Miracle-dz/UniFAR-FTUs huggingface dataset:
Depression of retinal glutamate transporter function leads to elevated intravitreal glutamate levels and ganglion cell death.

PURPOSE Elevated levels of extracellular glutamate have been implicated in the pathophysiology of neuronal loss in both central nervous system and ophthalmic disorders, including glaucoma. This increase in glutamate may result from a failure of glutamate transporters (molecules that ordinarily regulate extracellular glutamate; E:xcitatory A:mino A:cid T:ransporter; EAAT). Elevated glutamate levels can also lead to alterations in glutamate receptor expression. It was hypothesized that selective blockade of glutamate transporters would be toxic to retinal ganglion cells. METHODS Glutamate transporters were blocked either pharmacologically or with subtype-specific antisense oligonucleotides against EAAT1. Glutamate levels, transporter levels and ganglion cell survival were assayed. RESULTS Pharmacological inhibition of glutamate transporters with either an EAAT2 specific inhibitor or a nonspecific inhibitor of all the subtypes of transporters was toxic to ganglion cells. Treatment with oligonucleotides against the glutamate transporter EAAT1 decreased the levels of expression of the transporter, increased vitreal glutamate, and was toxic to ganglion cells. CONCLUSIONS These results demonstrate that normal function of EAAT1 and EAAT2 is necessary for retinal ganglion cell survival and plays an important role in retinal excitotoxicity. Manipulation of retinal glutamate transporter expression may become a useful tool in understanding retinal neuronal loss.
A decentralized fault-tolerant control scheme based on Active Fault Diagnosis

This paper deals with a decentralized fault-tolerant control methodology based on an Active Fault Diagnosis approach. The proposed technique addresses the important problem of monitoring interconnected Large-Scale Systems (LSS). The fault diagnosis approach is made of a passive set-based fault detection method and an active fault isolation technique, able to guarantee isolability subject to local input and state constraints. The proposed scheme can be implemented locally in a decentralized way. A significant feature is the decentralized design constructed on tube-based Model Predictive Control to possibly allow the disconnection of faulty subsystems or the reconfiguration of local controllers. The Active Fault Diagnosis tool is designed to support the decision-making process for the control and monitoring of the LSS.
The genome of the endophytic bacterium H. frisingense GSF30T identifies diverse strategies in the Herbaspirillum genus to interact with plants

The diazotrophic, bacterial endophyte Herbaspirillum frisingense GSF30T has been identified in biomass grasses grown in temperate climate, including the highly nitrogen-efficient grass Miscanthus. Its genome was annotated and compared with related Herbaspirillum species from diverse habitats, including H. seropedicae, and further well-characterized endophytes. The analysis revealed that Herbaspirillum frisingense lacks a type III secretion system that is present in some related Herbaspirillum grass endophytes. Together with the lack of components of the type II secretion system, the genomic inventory indicates distinct interaction scenarios of endophytic Herbaspirillum strains with plants. Differences in respiration, carbon, nitrogen and cell wall metabolism among Herbaspirillum isolates partially correlate with their different habitats. Herbaspirillum frisingense is closely related to strains isolated from the rhizosphere of phragmites and from well water, but these lack nitrogen fixation and metabolism genes. Within grass endophytes, the high diversity in their genomic inventory suggests that even individual plant species provide distinct, highly diverse metabolic niches for successful endophyte-plant associations.
A Hybrid Method for Opinion finding Task (KUNLP at TREC 2008 Blog Track)

This paper presents an approach for the Opinion Finding task at TREC 2008 Blog Track. For the Ad-hoc Retrieval subtask, we adopt language model to retrieve relevant documents. For the Opinion Retrieval subtask, we propose a hybrid model of lexicon-based approach and machine learning approach for estimating and ranking the opinionated documents. For the Polarized Opinion Retrieval subtask, we employ machine learning for predicting the polarity and linear combination technique for ranking polar documents. The hybrid model which utilize both lexicon-based approach and machine learning approach to predict and rank opinionated documents are the focuses of our participation this year. Regarding the hybrid method for opinion retrieval subtask, our submitted runs yield 15% improvement over baseline.
Impact of Time on Improvement of Outcome After Stroke

