Miracle-dz/UniFAR-FTUs huggingface dataset:
Panoptes: web‐based exploration of large scale genome variation data

Motivation The size and complexity of modern large‐scale genome variation studies demand novel approaches for exploring and sharing the data. In order to unlock the potential of these data for a broad audience of scientists with various areas of expertise, a unified exploration framework is required that is accessible, coherent and user‐friendly. Results Panoptes is an open‐source software framework for collaborative visual exploration of large‐scale genome variation data and associated metadata in a web browser. It relies on technology choices that allow it to operate in near real‐time on very large datasets. It can be used to browse rich, hybrid content in a coherent way, and offers interactive visual analytics approaches to assist the exploration. We illustrate its application using genome variation data of Anopheles gambiae, Plasmodium falciparum and Plasmodium vivax. Availability and implementation Freely available at https://github.com/cggh/panoptes, under the GNU Affero General Public License. Contact paul.vauterin@gmail.com
Complex Human-System Systems Design for C2

Human-System systems design is a critical part of Command and Control (C2) design, in order to improve the whole effectiveness of C2 design, the human beings and systems must be in harmony in the human-in-loop systems, which can be referred to as Cyber-physical-social systems (CPSS). Based on the coordination theory, self synchronization of a CPSS is both a self-organizing and self-adapting process, of which the end effect will be shown as the emergence of all the dependency relationships among the courses of action (COAs). Human-system systems design for C2 will be modeled in different views: the system view, the human view and the coordination view, being a loop iteration process.
The null hypothesis of GSEA, and a novel statistical model for competitive gene set analysis

Motivation: Competitive gene set analysis intends to assess whether a specific set of genes is more associated with a trait than the remaining genes. However, the statistical models assumed to date to underly these methods do not enable a clear cut formulation of the competitive null hypothesis. This is a major handicap to the interpretation of results obtained from a gene set analysis. Results: This work presents a hierarchical statistical model based on the notion of dependence measures, which overcomes this problem. The two levels of the model naturally reflect the modular structure of many gene set analysis methods. We apply the model to show that the popular GSEA method, which recently has been claimed to test the self‐contained null hypothesis, actually tests the competitive null if the weight parameter is zero. However, for this result to hold strictly, the choice of the dependence measures underlying GSEA and the estimators used for it is crucial. Contact: bdebrabant@health.sdu. dk Supplementary information: Supplementary material is available at Bioinformatics online.
A Comparison of Surgical Treatments for Superior Semicircular Canal Dehiscence: A Systematic Review.

OBJECTIVE We investigate the postoperative subjective and objective outcomes of different surgical treatments for superior semicircular canal dehiscence (SSCD): vestibular signs, auditory signs, vestibular evoked myogenic potential test, pure tone audiogram, speech audiogram, or video-nystagmography. DATA SOURCES An electronic search performed in the PubMed, Cochrane Library, and EMBASE databases on 15th of September 2015. A systematic search was conducted. Articles were included if written in English, Dutch, German, or French language. STUDY SELECTION Original studies reporting on the pre and postoperative subjective and/or objective outcomes of surgical treatments for superior semicircular canal dehiscence were included. DATA EXTRACTION The methodological quality of the studies was independently assessed by two reviewers using a constructed critical appraisal, to assess the directness of evidence and the risk of bias. The results of the pre and postoperative subjective and/or objective outcomes were extracted. DATA SYNTHESIS Comparative study was conducted. CONCLUSION Surgical treatment for SSCD is particularly effective for vestibular symptoms and there is no evidence for improvement of hearing loss after surgical treatment. Since plugging using transmastoid approach had a lower complication rate, lower revision rate, and a shorter hospital stay, this treatment is recommended in high disabled SSCD patients.
Collaborative biocuration—text-mining development task for document prioritization for curation

