Miracle-dz/UniFAR-FTUs huggingface dataset:
α‐Synuclein protects naive but not dbcAMP‐treated dopaminergic cell types from 1‐methyl‐4‐phenylpyridinium toxicity

The pre‐synaptic protein, α‐synuclein, has been associated with the pathogenesis of Parkinson's disease. The present study indicates that α‐synuclein, but not its mutants (A53T, A30P), can protect CNS dopaminergic cells from the parkinsonism‐inducing drug 1‐methyl‐4‐phenylpyridinium (MPP+), whereas it cannot protect from the dopaminergic toxin, 6‐hydroxydopamine, hydrogen‐peroxide, or the β‐amyloid peptide, A‐β. Protection from MPP+ was directly correlated with the preservation of mitochondrial function. Specifically, α‐synuclein rescued cells from MPP+ mediated decreases in mitochondrial dehydrogenase activity and loss of ATP levels by utilizing ketosis. It also prevented toxin‐induced activation of the creatine kinase/creatine phosphate system. Similarly, α‐synuclein protected cells from the complex I inhibitor rotenone and 3‐nitroproprionic acid, a complex II inhibitor. Wild‐type α‐synuclein‐mediated neuroprotection and subsequent alterations in energy were not found in dbcAMP‐differentiated cells. These results suggest that the normal physiological role for α‐synuclein may change during development.
CODEX: exploration of semantic changes between ontology versions

Life science ontologies substantially change over time to meet the requirements of their users and to include the newest domain knowledge. Thus, an important task is to know what has been modified between two versions of an ontology (diff). This diff should contain all performed changes as compact and understandable as possible. We present CODEX (Complex Ontology Diff Explorer), a tool that allows determining semantic changes between two versions of an ontology, which users can interactively analyze in multiple ways.
Long non-coding RNA produced by RNA polymerase V determines boundaries of heterochromatin

RNA-mediated transcriptional gene silencing is a conserved process where small RNAs target transposons and other sequences for repression by establishing chromatin modifications. A central element of this process are long non-coding RNAs (lncRNA), which in Arabidopsis thaliana are produced by a specialized RNA polymerase known as Pol V. Here we show that non-coding transcription by Pol V is controlled by preexisting chromatin modifications located within the transcribed regions. Most Pol V transcripts are associated with AGO4 but are not sliced by AGO4. Pol V-dependent DNA methylation is established on both strands of DNA and is tightly restricted to Pol V-transcribed regions. This indicates that chromatin modifications are established in close proximity to Pol V. Finally, Pol V transcription is preferentially enriched on edges of silenced transposable elements, where Pol V transcribes into TEs. We propose that Pol V may play an important role in the determination of heterochromatin boundaries. DOI: http://dx.doi. org/10.7554/eLife.19092. 001
Spiral intra macroblock refresh with motion vector restriction for low bit-rate video telephony over a 3G network

A method to limit the effect of error propagation in low bit-rate error resilient video coding has been proposed and implemented on a 3G prototype videophone. In conventional methods, the effect of the bit-stream error does not vanish rapidly since the refreshed macroblocks are affected by the errors in the unrefreshed macroblocks. To overcome this ineffectiveness, two techniques are used; one is motion vector restriction that limits the error propagation, and the other is the spiral intra macroblock refresh that minimizes coding efficiency degradation caused by the motion vector restriction. Further, the latter technique concentrates on the center area in the screen, where the subjective preference is closely related. Experiments show that the proposed method removes the effect of the error more rapidly than the conventional methods.
Correlation of Particular Bacterial PCR-Denaturing Gradient Gel Electrophoresis Patterns with Bovine Ruminal Fermentation Parameters and Feed Efficiency Traits

ABSTRACT The influence of rumen microbial structure and functions on host physiology remains poorly understood. This study aimed to investigate the interaction between the ruminal microflora and the host by correlating bacterial diversity with fermentation measurements and feed efficiency traits, including dry matter intake, feed conversion ratio, average daily gain, and residual feed intake, using culture-independent methods. Universal bacterial partial 16S rRNA gene products were amplified from ruminal fluid collected from 58 steers raised under a low-energy diet and were subjected to PCR-denaturing gradient gel electrophoresis (DGGE) analysis. Multivariate statistical analysis was used to relate specific PCR-DGGE bands to various feed efficiency traits and metabolites. Analysis of volatile fatty acid profiles showed that butyrate was positively correlated with daily dry matter intake (P < 0.05) and tended to have higher concentration in inefficient animals (P = 0.10), while isovalerate was associated with residual feed intake (P < 0.05). Our results suggest that particular bacteria and their metabolism in the rumen may contribute to differences in host feed efficiency under a low-energy diet. This is the first study correlating PCR-DGGE bands representing specific bacteria to metabolites in the bovine rumen and to host feed efficiency traits.
Effect of Weld Toe Burr Grinding on Fatigue Strength of Transverse Welded Specimens Made From DH36 Steel

