures of social desirability and physical trait aggression. The simpliﬁed reference tissue model with cerebellum as reference region was used to calculate BPND values in the whole striatum and limbic striatum. The two regions were selected since they showed strong association between D1-R availability and personality scores in the previous study. Pearson’s correlation coefﬁcients and replication Bayes factors were then employed to assess the replicability and robustness of previous results.ResultsThere were no signiﬁcant correlations (all p values > 0.3) between regional BPND values and personality scale scores. Replication Bayes factors showed strong to moderate evidence in favor no relationship between D1-receptor availability and social desirability (striatum BF01 = 12.4; limbic striatum BF01 = 7.2) or physical aggression scale scores (limbic striatum BF01 = 3.3), compared to the original correlations.DiscussionWe could not replicate the previous ﬁndings of associations between D1-R availability and either pro- or antisocial behavior as measured using the SSP. Rather, there was evidence in favor of failed replications of associations between BPND and scale scores. Potential reasons for these results are restrictive variance in both PET and personality outcomes due to high sample homogeneity, or that the previous ﬁndings were false positives.
Intestinal crypts recover rapidly from focal damage with coordinated motion of stem cells that is impaired by aging
Authors: Choi Jiahn , Rakhilin Nikolai , Gadamsetty Poornima , Joe Daniel J. , Tabrizian Tahmineh , Lipkin Steven M. , Huffman Derek M. , Shen Xiling , Nishimura Nozomi 
Published: November 2017

ABSTRACTDespite the continuous renewal and turnover of the small intestinal epithelium, the intestinal stem cell niche maintains a ‘soccer ball-like’, alternating pattern of stem and Paneth cells in the crypt. To study the robustness of the niche pattern, we used intravital two-photon microscopy in mice with fluorescently-labeled Lgr5+ intestinal stem cells and precisely perturbed the mosaic pattern with femtosecond laser ablation. Ablation of one to three cells initiated rapid motion of niche cells that restored the alternation in the crypt pattern within about two hours without any cell proliferation. Crypt cells then performed a coordinated dilation of the crypt lumen, which resulted in peristalsis-like motion that forced damaged cells out of the niche. Crypt cell motion was reduced with inhibition of the ROCK pathway and attenuated with old age, and both resulted in incomplete pattern recovery. This suggests that in addition to proliferation and self-renewal, motility of stem cells is critical for maintaining homeostasis. Reduction of this novel behavior of stem cells could contribute to disease and age-related changes.
Role of guard-cell ABA in determining maximal stomatal aperture and prompt vapor-pressure-deficit response
Authors: Yaaran Adi , Negin Boaz , Moshelion Menachem 
Published: November 2017

AbstractAbscisic acid (ABA) is known to be involved in stomatal closure. However, its role in stomatal response to rapid increases in the vapor pressure deficit (VPD) is unclear. To study this issue, we generated guard cell (GC)-specific ABA-insensitive Arabidopsis plants (GC-specific abi1-1; GCabi). Under normal conditions, the stomatal conductance (gs) and apertures of GCabi plants were greater than those of control plants. This supports GC ABA role as limiting maximal stomatal aperture under non-stressful conditions. When there was a rapid increase in VPD (0.15 to 1 kPa), the gs and stomatal apertures of GCabi decreased in a manner similar that observed in the WT control, but different from that observed in WT plants treated with fusicoccin. Low VPD increased the size of the stomatal apertures of the WT, but not of GCabi. We conclude that GC ABA does not play a significant role in the initial, rapid stomatal closure that occurs in response to an increase in VPD, but is important for stomatal adaptation to ambient VPD. We propose a biphasic angiosperm VPD-sensing model that includes an initial passive-hydraulic, ABA-independent phase and a subsequent ABA-dependent steady-state phase in which stomatal behavior is optimized for ambient VPD conditions.HighlightGuard-cell ABA does not play a significant role in the immediate closure of stomata following an increase in the VPD, but is important for stomatal adaptation to ambient VPD.
Structure of transmembrane helix 8 and possible membrane defects in CFTR
Authors: Corradi Valentina , Gu Ruo-Xu , Vergani Paola , Tieleman D. Peter 
Published: November 2017

