Miracle-dz/UniFAR-FTUs huggingface dataset:
Issues in co-morbid severe mental illnesses in HIV infected individuals

Patients with comorbid HIV and serious mental illnesses pose particular difficulties for clinicians. Presentation of several mental disturbances can be similar, and often significanlty complicate the management of advancing HIV disease. In this article, we will review the assessment and management of four serious mental conditions in HIV-infected patients: delirium, dementia, schizophrenia and bipolar disorder.
An in vivo verification of the intravoxel incoherent motion effect in diffusion‐weighted imaging of the abdomen

To investigate the vascular contribution to the measured apparent diffusion coefficient and to validate the Intra Voxel Incoherent Motion theory, the signal as a function of the b‐value was measured in the healthy pancreas with and without suppression of the vascular component and under varying echo times (TE = 50, 70, and 100 msec). The perfusion fraction f and the diffusion coefficient D were extracted from the measured DW‐data using the original Intra Voxel Incoherent Motion‐equation and a modified version of this equation incorporating relaxation effects. First, the perfusion fraction f in the blood suppressed pancreatic tissue decreased significantly (P = 0.03), whereas the diffusion coefficient D did not change with suppression (P = 0.43). Second, the perfusion fraction f increased significantly with increasing echo time (P = 0.0025), whereas the relaxation time compensated perfusion fraction f′ showed no significant dependence on TE (P = 0.31). These results verify a vascular contribution to the diffusion weighted imaging measurement at low b values and support the Intra Voxel Incoherent Motion‐theory. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.
Extraordinary isotopic fractionation in ozone photolysis

Analysis of experimental ozone absorption spectra reveals that ultraviolet photolysis within the structured Huggins band yields extraordinary wavelength‐dependent isotopic fractionation, oscillating between complete enrichment and complete depletion for changes of less than 2 nm in the excitation wavelength. Visible photolysis yields wavelength‐dependent fractionation that varies from −300‰ to +300‰. Photochemical modeling demonstrates photolysis contributes fractionation up to +45‰ to the heavy ozone anomaly in the middle stratosphere with measurable 17O and 18O isotopologue‐dependent variations as a function of altitude despite the fact that the extraordinary photolysis‐induced isotopic fractionation effect is dampened in the atmosphere due to the integration over all excitation wavelengths.
Within-Hospital Readmission: An Indicator of Readmission after Discharge from Psychiatric Hospitalization

Objective: Readmission after psychiatric hospitalization is widely used as a quality of care indicator by government funding agencies, policy-makers, and hospitals deciding on clinical priorities. Readmission rates are calculated accurately to allow these varied groups to correctly translate the knowledge into appropriate, tangible outcomes. We aimed to assess how well hospital readmission rates, calculated using only readmissions to the discharging institution, can approximate actual readmission rates. Method: We used administrative data sources to identify patients with a mental health discharge in the province of Ontario (2008–2011). We identified mental health readmissions within 30 and 90 days of discharge occurring to the hospital from which the patient was discharged (within-hospital readmissions), and compared readmission rates using only within-hospital admissions with actual readmission rates. Results: The percentage of readmissions occurring to the discharging institution ranged from 39% to 89% (median 73%) and from 37% to 86% (median 70%) for 30- and 90-day readmissions, respectively. Using only within-hospital readmissions to rank hospitals by their readmission rates, only 56% of hospitals for 30-day readmissions and 50% for 90-day readmissions were ranked in the same quartile as when actual readmission rates were used. Conclusions: These findings highlight the importance of measuring psychiatric readmissions at the system level, particularly for hospitals with lower discharge volumes. As well, the high likelihood that multiple hospitals are involved in the hospital-based care of people who require readmission requires consideration at clinical and policy levels.
Finding Skills through Ranked Semantic Match of Descriptions

