Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploiting parallelism in pattern matching: an information retrieval application

We propose a document-searching architecture based on high-speed hardware pattern matching to increase the throughput of an information retrieval system. We also propose a new parallel VLSI pattern-matching algorithm called the Data Parallel Pattern Matching (DPPM) algorithm, which serially broadcasts and compares the pattern to a block of data in parallel. The DPPM algorithm utilizes the high degree of integration of VLSI technology to attain very high-speed processing through parallelism. Performance of the DPPM has been evaluated both analytically and by simulation. Based on the simulation statistics and timing analysis on the hardware design, a search rate of multiple gigabytes per second is achievable using 2-μm CMOS technology. The potential performance of the proposed document-searching architecture is also analyzed using the simulation statistics of the DPPM algorithm.
Stable Image Colorization Algorithm Based on the Mixed L 0 / L 1 Norm Minimization

This paper proposes a colorization algorithm based on the mixed L0/L1 norm minimization. Authors have already proposed a colorization algorithm, however, it requires appropriate parameters, and its performance highly depends on these parameters. This paper introduces some heuristic and modifies the algorithm in order to reduce the dependence of parameters. Numerical examples show that the proposed algorithm colorizes the grayscale image efficiently.
Central arterial stiffness is increased among subjects with severe and very severe COPD: report from a population-based cohort study

Introduction Cardiovascular disease (CVD) is common in chronic obstructive pulmonary disease (COPD) and is, as productive cough, related to poorer prognosis in COPD. Central arterial stiffness is a marker of early atherosclerosis, but the association between COPD, productive cough, and arterial stiffness as a possible indicator of CVD is unclear. Objectives To compare both arterial stiffness among subjects with and without COPD and the impact of productive cough in a population-based cohort. Methods A population-based cohort, including 993 COPD and 993 non-COPD subjects, has been invited to annual examination since 2005. In 2010, 947 subjects, of which 416 had COPD (according to the GOLD spirometric criteria), participated in examinations including structured interview, spirometry, and measurements of central arterial stiffness as pulse wave velocity (PWV). Results PWV was higher in GOLD 3–4 compared to non-COPD (10.52 vs. 9.13 m/s, p=0.042). CVD and age ≥60 were both associated with significantly higher PWV in COPD as well as in non-COPD. In COPD, those with productive cough had higher PWV than those without, significantly so in GOLD 1 (9.59 vs. 8.92 m/s, p=0.024). In a multivariate model, GOLD 3–4 but not productive cough was associated with higher PWV, when adjusted for sex, age group, smoking habits, blood pressure, CVD, and pulse rate. Conclusions GOLD 3–4, age ≥60, and CVD were associated with increased arterial stiffness, and also increased in COPD subjects with productive cough compared to those without. Of importance, GOLD 3–4 but not productive cough remained associated with increased central arterial stiffness when adjusted for confounders.
Different dietary restriction regimens extend lifespan by both independent and overlapping genetic pathways in C. elegans

Dietary restriction (DR) has the remarkable ability to extend lifespan and healthspan. A variety of DR regimens have been described in species ranging from yeast to mammals. However, whether different DR regimens extend lifespan via universal, distinct, or overlapping pathways is still an open question. Here we examine the genetic pathways that mediate longevity by different DR regimens in Caenorhabditis elegans. We have previously shown that the low‐energy sensing AMP‐activated protein kinase AMPK/aak‐2 and the Forkhead transcription factor FoxO/daf‐16 are necessary for longevity induced by a DR regimen that we developed (sDR). Here we find that AMPK and FoxO are necessary for longevity induced by another DR regimen, but are dispensable for the lifespan extension induced by two different DR methods. Intriguingly, AMPK is also necessary for the lifespan extension elicited by resveratrol, a natural polyphenol that mimics some aspects of DR. Conversely, we test if genes previously reported to mediate longevity by a variety of DR methods are necessary for sDR‐induced longevity. Although clk‐1, a gene involved in ubiquinone biosynthesis, is also required for sDR‐induced lifespan extension, we find that four other genes (sir‐2.1, FoxA/pha‐4, skn‐1, and hsf‐1) are all dispensable for longevity induced by sDR. Consistent with the observation that different DR methods extend lifespan by mostly independent genetic mechanisms, we find that the effects on lifespan of two different DR regimens are additive. Understanding the genetic network by which different DR regimens extend lifespan has important implications for harnessing the full benefits of DR on lifespan and healthspan.
Elements of Formal Semantics

