Miracle-dz/UniFAR-FTUs huggingface dataset:
Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics

Significance We created a dataset of dinoflagellate transcriptomes to resolve internal phylogenetic relationships of the group. We show that the dinoflagellate theca originated once, through a process that likely involved changes in the metabolism of cellulose, and suggest that a late origin of dinosterol in the group is at odds with dinoflagellates being the source of this important biomarker before the Mesozoic. We also show that nonphotosynthetic dinoflagellates have retained nonphotosynthetic plastids with vital metabolic functions, and propose that one of these may be the evolutionary source of dinoflagellate bioluminescence. Finally, we reconstruct major molecular and morphological transitions in dinoflagellates and highlight the role of horizontal gene transfer in the origin of their unique nuclear architecture. Dinoflagellates are key species in marine environments, but they remain poorly understood in part because of their large, complex genomes, unique molecular biology, and unresolved in-group relationships. We created a taxonomically representative dataset of dinoflagellate transcriptomes and used this to infer a strongly supported phylogeny to map major morphological and molecular transitions in dinoflagellate evolution. Our results show an early-branching position of Noctiluca, monophyly of thecate (plate-bearing) dinoflagellates, and paraphyly of athecate ones. This represents unambiguous phylogenetic evidence for a single origin of the group’s cellulosic theca, which we show coincided with a radiation of cellulases implicated in cell division. By integrating dinoflagellate molecular, fossil, and biogeochemical evidence, we propose a revised model for the evolution of thecal tabulations and suggest that the late acquisition of dinosterol in the group is inconsistent with dinoflagellates being the source of this biomarker in pre-Mesozoic strata. Three distantly related, fundamentally nonphotosynthetic dinoflagellates, Noctiluca, Oxyrrhis, and Dinophysis, contain cryptic plastidial metabolisms and lack alternative cytosolic pathways, suggesting that all free-living dinoflagellates are metabolically dependent on plastids. This finding led us to propose general mechanisms of dependency on plastid organelles in eukaryotes that have lost photosynthesis; it also suggests that the evolutionary origin of bioluminescence in nonphotosynthetic dinoflagellates may be linked to plastidic tetrapyrrole biosynthesis. Finally, we use our phylogenetic framework to show that dinoflagellate nuclei have recruited DNA-binding proteins in three distinct evolutionary waves, which included two independent acquisitions of bacterial histone-like proteins.
Emergency Department Utilization by Children in the USA, 2010–2011

Introduction Epidemiological surveillance data for emergency department (ED) visits by children are imperative to guide resource allocation and to develop health policies that advance pediatric emergency care. However, there are sparse population-based data on patient-level information (e.g., the number of children who present to the emergency department [ED]). In this context, we aimed to investigate both the patient- and visit-level rates of ED utilization by children. Methods This was a retrospective cohort study using population-based multipayer data – state ED databases (SEDD) and state inpatient databases (SID) – from six geographically-dispersed U.S. states (California, Florida, Iowa, Nebraska, New York, and Utah) in 2010 and 2011. We identified all children aged <18 years who presented to the ED and described the patient-level ED visit rate, visit-level ED visit rate, and proportion of all ED visits made by children. We conducted the analysis using the 2011 SEDD and SID data. We also repeated the analysis using the 2010 data to determine the consistency of the results across different years. Results In 2011, 2.9 million children with a patient identifier presented to EDs in the six U.S. states. At the patient-level, 15 out of every 100 children presented to an ED at least once per year. Of these children, 25% presented to EDs 2–3 times per year with an approximately 1.5-fold variation across the states (e.g., 19% in Utah vs. 28% in Florida). In addition, 5% presented to EDs ≥4 times per year. At the visit-level, 6.7 million ED visits were made by children in 2011 – 34 ED visits per 100 children annually. ED visits by children accounted for 22% of all ED visits (including both adults and children), with a relatively small variation across the states (e.g., 20% in New York vs. 24% in Nebraska). Analysis of the 2010 data gave similar results for the ED utilization by children. Conclusion By using large population-based data, we found a substantial burden of ED visits at both patient- and visit-levels. These findings provide a strong foundation for policy makers and professional organizations to strengthen emergency care for children.
Restless ‘rest’: intrinsic sensory hyperactivity and disinhibition in post-traumatic stress disorder

