Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical Correlates and Heritability of Flow-Mediated Dilation in the Community: The Framingham Heart Study

Background—Studies in selected samples have linked impaired endothelial function with cardiovascular disease and its risk factors. The clinical correlates and heritability of endothelial function in the community have not been described. Methods and Results—We examined a measure of endothelial function, brachial artery flow-mediated dilation (FMD), expressed as both percent (FMD%) and actual dilation by ultrasound with the occlusion cuff below the elbow in 2883 Framingham Study participants (52.9% women; mean age, 61 years). A subset of 1096 participants performed a 6-minute walk test before FMD determination. Mean FMD% was 3.3±3.0% in women and 2.4±2.4% in men. In stepwise multivariable linear regression models, FMD% was inversely related to age, systolic blood pressure, body mass index (BMI), lipid-lowering medication, and smoking, whereas it was positively related to female gender, heart rate, and prior walk test. The estimated heritability of FMD% was 0.14. FMD actual dilation findings were similar, except that female sex and BMI were not significantly associated. Conclusions—Increasing age, systolic blood pressure, BMI, and smoking were associated with lower FMD% in our community-based sample, whereas prior exercise and increasing heart rate were associated with higher FMD%. The estimated heritability of FMD was modest. Future research will permit more complete characterization of the genetic and environmental determinants of endothelial function and its prognostic value in the community.
Selective Attention and Mental Flexibility are Reduced during the Interictal Period in Migraine

Background: Headache patients frequently complain about difficulties in attention and concentration, even when they are headache free, and psychometric studies concerning attentional deficits in migraine patients between attacks are scarce. Objective: To evaluate selective attention of migraine patients interictally and compare them with healthy volunteers. Patients and Methods: We performed, between February 2011 and July 2011, a case-control study including 45 university students suffering from migraine matched with 45 healthy students as controls. Migraine patients were evaluated in an interictal state. Subjects with another headache type, history of brain injury, epilepsy and visual disturbances were excluded. Mood disorders were assessed using the Hospital Anxiety and Depression (HAD) questionnaire. Selective attention was evaluated using the Delis–Kaplan Executive Functions System (D-KEFS) colour-word interference test. Results: Mean age of patients was 23.29±2.55 years, versus 22.89±2.04 years for controls (p=0.2). The selective attention score was −4.04±7.08 for patients, versus −1.31±7.73 for controls (p=0.02). The mean mental flexibility score was lower in migraine patients compared with controls (36.67±6.79 versus 41.33±6.23; p=0.01). Gender, anxiety, depression scores and migraine characteristics had no correlation with the selective attention score. Conclusion: Selective attention and mental flexibility capacities are significantly reduced in migraine patients during the interictal period. These abnormalities probably contribute to frequent attentional complaints among these patients.
XML in the Visualisation Pipeline

The extensible markup language (XML) has been applied successfully in a wide range of application domains and is beginning to find applications in visualisation. We explore the possibility that, rather than simply being used as an exchange format, XML might become a fundamental medium in an extended visualisation pipeline. We present examples from our software visualisation research to illustrate that increased rigour, as well as flexibility, can be delivered by integrating XML into the visualisation pipeline.
A COMPARISON OF CELL DISRUPTION PROCEDURES FOR THE RECOVERY OF INTRACELLULAR CAROTENOIDS FROM SPOROBOLOMYCES RUBERRIMUS H110

Carotenoids are intracellular pigments produced by microorganisms, including some species of yeasts, in the stationary phase of growth by the secondary metabolic pathways. In the present study, different methods of Sporobolomyces ruberrimus H110 yeast cell lysis were evaluated with the objective of optimizing the recovery of intracellular pigments. Three extraction methods were used: vortex (glass beads and quartz stones), planetary mill (glass beads and quartz stones) and dimethyl sulfoxide. For each one of the lysis agents studied, factorial designs were developed considering as independent variables the agitation speed and lysis agent concentration. A central composite planning was defined considering as independent variables the lysis agent concentration and agitation speed, analyzing as response the estimated total number of extracted carotenoids. From the methods studied, a better extraction of total carotenoid (1.74 mg.g -1 of cells and of 1.57 mg.g -1 of cells) using the planetary mill method with 135 mg of glass beads or irregular quartz stones,
Consistent Velocity Approximation for Finite Volume or Element Discretizations of Density Driven Flow in Porous Media

