Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamic Networks from Hierarchical Bayesian Graph Clustering

Biological networks change dynamically as protein components are synthesized and degraded. Understanding the time-dependence and, in a multicellular organism, tissue-dependence of a network leads to insight beyond a view that collapses time-varying interactions into a single static map. Conventional algorithms are limited to analyzing evolving networks by reducing them to a series of unrelated snapshots. Here we introduce an approach that groups proteins according to shared interaction patterns through a dynamical hierarchical stochastic block model. Protein membership in a block is permitted to evolve as interaction patterns shift over time and space, representing the spatial organization of cell types in a multicellular organism. The spatiotemporal evolution of the protein components are inferred from transcript profiles, using Arabidopsis root development (5 tissues, 3 temporal stages) as an example. The new model requires essentially no parameter tuning, out-performs existing snapshot-based methods, identifies protein modules recruited to specific cell types and developmental stages, and could have broad application to social networks and other similar dynamic systems.
Ability to Maintain Internal Arousal and Motivation Modulates Brain Responses to Emotions

Persistence (PS) is defined as the ability to generate and maintain arousal and motivation internally in the absence of immediate external reward. Low PS individuals tend to become discouraged when expectations are not rapidly fulfilled. The goal of this study was to investigate whether individual differences in PS influence the recruitment of brain regions involved in emotional processing and regulation. In a functional MRI study, 35 subjects judged the emotional intensity of displayed pictures. When processing negative pictures, low PS (vs. high PS) subjects showed higher amygdala and right orbito-frontal cortex (OFC) activity but lower left OFC activity. This dissociation in OFC activity suggests greater prefrontal cortical asymmetry for approach/avoidance motivation, suggesting an avoidance response to aversive stimuli in low PS. For positive or neutral stimuli, low PS subjects showed lower activity in the amygdala, striatum, and hippocampus. These results suggest that low PS may involve an imbalance in processing distinct emotional inputs, with greater reactivity to aversive information in regions involved in avoidance behaviour (amygdala, OFC) and dampened response to positive and neutral stimuli across circuits subserving motivated behaviour (striatum, hippocampus, amygdala). Low PS affective style was associated with depression vulnerability. These findings in non-depressed subjects point to a neural mechanism whereby some individuals are more likely to show systematic negative emotional biases, as frequently observed in depression. The assessment of these individual differences, including those that may cause vulnerability to depressive disorders, would therefore constitute a promising approach to risk assessment for depression.
Evalution of Random Forest Ensemble Classification for Land Cover Mapping Using TM and Ancillary Geographical Data

Large area land cover mapping, involving large volumes of data, are becoming more prevalent in remote sensing applications. Thus there is a pressing need for increased automation in the land cover mapping process. The main objective of this research was to map land cover in the Small Sanjiang Plain where marsh distributed concentively combined Landsat TM imagery with ancillary geographical data and compare the performance of three machine learning algrithms (MLAs) including random forest (RF), classification and regression tree (CART) and maximum likelihood classification (MLC). Comparisions were based on several criteria: overall accuracy, sensitivity to data set size and noise. Our results indicated that (1) Random Forest can achieve substantial improvements in accuracy over single classification trees and traditional MLC method, overall accuracy was 91.0%, kappa coefficient was 0.8943, with marsh class accuracy ranging from 77.4% to 90.0%; (2) Random forest was least sensitive to reduction in training sample size and it was most resistant to the presence of noise compared to CART and MLC. The comparison result revealed that random forest has potential to increase automation in large area land cover mapping while achieving reasonable map accuracy.
New Real-Time Reverse Transcriptase-Initiated PCR Assay with Single-Copy Sensitivity for Human Immunodeficiency Virus Type 1 RNA in Plasma

