Miracle-dz/UniFAR-FTUs huggingface dataset:
Trauma is a team sport.

Resources are mobilized. The trauma bay is prepared. Appropriate people converge: radiology, respiratory therapy, nursing, emergency physicians, and trauma physicians. The patient arrives in shock with unstable vital signs. The group hovers around the patient and moves like a well-oiled machine. Nursing staff attach the patient to the monitor and insert various catheters. An emergency doctor prepares to place an endotracheal tube, whereas respiratory therapy sets up the ventilator. Trauma surgeons insert a chest tube and use an ultrasound to assess bleeding in the abdomen. Radiology obtains films and the operating room staff communicate that they are ready for the patient, whereas the intensive care unit prepares a bed in anticipation. Total elapsed time is 20 minutes. Trauma is a team sport. All team members have specialty skills and decision processes they
Can diffusion-weighted imaging add information in the evaluation of breast lesions considered suspicious on magnetic resonance imaging?

Objective To assess the role of diffusion-weighted imaging (DWI) in the evaluation of breast lesions classified as suspicious on magnetic resonance imaging (MRI), correlating the findings with the results of the histological analysis. Materials and Methods This was a retrospective, descriptive study based on a review of the medical records of 215 patients who were submitted to MRI with DWI before undergoing biopsy at a cancer center. Apparent diffusion coefficient (ADC) values were calculated for each lesion, and the result of the histological analysis was considered the gold standard. Results The mean age was 49 years. We identified 252 lesions, 161 (63.9%) of which were found to be malignant in the histological analysis. The mean ADC value was higher for the benign lesions than for the malignant lesions (1.50 × 10–3 mm2/s vs. 0.97 × 10−3 mm2/s), the difference being statistically significant (p < 0.001). The ADC cut-off point with the greatest sensitivity and specificity on the receiver operating characteristic curve was 1.03 × 10−3 mm2/s. When the DWI and conventional MRI findings were combined, the accuracy reached 95.9%, with a sensitivity of 95.7% and a specificity of 96.4%. Conclusion The use of DWI could facilitate the characterization of breast lesions, especially those classified as BI-RADS 4, increasing the specificity and diagnostic accuracy of MRI.
Risk factors for low vision related functioning in the Mycotic Ulcer Treatment Trial: a randomised trial comparing natamycin with voriconazole

Background/aims The Mycotic Ulcer Treatment Trial I (MUTT I) was a double-masked, multicentre, randomised controlled trial, which found that topical natamycin is superior to voriconazole for the treatment of filamentous fungal corneal ulcers. In this study, we determine risk factors for low vision-related quality of life in patients with fungal keratitis. Methods The Indian visual function questionnaire (IND-VFQ) was administered to MUTT I study participants at 3 months. Associations between patient and ulcer characteristics and IND-VFQ subscale score were assessed using generalised estimating equations. Results 323 patients were enrolled in the trial, and 292 (90.4%) completed the IND-VFQ at 3 months. Out of a total possible score of 100, the average VFQ score for all participants was 81.3 (range 0–100, SD 23.6). After correcting for treatment arm, each logMAR line of worse baseline visual acuity in the affected eye resulted in an average 1.2 points decrease on VFQ at 3 months (95% CI −1.8 to 0.6, p<0.001). Those who required therapeutic penetrating keratoplasty had an average of 25.2 points decrease on VFQ after correcting for treatment arm (95% CI −31.8 to −18.5, p<0.001). Study participants who were unemployed had on average 28.5 points decrease on VFQ (95% CI −46.9 to −10.2, p=0.002) after correcting for treatment arm. Conclusions Monocular vision loss from corneal opacity due to fungal keratitis reduced vision-related quality of life. Given the relatively high worldwide burden of corneal opacity, improving treatment outcomes of corneal infections should be a public health priority. Trial registration number Clinicaltrials.gov Identifier: NCT00996736.
Neurocognitive Features of Attention Deficit Hyperactivity Disorder in a Non-Clinical Adult Sample

