bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interplay of pericentromeric genome organization and chromatin landscape regulates the expression ofDrosophila melanogasterheterochromatic genes
Authors: Saha Parna , Sowpati Divya Tej , Srivastava Ishanee , Mishra Rakesh Kumar 
Published: January 2019

AbstractTranscription of heterochromatic genes residing within the constitutive heterochromatin is paradoxical to the tenets of the epigenetic code.Drosophila melanogasterheterochromatic genes serve as an excellent model system to understand the mechanisms of their transcriptional regulation. Recent developments in chromatin conformation techniques have revealed that genome organization regulates the transcriptional outputs. Thus, using 5C-seq in S2 cells, we present a detailed characterization of the hierarchical genome organization ofDrosophilapericentromeric heterochromatin and its contribution to heterochromatic gene expression. We show that pericentromeric TAD borders are enriched in nuclear Matrix attachment regions while the intra-TAD interactions are mediated by various insulator binding proteins. Heterochromatic genes of similar expression levels cluster into Het TADs which indicates their transcriptional co-regulation. To elucidate how heterochromatic factors, influence the expression of heterochromatic genes, we performed 5C-seq in the HP1a or Su(var)3-9 depleted cells. HP1a or Su(var)3-9 RNAi results in perturbation of global pericentromeric TAD organization but the expression of the heterochromatic genes is minimally affected. Subset of active heterochromatic genes have been shown to have combination of HP1a/H3K9me3 with H3K36me3 at their exons. Interestingly, the knock-down of dMES-4 (H3K36 methyltransferase), downregulates expression of the heterochromatic genes. This indicates that the local chromatin interactions and the combination of heterochromatic factors (HP1a or H3K9me3) along with the H3K36me3 is crucial to drive the expression of heterochromatic genes. Furthermore, dADD1, present near the TSS of the active heterochromatic genes, can bind to both H3K9me3 or HP1a and facilitate the heterochromatic gene expression by regulating the H3K36me3 levels. Therefore, our findings provide mechanistic insights into the interplay of genome organization and chromatin factors at the pericentromeric heterochromatin that regulatesDrosophila melanogasterheterochromatic gene expression.
Fear in dreams and in wakefulness: evidence for day/night affective homeostasis
Authors: Sterpenich V , Perogamvros L , Tononi G , Schwartz S 
Published: January 2019

SUMMARYDespite partial experimental evidence, it is a long-standing and common belief that dreams serve an emotion regulation function. Revisiting this idea, recent neuroscientific theories have proposed that emotions experienced in dreams contribute to the resolution of emotional distress (e.g. fear extinction) and preparation for future waking affective reactions. Here we addressed one emerging common prediction from these theoretical accounts, namely that experiencing fear in dreams is associated with more adapted responses to threatening signals during wakefulness. Using a stepwise approach across two studies, we first identified brain regions activated when experiencing fear in dreams and then showed that frightening dreams modulated the response of these same regions to threatening stimuli during wakefulness. As predicted, more fear in dreams was associated with reduced activation of those fear-responsive regions during wakefulness. Specifically, in Study 1, we performed serial awakenings in 18 participants recorded throughout the night with high-density EEG and asked them whether they experienced any fear in their dreams. Insula activity increased (i.e. decreased delta and increased gamma power) for dreams containing fear. In Study 2, we tested 89 participants and found that those with higher incidence of fear in their dreams showed reduced fMRI response to fear-eliciting stimuli in the insula, amygdala and midcingulate cortex, while awake. Consistent with better emotion regulation processes, the same participants also displayed increased medial prefrontal cortex activity. These findings support that emotions in dreams and wakefulness engage similar neural substrates, and substantiate a link between emotional processes occurring during sleep and emotional brain functions during wakefulness.
Development of new food-sharing relationships among nonkin vampire bats
Authors: Carter Gerald G. , Farine Damien R. , Crisp Rachel J. , Vrtilek Julia K. , Ripperger Simon P. , Page Rachel A. 
Published: January 2019

