Miracle-dz/UniFAR-FTUs huggingface dataset:
Partial Halting in P Systems

We consider a new variant of the halting condition in P systems, i.e., a computation in a P system is already called halting if no multiset of rules containing a rule from each set of rules assigned to the membranes is applicable anymore, whereas usually a computation is called halting if no rule is applicable anymore in the whole system. This new variant of partial halting is especially investigated for (catalytic) P systems and antiport P systems working in different derivation modes.
Mimicking Primitive Photobacteria: Sustainable Hydrogen Evolution Based on Peptide-Porphyrin Co-Assemblies with a Self-Mineralized Reaction Center.

Molecular evolution, with self-organization of simple molecules towards complex functional systems, provides a new strategy for biomimetic architectonics and perspectives for understanding the complex processes of life. However, there remain many challenges to fabrication of systems comprising different types of units, which interact with one another to perform desired functions. Challenges arise from a lack of stability, dynamic properties, and functionalities that reconcile with a given environment. A co-assembling fiber system composed of simple peptide and porphyrin is presented. This material is considered a prebiotic assembly of molecules that can be rather stable and flexibly self-functionalized with the assistance of visible light in a "prebiotic soup"; acidic (pH 2), hot (70 °C), and mineral-containing (Na(+) , Ti(4+) , Pt(2+) , and so forth) water. The co-assembled peptide-porphyrin fiber, with self-mineralized reaction centers, may serve as a primitive photobacteria-like cellular model to achieve light harvesting, energy transfer, and ultimately sustainable hydrogen evolution.
On Schur Properties of Random Subsets of Integers

Abstract A classic result of I. Schur [9] asserts that for everyr⩾2 and fornsufficiently large, if the set [n]={1, 2, …, n} is partitioned intorclasses, then at least one of the classes contains a solution to the equationx+y=z. Any such solution withx≠ywill be called aSchur triple. Let us say thatA⊆[n] has theSchur propertyif for every partition (or 2-coloring) ofA=R∪B(forredandblue), there must always be formed somemonochromaticSchur triple, i.e., belonging entirely to eitherRorB. Our goal here is to show thatn1/2is a threshold for the Schur property in the following sense: for anyω=ω(n)→∞, almost all setsA⊆[n] with |A| ωn1/2do.
Compatibility of Rhizobial Genotypes within Natural Populations of Rhizobium leguminosarum Biovar viciae for Nodulation of Host Legumes

ABSTRACT Populations of Rhizobium leguminosarum biovar viciae were sampled from two bulk soils, rhizosphere, and nodules of host legumes, fava bean (Vicia faba) and pea (Pisum sativum) grown in the same soils. Additional populations nodulating peas, fava beans, and vetches (Vicia sativa) grown in other soils and fava bean-nodulating strains from various geographic sites were also analyzed. The rhizobia were characterized by repetitive extragenomic palindromic-PCR fingerprinting and/or PCR-restriction fragment length polymorphism (RFLP) of 16S-23S ribosomal DNA intergenic spacers as markers of the genomic background and PCR-RFLP of a nodulation gene region, nodD, as a marker of the symbiotic component of the genome. Pairwise comparisons showed differences among the genetic structures of the bulk soil, rhizosphere, and nodule populations and in the degree of host specificity within the Vicieae cross-inoculation group. With fava bean, the symbiotic genotype appeared to be the preponderant determinant of the success in nodule occupancy of rhizobial genotypes independently of the associated genomic background, the plant genotype, and the soil sampled. The interaction between one particular rhizobial symbiotic genotype and fava bean seems to be highly specific for nodulation and linked to the efficiency of nitrogen fixation. By contrast with bulk soil and fava bean-nodulating populations, the analysis of pea-nodulating populations showed preferential associations between genomic backgrounds and symbiotic genotypes. Both components of the rhizobial genome may influence competitiveness for nodulation of pea, and rhizosphere colonization may be a decisive step in competition for nodule occupancy.
0 6 0 1 1 3 0 v 2 1 5 A u g 2 0 0 6 Experimentally realizable quantum comparison of coherent states and its applications

