Miracle-dz/UniFAR-FTUs huggingface dataset:
Lysophosphatidic Acid and Autotaxin Stimulate Cell Motility of Neoplastic and Non-neoplastic Cells through LPA1*

Autotaxin (ATX) is a tumor cell motility-stimulating factor originally isolated from melanoma cell supernatant that has been implicated in regulation of invasive and metastatic properties of cancer cells. Recently, we showed that ATX is identical to lysophospholipase D, which converts lysophosphatidylcholine to a potent bioactive phospholipid mediator, lysophosphatidic acid (LPA), raising the possibility that autocrine or paracrine production of LPA by ATX contributes to tumor cell motility. Here we demonstrate that LPA and ATX mediate cell motility-stimulating activity through the LPA receptor, LPA1. In fibroblasts isolated from lpa1-/- mice, but not from wild-type or lpa2-/-, cell motility stimulated with LPA and ATX was completely absent. In the lpa1-/- cells, LPA-stimulated lamellipodia formation was markedly diminished with a concomitant decrease in Rac1 activation. LPA stimulated the motility of multiple human cancer cell lines expressing LPA1, and the motility was attenuated by an LPA1-selective antagonist, Ki16425. The present study suggests that ATX and LPA1 represent potential targets for cancer therapy.
Efficient Cache-oblivious String Algorithms for Bioinformatics

We present theoretical and experimental results on cache-efficient and parallel algorithms for some well-studied string problems in bioinformatics: 1. Pairwise alignment. Optimal pairwise global sequence alignment using affine gap penalty; 2. Median. Optimal alignment of three sequences using affine gap penalty; 3. RNA secondary structure prediction. Maximizing number of base pairs in RNA secondary structure with simple pseudoknots. For each of these three problems we present cache-oblivious algorithms that match the best-known time complexity, match or improve the best-known space complexity, and improve significantly over the cache-efficiency of earlier algorithms. We also show that these algorithms are easily parallelizable, and we analyze their parallel performance. We present experimental results that show that all three cache-oblivious algorithms run faster on current desktop machines than the best previous algorithm for the problem. For the first two problems we compare our code to publicly available software written by others, and for the last problem our comparison is to our implementation of Akutsu’s algorithm. We also include empirical results showing good performance for the parallel implementations of our algorithms for the first two problems. Our methods are applicable to several other dynamic programs for string problems in bioinformatics including local alignment, generalized global alignment with intermittent similarities, multiple sequence alignment under several scoring functions such as ‘sum-of-pairs’ objective function and RNA secondary structure prediction with simple pseudoknots using energy functions based on adjacent base pairs. ∗Department of Computer Sciences, University of Texas, Austin, TX 78712. Email: {shaikat,haison,vlr}@cs.utexas. edu. This work was supported in part by NSF Grant CCF-0514876 and NSF CISE Research Infrastructure Grant EIA-0303609.
Small artery structure in hypertension. Dual processes of remodeling and growth.

A lthough the causes of high blood pressure vary, it / \ is becoming clear that sustained hypertension is -Z A . associated with changes in cardiovascular structure: left ventricular hypertrophy and increased wall thickness:lumen diameter (wall:lumen) ratio of the blood vessels. To some extent, these alterations are natural physiological responses and are protective. However, the risk of circulatory death is closely related to left ventricular hypertrophy, and therefore, it is suggested increasingly that effective antihypertensive treatment requires normalization not only of blood pressure but also of cardiac structure. This may be the case also for the vascular changes, in particular at the level of the "resistance arteries" (defined here as precapillary arteries with diameters less than 500 fim; see Reference 2), these vessels being responsible for the increased peripheral resistance of essential hypertensive patients. Until recently, this possibility remained speculative because there were few quantitative data concerning resistance artery structure. However, over the past 10 years such data have become available, in particular with regard to the more proximal resistance vessels, so-called "small arteries" (see Reference 2). The purpose of this Brief Review is to identify the type of structural change that is found in small arteries in hypertensive individuals. In particular, we will discuss whether the altered structure can be ascribed to growth alone or whether it is due to "remodeling,"' that is, a rearrangement of otherwise normal material, which Baumbach and Heistad first noted in cerebral small arteries of spontaneously hypertensive rats (SHR) that are stroke-prone.
Effect of Interface Modification on the Mechanical Behavior of Carbon Nanotube Reinforced Composites Using Parallel Molecular Dynamics Simulations

