Miracle-dz/UniFAR-FTUs huggingface dataset:
Selfish Task Allocation

Recently there has been a lot of interest in problems at the intersection of Game Theory, Economics, and Computer Science. For example, there are interesting developments concerning algorithms for equilibria and cost sharing, algorithmic mechanism design, and the efficiency of systems with selfish users [17]. In this note, I will focus on the last area and in particular on the price of anarchy of scheduling or task allocation. I will discuss the issues of this area, mention the central results, and suggest some open problems. This is definitely not a review paper: My aim is to stimulate the reader, not to provide complete coverage of the area. The presentation favors simplicity to preciseness, examples to formal presentation, and intuition to rigor.
Result identification for biomedical abstracts using Conditional Random Fields

For biomedical research, the most important parts of an abstract are the result and conclusion sections. Some journals divide an abstract into several sections so that readers can easily identify those parts, but others do not. We propose a method that can automatically identify the result and conclusion sections of any biomedical abstracts by formulating this identification problem as a sequence labeling task. Three feature sets (Position, Named Entity, and Word Frequency) are employed with Conditional Random Fields (CRFs) as the underlying machine learning model. Experimental results show that the combination of our proposed feature sets can achieve F-measure, precision, and recall scores of 92.50%, 95.32% and 89.85%, respectively.
Deterministic regular expressions in linear time

Deterministic regular expressions are widely used in XML processing. For instance, all regular expressions in DTDs and XML Schemas are required to be deterministic. In this paper we show that determinism of a regular expression e can be tested in linear time. The best known algorithms, based on the Glushkov automaton, require O(σ|e|) time, where σ is the number of distinct symbols in e. We further show that matching a word w against an expression e can be achieved in combined linear time O(|e|+|w|), for a wide range of deterministic regular expressions: (i) star-free (for multiple input words), (ii) bounded-occurrence, i.e., expressions in which each symbol appears a bounded number of times, and (iii) bounded plus-depth, i.e., expressions in which the nesting depth of alternating plus (union) and concatenation symbols is bounded. Our algorithms use a new structural decomposition of the parse tree of e. For matching arbitrary deterministic regular expressions we present an O(|e| + |w|log log|e|) time algorithm.
Flux control and excess capacity in the enzymes of glycolysis and their relationship to flight metabolism in Drosophila melanogaster

An important question in evolutionary and physiological genetics is how the control of flux-base phenotypes is distributed across the enzymes in a pathway. This control is often related to enzyme-specific levels of activity that are reported to be in excess of that required for demand. In glycolysis, metabolic control is frequently considered vested in classical regulatory enzymes, each strongly displaced from equilibrium. Yet the contribution of individual steps to control is unclear. To assess enzyme-specific control in the glycolytic pathway, we used P-element excision-derived mutagenesis in Drosophila melanogaster to generate full and partial knockouts of seven metabolic genes and to measure tethered flight performance. For most enzymes, we find that reduction to half of the normal activity has no measurable impact on wing beat frequency. The enzymes catalyzing near-equilibrium reactions, phosphoglucose isomerase, phosphoglucomutase, and triosephosphate isomerase fail to show any decline in flight performance even when activity levels are reduced to 17% or less. At reduced activities, the classic regulatory enzymes, hexokinase and glycogen phosphorylase, show significant drops in flight performance and are nearer to saturation. Our results show that flight performance is canalized or robust to the activity variation found in natural populations. Furthermore, enzymes catalyzing near-equilibrium reactions show strong genetic dominance down to low levels of activity. This implies considerable excess enzyme capacity for these enzymes.
A robust beamformer with main beam control