Erika Andersson, Marcos Curty, and Igor Jex Department of Physics, SUPA, University of Strathclyde, Glasgow G4 0NG, UK Quantum Information Theory Group, Institut für Theoretische Physik I, and Max-Planck Research Group, Institute of Optics, Information and Photonics, Universität Erlangen-Nürnberg, Staudtstraße 7/B2, 91058 Erlangen, Germany Department of Physics, FNSPE Czech Technical University in Prague Břehová 7, 115 19 Praha 1, Czech Republic (Dated: August 16, 2006)
A Phyletically Rare Gene Promotes the Niche-specific Fitness of an E. coli Pathogen during Bacteremia

In bacteria, laterally acquired genes are often concentrated within chromosomal regions known as genomic islands. Using a recently developed zebrafish infection model, we set out to identify unique factors encoded within genomic islands that contribute to the fitness and virulence of a reference urosepsis isolate—extraintestinal pathogenic Escherichia coli strain CFT073. By screening a series of deletion mutants, we discovered a previously uncharacterized gene, neaT, that is conditionally required by the pathogen during systemic infections. In vitro assays indicate that neaT can limit bacterial interactions with host phagocytes and alter the aggregative properties of CFT073. The neaT gene is localized within an integrated P2-like bacteriophage in CFT073, but was rarely found within other proteobacterial genomes. Sequence-based analyses revealed that neaT homologues are present, but discordantly conserved, within a phyletically diverse set of bacterial species. In CFT073, neaT appears to be unameliorated, having an exceptionally A+T-rich composition along with a notably altered codon bias. These data suggest that neaT was recently brought into the proteobacterial pan-genome from an extra-phyletic source. Interestingly, even in G+C-poor genomes, as found within the Firmicutes lineage, neaT-like genes are often unameliorated. Sequence-level features of neaT homologues challenge the common supposition that the A+T-rich nature of many recently acquired genes reflects the nucleotide composition of their genomes of origin. In total, these findings highlight the complexity of the evolutionary forces that can affect the acquisition, utilization, and assimilation of rare genes that promote the niche-dependent fitness and virulence of a bacterial pathogen.
Physical Activity Level and Associated Factors Among Higher Secondary School Students in Banke, Nepal: A Cross-Sectional Study.

BACKGROUND This study was carried out to assess physical activity level and identify associated factors among higher secondary school students in Banke district, Nepal. METHODS A school-based, cross-sectional descriptive study was conducted among 405 students studying in grades 11 and 12 in 7 higher secondary schools selected randomly. A self-administered questionnaire based on the International Physical Activity Questionnaire was used to measure physical activity level. RESULTS Only 5% of students were found to be inactive, and domestic and transport-related activities were major contributors to total physical activity score. No significant difference existed for total physical activity and domain-specific and activity-specific scores across different age groups when males and females were tested separately. Being male (P = .046), lower economic status (P = .026), living at a distance of less than 30 minutes (P = .007), walking/cycling to school (P < .001), and studying in government school (P < .001) were associated with increased physical activity scores on multivariate logistic regression analysis. CONCLUSION Routine activities such as transport and household chores contributed greatly to total physical activity among students. This study highlights the need for physical activity promotion interventions at school addressing the associated factors and a need for greater focus on leisure-time physical activities.
A distance-based test of association between paired heterogeneous genomic data

