Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequential change of the hypervariable region of the hepatitis C virus genome in acute infection

Hepatitis C virus (HCV) infection is characterized by persistence of liver inflammation that often leads to end‐stage liver disease, although the mechanisms are not fully understood. A hyper‐variable region (HVR) has been reported in the E2/NS1 region of the HCV genome, in which striking diversity is found among different HCV isolates. To investigate the association of the HVR alterations with the clinical courses of HCV infection, a longitudinal analysis of the HVR in patients with acute HCV infection was carried out. Plasma samples were obtained at several times in three patients with acute hepatitis C. Plasma RNA was extracted and reverse transcribed, and DNA fragments that included the HVR were amplified by PCR. The sequences of the HVR were directly determined from the PCR products by the dideoxy chain termination method, from which amino acid sequences were deduced. In all cases, plasma HCV‐RNA disappeared with the improvement of the initial alanine aminotransferase (ALT) elevation, but HCV‐RNA reappeared about 1 year later with or without deterioration of the hepatitis. In a case of sporadic acute hepatitis, the HCV in the recurrent phase had seven amino acid substitutions in the HVR compared with that in the acute phase, although no amino acid changes were noted during the initial acute phase. In a case of posttransfusion hepatitis, a marked difference was observed between the acute and the recurrent phases, with an amino acid homology of 30% (8/27). The mutation rate of the HVR had a tendency to accelerate as the HCV infection progressed to the chronic stage. In conclusion, the HVR changes serially during the course of acute HCV infection, and these HVR changes may play a part in the chronicity of HCV infection. © 1994 Wiiey‐Liss, Inc.
Cluster-based Simulated Annealing for Mapping Cores onto 2D Mesh Networks on Chip

In network-on-chip (NoC) application design, core-to-node mapping is an important but intractable optimization problem. In the paper, we use simulated annealing to tackle the mapping problem in 2D mesh NoCs. In particular, we combine a clustering technique with the simulated annealing to speed up the convergence to near-optimal solutions. The clustering exploits the connectivity and distance relation in the network architecture as well as the locality and bandwidth requirements in the core communication graph. The annealing is cluster-aware and may be dynamically constrained within clusters. Our experiments suggest that simulated annealing can be effectively used to solve the mapping problem with a scalable size, and the combined strategy improves over the simulated annealing in execution time by up to 30% without compromising the quality of solutions.
Looking Forward and Looking Back: Older Adults' Views of the Impacts of Stopping Driving

ABSTRACT This project aimed to identify the impact of driving cessation from the perspectives of older drivers and former drivers. Participants included 17 adults aged 65–88 years residing in a city in Northwestern Ontario, Canada. Using a semi-structured interview guide (with questions regarding mobility, personal impact, impact on others, engagement with life, and finances), two focus groups were held with nine current drivers, and one-on-one interviews were held with six former drivers and two current drivers. Two themes emerged concerning stopping driving. The first theme included discussions on experiencing lifestyle changes, relationship impacts, and emotional impacts. The second, the adjustment to stopping driving, included practical adaptations, and emotional responses such as appreciation, resistance, acceptance, and being positive. Although the impacts of stopping driving were substantial, there were few discrepancies between what was anticipated and what was experienced. This information could assist with developing interventions to ease the transition to former-driver status.
Evaluating global e-government sites: A view using web diagnostics tools

Several governments across the world have embraced the digital revolution and continue to take advantage of the information and communication facilities offered by the Internet to offer public services. Conversely, citizens’ awareness and expectations of Internet based online-public-services have also increased in recent times. Although the numbers of the different national e-Government web portals have rapidly increased in the last three years, the success of these portals will largely depend on their accessibility, quality and privacy. This paper reports the results of an evaluative study of a cross-section of e-Government portals from these three perspectives, using a common set of performance metrics and Web diagnostic engines. Results show that not only are there wide variations in the spectrum of information and services provided by these portals, but that significant work still needs to be undertaken in order to make the portals examples of ‘best practice’ e-Government services.
Intracellular sorting and targeting of melanosomal membrane proteins: identification of signals for sorting of the human brown locus protein, gp75

