Miracle-dz/UniFAR-FTUs huggingface dataset:
Bit Weaving: A Non-Prefix Approach to Compressing Packet Classifiers in TCAMs

Ternary content addressable memories (TCAMs) have become the de facto standard in industry for fast packet classification. Unfortunately, TCAMs have limitations of small capacity, high power consumption, high heat generation, and high cost. The well-known range expansion problem exacerbates these limitations as each classifier rule typically has to be converted to multiple TCAM rules. One method for coping with these limitations is to use compression schemes to reduce the number of TCAM rules required to represent a classifier. Unfortunately, all existing compression schemes only produce prefix classifiers. Thus, they all miss the compression opportunities created by non-prefix ternary classifiers. In this paper, we propose bit weaving, the first non-prefix compression scheme. Bit weaving is based on the observation that TCAM entries that have the same decision and whose predicates differ by only one bit can be merged into one entry by replacing the bit in question with . Bit weaving consists of two new techniques, bit swapping and bit merging, to first identify and then merge such rules together. The key advantages of bit weaving are that it runs fast, it is effective, and it is composable with other TCAM optimization methods as a pre/post-processing routine. We implemented bit weaving and conducted experiments on both real-world and synthetic packet classifiers. Our experimental results show the following: 1) bit weaving is an effective standalone compression technique (it achieves an average compression ratio of 23.6%); 2) bit weaving finds compression opportunities that other methods miss. Specifically, bit weaving improves the prior TCAM optimization techniques of TCAM Razor and Topological Transformation by an average of 12.8% and 36.5%, respectively.
Porous silicon nanowires for lithium rechargeable batteries

Porous silicon nanowire is fabricated by a simple electrospinning process combined with a magnesium reduction; this material is investigated for use as an anode material for lithium rechargeable batteries. We find that the porous silicon nanowire electrode from the simple and scalable method can deliver a high reversible capacity with an excellent cycle stability. The enhanced performance in terms of cycling stability is attributed to the facile accommodation of the volume change by the pores in the interconnect and the increased electronic conductivity due to a multi-level carbon coating during the fabrication process.
Generating and Validating Abstracts of Meeting Conversations: a User Study

In this paper we present a complete system for automatically generating natural language abstracts of meeting conversations. This system is comprised of components relating to interpretation of the meeting documents according to a meeting ontology, transformation or content selection from that source representation to a summary representation, and generation of new summary text. In a formative user study, we compare this approach to gold-standard human abstracts and extracts to gauge the usefulness of the different summary types for browsing meeting conversations. We find that our automatically generated summaries are ranked significantly higher than human-selected extracts on coherence and usability criteria. More generally, users demonstrate a strong preference for abstract-style summaries over extracts.
Rabix: an open-source workflow executor supporting recomputability and interoperability of workflow descriptions

As biomedical data has become increasingly easy to generate in large quantities, the methods used to analyze it have proliferated rapidly. Reproducible and reusable methods are required to learn from large volumes of data reliably. To address this issue, numerous groups have developed workflow specifications or execution engines, which provide a framework with which to perform a sequence of analyses. One such specification is the Common Workflow Language, an emerging standard which provides a robust and flexible framework for describing data analysis tools and workflows. In addition, reproducibility can be furthered by executors or workflow engines which interpret the specification and enable additional features, such as error logging, file organization, optim1izations tocomputation and job scheduling, and allow for easy computing on large volumes of data. To this end, we have developed the Rabix Executora, an open-source workflow engine for the purposes of improving reproducibility through reusability and interoperability of workflow descriptions.
Demand for Modern Family Planning among Married Women Living with HIV in Western Ethiopia

