Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequence Pattern Mining Based on Markov Chain

Sequence pattern mining is one of the main challenges in data mining and especially in large biological sequence databases, which consist of a large number of DNA sequences. Many existing methods are time consuming and scan the database multiple times. In order to overcome such shortcomings, we propose a fast and efficient algorithm SPMM based on Markov chain for mining sequence patterns because the DNA sequences meet Markov property. We first present the relative concepts and definitions. And then SPMM algorithm is put forward in which transition probabilities matrix is computed for each DNA sequence. The sequence patterns can be identified according to the given threshold of minimum support degree. Some examples are given to illustrate SPMM in detail. The experimental results show that our SPMM algorithm can achieve not only faster speed, but also higher quality results as compared with other algorithms.
College Student Leadership Competencies Development: A Model

The study has designed a model for assessing student leadership competencies development and affecting factors in university. It is based on the findings in Fars provinceIran. 400 college students were randomly selected from 26 institutions. The study used qualitative (Focus group, individual in-depth interview and library) and quantitative (path analysis) methods. Numerous studies have been carried out examining the effect of involvement and environment variables, leadership attitude and leadership behavior on the student leadership competencies development. However, there is little research conducted on the effect of leadership attitude and leadership behavior such as mediatory variable on the student leadership competencies development. The model suggests that systematic thinking, challenging the process, inspiring a shared vision, enabling others to act, modeling the way and encouraging the heart are considered important in student leadership competencies development. The authors propose that student affair practitioners need to rethink some of the key assumptions of their student leadership and practices in order to meet the needs of a changing student body. Also, college and universities need to be cognizant of these differences, as they develop leadership programs, training opportunities, leadership course and cocurricular and extracurricular activities.
A balance of power: expressive, analyzable controller programming

Configuration languages for traditional network hardware are often fairly limited and hence easy to analyze. Programmable controllers for software-defined networks are far more flexible, but this flexibility results in more opportunities for mis-configuration and greatly complicates analyses. We propose a new network-programming paradigm that strikes a balance between expressive power and analysis, providing a highly analyzable core language while allowing the re-use of pre-existing code written in more complex production languages. As the first step we have created FlowLog, a declarative language for programming SDN controllers. We show that FlowLog is expressive enough to build some real controller programs. It is also a finite-state language, and thus amenable to many types of analysis, such as model-checking. In this paper we present FlowLog, show examples of controller programs, and discuss analyzing them.
Parametric coding of speech spectra

We suggest that a class of speech coders can be designed from criteria that are perception‐specific. Such a class represents a middle ground between ’’waveform’’ coders and speech‐specific ’’source’’ coders. We argue that, within perceptually acceptable limits, a bandpass portion of a speech signal can be represented by its short‐time spectral amplitude ‖ Sn ‖ and its phase derivative ? n. Both parameters are evaluated at the center frequency ωn of the passband whose spectral width is Wn rad/s. We show that the short‐time spectral amplitude is identical to the Hilbert envelope An of the passband waveform. As a by‐product, we show that the bandwidth occupied by both An2 and An2 ? n is the same as that for their parent bandpass signal, but their spectra are translated to the range 0 to Wn. No comparable statements can be adduced for An and ? n, but on practical grounds, we conjecture that useful low‐pass limits of less than Wn/2 can be applied to both. Finally, we outline techniques to utilize the passband par.
GST and its relatives do not measure differentiation

G ST and its relatives are often interpreted as measures of differentiation between subpopulations, with values near zero supposedly indicating low differentiation. However, GST necessarily approaches zero when gene diversity is high, even if subpopulations are completely differentiated, and it is not monotonic with increasing differentiation. Likewise, when diversity is equated with heterozygosity, standard similarity measures formed by taking the ratio of mean within‐subpopulation diversity to total diversity necessarily approach unity when diversity is high, even if the subpopulations are completely dissimilar (no shared alleles). None of these measures can be interpreted as measures of differentiation or similarity. The derivations of these measures contain two subtle misconceptions which cause their paradoxical behaviours. Conclusions about population differentiation, gene flow, relatedness, and conservation priority will often be wrong when based on these fixation indices or similarity measures. These are not statistical issues; the problems persist even when true population frequencies are used in the calculations. Recent advances in the mathematics of diversity identify the misconceptions, and yield mathematically consistent descriptive measures of population structure which eliminate the paradoxes produced by standard measures. These measures can be directly related to the migration and mutation rates of the finite‐island model.
Product news summarization for competitor intelligence using topic identification and artificial bee colony optimization