ABSTRACT More sensitive assays for human immunodeficiency virus type 1 (HIV-1) RNA are needed to detect, quantify, and characterize persistent viremia in patients who are receiving antiretroviral therapy and whose plasma HIV-1 RNA levels are suppressed to less than 50 to 75 copies/ml. We therefore developed an internally controlled real-time reverse transcriptase-initiated PCR assay that quantifies HIV-1 RNA concentrations down to 1 copy per ml of plasma. This assay with single-copy sensitivity (the single-copy assay) generates a reproducible linear regression plot of input copy number versus threshold cycle by using HIV-1 RNA transcripts at copy numbers ranging from 1 to 106 per reaction mixture. The single-copy assay was compared to the ultrasensitive AMPLICOR HIV-1 MONITOR assay and a more sensitive modification of the ultrasensitive assay by repeatedly testing a low-copy-number panel containing 200 to 0.781 copies of HIV-1 RNA per ml of plasma. This comparison showed that the single-copy assay had a greater sensitivity than the other assays and was the only assay that detected HIV-1 RNA at levels as low as 0.781 copies/ml. Testing of plasma samples from 15 patients who were receiving antiretroviral therapy and who had <75 HIV-1 RNA copies/ml revealed persistent viremia in all 15 patients, with HIV-1 RNA levels ranging from 1 to 32 copies/ml (median, 13 copies/ml). The greater sensitivity of the single-copy assay should allow better characterization of persistent viremia in patients who are receiving antiretroviral therapy and whose HIV-1 RNA levels are suppressed to below the detection limits of present assays.
Learning to Design Rehabilitation Devices Through the H-CARD Course: Project-Based Learning of Rehabilitation Technology Design

The aging population and the wish to improve quality of life, as well as the economic pressure to work longer, call for intuitive and efficient assistive and rehabilitation technologies. Therefore, we have developed a project based education paradigm in the design of assistive and rehabilitation devices. Using a miniature wireless sensing and feedback platform, the multimodal interactive motor assessment and training environment (MIMATE), students from different engineering backgrounds were able to develop innovative devices implementing rehabilitative games in the short span of a one-term course. We describe here this novel H-CARD course on the human-centered design of assistive and rehabilitative devices.
The Adhesion Molecule on Glia (AMOG) Is Widely Expressed by Astrocytes in Developing and Adult Mouse Brain

Adhesion molecule on glia (AMOG) is a 45–50 kD cell surface glycoprotein structurally similar to the Na, K‐ATPase β‐subunit and associated with the catalytic subunit of this enzyme. Previous immunofluorescence results had suggested that AMOG is transiently expressed on Bergmann glia during mouse cerebellar development, and antibody‐inhibition results have implicated it in the migration of granule neurons. We report that, while AMOG mRNA is detected in Bergmann glia during the migratory period, this astrocyte derivative continues to express AMOG mRNA at similar levels in adult mice suggesting a functional role for AMOG in adulthood. Evidence from RNA and protein blot analyses that AMOG is present before birth, increasing about ten fold in adult mouse brain and cerebellum is also provided. RNA blot analysis of astrocyte‐enriched cell populations and in situ hybridization results show that astrocytes synthesize AMOG mRNA in all regions of the developing and adult brain. In the adult, AMOG mRNA is more abundant in grey than white matter and, among grey matter regions, highest in cerebellar cortex. These results indicate a relationship between density of neuronal elements and AMOG expression. It is further speculated that AMOG is part of a Na,K‐ATPase complex expressed preferentially by astrocytes in mouse brain.
Swelling of Composite Laminates

Abstract : The swelling behavior of a graphite/epoxy (AS/3501-5) is shown to be described by a model which is based on the assumption that the swelling is negligible until the moisture concentration reaches a threshhold value and then increases linearly thereafter. The model also provides a means of measuring the volume fraction of voids. The analytical results, which take into account the curing stresses, are compared with the experimental data for the transverse and thickness strains of symmetric laminates as well as for the warpage of unsymmetric laminates. The initial absorption on virgin specimens facilitates the subsequent diffusion and the residual stresses appear to be responsible for the absorption being slower than the desorption during the early stages of moisture conditioning. Warpage of unsymmetric laminates is discussed in light of the cracks found in constituent plies. Finally derived is a temperature-relative humidity relationship which renders the graphite/epoxy composite laminates free of residual stresses. (Author)
Daily time series for cardiovascular hospital admissions and previous day's air pollution in London, UK.