The structural and functional integrity of cytoplasmic organelles is maintained by intracellular mechanisms that sort and target newly synthesized proteins to their appropriate cellular locations. In melanocytic cells, melanin pigment is synthesized in specialized organelles, melanosomes. A family of melanocyte-specific proteins, known as tyrosinase-related proteins that regulate melanin pigment synthesis, is localized to the melanosomal membrane. The human brown locus protein, tyrosinase-related protein-1 or gp75, is the most abundant glycoprotein in melanocytic cells, and is a prototype for melanosomal membrane proteins. To investigate the signals that allow intracellular retention and sorting of glycoprotein (gp)75, we constructed protein chimeras containing the amino-terminal extracellular domain of the T lymphocyte surface protein CD8, and transmembrane and cytoplasmic domains of gp75. In fibroblast transfectants, chimeric CD8 molecules containing the 36-amino acid cytoplasmic domain of gp75 were retained in cytoplasmic organelles. Signals in the gp75 cytoplasmic tail alone, were sufficient for intracellular retention and targeting of the chimeric proteins to the endosomal/lysosomal compartment. Analysis of subcellular localization of carboxy-terminal deletion mutants of gp75 and the CD8/gp75 chimeras showed that deletion of up amino acids from the gp75 carboxyl terminus did not affect intracellular retention and sorting, whereas both gp75 and CD8/gp75 mutants lacking the carboxyl-terminal 27 amino acids were transported to the cell surface. This region contains the amino acid sequence, asn-gln-pro-leu-leu-thr, and this hexapeptide is conserved among other melanosomal proteins. Further evidence showed that this hexapeptide sequence is necessary for intracellular sorting of gp75 in melanocytic cells, and suggested that a signal for sorting melanosomal proteins along the endosomal/lysosomal pathway lies within this sequence. These data provide evidence for common signals for intracellular sorting of melanosomal and lysosomal proteins, and support the notion that lysosomes and melanosomes share a common endosomal pathway of biogenesis.
Identification of CD24 as a Cancer Stem Cell Marker in Human Nasopharyngeal Carcinoma

Cancer stem cells (CSCs) represent a unique sub-population of tumor cells with the ability to initiate tumor growth and sustain self-renewal. Although CSC biomarkers have been described for various tumors, only a few markers have been identified for nasopharyngeal carcinoma (NPC). In this study, we show that CD24+ cells isolated from human NPC cell lines express stem cell genes (Sox2, Oct4, Nanog, Bmi-1, and Rex-1), and show activation of the Wnt/β-catenin signaling pathway. CD24+ cells possess typical CSC characteristics that include enhanced cell proliferation, increased colony and sphere formation, maintenance of cell differentiation potential in prolonged culture, and enhanced resistance to chemotherapeutic drugs. Notably, CD24+ cells produce tumors following inoculation of as few as 500 cells in immunodeficient NOD/SCID mice. CD24+ cells further show increased invasion ability in vitro, which correlates with enhanced expression of matrix metalloproteinase 2 and 9. In summary, our results suggest that CD24 represents a novel CSC biomarker in NPC.
Trait-Associated SNPs Are More Likely to Be eQTLs: Annotation to Enhance Discovery from GWAS

Although genome-wide association studies (GWAS) of complex traits have yielded more reproducible associations than had been discovered using any other approach, the loci characterized to date do not account for much of the heritability to such traits and, in general, have not led to improved understanding of the biology underlying complex phenotypes. Using a web site we developed to serve results of expression quantitative trait locus (eQTL) studies in lymphoblastoid cell lines from HapMap samples (http://www.scandb.org), we show that single nucleotide polymorphisms (SNPs) associated with complex traits (from http://www.genome.gov/gwastudies/) are significantly more likely to be eQTLs than minor-allele-frequency–matched SNPs chosen from high-throughput GWAS platforms. These findings are robust across a range of thresholds for establishing eQTLs (p-values from 10−4–10−8), and a broad spectrum of human complex traits. Analyses of GWAS data from the Wellcome Trust studies confirm that annotating SNPs with a score reflecting the strength of the evidence that the SNP is an eQTL can improve the ability to discover true associations and clarify the nature of the mechanism driving the associations. Our results showing that trait-associated SNPs are more likely to be eQTLs and that application of this information can enhance discovery of trait-associated SNPs for complex phenotypes raise the possibility that we can utilize this information both to increase the heritability explained by identifiable genetic factors and to gain a better understanding of the biology underlying complex traits.
ADHD diagnosis from multiple data sources with batch effects

The Attention Deficit Hyperactivity Disorder (ADHD) affects the school-age population and has large social costs. The scientific community is still lacking a pathophysiological model of the disorder and there are no objective biomarkers to support the diagnosis. In 2011 the ADHD-200 Consortium provided a rich, heterogeneous neuroimaging dataset aimed at studying neural correlates of ADHD and to promote the development of systems for automated diagnosis. Concurrently a competition was set up with the goal of addressing the wide range of different types of data for the accurate prediction of the presence of ADHD. Phenotypic information, structural magnetic resonance imaging (MRI) scans and resting state fMRI recordings were provided for nearly 1000 typical and non-typical young individuals. Data were collected by eight different research centers in the consortium. This work is not concerned with the main task of the contest, i.e., achieving a high prediction accuracy on the competition dataset, but we rather address the proper handling of such a heterogeneous dataset when performing classification-based analysis. Our interest lies in the clustered structure of the data causing the so-called batch effects which have strong impact when assessing the performance of classifiers built on the ADHD-200 dataset. We propose a method to eliminate the biases introduced by such batch effects. Its application on the ADHD-200 dataset generates such a significant drop in prediction accuracy that most of the conclusions from a standard analysis had to be revised. In addition we propose to adopt the dissimilarity representation to set up effective representation spaces for the heterogeneous ADHD-200 dataset. Moreover we propose to evaluate the quality of predictions through a recently proposed test of independence in order to cope with the unbalancedness of the dataset.
Externally Oriented Thinking of Obese Men and Women