With proliferation of web content, nowadays, various information about companies have become publicly available online. These information are mostly text documents such as news, reports, which can provide useful insight into various aspects about corporations. In order to extract useful information from this huge and diverse collection of texts, appropriate state-of-the-art text mining techniques are necessary. In this paper, a novel multi-document extractive text summarization technique, based on topic identification and artificial bee colony optimization, is described which can be used by companies for extracting important facts from the product-specific news items of their competitors and subsequently use them as one of the inputs for strategic business decision making. The results presented in this paper are based on the corpus created by collecting news items for a specific consumer electronics company from authentic news sites available on the internet. The quality of summary generated using this approach is found to be better on many aspects as compared to summaries generated by a well-known benchmark summarizer called MEAD.
Neuromyelitis optica spectrum disorders: comparison of clinical and magnetic resonance imaging characteristics of AQP4‐IgG versus MOG‐IgG seropositive cases in the Netherlands

Neuromyelitis optica spectrum disorders (NMOSDs) are a group of rare inflammatory demyelinating disorders of the central nervous system. The identification of specific antibodies directed to aquaporin 4 (AQP4‐IgG) led to the distinction from multiple sclerosis. However, up to 25% of the clinically diagnosed NMO patients are seronegative for AQP4‐IgG. A subgroup of these patients might be identified by antibodies directed to myelin oligodendrocyte glycoprotein (MOG‐IgG). Our objective was to investigate whether the clinical characteristics of these patients differ.
Dependency Analysis of Message Packet Queues in Interconnection Networks with Faults

Many contemporary communication networks carry different types of traffics, each bearing specific characteristics of their own. The arrival process of packets outsourced from every single source node is approximated to a Poisson arrival process. Mostly, in network performance models, the exponential nature of the inter-arrival time in fault-free networks is determined by the dependency between inter-arrival times. But in most of the communication environments, in addition to minimizing packet delays and maximizing the network throughput, continuous functionality in the presence of faulty components has become a major issue. On such basis, the dependency phenomenon between consecutive service times as well as between service and inter-arrival times for packet queues in interconnection networks and in the vicinity of the faulty components can be of great importance. In this paper, we analyze the effect of such dependencies in packet queues through simulation experiments. We also study the behavior of an M/G/l queue with Poisson processes in face of faults. This study can be used to justify the predicted packet delays obtained from analytical models under diverse traffic patterns and various network conditions and prove beneficial by enlightening the limitations of network analytical approaches in using approximation methods for evaluating network of queues.
Examining State Dependence and Place Attachment Within a Recreational Fishing Site Choice Model

Many contexts including the fidelity that recreationists have for sites may affect the choices of recreational sites by individuals. This study expands the choice model research on state dependence by examining state dependence at site and larger spatial scales. Analyses of recreational fishing site choices by anglers from northern Ontario, Canada suggest that anglers exhibit state dependence at both the site and larger spatial scales. Attempts to understand the importance of state dependence through self reports of place attachment dimensions among the anglers provided mixed results. No significant relationships were found between place identity and the importance of site or spatial state dependence to anglers. While having no significant effect on site state dependence, place dependence was positively associated with the importance of spatial state dependence among approximately 65% of the anglers. Evidently, anglers who viewed themselves as dependent upon a fishing area were more likely to take their fishing trips in a constrained space than were other anglers. These conclusions are influenced by the difference between the larger spatial scale for the place attachment questions (i.e., favorite fishing area) than for the choice model (i.e., fishing site).
Versorgungsindikatoren in der Psychiatrie und Psychosomatik ( VIPP ) – Ein Datenbank-Projekt Indicators of Patient Care in Psychiatric and Psychosomatic Facilities ( VIPP Project ) – A Database Project

