Miracle-dz/UniFAR-FTUs huggingface dataset:
Generalized Centroid Estimators in Bioinformatics

In a number of estimation problems in bioinformatics, accuracy measures of the target problem are usually given, and it is important to design estimators that are suitable to those accuracy measures. However, there is often a discrepancy between an employed estimator and a given accuracy measure of the problem. In this study, we introduce a general class of efficient estimators for estimation problems on high-dimensional binary spaces, which represent many fundamental problems in bioinformatics. Theoretical analysis reveals that the proposed estimators generally fit with commonly-used accuracy measures (e.g. sensitivity, PPV, MCC and F-score) as well as it can be computed efficiently in many cases, and cover a wide range of problems in bioinformatics from the viewpoint of the principle of maximum expected accuracy (MEA). It is also shown that some important algorithms in bioinformatics can be interpreted in a unified manner. Not only the concept presented in this paper gives a useful framework to design MEA-based estimators but also it is highly extendable and sheds new light on many problems in bioinformatics.
Fast and Slow Voltage Sensor Movements in HERG Potassium Channels

HERG encodes an inwardly-rectifying potassium channel that plays an important role in repolarization of the cardiac action potential. Inward rectification of HERG channels results from rapid and voltage-dependent inactivation gating, combined with very slow activation gating. We asked whether the voltage sensor is implicated in the unusual properties of HERG gating: does the voltage sensor move slowly to account for slow activation and deactivation, or could the voltage sensor move rapidly to account for the rapid kinetics and intrinsic voltage dependence of inactivation? To probe voltage sensor movement, we used a fluorescence technique to examine conformational changes near the positively charged S4 region. Fluorescent probes attached to three different residues on the NH2-terminal end of the S4 region (E518C, E519C, and L520C) reported both fast and slow voltage-dependent changes in fluorescence. The slow changes in fluorescence correlated strongly with activation gating, suggesting that the slow activation gating of HERG results from slow voltage sensor movement. The fast changes in fluorescence showed voltage dependence and kinetics similar to inactivation gating, though these fluorescence signals were not affected by external tetraethylammonium blockade or mutations that alter inactivation. A working model with two types of voltage sensor movement is proposed as a framework for understanding HERG channel gating and the fluorescence signals.
Multiscale AM-FM decompositions with GPU acceleration for diabetic retinopathy screening

A Computer Aided Diagnosis system based on multiscale amplitude-modulation frequency-modulation (AM-FM) methods has been recently developed for discriminating between normal and pathological retinal images. The original Matlab implementation of this system required large amounts of computational time and memory resources that would not permit real-time patient consultation. In this manuscript, we present a new implementation of the multiscale AM-FM decomposition, converted from MATLAB code into C/CUDA (Compute Unified Device Architecture) code, in order to take advantage of the graphics processing units (GPU) to significantly reduce the running time and memory resources.
A mixing board interface for graphics and visualization applications

We use a haptically enhanced mixing board with a video projector as an interface to various data visualization tasks. We report results of an expert review with four participants, qualitatively evaluating the board for three different applications: dynamic queries (abstract task), parallel coordinates interface (multi-dimensional combinatorial search), and ExoVis (3D spatial navigation). Our investigation sought to determine the strengths of this physical input given its capability to facilitate bimanual interaction, constraint maintenance, tight coupling of input and output, and other features. Participants generally had little difficulty with the mappings of parameters to sliders. The graspable sliders apparently reduced the mental exertion needed to acquire control, allowing participants to attend more directly to understanding the visualization. Participants often designated specific roles for each hand, but only rarely moved both hands simultaneously.
A Statistical Framework for Testing Modularity in Multidimensional Data