Molecular dynamics (MD) simulations play an important predictive role in understanding the behavior of nanoscale systems. In this paper, parallel MD simulations are used to understand the mechanical behavior of interfaces in CNT based composites. We present an algorithm for parallel implementation of MD simulations of carbon nanotube (CNT) based systems using reactive bond order potentials. We then use that algorithm to model the CNT-polymer interfaces with various levels of interaction as (a) described only by long range Van Der Waals interactions (b) chemically bonded with fixed matrix and (c) chemically bonded with matrix explicitly modeled. It is shown that interface strength based on non bonded interactions is very low (of the order of few MPa) and it can be significantly improved through surface chemical modification of CNTs (to an order of a few GPa). It is further noted that chemical bonding between functionalized nanotube and matrix during processing is essential to obtain good interface strength and hence a better composite. Keyword: Carbon nanotube composites, interfaces, parallel molecular dynamics.
Association between air pollution and low birth weight: a community-based study.

The relationship between maternal exposure to air pollution during periods of pregnancy (entire and specific periods) and birth weight was investigated in a well-defined cohort. Between 1988 and 1991, all pregnant women living in four residential areas of Beijing were registered and followed from early pregnancy until delivery. Information on individual mothers and infants was collected. Daily air pollution data were obtained independently. The sample for analysis included 74,671 first-parity live births were gestational age 37-44 weeks. Multiple linear regression and logistic regression were used to estimate the effects of air pollution on birth weight and low birth weight (< 2,500 g), adjusting for gestational age, residence, year of birth, maternal age, and infant gender. There was a significant exposure-response relationship between maternal exposures to sulfur dioxide (SO2) and total suspended particles (TSP) during the third trimester of pregnancy and infant birth weight. The adjusted odds ratio for low birth weight was 1.11 (95% CI, 1.06-1.16) for each 100 micrograms/m3 increase in SO2 and 1.10 (95% CI, 1.05-1.14) for each 100 micrograms/m3 increase in TSP. The estimated reduction in birth weight was 7.3 g and 6.9 g for each 100 micrograms/m3 increase in SO2 and in TSP, respectively. The birth weight distribution of the high-exposure group was more skewed toward the left tail (i.e., with higher proportion of births < 2,500 g) than that of the low-exposure group. Although the effects of other unmeasured risk factors cannot be excluded with certainty, our data suggests that TSP and SO2, or a more complex pollution mixture associated with these pollutants, contribute to an excess risk of low birth weight in the Beijing population. ImagesFigure 1.Figure 2.Figure 3.Figure 4.Figure 5.
Probabilistic color-by-numbers

We present a probabilistic factor graph model for automatically coloring 2D patterns. The model is trained on example patterns to statistically capture their stylistic properties. It incorporates terms for enforcing both color compatibility and spatial arrangements of colors that are consistent with the training examples. Using Markov Chain Monte Carlo, the model can be sampled to generate a diverse set of new colorings for a target pattern. This general probabilistic framework allows users to guide the generated suggestions via conditional inference or additional soft constraints. We demonstrate results on a variety of coloring tasks, and we evaluate the model through a perceptual study in which participants judged sampled colorings to be significantly preferable to other automatic baselines.
Constraint Programming Based Column Generation Heuristics for a Ship Routing and Berthing Time Assignment Problem

We develop a constraint programming based heuristic algorithm using column generation technique to solve a ship routing problem which the loading and unloading times of cargoes at pickup and drop-off locations are significant. In order to prevent congestions at the locations, we need to assign berthing time slots to each vessel to perform the loading and unloading tasks at different locations. This problem is motivated by the operations of a feeder vessel service company with company-owned cargo terminals, which the shipping company wishes to coordinate the routing and the berthing time of the vessels.
Relational particle models: II. Use as toy models for quantum geometrodynamics

