Miracle-dz/UniFAR-FTUs huggingface dataset:
Increasing the Power to Detect Causal Associations by Combining Genotypic and Expression Data in Segregating Populations

To dissect common human diseases such as obesity and diabetes, a systematic approach is needed to study how genes interact with one another, and with genetic and environmental factors, to determine clinical end points or disease phenotypes. Bayesian networks provide a convenient framework for extracting relationships from noisy data and are frequently applied to large-scale data to derive causal relationships among variables of interest. Given the complexity of molecular networks underlying common human disease traits, and the fact that biological networks can change depending on environmental conditions and genetic factors, large datasets, generally involving multiple perturbations (experiments), are required to reconstruct and reliably extract information from these networks. With limited resources, the balance of coverage of multiple perturbations and multiple subjects in a single perturbation needs to be considered in the experimental design. Increasing the number of experiments, or the number of subjects in an experiment, is an expensive and time-consuming way to improve network reconstruction. Integrating multiple types of data from existing subjects might be more efficient. For example, it has recently been demonstrated that combining genotypic and gene expression data in a segregating population leads to improved network reconstruction, which in turn may lead to better predictions of the effects of experimental perturbations on any given gene. Here we simulate data based on networks reconstructed from biological data collected in a segregating mouse population and quantify the improvement in network reconstruction achieved using genotypic and gene expression data, compared with reconstruction using gene expression data alone. We demonstrate that networks reconstructed using the combined genotypic and gene expression data achieve a level of reconstruction accuracy that exceeds networks reconstructed from expression data alone, and that fewer subjects may be required to achieve this superior reconstruction accuracy. We conclude that this integrative genomics approach to reconstructing networks not only leads to more predictive network models, but also may save time and money by decreasing the amount of data that must be generated under any given condition of interest to construct predictive network models.
Performance measurement and management: a literature review and a research agenda

Purpose – The purpose of this paper is to review the literature in the field of performance measurement and management (PMM) for small and medium enterprises (SMEs) and large companies and propose a research agenda for the future.Design/methodology/approach – This paper provides an update of Neely's work “The evolution of performance measurement research” The literature review has been carried out by using two different methodologies. Citation/co‐citation analysis has been used to explore “performance measurement” (PM) literature, while a chronological review of main frameworks/models developed both for large and small companies is presented in order to highlight “PMM” literature.Findings – The paper analyzes the literature on the field and carries out the most cited works and the common characteristics of them based on the key words used. The results of the literature review reveal a certain maturity of the literature related to large companies and a significant lack of PMM literature for SMEs. Finally t.
3D Cartesian Transport Sweep for Massively Parallel Architectures with PaRSEC

High-fidelity nuclear power plant core simulations require solving the Boltzmann transport equation. In discrete ordinates methods, the most computationally demanding operation of this equation is the sweep operation. Considering the evolution of computer architectures, we propose in this paper, as a first step toward heterogeneous distributed architectures, a hybrid parallel implementation of the sweep operation on top of the generic task-based runtime system: PaRSEC. Such an implementation targets three nested levels of parallelism: message passing, multi-threading, and vectorization. A theoretical performance model was designed to validate the approach and help the tuning of the multiple parameters involved in such an approach. The proposed parallel implementation of the Sweep achieves a sustained performance of 6.1 Tflop/s, corresponding to 33.9% of the peak performance of the targeted supercomputer. This implementation compares favourably with state-of-art solvers such as PartiSN, and it can therefore serve as a building block for a massively parallel version of the neutron transport solver DOMINO developed at EDF.
Skilled-motion plannings of multi-body systems based upon Riemannian distance

