bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surgical residents' interpretation of diagnostic radiologic imaging in the traumatically injured patient
Authors: Fakhoury Elias , Abolghasemi Daria , McKinney Justin , Naumova Alena , Wessner Scott , Elsawy Osama , Zuberi Jamshed , Madlinger Robert V. 
Published: September 2017

BACKGROUND
Senior surgical residents are of paramount importance in directing further therapeutic modalities based on their interpretation of critical diagnostic imaging. We propose that senior surgical residents are proficient with interpreting radiologic imaging studies in the trauma patient.

METHODS
A prospective cohort study was performed comparing surgery resident interpretations of computed tomography (CT) scans of the head, maxillofacial bones, spine (cervical, thoracic, lumbar), chest, abdomen, pelvis, and chest X-rays versus final radiologists' reports at a Level II trauma center from September 2014 to May 2015. A Cohen κ coefficient and a statistical analysis of variance testing were used to make multiple comparisons of the data.

RESULTS
There were 951 trauma alerts activated in the period stated. Of these, 860 met our age inclusion criteria (age, > 18 years). There were 204 images included with an overall accuracy of 81.3%. Residents were more than 70% successful interpreting seven of nine categories. They achieved an accuracy of 84.6%, 62.5%, and 75% in the cervical, thoracic, and lumbar spine categories, respectively. Forty-one of 50 CT scans of the head were interpreted correctly. Maxillofacial CT scans proved to be the weakest category, with only 50% read accurately. In regard to CT scans of the abdomen and pelvis, 80% proficiency was achieved. Abdominal x-rays were read correctly in all instances and chest x-rays 83.3%. On κ analysis, there was an overall moderate agreement between the two groups with K = 0.449, and an overall p less than 0.0005 (Table 1). A perfect agreement existed with abdominal x-rays.

CONCLUSION
Senior surgical residents are capable of interpreting critical images obtained in the trauma setting. When discordance existed with attending radiologists' interpretation, it did not change the clinical outcome or result in any critically missed findings.

Level of Evidence
Therapeutic/Care Management study, Level IV.
Management of Emergency Electroconvulsive Therapy in the Intensive Care Unit for Life-Threatening Psychiatric Conditions
Authors: Bulteau Samuel , Laforgue Edouard-Jules , Chimot Loïc , Dumont Romain , Loutrel Olivier , Etcheverrigaray François , Victorri-Vigneau Caroline , Massri Alexandre , Vanelle Jean-Marie , Sauvaget Anne 
Published: September 2017

Abstract
Catatonia can lead to severe complications and may be lethal but is often underdiagnosed. The clinical presentation can be similar to coma. In these situations, electroconvulsive therapy (ECT) can be used as first-line treatment to enable extubation, recovery of autonomy, and rapid discharge from intensive care. We report 4 cases of patients hospitalized in the intensive care unit with comatose clinical presentation and life-threatening condition caused by catatonia. All patients received ECT sessions, after which the catatonic symptoms partially or fully remitted. We discuss the clinical identification, general considerations, ECT feasibility, and parameters in the intensive care unit, as well as the differential diagnosis, drug precautions, and prevention concerns.
On the Keller–Rubinow model for Liesegang ring formation
Authors: Duley J. M. , Fowler A. C. , Moyles I. R. , O'Brien S. B. G. 
Published: September 2017

We study the model of Keller & Rubinow (Keller & Rubinow 1981J. Chem. Phys74, 5000–5007. (doi:10.1063/1.441752)) describing the formation of Liesegang rings due to Ostwald's supersaturation mechanism. Keller and Rubinow provided an approximate solution both for the growth and equilibration of the first band, and also for the formation of secondary bands, based on a presumed asymptotic limit. However, they did not provide a parametric basis for the assumptions in their solution, nor did they provide any numerical corroboration, particularly of the secondary band formation. Here, we provide a different asymptotic solution, based on a specific parametric limit, and we show that the growth and subsequent cessation of the first band can be explained. We also show that the model is unable to explain the formation of finite width secondary bands, and we confirm this result by numerical computation. We conclude that the model is not fully posed, lacking a transition variable which can describe the hysteretic switch across the nucleation threshold.
On the topology of the Lorenz system
Authors: Pinsky Tali 
Published: September 2017

