Miracle-dz/UniFAR-FTUs huggingface dataset:
Two‐Dimensional Particle‐in‐Cell Simulation of Magnetosonic Wave Excitation in a Dipole Magnetic Field

The excitation of magnetosonic waves in the meridian plane of a rescaled dipole magnetic field is investigated, for the first time, using a general curvilinear particle‐in‐cell simulation. Our simulation demonstrates that the magnetosonic waves are excited near the equatorial plane by tenuous ring distribution protons. The waves propagate nearly perpendicularly to the background magnetic field along both radially inward and outward directions. Different speeds of inward and outward propagation result in the asymmetrical distribution about the source region. The waves are accompanied by energization of both cool protons and electrons near the wave source region. The cool protons are heated perpendicularly, while the cool electrons can be heated in the parallel direction and also experience enhanced perpendicular drift at the presence of intense wave power. The implications of simulation results to the observations of magnetosonic waves and related particle heating in the inner magnetosphere are also discussed.
Regulation of early gene expression from the bovine papillomavirus genome in transiently transfected C127 cells

Expression of bovine papillomavirus (BPV) early gene products is required for viral DNA replication and establishment of the transformed phenotype. By the use of a highly efficient electroporation system, we have examined for the first time the transcriptional activity of BPV promoters in their natural genomic context in a replication-permissive cell line. We have determined that a qualitatively distinct stage of transcription is not detectable prior to DNA replication in transiently transfected cells. This suggests that the transcriptional activity of the BPV genome in stably transformed cells represents the early stage of BPV gene expression. Quantitative differences in promoter activity between transiently transfected and stably transformed cells suggest that subtle changes in gene expression may control progression of the viral life cycle. Deletion analysis demonstrated that the E2 transactivator protein stimulates all of the early promoters through sequences located in the upstream regulatory region. This E2-dependent enhancer was found to be highly redundant, and particular E2 binding sites did not display a preference for particular promoters. Despite this dependence on a common cis-acting sequence, the various promoters displayed different sensitivities to the E2 transactivator. The findings that E2 regulates all promoters and, with the exception of the E2 repressors, that no other known viral gene product appears to affect transcription indicate that the E2 system functions as the master regulator of BPV early gene expression.
Physiologic response to changing positive end-expiratory pressure during neurally adjusted ventilatory assist in sedated, critically ill adults.

BACKGROUND Neurally adjusted ventilatory assist (NAVA) delivers airway pressure (Paw) in proportion to neural inspiratory drive as reflected by electrical activity of the diaphragm (EAdi). Changing positive end-expiratory pressure (PEEP) impacts respiratory muscle load and function and, hence, EAdi. We aimed to evaluate how PEEP affects the breathing pattern and neuroventilatory efficiency during NAVA. METHODS In 20 adult patients, adequate assist (NAVAal) was first identified based on Paw and tidal volume (Vt) responses to systematic increases in NAVA level while using preset PEEP (PEEPbl). Thereafter, using NAVAal, PEEP was increased to 20 cm water (H(2)O) (PEEPhigh) and then lowered stepwise to 1 cm H(2)O (PEEP1). EAdi, Paw, and Vt were recorded. RESULTS Median NAVAal was 2.7 (interquartile range, 2.3-3.5) cm H(2)O/muV and was similar to NAVAal identified post hoc by 17 independent physicians (2.5 [2.0-3.4] cm H(2)O/muV; P = NS). Reducing PEEPhigh to PEEP1 increased inspiratory EAdi by 34% (2-67; P = .046) and was associated with an increase in mean Paw above PEEP from 8.5 (6.7-11.4) cm H(2)O to 12.2 (8.8-16.7) cm H(2)O (P = .008), whereas Vt and respiratory rate remained unchanged. The response pattern in Vt/EAdi, indicating changes in neuroventilatory efficiency, differed among patients. Tidal breathing occurred at the lowest EAdi cost in seven patients with PEEP1 or half PEEPbl, in six patients with PEEPbl, and in seven patients with PEEPhigh. CONCLUSIONS During NAVAal, increasing PEEP reduces respiratory drive. Patients adapt their neuroventilatory efficiency such that the individual ventilatory pattern is preserved over a wide range of PEEP levels. Monitoring Vt/EAdi during PEEP changes allows identification of a PEEP level at which tidal breathing occurs at minimal EAdi cost. TRIAL REGISTRATION clinicaltrials.gov; Identifier: NCT00529347.
Protein interaction network for Alzheimer's disease using computational approach