This paper focuses on the Riemannian distance and its application to skilled-motion plannings for the system. The Riemannian distance from one pose to another and vice versa is defined as the minimum curve-length measured by the Riemannian metric based upon the system inertia matrix among all curves connecting the two poses. The minimum-length curve in this meaning is called "geodesic" and reflects a movement of the system affected only by inertia-tensor-originated force (i.e., pure inertia, centrifugal, and Coriolis forces). In order to investigate in detail such a movement along the geodesic, some computer simulations are conducted in the cases of planar motions by a 4-DOF robot arm and biped walkings by a whole-body robot. It is shown through simulation results that movements attaining the Riemannian distance (natural movements in inertial actions) in the two cases tend to be similar to those in human skilled motions when human-scale robot models are chosen. Based upon the Riemannian distance, motion plannings for multi-body systems using physical properties inherent in their own physical structures are discussed.
Aspergillosis for Diagnosis of Invasive Pulmonary Tests with Bronchoalveolar Lavage Fluid Device , Conventional Culture , and PCR Beta-d-Glucan , Aspergillus Lateral-Flow Performance of Galactomannan

Published Ahead of Print 26 March 2014. 10.1128/JCM.00467-14. 2014, 52(6):2039. DOI: J. Clin. Microbiol. and D. Buchheidt C. Koidl, W. Buzina, M. Reinwald, C. R. Thornton, R. Krause Wölfler, B. Raggam, V. Posch, W. Duettmann, K. Hoenigl, A. M. Hoenigl, J. Prattes, B. Spiess, J. Wagner, F. Prueller, R. Aspergillosis for Diagnosis of Invasive Pulmonary Tests with Bronchoalveolar Lavage Fluid Device, Conventional Culture, and PCR Beta-d-Glucan, Aspergillus Lateral-Flow Performance of Galactomannan,
Use of Z-Score in Detection of Revenue Manipulations

The companies charged by U.S. SEC with earnings manipulations offences appear to have lower Z-Score than the rest of the companies. This study attempts to justify that Z-Score limits set by Altman for determination of bankruptcy state will also work in detection of earnings manipulations. The paper examines the validity of using Z-Score in establishing the sample of non-manipulating companies. It also offers the proof that the signs of earnings manipulations and earnings management coincide within the statements of the same company. The research provides the attempt to give a numeric criterion for establishing presence of earnings manipulation based on Z-Score.
Ecology and Evolution as Targets: the Need for Novel Eco-Evo Drugs and Strategies To Fight Antibiotic Resistance

ABSTRACT In recent years, the explosive spread of antibiotic resistance determinants among pathogenic, commensal, and environmental bacteria has reached a global dimension. Classical measures trying to contain or slow locally the progress of antibiotic resistance in patients on the basis of better antibiotic prescribing policies have clearly become insufficient at the global level. Urgent measures are needed to directly confront the processes influencing antibiotic resistance pollution in the microbiosphere. Recent interdisciplinary research indicates that new eco-evo drugs and strategies, which take ecology and evolution into account, have a promising role in resistance prevention, decontamination, and the eventual restoration of antibiotic susceptibility. This minireview summarizes what is known and what should be further investigated to find drugs and strategies aiming to counteract the “four P's,” penetration, promiscuity, plasticity, and persistence of rapidly spreading bacterial clones, mobile genetic elements, or resistance genes. The term “drug” is used in this eco-evo perspective as a tool to fight resistance that is able to prevent, cure, or decrease potential damage caused by antibiotic resistance, not necessarily only at the individual level (the patient) but also at the ecological and evolutionary levels. This view offers a wealth of research opportunities for science and technology and also represents a large adaptive challenge for regulatory agencies and public health officers. Eco-evo drugs and interventions constitute a new avenue for research that might influence not only antibiotic resistance but the maintenance of a healthy interaction between humans and microbial systems in a rapidly changing biosphere.
Regulation of gamma-glutamylcysteine synthetase subunit gene expression in retinal Müller cells by oxidative stress.