The effect of weld toe grinding on fatigue life of welded joint has been studied by a number of investigators who have established that improvement factor on fatigue life is greater for higher tensile steels as compared with mild steels [1]. To establish the effect of weld toe grinding on the fatigue strength of joints made from DH36 steel, transverse welded specimens were tested under constant amplitude loading. This work was carried out by DAEWOO Shipbuilding and Marine Engineering Co. within Lloyds Register/DSME Joint Project. It was shown that the improvement factor on fatigue strength due to weld toe burr grinding for DH36 steel is above 1.5 for high cycle fatigue range. © 2009 ASME
The prognostic significance of MCL1 copy number gain in esophageal squamous cell carcinoma

Background MCL1 copy number variations have been reported to be associated with cancer prognosis in several cancers. However, the role of MCL1 gain has not yet been determined in esophageal squamous cell carcinomas (ESCC). Methods Fluorescence in situ hybridization (FISH) for MCL1 was performed on 262 ESCC samples using tissue microarray (TMA). Results The median age of ESCC patients was 62 years (range 37–83), with frequencies between women (16.4%) and men (83.6%). Of the 262 tumors, 77 tumors (29.4%) had high MCL1 gain. In the multivariate analysis, lymph node metastasis (HR: 3.236, P<0.001 for DFS; HR: 3.501, P<0.001 for OS) and clinical stage (HR: 3.388, P<0.001 for DFS; HR: 3.616, P<0.001 for OS) were identified as independent worse prognostic factors. Interestingly, among patients without lymph node metastasis or stage I-II patients, high MCL1 gain was associated with better DFS (P=0.009 or 0.046) and OS (P=0.014 or 0.069) after disease free survival time was more than or equal to 12 months. Reversely, among patients with lymph node metastasis or stage III-IVa patients, high MCL1 gain was associated with poorer DFS (P=0.007 or 0.021) and OS (P=0.029 or 0.068) after disease free survival time was more than or equal to 29 months. Conclusion We observed that high MCL1 gain had bidirectional prognostic significance in ESCC patients with different lymph node status or clinical stage. These findings might provide the useful way of detailed risk stratification in patients with ESCC, and an insight into pathogenesis and mechanism of progression in ESCC.
Factors affecting e-training adoption: an examination of perceived cost, computer self-efficacy and the technology acceptance model

ABSTRACT The objective of this paper is to highlight the role that perceived cost, computer self-efficacy and the technology acceptance model (TAM) constructs have in e-training adoption in the Nigerian civil service. With the use of the SmartPLS 2.0 M3 software, a framework that included perceived cost, computer self-efficacy and TAM constructs (perceived usefulness (PU) and perceived ease of use (PEOU)) was tested on 450 heads of departments. Scales on perceived cost, computer self-efficacy, PU and PEOU developed by previous studies were modified accordingly and used. This paper found perceived cost to have a significant effect on e-training adoption. Computer self-efficacy was statistically insignificant through PEOU. In addition, PEOU had an indirect effect through PU. Therefore, only PU of the TAM constructs indicated strong predictive strength in e-training adoption. This paper showed that with e-training adoption, facilities such as computers can be put in place, which can improve the outlook of the civil service. In addition, the cost that is usually associated with traditional training can be reduced, increasing the opportunity to invest in other aspects of the civil service which can help in adding to the overall performance. Relationships were examined in this paper, which were shown to be favourable to e-training adoption in the Nigerian civil service.
Photothermal spectroscopy methods for chemical analysis

Absorption, Energy Transfer, and Excited-State Relaxation. Hydrodynamic Relaxation: Heat Transfer and Acoustics. Optical Principles for Photothermal Spectroscopy. Temperature Change and Optical Elements in Homogeneous Samples. Photothermal Spectroscopy in Homogeneous Samples. Analytical Measurement and Data Processing Considerations. Analytical Applications. Photothermal Spectroscopy of Heterogeneous Samples. Index.
Delayed posthypoxic leukoencephalopathy: a case series and review of the literature

