Miracle-dz/UniFAR-FTUs huggingface dataset:
Discrepant coagulation profile in HIV infection: elevated D-dimer but impaired platelet aggregation and clot initiation

Objectives:In HIV infection, cardiovascular disease (CVD) has emerged as a clinical problem, and elevated D-dimer has been reported. The pathophysiologic mechanisms underlying this remain unclear. We aimed to investigate whether untreated HIV-infected individuals display evidence of functional coagulopathy and whether this was associated with microbial translocation. Design:The study population consisted of 50 HIV-infected untreated individuals and 50 HIV-infected individuals on combination antiretroviral therapy (cART). Groups were matched for age, sex and current CD4+cell count. Methods:Coagulation analyses included D-dimer and the functional haemostatic whole blood tests, thromboelastography (TEG) and platelet aggregation (Multiplate, impedance aggregometry). Microbial translocation was assessed by plasma levels of lipopolysaccharide (LPS). Results:A larger proportion of untreated individuals compared with treated individuals had D-dimer above normal reference range (27.7 vs. 2.2%, P = 0.001). In both treated and untreated individuals, delayed clot initiation with TEG R-time above upper reference range (18 and 28%, respectively, both P < 0.001) and TEG angle below lower reference range [14% (P = 0.004) and 24% (P < 0.001), respectively] was found. In untreated individuals, 64.6% had aggregation response below threshold in at least two of four tests compared with 36.7% in treated individuals (P = 0.010). Untreated individuals with increased D-dimer levels were relatively hypercoagulable by thromboelastography. Furthermore, in untreated patients, a negative association between microbial translocation and platelet aggregation was found. Conclusion:Elevated D-dimer in untreated HIV-infected individuals was confirmed. However, in both untreated and treated individuals, reduced platelet aggregation and clot initiation was found. The impact of reduced platelet function in HIV infection and a potential role of microbial translocation warrant further investigation.
A Daily Temperature Record for Central Texas, 1896-2011

A continuous record of 882,693 daily maximum, minimum, and mean temperature measurements for seven weather stations in central Texas dating from August 1, 1896, to August 31, 2011, were screened and corrected for missing values and inhomogeneities. The resulting data were averaged to create a 115-year unbroken regional record of daily temperature for central Texas. This record indicates warming in daily, seasonal, and annual temperatures. Winter warm temperature extremes have increased over the period of record while warm temperature extremes during the summer months have remained largely unchanged. Summer heat wave days and the length of heat waves have increased significantly since 1897. Cooling degree days have increased and heating degree days have decreased throughout the period of record. The coldest day per year has warmed. Intense multi-year droughts dominate the summer temperature record and account for most of the hottest days per year, most high temperature extremes, and most heat waves. No significant linear trends were detected in summer temperature extremes, but the summer of 2011 was the hottest summer, had the hottest month, the second highest number of heat wave days per year, the longest consecutive heat wave, the highest number of days above the 95 th and 97.5 th percentiles, the highest number of days ≥ 100°F, and the hottest single daily maximum temperature in nearly 115 years. This thesis is approved for recommendation to the Graduate Council.
Feasibility study of bike sharing in Singapore

This study analysed the feasibility of a bike-sharing programme in Singapore based on a case study in the Jurong Lake district. Data were collected using a two-stage perception survey to gather the public’s general awareness and opinions about bike sharing and followed by estimating the likely take-up rate of bike sharing. The results showed that bike-sharing schemes would be suitable around mass rapid transit stations and low rental costs would encourage bike sharing. Finally, a distance-based mode-choice model was established for four scenarios (morning peak and good weather, morning peak and bad weather, evening peak and good weather and evening peak and bad weather), focusing on walking, bike sharing and taking a bus. Weather could have an obvious impact on the frequency of bike sharing.
Familial pulmonary alveolar proteinosis caused by mutations in CSF2RA

