Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating a Ranked List of Human Genetic Diseases by Associating Phenotype-Gene with Gene-Disease Bipartite Graphs

With vast amounts of medical knowledge available on the Internet, it is becoming increasingly practical to help doctors in clinical diagnostics by suggesting plausible diseases predicted by applying data and text mining technologies. Recently, Genome-Wide Association Studies (GWAS) have proved useful as a method for exploring phenotypic associations with diseases. However, since genetic diseases are difficult to diagnose because of their low prevalence, large number, and broad diversity of symptoms, genetic disease patients are often misdiagnosed or experience long diagnostic delays. In this article, we propose a method for ranking genetic diseases for a set of clinical phenotypes. In this regard, we associate a phenotype-gene bipartite graph (PGBG) with a gene-disease bipartite graph (GDBG) by producing a phenotype-disease bipartite graph (PDBG), and we estimate the candidate weights of diseases. In our approach, all paths from a phenotype to a disease are explored by considering causative genes to assign a weight based on path frequency, and the phenotype is linked to the disease in a new PDBG. We introduce the Bidirectionally induced Importance Weight (BIW) prediction method to PDBG for approximating the weights of the edges of diseases with phenotypes by considering link information from both sides of the bipartite graph. The performance of our system is compared to that of other known related systems by estimating Normalized Discounted Cumulative Gain (NDCG), Mean Average Precision (MAP), and Kendall’s tau metrics. Further experiments are conducted with well-known TF · IDF, BM25, and Jenson-Shannon divergence as baselines. The result shows that our proposed method outperforms the known related tool Phenomizer in terms of NDCG@10, NDCG@20, MAP@10, and MAP@20; however, it performs worse than Phenomizer in terms of Kendall’s tau-b metric at the top-10 ranks. It also turns out that our proposed method has overall better performance than the baseline methods.
Gain-scheduling control for mechatronic systems with position dependent dynamics

Abstract This paper presents a gain-scheduling-control technique f or mechatronic systems with position-dependent dynamics. The proposed method fits in the framework of tradit ional gain scheduling, where several controllers designed for fixed operating points are interpolat ed to construct a global gain-scheduling controller. A new interpolation approach is proposed starting from an af fi e interpolation between the poles, zeros and gains of the local controllers as a function of the varying pa rameter, resulting in a polynomial state-space representation. The presented method is applied on an indus trial pick-and-place machine which has positiondependent dynamics. Experimental results show the benefit o f the proposed method.
Outlier Detection: Applications And Techniques

Outliers once upon a time regarded as noisy data in statistics, has turned out to be an important problem which is being researched in diverse fields of research and application domains. Many outlier detection techniques have been developed specific to certain application domains, while some techniques are more generic. Some application domains are being researched in strict confidentiality such as research on crime and terrorist activities. The techniques and results of such techniques are not readily forthcoming. A number of surveys, research and review articles and books cover outlier detection techniques in machine learning and statistical domains individually in great details. In this paper we make an attempt to bring together various outlier detection techniques, in a structured and generic description. With this exercise, we hope to attain a better understanding of the different directions of research on outlier analysis for ourselves as well as for beginners in this research field who could then pick up the links to different areas of applications in details.
Subterranean: A 600 Mbit/sec cryptographic VLSI chip

A high-speed cryptographic coprocessor is presented. This coprocessor is named Subterranean and can be used for both cryptographic pseudorandom sequence generation (Substream) and cryptographic hashing (Subhash). In Substream mode the chip can be used for stream encryption/decryption under control of a 256-bit key. A cryptographic resynchronization mechanism is provided for fast accessibility of encrypted data by legitimate particles. Application fields include the real-time encryption of digital HDTV signals as well as high speed telecommunication and networking such as ATM. The chip has been fabricated within the INVOMEC/EUROCHIP educational VLSI Design Facilities in MIETEC 2.4 /spl mu/ CMOS technology. Measured samples are operating at encryption/decryption rates of 286 Mb/s and hashing rates of 572 Mb/s. The operation of the chip is demonstrated by a setup showing the real-time encryption and decryption of digitized PAL color composite video signals. The designed cryptographic module can be used as a stand-alone device or embedded as a mega-block in a larger chip. <<ETX>>
Muscle Pain: Sensory Implications and Interaction With Motor Control

