Miracle-dz/UniFAR-FTUs huggingface dataset:
De novo identification of highly diverged protein repeats by probabilistic consistency

MOTIVATION An estimated 25% of all eukaryotic proteins contain repeats, which underlines the importance of duplication for evolving new protein functions. Internal repeats often correspond to structural or functional units in proteins. Methods capable of identifying diverged repeated segments or domains at the sequence level can therefore assist in predicting domain structures, inferring hypotheses about function and mechanism, and investigating the evolution of proteins from smaller fragments. RESULTS We present HHrepID, a method for the de novo identification of repeats in protein sequences. It is able to detect the sequence signature of structural repeats in many proteins that have not yet been known to possess internal sequence symmetry, such as outer membrane beta-barrels. HHrepID uses HMM-HMM comparison to exploit evolutionary information in the form of multiple sequence alignments of homologs. In contrast to a previous method, the new method (1) generates a multiple alignment of repeats; (2) utilizes the transitive nature of homology through a novel merging procedure with fully probabilistic treatment of alignments; (3) improves alignment quality through an algorithm that maximizes the expected accuracy; (4) is able to identify different kinds of repeats within complex architectures by a probabilistic domain boundary detection method and (5) improves sensitivity through a new approach to assess statistical significance. AVAILABILITY Server: http://toolkit.tuebingen. mpg.de/hhrepid; Executables: ftp://ftp.tuebingen. mpg.de/pub/protevo/HHrepID
Direct reconstruction of fibre orientation using discrete ground truth interpolation

In this paper we present a novel approach to extracting fibre orientation information from the diffusion signal. We start the process by expanding the diffusion signal using spherical harmonics (SH) basis. In theory, this could lead to a mapping between SH coefficients and fibre orientations. In practice, finding such a mapping is non-trivial. Instead, we simulate the diffusion signal for a limited set of fibres (n different fibres with up to m fibre crossings) and store their corresponding SH coefficients in a database. We show that with such a database it is possible to find the precomputed fibre configuration closest to any SH expansion.
A New Algorithm for Maintaining Closed Frequent Itemsets in Data Streams by Incremental Updates

Online mining of closed frequent itemsets over streaming data is one of the most important issues in mining data streams. In this paper, we propose an efficient one-pass algorithm, NewMoment to maintain the set of closed frequent itemsets in data streams with a transaction-sensitive sliding window. An effective bit-sequence representation of items is used in the proposed algorithm to reduce the time and memory needed to slide the windows. Experiments show that the proposed algorithm not only attain highly accurate mining results, but also run significant faster and consume less memory than existing algorithm Moment for mining closed frequent itemsets over recent data streams
Data Anonymity Meets Non-discrimination

We investigate the relation between t-closeness, a well-known model of data anonymization, and α-protection, a model of data discrimination. We show that t-closeness implies bd(t)-protection, for a bound function bd() depending on the discrimination measure at hand. This allows us to adapt an inference control method, the Mondrian multidimensional generalization technique, to the purpose of non-discrimination data protection. The parallel between the two analytical models raises intriguing issues on the interplay between data anonymization and non-discrimination research in data mining.
On the Throughput Capacity of Opportunistic Multicasting with Erasure Codes

In this paper, we concentrate on opportunistic scheduling for multicast information. We pose the problem as a multicast throughput optimization problem. As a solution we present how one can jointly utilize fixed-rate and rateless erasure coding along with simple rate adaptation techniques in order to achieve the optimal multicast throughput per user. We first investigate the performance of the proposed system under i.i. d. channel conditions. Our analysis shows a linear gain for the multicast capacity over i.i. d. Rayleigh fading channels with respect to the number of users. Since the established results require coding over large number of blocks and hence induce large decoding delays, we extend our analysis to the cases where we code over shorter block lengths and thus quantify the delay-capacity tradeoffs under a simple setting. We further look into non-i.i. d. channel conditions and show achievable gains by modifying a scheduling heuristic whose fairness is well- established for opportunistic scheduling of unicast flows. Our overall evaluations demonstrate that under both i.i. d. and non-i.i. d. channel conditions, opportunistic multicasting with erasure coding can significantly improve the performance over the traditional techniques used in today's communication systems.
Culture and the Remembering of Trauma