Alzheimer's disease (AD) is the most common form of dementia. It is the sixth leading cause of death in old age people. Despite recent advances in the field of drug design, the medical treatment for the disease is purely symptomatic and hardly effective. Thus there is a need to understand the molecular mechanism behind the disease in order to improve the drug aspects of the disease. We provided two contributions in the field of proteomics in drug design. First, we have constructed a protein-protein interaction network for Alzheimer's disease reviewed proteins with 1412 interactions predicted among 969 proteins. Second, the disease proteins were given confidence scores to prioritize and then analyzed for their homology nature with respect to paralogs and homologs. The homology persisted with the mouse giving a basis for drug design phase. The method will create a new drug design technique in the field of bioinformatics by linking drug design process with protein-protein interactions via signal pathways. This method can be improvised for other diseases in future.
Ubiquitin Ligase gp78 Targets Unglycosylated Prion Protein PrP for Ubiquitylation and Degradation

Prion protein PrP is a central player in several devastating neurodegenerative disorders, including mad cow disease and Creutzfeltd-Jacob disease. Conformational alteration of PrP into an aggregation-prone infectious form PrPSc can trigger pathogenic events. How levels of PrP are regulated is poorly understood. Human PrP is known to be degraded by the proteasome, but the specific proteolytic pathway responsible for PrP destruction remains elusive. Here, we demonstrate that the ubiquitin ligase gp78, known for its role in protein quality control, is critical for unglycosylated PrP ubiquitylation and degradation. Furthermore, C-terminal sequences of PrP protein are crucial for its ubiquitylation and degradation. Our study reveals the first ubiquitin ligase specifically involved in prion protein PrP degradation and PrP sequences crucial for its turnover. Our data may lead to a new avenue to control PrP level and pathogenesis.
On Metric Temporal Description Logics

We introduce metric temporal description logics (mTDLs) as combinations of the classical description logic ALC with (a) LTLbin, an extension of the temporal logic LTL with succinctly represented intervals, and (b) metric temporal logic MTL, extending LTLbin with capabilities to quantitatively reason about time delays. Our main contributions are algorithms and tight complexity bounds for the satisfiability problem in these mTDLs: For mTDLs based on (fragments of) LTLbin, we establish complexity bounds ranging from EXPTIME to 2EXPSPACE. For mTDLs based on (fragments of) MTL interpreted over the naturals, we establish complexity bounds ranging from EXPSPACE to 2EXPSPACE.
Phase Transition and Hysteresis in an Ensemble of Stochastic Spiking Neurons

An ensemble of stochastic nonleaky integrate-and-fire neurons with global, delayed, and excitatory coupling and a small refractory period is analyzed. Simulations with adiabatic changes of the coupling strength indicate the presence of a phase transition accompanied by a hysteresis around a critical coupling strength. Below the critical coupling production of spikes in the ensemble is governed by the stochastic dynamics, whereas for coupling greater than the critical value, the stochastic dynamics loses its influence and the units organize into several clusters with self-sustained activity. All units within one cluster spike in unison, and the clusters themselves are phase-locked. Theoretical analysis leads to upper and lower bounds for the average interspike interval of the ensemble valid for all possible coupling strengths. The bounds allow calculating the limit behavior for large ensembles and characterize the phase transition analytically. These results may be extensible to pulse-coupled oscillators.
A Real-Time PCR for Detection and Quantification of Mycoplasma ovipneumoniae

A real-time PCR for detection and quantification of M. ovipneumoniae was developed using 9 recently sequenced M. ovipneumoniae genomes and primers targeting a putative adhesin gene p113. The assay proved to be specific and sensitive (with a detection limit of 22 genomic DNA) and could quantify M. ovipneumoniae DNA over a wide linear range, from 2.2 × 102 to 2.2 × 107 genomes.
Implicit Contact Handling for Deformable Objects