We propose a formal approach to Ontology-Based Semantic Matchmaking between Skills request and offer, devised as a virtual marketplace of knowledge. In such a knowledge market metaphor, skills are a peculiar kind of goods that have distinguishing characteristics with respect to traditional assets. Buyers are entities that need the skills of people, such as projects, departments and organizations; sellers are workers that offer their own skills. The formal framework supports the semantic match of descriptions provided by demanders and sellers of skills. In particular our approach overcomes simple subsumption matching and allows for match ranking and categorization. The implementation of the approach in a prototype facilitator, which embeds a NeoCLassic reasoner, is also described.
Constrained Texture Mapping And Foldover-free Condition

Texture mapping has been widely used in image processing and graphics to enhance the realism of CG scenes. However to perfectly match the feature points of a 3D model with the corresponding pixels in texture images, the parameterisation which maps a 3D mesh to the texture space must satisfy the positional constraints. Despite numerous research efforts, the construction of a mathematically robust foldover-free parameterisation subject to internal constraints is still a remaining issue. In this paper, we address this challenge by developing a two-step parameterisation method. First, we produce an initial parameterisation with a method traditionally used to solve structural engineering problems, called the bar-network. We then derive a mathematical foldover-free condition, which is incorporated into a Radial Basis Function based scheme. This method is therefore able to guarantee that the resulting parameterization meets the hard constraints without foldovers. Keywords-Foldover; constrained texture mapping; parameterization;
Solving the Quadratic Assignment Problem with the modified hybrid PSO algorithm

In this paper a particle swarm optimization algorithm is presented to solve the Quadratic Assignment Problem, which is a NP-Complete problem and is one of the most interesting and challenging combinatorial optimization problems in existence. A heuristic rule, the Smallest Position Value (SPV) rule, is developed to enable the Continuous particle swarm optimization algorithm to be applied to the sequencing problems. So, we use SPV to the QAP problem, which is a discrete problem. A simple but very efficient Hill Climbing method is embedded in the particle swarm optimization algorithm. We test our hybrid algorithm on some of the benchmark instances of QAPLIB, a well-known library of QAP instances. This algorithm is compared with some strategies to solve the problem. The computational results show that the modified hybrid Particle Swarm algorithm is able to find the optimal and best-known solutions on instances of widely used benchmarks from the QAPLIB. In most of instances, the proposed method outperforms other approaches. Experimental results illustrate the effectiveness of proposed approach on the quadratic assignment problem.
Blood oxygenation dependence of t1 and t2 in the isolated, perfused rabbit heart at 4.7t

An MR line scan protocol has been used to measure relaxation parameters (T1 and T2) in isolated, blood perfused rabbit hearts at various blood oxygenations. Hearts were retro‐gradely perfused at 37°C with a cardioplegic solution (modified St. Thomas' solution) containing sheep red blood cells and adenosine (1 mM) to maximally vasodilate the coronary vascular bed. Arresting the hearts eliminated motion complications and minimized arteriovenous oxygenation differences. The authors have found that under conditions of stable flow, there is a strong correlation between T2 in myocardial septa and hemoglobin (Hb) saturation, while tissue T1 is virtually independent of blood oxygenation. These effects are believed to be due to the paramagnetic agent deoxyhemoglobin.
Diverse Plant and Animal Genetic Records from Holocene and Pleistocene Sediments

Genetic analyses of permafrost and temperate sediments reveal that plant and animal DNA may be preserved for long periods, even in the absence of obvious macrofossils. In Siberia, five permafrost cores ranging from 400,000 to 10,000 years old contained at least 19 different plant taxa, including the oldest authenticated ancient DNA sequences known, and megafaunal sequences including mammoth, bison, and horse. The genetic data record a number of dramatic changes in the taxonomic diversity and composition of Beringian vegetation and fauna. Temperate cave sediments in New Zealand also yielded DNA sequences of extinct biota, including two species of ratite moa, and 29 plant taxa characteristic of the prehuman environment. Therefore, many sedimentary deposits may contain unique, and widespread, genetic records of paleoenvironments.
Metabolic engineering of terpene biosynthesis in plants using a trichome‐specific transcription factor MsYABBY5 from spearmint (Mentha spicata)