This research investigated the influence of culture and posttraumatic stress disorder (PTSD) on global autobiographical remembering (Study 1a) and on the phenomenological properties (Study 1b) and memory-content variables (Study 1c) of trauma-specific autobiographical remembering. Australian, British, and Iranian trauma survivors with and without PTSD completed the Autobiographical Memory Test, Self-Defining Memory Task, and Autobiographical Memory Questionnaire and provided trauma- and negative-memory narratives. We found that there were pan-cultural deficits and distortions in the global autobiographical remembering of participants with PTSD (Study 1a). In addition, the presence of PTSD moderated the usual effect of culture on the phenomenological properties of the trauma memory (Study 1b). Finally, participants with PTSD, regardless of cultural background, had significantly fewer expressions of autonomy and self-determination in their autobiographical remembering than did those without PTSD (Study 1c). The findings suggest that pan-culturally, individuals with PTSD have similar disruptions and distortions in their autobiographical remembering.
Z-Score Linear Discriminant Analysis for EEG Based Brain-Computer Interfaces

Linear discriminant analysis (LDA) is one of the most popular classification algorithms for brain-computer interfaces (BCI). LDA assumes Gaussian distribution of the data, with equal covariance matrices for the concerned classes, however, the assumption is not usually held in actual BCI applications, where the heteroscedastic class distributions are usually observed. This paper proposes an enhanced version of LDA, namely z-score linear discriminant analysis (Z-LDA), which introduces a new decision boundary definition strategy to handle with the heteroscedastic class distributions. Z-LDA defines decision boundary through z-score utilizing both mean and standard deviation information of the projected data, which can adaptively adjust the decision boundary to fit for heteroscedastic distribution situation. Results derived from both simulation dataset and two actual BCI datasets consistently show that Z-LDA achieves significantly higher average classification accuracies than conventional LDA, indicating the superiority of the new proposed decision boundary definition strategy.
Applicability of Family Therapy for Chinese Children and Adolescents Suffering from Anorexia Nervosa in a Chinese Context: A Preliminary Study

ABSTRACT This article presents the results of a preliminary study that assesses the applicability of family therapy for Chinese adolescents suffering from anorexia nervosa in Hong Kong, an area that had never been studied in the past. A total of 27 Chinese emaciated children and adolescents received family therapy and conventional psychiatric treatment from the university-based family treatment center, in collaboration with the psychiatric unit of the university hospital. The treatment outcome was evaluated by changes in body weight, body mass index, symptoms associated with the disorder, level of psychological distress, marital quality of parents, and perceived family functioning at three different phases, namely, at the pretreatment phase, immediately upon the completion of treatment, and 6 months after treatment. The results of this study have shown that family therapy combined with conventional psychiatric treatment was effective in restoring body weight, increasing the body mass index, and recovering menstruation. Six months after treatment, patients were clinically no longer symptomatic in Drive for Thinness and Perfectionism; six psychological dimensions of the Symptoms Checklist-90 (R) have changed from a dysfunctional range to a functional range; and the fathers perceived significant improvement in dyadic consensus. However, changes of perceived family functioning 6 months after treatment were statistically insignificant, suggesting limitations of the assessment measure in capturing changes in this area.
Monte Carlo Method Study of Terahertz Pulse Propagation in Biological Tissue

The terahertz pulse (THz pulse) propagation in biological tissue is simulated by Monte Carlo method (MCM). The migratory route of THz pulse in the tissue is presented. The computation model is based on the assumption that the refraction indexes of tissue and air are mismatch and both surfaces of the tissue have the reflection effect for THz pulse
Heart Rate Response to Exercise Stress Testing in Asymptomatic Women