Background and Purpose— Longitudinal conducted studies show that neurologic and functional recovery show faster recovery in the first weeks poststroke. The aim of the present study was to study the effects of progress of time on observed improvements in motor strength, synergisms, and activities during the first 16 weeks poststroke. Methods— Based on data from a previous study, 101 patients with first-ever ischemic middle cerebral artery strokes were prospectively investigated during the first 16 weeks after stroke. Progress of time was categorized into 8 biweekly time intervals and was used as the independent covariate in a first-order longitudinal regression model. The biweekly time change (progress of time) was related to improvement in upper and lower limb motor recovery assessed with Fugl-Meyer score and Motricity Index, reduction in visuospatial inattention based on the letter cancellation task, and improvement in walking ability, dexterity, and activities of daily living measured with the Functional Ambulation Categories, Action Research Arm test, and Barthel Index. Results— Time explained a significant change of 8.4 (42%) measurement units on the Barthel Index for the first 10 weeks poststroke, 1.1 (22%) measurement units on Functional Ambulation Categories, and 19% on the Action Research Arm test for the first 6 and 8 weeks poststroke. Approximately 25% (for Fugl-Meyer–arm) to 26% (for Motricity Index–arm) of the significant change in measurements units was explained by time alone for the upper limb compared with 33% for Fugl-Meyer–leg and 39% for Motricity Index–leg of the lower limb. Time accounted for a reduction of 16% in the letter cancellation task. Observed associations did not change after controlling for covariates such as age, gender, hemisphere of stroke, type of stroke, or intervention. Conclusion— Progress of time is an independent covariate that reflects spontaneous recovery of body functions and activities explaining ≈16% to 42% of the observed improvements in the first 6 to 10 weeks after stroke onset.
Occurrence of enterotoxigenic Aeromonas species in foods of animal origin in North East India.

OBJECTIVE The aim of the present study was to isolate and identify Aeromonas (A.) species and assess their toxin producing ability in foods of animal origin from North East India. MATERIALS AND METHODS A total of 332 animal food samples (fish, poultry meat, pork and chevon) of which 38 (11.44%) isolates were identified by the 16S rRNA technique were included in the study. The enterotoxigenicity of the isolates was measured by the Mouse Paw Oedema Test (MPOT), rabbit ileal loop (RIL) and vascular permeability reaction (VPR) test. RESULTS Maximum positivity was shown by the samples from fish (13.13%), followed by poultry meat (11.5%), pork (9.85%) and chevon (2.5%). A. hydrophila was the predominant species (92.10%) followed by A. sobria (5.26%) and A. caviae (2.63%). CONCLUSIONS All the Aeromonas strains isolated by culture methods expressed enterotoxigenicity by MPOT, RIL assay and VPR test.
Morphologic Findings of Coronary Atherosclerotic Plaques in Diabetics: A Postmortem Study

Objective—Coronary atherosclerotic plaque composition of diabetic subjects and localization of receptor for advanced glycation end products (RAGE) and its ligands have not been extensively studied. Method and Results—Hearts from diabetic subjects and age, race, and sex-matched nondiabetic subjects dying suddenly were examined. Coronary arteries were dissected and lesions were evaluated for plaque burden, necrotic core size, and inflammatory infiltrate. The expression of RAGE, the RAGE-binding protein (S100-A12, EN-RAGE), and cell death (apoptosis) were also determined. Lesions from type II diabetic subjects had larger mean necrotic cores (P= 0.01) and greater total and distal plaque load (P <0.001) than nondiabetic subjects. Necrotic core size correlated positively with diabetic status, independent of other risk factors. Intimal staining for macrophages, T-cells, and HLA-DR was also significantly greater in diabetic subjects (P =0.03, P =0.003, and P <0.0001), respectively. The association of increased macrophage infiltrate was independent of cholesterol levels and patient age. Expression of RAGE and EN-RAGE was significantly greater in diabetic subjects (P =0.004) and was associated with apoptotic smooth muscle cells and macrophages. Conclusion—In sudden coronary death, inflammation and necrotic core size play a greater role in the progression of atherosclerosis in diabetic subjects. The expression of RAGE and EN-RAGE may further compromise cell survival and promote plaque destabilization.
Validation of an Automated Computerized Analyzing System for Measuring Common Carotid Artery Intima–Media Thickness by Brightness Mode Ultrasound

