Miracle-dz/UniFAR-FTUs huggingface dataset:
Unique CRF01_AE Gag CTL Epitopes Associated with Lower HIV-Viral Load and Delayed Disease Progression in a Cohort of HIV-Infected Thais

Cytotoxic T Lymphocytes (CTLs) play a central role in controlling HIV-replication. Although numerous CTL epitopes have been described, most are in subtype B or C infection. Little is known about CTL responses in CRF01_AE infection. Gag CTL responses were investigated in a cohort of 137 treatment-naïve HIV-1 infected Thai patients with high CD4+ T cell counts, using gIFN Enzyme-Linked Immunospot (ELISpot) assays with 15-mer overlapping peptides (OLPs) derived from locally dominant CRF01_AE Gag sequences. 44 OLPs were recognized in 112 (81.8%) individuals. Both the breadth and magnitude of the CTL response, particularly against the p24 region, positively correlated with CD4+ T cell count and inversely correlated with HIV viral load. The breadth of OLP response was also associated with slower progression to antiretroviral therapy initiation. Statistical analysis and single peptide ELISpot assay identified at least 17 significant associations between reactive OLP and HLA in 12 OLP regions; 6 OLP-HLA associations (35.3%) were not compatible with previously reported CTL epitopes, suggesting that these contained new CTL Gag epitopes. A substantial proportion of CTL epitopes in CRF01_AE infection differ from subtype B or C. However, the pattern of protective CTL responses is similar; Gag CTL responses, particularly against p24, control viral replication and slow clinical progression.
Responses of raptors to habitat fragmentation : from individual responses to population susceptibility

The Black Harrier is an endemic, globally Vulnerable species with its core breeding range centered on the Fynbos Biome of the Western Cape, South Africa. Lowland habitats within this region, especially Renosterveld, a fertile vegetation type characterised by the shrub Dicerothamnus rhinocerotis, have been severely fragmented and degraded by activities associated primarily with agriculture. I hypothesise that the Black Harrier has lost a significant proportion of its preferred natural habitat due to this degradation. In order to test this hypothesis, I examine i) the dispersion of breeding pairs of harriers in relation to patches of varying size and quality, ii) the foraging range and habitat use of two provisioning males in a large lowland renosterveld patch and iii) the productivity of harriers breeding in different habitat types. I surveyed 79 lowland Renosterveld patches of varying size and quality in the Swartland and Overberg plains of south-western South Africa. No breeding harriers were found in 36 patches in the lowlands of the Swartland, and only seven (16%) of 43 surveyed patches in the Overberg contained breeding pairs of harriers. Harriers selected large patches (minimum patch size ±1 00 ha) for breeding: these tended to be the more ecologically intact ones. Within the range of patch sizes used by breeding Black Harriers, there was no evidence that patch size influenced breeding success, however, on a larger scale, breeding success was significantly higher in coastal habitats than in montane and lowland areas. Two radio-tracked provisioning males foraged 2.3-2.9 km from their nests. Although these foraging radii included substantial amounts of transformed habitat, the birds foraged almost exclusively in natural habitats, indicating a strong dependence on untransformed habitats. In terms of these results, out of almost 17 000 patches remaining in the Overberg, only ca 2.6% are of sufficient size to support a breeding pair of harriers; in addition, many of the smaller patches « 100ha) are likely to have a low degree of connectivity and are therefore unsuitable for harriers. Extrapolations suggest that before land transformation, the lowlands of the Overberg region alone may have supported about 390-1570 pairs of Black Harriers, of which perhaps no more than 60 pairs (15%) remain in the region. I conclude that Black Harriers have been severely impacted by habitat fragmentation and that historically the species was dependent on, and probably abundant in, lowland habitats. Conservation of the Black Harrier, with a world population currently estimated at 500-1000 pairs, depends on the preservation of large, ecologically intact patches of natural Fynbos vegetation. 25 Un ive rsi ty of Ca pe To wn
2016 Ieee International Conference on Big Data (big Data) Evaluating the Impact of Data Placement to Spark and Scidb with an Earth Science Use Case