Introduction People living with HIV (PLHIV) have diverse family planning (FP) needs. Little is reported on FP needs among women living with HIV in Ethiopia. Thus, the objective of the study was to assess the demand for modern FP among married women living with HIV in western Ethiopia. Methods A facility-based cross-sectional survey was conducted on 401 married women living with HIV selected from Nekemte Referral Hospital and Health Center, Nekemte, Oromia, Ethiopia. Convenience sampling of every other eligible patient was used to recruit respondents. Data were collected using a pretested, structured questionnaire. We first calculated frequency and percentage of unmet need, met need and total demand by each explanatory variable, and performed chi-squared testing to assess for differences in groups. We then fitted logistic regression models to identify correlates of unmet need for modern FP at 95% CL. Results The proportion of respondents with met need for modern FP among married women living with HIV was 61.6% (30.7% for spacing and 30.9% for limiting). Demand for family planning was reported in 77.0% (38.2% for spacing and 38.8% for limiting), making unmet need for modern FP prevalent in 15.4% (7.5% for spacing and 7.9% for limiting). Whereas age 25–34 years [adjusted odds ratio (AOR) (95% confidence interval (CI)) = . 397 (.204–.771)] was protective against unmet need for modern FP, not having knowledge of MTCT [AOR (95% CI) = 2.531 (1.689–9.290)] and not discussing FP with a partner [AOR (95% CI) = 3.616(1.869–6.996)] were associated with increased odds of unmet need for modern FP. Conclusions There is high unmet need for modern FP in HIV-positive married women in western Ethiopia. Health care providers and program managers at a local and international level should work to satisfy the unmet need for modern family planning.
G9a promotes proliferation and inhibits cell cycle exit during myogenic differentiation

Differentiation of skeletal muscle cells, like most other cell types, requires a permanent exit from the cell cycle. The epigenetic programming underlying these distinct cellular states is not fully understood. In this study, we provide evidence that the lysine methyltransferase G9a functions as a central axis to regulate proliferation and differentiation of skeletal muscle cells. Transcriptome analysis of G9a knockdown cells revealed deregulation of many cell cycle regulatory genes. We demonstrate that G9a enhances cellular proliferation by two distinct mechanisms. G9a blocks cell cycle exit via methylation-dependent transcriptional repression of the MyoD target genes p21Cip/Waf1 and Rb1. In addition, it activates E2F1-target genes in a methyltransferase activity-independent manner. We show that G9a is present in the E2F1/PCAF complex, and enhances PCAF occupancy and histone acetylation marks at E2F1-target promoters. Interestingly, G9a preferentially associates with E2F1 at the G1/S phase and with MyoD at the G2/M phase. Our results provide evidence that G9a functions both as a co-activator and a co-repressor to enhance cellular proliferation and inhibit myogenic differentiation.
SDEAP: a splice graph based differential transcript expression analysis tool for population data

MOTIVATION Differential transcript expression (DTE) analysis without predefined conditions is critical to biological studies. For example, it can be used to discover biomarkers to classify cancer samples into previously unknown subtypes such that better diagnosis and therapy methods can be developed for the subtypes. Although several DTE tools for population data, i.e. data without known biological conditions, have been published, these tools either assume binary conditions in the input population or require the number of conditions as a part of the input. Fixing the number of conditions to binary is unrealistic and may distort the results of a DTE analysis. Estimating the correct number of conditions in a population could also be challenging for a routine user. Moreover, the existing tools only provide differential usages of exons, which may be insufficient to interpret the patterns of alternative splicing across samples and restrains the applications of the tools from many biology studies. RESULTS We propose a novel DTE analysis algorithm, called SDEAP, that estimates the number of conditions directly from the input samples using a Dirichlet mixture model and discovers alternative splicing events using a new graph modular decomposition algorithm. By taking advantage of the above technical improvement, SDEAP was able to outperform the other DTE analysis methods in our extensive experiments on simulated data and real data with qPCR validation. The prediction of SDEAP also allowed us to classify the samples of cancer subtypes and cell-cycle phases more accurately. AVAILABILITY AND IMPLEMENTATION SDEAP is publicly available for free at https://github.com/ewyang089/SDEAP/wiki CONTACT: yyang027@cs.ucr. edu; jiang@cs.ucr. eduSupplementary information: Supplementary data are available at Bioinformatics online.
Contiki - a lightweight and flexible operating system for tiny networked sensors

