Miracle-dz/UniFAR-FTUs huggingface dataset:
Retrograde transport from the yeast Golgi is mediated by two ARF GAP proteins with overlapping function

ARF proteins, which mediate vesicular transport, have little or no intrinsic GTPase activity. They rely on the actions of GTPase‐activating proteins (GAPs) for their function. The in vitro GTPase activity of the Saccharomyces cerevisiae ARF proteins Arf1 and Arf2 is stimulated by the yeast Gcs1 protein, and in vivo genetic interactions between arf and gcs1 mutations implicate Gcs1 in vesicular transport. However, the Gcs1 protein is dispensable, indicating that additional ARF GAP proteins exist. We show that the structurally related protein Glo3, which is also dispensable, also exhibits ARF GAP activity. Genetic and in vitro approaches reveal that Glo3 and Gcs1 have an overlapping essential function at the endoplasmic reticulum (ER)–Golgi stage of vesicular transport. Mutant cells deficient for both ARF GAPs cannot proliferate, undergo a dramatic accumulation of ER and are defective for protein transport between ER and Golgi. The glo3Δ and gcs1Δ single mutations each interact with a sec21 mutation that affects a component of COPI, which mediates vesicular transport within the ER–Golgi shuttle, while increased dosage of the BET1, BOS1 and SEC22 genes encoding members of a v‐SNARE family that functions within the ER–Golgi alleviates the effects of a glo3Δ mutation. An in vitro assay indicates that efficient retrieval from the Golgi to the ER requires these two proteins. These findings suggest that Glo3 and Gcs1 ARF GAPs mediate retrograde vesicular transport from the Golgi to the ER.
Prospective Observational Study of Implantable Cardioverter‐Defibrillators in Primary Prevention of Sudden Cardiac Death: Study Design and Cohort Description

Background Primary‐prevention implantable cardioverter‐defibrillators (ICDs) reduce total mortality in patients with severe left ventricular systolic function. However, only a minority of patients benefit from these devices. We designed the Prospective Observational Study of Implantable Cardioverter‐Defibrillators (PROSE‐ICD) to identify risk factors and enhance our understanding of the biological mechanisms that predispose to arrhythmic death in patients undergoing ICD implantation for primary prevention of sudden death. Methods and Results This is a multicenter prospective cohort study with a target enrollment of 1200 patients. The primary end point is ICD shocks for adjudicated ventricular tachyarrhythmias. The secondary end point is total mortality. All patients undergo a comprehensive evaluation including history and physical examination, signal‐averaged electrocardiograms, and blood sampling for genomic, proteomic, and metabolomic analyses. Patients are evaluated every 6 months and after every known ICD shock for additional electrocardiographic and blood sampling. As of December 2011, a total of 1177 patients have been enrolled with more nonwhite and female patients compared to previous randomized trials. A total of 143 patients have reached the primary end point, whereas a total of 260 patients died over an average follow‐up of 59 months. The PROSE‐ICD study represents a real‐world cohort of individuals with systolic heart failure receiving primary‐prevention ICDs. Conclusions Extensive electrophysiological and structural phenotyping as well as the availability of serial DNA and serum samples will be important resources for evaluating novel metrics for risk stratification and identifying patients at risk for arrhythmic sudden death. Clinical Trial Registration URL: http://clinicaltrials.gov/ Unique Identifier: NCT00733590.
Learning Multiscale Representations of Natural Scenes Using Dirichlet Processes

We develop nonparametric Bayesian models for multiscale representations of images depicting natural scene categories. Individual features or wavelet coefficients are marginally described by Dirichlet process (DP) mixtures, yielding the heavy-tailed marginal distributions characteristic of natural images. Dependencies between features are then captured with a hidden Markov tree, and Markov chain Monte Carlo methods used to learn models whose latent state space grows in complexity as more images are observed. By truncating the potentially infinite set of hidden states, we are able to exploit efficient belief propagation methods when learning these hierarchical Dirichlet process hidden Markov trees (HDP-HMTs) from data. We show that our generative models capture interesting qualitative structure in natural scenes, and more accurately categorize novel images than models which ignore spatial relationships among features.
Polysialylated Neural Cell Adhesion Molecule Is Involved in Induction of Long-Term Potentiation and Memory Acquisition and Consolidation in a Fear-Conditioning Paradigm

