Miracle-dz/UniFAR-FTUs huggingface dataset:
Epistasis affecting litter size in mice

Litter size is an important reproductive trait as it makes a major contribution to fitness. Generally, traits closely related to fitness show low heritability perhaps because of the corrosive effects of directional natural selection on the additive genetic variance. Nonetheless, low heritability does not imply, necessarily, a complete absence of genetic variation because genetic interactions (epistasis and dominance) contribute to variation in traits displaying strong heterosis in crosses, such as litter size. In our study, we investigated the genetic architecture of litter size in 166 females from an F2 intercross of the SM/J and LG/J inbred mouse strains. Litter size had a low heritability (h2 = 12%) and a low repeatability (r = 33%). Using interval‐mapping methods, we located two quantitative trait loci (QTL) affecting litter size at locations D7Mit21 + 0 cM and D12Mit6 + 8 cM, on chromosomes 7 and 12 respectively. These QTL accounted for 12.6% of the variance in litter size. In a two‐way genome‐wide epistasis scan we found eight QTL interacting epistatically involving chromosomes 2, 4, 5, 11, 14, 15 and 18. Taken together, the QTL and their interactions explain nearly 49% (39.5% adjusted multiple r2) of the phenotypic variation for litter size in this cross, an increase of 36% over the direct effects of the QTL. This indicates the importance of epistasis as a component of the genetic architecture of litter size and fitness in our intercross population.
Analysis of Hypertext Isolation Techniques for XSS Prevention

Modern websites and web applications commonly integrate third-party and user-generated content to enrich the user’s experience. Developers of these applications are in need of a simple way to limit the capabilities of this less trusted, outsourced web content and thereby protect their users from cross-site scripting attacks. We summarize several recent proposals that enable developers to isolate untrusted hypertext, and could be used to define robust constraint environments that are enforceable by web browsers. A comparative analysis of these proposals is presented highlighting security, legacy browser compatibility and several other important qualities.
Observer-based robust adaptive fuzzy tracking control in robot arms

In this paper, an observer-based robust adaptive fuzzy tracking control for rigid robotic systems is presented with plant unknown. It is assumed that only the joint angular positions are measured, the joint angular velocities are estimated via a fuzzy observer. First, we design a nonlinear observer based on fuzzy basis functions (FBF) to estimate the joint angular velocities in which a fuzzy logic system is introduced to learn these unknown dynamics by an adaptive algorithm. Then, an indirect adaptive fuzzy controller based on observer is presented. The developed control scheme is simple and computationally efficient, since it does not require a knowledge of either the mathematical model or the parameterization of the robotic dynamics. Simulation results demonstrate the applicability of the proposed method in order to achieve desired performance.
The mechanics of memory-related software aging

Software aging is a phenomenon defined as the continuing degradation of software systems during runtime, being particularly noticeable in long-running applications. Memory-related aging effects are one of the most important problems in this research field. Therefore understanding their causes and how they work is a major requirement in designing dependable software systems. In this paper we go deep into how memory management works inside application process, focusing on two memory problems that cause software aging: fragmenting and leakage. We explain the mechanics of memory-related software aging effects dissecting a real and widely adopted memory allocator. Along with the theoretical explanation, we present an experimental study that illustrates how memory fragmenting and leakage occur and how they accumulate over time in order to cause system aging-related failures.
Psychological aspects of information seeking on the Internet

Two studies are presented that investigate information seeking behaviour on the Internet. In study one, soccer fans’ information seeking on the World Wide Web is investigated. In study two, access rates to a cancer information Web site are analysed. It is tentatively argued that there is a tendency for people to access information more commonly avoided in “real life”, although in the case of football fans, the tendency to “bask in reflected glory” remains when online, while cutting off reflected failure is minimised. Implications for understanding and researching psychological processes of Web browsing behaviour are discussed.
Three New Approaches to Privacy-preserving Add to Multiply Protocol and its Application