Wireless sensor networks are composed of large numbers of tiny networked devices that communicate untethered. For large scale networks, it is important to be able to download code into the network dynamically. We present Contiki, a lightweight operating system with support for dynamic loading and replacement of individual programs and services. Contiki is built around an event-driven kernel but provides optional preemptive multithreading that can be applied to individual processes. We show that dynamic loading and unloading is feasible in a resource constrained environment, while keeping the base system lightweight and compact.
Dispersion penalty reduction using an optical modulator with adjustable chirp

Using a unique Ti:LiNbO/sub 3/ modulator, the value of the modulation chirp parameter that minimizes the transmission power penalty caused by fiber chromatic dispersion was experimentally identified. System experiments at 5 Gb/s using nonreturn-to-zero (NRZ) amplitude-shift-keyed (ASK) transmission with direct detection reception are discussed, and the optimum values of the modulation chirp parameter versus distance for transmission at 1.5 mu m wavelength over fibre having zero dispersion at 1.3 mu m are identified. 5 Gb/s NRZ transmission was achieved through distances of 128, 192, and 256 km of conventional fiber while incurring dispersion penalties of -0.5, 0.1, and 1.1 dB respectively, by operating at the quantum chirp value. <<ETX>>
Moment expansion and nonuniform FFT applied to antenna reflection parameter characterization using a FDTD/WP-PML algorithm

This paper presents the results of the application of a moment expansion and a nonuniform FFT technique together with a FDTD algorithm in order to determinate the return loss parameter of printed antennas. The impedance characterization of wideband printed antennas with lossy substrates is introduced by means of an approach based on FDTD method and the WP-PML absorbing boundary condition. It was used a simple voltage source model where an excitation plane with an Gaussian vertical electrical field was imposed to a rectangular area just below the structure to be analyzed. Results obtained for the return loss of a multiband and an UWB printed antenna are compared to those determined from conventional FFT based methods available in the scientific literature as well as measurements previously done, in order to show the applicability of the methodology that has been developed herein. The results obtained for return loss parameter showed good agreements between the techniques proposed by this work and the results previous done.
Drug-Driven AMPA Receptor Redistribution Mimicked by Selective Dopamine Neuron Stimulation

Background Addictive drugs have in common that they cause surges in dopamine (DA) concentration in the mesolimbic reward system and elicit synaptic plasticity in DA neurons of the ventral tegmental area (VTA). Cocaine for example drives insertion of GluA2-lacking AMPA receptors (AMPARs) at glutamatergic synapes in DA neurons. However it remains elusive which molecular target of cocaine drives such AMPAR redistribution and whether other addictive drugs (morphine and nicotine) cause similar changes through their effects on the mesolimbic DA system. Methodology / Principal Findings We used in vitro electrophysiological techniques in wild-type and transgenic mice to observe the modulation of excitatory inputs onto DA neurons by addictive drugs. To observe AMPAR redistribution, post-embedding immunohistochemistry for GluA2 AMPAR subunit was combined with electron microscopy. We also used a double-floxed AAV virus expressing channelrhodopsin together with a DAT Cre mouse line to selectively express ChR2 in VTA DA neurons. We find that in mice where the effect of cocaine on the dopamine transporter (DAT) is specifically blocked, AMPAR redistribution was absent following administration of the drug. Furthermore, addictive drugs known to increase dopamine levels cause a similar AMPAR redistribution. Finally, activating DA VTA neurons optogenetically is sufficient to drive insertion of GluA2-lacking AMPARs, mimicking the changes observed after a single injection of morphine, nicotine or cocaine. Conclusions / Significance We propose the mesolimbic dopamine system as a point of convergence at which addictive drugs can alter neural circuits. We also show that direct activation of DA neurons is sufficient to drive AMPAR redistribution, which may be a mechanism associated with early steps of non-substance related addictions.
[Prevalence and factors associated to overweight and obesity in adolescents].