Post-traumatic stress disorder is characterized by exaggerated threat response, and theoretical accounts to date have focused on impaired threat processing and dysregulated prefrontal-cortex-amygdala circuitry. Nevertheless, evidence is accruing for broad, threat-neutral sensory hyperactivity in post-traumatic stress disorder. As low-level, sensory processing impacts higher-order operations, such sensory anomalies can contribute to widespread dysfunctions, presenting an additional aetiological mechanism for post-traumatic stress disorder. To elucidate a sensory pathology of post-traumatic stress disorder, we examined intrinsic visual cortical activity (based on posterior alpha oscillations) and bottom-up sensory-driven causal connectivity (Granger causality in the alpha band) during a resting state (eyes open) and a passive, serial picture viewing state. Compared to patients with generalized anxiety disorder (n = 24) and healthy control subjects (n = 20), patients with post-traumatic stress disorder (n = 25) demonstrated intrinsic sensory hyperactivity (suppressed posterior alpha power, source-localized to the visual cortex-cuneus and precuneus) and bottom-up inhibition deficits (reduced posterior→frontal Granger causality). As sensory input increased from resting to passive picture viewing, patients with post-traumatic stress disorder failed to demonstrate alpha adaptation, highlighting a rigid, set mode of sensory hyperactivity. Interestingly, patients with post-traumatic stress disorder also showed heightened frontal processing (augmented frontal gamma power, source-localized to the superior frontal gyrus and dorsal cingulate cortex), accompanied by attenuated top-down inhibition (reduced frontal→posterior causality). Importantly, not only did suppressed alpha power and bottom-up causality correlate with heightened frontal gamma power, they also correlated with increased severity of sensory and executive dysfunctions (i.e. hypervigilance and impulse control deficits, respectively). Therefore, sensory aberrations help construct a vicious cycle in post-traumatic stress disorder that is in action even at rest, implicating dysregulated triangular sensory-prefrontal-cortex-amygdala circuitry: intrinsic sensory hyperactivity and disinhibition give rise to frontal overload and disrupt executive control, fuelling and perpetuating post-traumatic stress disorder symptoms. Absent in generalized anxiety disorder, these aberrations highlight a unique sensory pathology of post-traumatic stress disorder (ruling out effects merely reflecting anxious hyperarousal), motivating new interventions targeting sensory processing and the sensory brain in these patients.
Strong concepts: Intermediate-level knowledge in interaction design research

Design-oriented research practices create opportunities for constructing knowledge that is more abstracted than particular instances, without aspiring to be at the scope of generalized theories. We propose an intermediate design knowledge form that we name strong concepts that has the following properties: is generative and carries a core design idea, cutting across particular use situations and even application domains; concerned with interactive behavior, not static appearance; is a design element and a part of an artifact and, at the same time, speaks of a use practice and behavior over time; and finally, resides on an abstraction level above particular instances. We present two strong concepts—social navigation and seamfulness—and discuss how they fulfil criteria we might have on knowledge, such as being contestable, defensible, and substantive. Our aim is to foster an academic culture of discursive knowledge construction of intermediate-level knowledge and of how it can be produced and assessed in design-oriented HCI research.
Work-efficient parallel non-maximum suppression for embedded GPU architectures

