Miracle-dz/UniFAR-FTUs huggingface dataset:
Cleavage of Phage DNA by the Streptococcus thermophilus CRISPR3-Cas System

Streptococcus thermophilus, similar to other Bacteria and Archaea, has developed defense mechanisms to protect cells against invasion by foreign nucleic acids, such as virus infections and plasmid transformations. One defense system recently described in these organisms is the CRISPR-Cas system (Clustered Regularly Interspaced Short Palindromic Repeats loci coupled to CRISPR-associated genes). Two S. thermophilus CRISPR-Cas systems, CRISPR1-Cas and CRISPR3-Cas, have been shown to actively block phage infection. The CRISPR1-Cas system interferes by cleaving foreign dsDNA entering the cell in a length-specific and orientation-dependant manner. Here, we show that the S. thermophilus CRISPR3-Cas system acts by cleaving phage dsDNA genomes at the same specific position inside the targeted protospacer as observed with the CRISPR1-Cas system. Only one cleavage site was observed in all tested strains. Moreover, we observed that the CRISPR1-Cas and CRISPR3-Cas systems are compatible and, when both systems are present within the same cell, provide increased resistance against phage infection by both cleaving the invading dsDNA. We also determined that overall phage resistance efficiency is correlated to the total number of newly acquired spacers in both CRISPR loci.
Defining Fairness in Reactive and Concurrent Systems

We define when a linear-time temporal property is a fairness property with respect to a given system. This captures the essence shared by most fairness assumptions that are used in the specification and verification of reactive and concurrent systems, such as weak fairness, strong fairness, k-fairness, and many others. We provide three characterizations of fairness: a language-theoretic, a game-theoretic, and a topological characterization. It turns out that the fairness properties are the sets that are “large” from a topological point of view, that is, they are the co-meager sets in the natural topology of runs of a given system. This insight provides a link to probability theory where a set is “large” when it has measure 1. While these two notions of largeness are similar, they do not coincide in general. However, we show that they coincide for ω-regular properties and bounded Borel measures. That is, an ω-regular temporal property of a finite-state system has measure 1 under a bounded Borel measure if and only if it is a fairness property with respect to that system. The definition of fairness leads to a generic relaxation of correctness of a system in linear-time semantics. We define a system to be fairly correct if there exists a fairness assumption under which it satisfies its specification. Equivalently, a system is fairly correct if the set of runs satisfying the specification is topologically large. We motivate this notion of correctness and show how it can be verified in a system.
Variation and constraint in Hox gene evolution

Despite enormous body plan variation, genes regulating embryonic development are highly conserved. Here, we probe the mechanisms that predispose ancient regulatory genes to reutilization and diversification rather than evolutionary loss. The Hox gene fushi tarazu (ftz) arose as a homeotic gene but functions as a pair-rule segmentation gene in Drosophila. ftz shows extensive variation in expression and protein coding regions but has managed to elude loss from arthropod genomes. We asked what properties prevent this loss by testing the importance of different protein motifs and partners in the developing CNS, where ftz expression is conserved. Drosophila Ftz proteins with mutated protein motifs were expressed under the control of a neurogenic-specific ftz cis-regulatory element (CRE) in a ftz mutant background rescued for segmentation defects. Ftz CNS function did not require the variable motifs that mediate differential cofactor interactions involved in homeosis or segmentation, which vary in arthropods. Rather, CNS function did require the shared DNA-binding homeodomain, which plays less of a role in Ftz segmentation activity. The Antennapedia homeodomain substituted for Ftz homeodomain function in the Drosophila CNS, but full-length Antennapedia did not rescue CNS defects. These results suggest that a core CNS function retains ftz in arthropod genomes. Acquisition of a neurogenic CRE led to ftz expression in unique CNS cells, differentiating its role from neighboring Hox genes, rendering it nonredundant. The inherent flexibility of modular CREs and protein domains allows for stepwise acquisition of new functions, explaining broad retention of regulatory genes during animal evolution.
Environmental Policy Uncertainty and Innovation in Environmental Technologies

The effect of uncertainty related to environmental damages or technological change has on the optimal level of environmental policy stringency has been extensively analysed in the literature. However, empirical evidence on the innovation efforts of firms in the face of actual policy uncertainty has not been examined formally. Drawing upon real options theory, it is hypothesised that for any given level of environmental policy stringency, environmental policy uncertainty can serve as a brake on investment in innovative activities which can reduce the cost of meeting environmental objectives. By increasing the benefits of ‘waiting’, policy uncertainty will reduce incentives to identify innovative environmental technologies. Using patent counts as a measure of environmental innovation, preliminary empirical evidence has been presented which supports this hypothesis.
Cheap and Small Counterexamples