Abstract Modular variation of multivariate traits results from modular distribution of effects of genetic and epigenetic interactions among those traits. However, statistical methods rarely detect truly modular patterns, possibly because the processes that generate intramodular associations may overlap spatially. Methodologically, this overlap may cause multiple patterns of modularity to be equally consistent with observed covariances. To deal with this indeterminacy, the present study outlines a framework for testing a priori hypotheses of modularity in which putative modules are mathematically represented as multidimensional subspaces embedded in the data. Model expectations are computed by subdividing the data into arrays of variables, and intermodular interactions are represented by overlapping arrays. Covariance structures are thus modeled as the outcome of complex and nonorthogonal intermodular interactions. This approach is demonstrated by analyzing mandibular modularity in nine rodent species. A total of 620 models are fit to each species, and the most strongly supported are heuristically modified to improve their fit. Five modules common to all species are identified, which approximately map to the developmental modules of the mandible. Within species, these modules are embedded within larger “super-modules,” suggesting that these conserved modules act as building blocks from which covariation patterns are built.
Genomic Loads and Genotypes of Respiratory Syncytial Virus: Viral Factors during Lower Respiratory Tract Infection in Chilean Hospitalized Infants

The clinical impact of viral factors (types and viral loads) during respiratory syncytial virus (RSV) infection is still controversial, especially regarding newly described genotypes. In this study, infants with RSV bronchiolitis were recruited to describe the association of these viral factors with severity of infection. RSV antigenic types, genotypes, and viral loads were determined from hospitalized patients at Hospital Roberto del Río, Santiago, Chile. Cases were characterized by demographic and clinical information, including days of lower respiratory symptoms and severity. A total of 86 patients were included: 49 moderate and 37 severe cases. During 2013, RSV-A was dominant (86%). RSV-B predominated in 2014 (92%). Phylogenetic analyses revealed circulation of GA2, Buenos Aires (BA), and Ontario (ON) genotypes. No association was observed between severity of infection and RSV group (p = 0.69) or genotype (p = 0.87). After a clinical categorization of duration of illness, higher RSV genomic loads were detected in infants evaluated earlier in their disease (p < 0.001) and also in infants evaluated later, but coursing a more severe infection (p = 0.04). Although types and genotypes did not associate with severity in our children, higher RSV genomic loads and delayed viral clearance in severe patients define a group that might benefit from new antiviral therapies.
Strength properties of concrete at elevated temperatures

A study is presented concerning the compressive strength, modulus of elasticity, and stress-strain relationships of concrete at elevated temperatures. A review of published results provides information for the development of upper and lower bound relationships for compressive strength and the modulus of elasticity and establishes exposure conditions for a lower bound thermal response. The relationships developed from the literature review are confirmed by the results of a verification test program. The strength and elasticity relationships provide a basis for the development of design stress-strain curves for concrete exposed to elevated temperatures.
Strain-induced crystallization behavior of phenolic resin crosslinked natural rubber/clay nanocomposites

Nanocomposites of natural rubber (NR) and unmodified clay were prepared by latex compounding method. Phenolic resin (PhOH) was used to crosslink NR. Crosslinked neat NR was also prepared for comparison. The structure–property relationship of uncrosslinked and crosslinked NR/clay nanocomposites was examined to verify the reinforcement mechanism. Microstructure of NR/clay nanocomposites was studied by using transmission electron microscopic (TEM), X-ray diffraction (XRD), wide angle X-ray diffraction (WAXD), and small angle X-ray scattering (SAXS) analyses. The results showed the evidence of intercalated clay together with clay tactoids for the nanocomposite samples. The highest tensile strength was achieved for the crosslinked NR/clay nanocomposite. The onset strain of deformation induced the crystallization of NR for nanocomposites was found at almost the same strain, and furthermore their crystallization was developed at lower strain than that of the crosslinked neat NR because of the clay orientation and alignment. However, at high strain region, the collaborative crystallization process related to the clay dispersion and conventional crosslink points in the NR was responsible to considerably high tensile strength of the crosslinked NR/clay nanocomposite. Based on these analyses, a mechanistic model for the strain-induced crystallization and orientational evolution of a network structure of PhOH-crosslinked NR/clay nanocomposite was proposed. © 2015 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015, 132, 42580.
Optical and Mechanical Anisotropy in Crystalline Polymers