Background—The definition of a normal heart rate (HR) response to exercise stress testing in women is poorly understood, given that most studies describing a normative response were predominately based on male data. Measures of an attenuated HR response (chronotropic incompetence) and age-predicted HR have not been validated in asymptomatic women. We investigated the association between HR response to exercise testing and age with prognosis in 5437 asymptomatic women. Methods and Results—Participants underwent a symptom-limited maximal stress test in 1992. HR reserve (change in HR from rest to peak), chronotropic index, and age-predicted peak HR were calculated. Deaths were identified to December 31, 2008. Mean age at baseline was 52 11 years, with 549 deaths (10%) over 15.9 2.2 years. Mean peak HR was inversely associated with age; mean peak HR 206–0.88(age). After adjusting for exercise capacity and traditional cardiac risk factors, risk of death was reduced by 3% for every 1–beat-per-minute increase in peak HR, and by 2% for every 1–beat-per-minute increase in HR reserve (P 0.001). Inability to achieve 85% age-predicted HR was not an independent predictor of mortality, but being 1 SD below the mean predicted HR or a chronotropic index 0.80 based on the prediction model established by this cohort were independent predictors of mortality (P 0.001 and P 0.023, respectively). Conclusions—Chronotropic incompetence is associated with an increased risk of death in asymptomatic women; however, the traditional male-based calculation overestimates the maximum HR for age in women. Sex-specific parameters of physiological HR response to exercise should be incorporated into clinical practice. (Circulation. 2010;122:130-137.)
Making Games for Health Engaging: The Influence of Cognitive Skills.

OBJECTIVE Serious games for health care are on the rise. These games are thought to be effective because they can provide information in a context that is engaging. However, it is likely that game-based health training is most effective for a subset of people with specific skills, traits, and experiences. Understanding the factors associated with optimum game outcomes will help us better describe the learners for whom they are appropriate. Toward this end, the present study examined specific cognitive skills related to the achievement of flow state while playing a game for health. MATERIALS AND METHODS In total, 59 college students were recruited from undergraduate classes to play a game for health and were assessed on levels of mindfulness, cognitive flexibility, and flow state. RESULTS The results suggest that the effect of cognitive flexibility on flow changes as a function of mindfulness. More specifically, the results suggest that there is a negative relationship between cognitive flexibility and flow in individuals low on mindfulness and a positive relationship between cognitive flexibility and flow in individuals high on mindfulness. CONCLUSIONS Game designers wishing to create effective game-based treatment supplements may wish to implement cognitive flexibility and mindfulness training.
Inducing Script Structure from Crowdsourced Event Descriptions via Semi-Supervised Clustering

We present a semi-supervised clustering approach to induce script structure from crowdsourced descriptions of event sequences by grouping event descriptions into paraphrase sets (representing event types) and inducing their temporal order. Our approach exploits semantic and positional similarity and allows for flexible event order, thus overcoming the rigidity of previous approaches. We incorporate crowdsourced alignments as prior knowledge and show that exploiting a small number of alignments results in a substantial improvement in cluster quality over state-of-the-art models and provides an appropriate basis for the induction of temporal order. We also show a coverage study to demonstrate the scalability of our approach.
Time-communication trade-offs for minimum spanning tree construction

This paper concerns the problem of constructing a minimum spanning tree (MST) in a synchronous distributed network with n nodes, where each node knows only the identities of itself and its neighbors. We assume the CONGEST model where messages are of size O(log n) bits. Spanning tree construction was long believed to require an amount of communication linear in the number of edges. In 2015, King, Kutten and Thorup presented a Monte Carlo algorithm which broke this communication bound. In particular it showed that an MST could be constructed with time and message complexity O(n log2 n/log log n), independent of the number of edges. Here we give trade-offs between time and communication. Our Monte Carlo algorithm runs in O(n/ϵ) time and O(n1+ϵ/ϵ log log n) messages for any 1 > ϵ ≥ log log n log n. For the spanning tree problem, we show a time bound of O(n) and a communication bound of O(n log n log log n) messages. We also provide the first algorithm that constructs an MST in time proportional to the diameter of the MST up to a logarithmic factor with o(m) communication.
HIV Nef Increases T Cell ERK MAP Kinase Activity*