Minimal counterexamples are desirable, but expensive to compute. We propose four algorithms for computing small counterexamples that approximate the shortest case. Three of these use a new algorithm for automata-theoretic linear-time model checking, based on an early algorithm by Dijkstra for detecting strongly connected components. All four of the approximation algorithms rely on transitions shuffling; we show that the default transition ordering can behave badly. The algorithms are compared to a standard shortest counterexample algorithm on a large public data set.
Peru: Providers' Compliance with Quality of Care Norms

Final report of the in-house project “Monitoring family planning providers’ compliance with the quality of care norms of Peru’s Ministry of Health”, conduced from 14 June through 30 September 1999. This study was funded by the U. S. AGENCY FOR INTERNATIONAL DEVELOPMENT (USAID) under the terms of Cooperative Agreement Number HRN-A-00-98-0012-00. The opinions expressed herein are those of the author and do not necessarily reflect the view of USAID. The study was requested by USAID/Peru as part of the activities of its PASARE Program and used Field Support funds.
ONTOSEARCH2: SEARCHING AND QUERYING WEB ONTOLOGIES

Ontologies are important components of web-based applications. While the Web makes an increasing number of ontologies widely available for applications, how to discover ontologies in the Web becomes a more challenging issue. Existing approaches are mainly based on keywords and metadata information of ontologies, rather than semantic entailments of ontologies. In this paper, we present a Semantic Web engine, called ONTOSEARCH2, which searches and queries Web ontologies by creating and storing a copy of ontologies in a tractable description logic. ONTOSEARCH2 allows formal querying of its repository, including both the structures and instances of ontologies, using the SPARQL query language. Furthermore, this paper reports on preliminary, but encouraging, benchmark results which compare ONTOSEARCH2’s response times on a number of queries with those of existing knowledge base management systems.
Developmental dyslexia: dysfunction of a left hemisphere reading network

This mini-review summarizes and integrates findings from recent meta-analyses and original neuroimaging studies on functional brain abnormalities in dyslexic readers. Surprisingly, there is little empirical support for the standard neuroanatomical model of developmental dyslexia, which localizes the primary phonological decoding deficit in left temporo-parietal (TP) regions. Rather, recent evidence points to a dysfunction of a left hemisphere reading network, which includes occipito-temporal (OT), inferior frontal, and inferior parietal regions.
The regulation of synaptogenesis during normal development and following activity blockade

The mature neuromuscular junction is characterized by the tight spatial colocalization of synaptic vesicles and acetylcholine receptor (AChR) clusters. Although a large body of work exists on the interactions between motoneurons and myotubes leading to synaptogenesis in tissue culture, how the neuromuscular junction acquires its highly specialized structure in vivo is not well understood, particularly during the earliest period of synaptogenesis. In this study, the development of the neuromuscular synapse in chick hindlimb muscles was examined and quantified by simultaneously labeling the pre- and postsynaptic elements from the time the main nerve trunks leave the lumbosacral plexus region to enter the developing limb (St 24) through the end of the motoneuron cell death period (St 36). Based on these results, synaptogenesis can be divided into several distinct stages that are intimately connected to the innervation sequence described in a previous paper (Dahm and Landmesser, 1988). Briefly, as large nerve trunks approach the developing muscles and the first AChR clusters are induced to form on nearby myotubes, none of these initial receptor clusters are in direct contact with a nerve profile. The first appearance of nerve-contacted clusters (synapses) is coincident with the growth of large, unbranched nerve trunks into the muscles. The next step is initiated by the formation of small nerve side branches that grow out from the larger intramuscular nerve trunks to bring most axons and myotubes into contact for the first time. As side branches form, synapses appear around them, and non-nerve-contacted receptor clusters disappear from around the main intramuscular nerve trunks. The next step in synaptogenesis is the restriction of synaptic vesicle antigen to sites of synaptic contact. These early stages of synaptogenesis are also characterized by the growth of the presynaptic terminal to match the length of the postsynaptic receptor cluster. This study showed that AChR cluster formation during early in vivo neuromuscular development does not require close anatomical nerve contact, but that the presence of the nerves is necessary for AChR clusters to form. This suggests that the nerves normally induce AChR clustering via the release of a diffusible substance, a suggestion substantiated by the observation that AChR clusters do not form on aneural myotubes in vivo. In order to assess the role of synapse formation in the regulation of motoneuron number, synaptogenesis was quantitatively examined after chronic neuromuscular blockade, which prevents motoneuron cell death. (ABSTRACT TRUNCATED AT 400 WORDS)
Incremental Negotiation and Coalition Formation for Resource-bounded Agents: Preliminary Report

