Miracle-dz/UniFAR-FTUs huggingface dataset:
A Novel Algorithm for String Matching with Mismatches

We present an online algorithm to deal with pattern matching in strings. The problem we investigate is commonly known as string matching with mismatches in which the objective is to report the number of characters that match when a pattern is aligned with every location in the text. The novel method we propose is based on the frequencies of individual characters in the pattern and the text. The algorithm consumes minimal space in the form of simple arrays, which reduces the cost overhead to maintain the complex data structures such as suffix trees or automaton.
The Effect of Basketball Training on the Muscle Strength of Adults With Mental Retardation

Tsimaras, VK, Samara, CA, Kotzamanidou, MC, Bassa, EI, Fotiadou, EG, and Kotzamanidis, CM. The effect of basketball training on the muscle strength of adults with mental retardation. J Strength Cond Res 23(9): 2638-2644, 2009-The purpose of this study was to evaluate the effect of basketball training on the muscle strength of adults with mental retardation (MR). Twenty-four adults with and without MR were separated into 3 groups. Eight adults (mean age 25.4 years) with normal IQ constituted the control group (NIQ). Eight adults (mean age 26.5 years) with MR and all participating in a 4-year systematic basketball exercise program constituted the trained group (MR-T), and 8 adults (mean age 25.3 years) with MR exercised occasionally for recreational reasons formed the MR-R group. Parameters measured were isometric and isokinetic concentric and eccentric muscle strength. All subjects performed a leg strength test on a Cybex Norm isokinetic dynamometer. Analysis of variance was used to examine mean differences between the values of the 3 groups. A significance level of 0.05 was used for all tests. The NIQ group showed a statistically significant difference in all measured values compared to the MR groups. The MR-T group presented higher absolute and relative torque scores for both knee extensors and flexors than the MR-R group, whereas the MR-R group presented statistically higher antagonistic activity for both knee extensors and flexors than the MR-T group. In addition, both MR groups presented statistically higher antagonistic activity for both knee extensors and flexors compared to the NIQ group. Data support participation on a systematic and well-designed basketball training program to improve muscle strength levels of adults with MR. Participation in basketball without necessarily focusing on developing specific fitness components may be an effective training strategy for the promotion of strength of adults with MR.
Cross-neutralizing human anti-poliovirus antibodies bind the recognition site for cellular receptor

Significance This study demonstrated that cross-neutralizing anti-poliovirus antibodies bind the site on poliovirus capsid surface that significantly overlaps the binding site of the cellular receptor. A second antibody with similar specificity was isolated by sequential phage display panning, suggesting that cross-reactive anti-poliovirus antibodies may be more prevalent in primates than previously recognized. Binding to the receptor recognition site explains unusually broad specificity of the antibodies. The antibodies bind type 1 and type 2 polioviruses at a slightly different angle, indicating that molecular details of virus–antibody interaction are different and suggesting that further screening or engineering may produce an antibody neutralizing all three serotypes of poliovirus. These results may be used for developing new antiviral strategies for the polio eradication campaign. Most structural information about poliovirus interaction with neutralizing antibodies was obtained in the 1980s in studies of mouse monoclonal antibodies. Recently we have isolated a number of human/chimpanzee anti-poliovirus antibodies and demonstrated that one of them, MAb A12, could neutralize polioviruses of both serotypes 1 and 2. This communication presents data on isolation of an additional cross-neutralizing antibody (F12) and identification of a previously unknown epitope on the surface of poliovirus virions. Epitope mapping was performed by sequencing of antibody-resistant mutants and by cryo-EM of complexes of virions with Fab fragments. The results have demonstrated that both cross-neutralizing antibodies bind the site located at the bottom of the canyon surrounding the fivefold axis of symmetry that was previously shown to interact with cellular poliovirus receptor CD155. However, the same antibody binds to serotypes 1 and 2 through different specific interactions. It was also shown to interact with type 3 poliovirus, albeit with about 10-fold lower affinity, insufficient for effective neutralization. Antibody interaction with the binding site of the cellular receptor may explain its broad reactivity and suggest that further screening or antibody engineering could lead to a universal antibody capable of neutralizing all three serotypes of poliovirus.
PLISS: Detecting and Labeling Places Using Online Change-Point Detection

We present PLISS (Place Labeling through Image Sequence Segmentation), a novel technique for place recognition and categorization from visual cues. PLISS operates on video or image streams and works by segmenting it into pieces corresponding to distinct places in the environment. An online Bayesian change-point detection framework that detects changes to model parameters is used to segment the image stream. Unlike current place recognition methods, in addition to using previously learned place models for labeling, PLISS can also detect and learn a previously unknown place or place category in an online manner. Moreover, since both the inferred boundaries of places (change-points) and the place labels are fully probabilistic, they can indicate when the inference is uncertain. New places and categories are detected using a systematic statistical hypothesis testing framework. We present extensive experiments on a large and difficult image dataset. We validate our claims by comparing results obtained using different types of features and by comparing results from PLISS against the state of the art.
Data Mining and Visualization