In this paper, a new robust beamforming approach which is capable of accurately controlling the main beam response is proposed. In this method, steering vector uncertainties are taken into account in the beamformer design problem with array magnitude response constraints. This allows us to control the main beam as prescribed. However, the resultant non-convex problem has a different formulation from that of the existing methods for robust beamforming with magnitude response constraints. Thus, existing techniques cannot be applied directly. To cope with this problem, the lower and upper norm bounds of the beamformer weight vector are first derived. The semidefinite relaxation technique is then employed as an approximate solver ending up with a grid search solution. Simulation results show that the proposed method is able to accurately control the main beam magnitude response in the presence of steering vector uncertainties.
Formalization of Viruses and Malware Through Process Algebras

Abstract virology has seen the apparition of successive viral models, all based on Turing-equivalent formalisms. Considering recent malware, these are only partially covered because functional formalisms do not support interactive computations. This article provides a basis for a unified malware model, founded on the Join-Calculus. In terms of expressiveness, the process-based model supports the fundamental notion of self-replication but also interactions, concurrency and non-termination to cover evolved malware. In terms of protection, detection undecidability and prevention by isolation still hold. Additional results are established: calculus fragments where detection is decidable, definition of a non-infection property, potential solutions to restrict propagation.
ICE: a passive, high-speed, state-continuity scheme

The amount of trust that can be placed in commodity computing platforms is limited by the likelihood of vulnerabilities in their huge software stacks. Protected-module architectures, such as Intel SGX, provide an interesting alternative by isolating the execution of software modules. To minimize the amount of code that provides support for the protected-module architecture, persistent storage of (confidentiality and integrity protected) states of modules can be delegated to the untrusted operating system. But precautions should be taken to ensure state continuity: an attacker should not be able to cause a module to use stale states (a so-called rollback attack), and while the system is not under attack, a module should always be able to make progress, even when the system could crash or lose power at unexpected, random points in time (i.e., the system should be crash resilient). Providing state-continuity support is non-trivial as many algorithms are vulnerable to attack, require on-chip non-volatile memory, wear-out existing off-chip secure non-volatile memory and/or are too slow for many applications. We present ICE, a system and algorithm providing state-continuity guarantees to protected modules. ICE's novelty lies in the facts that (1) it does not rely on secure non-volatile storage for every state update (e.g., the slow TPM chip). (2) ICE is a passive security measure. An attacker interrupting the main power supply or any other source of power, cannot break state-continuity. (3) Benchmarks show that ICE already enables state-continuous updates almost 5x faster than writing to TPM NVRAM. With dedicated hardware, performance can be increased 2 orders of magnitude. ICE's security properties are guaranteed by means of a machine-checked proof and a prototype implementation is evaluated on commodity hardware.
The Deepwater Horizon Oil Spill and Physical Health among Adult Women in Southern Louisiana: The Women and Their Children’s Health (WaTCH) Study

Background: The Deepwater Horizon Oil Spill (DHOS) is the largest oil spill in U.S. history, negatively impacting Gulf Coast residents and the surrounding ecosystem. To date, no studies have been published concerning physical health outcomes associated with the DHOS in the general community. Objectives: We characterized individual DHOS exposure using survey data and examined the association between DHOS exposure and physical health. Methods: Baseline data from 2,126 adult women residing in southern Louisiana and enrolled in the Women and Their Children’s Health study were analyzed. Exploratory factor analysis was used to characterize DHOS exposure. Odds ratios and 95% confidence intervals for the associations between DHOS exposure and physical health symptoms were estimated using multivariate logistic regression. Results: A two-factor solution was identified as the best fit for DHOS exposure: physical–environmental exposure and economic exposure. High physical–environmental exposure was significantly associated with all of the physical health symptoms, with the strongest associations for burning in nose, throat, or lungs (OR = 4.73; 95% CI: 3.10, 7.22), sore throat (OR = 4.66; 95% CI: 2.89, 7.51), dizziness (OR = 4.21; 95% CI: 2.69, 6.58), and wheezing (OR = 4.20; 95% CI: 2.86, 6.17). Women who had high-economic exposure were significantly more likely to report wheezing (OR = 1.92; 95% CI: 1.32, 2.79); headaches (OR = 1.81; 95% CI: 1.41, 2.58); watery, burning, itchy eyes (OR = 1.61; 95% CI: 1.20, 2.16); and stuffy, itchy, runny nose (OR = 1.56; 95% CI: 1.16, 2.08). Conclusions: Among southern Louisiana women, both physical–environmental and economic exposure to the DHOS were associated with an increase in self-reported physical health outcomes. Additional longitudinal studies of this unique cohort are needed to elucidate the impact of the DHOS on short- and long-term human health. Citation: Peres LC, Trapido E, Rung AL, Harrington DJ, Oral E, Fang Z, Fontham E, Peters ES. 2016. The Deepwater Horizon Oil Spill and physical health among adult women in southern Louisiana: the Women and Their Children’s Health (WaTCH) study. Environ Health Perspect 124:1208–1213; http://dx.doi. org/10.1289/ehp.1510348
Design and implementation of voice command using MFCC and HMMs method

