Miracle-dz/UniFAR-FTUs huggingface dataset:
Using the entire history in the analysis of nested case cohort samples

Countermatching designs can provide more efficient estimates than simple matching or case–cohort designs in certain situations such as when good surrogate variables for an exposure of interest are available. We extend pseudolikelihood estimation for the Cox model under countermatching designs to models where time‐varying covariates are considered. We also implement pseudolikelihood with calibrated weights to improve efficiency in nested case–control designs in the presence of time‐varying variables. A simulation study is carried out, which considers four different scenarios including a binary time‐dependent variable, a continuous time‐dependent variable, and the case including interactions in each. Simulation results show that pseudolikelihood with calibrated weights under countermatching offers large gains in efficiency if compared to case–cohort. Pseudolikelihood with calibrated weights yielded more efficient estimators than pseudolikelihood estimators. Additionally, estimators were more efficient under countermatching than under case–cohort for the situations considered. The methods are illustrated using the Colorado Plateau uranium miners cohort. Furthermore, we present a general method to generate survival times with time‐varying covariates. Copyright © 2016 John Wiley & Sons, Ltd.
Abnormal thymic stromal lymphopoietin expression in the duodenal mucosa of patients with coeliac disease

Objective The short isoform of thymic stromal lymphopoietin (TSLP), a cytokine constitutively expressed by epithelial cells, is crucial in preserving immune tolerance in the gut. TSLP deficiency has been implicated in sustaining intestinal damage in Crohn's disease. We explored mucosal TSLP expression and function in refractory and uncomplicated coeliac disease (CD), a T-cell-mediated enteropathy induced by gluten in genetically susceptible individuals. Design TSLP isoforms—long and short—and receptors—TSLPR and interleukin (IL)-7Rα—were assessed by immunofluorescence, immunoblotting and qRT-PCR in the duodenum of untreated, treated, potential and refractory patients with CD. The ability of the serine protease furin or CD biopsy supernatants to cleave TSLP was evaluated by immunoblotting. The production of interferon (IFN)-γ and IL-8 by untreated CD biopsies cultured ex vivo with TSLP isoforms was also assessed. Results Mucosal TSLP, but not TSLPR and IL-7Rα, was reduced in untreated CD and refractory CD in comparison to treated CD, potential CD and controls. Transcripts of both TSLP isoforms were decreased in active CD mucosa. Furin, which was overexpressed in active CD biopsies, was able to cleave TSLP in vitro. Accordingly, refractory and untreated CD supernatants showed higher TSLP-degrading capacity in comparison to treated CD and control supernatants. In our ex vivo model, both TSLP isoforms significantly downregulated IFN-γ and IL-8 production by untreated CD biopsies. Conclusions Reduced mucosal TSLP expression may contribute to intestinal damage in refractory and untreated CD. Further studies are needed to verify whether restoring TSLP might be therapeutically useful especially in refractory patients with CD.
Intrahepatic Cholestasis of Pregnancy: A Review of Diagnosis and Management.

Importance Intrahepatic cholestasis of pregnancy (ICP) complicates approximately 0.2% to 2% of pregnancies and can lead to increased fetal risks in pregnancy. Objective This review aims to increase the knowledge of women's health care providers regarding the diagnosis, management, and fetal risks associated with ICP. Results The diagnosis of ICP is based on symptoms of pruritus that typically include the palms and soles, as well as elevated bile acid levels. Other liver function tests such as alanine aminotransferase and aspartate aminotransferase are also frequently elevated, and other causes of liver dysfunction should be ruled out. Fetal risks of ICP include increased risk of preterm birth, meconium-stained amniotic fluid, respiratory distress syndrome, or stillbirth. There is evidence that as bile acid levels increase, so does the risk of adverse neonatal outcomes. Ursodeoxycholic acid treatment has been shown to improve maternal pruritus symptoms, as well as biochemical tests, but no treatment has been shown to definitively improve fetal outcomes. Conclusions and Relevance Providers should be aware of the signs and symptoms of ICP and provide accurate diagnosis and management of affected women. Women with a diagnosis of ICP should be treated with ursodeoxycholic acid to improve maternal symptoms. Given the increased risk of stillbirth in the setting of ICP, delivery may be considered at 37 weeks' gestation.
Intonational phonology of Catalan and its dialectal varieties