Many controversial numerical simulations of density driven ow prob lems presented in di erent papers suggest the necessity of careful and proper design of discretization One of the possible numerical artifact that appears if standard nite element or nite volume methods are formally applied is the pres ence of arti cial numerical velocities even for the case of hydrostatic conditions This subject is known as a consistent velocity approximation Voss and Souza where a restrictive assumption on the interpolation of pressure and density must be used in the computations of velocity from v K rp c g An algorithm that is so far used for the determination of consistent velocity can be validated only for a linearly variable density and only in the case of one dimensional hydrostatic equilibrium We present a new formulation of consistent velocity approximation for the arbitrary choice of discretization technique Such formulation can be validated exactly for a general nonlinear dependence of density with no assumptions about hydrostatic conditions Further a simple relation to previous consistency formu lation is given with the conclusion that it is equivalent for the linearly variable density This enables us to present the algorithm also for nite elements not found in literature triangles tetrahedras The new idea of consistent velocity approximation was used in the context of nite volume discretization Together with an upwind scheme it results in stable physically reasonable and grid nondependent behaviour of numerical solutions
Newtonian cell interactions shape natural killer cell education

Newton's third law of motion states that for every action on a physical object there is an equal and opposite reaction. The dynamic change in functional potential of natural killer (NK) cells during education bears many features of such classical mechanics. Cumulative physical interactions between cells, under a constant influence of homeostatic drivers of differentiation, lead to a reactive spectrum that ultimately shapes the functionality of each NK cell. Inhibitory signaling from an array of self‐specific receptors appear not only to suppress self‐reactivity but also aid in the persistence of effector functions over time, thereby allowing the cell to gradually build up a functional potential. Conversely, the frequent non‐cytolytic interactions between normal cells in the absence of such inhibitory signaling result in continuous stimulation of the cells and attenuation of effector function. Although an innate cell, the degree to which the fate of the NK cell is predetermined versus its ability to adapt to its own environment can be revealed through a Newtonian view of NK cell education, one which is both chronological and dynamic. As such, the development of NK cell functional diversity is the product of qualitatively different physical interactions with host cells, rather than simply the sum of their signals or an imprint based on intrinsically different transcriptional programs.
Influence of Room Acoustics on Choir Singing

Multitrack recordings of a mixed adult choir with 23 singers were collected in order to investigate the influence of varied room acoustical conditions on a choir’s performance with regard to intonation, loudness, tempo, and timing precision. Headset microphones were used to record each chorister separately while the collected sound of all singers was presented via headphones exerting acoustic simulations of rooms with different reverberation times of 0.0 (bypass), 1.77 and 4.79 s according to three singing conditions. The choir was asked to sing “Locus Iste” by Anton Bruckner (1824-1896). Objective measures were obtained from single audio track analyses using the monophonic pitch tracker pYIN plugin for Sonic Visualiser. These revealed that intonation was barely affected by simulated room acoustics whereas tempo was notably slower and timing precision declined in the condition where participants sang in a comparatively large virtual room. Subjective judgments gathered by a questionnaire inquiring on the singers’ experiences showed a clear preference for singing in the medium sized “Concertgebouw” (with reverberation time = 1.77 s), while the dry acoustical condition (bypass) was felt to be the best to sing in time. The significance of these results and their relationships to other musical and acoustical parameters are discussed. PACS number(s): 43.75. Rs, 43.75. Yy, 43.75. Bc, 43.75Cd Influence of Room Acoustics on Choir Singing 3
R-composition of Lyapunov functions

This paper introduces the use of R-functions to compose (R-composition) basic simple Lyapunov functions, like the conventional quadratic ones, to obtain a larger variety of functions. R-functions represent the natural extension of Boolean operators to real-valued functions and provide the basic tools to compute the analytic expression of intersection and union operations in a geometric setting. In the framework of Lyapunov approaches to prove stability of a dynamical system, the union of Lyapunov functions computed through the R-function approach is still a Lyapunov function. Moreover, as each Lyapunov function defines the shape and the orientation of a correspondent geometric Largest Estimate of the Domain of Attraction (LEDA), then the LEDA associated to the union of several Lyapunov functions corresponds to the union of the single LEDAs. R-composition of Lyapunov functions thus corresponds to a non-conventional Lyapunov function which can be used to improve the estimate of the Region of Asymptotic Stability (RAS) and at the same time to introduce more freedom in the choice of the shape of the correspondent level sets, that in general are non-convex. An example of the R-composition of Lyapunov functions is illustrated to solve a classic RAS estimation problem.
Metabolome-scale prediction of intermediate compounds in multistep metabolic pathways with a recursive supervised approach