We present an algorithm for robust and efficient contact handling of deformable objects. By being aware of the internal dynamics of the colliding objects, our algorithm provides smooth rolling and sliding, stable stacking, robust impact handling, and seamless coupling of heterogeneous objects, all in a unified manner. We achieve dynamicsawareness through a constrained dynamics formulation with implicit complementarity constraints, and we present two major contributions that enable an efficient solution of the constrained dynamics problem: a time stepping algorithm that robustly ensures non‐penetration and progressively refines the formulation of constrained dynamics, and a new solver for large mixed linear complementarity problems, based on iterative constraint anticipation. We show the application of our algorithm in challenging scenarios such as multi‐layered cloth moving at high velocities, or colliding deformable solids simulated with large time steps.
Voting with Rank Dependent Scoring Rules

Positional scoring rules in voting compute the score of an alternative by summing the scores for the alternative induced by every vote. This summation principle ensures that all votes contribute equally to the score of an alternative. We relax this assumption and, instead, aggregate scores by taking into account the rank of a score in the ordered list of scores obtained from the votes. This defines a new family of voting rules, rank-dependent scoring rules (RDSRs), based on ordered weighted average (OWA) operators, which, include all scoring rules, and many others, most of which of new. We study some properties of these rules, and show, empirically, that certain RDSRs are less manipulable than Borda voting, across a variety of statistical cultures.
FAST MOLECULAR OUTFLOWS IN LUMINOUS GALAXY MERGERS: EVIDENCE FOR QUASAR FEEDBACK FROM HERSCHEL

We report the results from a systematic search for molecular (OH 119 μm) outflows with Herschel/PACS in a sample of 43 nearby (z < 0.3) galaxy mergers, mostly ultraluminous infrared galaxies (ULIRGs) and QSOs. We find that the character of the OH feature (strength of the absorption relative to the emission) correlates with that of the 9.7 μm silicate feature, a measure of obscuration in ULIRGs. Unambiguous evidence for molecular outflows, based on the detection of OH absorption profiles with median velocities more blueshifted than −50 km s−1, is seen in 26 (70%) of the 37 OH-detected targets, suggesting a wide-angle (∼145°) outflow geometry. Conversely, unambiguous evidence for molecular inflows, based on the detection of OH absorption profiles with median velocities more redshifted than +50 km s−1, is seen in only four objects, suggesting a planar or filamentary geometry for the inflowing gas. Terminal outflow velocities of ∼−1000 km s−1 are measured in several objects, but median outflow velocities are typically ∼−200 km s−1. While the outflow velocities show no statistically significant dependence on the star formation rate, they are distinctly more blueshifted among systems with large active galactic nucleus (AGN) fractions and luminosities [log (LAGN/L☉) ⩾ 11.8 ± 0.3]. The quasars in these systems play a dominant role in driving the molecular outflows. However, the most AGN dominated systems, where OH is seen purely in emission, show relatively modest OH line widths, despite their large AGN luminosities, perhaps indicating that molecular outflows subside once the quasar has cleared a path through the obscuring material.
Sparse Modeling for Image and Vision Processing

In recent years, a large amount of multi-disciplinary research has been conducted on sparse models and their applications. In statistics and machine learning, the sparsity principle is used to perform model selection - that is, automatically selecting a simple model among a large collection of them. In signal processing, sparse coding consists of representing data with linear combinations of a few dictionary elements. Subsequently, the corresponding tools have been widely adopted by several scientific communities such as neuroscience, bioinformatics, or computer vision. The goal of this monograph is to offer a self-contained view of sparse modeling for visual recognition and image processing. More specifically, we focus on applications where the dictionary is learned and adapted to data, yielding a compact representation that has been successful in various contexts.
DRAM1 Regulates Autophagy Flux through Lysosomes