Einleitung: Am 17.11. 2012 wurde der Katalog für das pauschalierende Entgeltsystem für die Psychiatrie und Psychosomatik (PEPP) in Kraft gesetzt. Es stehen Fragen zum Aufbau der Entgelte sowie vermuteter Anreizwirkungen dieser Systemveränderung im Fokus. Weder auf nationale bzw. internationale Erfahrungen noch auf ausreichende nationale Versorgungsdaten kann zurückgegriffen werden, so dass ein Bedarf für eine umfangreiche Datensammlung psychiatrischer und psychosomatischer Behandlungsfälle besteht. Material und Methoden: Das Projekt „Versorgungsindikatoren in der Psychiatrie und Psychosomatik (VIPP)“ hat das Ziel, routinedatenbasiert die aktuelle Versorgungssituation abzubilden. Der §-21-Datensatz stellt das Kernstück des Datensatzes dar. Eine Besonderheit besteht darin, dass weitere Datenquellen in diese Datenbank integriert sind. Eine jährliche Fallzahl von 100000 ist bereits überschritten. Bei den teilnehmenden Einrichtungen handelt es sich um Fachkrankenhäuser, Abteilungspsychiatrien und Universitäten, so dass eine große Bandbreite an Leistungserbringern und Behandlungen abgebildet wird. Die gepoolten Daten lassen die Identifizierung der einzelnen Klinik nicht zu. Teilnehmer erhalten einen webbasierten Zugang und können jederzeit selbstständig analysieren. Ergebnisse: Mittels Beispielen zur Kodierqualität und zuWiederaufnahmeratenwird demonstriert, wie vielfältig die Datenbankanalysen möglich sind und welches enorme Potenzial in dieser Datenbank liegt. Diskussion: Auf der Grundlage dieser VIPP-Datenbank lassen sich belastbare Versorgungsindikatoren und Längsschnittanalysen entwickeln. Aus den Ergebnissen können Kennzahlen und fachlich inhaltliche sowie gesundheitsökonomische Strategien abgeleitet werden, und es kann rechtzeitig auf die Stärken und Schwächen der VersorgungsAbstract !
Excess Supply of Nutrients, Fungal Community, and Plant Litter Decomposition: A Case Study of Avian-Derived Excreta Deposition in Conifer Plantations

1.1 Excess supply of nutrients and terrestrial ecosystems Human activities have greatly accelerated emissions of both carbon dioxide and biologically reactive nutrients such as nitrogen (N) to the atmosphere (Canfield et al., 2010), which cause environmental changes affecting ecosystem processes and biodiversity in forests. Excess supply of N of anthropogenic origin to forest soils, such as combustion of fossil fuels, production of N fertilizers, and cultivation of N-fixing legumes, is an example of such environmental changes often leading to a decrease of the rate of carbon dioxide evolution and decomposition (Fog, 1988; Berg and Matzner, 1997) and a concomitant increase in the amount of soil carbon stock (deVries et al., 2006; Zak et al., 2008). These changes are primarily attributable to the reduced activity of fungal ligninolytic enzymes that play crucial roles in the turnover of soil organic carbon and are known to be sensitive to N deposition (Sinsabaugh, 2010). However, such changes in the enzymatic activity are not consistently associated with changes in the abundance and diversity of fungi that are responsible for the activity (Waldrop and Zak, 2006; Blackwood et al., 2007; Hassett et al., 2009). This discrepancy merits further studies to examine the response of ecological and functional properties of fungal communities to excess supply of N and its consequences on the dynamics of carbon and N in forest soils. The transfer of nutrients by waterbirds from aquatic to terrestrial ecosystems provides similar situations to the anthropogenic supply of nutrients because birds feed on fish in the aquatic zone and deposit their waste rich in nutrients to the terrestrial parts of their habitats. Such allochthonous input of N and other nutrients to terrestrial ecosystems can lead locally to substantial enrichment of soils and plants and alter food webs, nutrient cycling, and
The Magnitude of Decrease in Hepatic Very Low Density Lipoprotein Apolipoprotein B Secretion Is Determined by the Extent of 3-Hydroxy-3-Methylglutaryl Coenzyme A Reductase Inhibition in Miniature Pigs1.

