Miracle-dz/UniFAR-FTUs huggingface dataset:
Local Normal Forms for First-Order Logic with Applications to Games and Automata

Building on work of Gaifman [Gai82] it is shown that every first-order formula is logically equivalent to a formula of the form ∃ x_1,. ,x_l, \forall y, φ where φ is r-local around y, i.e. quantification in φ is restricted to elements of the universe of distance at most r from y. \par From this and related normal forms, variants of the Ehrenfeucht game for first-order and existential monadic second-order logic are developed that restrict the possible strategies for the spoiler, one of the two players. This makes proofs of the existence of a winning strategy for the duplicator, the other player, easier and can thus simplify inexpressibility proofs. \par As another application, automata models are defined that have, on arbitrary classes of relational structures, exactly the expressive power of first-order logic and existential monadic second-order logic, respectively.
Genes Involved in Control of Galactose Uptake inLactobacillus brevis and Reconstitution of the Regulatory System in Bacillus subtilis

ABSTRACT The heterofermentative lactic acid bacterium Lactobacillus brevis transports galactose and the nonmetabolizable galactose analogue thiomethyl-β-galactoside (TMG) by a permease-catalyzed sugar:H+ symport mechanism. Addition of glucose to L. brevis cells loaded with [14C]TMG promotes efflux and prevents accumulation of the galactoside, probably by converting the proton symporter into a uniporter. Such a process manifests itself physiologically in phenomena termed inducer expulsion and exclusion. Previous evidence suggested a direct allosteric mechanism whereby the phosphocarrier protein, HPr, phosphorylated at serine-46 [HPr(Ser-P)], binds to the galactose:H+ symporter to uncouple sugar transport from proton symport. To elucidate the molecular mechanism of inducer control in L. brevis, we have cloned the genes encoding the HPr(Ser) kinase, HPr, enzyme I, and the galactose:H+ symporter. The sequences of these genes were determined, and the relevant phylogenetic trees are presented. Mutant HPr derivatives in which the regulatory serine was changed to either alanine or aspartate were constructed. The clonedgalP gene was integrated into the chromosome ofBacillus subtilis, and synthesis of the mutant HPr proteins in this organism was shown to promote regulation of GalP, as expected for a direct allosteric mechanism. We have thus reconstituted inducer control in an organism that does not otherwise exhibit this phenomenon. These results are consistent with the conclusion that inducer exclusion and expulsion in L. brevis operates via a multicomponent signal transduction mechanism wherein the presence of glycolytic intermediates such as fructose 1,6-bisphosphate (the intracellular effector), derived from exogenous glucose (the extracellular effector), activates HPr(Ser) kinase (the sensor) to phosphorylate HPr on Ser-46 (the messenger), which binds to the galactose:H+ symporter (the target), resulting in uncoupling of sugar transport from proton symport (the response). This cascade allows bacteria to quickly respond to changes in external sugar concentrations. Understanding the molecular mechanism of inducer control advances our knowledge of the link between metabolic and transport processes in bacteria.
What is the spatial extent of an object?

This paper discusses the question: Can we improve the recognition of objects by using their spatial context? We start from Bag-of-Words models and use the Pascal 2007 dataset. We use the rough object bounding boxes that come with this dataset to investigate the fundamental gain context can bring. Our main contributions are: (I) The result of Zhang et al. in CVPR07 that context is superfluous derived from the Pascal 2005 data set of 4 classes does not generalize to this dataset. For our larger and more realistic dataset context is important indeed. (II) Using the rough bounding box to limit or extend the scope of an object during both training and testing, we find that the spatial extent of an object is determined by its category: (a) well-defined, rigid objects have the object itself as the preferred spatial extent. (b) Non-rigid objects have an unbounded spatial extent : all spatial extents produce equally good results. (c) Objects primarily categorised based on their function have the whole image as their spatial extent. Finally, (III) using the rough bounding box to treat object and context separately, we find that the upper bound of improvement is 26% (12% absolute) in terms of mean average precision, and this bound is likely to be higher if the localisation is done using segmentation. It is concluded that object localisation, if done sufficiently precise, helps considerably in the recognition of objects for the Pascal 2007 dataset.
Mechanobiology of Skeletal Regeneration