Relational particle models are employed as toy models for the study of the problem of time in quantum geometrodynamics. These models' analogue of the thin sandwich is resolved. It is argued that the relative configuration space and shape space of these models are close analogues from various perspectives of superspace and conformal superspace, respectively. The geometry of these spaces and quantization thereupon is presented. A quantity that is frozen in the scale-invariant relational particle model is demonstrated to be an internal time in a certain portion of the relational particle reformulation of Newtonian mechanics. The semiclassical approach for these models is studied as an emergent time resolution for these models, as are consistent records approaches.
Concept of feedback-free high-frequency loss modulation in detuned duo-cavity vertical cavity surface-emitting laser

The authors propose and demonstrate a novel concept for ultrahigh-speed loss modulation of a vertical cavity surface-emitting laser (VCSEL). A duo-cavity device architecture is used to optically decouple the ac feedback component of a loss-modulation section from the VCSEL active region. The elimination of feedback allows modulation of the VCSEL output far beyond the optoelectronic relaxation frequency by eliminating both resonance and intrinsic high-frequency response roll-off. Precise detuning of the resonances of both coupled cavities is used to achieve ac feedback elimination by control of thickness during molecular beam epitaxy growth. Variation in the applied bias at the multiple-quantum-well modulator section allows adjustment of detuning to change coupling between the two sections, resulting in resonance features in the modulation response. In the ideal case, the resulting resonance-free high-frequency modulation response is limited only by parasitics of the modulator section. A flat (±3 dB) modul.
Genetic Interactions Due to Constitutive and Inducible Gene Regulation Mediated by the Unfolded Protein Response in C. elegans

The unfolded protein response (UPR) is an adaptive signaling pathway utilized to sense and alleviate the stress of protein folding in the endoplasmic reticulum (ER). In mammals, the UPR is mediated through three proximal sensors PERK/PEK, IRE1, and ATF6. PERK/PEK is a protein kinase that phosphorylates the alpha subunit of eukaryotic translation initiation factor 2 to inhibit protein synthesis. Activation of IRE1 induces splicing of XBP1 mRNA to produce a potent transcription factor. ATF6 is a transmembrane transcription factor that is activated by cleavage upon ER stress. We show that in Caenorhabditis elegans, deletion of either ire-1 or xbp-1 is synthetically lethal with deletion of either atf-6 or pek-1, both producing a developmental arrest at larval stage 2. Therefore, in C. elegans, atf-6 acts synergistically with pek-1 to complement the developmental requirement for ire-1 and xbp-1. Microarray analysis identified inducible UPR (i-UPR) genes, as well as numerous constitutive UPR (c-UPR) genes that require the ER stress transducers during normal development. Although ire-1 and xbp-1 together regulate transcription of most i-UPR genes, they are each required for expression of nonoverlapping sets of c-UPR genes, suggesting that they have distinct functions. Intriguingly, C. elegans atf-6 regulates few i-UPR genes following ER stress, but is required for the expression of many c-UPR genes, indicating its importance during development and homeostasis. In contrast, pek-1 is required for induction of approximately 23% of i-UPR genes but is dispensable for the c-UPR. As pek-1 and atf-6 mainly act through sets of nonoverlapping targets that are different from ire-1 and xbp-1 targets, at least two coordinated responses are required to alleviate ER stress by distinct mechanisms. Finally, our array study identified the liver-specific transcription factor CREBh as a novel UPR gene conserved during metazoan evolution.
Cytogenetic Analysis of Gemistocytic Cells in Gliomas