MOTIVATION Due to rapid technological advances, a wide range of different measurements can be obtained from a given biological sample including single nucleotide polymorphisms, copy number variation, gene expression levels, DNA methylation and proteomic profiles. Each of these distinct measurements provides the means to characterize a certain aspect of biological diversity, and a fundamental problem of broad interest concerns the discovery of shared patterns of variation across different data types. Such data types are heterogeneous in the sense that they represent measurements taken at different scales or represented by different data structures. RESULTS We propose a distance-based statistical test, the generalized RV (GRV) test, to assess whether there is a common and non-random pattern of variability between paired biological measurements obtained from the same random sample. The measurements enter the test through the use of two distance measures, which can be chosen to capture a particular aspect of the data. An approximate null distribution is proposed to compute P-values in closed-form and without the need to perform costly Monte Carlo permutation procedures. Compared with the classical Mantel test for association between distance matrices, the GRV test has been found to be more powerful in a number of simulation settings. We also demonstrate how the GRV test can be used to detect biological pathways in which genetic variability is associated to variation in gene expression levels in an ovarian cancer sample, and present results obtained from two independent cohorts. AVAILABILITY R code to compute the GRV test is freely available from http://www2.imperial. ac.uk/∼gmontana
Selective attention modulates implicit learning

The effect of selective attention on implicit learning was tested in four experiments using the “contextual cueing” paradigm (Chun & Jiang, 1998, 1999). Observers performed visual search through items presented in an attended colour (e.g., red) and an ignored colour (e.g., green). When the spatial configuration of items in the attended colour was invariant and was consistently paired with a target location, visual search was facilitated, showing contextual cueing (Experiments 1, 3, and 4). In contrast, repeating and pairing the configuration of the ignored items with the target location resulted in no contextual cueing (Experiments 2 and 4). We conclude that implicit learning is robust only when relevant, predictive information is selectively attended.
Small Cell Offloading Through Cooperative Communication in Software-Defined Heterogeneous Networks

To meet the ever-growing demand for a higher communicating rate and better communication quality, more and more small cells are overlaid under the macro base station (MBS) tier, thus forming the heterogeneous networks. Small cells can ease the load pressure of MBS but lack of the guarantee of performance. On the other hand, cooperation draws more and more attention because of the great potential of small cell densification. Some technologies matured in wired network can also be applied to cellular networks, such as software-defined networking (SDN). SDN helps simplify the structure of multi-tier networks. In addition, it is more reasonable for the SDN controller to implement cell coordination. In this paper, we propose a method to offload users from MBSs through small cell cooperation in heterogeneous networks. Association probability is the main indicator of offloading. By using the tools from stochastic geometry, we then obtain the coverage probabilities when users are associated with different types of BSs. All the cell association and cooperation are conducted by the SDN controller. Then, on this basis, we compare the overall coverage probabilities, achievable rate, and energy efficiency with and without cooperation. Numerical results show that small cell cooperation can offload more users from MBS tier. It can also increase the system's coverage performance. As small cells become denser, cooperation can bring more gains to the energy efficiency of the network.
Subject Areas : health and disease and epidemiology Keywords : stem cells , pluripotency , induced pluripotent stem cells , embryonic stem cells

In recent times, the epigenetic study of pluripotency based on cellular reprogramming techniques led to the creation of induced pluripotent stem cells. It has come to represent the forefront of a new wave of alternative therapeutic approaches in the field of stem cell therapy. Progress in drug development has saved countless lives, but there are numerous intractable diseases where curative treatment cannot be achieved through pharmacological intervention alone. Consequently, there has been an unfortunate rise in incidences of organ failures, degenerative disorders and cancers, hence novel therapeutic interventions are required. Stem cells have unique selfrenewal and multilineage differentiation capabilities that could be harnessed for therapeutic purposes. Although a number of mature differentiated cells have been characterized in vitro, few have been demonstrated to function in a physiologically relevant context. Despite fervent levels of enthusiasm in the field, the reality is that other than the employment of haematopoietic stem cells, many other therapies have yet to be thoroughly proven for their therapeutic benefit and safety in application. This review shall focus on a discussion regarding the current status of stem cell therapy, the issues surrounding it and its future prospects with a general background on the regulatory networks underlying pluripotency.
Extension of epipolar image analysis to circular camera movements