Motivation: Metabolic pathway analysis is crucial not only in metabolic engineering but also in rational drug design. However, the biosynthetic/biodegradation pathways are known only for a small portion of metabolites, and a vast amount of pathways remain uncharacterized. Therefore, an important challenge in metabolomics is the de novo reconstruction of potential reaction networks on a metabolome-scale. Results: In this article, we develop a novel method to predict the multistep reaction sequences for de novo reconstruction of metabolic pathways in the reaction-filling framework. We propose a supervised approach to learn what we refer to as ‘multistep reaction sequence likeness’, i.e. whether a compound–compound pair is possibly converted to each other by a sequence of enzymatic reactions. In the algorithm, we propose a recursive procedure of using step-specific classifiers to predict the intermediate compounds in the multistep reaction sequences, based on chemical substructure fingerprints/descriptors of compounds. We further demonstrate the usefulness of our proposed method on the prediction of enzymatic reaction networks from a metabolome-scale compound set and discuss characteristic features of the extracted chemical substructure transformation patterns in multistep reaction sequences. Our comprehensively predicted reaction networks help to fill the metabolic gap and to infer new reaction sequences in metabolic pathways. Availability and implementation: Materials are available for free at http://web.kuicr.kyoto-u.ac. jp/supp/kot/ismb2014/ Contact: goto@kuicr.kyoto-u.ac. jp Supplementary information: Supplementary data are available at Bioinformatics online.
A Markov chain based method for NoC end-to-end latency evaluation

This paper presents a generic analytical method to estimate communication latency between a source and a destination of a given Network-on-Chip. This method is based on Markov chain stochastic processes. In order to solve the limiting problem of state-space explosion in complex stochastic processes, we propose to construct a reduced Markov chain model for each node of the path, and to recursively use the local mean latencies to obtain the mean latency of the complete path. Comparison between the analytical results obtained by our method and those of a corresponding SystemC CABA simulation platform shows the accuracy of our method.
Multi-objective optimal distributed generation placement using simulated annealing

In this paper, the simulated annealing (SA) is applied to solve the multi-objective optimal placement of distributed generation (DG). The result on the IEEE 30 bus test system shows that the SA can find the optimal location and size with the less computing time than genetic algorithm (GA) and tabu search (TS) as well as the result of multi-objective problem can conclude that the DGs placing in the optimal location are indeed capable of obtaining higher quality solution efficiently comparing with single objective. With the optimal placement of DGs, the system can reduced power loss about 22%, emission about 27.5% and system contingency about 43% comparing with the system without DG.
The SNX-PX-BAR Family in Macropinocytosis: The Regulation of Macropinosome Formation by SNX-PX-BAR Proteins

Background Macropinocytosis is an actin-driven endocytic process, whereby membrane ruffles fold back onto the plasma membrane to form large (>0.2 µm in diameter) endocytic organelles called macropinosomes. Relative to other endocytic pathways, little is known about the molecular mechanisms involved in macropinocytosis. Recently, members of the Sorting Nexin (SNX) family have been localized to the cell surface and early macropinosomes, and implicated in macropinosome formation. SNX-PX-BAR proteins form a subset of the SNX family and their lipid-binding (PX) and membrane-curvature sensing (BAR) domain architecture further implicates their functional involvement in macropinosome formation. Methodology/Principal Findings We exploited the tractability of macropinosomes through image-based screening and systematic overexpression of SNX-PX-BAR proteins to quantitate their effect on macropinosome formation. SNX1 (40.9+/−3.19 macropinosomes), SNX5 (36.99+/−4.48 macropinosomes), SNX9 (37.55+/−2.4 macropinosomes), SNX18 (88.2+/−8 macropinosomes), SNX33 (65.25+/−6.95 macropinosomes) all exhibited statistically significant (p<0.05) increases in average macropinosome numbers per 100 transfected cells as compared to control cells (24.44+/−1.81 macropinosomes). SNX1, SNX5, SNX9, and SNX18 were also found to associate with early-stage macropinosomes within 5 minutes following organelle formation. The modulation of intracellular PI(3,4,5)P3 levels through overexpression of PTEN or a lipid phosphatase-deficient mutant PTEN(G129E) was also observed to significantly reduce or elevate macropinosome formation respectively; coexpression of PTEN(G129E) with SNX9 or SNX18 synergistically elevated macropinosome formation to 119.4+/−7.13 and 91.4+/−6.37 macropinosomes respectively (p<0.05). Conclusions/Significance SNX1, SNX5, SNX9, SNX18, and SNX33 were all found to elevate macropinosome formation and (with the exception of SNX33) associate with early-stage macropinosomes. Moreover the effects of SNX9 and SNX18 overexpression in elevating macropinocytosis is likely to be synergistic with the increase in PI(3,4,5)P3 levels, which is known to accumulate on the cell surface and early-stage macropinocytic cups. Together these findings represent the first systematic functional study into the impact of the SNX-PX-BAR family on macropinocytosis.
Sugar–Protein Connectivity Impacts on the Immunogenicity of Site-Selective Salmonella O-Antigen Glycoconjugate Vaccines