It has been postulated that the rate of hepatic very low density lipoprotein (VLDL) apolipoprotein (apo) B secretion is dependent upon the activity of 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase. To test this hypothesis in vivo, apoB kinetic studies were carried out in miniature pigs before and after 21 days treatment with high-dose (10 mg/kg/day), atorvastatin (A) or simvastatin (S) (n = 5). Pigs were fed a diet containing fat (34% of calories) and cholesterol (400 mg/day; 0.1%). Statin treatment decreased plasma total cholesterol [31 (A) vs. 20% (S)] and low density lipoprotein (LDL) cholesterol concentrations [42 (A) vs. 24% (S)]. Significant reductions in plasma total triglyceride (46%) and VLDL triglyceride (50%) concentrations were only observed with (A). Autologous [131I]VLDL, [125I]LDL, and [3H]leucine were injected simultaneously, and apoB kinetic parameters were determined by triple-isotope multicompartmental analysis using SAAM II. Statin treatment decreased the VLDL apoB pool size [49 (A) vs. 24% (S)] and the hepatic VLDL apoB secretion rate [50 (A) vs. 33% (S)], with no change in the fractional catabolic rate (FCR). LDL apoB pool size decreased [39 (A) vs. 26% (S)], due to reductions in both the total LDL apoB production rate [30 (A) vs. 21% (S)] and LDL direct synthesis [32 (A) vs. 23% (S)]. A significant increase in the LDL apoB FCR (15%) was only seen with (A). Neither plasma VLDL nor LDL lipoprotein compositions were significantly altered. Hepatic HMG-CoA reductase was inhibited to a greater extent with (A), when compared with (S), as evidenced by 1) a greater induction in hepatic mRNA abundances for HMG-CoA reductase (105%) and the LDL receptor (40%) (both P < 0.05); and 2) a greater decrease in hepatic free (9%) and esterified cholesterol (25%) (both P < 0.05). We conclude that both (A) and (S) decrease hepatic VLDL apoB secretion, in vivo, but that the magnitude is determined by the extent of HMG-CoA reductase inhibition.
Video-based activity level recognition for assisted living using motion features

Activities of daily living of the elderly is often monitored using passive sensor networks. With the reduction of camera prices, there is a growing interest of video-based approaches to provide a smart, safe and independent living environment for the elderly. In this paper, activity level in context of tracking the movement pattern of an individual as a metric to monitor the daily living of the elderly is explored. Activity levels can be an effective indicator that would denote the amount of busyness of an individual by modelling motion features over time. The novel framework uses two different variants of the motion features captured from two camera angles and classifies them into different activity levels using neural networks. A new dataset for assisted living research called the Sheffield Activities of Daily Living (SADL) dataset is used where each activity is simulated by 6 subjects and is captured under two different illumination conditions within a simulated assisted living environment. The experiments show that the overall detection rate using a single camera setup and a dual camera setup is above 80%.
Reliability-Oriented bioinformatic networks visualization

SUMMARY We present our protein-protein interaction (PPI) network visualization system RobinViz (reliability-oriented bioinformatic networks visualization). Clustering the PPI network based on gene ontology (GO) annotations or biclustered gene expression data, providing a clustered visualization model based on a central/peripheral duality, computing layouts with algorithms specialized for interaction reliabilities represented as weights, completely automated data acquisition, processing are notable features of the system. AVAILABILITY RobinViz is a free, open-source software protected under GPL. It is written in C++ and Python, and consists of almost 30 000 lines of code, excluding the employed libraries. Source code, user manual and other Supplementary Material are available for download at http://code.google. com/p/robinviz/.
Novel Bioinformatics Method for Identification of Genome-Wide Non-Canonical Spliced Regions Using RNA-Seq Data