With the emergence of GPU computing, deep neural networks have become a widely used technique for advancing research in the field of image and speech processing. In the context of object and event detection, sliding-window classifiers require to choose the best among all positively discriminated candidate windows. In this paper, we introduce the first GPU-based non-maximum suppression (NMS) algorithm for embedded GPU architectures. The obtained results show that the proposed parallel algorithm reduces the NMS latency by a wide margin when compared to CPUs, even clocking the GPU at 50% of its maximum frequency on an NVIDIA Tegra K1. In this paper, we show results for object detection in images. The proposed technique is directly applicable to speech segmentation tasks such as speaker diarization.
Patterns of Empiric Antibiotic Administration for Presumed Early-Onset Neonatal Sepsis in Neonatal Intensive Care Units in the United States

Abstract Objective To evaluate current patterns in empiric antibiotic use for early-onset neonatal sepsis (EONS). Study Design Retrospective population-based cohort study of newborns admitted on postnatal day 0 to 1 and discharged from NICUs participating in the Pediatric Health Information System (PHIS 2006–2013). Analyses included frequency of antibiotic initiation within 3 days of birth, duration of first course, and variation among hospitals. Results Of 158,907 newborns, 118,624 (74.7%) received antibiotics on or before postnatal day 3. Within 3 days of treatment, 49.4% (n = 58,610) were discharged home or remained hospitalized without antibiotics. There was marked interhospital variation in the proportion of infants receiving antibiotics (range: 52.3–90.9%, mean 77.9%, SD 11.0%) and in treatment days (range: 3.2–8.6, mean 5.3, SD 1.4). Facilities with higher number of newborns started on antibiotics had longer courses (r = 0.643, p < 0.001). The cost of admissions for infants born at ≥35 weeks started on antibiotics and discharged home after no more than 3 days of antibiotics was $76,692,713. Conclusion Site variation in antibiotic utilization suggests antibiotic overtreatment of infants with culture unconfirmed EONS is common and costly.
Women in Industry

try. Though complete national statistics of women employed in industry are not available, an investigator in behalf of the International Journal of Public Health has been able to make a rough survey which discloses marked differences in the number of women workers and the conditions under which they work. In Japan (1) about two-thirds of the factory workers, or about half a million, are women and girls. The U.S. census for 1910 (2) gave the general figure of 8,000,000 women engaged
Structural Alteration of the Dorsal Visual Network in DLB Patients with Visual Hallucinations: A Cortical Thickness MRI Study

Visual hallucinations (VH) represent one of the core features in discriminating dementia with Lewy bodies (DLB) from Alzheimer’s Disease (AD). Previous studies reported that in DLB patients functional alterations of the parieto-occipital regions were correlated with the presence of VH. The aim of our study was to assess whether morphological changes in specific cortical regions of DLB could be related to the presence and severity of VH. We performed a cortical thickness analysis on magnetic resonance imaging data in a cohort including 18 DLB patients, 15 AD patients and 14 healthy control subjects. Relatively to DLB group, correlation analysis between the cortical thickness and the Neuropsychiatric Inventory (NPI) hallucination item scores was also performed. Cortical thickness was reduced bilaterally in DLB compared to controls in the pericalcarine and lingual gyri, cuneus, precuneus, superior parietal gyrus. Cortical thinning was found bilaterally in AD compared to controls in temporal cortex including the superior and middle temporal gyrus, part of inferior temporal cortex, temporal pole and insula. Inferior parietal and supramarginal gyri were also affected bilaterally in AD as compared to controls. The comparison between DLB and AD evidenced cortical thinning in DLB group in the right posterior regions including superior parietal gyrus, precuneus, cuneus, pericalcarine and lingual gyri. Furthermore, the correlation analysis between cortical thickness and NPI hallucination item scores showed that the structural alteration in the dorsal visual regions including superior parietal gyrus and precuneus closely correlated with the occurrence and severity of VH. We suggest that structural changes in key regions of the dorsal visual network may play a crucial role in the physiopathology of VH in DLB patients.
Cost-Benefit Analysis of V2G Implementation in Distribution Networks Considering PEVs Battery Degradation

