Miracle-dz/UniFAR-FTUs huggingface dataset:
Defective Mitochondrial Oxidative Phosphorylation in Myopathies with Tubular Aggregates Originating from Sarcoplasmic Reticulum

Abnormalities of the sarcotubular system presenting as tubular aggregates (TAs) have been described in a variety of neuromuscular disorders. Here, we report on immunohistochemical and biochemical findings in 7 patients (2 familial and 5 sporadic cases) suffering from myopathies with TAs. In muscle biopsy specimens from 5 of the 7 patients, TAs were immunopositive for the ryanodine receptor (RYR 1) of the sarcoplasmic reticulum (SR), the SR Ca2+ pump (SERCA2-ATPase), and the intraluminal SR Ca2+ binding protein calsequestrin, indicating an SR origin of these aggregates. Furthermore, these 5 cases showed decreased respiratory chain enzyme activities (NADH:CoQ oxidoreductase, complex I and cytochrome c oxidase [COX], complex IV), while the remaining 2 patients exhibited normal values. Our findings indicate a functional link between mitochondrial dysfunction and the presence of TAs originating from the sarcoplasmic reticulum.
Real-time multi-perspective rendering on graphics hardware

Multi-perspective rendering has a variety of applications; examples include lens refraction, curved mirror reflection, caustics, as well depiction and visualization. However, multi-perspective rendering is not yet practical on polygonal graphics hardware, which so far has utilized mostly single-perspective (pin-hole or orthographic) projections.In this paper, we present a methodology for real-time multi-perspective rendering on polygonal graphics hardware. Our approach approximates a general multi-perspective projection surface (such as a curved mirror and lens) via a piecewise-linear triangle mesh, upon which each triangle is a simple multi-perspective camera, parameterized by three rays at triangle vertices. We derive analytic formula showing that each triangle projection can be implemented as a pair of vertex and fragment programs on programmable graphics hardware. We demonstrate real-time performance of a variety of applications enabled by our technique, including reflection, refraction, caustics, and visualization.
Mitogenome Phylogenetics: The Impact of Using Single Regions and Partitioning Schemes on Topology, Substitution Rate and Divergence Time Estimation

The availability of mitochondrial genome sequences is growing as a result of recent technological advances in molecular biology. In phylogenetic analyses, the complete mitogenome is increasingly becoming the marker of choice, usually providing better phylogenetic resolution and precision relative to traditional markers such as cytochrome b (CYTB) and the control region (CR). In some cases, the differences in phylogenetic estimates between mitogenomic and single-gene markers have yielded incongruent conclusions. By comparing phylogenetic estimates made from different genes, we identified the most informative mitochondrial regions and evaluated the minimum amount of data necessary to reproduce the same results as the mitogenome. We compared results among individual genes and the mitogenome for recently published complete mitogenome datasets of selected delphinids (Delphinidae) and killer whales (genus Orcinus). Using Bayesian phylogenetic methods, we investigated differences in estimation of topologies, divergence dates, and clock-like behavior among genes for both datasets. Although the most informative regions were not the same for each taxonomic group (COX1, CYTB, ND3 and ATP6 for Orcinus, and ND1, COX1 and ND4 for Delphinidae), in both cases they were equivalent to less than a quarter of the complete mitogenome. This suggests that gene information content can vary among groups, but can be adequately represented by a portion of the complete sequence. Although our results indicate that complete mitogenomes provide the highest phylogenetic resolution and most precise date estimates, a minimum amount of data can be selected using our approach when the complete sequence is unavailable. Studies based on single genes can benefit from the addition of a few more mitochondrial markers, producing topologies and date estimates similar to those obtained using the entire mitogenome.
Applications of Next-Generation Sequencing Technologies to Diagnostic Virology

Novel DNA sequencing techniques, referred to as “next-generation” sequencing (NGS), provide high speed and throughput that can produce an enormous volume of sequences with many possible applications in research and diagnostic settings. In this article, we provide an overview of the many applications of NGS in diagnostic virology. NGS techniques have been used for high-throughput whole viral genome sequencing, such as sequencing of new influenza viruses, for detection of viral genome variability and evolution within the host, such as investigation of human immunodeficiency virus and human hepatitis C virus quasispecies, and monitoring of low-abundance antiviral drug-resistance mutations. NGS techniques have been applied to metagenomics-based strategies for the detection of unexpected disease-associated viruses and for the discovery of novel human viruses, including cancer-related viruses. Finally, the human virome in healthy and disease conditions has been described by NGS-based metagenomics.
Differential prognosis of reading backwardness and specific reading retardation.