Catalan is a Romance language that is spoken by about 10 million people in a region that lies within four adjacent European states, Andorra, Italy, France, and Spain. Fig. 2.1 shows a map of the geographical areas where Catalan is spoken, subdivided into its major and traditionally accepted dialects (Veny 1982): Central Catalan and Northwestern Catalan (spoken in Catalonia, Aragon, and Andorra), Valencian Catalan (Valencian region), Balearic Catalan (Balearic Islands), Northern Catalan (in the Roussillon region of southern France, roughly equivalent to the current département of Pyrénées-Orientales), and Algherese Catalan (in the city of l’Alguer, Sardinia). Breaking down the total number of roughly 10 million Catalan speakers by geographic area, Catalonia and the Valencian region provide the great majority, with 5,703,000 and 2,952,000 respectively, followed by the Balearic community with 735,000 speakers. The remaining territories provide much smaller figures, with 61,000 speakers in Andorra, 142,000 speakers in southern France, and 24,000 in the city of l’Alguer (Sardinia, Italy) (data from Pons and Sorolla 2009). With respect to its legal status, Catalan is the official language in Andorra; within Spain it is co-official
Selenium toxicity to survival and reproduction of Collembola and Enchytraeids in a sandy loam soil

We investigated the toxicity of selenium (Se) to the soil invertebrates Folsomia candida (Collembola) and Enchytraeus crypticus (potworm). Studies were designed to generate ecotoxicological benchmarks for developing ecological soil screening levels (Eco‐SSLs) for risk assessments of contaminated soils. For the present studies, we selected Sassafras sandy loam, an aerobic upland soil with soil characteristics (low levels of clay and organic matter, soil pH adjusted from 5.2 to 7.1) that support high relative bioavailability of the anionic Se species that is typically found in aerobic soil. The Se was amended into soil as sodium selenate, subjected to weathering and aging using 21 d of alternating cycles of air‐drying/rehydration to 60% of the water‐holding capacity of the Sassafras sandy loam soil, under ambient greenhouse conditions. Effective concentrations at 20 and 50% (EC20 and EC50) levels for production of juveniles (reproduction) were 4.7 and 10.9 mg of Se/kg of soil (dry mass basis), respectively, for Collembola, and 4.4 and 6.2 mg/kg, respectively, for the potworms. The data enabled the derivation of toxicity benchmarks, contributing to the development of a soil invertebrate‐based Eco‐SSL of 4.1 mg/kg for Se. Environ Toxicol Chem 2018;37:846–853. Published 2017 Wiley Periodicals Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America.
Spatially Constrained Location Prior for scene parsing

Semantic context is an important and useful cue for scene parsing in complicated natural images with a substantial amount of variations in objects and the environment. This paper proposes Spatially Constrained Location Prior (SCLP) for effective modelling of global and local semantic context in the scene in terms of inter-class spatial relationships. Unlike existing studies focusing on either relative or absolute location prior of objects, the SCLP effectively incorporates both relative and absolute location priors by calculating object co-occurrence frequencies in spatially constrained image blocks. The SCLP is general and can be used in conjunction with various visual feature-based prediction models, such as Artificial Neural Networks and Support Vector Machine (SVM), to enforce spatial contextual constraints on class labels. Using SVM classifiers and a linear regression model, we demonstrate that the incorporation of SCLP achieves superior performance compared to the state-of-the-art methods on the Stanford background and SIFT Flow datasets.
Involvement of shared mucosal‐associated microbiota in the duodenum and rectum in diarrhea‐predominant irritable bowel syndrome

Most studies of diarrhea‐predominant irritable bowel syndrome (IBS‐D) focused on microbiota dysbiosis in a single segment of the intestine such as the colon. However, the intestine as a whole is involved in IBS‐D and knowledge about the role of microbiota shared by the duodenum and rectum in IBS‐D is limited. Here, we investigated the characteristics of mucosal microbiota shared by the duodenum and rectum in IBS‐D patients.
Check before storing: what is the performance price of content integrity verification in LRU caching?

In some network and application scenarios, it is useful to cache content in network nodes on the fly, at line rate. Resilience of in-network caches can be improved by guaranteeing that all content therein stored is valid. Digital signatures could be indeed used to verify content integrity and provenance. However, their operation may be much slower than the line rate, thus limiting caching of cryptographically verified objects to a small subset of the forwarded ones. How this affects caching performance? To answer such a question, we devise a simple analytical approach which permits to assess performance of an LRU caching strategy storing a randomly sampled subset of requests. A key feature of our model is the ability to handle traffic beyond the traditional Independent Reference Model, thus permitting us to understand how performance vary in different temporal locality conditions. Results, also verified on real world traces, show that content integrity verification does not necessarily bring about a performance penalty; rather, in some specific (but practical) conditions, performance may even improve.
802.11b/g link level measurements for an outdoor wireless campus network

