Miracle-dz/UniFAR-FTUs huggingface dataset:
Case-control study of binary disease trait considering interactions between SNPs and environmental effects using logistic regression

In this paper, we propose a combination of logistic regression and genetic algorithm for the association study of the binary disease trait. We use a logistic regression model to describe the relation of multiple SNPs, environments and the target binary trait. The logistic regression model can capture the continuous effects of environments without categorization, which causes the loss of the information. To construct an accurate prediction rule for binary trait, we adopted Akaike information criterion (AIC) to find the most effective set of SNPs and environments. That is, the set of SNPs and environments that gives the smallest AIC is chosen as the optimal set. Since the number of combinations of SNPs and environments is usually huge, we propose the use of the genetic algorithm for choosing the optimal SNPs and environments in the sense of AIC. We show the effectiveness of the proposed method through the analysis of the case/control populations of diabetes patients. We succeeded in finding an efficient set to predict types of diabetes and some SNPs which have strong interactions to age while it is not significant as a single locus.
Can coarse‐grain patterns in insect atlas data predict local occupancy?

Species atlases provide an economical way to collect data with national coverage, but are typically too coarse‐grained to monitor fine‐grain patterns in rarity, distribution and abundance. We test the performance of ten downscaling models in extrapolating occupancy across two orders of magnitude. To provide a greater challenge to downscaling models, we extend previous downscaling tests with plants to highly mobile insect taxa (Odonata) with a life history that is tied to freshwater bodies for reproduction. We investigate the species‐level correlates of predictive accuracy for the best performing model to understand whether traits driving spatial structure can cause interspecific variation in downscaling success.
Integrated optical isolators with sputter-deposited thin-film magnets

This letter describes the use of a compact sputter-deposited thin-film magnet that is directly integrated onto a waveguide isolator fabricated in magnetic thin-film garnets. Film magnets of different thicknesses are sputtered onto the waveguides, and isolation ratios of 29 dB are obtained with negligible excess loss. Stress-birefringent effects due to the ferromagnetic film overlayer are eliminated by the use of an aluminum compliant buffer.
mosaik - A modular platform for the evaluation of agent-based Smart Grid control

Smart Grids rely on the use of ICT for managing large numbers of active components and sensors to keep demand and generation of electricity at equilibrium while operating multiple resources within their operational limits. Due to the distributed nature of these resources, their heterogeneity as well as their sheer number, is a challenging task. Control strategies as well as novel paradigms need to be developed and thoroughly evaluated through extensive simulations. In order to yield scientifically sound and reliable results, these simulations have to rely on valid and (ideally) established models, e.g., from industry. Therefore, it is desirable to reuse these models as often as possible by combining them into new, potentially large-scale test scenarios. The introduced mosaik framework presents a flexible architecture as well as a powerful modeling and specification language to automate the process of composing existing models and simulation platforms into large-scale simulation scenarios.
Identifying the transporters of different flavonoids in plants

We recently identified a new component of flavonoid transport pathways in Arabidopsis. The MATE protein FFT (Flower Flavonoid Transporter) is primarily found in guard cells and seedling roots, and mutation of the transporter results in floral and growth phenotypes. The nature of FFT’s substrate requires further exploration but our data suggest that it is a kaempferol diglucoside. Here we discuss potential partner H+-ATPases and possible redundancy among the close homologues within the large Arabidopsis MATE family.
Evolving visual metaphors and dynamic tools for bioinformatics visualization

Bioinformatics poses a challenging domain for computer generated visualization techniques. For starters, is this a domain of scientific or information visualization? Typical scientific data sets have inherent spatial metaphors such as fluid flow in the human heart or chemical bonding of molecules. In contrast, exploration of cyberspace or searching of document repositories are traditional information visualization problems requiring the creation of a visual metaphor. How do we handle data mining of genomic information where the visual metaphor might not be obvious but the results can push forward scientific discovery?
Area-Throughput Trade-Offs for SHA-1 and SHA-256 Hash Functions' Pipelined Designs