We explore a class of task allocation mechanisms that are incremental and can be tuned to the computational resource limitations of agents Our focus is on dis tributed task and resource allocation problems involv ing coalitions of cooperative agents that must negotiate among themselves on the distribution of tasks Our emphasis is on the design of mechanisms with desir able real time and dynamic properties We describe preliminary work in four areas the design of what we call time bounded commitment networks that are ex tensions of task auctions and contract nets and that support a notion of reciprocal commitment anytime algorithms for combinatorial task allocation that take into account both positive and negative task interac tions organizational frameworks for e cient task allo cation in highly dynamic domains involving hundreds of agents and logical tools for analyzing dynamic emer gent properties of agent societies
Smoothing irregularly sampled signals by convolutional RBF networks

Convolutional radial basis function (RBF) networks are introduced for smoothing out irregularly sampled signals. The proposed technique involves training an RBF network and then convolving it with a Gaussian smoothing kernel in an analytical manner. Since the convolution results in an analytic form, the computation necessary for numerical convolution is avoided. Convolutional RBF networks need training only once, do not depend on any particular details of the training methods used, and different degrees of smoothing are immediately available.
Prevalence of Antibodies against Hantaviruses in Serum and Saliva of Adults Living or Working on Farms in Yorkshire, United Kingdom

Hantaviruses are an established cause of haemorrhagic fever with renal syndrome (HFRS) in Europe. Following a confirmed case of HFRS in the UK, in an individual residing on a farm in North Yorkshire and the Humber, a tidal estuary on the east coast of Northern England, and the subsequent isolation of a Seoul hantavirus from rats trapped on the patient’s farm, it was considered appropriate to further investigate the public health risk of this virus in the region. Of a total 119 individuals tested, nine (7.6%) were seropositive for hantavirus antibodies. Seven of the seropositive samples showed a stronger reaction to Seoul and Hantaan compared to other clinically relevant hantaviruses. Observation of rodents during the day, in particular mice, was associated with a reduced risk of seropositivity. In addition to one region known to be at risk following an acute case, five further potential risk areas have been identified. This study supports recently published evidence that hantaviruses are likely to be of public health interest in the region.
Smoothing Problem in 2D Images with Tissue-like P Systems and Parallel Implementation

Smoothing is often used in Digital Imagery to reduce noise within an image. In this paper we present a Membrane Computing algorithm for smoothing 2D images in the framework of tissue-like P systems. The algorithm has been implemented by using a novel device architecture called CUDA, (Compute Unified Device Architecture). We present some examples, compare the obtained time and present some research lines for the future.
Clearing the garden-path: improving sentence processing through cognitive control training

How do general-purpose cognitive abilities affect language processing and comprehension? Recent research emphasises a role for cognitive control—also called executive function (EF)—when individuals must override early parsing decisions as new evidence conflicts with their developing interpretation. We tested if training on non-syntactic EF tasks improves readers' ability to recover from misanalysis during language processing. Participants completed pre/post-reading assessments containing temporarily ambiguous sentences susceptible to misinterpretation. Performance increases on a training task targeting conflict-resolution processes (n-back with “lures”) predicted improvements in garden-path recovery. N-back responders—those demonstrating reliable training gains—significantly increased their comprehension accuracy across assessments. Their posttest eye-movement patterns also revealed significantly improved real-time revision following entry into disambiguating sentence regions where cognitive control is hypothesised to engage. Untrained participants and n-back non-responders showed no performance changes. The results provide insight into how nonlinguistic functions contribute to parsing and interpretation and suggest that certain language skills are amenable to improvement via domain-general EF training.
PROBING THE ORIGINS OF THE C iv AND Fe Kα BALDWIN EFFECTS

We use UV/optical and X-ray observations of 272 radio-quiet Type 1 active galactic nuclei and quasars to investigate the C iv Baldwin Effect (BEff). The UV/optical spectra are drawn from the Hubble Space Telescope, International Ultraviolet Explorer and Sloan Digital Sky Survey archives. The X-ray spectra are from the Chandra and XMM-Newton archives. We apply correlation and partial-correlation analyses to the equivalent widths (EWs), continuum monochromatic luminosities, and αox, which characterizes the relative X-ray to UV brightness. The EW of the C iv λ1549 emission line is correlated with both αox and luminosity. We find that by regressing lν(2500 Å) with EW(C iv) and αox, we can obtain tighter correlations than by regressing lν(2500 Å) with only EW(C iv). Both correlation and regression analyses imply that lν(2500 Å) is not the only factor controlling the changes of EW(C iv); αox (or, equivalently, the soft X-ray emission) plays a fundamental role in the formation and variation of C iv. Variability contributes at least 60% of the scatter of the EW(C iv)–lν(2500 Å) relation and at least 75% of the scatter of the of the EW(C iv)–αox relation. In our sample, narrow Fe Kα 6.4 keV emission lines are detected in 50 objects. Although narrow Fe Kα exhibits a BEff similar to that of C iv, its EW has almost no dependence on either αox or EW(C iv). This suggests that the majority of narrow Fe Kα emission is unlikely to be produced in the broad emission-line region. We do find suggestive correlations between the emission-line luminosities of C iv and Fe Kα, which could be potentially used to estimate the detectability of the Fe Kα line of quasars from rest-frame UV spectroscopic observations.
Wiener Filters in Gaussian Mixture Signal Estimation With  \(\ell _\infty \) -Norm Error