Abstract : Cognitive difficulties are frequently documented in clinical Attention Deficit Hyperactivity Disorder (ADHD) samples. Whether these cognitive weaknesses are associated with ADHD symptoms in non-clinical samples is unknown. The current study examined the relationship between ADHD symptoms and cognitive performance in a non-clinical adult sample of 75 men and women ages 20 to 49. Self-report measures of ADHD symptoms and neuropsychological assessments examining sustained attention, inhibition, impulsivity, and working memory were administered. Results revealed the following: (1) individuals with high total ADHD scores had difficulty sustaining attention on a repeated trial task; (2) hyperactive/impulsive scores had a significant positive correlation with impulsivity but not with disinhibition; and (3) inattentive scores had a negative trend correlation only with a simple auditory/verbal working memory task. The study revealed that even individuals with sub-clinical ADHD symptoms had similar difficulties associated with sustained attention, impulsivity, and simple verbal working memory in neurocognitive tests.
HIV-1 Diversity in the Envelope Glycoproteins: Implications for Viral Entry Inhibition

Entry of HIV-1 into a host cell is a multi-step process, with the viral envelope gp120 and gp41 acting sequentially to mediate the viral attachment, CD4 binding, coreceptor binding, and fusion of the viral and host membranes. The emerging class of antiretroviral agents, collectively known as entry inhibitors, interfere in some of these steps. However, viral diversity has implications for possible differential responses to entry inhibitors, since envelope is the most variable of all HIV genes. Different HIV genetic forms carry in their genomes genetic signatures and polymorphisms that could alter the structure of viral proteins which are targeted by drugs, thus impairing antiretroviral binding and efficacy. This review will examine current research that describes subtype differences in envelope at the genetic level and the effects of mutations on the efficacy of current entry inhibitors.
Does Generalization Occur Following Computer-Based Cognitive Retraining?—An Exploratory Study

ABSTRACT Computer-based cognitive retraining (CBCR) intervention has gained great popularity in recent years. This study aimed to investigate the occurrence of skill generalization to daily living task for individuals with acquired brain injury (ABI) after completion of eight modules of a commercially available CBCR program, the Parrot Software. The study investigated changes in individuals’ global cognition as measured by the Montreal Cognitive Assessment, and changes in individuals’ performance during a medication-box sorting task, a novel instrumental activity of daily living. The medication-box sorting task resembled real life medication management with daily prescribed and over-the-counter medications. Twelve individuals with ABI from a community-based program completed the study. Results indicated that CBCR intervention brought about improvement in global cognition, but the improvement did not appear in any particular cognitive domain. Additionally, the gains in global cognition failed to enhance performance in the medication-box sorting task. This exploratory study demonstrated that while CBCR may be a promising intervention for improving global cognition in individuals with ABI, additional intervention might be needed for generalization to occur to a novel daily task. Future studies should look for the ultimate therapeutic outcome from CBCR interventions or include interventions that could bridge the gap between CBCR intervention and performance improvement in daily living occupations.
CD 40-stimulated B Lymphocytes Pulsed with Tumor Antigens Are Effective Antigen-presenting Cells That Can Generate Specific T Cells 1