High-throughput designs of hash functions are strongly demanded due to the need for security in every transmitted packet of worldwide e-transactions. Thus, optimized and non-optimized pipelined architectures have been proposed raising, however, important questions. Which is the optimum number of the pipeline stages? Is it worth to develop optimized designs or could the same results be achieved by increasing only the pipeline stages of the non-optimized designs? The paper answers the above questions studying extensively many pipelined architectures of SHA-1 and SHA-256 hashes, implemented in FPGAs, in terms of throughput/area (T/A) factor. Also, guides for developing efficient security schemes designs are provided.
REPRODUCTIVE PERFORMANCE OF RED CHITTAGONG CATTLE IN A NUCLEUS HERD

The present study was undertaken to estimate the performance of some reproductive traits of Red Chittagong Cattle (RCC) is an important indigenous Farm Animal Genetic Resource of Bangladesh having some efficient reproductive capabilities. The effect of parity on these traits was also studied. The study was conducted in the nucleus herd of RCC Project at Bangladesh Agricultural University (BAU) dairy farm taking data from 2005 to 2008. The traits considered for this study were age at sexual maturity, age at first calving, number of service per conception, conception rate, calving interval, post partum heat period, gestation length and service period of RCC cows. The mean (±SE) values of the said traits are 28.75 ± 1.26 months, 40.93 ± 1.74 months, 1.55 ± 0.08, 78.91 ± 2.82 %, 14.42 ± 0.33 months, 127.71 ± 7.02 days, 282.11 ± 0.58 days and 151.72 ± 6.83 days, respectively. All the traits studied did not differ significantly (P>0.05) between different parities.
Music and dementia: Observing effects and searching for underlying theories

Is music helpful for people with dementia, and if so, why? Opinions are divided: on the one hand, the Cochrane Review of music therapy for people with dementia concluded that there was ‘no substantial evidence to support nor discourage the use of music therapy in the care of older people with dementia’ (Vink, Birks, Bruinsma, & Scholten, 2006); on the other hand, small–scale studies have suggested that music is useful in improving the state of individuals with dementia (Brotons, Koger, & Pickett—Cooper, 1997; Sherratt, Thornton, & Hatton, 2004a; Witzke, Rhone, Backhaus, & Shaver, 2008). This question is particularly important as dementia care constitutes an ‘unsolved’ problem. Though pharmaceutical treatments have been developed, there are many aspects of the condition that remain untreatable using these methods from which there are also often unwanted side effects. There is much debate regarding the extent to which music is therapeutically useful in dementia. On the practical side, there are many music therapists worldwide working with individuals with dementia, and outreach programs that include music are increasing in popularity. As in other areas of music therapy, however, there is insufficient rigorous evidence about the effect of music in the form of systematic testing or randomised controlled trials. Moreover, there is only partial understanding of the processes underlying the interventions and results of music therapy. Three dominant groups of symptoms of dementia, which have been suggested to be positively influenced by music, form the focus of the current discussion: memory (particularly autobiographical memory) and language retention; mood and depression; and aggression and agitation. However, a lack of an evidence base for the use of music in dementia care, and an understanding of the underlying processes related to behavioural observations, remain. This Editorial illustrates the evidence to date and, in an attempt to explore the possible reasons for the reported success of music in this context and better understand these underlying processes, brings together evidence and theories from the fields of music and dementia, music psychology and the study of diverse health conditions. In order to contextualise the existing evidence, and possible underlying processes and approaches to investigating those processes, a brief discussion of the types of dementia that have been focussed on in music research and definitions of music in therapeutic and other contexts is presented. Dementias: Definitions and needs
The uniqueness of speech among motor systems

