Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of IL-28B Polymorphisms and Serum IP-10 in Hepatitis C Infected Chimpanzees

In humans, clearance of hepatitis C virus (HCV) infection is associated with genetic variation near the IL-28B gene and the induction of interferon-stimulated genes, like IP-10. Also in chimpanzees spontaneous clearance of HCV is observed. To study whether similar correlations exist in these animals, a direct comparison of IP-10 and IL-28B polymorphism between chimpanzees and patients was performed. All chimpanzees studied were monomorphic for the human IL-28B SNPs which are associated with spontaneous and treatment induced HCV clearance in humans. As a result, these particular SNPs cannot be used for clinical association studies in chimpanzees. Although these human SNPs were absent in chimpanzees, gene variation in this region was present however, no correlation was observed between different SNP-genotypes and HCV outcome. Strikingly, IP-10 levels in chimpanzees correlated with HCV-RNA load and γGT, while such correlations were not observed in humans. The correlation between IP-10, γGT and virus load in chimpanzees was not found in patients and may be due to the lack of lifestyle-related confounding factors in chimpanzees. Direct comparison of IP-10 and IL-28B polymorphism between chimpanzees and patients in relation to HCV infection, illustrates that the IFN-pathways are important during HCV infection in both species. The Genbank EMBL accession numbers assigned to chimpanzees specific sequences near the IL-28B gene are HE599784 and HE599785.
Induction of Cell-Mediated Immune Responses in Mice by DNA Vaccines That Express Hepatitis C Virus NS3 Mutants Lacking Serine Protease and NTPase/RNA Helicase Activities

Effective therapeutic vaccines against virus infection must induce sufficient levels of cell-mediated immune responses against the target viral epitopes and also must avoid concomitant risk factors, such as potential carcinogenic properties. The nonstructural protein 3 (NS3) of hepatitis C virus (HCV) carries a variety of CD4+ and CD8+ T cell epitopes, and induces strong HCV-specific T cell responses, which are correlated with viral clearance and resolution of acute HCV infection. On the other hand, NS3 possesses serine protease and nucleoside triphosphatase (NTPase)/RNA helicase activities, which not only play important roles in viral life cycle but also concomitantly interfere with host defense mechanisms by deregulating normal cellular functions. In this study, we constructed a series of DNA vaccines that express NS3 of HCV. To avoid the potential harm of NS3, we introduced mutations to the catalytic triad of the serine protease (H57A, D81A and S139A) and the NTPase/RNA helicase domain (K210N, F444A, R461Q and W501A) to eliminate the enzymatic activities. Immunization of BALB/c mice with each of the DNA vaccine candidates (pNS3[S139A/K210N], pNS3[S139A/F444A], pNS3[S139A/R461Q] and pNS3[S139A/W501A]) that expresses an NS3 mutant lacking both serine protease and NTPase/helicase activities induced T cell immune responses to the degree comparable to that induced by the wild type NS3 and the NS3/4A complex, as demonstrated by interferon-γ production and cytotoxic T lymphocytes activities against NS3. The present study has demonstrated that plasmids expressing NS3 mutants, NS3(S139A/K210N), NS3(S139A/F444A), NS3(S139A/R461Q) and NS3(S139A/W501A), which lack both serine protease and NTPase/RNA helicase activities, would be good candidates for safe and efficient therapeutic DNA vaccines against HCV infection.
Property-based typing with LITEQ

Coding against the semantic web can be quite difficult as the basic concepts of RDF data and programming languages differ greatly. Existing mappings from RDF to programming languages are mostly schema-centric. However, this can be problematic as many data sources lack schematic information. To alleviate this problem, we present a data centric approach that focuses on the properties of the instance data found in RDF and that lets a developer create types in his programming language by specifying properties that need to be present. This resembles a type definition rooted in description logics. We show how such a type definition can look like and demonstrate how a program using such type definitions can can be written.
A domain-specific controlled English language for automated regulatory compliance (industrial paper)

