Miracle-dz/UniFAR-FTUs huggingface dataset:
HAR+: Archive and metadata distribution! Why not both?

Size of the data used in today's enterprises has been expanding at a huge range from last few years. Simultaneously, the need to process and analyze the large volumes of data has also increased. Hadoop Distributed File System (HDFS), is an open source implementation of Apache, designed for running on commodity hardware to handle applications having large datasets (TB, PB). HDFS architecture is based on single master (Name Node), which handles the metadata for large number of slaves. To get maximum efficiency, Name Node stores all of the metadata in its RAM. So, when dealing with huge number of small files, Name Node often becomes a bottleneck for HDFS as it might run out of memory. Apache Hadoop uses Hadoop ARchive (HAR) to deal with small files. But it is not so efficient for multi-NameNode environment, which requires automatic scaling of metadata. In this paper, we have designed hashtable based architecture, Hadoop ARchive Plus (HAR+) using sha256 as the key, which is a modification of existing HAR. HAR+ is designed to provide more reliability which can also provide auto scaling of metadata. Instead of using one NameNode for storing the metadata, HAR+ uses multiple NameNodes. Our result shows that HAR+ reduces the load of a single NameNode in significant amount. This makes the cluster more scalable, more robust and less prone to failure unlike of Hadoop ARchive.
Physical and Psychosocial Contributors to Quality of Life in Veterans With Hepatitis C Not on Antiviral Therapy

Background and Aims: Treatment-naive hepatitis C virus (HCV)-infected patients report impaired health-related quality of life (HRQOL), although causes are unclear. Psychosocial factors may be major determinants of HRQOL. Methods: We administered a general (Short Form-36; SF-36) and a liver-specific (Chronic Liver Disease Questionnaire; CLDQ) HRQOL measure to 62 HCV-infected veterans being considered for antiviral therapy. Psychosocial assessment included the Structured Clinical Interview for DSM-IV Axis I Disorders/Non-Patient (SCID-I/NP), Beck Depression Inventory-II (BDI-II), Beck Anxiety Inventory (BAI), Abbreviated Cook-Medley (ACM) anger measure, and Medical Outcomes Study Social Support Measure (SSM). We examined the potential determinants of HRQOL, including psychosocial measures, demographic measures (age, sex, race/ethnicity), clinical measures (presence of cirrhosis, comorbid medical conditions), and viral data (quantitative PCR). Results: SF-36 scores were significantly lower in HCV-infected patients than published U.S. population norms but similar to those reported by previous studies of HCV-infected samples. CLDQ scores were very similar to those reported by previous studies. Demographic, clinical, and viral indicators were not statistically associated with HRQOL, and neither was the presence of a substance abuse or psychotic disorder. Lower BDI-II and BAI scores were associated with better general and disease-specific HRQOL. Lower SSM scores were associated with lower scores on SF-36 but not CLDQ; however, this effect did not persist in multiple linear regression analyses. In these, BDI-II was the strongest independent predictor of both SF-36 and CLDQ. Conclusions: Psychosocial factors, especially depression, are strong indicators of impaired HRQOL for HCV-infected veterans not receiving antiviral therapy. Screening and treatment of psychosocial factors is recommended.
Congenital complete heart block and successful vaginal delivery.

BACKGROUND Congenital complete heart block is an uncommon fetal arrhythmia characterized by complete dissociation of the atrial and ventricular contractions. CASES Two patients were diagnosed with isolated congenital complete heart block in the second trimester of pregnancy. Successful vaginal delivery was achieved by both. CONCLUSION A monitoring protocol algorithm to be used by the clinician in managing term patients with isolated complete congenital heart block is presented. Vaginal delivery can be safely accomplished in patients with isolated congenital complete heart block, with the use of ultrasound and fetal scalp blood sampling to assess fetal well-being during labor and delivery.
Methamphetamine-induced disruption of frontostriatal reward learning signals: relation to psychotic symptoms.