This paper considers evidence that the speech muscles are unique in their genetic, developmental, functional and phenotypical properties. The literature was reviewed using PubMed, ScienceDirect, ComDisDome and other literature‐retrieval systems to identify studies reporting on the craniofacial and laryngeal muscles. Particular emphasis was given to studies of muscle fibre composition. A number of studies on mandibular, lingual, palatal and laryngeal muscles in humans show that these muscles are distinct from limb and other muscles. These speech‐related muscles typically contain diverse fibre types and these types can vary regionally within a muscle. In general, the muscles of the speech production system are designed for fast and/or variable contraction and fatigue resistance. The craniofacial and laryngeal muscles are unique among the muscle systems of the human body and the specialized properties of these muscles are relevant to understanding the biomechanics of speech and various speech disorders.
Trends in HIV acquisition, risk factors and prevention policies among youth in Uganda, 1999–2011

Objective:The objective of this study is to understand how trends in HIV acquisition among youth can be influenced by change in HIV risk factors, social factors and prevention and treatment programmes. Design:Trends in HIV incidence (per 1000 person-years), by sex and age group, were estimated using data from youth (15–24 years: n = 22 164) in the Rakai Community Cohort Study. Trends in HIV incidence were compared with trends in previously identified HIV risk factors, social factors and programmes. Methods:Poisson and linear regression were used to test for statistical significance and decomposition was used to calculate attribution of risk factors to HIV incidence. Results:Substantial declines between 1999 and 2011 occurred in sexual experience, multiple partners and sexual concurrency among adolescents and young adults. HIV acquisition declined substantially (86%, P = 0.006) among adolescent women (15–19 years) but not among men or young adult women. Changes in HIV incidence and risk behaviours coincided with increases in school enrolment, decline in adolescent marriage, availability of antiretroviral therapy (ART) and increases in male medical circumcision (MMC). Much of the decline in HIV incidence among adolescent women (71%) was attributable to reduced sexual experience; the decline in sexual experience was primarily attributable to increasing levels of school enrolment. Conclusion:Dramatic decreases in HIV incidence occurred among adolescent women in Rakai. Changes in school enrolment and sexual experience were primarily responsible for declining HIV acquisition over time among adolescent women. Given limited improvement among young men and young adult women, the need for effective HIV prevention for young people remains critical.
Tandem processing of fepstrum features

In our previous work [1, 2], we have introduced Fepstrum - an improved modulation spectrum estimation technique that overcomes certain theoretical as well as practical shortcomings in the previously published modulation spectrum related techniques[7, 8, 9]. In this paper, we provide further extensive ASR results using the Tandem processed Fepstrum features over the TIMIT corpus. The results are compared with TRAPS features derived from hierarchical and parallel structures of neural networks[3]. Unlike the multiple neural networks trained over multiple time-frequency patches or the frequency bands as in [3], we train a single neural network with the concatenated Fep-strum and MFCC features to derive Tandem(Fepstrum+MFCC) features. Theresultantphonemerecognitionaccuracyofthecon-catenated Tandem(Fepstrum+MFCC)+MFCC feature is 76.5% on the TIMIT core test set and 77.6% on the complete test set making these one of the best reported results on the TIMIT continuous phoneme recognition task.
Entanglement distillation : a discourse on bound entanglement in quantum information theory

PhD thesis (University of York). The thesis covers in a unified way the material presented in quant-ph/0403073, quant-ph/0502040, quant-ph/0504160, quant-ph/0510035, quant-ph/0512012 and quant-ph/0603283. It includes two large review chapters on entanglement and distillation.
Candidate Gene Association Studies in Sporadic Alzheimer’s Disease

The genetics of Alzheimer’s disease (AD) is complex. Three genes (amyloid precursor protein, presenilin 1 and presenilin 2) have been described in the relatively rare, early-onset, autosomal dominant familial form of AD. In the common, non-familial (sporadic) late-onset AD, the major known genetic risk factor is the Ε4 allele of the apolipoprotein E (APOE) gene. However, at least half of the people who develop AD do not carry this allele, and not all people who do carry this allele develop AD even if they live to an old age. Therefore, approximately 30 other candidate genes involving a protein in a critical pathway in the pathogenesis of disease (principally interaction with amyloid-β, oxidative stress and inflammation/apoptosis) have been considered as risk factors for sporadic AD. Then these genes have been sequenced in search of genetic variability or polymorphisms, and each putative polymorphism has been reported to alter the risk of AD either directly or by an interaction with the APOE Ε4 allele. However, positive-association studies with these candidate genes have not been consistently confirmed.
Strong sequence conservation among horizontally transmissible, minimally pathogenic feline leukemia viruses