AbstractIn an individualized animal society, social bonds can foster cooperation and enhance survival and reproduction. Cooperative bonds often exist among kin, but nonkin can also develop high-investment cooperative bonds that share similarities with human friendship. How do such bonds form? One theory suggests that strangers should ‘test the waters’ of a new relationship by making small initial cooperative investments and gradually escalating them with good partners. This ‘raising-the-stakes’ strategy is demonstrated by human strangers in short-term economic games, but it remains unclear whether it applies to helping in a natural long-term social bond. Here we show evidence that unfamiliar vampire bats (Desmodus rotundus) selectively escalate low-cost investments in allogrooming before developing higher-cost food-sharing relationships. We introduced females from geographically distant sites in pairs or groups and observed that bats established new reciprocal grooming relationships, and that increasing grooming rates predicted the occurrence of first food donations, at which point grooming rates no longer increased. New food-sharing relationships emerged reciprocally in 14% of female pairs, typically over 10-15 months, and developed faster when strangers lacked alternative familiar partners. A gradual grooming-to-sharing transition among past strangers suggests that ‘raising the stakes’ might be more evident when tracking multiple cooperative behaviours as new relationships form, rather than measuring a single behavior in an established relationship. ‘Raising the stakes’ could play a similar underappreciated role across a broader spectrum of social decisions with long-term consequences, such as joining a new social group or forming a long-term pair-bond.Significance statementVampire bats form long-term cooperative social bonds that involve reciprocal food sharing. How do two unrelated bats go from being strangers to having a high-investment food-sharing relationship? We introduced unfamiliar bats and found evidence that low-cost grooming paves the way for higher-cost food donations. Food sharing emerged in a reciprocal fashion and it emerged faster when two strangers did not have access to their original groupmates. The bats that formed new food-sharing relationships had a history of escalating reciprocal grooming up until the food sharing began. Our finding that unfamiliar nonkin vampire bats appear to gradually and selectively transition from low-cost to high-cost cooperative behaviors is the first evidence that nonhuman individuals ‘raise the stakes’ when forming new cooperative relationships.
Spatial Regulation of Polo-like Kinase Activity during C. elegans Meiosis by the Nucleoplasmic HAL-2/HAL-3 Complex
Authors: Roelens Baptiste , Barroso Consuelo , Montoya Alex , Cutillas Pedro , Zhang Weibin , Woglar Alexander , Girard Chloe , Martinez-Perez Enrique , Villeneuve Anne M. 
Published: January 2019

AbstractProper partitioning of homologous chromosomes during meiosis relies on the coordinated execution of multiple interconnected events: Homologs must locate, recognize and align with their correct pairing partners. Further, homolog pairing must be coupled to assembly of the synaptonemal complex (SC), a meiosis-specific tripartite structure that maintains stable associations between the axes of aligned homologs and regulates formation of crossovers between their DNA molecules to create linkages that enable their segregation. Here we identify HAL-3 (Homolog Alignment 3) as an important player in coordinating these key events during C. elegans meiosis. HAL-3 and the previously-identified HAL-2 are interacting and interdependent components of a protein complex that localizes to the nucleoplasm of germ cells. hal-3 (or hal-2) mutants exhibit multiple meiotic prophase defects including failure to establish homolog pairing, inappropriate loading of SC subunits onto unpaired chromosome axes, and premature loss of synapsis checkpoint protein PCH-2. Further, loss of hal function results in misregulation of the subcellular localization and activity of polo-like kinases (PLK-1 and PLK-2), which dynamically localize to different defined subnuclear sites during wild-type prophase progression to regulate distinct cellular events. Moreover, loss of PLK-2 activity partially restores tripartite SC structure in a hal mutant background, suggesting that the defect in pairwise SC assembly in hal mutants reflects inappropriate PLK activity. Together our data support a model in which the nucleoplasmic HAL-2/HAL-3 protein complex constrains both localization and activity of meiotic Polo-like kinases, thereby preventing premature interaction with stage-inappropriate targets.
Distinct ROPGEFs successively drive polarization and outgrowth of root hairs
Authors: Denninger Philipp , Reichelt Anna , Schmidt Vanessa A. F. , Mehlhorn Dietmar G. , Asseck Lisa Y. , Stanley Claire E. , Keinath Nana F. , Evers Jan-Felix , Grefen Christopher , Grossmann Guido 
Published: January 2019