We present a new paradigm for three-dimensional chaos, and specifically for the Lorenz equations. The main difficulty in these equations and for a generic flow in dimension 3 is the existence of singularities. We show how to use knot theory as a way to remove the singularities. Specifically, we claim: (i) for certain parameters, the Lorenz system has an invariant one-dimensional curve, which is a trefoil knot. The knot is a union of invariant manifolds of the singular points. (ii) The flow is topologically equivalent to an Anosov flow on the complement of this curve, and moreover to a geodesic flow. (iii) When varying the parameters, the system exhibits topological phase transitions, i.e. for special parameter values, it will be topologically equivalent to an Anosov flow on a knot complement. Different knots appear for different parameter values and each knot controls the dynamics at nearby parameters.
Integration of anatomy ontologies and evo-devo using structured Markov models suggests a new framework for modeling discrete phenotypic traits
Authors: Tarasov Sergei 
Published: September 2017

AbstractModeling discrete phenotypic traits for either ancestral character state reconstruction or morphology-based phylogenetic inference suffers from ambiguities of character coding, homology assessment, dependencies, and selection of adequate models. These drawbacks occur because trait evolution is driven by two key processes – hierarchical and hidden – which are not accommodated simultaneously by the available phylogenetic methods. The hierarchical process refers to the dependencies between anatomical body parts, while the hidden process refers to the evolution of gene regulatory networks underlying trait development. Herein, I demonstrate that these processes can be efficiently modeled using structured Markov models equipped with hidden states, which resolves the majority of the problems associated with discrete traits. Integration of structured Markov models with anatomy ontologies can adequately incorporate the hierarchical dependencies, while the use of the hidden states accommodates hidden evolution of gene regulatory networks and substitution rate heterogeneity. I assess the new models using simulations and theoretical synthesis. The new approach solves the long-standing tail color problem (that aims at coding tail when it is absent) and presents a previously unknown issue called the “two-scientist paradox”. The latter issue refers to the confounding nature of the coding of a trait and the hidden processes driving the trait’s evolution; failing to account for the hidden process may result in a bias, which can be avoided by using hidden state models. All this provides a clear guideline for coding traits into characters. This paper gives practical examples of using the new framework for phylogenetic inference and comparative analysis.
Regulator of calcineurin-2 is a centriolar protein with a role in cilia length control
Authors: Stevenson Nicola L. , Bergen Dylan J.M. , Xu Amadeus , Wyatt Emily , Henry Freya , McCaughey Janine , Vuolo Laura , Hammond Chrissy L. , Stephens David J. 
Published: September 2017

AbstractAlmost every cell in the human body extends a primary cilium. Defective cilia function leads to a set of disorders known as ciliopathies characterised by debilitating developmental defects affecting many tissues. Here we report a new role for regulator of calcineurin 2, RCAN2, in primary cilia function. It localises to centrioles and the basal body and is required to maintain normal cilia length. RCAN2 was identified as the most strongly upregulated gene from a comparative RNAseq analysis of cells in which expression of the Golgi matrix protein giantin had been abolished by gene editing. In contrast to previous work where we showed that depletion of giantin by RNAi results in defects in ciliogenesis and in cilia length control, giantin knockout cells generate normal cilia on serum withdrawal. Furthermore, giantin knockout zebrafish show increased expression of RCAN2. Importantly, suppression of RCAN2 expression in giantin knockout cells results in the same defects in cilia length control seen on RNAi of giantin itself. Together these data define RCAN2 as a regulator of cilia function that can compensate for loss of giantin function.
A blood-based signature of cerebrospinal fluid Aβ1–42status
Authors: Goudey Benjamin , Fung Bowen J , Schieber Christine ,   for the Alzheimer’s Disease Metabolomics Consortium,   for the Alzheimer’s Disease Neuroimaging Initiative, Faux Noel G 
Published: September 2017