The more frequent human interaction to technology demands the development of methods of interaction with the machine to a more natural. Sound which is the most frequently used communication humans makes it one of the natural methods of interaction. Thus the development of a system that can recognize human speech as an action on the machine can be an option for those problems. Voice command is a speech recognition system to give the functions and actions on a system that has been defined as Command and Control systems. Amplitude value is taken from the input sound signal, so we get a set of real numbers is the value input for feature extraction. Feature extraction methods used in this paper are Mel frequency cepstral coefficient (MFCC). Early stages of MFCC is splitting the input signal amplitude values into frames which are processed using the mel-filterbak adapted from the human hearing system. The results of feature extraction made into a codebook which is used as an input symbol on HMM to form a model of every word. On testing step the characteristics of the test signal that has been quantized, then matched with the model that has been created in the previous step. From the test results, the system can recognize spoken words of speakers with an average accuracy of 93.89% in the environment without noise, and 58.1% in environments with noise.
Interactions between Type 1 Interferons and the Th17 Response in Tuberculosis: Lessons Learned from Autoimmune Diseases

The classical paradigm of tuberculosis (TB) immunity, with a central protective role for Th1 responses and IFN-γ-stimulated cellular responses, has been challenged by unsatisfactory results of vaccine strategies aimed at enhancing Th1 immunity. Moreover, preclinical TB models have shown that increasing IFN-γ responses in the lungs is more damaging to the host than to the pathogen. Type 1 interferon signaling and altered Th17 responses have also been associated with active TB, but their functional roles in TB pathogenesis remain to be established. These two host responses have been studied in more detail in autoimmune diseases (AID) and show functional interactions that are of potential interest in TB immunity. In this review, we first identify the role of type 1 interferons and Th17 immunity in TB, followed by an overview of interactions between these responses observed in systemic AID. We discuss (i) the effects of GM-CSF-secreting Th17.1 cells and type 1 interferons on CCR2+ monocytes; (ii) convergence of IL-17 and type 1 interferon signaling on stimulating B-cell activating factor production and the central role of neutrophils in this process; and (iii) synergy between IL-17 and type 1 interferons in the generation and function of tertiary lymphoid structures and the associated follicular helper T-cell responses. Evaluation of these autoimmune-related pathways in TB pathogenesis provides a new perspective on recent developments in TB research.
TASC: Description of the TASC System Used for MUC-7

TASC has recently developed a technology for learning scenario-templateextraction grammars from examples provided by end-users with no special computational or linguistic knowledge. For straightforward scenario-template problems, complete extraction systems can be learned from scratch in a few hours. The learned systems are fast, robust, and as accurate as carefully handcrafted systems. For more complex extraction problems, such as the MUC-7 task, the grammars can still be learned automatically, but some computational-linguistic work may be required for complex template merging and inference.
Color Image Enhancement Using Multiscale Retinex with Modified Color Restoration Technique