Summary. Multiple regression techniques have been used very infrequently to define samples of children with reading difficulties. Earlier studies have shown that children with specific reading retardation differ from generally backward readers on sex distribution, IQ distribution, and other factors. The present paper reports preliminary results of a five-year follow-up of disabled readers and provides evidence that whilst the prognosis for any reading disability is poor, children with specific reading retardation have a poorer prognosis than backward readers. The distinction between backwardness and retardation in reading is therefore seen to be both meaningful and of prognostic importance.
An analysis of SEI software process assessment results: 1987-1991

The authors focus on the results of Software Engineering Institute (SEI) software process assessments conducted over a four-year period beginning in 1987. They contribute to the existing body of knowledge on the state of practice of software engineering in the United States by characterizing software sites from a process maturity perspective and profiling site software process weaknesses. The data analyzed are drawn from SEI software process assessments of 59 government and industry software sites. This work is an analysis of existing assessment data rather than a designed study. <<ETX>>
Development of a New Rapid Isolation Device for Circulating Tumor Cells (CTCs) Using 3D Palladium Filter and Its Application for Genetic Analysis

Circulating tumor cells (CTCs) in the blood of patients with epithelial malignancies provide a promising and minimally invasive source for early detection of metastasis, monitoring of therapeutic effects and basic research addressing the mechanism of metastasis. In this study, we developed a new filtration-based, sensitive CTC isolation device. This device consists of a 3-dimensional (3D) palladium (Pd) filter with an 8 µm-sized pore in the lower layer and a 30 µm-sized pocket in the upper layer to trap CTCs on a filter micro-fabricated by precise lithography plus electroforming process. This is a simple pump-less device driven by gravity flow and can enrich CTCs from whole blood within 20 min. After on-device staining of CTCs for 30 min, the filter cassette was removed from the device, fixed in a cassette holder and set up on the upright fluorescence microscope. Enumeration and isolation of CTCs for subsequent genetic analysis from the beginning were completed within 1.5 hr and 2 hr, respectively. Cell spike experiments demonstrated that the recovery rate of tumor cells from blood by this Pd filter device was more than 85%. Single living tumor cells were efficiently isolated from these spiked tumor cells by a micromanipulator, and KRAS mutation, HER2 gene amplification and overexpression, for example, were successfully detected from such isolated single tumor cells. Sequential analysis of blood from mice bearing metastasis revealed that CTC increased with progression of metastasis. Furthermore, a significant increase in the number of CTCs from the blood of patients with metastatic breast cancer was observed compared with patients without metastasis and healthy volunteers. These results suggest that this new 3D Pd filter-based device would be a useful tool for the rapid, cost effective and sensitive detection, enumeration, isolation and genetic analysis of CTCs from peripheral blood in both preclinical and clinical settings.
Durable Scar Size Reduction Due to Allogeneic Mesenchymal Stem Cell Therapy Regulates Whole‐Chamber Remodeling