Background and Purpose Evaluation of subclinical atherosclerosis by B-mode carotid ultrasound intima–media thickness (IMT) is an endorsed technique whose ease and precision is improved by use of automated IMT measurement algorithms. We report results of a validation study of SonoCalc, an automated IMT software program. Methods Three vascular sonographers measured the mean common carotid artery IMT twice of 120 near and far wall CCA segments from 30 subjects by manual electronic instrument calipers and with SonoCalc. Results Accuracy analysis indicated the equivalence of SonoCalc IMT measurements to those with manual electronic instrument calipers (p < 0.0001). The coefficient of variation (CV) was calculated for each set of duplicate SonoCalc and manual electronic instrument calipers measurements. The average SonoCalc-manual electronic instrument calipers CV differences significantly favored SonoCalc (p < 0.0001). Conclusion This study demonstrated that the use of the SonoCalc and the manual electronic instrument calipers produced measurements whose differences were statistically insignificant. Furthermore, the analysis to assess reproducibility of the two methods showed that the SonoCalc method was significantly more reproducible than the manual electronic instrument calipers methods.
Numerical investigation of hydrogen consumption in Proton Exchange Membrane Fuel Cell by using computational fluid dynamics (CFD) simulation

Proton exchange membrane fuel cell (PEMFC) is the most important system that converts chemical energy into electricity by using hydrogen oxidation and oxygen reduction reactions. With this approach, a 3-D (CFD) thermo-fluid model was studied using a commercial code ANSYS fluent for investigating the performance of the PEMFC system. The developed model can evaluate the distribution of gas species like the mass fraction of hydrogen, as well as the distribution of water in PEMFC. The results are used to investigate the influence of temperature and cell voltage on the consumption of hydrogen from inlet z= 0mm to outlet z=50 mm. The obtained polarization curve I-V is compared with the literature findings. The analysis shows a good agreement between our findings and the experimental results. The CFD simulation shows that the cell voltage affects considerably the hydrogen consumption; at 333 K, it can be seen that the hydrogen mass fraction decreases from 80% to 67% at 0.7 V and 80% to 73 % at 0.9 V. By comparing the hydrogen mass fractions; at a low cell voltage the hydrogen mass fraction dropped by only 7%, while at a high cell voltage the hydrogen mass fraction dropped by about 13% from the inlet to outlet. Consequently; our analyses show high consumption of hydrogen at low cell voltages.
Variable Episomal Silencing of a Recombinant Herpesvirus Renders Its Encoded GFP an Unreliable Marker of Infection in Primary Cells

The availability of reliable recombinant reporter virus systems has been a great boon to the study of Kaposi's sarcoma-associated herpesvirus (KSHV/HHV-8). Unexpectedly, we found that expression of the ostensibly constitutive green fluorescent protein (GFP) marker was progressively lost during unselected passage in primary rat mesenchymal precursor cells (MM), despite efficient maintenance of latent viral gene expression and episomal partitioning. This repression of EF1-α promoter-driven GFP expression appeared to be passage-dependent, however, since functionally immortalized MM cells derived from long serial passage retained stable expression of GFP following rKSHV.219 infection. Chromatin analysis of cultures that we had infected in parallel demonstrated an increase in repressive H3K27 tri-methylation across the viral episome with the exception of the LANA control region in MM cells infected at early rather than late passage post-isolation. The silencing of GFP expression in the MM cells was reversible in a dose-dependent fashion by the histone deacetylase inhibitor valproic acid, further implicating cellular silencing on incoming viral genomes, and underscoring potential differences in viral gene regulation between primary and functionally immortalized cells. Furthermore, using multispectral imaging flow cytometry, we also determined that the extent of GFP expression per cell among those that were positive did not correlate with the number of LANA dots per nucleus nor the extent of overall LANA expression per cell. This suggests a more complex mode of local gene regulation, rather than one that simply reflects the relative intracellular viral copy number. In sum, we have demonstrated the significant potential for false-negative data when using a constitutive marker gene as a sole means of evaluating herpesviral infection, especially in primary cells.
Investigation of the Transverse Spread of Erbium Ions Implanted in SOI