OBJECTIVE: To test for a significant association between air pollution and emergency hospital admissions for circulatory diseases (international classification of diseases-9 390-459) in London, England, that would be consistent with a causal effect of pollution on the previous day. METHODS: Long term concurrent trends, temperature, humidity, day of the week, influenza epidemic of 1989, and cyclical covariations with periodicity > 20 days in daily measures of pollution and admissions for 1987-94 were allowed for. RESULTS: There were 373556 admissions. No association was found between O3 and circulatory diseases. Four other pollutants were associated with acute myocardial infarction and circulatory diseases combined. P values and attributable cases (95% confidence intervals) for acute myocardial infarction were: black smoke P = 0.003, 2.5% (0.8% to 4.3%); NO2 P = 0.002, 2.7% (0.8% to 4.6%); CO P = 0.001, 2.1% (0.7% to 3.5%); and SO2 P = 0.0006, 1.7% (0.7% to 2.6%). There were also associations between black smoke and angina (P = 0.02), NO2 and arrhythmia (P = 0.04), and CO and other circulatory diseases (P = 0.004), but none with heart failure. Acute myocardial infarction was the only diagnosis for which there were significant associations with and without adjustment for cyclical terms. The associations with acute myocardial infarction were significant only in the cool season. CONCLUSION: Population data were consistent with 1 in 50 heart attacks currently presenting at London hospitals being triggered by outdoor air pollution. Further research is now needed to investigate whether background concentrations of black smoke, NO2, CO, and SO2 are a preventable cause of myocardial infarction. These results, if applied to all myocardial infarctions in the United Kingdom, indicate a potential saving of 6000 heart attacks a year.
Benefits of Swim Training for Children and Adolescents with Asthma

PURPOSE To r eview scientific evidence related to the benefits of swimming and present an evidence‐based approach to prescribing swim training for children and adolescents with asthma. DATA SOURCES Extensive literature review of all research that has been done on swim training in asthmatic children and adolescents, using the databases CINAHL, Medline, and ProQuest. CONCLUSIONS When swimming is compared to other sports in the scientific literature, it has been found to have a lower asthmogenicity. It has also been shown to decrease the severity of asthma symptoms. Swimming may be an effective nonpharma‐cological intervention for the child or adolescent with asthma. IMPLICATIONS FOR PRACTICE Research findings are summarized regarding the benefits of swim training on children and adolescents with asthma, and a stepped three‐level approach to swim prescription is outlined along with safety recommendations.
Evaluation of Oral and Nasal Odor in Patients with and without Cleft Lip and Palate: Preliminary Report

Objective To evaluate oral and nasal halitosis parameters in patients with and without clefts. Design Randomized and prospective study. Patients with and without clefts were evaluated as to oral and nasal halitosis. Setting University of São Paulo, Bauru Dental School and Hospital for Rehabilitation of Craniofacial Anomalies, Bauru, Brazil. Patients Twelve patients with clefts and 12 without clefts were evaluated, and no exclusion criteria were followed. Interventions Nasal and oral halitosis were measured with the use of a portable sulfide monitor during a single visit. Results One hundred percent of the patients with clefts had altered values for volatile sulfur compounds. Only 33.3% of the patients without clefts had at least one strong value for nasal halimeter measurements, and 58.3% of these patients showed alteration in the nasal values. Statistical evaluation, made using the Mann-Whitney U test, classifying the nasal halimeter values as normal, weak, and strong, showing a statistical significant group difference (p = .003). There was no significant difference in the oral halimeter values between the two groups. Conclusions Patients with cleft lip and palate had a tendency to present higher values for the nasal halimeter measurements, when compared with patients without clefts.
Ureteral stricture formation after ureteroscope treatment of impacted calculi: A prospective study