Modern enterprises operate in an unprecedented regulatory environment where increasing regulation and heavy penalties on non-compliance have placed regulatory compliance among the topmost concerns of enterprises worldwide. Previous research in the field of compliance has established that the manual specification of the regulations used by GRC frameworks not only fails to ensure their proper coverage but also negatively affects the turnaround time both in proving and maintaining the compliance. Our key contribution in this paper is an implementation of a controlled natural English like (domain-specific) language that can be used by domain experts to specify regulations for automated compliance checking. We demonstrate this language using examples from industry regulations in banking and financial services domain.
A novel developmental rodent model to investigate the neural basis of episodic memory

Episodic memory is the recollection of unique autobiographical events, including rich detail of times, places and associated contextual information. In neurodegenerative diseases, such as Alzheimer’s disease, episodic memory is greatly impaired. The ability to recall episodic memories is thought to develop later in childhood than other types of memory such as novelty recognition, however this ontogeny in animals is so far unconfirmed due to a lack of suitable behavioral tests. The aim of this thesis was to develop a protocol suitable for testing the development of memory in juvenile rats, and to understand if rats show a similar ontogenic profile of memory as humans. A novel protocol was developed and first tested in adult rats. The protocol was compressed into two days of testing using a battery of spontaneous object recognition tasks to allow testing of narrow critical developmental time windows. The tasks were then used to assess the ontogeny of different types of memory in rats from p25 to adulthood. The Object Place Context (OPC) task was used as a model of episodic memory and used alongside the Novel Object Recognition (NOR), Object Context (OC) and Object Place (OP) tasks, all of which were tested in two days. It was discovered that all ages tested could perform basic object recognition (NOR task). Associative contextual memory (OC task) developed between p38 and 42 and both spatial (OP task) and episodic memory (OPC task) developed between p46 and 48. Further investigations pinpointed this spatial and episodic memory development to overnight between p47 and p48. Immunohistochemistry allowed the investigation of the anatomical locus of the episodic memory task, and showed subtle increases in the CA3 in p48 rats. It was concluded that rats do show a similar ontogenic profile of memory a humans, with recognition memory developing before episodic memory. This information will be invaluable when studying disease during development, and may also be extrapolated to understand disease of old age.
Effects of Physical Living Environment on the Social Interaction and Perceived Sense of Community among Students in University Dormitory

College students living in university dormitory continuously experience unique physical and social living conditions, being away from their hometown and loving families. Most college students has engaged in a very limited social activities in dormitory area. Studies have shown that sense of community(SOC) is closely related to students' social activities. However, few research have examined the relationship between physical environment and sense of community. Therefore, this research aims to evaluate the effects of physical environment of dormitory on students' perceived sense of community and their social interaction. Extensive literature review found that developing social interaction and building a sense of student community improve students' overall residential satisfaction with dormitory and personal academic growth. Survey on A university dormitory and Chi square analysis () indicated that each group's individual characteristics such as gender, grade, living period, and personality were statistically significant on the level of SOC at the level of p=. 01. Individual analysis of SOC showed that sense of belonging was higher than shared emotional connection, which means certain level of intervention is needed. Pearson correlation analysis validated that there exists statistically significant relationship between physical environment and SOC. Further it also found that the most important predictor in facilitating social interaction were comfortable, quiet, and enough social space around the dormitory.
Communications in Mathematical Physics Reconstruction of Random Colourings

Reconstruction problems have been studied in a number of contexts including biology, information theory and statistical physics. We consider the reconstruction problem for random k-colourings on the ∆-ary tree for large k. Bhatnagar et al. [2] showed non-reconstruction when ∆ ≤ 1 2k log k−o(k log k). We tighten this result and show nonreconstruction when ∆ ≤ k[log k+log log k+1−log 2−o(1)], which is very close to the best known bound establishing reconstruction which is ∆ ≥ k[log k+log log k+1+o(1)].
Homologous chromosome pairing in Schizosaccharomyces pombe