— We investigate the impact of data placement on two Big Data technologies, Spark and SciDB, with a use case from Earth Science where data arrays are multidimensional. Simultaneously, this investigation provides an opportunity to evaluate the performance of the technologies involved. Two datastores, HDFS and Cassandra, are used with Spark for our comparison. It is found that Spark with Cassandra performs better than with HDFS, but SciDB performs better yet than Spark with either datastore. The investigation also underscores the value of having data aligned for the most common analysis scenarios in advance on a shared nothing architecture. Otherwise, repartitioning needs to be carried out on the fly, degrading overall performance.
Fetal Versus Maternal and Gestational Age Effects of Repetitive Antenatal Glucocorticoids

Background. Although single courses of antenatal glucocorticoids decrease respiratory distress syndrome and mortality, repetitive courses of antenatal glucocorticoids are being given to women at risk of preterm delivery without evidence of benefit or appreciation of potential risks. Objectives. To evaluate the effects of single and repetitive antenatal glucocorticoid exposures on fetal growth and postnatal lung function in sheep. Methods. Pregnant ewes were randomized to three protocols that included one or three doses (at 7-day intervals) of 0.5 mg/kg of betamethasone (β) given to the ewe or fetus beginning at gestations ranging from 104 to 128 days' gestation with delivery at 125, 135, and 146 days' gestation. Postnatal assessments included measurements of gas exchange, compliance, ventilation efficiency, static lung volume, and lung tissue and alveolar wash saturated phosphatidylcholine. Results. Single or repetitive maternal β but not fetal β caused fetal growth retardation at delivery at 125, 135, and 146 days' gestation. Single-dose fetal β had no effect on postnatal lung function whereas single-dose maternal β significantly increased compliance, lung volume, and tissue and alveolar surfactant after preterm delivery. Although three-dose fetal β improved all indicators of postnatal lung function, three-dose maternal β resulted in larger responses. The added benefits of repetitive β relative to a single-dose β on postnatal lung function after preterm delivery were not as great when therapy was begun later in gestation. Postnatal lung function after delivery at 146 days' gestation (term is 150 days) was improved after repetitive maternal β at early gestational age. Conclusions. In sheep, single or repetitive maternal β causes growth retardation from 104 to 121 days' gestation and the growth retardation persists to term. In contrast, single or repetitive fetal β does not cause fetal growth retardation and is less potent at improving postnatal lung function and increasing surfactant pools. There are potential benefits as well as risks for the use of repetitive antenatal glucocorticoids. Randomized, controlled trials in humans are essential given the widespread use of repetitive courses of antenatal glucocorticoids in women at risk of preterm delivery. respiratory distress syndrome, maturation, prematurity, growth retardation, surfactant.
Cluster Analysis and Priority Sorting in Huge Point Clouds for Building Reconstruction

Terrestrial laser scanners produce point clouds with a huge number of points within a very limited surrounding. In built-up areas, many of the man-made objects are dominated by planar surfaces. We introduce a RANSAC based preprocessing technique that transforms the irregular point cloud into a set of locally delimited surface patches in order to reduce the amount of data and to achieve a higher level of abstraction. In a second step, the resulting patches are grouped to large planes while ignoring small and irrelevant structures. The approach is tested with a dataset of a built-up area which is described very well needing only a small number of geometric primitives. The grouping emphasizes man-made structures and could be used as a preclassification
Medial Prefrontal Cortex Neuronal Activation and Synaptic Alterations after Stress-Induced Reinstatement of Palatable Food Seeking: A Study Using c-fos-GFP Transgenic Female Rats

