Miracle-dz/UniFAR-FTUs huggingface dataset:
Results Inhibition of Proteasome Activity Results in Prolonged TAP-Class I Association and Impaired Intracellular Transport of Class I Molecules

Newly assembled heavy chain-[32m heterodimers of class I histocompatibility molecules associate with the endoplasmic reticulum (ER) peptide transporter, TAP, and subsequently dissociate from TAP in parallel with their transport from the ElL to the Golgi apparatus. It appears that TAP-associated class I molecules are waiting to bind appropriate peptides before they dissociate from TAP and leave the E R since binding of high affinity peptides to class I molecules in vitro leads to dissociation of TAP-class I complexes. In further support of this notion, we report that limiting peptide supply through inhibition of proteasome activities prolongs the association of mouse class I molecules with TAP and concomitantly slows their transport to the Golgi apparatus. By using a series of deletion mutants and hybrid class I molecules we demonstrate that the extracellular domains of class I molecules are sufficient for their peptide-regulated interaction with TAP. Furthermore, based on the inability of an or. 3 domain-specific mAb to recognize TAP-class I complexes and the fact that a point mutant of the D d molecule at residue 222 is unable to bind to TAP, it is likely that a major site of interaction with TAP resides in the membrane-proximal region of the heavy chain % domain. Finally, we examined the relationship between the interaction of mouse heavy chain-[32m heterodimers with TAP and with the resident ElL chaperone, calnexin. Most heterodimers that bound to TAP were found to associate simultaneously with calnexin. Upon delivery of peptide to class I molecules in permeabilized cells, dissociation from TAP was observed but the interaction with calnexin was largely maintained. Therefore, both TAP and calnexin may participate in the ER retention ofpeptide-deficient class I molecules. However, since release from calnexin occurs after dissociation from TAP, it appears that calnexin ultimately determines if a class I molecule is to be exported from the ElL.
Analytical Eye-Diagram Determination for the Efficient and Accurate Signal Integrity Verification of Single Interconnect Lines

In this paper, a new efficient and accurate analytical eye-diagram determination technique for interconnect lines is presented. The simplest input test signal model for the intersymbol interference analysis of high-speed data links is mathematically formulated. Since input test patterns for eye boundaries are determined analytically, it is considered very convenient and efficient. The proposed technique shows excellent agreement with the SPICE-based simulation in both eye height and jitter, i.e., within 5% error for nondiscontinuous data paths and 10% error for discontinuous data paths. The method is much more computation-time-efficient than the pseudorandom bit sequence-based SPICE simulation in the order of magnitude.
A Lead ANRIL Polymorphism Is Associated with Elevated CRP Levels in Periodontitis: A Pilot Case-Control Study

Elevated high sensitive C-reactive protein (hsCRP) is a marker for systemic inflammation and a risk marker for atherosclerotic cardiovascular disease (ACVD), and has also been associated with periodontitis. Inter-individual variation for hsCRP in periodontitis has been shown. ANRIL is the strongest genetic susceptibility locus for both periodontitis and ACVD, and it is speculated that genetic variation in ANRIL may modulate inflammatory processes. Therefore, we explored the possible association between hsCRP plasma levels and a leading ANRIL single nucleotide polymorphism (SNP) in periodontitis patients and controls. 171 healthy subjects with North European descent (115 periodontitis and 56 controls) were included in this case-control study. hsCRP levels were determined and subjects were genotyped for the leading ANRIL SNP rs1333048. In a multivariate analysis, periodontitis, female gender, increasing BMI and homozygosity for the major allele (AA-genotype) of rs1333048 were significantly associated with elevated hsCRP plasma levels (p = 0.012, p = 0.004, p = 0.007 and p = 0.003, respectively). Periodontitis patients with rs1333048 AA-genotype showed higher levels of hsCRP than those carrying the minor C allele (median: 4.5 mg/L vs. 1.6 mg/L, padjusted = 0.007). This study is the first to show that, in addition to gender and BMI, also a leading SNP in ANRIL is explanatory for inter-individual variation in hsCRP levels in periodontitis patients of North European descent.
Chemical investigation of metabolites produced by an endophytic fungi Phialemonium curvatum from the leaves of Passiflora edulis