Draft version of Chapters 1 and 2. Comments welcome! See webpage for future updates and mailing list: Elements of Formal Semantics will aim at introducing some of the foundational concepts, principles and techniques in formal semantics of natural language. It is planned as a basic but sophisticated introduction for readers who have some elementary background in set theory and linguistics. No mastery of logic, advanced math, or theoretical linguistics is presupposed. The book will bring central semantic concepts and tools to the forefront, without letting them be complicated by detailed empirical discussions, logical background or specifics of semantic theories. By motivating the introduction of each basic tool and concept by the analysis of concrete examples in English, the book attempts to attract the reader's attention to the beauty of capturing intricate semantic phenomena using elegant and rigorously-defined mathematical techniques.
Aldehyde Dehydrogenase Discriminates the CD133 Liver Cancer Stem Cell Populations

Recent efforts in our study of cancer stem cells (CSC) in hepatocellular carcinoma (HCC) have led to the identification of CD133 as a prominent HCC CSC marker. Findings were based on experiments done on cell lines and xenograft tumors where expression of CD133 was detected at levels as high as 65%. Based on the CSC theory, CSCs are believed to represent only a minority number of the tumor mass. This is indicative that our previously characterized CD133+ HCC CSC population is still heterogeneous, consisting of perhaps subsets of cells with differing tumorigenic potential. We hypothesized that it is possible to further enrich the CSC population by means of additional differentially expressed markers. Using a two-dimensional PAGE approach, we compared protein profiles between CD133+ and CD133− subpopulations isolated from Huh7 and PLC8024 and identified aldehyde dehydrogenase 1A1 as one of the proteins that are preferentially expressed in the CD133+ subfraction. Analysis of the expression of several different ALDH isoforms and ALDH enzymatic activity in liver cell lines found ALDH to be positively correlated with CD133 expression. Dual-color flow cytometry analysis found the majority of ALDH+ to be CD133+, yet not all CD133+ HCC cells were ALDH+. Subsequent studies on purified subpopulations found CD133+ALDH+ cells to be significantly more tumorigenic than their CD133−ALDH+ or CD133−ALDH− counterparts, both in vitro and in vivo. These data, combined with those from our previous work, reveal the existence of a hierarchical organization in HCC bearing tumorigenic potential in the order of CD133+ALDH+ > CD133+ALDH− > CD133−ALDH−. ALDH, expressed along CD133, can more specifically characterize the tumorigenic liver CSC population. (Mol Cancer Res 2008;6(7):1146–53)
Enhancing Accuracy for Protein Prediction Secondary Structure by a New Hybrid Method

of protein secondary structure is an important step on the way to spell out its three dimensional structure and its function. This paper describes a new technique for prediction of secondary structure of protein based on contemporary machine learning methodology and data mining approach. More than one method has been developed to predict the protein secondary structure from the amino acids sequence; these methods show that we can achieve accuracy up to 80%. The work in this research is consists of three parts. In the first part, the secondary structure of each amino acid is predict alone with naive bays classifier, this method is based on amino acid preferences for different secondary structure. In the second part, an evolutionary algorithm to ameliorate this prediction is used; this method is based on physicochemical properties of protein regions. In the last part, a fragments bank which contains the protein fragments frequently detected in the Protein Data Bank (PDB) was developed; this method is based on the sequence alignment of protein but with a reduced database. The results of this research shows that the proposed method is improved the best know predictive accuracy by 4.5%, and attaint 85% accuracy with different datasets. Keywordssecondary structure prediction, Bays, Genetic algorithm, K nearest neighbor, Data mining, Amino acids, Hybrid method, supervised learning.
A COURSE IN HOMOLOGICAL ALGEBRA