Muscle hyperalgesia and referred pain plays an important role in chronic musculoskeletal pain. New knowledge on the involved basic mechanisms and better methods to assess muscle pain in the clinic are needed to revise and optimize the treatment regimes. Increased muscle sensitivity is manifested as (1) pain evoked by a normally non-nociceptive stimulus (allodynia), (2) increased pain intensity evoked by nociceptive stimuli (hyperalgesia), or (3) increased referred pain areas with associated somatosensory changes. Quantitative sensory testing provides the possibility to evaluate these manifestations in a standardized way in patients suffering from musculoskeletal pain or in healthy volunteers. Some manifestations of sensitisation, such as expanded referred muscle pain areas in chronic musculoskeletal pain patients, can be explained from animal experiments showing extrasegmental spread of sensitisation. An important part of the pain manifestations (eg, tenderness and referred pain) related to chronic musculoskeletal disorders may be due to peripheral and central sensitization, which play a role in the transition from acute to chronic pain. In recent years, it has become evident that muscle pain can interfere with motor control strategies and different patters of interaction are seen during rest, static contractions, and dynamic conditions.
Increased creatine kinase MB in the absence of acute myocardial infarction.

Although measurement of CK-MB is a very sensitive, specific, and cost-effective test for use in diagnosis or exclusion of acute myocardial infarction, it should not be used as the sole diagnostic indicator, and all positive values must be critically analyzed to exclude other causes of increased values in serum. This is particularly important when the population being tested consists of patients with multiple medical problems, with low to medium probability of myocardial infarction, and without clinical or other biochemical (i.e., LDH 1) evidence of acute myocardial infarction. When the temporal pattern and absolute CK-MB values are considered together with the patient's clinical status, the diagnostic specificity is dramatically increased. In addition, one must be familiar with the limitations of individual assay systems in order to exclude method-related artifactual values.
Human-Centric Images and Videos Analysis

This article summarizes the corresponding half-day tutorial at ACM Multimedia 2015. This tutorial reviews recent progresses in human-centric images and videos analysis: 1) fashion analysis: parsing, attribute prediction and retrieval; 2) action analysis: discriminative feature selection, pooling and fusion; 3) person verification: cross-domain person verification via learning a generalized similarity measure, and bit-scalable deep hashing with regularized similarity learning.
Full-Malaria/Parasites and Full-Arthropods: databases of full-length cDNAs of parasites and arthropods, update 2009

Full-Malaria/Parasites is a database for transcriptome studies of apicomplexa and other parasites, which is based on our original full-length cDNA sequences and physical cDNA clone resources. In this update, the database has been expanded to contain the shogun sequencing for the entire sequences of 14 818 non-redundant full-length cDNA clones from six apicomplexa parasites and 6.8 million of transcription start sites (TSS), both of which had been produced by novel protocols using the oligo-capping method and the Illumina GA sequencer. The former should be the ultimate data for exact annotation of the expressed genes, while the latter should be useful for ultra-deep expression analysis. Furthermore, we have launched Full-Arthropods, a full-length cDNA database for arthropods of medical importance. Full-Arthropods contains 50 343 one-pass sequences, 10 399 shotgun complete sequences and 22.4 million TSS tags in anopheles mosquitoes that transmit malaria, tsetse flies that transmit trypanosomiasis and dust mites that cause allergic dermatitis and bronchial asthma. By providing the largest integrated full-length cDNA data resources in the apicomplexa parasites as well as their vectors, Full-Malaria/Parasites and Full-Arthropods should help combat parasitic diseases. Full-Malaria/Parasites and Full-Arthropods are accessible from http://fullmal.hgc. jp/.
Construction of protein backbone pieces using segment-based FBCCD and Cryo-EM skeleton

