bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ecological scaffolding and the evolution of individuality: the transition from cells to multicellular life
Authors: Black Andrew J , Bourrat Pierrick , Rainey Paul B 
Published: June 2019

ABSTRACTEvolutionary transitions in individuality are central to the emergence of biological complexity. Recent experiments provide glimpses of processes underpinning the transition from single cells to multicellular life and draw attention to the critical role of ecology. Here we emphasise this ecological dimension and argue that its current absence from theoretical frameworks hampers development of general explanatory solutions. Using mechanistic mathematical models, we show how a minimal ecological structure comprised of patchily distributed resources and between patch dispersal can scaffold Darwinian-like properties on collectives of cells. This scaffolding causes cells to participate directly in the process of evolution by natural selection as if they were members of multicellular collectives, with collectives participating in a death-birth process arising from the interplay between the timing of dispersal events and the rate of resource utilisation by cells. When this timescale is sufficiently long and new collectives are founded by single cells, collectives experience conditions that favour evolution of a reproductive division of labour. Together our simple model makes explicit key events in the major evolutionary transition to multicellularity. It also makes predictions concerning the life history of certain pathogens and serves as an ecological recipe for experimental realisation of evolutionary transitions.
Impact of RNA Extraction and Target Capture Methods on RNA Sequencing Using Formalin-Fixed, Paraffin Embedded Tissues
Authors: Hilker Christopher A. , Bhagwate Aditya V. , Jang Jin Sung , Meyer Jeffrey G , Nair Asha A. , Davila Jaime I. , McDonald Amber M. , Winters Jennifer L. , Wehrs Rebecca N. , Jackson Rory A. , Gorman Joshua A. , Cicek Mine S. , Oliveira Andre M. , Thompson E. Aubrey , Eckloff Bruce W. , Halling Kevin C. , Sun Zhifu A. , Jen Jin 
Published: June 2019

AbstractFormalin fixed paraffin embedded (FFPE) tissues are commonly used biospecimen for clinical diagnosis. However, RNA degradation is extensive when isolated from FFPE blocks making it challenging for whole transcriptome profiling (RNA-seq). Here, we examined RNA isolation methods, quality metrics, and the performance of RNA-seq using different approaches with RNA isolated from FFPE and fresh frozen (FF) tissues. We evaluated FFPE RNA extraction methods using six different tissues and five different methods. The reproducibility and quality of the prepared libraries from these RNAs were assessed by RNA-seq. We next examined the performance and reproducibility of RNA-seq for gene expression profiling with FFPE and FF samples using targeted (Kinome capture) and whole transcriptome capture based sequencing. Finally, we assessed Agilent SureSelect All-Exon V6+UTR capture and the Illumina TruSeq RNA Access protocols for their ability to detect known gene fusions in FFPE RNA samples. Although the overall yield of RNA varied among extraction methods, gene expression profiles generated by RNA-seq were highly correlated (>90%) when the input RNA was of sufficient quality (≥DV200 30%) and quantity (≥ 100 ng). Using gene capture, we observed a linear relationship between gene expression levels for shared genes that were captured using either All-Exon or Kinome kits. Gene expression correlations between the two capture-based approaches were similar using RNA from FFPE and FF samples. However, TruSeq RNA Access protocol provided significantly higher exon and junction reads when compared to the SureSelect All-Exon capture kit and was more sensitive for fusion gene detection. Our study established pre and post library construction QC parameters that are essential to reproducible RNA-seq profiling using FFPE samples. We show that gene capture based NGS sequencing is an efficient and highly reproducible strategy for gene expression measurements as well as fusion gene detection.
Coordination of multiple joints increases bilateral connectivity with ipsilateral sensorimotor cortices
Authors: Wilkins Kevin B. , Yao Jun 
Published: June 2019

