Miracle-dz/UniFAR-FTUs huggingface dataset:
Association between HLA-DQ genotypes and haplotypes vs Helicobacter pylori infection in an Indonesian population.

BACKGROUND Helicobacter pylori is an important gastrointestinal pathogen related to the development of not only atrophic gastritis and peptic ulcer, but also gastric cancer. Human leukocyte antigens (HLA) may play particular roles in host immune responses to bacterial antigens. This study aimed to investigate the association between HLA-DQA1 and DQB1 genotypes and haplotypes vs H. pylori infection in an Indonesian population. METHODS We selected 294 healthy participants in Mataram, Lombok Island, Indonesia. H. pylori infection was determined by urea breath test (UBT). We analyzed HLA-DQA1 and DQB1 genotypes by PCR-RFLP and constructed haplotypes of HLA-DQA1 and DQB1 genes. Multiple comparisons were conducted according to the Bonferroni method. RESULTS The H. pylori infection rate was 11.2% in this Indonesian population. The DQB1*0401 genotype was noted to be associated with a high risk of H. pylori infection, compared with the DQB1*0301 genotype. None of the HLA-DQA1 or DQB1 haplotypes were related to the risk of H. pylori infection. CONCLUSIONS The study suggests that HLADQB1 genes play important roles in H. pylori infection, but there was no statistically significant association between HLA-DQA1 or DQB1 haplotypes and H.pylori infection in our Lombok Indonesian population.
Early Childhood Diarrhea Predicts Impaired School Performance

Objective: Diarrhea is a leading cause of mortality worldwide; however, its long-term morbidity is poorly understood. Recently, early childhood diarrhea (ECD) has been associated with impaired physical fitness, growth and cognitive function 6 to 9 years later. We studied the effects of ECD on school functioning in a shantytown in northeastern Brazil. Design: We administered 77 educational surveys. Complete diarrhea surveillance (ie, >90%) in the first 2 years of life and demographic and anthropometric information were available for 73 children. Age at starting school was calculated for 62 children, whereas age appropriateness for the current grade (AFG) was calculated for all 73 children who were >6 years old. Stepwise regression was used to examine the independent effect of ECD on school functioning after controlling for socioeconomic factors, maternal education, breast feeding, growth and cognitive functioning. Results: ECD correlated with age at starting school (r = 0.55, P = 0.0005) and remained a significant predictor even after controlling for family demographics, days of breast feeding, early growth and TONI-3 test of nonverbal intelligence. This was true despite significant correlations of ECD with growth shortfalls and impaired cognitive functioning. ECD also correlated with AFG (r = 0.38, P = 0.001). Only TONI-3 test scores explained this association, suggesting that ECD may hinder school performance, but only in part school readiness, by impairing cognitive function as measured by performance on the TONI-3 nonverbal intelligence test. Conclusions: These findings document effects of early childhood diarrhea on later school readiness and performance and hence potential long-term human and economic costs of ECD, which warrant further attention and far greater investment for the control of ECD and its consequences.
A Bayesian Model for Unsupervised Semantic Parsing

We propose a non-parametric Bayesian model for unsupervised semantic parsing. Following Poon and Domingos (2009), we consider a semantic parsing setting where the goal is to (1) decompose the syntactic dependency tree of a sentence into fragments, (2) assign each of these fragments to a cluster of semantically equivalent syntactic structures, and (3) predict predicate-argument relations between the fragments. We use hierarchical Pitman-Yor processes to model statistical dependencies between meaning representations of predicates and those of their arguments, as well as the clusters of their syntactic realizations. We develop a modification of the Metropolis-Hastings split-merge sampler, resulting in an efficient inference algorithm for the model. The method is experimentally evaluated by using the induced semantic representation for the question answering task in the biomedical domain.
Voice quality and loudness in affect perception

Different voice qualities tend to vary in terms of their intrinsic loudness. Perceptual experiments have shown that voice quality variation can be strongly associated with the affective colouring of an utterance. The question addressed in this paper concerns the role that the intrinsic loudness variation might play in this voice quality-to-affect mapping. To test the hypothesis that the intrinsic loudness variation is not a major determinant of the perceived affective colouring, listeners rated the affective colouring of two series of stimuli: one series varied in voice quality and contained intrinsic loudness variation; the other series were of a constant voice quality, but matched loudness variations of the first series. The results overall support the hypothesis that loudness contributes relatively little to the perceived affective colouring of specific voice qualities. But variation in loudness (in the absence of voice quality variation) is not entirely irrelevant: some contribution of loudness to certain high activation affects was also found.
Multi2Sim: A simulation framework for CPU-GPU computing