Summary In many aromatic plants including spearmint (Mentha spicata), the sites of secondary metabolite production are tiny specialized structures called peltate glandular trichomes (PGT). Having high commercial values, these secondary metabolites are exploited largely as flavours, fragrances and pharmaceuticals. But, knowledge about transcription factors (TFs) that regulate secondary metabolism in PGT remains elusive. Understanding the role of TFs in secondary metabolism pathway will aid in metabolic engineering for increased yield of secondary metabolites and also the development of new production techniques for valuable metabolites. Here, we isolated and functionally characterized a novel MsYABBY5 gene that is preferentially expressed in PGT of spearmint. We generated transgenic plants in which MsYABBY5 was either overexpressed or silenced using RNA interference (RNAi). Analysis of the transgenic lines showed that the reduced expression of MsYABBY5 led to increased levels of terpenes and that overexpression decreased terpene levels. Additionally, ectopic expression of MsYABBY5 in Ocimum basilicum and Nicotiana sylvestris decreased secondary metabolite production in them, suggesting that the encoded transcription factor is probably a repressor of secondary metabolism.
Long-run cost analysis by approximation of linear operators over dioids

In this paper we present a semantics-based framework for analysing the quantitative behaviour of programs with respect to resource usage. We start from an operational semantics in which costs are modelled using a dioid structure. The dioid structure of costs allows the definition of the quantitative semantics as a linear operator. We then develop a theory of approximation of such a semantics, which is akin to what is offered by the theory of abstract interpretation for analysing qualitative properties, in order to compute effectively global cost information from the program. We focus on the notion of long-run cost, which models the asymptotic average cost of a program. The abstraction of the semantics has to take two distinct notions of order into account: the order on costs and the order on states. We prove that our abstraction technique provides a correct approximation of the concrete long-run cost of a program.
Ibrutinib is an irreversible molecular inhibitor of ITK driving a Th1-selective pressure in T lymphocytes.

Given its critical role in T-cell signaling, interleukin-2-inducible kinase (ITK) is an appealing therapeutic target that can contribute to the pathogenesis of certain infectious, autoimmune, and neoplastic diseases. Ablation of ITK subverts Th2 immunity, thereby potentiating Th1-based immune responses. While small-molecule ITK inhibitors have been identified, none have demonstrated clinical utility. Ibrutinib is a confirmed irreversible inhibitor of Bruton tyrosine kinase (BTK) with outstanding clinical activity and tolerability in B-cell malignancies. Significant homology between BTK and ITK alongside in silico docking studies support ibrutinib as an immunomodulatory inhibitor of both ITK and BTK. Our comprehensive molecular and phenotypic analysis confirms ITK as an irreversible T-cell target of ibrutinib. Using ibrutinib clinical trial samples along with well-characterized neoplastic (chronic lymphocytic leukemia), parasitic infection (Leishmania major), and infectious disease (Listeria monocytogenes) models, we establish ibrutinib as a clinically relevant and physiologically potent ITK inhibitor with broad therapeutic utility. This trial was registered at www.clinicaltrials. gov as #NCT01105247 and #NCT01217749.
UdL at SemEval-2017 Task 1: Semantic Textual Similarity Estimation of English Sentence Pairs Using Regression Model over Pairwise Features

This paper describes the model UdL we proposed to solve the semantic textual similarity task of SemEval 2017 workshop. The track we participated in was estimating the semantics relatedness of a given set of sentence pairs in English. The best run out of three submitted runs of our model achieved a Pearson correlation score of 0.8004 compared to a hidden human annotation of 250 pairs. We used random forest ensemble learning to map an expandable set of extracted pairwise features into a semantic similarity estimated value bounded between 0 and 5. Most of these features were calculated using word embedding vectors similarity to align Part of Speech (PoS) and Name Entities (NE) tagged tokens of each sentence pair. Among other pairwise features, we experimented a classical tf-idf weighted Bag of Words (BoW) vector model but with character-based range of n-grams instead of words. This sentence vector BoW-based feature gave a relatively high importance value percentage in the feature importances analysis of the ensemble learning.
Insulin Detemir Reduces Weight Gain as a Result of Reduced Food Intake in Patients With Type 1 Diabetes