Abstract Phialemonium curvatum, an endophytic fungus isolated from the leaves of Passiflora edulis was cultured in potato dextrose broth (PDB) media and chromatographic separation of the EtOAc extract of the broth and mycelium led to the isolation of 4-hydroxybenzoic acid (1), 3-indole acetic acid (2), solaniol (3), uracil (4), uridine (5) and glycerol (6). Compound 2 showed a weak antifungal activity against Cladosporium cladosporioides. This is the first report of the isolation of the endophytic fungus P. curvatum from P. edulis and complete 13CNMR assignments of 3.
The Role of the Multifunctional BAG3 Protein in Cellular Protein Quality Control and in Disease

In neurons, but also in all other cells the complex proteostasis network is monitored and tightly regulated by the cellular protein quality control (PQC) system. Beyond folding of newly synthesized polypeptides and their refolding upon misfolding the PQC also manages the disposal of aberrant proteins either by the ubiquitin-proteasome machinery or by the autophagic-lysosomal system. Aggregated proteins are primarily degraded by a process termed selective macroautophagy (or aggrephagy). One such recently discovered selective macroautophagy pathway is mediated by the multifunctional HSP70 co-chaperone BAG3 (BCL-2-associated athanogene 3). Under acute stress and during cellular aging, BAG3 in concert with the molecular chaperones HSP70 and HSPB8 as well as the ubiquitin receptor p62/SQSTM1 specifically targets aggregation-prone proteins to autophagic degradation. Thereby, BAG3-mediated selective macroautophagy represents a pivotal adaptive safeguarding and emergency system of the PQC which is activated under pathophysiological conditions to ensure cellular proteostasis. Interestingly, BAG3-mediated selective macroautophagy is also involved in the clearance of aggregated proteins associated with age-related neurodegenerative disorders, like Alzheimer’s disease (tau-protein), Huntington’s disease (mutated huntingtin/polyQ proteins), and amyotrophic lateral sclerosis (mutated SOD1). In addition, based on its initial description BAG3 is an anti-apoptotic protein that plays a decisive role in other widespread diseases, including cancer and myopathies. Therefore, in the search for novel therapeutic intervention avenues in neurodegeneration, myopathies and cancer BAG3 is a promising candidate.
TouchViz: (multi)touching multivariate data

In this paper we describe TouchViz, an information visualization system for tablets that encourages rich interaction, exploration, and play through references to physical models. TouchViz turns data into physical objects that experience forces and respond to the user. We describe the design of the system and conduct a user study to explore its use, finding that it supports many different models of data exploration and encourages users to have fun exploring data.
SensorSift: balancing sensor data privacy and utility in automated face understanding

We introduce SensorSift, a new theoretical scheme for balancing utility and privacy in smart sensor applications. At the heart of our contribution is an algorithm which transforms raw sensor data into a 'sifted' representation which minimizes exposure of user defined private attributes while maximally exposing application-requested public attributes. We envision multiple applications using the same platform, and requesting access to public attributes explicitly not known at the time of the platform creation. Support for future-defined public attributes, while still preserving the defined privacy of the private attributes, is a central challenge that we tackle. To evaluate our approach, we apply SensorSift to the PubFig dataset of celebrity face images, and study how well we can simultaneously hide and reveal various policy combinations of face attributes using machine classifiers. We find that as long as the public and private attributes are not significantly correlated, it is possible to generate a sifting transformation which reduces private attribute inferences to random guessing while maximally retaining classifier accuracy of public attributes relative to raw data (average PubLoss = .053 and PrivLoss = .075, see Figure 4). In addition, our sifting transformations led to consistent classification performance when evaluated using a set of five modern machine learning methods (linear SVM, kNearest Neighbors, Random Forests, kernel SVM, and Neural Nets).
Influence of isotropic skull models on EEG source localization