Polysialic acid (PSA) regulates functions of the neural cell adhesion molecule (NCAM) during development and in neuroplasticity in the adult; the underlying mechanisms at different phases of learning and memory consolidation are, however, unknown. To investigate the contributions of PSA versus the extracellular domain of the NCAM glycoprotein backbone to synaptic plasticity, we applied NCAM, PSA-NCAM, and PSA to acute slices of the hippocampal CA1 region of NCAM-deficient mice and measured their effects on long-term potentiation (LTP). Remarkably, only PSA and PSA-NCAM, but not NCAM restored normal LTP. Application of these molecules to the dorsal hippocampus of wild-type mice showed that PSA-NCAM and PSA, but not NCAM, injected before fear conditioning, impaired formation of hippocampus-dependent contextual memory. Consolidation of contextual memory was affected by PSA-NCAM only when injected during its late, but not early phases. None of the tested compounds disturbed extrahippocampal-cued memory. Mice lacking the polysialyltransferase (ST8SialV/PST) responsible for attachment of PSA to NCAM in adulthood showed a mild deficit only in hippocampal contextual learning, when compared with NCAM-deficient mice that were disturbed in both contextual and cued memories. Contextual and tone memory in NCAM-deficient mice could be partially restored by injection of PSA-NCAM, but not of NCAM, into the hippocampus, suggesting that the impact of PSA-NCAM in synaptic plasticity and learning is not mediated by modulation of NCAM–NCAM homophilic interactions. In conclusion, our data support the view that polysialylated NCAM is involved in both formation and late consolidation of contextual memory.
Geometric incidence theorems via Fourier analysis

We show that every non-trivial Sobolev bound for generalized Radon transforms which average functions over families of curves and surfaces yields an incidence theorem for suitably regular discrete sets of points and curves or surfaces in Euclidean space. This mechanism allows us to deduce geometric results not readily accessible by combinatorial methods.
Pelletization of Iron Oxide Based Sorbents for Hydrogen Sulfide Removal

Biogas derived from anaerobic digestion of biological wastes has been extensively used for heating purposes and/or electricity generation. Presence of hydrogen sulfide (H2S) in biogas affects engine performance adversely, thus reducing H2S content is a valuable part in practical application before utilizing biogas. Adsorptive separation is very appealing due to being an economical and effective method including the use of iron oxide based adsorbents. Pelletization of iron oxide adsorbents has never been reported among the adsorbents described to date. Therefore, H2S capture in two iron oxides (ferric oxide (Fe2O3) and magnetite (Fe3O4)) was experimentally investigated to determine technical feasibility of shaping pellets based on active iron oxide sorbent in removing H2S from a simulated gas stream (0.35 vol.% H2S balanced in N2). Many factors affecting the behavior of gas adsorption such as gas in-flow rate, adsorption temperature, binder loadings and textural characteristics were considered. The pellet strengths were also undertaken using a bulk crushing strength analyzer. The results indicated that higher temperature favors the diffusion of H2S molecules from the surface into the bulk of iron oxides. The H2S-sorption capacity of Fe3O4 sorbent was higher than that of Fe2O3 sorbent corresponding with the different pore volume and surface area in each adsorbent. With the same active Fe3O4, the extruded pellet produced with starch binder showed the excellent H2S uptake and crushing resistance. The higher gas in-flow rate had positive impact to contacting efficiency and mass transfer of solid and gas phase. The adsorbed H2S gas can be readily desorbed from the pellets with the desorption temperature below 60°C and the H2S-sorption capacity was consistent over repeated cycles. The pellets can be reused several times for consecutive adsorption/desorption cycles, without loss of performance in a large-scale reactor and therefore represent serious candidates for use in commercial absorbers.
Diagnostic Value of Fecal Calprotectin (S100 A8/A9) Test in Children with Chronic Abdominal Pain