Outdoor WLAN communication is envisioning an increasing interest, due to the massive emergence and deployment of outdoor wireless mesh networks. This paper provides a report on an extensive measurement campaign carried out in an outdoor wireless LAN campus scenario. A public domain driver, namely MADWiFi, has been modified in order to achieve a high (per-node and per-frame) measurement granularity, and in order to distinguish the different causes that contribute to link-layer errors. The main result of our experimental investigation is that, unlike 802.11b, which appears a robust technology in most of the operational conditions, 802.11g may lead to severe inefficiencies when employed in an outdoor scenario
Review of Multifarious Applications of Poly (Lactic Acid)

ABSTRACT Poly (lactic acid) is considered to be a promising alternative to petroleum-based polymers due to its renewability, biodegradability, biocompatibility, and good mechanical properties. Because of the high cost, the applications of poly (lactic acid) were limited to the medical field. Over the past decade, improvements in polymerization allow the economical mass production of high molecular weight poly (lactic acid). Therefore, the applications of poly (lactic acid) have recently spread to domestic, commercial packaging, and textile applications. This review outlines the chemical, thermal characteristics of poly (lactic acid) and discusses the use of poly (lactic acid) in medical applications such as sutures, stents, drug carrier, orthopaedic devices, scaffolds, as well as commercial applications in textile and packaging fields with superior properties such as high wicking performance, good dyeability, antibacterial feature, good ultraviolet resistance, high water vapor transmission rates, shrink wrapping, and dead fold property. While the drawbacks of poly (lactic acid) utilized in these fields are also discussed. It is clear that the advantages of using poly (lactic acid) outlined in this review will ensure that the market for poly (lactic acid) products will continue to expand. GRAPHICAL ABSTRACT
Proteochemometrics-Based Prediction of Peptide Binding to HLA-DP Proteins

Human leukocyte antigens (HLA) class II proteins are involved in the antigen processing in the antigen presenting cells. They form complexes with antigen peptide fragments. The peptide-HLA protein complexes are presented on the cell surface where they are recognized by helper T cells (Th cells). HLA-DP is one of the three HLA class II loci. The HLA-DP proteins are associated with a significant number of autoimmune diseases, as well as with a susceptibility or resistance to a number of infectious agents. In the present study, we apply proteochemometrics-a method for bioactivity modeling of multiple ligands binding to multiple target proteins-to derive and validate a robust model for peptide binding prediction to the 7 most frequent HLA-DP proteins. The model is able to identify 86% of the binders in the top 10% of the best predicted nonamers generated from one protein.
The Workplace Experiences of Women with Fibromyalgia.

PURPOSE Fibromyalgia (FM) is a common pain syndrome that mostly affects women. Chronic pain and other symptoms often chalenge work for women with FM. This study aimed to explore how women with FM experience their work situations. METHOD A purposive sample of 15 women with FM was interviewed with in-depth qualitative interviews. Data were analysed using a hermeneutic approach. RESULTS The results revealed that women with FM experienced incapacity to work as they had previously and eventually accepted that their work life had changed or reached its end. Since their work had great significance in their lives, feelings of loss and sorrow were common. Women who were working, unemployed, or on sick leave described feelings of fear for their future work situations. CONCLUSIONS Women with FM greatly value their work. Their wish to perform work as before is however, not consistent with their abilities. As such, women with FM need support in continuing to work for as long as possible, after which they need support in finding new values in life.
The importance of studying oral and craniofacial manifestations of Mendelian phenotypes.

One of the main goals of the Human Genome Project (HGP), completed in April of 2003 (All About the Human Genome Project, 2015), was to improve understanding of human disease. This wonderful roadmap accelerated the discovery of genes that increased risk for more common, complex diseases such as diabetes, but also hereditary disorders that are found in families and passed from parents to children (Mendelian phenotypes) (Chong et al, 2015). The value of studying Mendelian phenotypes is that the identification of the germline mutation (single-nucleotide variant) or copy-number variants that are responsible for the phenotype expands our understanding of the protein that is encoded by the gene, its function, how it is expressed, and how altered forms of the protein may contribute to more common, similar diseases in the general population.
Longitudinal Links between Executive Function, Anger, and Aggression in Middle Childhood