A series of glycoconjugates with defined connectivity were synthesized to investigate the impact of coupling Salmonella typhimurium O-antigen to different amino acids of CRM197 protein carrier. In particular, two novel methods for site-selective glycan conjugation were developed to obtain conjugates with single attachment site on the protein, based on chemical modification of a disulfide bond and pH-controlled transglutaminase-catalyzed modification of lysine, respectively. Importantly, conjugation at the C186-201 bond resulted in significantly higher anti O-antigen bactericidal antibody titers than coupling to K37/39, and in comparable titers to conjugates bearing a larger number of saccharides. This study demonstrates that the conjugation site plays a role in determining the immunogenicity in mice and one single attachment point may be sufficient to induce high levels of bactericidal antibodies.
Large Margin LAD Classifiers

In this report we present an optimization approach for model construction in Logical Analysis of Data (LAD) that unifies the distinct tasks of pattern generation and creation of a discriminant function. We also investigate how accurate are the LAD models built with such an algorithm and how they compare with other classification models. The main novelty in our algorithm is that the underlying optimization model proposed is more general than other existing methods for model construction in LAD. Moreover, the resulting algorithm is practically parameterfree, which considerably simplifies the task of constructing an accurate LAD model for a new dataset. Acknowledgements: We are deeply thankful to Alex Kogan, for helpful discussions on a preliminary version of this text. The first author would like to acknowledge the generous support of a DIMACS Graduate Student Award.
In their words

The strong and consistent relationship between criminal involvement and victimization is one of the most persistent documented findings within criminological research. However, there is little study on the nature and extent of why this overlap exists with even less research focusing on the perspective of the offenders who identify themselves as victims. The current study analyzes the personal experiences of female offenders at the Greene County Jail, Missouri. Our findings indicate a substantial overlap in lifestyle and risk behavior of female offenders who also identify as victims of crime. Important theoretical and policy implications are discussed.
Running Title : KSHV encoded Rta induces cell cycle arrest 4 5

21 The Kaposi's sarcoma-associated herpesvirus (KSHV) encoded immediate early gene, replication 22 and transcription activator (K-Rta) is a key viral protein that serves as the master regulator for 23 viral lytic replication. In this study, we investigated the role of K-Rta in cell cycle regulation and 24 found that the expression of K-Rta in doxycycline (Dox)-inducible BJAB cells induced cell cycle 25 arrest in G0/G1 phase. Western blot analysis of key cell cycle regulators revealed that K-Rta-26 mediated cell cycle arrest was associated with a decrease in Cyclin A and phosphorylated Rb 27 (pS807/ pS811) protein levels, both markers of S phase progression and an increase in protein 28 levels for p27, a cyclin-dependent kinase inhibitor. Further, we found that K-Rta does not affect 29 the transcription of p27 but regulates p27 at the post-translational level by inhibiting its 30 proteosomal degradation. Immunofluorescence staining and cell fractionation experiments 31 revealed largely nuclear compartmentalization of p27 in K-Rta expressing cells demonstrating 32 that K-Rta not only stabilizes p27 but also modulates its cellular localization. Finally, shRNA 33 knockdown of p27 significantly abrogates cell cycle arrest in K-Rta expressing cells supporting 34 its key role in K-Rta mediated cell cycle arrest. Our findings are consistent with previous studies 35 which showed that expression of immediate early genes of several herpes viruses including HSV, 36 EBV and CMV results in cell cycle arrest at the G0/G1 phase, possibly to avoid competition of 37 resources needed for host cell replication during the S phase. 39 Kaposi's sarcoma-associated herpesvirus (KSHV), also known as Human herpesvirus-8 40 (HHV-8) is a member of gammaherpesvirus family that includes Epstein Barr Virus (EBV), 41 Herpesvirus saimiri (HVS) and Murid herpesvirus 68 (MHV 68) (1). KSHV is the etiological 42 agent of Kaposi's sarcoma (KS), the most common tumor associated with HIV infection and for 43 at least two other malignancies, pleural effusion lymphoma (PEL) and multicentric Castleman's 44 disease (MCD) (2-4). Like all herpesviruses, the life cycle of KSHV consists of latent and lytic 45 phases. The latent phase is characterized by a restricted pattern of viral gene expression that 46 facilitates the evasion of immune surveillance and the establishment of lifelong persistent 47 infection. The lytic phase drives the replication cycle and a majority of the viral genes are 48 expressed in this phase. This phase mainly allows for the spread of the virus in the infected 49 …
Memory allocation costs in large C and C++ programs

Dynamic storage allocation is an important part of a large class of computer programs written in C and C + +. High‐performance algorithms for dynamic storage allocation have been, and will continue to be, of considerable interest. This paper presents detailed measurements of the cost of dynamic storage allocation in 11 diverse C and C + + programs using five very different dynamic storage allocation implementations, including a conservative garbage collection algorithm. Four of the allocator implementations measured are publicly available on the Internet. A number of the programs used in these measurements are also available on the Internet to facilitate further research in dynamic storage allocation. Finally, the data presented in this paper is an abbreviated version of more extensive statistics that are also publicly available on the Internet.