The fascinating thing is that zeroth syzygies and first syzygies have an intrinsic significance in terms of the duality functor A 7→ A∗ = HomΛ(A, Λ). Namely, a left Λ-module A is a first syzygy if and only if it is the dual of some right Λ-module, and is a zeroth syzygy if and only if natural isomorphism A → A∗∗ is monic. Another interesting fact is that A∗ = 0 if and only if A ≈ ExtΛ(B, Λ) for some right Λ-module B . We will now proceed to prove these results.
A Magnetometer-Based Approach for Studying Human Movements

This paper investigates the use of body-mounted magnetic field sensors for the analysis of certain human movements. We demonstrate that, in several usual dynamic situations, magnetometers allow to estimate accurately a body inclination while being insensitive to its acceleration. Doing this, it is then possible to combine this information together with the one provided by an accelerometer to separate in a very accurate way the gravitational and kinematical components of acceleration. The proposed method is illustrated by the study of the sit-to-stand movement, estimating trunk inclination and absolute acceleration.
Learning to Summarize Web Documents Using Social Information

This paper presents a method named SoSVMRank, which integrates the social information of a Web document to generate a high-quality summarization. In order to do that, the summarization was formulated as a learning to rank task, in which the order of a sentence or comment was determined by its informative information. The informative information was measured by a set of local and social features in which the social features were exploited to support the local ones when modeling a sentence or comment. To enrich information, new features were also proposed. After ranking, top m ranked sentences and comments were selected as the summarization. Our method was extensively evaluated on two datasets. Promising results indicate that: (1) by using new features, our method achieves improvements in both ROUGE-1 and ROUGE-2 of the summarization over state-of-the-art baselines and (2) integrating social information benefits the summarization.
Anti‐transforming growth factor β‐induced protein antibody ameliorates vascular barrier dysfunction and improves survival in sepsis

Sepsis is a systemic inflammatory response syndrome resulting from a microbial infection. Transforming growth factor β‐induced protein (TGFBIp) is an extracellular matrix protein expressed by human endothelial cells and platelets that induces sepsis through interaction with integrin αvβ5. The aim of this study was to investigate the role of TGFBIp in vascular permeability and the underlying mechanisms using TGFBIp‐neutralizing antibody.
Hadoop Memory Usage Model

Hadoop MapReduce is a powerful open-source framework towards big data processing. For ordinary users, it is not hard to write MapReduce programs but hard to specify memory-related configurations. To help users analyze, predict and optimize job’s memory consumption, this technical report presents a fine-grained memory usage model. The proposed model reveals the relationship among memory usage, dataflow, configurations and user code. The task scheduler can also benefit from this model for better scheduling. 1 Background Although MapReduce is a simple divide-and-conquer programming paradigm, its detailed implementation is rather complex. This section talks bout the basic knowledge of Hadoop internals. System layers subsection describes the different views towards task’s memory usage in different layers. MapReduce dataflow depicts the concrete data processing steps that each job will go through. JVM internals discusses the memory management mechanism of JVM (Java Virtual Machine). 1.1 System layers To achieve flexibility and isolation, Hadoop MapReduce consists of three system layers shown in Figure 1.1. However, this complex architecture will aggravate user’s difficulty in understanding and optimizing job’s performance, especially the memory consumption. In user layer, before submitting the job, users are required to prepare the dataset, write user code and specify appropriate configurations. In framework layer, each job is divided into several small map and reduce tasks. After that, each task will be scheduled onto an appropriate node. In execution layer, the node will launch each task as a separate process (i.e., a JVM instance, JVM reuse is an exception). Then, each task will perform the relatively fixed processing steps which are pre-defined by the framework. Since JVM divides the heap space into two generations and manages them separately, execution layer is the only one that knows the real fine-grained memory usage. The blue-green graph in Figure 1.1 shows the realtime usage in New and Old generations of a JVM instance. Framework just treats memory as a large continuous space and has little idea of the real usage. The memory space is intensively used for both data storage (e.g., storing intermediate data) and data processing (e.g., map() reads and processes the input data). At the highest layer, users usually feel hard to understand job’s memory usage, not to mention optimizing the usage in the large space of configurations. However, new resource management and scheduling frameworks such as YARN [6] and Mesos [8] not only require users to specify the maximum memory consumption but also schedule tasks according to the consumption. Inappropriate configurations may lead to job’s runtime error, performance degradation or the waste of memory.
Sexual Seroadaptation: Lessons for Prevention and Sex Research from a Cohort of HIV-Positive Men Who Have Sex with Men