OBJECTIVE Frontostriatal circuitry is critical to learning processes, and its disruption may underlie maladaptive decision making and the generation of psychotic symptoms in schizophrenia. However, there is a paucity of evidence directly examining the role of modulatory neurotransmitters on frontostriatal function in humans. In order to probe the effects of modulation on frontostriatal circuitry during learning and to test whether disruptions in learning processes may be related to the pathogenesis of psychosis, the authors explored the brain representations of reward prediction error and incentive value, two key reinforcement learning parameters, before and after methamphetamine challenge. METHOD Healthy volunteers (N=18) underwent functional MRI (fMRI) scanning while performing a reward learning task on three occasions: after placebo, after methamphetamine infusion (0.3 mg/kg body weight), and after pretreatment with 400 mg of amisulpride and then methamphetamine infusion. Brain fMRI representations of learning signals, calculated using a reinforcement Q-learning algorithm, were compared across drug conditions. RESULTS In the placebo condition, reward prediction error was coded in the ventral striatum bilaterally and incentive value in the ventromedial prefrontal cortex bilaterally. Reward prediction error and incentive value signals were disrupted by methamphetamine in the left nucleus accumbens and left ventromedial prefrontal cortex, respectively. Psychotic symptoms were significantly correlated with incentive value disruption in the ventromedial prefrontal and posterior cingulate cortex. Amisulpride pretreatment did not significantly alter methamphetamine-induced effects. CONCLUSIONS The results demonstrate that methamphetamine impairs brain representations of computational parameters that underpin learning. They also demonstrate a significant link between psychosis and abnormal monoamine-regulated learning signals in the prefrontal and cingulate cortices.
Approximative covariance interpolation with a quadratic penalty

Given output data of a stationary stochastic process estimates of the covariances parameters can be obtained. These estimates can be used to determine ARMA models to approximately fit the data by matching the covariances exactly. However, the estimates of the covariances may contain large errors, especially if they are determined from short data sequences, and thus it makes sense to match the covariances only in an approximative way. Here we consider a convex method for solving an approximative covariance interpolation problem while maximizing the entropy and penalize the quadratic deviation from the nominal covariances.
Simple and effective link-time optimization of Modula-3 programs

Modula-3 supports development of modular programs by separating an object's interface from its implementation. This separation induces a runtime overhead in the implementation of objects, because it prevents the compiler from having complete information about a program's type hierarchy. This overhead can be reduced at link time, when the entire type hierarchy becomes available. We describe opportunities for link-time optimization of Modula-3, present two link-time optimizations that reduce the runtime costs of Modula-3's opaque types and methods, and show how link-time optimization could provide C++ which the benefits of opaques types at no additional runtime cost. Our optimization techniques are implemented in mld, a retargetable linker for the MIPS, SPARC, and Intel 486, mld links a machine-independent intermediate code that is suitable for link-time optimization and code generation. Linking intermediate code simplifies implementation of the optimizations and makes it possible to evaluate them on a wide range of architectures. mld's optimizations are effective: they reduce the total number of instructions executed by up to 14% and convert as many as 79% of indirect calls to direct calls.
Increased Adipogenesis of Human Adipose-Derived Stem Cells on Polycaprolactone Fiber Matrices

With accelerating rates of obesity and type 2 diabetes world-wide, interest in studying the adipocyte and adipose tissue is increasing. Human adipose derived stem cells - differentiated to adipocytes in vitro - are frequently used as a model system for white adipocytes, as most of their pathways and functions resemble mature adipocytes in vivo. However, these cells are not completely like in vivo mature adipocytes. Hosting the cells in a more physiologically relevant environment compared to conventional two-dimensional cell culturing on plastic surfaces, can produce spatial cues that drive the cells towards a more mature state. We investigated the adipogenesis of adipose derived stem cells on electro spun polycaprolactone matrices and compared functionality to conventional two-dimensional cultures as well as to human primary mature adipocytes. To assess the degree of adipogenesis we measured cellular glucose-uptake and lipolysis and used a range of different methods to evaluate lipid accumulation. We compared the averaged results from a whole population with the single cell characteristics – studied by coherent anti-Stokes Raman scattering microscopy - to gain a comprehensive picture of the cell phenotypes. In adipose derived stem cells differentiated on a polycaprolactone-fiber matrix; an increased sensitivity in insulin-stimulated glucose uptake was detected when cells were grown on either aligned or random matrices. Furthermore, comparing differentiation of adipose derived stem cells on aligned polycaprolactone-fiber matrixes, to those differentiated in two-dimensional cultures showed, an increase in the cellular lipid accumulation, and hormone sensitive lipase content. In conclusion, we propose an adipocyte cell model created by differentiation of adipose derived stem cells on aligned polycaprolactone-fiber matrices which demonstrates increased maturity, compared to 2D cultured cells.
MicroRNA identity and abundance in developing swine adipose tissue as determined by solexa sequencing

