Miracle-dz/UniFAR-FTUs huggingface dataset:
Predicting spontaneous clearance of acute hepatitis C virus in a large cohort of HIV-1-infected men

Objective An epidemic of acute hepatitis C virus (HCV) infection in HIV-positive men-who-have-sex-with-men (MSM) is emerging in Europe, Australia and the USA. The aim of this study was to characterise the natural history of primary HCV in this setting and to assess host and viral factors which predict spontaneous clearance. Methods This prospective longitudinal cohort study was carried out in 112 HIV-positive patients who were followed in a single centre (the St Mary's Acute HCV Cohort). Plasma and peripheral blood mononuclear cells (PBMCs) were obtained at monthly intervals for 3 months and at 3-monthly intervals thereafter for a median of 45 months (IQR=29–69 months). The primary end point was spontaneous clearance of HCV. Cox regression was used to assess the impact of clinical and virological variables on outcome, including liver function, CD4 count, rate of HCV RNA decline, T cell response and clonal sequence evolution within the HCV E2 envelope gene. Results 15% of patients cleared HCV spontaneously, while 85% progressed towards chronicity. The latter group included a significant proportion of ‘fluctuating’ progressors (37.5%), in whom a fall followed by a rise (>1 log10) in viraemia was observed. This was associated with superinfection with new HCV strains and partially effective T cell responses. Spontaneous clearance was strongly associated with a 2.2 log10 viral load drop within 100 days of infection (HR=1.78; p<0.0001), elevated bilirubin (≥40 μmol/l; HR=5.04; p=0.006), elevated alanine aminotransferase (ALT; ≥1000 IU/ml; HR=2.62; p=0.048) and baseline CD4 count ≥650×106/l (HR=2.66; p=0.045), and only occurred in patients with genotype 1 infection. Evolution to spontaneous clearance occurred in patients with low viral diversity in the presence of an early multispecific T cell response. Conclusions Spontaneous clearance of acute HCV in HIV-positive men can be predicted by a rapid decline in viral load, high CD4 count, elevated bilirubin and ALT, and is associated with low viral diversity and strong T cell responses.
Impact of nocturia on sleep and quality of life: A brief, selected review for the International Consultation on Incontinence Research Society (ICI‐RS) nocturia think tank

Nocturia, the need to awaken at night to void, is a highly prevalent disorder that negatively affects nocturnal sleep, increases daytime tiredness, and adversely impacts quality of life. In this selective review, we provide the reader an overview of current work in this area. From the perspective of disturbed sleep, two divergent perspectives have emerged from the literature when discussing nocturia. The first is that a patient awakens because of an urge to urinate. The second is that a patient awakens during the night for some reason unrelated to urinary urge (e.g., an awakening from an environmental source or from intrinsic lightening of sleep) and then decides to void while awake. In the few studies that have inquired about nocturia as a cause of awakenings, nocturia often ranks above the traditional psychological or physical factors. Not only is nocturia likely to disrupt sleep, but it may impact waking quality of life as well. A number of generic and nocturia‐related questionnaires have been used to quantify the effect of nocturia on quality of life. In this short paper, we introduce the reader to several key studies in these important areas. Neurourol. Urodynam. 33:S15–S18, 2014. © 2014 Wiley Periodicals, Inc.
Grasping the dice by dicing the grasp

Many methods for generating and analyzing grasps have been developed in the recent years. They gave insight and comprehension of grasping with robot hands but many of them are rather complicated to implement and of high computational complexity. In this paper we study if the basic quality criterion for grasps, the force-closure property, is in principle easy or difficult to reach. We show that it is not necessary to generate optimal grasps, due to a certain quality measure, for real robot grasping tasks where an average quality grasp is acceptable. We present statistical data that confirm our opinion that a randomized grasp generation algorithm is fast and suitable for the planning of robot grasping tasks.
Recent advances in diagnosis and treatment of microscopic colitis

Microscopic colitis, comprising collagenous colitis and lymphocytic colitis, is a common cause of chronic diarrhea. It is characterized clinically by chronic watery diarrhea and a macroscopically normal colonic mucosa where diagnostic histopathological features are seen on microscopic examination. The annual incidence of each disorder is 4-6/100,000 inhabitants, with a peak incidence in individuals 60-70 years old and a noticeable female predominance in collagenous colitis. The etiology is unknown. Chronic diarrhea, abdominal pain, weight loss, fatigue, and fecal incontinence are common symptoms that impair the health-related quality of life of the patient. There is an association with other autoimmune disorders, such as celiac disease, thyroid disorders, diabetes mellitus, and arthritis. Budesonide is the best-documented treatment, both short-term and long-term. Recurrence of symptoms is common after withdrawal of successful budesonide therapy, and the optimal long-term treatment strategy needs further study. The long-term prognosis is good, and the risk of complications including colon cancer is low. We review the epidemiology, clinical features, diagnosis and treatment of microscopic colitis.
Towards unlocking web video: Automatic people tracking and clustering