Objectives. The aim of the study was to establish whether fecal calprotectin concentration (FCC) may be useful in children with chronic abdominal pain to differentiate between inflammatory bowel disease (IBD), other inflammatory gastrointestinal disorders, and functional gastrointestinal disorders. Methods. The study included 163 patients (median age 13 years), who were assigned to four study groups: group 0 (control), 22 healthy children; group 1, 33 children with functional gastrointestinal disorders; group 2, 71 children with inflammatory gastrointestinal disorders other than IBD; group 3, 37 children with IBD. FCC was measured using ELISA assay. Results. In group 0 and group 1 FCCs were below 100 μg/g. Low FCCs were found in 91% of patients in group 2. In patients with IBD FCCs were markedly elevated with median value of 1191.5 μg/g. However, in children with inflammatory gastrointestinal disorders other than IBD and in children with IBD mean FCCs were significantly higher compared with the control group. Significant differences in FCCs were also found between group 1 and group 2, between group 1 and group 3, and between group 2 and group 3. Conclusion. FCC is the best parameter allowing for differentiation between IBD, other inflammatory gastrointestinal disorders, and functional gastrointestinal disorders. High FCC is associated with a high probability of IBD and/or other inflammatory gastrointestinal disorders, and it allows excluding functional gastrointestinal disorders.
Cytoplasmic Poly(A) Binding Proteins Regulate Telomerase Activity and Cell Growth in Human Papillomavirus Type 16 E6-Expressing Keratinocytes

ABSTRACT The high-risk human papillomavirus (HPV) E6 and E7 oncoproteins are critical to the immortalization of keratinocytes. HPV type 16 (HPV16) E6 interacts with endogenous proteins to activate hTERT, the catalytic subunit of telomerase, thus avoiding cellular senescence signals. NFX1-123, the longer splice variant of NFX1, interacts with HPV16 E6, as well as cytoplasmic poly(A) binding proteins 1 and 4 (PABPC1 and PABPC4). HPV16 E6 affects hTERT expression posttranscriptionally through NFX1-123, as NFX1-123 interacts with hTERT mRNA and stabilizes it, leading to greater telomerase activity. The PAM2 motif of NFX1-123, with which it binds PABPCs, is required for the posttranscriptional regulation of hTERT by HPV16 E6 and NFX1-123. There is increasing evidence that RNA and DNA viruses utilize RNA-processing proteins, and specifically PABPCs, in the normal virus life cycle, and there is also evidence that RNA-processing proteins are perturbed in cancers. Here, we show that PABPCs are critical in hTERT regulation by HPV16 E6. Although the amount and cellular localization of PABPCs were largely unchanged in cervical cancer cell lines with or without HPV16 and in human foreskin keratinocytes (HFKs) with or without HPV16 E6, knockdown of PABPCs decreased hTERT mRNA and telomerase activity and overexpression of PABPC4 increased these in HPV16 E6-expressing HFKs. In contrast, knockdown of PABPCs in C33A cells had no effect on hTERT mRNA or telomerase activity. Additionally, overexpression of PABPC4 and hTERT led to greater growth of cultured HPV16 E6-expressing HFKs. This is the first evidence that PABPCs have a targeted role in hTERT regulation leading to a growth advantage in cells expressing HPV16 E6.
An analysis of usage locality for data-centric web services

The growing popularity of XML Web Services is resulting in a significant increase in the proportion of Internet traffic that involves requests to and responses from Web Services. Unfortunately, web service responses, because they are generated dynamically, are considered “uncacheable” by traditional caching infrastructures. One way of remedying this situation is by developing alternative caching infrastructures, which improve performance using on-demand service replication, data ooading, and request redirection. These infrastructures benefit from two characteristics of web service trac
Epigenetic Influences in the Aetiology of Cancers Arising from Breast and Prostate: A Hypothesised Transgenerational Evolution in Chromatin Accessibility