SUMMARYRoot hairs are tubular protrusions of the root epidermis that significantly enlarge the exploitable soil volume in the rhizosphere. Trichoblasts, the cell type responsible for root hair formation, switch from cell elongation to tip growth through polarization of the growth machinery to a pre-defined root hair initiation domain (RHID) at the plasma membrane. The emergence of this polar domain resembles the establishment of cell polarity in other eukaryotic systems [1–3]. Rho-type GTPases of plants (ROPs) are among the first molecular determinants of the RHID [4, 5] and later play a central role in polar growth [6]. Numerous studies have elucidated mechanisms that position the RHID in the cell [7–9] or regulate ROP activity [10–18]. The molecular players that target ROPs to the RHID and initiate outgrowth, however, have not been identified. We dissected the timing of the growth machinery assembly in polarizing hair cells and found that positioning of molecular players and outgrowth are temporally separate processes that are each controlled by specific ROP guanine nucleotide exchange factor (GEFs). A functional analysis of trichoblast-specific GEFs revealed GEF3 to be required for normal ROP polarization and thus efficient root hair emergence, while GEF4 predominantly regulates subsequent tip growth. Ectopic expression of GEF3 induced the formation of spatially confined, ROP-recruiting domains in other cell types, demonstrating the role of GEF3 to serve as a membrane landmark during cell polarization. Our findings suggest that morphogenetic programs in plants employ distinct regulatory modules for the alignment and activation of the cellular growth machinery.
PAN: Personalized Annotation-based Networks for the Prediction of Breast Cancer Relapse
Authors: Nguyen Thin , Lee Samuel C. , Quinn Thomas P. , Truong Buu , Li Xiaomei , Tran Truyen , Venkatesh Svetha , Le Thuc Duy 
Published: January 2019

AbstractThe classification of clinical samples based on gene expression data is an important part of precision medicine. However, it has proved difficult to accurately predict survival outcomes and treatment responses for cancer patients. In this manuscript, we show how transforming gene expression data into a set of personalized (sample-specific) networks can allow us to harness existing graph-based methods to improve classifier performance. Existing approaches to personalized gene networks all have the limitation that they depend on other samples in the data and must get re-computed whenever a new sample is introduced. Here, we propose a novel method, called Personalized Annotation-based Networks (PAN), that avoids this limitation by using curated annotation databases to transform gene expression data into a graph. These databases organize genes into overlapping gene sets, called annotations, that we use to build a network where nodes represent functional terms and edges represent the similarity between them. Unlike competing methods, PANs are calculated for each sample independent of the population, making it a more efficient way to obtain single-sample networks. Using three breast cancer datasets as a case study (METABRIC and a super-set of GEO studies), we show that PAN classifiers not only predict cancer relapse better than gene features alone, but also outperform PPI and population-level graph-based classifiers. This work demonstrates the practical advantages of graph-based classification for high-dimensional genomic data, while offering a new approach to making sample-specific networks.Supplementary informationThe codes and data are available at https://github.com/thinng/PAN.ContactThuc.Le@unisa.edu.au
Multi-Neuromodulator Measurements across Fronto-Striatal Network Areas of the Behaving Macaque using Solid-Phase Microextraction
Authors: Hassani Seyed-Alireza , Lendor Sofia , Boyaci Ezel , Pawliszyn Janusz , Womelsdorf Thilo 
Published: January 2019

