Miracle-dz/UniFAR-FTUs huggingface dataset:
GRB 091024A AND THE NATURE OF ULTRA-LONG GAMMA-RAY BURSTS

We present a broadband study of gamma-ray burst (GRB) 091024A within the context of other ultra-long-duration GRBs. An unusually long burst detected by Konus–Wind (KW), Swift, and Fermi, GRB 091024A has prompt emission episodes covering ∼1300 s, accompanied by bright and highly structured optical emission captured by various rapid-response facilities, including the 2 m autonomous robotic Faulkes North and Liverpool Telescopes, KAIT, S-LOTIS, and the Sonoita Research Observatory. We also observed the burst with 8 and 10 m class telescopes and determine the redshift to be z = 1.0924 ± 0.0004. We find no correlation between the optical and γ-ray peaks and interpret the optical light curve as being of external origin, caused by the reverse and forward shock of a highly magnetized jet (RB ≈ 100–200). Low-level emission is detected throughout the near-background quiescent period between the first two emission episodes of the KW data, suggesting continued central-engine activity; we discuss the implications of this ongoing emission and its impact on the afterglow evolution and predictions. We summarize the varied sample of historical GRBs with exceptionally long durations in gamma-rays (≳1000 s) and discuss the likelihood of these events being from a separate population; we suggest ultra-long GRBs represent the tail of the duration distribution of the long GRB population.
Life Cycle and Morphology of a Cambrian Stem-Lineage Loriciferan

Cycloneuralians form a rich and diverse element within Cambrian assemblages of exceptionally preserved fossils. Most resemble priapulid worms whereas other Cycloneuralia (Nematoda, Nematomorpha, Kinorhyncha, Loricifera), well known at the present day, have little or no fossil record. First reports of Sirilorica Peel, 2010 from the lower Cambrian Sirius Passet fauna of North Greenland described a tubular lorica covering the abdomen and part of a well developed introvert with a circlet of 6 grasping denticles near the lorica. The introvert is now known to terminate in a narrow mouth tube, while a conical anal field is also developed. Broad muscular bands between the plates in the lorica indicate that it was capable of movement by rhythmic expansion and contraction of the lorica. Sirilorica is regarded as a macrobenthic member of the stem-lineage of the miniaturised, interstitial, present day Loricifera. Like loriciferans, Sirilorica is now known to have grown by moulting. Evidence of the life cycle of Sirilorica is described, including a large post-larval stage and probably an initial larva similar to that of the middle Cambrian fossil Orstenoloricusshergoldii .
Assembly of long error-prone reads using de Bruijn graphs

Significance When the long reads generated using single-molecule se-quencing (SMS) technology were made available, most researchers were skeptical about the ability of existing algorithms to generate high-quality assemblies from long error-prone reads. Nevertheless, recent algorithmic breakthroughs resulted in many successful SMS sequencing projects. However, as the recent assemblies of important plant pathogens illustrate, the problem of assembling long error-prone reads is far from being resolved even in the case of relatively short bacterial genomes. We propose an algorithmic approach for assembling long error-prone reads and describe the ABruijn assembler, which results in accurate genome reconstructions. The recent breakthroughs in assembling long error-prone reads were based on the overlap-layout-consensus (OLC) approach and did not utilize the strengths of the alternative de Bruijn graph approach to genome assembly. Moreover, these studies often assume that applications of the de Bruijn graph approach are limited to short and accurate reads and that the OLC approach is the only practical paradigm for assembling long error-prone reads. We show how to generalize de Bruijn graphs for assembling long error-prone reads and describe the ABruijn assembler, which combines the de Bruijn graph and the OLC approaches and results in accurate genome reconstructions.
Repetitive Transcranial Magnetic Stimulation, Cognition, and Multiple Sclerosis: An Overview