Background Intramyocardial injection of mesenchymal stem cells (MSCs) in chronic ischemic cardiomyopathy is associated with reverse remodeling in experimental models and humans. Here, we tested the hypothesis that allogeneic MSC therapy drives ventricular remodeling by producing durable and progressive scar size reduction in ischemic cardiomyopathy. Methods and Results Gottingen swine (n=12) underwent left anterior descending coronary artery myocardial infarction (MI), and 3 months post‐MI animals received either intramyocardial allogeneic MSC injection (200 mol/L cells; n=6) or left ventricle (LV) catheterization without injection (n=6). Swine were followed with serial cardiac magnetic resonance imaging for 9 months to assess structural and functional changes of the LV. Intramyocardial injection was performed using an integrated imaging platform combining electroanatomical mapping unipolar voltage and 3‐dimensional cardiac magnetic resonance imaging angiography–derived anatomy to accurately target infarct border zone injections. MSC‐treated animals had a 19.62±2.86% reduction in scar size at 3 months postinjection, which progressed to 28.09±2.31% from 3 to 6 months postinjection (P<0.0001). MSC‐treated animals had unchanged end‐diastolic volume (EDV; P=0.08) and end‐systolic volume (ESV; P=0.28) from preinjection to 6 months postinjection, whereas controls had progressive dilatation in both EDV (P=0.0002) and ESV (P=0.0002). In addition, MSC‐treated animals had improved LV sphericity index. Percentage change in infarct size correlated with percentage change in EDV (r=0.68; P=0.01) and ESV (r=0.77; P=0.001). Ejection fraction increased from 29.69±1.68% to 35.85±2.74% at 3 months post‐MSC injection and progressed to 39.02±2.42% 6 months postinjection (P=0.0001), whereas controls had a persistently depressed ejection fraction during follow‐up (P=0.33). Conclusion Intramyocardial injection of allogeneic MSCs leads to a sustained and progressive reduction in infarct size, which in turn drives reverse remodeling and increases in ejection fraction. These findings support ongoing biological activity of cell therapy for substantial periods and suggest optimal end points for future clinical trials.
Effect of perspective change in body ownership transfer to teleoperated android robot

We previously investigated body ownership transfer to a teleoperated android body caused by motion synchronization between the robot and its operator. Although visual feedback is the only information provided from the robot, due to body ownership transfer, some operators feel as if they were touched when the robot's body was touched. This illusion can help operators transfer their presence to the robotic body during teleoperation. By enhancing this phenomenon, we can improve our communication interface and the quality of the interaction between operator and interlocutor. In this paper, we examined how the change in the operator's perspective affects the body ownership transfer during teleoperation. Based on past studies on the rubber hand illusion, we hypothesized that the perspective change will suppress the body owner transfer. Our results, however, showed that in any perspective condition, the participants felt the body ownership transfer. This shows that its generation process may differ in the body ownership transfer for teleoperated androids and the rubber hand illusion.
Spontaneous local variations in ongoing neural activity bias perceptual decisions

Neural variability in responding to identical repeated stimuli has been related to trial-by-trial fluctuations in ongoing activity, yet the neural and perceptual consequences of these fluctuations remain poorly understood. Using functional neuroimaging, we recorded brain activity in subjects who reported perceptual decisions on an ambiguous figure, Rubin's vase-faces picture, which was briefly presented at variable intervals of ≥20 s. Prestimulus activity in the fusiform face area, a cortical region preferentially responding to faces, was higher when subjects subsequently perceived faces instead of the vase. This finding suggests that endogenous variations in prestimulus neuronal activity biased subsequent perceptual inference. Furnishing evidence that evoked sensory responses, we then went on to show that the pre- and poststimulus activity interact in a nonlinear way and the ensuing perceptual decisions depend upon the prestimulus context in which they occur.
Estimating County Cost of Living Indexes : The Issue of Urban Versus Rural

This paper summarizes the outcome of a survey of cost of living/price index programs at the county level in the U.S. Additionally, it presents results of econometric analyses of price level data by counties for two states, Florida and Minnesota. Unlike previous studies that use a sample of urban counties and/or metropolitan areas, this analysis uses all units of the defined geographical area. It reviews the differences that occur from applying the same analytical methods to different data groupings, specifically, urban and rural counties. Finally, it points out issues that regional statisticians must consider when developing indexes for counties within their states. Acknowledgement: This research was conducted while Blanciforti was a research assistant professor at the Regional Research Institute and assistant professor of Resource Economics at West Virginia University and Kranner was a graduate research assistant with the Regional Research Institute in Resource Economics.
Mortality Associated With Discordant Responses to Antiretroviral Therapy in Resource-Constrained Settings