Primary pulmonary alveolar proteinosis (PAP) is a rare syndrome characterized by accumulation of surfactant in the lungs that is presumed to be mediated by disruption of granulocyte/macrophage colony-stimulating factor (GM-CSF) signaling based on studies in genetically modified mice. The effects of GM-CSF are mediated by heterologous receptors composed of GM-CSF binding (GM-CSF-Rα) and nonbinding affinity-enhancing (GM-CSF-Rβ) subunits. We describe PAP, failure to thrive, and increased GM-CSF levels in two sisters aged 6 and 8 yr with abnormalities of both GM-CSF-Rα–encoding alleles (CSF2RA). One was a 1.6-Mb deletion in the pseudoautosomal region of one maternal X chromosome encompassing CSF2RA. The other, a point mutation in the paternal X chromosome allele encoding a G174R substitution, altered an N-linked glycosylation site within the cytokine binding domain and glycosylation of GM-CSF-Rα, severely reducing GM-CSF binding, receptor signaling, and GM-CSF–dependent functions in primary myeloid cells. Transfection of cloned cDNAs faithfully reproduced the signaling defect at physiological GM-CSF concentrations. Interestingly, at high GM-CSF concentrations similar to those observed in the index patient, signaling was partially rescued, thereby providing a molecular explanation for the slow progression of disease in these children. These results establish that GM-CSF signaling is critical for surfactant homeostasis in humans and demonstrate that mutations in CSF2RA cause familial PAP.
Towards A Soft Computing Approach to Document Clustering

Soft computing refers to partnership of methods to produce an approximate and low cost solution for hard problems. We believe that document clustering is one such problem and trust that the soft computing approach will be a good candidate for this problem. In this paper, we propose a generalized document clustering approach using soft computing techniques. We define two methods for document clustering using k-Mean partition algorithm: (i) A Genetic Algorithm (GA) based k-Mean algorithm that optimized to find a local optimal solution and (ii) A Harmony Search (HS) based k-Mean algorithm that optimized to find a global optimal solution. We also proposed a novel soft computing partnership method (Hybrid) that uses solution produced from either (GA k-Mean) or (HS k-Mean) method to seed the other for improvement. We extensively performed experiments with our proposed method on standard text mining datasets like: (i) NEWS20, (ii) Reuters and (iii) WebKB-courses-courses and evaluated the results on Purity and Silhouette. In comparison the proposed outperform the basic k-Mean and the hybrid approach performs exceptionally good.
Release of ATP and glutamate in the nucleus tractus solitarii mediate pulmonary stretch receptor (Breuer–Hering) reflex pathway

The Breuer–Hering inflation reflex is initiated by activation of the slowly adapting pulmonary stretch receptor afferents (SARs), which monosynaptically activate second‐order relay neurones in the dorsal medullary nucleus of the solitary tract (NTS). Here we demonstrate that during lung inflation SARs release both ATP and glutamate from their central terminals to activate these NTS neurones. In anaesthetized and artificially ventilated rats, ATP‐ and glutamate‐selective microelectrode biosensors placed in the NTS detected rhythmic release of both transmitters phase‐locked to lung inflation. This release of ATP and glutamate was independent of the centrally generated respiratory rhythm and could be reversibly abolished during the blockade of the afferent transmission in the vagus nerve by topical application of local anaesthetic. Microionophoretic application of ATP increased the activity of all tested NTS second‐order relay neurones which receive monosynaptic inputs from the SARs. Unilateral microinjection of ATP into the NTS site where pulmonary stretch receptor afferents terminate produced central apnoea, mimicking the effect of lung inflation. Application of P2 and glutamate receptor antagonists (pyridoxal‐5′‐phosphate‐6‐azophenyl‐2′,4′‐disulphonic acid, suramin and kynurenic acid) significantly decreased baseline lung inflation‐induced firing of the second‐order relay neurones. These data demonstrate that ATP and glutamate are released in the NTS from the central terminals of the lung stretch receptor afferents, activate the second‐order relay neurones and hence mediate the key respiratory reflex – the Breuer–Hering inflation reflex.
Image registration based on a novel 2-D adaptive filter algorithm