Expressions have been derived for the optical birefringence and elastic moduli of an idealized semicrystalline polymer in terms of the molecular orientation. The predicted birefringence and moduli show qualitative agreement with previous experimental data for polyethylene at low extension ratios. A result of particular interest is that this treatment predicts the observed minimum in the Young's modulus with increasing orientation.
The long noncoding RNA Gm15055 represses Hoxa gene expression by recruiting PRC2 to the gene cluster

The Hox genes encode transcription factors that determine embryonic pattern formation. In embryonic stem cells, the Hox genes are silenced by PRC2. Recent studies have reported a role for long noncoding RNAs in PRC2 recruitment in vertebrates. However, little is known about how PRC2 is recruited to the Hox genes in ESCs. Here, we used stable knockdown and knockout strategies to characterize the function of the long noncoding RNA Gm15055 in the regulation of Hoxa genes in mouse ESCs. We found that Gm15055 is highly expressed in mESCs and its expression is maintained by OCT4. Gm15055 represses Hoxa gene expression by recruiting PRC2 to the cluster and maintaining the H3K27me3 modification on Hoxa promoters. A chromosome conformation capture assay revealed the close physical association of the Gm15055 locus to multiple sites at the Hoxa gene cluster in mESCs, which may facilitate the in cis targeting of Gm15055 RNA to the Hoxa genes. Furthermore, an OCT4-responsive positive cis-regulatory element is found in the Gm15055 gene locus, which potentially regulates both Gm15055 itself and the Hoxa gene activation. This study suggests how PRC2 is recruited to the Hoxa locus in mESCs, and implies an elaborate mechanism for Hoxa gene regulation in mESCs.
MS characterization of multiple forms of alpha‐amylase in human saliva

Alpha‐amylase is a major and well‐characterized component of human saliva. Recent proteomic studies suggested that this protein could be observed in more than twenty spots on 2‐D gels of salivary proteins. The aim of this work was to investigate this unexpected redundancy. 2‐D gel electrophoresis was combined with systematic MALDI‐TOF MS analysis. More than 140 protein spots identifying the alpha‐amylase were shown to constitute a stable but very complex pattern. Careful analysis of mass spectra and simultaneous hierarchical clustering of the observed peptides and of the electrophoretic features of spots allowed one to define three major groups. A main class grouping 90 spots was shown to correspond to full length alpha‐amylases that can be assumed to include isoforms and post‐translationally modified forms, a subset of this class being demonstrated to be N‐glycosylated. A second group included short alpha‐amylases that are differently truncated in a non‐random manner, very likely in the oral cavity. The last class grouped alpha‐amylase forms showing both the N‐ and C‐terminal sequences of the enzyme but displaying a molecular weight that was up to 50% lower than that of the native protein. It is speculated that the last group of alpha‐amylase spots could correspond to proteins submitted to internal deletions prior to the secretion.
Direct Visualization of the Movement of the Monomeric Axonal Transport Motor UNC-104 along Neuronal Processes in LivingCaenorhabditis elegans

The formation and function of axons depends on the microtubule-based transport of cellular components from their sites of synthesis in the neuronal cell body to their sites of utilization at the axon terminus. To directly visualize this axonal transport in a living organism, we constructed transgenic lines ofCaenorhabditis elegans that express green fluorescent protein fused to the monomeric synaptic vesicle transport motor, UNC-104. This UNC-104:: GFP construct rescued the Unc-104 mutant phenotype and was expressed throughout the nervous system. Using time-lapse confocal fluorescence microscopy, we were able to visualize fluorescent motor proteins moving in both directions along neuronal processes, some of which were identified definitely as axons and others as dendrites. Using kymograph analysis, we followed the movement of >900 particles. Most of them moved in one direction, but not necessarily at the same velocity. Ten percent of the observed particles reversed direction of movement during the period of observation, and 10% exhibited periods of movement interspersed with pauses. During episodes of persistent movement, particles moved at an average velocity of 1.02 μm/sec, which is close to the in vitrovelocity of microtubule gliding driven by purified monomeric kinesin at high motor density. To our knowledge, this is the first direct visualization and analysis of the movement of specifically labeled microtubule motor proteins along axons in vivo.
An Obstacle to a Decomposition Theorem for Near-Regular Matroids