We have previously reported that the mitochondria inhibitor 3-nitropropionic acid (3-NP), induces the expression of DNA damage-regulated autophagy modulator1 (DRAM1) and activation of autophagy in rat striatum. Although the role of DRAM1 in autophagy has been previously characterized, the detailed mechanism by which DRAM1 regulates autophagy activity has not been fully understood. The present study investigated the role of DRAM1 in regulating autophagy flux. In A549 cells expressing wilt-type TP53, 3-NP increased the protein levels of DRAM1 and LC3-II, whereas decreased the levels of SQSTM1 (sequestosome 1). The increase in LC3-II and decrease in SQSTM1 were blocked by the autophagy inhibitor 3-methyl-adenine. Lack of TP53 or knock-down of TP53 in cells impaired the induction of DRAM1. Knock-down of DRAM1 with siRNA significantly reduced 3-NP-induced upregulation of LC3-II and downregulation of SQSTM1, indicating DRAM1 contributes to autophagy activation. Knock-down of DRAM1 robustly decreased rate of disappearance of induced autophagosomes, increased RFP-LC3 fluorescence dots and decreased the decline of LC3-II after withdraw of rapamycin, indicating DRAM1 promotes autophagy flux. DRAM1 siRNA inhibited lysosomal V-ATPase and acidification of lysosomes. As a result, DRAM1 siRNA reduced activation of lysosomal cathepsin D. Similar to DRAM1 siRNA, lysosomal inhibitors E64d and chloroquine also inhibited clearance of autophagosomes and activation of lysosomal cathapsin D after 3-NP treatment. These data suggest that DRAM1 plays important roles in autophagy activation induced by mitochondria dysfunction. DRAM1 affects autophagy through argument of lysosomal acidification, fusion of lysosomes with autophagosomes and clearance of autophagosomes.
Microbial Community Analysis of a Methane-Producing Biocathode in a Bioelectrochemical System

A methane-producing biocathode that converts CO2 into methane was studied electrochemically and microbiologically. The biocathode produced methane at a maximum rate of 5.1 L CH4/m2 projected cathode per day (1.6 A/m2) at −0.7 V versus NHE cathode potential and 3.0 L CH4/m2 projected cathode per day (0.9 A/m2) at −0.6 V versus NHE cathode potential. The microbial community at the biocathode was dominated by three phylotypes of Archaea and six phylotypes of bacteria. The Archaeal phylotypes were most closely related to Methanobacterium palustre and Methanobacterium aarhusense. Besides methanogenic Archaea, bacteria seemed to be associated with methane production, producing hydrogen as an intermediate. Biomass density varied greatly with part of the carbon electrode covered with a dense biofilm, while only clusters of cells were found on other parts. Based on our results, we discuss how inoculum enrichment and changing operational conditions may help to increase biomass density and to select for microorganisms that produce methane.
Determining Moisture Content in Small Wheat Samples by Dual-frequency RF Impedance Sensing

A technique is described for estimating moisture content of small samples of hard red winter wheat (10 to 30 kernels) by impedance measurements at 1 and 4.5 MHz on a parallel-plate capacitor holding the sample between the plates. The measurement system was calibrated by measurements on samples, ranging from 9 to 20% moisture content, wet basis, from three wheat cultivars grown in 1991 and 1992. Validation measurements were taken for prediction of moisture content of small wheat samples from three different cultivars harvested in 1992. Moisture contents of the small samples were predicted with a five-variable equation involving differences in the real and imaginary components of the complex impedance at the two frequencies. The standard error was 0.9% moisture content. The study established a basis for further development of the rapid, nondestructive method for estimating moisture content of small wheat samples.
Synapse Loss in Cortex of Agrin-Deficient Mice after Genetic Rescue of Perinatal Death

Agrin-deficient mice die at birth because of aberrant development of the neuromuscular junctions. Here, we examined the role of agrin at brain synapses. We show that agrin is associated with excitatory but not inhibitory synapses in the cerebral cortex. Most importantly, we examined the brains of agrin-deficient mice whose perinatal death was prevented by the selective expression of agrin in motor neurons. We find that the number of presynaptic and postsynaptic specializations is strongly reduced in the cortex of 5- to 7-week-old mice. Consistent with a reduction in the number of synapses, the frequency of miniature postsynaptic currents was greatly decreased. In accordance with the synaptic localization of agrin to excitatory synapses, changes in the frequency were only detected for excitatory but not inhibitory synapses. Moreover, we find that the muscle-specific receptor tyrosine kinase MuSK, which is known to be an essential component of agrin-induced signaling at the neuromuscular junction, is also localized to a subset of excitatory synapses. Finally, some components of the mitogen-activated protein (MAP) kinase pathway, which has been shown to be activated by agrin in cultured neurons, are deregulated in agrin-deficient mice. In summary, our results provide strong evidence that agrin plays an important role in the formation and/or the maintenance of excitatory synapses in the brain, and we provide evidence that this function involves MAP kinase signaling.
Combined deficiency of alpha and epsilon sarcoglycan disrupts the cardiac dystrophin complex