Privacy-preserving Data Mining aims at securely extracting knowledge from two or more parties' private data. Secure Multi-party Computation is the paramount approach to it. In this paper, we study Privacy-preserving Add and Multiply Exchanging Technology and present three new different approaches to Privacy-preserving Add to Multiply Protocol. After that, we analyze and compare the three different approaches about the communication overheads, the computation efforts and the security. In addition, we extend Privacy-preserving Add to Multiply Protocol to Privacy-preserving Adding to Scalar Product Protocol, which is more secure and more useful in the high security situations of Privacy-preserving Data Mining. Meantime, we present a solution for the new protocol.
ESTIMATES OF VARIANCE COMPONENTS IN RANDOM EFFECTS META-ANALYSIS : SENSITIVITY TO VIOLATIONS OF NORMALITY AND VARIANCE HOMOGENEITY

Meta-analysis is a statistical technique through which information obtained from a collection of independent studies is analyzed and synthesized, potentially providing a more complete representation of the phenomenon under investigation. Models for meta-analysis may be roughly divided into those based upon fixed effects and those based upon random effects (Field, 2001; Hedges, 1994; Hedges & Vevea, 1998; Raudenbush, 1994). The primary goal of meta-analysis is to obtain estimates of population effect sizes and confidence bands around those estimates. For example, recent research in the area of educational reform related to the National Science Foundation’s Systemic Initiatives (Kromrey et al., 2002) has investigated the use of effect sizes as indices of the effectiveness of systemic change. These efforts have been directed towards synthesizing student outcome differences across subject areas, grade levels, and years of participation. Because sample effect sizes obtained for a metaanalysis typically present different magnitudes of estimation error, weighted means and variances are used to obtain the estimates of population effect sizes and confidence bands. For fixed effects models, these weights are given by
Evaluation of MTBDRplus and MTBDRsl in Detecting Drug-Resistant Tuberculosis in a Chinese Population

Background. This study aims to evaluate GenoType MTBDRplus and GenoType MTBDRsl for their ability to detect drug-resistant tuberculosis in a Chinese population. Methods. We collected 112 Mycobacteria tuberculosis strains from Jiangsu province, China. The conventional DST and line probe assay were used to detect drug resistance to rifampicin (RFP), isoniazid (INH), ofloxacin (OFX), kanamycin (Km), and ethambutol (EMB). Results. The sensitivity and specificity were 100% and 50% for RFP and 86.11% and 47.06% for INH, respectively. The most common mutations observed in MTBDRplus were rpoBWT8 omission + MUT3 presence, katGWT omission + MUT1 presence, and inhAWT1 omission + MUT1 presence. For drug resistance to OFX, Km, and EMB, the sensitivity of MTBDRsl was 94.74%, 62.50%, and 58.82%, respectively, while the specificity was 92.59%, 98.81%, and 91.67%, respectively. The most common mutations were gyrAWT3 omission + MUT3C presence, rrsMUT1 presence, embBWT omission + MUT1B presence, and embBWT omission + MUT1A presence. Sequencing analysis found several uncommon mutations. Conclusion. In combination with DST, application of the GenoType MTBDRplus and GenoType MTBDRsl assays might be a useful additional tool to allow for the rapid and safe diagnosis of drug resistance to RFP and OFX.
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Edited by Owen Holland About Authors Editorial Introduction Owen Holland Axioms and Tests for the Presence of Igor Aleksander Minimal Consciousness in Agents & Barry Dunmall Consciousness in Meme Machines Susan Blackmore CyberChild: A Simulation Test-Bed Rodney M.J. Cotterill for Consciousness Studies IDA: A Conscious Artifact? Stan Franklin Can a Machine Be Conscious? How? Stevan Hamad Robots With Internal Models: Owen Holland A Route to Machine Consciousness? & Rod Goodman Level-Headed Mysterianism Jesse J. Prinz and Artificial Experience Virtual Machines and Consciousness Aaron Sloman & Ron Chrisley Language Re-Entrance and the 'Inner Voice' Luc Steels The Borg or Borges? William Irwin Thompson
New local estimation procedure for a non‐parametric regression function for longitudinal data