Homologous chromosome pairing is a central feature of meiosis I, contributing to the correct segregation of chromosomes during meiosis. The fission yeast, Schizosaccharomyces pombe, has been widely used to study meiotic chromosome dynamics, partly because studies in this yeast are simplified due to the lack of post‐pairing synaptic structures. Chromosome pairing in Sz. pombe occurs differentially throughout the genome. Telomeres cluster at the spindle pole body (SPB) at the onset of meiosis, imposing a spatial restriction on pairing events. Subsequently, centromeres dissociate from the SPB and pair in a recombination‐ and heterochromatin (Swi6)‐independent fashion. Pairing of telomere distal regions occurs during meiotic prophase, concomitant with a dynamic association/dissociation of homologous regions, with interhomologue associations becoming increasingly stable. The stabilization of paired regions is enhanced by factors required for the initiation of meiotic recombination, suggesting that recombination stabilizes paired regions. However, substantial pairing is initiated in the absence of recombination; this is dependent upon another factor, the conserved Meu13 protein, demonstrating that recombination is not required for initial pairing interactions. During meiotic prophase Sz. pombe exhibits a pronounced dynein‐dependent nuclear oscillation, which drives the pairing of centromeric and interstitial regions. Dynein is also required for the significant levels of achiasmate reductional segregation observed in Sz. pombe, possibly implicating the centromere‐associated pairing with achiasmate homologue segregation. Whilst Sz. pombe does not form discernable synaptic structures continuously along the meiotic chromosomes, it does form proteinacious, meiosis‐specific, linear structures (linear elements). However, the role, if any, of these structures in mediating homologue pairing is unknown. Copyright © 2006 John Wiley & Sons, Ltd.
Clinical Interventions in Aging Dovepress Cognitive Effects of Calligraphy Therapy for Older People: a Randomized Controlled Trial in Hong Kong

Background: This pilot study investigated the effects of calligraphy therapy on cognitive function in older Hong Kong Chinese people with mild cognitive impairment. Methods: A single-blind, randomized controlled trial was carried out in a sample of 31 adults aged 65 years or older with mild cognitive impairment. They were randomly assigned to receive either intensive calligraphy training led by a trained research assistant for eight weeks (calligraphy group, n = 14) or no calligraphy treatment (control group, n = 17). Participants' cognitive function was assessed by the Chinese version of the Mini-Mental State Examination (CMMSE) before and after calligraphy treatment. Repeated measures analysis of variance and paired samples t-tests were used to analyze the data. Results: A significant interaction effect of time and intervention was detected [F (1, 29) = 9.11, P = 0.005, η 2 = 0.24]. The calligraphy group was found to have a prominent increase in CMMSE global score, and scores in the cognitive areas of orientation, attention, and calculation after two months (∆M = 2.36, P , 0.01), whereas their counterparts in the control group experienced a decline in CMMSE score (∆M = −0.41, P , 0.05). Conclusion: Calligraphy therapy was effective for enhancing cognitive function in older people with mild cognitive impairment and should be incorporated as part of routine programs in both community and residential care settings.
Quality assessment of EEG signals based on statistics of signal fluctuations

The quality of the non-invasive EEG signals was always affected by the changes in the contact impedances and the artifacts from eye blinking, eye movements and body movements. An effective quality assessment method is needed to assess the qualities of the EEG signals. This paper proposed a novel method to assess the signal quality of EEG signals based on block-based measurements of the fluctuations of the second-order power amplitudes of the EEG signals. The initial signal quality scores were generated by fusion of the mean power amplitudes and the signal fluctuations of the motor imagery state with reference to background idling state. These scores were subsequently mapped to different quality levels by using fuzzy-c means clustering. Experimental results were conducted on the basis of 3 data sets of 15 healthy subjects performing motor imagery of hand movements and idle, for both gel-based and gel-less electrodes. The results obtained demonstrated that the proposed method was capable of evaluating the quality of the EEG signals, as supported by the clear separation of the assigned quality levels between gel-based and gel-less electrodes. This further validated the assumption that generally the quality of the EEG signals acquired based on the gel-based electrodes was better than that of the gel-less electrodes.
VILLUS EPITHELIAL INJURY INDUCED BY INFECTION WITH THE NEMATODE NIPPOSTRONGYLUS BRASILIENSIS IS ASSOCIATED WITH UPREGULATION OF GRANZYME B