In this paper, a new technique for the enhancement of color image using multiscale retinex with modified color restoration has been proposed. The basic steps of multiscale retinex algorithm have been analyzed, modified and various operations are performed in an orderly manner. The enhancement effects are visually effective. In addition, it adds true color constancy to an image. The experimental results show that multiscale retinex method based on color restoration technique is an efficient and computationally inexpensive. The proposed method not only provides true color fidelity for poor quality images but also averages the color components to gray value for balancing colors.
Methylation of tumor suppressor genes in ovarian cancer

Aberrant methylation of gene promoter regions is one of the mechanisms for inactivation of tumor suppressor genes in human malignancies. In this study, the methylation pattern of 24 tumor suppressor genes was analyzed in 75 samples of ovarian cancer using the methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) assay. Of the 24 tumor suppressor genes examined, aberrant methylation was observed in 17. The three most frequently methylated genes were CDKN2B, CDH13 and RASSF1, followed by ESR1 and MLH1. Methylation frequencies ranged from 1.3% for CDKN2A, RARβ, CASP8, VHL and TP73 to 24% for CDKN2B. The corresponding normal DNA from each patient was also investigated. Methylation was detected in tumors, although not in normal tissues, with the exception of two samples, indicating aberrant methylation in tumors. Clear cell carcinoma samples exhibited a higher frequency of CDKN2B promoter hypermethylation compared to those of other histological types (P=0.05). Our data indicate that methylation of the CDKN2B gene is a frequent event in ovarian carcinogenesis and that analysis of only three genes is sufficient to detect the presence of methylation in 35% of ovarian cancer cases. However, more studies using a much larger sample size are needed to define the potential role of DNA methylation as a marker for ovarian cancer.
Management of colorectal cancer

Colorectal cancer is one of the most frequent solid tumors in the Western world. Treatment options are dependent on the stage of the disease, the performance status of the patient, and increasingly the molecular makeup of the tumor. In countries with surveillance programs, the incidence rate as well as the mortality rate has gone down because of the earlier stages at which the tumors are detected. For rectal cancer, standard of care differs from that of colon cancer with regard to perioperative treatment. In the metastatic setting, treatment options are uniform for colorectal cancer. Over the years, treatment options have emerged from single-agent 5-fluorouracil (5-FU) treatment to combination regimens using 5-FU and oxaliplatin or irinotecan or both. Treatment efficacy in the metastatic setting has been increased with the introduction of targeted substances. These include (a) the anti-vascular endothelial growth factor-A (anti-VEGF-A) antibody bevacizumab, (b) the anti-epidermal growth factor receptor (anti-EGFR) antibodies cetuximab and panitumumab, (c) the anti-angiogenic multi-kinase inhibitor regorafenib, and (d) the anti-angiogenic compound aflibercept. Anti-EGFR antibodies have shown efficacy only in the subpopulations of tumors that do not have any mutation in KRAS and NRAS exon 2, 3, 4. Physicians have the choice in the first line to use anti-EGFR or anti-VEGF inhibitors in combination with chemotherapy based on treatment goals and patient performance. In recent years, tumor location has been shown to be prognostic and predictive for clinical outcome. Right-sided sporadic colon cancers differ significantly in molecular characteristics and, with the exception of microsatellite instability (MSI-H) tumors, are associated with poor prognosis. Tumors based on hereditary non-polyposis colorectal cancer, on the other hand, have excellent prognosis in stage II and III disease. Recent efforts have focused on the molecular classification of colorectal cancer with the purpose of establishing molecularly defined subgroups.
A Quantitative Study on the Re-executability of Publicly Shared Scientific Workflows