We report the first complete nucleotide sequence (8,440 base pairs) of a biologically active feline leukemia virus (FeLV), designated FeLV-61E (or F6A), and the molecular cloning, biological activity, and env-long terminal repeat (LTR) sequence of another FeLV isolate, FeLV-3281 (or F3A). F6A corresponds to the non-disease-specific common-form component of the immunodeficiency disease-inducing strain of FeLV, FeLV-FAIDS, and was isolated from tissue DNA of a cat following experimental transmission of naturally occurring feline acquired immunodeficiency syndrome. F3A clones were derived from a subgroup-A-virus-producing feline tumor cell line. Both are unusual relative to other molecularly cloned FeLVs studied to date in their ability to induce viremia in weanling (8-week-old) cats and in their failure to induce acute disease. The F6A provirus is organized into 5'-LTR-gag-pol-env-LTR-3' regions; the gag and pol open reading frames are separated by an amber codon, and env is in a different reading frame. The deduced extracellular glycoproteins of F6A, F3A, and the Glasgow-1 subgroup A isolate of FeLV (M. Stewart, M. Warnock, A. Wheeler, N. Wilkie, J. Mullins, D. Onions, and J. Neil, J. Virol. 58:825-834, 1986) are 98% homologous, despite having been isolated from naturally infected cats 6 to 13 years apart and from widely different geographic locations. As a group, their envelope gene sequences differ markedly from those of the disease-associated subgroup B and acutely pathogenic subgroup C viruses. Thus, F6A and F3A correspond to members of a highly conserved family and represent prototypes of the horizontally transmitted, minimally pathogenic FeLV present in all naturally occurring infections.
An empirical study on cloud computing requirements for better mobile learning services

Information technology and its applications change not only the way students learn but also how they are taught. M-learning provides many advantages to our education system. Cloud computing is the new technology that has started to be widely adopted for use with several applications by many education providers. A number of issues that have delayed the complete adoption of M-learning applications through cloud computing services still need to be solved. This paper defines an appropriate set of requirements, i.e. availability, quick response, flexibility and ease of use, long-term storage, elasticity and scalability, integrity, privacy and confidentiality and the control of information flow. The dimensions of these requirements are tailored to criteria developed from the literature study, standards for software quality and their guidelines. The paper then highlights the level of importance of each defined requirement for higher educational institutions, training centres, research laboratories, infant and junior schools.
EDDS: An Enhanced Density-Based Method for Clustering Data Streams

Data stream clustering is an active area of research in big data. It refers to clustering constantly arriving new data records and updating existing cluster patterns and outliers in light of the newly arriving data. Density-based algorithms for solving this problem have the promise for finding arbitrary shape clusters and detecting anomalies without prior knowledge of the number of clusters. In this paper, a new incremental algorithm known as Enhanced Density-based Data Stream (EDDS) is developed to overcome limitations with the existing solutions. The algorithm detects clusters and outliers in an incoming data chunk, merges new clusters from the chunk with the existing clusters, and filters out new outliers for the next round. It modified the traditional DBSCAN algorithm to summarise each cluster in terms of a set of surface-core points. The algorithm applies the density-reachable concept of DBSCAN as its merging strategy and prunes the internal core points using a heuristic solution. The algorithm also removes the aged core points and outliers depending on a fading function. The paper investigates three versions of the algorithm for three possible representations of clusters where either all core points are maintained (EDDS-I), only core points of the new clusters from the incoming chunk are kept (EDDS-II), or only the surface-core points of the cluster shapes are kept (EDDS-III) to examine the balance between the efficiency gain for the algorithm and the amount of overhead time committed for pruning internal core points. The algorithm was evaluated on selected datasets using various quality measures. The experimental results indicate improvements in terms of clustering correctness with a comparable time complexity over the existing solutions for solving the same kind of problems.
The dihydrofolate reductase amplicons in different methotrexate-resistant Chinese hamster cell lines share at least a 273-kilobase core sequence, but the amplicons in some cell lines are much larger and are remarkably uniform in structure