In this paper, we study the image registration problem by a proposed novel 2-D adaptive projection algorithm. Different to the existing adaptive filtering methods, the unknown transformation coefficients can be updated by taking account of the information both along the horizontal and the vertical directions on a 2-D plane simultaneously, which is essentially a 2-D adaptive one. Experiments are presented to illustrate the effectiveness of our proposed algorithm.
Kernels for sequentially ordered data

We present a novel framework for kernel learning with sequential data of any kind, such as time series, sequences of graphs, or strings. Our approach is based on signature features which can be seen as an ordered variant of sample (cross-)moments; it allows to obtain a "sequentialized" version of any static kernel. The sequential kernels are efficiently computable for discrete sequences and are shown to approximate a continuous moment form in a sampling sense. A number of known kernels for sequences arise as "sequentializations" of suitable static kernels: string kernels may be obtained as a special case, and alignment kernels are closely related up to a modification that resolves their open non-definiteness issue. Our experiments indicate that our signature-based sequential kernel framework may be a promising approach to learning with sequential data, such as time series, that allows to avoid extensive manual pre-processing.
Effect of physical activity on lipid levels in a population‐based sample of men with and without the Arg192 variant of the human paraoxonase gene

The prevalence of cardiovascular risk factors in Gerona, Spain, is high for the low myocardial infarction incidence and mortality rates in the province. Physical activity is a protective factor against coronary heart disease. We investigated whether the genetic variants Q and R of the paraoxonase Gln‐Arg 192 polymorphism were involved in different responses of lipids to physical activity. Serum triglycerides, HDL‐cholesterol concentrations, and the paraoxonase Gln‐Arg 192 polymorphism were determined in 262 men randomly selected from a representative population sample in a cross‐sectional study conducted in Gerona, Spain. The Minnesota Leisure Time Physical Activity Questionnaire was used to assess energy expenditure in leisure time physical activity. No differences were found in lipid levels among tertiles of physical activity distribution in subjects with the QQ genotype. However, R carriers showed a significant decreasing trend in triglyceride levels and in log‐triglyceride‐to‐HDL‐cholesterol ratio and a significant increasing trend in HDL‐cholesterol concentration with the amount of physical activity. R carriers included in the low tertile of physical activity distribution had HDL‐cholesterol levels significantly lower than those of QQ homozygous men in the same physical activity category (1.04 mmol/L vs. 1.22 mmol/L, P = 0.024). R carriers of the higher tertile of physical activity distribution showed the most favorable lipid profile in this genetic group. A statistically‐significant interaction between paraoxonase genotypes and physical activity was observed for log triglycerides (P = 0.018), HDL‐cholesterol concentration (P = 0.017), and log triglyceride‐to‐HDL‐cholesterol ratio (P = 0.008). The beneficial association of the amount of physical activity and lipid traits found in men with the R allele suggests that this population subgroup needs to be physically active to achieve a favorable lipoprotein phenotype similar to that observed in QQ homozygous men. Genet. Epidemiol. 18:276–286, 2000. © 2000 Wiley‐Liss, Inc.
Major Clades of Australasian Rutoideae (Rutaceae) Based on rbcL and atpB Sequences