Summary. The paper develops a new estimation of non‐parametric regression functions for clustered or longitudinal data. We propose to use Cholesky decomposition and profile least squares techniques to estimate the correlation structure and regression function simultaneously. We further prove that the estimator proposed is as asymptotically efficient as if the covariance matrix were known. A Monte Carlo simulation study is conducted to examine the finite sample performance of the procedure proposed, and to compare the procedure with the existing procedures. On the basis of our empirical studies, the newly proposed procedure works better than naive local linear regression with working independence error structure and the gain in efficiency can be achieved in moderate‐sized samples. Our numerical comparison also shows that the newly proposed procedure outperforms some existing procedures. A real data set application is also provided to illustrate the estimation procedure proposed.
The Four Distal Tyrosines Are Required for LAT-dependent Signaling in FcɛRI-mediated Mast Cell Activation

The linker for activation of T cells (LAT) is an adaptor protein critical for FcɛRI-mediated mast cell activation. LAT is a substrate of the tyrosine kinases activated after TCR and FcɛRI engagement. After phosphorylation of the cytosolic domain of LAT, multiple signaling molecules such as phospholipase C–γ1, Grb2, and Gads associate with phosphorylated LAT via their SH2 domains. The essential role of the four distal tyrosines in TCR-mediated signaling and T cell development has been demonstrated by experiments using LAT-deficient cell lines and genetically modified mice. To investigate the role of these four tyrosines of LAT in FcɛRI-mediated mast cell activation, bone marrow–derived mast cells from LAT-deficient mice were infected with retroviral vectors designed to express wild-type or mutant LAT. Examination of bone marrow–derived mast cells expressing various tyrosine to phenylalanine mutants in LAT demonstrates a differential requirement for these different binding sites. In these studies, assays of biochemical pathways, degranulation, and cytokine and chemokine release were performed. Finally, the role of these tyrosines was also evaluated in vivo using genetically modified animals. Deletion of all four distal tyrosines, and in particular, loss of the primary phospholipase C–γ-binding tyrosine had a significant effect on antigen-induced histamine release.
NECLA at the Medical Natural Language Processing Pilot Task (MedNLP)

This paper gives an overview of NECLA’s submitted systems for the De-Identification and Complaint & Diagnosis subtasks of the Medical Natural Language Processing Pilot Task (MedNLP)[5]. Our systems combine features derived from Part of Speech (POS) tags, a domain-specific dictionary, the Unified Medical Language System (UMLS) metathesaurus and semantic network, and a small set of heuristics based on trigger-words and polarity propagation through sentence dependency parse trees.
Rigorous numerics for analytic solutions of differential equations: the radii polynomial approach

Judicious use of interval arithmetic, combined with careful pen and paper estimates, leads to effective strategies for computer assisted analysis of nonlinear operator equations. The method of radii polynomials is an efficient tool for bounding the smallest and largest neighborhoods on which a Newton-like operator associated with a nonlinear equation is a contraction mapping. The method has been used to study solutions of ordinary, partial, and delay differential equations such as equilibria, periodic orbits, solutions of initial value problems, heteroclinic and homoclinic connecting orbits in the C category of functions. In the present work we adapt the method of radii polynomials to the analytic category. For ease of exposition we focus on studying periodic solutions in Cartesian products of infinite sequence spaces. We derive the radii polynomials for some specific application problems, and give a number of computer assisted proofs in the analytic framework.
Hybrid assistive system-the motor neuroprosthesis

Two approaches are currently applied for motor rehabilitation of paralyzed humans: functional electrical stimulation (FES) and mechanical bracing. Both assistive systems have limited application due to several factors. The combination of FES and an externally powered and controlled brace is called a hybrid assistive system (HAS). The HAS presented here is a combination of multichannel surface FES and self-fitting modular orthosis. Energy expenditure and a reduction of force load on the upper extremities are criteria for the efficacy of HAS. The control system of HAS is nonnumerical and based on artificial reflexes. <<ETX>>
Differential effects of developmental cerebellar abnormality on cognitive and motor functions in the cerebellum: an fMRI study of autism.