Accurate simulation is essential for the proper design and evaluation of any computing platform. Upon the current move toward the CPU-GPU heterogeneous computing era, researchers need a simulation framework that can model both kinds of computing devices and their interaction. In this paper, we present Multi2Sim, an open-source, modular, and fully configurable toolset that enables ISA-level simulation of an ×86 CPU and an AMD Evergreen GPU. Focusing on a model of the AMD Radeon 5870 GPU, we address program emulation correctness, as well as architectural simulation accuracy, using AMD's OpenCL benchmark suite. Simulation capabilities are demonstrated with a preliminary architectural exploration study, and workload characterization examples. The project source code, benchmark packages, and a detailed user's guide are publicly available at www.multi2sim. org.
Intermediary role of macrophages in the passage of suppressor signals between T-cell subsets

We have examined the ability of macrophages (Mphi) to transmit T-cell derived suppressor signals to other T cells. The suppressor signal studied is an antigen-specific factor which suppresses the ability of adoptively transferred, sensitized lymphocytes to express contact hypersensitivity in normal recipients. We have found that this factor binds to peritoneal exudate Mphi via cell surface structures which can be blocked with heat-aggregated gamma globulin. Dead (HK) Mphi bind the factor but fail to present it in a functional way to assay (immune) T cells, whereas live (L) Mphi perform both functions. Further, L Mphi can retrieve the factor in an active form from the surfaces of HK Mphi. Based on these and other findings (1-5), we discuss the possibility that Mphi may play as important a role in presenting T-cell communication signals to the cells of the immune system as they do in presenting antigen.
A computerized procedure for long‐life fatigue assessment under complex multiaxial loading

A computerized procedure is presented and evaluated for application examples of long-life fatigue analyses of metallic materials under complex multiaxial loading. The method is based on the stress invariants and uses the minimum circumscribed ellipse approach for evaluating the effective shear stress amplitude under complex multiaxial loading. The applicability of the procedure for handling non-proportional loading is examined through typical examples such as combined normal/shear stresses and combined bi-axial normal stresses with complex stress time histories. The effects of phase shift angles, frequency ratios and waveforms on fatigue endurance were re-analysed and compared with available experimental results from the literature. The comparison shows that the presented procedure based on stress invariants is a potential conservative engineering approach, very suitable for fast fatigue evaluation in the integrated computer aided fatigue design.
Virtual Sensory Feedback for Gait Improvement in Neurological Patients

We review a treatment modality for movement disorders by sensory feedback. The natural closed-loop sensory-motor feedback system is imitated by a wearable virtual reality apparatus, employing body-mounted inertial sensors and responding dynamically to the patient’s own motion. Clinical trials have shown a significant gait improvement in patients with Parkinson’s disease using the apparatus. In contrast to open-loop devices, which impose constant-velocity visual cues in a “treadmill” fashion, or rhythmic auditory cues in a “metronome” fashion, requiring constant vigilance and attention strategies, and, in some cases, instigating freezing in Parkinson’s patients, the closed-loop device improved gait parameters and eliminated freezing in most patients, without side effects. Patients with multiple sclerosis, previous stroke, senile gait, and cerebral palsy using the device also improved their balance and gait substantially. Training with the device has produced a residual improvement, suggesting virtual sensory feedback for the treatment of neurological movement disorders.
Bevacizumab in Recurrent Glioma: Patterns of Treatment Failure and Implications

Glioblastoma, the most common primary malignant brain tumor in adults, is highly aggressive and associated with a poor prognosis. Bevacizumab, a monoclonal antibody against the vascular endothelial growth factor receptor, has increasingly been used in the treatment of recurrent glioblastoma. It has achieved excellent rates of radiographic response, but most patients will progress after only a few months. Upon recurrence, tumors may not enhance, secondary to vascular normalization. We describe four patterns of radiographic progression commonly associated with Bevacizumab failure: 1) Distant enhancing tumor, 2) Local tumor progression without enhancement, 3) Diffuse gliomatosis-like infiltration, and 4) Local or multifocal progression, with enhancement. Some have noted an increased incidence of distant or diffuse disease upon recurrence, suggestive of a transition to a more aggressive phenotype, but a review of the literature suggests there is no conclusive evidence that Bevacizumab treatment is associated with an increased rate of distant or diffuse recurrence.
GTPase Crosstalk by Abr

Emily M. Vaughan,1,2,* Ann L. Miller,2 Hoi-Ying E. Yu,1,3 and William M. Bement1,2,4 1Program in Cellular and Molecular Biology 2Department of Zoology University of Wisconsin-Madison, 1117 West Johnson Street, Madison WI 53706, USA 3Geisinger Medical Laboratories, 100 North Academy Avenue, Danville, PA 17822-0131, USA 4Laboratory of Cell and Molecular Biology, University of Wisconsin-Madison, 1525 Linden Drive, Madison WI 53706, USA
Real‐Time Depth‐of‐Field Rendering Using Point Splatting on Per‐Pixel Layers