Workflows have become a popular means for implementing experiments in computational sciences. They are beneficial over other forms of implementation, as they require a formalisation of the experiment process, they provide a standard set of functions to be used, and provide an abstraction of the underlying system. Thus, they facilitate understandability and repeatability of experimental research. Also, additional meta data standards such as Research Objects, which allow to add more meta-data about the research process, shall enable better reproducibility of experiments. However, as several studies have shown, merely implementing an experiment as a workflow in a workflow engine is not sufficient to achieve these goals, as still a number of challenges and pitfalls prevail. In this paper, we want to quantify how many workflow executions are easy to repeat. To this end, we automatically obtain and analyse a set of almost 1,500 workflows available in the myExperiment platform, focusing on the ones authored in the Taverna workflow language. We provide statistics on the types of processing steps used, and investigate what vulnerabilities in regards to re-execution are faced. We then try to automatically execute the workflows. Form these results, we conclude which are the most common causes for failures, and analyse how these can be countered, with existing or yet to be developed approaches.
User Interface Constraints for Immersive Virtual Environment Applications

Applications of Virtual Environments (VEs) are rapidly becoming more complex and interactive. They are not restricted to tasks that are solely perceptual in nature; rather, they involve both perception and action on the part of the user. With this increased complexity comes a host of problems relating to the user interface (UI) of such systems. Researchers have produced a body of work on displays, input devices, and other hardware, but very few guidelines have been suggested for user interface software in 3D VEs. In this paper, we discuss the usage and implementation of constraints, a fundamental principle for desktop user interfaces, in highly interactive virtual environment systems. Our claims are supported with examples from the literature and from our own experience with the Conceptual Design Space
The Evaluator Effect in Usability Studies: Problem Detection and Severity Judgments

Usability studies are commonly used in industry and applied in research as a yardstick for other usability evaluation methods. Though usability studies have been studied extensively, one potential threat to their reliability has been left virtually untouched: the evaluator effect. In this study, four evaluators individually analyzed four videotaped usability test sessions. Only 20% of the 93 detected problems were detected by all evaluators, and 46% were detected by only a single evaluator. From the total set of 93 problems the evaluators individually selected the ten problems they considered most severe. None of the selected severe problems appeared on all four evaluators' top-10 lists, and 4 of the 11 problems that were considered severe by more than one evaluator were only detected by one or two evaluators. Thus, both detection of usability problems and selection of the most severe problems are subject to considerable individual variability.
Se p 20 06 ENLARGEABILITY AND INDEX THEORY : INFINITE COVERS

In [5] we showed non-vanishing of the universal index elements in the K-theory of the maximal C∗-algebras of the fundamental groups of enlargeable spin manifolds. The underlying notion of enlargeability was the one from [3], involving contracting maps defined on finite covers of the given manifolds. In the paper at hand, we weaken this assumption to the one in [4] where infinite covers are allowed. The new idea is the construction of a geometrically given C∗-algebra with trace which encodes the information given by these infinite covers. Along the way we obtain an easy proof of a relative index theorem relevant in this context. 1. Overview of results This paper is a sequel to [5]. We quickly review the relevant mathematics and the motivation for our research. Since the work of Lichnerowicz it has been known that index theory can be used to construct computable obstructions to the existence of positive scalar curvature metrics on closed spin manifoldsM: If such a metric exists onM , then Â(M), a characteristic number of M involving its Pontryagin classes, vanishes. However, the converse is not true: In [3] it was shown (again by index theoretic methods) that also enlargeability (see the definition below) of M is an obstruction to the existence of a positive scalar curvature metric. Furthermore, it is well known that there are enlargeable manifolds with vanishing Â-genus (for example tori). The Â-obstruction was gradually refined and in its most sophisticated form constructed by Rosenberg [7] as an element α max(M) ∈ KOn(C ∗ max,Rπ1(M)) in the real K-theory of the maximal C-algebra of π1(M). It is often assumed that this obstruction subsumes all other index theoretic obstructions against positive scalar curvature metrics on M . Results We thank S. Stolz and A. Thom for useful conversations regarding the research in this paper. Both authors are members of the DFG emphasis programme “Globale Differentialgeometrie” whose support is gratefully acknowledged.