Cryo-Electron Microscopy is a biophysical technique that generates volumetric images of macromolecules. Although it is hard to distinguish the backbone from the density map at medium resolutions such as 5-10Å, the location of major secondary structure traces and the skeleton can be detected from such density maps. We introduce an effective method to construct pieces of backbone conformations for α-helices, β-strands and loops using α-traces, β-traces and skeleton trace that can be detected from a density map. A test of nineteen cases shows that our fragment-based FBCCD method can quickly build a model that aligns well with a spline trace with a small RMSD from the native.
Statistical Analysis of Timing Errors

Human rhythmic activities are variable. Cycle-to-cycle fluctuations form the behavioral observable. Traditional analysis focuses on statistical measures such as mean and variance. In this article we show that, by treating the fluctuations as a time series, one can apply techniques such as power spectra and rescaled range analysis to gain insight into the mechanisms underlying the remarkable abilities of humans to perform a variety of rhythmic movements, from maintaining memorized temporal patterns to anticipating and timing their movements to predictable sensory stimuli.
Conflicts between plants and pollinators that reproduce within inflorescences: evolutionary variations on a theme

The high diversity of mutualisms has probably limited the development of a general theory about their evolution and their stability. Here we review conflicts of interests occurring in the 13 known nursery pollination systems, where pollinators reproduce within the inflorescence they pollinate. We found three main conflicts of interest between mutualists that correspond to the following evolutionary questions: 1) Why do plants not kill their pollinators' larvae? 2) Why do pollinators visit deceptive flowers? and 3) Why do pollinators pollinate? We show that the reproductive system of the plant is strongly correlated not only with the set of conflicts of interests that actually occur but also with the proximal resolution of these conflicts. In many cases the evolutionary stability of nursery pollination mutualisms relies on the avoidance of intra-specific competition among pollinator larvae. This stabilizing factor could perhaps also explain the absence of overexploitation in other mutualisms.
Leadership and Corporate Social Irresponsibility 1 Running Head: Leadership and Corporate Social Irresponsibility Illuminating the Black Box: the Role of Leaders on Organizational Outcomes

While managers and researchers have invested considerable effort into understanding what factors affect corporate social responsibility (CSR), less is known about corporate social irresponsibility (CSiR). Drawing on strategic leadership and moral licensing research, we address this gap by considering the relationship between CSR and CSiR. We predict that prior CSR is positively associated with subsequent CSiR because the moral credits achieved through CSR enables leaders to engage in less ethical stakeholder treatment. Further, we hypothesize that leaders' moral identity will moderate the CSR-CSiR relationship, such that the relationship will be stronger when CEOs are high moral identifiers rather than low moral identifiers. Through an archival study of 49 Fortune 500 firms we find support for our hypotheses.
Camera calibration methods evaluation procedure for images rectification and 3D reconstruction

Camera calibration and images rectification are two necessary steps in most 3D reconstruction methods using image acquisition. This paper proposes an evaluation procedure for camera calibration methods for the case of 3D reconstruction using rectified multi-stereo images. The evaluation is based on the accuracy of the rectification and of the 3D reconstruction which are directly related to the calibration precision. Three methods are thus compared: Faugeras-Toscani, Zhang and a robust calibration algorithm. The procedure can be applied for computer vision systems with an arbitrary number of cameras and for any other calibration method. We show that, although the three methods provide significantly different intrinsic and stereo system parameter estimations, the rectified images of the planar target that we use for evaluation are relatively coherent and lead to close 3D reconstruction errors
Dynamic Regulation of Chloroplast Transcription’