Setting During endoplasmic reticulum (ER) stress, the endoribonuclease (RNase) Ire1α initiates removal of a 26 nt region from the mRNA encoding the transcription factor Xbp1 via an unconventional mechanism (atypically within the cytosol). This causes an open reading frame-shift that leads to altered transcriptional regulation of numerous downstream genes in response to ER stress as part of the unfolded protein response (UPR). Strikingly, other examples of targeted, unconventional splicing of short mRNA regions have yet to be reported. Objective Our goal was to develop an approach to identify non-canonical, possibly very short, splicing regions using RNA-Seq data and apply it to ER stress-induced Ire1α heterozygous and knockout mouse embryonic fibroblast (MEF) cell lines to identify additional Ire1α targets. Results We developed a bioinformatics approach called the Read-Split-Walk (RSW) pipeline, and evaluated it using two Ire1α heterozygous and two Ire1α-null samples. The 26 nt non-canonical splice site in Xbp1 was detected as the top hit by our RSW pipeline in heterozygous samples but not in the negative control Ire1α knockout samples. We compared the Xbp1 results from our approach with results using the alignment program BWA, Bowtie2, STAR, Exonerate and the Unix “grep” command. We then applied our RSW pipeline to RNA-Seq data from the SKBR3 human breast cancer cell line. RSW reported a large number of non-canonical spliced regions for 108 genes in chromosome 17, which were identified by an independent study. Conclusions We conclude that our RSW pipeline is a practical approach for identifying non-canonical splice junction sites on a genome-wide level. We demonstrate that our pipeline can detect novel splice sites in RNA-Seq data generated under similar conditions for multiple species, in our case mouse and human.
Engagement in the local community and civic socialisation : an analysis of neighbourhood and household context using the British Household Panel Survey

This thesis sets out to examine the notion that social context throughout the life course plays an important role in the development of social capital. It explores this using the British Household Panel Survey (BHPS), a longitudinal data set, using data from England and Wales. It argues that social capital can be thought of as being composed of different dimensions which develop differentially over time. It frames the research within the context of the local community and examines three distinct dimensions of social capital: participation in local groups, neighbourhood attachment, and interpersonal trust. Frameworks are developed within which each is hypothesised to develop at different times and within different contexts. Different expectations are outlined which suggest how they should develop within a view of social capital based on Putnam (2000) and his predictions concerning social participation and trust. These are contrasted with theories and findings form the literature on political socialisation and Uslaner? s (2002) conception of trust as a deep rooted moral trait.It is shown that participation in local groups, neighbourhood attachment and interpersonal trust, do develop at different stages and in different contexts. Moreover, it is shown that growing up in a highly trusting environment may predict participation and engagement later in life.
Wikipedia-based Unsupervised Query Classification

In this paper we present an unsupervised approach to Query Classification. The approach exploits the Wikipedia encyclopedia as a corpus and the statistical distribution of terms, from both the category labels and the query, in order to select an appropriate category. We have created a classifier that works with 55 categories extracted from the search section of the Bridgeman Art Library website. We have also evaluated our approach using the labeled data of the KDD-Cup 2005 Knowledge Discovery and Data Mining competition (800,000 real user queries into 67 target categories) and obtained promising results.
Circuit design for beyond von Neumann applications using emerging memory: From nonvolatile logics to neuromorphic computing

Emerging memory devices enable performance improvements in memory applications and make possible chip designs using beyond von Neumann architectures. This paper explores the use of emerging memory devices in applications of nonvolatile logics and neuromorphic computing, and provides a review of several silicon examples of nonvolatile logics. This paper also discusses the challenges involved in the design of circuits for nonvolatile logics and neuromorphic computing systems based on emerging memory devices.