We have previously cloned and characterized two different dihydrofolate reductase amplicon types from a methotrexate-resistant Chinese hamster ovary cell line (CHOC 400). The largest of these (the type I amplicon) is 273 kilobases (kb) in length. In the present study, we utilized clones from the type I amplicon as probes to analyze the size and variability of the amplified DNA sequences in five other independently isolated methotrexate-resistant Chinese hamster cell lines. Our data indicated that the predominant amplicon types in all but one of these cell lines are larger than the 273-kb type I sequence. In-gel renaturation experiments as well as hybridization analysis of large SfiI fragments separated by pulse-field gradient gel electrophoresis showed that two highly resistant cell lines (A3 and MK42) have amplified very homogeneous core sequences that are estimated to be at least 583 and 653 kb in length, respectively. Thus, the sizes of the major amplicon types can be different in different drug-resistant Chinese hamster cell lines. However, there appears to be less heterogeneity in size and sequence arrangement within a given methotrexate-resistant Chinese hamster cell line than has been reported for several other examples of DNA sequence amplification in mammalian systems.
Employment Discrimination on Civil Servant Recruitment

: Employment right is linked to the people’s livelihood in our society. As a most important and representative part in the labor market, the employment of public servants is always taking much attention. But the discrimination in the employment of public servants has always existed and, to become a controversy in our society. The paper try to discuss this problem from four parts as follows: First, the employment of public servants has a representative status in our labor market. The second part is about the discrimination in the employment of public servants. The third part is about the right of equality and its significance. The last part is to analysis the legal predicament about discrimination in the employment of public servants in China.
Microcirculatory dysfunction in sepsis: a pathogenetic basis for therapy?

Sepsis is a frequent complication of multiple organ dysfunction syndrome and remains a major problem of intensive care medicine. It is also a common factor in the final cause of death in hospital populations. Clinical observations, assisted by invasive monitoring techniques as well as pathological–anatomical studies, clearly indicate that microcirculatory dysfunction lies at the centre of sepsis pathogenesis. Numerous animal models, from rodents to primates, many of which employ bacteria or their toxins, especially endotoxins, have helped to shed light on the pathomechanisms leading to this dysregulation in the peripheral circulation. Among these are activation of humoral and cellular inflammatory mediator systems, with special emphasis on neutrophil–endothelial interactions, affecting endothelial barrier function and vasoregulation and ultimately leading to severely perturbed oxygen transport and utilization. In vitro studies have provided more insight into the molecular mechanisms involved in this microcirculatory dysfunction, although much more attention must be directed towards microvascular endothelial cells and the role of heterogeneity of response in various vascular beds. These experimental data must in turn be validated by comparing with the human in situ situation, both clinical and morphological. This review aims at a critical appraisal of the clinical and experimental evidence for sepsis‐induced dysregulation of the microcirculation and how knowledge of the underlying cellular and molecular pathology could be used to make therapy more rational and effective. To date, therapeutic approaches, such as anti‐cytokine and anti‐oxidant regimens, which have been highly successful in experimental models, have failed to demonstrate clinical efficacy. Newer approaches, such as targeting the coagulation system, nitric oxide synthesis or intracellular signal transduction, are also discussed. The necessity to focus on the role of anti‐inflammatory mediators, as well as the pathogenetic significance of important molecular groups, such as the heat shock proteins, which until now have been given scant attention, will be stressed. Copyright © 2000 John Wiley & Sons, Ltd.