Intestinal parasite infections induce thymus-dependent villus atrophy, but the effector mechanisms directly responsible for the development of villus atrophy are not thoroughly understood. In this study, we analyzed the expression of cytotoxic factors or ligands in athymic nude rnu/rnu rats and their littermate euthymic rnu/+ rats infected with the nematode Nippostrongylus brasiliensis. Morphometric analyses showed that partial villus atrophy developed 10 days after infection in euthymic but not in athymic rats, whereas crypt hyperplasia occurred in both types of animal. Reverse transcription–polymerase chain reaction analyses of the isolated jejunal epithelial fraction showed that the development of villus atrophy in euthymic rats was positively correlated with an increase of granzyme B transcript levels but not with Fas ligand or tumor necrosis factor-α expression. In addition, the number of granzyme B–immunoreactive cells was increased significantly in euthymic rat villus epithelium and the propria mucosa after infection. The CD8+ cell number did not change significantly. Collectively, these findings showed that significant increases in the number of cells that express the cytotoxic factor granzyme B occur in the nematode-infected small intestine of immunocompetent hosts. The type of cells that express granzyme B and their role in the progression of enteropathy remain to be elucidated.
Screening adolescents for problem drinking: performance of brief screens against DSM-IV alcohol diagnoses.

OBJECTIVE The performance of three brief screens, the CAGE, TWEAK and Alcohol Use Disorders Identification Test (AUDIT), was evaluated against a DSM-IV diagnosis of alcohol abuse or dependence in an adolescent sample. METHOD Adolescents (13-19 years old) who presented to an emergency department for treatment of an injury, and who tested negative for blood alcohol concentration at time of admission, were administered a structured diagnostic interview and modified versions of the CAGE, TWEAK and AUDIT. RESULTS Of the 415 adolescents for whom complete data were available, 18% met criteria for a DSM-IV alcohol use disorder according to the Diagnostic Interview Schedule for Children (version 2.3). Teens who reported alcohol use in the last year (n = 261, 58% male, 71% white) were included in analyses that compared the performance of the three screening instruments. Receiver Operating Characteristic analysis indicated that the AUDIT demonstrated the best performance across the range of its cut-scores, with optimal performance at a cut-score of 4. The TWEAK performed optimally at a cut-score of 2 and the CAGE at a cut-score of 1. CONCLUSIONS Routine alcohol screening among adolescents seen in a hospital setting is indicated. Two important directions for future research include the identification of adolescent-specific alcohol screening items, and the validation of an adolescent-specific definition of problem drinking that addresses limitations of DSM-IV alcohol diagnoses when applied to adolescents.
Impact of single-walled carbon nanotubes on the embryo: a brief review

Carbon nanotubes (CNTs) are considered one of the most interesting materials in the 21st century due to their unique physiochemical characteristics and applicability to various industrial products and medical applications. However, in the last few years, questions have been raised regarding the potential toxicity of CNTs to humans and the environment; it is believed that the physiochemical characteristics of these materials are key determinants of CNT interaction with living cells and hence determine their toxicity in humans and other organisms as well as their embryos. Thus, several recent studies, including ours, pointed out that CNTs have cytotoxic effects on human and animal cells, which occur via the alteration of key regulator genes of cell proliferation, apoptosis, survival, cell–cell adhesion, and angiogenesis. Meanwhile, few investigations revealed that CNTs could also be harmful to the normal development of the embryo. In this review, we will discuss the toxic role of single-walled CNTs in the embryo, which was recently explored by several groups including ours.
Bisector Graphs for Min-/Max-Volume Roofs over Simple Polygons