Naive-Bayes induction algorithms were previously shown to be surprisingly accurate on many classifi- cation tasks even when the conditional independence assumption on which they are based is violated. However, most studies were done on small databases. We show that in some larger databases, the accuracy of Naive-Bayes does not scale up as well as decision trees. We then propose a new algorithm, NBTree, which induces a hybrid of decision-tree classifiers and Naive-Bayes classifiers: the decision-tree nodes contain univariate splits as regular decision-trees, but the leaves contain Naive-Bayesian classifiers. The approach re-tains the interpretability of Naive-Bayes and decision trees, while resulting in classifiers that frequently outperform both constituents, especially in the larger databases tested.
Targeted tumor dual mode CT/MR imaging using multifunctional polyethylenimine-entrapped gold nanoparticles loaded with gadolinium

Abstract We report the construction and characterization of polyethylenimine (PEI)-entrapped gold nanoparticles (AuNPs) chelated with gadolinium (Gd) ions for targeted dual mode tumor CT/MR imaging in vivo. In this work, polyethylene glycol (PEG) monomethyl ether-modified PEI was sequentially modified with Gd chelator and folic acid (FA)-linked PEG (FA-PEG) was used as a template to synthesize AuNPs, followed by Gd(III) chelation and acetylation of the remaining PEI surface amines. The formed FA-targeted PEI-entrapped AuNPs loaded with Gd (FA-Gd-Au PENPs) were well characterized in terms of structure, composition, morphology, and size distribution. We show that the FA-Gd-Au PENPs with an Au core size of 3.0 nm are water dispersible, colloidally stable, and noncytotoxic in a given concentration range. Thanks to the coexistence of Au and Gd elements within one nanoparticulate system, the FA-Gd-Au PENPs display a better X-ray attenuation property than clinical iodinated contrast agent (e.g. Omnipaque) and reasonable r1 relaxivity (1.1 mM−1s−1). These properties allow the FA-targeted particles to be used as an efficient nanoprobe for dual mode CT/MR imaging of tumors with excellent FA-mediated targeting specificity. With the demonstrated organ biocompatibility, the designed FA-Gd-Au PENPs may hold a great promise to be used as a nanoprobe for CT/MR dual mode imaging of different FA receptor-overexpressing tumors.
Cooperative surveillance of multiple targets using mutual information

This work presents a method to control multiple, but diverse pan-tilt-zoom cameras which are sharing overlapping views of the same spatial location for the purpose of observation of this scene. We cast this control input selection problem in an information-theoretic framework, where we maximise the expected mutual information gain in the scene model with respect to the observation parameters. The scene model yielding this information comprises several dynamic targets, augmented by one which has not yet been detected. The information content of the former is supplied directly by the uncertainties computed using a Sequential Kalman Filter tracker for the observed targets, while the undetected is modelled using a Poisson process for every element of a common ground plane. Together these yield an informationtheoretic utility for each parameter setting for each camera, triggering collaborative explorative behaviour of the system. Overall this yields a framework in which heterogeneous active camera types can be integrated cleanly and consistently, obviating the need for a wide-angle supervisor camera or other artificial restrictions on the camera parameter settings.
Learning Semi-Supervised Representation Towards a Unified Optimization Framework for Semi-Supervised Learning

State of the art approaches for Semi-Supervised Learning (SSL) usually follow a two-stage framework -- constructing an affinity matrix from the data and then propagating the partial labels on this affinity matrix to infer those unknown labels. While such a two-stage framework has been successful in many applications, solving two subproblems separately only once is still suboptimal because it does not fully exploit the correlation between the affinity and the labels. In this paper, we formulate the two stages of SSL into a unified optimization framework, which learns both the affinity matrix and the unknown labels simultaneously. In the unified framework, both the given labels and the estimated labels are used to learn the affinity matrix and to infer the unknown labels. We solve the unified optimization problem via an alternating direction method of multipliers combined with label propagation. Extensive experiments on a synthetic data set and several benchmark data sets demonstrate the effectiveness of our approach.
Decreased salivary output in patients with Gaucher disease.