Objectives:We assessed mortality associated with immunologic and virologic patterns of response at 6 months of highly active antiretroviral therapy (HAART) in HIV-infected individuals from resource-limited countries in Africa and South America. Methods:Patients who initiated HAART between 1996 and 2007, aged 16 years or older, and had at least 1 measurement (HIV-1 RNA plasma viral load or CD4 cell count) at 6 months of therapy (3-9 month window) were included. Therapy response was categorized as complete, discordant (virologic only or immunologic only), and absent. Associations between 6-month response to therapy and all-cause mortality were assessed by Cox proportional hazards regression. Robust standard errors were calculated to account for intrasite correlation. Results:A total of 7160 patients, corresponding to 15,107 person-years, were analyzed. In multivariable analysis adjusted for age at HAART initiation, baseline clinical stage and CD4 cell count, year of HAART initiation, clinic, occurrence of an AIDS-defining condition within the first 6 months of treatment, and discordant and absent responses were associated with increased risk of death. Conclusions:Similar to reports from high-income countries, discordant immunologic and virologic responses were associated with intermediate risk of death compared with complete and no response in this large cohort of HIV-1 patients from resource-limited countries. Our results support a recommendation for wider availability of plasma viral load testing to monitor antiretroviral therapy in these settings.
Naturally occurring tuberculosis in white-tailed deer.

OBJECTIVE To determine the distribution of lesions and extent of tissues infected with Mycobacterium bovis in a captive population of white-tailed deer. DESIGN Cross-sectional study. ANIMALS 116 captive white-tailed deer. PROCEDURE Deer were euthanatized, and postmortem examinations were performed. Tissues with gross lesions suggestive of tuberculosis were collected for microscopic analysis and bacteriologic culture. Tissues from the head, thorax, and abdomen of deer with no gross lesions were pooled for bacteriologic culture. Tonsillar, nasal, oral, and rectal swab specimens, fecal samples, and samples of hay and pelleted feed, soil around feeding sites, and water from 2 natural ponds were collected for bacteriologic culture. RESULTS Mycobacterium bovis was isolated from 14 of 116 (12%) deer; however, only 9 of 14 had lesions consistent with tuberculosis. Most commonly affected tissues included the medial retropharyngeal lymph node and lung. Five of 14 tuberculous deer had no gross lesions; however, M bovis was isolated from pooled tissue specimens from the heads of each of these deer. Bacteriologic culture of tonsillar swab specimens from 2 of the infected deer yielded M bovis. Mean (+/- SEM) age of tuberculous deer was 2.5 +/- 0.3 years (range, 0.5 to 6 years). Mycobacterium bovis was not isolated from feed, soil, water, or fecal samples. CONCLUSIONS AND CLINICAL RELEVANCE Examination of hunter-killed white-tailed deer for tuberculosis commonly includes only the lymph nodes of the head. Results of such examinations may underestimate disease prevalence by as much as 57%. Such discrepancy should be considered when estimating disease prevalence.
Assessment of geotechnical properties of uncemented/cemented clayey soil incorporated with waste crumb rubber

Discarded waste tires are becoming a serious threat to health, environment, and ecological systems worldwide if it is not disposed of properly. Every year 1000 million of waste tires are discarded. This number may grow up to 1200 million by the year 2030. On the other hand, construction of civil engineering structures such as buildings, dams, highways, etc. are at high risk of differential settlement, especially in the case of weak or soft clay, which is due to its low shear strength and high compressibility. The paper aims to assess geotechnical properties of uncemented/cemented clayey soil incorporated with waste crumb rubber. Compaction parameters, unconfined compressive strength, split tensile strength, toughness index, CBR values and swelling pressure of rubberized uncemented/cemented clayey soil (3%, and 6% cement and different percentage of crumb rubber) have been obtained. After rigorous extensive study, it has been concluded that unconfined compressive strength and split tensile strength of rubberized cemented clayey soil decreases with the increase of the percentage of crumb rubber whereas the axial, and diametral strain are found to be increased with the addition of crumb rubber up to 5% after that it starts to decrease. The CBR values, swelling pressure, and toughness index of uncemented/cemented clayey soil was significantly affected by incorporation of crumb rubber. SEM studies have also been incorporated in this investigation.
Sandwich problem for Π - and ∆ -free multigraphs and its applications to positional games