Background Surveillance data on sexually transmitted infections (STIs) and behavioral characteristics identified in studies of the risk of seroconversion are often used as to track sexual behaviors that spread HIV. However, such analyses can be confounded by “seroadaptation”—the restriction of unprotected anal intercourse (UAI), especially unprotected insertive UAI, to seroconcordant partnerships. Methods We utilized sexual network methodology and repeated-measures statistics to test the hypothesis that seroadaptive strategies reduce the risk of HIV transmission despite numerous partnerships and frequent UAI. Principal Findings In a prospective cohort study of HIV superinfection including 168 HIV-positive men who have sex with men (MSM), we found extensive seroadaptation. UAI was 15.5 times more likely to occur with a positive partner than a negative one (95% confidence interval [CI], 9.1–26.4). Receptive UAI was 4.3 times more likely in seroconcordant partnerships than with negative partners (95% CI, 2.8–6.6), but insertive UAI was 13.6 times more likely with positives (95% CI, 7.2–25.6). Our estimates suggest that seroadaptation reduced HIV transmissions by 98%. Conclusion Potentially effective HIV prevention strategies, such as seroadaptation, have evolved in communities of MSM before they have been recognized in research or discussed in the public health forum. Thus, to be informative, studies of HIV risk must be designed to assess seroadaptive behaviors rather than be limited to individual characteristics, unprotected intercourse, and numbers of partners. STI surveillance is not an effective indicator of trends in HIV incidence where there are strong patterns of seroadaptation.
The macroevolutionary consequences of phenotypic integration: from development to deep time

Phenotypic integration is a pervasive characteristic of organisms. Numerous analyses have demonstrated that patterns of phenotypic integration are conserved across large clades, but that significant variation also exists. For example, heterochronic shifts related to different mammalian reproductive strategies are reflected in postcranial skeletal integration and in coordination of bone ossification. Phenotypic integration and modularity have been hypothesized to shape morphological evolution, and we extended simulations to confirm that trait integration can influence both the trajectory and magnitude of response to selection. We further demonstrate that phenotypic integration can produce both more and less disparate organisms than would be expected under random walk models by repartitioning variance in preferred directions. This effect can also be expected to favour homoplasy and convergent evolution. New empirical analyses of the carnivoran cranium show that rates of evolution, in contrast, are not strongly influenced by phenotypic integration and show little relationship to morphological disparity, suggesting that phenotypic integration may shape the direction of evolutionary change, but not necessarily the speed of it. Nonetheless, phenotypic integration is problematic for morphological clocks and should be incorporated more widely into models that seek to accurately reconstruct both trait and organismal evolution.
Collagen Induced Thrombus Formation at the Apex of Eccentric Stenoses - A Time Course Study with Non-Anticoagulated Human Blood