Delayed posthypoxic leukoencephalopathy (DPHL) is a rare and underrecognized entity where patients manifest a neurological relapse after initial recovery from an acute hypoxic episode. We sought to describe the magnetic resonance imaging (MRI) findings in a group of patients with DPHL and review the available literature.
Status of Neutrophils, Lymphocytes and Platelets in Patients with Recurrent Aphthous Stomatitis: A Retrospective Study

Introduction: The aim of this study was to evaluate the neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), and mean platelet volume (MPV) in patients with recurrent aphthous stomatitis (RAS). Materials and Methods: Eighty patients who were diagnosed with RAS between January 2014 and January 2016 were included in this study. Eighty age- and gender-matched healthy subjects were also enrolled as a control group. Neutrophil, lymphocyte, and platelet counts were compared between groups, in addition to NLR, PLR, and MPV values. Results: There was no significant difference in terms of lymphocyte count, platelet count, PLR, or MPV values between the two groups (P>0.05). However, white blood count, neutrophil count, and NLR were significantly higher in patients with RAS compared with the control group (P<0.05). Conclusion: The present study revealed an increased NLR among RAS patients compared with healthy controls. This suggests that development of RAS involves an inflammatory process. We believe that NLR could be used as a cheap and simple marker of inflammation.
Blood pressure improvement with continuous positive airway pressure is independent of obstructive sleep apnea severity.

STUDY OBJECTIVES We sought to perform a patient-level meta-analysis using the individual patient data of the trials identified in our previous study-level meta-analysis investigating the effect of positive airway pressure (PAP) treatment for obstructive sleep apnea (OSA) on blood pressure (BP). DESIGN Patient-level meta-analysis. SETTING N/A. PARTICIPANTS 968 adult OSA subjects without major comorbidities drawn from eight randomized controlled trials. INTERVENTIONS Therapeutic PAP versus non-therapeutic control conditions (sham-PAP, pill placebo or standard care) over at least one week. MEASUREMENTS AND RESULTS The mean reductions in BP between PAP and non-therapeutic control arms were -2.27 mm Hg (95% CI -4.01 to -0.54) for systolic BP and -1.78 mm Hg (95% CI -2.99 to -0.58) for diastolic BP. The presence of uncontrolled hypertension at baseline was significantly associated with a reduction in systolic BP of 7.1 mm Hg and diastolic BP of 4.3 mm Hg after controlling for OSA severity (apnea-hypopnea index, Epworth Sleepiness Scale score, PAP level), patient demographics (age, gender, body mass index, use of antihypertensive medication/s), and measures of PAP efficacy (PAP adherence and treatment duration). CONCLUSIONS OSA patients with uncontrolled hypertension are likely to gain the largest benefit from PAP in terms of a substantial reduction in BP, even after controlling for disease severity.
Chronic Thromboembolic Pulmonary Hypertension (CTEPH): Results From an International Prospective Registry

Background— Chronic thromboembolic pulmonary hypertension (CTEPH) is often a sequel of venous thromboembolism with fatal natural history; however, many cases can be cured by pulmonary endarterectomy. The clinical characteristics and current management of patients enrolled in an international CTEPH registry was investigated. Methods and Results— The international registry included 679 newly diagnosed (⩽6 months) consecutive patients with CTEPH, from February 2007 until January 2009. Diagnosis was confirmed by right heart catheterization, ventilation-perfusion lung scintigraphy, computerized tomography, and/or pulmonary angiography. At diagnosis, a median of 14.1 months had passed since first symptoms; 427 patients (62.9%) were considered operable, 247 (36.4%) nonoperable, and 5 (0.7%) had no operability data; 386 patients (56.8%, ranging from 12.0%– 60.9% across countries) underwent surgery. Operable patients did not differ from nonoperable patients relative to symptoms, New York Heart Association class, and hemodynamics. A history of acute pulmonary embolism was reported for 74.8% of patients (77.5% operable, 70.0% nonoperable). Associated conditions included thrombophilic disorder in 31.9% (37.1% operable, 23.5% nonoperable) and splenectomy in 3.4% of patients (1.9% operable, 5.7% nonoperable). At the time of CTEPH diagnosis, 37.7% of patients initiated at least 1 pulmonary arterial hypertension–targeted therapy (28.3% operable, 53.8% nonoperable). Pulmonary endarterectomy was performed with a 4.7% documented mortality rate. Conclusions— Despite similarities in clinical presentation, operable and nonoperable CTEPH patients may have distinct associated medical conditions. Operability rates vary considerably across countries, and a substantial number of patients (operable and nonoperable) receive off-label pulmonary arterial hypertension–targeted treatments.
CD4 T cells guarantee optimal competitive fitness of CD8 memory T cells