BACKGROUND Gaucher disease, the most common sphingolipid storage disease, results in accumulation of glucocerebroside in macrophages or "Gaucher cells". In a preliminary screening of 109 patients with type I disease, when asked specifically about dry mouth, approximately one quarter claimed to suffer from this symptom. AIM To ascertain whether decreased salivary output is a feature of Gaucher disease. DESIGN Prospective case-control study. METHODS Salivary output was measured in 65 adult patients and 65 healthy controls using the Saxon test with Hochberg's modification. RESULTS Mean salivary output was 1.91+/-1.19 g/min in the patient group vs. 2.74+/-1.17 g/min in the control group (p<0.001). This difference was greater among males. These results were not improved in the patients receiving enzyme replacement therapy, which is effective in ameliorating most Gaucher-related signs and symptoms. DISCUSSION Recent studies have implicated an association between sicca syndrome and viral hepatitis C infection, which may imply an immunological trigger for these findings, but in this specific cohort, only three patients were reactive for hepatitis C. Follow-up of patients, both untreated and receiving enzyme therapy, is needed to delineate the association with salivary hypofunction, and ascertain whether enzyme therapy may induce sicca symptoms.
Quenching of Steels

This chapter examines the cooling of steels from the austenite region. It describes the processes of determining the severity of quench. The chapter examines the methods to estimate the quench required if the size and shape of the part are known and the required cooling rate is known. The cooling rate correlation is used to calculate the hardness distribution across the diameter of cylinders. The calculations are used to illustrate the sensitivity of the hardness distribution to the severity of quench and the hardenability. The chapter discusses the methods of determining cooling rates in quenched steel components. It describes the formation of residual stresses in materials in which no phase change occurs on cooling. The chapter also examines the effect on the residual stresses of the phase changes in austenite. It provides information on two types of quench cracks in quenched steels, namely, microcracking and gross cracking during quenching.
Minimal alveolar concentration of sevoflurane for maintaining bispectral index below 50 in morbidly obese patients

Morbid obesity is associated with important differences in pharmacokinetics and pharmacodynamics. The aim of this study was to determine minimum alveolar concentration of sevoflurane for maintaining bispectral index (BIS) below 50 (MACBIS50) in morbidly obese patients undergoing bariatric surgery using the Continual Reassessment Method (CRM) method.
CODE (Common Ontology DEvelopment): A Knowledge Integration Approach from Multiple Ontologies

Ontology is used widely as a knowledge representation form. In the recent years, there is substantial growth of ontology utilization and development in different application domains that requires standardization and semantic interoperability. The increasing number in ontology development leads to overlapping in domain ontologies. Our approach called CODE (Common Ontology Development) is created to address the need for knowledge integration and reuse from distributed knowledge across multiple underlying ontologies. CODE is fully automated and it is a complete framework that aims to preserve source ontology knowledge. It uses natural language processing and scenario-based rules to ensure the accuracy of the integration mechanism. In addition, CODE can be used to merge more than two ontologies at the same time. To evaluate knowledge preservation and correctness in the proposed approach, SPARQL queries are used on the new integrated ontology and the results are verified against the source ontologies.
Current Exercise Behaviors Of Breast Cancer Patients Diagnosed With Chemotherapy-induced Peripheral Neuropathy

Introduction: Chemotherapy-induced peripheral neuropathy (CIPN) is a common, dose-limiting effect of cancer therapy. The neuropathic pain associated with CIPN often has negative implications on an individual's quality of life (QOL) and has long been recognized as one of the more difficult types of pain to treat. Treatment of neuropathic pain due to CIPN often requires a multidisciplinary approach, with much attention focused on the use of pharmacological therapies. However, in most instances, these agents have been shown to have additional negative side effects for cancer patients. Thus, other interventions that address the symptoms of CIPN should be considered. One such possible intervention is exercise rehabilitation, which has previously been reported effective in attenuating numerous cancer treatment-related toxicities and enhancing the QOL of patients. However, to our knowledge, there have been no published clinical trials examining the role of exercise in preserving neurological function following chemotherapy. As such, the purpose of this investigation was to examine the current exercise habits of breast cancer patients who are diagnosed with CIPN and the impact on pain and QOL. Methods: 300 women listed in the Breast Cancer Registry of Greater Cincinnati database were recruited by mail and asked to complete three questionnaires (McGill QOL, Leeds Assessment of Neuropathic Symptoms and Signs, and Current Exercise Behaviors). Data was analyzed at the 0.05 level of significance using a student's t-test and a Pearson's product moment correlation. Results: 134 completed surveys were returned and analyzed (44.6% response rate). Overall, QOL and exercise behaviors were moderately correlated (r = 0.56). Patients reported exercising an average of 2.3 d/wk and an overall QOL of 4.7. Of the patients completing the recommended amount of physical activity (EX, n = 21), QOL was 6.3, which was significantly higher than patients who did not meet these recommendations (SED, n = 113, p<0.001). Likewise, only 15% of EX patients reported experiencing pain compared to 72% of SED patients (p<0.001). Conclusions: Based on these data, it seems likely that an exercise intervention would be successful in attenuating symptoms of CIPN and improving the overall QOL of breast cancer patients.
Evolution of Social Insect Polyphenism Facilitated by the Sex Differentiation Cascade