Purpose Urinary calculi is a familiar disease. A well-known complication of endourological treatment for impacted ureteral stones is the formation of ureteral strictures, which has been reported to occur in 14.2% to 24% of cases. Materials and Methods This was a prospective study. Ureterotripsy treatment was used on patients with impacted ureteral stones. Then, after 3 months and 6 months, the condition of these patients was assessed by means of a kidney-ureter-bladder (KUB) ultrasound. If the KUB ultrasound indicated moderate to serious hydronephrosis, the patient was further assessed by means of a computed tomography intravenous urogram or retrograde pyelogram to confirm the occurrence of ureteral strictures. Results Of the 77 patients who participated in the study, 5 developed ureteral strictures. Thus, the stricture rate was 7.8%. An analysis of the intraoperative risk factors including perforation of the ureter, damage to the mucous membrane, and residual stone impacted within the ureter mucosa revealed that none of these factors contributed significantly to the formation of the ureteric strictures. The stone-related risk factors that were taken into consideration were stone size, stone impaction site, and duration of impaction. These stone factors also did not contribute significantly to the formation of the ureteral strictures. Conclusions This prospective study failed to identify any predictable factors for ureteral stricture formation. It is proposed that all patients undergo a simple postoperative KUB ultrasound screening 3 months after undergoing endoscopic treatment for impacted ureteral stones.
Cost-effectiveness of counseling and testing and partner notification: a decision analysis.

OBJECTIVE Counseling and testing and partner notification are effective HIV prevention strategies, but they can be resource intensive. This paper evaluates the cost-effectiveness of partner notification and counseling and testing offered in HIV and sexually transmitted disease (STD) clinics in preventing future HIV infections in the United States of America. METHODS Decision trees were developed from both societal and provider perspectives. The counseling and testing and partner notification models incorporate estimates of HIV prevalence, return rates for counseling, risk of HIV transmission within 1 year, and the effectiveness of counseling. Cost estimates for counseling and testing and partner notification programs and lifetime treatment cost of HIV for the United States of America were obtained from published literature. Extensive sensitivity analyses of model parameters were conducted. RESULTS For a cohort of 10,000 individuals at a clinic with an HIV seroprevalence of 1.5%, we estimate that counseling and testing prevents eight HIV infections and saves society almost $1,000,000. We estimate that partner notification for the 113 infected persons identified by counseling and testing, prevents another 1.2 HIV infections and saves an additional $181,000. To the provider (HIV and STD clinics), this translates to a cost of $32,000 per case prevented by counseling and testing and an additional $28,000 for partner notification. Model results are most sensitive to assumptions of HIV prevalence, risk of transmission, and treatment cost of HIV. CONCLUSIONS Counseling and testing and partner notification are cost effective in preventing HIV transmission in this setting. This model can be adapted to assess the cost-effectiveness of counseling and testing and partner notification in other settings.
Comparative Metagenomics Reveals Host Specific Metavirulomes and Horizontal Gene Transfer Elements in the Chicken Cecum Microbiome

Background The complex microbiome of the ceca of chickens plays an important role in nutrient utilization, growth and well-being of these animals. Since we have a very limited understanding of the capabilities of most species present in the cecum, we investigated the role of the microbiome by comparative analyses of both the microbial community structure and functional gene content using random sample pyrosequencing. The overall goal of this study was to characterize the chicken cecal microbiome using a pathogen-free chicken and one that had been challenged with Campylobacter jejuni. Methodology/Principal Findings Comparative metagenomic pyrosequencing was used to generate 55,364,266 bases of random sampled pyrosequence data from two chicken cecal samples. SSU rDNA gene tags and environmental gene tags (EGTs) were identified using SEED subsystems-based annotations. The distribution of phylotypes and EGTs detected within each cecal sample were primarily from the Firmicutes, Bacteroidetes and Proteobacteria, consistent with previous SSU rDNA libraries of the chicken cecum. Carbohydrate metabolism and virulence genes are major components of the EGT content of both of these microbiomes. A comparison of the twelve major pathways in the SEED Virulence Subsystem (metavirulome) represented in the chicken cecum, mouse cecum and human fecal microbiomes showed that the metavirulomes differed between these microbiomes and the metavirulomes clustered by host environment. The chicken cecum microbiomes had the broadest range of EGTs within the SEED Conjugative Transposon Subsystem, however the mouse cecum microbiomes showed a greater abundance of EGTs in this subsystem. Gene assemblies (32 contigs) from one microbiome sample were predominately from the Bacteroidetes, and seven of these showed sequence similarity to transposases, whereas the remaining sequences were most similar to those from catabolic gene families. Conclusion/Significance This analysis has demonstrated that mobile DNA elements are a major functional component of cecal microbiomes, thus contributing to horizontal gene transfer and functional microbiome evolution. Moreover, the metavirulomes of these microbiomes appear to associate by host environment. These data have implications for defining core and variable microbiome content in a host species. Furthermore, this suggests that the evolution of host specific metavirulomes is a contributing factor in disease resistance to zoonotic pathogens.
Robust Recovery of Signals From a Structured Union of Subspaces