This study examined the association of scores on alexithymia and obesity. The obese group (n = 47) reported significantly higher total scores on the Toronto Alexithymia Scale than the nonobese group (n = 190). Of the four factors of alexithymia, although significant differences were not found in the statistical analysis with a Bonferroni correction, scores on externally-oriented thinking (so-called “pensée operatoire”) were higher for the obese group than the nonobese group. The results suggest that persons with simple obesity are prone to alexithymia, in particular externally-oriented thinking.
Identification of Compounds in the Essential Oil of Nutmeg Seeds (Myristica fragrans Houtt.) That Inhibit Locomotor Activity in Mice

The present study was designed to evaluate the inhibitory effect of nutmeg (Myristica fragrans Houtt.) seed essential oil on the locomotor activity of mice in a wheel cage. Active compounds in the essential oil were identified by off-line solid phase extraction (SPE-C18) and GC/MS analysis. The essential oil was administered by inhalation at doses of 0.1, 0.3, and 0.5 mL/cage. The results showed that inhalation of nutmeg seed essential oil at a dose of 0.5 mL/cage decreased locomotion by 68.62%; and inhalation of 0.1 and 0.3 mL/cage inhibited locomotion by 62.81% and 65.33%, respectively. Generally, larger doses and longer administrations of nutmeg seed essential oil exhibited greater locomotor inhibition. Subsequently, the plasma concentrations of essential oil compounds were measured. The most concentrated compound in the plasma was myristicin. Half an hour after the addition of 1 mL/cage of nutmeg seed oil, the plasma concentration of myristicin was 3.7 μg/mL; one and two hours after the addition, the blood levels of myristicin were 5.2 μg/mL and 7.1 μg/mL, respectively. Other essential oil compounds identified in plasma were safrole (two-hour inhalation: 1.28 μg/mL), 4-terpineol (half-hour inhalation: 1.49 μg/mL, one-hour inhalation: 2.95 μg/mL, two-hour inhalation: 6.28 μg/mL) and fatty esters. The concentrations of the essential oil compounds in the blood plasma were relatively low (μg/mL or ppm). In conclusion, the volatile compounds of nutmeg seed essential oil identified in the blood plasma may correlate with the locomotor-inhibiting properties of the oil when administered by inhalation.
Model confirmation in climate economics

Significance Benefit–cost integrated assessment models (BC-IAMs) combine climate science, impacts studies, and representations of long-run economic growth to estimate the costs and benefits of climate policy. They provide valuable qualitative insights into how policy outcomes might depend on ethical and empirical assumptions. Increasingly, however, BC-IAMs are being used to inform quantitative policy choices, despite their economic components being largely untested, or untestable, over relevant time scales. We demonstrate the potential benefits of model confirmation exercises for policy applications, demonstrating that the economic growth model used by a prominent BC-IAM had little predictive power over the 20th century. Insofar as possible, out-of-sample empirical tests of the economic components of BC-IAMs should inform their future development for real-world applications. Benefit–cost integrated assessment models (BC-IAMs) inform climate policy debates by quantifying the trade-offs between alternative greenhouse gas abatement options. They achieve this by coupling simplified models of the climate system to models of the global economy and the costs and benefits of climate policy. Although these models have provided valuable qualitative insights into the sensitivity of policy trade-offs to different ethical and empirical assumptions, they are increasingly being used to inform the selection of policies in the real world. To the extent that BC-IAMs are used as inputs to policy selection, our confidence in their quantitative outputs must depend on the empirical validity of their modeling assumptions. We have a degree of confidence in climate models both because they have been tested on historical data in hindcasting experiments and because the physical principles they are based on have been empirically confirmed in closely related applications. By contrast, the economic components of BC-IAMs often rely on untestable scenarios, or on structural models that are comparatively untested on relevant time scales. Where possible, an approach to model confirmation similar to that used in climate science could help to build confidence in the economic components of BC-IAMs, or focus attention on which components might need refinement for policy applications. We illustrate the potential benefits of model confirmation exercises by performing a long-run hindcasting experiment with one of the leading BC-IAMs. We show that its model of long-run economic growth—one of its most important economic components—had questionable predictive power over the 20th century.
A Computational Model for the AMPA Receptor Phosphorylation Master Switch Regulating Cerebellar Long-Term Depression