Skeletal regeneration is accomplished by a cascade of biologic processes that may include differentiation of pluripotential tissue, endochondral ossification, and bone remodeling. It has been shown that all these processes are influenced strongly by the local tissue mechanical loading history. This article reviews some of the mechanobiologic principles that are thought to guide the differentiation of mesenchymal tissue into bone, cartilage, or fibrous tissue during the initial phase of regeneration. Cyclic motion and the associated shear stresses cause cell proliferation and the production of a large callus in the early phases of fracture healing. For intermittently imposed loading in the regenerating tissue: (1) direct intramembranous bone formation is permitted in areas of low stress and strain; (2) low to moderate magnitudes of tensile strain and hydrostatic tensile stress may stimulate intramembranous ossification; (3) poor vascularity can promote chondrogenesis in an otherwise osteogenic environment; (4) hydrostatic compressive stress is a stimulus for chondrogenesis; (5) high tensile strain is a stimulus for the net production of fibrous tissue; and (6) tensile strain with a superimposed hydrostatic compressive stress will stimulate the development of fibrocartilage. Finite element models are used to show that the patterns of tissue differentiation observed in fracture healing and distraction osteogenesis can be predicted from these fundamental mechanobiologic concepts. In areas of cartilage formation, subsequent endochondral ossification normally will proceed, but it can be inhibited by intermittent hydrostatic compressive stress and accelerated by octahedral shear stress (or strain). Later, bone remodeling at these sites can be expected to follow the same mechanobiologic adaptation rules as normal bone.
Development and psychometric evaluation of the FACE-Q Aging Appraisal Scale and Patient-Perceived Age Visual Analog Scale.

BACKGROUND The primary outcome measures for patients who undergo aesthetic facial procedures are quality of life and satisfaction with appearance. The FACE-Q, a new patient-reported outcome (PRO) instrument composed of independently functioning scales, is designed to measure a broad range of important outcomes in patients who undergo cosmetic surgical and/or nonsurgical facial procedures. OBJECTIVES The authors describe the development and psychometric evaluation of the FACE-Q Aging Appraisal Scale and the FACE-Q Patient-Perceived Age Visual Analog Scale (VAS). METHODS International guidelines for creating PRO instruments were strictly observed throughout development of the FACE-Q scales. Qualitative methods were used to identify the concepts most important to patients who received aesthetic facial procedures. These were turned into "items"-and the resultant FACE-Q Aging Appraisal Scale was field tested, along with the Patient-Perceived Age VAS, in 288 patients who underwent cosmetic surgical and/or nonsurgical facial procedures. RESULTS Rasch measurement theory and traditional psychometric methods confirmed the reliability and validity of the scales. CONCLUSIONS The FACE-Q Aging Appraisal Scale and Patient-Perceived Age VAS are psychometrically sound, condition-specific PRO instruments with excellent reliability and validity. They enable accurate outcome assessments in patients who undergo aesthetic facial procedures.
Efficient rate-distortion optimized mode selection of H.264/AVC intra coding

Rate-distortion optimization (RDO) can significantly improves encoder performance in H.264-like video coding applications. In H.264/AVC, rate-distortion optimization (RDO) method has to code the video by exhaustively trying all the mode combinations including the different intra- and inter-prediction modes. Therefore, the complexity and computation load of video coding in H.264/AVC increase drastically compared to any previous standards. This paper reviewed the conventional fast cost functions of the intra encoder and proposed an enhanced low complex cost function for H.264/AVC intra 4×4 mode selections. The enhanced cost function uses sum of absolute Hadamard-transformed differences (SATD) and mean absolute deviation of the residual block to estimate distortion part of the cost function. A threshold based large coefficients count is also used for estimating the bit-rate part. The proposed method improves the rate-distortion performance of the conventional fast cost functions while maintaining low complexity requirement. As the results, the encoding process can be significantly accelerated with use of the proposed cost function. Simulation results confirmed that the proposed method reduced about 85% of computation of original encoder with negligible rate-distortion performance degradation.
Global burden of Shigella infections: implications for vaccine development and implementation of control strategies.