The human immunodeficiency regulatory protein Nef enhances viral replication and is central to viral pathogenesis. Although Nef has displayed a capacity to associate with a diverse assortment of cellular molecules and to increase T cell activity, the biochemical activity of Nef in T cells remains poorly defined. In this report we examine the bioactivity of Nef in primary CD4 T cells and, in particular, focus on the biochemical pathways known to be central to T cell activity. The extracellular signal-regulated kinase (ERK) mitogen-activated protein (MAP) kinase pathway was dramatically affected by Nef expression with increases in ERK, MEK, and Elk induction. The capacity of Nef to increase the MAP kinase pathway activity was dependent on T cell receptor stimulation. By increasing ERK MAP kinase activity, Nef is functionally associated with a kinase known to affect T cell activity, viral replication, and viral infectivity.
Maximum-likelihood sequence detection with closed-form metrics in OOK optical systems impaired by GVD and PMD

This paper thoroughly investigates the maximum-likelihood sequence detection (MLSD) receiver for the optical ON-OFF keying (OOK) channel in the presence of both polarization mode dispersion and group velocity dispersion (GVD). A reliable method is provided for computing the relevant performance for any possible value of the system parameters, with no constraint on the sampling rate. With one sample per bit time, a practically exact expression of the statistics of the received samples is found, and therefore the performance of a synchronous MLSD receiver is evaluated and compared with that of other electronic techniques such as combined feedforward and decision-feedback equalizers (FFE and DFE). It is also shown that the ultimate performance of electronic processing can be obtained by sampling the received signal at twice the bit rate. An approximate accurate closed-form expression of the receiver metrics is also identified, allowing for the implementation of a practically optimal MLSD receiver
Proving Invariants via Rewriting and Abstra tion

We present a deductive method for proving invariants of reactive systems. Our approach uses term rewriting to reduce invariant proofs to reachability analysis on a finite graph. This substantially automates invariant proofs by obviating the need to define inductive invariants while still benefitting from the expressiveness of deductive methods. We implement a procedure supporting this approach which interfaces with the ACL2 theorem prover. The interface affords sound extension of our procedure with rewrite rules based on proven theorems. We demonstrate the method in the verification of cache coherence protocols.
A Homomorphic Crypto System for Electronic Election Schemes

This research investigates the applications of homomorphic encryption systems in electronic voting schemes. We make use of Paillier cryptosystem which exhibits additive homomorphic properties. The other homomorphic cryptosystems RSA and Elgamal are not considered, since they exhibit only multiplicative homomorphic property. Our proposed method increases the level of security when compared to Elgamal method. It is more flexible when compared to previous schemes. We also propose data packing for efficient storage of election data. Finally, we demonstrate the advantages of the homomorphic encryption in voting schemes by comparing with other electronic voting scheme.
Deconfinement Transition for Quarks on a Line

Abstract We examine the statistical mechanics of a one-dimensional gas of both adjoint and fundamental representation quarks which interact with each other through (1+1)-dimensionalU(N) gauge fields. Using large-Nexpansion we show that, when the density of fundamental quarks is small, there is a first-order phase transition at a critical temperature and adjoint quark density which can be interpreted as deconfinement. When the fundamental quark density is comparable to the adjoint quark density, the phase transition becomes a third order one. We formulate a way to distinguish the phases by considering the expectation values of high winding number Polyakov loop operators.
Increasing prevalence of the metabolic syndrome among u.s. Adults.