ABSTRACTIt is increasingly recognized that Alzheimer’s disease (AD) exists before dementia is present and that shifts in amyloid beta occur long before clinical symptoms can be detected. Early detection of these molecular changes is a key aspect for the success of interventions aimed at slowing down rates of cognitive decline. Recent evidence indicates that of the two established methods for measuring amyloid, a decrease in cerebrospinal fluid (CSF) amyloidβ1–42(Aβ1–42) may be an earlier indicator of Alzheimer’s disease risk than measures of amyloid obtained from Positron Emission Tomography (PET). However, CSF collection is highly invasive and expensive. In contrast, blood collection is routinely performed, minimally invasive and cheap. In this work, we develop a blood-based signature that can provide a cheap and minimally invasive estimation of an individual’s CSF amyloid status using a machine learning approach. We show that a Random Forest model derived from plasma analytes can accurately predict subjects as having abnormal (low) CSF Aβ1–42levels indicative of AD risk (0.84 AUC, 0.78 sensitivity, and 0.73 specificity). Refinement of the modeling indicates that onlyAPOEε4carrier status and four plasma analytes (CGA, Aβ1–42, Eotaxin 3, APOE) are required to achieve a high level of accuracy. Furthermore, we show across an independent validation cohort that individuals with predicted abnormal CSF Aβ1–42levels transitioned to an AD diagnosis over 120 months significantly faster than those with predicted normal CSF Aβ1–42levels and that the resulting model also validates reasonably across PET Aβ1-42status (0.78 AUC).This is the first study to show that a machine learning approach, using plasma protein levels, age andAPOEε4carrier status, is able to predict CSF Aβ1–42status, the earliest risk indicator for AD, with high accuracy.
Diminished dynamic cerebral autoregulatory capacity with forced oscillations in mean arterial pressure with elevated cardiorespiratory fitness
Authors: Labrecque Lawrence , Rahimaly Kevan , Imhoff Sarah , Paquette Myriam , Le Blanc Olivier , Malenfant Simon , Lucas Samuel JE , Bailey Damian M. , Smirl Jonathan D. , Brassard Patrice 
Published: September 2017

AbstractThe effect that cardiorespiratory fitness has on the dynamic cerebral autoregulatory capacity during changes in mean arterial pressure (MAP) remains equivocal. Using a multiple-metrics approach, challenging MAP across the spectrum of physiological extremes (i.e. spontaneous through forced MAP oscillations), we characterized dynamic cerebral autoregulatory capacity in 19 male endurance athletes and 8 controls via three methods: [1] onset of regulation (i.e., time delay before an increase in middle cerebral artery (MCA) conductance [MCA flow velocity (MCAv)/mean arterial pressure (MAP)] and rate of regulation, after transient hypotension induced by sit-to-stand, and transfer function analysis (TFA) of MAP and MCAv responses during [2] spontaneous and [3] forced oscillations (5-min of squat-stand maneuvers performed at 0.05 and 0.10 Hz). Reductions in MAP and mean MCAv (MCAVmean) during initial orthostatic stress (0-30 s after sit-to-stand) and the prevalence of orthostatic hypotension were also determined. Onset of regulation was delayed after sit-to-stand in athletes (3.1±1.7 vs. 1.5±1.0 s; p=0.03), but rate of regulation was not different between groups (0.24±0.05 vs. 0.21±0.09 s-1; p=0.82). While both groups had comparable TFA metrics during spontaneous oscillations, athletes had higher TFA gain during 0.10 Hz squat-stand vs. recreational controls (p=0.01). Reductions in MAP (p=0.15) and MCAVmean(p=0.11) during orthostatic stress and the prevalence of initial orthostatic hypotension (p=0.65) were comparable between groups. These results indicate an intact ability of the cerebral vasculature to react to spontaneous oscillations but an attenuated capability to counter rapid and large changes in MAP in individuals with elevated cardiorespiratory fitness.New findingsWhat is the central question of this study?What is the impact of cardiorespiratory fitness on dynamic cerebral autoregulatory capacity?What is the main finding and its importance?Our results indicate an intact ability of the cerebral vasculature to react to spontaneous oscillations but an attenuated capability to counter rapid and large changes in mean arterial pressure in individuals with elevated cardiorespiratory fitness.
Limitations of compensatory plasticity: the organization of the primary sensorimotor cortex in foot-using bilateral upper limb dysplasics
Authors: Striem-Amit Ella , Vannuscorps Gilles , Caramazza Alfonso 
Published: September 2017