OBJECTIVE Insulin detemir lacks the usual propensity for insulin to cause weight gain. We investigated whether this effect was a result of reduced energy intake and/or increased energy expenditure. RESEARCH DESIGN AND METHODS A 32-week, randomized crossover design trial was undertaken in 23 patients with type 1 diabetes. Patients on a basal-bolus regimen (with insulin aspart as the bolus insulin) were randomly assigned to insulin detemir or NPH insulin as a basal insulin for 16 weeks, followed by the other basal insulin for 16 weeks. At the end of each 16-week period, total energy expenditure, resting energy expenditure, diet-induced thermogenesis, activity energy expenditure, energy intake, weight change, glycemic control, hypoglycemic episodes, and hormones that affect satiety and fuel partitioning were measured. RESULTS After 16 weeks, weight change was −0.69 ± 1.85 kg with insulin detemir and +1.7 ± 2.46 kg with NPH insulin (P < 0.001). Total energy intake was significantly less with insulin detemir (2,016 ± 501 kcal/day) than with NPH insulin (2,181 ± 559 kcal/day) (P = 0.026). There was no significant difference in any measure of energy expenditure, HbA1c percentage, or number of hypoglycemic episodes. Leptin was lower and resistin was higher with insulin detemir compared with NPH insulin (P = 0.039, P = 0.047). After the meal, ghrelin and pancreatic polypeptide levels (P = 0.002, P = 0.001) were higher with insulin detemir. CONCLUSIONS The reduced weight gain with insulin detemir compared with NPH insulin is attributed to reduced energy intake rather than increased energy expenditure. This may be mediated by a direct or indirect effect of insulin detemir on the hormones that control satiety.
Biplexiform ganglion cells, characterized by dendrites in both outer and inner plexiform layers, are regular, mosaic-forming elements of teleost fish retinae

Abstract Biplexiform ganglion cells were labelled by retrograde transport of HRP in five species of marine fish from the neoteleost acanthopterygian orders Perciformes and Scorpaeniformes. Their forms and spatial distributions were studied in retinal flatmounts and thick sections. Biplexiform ganglion cells possessed sparsely branched, often varicose, dendrites that ramified through the inner nuclear layer (INL) to reach the outer plexiform layer (OPL), as well as conventional arborizations in the most sclerad part of the inner plexiform layer (IPL). Their somata were of above-average size and were displaced into the vitread border of the INL. Mean soma areas ranged from 99 ± 6 μm2 in Bathymaster derjugini (Perciformes) to 241 ± 12 μm2 in Hexagrammos stelleri (Scorpaeniformes), but were similar in each species to those of the outer-stratified alpha-like ganglion cells, whose dendritic trees occupied the same IPL sublamina. In the best-labelled specimens, biplexiform cells formed clear mosaics with spacings and degrees of regularity much like those of other large ganglion cells, but spatially independent of them. Biplexiform mosaics were plotted in three species, and analyzed by nearest-neighbor distance and spatial correlogram methods. The exclusion radius, an estimate of minimum mosaic spacing, ranged from 113 urn in Hexagrammos stelleri, through 150 μm in Ernogrammus hexagraminus (Perciformes), to 240 μm in Myoxocephalus stelleri (Scorpaeniformes). A spatial cross-correlogram analysis of the distributions of biplexiform and outer-stratified alpha-like cells in Hexagrammos demonstrated the spatial independence of their mosaics. Similar cells were previously observed not only in the freshwater cichlid Oreochromis spilurus (Perciformes) but also in the goldfish Carassius auratiis (Cypriniformes) which, being an ostariophysan teleost, is only distantly related. Thus, biplexiform ganglion cells may be regular elements of all teleost fish retinae. Their functional role remains unknown.
Physical Activity and Inflammatory Markers Over 10 Years: Follow-Up in Men and Women From the Whitehall II Cohort Study