We investigated the influence of using simplified skull models on electroencephalogram (EEG) source localization. The simplified skull models were derived from CT and MR images, with isotropic conductivity modeled as either heterogeneous or homogeneous. A total of four simplified head models were compared against a reference model with a skull accurately segmented with CT images. Our results show that the use of a simplified geometry for the skull, can lead to errors of approximately 1 cm for sources located in the central and temporal regions of the brain.
Experimental and numerical modelling of aerated flows over stepped spillways

Stepped spillways are a popular design choice for reservoir overflows due to the high rates of energy dissipation and air entrainment compared to smooth spillways. Air entrainment is important in spillway flows as it affects the pressures acting on the spillway surface, which in adverse conditions can damage the spillway. Air entrainment also causes flow bulking which increases the depth of flow. This study presents free surface and pressure data for aerated flows over an experimental stepped spillway, with pressures measured at different positions across the width of the channel. Within the step cavities, recirculating vortices are observed in both the stream-wise and cross-stream directions, with the direction of circulation alternating at each subsequent step. These 3D effects cause the pressures acting on the step edges to vary across the width of the channel. The Volume of Fluid (VOF) and Eulerian multiphase numerical models are used to predict flows over the spillway. The Eulerian multiphase model shows high levels of air entrainment and is able to predict the position of the free surface to reasonable accuracy. The VOF model, conversely, does not show any air entrainment and therefore under predicts the position of the free surface. The accuracy to which each numerical model predicts pressures on the step faces varies depending on the measurement location. Both of the numerical models accurately simulate the direction of circulation of the 3D vortices within the step cavities. Simulations with varying channel widths, conducted using the VOF model, show that the pattern of 3D vortices repeats as the channel width is increased.
Spatial Genetic Structure and Life History Traits in Cerrado Tree Species: Inferences for Conservation

Spatial Genetic Structure (SGS) is correlated with life history traits and is affected by ecological and demographic processes. We discuss here the SGS within populations of three species from Cerrado Biome, Caryocar brasiliense, Dipteryx alata and Tibouchina papyrus, which vary in life history traits. Our working hypothesis was that self-incompatible and wind-dispersed species present no SGS due to long distance pollen gene flow. SGS analyses were based on polymorphism at microsatellite loci. Weak SGS was found for the three species, but the mammal dispersed species, C. brasiliense and D. alata, presented stronger SGS than the wind dispersed species. T. papyrus. Although D. alata presented the highest value of Sp (intensity of SGS), breeding system was not related with SGS because the other two self-compatible species presented contrasting patterns of SGS. The three species may be highly affected by fragmentation, especially the wind-dispersed species T. papyrus, due to endemism and habitat vulnerability.
Muscle reflex in heart failure: the role of exercise training

Exercise evokes sympathetic activation and increases blood pressure and heart rate (HR). Two neural mechanisms that cause the exercise-induced increase in sympathetic discharge are central command and the exercise pressor reflex (EPR). The former suggests that a volitional signal emanating from central motor areas leads to increased sympathetic activation during exercise. The latter is a reflex originating in skeletal muscle which contributes significantly to the regulation of the cardiovascular and respiratory systems during exercise. The afferent arm of this reflex is composed of metabolically sensitive (predominantly group IV, C-fibers) and mechanically sensitive (predominately group III, A-delta fibers) afferent fibers. Activation of these receptors and their associated afferent fibers reflexively adjusts sympathetic and parasympathetic nerve activity during exercise. In heart failure, the sympathetic activation during exercise is exaggerated, which potentially increases cardiovascular risk and contributes to exercise intolerance during physical activity in chronic heart failure (CHF) patients. A therapeutic strategy for preventing or slowing the progression of the exaggerated EPR may be of benefit in CHF patients. Long-term exercise training (ExT), as a non-pharmacological treatment for CHF increases exercise capacity, reduces sympatho-excitation and improves cardiovascular function in CHF animals and patients. In this review, we will discuss the effects of ExT and the mechanisms that contribute to the exaggerated EPR in the CHF state.
Confirmation of Matheron's conjecture on the covariogram of a planar convex body