Cardiomyopathy is a puzzling complication in addition to skeletal muscle pathology for patients with mutations in β-, γ- or δ-sarcoglycan (SG) genes. Patients with mutations in α-SG rarely have associated cardiomyopathy, or their cardiac pathology is very mild. We hypothesize that a fifth SG, ɛ-SG, may compensate for α-SG deficiency in the heart. To investigate the function of ɛ-SG in striated muscle, we generated an Sgce-null mouse and a Sgca-;Sgce-null mouse, which lacks both α- and ɛ-SGs. While Sgce-null mice showed a wild-type phenotype, with no signs of muscular dystrophy or heart disease, the Sgca-;Sgce-null mouse developed a progressive muscular dystrophy and a more anticipated and severe cardiomyopathy. It shows a complete loss of residual SGs and a strong reduction in both dystrophin and dystroglycan. Our data indicate that ɛ-SG is important in preventing cardiomyopathy in α-SG deficiency.
Interrelation of energy intake, body size, and physical activity with prostate cancer in a large prospective cohort study.

Energy restriction reduces prostate tumor growth in transplantable tumor models in rodents, which suggests that excessive energy intake may contribute to the risk of prostate cancer. The association of total energy intake across the normal range with prostate cancer has not been consistent in epidemiological studies. We prospectively evaluated the joint associations of energy intake and body size or physical activity with prostate cancer. Participants were 46786 male health professionals ages 40-75 years at baseline in 1986 who were free of cancer diagnosis. Between 1986 and 2000, we documented 2896 incident prostate cancer cases (excluding stage T1a) by review of medical records and histopathology reports. Of these, 339 were metastatic or fatal cases. We used Cox proportional hazards regression to estimate the multivariate relative risk (RR) of prostate cancer associated with energy intake measured using a food frequency questionnaire, overall and stratified by body mass index, waist size, physical activity, as well as by age and family history of prostate cancer. There was no association between energy intake and total prostate cancer incidence. However, a modest increased risk of metastatic or fatal disease with energy intake was suggested [RR comparing extreme quintiles: 1.38, 95% confidence interval (CI) 0.96-1.98, P(trend) = 0.06]. This association was most pronounced in men with a lower body mass index (in stratum < 24 kg/m(2): RR = 1.76, 95% CI 0.92-3.39; P(interaction) = 0.04), smaller waist size [in stratum <or= 37 inches: RR = 1.91, 95% CI 0.83-4.36; P(interaction) = 0.03], and who were more physically active [in stratum >or= median: RR = 1.74, 95% CI 0.93-3.26; P(interaction) = 0.09]. Also, the association of energy intake with metastatic and fatal prostate cancer was restricted to men who were younger [in stratum <or= 65 years old: RR = 2.60, 95% CI 1.26-5.39; P(interaction) = 0.04] or who had a positive family history [RR = 3.33, 95% CI 1.26-8.76; P(interaction) = 0.04]. Although energy intake is known to be imperfectly measured by questionnaire, we observed a positive association between energy intake and metastatic or fatal prostate cancer among men who were leaner, more physically active, younger, and who had a family history of prostate cancer. Our observations suggest the testable hypothesis that the elevated risk of clinically important prostate cancer in men with a high energy intake may be attributable to certain metabolic profiles that favor enhanced growth factor production over an increase in adiposity.
CMIP5 Diversity in Southern Westerly Jet Projections Related to Historical Sea Ice Area: Strong Link to Strengthening and Weak Link to Shift

AbstractA major feature of projected changes in Southern Hemisphere climate under future scenarios of increased greenhouse gas concentrations is the poleward shift and strengthening of the main eddy-driven belt of mid-latitude near-surface westerly winds (the westerly jet). However, there is large uncertainty in projected twenty-first century westerly jet changes across different climate models.Here the World Climate Research Programme’s Coupled Model Intercomparison Project phase 5 (CMIP5) models were evaluated to assess linkages between diversity in simulated sea ice area (SIA), Antarctic amplification and diversity in projected 21st century changes in the westerly jet following the Representative Concentration Pathway 8.5 scenario (RCP8.5). To help disentangle cause and effect in the coupled model analysis, uncoupled atmosphere-only fixed sea-surface experiments from CMIP5 were also evaluated.It is shown that across all seasons approximately half of the variance in projected RCP8.5 jet strengthening is.