The Critical Assessment of Information Extraction systems in Biology (BioCreAtIvE) challenge evaluation is a community-wide effort for evaluating text mining and information extraction systems for the biological domain. The ‘BioCreative Workshop 2012’ subcommittee identified three areas, or tracks, that comprised independent, but complementary aspects of data curation in which they sought community input: literature triage (Track I); curation workflow (Track II) and text mining/natural language processing (NLP) systems (Track III). Track I participants were invited to develop tools or systems that would effectively triage and prioritize articles for curation and present results in a prototype web interface. Training and test datasets were derived from the Comparative Toxicogenomics Database (CTD; http://ctdbase.org) and consisted of manuscripts from which chemical–gene–disease data were manually curated. A total of seven groups participated in Track I. For the triage component, the effectiveness of participant systems was measured by aggregate gene, disease and chemical ‘named-entity recognition’ (NER) across articles; the effectiveness of ‘information retrieval’ (IR) was also measured based on ‘mean average precision’ (MAP). Top recall scores for gene, disease and chemical NER were 49, 65 and 82%, respectively; the top MAP score was 80%. Each participating group also developed a prototype web interface; these interfaces were evaluated based on functionality and ease-of-use by CTD’s biocuration project manager. In this article, we present a detailed description of the challenge and a summary of the results.
Development and validation of the Alzheimer's prevention beliefs measure in a multi‐ethnic cohort—a behavioral theory approach

Background Understanding health beliefs and how they influence willingness will enable the development of targeted curricula that maximize public engagement in Alzheimer's disease (AD) risk reduction behaviors. Methods Literature on behavioral theory and community input was used to develop and validate a health beliefs survey about AD risk reduction among 428 community‐dwelling adults. Principal component analysis was performed to assess internal consistency. Linear regression was performed to identify key predictors of Willingness to engage in AD risk reduction behaviors. Results The measure as well as the individual scales (Benefits, Barriers, Severity, Susceptibility and Social Norm) were found to be internally consistent. Overall, as Benefits and Barriers scores increased, Willingness scores also increased. Those without prior AD experience or family history had lower willingness scores. Finally, we observed an interaction between age and norms, suggesting that social factors related to AD prevention may differentially affect people of different ages. Conclusions The Alzheimer Prevention Beliefs Measure provides assessment of several health belief factors related to AD prevention. Age, Family History, Logistical Barriers and total Benefits are significant determinants of willingness to engage in AD risk reduction behaviors, such as seeing a doctor or making a lifestyle change.
Microscopy Techniques for Immunolocalisation of Nitrated Proteins in Different Tissues

Immunohistochemistry is an important tool in the investigation of posttranslational protein modifications; facilitating the identification of modified proteins at cellular level. Nitration of tyrosine residues (NO2Tyr) has been detected in multiple species, organ systems, and cell types during both acute and chronic inflammation. This post-translational protein modification is a marker of oxidative injury that is frequently linked to altered protein function during inflammatory conditions. The existence of multiple distinct, yet redundant pathways for tyrosine nitration underscores the potential significance of this process in inflammation and cell signaling. Methods that allow for definitive NO2Tyr identification in tissues depend on the immunoreactivity of the NO2Tyr adduct to antibodies raised against artificially nitrated proteins. In previous reports we have utilized both immunofluorescence and light microscopy to reveal the occurrence of protein nitration in glaucomatous retinal damage, ocular inflammation, liver and kidney damage. Elevated levels of NO2Tyr in all of these diseases imply the formation of secondary species capable of nitration reactions.
Effects of Augmented Exercise Therapy Time After Stroke: A Meta-Analysis