The Er (erbium) ions at energies of 200 500 keV and dose of 2×1015 ions/cm2 were implanted into the optical waveguide material SOI (Silicon on insulator) at room temperature ( RT ) under the angles of 0°, 45° and 60°, respectively. The range distribution of 200 500 keV, 2×1015 ions/cm2 Er ions implanted in SOI samples were measured by Rutherford backscattering (RBS) technique. The transverse distribution of 200 500 keV Er ions in SOI samples were calculated according to the experimental principle proposed by Seijiro Furukawa et al. The measured results are compared with Monte Carlo code, SRIM (Stopping and Range of Ions in Matter) predictions. It is found that the measured experimental values are in good agreement with the SRIM 2012 theoretical simulation results. Keywords—electro-optical materials; transverse distribution; Rutherford backscattering technique; ion implantation
Urinary bisphenol-A, phthalate metabolites and body composition in US adults, NHANES 1999–2006

Abstract Background: Exposure to bisphenol-A (BPA) and phthalates is highly prevalent. Prior studies have not assessed associations between urinary levels of BPA and phthalate metabolites and body composition. Methods: National Health and Nutrition Examination Survey (NHANES) data from 1999 to 2006 on adults aged ≥20 were analyzed by linear regression for associations between urinary BPA, monoethyl phthalate, monobutyl phthalate (MBP), monoethylhexyl phthalate (MEHP), and monobenzyl phthalate (MBzP) and lean mass, fat mass, and percent body fat. Results: BPA and phthalate metabolites were not independently associated with fat mass or percent body fat. Significant inverse associations were observed with lean mass, with the strongest association observed for BPA in men (mean lean mass 1.39 kg lower for quartile 4 vs. quartile 1, p trend = 0.02). Conclusions: BPA and some phthalates could have important, negative effects on muscle and may affect conditions related to deficits in lean mass, though additional research is needed.
Mapping of Post-translational Modifications of Transition Proteins, TP1 and TP2, and Identification of Protein Arginine Methyltransferase 4 and Lysine Methyltransferase 7 as Methyltransferase for TP2*

Background: Transition proteins replace 90% of the nucleosomal histones during nucleo-histone to nucleo-protamine chromatin reconfiguration in mammalian spermiogenesis. Results: Major transition proteins, TP1 and TP2, harbor several post-translational modifications. TP2 is methylated by PRMT4 and KMT7 methyltransferase. Conclusion: Endogenous transition proteins, TP1 and TP2, exhibit extensive post-translational modifications. Significance: This work provides insight into the chromatin remodeling events during spermiogenesis and establishment of the sperm epigenome. In a unique global chromatin remodeling process during mammalian spermiogenesis, 90% of the nucleosomal histones are replaced by testis-specific transition proteins, TP1, TP2, and TP4. These proteins are further substituted by sperm-specific protamines, P1 and P2, to form a highly condensed sperm chromatin. In spermatozoa, a small proportion of chromatin, which ranges from 1 to 10% in mammals, retains the nucleosomal architecture and is implicated to play a role in transgenerational inheritance. However, there is still no mechanistic understanding of the interaction of chromatin machinery with histones and transition proteins, which facilitate this selective histone replacement from chromatin. Here, we report the identification of 16 and 19 novel post-translational modifications on rat endogenous transition proteins, TP1 and TP2, respectively, by mass spectrometry. By in vitro assays and mutational analysis, we demonstrate that protein arginine methyltransferase PRMT4 (CARM1) methylates TP2 at Arg71, Arg75, and Arg92 residues, and lysine methyltransferase KMT7 (Set9) methylates TP2 at Lys88 and Lys91 residues. Further studies with modification-specific antibodies that recognize TP2K88me1 and TP2R92me1 modifications showed that they appear in elongating to condensing spermatids and predominantly associated with the chromatin-bound TP2. This work establishes the repertoire of post-translational modifications that occur on TP1 and TP2, which may play a significant role in various chromatin-templated events during spermiogenesis and in the establishment of the sperm epigenome.
Effect of lipopolysaccharide (LPS) chain length on interactions of bactericidal/permeability-increasing protein and its bioactive 23-kilodalton NH2-terminal fragment with isolated LPS and intact Proteus mirabilis and Escherichia coli