Multiple sclerosis (MS) affects cognition in the majority of patients. A major aspect of the disease is brain volume loss (BVL), present in all phases and types (relapsing and progressive) of the disease and linked to both motor and cognitive disabilities. Due to the lack of effective pharmacological treatments for cognition, cognitive rehabilitation and other nonpharmacological interventions such as repetitive transcranial magnetic stimulation (rTMS) have recently emerged and their potential role in functional connectivity is studied. With recently developed advanced neuroimaging and neurophysiological techniques, changes related to alterations of the brain's functional connectivity can be detected. In this overview, we focus on the brain's functional reorganization in MS, theoretical and practical aspects of rTMS utilization in humans, and its potential therapeutic role in treating cognitively impaired MS patients.
Examining Perceptions of Computerized Physician Order Entry in a Neonatal Intensive Care Unit

Summary Background: Computerized provider order entry (CPOE) is a technology with potential to transform care delivery. While CPOE systems have been studied in adult populations, less is known about the implementation of CPOE in the neonatal intensive care unit (NICU) and perceptions of nurses and physicians using the system. Objective: To examine perceptions of clinicians before and after CPOE implementation in the NICU of a pediatric hospital. Methods: A cross-sectional survey of clinicians working in a Level III NICU was conducted. The survey was distributed before and after CPOE implementation. Participants were asked about their perception of CPOE on patient care delivery, implementation of the system, and effect on job satisfaction. A qualitative section inquired about additional concerns surrounding implementation. Responses were tabulated and analyzed using the Chi-square test. Results: The survey was distributed to 158 clinicians with a 47% response rate for pre-implementation and 45% for post-implementation. Clinicians understood why CPOE was implemented, but felt there was incomplete technical training. The expectation for increased job satisfaction and ability to recruit high-quality staff was high. However, there was concern about the ability to deliver appropriate treatments before and after implementation. Physicians were more optimistic about CPOE implementation than nurses who remained concerned that workflow may be altered. Conclusions: Introducing CPOE is a potentially risky endeavor and must be done carefully to mitigate harm. Although high expectations of the system can be met, it is important to attend to differing expectations among clinicians with varied levels of comfort with technology. Interdisciplinary collaboration is critical in planning a functioning CPOE to ensure that efficient workflow is maintained and appropriate supports for individuals with a lower degree of technical literacy is available. Citation: Beam KS, Cardoso M, Sweeney M, Binney G, Weingart SN. Examining perceptions of computerized physician order entry in a neonatal intensive care unit. Appl Clin Inform 2017; 8: 337–347 https://doi.org/10.4338/ACI-2016-09-RA-0153
Safety of endovascular treatment in acute stroke patients taking oral anticoagulants

Background The endovascular treatment of acute cerebral ischemia has been proven beneficial without major safety concerns. To date, the role of endovascular treatment in patients treated with oral anticoagulants, which may be associated with periprocedural intracranial bleeding, remains uncertain. Aims The objective of the current analysis is to evaluate the safety of endovascular treatment in patients treated with oral anticoagulants. Methods The ENDOSTROKE-Registry is a commercially independent, prospective observational study in 12 stroke centers in Germany and Austria collecting pre-specified variables about endovascular stroke therapy. Results Data from 815 patients (median age 70 (interquartile range (IQR) 20), 57% male) undergoing endovascular treatment with known anticoagulation status were analyzed. A total of 85 (median age 76 (IQR 8), 52% male) patients (10.4%) took vitamin-K-antagonists prior to endovascular treatment. Anticoagulation status as measured with international normalized ratio was above 2.0 in 31 patients. Intracranial hemorrhage occurred in 11.8% of patients taking vitamin-K-antagonists compared to no-vitamin-K-antagonists (12.2%, p = 0.909). After adjustment for confounding factors which were unbalanced at univariate level such as NIHSS and age, anticoagulation status was not found to significantly influence clinical outcome (modified Rankin Scale 3–6) and occurrence of intracranial hemorrhage in a multivariate logistic regression analysis. Conclusion Prior use of vitamin-K-antagonists was not associated with a higher rate of periprocedural intracranial hemorrhage after endovascular treatment or worse outcome. Endovascular treatment should be considered as an important treatment option in patients taking vitamin-K-antagonists.
Safe Practices for Copy and Paste in the EHR