Seymour's decomposition theorem [J. Combin. Theory Ser. B, 28 (1980), pp. 305-359] for regular matroids states that any matroid representable over both $\mathrm{GF}(2)$ and $\mathrm{GF}(3)$ can be obtained from matroids that are graphic, cographic, or isomorphic to $R_{10}$ by 1-, 2-, and 3-sums. It is hoped that similar characterizations hold for other classes of matroids, notably for the class of near-regular matroids. Suppose that all near-regular matroids can be obtained from matroids that belong to a few basic classes through $k$-sums. Also suppose that these basic classes are such that, whenever a class contains all graphic matroids, it does not contain all cographic matroids. We show that, in that case, 3-sums will not suffice.
Evaluability Assessment

Using a local cross-cultural health service program as a framework, the authors describe the process of an evaluability assessment (EA) and illustrate how it can be a catalyst for program change. An EA is a process that improves evaluation. The key product was a logic model, which traces the links between objectives, activities, and outcomes. Four key insights emerged. First, the distinction of who was included and excluded in the target population, originally ambiguous, was clearly defined. Second, through the development of the logic model, staff members were able to analyze their goals and assumptions and critically explore possible gaps between expected outcomes and activities. Third, the EA enabled reflection on and clarification of both process and outcome measures. Finally, global goals were pared down to better match the project capacity. Developing an evaluability assessment was a cost-effective way to collaborate with staff to develop a clearer, more evaluable project.
Antibiotic Resistance in Sepsis Patients: Evaluation and Recommendation of Antibiotic Use

Background: The appropriate selection of empirical antibiotics based on the pattern of local antibiotic resistance can reduce the mortality rate and increase the rational use of antibiotics. Aims: We analyze the pattern of antibiotic use and the sensitivity patterns of antibiotics to support the rational use of antibiotics in patients with sepsis. Materials and Methods: A retrospective observational study was conducted in adult sepsis patient at one of Indonesian hospital during January-December 2011. Data were collected from the hospital medical record department. Descriptive analysis was used in the processing and interpretation of data. Results: A total of 76 patients were included as research subjects. Lung infection was the highest source of infection. In the 66.3% of clinical specimens that were culture positive for microbes, Klebsiella pneumoniae, Escherichia coli, Staphylococcus hominis were detected with the highest frequency. The six most frequently used antibiotics, levofloxacin, ceftazidime, ciprofloxacin, cefotaxime, ceftriaxone, and erythromycin, showed an average resistance above 50%. Conclusions: The high use of antibiotic with a high level resistance requires a policy to support its rational use. Local microbial pattern based on site infection and pattern of antibiotics sensitivity test can be used as supporting data to optimize appropriateness of empirical antibiotics therapy in sepsis patients.
Short-Term Visual Deprivation Does Not Enhance Passive Tactile Spatial Acuity