Background Rutaceae subfamily Rutoideae (46 genera, c. 660 species) is diverse in both rainforests and sclerophyll vegetation of Australasia. Australia and New Caledonia are centres of endemism with a number of genera and species distributed disjunctly between the two regions. Our aim was to generate a high-level molecular phylogeny for the Australasian Rutoideae and identify major clades as a framework for assessing morphological and biogeographic patterns and taxonomy. Methodology/Principal Findings Phylogenetic analyses were based on chloroplast genes, rbcL and atpB, for 108 samples (78 new here), including 38 of 46 Australasian genera. Results were integrated with those from other molecular studies to produce a supertree for Rutaceae worldwide, including 115 of 154 genera. Australasian clades are poorly matched with existing tribal classifications, and genera Philotheca and Boronia are not monophyletic. Major sclerophyll lineages in Australia belong to two separate clades, each with an early divergence between rainforest and sclerophyll taxa. Dehiscent fruits with seeds ejected at maturity (often associated with myrmecochory) are inferred as ancestral; derived states include woody capsules with winged seeds, samaras, fleshy drupes, and retention and display of seeds in dehisced fruits (the last two states adaptations to bird dispersal, with multiple origins among rainforest genera). Patterns of relationship and levels of sequence divergence in some taxa, mostly species, with bird-dispersed (Acronychia, Sarcomelicope, Halfordia and Melicope) or winged (Flindersia) seeds are consistent with recent long-distance dispersal between Australia and New Caledonia. Other deeper Australian/New Caledonian divergences, some involving ant-dispersed taxa (e.g., Neoschmidia), suggest older vicariance. Conclusions/Significance This comprehensive molecular phylogeny of the Australasian Rutoideae gives a broad overview of the group’s evolutionary and biogeographic history. Deficiencies of infrafamilial classifications of Rutoideae have long been recognised, and our results provide a basis for taxonomic revision and a necessary framework for more focused studies of genera and species.
Using Kappa Distributions to Identify the Potential Energy

This paper reports on the properties of kappa distributions in the presence of a potential energy. The constructed phase space kappa distribution leads to a polytropic relationship between the local density and temperature. The kappa and polytropic indices are connected via a characteristic and universal relationship: their sum is a constant depending specifically on the potential features. Determining this constant comprises a method essential for revealing the functional form and understanding the nature of the particle potential energy. The method is applied to the solar wind proton plasma at 1 AU. It is shown that a satisfactory physical interpretation of the potential affecting solar wind protons can be given by the interplanetary radial electric field.
Fructose and Pectin Detection in Fruit-Based Food Products by Surface-Enhanced Raman Spectroscopy

Surface-Enhanced Raman Spectroscopy (SERS) enables the investigation of samples with weak specific Raman signals, such as opaque samples, including fruit juices and pulp. In this paper, biological apple juices and apple/pear pulp have been studied in order to evidence the presence of fructose and pectin, which are components of great relevance for quality assessment of these kinds of products. In order to perform SERS measurements a low-cost home-made substrate consisting of a glass slide decorated with 30-nm-sized gold nanoparticles has been designed and used. By employing a conventional micro-Raman spectroscopy set-up and a suitable data treatment based on “wavelet” denoising algorithms and background subtraction, spectra of pectin and fructose with clear Raman features have been obtained. The results have confirmed the potential of SERS in the food industry for product characterization, also considering the low-cost and the relative ease of the fabrication process of the employed SERS substrate.
Toxicant Exposure in Cigarette Reducers versus Light Smokers

Background: The extent of exposure to tobacco toxicants in smokers who have reduced their cigarette intake compared with smokers who are light smokers is relatively unknown. The goal of this study is to investigate the occurrence of compensatory smoking in reducers compared with light smokers by measuring toxicant exposure. Methods: Participants in two smoking reduction intervention studies (N = 64) were selected for comparison with a group of light smokers (N = 62) who smoked the same number of cigarettes as the reducers. A compensatory smoking score was defined (biomarker level for reducer/biomarker level for light smoker) and calculated for urinary 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL) and its glucuronides (total NNAL), metabolites of the tobacco-specific lung carcinogen 4-(methylnitrosamino)-I-(3-pyridyl)-1-butanone, to measure the degree of smoking compensation in reducers when compared with the light smokers. Results: The mean level of creatinine-adjusted total NNAL for reducers was over twice that of light smokers even when they smoked about the same number of cigarettes per day. The difference of the mean total NNAL concentrations between light smokers and reducers was highly significant (P < 0.0001). Wide variability in total NNAL concentrations was also observed in reducers, with the extent of this variability between light smokers and reducers being significantly different (P = 0.0005). The level of individual reduction was shown to be a consistent predictor of compensatory smoking (r = 0.50; adjusted Ps = 0.002), with greater cigarette reduction associated with more compensation. Conclusions: Compensatory smoking limits the harm reduction value of decreased smoking of cigarettes. (Cancer Epidemiol Biomarkers Prev 2006;15(12):2355–8)
DOC1R: a MAP kinase substrate that control microtubule organization of metaphase II mouse oocytes