The covariogramgK of a convex bodyK in E d is the function which associates to each x2 E d the volume of the intersection ofK withKCx. In 1986 G. Matheron conjectured that for dD 2 the covariogramgK determinesK within the class of all planar convex bodies, up to transla- tions and reflections in a point. This problem is equivalent to some problems in stochastic geometry and probability as well as to a particular case of the phase retrieval problem in Fourier analysis. It is also relevant for the inverse problem of determining the atomic structure of a quasicrystal from its X-ray diffraction image. In this paper we confirm Matheron's conjecture completely.
ASM'15: The 1st International Workshop on Affect and Sentiment in Multimedia

In recent years, there has been a dramatic proliferation of research on multimedia retrieval and indexing based on highly subjective concepts such as emotion, sentiment, preference and aesthetics [1, 2, 4, 5]. These retrieval methods are considered human-centered, intuitive, and beyond the conventional keywordor object-based retrieval paradigm. In addition, the problem is considered challenging because it requires multidisciplinary understanding of human behavior and perception as well as multimodal integration of different modalities (music, image, video, text) for better performance. The challenges in affective multimedia analysis are not limited to the technical problems but also to the way we use and assess emotional concepts, representations and responses. Therefore, research in affective analysis should pay a careful attention to the definitions, limitations and the developments in the psychology of emotions [3]. ASM workshop provides a forum to present and discuss the emerging field of affect and sentiment analysis in multimedia. Unlike the affect and social signal processing track at the main conference, we focus mainly on multimedia content analysis and its applications for automatic sentiment and affective analysis. Being a workshop, we also provide more space for focused discussions.
An online credential repository for the Grid: MyProxy

Grid portals, based on standard Web technologies, are increasingly used to provide user interfaces for computational and data grids. However, such Grid portals do not integrate cleanly with existing Grid security systems such as the Grid Security Infrastructure (GSI), due to lack of delegation capabilities in Web security mechanisms. We solve this problem using an online credentials repository system, called MyProxy. MyProxy allows Grid portals to use the GSI to interact with Grid resources in a standard, secure manner. We examine the requirements of Grid portals, give an overview of the GSI, and demonstrate how MyProxy enables them to function together. The architecture and security of the MyProxy system are described in detail.
Non-invasive remote limb ischemic postconditioning protects rats against focal cerebral ischemia by upregulating STAT3 and reducing apoptosis

The signal transducer and activator of transcription 3 (STAT3) signaling pathway has been implicated in cell apoptosis and inflammatory processes. Ischemic preconditioning (IPC) and ischemic postconditioning (IPTC) inhibit both of these processes. In the present study, we investigated the role of phosphorylated STAT3 (p-STAT3)-mediated apoptosis and inflammation following non-invasive remote limb IPTC (NRIPoC) using a classic rat model of focal cerebral ischemia. Forty-five adult male Sprague-Dawley rats were divided randomly into 3 groups (n=15 per group): the sham-operated, ischemia/reperfusion (I/R) and NRIPoC groups. NRIPoC was implemented at the beginning of reperfusion. At 24 h after cerebral reperfusion, we evaluated the neurological deficit score (NDS), assessed the cerebral infarct size and tissue morphology, and evaluated neuronal apoptosis. The protein expression levels of Bcl-2, Bax, nuclear factor-κB (NF-κB), tumor necrosis factor-α (TNF-α) and p-STAT3 in the penumbra region were assessed by western blot analysis. The cerebral infarct volume, the number of apoptotic cells and the protein expression levels of Bcl-2, Bax, NF-κB and TNF-α were all found to be increased in the I/R group compared with the sham-operated group. However, these levels were decreased in the NRIPoC group compared with the I/R group. The number of apoptotic cells in the penumbra in the I/R group was increased compared with that in the NRIPoC and sham-operated groups. The protein expression of p-STAT3 was increased in the NRIPoC group compared with the sham-operated and I/R groups. These results indicate that the protective effects of NRIPoC against cerebral I/R injury may be related to the attenuation of neuronal apoptosis and inflammation through the activation of STAT3.
A study of participants' experience of Yirra : An adolescent treatment program