ABSTRACTThe cystic fibrosis transmembrane conductance regulator (CFTR) is an ion channel that regulates the flow of anions across epithelia. Mutations in CFTR cause cystic fibrosis. CFTR belongs to the ATP-Binding Cassette (ABC) transporter superfamily, and gating is controlled by phosphorylation and ATP binding and hydrolysis. Recent ATP-free and ATP-bound structures of zebrafish CFTR revealed an unwound segment of transmembrane helix (TM) 8, which appears to be a unique feature of CFTR not present in other ABC transporter structures. Here, by means of 1 μs long molecular dynamics simulations, we investigate the interactions formed by this TM8 segment with nearby helices, in both ATP-free and ATP-bound states. We highlight the structural role of TM8 in maintaining the functional architecture of the pore and we describe a distinct membrane defect that is found near TM8 only in the ATP-free state. The results of the MD simulations are discussed in the context of the gating mechanism of CFTR.
Ant nurse workers exhibit behavioral and transcriptomic signatures of specialization on larval stage
Authors: Walsh Justin T. , Warner Michael R. , Kase Adrian , Cushing Benjamin J. , Linksvayer Timothy A. 
Published: November 2017

AbstractDivision of labor within and between the worker and queen castes is thought to underlie the tremendous success of social insects. Colonies might benefit if subsets of nurse workers specialize further in caring for larvae of a certain stage or caste, given that larval nutritional requirements depend on stage and caste. We used short- (<1 hr) and long-term (ten days) behavioral observations to determine whether nurses of the pharaoh ant (Monomorium pharaonis) exhibit such specialization. We found that nurses were behaviorally specialized based on larval instar but not on larval caste. This specialization was widespread, with 56% of nurses in the short-term and between 22-27% in the long-term showing significant specialization. Additionally, we identified ∼200 genes that were differentially expressed in nurse head and abdominal tissues between nurses feeding young versus old larvae. These included 18 genes predicted to code for secreted proteins, which may be passed from nurses to larvae via trophallaxis, as well as vitellogenin and major royal jelly protein-1, which have previously been implicated in the transfer of nutrition from nurse to larvae and the regulation of larval development and caste in social insects. Altogether, our results provide the first evidence in any social insect for a division of labor among nurse workers based on larval stage, and our study begins to elucidate the molecular mechanisms underlying this specialization.
Maternal proteins that are phospho-regulated upon egg activation include crucial factors for oogenesis, egg activation and embryogenesis inDrosophila melanogaster
Authors: Zhang Zijing , Krauchunas Amber R. , Huang Stephanie , Wolfner Mariana F. 
Published: November 2017

ABSTRACTEgg activation is essential for the successful transition from a mature oocyte to a developmentally competent egg. It consists of a series of events including the resumption and completion of meiosis, initiation of translation of some maternal mRNAs and destruction of others, and changes to the vitelline envelope. This drastic change of cell state is accompanied by large scale alteration of the phospho-proteome of the cell. Despite the importance of this transition in cell and developmental state, it has been difficult to find many of its regulators. We hypothesize that phosphorylation state changes between oocyte and early embryo regulate the activities of proteins that are necessary during or after this transition, and thus that the set of phospho-regulated proteins would be an enriched source for finding critical players in the egg-to-embryo transition. To test this, we used germline-specific RNAi to examine the function of 189 maternal proteins that are phospho-regulated during egg activation inDrosophila melanogaster. We identified 53 genes whose knockdown reduced or abolished egg production, as well as 50 genes for which maternal knockdown led to significant impairment or abolishment of the eggs’ ability to hatch (hatchability). We observed different stages of developmental arrest in the embryos with impaired hatchability and several distinct categories of abnormalities in the maternal knockdown embryos that arrest early in development, suggesting potential roles of the candidates in egg activation and early embryogenesis. Our results, validated by our detection of multiple genes with previously-documented maternal-effect phenotypes among the proteins we tested, revealed 15 genes with new roles in egg activation and early embryogenesis. Given that protein phospho-regulation also occurs during this transition in other organisms, we suggest that the phospho-regulated proteins may provide an enriched dataset for identifying important players in the egg-to-embryo transition.
Hyperedge bundling: A practical solution to spurious interactions in MEG/EEG source connectivity analyses
Authors: Wang Sheng H. , Lobier Muriel , Siebenhühner Felix , Puoliväli Tuomas , Palva Satu , Matias Palva J. 
Published: November 2017