AbstractAlthough most activities of daily life require simultaneous coordination of both proximal and distal joints, motor preparation during such movements has not been well studied. Previous results for motor preparation have focused on hand/finger movements. For simple hand/finger movements, results have found that such movements typically evoke activity primarily in the contralateral motor cortices. However, increasing the complexity of the finger movements, such as during a distal sequential finger-pressing task, leads to additional recruitment of ipsilateral resources. It has been suggested that this involvement of the ipsilateral hemisphere is critical for temporal coordination of distal joints. The goal of the current study was to examine whether increasing simultaneous coordination of multiple joints (both proximal and distal) leads to a similar increase in coupling with ipsilateral sensorimotor cortices during motor preparation compared to a simple distal movement such as hand opening. To test this possibility, 12 healthy individuals participated in a high-density EEG experiment in which they performed either hand opening or simultaneous hand opening while lifting at the shoulder on a robotic device. We quantified within- and cross-frequency cortical coupling across the sensorimotor cortex for the two tasks using dynamic causal modeling. Both hand opening and simultaneous hand opening while lifting at the shoulder elicited coupling from secondary motor areas to primary motor cortex within the contralateral hemisphere exclusively in the beta band, as well as from ipsilateral primary motor cortex. However increasing the task complexity by combining hand opening while lifting at the shoulder also led to an increase in coupling within the ipsilateral hemisphere as well as interhemispheric coupling between hemispheres that expanded to theta, mu, and gamma frequencies. These findings demonstrate that increasing the demand of joint coordination between proximal and distal joints leads to increases in communication with the ipsilateral hemisphere as previously observed in distal sequential finger tasks.
Armadillo repeat-containing protein 1 is a dual localization protein associated with mitochondrial intermembrane space bridging complex
Authors: Wagner Fabienne , Kunz Tobias C. , Chowdhury Suvagata R. , Thiede Bernd , Fraunholz Martin , Eger Debora , Kozjak-Pavlovic Vera 
Published: June 2019

AbstractCristae architecture is important for the function of mitochondria, the organelles that play the central role in many cellular processes. The mitochondrial contact site and cristae organizing system (MICOS) together with the sorting and assembly machinery (SAM) forms the mitochondrial intermembrane space bridging complex (MIB), a large protein complex present in mammalian mitochondria that partakes in the formation and maintenance of cristae. We report here a new subunit of the mammalian MICOS/MIB complex, an armadillo repeat-containing protein 1 (ArmC1). ArmC1 localizes both to cytosol and mitochondria, where it associates with the outer mitochondrial membrane through its carboxy-terminus. ArmC1 interacts with other constituents of the MICOS/MIB complex and its amounts are reduced upon MICOS/MIB complex depletion. Mitochondria lacking ArmC1 do not show defects in cristae structure, respiration or protein content, but appear fragmented and with reduced motility. ArmC1 represents therefore a peripheral MICOS/MIB component that appears to play a role in mitochondrial distribution in the cell.
Deconstructing hunting behavior reveals a tightly coupled stimulus-response loop
Authors: Mearns Duncan S. , Semmelhack Julia L. , Donovan Joseph C. , Baier Herwig 
Published: June 2019

AbstractAnimals build behavioral sequences out of simple stereotyped actions. A comprehensive characterization of these actions and the rules underlying their temporal organization is necessary to understand sensorimotor transformations performed by the brain. Here, we use unsupervised methods to study behavioral sequences in zebrafish larvae. Generating a map of swim bouts, we reveal that fish modulate their tail movements along a continuum. We cluster bouts that share common kinematic features and contribute to similar behavioral sequences into seven modules. Behavioral sequences comprising a subset of modules bring prey into the anterior dorsal visual field of the larvae. Fish then release a capture maneuver comprising a stereotyped jaw movement and fine-tuned stereotyped tail movements to capture prey at various distances. We demonstrate that changes to chaining dynamics, but not module production, underlie prey capture deficits in two visually impaired mutants. Our analysis thus reveals the temporal organization of a vertebrate hunting behavior, with the implication that different neural architectures underlie prey pursuit and capture.
Changes-of-mind in the absence of new post-decision evidence
Authors: Atiya Nadim A. A. , Zgonnikov Arkady , Schoemann Martin , Scherbaum Stefan , O’Hora Denis , Wong-Lin KongFatt 
Published: June 2019