OBJECTIVE Recent years have seen a revolution in views regarding cerebellar function. New findings suggest that the cerebellum plays a role in multiple functional domains: cognitive, affective, and sensory as well as motor. These findings imply that developmental cerebellar pathology could play a role in certain nonmotor functional deficits, thereby calling for a broader investigation of the functional consequences of cerebellar pathology. Autism provides a useful model, since over 90% of autistic cerebella examined at autopsy have shown well-defined cerebellar anatomic abnormalities. The aim of the present study was to examine how such pathology ultimately impacts cognitive and motor function within the cerebellum. METHOD Patterns of functional magnetic resonance imaging (fMRI) activation within anatomically defined cerebellar regions of interest were examined in eight autistic patients (ages 14-38 years) and eight matched healthy comparison subjects performing motor and attention tasks. For the motor task, subjects pressed a button at a comfortable pace, and activation was compared with a rest condition. For the attention task, visual stimuli were presented one at a time at fixation, and subjects pressed a button to every target. Activation was compared with passive visual stimulation. RESULTS While performing these tasks, autistic individuals showed significantly greater cerebellar motor activation and significantly less cerebellar attention activation. CONCLUSIONS These findings shed new light on the cerebellar role in attention deficits in autism and suggest that developmental cerebellar abnormality has differential functional implications for cognitive and motor systems.
M(o)TOR of aging: MTOR as a universal molecular hypothalamus

A recent ground-breaking publication described hypothalamus-driven programmatic aging. As a Russian proverb goes “everything new is well-forgotten old”. In 1958, Dilman proposed that aging and its related diseases are programmed by the hypothalamus. This theory, supported by beautiful experiments, remained unnoticed just to be re-discovered recently. Yet, it does not explain all manifestations of aging. And would organism age without hypothalamus? Do sensing pathways such as MTOR (mechanistic Target of Rapamycin) and IKK-beta play a role of a “molecular hypothalamus” in every cell? Are hypothalamus-driven alterations simply a part of quasi-programmed aging manifested by hyperfunction and secondary signal-resistance? Here are some answers.
Racial Segregation and Poverty by

This paper examines the relationship between racial segregation and poverty. Using data primarily from the 2000 Census, I control extensively for metropolitan area characteristics and other factors. In addition, I use metropolitan area physical geography characteristics as instruments for racial segregation as one approach to address the problem of endogeneity bias. I find significant and positive effects of black (Latino)-white segregation on black and Latino poverty, respectively, that remains evident across a variety of model specifications. Evidence from two-stage least squares estimates reveals that the effect on Latino poverty seems more plagued by endogeneity bias than that on black poverty. Simulations show that if black-white levels of segregation were reduced from hyper segregation (actual) levels to low levels of segregation the black-white poverty rate gap would close by fifty percent. The influence of segregation on poverty varies across important metropolitan characteristics such as region, metro size and percent of the population that minority.
Non-intrusive Movement Detection in CARA Pervasive Healthcare Application

Pervasive healthcare promises to support the desire of many elderly for independent living and at-home care. This paper presents the CARA (Context Aware Real-time Assistant) system whose design goal is to provide a pervasive real-time intelligent at-home healthcare solution. While this is the goal it is recognized that current practice and current user requirements of both the subject (such as an elderly person) and caregiver (such as a medical consultant) may differ from our ultimate goal. Recognizing this, we have built a solution that supports scenarios of use of CARA other than as a fully automatic pervasive healthcare solution. In this paper we describe a scenario where the full wireless medical BAN (body area network) is used remotely under supervision, and supplementary continuous monitoring of the patient is done in a non-intrusive way via a movement sensor. This movement monitoring is integrated with the CARA system and can make use of CARA’s intelligent analysis as well as its recording and playback facilities. While this scenario does not use the full capabilities of the CARA system, it provides a less disruptive introduction to the technology for an elderly person, and leads easily to incremental further incorporation of the technology. The full CARA system has sensors to continuously measure physiological signals, and it can either store the data on a server or stream the data to a remote location in real-time. Implemented as a rich internet application, the only tool required of a remote caregiver is a web browser with the commonly-available Adobe Flash plug-in. Thus the CARA system can be accessed on any internet-connected PC or appropriate smart device. The results of experiments are presented that illustrate the effectiveness of the system in analyzing a patient’s movement, and its performance over the internet. KeywordsPervasive Healthcare, Data Review, Remote Monitoring, Movement Monitoring, Rich Internet Application
Matching technological evaluation to the key attributes of a technology