Previous research has indicated that executive function (EF) is negatively associated with aggressive behavior in childhood. However, there is a lack of longitudinal studies that have examined the effect of deficits in EF on aggression over time and taken into account different forms and functions of aggression at the same time. Furthermore, only few studies have analyzed the role of underlying variables that may explain the association between EF and aggression. The present study examined the prospective paths between EF and different forms (physical and relational) and functions (reactive and proactive) of aggression. The habitual experience of anger was examined as a potential underlying mechanism of the link between EF and aggression, because the tendency to get angry easily has been found to be both a consequence of deficits in EF and a predictor of aggression. The study included 1,652 children (between 6 and 11 years old at the first time point), who were followed over three time points (T1, T2, and T3) covering 3 years. At T1, a latent factor of EF comprised measures of planning, rated via teacher reports, as well as inhibition, set shifting, and working-memory updating, assessed experimentally. Habitual anger experience was assessed via parent reports at T1 and T2. The forms and functions of aggression were measured via teacher reports at all three time points. Structural equation modeling revealed that EF at T1 predicted physical, relational, and reactive aggression at T3, but was unrelated to proactive aggression at T3. Furthermore, EF at T1 was indirectly linked to physical aggression at T3, mediated through habitual anger experience at T2. The results indicate that deficits in EF influence the later occurrence of aggression in middle childhood, and the tendency to get angry easily mediates this relation.
The contribution of lesion location to upper limb deficit after stroke

Background Motor deficit after stroke is related to regional anatomical damage. Objective To examine the influence of lesion location on upper limb motor deficit in chronic patients with stroke. Methods Lesion likelihood maps were created from T1-weighted structural MRI in 33 chronic patients with stroke with either purely subcortical lesions (SC, n=19) or lesions extending to any of the cortical motor areas (CM, n=14). We estimated lesion likelihood maps over the whole brain and applied multivoxel pattern analysis to seek the contribution weight of lesion likelihood to upper limb motor deficit. Among 5 brain regions of interest, the brain region with the greatest contribution to motor deficit was determined for each subgroup. Results The corticospinal tract was most likely to be damaged in both subgroups. However, while damage in the corticospinal tract was the best indicator of motor deficit in the SC patients, motor deficit in the CM patients was best explained by damage in brain areas activated during handgrip. Conclusions Quantification of structural damage can add to models explaining motor outcome after stroke, but assessment of corticospinal tract damage alone is unlikely to be sufficient when considering patients with stroke with a wide range of lesion topography.
Soil Quality Evaluation Using the Soil Management Assessment Framework (SMAF) in Brazilian Oxisols with Contrasting Texture

The Soil Management Assessment Framework (SMAF) was developed in the U.S.A. and has been used as a tool for assessing and quantifying changes in soil quality/health (SQ) induced by land uses and agricultural practices in that region and elsewhere throughout the world. An initial study using SMAF in Brazil was recently published, but additional research for a variety of soils and management systems is still needed. Our objective was to use data from five studies in southern Brazil to evaluate the potential of SMAF for assessing diverse land-use and management practices on SQ. The studies examined were: (i) horizontal and vertical distribution of soil properties in a long-term orange orchard; (ii) impacts of long-term land-use change from native vegetation to agricultural crops on soil properties; (iii) effects of short-term tillage on soil properties in a cassava production area; (iv) changes in soil properties due to mineral fertilizer and pig slurry application coupled with soil tillage practices; and (v) row and inter-row sowing effects on soil properties in a long-term no-tillage area. The soils were classified as Oxisols, with clay content ranging from 180 to 800 g kg-1. Six SQ indicators [pH(H2O), P, K, bulk density, organic C, and microbial biomass] were individually scored using SMAF curves and integrated into an overall Soil Quality Index (SQI) focusing on chemical, physical, and biological sectors. The SMAF was sensitive for detecting SQ changes induced by different land uses and management practices within this wide textural range of Brazilian Oxisols. The SMAF scoring curve algorithms properly transformed the indicator values expressed in different units into unitless scores ranging from 0-1, thus enabling the individual indicators to be combined into an overall index for evaluating land-use and management effects on soil functions. Soil sector scores (i.e., chemical, physical, and biological) identify the principal soil limitations and can therefore be used to establish priorities for specific management actions. The SMAF can be used as a tool for assessing SQ in Brazilian soils, thus helping farmers, land managers, and politicians make better decisions regarding sustainable land-use and management practices.
Progress Report on Disassembly and Post-Irradiation Experiments for UCSB ATR-2 Experiment

The reactor pressure vessel (RPV) in a light-water reactor (LWR) represents the first line of defense against a release of radiation in case of an accident. Thus, regulations that govern the operation of commercial nuclear power plants require conservative margins of fracture toughness, both during normal operation and under accident scenarios. In the unirradiated condition, the RPV has sufficient fracture toughness such that failure is implausible under any postulated condition, including pressurized thermal shock (PTS) in pressurized water reactors (PWR). In the irradiated condition, however, the fracture toughness of the RPV may be severely degraded, with the degree of toughness loss dependent on the radiation sensitivity of the materials. As stated in previous progress reports, the available embrittlement predictive models, e.g. [1], and our present understanding of radiation damage are not fully quantitative, and do not treat all potentially significant variables and issues, particularly considering extension of operation to 80y.