Few studies provide data on the global morbidity and mortality caused by infection with Shigella spp. ; such estimates are needed, however, to plan strategies of prevention and treatment. Here we report the results of a review of the literature published between 1966 and 1997 on Shigella infection. The data obtained permit calculation of the number of cases of Shigella infection and the associated mortality occurring worldwide each year, by age, and (as a proxy for disease severity) by clinical category, i.e. mild cases remaining at home, moderate cases requiring outpatient care, and severe cases demanding hospitalization. A sensitivity analysis was performed to estimate the high and low range of morbid and fatal cases in each category. Finally, the frequency distribution of Shigella infection, by serogroup and serotype and by region of the world, was determined. The annual number of Shigella episodes throughout the world was estimated to be 164.7 million, of which 163.2 million were in developing countries (with 1.1 million deaths) and 1.5 million in industrialized countries. A total of 69% of all episodes and 61% of all deaths attributable to shigellosis involved children under 5 years of age. The median percentages of isolates of S. flexneri, S. sonnei, S. boydii, and S. dysenteriae were, respectively, 60%, 15%, 6%, and 6% (30% of S. dysenteriae cases were type 1) in developing countries; and 16%, 77%, 2%, and 1% in industrialized countries. In developing countries, the predominant serotype of S. flexneri is 2a, followed by 1b, 3a, 4a, and 6. In industrialized countries, most isolates are S. flexneri 2a or other unspecified type 2 strains. Shigellosis, which continues to have an important global impact, cannot be adequately controlled with the existing prevention and treatment measures. Innovative strategies, including development of vaccines against the most common serotypes, could provide substantial benefits.
Mutual information of non-coherent Rayleigh fading channels with Gaussian input

In this paper, the mutual information of a discrete time Rayleigh fading channel is considered, where neither the transmitter nor the receiver has the knowledge of the channel state information. We derive a closed form expression for the mutual information of single input single output Rayleigh fading channel when the input distribution is complex Gaussian. We compare the channel capacity and the mutual information attained with Gaussian input using the derived closed form expressions. Furthermore, we argue that the mutual information is bounded by the signal to noise ratio with the simulation results showing the sub optimality of Gaussian signalling in non-coherent Rayleigh fading channels.
Interaction of HRC (Histidine-rich Ca2+-Binding Protein) and Triadin in the Lumen of Sarcoplasmic Reticulum*

HRC (histidine-rich Ca2+binding protein) has been identified from skeletal and cardiac muscle and shown to bind Ca2+ with high capacity and low affinity. While HRC resides in the lumen of the sarcoplasmic reticulum, the physiological function of HRC is largely unknown. In the present study, we have performed co-immunoprecipitation experiments and show that HRC binds directly to triadin, which is an integral membrane protein of the sarcoplasmic reticulum. Using a fusion protein binding assay, we further identified the histidine-rich acidic repeats of HRC as responsible for the binding of HRC to triadin. These motifs may represent a novel protein-protein interaction domain. The HRC binding domain of triadin was also localized by fusion protein binding assay to the lumenal region containing the KEKE motif that was previously shown to be involved in the binding of triadin to calsequestrin. Notably, the interaction of HRC and triadin is Ca2+-sensitive. Our data suggest that HRC may play a role in the regulation of Ca2+release from the sarcoplasmic reticulum by interaction with triadin.
A high step-up current fed multi-resonant converter with output voltage doubler