AbstractDecisions are occasionally accompanied by changes-of-mind. While considered a hallmark of cognitive flexibility, the mechanisms underlying changes-of-mind remain elusive. Previous studies on perceptual decision making have focused on changes-of-mind that are primarily driven by the accumulation of additional noisy sensory evidence after the initial decision. In a motion discrimination task, we demonstrate that changes-of-mind can occur even in the absence of additional evidence after the initial decision. Unlike previous studies of changes-of-mind, the majority of changes-of-mind in our experiment occurred in trials with prolonged initial response times. This suggests a distinct mechanism underlying such changes. Using a neural circuit model of decision uncertainty and change-of-mind behaviour, we demonstrate that this phenomenon is associated with top-down signals mediated by an uncertainty-monitoring neural population. Such a mechanism is consistent with recent neurophysiological evidence showing a link between changes-of-mind and elevated top-down neural activity. Our model explains the long response times associated with changes-of-mind through high decision uncertainty levels in such trials, and accounts for the observed motor response trajectories. Overall, our work provides a computational framework that explains changes-of-mind in the absence of new post-decision evidence.Authors SummaryWe used limited availability of sensory evidence during a standard motion discrimination task, and demonstrated that changes-of-mind could occur long after sensory information was no longer available. Unlike previous studies, our experiment further indicated that changes-of-mind were strongly linked to slow response time. We used a reduced version of a previously developed neural computational model of decision uncertainty and change-of-mind to account for these experimental observations. Importantly, our model showed that the replication of these experimental results required a strong link between change-of-mind and high decision uncertainty (i.e. low decision confidence), supporting the notion that change-of-mind are related to decision uncertainty or confidence.
The sensitivity of seabird populations to density‐dependence, environmental stochasticity and anthropogenic mortality
Authors: Miller Julie A. O. , Furness Robert W. , Trinder Mark , Matthiopoulos Jason 
Published: June 2019

AbstractThe balance between economic growth and wildlife conservation is a priority for many governments. Enhancing realism in assessment of population‐level impacts of anthropogenic mortality can help achieve this balance. Population Viability Analysis (PVA) is commonly applied to investigate population vulnerability, but outcomes of PVA are sensitive to formulations of density‐dependence, environmental stochasticity and life history. Current practice in marine assessments is to use precautionary models that assume no compensation from density‐dependence or rescue‐effects via “re‐seeding” from other colonies. However, if we could empirically quantify regulatory population processes, the responses of populations to additional anthropogenic mortality may be assessed with more realism in PVA.Using Bayesian state‐space models fitted to population time series from three sympatric seabird populations, selected for varied life histories, we inferred the extent to which their dynamics are driven by environmental stochasticity and density‐dependence.Based on these inferences, we conducted an exhaustive PVA across credible parameterizations for intrinsic and extrinsic population regulation, simulated as a closed and re‐seeded system. Scenarios of anthropogenic mortality, along a sliding scale of precaution, were applied both proportionally and as a fixed quota using Potential Biological Removal (PBR).Baseline results from fitting revealed clear environmental regulation in two of our three species. Crucially, we found that for our empirically derived, realistic model parameterizations there are risks of decline to real populations even under very precautionary mortality scenarios. We find that PBR is dubious in application as a sustainable tool for population assessment when we account for regulation. Closed versus re‐seeded models showed a large divergence in outcomes, with sharper declines in closed simulations. Fixed‐quota mortality typically induced greater population declines comparative to proportional mortality, subject to regulation and re‐seeding.Synthesis and applications. Practitioners using arbitrary formulations of population regulation risk over‐precaution (economic constraint) or under‐precaution (endangering populations). The demands of increased economic development and preservation of wildlife require that methodologies apply techniques that confer reality and rigour to assessment. The current practice of employing models lacking density‐dependence and empirical environmental information imposes limitations in the efficacy of estimating impacts. Here, we provide a method to quantify the conditions that predominantly regulate a population and exacerbate the risk of decline from anthropogenic mortality. It is in the interests of both developers and conservationists to apply methods in population impact assessments that capture realism in the processes driving population dynamics.
Invasion of Euryops floribundus in degraded South African communal grassland: Unpacking the invasion relationship with elevation, soil properties, the quality and quantity of the herbaceous layer
Authors: Masibonge Gxasheka , Tefera Solomon , Mota Lesoli 
Published: June 2019