Although they are considered as antigen-presenting cells, the role of antigen-unspecific B lymphocytes in antigen presentation and T-lymphocyte stimulation remains controversial. In this paper, we tested the capacity of normal human peripheral activated B cells to stimulate T cells using melanoma antigens or melanoma cell lysates. B lymphocytes activated through CD40 ligation and then pulsed with tumor antigens efficiently processed and presented MHC class II-restricted peptides to specific CD4 T-cell clones. This suggests that CD40-activated B cells have the functional and molecular competence to present MHC class II epitopes when pulsed with exogenous antigens, thereby making them a relevant source of antigen-presenting cells to generate T cells. To test this hypothesis, CD40-activated B cells were pulsed with a lysate prepared from melanoma cells and used to stimulate peripheral autologous T cells. Interestingly, T cells specific to melanoma antigens were generated. Additional analysis of these T-cell clones revealed that they recognized MHC class II-restricted epitopes from tyrosinase, a known melanoma tumor antigen. The efficient antigen presentation by antigen-unspecific activated B cells was correlated with a down-regulation in the expression of HLADO, a B cell-specific protein known to interfere with HLA-DM function. Because HLA-DM is important in MHC class II peptide loading, the observed decrease in HLA-DO may partially explain the enhanced antigen presentation after B-cell activation. Results globally suggest that when they are properly activated, antigen-unspecific B-lymphocytes can present exogenous antigens by MHC class II molecules and stimulate peripheral antigen-specific T cells. Antigen presentation by activated B cells could be exploited for immunotherapy by allowing the in vitro generation of T cells specific against antigens expressed by tumors or viruses.
A molecular dynamics study of the structural stability of HIV‐1 protease under physiological conditions: The role of Na+ ions in stabilizing the active site

HIV‐1 protease is most active under weakly acidic conditions (pH 3.5–6.5), when the catalytic Asp25 and Asp25′ residues share 1 proton. At neutral pH, this proton is lost and the stability of the structure is reduced. Here we present an investigation of the effect of pH on the dynamics of HIV‐1 protease using MD simulation techniques. MD simulations of the solvated HIV‐1 protease with the Asp25/25′ residues monoprotonated and deprotonated have been performed. In addition we investigated the effect of the inclusion of Na+ and Cl− ions to mimic physiological salt conditions. The simulations of the monoprotonated form and deprotonated form including Na+ show very similar behavior. In both cases the protein remained stable in the compact, “self‐blocked” conformation in which the active site is blocked by the tips of the flaps. In the deprotonated system a Na+ ion binds tightly to the catalytic dyad shielding the repulsion between the COO− groups. Ab initio calculations also suggest the geometry of the active site with the Na+ bound closely resembles that of the monoprotonated case. In the simulations of the deprotonated form (without Na+ ions), a water molecule bound between the Asp25 Asp25′ side‐chains. This disrupted the dimerization interface and eventually led to a fully open conformation. Proteins 2005. © 2004 Wiley‐Liss, Inc.
Activation of cerebellar parallel fibers monitored in transgenic mice expressing a fluorescent Ca2+ indicator protein

Genetically encoded fluorescent Ca2+ indicator proteins (FCIPs) are promising tools to study Ca2+ signaling in large assemblies of nerve cells. Currently, there are few examples of stable transgenic mouse lines that functionally express such sensors in well‐defined neuronal cell populations. Here we report the generation and characterization of transgenic mice expressing an FCIP under the 5′ regulatory sequences of the Kv3.1 potassium channel promoter. In the cerebellar cortex, expression was restricted to granule cells. We first demonstrated reliable measurements of Ca2+ transients from beams of parallel fibers and compared the FCIP signals with intrinsic autofluorescence signals. We demonstrate that, in a transgenic line that exhibits a high expression level of the FCIP, autofluorescence signals are negligible and stimulation‐induced fluorescence transients represent FCIP signals. Using frontal cerebellar slices we imaged antidromic activation of granule cells following electrical stimulation of parallel fibers and orthodromic activation of beams of parallel fibers following electrical stimulation of granule cells. We found that paired pulse‐induced presynaptic Ca2+ transients of parallel fibers are not affected by blockade of N‐methyl‐d‐aspartate receptors.
A Synthetic Triterpenoid, CDDO-Me, Inhibits IκBα Kinase and Enhances Apoptosis Induced by TNF and Chemotherapeutic Agents through Down-Regulation of Expression of Nuclear Factor κB–Regulated Gene Products in Human Leukemic Cells