Epidemiological studies have consistently supported the notion that environmental and/or dietary factors play a central role in the aetiology of cancers of the breast and prostate. However, for more than five decades investigators have failed to identify a single cause-and-effect factor, which could be implicated; identification of a causative entity would allow the implementation of an intervention strategy in at-risk populations. This suggests a more complex pathoaetiology for these cancer sites, compared to others. When one examines the increases or decreases in incidence of specific cancers amongst migrant populations, it is notable that disease arising in colon or stomach requires one or at most two generations to exhibit a change in incidence to match that of high-incidence regions, whereas for breast or prostate cancer, at least three generations are required. This generational threshold could suggest a requirement for nonmutation-driven epigenetic alterations in the F0/F1 generations (parental/offspring adopting a more westernized lifestyle), which then predisposes the inherited genome of subsequent generations to mutagenic/genotoxic alterations leading to the development of sporadic cancer in these target sites. As such, individual susceptibility to carcinogen insult would not be based per se on polymorphisms in activating/detoxifying/repair enzymes, but on elevated accessibility of crucial target genes (e.g., oncogenes, tumour suppressor genes) or hotspots therein to mutation events. This could be termed a genomic susceptibility organizational structure (SOS). Several exposures including alcohol and heavy metals are epigens (i.e., modifiers of the epigenome), whereas others are mutagenic/genotoxic, for example, heterocyclic aromatic amines; humans are continuously and variously exposed to mixtures of these agents. Within such a transgenerational multistage model of cancer development, determining the interaction between epigenetic modification to generate a genomic SOS and genotoxic insult will facilitate a new level of understanding in the aetiology of cancer.
A Novel Unascertained C-Means Clustering with Application

Using the theory and method of unascertained measure, a novel unascertained C-means clustering model and the clustering weight are established. The basic knowledge of the unascertained sets and concept of unascertained clustering was introduced briefly. Then, the unascertained measure was defined and clustering weight were set up. Experimental results show that the presented algorithm performs more robust to noise than the fuzzy C-means clustering (FCM) algorithm do. Furthermore, the results of stock market board analysis using proposed method that indicates the unascertained C-means clustering model provides a quantitative objective and efficient method of stock market board analysis, and hence is suitable to stock market board analysis.
Keratinase Production by Three Bacillus spp. Using Feather Meal and Whole Feather as Substrate in a Submerged Fermentation

Three Bacillus species (B. subtilis LFB-FIOCRUZ 1270, B. subtilis LFB-FIOCRUZ 1273, and B. licheniformis LFB-FIOCRUZ 1274), isolated from the poultry industry, were evaluated for keratinase production using feathers or feather meal as the sole carbon and nitrogen sources in a submerged fermentation. The three Bacillus spp. produced extracellular keratinases and peptidases after 7 days. Feather meal was the best substrate for keratinase and peptidase production in B. subtilis 1273, with 412 U/mL and 463 U/ml. The three strains were able to degrade feather meal (62–75%) and feather (40–95%) producing 3.9–4.4 mg/ml of soluble protein in feather meal medium and 1.9–3.3 mg/ml when feather medium was used. The three strains produced serine peptidases with keratinase and gelatinase activity. B. subtilis 1273 was the strain which exhibited the highest enzymatic activity.
RrgA and RrgB Are Components of a Multisubunit Pilus Encoded by the Streptococcus pneumoniae rlrA Pathogenicity Islet

ABSTRACT The rlrA pathogenicity islet in Streptococcus pneumoniae TIGR4 encodes three surface proteins, RrgA, RrgB, and RrgC, and three sortase enzymes. Using transmission electron microscopy, cell fractionation, cell wall sorting signal domain swapping, and Western blotting, we show that RrgA and RrgB are incorporated into a multisubunit pilus in S. pneumoniae.
On the performance of GPU public-key cryptography

Graphics processing units (GPUs) have become increasingly popular over the last years as a cost-effective means of accelerating various computationally intensive tasks. We study the particular case of modular exponentiation, the crucial operation behind most modern public-key cryptography algorithms. We focus our attention on the NVIDIA GT200 architecture, currently one of the most popular for general purpose GPU computation.
Implications of Halo Inside-Out Growth for the X-Ray Properties of Nearby Galaxy Systems within the Preheating Scenario