Plastids are ubiquitous DNA-containing organelles present in plant cells. These organelles carry out numerous metabolic functions including photosynthesis, starch synthesis, and steps in lipid, terpenoid, amino acid, tetrapyrrole, and plant hormone biosynthesis. Some of these functions are highly expressed in differentiated plastids. For example, chloroplasts are specialized for photosynthesis, chromoplasts for carotenoid biosynthesis and storage, and amyloplasts for starch biosynthesis. Although basal levels of plastid gene expression are observed in a11 plastid types, a large increase in plastid transcription is observed during chloroplast biogenesis. This suggests that one central regulatory point of chloroplast differentiation is the activation of chloroplast transcription. However, chloroplast development requires coordinated expression of plastid and nuclear genes, and, therefore, activation of plastid gene transcription must be coordinated with the activation of nuclear gene expression by signals that can be transmitted between plastids and the nucleus. The study of chloroplast gene expression also provides an opportunity to understand how plants sense and alter gene expression in response to light. Light is a substrate for photosynthesis, a trigger of plant developmental processes, and a potential source of injury that modulates chloroplast transcription.
Touch-driven interaction via an NFC-enabled smartphone

With the advent of smart home technologies, convenient and intuitive cyber-physical interaction methods are in great need. We demonstrate a touch-driven interaction system with home appliances via an NFC-enabled smartphone. By touching the phone to NFC tagged devices, we can establish connection and exchange information, control devices from phone, and share media between them. We also demonstrate three applications, Touch&Connect, Touch&Listen, and Touch&Watch, to demonstrate touch-driven interaction in a smart home environment.
A probability based approach on ananlyzing dynamics of oscillators on a bidirectional ring with propagation delay

In this paper, we presented a model of pulse-coupled oscillators distributed on a bidirectional ring with propagation delay. In numerical simulations based on this model, we observed phenomena of asynchrony in a certain range of delay factor $\alpha$. To find the cause of these phenomena, we used a new probability based approach of analyzing. In this approach, the mathematical expectation of influence on one oscillator's phase change caused by its neighbor, which is regarded as a random factor, is calculated. By adding this expectation of influence into the firing map $h(\phi)$ introduced by Mirolla and Strogatz, a probability firing map $H$ is invented. By observing the behavior of $H$ 's iteration from $H$ 's graph, we successfully constructed a connection between the asynchrony phenomena and $H$ 's graph.
Loneliness and risk of Alzheimer disease.

CONTEXT Social isolation in old age has been associated with risk of developing dementia, but the risk associated with perceived isolation, or loneliness, is not well understood. OBJECTIVE To test the hypothesis that loneliness is associated with increased risk of Alzheimer disease (AD). DESIGN Longitudinal clinicopathologic cohort study with up to 4 years of annual in-home follow-up. PARTICIPANTS A total of 823 older persons free of dementia at enrollment were recruited from senior citizen facilities in and around Chicago, Ill. Loneliness was assessed with a 5-item scale at baseline (mean +/- SD, 2.3 +/- 0.6) and annually thereafter. At death, a uniform postmortem examination of the brain was conducted to quantify AD pathology in multiple brain regions and the presence of cerebral infarctions. MAIN OUTCOME MEASURES Clinical diagnosis of AD and change in previously established composite measures of global cognition and specific cognitive functions. RESULTS During follow-up, 76 subjects developed clinical AD. Risk of AD was more than doubled in lonely persons (score 3.2, 90th percentile) compared with persons who were not lonely (score 1.4, 10th percentile), and controlling for indicators of social isolation did not affect the finding. Loneliness was associated with lower level of cognition at baseline and with more rapid cognitive decline during follow-up. There was no significant change in loneliness, and mean degree of loneliness during the study was robustly associated with cognitive decline and development of AD. In 90 participants who died and in whom autopsy of the brain was performed, loneliness was unrelated to summary measures of AD pathology or to cerebral infarction. CONCLUSION Loneliness is associated with an increased risk of late-life dementia but not with its leading causes.
Análisis ecoturístico de la actividad de snorkelling en Majayura (Cartagena, Colombia)