Charging of plug-in electric vehicles (PEVs), especially as market penetration increases, is an important challenge for today's power systems. This paper presents a stochastic methodology for smart charging of PEVs. All of the associated uncertainties are taken into account in the proposed methodology. Moreover, a comprehensive model for impact of charging/discharging strategies on the battery pack degradation in the vehicle has been included. The proposed approach is applied to a typical distribution network that contains wind-based distributed generation (DG) units. A cost-benefit analysis is carried out to extract the benefits of Vehicle to Grid (V2G) implementation in distribution network. The simulation results show that the V2G implementation without considering battery degradation is economical. However, when considering a battery degradation cost, V2G implementation without wind generation is not beneficial, while it is economical when considering wind DG. Moreover, the smart charging is economical in all conditions and also it reduces the battery degradation cost in comparison with uncoordinated charging.
Thermal and dynamic glass transition in ultrathin films of homopolymers and a miscible polymer blend

Despite the decade long controversial discussion on the effect of nanometer confinement on the glass transition temperature (Tg) of ultrathin polymer films, there is still no consistent picture. Here, the dynamic calorimetric glass transition of ultrathin films of a blend, which is miscible in the bulk, is directly investigated by specific heat spectroscopy. By a self-assembling process, a nanometer thick surface layer with a higher molecular mobility is formed at the polymer/air interface. By measuring the dynamic calorimetric Tg in dependence on the film thickness, it was shown that the Tg of the whole film was strongly influenced by that nanometer thick surface layer, with a lower Tg. Since the observed thickness dependence of the dynamic Tg is similar to the thickness dependence of the Tg for thin films of homopolymers, it is concluded that also for homopolymer a highly mobile surface layer is relevant for the widely observed Tg depression.
Stabilisation of atherosclerotic plaques

Summary Plaque rupture and subsequent thrombotic occlusion of the coronary artery account for as many as three quarters of myocardial infarctions. The concept of plaque stabilisation emerged about 20 years ago to explain the discrepancy between the reduction of cardiovascular events in patients receiving lipid lowering therapy and the small decrease seen in angiographic evaluation of atherosclerosis. Since then, the concept of a vulnerable plaque has received a lot of attention in basic and clinical research leading to a better understanding of the pathophysiology of the vulnerable plaque and acute coronary syndromes. From pathological and clinical observations, plaques that have recently ruptured have thin fibrous caps, large lipid cores, exhibit outward remodelling and invasion by vasa vasorum. Ruptured plaques are also focally inflamed and this may be a common denominator of the other pathological features. Plaques with similar characteristics, but which have not yet ruptured, are believed to be vulnerable to rupture. Experimental studies strongly support the validity of anti-inflammatory approaches to promote plaque stability. Unfortunately, reliable non-invasive methods for imaging and detection of such plaques are not yet readily available. There is a strong biological basis and supportive clinical evidence that low-density lipoprotein lowering with statins is useful for the stabilisation of vulnerable plaques. There is also some clinical evidence for the usefulness of antiplatelet agents, beta blockers and renin-angiotensin-aldosterone system inhibitors for plaque stabilisation. Determining the causes of plaque rupture and designing diagnostics and interventions to prevent them are urgent priorities for current basic and clinical research in cardiovascular area.
Evaluating the antioxidant effects of human hair protein extracts

Abstract The intrinsically high cysteine content in human hair keratins and keratin associated proteins confer hair its outstanding mechanical strength through the formation of strong intermolecular disulfide bonds. In addition, these proteins offer the potential to be exploited as potent antioxidants. This report presents our findings on the antioxidant effects of human hair protein extracts and their consequent protective role against oxidative stress in human dermal fibroblast (HDF) cultures. Protein extracts were obtained from human hair using sodium sulfide as the reducing agent, and characterized using SDS-PAGE, Western blotting, MALDI-ToF mass spectrometry and amino acid analysis. Cysteine was found to account for 11.2 mol % in the extracted fractions. By measuring 2,2-diphenyl-1-picryl-hydrazyl-hydrate (DPPH) radical scavenging activity, the hair protein fractions were shown to possess significant antioxidant ability (IC50 = 16.22 μM). As a supplement in cell culture media, the extracts protected HDFs from H2O2 induced oxidative stress, which was demonstrated by the maintenance of cell viability and reduced reactive oxygen species production. Besides offering mechanical support as a scaffolding material, the unique antioxidizing ability of human hair protein extracts may also be exploited in biomedical applications.
Large-scale first principles and tight-binding density functional theory calculations on hydrogen-passivated silicon nanorods