A high step-up current fed multi-resonant converter (CFMRC) has been proposed recently for renewable energy harvesting where the sustainable power sources such as PV panels and fuel cells are characterized by low-voltage, high-current output. An output voltage doubler is applied to the previously proposed CFMRC for the purpose of reducing the turns-ratio of the transformer. Compared to the CFMRC with full bridge rectifier, the CFMRC with output voltage doubler simplifies the transformer structure and hence reduces the cost. By applying the interleaving technique, the ac resistances of the transformer windings are greatly reduced. When running a 150 W prototype at 255 kHz with 23 V input and 350 V output, a peak efficiency of 95.95% is achieved.
Hardware Implementation of Secure Shamir's Secret Sharing Scheme

Shamir's secret sharing scheme is an effective way to distribute secret to a group of shareholders. But this scheme is vulnerable to cheaters and attackers and thus how to protect the system from cheating and attacks is a big problem. In this paper, we proposed to use robust codes and algebraic manipulation detection (AMD) codes to protect the secret sharing module. Simulation and synthesis results show that the proposed architecture can improve the security level significantly even under strong cheating and attack models with some extra area and timing overheads.
Understanding Student Satisfaction in a Mobile Learning Environment: The Role of Internal and External Facilitators

This paper presents and empirically validates a model of student satisfaction with mobile learning. The proposed model draws on Optimal Stimulation Theory and Learning Approach Theory from the psychology and education literature, respectively, and integrates them with prior findings from the Information Systems user satisfaction domain. The proposed model is empirically validated using a field survey of MBA students participating in a Blackberry mobile learning pilot project at a major Canadian university. The results confirm the theoretical analysis, suggesting that external facilitating factors within a mobile learner‘s environment and internal facilitating factors associated with the mobile learner him/herself influence utilitarian and hedonic antecedents to student satisfaction with mobile learning.
In silico abstraction of zinc finger nuclease cleavage profiles reveals an expanded landscape of off-target sites

Gene-editing nucleases enable targeted modification of DNA sequences in living cells, thereby facilitating efficient knockout and precise editing of endogenous loci. Engineered nucleases also have the potential to introduce mutations at off-target sites of action. Such unintended alterations can confound interpretation of experiments and can have implications for development of therapeutic applications. Recently, two improved methods for identifying the off-target effects of zinc finger nucleases (ZFNs) were described–one using an in vitro cleavage site selection method and the other exploiting the insertion of integration-defective lentiviruses into nuclease-induced double-stranded DNA breaks. However, application of these two methods to a ZFN pair targeted to the human CCR5 gene led to identification of largely non-overlapping off-target sites, raising the possibility that additional off-target sites might exist. Here, we show that in silico abstraction of ZFN cleavage profiles obtained from in vitro cleavage site selections can greatly enhance the ability to identify potential off-target sites in human cells. Our improved method should enable more comprehensive profiling of ZFN specificities.
Why are Target Interest Rate Changes so Persistent?

While the degree of policy inertia in central banks' reaction functions is a central ingredient in theoretical and empirical monetary economics, the source of the observed policy inertia in the U.S. is controversial, with tests of competing hypotheses such as interest-smoothing and persistent-shocks theories being inconclusive. This paper employs real time data; nested specifications with flexible time series structures; narratives; interest rate forecasts of the Fed, financial markets, and professional forecasters; and instrumental variables to discriminate competing explanations of policy inertia. The presented evidence strongly favors the interest-smoothing explanation and thus can help resolve a key puzzle in monetary economics.
Citizen scientists document geographic patterns in pollinator communities