The C-28 methyl ester of 2-cyano-3,12-dioxoolean-1,9-dien-28-oic acid (CDDO-Me), a synthetic triterpenoid based on naturally occurring ursolic and oleanolic acids, induces apoptosis in tumor cells, induces differentiation, and inhibits inflammatory response through a poorly understood mechanism. Because the nuclear transcription factor nuclear factor κB (NF-κB) has been shown to suppress apoptosis and promote proliferation and is linked with inflammation and differentiation, we postulated that CDDO-Me modulates NF-κB activity and NF-κB-regulated gene expression. Using human leukemia cell lines and patient samples, we show that CDDO-Me potently inhibits both constitutive and inducible NF-κB activated by tumor necrosis factor (TNF), interleukin (IL)-1β, phorbol ester, okadaic acid, hydrogen peroxide, lipopolysaccharide, and cigarette smoke. CDDO-Me was more potent than CDDO and its imidazole derivative. NF-κB suppression occurred through inhibition of IκBα kinase activation, IκBα phosphorylation, IκBα degradation, p65 phosphorylation, p65 nuclear translocation, and NF-κB-mediated reporter gene transcription. This inhibition correlated with suppression of NF-κB-dependent genes involved in antiapoptosis (IAP2, cFLIP, TRAF1, survivin, and bcl-2), proliferation (cyclin d1 and c-myc), and angiogenesis (VEGF, cox-2, and mmp-9). CDDO-Me also potentiated the cytotoxic effects of TNF and chemotherapeutic agents. Overall, our results suggest that CDDO-Me inhibits NF-κB through inhibition of IκBα kinase, leading to the suppression of expression of NF-κB-regulated gene products and enhancement of apoptosis induced by TNF and chemotherapeutic agents.
New antithrombotic drugs: a revolution in stroke management

Embolism of cardiac origin accounts for 20% of ischaemic strokes. Atrial fibrillation is by far the most common cause of cardioembolic stroke, and anticoagulation is the treatment generally indicated for secondary, and in many cases, primary prevention. The decision to prescribe warfarin is usually based on an accurate assessment of the likely absolute annual risk of stroke without warfarin, and whether or not such benefits of warfarin treatment are likely to outweigh the risk of bleeding associated with its use.
Correlated behavior implicates stromules in increasing the interactive surface between plastids and ER tubules

Stromules are extended by plastids but the underlying basis for their extension and retraction had not been understood until recently. Our live-imaging aided observations on coincident plastid stromule branching and ER tubule dynamics open out new areas of investigation relating to these rapid subcellular interactions. The addendum provides a testable hypothesis on the formation of stromules, which argues against the need for new membrane incorporation and suggests that stromal extensions might result from a remodeling of the plastid envelope membrane in an ER aided manner.
Screening for chronic kidney disease complications in US adults: racial implications of a single GFR threshold.

BACKGROUND AND OBJECTIVES An ideal and effective screening tool should perform equally across ethnic groups. The objective of this study was to determine whether the widely advocated creatinine-based estimated GFR (eGFR) threshold of 60 ml/min per 1.73 m(2) identifies the typical metabolic abnormalities related to chronic kidney disease equally well in minority and nonminority adults. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS This objective was addressed using data for 8918 minority and nonminority adult participants in the National Health and Nutrition Examination Survey 2003 through 2006, which used stratified, multistage, probability sampling methods to assemble a nationwide probability sample of the noninstitutionalized population of the United States. Metabolic abnormalities including BP, potassium, hemoglobin, bicarbonate, uric acid, calcium, phosphorus, and parathyroid hormone were defined by fifth or 95th percentile values. RESULTS Among participants with eGFR <60 ml/min per 1.73 m(2), black individuals were more likely than white individuals to have low hemoglobin (adjusted odds ratio [aOR] 3.76; 95% confidence interval [CI] 1.94 to 7.28), elevated uric acid (aOR 2.15; 95% CI 1.26 to 3.68), and elevated parathyroid hormone (aOR 3.93; 95% CI 2.33 to 6.66). CONCLUSIONS Metabolic consequences of reduced eGFR are more common in black individuals and seem to be present at levels well above 60 ml/min per 1.73 m(2); thus, black individuals should be screened for the metabolic complications of chronic kidney at higher GFR levels.
V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput sequencing data