Background and Purpose— To present a systematic review of studies that addresses the effects of intensity of augmented exercise therapy time (AETT) on activities of daily living (ADL), walking, and dexterity in patients with stroke. Summary of Review— A database of articles published from 1966 to November 2003 was compiled from MEDLINE, CINAHL, Cochrane Central Register of Controlled Trials, PEDro, DARE, and PiCarta using combinations of the following key words: stroke, cerebrovascular disorders, physical therapy, physiotherapy, occupational therapy, exercise therapy, rehabilitation, intensity, dose–response relationship, effectiveness, and randomized controlled trial. References presented in relevant publications were examined as well as abstracts in proceedings. Studies that satisfied the following selection criteria were included: (1) patients had a diagnosis of stroke; (2) effects of intensity of exercise training were investigated; and (3) design of the study was a randomized controlled trial (RCT). For each outcome measure, the estimated effect size (ES) and the summary effect size (SES) expressed in standard deviation units (SDU) were calculated for ADL, walking speed, and dexterity using fixed and random effect models. Correlation coefficients were calculated between observed individual effect sizes on ADL of each study, additional time spent on exercise training, and methodological quality. Cumulative meta-analyses (random effects model) adjusted for the difference in treatment intensity in each study was used for the trials evaluating the effects of AETT provided. Twenty of the 31 candidate studies, involving 2686 stroke patients, were included in the synthesis. The methodological quality ranged from 2 to 10 out of the maximum score of 14 points. The meta-analysis resulted in a small but statistically significant SES with regard to ADL measured at the end of the intervention phase. Further analysis showed a significant homogeneous SES for 17 studies that investigated effects of increased exercise intensity within the first 6 months after stroke. No significant SES was observed for the 3 studies conducted in the chronic phase. Cumulative meta-analysis strongly suggests that at least a 16-hour difference in treatment time between experimental and control groups provided in the first 6 months after stroke is needed to obtain significant differences in ADL. A significant SES supporting a higher intensity was also observed for instrumental ADL and walking speed, whereas no significant SES was found for dexterity. Conclusion— The results of the present research synthesis support the hypothesis that augmented exercise therapy has a small but favorable effect on ADL, particularly if therapy input is augmented at least 16 hours within the first 6 months after stroke. This meta-analysis also suggests that clinically relevant treatment effects may be achieved on instrumental ADL and gait speed.
Altered Expression of miR-181a-5p and miR-23a-3p Is Associated With Obesity and TNF&agr;-Induced Insulin Resistance

Context The proinflammatory cytokine TNFα is a key player in insulin resistance (IR). The role of miRNAs in inflammation associated with IR is poorly understood. Objective To investigate miR-181a-5p and miR-23a-3p expression profiles in obesity and to study their role in TNFα-induced IR in adipocytes. Design Two separate cohorts were used. Cohort 1 was used in adipose tissue (AT) expression studies and included 28 subjects with body mass index (BMI) <30 kg/m2 and 30 with BMI ≥30 kg/m2. Cohort 2 was used in circulating serum miRNA studies and included 101 subjects with 4 years of follow-up (48 case subjects and 53 control subjects). miR-181a-5p and miR-23a-3p expression was assessed in subcutaneous and visceral AT. Functional analysis was performed in adipocytes, using miRNA mimics and inhibitors. Key molecules of the insulin pathway, AKT, PTEN, AS160, and S6K, were analyzed. Results Expression of miR-181a-5p and miR-23a-3p was reduced in adipose tissue from obese and diabetic subjects and was inversely correlated to adiposity and homeostasis model assessment of IR index. Overexpression of miR-181a-5p and miR-23a-3p in adipocytes upregulated insulin-stimulated AKT activation and reduced TNFα-induced IR, regulating PTEN and S6K expression. Serum levels of miR-181a-5p were reduced in case vs control subjects at baseline, suggesting a prognostic value. Variable importance in projection scores revealed miR-181a-5p had more effect on the model than insulin or glucose at 120 minutes. Conclusion miR-181a-5p and miR-23a-3p may prevent TNFα-induced IR in adipocytes through modulation of PTEN and S6K expression.
Shadow obstacle model for realistic corner-turning behavior in crowd simulation

This paper describes a novel model known as the shadow obstacle model to generate a realistic corner-turning behavior in crowd simulation. The motivation for this model comes from the observation that people tend to choose a safer route rather than a shorter one when turning a corner. To calculate a safer route, an optimization method is proposed to generate the corner-turning rule that maximizes the viewing range for the agents. By combining psychological and physical forces together, a full crowd simulation framework is established to provide a more realistic crowd simulation. We demonstrate that our model produces a more realistic corner-turning behavior by comparison with real data obtained from the experiments. Finally, we perform parameter analysis to show the believability of our model through a series of experiments.
Two novel low power and very high speed pulse triggered flip‐flops