We studied the contribution of CD4 T cell help to survival and competitive fitness of CD8 memory T cells specific for influenza virus nucleoprotein. In agreement with recent studies, the optimal generation of functional memory CD8 T cells required CD4 help, although long‐term maintenance of resting CD8 memory T cells did not absolutely depend on the presence of CD4 T cells. Nonetheless, CD4 T cells were essential during differentiation of CD8 memory T cells to imprint on them the capacity to compete effectively with other memory T cells. CD8 memory cells generated with help survived better in secondary polyclonal hosts, and co‐transfer into lymphopenic hosts together with "un‐helped" CD8 memory cells showed improved homeostatic expansion of CD8 memory cells that had been generated with CD4 help. Therefore, the requirement for CD4 help in CD8 T cell memory extends to homeostatic parameters that ensure the maintenance and competitive fitness of memory clones.
Beyond uniformity and independence: analysis of R-trees using the concept of fractal dimension

We propose the concept of fractal dimension of a set of points, in order to quantify the deviation from the uniformity distribution. Using measurements on real data sets (road intersections of U.S. counties, star coordinates from NASA's Infrared-Ultraviolet Explorer etc.) we provide evidence that real data indeed are skewed, and, moreover, we show that they behave as mathematical fractals, with a measurable, non-integer fractal dimension. Armed with this tool, we then show its practical use in predicting the performance of spatial access methods, and specifically of the R-trees. We provide the first analysis of R-trees for skewed distributions of points: We develop a formula that estimates the number of disk accesses for range queries, given only the fractal dimension of the point set, and its count. Experiments on real data sets show that the formula is very accurate: the relative error is usually below 5%, and it rarely exceeds 10%. We believe that the fractal dimension will help replace the uniformity and independence assumptions, allowing more accurate analysis for any spatial access method, as well as better estimates for query optimization on multi-attribute queries.
CTP:Phosphocholine Cytidylyltransferase α Is a Cytosolic Protein in Pulmonary Epithelial Cells and Tissues*

CTP:phosphocholine cytidylyltransferase (CCT) is a rate-determining enzyme in de novo synthesis of phosphatidylcholine (PC). The lung requires a steady synthesis of PC for lung surfactant of which disaturated PC is the essential active agent. Surfactant synthesis occurs in alveolar type II cells. Studies with non-pulmonary cells have suggested that CCT is both a nuclear and cytoplasmic protein. The unusual requirements of the lung for PC synthesis and, therefore, CCT activity suggest a unique mechanism of regulation and possibly localization of CCT. The localization of CCTα in lung epithelial cells and, of greater consequence, lung tissues are yet unknown. Three isoforms of CCT have been identified. Herein we investigated the localization of the ubiquitously expressed CCTα isoform. To ascertain CCTα localization in lungs and lung-related epithelial cells, we employed a number of localization methods. Immunogold electron microscopy using polyclonal antibodies raised to either the carboxyl terminus, catalytic domain, or amino terminus of CCTα localized CCTα mostly to the exterior plasma membrane or regions of the endoplasmic reticulum (ER) in both A549 and MLE-15 epithelial lung cell lines and primary cultures of fetal rat lung epithelial cells. In contrast to other studies, little or no nuclear labeling was observed. Indirect immunofluorescence of these cells with anti-CCTα antibodies resulted in a similar distribution. Indirect visualization of both hemagglutinin- and FLAG-tagged CCTα as well as direct visualization of enhanced green fluorescence protein-CCTα fusion protein corroborated a cytoplasmic localization of CCTα in pulmonary cells. Moreover, analysis of lung tissue from fetal and adult mouse by either immunogold electron microscopy or indirect immunofluorescence yielded a strong cytoplasmic CCTα signal with virtually no nuclear localization in epithelial cells lining the airways. The cytoplasmic localization of CCTα in type II cells was further substantiated with transgenic mice overexpressing FLAG-tagged CCTα using the lung-specific human surfactant protein C (SP-C) promoter. We conclude that CCTα does not localize to the nucleus in pulmonary tissues, and, therefore, nuclear localization of CCTα is not a universal event.
Tunable thermal switching via DNA-based nano-devices