We present a real‐time method for rendering a depth‐of‐field effect based on the per‐pixel layered splatting where source pixels are scattered on one of the three layers of a destination pixel. In addition, the missing information behind foreground objects is filled with an additional image of the areas occluded by nearer objects. The method creates high‐quality depth‐of‐field results even in the presence of partial occlusion, without major artifacts often present in the previous real‐time methods. The method can also be applied to simulating defocused highlights. The entire framework is accelerated by GPU, enabling real‐time post‐processing for both off‐line and interactive applications.
Thermal diffusivity and conductivity of crystalline polymers

The thermal diffusivity and conductivity of the isotropic and drawn samples of five semicrystalline polymers—nylon 6, poly(ethylene terephthalate), poly(butylene terephthalate), polybutene-1, and poly(4-methylpentene-1)—were measured by the flash method over the temperature range 100–350 K. The temperature dependence of the thermal diffusivity was found to follow a simple phenomenological pattern, while a more detailed understanding of the temperature dependence and the effect of orientation on thermal conductivity was obtained by using the modified Maxwell model.
2013 7th International Conference on Pervasive Computing Technologies for Healthcare and Workshops Pvt -touch: Adapting a Reaction Time Test for Touchscreen Devices

The Psychomotor Vigilance Task (PVT) is a vali­ dated reaction time (RT) test used to assess aspects of sleep loss including alertness and sleepiness. PVT typically requires a phys­ ical button to assess RT, which minimizes the effect of execution time (the time taken to perform a gesture) on RT. When translat­ ing this application to mobile devices, a touchscreen version is useful for widespread in situ sleepiness assessments to produce more ecologically valid data. We describe the Android-based implementation of a touchscreen version of PVT, called PVT ­ Touch. In an evaluation (N=20), we compared four different touchscreen input techniques to a physical button: touch down, finger lift,finger tilt, and goal crossing. We found that touch down was comparable to the physical button approach used in tradi­ tional PVT in execution time and in several measures associated with sleepiness, and was preferred by most participants. We also found that finger lift may be a more precise but less intuitive measure, which may warrant further study.
Cooperative Localization in WSNs Using Gaussian Mixture Modeling: Distributed ECM Algorithms

We study cooperative sensor network localization in a realistic scenario where the underlying measurement errors more probably follow a non-Gaussian distribution; the measurement error distribution is unknown without conducting massive offline calibrations; and non-line-of-sight identification is not performed due to the complexity constraint and/or storage limitation. The underlying measurement error distribution is approximated parametrically by a Gaussian mixture with finite number of components, and the expectation-conditional maximization (ECM) criterion is adopted to approximate the maximum-likelihood estimator of the unknown sensor positions and an extra set of Gaussian mixture model parameters. The resulting centralized ECM algorithms lead to easier inference tasks and meanwhile retain several convergence properties with a proof of the “space filling” condition. To meet the scalability requirement, we further develop two distributed ECM algorithms where an average consensus algorithm plays an important role for updating the Gaussian mixture model parameters locally. The proposed algorithms are analyzed systematically in terms of computational complexity and communication overhead. Various computer based tests are also conducted with both simulation and experimental data. The results pin down that the proposed distributed algorithms can provide overall good performance for the assumed scenario even under model mismatch, while the existing competing algorithms either cannot work without the prior knowledge of the measurement error statistics or merely provide degraded localization performance when the measurement error is clearly non-Gaussian.
Human Artificial Chromosome with a Conditional Centromere for Gene Delivery and Gene Expression

Human artificial chromosomes (HACs), which carry a fully functional centromere and are maintained as a single-copy episome, are not associated with random mutagenesis and offer greater control over expression of ectopic genes on the HAC. Recently, we generated a HAC with a conditional centromere, which includes the tetracycline operator (tet-O) sequence embedded in the alphoid DNA array. This conditional centromere can be inactivated, loss of the alphoidtet-O (tet-O HAC) by expression of tet-repressor fusion proteins. In this report, we describe adaptation of the tet-O HAC vector for gene delivery and gene expression in human cells. A loxP cassette was inserted into the tet-O HAC by homologous recombination in chicken DT40 cells following a microcell-mediated chromosome transfer (MMCT). The tet-O HAC with the loxP cassette was then transferred into Chinese hamster ovary cells, and EGFP transgene was efficiently and accurately incorporated into the tet-O HAC vector. The EGFP transgene was stably expressed in human cells after transfer via MMCT. Because the transgenes inserted on the tet-O HAC can be eliminated from cells by HAC loss due to centromere inactivation, this HAC vector system provides important novel features and has potential applications for gene expression studies and gene therapy.
Optimal tuning of PI controllers for first order plus dead time/long dead time models using dimensional analysis