OBJECTIVE To assess the prevalence and factors associated to overweight and obesity in urban area adolescents. METHODS A cross-sectional population-based study was carried out in the municipality of Pelotas, Southern Brazil, between 2001 and 2002. Adolescents between 15 and 18 years old were weighed, measured and asked to complete a self-administered questionnaire. Of 90 areas drawn, 86 dwellings were visited in each area, comprising a total of 960 adolescents interviewed. Overweight and obesity prevalences were defined based on the body mass index, according to cutoff values and adjusted to age and sex. Multivariate analysis with Poisson regression was performed using a hierarchical model of variables associated to overweight and obesity. RESULTS Overweight and obesity prevalences were 20.94% and 5% respectively. There was found an inverse relationship between obesity and age and schooling. An association of overweight and obesity with reporting parents' obesity (p=0.03) and adolescents' sexual maturation (p=0.01) was seen. Dieting and skipping meals were associated to obesity with a risk of 3.98 (95% CI: 1.83-8.67) and 2.54 (95% CI: 1.22-5.29) respectively. CONCLUSIONS Overweight and obesity prevalences in the area studied are of concern despite adolescents' behaviors to prevent to obesity. There is a need to implement more effective campaigns to provide better guidance to adolescents.
Observations on some reproductive features of Carasobarbus luteus (Heckel, 1843) from the Shatt Al-Arab River, Southern Iraq

The present study was conducted from December 2013 to November 2014 to investigate the reproductive features of Himri Carasobarbus luteus in the Northern reaches of Shatt Al-Arab river in Southern Iraq. The samples were collected using seine, gill, cast nets as well as electrofishing. A total of 351 specimens from himri were caught but only mature individuals were chosen to estimate the absolute and relative fecundity and egg diameters. The results of the present research revealed that the highest GSI values were recorded in male and female (4.63 and 11.99) during the April month. Absolute fecundity was increased with length, weight and gonads weight, and it was ranged as 2098 eggs for 131 mm total length and 35 g weight to 14147 eggs for 209 mm total length and 131 g weight. Relationship between length, weight and reproductive parameters were highly significant. A highest relative condition factor of females (1.24) was calculated in March 2014.
Casein kinase 1 regulates human hypoxia-inducible factor HIF-1

Hypoxia-inducible factor 1 (HIF-1), a transcriptional activator that mediates cellular response to hypoxia and a promising target of anticancer therapy, is essential for adaptation to low oxygen conditions, embryogenesis and tumor progression. HIF-1 is a heterodimer of HIF-1α, expression of which is controlled by oxygen levels as well as by various oxygen-independent mechanisms, and HIF-1β (or ARNT), which is constitutively expressed. In this work, we investigate the phosphorylation of the N-terminal heterodimerization (PAS) domain of HIF-1α and identify Ser247 as a major site of in vitro modification by casein kinase 1δ (CK1δ). Mutation of this site to alanine, surprisingly, enhanced the transcriptional activity of HIF-1α, a result phenocopied by inhibition or small interfering RNA (siRNA)-mediated silencing of CK1δ under hypoxic conditions. Conversely, overexpression of CK1δ or phosphomimetic mutation of Ser247 to aspartate inhibited HIF-1α activity without affecting its stability or nuclear accumulation. Immunoprecipitation and in vitro binding experiments suggest that CK1-dependent phosphorylation of HIF-1α at Ser247 impairs its association with ARNT, a notion also supported by modeling the structure of the complex between HIF-1α and ARNT PAS-B domains. We suggest that modification of HIF-1α by CK1 represents a novel mechanism that controls the activity of HIF-1 during hypoxia by regulating the interaction between its two subunits.
Inference of Cause and Effect with Unsupervised Inverse Regression