DNA has a well-defined structural transition—the denaturation of its double-stranded form into two single strands—that strongly affects its thermal transport properties. We show that, according to a widely implemented model for DNA denaturation, one can engineer DNA ‘heattronic’ devices that have a rapidly increasing thermal conductance over a narrow temperature range across the denaturation transition (∼350 K). The origin of this rapid increase of conductance, or ‘switching’, is the softening of the lattice and suppression of nonlinear effects as the temperature crosses the transition temperature and DNA denatures. Most importantly, we demonstrate that DNA nano-junctions have a broad range of thermal tunability by varying the sequence and length, and exploiting the underlying nonlinear behavior. We discuss the role of disorder in the base sequence, as well as the relation to genomic DNA. These results set the basis for developing thermal devices out of materials with nonlinear structural dynamics, as well as understanding the underlying mechanisms of DNA denaturation.
Viscoelastic Tension-Compression Nonlinearity in Asphalt Concrete

AbstractA new one-dimensional (1D) viscoelastic creep formulation is proposed for modeling the recoverable deformation component in asphalt concrete (AC). The formulation is designed to accommodate different tensile and compressive properties in analogy with bimodular elasticity. It is structured as a Volterra equation of the second kind with a kernel that alternates between tensile and compressive compliances based on the sign of the viscoelastic (VE) strain. If the response is only in one direction, or if the viscoelastic properties are identical in both directions, the model degenerates to the linear Boltzmann superposition. As a demonstrative application, the theory was utilized to match the response of an asphalt specimen exposed to several load–unload–rest sequences in uniaxial tension–compression. It was found that two dissimilar creep functions were needed to achieve excellent reproducibility. At short times the two were almost overlapping while for longer times they departed such that the complia.
Incremental Prognostic Value of Left Ventricular Global Longitudinal Strain in Patients With Aortic Stenosis and Preserved Ejection Fraction

Background—We sought to assess the utility of left ventricular global longitudinal strain (LV-GLS) in predicting mortality in moderate to severe and paradoxical severe aortic stenosis (AS) patients with preserved ejection fraction. Methods and Results—We studied 395 AS patients (70±14 years, 57% men) with aortic valve area <1.3 cm2 evaluated between January to June 2008 (excluding severe other valve disease and LV ejection fraction <50%). Clinical and echocardiographic data were recorded. LV-GLS was analyzed using Velocity Vector Imaging. AS patients were classified as (a) moderate–severe (n=93; aortic valve area, 1.1–1.3 cm2), (b) standard severe (n=161; aortic valve area, ⩽1 cm2; mean gradient ≥40 mm Hg), and (c) paradoxical severe (n=141; aortic valve area, ⩽1 cm2 and mean gradient <40 mm Hg). Additive Euroscore was 7±3. The association of LV-GLS with all-cause mortality was assessed after risk-adjustment using Cox proportional hazards models. Median LV-GLS was −14.8% (interquartile range, −17.2%, −12.1%). At 4.4±1.4 years, there were 92 (23%) deaths. On multivariable Cox analysis, additive Euroscore (hazard ratio, 1.19; 1.13–1.27; P<0.001), New York Heart Association class (hazard ratio, 1.44; 1.11–1.87; P<0.001), AV surgery with time-dependent covariate analysis (hazard ratio, 0.29; 0.19–0.45; P<0.001), and LV-GLS (hazard ratio, 1.05; 1.03–1.07; P<0.001) were independent predictors of mortality. LV-GLS <−12.1% (4th quartile) was associated with significantly reduced survival. Addition of LV-GLS to clinical parameters (additive Euroscore+New York Heart Association class) led to significant improvement in prediction of mortality (&khgr;2 increased from 48 to 58; P<0.01). Conclusions—LV-GLS independently predicts mortality in moderate–severe and severe AS patients with preserved LV ejection fraction, providing incremental prognostic utility, in addition to standard clinical and echocardiographic parameters.