For first order plus dead time models, an optimal method for tuning PI controllers is presented using dimensional analysis and numerical optimisation techniques. Considering a step change in setpoint, optimal equations for determining PI parameters are obtained through minimising the integral of absolute error (IAE). The optimisation process is constrained to guarantee a minimum Gain margin (G.M.) of 2 and a minimum Phase Margin (P.M.) of 60°. The proposed formulas can also be used for first order systems with long dead time. Simulation results show that the proposed method has a considerable superiority over conventional techniques. In addition, the closed loop system shows a robust performance in the face of model parameters uncertainties.
Human Genomic Sequences That Inhibit Splicing

ABSTRACT Mammalian genes are characterized by relatively small exons surrounded by variable lengths of intronic sequence. Sequences similar to the splice signals that define the 5′ and 3′ boundaries of these exons are also present in abundance throughout the surrounding introns. What causes the real sites to be distinguished from the multitude of pseudosites in pre-mRNA is unclear. Much progress has been made in defining additional sequence elements that enhance the use of particular sites. Less work has been done on sequences that repress the use of particular splice sites. To find additional examples of sequences that inhibit splicing, we searched human genomic DNA libraries for sequences that would inhibit the inclusion of a constitutively spliced exon. Genetic selection experiments suggested that such sequences were common, and we subsequently tested randomly chosen restriction fragments of about 100 bp. When inserted into the central exon of a three-exon minigene, about one in three inhibited inclusion, revealing a high frequency of inhibitory elements in human DNA. In contrast, only 1 in 27 Escherichia coli DNA fragments was inhibitory. Several previously identified silencing elements derived from alternatively spliced exons functioned weakly in this constitutively spliced exon. In contrast, a high-affinity site for U2AF65 strongly inhibited exon inclusion. Together, our results suggest that splicing occurs in a background of repression and, since many of our inhibitors contain splice like signals, we suggest that repression of some pseudosites may occur through an inhibitory arrangement of these sites.
Diagnostic reference levels for the most frequent radiological examinations carried out in Brazil.

OBJECTIVES A large-scale survey of doses to patients undergoing the most frequent radiological examinations was carried out in health services in São Paulo (347 radiological examinations per 1 000 inhabitants), the most populous Brazilian state. METHODS A postal dosimetric kit with thermoluminescence dosimeters was used to evaluate the entrance surface dose (ESD) to patients. A stratified sampling technique applied to the national health database furnished important data on the distribution of equipment and the annual number of examinations. Chest, head (skull and sinus), and spine (cervical, thoracic, and lumbar) examinations were included in the trial. A total of 83 rooms and 868 patients were included, and 1 415 values of ESD were measured. RESULTS The data show large coefficients of variation in tube charge, giving rise to large variations in ESD values. Also, a series of high ESD values associated with unnecessary localizing fluoroscopy were detected. Diagnostic reference levels were determined, based on the 75th percentile (third quartile) of the ESD distributions. For adult patients, the diagnostic reference levels achieved are very similar to those obtained in international surveys. However, the situation is different for pediatric patients: the ESD values found in this survey are twice as large as the international recommendations for chest radiographs of children. CONCLUSIONS Despite the reduced number of ESD values and rooms for the pediatric patient group, it is recommended that practices in chest examinations be revised and that specific national reference doses and image quality be established after a broader survey is carried out.
Methodological Quality of Animal Studies of Neuroprotective Agents Currently in Phase II/III Acute Ischemic Stroke Trials

Background and Purpose— Numerous neuroprotective agents have proven effective in animal stroke studies, but every drug has failed to achieve its primary outcome when brought forward to clinical trials. We analyzed the quality and adequacy of animal studies supporting the efficacy of NXY-059 and other neuroprotective agents that are currently being investigated in phase II/III trials. Methods— We conducted a systematic search of all neuroprotective drugs in Phase II or III trials and collected data from animal studies of focal cerebral ischemia testing agents systemically administered within 24 hours of occlusion. The methodological rigor of each individual study was evaluated using 5 criteria derived from the STAIR guidelines. The adequacy of the preclinical “package” for each drug was then evaluated by combining the results of all studies for each drug to determine which of a further 5 STAIR criteria were met before moving forward from animal to human studies. Results— Our search yielded 13 agents of which 10 had published data in peer-reviewed journals. There is substantial within-drug variability in the quality of preclinical studies as well as substantial variation in the completeness of the collective preclinical literature for different drugs. There has been little or no improvement in the quality of animal studies since NXY-059, and current agents have not been subjected to a more complete preclinical evaluation. Conclusion— There is significant heterogeneity in the quality of animal testing for neuroprotective agents in stroke. Drugs in the post-SAINT era have not been subjected to more thorough preclinical evaluation.