SummaryWhat forces direct brain organization and its plasticity? When a brain region is deprived of its input would this region reorganize based on compensation for the disability and experience, or would strong limitations of brain structure limit its plasticity? People born without hands activate their sensorimotor hand region while moving body parts used to compensate for this ability (e.g. their feet). This has been taken to suggest a neural organization based on functions, such as performing manual-like dexterous actions, rather than on body parts. Here we test the selectivity for functionally-compensatory body parts in the sensorimotor cortex of people born without hands. Despite clear compensatory foot use, the sensorimotor hand area in the dysplasic subjects showed preference for body parts whose cortical territory is close to the hand area, but which are not compensatorily used as effectors. This suggests that function-based organization, originally proposed for congenital blindness and deafness, does not apply to cases of the primary sensorimotor cortex deprivation in dysplasia. This is consistent with the idea that experience-independent functional specialization occurs at relatively high levels of representation. Indeed, increased and selective foot movement preference in the dysplasics was found in the association cortex, in the inferior parietal lobule. Furthermore, it stresses the roles of neuroanatomical constraints such as topographical proximity and connectivity in determining the functional development of brain regions. These findings reveal limitations to brain plasticity and to the role of experience in shaping the functional organization of the brain.Significance StatementWhat determines the role of brain regions, and their plasticity when typical inputs or experience is not provided? To what extent can extreme compensatory use affect brain organization? We tested the functional reorganization of the primary sensorimotor cortex hand area in people born without hands, who use their feet for every-day tasks. We found that it is preferentially activated by close-by body-parts which cannot serve as effectors, and not by the feet. In contrast, foot-selective compensatory plasticity was found in the association cortex, in an area involved in tool use. This shows limitations of compensatory plasticity and experience in modifying brain organization of early topographical cortex, as compared to association cortices where function-based organization is the driving factor.ClassificationBiological Sciences\Neuroscience
Big trouble with little inserts: boundaries in metagenomic screenings usinglacZα based vectors
Authors: Alves Luana de Fátima , Borelli Tiago Cabral , Westmann Cauã Antunes , Silva-Rocha Rafael , Guazzaroni María-Eugenia 
Published: September 2017

AbstractThe vast biochemical repertoire found in microbial communities from a wide-range of environments allows screening and isolation of novel enzymes with improved catalytic features. In this sense, metagenomics approaches have been of high relevance for providing enzymes used in diverse industrial applications. For instance, glycosyl hydrolases, which catalyze the hydrolysis of carbohydrates to sugars, are essential for bioethanol production from renewable resources. In the current study, we have focused on the prospection of protease and glycosyl hydrolase activities from microbial communities inhabiting a soil sample by using thelacZα-based plasmid pSEVA232 in the generation of a screenable metagenomic library. For this, we used a functional screen based on skimmed milk agar and a pH indicator dye as previously reported in literature. Although we effectively identified nine positive clones in the screenings, subsequent experiments revealed that this phenotype was not because of the hydrolytic activity encoded in the metagenomic fragments, but rather due to the insertion of small metagenomic DNA fragmentsin framewithin the coding region of thelacZαalpha gene present in the original vector. We concluded that the current method has a higher tendency for false positive recovery of clones, when used in combination with alacZα-based vector. Finally, we discuss the molecular explanation for positive phenotype recovering and highlight the importance of reporting boundaries in metagenomic screenings methodologies.
Functional genomics of lipid metabolism in the oleaginous yeastRhodosporidium toruloides
Authors: Coradetti Samuel T , Pinel Dominic , Geiselman Gina , Ito Masakazu , Mondo Stephen , Reilly Morgann C , Cheng Ya-Fang , Bauer Stefan , Grigoriev Igor V , Gladden John M , Simmons Blake A , Brem Rachel B , Arkin Adam P , Skerker Jeffrey M 
Published: September 2017