OBJECTIVE The prevalence of the metabolic syndrome is high among U.S. adults. Our purpose was to determine whether the prevalence of this syndrome has changed since 1988-1994. RESEARCH DESIGN AND METHODS A total of 6,436 men and women aged > or = 20 years from the National Health and Nutrition Examination Survey (NHANES) III (1988-1994) and 1,677 participants from NHANES 1999-2000 were included in the analyses. We used the definition of the metabolic syndrome developed by the Third Report of the National Cholesterol Education Program Expert Panel on Detection, Evaluation, and Treatment of High Blood Cholesterol in Adults. RESULTS The unadjusted prevalence of the metabolic syndrome was 23.1% in NHANES III and 26.7% in NHANES 1999-2000 (P = 0.043), and the age-adjusted prevalences were 24.1 and 27.0% (P = 0.088), respectively. The age-adjusted prevalence increased by 23.5% among women (P = 0.021) and 2.2% among men (P = 0.831). Increases in high blood pressure, waist circumference, and hypertriglyceridemia accounted for much of the increase in the prevalence of the metabolic syndrome, particularly among women. CONCLUSIONS The increased prevalence of the metabolic syndrome is likely to lead to future increases in diabetes and cardiovascular disease.
The mantle of the heavens: Reflections on the 2014 nobel prize for medicine or physiology

The award of the Nobel Prize in Medicine or Physiology in 2014 for the discovery of place and grid cells was both a personal award to three great scientists and also a mark of the maturity of systems neuroscience as a discipline. This article offers both personal and scientific reflections on these discoveries, detailing both how getting to know all three winners had an impact on my life and the research questions that we shared in common work together. It ends with brief reflections on three important outstanding questions. © 2015 Wiley Periodicals, Inc.
Molecular and clinical analysis of Japanese patients with persistent congenital hyperinsulinism: predominance of paternally inherited monoallelic mutations in the KATP channel genes.

BACKGROUND Preoperative identification of the focal form of congenital hyperinsulinism is important for avoiding unnecessary subtotal pancreatectomy. However, neither the incidence nor the histological spectrum of the disease is known for Japanese patients. AIMS The aim of the study was to elucidate the molecular and histological spectrum of congenital hyperinsulinism in Japan. SUBJECTS Thirty-six Japanese infants with persistent congenital hyperinsulinism were included in the study. METHODS All exons of the ATP-sensitive potassium channel (K(ATP) channel) genes (KCNJ11 and ABCC8), the GCK gene, and exons 6 and 7 and 10-12 of the GLUD1 gene were amplified from genomic DNA and directly sequenced. In patients with K(ATP) channel mutations, the parental origin of each mutation was determined, and the results were compared with the histological findings of surgically treated patients. In one of the patients with scattered lesions, islets were sampled by laser capture microdissection for mutational analysis. RESULTS Mutations were identified in 24 patients (66.7%): five in GLUD1 and 19 in the K(ATP) channel genes. Sixteen had a paternally derived, monoallelic K(ATP) channel mutation predictive of the focal form. In 10 patients who underwent pancreatectomy, the molecular diagnosis correctly predicted the histology, more accurately than [18F]-3,4-dihydroxyphenylalanine positron emission tomography scans. Three patients showed focal lesions that occupied larger areas of the pancreas. Preferential loss of the maternal allele was observed in these islets. CONCLUSION The majority of the Japanese patients with K(ATP) channel hyperinsulinism (84.2%) demonstrated paternally inherited monoallelic mutations that accurately predicted the presence of the focal form.
The Identification of Social Learning in Online Markets

I investigate the identification of social learning in online markets. In these markets, there is often a two-stage decision making process where a consumer first chooses whether or not to search a product and then chooses whether or not to buy it. Additionally, the social learning signals are regularly observable before the search decision. I posit that the ideal test for learning involves estimating the effect of a signal on the search probability, but one can also identify learning by finding the signal's effect on the purchase probability. However, using the purchase decision results in an increased likelihood that learning is incorrectly rejected. To demonstrate this, I perform three empirical exercises. The first uses simulation, while the others use data from an experimental and a real-world online market for music. The advantage of the latter two data sets is that I observe both a search decision (listening to the sample of a song) and a purchase decision (the downloading of a song). The results of the paper suggest a possible explanation for the difference in the amount of empirical evidence supporting word-of-mouth versus observational learning. Further, it provides researchers and managers a road map for identifying learning in line markets.