High-throughput sequencing technologies are used increasingly, not only in viral genomics research but also in clinical surveillance and diagnostics. These technologies facilitate the assessment of the genetic diversity in intra-host virus populations, which affects transmission, virulence, and pathogenesis of viral infections. However, there are two major challenges in analysing viral diversity. First, amplification and sequencing errors confound the identification of true biological variants, and second, the large data volumes represent computational limitations. To support viral high-throughput sequencing studies, we developed V-pipe, a bioinformatics pipeline combining various state-of-the-art statistical models and computational tools for automated end-to-end analyses of raw sequencing reads. V-pipe supports quality control, read mapping and alignment, low-frequency mutation calling, and inference of viral haplotypes. For generating high-quality read alignments, we developed a novel method, called ngshmmalign, based on profile hidden Markov models and tailored to small and highly diverse viral genomes. V-pipe also includes benchmarking functionality providing a standardized environment for comparative evaluations of different pipeline configurations. We demonstrate this capability by assessing the impact of three different read aligners (Bowtie 2, BWA MEM, ngshmmalign) and two different variant callers (LoFreq, ShoRAH) on the performance of calling single-nucleotide variants in intra-host virus populations. V-pipe supports various pipeline configurations and is implemented in a modular fashion to facilitate adaptations to the continuously changing technology landscape. V-pipe is freely available at https://github.com/cbg-ethz/V-pipe.
Transfer Effects of Successive Discrimination-Reversal Training in Chimpanzees

Chimpanzees receiving successive discrimination-reversal training on a single pair of stimuli transferred almost perfectly to two additional reversal tasks and to a "learning-set" series of 180 discrimination problems. A "win-stay, lose-shift" strategy, however it is acquired, seems to be a sufficient basis for one-trial discrimination learning.
Configurational Approach to uncovering the effect of Enterprise Architecture Design on Organizational Performance

Despite this growing adoption of enterprise architecture (EA), there has been little research that provides compelling empirical evidence of the EA impact on organizational performance. We argue that the lack of strong empirical evidence is due to the complexity of EA configurations and the limitations of the traditional correlation-based methods for uncovering the complex relationships. This research intends to examine how EA elements are combined with organizational and environmental elements to produce high or low organizational performance. We identify four EA design factors including centralization, modularity, standardization, and open platforms. Then, we analyze empirical field data, using fuzzy-set qualitative comparative analysis (fsQCA), an emerging set-theoretic configurational methodology. We seek to explain that the way of configuring EA design factors matters for the EA impact on organizational performance and the multifaceted role of each factor over the equifinal configurations. We present our preliminary result and discuss its implications for EA design.
A Robust Wavelet-Aggregated Signal for Geophysical Monitoring Problems

A modification of the method of wavelet-aggregated signal intended for the analysis of multidimen- sional time series of monitoring systems, with account taken of the existence of large outliers in the values of wavelet coefficients, is considered. This property follows from the ability of wavelet expansions to accumulate a maximum amount of information in a relatively small amount of coefficients, as well as from the nature of the data analyzed, in which outliers are not due to errors of recording systems. The non-Gaussian property of the distribution of wavelet coefficients requires modification of conventional schemes used for the multidimen- sional analysis of canonical and principal components in order to make results of this analysis statistically more reliable. An approach to the solution of this problem is presented, along with its applications to the analysis of geophysical data (time series of monitoring systems and seismic catalogs) and comparison of their results with those obtained by applying the previous nonrobust approach.
Euskarazko denbora-egiturak. Azterketa eta etiketatze-esperimentua

Time information extraction is very useful in natural language processing (NLP), as it can be used in text simplification, information extraction and machine translation systems. In this paper we present the first steps of making that information accessible for Basque language: on one hand, Basque structures that convey time have been analysed based on grammars and, on the other hand, first decisions on tagging those on real texts have been taken. Also, we give account of an annotating experiment we have carried out on a financial news corpus.