Relapse to maladaptive eating habits during dieting is often provoked by stress and there is evidence for a role of ovarian hormones in stress responses and feeding. We studied the role of these hormones in stress-induced reinstatement of food seeking and medial prefrontal cortex (mPFC) neuronal activation in c-fos-GFP transgenic female rats, which express GFP in strongly activated neurons. Food-restricted ovariectomized or sham-operated c-fos-GFP rats were trained to lever-press for palatable food pellets. Subsequently, lever-pressing was extinguished and reinstatement of food seeking and mPFC neuronal activation was assessed after injections of the pharmacological stressor yohimbine (0.5–2 mg/kg) or pellet priming (1–4 noncontingent pellets). Estrous cycle effects on reinstatement were also assessed in wild-type rats. Yohimbine- and pellet-priming-induced reinstatement was associated with Fos and GFP induction in mPFC; both reinstatement and neuronal activation were minimally affected by ovarian hormones in both c-fos-GFP and wild-type rats. c-fos-GFP transgenic rats were then used to assess glutamatergic synaptic alterations within activated GFP-positive and nonactivated GFP-negative mPFC neurons following yohimbine-induced reinstatement of food seeking. This reinstatement was associated with reduced AMPA receptor/NMDA receptor current ratios and increased paired-pulse facilitation in activated GFP-positive but not GFP-negative neurons. While ovarian hormones do not appear to play a role in stress-induced relapse of food seeking in our rat model, this reinstatement was associated with unique synaptic alterations in strongly activated mPFC neurons. Our paper introduces the c-fos-GFP transgenic rat as a new tool to study unique synaptic changes in activated neurons during behavior.
Analysis and prediction of helix–helix interactions in membrane channels and transporters

Membrane proteins span a large variety of different functions such as cell‐surface receptors, redox proteins, ion channels, and transporters. Proteins with functional pores show different characteristics of helix–helix packing as other helical membrane proteins. We found that the helix–helix contacts of 13 nonhomologous high‐resolution structures of membrane channels and transporters are mainly accomplished by weakly polar amino acids (G > S > T > F) that preferably create contacts every fourth residue, typical for right‐handed helix crossings. There is a strong correlation between the now available biological hydrophobicity scale and the propensities of the weakly polar and hydrophobic residues to be buried at helix–helix interfaces or to be exposed to the lipids in membrane channels and transporters. The polar residues, however, make no major contribution towards the packing of their transmembrane helices, and are therefore subsumed to be primarily exposed to the polar milieu during the folding process. The contact formation of membrane channels and transporters is therefore ruled by the solubility of the residues, which we suppose to be the driving force for the assembly of their transmembrane helices. By contrast, in 14 nonhomologous high‐resolution structures of other membrane protein coils, also large and polar amino acids (D > S > M > Q) create characteristic contacts every 3.5th residues, which is a signature for left‐handed helix crossings. Accordingly, it seems that dependent on the function, different concepts of folding and stabilization are realized for helical membrane proteins. Using a sequence‐based matrix prediction method these differences are exploited to improve the prediction of buried and exposed residues of transmembrane helices significantly. When the sequence motifs typical for membrane channels and transporters were applied for the prediction of helix–helix contacts the quality of prediction rises by 16% to an average value of 76%, compared to the same approach when only single amino acid positions are taken into account. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Oral health-related quality of life in 6- to 12-year-old schoolchildren in Spain.

BACKGROUND There is a lack of large epidemiological studies researching the major factors of the oral well-being in schoolchildren. AIMS To quantify the impact of the different clinical conditions related to caries and periodontal and dento-facial anomalies on the quality of life captured by the Child-OIDP. DESIGN A standardized epidemiological study was conducted on 2041 Spanish schoolchildren, aged 6-12 years, to assess caries and periodontal and dento-facial disease. Data on oral health-related quality of life were collected using the Child-OIDP. Bivariate and multivariate analyses were performed to evaluate the modulating factors in the perceived oral well-being. RESULTS The prevalence of impact in this sample was 45.7%, mostly for eating (24.3%) but also for smiling (16.2%); however, 72.5% of the subjects had at least one type of normative needs, mainly for periodontal treatment (52.3%), followed by caries (32.3%) and orthodontic treatments (20.6%). The main predictors of the impact on quality of life were perceived dental treatment needs, caries, and periodontal diseases. Also, some demographic (age and gender) and behavioural factors (consumption of sweets) modulated the impact on several domains. Moreover, subjects who rated their general health as good or very good reported a significantly better oral well-being than their counterparts. CONCLUSIONS Pain and aesthetic-related domains (i.e., problems when eating or smiling) are the major components of the oral health-related quality of life perceived by Spanish schoolchildren. Perceived treatment needs as well as dental and periodontal status were the strongest predictors of oral well-being.
Conservation of the metabolomic response to starvation across two divergent microbes