The major transition to eusociality required the evolution of a switch to canalize development into either a reproductive or a helper, the nature of which is currently unknown. Following predictions from the ‘theory of facilitated variation’, we identify sex differentiation pathways as promising candidates because of their pre-adaptation to regulating development of complex phenotypes. We show that conserved core genes, including the juvenile hormone-sensitive master sex differentiation gene doublesex (dsx) and a krüppel homolog 2 (kr-h2) with putative regulatory function, exhibit both sex and morph-specific expression across life stages in the ant Cardiocondyla obscurior. We hypothesize that genes in the sex differentiation cascade evolved perception of alternative input signals for caste differentiation (i.e. environmental or genetic cues), and that their inherent switch-like and epistatic behavior facilitated signal transfer to downstream targets, thus allowing them to control differential development into morphological castes.
Diabetes Susceptibility Genes Pdx1 and Clec16a Function in a Pathway Regulating Mitophagy in β-Cells

Mitophagy is a critical regulator of mitochondrial quality control and is necessary for elimination of dysfunctional mitochondria to maintain cellular respiration. Here, we report that the homeodomain transcription factor Pdx1, a gene associated with both type 2 diabetes and monogenic diabetes of the young, regulates mitophagy in pancreatic β-cells. Loss of Pdx1 leads to abnormal mitochondrial morphology and function as well as impaired mitochondrial turnover. High-throughput expression microarray and chromatin occupancy analyses reveal that Pdx1 regulates the expression of Clec16a, a type 1 diabetes gene and itself a key mediator of mitophagy through regulation of the E3 ubiquitin ligase Nrdp1. Indeed, expression of Clec16a and Nrdp1 are both reduced in Pdx1 haploinsufficient islets, and reduction of Pdx1 impairs fusion of autophagosomes containing mitochondria to lysosomes during mitophagy. Importantly, restoration of Clec16a expression after Pdx1 loss of function restores mitochondrial trafficking during mitophagy and improves mitochondrial respiration and glucose-stimulated insulin release. Thus, Pdx1 orchestrates nuclear control of mitochondrial function in part by controlling mitophagy through Clec16a. The novel Pdx1-Clec16a-Nrdp1 pathway we describe provides a genetic basis for the pathogenesis of mitochondrial dysfunction in multiple forms of diabetes that could be targeted for future therapies to improve β-cell function.
Gossip-based aggregation in large dynamic networks

As computer networks increase in size, become more heterogeneous and span greater geographic distances, applications must be designed to cope with the very large scale, poor reliability, and often, with the extreme dynamism of the underlying network. Aggregation is a key functional building block for such applications: it refers to a set of functions that provide components of a distributed system access to global information including network size, average load, average uptime, location and description of hotspots, and so on. Local access to global information is often very useful, if not indispensable for building applications that are robust and adaptive. For example, in an industrial control application, some aggregate value reaching a threshold may trigger the execution of certain actions; a distributed storage system will want to know the total available free space; load-balancing protocols may benefit from knowing the target average load so as to minimize the load they transfer. We propose a gossip-based protocol for computing aggregate values over network components in a fully decentralized fashion. The class of aggregate functions we can compute is very broad and includes many useful special cases such as counting, averages, sums, products, and extremal values. The protocol is suitable for extremely large and highly dynamic systems due to its proactive structure---all nodes receive the aggregate value continuously, thus being able to track any changes in the system. The protocol is also extremely lightweight, making it suitable for many distributed applications including peer-to-peer and grid computing systems. We demonstrate the efficiency and robustness of our gossip-based protocol both theoretically and experimentally under a variety of scenarios including node and communication failures.
Rheology of blood.

The non-Newtonian flow properties of resuspended red cells were determined in vitro by means of a capillary viscometer. In order to evaluate the rheological effect of the suspending medium, viscosity measurements were made over a wide range of shearing stresses using both plasma and an acid-citrate-dextrose solution as diluents. At low shearing stresses, the plasma exhibited non-Newtonian flow behavior. Using a technique of treating the data to obtain rate-of-shear versus shearing-stress curves without prior assumption of a flow equation showed that whole blood over a wide range of shear stresses and a twofold range of capillary radii did not show any dependence of the viscosity on the capillaries employed. This procedure was also used to examine the data of other workers. In an attempt to determine the shape factor for the red cell, an extrapolation to infinite dilution and zero rate of shear was made. The shape factor can be estimated to be 2.5±1.5 for red cell.