Gemistocytes are glial cells characterized by voluminous, eosinophilic cytoplasm and a peripherally positioned, often flattened nucleus. Gemistocytes, usually present in anoxic-ischemic brains, are regularly encountered in glial neoplasms. The presence of gemistocytes in gliomas has been associated with an unfavorable clinical course, notwithstanding the low proliferative potential of these cells. It is not known whether gemistocytes residing in gliomas are dormant tumor cells, or alternatively, represent interspersed reactive glial cells. Whereas gemistocytic astrocytomas have been subject to various genetic investigations, no genomic analysis comparing individual cells in gliomas has been reported so far. In the present study, 3 astrocytomas, 3 oligodendrogliomas, and 3 mixed oligoastrocytomas, all harboring gemistocytic cells, were genetically analyzed by DNA in situ hybridization to paraffin-embedded, formalin-fixed tissue samples with optimal preservation of cellular morphology. To this end, probes for the centromeric regions of chromosome 7 and 10, known to show copy number aberrations in gliomas, were used. In addition, probes for centromeric regions of chromosomes 1 and 17 were used for the ploidy status of the tumors. The spot counts for the various chromosomes were statistically compared. Gains of chromosome 7 were found in 1 anaplastic astrocytoma, 1 anaplastic oligodendroglioma, and 1 anaplastic oligoastrocytoma. Loss of chromosome 10 was seen in 2 anaplastic astrocytomas, in 1 anaplastic oligodendroglioma, and in 1 anaplastic oligoastrocytoma. In 3 cases, significant differences in spot distributions between gemistocytes and non-gemistocytes were found, but the other cases showed no difference in spot distribution. It is concluded that, although many gemistocytic cells in gliomas may be considered reactive cells, in a subset of tumors, part of the gemistocytic cells should be considered neoplastic.
Reinforcement of Denture Base Resin

The fracture resistance of polymethyl methacrylate (PMMA) the most popular denture base materials, is not satisfactory. The aim of this study is to improve the mechanical properties of PMMA by adding filler particles. Different inorganic filler particles including micronised glass flakes, acryl silane micronised, glass flakes 350nm, TiO2 and ZrO2 with different ratios by weight were incorporated into heat-cure plain PMMA and processed with optimal condition [2.5:1 Powder/ monomer ratio, conventional packing method and water bath curing for 2 hours at 95°C] to produce 12mm diameter and 2mm thick discs. Plain PMMA without additives was prepared as a test control. Three types of mechanical tests, biaxial flexure, microindentation fracture toughness and Vickers hardness were carried out on the samples. It was found that incorporating the particles did not improve the biaxial flexural strength of the resin. However, TiO2, ZrO2 and micronised glass flakes increased the fracture toughness of the resin. The hardness of PMMA was improved by the incorporation of all the particles.
The pulse of the city through Twitter: relationships between land use and spatiotemporal demographics

Social network data offer interesting opportunities in urban studies. In this study, we used Twitter data to analyse city dynamics over the course of the day. Users of this social network were grouped according to city zone and time slot in order to analyse the daily dynamics of the city and the relationship between this and land use. First, daytime activity in each zone was compared with activity at night in order to determine which zones showed increased activity in each of the time slots. Then, typical Twitter activity profiles were obtained based on the predominant land use in each zone, indicating how land uses linked to activities were activated during the day, but at different rates depending on the type of land use. Lastly, a multiple regression analysis was performed to determine the influence of the different land uses on each of the major time slots (morning, afternoon, evening and night) through their changing coefficients. Activity tended to decrease throughout the day for most land uses (e.g. offices, education, health and transport), but remained constant in parks and increased in retail and residential zones. Our results show that social network data can be used to improve our understanding of the link between land use and urban dynamics.
Locality-Aware CTA Clustering for Modern GPUs