AbstractDifferent neuromodulators rarely act independent from each other to modify neural processes but are instead co-released, gated, or modulated. To understand this interdependence of neuromodulators and their collective influence on local circuits during different brain states, it is necessary to reliably extract local concentrations of multiple neuromodulators in vivo. Here we describe results using solid phase microextraction (SPME), a method providing sensitive, multi-neuromodulator measurements. SPME is a sampling method that is coupled with mass spectrometry to quantify collected analytes. Reliable measurements of glutamate, dopamine, acetylcholine and choline were made simultaneously within frontal cortex and striatum of two macaque monkeys (Macaca mulatta) during goal-directed behavior. We find glutamate concentrations several orders of magnitude higher than acetylcholine and dopamine in all brain regions. Dopamine was reliably detected in the striatum at tenfold higher concentrations than acetylcholine. Acetylcholine and choline concentrations were detected with high consistency across brain areas, within monkeys and between monkeys. These findings illustrate that SPME microprobes provide a versatile novel tool to characterize multiple neuromodulators across different brain areas in vivo to understand the interdependence and co-variation of neuromodulators during goal directed behavior. Such data will be important to better distinguish between different behavioral states and characterize dysfunctional brain states that may be evident in psychiatric disorders.
Capturing cell type-specific chromatin structural patterns by applying topic modeling to single-cell Hi-C data
Authors: Kim Hyeon-Jin , Gürkan Yardımcı Galip , Bonora Giancarlo , Ramani Vijay , Liu Jie , Qiu Ruolan , Lee Choli , Hesson Jennifer , Ware Carol B. , Shendure Jay , Duan Zhijun , Stafford Noble William 
Published: January 2019

AbstractSingle-cell Hi-C (scHi-C) interrogates genome-wide chromatin interaction in individual cells, allowing us to gain insights into 3D genome organization. However, the extremely sparse nature of scHi-C data poses a significant barrier to analysis, limiting our ability to tease out hidden biological information. In this work, we approach this problem by applying topic modeling to scHi-C data. Topic modeling is well-suited for discovering latent topics in a collection of discrete data. For our analysis, we generate twelve different single-cell combinatorial indexed Hi-C (sciHi-C) libraries from five human cell lines (GM12878, H1Esc, HFF, IMR90, and HAP1), consisting over 25,000 cells. We demonstrate that topic modeling is able to successfully capture cell type differences from sciHi-C data in the form of “chromatin topics.” We further show enrichment of particular compartment structures associated with locus pairs in these topics.
TRPV4 inhibition prevents increased water diffusion and blood-retina barrier breakdown in the retina of streptozotocin-induced diabetic mice
Authors: Ríos Maricruz Orduña , Imm Ramsés Noguez , Godínez Nicole Marilú Hernández , Cortes Ana María Bautista , Liedtke Wolfgang , Torres Ataúlfo Martínez , Concha Luis , Thébault Stéphanie 
Published: January 2019

AbstractA better understanding of the molecular and cellular mechanisms involved in retinal hydro-ionic homeostasis imbalance during diabetic macular edema (DME) is needed to gain insights into retinal physio(patho)logy that will help elaborating innovative therapies with lower health care costs. Transient receptor potential cation channel subfamily vanilloid member 4 (TRPV4) plays an intricate role in homeostatic processes that needs to be deciphered in normal and diabetic retina. Based on previous findings showing that TRPV4 antagonists resolve blood-retina barrier (BRB) breakdown in diabetic rats, we evaluated whether TRPV4 channel inhibition prevents and reverts retinal edema in streptozotocin(STZ)-induced diabetic mice. We assessed retinal edema using common metrics, including retinal morphology/thickness (histology) and BRB integrity (albumin-associated tracer), and also by quantifying water mobility through apparent diffusion coefficient (ADC) measures. ADC was measured by diffusion-weighted magnetic resonance imaging (DW-MRI), acquiredex vivoat 4 weeks after STZ injection in diabetes and control groups. DWI images were also used to assess retinal thickness. TRPV4 was genetically ablated or pharmacologically inhibited as follows: left eyes were used as vehicle control and right eyes were intravitreally injected with TRPV4-selective antagonist GSK2193874, 24 h before the end of the 4 weeks of diabetes. Histological data show that retinal thickness was similar in nondiabetic and diabetic wt groups but increased in diabeticTrpv4−/−mice. In contrast, DWI shows retinal thinning in diabetic wt mice that was absent in diabeticTrpv4−/−mice. Disorganized outer nuclear layer was observed in diabetic wt but not in diabeticTrpv4−/−retinas. We further demonstrate increased water diffusion and BRB hyperpermeability in diabetic wt mice, effects that were absent in diabeticTrpv4−/−mice. Retinas of diabetic mice treated with PBS showed increased water diffusion that was not inhibited by GSK2193874. ADC maps in nondiabeticTrpv4−/−mouse retinas showed restricted diffusion. Our data provide evidence that water diffusion is increased in diabetic mouse retinas and that TRPV4 function contributes to retinal hydro-ionic homeostasis and structure under control conditions, and to the development of BRB breakdown and increased water diffusion in the retina under diabetes conditions. A single intravitreous injection of TRPV4 antagonist is however not sufficient to revert these alterations in diabetic mouse retinas.
Engineering-out hazards: digitising the management working safety in confined spaces
Authors: Parn Erika A. , Edwards David , Riaz Zainab , Mehmood Fahad , Lai Joseph 
Published: January 2019