For the success of fertilization, spindles of vertebrate oocytes must remain stable and correctly organized during the arrest in metaphase II of meiosis. Using a two-hybrid screen with MAPK as a bait, we have recently identified MISS (MAPK interacting and spindle stabilizing) which controls mouse oocyte metaphase II spindle stability. Using the same screen, we identify another MAPK partner, DOC1R (Deleted in oral cancer one related), a murine homologue of a potential human tumor suppressor gene. We characterize DOC1R during mouse oocyte meiosis resumption. DOC1R is regulated by phosphorylation during meiotic maturation by MPF (M-phase promoting factor) and by the MOS/. /MAPK pathway. DOC1R and a DOC1R-GFP fusion localize to microtubules during meiotic maturation. Consistent with this microtubular localization, we show, by antisense and double-stranded RNA injection, that depletion of DOC1R induces microtubule defects in metaphase II oocytes. These defects are rescued by overexpressing a Xenopus DOC1R, showing that they are specific to DOC1R. Thus, the discovery of DOC1R, a substrate of MAPK that regulates microtubule organization of metaphase II mouse oocytes, reinforces the importance of this pathway in the control of spindle stability during the metaphase II arrest.
Computational Creativity Theory: The FACE and IDEA Descriptive Models

We introduce computational creativity theory (CCT) as an analogue in computational creativity research to computational learning theory in machine learning. In its current draft, CCT comprises the FACE descriptive model of creative acts as tuples of generative acts, and the IDEA descriptive model of the impact such creative acts may have. To introduce these, we simplify various assumptions about software development, background material given to software, how creative acts are performed by computer, and how audiences consume the results. We use the two descriptive models to perform two comparisons studies, firstly for mathematical discovery software, and secondly for visual art generating programs. We conclude by discussing possible additions, improvements and refinements to CCT.
Novel Intermolecular Iterative Mechanism for Biosynthesis of Mycoketide Catalyzed by a Bimodular Polyketide Synthase

In recent years, remarkable versatility of polyketide synthases (PKSs) has been recognized; both in terms of their structural and functional organization as well as their ability to produce compounds other than typical secondary metabolites. Multifunctional Type I PKSs catalyze the biosynthesis of polyketide products by either using the same active sites repetitively (iterative) or by using these catalytic domains only once (modular) during the entire biosynthetic process. The largest open reading frame in Mycobacterium tuberculosis, pks12, was recently proposed to be involved in the biosynthesis of mannosyl-β-1-phosphomycoketide (MPM). The PKS12 protein contains two complete sets of modules and has been suggested to synthesize mycoketide by five alternating condensations of methylmalonyl and malonyl units by using an iterative mode of catalysis. The bimodular iterative catalysis would require transfer of intermediate chains from acyl carrier protein domain of module 2 to ketosynthase domain of module 1. Such bimodular iterations during PKS biosynthesis have not been characterized and appear unlikely based on recent understanding of the three-dimensional organization of these proteins. Moreover, all known examples of iterative PKSs so far characterized involve unimodular iterations. Based on cell-free reconstitution of PKS12 enzymatic machinery, in this study, we provide the first evidence for a novel “modularly iterative” mechanism of biosynthesis. By combination of biochemical, computational, mutagenic, analytical ultracentrifugation and atomic force microscopy studies, we propose that PKS12 protein is organized as a large supramolecular assembly mediated through specific interactions between the C- and N-terminus linkers. PKS12 protein thus forms a modular assembly to perform repetitive condensations analogous to iterative proteins. This novel intermolecular iterative biosynthetic mechanism provides new perspective to our understanding of polyketide biosynthetic machinery and also suggests new ways to engineer polyketide metabolites. The characterization of novel molecular mechanisms involved in biosynthesis of mycobacterial virulent lipids has opened new avenues for drug discovery.