We present a computational study by density functional theory (DFT) of entire silicon nanorods with up to 1648 atoms without any periodicity or symmetry imposed. The nanorods have been selected to have varying aspect ratios and levels of surface passivation with hydrogen. The structures of the nanorods have been optimized using a density functional tight-binding approach, while energies and electronic properties have been computed using linear-scaling DFT with plane-wave accuracy with the ONETEP (Skylaris et al 2005 J. Chem. Phys. 122 084119) program. The aspect ratio and surface passivation (1 × 1 and 2 × 1 reconstructions) along with the size of the nanorods which leads to quantum confinement along all three dimensions, significantly affect their electronic properties. The structures of the nanorods also show interesting behaviour as, depending on their characteristics, they can in certain areas retain the structure of bulk silicon while in other parts significantly deviate from it.
Maternal components of RNA‐directed DNA methylation are required for seed development in Brassica rapa

Small RNAs trigger repressive DNA methylation at thousands of transposable elements in a process called RNA-directed DNA methylation (RdDM). The molecular mechanism of RdDM is well characterized in Arabidopsis, yet the biological function remains unclear, as loss of RdDM in Arabidopsis causes no overt defects, even after generations of inbreeding. It is known that 24 nucleotide Pol IV-dependent siRNAs, the hallmark of RdDM, are abundant in flowers and developing seeds, indicating that RdDM might be important during reproduction. Here we show that, unlike Arabidopsis, mutations in the Pol IV-dependent small RNA pathway cause severe and specific reproductive defects in Brassica rapa. High rates of abortion occur when seeds have RdDM mutant mothers, but not when they have mutant fathers. Although abortion occurs after fertilization, RdDM function is required in maternal somatic tissue, not in the female gametophyte or the developing zygote, suggesting that siRNAs from the maternal soma might function in filial tissues. We propose that recently outbreeding species such as B. rapa are key to understanding the role of RdDM during plant reproduction.
Detection of MicroRNA in Hepatic Cirrhosis and Hepatocellular Carcinoma in Hepatitis C Genotype-4 in Egyptian Patients

Background In Egypt, the prevalence of chronic hepatitis C (CHC) infection is 13.8% of whole population and about 80% of the patients with hepatocellular carcinoma have underling hepatitis C. Aim This study was designed to assess the diagnostic value of plasma miR-122 and miR-21 in patients with CHC, genotype-4, to detect fibrosis progression versus noninvasive indices and their diagnostic value in detection of early stages of hepatocellular carcinoma (HCC). Methodology A prospective study that included 180 patients, divided into 3 groups: healthy controls (group I), CHC patients (group II), and hepatitis C patients with HCC (group III); all cases were subjected to thorough clinical, radiological, and laboratory investigations. Selected biomarkers were evaluated and correlated with degree of liver damage. Results revealed that miR-122 followed by miR-21 had the highest efficiency in prediction of liver cell damage. Also, miR-21 was strongly correlated with vascular endothelial growth factor (VEGF) and alpha fetoprotein (α-FP) in HCC patients. Conclusions Plasma miR-122 and miR-21 had strong correlation with degree fibrosis in HCV genotype-4 patients; consequently they can be considered as potential biomarker for early detection of hepatic fibrosis. Moreover, miR-21 can be used as a potential biomarker, for early detection of HCC combined with VEGF and α-FP.