An n - multigraph G = ( V ; E i | i ∈ I ) is a complete graph G = ( V , E ) whose edges are covered by n = | I | sets, E = ∪ i ∈ I E i , some of which might be empty. If this cover is a partition, then G is called an n-graph . We say that an n -graph G ′ = ( V ; E ′ i | i ∈ I ) is an edge subgraph of an n -multigraph G = ( V ; E i | i ∈ I ) if E ′ i ⊆ E i for all i ∈ I . We denote by ∆ the n -graph on three vertices with three nonempty sets each containing a single edge, and by Π the four-vertex n -graph with two non-empty sets each of which contains the edges of a P 4 . In this paper, we recognize in polynomial time whether a given n -multigraph G contains a Π - and ∆ -free n -subgraph, or not, and if yes, provide a polynomial delay algorithm generating all such subgraphs. The above decision problem can be viewed as a generalization of the sandwich problem for P 4 -free graphs solved by Golumbic, Kaplan, and Shamir in 1995. As a motivation and application, we consider the n -person positional game forms, which are known to be in a one-to-one correspondence with the Π - and ∆ -free n -graphs. Given a game form g , making use of the above result, we recognize in polynomial time whether g is a subform of a positional (that is, tight and rectangular) game form and, if yes, we generate with polynomial delay all such positional extensions of g .
Test-data compression with low number of channels and short test time

The paper describes a modified Smart BIST methodology that provides test data volume compression. The test equipment is easily applicable because it is based on the standard scan methodology. The method is based on continuous LFSR reseeding decompression that is used in such a way that it enables lockout escaping within a small number of clock cycles. It requires a separate controlling of the LFSR decompressor and the scan chain clock inputs. We propose a modified LFSR with state skipping for the pattern decompression that does not require a phase shifter and saves hardware. A pattern encoding algorithm minimizing the number of clock cycles of the decompressor needed for decoding test patterns is also proposed. The parameters can be tuned in such a way that the method provides similar data magnitude reduction and decompressor hardware overhead as other test compression methods but it substantially reduces test time, number of tester channels and hardware overhead. Experimental results of benchmark circuit testing show that the modified Smart BIST methodology provides unreduced test coverage, low hardware overhead and short test sequences.
The Flavonoid Luteolin Worsens Chemical-Induced Colitis in NF-κBEGFP Transgenic Mice through Blockade of NF-κB-Dependent Protective Molecules

Background The flavonoid luteolin has anti-inflammatory properties both in vivo and in vitro. However, the impact of luteolin on experimental models of colitis is unknown. Methodology/Principal Findings To address the therapeutic impact of luteolin, NF-κBEGFP transgenic mice were fed a chow diet containing 2% luteolin- or isoflavone-free control chow (AIN-76), and acute colitis was induced using 3% dextran sodium sulfate (DSS). Additionally, development of spontaneous colitis was evaluated in IL-10−/−;NF-κBEGFP transgenic mice fed 2% luteolin chow diet or control chow diet. Interestingly, NF-κBEGFP transgenic mice exposed to luteolin showed worse DSS-induced colitis (weight loss, histological scores) compared to control-fed mice, whereas spontaneous colitis in IL-10−/−;NF-κBEGFP mice was significantly attenuated. Macroscopic imaging of live resected colon showed enhanced EGFP expression (NF-κB activity) in luteolin-fed mice as compared to control-fed animals after DSS exposure, while cecal EGFP expression was attenuated in luteolin-fed IL-10−/− mice. Interestingly, confocal microscopy showed that EGFP positive cells were mostly located in the lamina propria and not in the epithelium. Caspase 3 activation was significantly enhanced whereas COX-2 gene expression was reduced in luteolin-fed, DSS-exposed NF-κBEGFP transgenic mice as assessed by Western blot and immunohistochemical analysis. In vitro, luteolin sensitized colonic epithelial HT29 cells to TNFα-induced apoptosis, caspase 3 activation, DNA fragmentation and reduced TNFα-induced C-IAP1, C-IAP2 and COX-2 gene expression. Conclusions/Significance We conclude that while luteolin shows beneficial effects on spontaneous colitis, it aggravates DSS-induced experimental colitis by blocking NF-κB-dependent protective molecules in enterocytes.