MicroRNAs (miRNAs) are small ∼22‐nt regulatory RNAs that regulate the stability and translation of cognate mRNAs. MiRNAs participate in the regulation of adipogenesis, and identification of the full repertoire of miRNAs expressed in adipose tissue is likely to significantly increase our understanding of adipose tissue growth and development. Here, we adopted a deep sequencing approach to determine the identity and abundance of miRNAs in developing swine adipose tissue. Via this approach, we identified the sequences and relative expression levels of 227 conserved miRNAs (of which 59 were novel) and 66 potential porcine miRNAs. The expression levels displayed a large range, as reflected by the number of sequence reads, which varied from several counts for rare miRNAs to several million reads for the most abundant miRNAs. The abundant miRNAs principally belonged to 32 miRNA gene families, including miR‐143, miR‐103, let‐7, and miR‐148. Of the conserved miRNAs, 93 miRNAs were up‐regulated and 33 miRNAs were down‐regulated in the adult pig adipose tissue. Moreover, we observed sequence variants and seed edits of the miRNAs. KEGG pathway analysis and GO term enrichment suggested that highly expressed miRNAs are involved in adipose tissue development, signal transduction, cell–cell and cell–extracellular matrix communication, neural development and function, and lipid metabolism including carboxylic acid, oxoacid, fatty acid, steroid, glycerolipid, alcohol and phospholipid metabolism. Our results expand the number of known porcine miRNAs and provide a thorough account of the miRNA transcriptome in porcine adipose tissue. J. Cell. Biochem. 112: 1318–1328, 2011. © 2011 Wiley‐Liss, Inc.
INFERENCES ABOUT QUANTITATIVE INHERITANCE BASED ON NATURAL POPULATION STRUCTURE IN THE YELLOW MONKEYFLOWER, MIMULUS GUTTATUS

We used a nonmanipulative, marker‐based method to study quantitative genetic inheritance in two habitats of a common monkeyflower population. The method involved regressing quantitative trait similarity on marker‐estimated relatedness between individuals sampled in the field. We sampled 300 adult plants from each of two transects, one along a stream habitat and another through a meadow habitat. For each plant we measured 10 quantitative characters and assayed 10 polymorphic isozyme loci. In the meadow habitat, relatedness of plants within 1 m was moderate (r = 0.125, corresponding to half‐sibs) as was actual variance of relatedness (Vr = 0.044). Significant heritabilities of 50–70% were found for corolla width and the fitness characters of flower number and plant weight. Genetic correlations were strongly positive, but sharing of environmental effects within 1 m was weak. In the stream habitat, levels of relatedness were lower and similar heritabilities were indicated. To detect dominance variance and the correlation of phenotypes due to shared inbreeding, we also estimated higher‐order coefficients of relationship and inbreeding, but these did not significantly differ from zero. Laboratory‐based estimates of heritability in the field were lower than the marker‐based estimates, indicating that natural heritabilities and genetic correlations may be stronger than indicated by controlled studies.
X-chromosome inactivation mosaicism in the three germ layers and the germ line of the mouse embryo.

Electrophoretic variant forms of the X-linked enzyme phosphoglycerate kinase (PGK-1, E.C.2,7,2,3) have been used to examine X-chromosome mosaicism in tissues from 12 1/2-day post coitum heterozygous female mouse embryos. Samples of yolk-sac endoderm, neural ectoderm, heart (mesoderm), liver (endoderm) and germ cells were analysed from each embryo. In all tissues except yolk-sac endoderm, both PGK-1 isozymes were expressed. The extent of covariance among tissues with respect to the PGK-1 isozyme contribution is consistent with all tissues being derived from the same pool of cells after X-inactivation. The covariance among tissues gives an estimate of the size of this pool (47 cells) and places the earliest time of X-inactivation in epiblast cells between 4 1/2 and 5 1/2 days post coitum. From the independent variance among tissues within an individual, the average primordial precursor pool size for the three germ layers and the germ line itself was estimated as 193 cells.
Linear precoding for mutual information maximization in MIMO systems