Traditional sampling theories consider the problem of reconstructing an unknown signal x from a series of samples. A prevalent assumption which often guarantees recovery from the given measurements is that x lies in a known subspace. Recently, there has been growing interest in nonlinear but structured signal models, in which x lies in a union of subspaces. In this paper, we develop a general framework for robust and efficient recovery of such signals from a given set of samples. More specifically, we treat the case in which x lies in a sum of k subspaces, chosen from a larger set of m possibilities. The samples are modeled as inner products with an arbitrary set of sampling functions. To derive an efficient and robust recovery algorithm, we show that our problem can be formulated as that of recovering a block-sparse vector whose nonzero elements appear in fixed blocks. We then propose a mixed lscr2/lscr1 program for block sparse recovery. Our main result is an equivalence condition under which the proposed convex algorithm is guaranteed to recover the original signal. This result relies on the notion of block restricted isometry property (RIP), which is a generalization of the standard RIP used extensively in the context of compressed sensing. Based on RIP, we also prove stability of our approach in the presence of noise and modeling errors. A special case of our framework is that of recovering multiple measurement vectors (MMV) that share a joint sparsity pattern. Adapting our results to this context leads to new MMV recovery methods as well as equivalence conditions under which the entire set can be determined efficiently.
Immune Responses to rAAV6: The Influence of Canine Parvovirus Vaccination and Neonatal Administration of Viral Vector

Recombinant adeno-associated viral (rAAV) vectors promote long-term gene transfer in many animal species. Significant effort has focused on the evaluation of rAAV delivery and the immune response in both murine and canine models of neuromuscular disease. However, canines provided for research purposes are routinely vaccinated against canine parvovirus (CPV). rAAV and CPV possess significant homology and are both parvoviruses. Thus, any immune response generated to CPV vaccination has the potential to cross-react with rAAV vectors. In this study, we investigated the immune response to rAAV6 delivery in a cohort of CPV-vaccinated canines and evaluated multiple vaccination regimens in a mouse model of CPV-vaccination. We show that CPV-vaccination stimulates production of neutralizing antibodies with minimal cross-reactivity to rAAV6. In addition, no significant differences were observed in the magnitude of the rAAV6-directed immune response between CPV-vaccinated animals and controls. Moreover, CPV-vaccination did not inhibit rAAV6-mediated transduction. We also evaluated the immune response to early rAAV6-vaccination in neonatal mice. The influence of maternal hormones and cytokines leads to a relatively permissive state in the neonate. We hypothesized that immaturity of the immune system would permit induction of tolerance to rAAV6 when delivered during the neonatal period. Mice were vaccinated with rAAV6 at 1 or 5 days of age, and subsequently challenged with rAAV6 exposure during adulthood via two sequential IM injections, 1 month apart. All vaccinated animals generated a significant neutralizing antibody response to rAAV6-vaccination that was enhanced following IM injection in adulthood. Taken together, these data demonstrate that the immune response raised against rAAV6 is distinct from that which is elicited by the standard parvoviral vaccines and is sufficient to prevent stable tolerization in neonatal mice.