Summary Background: Copy and paste functionality can support efficiency during clinical documentation, but may promote inaccurate documentation with risks for patient safety. The Partnership for Health IT Patient Safety was formed to gather data, conduct analysis, educate, and disseminate safe practices for safer care using health information technology (IT). Objective: To characterize copy and paste events in clinical care, identify safety risks, describe existing evidence, and develop implementable practice recommendations for safe reuse of information via copy and paste. Methods: The Partnership 1) reviewed 12 reported safety events, 2) solicited expert input, and 3) performed a systematic literature review (2010 to January 2015) to identify publications addressing frequency, perceptions/attitudes, patient safety risks, existing guidance, and potential interventions and mitigation practices. Results: The literature review identified 51 publications that were included. Overall, 66% to 90% of clinicians routinely use copy and paste. One study of diagnostic errors found that copy and paste led to 2.6% of errors in which a missed diagnosis required patients to seek additional unplanned care. Copy and paste can promote note bloat, internal inconsistencies, error propagation, and documentation in the wrong patient chart. Existing guidance identified specific responsibilities for authors, organizations, and electronic health record (EHR) developers. Analysis of 12 reported copy and paste safety events was congruent with problems identified from the literature review. Conclusion: Despite regular copy and paste use, evidence regarding direct risk to patient safety remains sparse, with significant study limitations. Drawing on existing evidence, the Partnership developed four safe practice recommendations: 1) Provide a mechanism to make copy and paste material easily identifiable; 2) Ensure the provenance of copy and paste material is readily available; 3) Ensure adequate staff training and education; 4) Ensure copy and paste practices are regularly monitored, measured, and assessed.
Bayesian Optimisation of Large-Scale Biophysical Networks

The relationship between structure and function in the human brain is well established, but not yet well characterised. Large-scale biophysical models allow us to investigate this relationship, by leveraging structural information (e.g. derived from diffusion tractography) in order to couple dynamical models of local neuronal activity into networks of interacting regions distributed across the cortex. In practice however, these models are difficult to parametrise, and their simulation is often delicate and computationally expensive. This undermines the experimental aspect of scientific modelling, and stands in the way of comparing different parametrisations, network architectures, or models in general, with confidence. Here, we advocate the use of Bayesian optimisation for assessing the capabilities of biophysical network models, given a set of desired properties (e.g. band-specific functional connectivity); and in turn the use of this assessment as a principled basis for incremental modelling and model comparison. We adapt an optimisation method designed to cope with costly, high-dimensional, non-convex problems, and demonstrate its use and effectiveness. We find that this method is able to converge to regions of high functional similarity with real MEG data, with very few samples given the number of parameters, without getting stuck in local extrema, and while building and exploiting a map of uncertainty defined smoothly across the parameter space. We compare the results obtained using different methods of structural connectivity estimation from diffusion tractography, and find that one method leads to better simulations.
Effects of Reduced pH on Macoma balthica Larvae from a System with Naturally Fluctuating pH-Dynamics

Ocean acidification is causing severe changes in the inorganic carbon balance of the oceans. The pH conditions predicted for the future oceans are, however, already regularly occurring in the Baltic Sea, and the system might thus work as an analogue for future ocean acidification scenarios. The characteristics of the Baltic Sea with low buffering capacity and large natural pH fluctuations, in combination with multiple other stressors, suggest that OA effects may be severe, but remain largely unexplored. A calcifying species potentially affected by low pH conditions is the bivalve Macoma balthica (L.). We investigated larval survival and development of M. balthica by exposing the larvae to a range of pH levels: 7.2, 7.4, 7.7 and 8.1 during 20 days in order to learn what the effects of reduced pH are on the larval biology and thus also potentially for the population dynamics of this key species. We found that even a slight pH decrease causes significant negative changes during the larval phase, both by slowing growth and by decreasing survival. The growth was slower in all reduced pH treatments compared to the control treatment. The size of 250 µm that is considered indicative to imminent settling in our system was reached by 22% of the larvae grown in control conditions after 20 days, whereas in all reduced pH treatments the size of 250 µm was reached by only 7–14%. The strong impact of ocean acidification on larvae is alarming as slowly growing individuals are exposed to higher predation risk in response to the longer time they are required to spend in the plankton, further decreasing the ecological competence of the species.
Twenty-first century climate change and submerged aquatic vegetation in a temperate estuary: the case of Chesapeake Bay