Two novel low power and high‐speed pulse triggered flip‐flops were presented in this paper. Short circuit current was controlled, and race condition between pull‐up and pull‐down branches was removed, which caused reduction of power consumption. On the other hand, the number of stack transistors in the discharging path was reduced which decreased delay of the flip‐flops. The first proposed flip‐flop reduced the number of transistors and the second proposed flip‐flop used conditional data mapping and removed floating node of the first flip‐flop. Post‐layout simulation result showed that the first proposed flip‐flop reduced 21% of power delay product and the second proposed flip‐flop reduced 16% of power delay product in comparison with other flip‐flops in 50% of data switching activities. Copyright © 2014 John Wiley & Sons, Ltd.
Chronic obstructive pulmonary disease exacerbation in the intensive care unit: clinical, functional and quality of life at discharge and 3 months of follow up

Objective The purpose of this study was to evaluate the clinical/functional aspects and quality of life of chronic obstructive pulmonary disease patients who were discharged after an intensive care unit admission for acute respiratory failure. Methods This prospective study included chronic obstructive pulmonary disease patients who were admitted to two intensive care units between December of 2010 and August of 2011 and evaluated over three visits after discharge. Thirty patients were included, and 20 patients completed the three-month follow up. Results There was a significant improvement in the following: forced expiratory flow in one second (L) (1.1/1.4/1.4; p = 0.019), six-minute walk test (m) (- /232.8 /272.6; p = 0.04), BODE score (7.5/5.0/3.8; p = 0.001), cognition measured by the Mini Mental State Examination (21/23.5/23.5; p = 0.008) and quality of life measured by the total Saint George Respiratory Questionnaire score (63.3/56.8/51, p = 0.02). The mean difference in the total score was 12.3 (between visits 1 and three). Important clinical differences were observed for the symptom score (18.8), activities score (5.2) and impact score (14.3). The majority of participants (80%) reported they would be willing to undergo a new intensive care unit admission. Conclusion Despite the disease severity, there was a significant clinical, functional and quality of life improvement at the end of the third month. Most patients would be willing to undergo a new intensive care unit admission.
University of Southern Denmark Thyroid fine-needle aspiration and the bethesda classification system

INTRODUCTION: Fine-needle aspiration (FNA) is a cornerstone in diagnosing thyroid nodules. For decades, Danish FNA have been categorised into the groups: “FNA not performed”, “Inadequate”, “Cystic”, “Inconclusive”, “Benign”, “Suspicious”, “Malignant” and “Information missing”. Internationally, The Bethesda Classification System (TBCS) is increasingly accepted, especially owing to a detailed specification of FNA suspicious for malignancy. The Danish “Suspicious” group is very broad and includes atypia, follicular neoplasia and FNA suspicious of other malignancies. The purpose of this study was to apply TBCS to the Danish “Suspicious” FNA group and to estimate the frequency of malignancy in the individual Bethesda groups (BG). METHODS: This descriptive study is based on a prospective cohort from the THYKIR database. It includes 479 patients with a “Suspicious” FNA and surgical treatment in The Region of Southern Denmark from 2001 to 2013. Based on pathology records, FNA was classified according to the TBCS. Malignancy was determined by the histological diagnosis from the THYKIR database. RESULTS: The Danish “Suspicious” group was allocated to the BG I, II, III, IV, V and VI with a malignancy risk of 36.4%, 13.3%, 17.2%, 16.1%, 55.3% and 88.2%, respectively. CONCLUSIONS: The Danish “Suspicious” group contains a broad spectrum of BG with varying malignancy risk. The results indicate a need for standardisation of the Danish FNA classification. A national introduction of the TBCS might secure an international and comparable standard.
Oral Monomethyl Fumarate Therapy Ameliorates Retinopathy in a Humanized Mouse Model of Sickle Cell Disease.