We address the problem of causal discovery in the two-variable case, given a sample from their joint distribution. Since X → Y and Y → X are Markov equivalent, conditional-independence-based methods [Spirtes et al., 2000, Pearl, 2009] can not recover the causal graph. Alternative methods, introduce asymmetries between cause and effect by restricting the function class (e.g., [Hoyer et al., 2009]). The proposed causal discovery method, CURE (Causal discovery with Unsupervised inverse REgression), is based on the principle of independence of causal mechanisms [Janzing and Scholkopf, 2010]. For the case of only two variables, it states that the marginal distribution of the cause, say P(X), and the conditional of the effect given the cause P(Y|X) are "independent", in the sense that they do not contain information about each other. This independence can be violated in the backward direction: the distribution of the effect P(Y) and the conditional P(X|Y) may contain information about each other because each of them inherits properties from both P(X) and P(Y|X), hence introducing an asymmetry between cause and effect. For deterministic causal relations (Y = f(X)), all the information about the conditional P(Y|X) is contained in the function f. In this case, previous work [Janzing et al., 2012] formalizes "independence" as uncorrelatedness between log f' and the density of P(X), both viewed as random variables. For non-deterministic relations, we propose an implicit notion of independence, namely that pY|X cannot be estimated based on pX (lower case denotes density). However, it may be possible to estimate pY|X based on the density of the effect, pY. In practice, we are given empirical data x ∈ ℝN, y ∈ ℝN from P(X,Y) and estimate pX|Y based on y (intentionally hiding x). The relationship between the observed y and the latent x is modeled by a Gaussian Process (GP). Then, the required conditional pX|Y is estimated as pyX|Y : (x, y) → p(x|y, y), with p(x|y, y) estimated by marginalizing out the latent x and the GP hyperparameters. CURE infers the causal direction using the procedure above two times: one to estimate pX|Y based only on y and another to estimate pY|X based only on x. If the first estimation is better, X → Y is inferred. Otherwise, Y → X. To evaluate the conditional's estimation, we compare it to the one using both x and y. CURE was evaluated on synthetic and real data and often outperformed existing methods. On the downside, its computational cost is comparably high. This work was recently published at AISTATS 2015 [Sgouritsa et al., 2015].
Fork Algebras in Algebra, Logic and Computer Science

Since the main themes at the Helena Rasiowa memorial were algebra, logic and computer science, we will present a survey of results on fork algebras from these points of view. In this paper we study fork algebras from the points of view of their algebraic and logical properties and applications. These results will prove to be essential, in a future work, for the definition of a wide-spectrum calculus for program construction.
A web-based tool for managing architectural design decisions

Software architectures represent the design for describing the main parts of a software system. In software projects, different stakeholders with different roles may need to share the documentation generated during the project. Also, during the architecture construction phase we need to communicate the architecture to the stakeholders involved in the process, but the lack of tools for documenting, managing and sharing this architectural knowledge constitutes a big barrier. In other cases it can be useful to recreate the design decisions taken because such decisions are frequently lost during the development process. To cover these issues, we outline in this paper a web-based tool able to record and manage architecture design decisions.
Neutrophils Suppress Intraluminal NK Cell-Mediated Tumor Cell Clearance and Enhance Extravasation of Disseminated Carcinoma Cells.

UNLABELLED Immune cells promote the initial metastatic dissemination of carcinoma cells from primary tumors. In contrast to their well-studied functions in the initial stages of metastasis, the specific roles of immunocytes in facilitating progression through the critical later steps of the invasion-metastasis cascade remain poorly understood. Here, we define novel functions of neutrophils in promoting intraluminal survival and extravasation at sites of metastatic dissemination. We show that CD11b(+)/Ly6G(+) neutrophils enhance metastasis formation via two distinct mechanisms. First, neutrophils inhibit natural killer cell function, which leads to a significant increase in the intraluminal survival time of tumor cells. Thereafter, neutrophils operate to facilitate extravasation of tumor cells through the secretion of IL1β and matrix metalloproteinases. These results identify neutrophils as key regulators of intraluminal survival and extravasation through their cross-talk with host cells and disseminating carcinoma cells. SIGNIFICANCE This study provides important insights into the systemic contributions of neutrophils to cancer metastasis by identifying how neutrophils facilitate intermediate steps of the invasion-metastasis cascade. We demonstrate that neutrophils suppress natural killer cell activity and increase extravasation of tumor cells. Cancer Discov; 6(6); 630-49. ©2016 AACR.This article is highlighted in the In This Issue feature, p. 561.