We study the design of linear precoders for maximization of the mutual information in MIMO systems with arbitrary constellations and with perfect channel state information at the transmitter. We derive the structure of the optimum precoder and we show that the mutual information is concave in a quadratic function of the precoder coefficients. An iterative algorithm is also proposed to find this optimum value.
Alpha sarcoglycan is required for FGF-dependent myogenic progenitor cell proliferation in vitro and in vivo

Mice deficient in α-sarcoglycan (Sgca-null mice) develop progressive muscular dystrophy and serve as a model for human limb girdle muscular dystrophy type 2D. Sgca-null mice suffer a more severe myopathy than that of mdx mice, the model for Duchenne muscular dystrophy. This is the opposite of what is observed in humans and the reason for this is unknown. In an attempt to understand the cellular basis of this severe muscular dystrophy, we isolated clonal populations of myogenic progenitor cells (MPCs), the resident postnatal muscle progenitors of dystrophic and wild-type mice. MPCs from Sgca-null mice generated much smaller clones than MPCs from wild-type or mdx dystrophic mice. Impaired proliferation of Sgca-null myogenic precursors was confirmed by single fiber analysis and this difference correlated with Sgca expression during MPC proliferation. In the absence of dystrophin and associated proteins, which are only expressed after differentiation, SGCA complexes with and stabilizes FGFR1. Deficiency of Sgca leads to an absence of FGFR1 expression at the membrane and impaired MPC proliferation in response to bFGF. The low proliferation rate of Sgca-null MPCs was rescued by transduction with Sgca-expressing lentiviral vectors. When transplanted into dystrophic muscle, Sgca-null MPCs exhibited reduced engraftment. The reduced proliferative ability of Sgca-null MPCs explains, at least in part, the severity of this muscular dystrophy and also why wild-type donor progenitor cells engraft efficiently and consequently ameliorate disease.
Pilus Phase Variation Switches Gonococcal Adherence to Invasion by Caveolin-1-Dependent Host Cell Signaling

Many pathogenic bacteria cause local infections but occasionally invade into the blood stream, often with fatal outcome. Very little is known about the mechanism underlying the switch from local to invasive infection. In the case of Neisseria gonorrhoeae, phase variable type 4 pili (T4P) stabilize local infection by mediating microcolony formation and inducing anti-invasive signals. Outer membrane porin PorBIA, in contrast, is associated with disseminated infection and facilitates the efficient invasion of gonococci into host cells. Here we demonstrate that loss of pili by natural pilus phase variation is a prerequisite for the transition from local to invasive infection. Unexpectedly, both T4P-mediated inhibition of invasion and PorBIA-triggered invasion utilize membrane rafts and signaling pathways that depend on caveolin-1-Y14 phosphorylation (Cav1-pY14). We identified p85 regulatory subunit of PI3 kinase (PI3K) and phospholipase Cγ1 as new, exclusive and essential interaction partners for Cav1-pY14 in the course of PorBIA-induced invasion. Active PI3K induces the uptake of gonococci via a new invasion pathway involving protein kinase D1. Our data describe a novel route of bacterial entry into epithelial cells and offer the first mechanistic insight into the switch from local to invasive gonococcal infection.
Measuring multimedia quality in mobile networks with an objective parametric model

The perceived quality of a multimedia stream can be estimated with good accuracy with a parametric no-reference opinion model taking codec, total coded bitrate, packet loss rate, and buffering events as input. A rebuffering event in a multimedia stream severely reduces the perceived quality with up to 1.5 MOS units for a QCIF video. High packet loss rates can reduce the quality with as much as 2.5 MOS units. The effect of these two degradation types has been combined in a non-linear way together with information about codec and coded bitrate to form a parametric no-reference objective opinion model. The model shows good performance with RMSE of 0.33 and correlation coefficient of 0.93.
Improving accuracy of protein contact prediction using balanced network deconvolution