Piecewise-linear terrains (“roofs”) over simple polygons were studied by Aichholzer et al. (1995) in their work on straight skeletons of polygons. We show how to construct a roof over a simple polygon that has minimum (or maximum) volume among all roofs that drain water. Such a maximum-volume (minimum-volume) roof can have quadratic (maybe cubic, resp.) number of facets. Our algorithm for computing such a roof extends the standard wavefront propagation known from the theory of straight skeletons by two additional events. Both the minimum-volume and the maximum-volume roof of a simple polygon with n vertices can be computed in O ( n 3 log n ) time.
Affordable Care Act and healthcare delivery: A comparison of California and Florida hospitals and emergency departments

Importance The Affordable Care Act (ACA) has expanded access to health insurance for millions of Americans, but the impact of Medicaid expansion on healthcare delivery and utilization remains uncertain. Objective To determine the early impact of the Medicaid expansion component of ACA on hospital and ED utilization in California, a state that implemented the Medicaid expansion component of ACA and Florida, a state that did not. Design Analyze all ED encounters and hospitalizations in California and Florida from 2009 to 2014 and evaluate trends by payer and diagnostic category. Data were collected from State Inpatient Databases, State Emergency Department Databases and the California Office of Statewide Health Planning and Development. Setting Hospital and ED encounters. Participants Population-based study of California and Florida state residents. Exposure Implementation of Medicaid expansion component of ACA in California in 2014. Main outcomes or measures Changes in ED visits and hospitalizations by payer, percentage of patients hospitalized after an ED encounter, top diagnostic categories for ED and hospital encounters. Results In California, Medicaid ED visits increased 33% after Medicaid expansion implementation and self-pay visits decreased by 25% compared with a 5.7% increase in the rate of Medicaid patient ED visits and a 5.1% decrease in rate of self-pay patient visits in Florida. In addition, California experienced a 15.4% increase in Medicaid inpatient stays and a 25% decrease in self pay stays. Trends in the percentage of patients admitted to the hospital from the ED were notable; a 5.4% decrease in hospital admissions originating from the ED in California, and a 2.1% decrease in Florida from 2013 to 2014. Conclusions and relevance We observed a significant shift in payer for ED visits and hospitalizations after Medicaid expansion in California without a significant change in top diagnoses or overall rate of these ED visits and hospitalizations. There appears to be a shift in reimbursement burden from patients and hospitals to the government without a dramatic shift in patterns of ED or hospital utilization.
Adaptive parameter control for quantum-behaved particle swarm optimization on individual level

Particle swarm optimization (PSO) is a population-based evolutionary search technique, which has comparable performance with genetic algorithm. The existing PSOs, however, are not global-convergence-guaranteed algorithms. In the previous work, we proposed quantum-behaved particle swarm optimization (QPSO) algorithm that outperforms traditional PSOs in search ability as well as having less parameter to control. This paper focuses on discussing two adaptive parameter control methods for QPSO. After the ideology of QPSO is formulated, the experiment results of stochastic simulation are given to show how to select the parameter value to guarantee the convergence of the particle in QPSO. Finally, two adaptive parameter control methods are presented and experiment results on benchmark functions testify their efficiency.
Cog Gap : Cognitive and Opportunistic Gateway Access for Wireless Mesh Networks

The performance of conventional gateway access optimization techniques deteriorate dramatically when traffic load is dynamic. In this article, we propose a novel gateway access algorithm called ‘Cog Gap’, which is a cognitive method and is designed for Wireless Mesh Networks to maximize the network utilization. The proposed Cog Gap utilizes a destination-hub access model, where multiple gateway nodes are connected by wired links, and packets from a source node can be sent from any connected gateway nodes to increase transmission opportunities. In Cog Gap, we use the Hidden Markov Model (HMM) and the expectation maximization method to handle uncertain traffic pattern and the loss of probing results. A traffic allocation algorithm is then proposed to optimize dynamic multi-gateway access. By modeling the route state determination and transition, we transform the opportunistic gateway access problem into a Markov decision process (MDP) problem. A heuristic and adaptive algorithm named hindsight optimal is used in solving MDP. Simulation results have proven that the proposed Cog Gap algorithm can make full use of the transmission opportunities and does not incur noticeable protocol overhead.