ABSTRACT Introduction: The Chesapeake Bay was once renowned for expansive meadows of submerged aquatic vegetation (SAV). However, only 10% of the original meadows survive. Future restoration efforts will be complicated by accelerating climate change, including physiological stressors such as a predicted mean temperature increase of 2–6°C and a 50–160% increase in CO2 concentrations. Outcomes: As the Chesapeake Bay begins to exhibit characteristics of a subtropical estuary, summer heat waves will become more frequent and severe. Warming alone would eventually eliminate eelgrass (Zostera marina) from the region. It will favor native heat-tolerant species such as widgeon grass (Ruppia maritima) while facilitating colonization by non-native seagrasses (e.g., Halodule spp.). Intensifying human activity will also fuel coastal zone acidification and the resulting high CO2/low pH conditions may benefit SAV via a “CO2 fertilization effect. ” Discussion: Acidification is known to offset the effects of thermal stress and may have similar effects in estuaries, assuming water clarity is sufficient to support CO2-stimulated photosynthesis and plants are not overgrown by epiphytes. However, coastal zone acidification is variable, driven mostly by local biological processes that may or may not always counterbalance the effects of regional warming. This precarious equipoise between two forces – thermal stress and acidification – will be critically important because it may ultimately determine the fate of cool-water plants such as Zostera marina in the Chesapeake Bay. Conclusion: The combined impacts of warming, coastal zone acidification, water clarity, and overgrowth of competing algae will determine the fate of SAV communities in rapidly changing temperate estuaries.
Anticonvulsant and Antioxidant Effects of Musa sapientum Stem Extract on Acute and Chronic Experimental Models of Epilepsy

Background: Musa sapientum (banana) plant extract has been shown to possess antioxidant activity in previous studies. Neuronal injury resulting from oxidative stress is an important factor involved in pathogenesis of epilepsy. Objective: The present study aimed to evaluate the anticonvulsant activity of M. sapientum stem extract (MSSE) in acute and chronic experimental models in mice and its effects on various markers of oxidative stress in the brain of pentylenetetrazole (PTZ)-kindled animals. Material and Methods: Maximal electroshock seizures (MES) and PTZ-induced convulsion models were used for acute studies. For the chronic study, the effect of MSSE on the development of kindling was studied. For the evaluation of the effects of MSSE on oxidative stress in brain, malondialdehyde (MDA) and reduced glutathione (GSH) levels were estimated in the brains of the kindled animals. Results: MSSE significantly increased the latency to onset of myoclonic jerks and the duration of clonic convulsions following PTZ administration. The MSSE pretreated group showed significantly reduced mean seizure score on PTZ-induced kindling. There was a significant increase in the brain MDA levels and decrease in GSH levels in response to PTZ-induced kindling. On MSSE pretreatment, there was a significant decrease in the MDA levels in the brains, though the increase in the GSH levels was not significant. Conclusion: The results from this study suggest the presence of significant anticonvulsant activity in MSSE, in both acute and chronic PTZ-induced seizure models, which could be due to its antioxidant activity, as is reflected by the change in oxidative stress markers in brain.
Relative Abundance of Integral Plasma Membrane Proteins in Arabidopsis Leaf and Root Tissue Determined by Metabolic Labeling and Mass Spectrometry

Metabolic labeling of proteins with a stable isotope (15N) in intact Arabidopsis plants was used for accurate determination by mass spectrometry of differences in protein abundance between plasma membranes isolated from leaves and roots. In total, 703 proteins were identified, of which 188 were predicted to be integral membrane proteins. Major classes were transporters, receptors, proteins involved in membrane trafficking and cell wall-related proteins. Forty-one of the integral proteins, including nine of the 13 isoforms of the PIP (plasma membrane intrinsic protein) aquaporin subfamily, could be identified by peptides unique to these proteins, which made it possible to determine their relative abundance in leaf and root tissue. In addition, peptides shared between isoforms gave information on the proportions of these isoforms. A comparison between our data for protein levels and corresponding data for mRNA levels in the widely used database Genevestigator showed an agreement for only about two thirds of the proteins. By contrast, localization data available in the literature for 21 of the 41 proteins show a much better agreement with our data, in particular data based on immunostaining of proteins and GUS-staining of promoter activity. Thus, although mRNA levels may provide a useful approximation for protein levels, detection and quantification of isoform-specific peptides by proteomics should generate the most reliable data for the proteome.
Monovalent Cation Permeation through the Connexin40 Gap Junction Channel