Residue contact map is essential for protein three‐dimensional structure determination. But most of the current contact prediction methods based on residue co‐evolution suffer from high false‐positives as introduced by indirect and transitive contacts (i.e., residues A–B and B–C are in contact, but A–C are not). Built on the work by Feizi et al. (Nat Biotechnol 2013; 31:726–733), which demonstrated a general network model to distinguish direct dependencies by network deconvolution, this study presents a new balanced network deconvolution (BND) algorithm to identify optimized dependency matrix without limit on the eigenvalue range in the applied network systems. The algorithm was used to filter contact predictions of five widely used co‐evolution methods. On the test of proteins from three benchmark datasets of the 9th critical assessment of protein structure prediction (CASP9), CASP10, and PSICOV (precise structural contact prediction using sparse inverse covariance estimation) database experiments, the BND can improve the medium‐ and long‐range contact predictions at the L/5 cutoff by 55.59% and 47.68%, respectively, without additional central processing unit cost. The improvement is statistically significant, with a P‐value < 5.93 × 10−3 in the Student's t‐test. A further comparison with the ab initio structure predictions in CASPs showed that the usefulness of the current co‐evolution‐based contact prediction to the three‐dimensional structure modeling relies on the number of homologous sequences existing in the sequence databases. BND can be used as a general contact refinement method, which is freely available at: http://www.csbio. sjtu.edu. cn/bioinf/BND/. Proteins 2015; 83:485–496. © 2014 Wiley Periodicals, Inc.
Spatially Modulated Gain Erbium-Doped Ti:LiNbO3 Waveguide Laser

In this letter, we present the first 1.5-μm single frequency Fabry-Pérot laser device that is free of spatial hole burning. The laser was realized using erbium-doped LiNbO3 waveguide. The optical gain of this laser is spatially distributed in such a manner to coincide with the standing wave pattern of the oscillating laser field. Thereby, the spatial hole burning was eliminated. Clean 1531-nm single-frequency operation was demonstrated.
Influence of postangioplasty beta-irradiation on endothelial function in porcine coronary arteries.

BACKGROUND Postangioplasty (PTCA) intracoronary radiation therapy (ICRT) has been demonstrated to limit restenosis. The consequences of these procedures on coronary reactivity are unknown. METHODS AND RESULTS Porcine coronary arteries were studied after PTCA immediately (n=5) and 6 weeks (n=5) after ICRT (n=5 and 5, respectively), after combined PTCA+ICRT (n=5 and 7, respectively), and after no intervention (n=11). A 3-cm-long source train of Sr/Y(90) was used in vivo to deliver 16 Gy at a depth of 2 mm from the source center, as used in clinical trials. Arterial rings were mounted on myographs to record isometric tension. After achieving steady-state contraction to depolarizing physiological solution containing 40 mmol/L KCl, measured baseline tension was significantly elevated immediately after all interventions. It returned to normal levels 6 weeks after PTCA and ICRT alone but was significantly reduced if combined. Active contractions induced by 40 mmol/L KCl were maintained after combined therapy both immediately after and at 6 weeks. In these depolarizing conditions, nitric oxide-dependent relaxation to substance P was trivial after PTCA+ICRT and reduced after ICRT, whereas in the presence of physiological solution and N(omega)-nitro-L-arginine, substance P-induced relaxation was reduced after PTCA and abolished after PTCA+ICRT 6 weeks after intervention. In rings without endothelium, the relaxation mediated by sodium nitroprusside (0.1 micromol/L) was reduced immediately after PTCA and at 6 weeks. CONCLUSIONS PTCA+ICRT altered the passive mechanical properties of porcine coronary arterial wall. Furthermore, at 6 weeks, receptor-operated release of endothelium-derived nitric oxide and endothelium-derived hyperpolarizing factor was reduced by ICRT and PTCA alone, respectively, and was prevented by their combination.
Cell-to-Cell Spread of Retroviruses

Viruses from several families use direct cell-to-cell infection to disseminate between cells. Retroviruses are a relatively recent addition to this list, and appear to spread cell-to-cell by induction of multimolecular complexes termed virological synapses that assemble at the interface between infected and receptor-expressing target cells. Over the past five years, detailed insight into the cellular and molecular basis of virological synapse-mediated retroviral cell-to-cell spread has been obtained, but important questions and controversies have been raised that remain to be resolved. This review will focus on recent advances in the field with emphasis on areas in which work still needs to be done.