Miracle-dz/UniFAR-FTUs huggingface dataset:
Biochemical Characterization of Highly Purified Leucine-Rich Repeat Kinases 1 and 2 Demonstrates Formation of Homodimers

Leucine-rich repeat kinase 1 and 2 (LRRK1 and LRRK2) are large multidomain proteins containing kinase, GTPase and multiple protein-protein interaction domains, but only mutations in LRRK2 are linked to familial Parkinson's disease (PD). Independent studies suggest that LRRK2 exists in the cell as a complex compatible with the size of a dimer. However, whether this complex is truly a homodimer or a heterologous complex formed by monomeric LRRK2 with other proteins has not been definitively proven due to the limitations in obtaining highly pure proteins suitable for structural characterization. Here, we used stable expression of LRRK1 and LRRK2 in HEK293T cell lines to produce recombinant LRRK1 and LRRK2 proteins of greater than 90% purity. Both purified LRRKs are folded, with a predominantly alpha-helical secondary structure and are capable of binding GTP with similar affinity. Furthermore, recombinant LRRK2 exhibits robust autophosphorylation activity, phosphorylation of model peptides in vitro and ATP binding. In contrast, LRRK1 does not display significant autophosphorylation activity and fails to phosphorylate LRRK2 model substrates, although it does bind ATP. Using these biochemically validated proteins, we show that LRRK1 and LRRK2 are capable of forming homodimers as shown by single-particle transmission electron microscopy and immunogold labeling. These LRRK dimers display an elongated conformation with a mean particle size of 145 Å and 175 Å respectively, which is disrupted by addition of 6M guanidinium chloride. Immunogold staining revealed double-labeled particles also in the pathological LRRK2 mutant G2019S and artificial mutants disrupting GTPase and kinase activities, suggesting that point mutations do not hinder the dimeric conformation. Overall, our findings indicate for the first time that purified and active LRRK1 and LRRK2 can form dimers in their full-length conformation.
Comparison of energy expenditure elevations after submaximal and supramaximal running.

Although exercise intensity has been identified as a major determinant of the excess postexercise oxygen consumption (EPOC), no studies have compared the EPOC after submaximal continuous running and supramaximal interval running. Eight male middle-distance runners [age = 2.1 +/- 3.1 (SD) yr; mass = 67.8 +/- 5.1 kg; maximal oxygen consumption (VO2max) = 69.2 +/- 4.0 ml.kg-1.min-1] therefore completed two equated treatments of treadmill running (continuous running: 30 min at 70% VO2max; interval running: 20 x 1-min intervals at 105% VO2max with intervening 2-min rest periods) and a control session (no exercise) in a counter-balanced research design. The 9-h EPOC values were 6.9 +/- 3.8 and 15.0 +/- 3.3 liters (t-test:P = 0.001) for the submaximal and supramaximal treatments, respectively. These values represent 7.1 and 13.8% of the net total oxygen cost of both treatments. Notwithstanding the higher EPOC for supramaximal interval running compared with submaximal continuous running, the major contribution of both to weight loss is therefore via the energy expended during the actual exercise.
Comprehensive Indoor Smoking Bans and Smoking Prevalence: Evidence from the BRFSS

In an effort to reduce exposure to secondhand smoke, many governments have enacted smoke-free laws in public spaces. To the extent that smoke-free laws change perceptions, norms, and attitudes about tobacco use, these laws may also reduce the prevalence and intensity of cigarette consumption. Using nationally representative data on over four million individuals spanning 15 years, we study the average effect of comprehensive, state-level indoor smoking bans on smoking prevalence in the United States. Our research design exploits within-state variation in smoking prevalence, as well as the rapid diffusion of comprehensive bans across states between 2002 and 2010. Our results suggest that a comprehensive indoor smoking ban is associated with a 2.35 percent to 3.29 percent average reduction in smoking prevalence, a range that is robust to various specifications. These effects are roughly equivalent to a $0.95 to $1.33 increase in the average state’s cigarette tax in 2010. Finally, we demonstrate that state-level indoor bans in bars may significantly decrease smoking prevalence in specific subpopulations, particularly young, female, low-income, and binge-drinking individuals.
Restricted algebras on inverse semigroups III, Fourier algebra