Epipolar image analysis is a robust method for 3D scene depth reconstruction that uses all available views of an image sequence simultaneously. It is restricted to horizontal, linear, and equidistant camera movements. In this paper, we present a concept for an extension of epipolar image analysis to other camera configurations like, e.g., circular movements. Instead of searching for straight lines in the epipolar image, we explicitly compute the trajectories of particular points through the image cube. Variation of the unknown depth leads to different curves. From those, the one corresponding to the true depth is selected by evaluating color constancy along the curve. In order to handle occlusions correctly an explicit occlusion compatible ordering scheme is derived for the case of circular movements. To compensate the influence of perspective projection we introduce a depth corrected epipolar image analysis algorithm which we call image cube trajectory analysis (ICT).
Visuospatial information in the retinotectal system of xenopus before correct image formation by the developing eye

The retinotectal pathway of Xenopus laevis is a well‐established experimental model for studying activity‐dependent processes during visual system development. Such processes can be guided by stimulus‐evoked activity patterns, which depend on the refractive characteristics of the eye. Previous work has shown that many animals are hyperopic at early developmental stages due to immature refractive properties. Whether this is also the case for Xenopus laevis is unknown. Here, we measure the focal length of the lens and the size of the eye of embryos at different stages and find that Xenopus laevis exhibits a similar shift from hyperopia to emmetropia. At early stages, immediately after innervation of the tectum by the optic nerve, Xenopus embryos are hyperopic. Soon afterwards the focal length of the lens decreases and the eye converges to a state of emmetropia. Despite being hyperopic we find that some visuospatial information is available to the young circuit. Calculations based on the optical properties of the eye show that even when the animals are hyperopic the blurred retinal image provides a crude spatial resolution. Furthermore, using whole‐cell recordings in the optic tectum combined with visual stimulation through the intact eye, we show that tectal neurons in hyperopic embryos have spatially restricted glutamatergic receptive fields. Our data demonstrate that Xenopus laevis eyes undergo a process of developmental emmetropization, and suggest that despite an initial stage of suboptimal image formation there is potentially enough information to guide activity‐dependent refinements of the retinotectal pathway from the onset of vision. © 2011 Wiley Periodicals, Inc. Develop Neurobiol 72: 507–519, 2012
Detecting Identity by Descent and Homozygosity Mapping in Whole-Exome Sequencing Data

The detection of genetic segments of Identical by Descent (IBD) in Genome-Wide Association Studies has proven successful in pinpointing genetic relatedness between reportedly unrelated individuals and leveraging such regions to shortlist candidate genes. These techniques depend on high-density genotyping arrays and their effectiveness in diverse sequence data is largely unknown. Due to decreasing costs and increasing effectiveness of high throughput techniques for whole-exome sequencing, an influx of exome sequencing data has become available. Studies using exomes and IBD-detection methods within known pedigrees have shown that IBD can be useful in finding hidden genetic candidates where known relatives are available. We set out to examine the viability of using IBD-detection in whole exome sequencing data in population-wide studies. In doing so, we extend GERMLINE, a method to detect IBD from exome sequencing data by finding small slices of matching alleles between pairs of individuals and extending them into full IBD segments. This algorithm allows for efficient population-wide detection in dense data. We apply this algorithm to a cohort of Crohn's Disease cases where whole-exome and GWAS array data is available. We confirm that GWAS-based detected segments are highly accurate and predictive of underlying shared variation. Where segments inferred from GWAS are expected to be of high accuracy, we compare exome-based detection accuracy of multiple detection strategies. We find detection accuracy to be prohibitively low in all assessments, both in terms of segment sensitivity and specificity. Even after isolating relatively long segments beyond 10cM, exome-based detection continued to offer poor specificity/sensitivity tradeoffs. We hypothesize that the variable coverage and platform biases of exome capture account for this decreased accuracy and look toward whole genome sequencing data as a higher quality source for detecting population-wide IBD.
Systematic review of measures and their concepts used in published studies focusing on rehabilitation in the acute hospital and in early post-acute rehabilitation facilities