Cache is designed to exploit locality; however, the role of on-chip L1 data caches on modern GPUs is often awkward. The locality among global memory requests from different SMs (Streaming Multiprocessors) is predominantly harvested by the commonly-shared L2 with long access latency; while the in-core locality, which is crucial for performance delivery, is handled explicitly by user-controlled scratchpad memory. In this work, we disclose another type of data locality that has been long ignored but with performance boosting potential --- the inter-CTA locality. Exploiting such locality is rather challenging due to unclear hardware feasibility, unknown and inaccessible underlying CTA scheduler, and small in-core cache capacity. To address these issues, we first conduct a thorough empirical exploration on various modern GPUs and demonstrate that inter-CTA locality can be harvested, both spatially and temporally, on L1 or L1/Tex unified cache. Through further quantification process, we prove the significance and commonality of such locality among GPU applications, and discuss whether such reuse is exploitable. By leveraging these insights, we propose the concept of CTA-Clustering and its associated software-based techniques to reshape the default CTA scheduling in order to group the CTAs with potential reuse together on the same SM. Our techniques require no hardware modification and can be directly deployed on existing GPUs. In addition, we incorporate these techniques into an integrated framework for automatic inter-CTA locality optimization. We evaluate our techniques using a wide range of popular GPU applications on all modern generations of NVIDIA GPU architectures. The results show that our proposed techniques significantly improve cache performance through reducing L2 cache transactions by 55%, 65%, 29%, 28% on average for Fermi, Kepler, Maxwell and Pascal, respectively, leading to an average of 1.46x, 1.48x, 1.45x, 1.41x (up to 3.8x, 3.6x, 3.1x, 3.3x) performance speedups for applications with algorithm-related inter-CTA reuse.
Aspects of Traditional versus Virtual Laboratory for Education in Instrumentation and Measurement

Nowadays the multimedia tools have an important role in both the management of the lectures and the organization of the course program on instrumentation and measurement. In this new scenario, the virtual laboratory (VL) represents the environment in which the learning activities are performed. Starting from this observation, in the paper an overview of the state of the art of the VL-based education on instrumentation and measurement is given. The fundamental aspects concerning both the software and the hardware to design the VL are examined. Attention it is also devoted to innovative requirements and interesting open questions arising from the large diffusion of the VLs
A graph Laplacian regularization for hyperspectral data unmixing

This paper introduces a graph Laplacian regularization in the hyperspectral unmixing formulation. The proposed regularization relies upon the construction of a graph representation of the hyperspectral image. Each node in the graph represents a pixel's spectrum, and edges connect similar pixels. The proposed graph framework promotes smoothness in the estimated abundance maps and collaborative estimation between homogeneous areas of the image. The resulting convex optimization problem is solved using the Alternating Direction Method of Multipliers (ADMM). A special attention is given to the computational complexity of the algorithm, and Graph-cut methods are proposed in order to reduce the computational burden. Finally, simulations conducted on synthetic and real data illustrate the effectiveness of the graph Laplacian regularization with respect to other classical regularizations for hyperspectral unmixing.
Hemodynamics and epoprostenol use are associated with thrombocytopenia in pulmonary arterial hypertension.

BACKGROUND Thrombocytopenia develops in some patients with advanced pulmonary arterial hypertension (PAH) while receiving IV epoprostenol therapy. In this study, we evaluate whether epoprostenol use, other PAH medication use, hemodynamics, or PAH etiology are associated with thrombocytopenia in PAH. METHODS Platelet counts were evaluated in 47 PAH patients receiving IV epoprostenol, and in 44 patients with an inadequate response to initial therapy with oral agents in a cross-sectional study. Associations between thrombocytopenia (platelet count < 150,000/mL) and epoprostenol use, hemodynamics, PAH etiology, and use of other PAH medications were evaluated in univariable and multivariable analyses. RESULTS PAH subtypes included idiopathic (69%), fenfluramine (18%), connective tissue disease (10%), and congenital heart disease (2%)-associated PAH. Thrombocytopenia was observed in 34% of patients treated with epoprostenol, compared with 15% of patients receiving oral therapy (odds ratio [OR], 2.9; p < 0.05), and the association between epoprostenol and thrombocytopenia remained significant after adjustment for differences in hemodynamics (OR, 5.0; p < 0.05). Right atrial pressure (OR, 1.12 per mm Hg; p < 0.05) and mixed venous oxygen saturation (Svo(2)) [OR, 0.92 per percentage; p < 0.05] were also associated with thrombocytopenia in univariable analyses; after logistic regression analysis, both the use of epoprostenol and Svo(2) were independently associated with thrombocytopenia. In a separate analysis including only patients with current or prior epoprostenol use, epoprostenol dose and right atrial pressure were inversely associated with platelet count. CONCLUSION Epoprostenol use and severity of hemodynamic abnormalities are associated with thrombocytopenia in PAH, and these effects appear to be independent and additive.