The unitary conductances and permeability sequences of the rat connexin40 (rCx40) gap junction channels to seven monovalent cations and anions were studied in rCx40-transfected neuroblastoma 2A (N2A) cell pairs using the dual whole cell recording technique. Chloride salt cation substitutions (115 mM principal salt) resulted in the following junctional maximal single channel current-voltage relationship slope conductances (γj in pS): CsCl (153), RbCl (148), KCl (142), NaCl (115), LiCl (86), TMACl (71), TEACl (63). Reversible block of the rCx40 channel was observed with TBA. Potassium anion salt γj are: Kglutamate (160), Kacetate (160), Kaspartate (158), KNO3 (157), KF (148), KCl (142), and KBr (132). Ion selectivity was verified by measuring reversal potentials for current in rCx40 gap junction channels with asymmetric salt solutions in the two electrodes and using the Goldman-Hodgkin-Katz equation to calculate relative permeabilities. The permeabilities relative to Li+ are: Cs+ (1.38), Rb+ (1.32), K+ (1.31), Na+ (1.16), TMA+ (0.53), TEA+ (0.45), TBA+ (0.03), Cl− (0.19), glutamate− (0.04), and NO3− (0.14), assuming that the monovalent anions permeate the channel by forming ion pairs with permeant monovalent cations within the pore thereby causing proportionate decreases in the channel conductance. This hypothesis can account for why the predicted increasing conductances with increasing ion mobilities in an essentially aqueous channel were not observed for anions in the rCx40 channel. The rCx40 effective channel radius is estimated to be 6.6 Å from a theoretical fit of the relationship of relative permeability and cation radius.
Synaptic Alterations in Mouse Models for Alzheimer Disease—A Special Focus on N-Truncated Abeta 4-42

This commentary reviews the role of the Alzheimer amyloid peptide Aβ on basal synaptic transmission, synaptic short-term plasticity, as well as short- and long-term potentiation in transgenic mice, with a special focus on N-terminal truncated Aβ4-42. Aβ4-42 is highly abundant in the brain of Alzheimer’s disease (AD) patients. It demonstrates increased neurotoxicity compared to full length Aβ, suggesting an important role in the pathogenesis of AD. Transgenic Tg4-42 mice, a model for sporadic AD, express human Aβ4-42 in Cornu Ammonis (CA1) neurons, and develop age-dependent hippocampal neuron loss and neurological deficits. In contrast to other transgenic AD mouse models, the Tg4-42 model exhibits synaptic hyperexcitability, altered synaptic short-term plasticity with no alterations in short- and long-term potentiation. The outcomes of this study are discussed in comparison with controversial results from other AD mouse models.
Development of Parametric Kelvin Structures will Closed Cells

This work presents the design of a parametric Kelvin structure in which the relative density of the geometry can be varied by adjusting three parameters: cell diameter, cell wall thickness and cell chamfer radius, the structure consistsing of a tessellation of hollow truncated octahedral. The developed model was evaluated in terms of compressive stiffness for the case of a rigid polyurethane foam of 0.256 relative density. Three models were analyzed in order to determine the influence of geometric characteristics on mechanical properties: a model that presented no chamfer a model that presented a medium-sized chamfer and a model that presented a large chamfer. A mesh convergence study was performed which analyzed the results in terms of accuracy and time expenses for three element sizes for both linear and quadratic elements. Due to the orthotropic nature of the model, its response on both possible loading directions was investigated. Simulation results were compared with experimental results and yielded accurate results for one loading direction, when using the material properties for solid polyurethane described in literature.