Summary Atherosclerotic plaque rupture may trigger the formation of a mural thrombus. This thrombus formation is apparently affected by very high and complex shear conditions introduced by the luminal narrowing (stenosis) of the atheroma. To study the impact of such blood flow behaviour on thrombus formation we employed a model system where collagen-induced thrombogenesis is studied at the apex of well-defined eccentric stenoses. Thrombus formation in non-anticoagulated human blood drawn directly from an antecubital vein over the collagen coated stenosis apex for periods of 0.5, 1, 3 or 5 min was quantified by morphometry. The stenoses reduced the cross-sectional area of the blood flow channel by 60, 80 and 89%, which corresponded to apex wall shear rates of 2600, 10,500 and 32,000 s−1, respectively. Platelet-collagen adhesion decreased by increasing shear at the stenosis apex. The corresponding adhesion rates were highest at 1 min, then they gradually decreased upon prolongation of the perfusion time. The platelet thrombus volume increased in concert with increasing shear rate up to 10,500 s−1, whereas, at 32,000 s−1, the volume was decreased. The corresponding growth rates and rates of thrombus occlusion at the apex levelled off at 3 min. Significant fibrin deposition was not observed before 3 min, and was most pronounced at 10,500 and 32,000 s−1. The plasma levels of fibrinopeptide A and P-thromboglobulin increased in concert with increasing shear and perfusion time, particularly at the two highest shear conditions. Thus, hallmarks of thrombus formation at these stenoses with increasing shear are decreased platelet-collagen adhesion, and increased platelet-platelet interaction and fibrin deposition. A fibrin tail downstream to the collagen-attached platelet thrombus is regularly observed when thrombus occlusion exceeds 40%. However, the reduced thrombus growth at the most occlusive stenosis (89%) is presumably due to the high shear stresses which may reduce the rate of platelet incorporation into the thrombus and/or tear off thrombus fragments.
The Molting Biomarker Molecule Exists as 2‐Acetamido‐2‐deoxy‐gluconic Acid in Urine of Blue Crabs and Helmet Crabs

N‐Acetyl‐d‐glucosamino‐1,5‐lactone 1 has been reported as a candidate component of the sex pheromone mixture of female blue crabs, Callinectes sapidus, since it is present in the urine of reproductive females and males detect it. Theoretically, 1 can convert to a 1,4‐lactone isomer 2 or to the corresponding carboxylic acid, 2‐acetamido‐2‐deoxygluconic acid 3 by hydrolysis in aqueous solution. In this study, we examined the biologically relevant state of equilibrium mixture of 1, 2, and 3 in crab urine using ESI‐MS and NMR analyses. The ESI‐MS analysis showed that the dominant form of solubilized synthetic 1 is lactone 1 and/or 2, immediately after solubilization in deuterated water, seawater, and phosphate buffer and gradually changing to carboxylic acid 3 which becomes most predominant in phosphate buffer. The NMR analysis showed that synthetic 1 converts to other forms in deuterated water and seawater, and reaches an equilibrium mixture of at least three forms within 24 h. In contrast, 1 converts to a single state of another form in deuterated water with 35 mm phosphate buffer pH 7.6 within 24 h, which is identical to the state in urine with or without phosphate buffer. Thus, we conclude that the molting biomarker sensed by male crabs is 3.
Time‐Series Analysis of Air Pollution and Cause Specific Mortality

Ten large European cities provided data on daily air pollution as well as mortality from respiratory and cardiovascular mortality. We used Poisson autoregressive models that controlled for trend, season, influenza epidemics, and meteorologic influences to assess the short-term effects of air pollution at each city. We then compared and pooled the city-specific results in a meta-analysis. The pooled relative risks of daily deaths from cardiovascular conditions were 1.02 [95% confidence interval (CI) = 1.01–1. 04] for a 50 $$g/m3 increment in the concentration of black smoke and 1.04 (95% CI = 1.01–1.06) for an increase in sulfur dioxide levels in western European cities. For respiratory diseases, these figures were 1.04 (95% CI = 1.021.07) and 1.05 (95% CI = 1.03–1.07), respectively. These associations were not found in the five central European cities. Eight-hour averages of ozone were also moderately associated with daily mortality in western European cities (relative risk = 1.02; 95% CI = 1.00–1.03 for cardiovascular conditions and relative risk = 1.06; 95% CI = 1.02–1.10 for respiratory conditions). Nitrogen dioxide did not show consistent relations with daily mortality. These results are similar to previously published data and add credence to the causal interpretation of these associations at levels of air pollution close to or lower than current European standards. (Epidemiology 1998; 9:495–503)