Los arrecifes de coral en las áreas marinas protegidas son un importante atractivo turístico cuyo sobreúso para fines turísticos puede generar cambios en su estructura. El propósito de esta investigación es describir la actividad de snorkelling en un sendero del Parque Nacional Natural Corales del Rosario y San Bernardo (Colombia) durante un período de alta afluencia turística y evidenciar oportunidades de manejo. Se evalúan cambios en la cobertura bentónica en dos transectos con y sin snorkelling y se realiza una descripción de las prácticas en uso de los guías por medio de observaciones participantes y entrevistas. No hubo cambios temporales en la cobertura de los componentes bénticos, pero sí hubo diferencias entre el sendero sin y con turismo. Se registró mayor número de contactos al sustrato por parte de los turistas al inicio de la actividad. A partir de la descripción de la actividad, se presentan recomendaciones para mejorar sus condiciones, tanto para el ecosistema como para los usuarios.
Divergence hitchhiking and the spread of genomic isolation during ecological speciation-with-gene-flow

In allopatric populations, geographical separation simultaneously isolates the entire genome, allowing genetic divergence to accumulate virtually anywhere in the genome. In sympatric populations, however, the strong divergent selection required to overcome migration produces a genetic mosaic of divergent and non-divergent genomic regions. In some recent genome scans, each divergent genomic region has been interpreted as an independent incidence of migration/selection balance, such that the reduction of gene exchange is restricted to a few kilobases around each divergently selected gene. I propose an alternative mechanism, ‘divergence hitchhiking’ (DH), in which divergent selection can reduce gene exchange for several megabases around a gene under strong divergent selection. Not all genes/markers within a DH region are divergently selected, yet the entire region is protected to some degree from gene exchange, permitting genetic divergence from mechanisms other than divergent selection to accumulate secondarily. After contrasting DH and multilocus migration/selection balance (MM/SB), I outline a model in which genomic isolation at a given genomic location is jointly determined by DH and genome-wide effects of the progressive reduction in realized migration, then illustrate DH using data from several pairs of incipient species in the wild.
A generic method to increase the prediction accuracy of visual quality metrics

A new simple, effective and generic method is presented that allows to increase the prediction accuracy of visual quality metrics. This method is based on the observation, that the correlation between subjective results and objective metrics is very high for one special sequence or image coded at several bit rates with the same codec. This can be used to decrease the absolute error between the predicted visual quality and the actual visual quality and therefore increase the overall correlation between prediction results and results from subjective tests. Using the described method PSNR is extended to PSNR. Comparing this new metric PSNR to two popular image quality metrics shows that the prediction accuracy can be increased significantly.
Population synthesis of gamma-ray bursts with precursor activity and the spinar paradigm

We study statistical properties of long gamma-ray bursts (GRBs) produced by the collapsing cores of WR stars in binary systems. Fast rotation of the cores enables a two-stage collapse scenario, implying the formation of a spinar-like object. A burst produced by such a collapse consists of two pulses, whose energy budget is enough to explain observed GRBs. We calculate models of spinar evolution using results from a population synthesis of binary systems (done by the ‘Scenario Machine’) as initial parameters for the rotating massive cores. Among the resulting bursts, events with a weaker first peak, namely precursor, are identified, and the precursor-to-main-pulse time separations fully agree with the range of the observed values. The calculated fraction of long GRBs with precursor (about 10 per cent of the total number of long GRBs) and the durations of the main pulses are also consistent with observations. Precursors with lead times greater by up to one order of magnitude than those observed so far are expected to be about a factor of 2 less numerous. Independently of the GRB model assumed, we predict the existence of precursors that arrive up to ≳103 s in advance of the main events of GRBs.
One-pion transitions between heavy baryons in the constituent quark model

Single pion transitions of S wave to S wave, P wave to S wave and P wave to P wave heavy baryons are analyzed in the framework of the Heavy Quark Symmetry limit (HQS). We use a constituent quark model picture for the light diquark system with an underlying SU(2N_{f}) X O(3) symmetry to reduce the number of the HQS coupling factors required to describe these transitions. We also use the quantum theory of angular momentum to rewrite the one-pion transitions constituent quark model results in a more general form using the 6j- and 9j-symbols. We finally estimate the decay rates of some single pion transitions between charm baryon states.