PURPOSE To study regulation of gamma-glutamylcysteine synthetase (GCS) heavy and light subunit gene expression in Müller cells under conditions of oxidative stress. METHODS Experiments were carried out with an SV40 transformed cell line (rMC-1) that exhibits the phenotype of rat retinal Müller cells. Endogenous glutathione levels were modified by treating cells with diethyl maleate (DEM), D,L-buthionine sulfoximine (BSO), or tert-butylhydroquinone (TBH). In other experiments, cells were grown in either high (28 mM) or normal (5.5 mM) glucose medium for 1 week to examine the effects of hyperglycemia. Cells were processed for reduced glutathione (GSH) measurement, RNA extraction, cell count, and, in some cases, lactate dehydrogenase activity. The steady state mRNA levels of GCS heavy and light subunits were measured by northern blot analysis using specific cDNA probes. Changes in mRNA levels were normalized to beta-actin or 18S rRNA. RESULTS Treatment with DEM for 30 minutes depleted cell GSH to 20% to 30% of the normal value. GSH content recovered completely 6 hours after returning to normal medium. BSO treatment for 12 hours followed by a medium change for 6 hours resulted in a cell GSH level that was 26% that of untreated cells. If cells were left in BSO for 18 hours, however, GSH levels were reduced to < 1%. Treatment with TBH for 12 hours led to a 77% increase in cellular GSH level. Treatment with DEM, TBH, or BSO for 18 hours led to a significant induction of the mRNA level of the GCS subunits, regardless of glucose concentration in the medium. Shorter BSO treatment exerted no effect. Prolonged hyperglycemia resulted in 30% lower GSH level, 55% lower GCS heavy subunit, and 30% lower GCS light subunit mRNA levels. CONCLUSIONS Oxidative stress induced the gene expression of GCS heavy and light subunits in Müller cells. The effect of BSO on mRNA levels correlated with the degree of GSH depletion. Prolonged hyperglycemia lowered GCS subunit mRNA and GSH levels.
WSF: An HTTP-Level Firewall for Hardening Web Servers

Due to both complexity of administration, insufficient checks on input data in many web applications, as well as lack of a single place to enforce security policy, web servers remain prone to external tampering. This paper proposes WSF (web server firewall) to protect web systems with three new mechanisms. First, WSF provides a language for specifying fine grained access control policy and enforcing it at the perimeter of a web server. Second, to prevent abuse of web application with malicious parameters, WSF allows web application developers to specify the restriction on application running parameters, rather than requiring them to enumerating all possible invalid input patterns, which substantially simplify input validation. Finally, WSF collects web user behavior statistics, which helps administrators to detect abnormal activities and adjust the access control policy heuristically.
Easy Questions First? A Case Study on Curriculum Learning for Question Answering

Cognitive science researchers have emphasized the importance of ordering a complex task into a sequence of easy to hard problems. Such an ordering provides an easier path to learning and increases the speed of acquisition of the task compared to conventional learning. Recent works in machine learning have explored a curriculum learning approach called self-paced learning which orders data samples on the easiness scale so that easy samples can be introduced to the learning algo-rithm ﬁrst and harder samples can be introduced successively. We introduce a number of heuristics that improve upon self-paced learning. Then, we argue that incorporating easy, yet, a diverse set of samples can further improve learning. We compare these curriculum learning proposals in the context of four non-convex models for QA and show that they lead to real improvements in each of them.
Syntactic cues to the noun and verb distinction in Mandarin child-directed speech

The syntactic structure of sentences in which a new word appears may provide listeners with cues to that new word’s form class. In English, for example, a noun tends to follow a determiner (a/an/the), while a verb precedes the morphological inflection [ing]. The presence of these markers may assist children in identifying a word’s form class and thus glean some information about its meaning. This study examined whether Mandarin, a language that has a relatively impoverished morphosyntactic system, offers reliable morphosyntactic cues to the noun–verb distinction in child-directed speech (CDS). Using the CHILDES Beijing corpora, Study 1 found that Mandarin CDS has reliable morphosyntactic markers to the noun–verb distinction. Study 2 examined the relationship between mothers’ use of a set of early-acquired nouns and verbs in the Beijing corpora and the age of acquisition (AoA) of these words. Results showed that the occurrence of the form class markers is a reliable predictor of the AoA for the early-acquired nouns and verbs.
Manipulation of Network Traffic Traces for Security Evaluation