We present an entirely analytic model for a preheated, polytropic intergalactic medium in hydrostatic equilibrium within an NFW dark halo potential in which the evolution of the halo structure between major merger events proceeds inside out by accretion. This model is used to explain, within a standard ΛCDM cosmogony, the observed X-ray properties of nearby relaxed, non-cooling flow groups and clusters of galaxies. We find that our preferred solution to the equilibrium equations produces scaling relations in excellent agreement with observations, while simultaneously accounting for the typical structural characteristics of the distribution of the diffuse baryons. In the class of preheating models, ours stands out because it offers a unified description of the intrahalo medium for galaxy systems with total masses above ~2 × 1013 M☉, does not produce baryonic configurations with large isentropic cores, and reproduces faithfully the observed behavior of the gas entropy at large radii. All this is achieved with a moderate level of energy injection of about half a kilo-electron volt, which can be easily accommodated within the limits of the total energy released by the most commonly invoked feedback mechanisms, as well as with a polytropic index of 1.2, consistent with both many observational determinations and predictions from high-resolution gasdynamical simulations of non-cooling flow clusters. More interestingly, our scheme offers a physical motivation for the adoption of this specific value of the polytropic index, as it is the one that best ensures the conservation after halo virialization of the balance between the total specific energies of the gas and dark matter components for the full range of masses investigated.
Chinese-speaking adults' understanding of argument structure

Syntactic constructions roughly correspond to sentence meanings. Jiang and Haryu (2014) found that Chinese children can associate subject-verb-object (SVO) constructions with causative events at age 2, but do not always map subject-verb (SV) constructions to noncausative events, even after reaching 5 years of age. The latter results may be attributed to the fact that Chinese allows argument-dropping. That is, an SV sentence in Chinese sometimes includes an intransitive verb, but other times includes a transitive verb with the object dropped. This paper investigated Chinese adults' knowledge of syntax-semantics correspondence. Experiment 1 found that Chinese adults did not always map SV sentences to noncausative events, while they almost always mapped SVO sentences to causative events. Experiment 2 found that they preferred to use SV and SVO constructions to describe noncausative and causative events, respectively. Chinese adults understand that causative and noncausative events should typically be described using transitive and intransitive constructions, respectively. However, when inferring to which event (causative or noncausative) the given sentence should be mapped, their performance seems to be regulated by actual SV sentence usage in Chinese.
CA-MAC: Context Adaptive MAC Protocol for Wireless Sensor Networks

Energy efficiency is a critical issue for sensor network. In this paper we propose an energy efficient context adaptive MAC protocol for wireless sensor networks. The existing approaches try to minimize energy consumption by controlling the duty cycle of transmission period. The proposed protocol achieves that by letting each node stay in the sleep mode if the number of packets in the buffer is smaller than the threshold, while the threshold value is decided according to the distance of the node to the sink node. The variable threshold for each switch node, however, may cause increased latency. This problem is solved by immediately transmitting the packets of high priority context data. Computer simulation using OMNeT++ reveals that the proposed protocol significantly reduces the energy consumption compared with the existing S-MAC and T-MAC protocol.
Fracture behavior of silica nanoparticles reinforced rubber/epoxy composite

Hybrid composites consisting of soft rubber (carboxyl-terminated butadiene acrylonitrile, CTBN) and silica nanoparticles with average particle size of 20 nm were studied for improving toughness of epoxy resins (diglycidyl ether of bisphenol A, DGEBA). The hybrid carboxyl-terminated butadiene acrylonitrile /silica nanoparticles epoxy systems exhibited improvements in the Young’s modulus, and more importantly, fracture toughness (KIC), which can be explained by synergistic impact from the inherent characteristics of each filler. In this study, the highest KIC was reached with addition of small amounts of silica nanoparticles (5 vol.%) to the epoxy containing 15 vol.% carboxyl-terminated butadiene acrylonitrile, where the KIC was distinctly higher than with the epoxy containing carboxyl-terminated butadiene acrylonitrile or silica nanoparticles alone. Cavitation of rubber particles with matrix dilation and particle debonding with subsequent void growth were determined as the toughening mechanisms responsible for the toughness improvements for epoxy. The evidence indicates that debonding of the silica nanoparticles causes a weakening of the matrix–particle interface. The toughness enhancement in hybrid nanocomposites involves an increase in silica nanoparticles particle debonding an increase in plastic zone size, which allows the epoxy matrix to dissipate more fracture energy.
Smart Control for Passive Greenhouses

The paper is focused on a new passive greenhouse architecture, provided with cold water heat pumps, wind generator and solar panels. This greenhouse is independent of any energetic infrastructure (electric, gas, hot water). The sizing of each element and the automate control are critical in order to reduce the costs. A simplified mathematical model, able to assist the design and the automate control, is provided. A fuzzyinterpolative adaptive controller with internal model is introduced.