AbstractShrub invasion is a recent occurrence in African grassland ecosystems. This study assessed the distribution of Euryops floribundus (a native shrub species) along an elevation and invasion intensity gradients, and its relationship with soil and herbaceous vegetation in a South African grassland. Shrub density increased (p < 0.05) from the uplands (2,301 plants/ha) to the bottomlands (4,888 plants/ha). Themeda triandra (a highly palatable grass) was dominant at the uplands and sloping sites, whereas Eragrostis plana and Sporobolus africanus (poorly palatable grasses) dominated the bottomlands. Upland soils had the highest organic carbon (OC), phosphorous (P), calcium and nitrogen (N) contents, but the lowest shrub density and herbaceous biomass. Canonical correspondence analysis indicated that elevation, soil OC and N contents determine important vegetation variables along the elevation gradient. In the shrub density gradient, soil P, OC and N responded positively to E. floribundus density. Grass biomass in the moderate and heavily invaded sites was high, but the abundance of palatable grasses declined, suggesting that E. floribundus invasion may be concomitant with a decrease in rangeland condition in terms of quality forage provision.
Genetic variants on chromosomes 7p31 and 12p12 are associated with abnormal atrial electrical activation in patients with early‐onset lone atrial fibrillation
Authors: Seifert Mariam B. , Olesen Morten S. , Christophersen Ingrid E. , Nielsen Jonas B. , Carlson Jonas , Holmqvist Fredrik , Tveit Arnljot , Haunsø Stig , Svendsen Jesper H. , Platonov Pyotr G. 
Published: June 2019

AbstractBackgroundAbnormal P‐wave morphology (PWM) has been associated with a history of atrial fibrillation (AF) in earlier studies. Although lone AF is believed to have substantial genetic basis, studies on associations between single nucleotide polymorphisms (SNP) linked to lone AF and PWM have not been reported. We aimed to assess whether SNPs previously associated with lone AF (rs2200733, rs13376333, rs3807989, and rs11047543) are also linked to P‐wave abnormalities.MethodsFour SNPs were studied in 176 unrelated individuals with early‐onset lone AF (age at onset <50 years), median age 38 years (19–63 years), 149 men. Using sinus rhythm ECG, orthogonal PWM was classified as Type 1—positive in leads X and Y and negative in lead Z, Type 2—positive in leads X and Y and biphasic (−/+) in lead Z, Type 3—positive in lead X and biphasic in lead Y (+/−), and the remaining as atypical.ResultsTwo SNPs were found to be significantly associated with altered P‐wave morphology distribution: rs3807989 near the gene CAV1/CAV2 and rs11047543 near the gene SOX5. Both SNPs were associated with a higher risk of non‐Type 1 P‐wave morphology (rs3807989: OR = 4.8, 95% CI = 2.3–10.2, p < 0.001; rs11047543: OR = 4.7, 95% CI = 1.1–20.5, p = 0.04). No association was observed for rs2200733 and rs13376333.ConclusionIn this study, the two variants rs3807989 and rs11047543, previously associated with PR interval and lone AF, were associated with altered P‐wave morphology distribution in patients with early‐onset lone AF. These findings suggest that common genetic variants may modify atrial conduction properties.
Deregulation, workplace, and women: Nurses in private health care in India
Authors: Basu Hemantika 
Published: June 2019

AbstractThe paper examines the growth of private health care in India in the context of its regulatory provisions and questions the work and employment conditions of female care workers (nurses) employed there. Nurses constitute 80% of the total workers in each nursing home/hospital. In the wake of increased demand for private health care since mid‐1990s, insertion of technology and investment is inducing transformation of nursing homes into multi‐ and super‐speciality hospitals resulting in changes in work organization of nurses. This has led to demand for larger numbers of workers. Employers gain by the segmentation in the nursing labor market, paying low wages. Workers face widespread social discrimination, long working hours, and high work intensity. The deplorable situation of a significant section of workers employed in this sector indicates state failure to control the private health sector. Lack of effective standards of work impacts nature of work of the workforce employed in various levels in the healthcare system.
3‐Arylindanones and related compounds as antiproliferative agents against colorectal cancer
Authors: Srivastava Ankita , Ravi Kusumoori , Fatima Kaneez , Maheshwari Mayank , Ashraf Raghib , Hasanain Mohammad , Yadav Pankaj , Iqbal Hina , Kumar Yogesh , Luqman Suaib , Chanda Debabrata , Khan Feroz , Shanker Karuna , Sarkar Jayanta , Negi Arvind Singh 
Published: June 2019