How to select technological evaluation methods is a very intractable problem technology assessors face. This study suggests a methodology which would allow the matching of technology evaluation techniques with the technologies to be assessed, by mapping them both onto a common scale. An attribute form, which is standard and easily processed by computer, is constructed to describe and record assessment techniques and a solution to assessment technique selection based on those attributes is presented. A logical structure of the assessment techniques system is built after the common characters among different assessment methods are analyzed. This exploratory method will help in computer-aided selection of complementary and appropriate techniques for a technology evaluation.
Droplet-based pyrosequencing using digital microfluidics.

The feasibility of implementing pyrosequencing chemistry within droplets using electrowetting-based digital microfluidics is reported. An array of electrodes patterned on a printed-circuit board was used to control the formation, transportation, merging, mixing, and splitting of submicroliter-sized droplets contained within an oil-filled chamber. A three-enzyme pyrosequencing protocol was implemented in which individual droplets contained enzymes, deoxyribonucleotide triphosphates (dNTPs), and DNA templates. The DNA templates were anchored to magnetic beads which enabled them to be thoroughly washed between nucleotide additions. Reagents and protocols were optimized to maximize signal over background, linearity of response, cycle efficiency, and wash efficiency. As an initial demonstration of feasibility, a portion of a 229 bp Candida parapsilosis template was sequenced using both a de novo protocol and a resequencing protocol. The resequencing protocol generated over 60 bp of sequence with 100% sequence accuracy based on raw pyrogram levels. Excellent linearity was observed for all of the homopolymers (two, three, or four nucleotides) contained in the C. parapsilosis sequence. With improvements in microfluidic design it is expected that longer reads, higher throughput, and improved process integration (i.e., "sample-to-sequence" capability) could eventually be achieved using this low-cost platform.
Rendezvous of Unicycles with Continuous and Time-Invariant Local Feedback

Abstract In this paper, a local feedback control strategy is devised to drive a group of nonholonomic unicycle-type vehicles to a rendezvous point. The proposed control law is continuous and time-invariant. Using tools from graph theory, convergence and ultimate boundedness properties of the overall system are examined. Similar to the results for the rendezvous problem for vehicles governed by linear dynamics, the convergence of the studied overall multi-agent system relies on the connectivity of the interaction graph. The validity of this control law is verified by computer simulations.
A New View on Young Pulsars in Supernova Remnants: Slow, Radio-quiet, & X-ray Bright

We propose a simple explanation for the apparent dearth of radio pulsars associated with young supernova remnants (SNRs). Recent X-ray observations of young remnants have revealed slowly rotating (P ~ 10-s) central pulsars with pulsed emission above 2 keV, lacking in detectable radio emission. Some of these objects apparently have enormous magnetic fields, evolving in a manner distinct from the Crab pulsar. We argue that these X-ray pulsars can account for a substantial fraction of the long sought after neutron stars in SNRs and that Crab-like pulsars are perhaps the rarer, but more highly visible example of these stellar embers. Magnetic field decay likely accounts for their high X-ray luminosity, which cannot be explained as rotational energy loss, as for the Crab-like pulsars. We suggest that the natal magnetic field strength of these objects control their subsequent evolution. There are currently almost a dozen slow X-ray pulsars associated with young SNRs. Remarkably, these objects, taken together, represent at least half of the confirmed pulsars in supernova remnants. This being the case, these pulsars must be the progenitors of a vast population of previously unrecognized neutron stars.