The Fourier and Fourier-Stieltjes algebras $A(G)$ and $B(G)$ of a locally compact group $G$ are introduced and studied in 60's by Piere Eymard in his PhD thesis. If $G$ is a locally compact abelian group, then $A(G)\simeq L^1(\hat{G})$, and $B(G)\simeq M(\hat{G})$, via the Fourier and Fourier-Stieltjes transforms, where $\hat{G}$ is the Pontryagin dual of $G$. Recently these algebras are defined on a (topological or measured) groupoid and have shown to share many common features with the group case. This is the last in a series of papers in which we have investigated a "restricted" form of these algebras on a unital inverse semigroup $S$.
Mutual Information for Testing Gene-Environment Interaction

Despite current enthusiasm for investigation of gene-gene interactions and gene-environment interactions, the essential issue of how to define and detect gene-environment interactions remains unresolved. In this report, we define gene-environment interactions as a stochastic dependence in the context of the effects of the genetic and environmental risk factors on the cause of phenotypic variation among individuals. We use mutual information that is widely used in communication and complex system analysis to measure gene-environment interactions. We investigate how gene-environment interactions generate the large difference in the information measure of gene-environment interactions between the general population and a diseased population, which motives us to develop mutual information-based statistics for testing gene-environment interactions. We validated the null distribution and calculated the type 1 error rates for the mutual information-based statistics to test gene-environment interactions using extensive simulation studies. We found that the new test statistics were more powerful than the traditional logistic regression under several disease models. Finally, in order to further evaluate the performance of our new method, we applied the mutual information-based statistics to three real examples. Our results showed that P-values for the mutual information-based statistics were much smaller than that obtained by other approaches including logistic regression models.
Detection of Immunoglobulin G Antibodies to Neospora caninum in Humans: High Seropositivity Rates in Patients Who Are Infected by Human Immunodeficiency Virus or Have Neurological Disorders

ABSTRACT Considering that little is known about the epidemiology of Neospora caninum infection in humans, particularly in populations with high Toxoplasma gondii infection rates, the present study aimed to investigate the presence of antibodies to N. caninum in T. gondii-seropositive and -seronegative individuals. A total of 256 serum samples divided into four groups (61 samples from human immunodeficiency virus [HIV]-positive patients, 50 samples from patients with neurological disorders, 91 samples from newborns, and 54 samples from healthy subjects) were assessed for N. caninum and T. gondii serologies by indirect fluorescent-antibody test, enzyme-linked immunosorbent assay, and immunoblotting (IB). Immunoglobulin G antibodies to N. caninum were predominantly detected in HIV-infected patients (38%) and patients with neurological disorders (18%), while newborns and healthy subjects showed lower seropositivity rates (5% and 6%, respectively). Seropositivity to N. caninum was significantly associated with seropositivity to T. gondii in both HIV-infected patients and patients with neurological disorders. Seroreactivity to N. caninum was confirmed by IB, with positive sera predominantly recognizing the 29-kDa antigen of N. caninum. The results of this study indicate the presence of N. caninum infection or exposure in humans, particularly in HIV-infected patients or patients with neurological disorders, who could have opportunistic and concurrent infections with T. gondii. These findings may bring a new concern for the unstable clinical health of HIV-infected patients and the actual role of N. caninum infection in immunocompromised patients.
Developmental Plasticity in Macrophiothrix Brittlestars: Are Morphologically Convergent Larvae Also Convergently Plastic?