The target-specific cytotoxicity for gram-negative bacteria and the endotoxin-neutralizing activity of the 55-kDa bactericidal/Permeability-increasing protein (BPI) and its bioactive 23-kDa NH2-terminal fragment depend on the strong attraction of BPI for the lipid A region of lipopolysaccharides (LPS). We have shown before that smooth gram-negative bacteria with long-chain LPS are more resistant to BPI (especially holo-BPI) than are rough strains. It has been suggested that the high BPI resistance of some gram-negative bacteria, such as Proteus mirabilis, might also reflect the structural diversity of lipid A. To explore this possibility, we compared the antibacterial activity and binding of natural and recombinant holo-BPI and a recombinant NH2-terminal fragment (rBPI-23) to an isogenic rough (Re-LPS chemotype) and a smooth (S-LPS chemotype) strain of P. mirabilis and to LPS isolated from the two strains. Holo-BPI and rBPI-23 were both potently active against the Re strain of P. mirabilis (90% lethal dose, 20 nM). In contrast, the smooth strain was > or = 100 times more resistant to holo-BPI but only 10 times more resistant to rBPI-23. rBPI-23 was also more potent against several Escherichia coli strains from clinical bacteremia isolates. Differences in the antibacterial potency of BPI toward the Re and S strains of P. mirabilis correlated with differences in the binding of holo-BPI and rBPI-23 to these bacteria. In contrast, the binding of biosynthetically (in vitro transcribed and translated) 35S-labeled holo-BPI and NH2-terminal fragment to isolated Re- and S-LPS from P. mirabilis in solution was similar. Moreover, in the Limulus amebocyte lysate assay, holo-BPI and rBPI-23 potently neutralized both forms of LPS with equal effectiveness. Together, these results strongly suggest that BPI recognizes Proteus lipid A and that the relative resistance of (smooth) P. mirabilis to holo-BPI is due to the inhibitory effect of long polysaccharide chains of tightly packed LPS in the envelope.
An Efficient Biomechanical Tongue model for Speech Research.

This paper describes our investigation of a fast 3D finite element method (FEM) for biomedical simulation of a muscle-activated human tongue. Our method uses a linear stiffness-warping scheme to achieve simulation speeds which are within a factor 10 of real-time rates at the expense of a small loss in accuracy. Muscle activations are produced by an arrangement of forces acting along selected edges of the FEM geometry. The model's dynamics are integrated using an implicit Euler formulation, which can be solved using either the conjugate gradient method or a direct sparse solver. To assess the utility of this model, we compare its accuracy against slower, but less approximate, simulations of a reference tongue model prepared using the FEM simulation package ANSYS.
Automatic SystemC Code Generation from UML Models at Early Stages of Systems on Chip Design

In this paper, we present our approach for automatic SystemC code generation from UML models at early stages of Systems On Chip (SOC) design. A particularity of our proposed approach is the fact that SystemC code generation process is performed through two levels of abstraction. In the first level, we use UML hierarchic sequence diagrams to generate a SystemC code that targets algorithmic space exploration and simulation. In the second level of abstraction, messages that occur in sequence diagrams are implemented using UML activity diagrams whose actions are expressed in the C++ Action Language (AL) included in the Rhapsody environment from which a full SystemC code is generated for both simulation and synthesis.
A genomic view of the peopling of the americas

Whole-genome studies have documented that most Native American ancestry stems from a single population that diversified within the continent more than twelve thousand years ago. However, this shared ancestry hides a more complex history whereby at least four distinct streams of Eurasian migration have contributed to present-day and prehistoric Native American populations. Whole genome studies enhanced by technological breakthroughs in ancient DNA now provide evidence of a sequence of events involving initial migration from a structured Northeast Asian source population, followed by a divergence into northern and southern Native American lineages. During the Holocene, new migrations from Asia introduced the Saqqaq/Dorset Paleoeskimo population to the North American Arctic ~4,500 years ago, ancestry that is potentially connected with ancestry found in Athabaskan-speakers today. This was then followed by a major new population turnover in the high Arctic involving Thule-related peoples who are the ancestors of present-day Inuit. We highlight several open questions that could be addressed through future genomic research.