AbstractInter-areal functional connectivity (FC), neuronal synchronization in particular, is thought to constitute a key systems-level mechanism for coordination of neuronal processing and communication between brain regions. Evidence to support this hypothesis has been gained largely using invasive electrophysiological approaches. In humans, neuronal activity can be non-invasively recorded only with magneto- and electroencephalography (MEG/EEG), which have been used to assess FC networks with high temporal resolution and whole-scalp coverage. However, even in source-reconstructed MEG/EEG data, signal mixing, or “source leakage”, is a significant confounder for FC analyses and network localization.Signal mixing leads to two distinct kinds of false-positive observations: artificial interactions (AI) caused directly by mixing and spurious interactions (SI) arising indirectly from the spread of signals from true interacting sources to nearby false loci. To date, several interaction metrics have been developed to solve the AI problem, but the SI problem has remained largely intractable in MEG/EEG all-to-all source connectivity studies. Here, we advance a novel approach for correcting SIs in FC analyses using source-reconstructed MEG/EEG data.Our approach is to bundle observed FC connections into hyperedges by their adjacency in signal mixing. Using realistic simulations, we show here that bundling yields hyperedges with good separability of true positives and little loss in the true positive rate. Hyperedge bundling thus significantly decreases graph noise by minimizing the false-positive to true-positive ratio. Finally, we demonstrate the advantage of edge bundling in the visualization of large-scale cortical networks with real MEG data. We propose that hypergraphs yielded by bundling represent well the set of true cortical interactions that are detectable and dissociable in MEG/EEG connectivity analysis.HighlightsA true interaction often is “ghosted” into a multitude of spurious edges (SI)Effective in controlling and illustrating SIHyperedges have much improved TPR and graph qualityAdvantages in visualizing connectivity
Financial constraints and production efficiency
Authors: Khanal Aditya R. , Regmi Madhav 
Published: November 2017

PurposeThe purpose of this paper is to study the production and efficiency of rice growers in drought prone areas with special attention given to economic and financial factors.Design/methodology/approachThe authors use a parametric stochastic frontier approach and a non-parametric data envelopment analysis.FindingsThe study found that financial and liquidity constraints negatively influence production efficiency while off-farm work positively influences efficiency in drought prone areas.Originality/valueMany biotic and abiotic factors affect the production efficiency of rice growers. Among abiotic stress, drought is the strongest constraint affecting nearly one third of the total rice area in Asia and causing significant economic losses. Farmers’ economic conditions and financial constraints further exacerbate the situation. However, very few studies have analyzed the efficiency in drought prone areas and the influence of economic and financial factors. This study contributes to in this regard by augmenting economic and financial factors in the efficiency estimation of drought prone areas using parametric and non-parametric approach.
Family firms and collaborative innovation: present debates and future research
Authors: Bigliardi Barbara , Galati Francesco 
Published: November 2017

PurposeThe purpose of this paper is threefold: first, to identify the unique characteristics of family firms in terms of the ability to manage and the willingness to engage in collaborative innovation; second, to investigate the existence of contingent factors affecting the heterogeneity of family firms’ behavior regarding these dimensions; and third, to propose a future research agenda.Design/methodology/approachThis study consists of a systematic literature review.FindingsBased on the results of a systematic review, the authors explain why family firms have a different behavior in terms of collaborative innovation if compared to the non-family counterparts and, following the contingent-based perspective, the authors also explain how different contingent factors can contribute to cause the heterogeneity of family firms’ behavior when facing collaborative innovation. Finally, the authors present a research agenda aimed at stimulating and guiding future research.Research limitations/implicationsThe main limitation of the review is the wide definition of collaborative innovation provided at the beginning of the manuscript, in the introduction. In fact, with the aim of including all the studies dealing with collaborative innovation in the family firms’ context, the authors adopt a broad definition of external collaborative innovation that encompasses each process by which organizations work together to achieve an innovation outcome.Originality/valueTo the knowledge, this is the first systematic review addressing this relevant topic and proposing a future research agenda. The authors believe it could represent an important guide (but also a stimulus) for scholars interesting in the topic.