Consider the estimation of a signal x ∈ RN from noisy observations r = x + z, where the input x is generated by an independent and identically distributed (i.i.d.) Gaussian mixture source, and z is additive white Gaussian noise in parallel Gaussian channels. Typically, the l2-norm error (squared error) is used to quantify the performance of the estimation process. In contrast, we consider the l∞-norm error (worst case error). For this error metric, we prove that, in an asymptotic setting where the signal dimension N → ∞, the l∞-norm error always comes from the Gaussian component that has the largest variance, and the Wiener filter asymptotically achieves the optimal expected l∞-norm error. The i.i. d. Gaussian mixture case can be extended to i.i. d. Bernoulli-Gaussian distributions, which are often used to model sparse signals. Finally, our results can be extended to linear mixing systems with i.i. d. Gaussian mixture inputs, in settings where a linear mixing systems with i.i. d. Gaussian mixture inputs, in settings where a linear mixing system can be decoupled to parallel Gaussian channels.
Racial and Ethnic Health Disparities: Influences, Actors, and Policy Opportunities

Much has been written on the existence of racial and ethnic differences in health status and health care access and quality in the United States. Researchers, think tanks, government entities, and advocacy organizations have worked to summarize many of the root causes, environmental and behavioral influences, and health system factors that play a role. Yet sustained and significant change has been elusive. Efforts to reduce disparities will continue to fall short unless the complex interplay of influences are understood and addressed, and synergies among actors who can impact those influences are realized. The Kaiser Permanente Institute for Health Policy has produced this review and synthesis of the literature to spur thinking and discussion among those who inform, influence, and make public and private policy impacting health. Areas of analysis include the landscape of influences on health disparities, which policy actors are best positioned to intervene, and where those actors may have the most impact. Given the complex nature of disparities, to date most action has focused on individual sectors of health or social policy, such as coverage for the uninsured, linguistically appropriate care, or neighborhood improvements to support healthy eating and active living.
A PRIMAL-DUAL EXTERIOR POINT ALGORITHM FOR LINEAR PROGRAMMING PROBLEMS

The aim of this paper is to present a new simplex type algorithm for the Linear Programming Problem. The Primal - Dual method is a Simplex - type pivoting algorithm that generates two paths in order to converge to the optimal solution. The first path is primal feasible while the second one is dual feasible for the original problem. Specifically, we use a three-phase-implementation. The first two phases construct the required primal and dual feasible solutions, using the Primal Simplex algorithm. Finally, in the third phase the Primal - Dual algorithm is applied. Moreover, a computational study has been carried out, using randomly generated sparse optimal linear problems, to compare its computational efficiency with the Primal Simplex algorithm and also with MATLAB's Interior Point Method implementation. The algorithm appears to be very promising since it clearly shows its superiority to the Primal Simplex algorithm as well as its robustness over the IPM algorithm.
Assessment of community functioning in people with schizophrenia and other severe mental illnesses: a white paper based on an NIMH-sponsored workshop.

People with schizophrenia frequently have significant problems in community functioning. Progress in developing effective interventions to ameliorate these problems has been slowed by the absence of reliable and valid measures that are suitable for use in clinical trials. The National Institute of Mental Health convened a workgroup in September 2005 to examine this issue and make recommendations to the field that would foster research in this area. This article reports on issues raised at the meeting. Many instruments have been developed to assess community functioning, but overall insufficient attention has been paid to psychometric issues and many instruments are not suitable for use in clinical trials. Consumer self-report, informant report, ratings by clinicians and trained raters, and behavioral assessment all can provide useful and valid information in some circumstances and may be practical for use in clinical trials. However, insufficient attention has been paid to when and how different forms of assessment and sources of information are useful or how to understand inconsistencies. A major limiting factor in development of reliable and valid instruments is failure to develop a suitable model of functioning and its primary mediators and moderators. Several examples that can guide thinking are presented. Finally, the field is limited by the absence of an objective gold standard of community functioning. Hence, outcomes must be evaluated in part by "clinical significance. " This criterion is problematic because different observers and constituencies often have different opinions about what types of change are clinically important and how much change is significant.