This paper describes a system for automatically extracting meta-information on people from videos on the Web. The system contains multiple modules which automatically track people, including both faces and bodies, and clusters the people into distinct groups. We present new technology and significantly modify existing algorithms for body-detection, shot-detection and grouping, tracking, and track-clustering within our system. The system was designed to work effectivity on Web content, and thus exhibits robust tracking and clustering behavior over a broad spectrum of professional and semi-professional video content. In order to quantify and evaluate our system we created a large ground-truth data-set of people within video. Finally, we provide actual video examples of our algorithm and find that the results are quite strong over a broad range of content.
A Novel Solution Based on Differential Evolution for Short-Term Combined Economic Emission Hydrothermal Scheduling

This paper presents a novel approach based on differential evolution for short-term combined economic emission hydrothermal scheduling, which is formulated as a bi-objective problem: 1) minimizing fuel cost and 2) minimizing emission cost. A penalty factor approach is employed to convert the bi-objective problem into a single objective one. In the proposed approach, heuristic rules are proposed to handle water dynamic balance constraints and heuristic strategies based on priority list are employed to repair active power balance constraints violations. A feasibility-based selection technique is also devised to handle the reservoir storage volumes constraints. The feasibility and effectiveness of the proposed approach are demonstrated and the test results are compared with those of other methods reported in the literature. Numerical experiments show that the proposed method can obtain better-quality solutions with higher precision than any other optimization methods. Hence, the proposed method can well be extended for solving the large-scale hydrothermal sched-uling.
Vulnerability and adaptive strategies to the impact of climate change and variability. The case of rural households in semi-arid Tanzania

This study assesses the community vulnerability and existing adaptive strategies to the impact of climate change in semi-arid areas of Tanzania. The study was undertaken in Shinyanga rural district. The study methods included focus group discussions, key informant and household interviews. Findings from the study showed that the local communities are aware that the climate is changing, as characterized by variability in rainfall patterns and increasing temperature. Rainfall amounts have decreased and became more unpredictable, and drought prolonged. Temperatures have also increased. Consequently, there has been declining crop productivity and increasing food insecurity. Such situation has increased the vulnerability of local community livelihoods to the impacts of climate change. Different socio-economic groups of households (the well-off, intermediate and poor) have differently pursued multiple adaptation strategies, including growing of drought tolerant crops, increasing wetlands cultivation and diversification to non-farm activities, depending on their livelihood assets. The poor groups with limited livelihood assets were reported to be more vulnerable to impacts of climate change and more food insecure as compared to the well-off group, mainly due to their low adaptive capacity. The study concluded that livelihood diversification strategies, including integration of on-farm and non-farm activities, are crucial to enhance adaptive capacity and ensure sustainable rural livelihood in a changing climate.
Ridge preservation techniques for implant therapy.

PURPOSE The aim of this review was to evaluate the techniques and outcomes of postextraction ridge preservation and the efficacy of these procedures in relation to subsequent implant placement. MATERIALS AND METHODS A MEDLINE/PubMed search was conducted and the bibliographies of reviews from 1999 to March 2008 were assessed for appropriate studies. Randomized clinical trials, controlled clinical trials, and prospective/retrospective studies with a minimum of five patients were included. RESULTS A total of 135 abstracts were identified, from which 53 full-text articles were further examined, leading to 37 human studies that fulfilled the search criteria. Many different techniques, methodologies, durations, and materials were presented in the publications reviewed, making direct comparison difficult. CONCLUSIONS Despite the heterogeneity of the studies, it was concluded that ridge preservation procedures are effective in limiting horizontal and vertical ridge alterations in postextraction sites. There is no evidence to support the superiority of one technique over another. There is also no conclusive evidence that ridge preservation procedures improve the ability to place implants.
Do all ischemic stroke subtypes benefit from organized inpatient stroke care?