We followed 68 cellular metabolites after carbon or nitrogen starvation of Escherichia coli and Saccharomyces cerevisiae, using a filter-culture methodology that allows exponential growth, nondisruptive nutrient removal, and fast quenching of metabolism. Dynamic concentration changes were measured by liquid chromatography–tandem mass spectrometry and viewed in clustered heat-map format. The major metabolic responses anticipated from metabolite-specific experiments in the literature were observed as well as a number of novel responses. When the data were analyzed by singular value decomposition, two dominant characteristic vectors were found, one corresponding to a generic starvation response and another to a nutrient-specific starvation response that is similar in both organisms. Together these captured a remarkable 72% of the metabolite concentration changes in the full data set. The responses described by the generic starvation response vector (42%) included, for example, depletion of most biosynthetic intermediates. The nutrient-specific vector (30%) included key responses such as increased phosphoenolpyruvate signaling glucose deprivation and increased α-ketoglutarate signaling ammonia deprivation. Metabolic similarity across organisms extends from the covalent reaction network of metabolism to include many elements of metabolome response to nutrient deprivation as well.
Closing the Gap in the Capacity of Wireless Networks Via Percolation Theory

An achievable bit rate per source-destination pair in a wireless network of n randomly located nodes is determined adopting the scaling limit approach of statistical physics. It is shown that randomly scattered nodes can achieve, with high probability, the same 1/radicn transmission rate of arbitrarily located nodes. This contrasts with previous results suggesting that a 1/radicnlogn reduced rate is the price to pay for the randomness due to the location of the nodes. The network operation strategy to achieve the result corresponds to the transition region between order and disorder of an underlying percolation model. If nodes are allowed to transmit over large distances, then paths of connected nodes that cross the entire network area can be easily found, but these generate excessive interference. If nodes transmit over short distances, then such crossing paths do not exist. Percolation theory ensures that crossing paths form in the transition region between these two extreme scenarios. Nodes along these paths are used as a backbone, relaying data for other nodes, and can transport the total amount of information generated by all the sources. A lower bound on the achievable bit rate is then obtained by performing pairwise coding and decoding at each hop along the paths, and using a time division multiple access scheme
TECPR2 Associated Neuroaxonal Dystrophy in Spanish Water Dogs

Clinical, pathological and genetic examination revealed an as yet uncharacterized juvenile-onset neuroaxonal dystrophy (NAD) in Spanish water dogs. Affected dogs presented with various neurological deficits including gait abnormalities and behavioral deficits. Histopathology demonstrated spheroid formation accentuated in the grey matter of the cerebral hemispheres, the cerebellum, the brain stem and in the sensory pathways of the spinal cord. Iron accumulation was absent. Ultrastructurally spheroids contained predominantly closely packed vesicles with a double-layered membrane, which were characterized as autophagosomes using immunohistochemistry. The family history of the four affected dogs suggested an autosomal recessive inheritance. SNP genotyping showed a single genomic region of extended homozygosity of 4.5 Mb in the four cases on CFA 8. Linkage analysis revealed a maximal parametric LOD score of 2.5 at this region. By whole genome re-sequencing of one affected dog, a perfectly associated, single, non-synonymous coding variant in the canine tectonin beta-propeller repeat-containing protein 2 (TECPR2) gene affecting a highly conserved region was detected (c.4009C>T or p.R1337W). This canine NAD form displays etiologic parallels to an inherited TECPR2 associated type of human hereditary spastic paraparesis (HSP). In contrast to the canine NAD, the spinal cord lesions in most types of human HSP involve the sensory and the motor pathways. Furthermore, the canine NAD form reveals similarities to cases of human NAD defined by widespread spheroid formation without iron accumulation in the basal ganglia. Thus TECPR2 should also be considered as candidate gene for human NAD. Immunohistochemistry and the ultrastructural findings further support the assumption, that TECPR2 regulates autophagosome accumulation in the autophagic pathways. Consequently, this report provides the first genetic characterization of juvenile canine NAD, describes the histopathological features associated with the TECPR2 mutation and provides evidence to emphasize the association between failure of autophagy and neurodegeneration.
Understanding Cellular Mechanisms Underlying Airway Epithelial Repair: Selecting the Most Appropriate Animal Models