Yirra is a residential treatment program for young people who are experiencing problems associated with their substance use. The design of this program was influenced both by consultation with other youth services, and by current literature and theories regarding the most effective approaches to delivery of youth substance use services. Yirra has been in operation since February, 1992, and to date has not been formally evaluated. 'l'his research represents the first stage of evaluation of Yirra. The Phenomenological approach to enquiry was aimed at gaining some understanding of the experience of being at Yirra, from the perspective of the young people in the program. Over a three month period, all program participants who had been in the program for a week were invited to take part in taped interviews. Data gathering also included participant observation and program document analysis. As the Yirra program was designed specifically for adolescents, the Phenomenological approach to data analysis also included analysis based on the theories of adolescent development of Piaget and Eiikson.
Prenatal Diethylstilbestrol Exposure and Risk of Breast Cancer

It has been hypothesized that breast cancer risk is influenced by prenatal hormone levels. Diethylstilbestrol (DES), a synthetic estrogen, was widely used by pregnant women in the 1950s and 1960s. Women who took the drug have an increased risk of breast cancer, but whether risk is also increased in the daughters who were exposed in utero is less clear. We assessed the relation of prenatal DES exposure to risk of breast cancer in a cohort of DES-exposed and unexposed women followed since the 1970s by mailed questionnaires. Eighty percent of both exposed and unexposed women completed the most recent questionnaire. Self-reports of breast cancer were confirmed by pathology reports. Cox proportional hazards regression was used to compute incidence rate ratios (IRR) for prenatal DES exposure relative to no exposure. During follow-up, 102 incident cases of invasive breast cancer occurred, with 76 among DES-exposed women (98,591 person-years) and 26 among unexposed women (35,046 person-years). The overall age-adjusted IRR was 1.40 [95% confidence interval (95% CI), 0.89-2.22]. For breast cancer occurring at ages ≥40 years, the IRR was 1.91 (95% CI, 1.09-3.33) and for cancers occurring at ages ≥50 years, it was 3.00 (95% CI, 1.01-8.98). Control for calendar year, parity, age at first birth, and other factors did not alter the results. These results, from the first prospective study on the subject, suggest that women with prenatal exposure to DES have an increased risk of breast cancer after age 40 years. The findings support the hypothesis that prenatal hormone levels influence breast cancer risk. (Cancer Epidemiol Biomarkers Prev 2006;15(8):1509–14)
Community extinction patterns in coloured environments

Understanding community responses to environmental variation is a fundamental aspect of ecological research, with direct ecological, conservation and economic implications. Here, we examined the role of the magnitude, correlation and autocorrelation structures of environmental variation on species' extinction risk (ER), and the probability of actual extinction events in model competitive communities. Both ER and probability increased with increasing positive autocorrelation when species responded independently to the environment, yet both decreased with a strong correlation between species-specific responses. These results are framed in terms of the synchrony between—and magnitude of variation within—species population sizes and are explained in terms of differences in noise amplification under different conditions. The simulation results are robust to changes in the strength of interspecific density dependence, and whether noise affects density-independent or density-dependent population processes. Similar patterns arose under different ranges of noise severity when these different model assumptions were examined. We compared our results with those from an analytically derived solution, which failed to capture many features of the simulation results.