The expression of long-term depression (LTD) in cerebellar Purkinje cells results from the internalisation of α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid receptors (AMPARs) from the postsynaptic membrane. This process is regulated by a complex signalling pathway involving sustained protein kinase C (PKC) activation, inhibition of serine/threonine phosphatase, and an active protein tyrosine phosphatase, PTPMEG. In addition, two AMPAR-interacting proteins–glutamate receptor-interacting protein (GRIP) and protein interacting with C kinase 1 (PICK1)–regulate the availability of AMPARs for trafficking between the postsynaptic membrane and the endosome. Here we present a new computational model of these overlapping signalling pathways. The model reveals how PTPMEG cooperates with PKC to drive LTD expression by facilitating the effect of PKC on the dissociation of AMPARs from GRIP and thus their availability for trafficking. Model simulations show that LTD expression is increased by serine/threonine phosphatase inhibition, and negatively regulated by Src-family tyrosine kinase activity, which restricts the dissociation of AMPARs from GRIP under basal conditions. We use the model to expose the dynamic balance between AMPAR internalisation and reinsertion, and the phosphorylation switch responsible for the perturbation of this balance and for the rapid plasticity initiation and regulation. Our model advances the understanding of PF-PC LTD regulation and induction, and provides a validated extensible platform for more detailed studies of this fundamental synaptic process.
On the convergence of relaxation schemes to couple phasor-mode and electromagnetic transients simulations

Hybrid simulations combining phasor-mode and electromagnetic transients models aim at taking advantage of computational speed of the former and accuracy of the latter. For simulation accuracy, a relaxation process is used, which consists of iterating between both models. The convergence properties of this relaxation process are investigated. The speed of convergence is assessed when the variables exchanged at the interface between both models are respectively pure voltage/current sources, Norton/Thévenin equivalents, or a combination of them. Iteratively updated Norton/Thévenin equivalents are shown to drastically reduce the number of relaxation iterations.
Geographic/ethnic variability of chromosomal and molecular abnormalities in leukemia

In 1963, Jean Bernard, a French hematologist, opened a new chapter in hematology called geographic hematology (‘Hématologie Géographique’). He distinguished two research avenues. One dealt with the differences between the various populations (ethnic hematology), the other with various environmental factors (environmental hematology). In recent years, focus has been put on analyzing the genetic susceptibility in cancer and hematological malignancies, particularly in childhood acute lymphoblastic leukemia, using specific gene or (genome-wide association study) approach. However, almost 30 years ago, it was suggested by a few workers that chromosomal abnormalities observed in leukemia could have a geographic and/or ethnic distribution. In this review, we analyze the literature on chromosomal and molecular abnormalities in several types of leukemia.
Long-Term Monitoring of Fecal Steroid Hormones in Female Snow Leopards (Panthera uncia) during Pregnancy or Pseudopregnancy

Knowledge of the basic reproductive physiology of snow leopards is required urgently in order to develop a suitable management conditions under captivity. In this study, the long-term monitoring of concentrations of three steroid hormones in fecal matter of three female snow leopards was performed using enzyme immunoassays: (1) estradiol-17β, (2) progesterone and (3) cortisol metabolite. Two of the female animals were housed with a male during the winter breeding season, and copulated around the day the estradiol-17β metabolite peaked subsequently becoming pregnant. The other female was treated in two different ways: (1) first housed with a male in all year round and then (2) in the winter season only. She did not mate with him on the first occasion, but did so latter around when estradiol-17β metabolite peaked, and became pseudopregnant. During pregnancy, progesterone metabolite concentrations increased for 92 or 94 days, with this period being approximately twice as long as in the pseudopregnant case (31, 42, 49 and 53 days). The levels of cortisol metabolite in the pseudopregnant female (1.35 µg/g) were significantly higher than in the pregnant females (0.33 and 0.24 µg/g) (P<0.05). Similarly, during the breeding season, the levels of estradiol-17β metabolite in the pseudopregnant female (2.18 µg/g) were significantly higher than those in the pregnant females (0.81 and 0.85 µg/g) (P<0.05). Unlike cortisol the average levels of estradiol-17β during the breeding season were independent of reproductive success. The hormone levels may also be related to housing conditions and the resulting reproductive success in female leopards. The female housed with a male during the non-breeding season had high levels of cortisol metabolites and low levels of estradiol-17β in the breeding season, and failed to become pregnant. This indicates that housing conditions in snow leopards may be an important factor for normal endocrine secretion and resulting breeding success.