An important unresolved question in sensory neuroscience is whether, and if so with what time course, tactile perception is enhanced by visual deprivation. In three experiments involving 158 normally sighted human participants, we assessed whether tactile spatial acuity improves with short-term visual deprivation over periods ranging from under 10 to over 110 minutes. We used an automated, precisely controlled two-interval forced-choice grating orientation task to assess each participant's ability to discern the orientation of square-wave gratings pressed against the stationary index finger pad of the dominant hand. A two-down one-up staircase (Experiment 1) or a Bayesian adaptive procedure (Experiments 2 and 3) was used to determine the groove width of the grating whose orientation each participant could reliably discriminate. The experiments consistently showed that tactile grating orientation discrimination does not improve with short-term visual deprivation. In fact, we found that tactile performance degraded slightly but significantly upon a brief period of visual deprivation (Experiment 1) and did not improve over periods of up to 110 minutes of deprivation (Experiments 2 and 3). The results additionally showed that grating orientation discrimination tends to improve upon repeated testing, and confirmed that women significantly outperform men on the grating orientation task. We conclude that, contrary to two recent reports but consistent with an earlier literature, passive tactile spatial acuity is not enhanced by short-term visual deprivation. Our findings have important theoretical and practical implications. On the theoretical side, the findings set limits on the time course over which neural mechanisms such as crossmodal plasticity may operate to drive sensory changes; on the practical side, the findings suggest that researchers who compare tactile acuity of blind and sighted participants should not blindfold the sighted participants.
Prevalence of Psychiatric Symptoms in ALL Patients during Maintenance Therapy

Background Cancer diagnosis may cause deep emotional and affective problems in patients and their families. Nowadays, however, despite its rising prevalence, cancer is no longer synonymous with death. Given the significance of emotional well-being in cancer patients, we decided to assess the frequency of psychological problems in seven to seventeen year-olds with acute lymphoblastic leukemia. Materials and Methods Our sample included 42 children and adolescents with ALL referred to pediatric hematology department of Dr. Sheikh hospital, who were put under maintenance course of the treatment. Psychiatric disorders such as anxiety, depression and behavioral disturbances were examined by using RCMAS, CDI and SDQ questionnaires respectively. Results The entire population showed depressive symptoms.59. 5% of patients (25 person) suffered from anxiety and 26.2% (11 person) had behavioral problems. No significant relation was found between depressive symptoms, and age (p=0.77), sex (p=0.97), length of disease (p=0.50), and type of treatment (p=0.064). Anxiety did not show any significant relation with age (p= 0.63), sex (p= 0.32), length of disease (p= 0.16) and treatment type (p= 0.064). Similarly behavioral disturbances did not indicate any suggestive relation with age (p= 0.20), sex (p= 0.56), length of disease (p= 0.81) and type of treatment (p= 0.19). Conclusion Our findings suggest a high prevalence of psychiatric disorders in children and adolescents with ALL. It is strongly recommended, therefore, that besides somatic symptoms, careful attention be paid to psychological disorders. This can prevent rapid development of the disease reduce treatment costs, and improve the quality of life for both patients and their families.
HEATR2 Plays a Conserved Role in Assembly of the Ciliary Motile Apparatus

Cilia are highly conserved microtubule-based structures that perform a variety of sensory and motility functions during development and adult homeostasis. In humans, defects specifically affecting motile cilia lead to chronic airway infections, infertility and laterality defects in the genetically heterogeneous disorder Primary Ciliary Dyskinesia (PCD). Using the comparatively simple Drosophila system, in which mechanosensory neurons possess modified motile cilia, we employed a recently elucidated cilia transcriptional RFX-FOX code to identify novel PCD candidate genes. Here, we report characterization of CG31320/HEATR2, which plays a conserved critical role in forming the axonemal dynein arms required for ciliary motility in both flies and humans. Inner and outer arm dyneins are absent from axonemes of CG31320 mutant flies and from PCD individuals with a novel splice-acceptor HEATR2 mutation. Functional conservation of closely arranged RFX-FOX binding sites upstream of HEATR2 orthologues may drive higher cytoplasmic expression of HEATR2 during early motile ciliogenesis. Immunoprecipitation reveals HEATR2 interacts with DNAI2, but not HSP70 or HSP90, distinguishing it from the client/chaperone functions described for other cytoplasmic proteins required for dynein arm assembly such as DNAAF1-4. These data implicate CG31320/HEATR2 in a growing intracellular pre-assembly and transport network that is necessary to deliver functional dynein machinery to the ciliary compartment for integration into the motile axoneme.