It is widely recognized that plants are visited by a diverse community of pollinators that are highly variable in space and time, but biologists are often unable to investigate the pollinator climate across species’ entire ranges. To study the community of pollinators visiting the spring ephemerals Claytonia virginica and Claytonia caroliniana, we assembled a team of citizen scientists to monitor pollinator visitation to plants throughout the species’ ranges. Citizen scientists documented some interesting differences in pollinator communities; specifically, that western C. virginica and C. caroliniana populations are visited more often by the pollen specialist bee Andrena erigeniae and southern populations are visited more often by the bombyliid fly Bombylius major. Differences in pollinator communities throughout the plants’ range will have implications for the ecology and evolution of a plant species, including that differences may affect the male fitness of individual plants or the reproductive success of plant populations, or both.
Asymmetry of the Budding Yeast Tem1 GTPase at Spindle Poles Is Required for Spindle Positioning But Not for Mitotic Exit

The asymmetrically dividing yeast S. cerevisiae assembles a bipolar spindle well after establishing the future site of cell division (i.e., the bud neck) and the division axis (i.e., the mother-bud axis). A surveillance mechanism called spindle position checkpoint (SPOC) delays mitotic exit and cytokinesis until the spindle is properly positioned relative to the mother-bud axis, thereby ensuring the correct ploidy of the progeny. SPOC relies on the heterodimeric GTPase-activating protein Bub2/Bfa1 that inhibits the small GTPase Tem1, in turn essential for activating the mitotic exit network (MEN) kinase cascade and cytokinesis. The Bub2/Bfa1 GAP and the Tem1 GTPase form a complex at spindle poles that undergoes a remarkable asymmetry during mitosis when the spindle is properly positioned, with the complex accumulating on the bud-directed old spindle pole. In contrast, the complex remains symmetrically localized on both poles of misaligned spindles. The mechanism driving asymmetry of Bub2/Bfa1/Tem1 in mitosis is unclear. Furthermore, whether asymmetry is involved in timely mitotic exit is controversial. We investigated the mechanism by which the GAP Bub2/Bfa1 controls GTP hydrolysis on Tem1 and generated a series of mutants leading to constitutive Tem1 activation. These mutants are SPOC-defective and invariably lead to symmetrical localization of Bub2/Bfa1/Tem1 at spindle poles, indicating that GTP hydrolysis is essential for asymmetry. Constitutive tethering of Bub2 or Bfa1 to both spindle poles impairs SPOC response but does not impair mitotic exit. Rather, it facilitates mitotic exit of MEN mutants, likely by increasing the residence time of Tem1 at spindle poles where it gets active. Surprisingly, all mutant or chimeric proteins leading to symmetrical localization of Bub2/Bfa1/Tem1 lead to increased symmetry at spindle poles of the Kar9 protein that mediates spindle positioning and cause spindle misalignment. Thus, asymmetry of the Bub2/Bfa1/Tem1 complex is crucial to control Kar9 distribution and spindle positioning during mitosis.
RNA-Seq Gene Profiling - A Systematic Empirical Comparison

Accurately quantifying gene expression levels is a key goal of experiments using RNA-sequencing to assay the transcriptome. This typically requires aligning the short reads generated to the genome or transcriptome before quantifying expression of pre-defined sets of genes. Differences in the alignment/quantification tools can have a major effect upon the expression levels found with important consequences for biological interpretation. Here we address two main issues: do different analysis pipelines affect the gene expression levels inferred from RNA-seq data? And, how close are the expression levels inferred to the “true” expression levels? We evaluate fifty gene profiling pipelines in experimental and simulated data sets with different characteristics (e.g, read length and sequencing depth). In the absence of knowledge of the ‘ground truth’ in real RNAseq data sets, we used simulated data to assess the differences between the “true” expression and those reconstructed by the analysis pipelines. Even though this approach does not take into account all known biases present in RNAseq data, it still allows to estimate the accuracy of the gene expression values inferred by different analysis pipelines. The results show that i) overall there is a high correlation between the expression levels inferred by the best pipelines and the true quantification values; ii) the error in the estimated gene expression values can vary considerably across genes; and iii) a small set of genes have expression estimates with consistently high error (across data sets and methods). Finally, although the mapping software is important, the quantification method makes a greater difference to the results.