Testing network-based security tools such as Intrusion Detection and Prevention Systems (IDS/IPS) differs from testing ordinary network tools (e.g., routers and switches). Basically, in addition to the parameters (such as bandwidth utilization, routing information and packets timing) that are important for network tools, security tools are more sensitive to issues like traffic composition, contents, and session level parameters. Generating a realistic synthetic traffic that keeps all the characteristics of the real traffic has proved to be difficult. For this reason, security testers often use real traffic traces in their test or evaluation. However, the available traces are often limited in number or size. Therefore, it is necessary to merge and manipulate traces to create a test environment that would be representative of the operational environment, and to inject attacks into the traffic. A variety of tools for recording, replaying as well as forging packets can be obtained easily, but there exist very few tools for manipulating traces so as to modify the traffic composition from the networking viewpoint. Among them, surprisingly there is no tool for manipulating traces without destructing their security-relevant characteristics. In this paper, we present a brief survey for trace manipulation and packet forging tools. Then we determine the requirements of tools for manipulating traces and injecting attacks while keeping their original characteristics. Finally, we present the architecture, and the implementation of our tool intended to fill this lack in security testing tools.
A Mobile Trusted Platform Module (mTPM) Architecture

We present the architecture of a mobile Trusted Platform Module (mTPM). Current implementations of TPM architectures assume physical bindings between the TPM and a single hardware platform. In this paper we introduce an alternative where a TPM is bound to a single virtual machine (VM) on a portable device, following the speciﬁcations provided by the Trusted Computing Group (TCG). By communicating with the VM infrastructure on the host machine, an mTPM offers various security functions similar as a physical TPM does. The mTPM is a mobile solution that will be beneﬁcial to any professional who requires a portable, secure computing environment.
It takes two—coincidence coding within the dual olfactory pathway of the honeybee

To rapidly process biologically relevant stimuli, sensory systems have developed a broad variety of coding mechanisms like parallel processing and coincidence detection. Parallel processing (e.g., in the visual system), increases both computational capacity and processing speed by simultaneously coding different aspects of the same stimulus. Coincidence detection is an efficient way to integrate information from different sources. Coincidence has been shown to promote associative learning and memory or stimulus feature detection (e.g., in auditory delay lines). Within the dual olfactory pathway of the honeybee both of these mechanisms might be implemented by uniglomerular projection neurons (PNs) that transfer information from the primary olfactory centers, the antennal lobe (AL), to a multimodal integration center, the mushroom body (MB). PNs from anatomically distinct tracts respond to the same stimulus space, but have different physiological properties, characteristics that are prerequisites for parallel processing of different stimulus aspects. However, the PN pathways also display mirror-imaged like anatomical trajectories that resemble neuronal coincidence detectors as known from auditory delay lines. To investigate temporal processing of olfactory information, we recorded PN odor responses simultaneously from both tracts and measured coincident activity of PNs within and between tracts. Our results show that coincidence levels are different within each of the two tracts. Coincidence also occurs between tracts, but to a minor extent compared to coincidence within tracts. Taken together our findings support the relevance of spike timing in coding of olfactory information (temporal code).
Integrating EDF in Hierarchical Scheduled Real-time Systems

An example implementation of a HSF built on top of a commercial real-time operating system (RTOS), VxWorks, is presented by Behnam et al. [2]. Similarly, we currently extend μC/OS-II [3] with hierarchical scheduling support. Opposite to the approach in VxWorks taken by Behnam et al. [2], μC/OS-II provides the kernel sources. The availability of kernel sources might lead to a different design and expectably a better performance.
Dialogue Concerning Two Views on Quantum Coherence: Factist and Fictionist