AbstractDiverse benzylidene indanones and their derivatives were synthesized as anticancer agents. Two of the analogues, that is 7 and 22, exhibited significant antiproliferative activity against several human cancer cell lines. Both the compounds possessed antimitotic activity and induced apoptosis in DLD1 colorectal adenocarcinoma cells through activation of caspase pathways. In cell cycle analysis, both the compounds induced predominantly G2/M phase arrest in DLD1 cells. Molecular docking studies revealed that compound 7 occupies colchicine binding pocket of β‐tubulin. Both the compounds were safe in acute oral toxicity in rodents. Both the compounds are further being optimized for better efficacy.
Susceptibility‐directed anticoagulation after pancreas transplantation: A single‐center retrospective study
Authors: Raveh Yehuda , Ciancio Gaetano , Burke George W. , Figueiro Jose , Chen Linda , Morsi Mahmoud , Namias Nicholas , Singh Bhavna P. , Lindsay Martine , Alfahel Waseem , Sleem Mahmoud S. , Nicolau‐Raducu Ramona 
Published: June 2019

AbstractPancreas transplant achieves consistent long‐term euglycemia in type 1 diabetes. Allograft thrombosis (AT) causes the majority of early graft failure. We compared outcomes of four anticoagulation regimens administered to 95 simultaneous kidney‐pancreas or isolated pancreas transplanted between 1/1/2015 and 11/20/2018. Early postoperative anticoagulation regimens included the following: none, subcutaneous heparin/aspirin, with or without dextran, and heparin infusion. The regimens were empirically selected based on each surgeon's assessment of hemostasis of the operative field and personal preference. A sonographic‐based global scoring system of AT is presented. The 47‐month recipients and graft survival were 95% and 86%, respectively. Recipients with or without AT had similar survival. Five and four grafts were lost due to death and AT, respectively. Outcomes of prophylaxis regimens correlated with intensity of anticoagulation. Compared with no anticoagulation, an increase in hemorrhagic complications occurred exclusively with iv heparin. The higher arterial AT score found in regimens lacking antiplatelet therapy highlights the importance of early antiaggregants therapy. Abnormal fibrinolysis was associated with an increase in AT score. Platelet dysfunction, warm ischemia time, and enteric drainage were predictive of AT and, along with other known risk factors, were incorporated into an algorithm that matches intensity of early postoperative anticoagulation to the thrombotic risk.
The role of gene fusions in melanocytic neoplasms
Authors: Quan Victor L. , Panah Elnaz , Zhang Bin , Shi Katherine , Mohan Lauren S. , Gerami Pedram 
Published: June 2019

AbstractRecent advances in next generation sequencing (NGS) have allowed for efficient whole transcriptome sequencing, leading to the identification of important kinase fusions as the primary driver in some melanocytic neoplasms. These fusions typically occur mutually exclusively of one another and other well‐known initiating mutations such as BRAF, NRAS, NF1, KIT, and GNAQ. Fusions are found in over 50% of Spitz neoplasms, including ALK, BRAF, NTRK1, NTRK3, ROS1, MET, MAP3K8, and RET. Familiarity with the typical morphologic features of certain fusion‐driven melanocytic neoplasms can help with classification, diagnosis, and identification of targeted molecular therapies in malignant cases. Spitz tumors with ALK, NTRK1, and NTRK3 fusions have characteristic morphologic features. BRAF and MAP3K8 fusions, in particular, tend to be epithelioid, high grade, and more frequent in Spitz melanoma than other fusion subtypes. Sporadic cases of pigmented epithelioid melanocytoma may have PRKCA fusions and sheets of monomorphic epithelioid melanocytes. Fusion events are also enriched among melanomas without the key mutations BRAF, NRAS, or NF1. Although NGS is the most reliable method to detect fusions, immunohistochemistry and fluorescence in situ hybridization are cost‐effective alternatives in some cases. We describe recent discoveries regarding the role of kinase fusions in melanocytic neoplasms and their associated morphologies.