The pluteus larval forms of sea urchins (echinoids) and brittlestars (ophiuroids) use an internal skeleton to project arms that bear a long ciliated band used in swimming and feeding. The length of this ciliated band influences rates of maximum food clearance for larvae of both echinoderm classes and affects rates of growth and development in the plankton. Phylogenetic and morphological evidence, however, tend to support the view that the pluteus morphologies of the two classes are independently derived. Studies with echinoplutei have shown that investment in skeletal growth and ciliated band length changes in response to food conditions, with poorly fed larvae investing more in growth of the larval skeleton and arms either absolutely or in relation to other larval or developing postlarval structures. We present evidence for similar plasticity of skeletal growth in ophioplutei. We examined four species in the brittlestar genus Macrophiothrix that spanned a 3.8-fold range in egg size. Sibling larvae in 14 male-female crosses were reared with high (H) or low (L) food rations, and measurements were recorded for five skeletal arm rods and three non-arm body dimensions. The expression of adaptive plasticity (significantly longer arms in L versus H cultures on a given day) was apparent for most crosses in M. koehleri, the species with the smallest egg size. In the single cross for M. longipeda, larvae from L cultures had longer arms for their body length or stomach width than did larvae from H cultures. In these cases, plasticity was similar in timing, persistence, and magnitude to previously published results from echinoplutei. If internal skeletons are independently derived in the two classes, then plasticity in the expression of this homoplastic trait may itself be homoplastic.
Vertical Coupling From the Lower Atmosphere to the Ionosphere: Observations Inferred From Indian MST Radar, GPS Radiosonde, Ionosonde, Magnetometer, OLR (NOAA), and SABER/TIMED Instrument Over Gadanki

Simultaneous wind observations from Mesosphere Stratosphere Troposphere (MST) radar collectively with Global Positioning System (GPS) radiosonde over Gadanki, covering altitude range of 3.6–20 km (January–December 2009; 365 days), divulge the propagation of lower atmospheric waves up to the ionosphere. It is combined with temperature data (20–110 km) observed from Sounding of the Atmosphere using the Broadband Emission Radiometry (SABER) instrument onboard Thermosphere Ionosphere Mesosphere Energetics and Dynamics (TIMED) satellite, ionosonde observations, and daily Outgoing Longwave Radiation (OLR) data acquired from the National Ocean and Atmospheric Administration (NOAA; centered around Gadanki [13.5°N, 79.2°E]) for the same time period. Long‐period oscillations with periodicities of ~64, ~32, and ~21 days are witnessed along with the well‐known oscillations of ~16, ~6.4, and ~5.3 days. Most of the long‐period oscillations are dominantly perceived during the summer months (April–June 2009), which can even exist up to September. These long‐period oscillations are found to propagate from lower tropospheric heights up to ionospheric heights with large vertical wavelengths (~300–400 km, in some cases) near to transition zones of atmospheric layers (e.g., tropopause, stratopause, and mesopause). Signatures of vertical coupling of atmosphere through large vertical wavelengths (indicating possible intraseasonal connections) is clearly observed in the equatorial electrojet current and the peak plasma frequencies of ionospheric layers (E and F regions). Noticeable reduction of the wave oscillations in spatial scale with upsurge in spatial damping is evidently visible, in the tropical stratosphere and mesosphere, which can be attributed to stratospheric ozone.
Intimate partner violence as a factor associated with risky sexual behaviours and alcohol misuse amongst men in South Africa