PurposeThis paper aims to report upon the further development of a hybrid application programming interface (API) plug-in to building information modelling (BIM) entitled confined spaces safety monitoring system “CoSMoS”. Originally designed to engineer-out environmental hazards associated with working in a building’s confined spaces (during the construction phase of a building’s life-cycle), this second generation version is expanded upon to use archival records to proactively learn from data generated within a sensor network during the building’s operations and maintenance (O&M) phase of asset management (AM).Design/methodology/approachAn applied research methodological approach adopted used a two-phase process. In phase one, a conceptual model was created to provide a “blueprint map” to integrate BIM, sensor-based networks and data analytics (DA) into one integral system. A literature review provided the basis for the conceptual model’s further development. In phase two, the conceptual model was transposed into the prototype’s development environment as a proof of concept using primary data accrued from a large educational building.FindingsAn amalgamation of BIM, historical sensor data accrued and the application of DA demonstrate that CoSMoS provides an opportunity for the facilities management (FM) team to monitor pertinent environmental conditions and human behaviour within buildings that may impact upon occupant/worker safety. Although working in confined spaces is used to demonstrate the inherent potential of CoSMoS, the system could readily be expanded to analyse sensor-based network’s historical data of other areas of building performance, maintenance and safety.Originality/valueThis novel prototype has automated safety applications for FM during the asset lifecycle and maintenance phase of a building’s O&M phase of AM. Future work is proposed in several key areas, namely, develop instantaneous indicators of current safety performance within a building; and develop lead indicators of future safety performance of buildings.
Psychological contract fulfilment, engagement and nurse professional turnover intention
Authors: Sheehan Cathy , Tham Tse Leng , Holland Peter , Cooper Brian 
Published: January 2019

Purpose
The purpose of this paper is to analyse the effect of nurses’ experience of the fulfilment of their psychological contract on their intention to leave the nursing profession and to consider employee engagement as a mediator between the fulfilment of the psychological contract of nurses and their intention to leave their profession.

Design/methodology/approach
The authors used a quantitative, cross-sectional research design. In total, 1,039 Australian nurses completed an anonymous online survey conducted via the Australian Nursing and Midwifery Federation website. Structural equation modelling was used to test the hypotheses.

Findings
The fulfilment of promises related to interesting job content and social atmosphere were negatively associated with intentions to leave the nursing profession, and these relationships were mediated by engagement. The fulfilment of promises related to career development, financial rewards and work–life balance were not associated with intentions to leave the nursing profession.

Research limitations/implications
To ensure professional nurse retention, it is necessary to not just promise nurses interesting jobs and a supportive social atmosphere, but to manage nurse perceptions regarding the fulfilment of these promises.

Originality/value
Although there has been extensive research on nurse intention to leave their current job, the important area of nurse professional turnover has received less attention. The research highlights the importance of fulfilling expectations and promises related to interesting nurse job content that encourages nurse responsibility and autonomy as well as promises of a social atmosphere that includes co-operative relationships and good communication with colleagues.