AbstractThe basidomycete yeastRhodosporidium toruloides(a.k.a.Rhodotorula toruloides)accumulates high concentrations of lipids and carotenoids from diverse carbon sources. It has great potential as a model for the cellular biology of lipid droplets and for sustainable chemical production. We developed a method for high-throughput genetics (RB-TDNAseq), using sequence-barcodedAgrobacterium tumefaciensT-DNA insertions into theR. toruloidesgenome. We identified 1337 putative essential genes with low T-DNA insertion rates. We functionally profiled genes required for fatty acid catabolism and lipid accumulation, validating results with 35 targeted deletion strains. We found that both mitochondrial and peroxisomal enzymes were required for growth on fatty acids, with different peroxisomal enzymes required on different fatty acids. We identified a high-confidence set of 150 genes affecting lipid accumulation, including genes with predicted function in signaling cascades, gene expression, protein modification and vesicular trafficking, autophagy, amino acid synthesis and tRNA modification, as well as genes of unknown function. These results greatly advance our understanding of lipid metabolism in this oleaginous species, identify key biological processes to be further explored and optimized for production of lipid-based bioproducts, and demonstrate a general approach for barcoded mutagenesis that should enable functional genomics in diverse fungi.
Simultaneously measuring image features and resolution in live-cell STED images
Authors: Barentine Andrew E. S. , Schroeder Lena K. , Graff Michael , Baddeley David , Bewersdorf Joerg 
Published: September 2017

AbstractReliable interpretation and quantification of cellular features in fluorescence microscopy requires an accurate estimate of microscope resolution. This is typically obtained by measuring the image of a non-biological proxy for a point-like object, such as a fluorescent bead. While appropriate for confocal microscopy, bead-based measurements are problematic for Stimulated Emission Depletion (STED) and similar techniques where the resolution depends critically on the choice of fluorophore and acquisition parameters. We demonstrate that for a known geometry, e.g. tubules, the resolution can be accurately measured by fitting a model that accounts for both the Point Spread Function (PSF) and the fluorophore distribution. To address the problem of coupling between tubule diameter and PSF width, we developed a technique, Nested-loop Ensemble PSF (NEP) fitting. NEP fitting enables extraction of the size of cellular features and the PSF in fixed-cell and live-cell images without relying on beads or pre-calibration. We validate our technique using fixed microtubules and apply it to measure the diameter of endoplasmic reticulum tubules in live COS-7 cells. NEP fitting has been implemented as a plugin for the PYthon Microscopy Environment (PYME), a freely available and open source software.
Brain-behavior patterns define a dimensional biotype in medication-naïve adults with attention-deficit hyperactivity disorder
Authors: Lin Hsiang-Yuan , Cocchi Luca , Zalesky Andrew , Lv Jinglei , Perry Alistair , Tseng Wen-Yih Isaac , Kundu Prantik , Breakspear Michael , Gau Susan Shur-Fen 
Published: September 2017

AbstractBackgroundChildhood-onset attention-deficit hyperactivity disorder (ADHD) in adults is clinically heterogeneous and commonly presents with different patterns of cognitive deficits. It is unclear if this clinical heterogeneity expresses a dimensional or categorical difference in ADHD.MethodsWe first studied differences in functional connectivity in multi-echo resting-state functional magnetic resonance imaging (rs-fMRI) acquired from 80 medication-naïve adults with ADHD and 123 matched healthy controls. We then used canonical correlation analysis (CCA) to identify latent relationships between symptoms and patterns of altered functional connectivity (dimensional biotype) in patients. Clustering methods were implemented to test if the individual associations between resting-state brain connectivity and symptoms reflected a non-overlapping categorical biotype.ResultsAdults with ADHD showed stronger functional connectivity compared to healthy controls, predominantly between the default-mode, cingulo-opercular and subcortical networks. CCA identified a single mode of brain-symptom co-variation, corresponding to an ADHD dimensional biotype. This dimensional biotype is characterized by a unique combination of altered connectivity correlating with symptoms of hyperactivity-impulsivity, inattention, and intelligence. Clustering analyses did not support the existence of distinct categorical biotypes of adult ADHD.ConclusionsOverall, our data advance a novel finding that the reduced functional segregation between default-mode and cognitive control networks supports a clinically important dimensional biotype of childhood-onset adult ADHD. Despite the heterogeneity of its presentation, our work suggests that childhood-onset adult ADHD is a single disorder characterized by dimensional brain-symptom mediators.