ABSTRACT Globally intimate partner violence (IPV) is a public health problem that can be perpetrated by both males and females, although males are more likely to inflict severe IPV-related injuries on their female partners. In low- and middle-income countries like South Africa, few studies have conducted research to determine whether IPV perpetration by men may be a risk factor for engaging in other risk behaviours. The aim of this study is to determine whether IPV perpetration by men is a risk factor for engaging in other risk behaviours with a particular focus on risky sexual behaviours and alcohol misuse. The data for this study were drawn from a multilevel intervention study, which addressed the nexus of alcohol abuse and HIV prevention among men in South Africa. Men were screened and recruited from informal drinking places within 12 communities situated in one of the oldest, predominantly Xhosa-speaking African townships in Cape Town. Univariate and multivariate logistic regression models were used to analyse the associations between IVP and potential explanatory variables. Of the 975 men included in the survey, 39.9% reported to have been involved in Intimate Partner Violence. IPV perpetration was significantly more likely among men who reported having a child [OR 1.51 (1.07–2.14) p = . 019], having a casual sexual partner [OR 1.51 (1.11–2.05) p = . 008], and those with possible alcohol dependence [OR 3.46 (1.17–10.20) p = . 024]. IPV was significantly less likely among men with matric educational qualification than those with no education [OR 0.30 (95% CI: 0.09–1.02) p = . 053] and among those who reported using a condom at last sex [OR 0.69 (0.50–0.97) p = . 034]. We therefore recommend that interventions aimed at reducing IPV need to address risky sexual and drinking behaviours amongst men simultaneously, while also focusing on intimate relationship power dynamics and gendered norms amongst couples.
New Path Based Index Structure for Processing CAS Queries over XML Database

Querying nested data has become one of the most challenging issues for retrieving desired information from the Web. Today diverse applications generate a tremendous amount of data in different formats. These data and information exchanged on the Web are commonly expressed as nested representation such as XML, JSON, etc. Unlike the traditional database system, they don't have a rigid schema. In general, the nested data is managed by storing data and its structures separately which significantly reduces the performance of data retrieving. Ensuring efficiency of processing queries which locates the exact positions of the elements has become a big challenging issue. There are different indexing structures which have been proposed in the literature to improve the performance of the query processing on the nested structure. Most of the past researches on nested structure concentrate on the structure alone. This paper proposes new index structure which combines siblings of the terminal nodes as one path which efficiently processes twig queries with less number of lookups and joins. The proposed approach is compared with some of the existing approaches. The results also show that they are processed with better performance compared to the existing ones.
Comparison of conventional and step-wise shockwave lithotripsy in management of urinary calculi.

PURPOSE In this clinical study, our aim was to evaluate the results of conventional and step-wise shockwave lithotripsy (SWL) in the management of urinary calculi. PATIENTS AND METHODS Fifty consecutive patients seen in our outpatient urology clinic were included and randomized in the clinical study. SWL was performed using a Dornier Compact Delta instrument. Treatment energy was set on 13 kV in the conventional group. In the step-wise SWL group, the patients were subjected to gradually increased (with every 500 shocks) output voltage as 11, 12, and 13 kV, respectively. The SWL session was completed with 13 kV thereafter. The maximum number of shocks in both groups was limited to 3,000. RESULTS Twenty-five patients in the conventional group and 25 patients in the step-wise SWL were included. The mean ages in the step-wise SWL group and the conventional group were 39.9 and 41.4 years (P > 0.05), respectively. The mean stone size was 0.83 +/- 0.51 cm in the step-wise SWL group and 0.70 +/- 0.41 cm in the conventional group (P > 0.05). There was no difference between the two groups as to the localization of stones in the ureter or kidney. Also, no statistical difference was observed in the number of lithotripsy treatments between the two groups. When we compared the results of two treatment procedures 8 weeks after the initial treatment, the success rate was significantly higher in the step-wise SWL group than in the conventional group (stone-free rate 96% (24/25) v 72% (18/25), P < 0.05)). CONCLUSIONS Step-wise SWL yielded better outcomes than conventional SWL without increased morbidity. Stepwise SWL can be considered as a management option for urinary calculi.
Gathering and ranking photos of named entities with high precision, high recall, and diversity