Background: There are limited data on the effectiveness of organized stroke care in different ischemic stroke subtypes in the real-world setting. We analyzed the effect of organized stroke care in all stroke subtypes in a longitudinal cohort study using data from the Registry of the Canadian Stroke Network. Methods: Between July 2003 and September 2007, there were 6,223 consecutive patients with ischemic stroke subtype information by Trial of Org 10172 in Acute Stroke Treatment criteria. Subtypes were categorized as large artery atherosclerotic disease, lacunar, cardioembolic, or other. The amount of organized stroke care was quantified using the previously published organized care index (OCI), graded 0-3 based on the presence or absence of occupational therapy or physiotherapy, stroke team assessment, and admission to a stroke unit. Results: Mortality at 30 days was associated with both stroke subtype and OCI. Higher OCI (defined as score 2-3 compared to 0-1) was strongly associated with lower odds of 30-day mortality in each ischemic stroke subtype (adjusted odds ratio estimates ranged from 0.16 to 0.43, p < 0.001, controlling for age, gender, stroke severity, and medical comorbidities by logistic regression). These estimates were essentially unchanged after excluding patients treated with palliative care. Numbers needed to treat, to prevent 1 death at 30 days, ranged from 4 to 9 across the subtypes. Conclusions: A strong association between higher OCI and lower 30-day mortality was apparent in each ischemic stroke subtype. These data suggest that organized stroke care should be provided to stroke patients regardless of stroke subtype.
Assessment of Estrogenic Endocrine-Disrupting Chemical Actions in the Brain Using in Vivo Somatic Gene Transfer

Estrogenic endocrine-disrupting chemicals abnormally stimulate vitellogenin gene expression and production in the liver of many male aquatic vertebrates. However, very few studies demonstrate the effects of estrogenic pollutants on brain function. We have used polyethylenimine-mediated in vivo somatic gene transfer to introduce an estrogen response element–thymidine kinase–luciferase (ERE-TK-LUC) construct into the brain. To determine if waterborne estrogenic chemicals modulate gene transcription in the brain, we injected the estrogen-sensitive construct into the brains of Nieuwkoop-Faber stage 54 Xenopus laevis tadpoles. Both ethinylestradiol (EE2; p < 0.002) and bisphenol A (BPA; p < 0.03) increased luciferase activity by 1.9- and 1.5-fold, respectively. In contrast, low physiologic levels of 17β-estradiol had no effect (p > 0.05). The mixed antagonist/agonist tamoxifen was estrogenic in vivo and increased (p < 0.003) luciferase activity in the tadpole brain by 2.3-fold. There have been no previous reports of somatic gene transfer to the fish brain; therefore, it was necessary to optimize injection and transfection conditions for the adult goldfish (Carassius auratus). Following third brain ventricle injection of cytomegalovirus (CMV)-green fluorescent protein or CMV-LUC gene constructs, we established that cells in the telencephalon and optic tectum are transfected. Optimal transfections were achieved with 1 μg DNA complexed with 18 nmol 22 kDa polyethylenimine 4 days after brain injections. Exposure to EE2 increased brain luciferase activity by 2-fold in males (p < 0.05) but not in females. Activation of an ERE-dependent luciferase reporter gene in both tadpole and fish indicates that waterborne estrogens can directly modulate transcription of estrogen-responsive genes in the brain. We provide a method adaptable to aquatic organisms to study the direct regulation of estrogen-responsive genes in vivo.
The Insertion Encoding of Permutations

We introduce the insertion encoding , an encoding of finite permutations. Classes of permutations whose insertion encodings form a regular language are characterized. Some necessary conditions are provided for a class of permutations to have insertion encodings that form a context free language. Applications of the insertion encoding to the evaluation of generating functions for classes of permutations, construction of polynomial time algorithms for enumerating such classes, and the illustration of bijective equivalence between classes are demonstrated.
A macroevolutionary perspective on species range limits

Understanding the factors that determine the geographic range limits of species is important for many questions in ecology, evolution and conservation biology. These limits arise from complex interactions among ecology and dispersal ability of species and the physical environment, but many of the underlying traits can be conserved among related species and clades. Thus, the range limits of species are likely to be influenced by their macroevolutionary history. Using palaeontological and biogeographic data for marine bivalves, we find that the range limits of genera are significantly related to their constituent species richness, but the effects of age are weak and inconsistent. In addition, we find a significant phylogenetic signal in the range limits at both genus and family levels, although the strength of this effect shows interoceanic variation. This phylogenetic conservatism of range limits gives rise to an evolutionary pattern where wide-ranging lineages have clusters of species within the biogeographic provinces, with a few extending across major boundaries.
Macrophages as APC and the Dendritic Cell Myth

Dendritic cells have been considered an immune cell type that is specialized for the presentation of Ag to naive T cells. Considerable effort has been applied to separate their lineage, pathways of differentiation, and effectiveness in Ag presentation from those of macrophages. This review summarizes evidence that dendritic cells are a part of the mononuclear phagocyte system and are derived from a common precursor, responsive to the same growth factors (including CSF-1), express the same surface markers (including CD11c), and have no unique adaptation for Ag presentation that is not shared by other macrophages.
The memory of ENSO revisited by a 2‐factor Gegenbauer process