AIMS Sickle retinopathy (SR) is a major cause of blindness in sickle cell disease (SCD). The genetic mutation responsible for SCD is known, however; oxidative stress and inflammation also figure prominently in the development and progression of pathology. Development of therapies for SR is hampered by the lack of (a) animal models that accurately recapitulate human SR and (b) strategies for noninvasive yet effective retinal drug delivery. This study addressed both issues by validating the Townes humanized SCD mouse as a model of SR and demonstrating the efficacy of oral administration of the antioxidant fumaric acid ester monomethyl fumarate (MMF) in the disease. RESULTS In vivo ophthalmic imaging, electroretinography, and postmortem histological RNA and protein analyses were used to monitor retinal health and function in normal (HbAA) and sickle (HbSS) hemoglobin-producing mice over a one-year period and in additional HbAA and HbSS mice treated with MMF (15 mg/ml) for 5 months. Functional and morphological abnormalities and molecular hallmarks of oxidative stress/inflammation were evident early in HbSS retinas and increased in number and severity with age. Treatment with MMF, a known inducer of Nrf2, induced γ-globin expression and fetal hemoglobin production, improved hematological profiles, and ameliorated SR-related pathology. Innovation and Conclusion: United States Food and Drug Administration-approved formulations in which MMF is the primary bioactive ingredient are currently available to treat multiple sclerosis; such drugs may be effective for treatment of ocular and systemic complications of SCD, and given the pleiotropic effects, other nonsickle-related diseases in which oxidative stress, inflammation, and retinal vascular pathology figure prominently. Antioxid. Redox Signal. 25, 921-935.
Macroarchitectural and Microarchitectural Approach Brain Development : Closing the Gap between aDrosophila

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Sleep extension is a feasible lifestyle intervention in free-living adults who are habitually short sleepers: a potential strategy for decreasing intake of free sugars? A randomized controlled pilot study

ABSTRACT Background Evidence suggests that short sleep duration may be a newly identified modifiable risk factor for obesity, yet there is a paucity of studies to investigate this. Objective We assessed the feasibility of a personalized sleep extension protocol in adults aged 18–64 y who are habitually short sleepers (5 to <7 h), with sleep primarily measured by wrist actigraphy. In addition, we collected pilot data to assess the effects of extended sleep on dietary intake and quality measured by 7-d food diaries, resting and total energy expenditure, physical activity, and markers of cardiometabolic health. Design Forty-two normal-weight healthy participants who were habitually short sleepers completed this free-living, 4-wk, parallel-design randomized controlled trial. The sleep extension group (n = 21) received a behavioral consultation session targeting sleep hygiene. The control group (n = 21) maintained habitual short sleep. Results Rates of participation, attrition, and compliance were 100%, 6.5%, and 85.7%, respectively. The sleep extension group significantly increased time in bed [0:55 hours:minutes (h:mm); 95% CI: 0:37, 1:12 h:mm], sleep period (0:47 h:mm; 95% CI: 0:29, 1:05 h:mm), and sleep duration (0:21 h:mm; 95% CI: 0:06, 0:36 h:mm) compared with the control group. Sleep extension led to reduced intake of free sugars (–9.6 g; 95% CI: –16.0, –3.1 g) compared with control (0.7 g; 95% CI: –5.7, 7.2 g) (P = 0.042). A sensitivity analysis in plausible reporters showed that the sleep extension group reduced intakes of fat (percentage), carbohydrates (grams), and free sugars (grams) in comparison to the control group. There were no significant differences between groups in markers of energy balance or cardiometabolic health. Conclusions We showed the feasibility of extending sleep in adult short sleepers. Sleep extension led to reduced free sugar intakes and may be a viable strategy to facilitate limiting excessive consumption of free sugars in an obesity-promoting environment. This trial was registered at www.clinicaltrials. gov as NCT02787577.