Understanding the mechanisms underlying the process of regeneration and repair of airway epithelial structures demands close characterization of the associated cellular and molecular events. The choice of an animal model system to study these processes and the role of lung stem cells is debatable since ideally the chosen animal model should offer a valid comparison with the human lung. Species differences may include the complex three-dimensional lung structures, cellular composition of the lung airway as well as transcriptional control of the molecular events in response to airway epithelium regeneration, and repair following injury. In this paper, we discuss issues related to the study of the lung repair and regeneration including the role of putative stem cells in small- and large-animal models. At the end of this paper, the author discuss the potential for using sheep as a model which can help bridge the gap between small-animal model systems and humans.
Electronic states of the pristine and alkali-metal-intercalated monolayer graphite/Ni(111) systems.

The electronic states of the pristine and alkali-metal-intercalated monolayer graphite (MG)/Ni(111) systems are investigated by using angle-resolved ultraviolet photoelectron spectroscopy and x-ray-photoelectron spectroscopy (XPS). The electronic structure of the MG is modified largely by hybridization of the \ensuremath{\pi} orbitals of the graphite layer with the d orbitals of the substrate. The deposition of alkali-metal atoms onto the graphite overlayer at room temperature results in the penetration of the adsorbates into the interface between the MG and the Ni(111) surface. This intercalation causes the change in the band structure of the system because of the dilation of the MG-Ni interlayer distance. The intercalation of the alkali-metal atoms also shows the broadening of the XPS peak of the C 1s core level of the MG.
Knowledge-Based Constraint Satisfaction for Spatial Reasoning

This linguistically motivated work addresses issues in reasoning intelligently over spatial descriptions of simple, static scenes to produce plausible graphical interpretations. It uses a combined representation that couples a semantic network for explicit knowledge with a knowledge base of frames for implicit knowledge. The knowledge base contains generalized rules for interpreting what objects are and how they should and should not be interpreted alone and in spatial interrelationships. The linguistic emphasis is on the semantics and pragmatics of underspecification, vagueness, uncertainty, and context in reasoning over spatial language and knowledge.
Nearly-optimal simple explicit MPC regulators with recursive feasibility guarantees

Explicit Model Predictive Control (MPC) is an attractive control strategy, especially when one aims at a fast, computationally less demanding implementation of MPC. Although leading to a fast implementation of optimization-based control, the main downside of explicit MPC is its high complexity in terms of memory occupancy, which often limits practical applicability of such a control methodology. Therefore in this paper we propose to obtain simple explicit MPC controllers that provide guarantees of recursive satisfaction of input and state constraints. The task is accomplished by optimizing, off-line, the parameters of the feedback law such that an integrated square error between the optimal, but complex controller and its simpler replacement is minimized. We show that the task can be formulated as a quadratic optimization problem which always yields an admissible solution. In this way, suboptimality of simple feedbacks with respect to their complex optimal counterparts is significantly mitigated.
Produção leiteira no Paraná : um estudo considerando os efeitos espaciais

The objective of this research is to study the spatial distribution of production of the dairy industry of cities of Parana. To this end, we use the method of Exploratory Spatial Data Analysis (ESDA) by means of Moran's I statistics and the analysis of identification of clusters. The results point to the West, Southwest and Central and Eastern Parana as areas of highest value of production rates. The results demonstrate the regional differences of Parana in relation to dairy farming. The analysis indicates the heterogeneity among dairy farmers of the state. The variables: number of property, power and capital are the ones most relevant to the formation of the gross output of the state. This highlights the modernization process by which the dairy farming has experienced over the past years.