This article specifies a multi‐factor long memory process, namely Gegenbauer process, particularly adapted for data with slow damping correlations and cyclical patterns, and explores the use of this representation in the inter‐annual climate variability range capture by indices of the El Niño Southern Oscillation (ENSO). The empirical results suggest that sea surface temperature (SST) indices are stationary long memory processes. It is found that the indices in the eastern and central Pacific exhibit different dynamics. The variability of the eastern equatorial Pacific SST indices (Niño 1 − 2 and Niño 3) is characterized by a large component of long‐memory behaviour associated with the quasi‐biennial and the semi‐annual frequency. In contrast, the variability of the central Pacific SST indices (Niño 3.4 and Niño 4) is characterized by a large component of long‐memory behaviour associated with the annual and the semi‐annual frequency. These results are consistent with recent studies that suggest that ENS0 SST anomalies in the equatorial Pacific can be considered to consist of two processes. The use of Gegenbauer processes can be considered as an alternative competitive procedure in the analysis of cyclical long memory climatological time series from a different time series perspective.
Do the risks and consequences of hospitalized fall injuries among older adults in California vary by type of fall?

BACKGROUND Research on fall injuries in older persons generally does not examine different types of falls separately. (The main types are same level, from one level to another, and on or from stairs and steps.) There is no a priori reason to believe that various types of falls have similar demographic risk factors and consequences. Therefore, we examined patterns in types of falls, place of falls, and consequences of fall injuries as Californians move through their later decades. METHODS We analyzed all computerized patient discharge records for all adults 20 years and over hospitalized with a fall as the principal external cause of injury in California nonfederal acute care hospitals, from 1995 through 1997 (N = 242,166). Older-adult age groups were compared with all younger adults. Place of fall, hospital charges, and disposition at discharge were analyzed by type of fall. RESULTS The three main types of fall injury increase with age, but each type shows variation by age and sex. Women have the highest rates for the main types but not for the less common types. Hospitalized falls vary by place of fall. Mean hospital charges ($17,086) vary by type of fall, with falls from one level to another having the largest mean hospital charge ($19,632). Disposition at discharge does not vary by type of fall. CONCLUSIONS We found significant variation in demographic factors, place of fall, and mean hospital charges for falling by type of fall, suggesting that future research should focus on individual types of falls rather than on aggregated falls.
Chemostat Production of Plantaricin C ByLactobacillus plantarum LL441

ABSTRACT Plantaricin C, a bacteriocin synthesized by Lactobacillus plantarum LL441, was optimally produced in chemostats kept at pH 5.0, 30°C, 150 rpm, and a dilution rate of 0.05 h−1 when glucose was used as carbon source and a dilution rate of 0.10 to 0.12 h−1 when sucrose or fructose was used instead. Production was abolished at high dilution rates, i.e., when the cells grew rapidly in all carbon sources.
Extended Substitution Cipher Chaining mode (ESCC)

In this paper, we present a new tweakable narrow-block mode of operation, the Extended Substitution Cipher Chaining mode (ESCC), that can be efficiently deployed in disk encryption applications. ESCC is an extension of Substitution Cipher Chaining mode (SCC) [5]. Unlike SCC, ESCC is resistant to the attacks in [6, 7, 8].
Does a Local B‐Minimum Appear in the Tail Current Sheet During a Substorm Growth Phase?

Magnetic configurations with dBz/dr > 0 in the midtail current sheet are potentially unstable to various instabilities associated with the explosive substorm onset. Their existence is hard to confirm with observations of magnetospheric spacecraft. Here we use remote sensing by low‐altitude spacecraft that measured the loss cone filling rate during electron‐rich solar particle event, providing information about magnetic properties of the tail current sheet. We found a latitudinally localized anisotropic 30 keV electron loss cone region embedded inside an extended region of isotropic solar electron precipitation. It was persistently observed for more than 0.5 h during isolated growth phase event by six Polar Operational Environmental Satellites spacecraft, which crossed the premidnight auroral oval. The embedded anisotropic region was observed 1° poleward of the outer radiation belt boundary over 4–5 h wide magnetic local time sector, suggesting a persistent ridge‐type Bz2/j maximum in the equatorial plasma sheet at distances 15–20 RE. We discuss infrequent observations of such events taking into account recent results of global magnetohydrodynamic simulations.
WAR: Webserver for aligning structural RNAs

We present an easy-to-use webserver that makes it possible to simultaneously use a number of state of the art methods for performing multiple alignment and secondary structure prediction for noncoding RNA sequences. This makes it possible to use the programs without having to download the code and get the programs to run. The results of all the programs are presented on a webpage and can easily be downloaded for further analysis. Additional measures are calculated for each program to make it easier to judge the individual predictions, and a consensus prediction taking all the programs into account is also calculated. This website is free and open to all users and there is no login requirement. The webserver can be found at: http://genome.ku. dk/resources/war.