Purpose: To identify outcome measures cited in published studies focusing on rehabilitation in the acute hospital and in early post-acute rehabilitation facilities, and to identify and quantify the concepts contained in these measures using the ICF as a reference. Methods: Electronic searches of Medline, Embase, CINAHL, Pedro and the Cochrane Library from 1997 to March 2002 were carried out. In a first step, abstracts of the retrieved studies were checked and data on the outcome measures and certain characteristics of the included studies were extracted. In a second step, the items of the questionnaires and their underlying concepts were specified. These concepts were then linked to ICF categories using standardized linkage rules. Results: From the 1,657 abstracts retrieved, 259 studies met the inclusion criteria. In a second step, 277 formal assessment instruments and 351 single clinical measures were retrieved. A total of 1,353 concepts were extracted from the clinical and technical measures. Ninety-six percent of these concepts could be linked to ICF categories. Fifty-six second-level ICF categories representing the concepts contained in the measures. Twenty-six (46%) of the 56 categories belong to the component Body Functions, five (9%) to the component Body Structures, and 25 (45%) to the component Activities and Participation. Conclusions: The ICF provides a valuable reference to identify and quantify the concepts of outcome measures focusing on rehabilitation in the acute hospital and in early post-acute rehabilitation facilities. Our findings indicate a need to define and to agree on ‘what should be measured’ in rehabilitation care to allow for a comparison of patient populations.
Stepwise Approach to Problematic Hypoglycemia in Korea: Educational, Technological, and Transplant Interventions

Impaired awareness of hypoglycemia has been found to be prevalent in 20% to 40% of people with type 1 diabetes. If a similar prevalence exists in Koreans with type 1 diabetes, at a minimum, thousands of people with type 1 diabetes suffer at least one unpredicted episode of severe hypoglycemia per year in Korea. For patients with problematic hypoglycemia, an evidence-based stepwise approach was suggested in 2015. The first step is structured education regarding multiple daily injections of an insulin analog, and the second step is adding a technological intervention, such as continuous subcutaneous insulin infusion or real-time continuous glucose monitoring. The next step is a sensor-augmented pump, preferably with a low glucose suspension feature or very frequent contact, and the final step is islet or pancreas transplantation. In Korea, however, none of these treatments are reimbursed by the National Health Insurance, and thus have not been widely implemented. The low prevalence of type 1 diabetes means that Korean physicians are relatively unfamiliar with the new technologies in this field. Therefore, the roles of new technologies and pancreas or islet transplantation in the treatment of problematic hypoglycemia need to be defined in the current clinical setting of Korea.
Chronic Thrombus Detection With In Vivo Magnetic Resonance Imaging and a Fibrin-Targeted Contrast Agent

Background—Arterial thrombosis plays a critical role in acute coronary syndromes and stroke. Therefore, the ability to detect thrombus in vivo has a significant clinical implication. Magnetic resonance imaging (MRI) has shown promise in noninvasive thrombus detection. However, thrombus characterization and age definition remain difficult. We sought to evaluate the use of a fibrin-targeted peptide (EP-2104R) for MR thrombus detection and to compare this modality with non–contrast-enhanced (NCE) MRI and with Gd-DTPA injection at various ages and time points after thrombus generation. Methods and Results—Carotid artery thrombosis was induced by external injury and stasis in 18 rabbits. T1-weighted MRI was performed before and after contrast agent injection, within 6 hours of thrombus induction, at 48 hours, at 1 week, and every week up to 8 weeks after injury. Correlation with histopathology was performed. The fibrin-targeted contrast agent accurately detected all thrombi, regardless of their size, location, and age. Although thrombus signal intensity after injection decreased with thrombus age (P<0.001), enhancement at 8 weeks was still present. Gd-DTPA injection was not associated with an improvement of thrombus detection. EP-2104R was superior to both NCE and Gd-DTPA injection (P<0.001). Histopathologic examination showed thrombus organization over time. Fibrin was gradually replaced by fibrous tissue. A strong correlation was found between thrombus enhancement and collagen content of the organizing thrombus with time (R=−0.89; P<0.001). Conclusions—In an experimental animal model of carotid thrombosis, we have demonstrated the superiority of a fibrin-targeted MR contrast agent for in vivo detection of chronic or organized thrombus, compared with NCE MRI and Gd-DTPA injection.