Background— Inflammatory processes are putative mechanisms underlying the cardioprotective effects of physical activity. An inverse association between physical activity and inflammation has been demonstrated, but no long-term prospective data are available. We therefore examined the association between physical activity and inflammatory markers over a 10-year follow-up period. Methods and Results— Participants were 4289 men and women (mean age, 49.2 years) from the Whitehall II cohort study. Self-reported physical activity and inflammatory markers (serum high-sensitivity C-reactive protein and interleukin-6) were measured at baseline (1991) and follow-up (2002). Forty-nine percent of the participants adhered to standard physical activity recommendations for cardiovascular health (2.5 h/wk moderate to vigorous physical activity) across all assessments. Physically active participants at baseline had lower C-reactive protein and interleukin-6 levels, and this difference remained stable over time. Compared with participants who rarely adhered to physical activity guidelines over the 10-year follow-up, the high-adherence group displayed lower loge C-reactive protein (&bgr;=−0.07; 95% confidence interval, −0.12 to −0.02) and loge interleukin-6 (&bgr;=−0.07; 95% confidence interval, −0.10 to −0.03) at follow-up after adjustment for a range of covariates. Compared with participants who remained stable, those who reported an increase in physical activity of at least 2.5 h/wk displayed lower loge C-reactive protein (&bgr; coefficient=−0.05; 95% confidence interval, −0.10 to −0.001) and loge interleukin-6 (&bgr; coefficient=−0.06; 95% confidence interval, −0.09 to −0.03) at follow-up. Conclusions— Regular physical activity is associated with lower markers of inflammation over 10 years of follow-up and thus may be important in preventing the proinflammatory state seen with aging.
Evaluation of Optimal ω-tile sets for fast texture synthesis

Texture synthesis is widely recognized to be important for computer graphics applications. However, the traditional texture synthesis algorithm based on ω-tile did not provide the quantitative analysis of all sets of ω-tiles. In this paper, all possible sets of 4, 8 and 16 ω-tiles that meet certain criteria are presented firstly. Secondly, a novel evaluation system is proposed to measure the quality of different ω-tile sets through the evaluation of color diversity, local match performance and global match performance, meanwhile, weight is utilized to reflect the distinct focus on different texture types. Thirdly, a fast search algorithm is raised to choose the optimal matching texture and best cutting curve, in contrast to previous approaches, this operation insures efficient and real-time texture synthesis. The outcomes of experiments verify the high quality and efficiency of the proposed evaluation system and search algorithm.
Predicting Treatment Response from Resting State fMRI Data: Comparison of Parcellation Approaches

Resting state fMRI reveals intrinsic network characteristics present in the brain. They are correlated with behavioral measures, and have made surprising insights in the brains' connectivity structure possible. At the core of many of those studies is the correlation of behavioral measures, and the characteristics of networks among a set of brain regions. In this paper we evaluate methods that identify functional networks in resting state fMRI in light of predicting treatment response of patients suffering from social anxiety disorder. Results illustrate differences in prediction when obtaining network labelings by population-wide-clustering, subject-specific parcellation, transferring anatomical region labels, or mapping networks from a previous large scale resting state study.
A Technological, Pedagogical and Content Knowledge (TPACK) Framework in the context of a Social Networking Site used for Academic Engagement

Research into the use of social media for academic purposes is increasingly emerging. Such research suggests that a social networking site (SNS) could be used as an innovative tool for teaching purposes. However, much of previous research has focused on outlining the experience of students and the empirical evidence to date reports how a SNS may develop a higher level of academic engagement amongst students. In addition, research in this field has overlooked review of the pedagogy involved in utilising a SNS for education purposes successfully. Previously, Koehler and Mishra [1] proposed the TPACK framework to explore the relationship of technology in teaching which builds the basis for this research. This paper explores the suitability of the TPACK framework in the context of utilising SNSs and reviews its relevance to the adoption of a SNS as a teaching tool. Initial observations suggests that the current TPACK framework overlooks some important elements which are relevant to the adoption of SNS.