A controversy that has arisen many times over in disparate contexts is whether quantum coherences between eigenstates of certain quantities are fact or fiction. We present a pedagogical introduction to the debate in the form of a hypothetical dialogue between proponents from each of the two camps: a factist and a fictionist. A resolution of the debate can be achieved, we argue, by recognizing that quantum states do not only contain information about the intrinsic properties of a system but about its extrinsic properties as well, that is, about its relation to other systems external to it. Specifically, the coherent quantum state of the factist is the appropriate description of the relation of the system to one reference frame, while the incoherent quantum state of the fictionist is the appropriate description of the relation of the system to another, uncorrelated, reference frame. The two views, we conclude, are alternative but equally valid paradigms of description.
The Econometric Approach to Efficiency Analysis

The Econometrics of Panel DataSpringer Handbook of Science and Technology IndicatorsPanel Data EconometricsThe Econometrics of Panel DataA Practitioner's Guide to Stochastic Frontier Analysis Using StataBenchmarking for Performance EvaluationEssays on Microeconomics and Industrial OrganisationHealth System EfficiencyInternational Journal of Production EconomicsEconometric Analysis of Model Selection and Model TestingInternational Applications of Productivity and Efficiency AnalysisAdvanced Robust and Nonparametric Methods in Efficiency AnalysisEconometrics and the Philosophy of EconomicsThe Measurement of Productive EfficiencyMeasuring Efficiency in Health CareFinancial, Macro and Micro Econometrics Using REconometric Analysis of Cross Section and Panel DataApplied EconometricsProductivity and Efficiency AnalysisEconometric Model SelectionProductivity and Efficiency AnalysisStochastic Frontier AnalysisThe Oxford Handbook of Health EconomicsThe Measurement of Productive Efficiency and Productivity GrowthNew Directions in Productivity Measurement and Efficiency AnalysisA Primer on Efficiency Measurement for Utilities and Transport RegulatorsPanel Data EconometricsProduction and Efficiency Analysis with RApplications of Modern Production TheoryThe Measurement of Productive EfficiencyNonparametric Econometric Methods and ApplicationAn Introduction to Efficiency and Productivity AnalysisHealth, the Medical Profession, and RegulationThe Analysis of Household SurveysData Envelopment AnalysisProgramming Collective IntelligenceEfficiency AnalysisProductivity and Efficiency AnalysisMeasurement of Productivity and EfficiencyProduction Frontiers
Localization of the Kinesin-like Protein Xklp2 to Spindle Poles Requires a Leucine Zipper, a Microtubule-associated Protein, and Dynein

Xklp2 is a plus end–directed Xenopus kinesin-like protein localized at spindle poles and required for centrosome separation during spindle assembly in Xenopus egg extracts. A glutathione-S-transferase fusion protein containing the COOH-terminal domain of Xklp2 (GST-Xklp2-Tail) was previously found to localize to spindle poles (Boleti, H., E. Karsenti, and I. Vernos. 1996. Cell. 84:49–59). Now, we have examined the mechanism of localization of GST-Xklp2-Tail. Immunofluorescence and electron microscopy showed that Xklp2 and GST-Xklp2-Tail localize specifically to the minus ends of spindle pole and aster microtubules in mitotic, but not in interphase, Xenopus egg extracts. We found that dimerization and a COOH-terminal leucine zipper are required for this localization: a single point mutation in the leucine zipper prevented targeting. The mechanism of localization is complex and two additional factors in mitotic egg extracts are required for the targeting of GST-Xklp2-Tail to microtubule minus ends: (a) a novel 100-kD microtubule-associated protein that we named TPX2 (Targeting protein for Xklp2) that mediates the binding of GST-Xklp2-Tail to microtubules and (b) the dynein–dynactin complex that is required for the accumulation of GST-Xklp2-Tail at microtubule minus ends. We propose two molecular mechanisms that could account for the localization of Xklp2 to microtubule minus ends.