Knowledge-sharing communities like Wikipedia and automated extraction methods like those of DBpedia enable the construction of large machine-processible knowledge bases with relational facts about entities. These endeavors lack multimodal data like photos and videos of people and places. While photos of famous entities are abundant on the Internet, they are much harder to retrieve for less popular entities such as notable computer scientists or regionally interesting churches. Querying the entity names in image search engines yields large candidate lists, but they often have low precision and unsatisfactory recall. Our goal is to populate a knowledge base with photos of named entities, with high precision, high recall, and diversity of photos for a given entity. We harness relational facts about entities for generating expanded queries to retrieve different candidate lists from image search engines. We use a weighted voting method to determine better rankings of an entity's photos. Appropriate weights are dependent on the type of entity (e.g., scientist vs. politician) and automatically computed from a small set of training entities. We also exploit visual similarity measures based on SIFT features, for higher diversity in the final rankings. Our experiments with photos of persons and landmarks show significant improvements of ranking measures like MAP and NDCG, and also for diversity-aware ranking.
Towards heterogeneous robot teams for disaster mitigation: Results and performance metrics from RoboCup rescue

Urban Search and Rescue is a growing area of robotic research. The RoboCup Federation has recognized this, and has created the new Virtual Robots competition to complement its existing physical robot and agent competitions. In order to successfully compete in this competition, teams need to field multi‐robot solutions that cooperatively explore and map an environment while searching for victims. This paper presents the results of the first annual RoboCup Rescue Virtual competition. It provides details on the metrics used to judge the contestants as well as summaries of the algorithms used by the top four teams. This allows readers to compare and contrast these effective approaches. Furthermore, the simulation engine itself is examined and real‐world validation results on the engine and algorithms are offered. © 2007 Wiley Periodicals, Inc.
Disruption of gingipain oligomerization into non-covalent cell-surface attached complexes

Abstract RgpA and Kgp gingipains are non-covalent complexes of endoprotease catalytic and hemagglutinin-adhesin domains on the surface of Porphyromonas gingivalis. A motif conserved in each domain has been suggested to function as an oligomerization motif. We tested this hypothesis by mutating motif residues to hexahistidine or insertion of hexahistidine tag to disrupt the motif within the Kgp catalytic domain. All modifications led to the secretion of entire Kgp activity into the growth media, predominantly in a form without functional His-tag. This confirmed the role of the conserved motif in correct posttranslational proteolytic processing and assembly of the multidomain complexes.
Gaussian Process Networks

In this paper we address the problem of learning the structure of a Bayesian network in domains with continuous variables. This task requires a procedure for comparing different candidate structures. In the Bayesian framework, this is done by evaluating the marginal likelihood of the data given a candidate structure. This term can be computed in closed-form for standard parametric families (e.g., Gaussians), and can be approximated, at some computational cost, for some semi-parametric families (e.g., mixtures of Gaussians). We present a new family of continuous variable probabilistic networks that are based on Gaussian Process priors. These priors are semiparametric in nature and can learn almost arbitrary noisy functional relations. Using these priors, we can directly compute marginal likelihoods for structure learning. The resulting method can discover a wide range of functional dependencies in multivariate data. We develop the Bayesian score of Gaussian Process Networks and describe how to learn them from data. We present empirical results on artificial data as well as on real-life domains with non-linear dependencies.
Small Cell Tumors of Bone

Bone tumors are fortunately rare, but small cell tumors of bone are a relatively common subset of these lesions. They comprise of a diverse group of primary and metastatic neoplasms in both children and adults. The most common small cell tumors of bone include Ewing sarcoma/primitive neuroectodermal tumor, small cell osteosarcoma, multiple myeloma, lymphoma, leukemia, neuroblastoma, rhabdomyosarcoma, and Langerhans cell histiocytosis. Although each entity has its distinctive features, the differential diagnosis of this group of tumors is still challenging because they are all “small, blue, and round cell tumors”, histologically. The correct diagnosis of small cell tumors of bone depends on an evaluation of clinical, radiologic, pathologic, and genetic features. Patients' age and sex are very important, as are the signs and symptoms at presentation. Radiologically, which bone is involved, the specific portion of the bone (epiphysis, metaphysis, or diaphysis; cortex vs. medulla) involved, and the radiographic manifestations (lytic, blastic, or mixed lytic and blastic) are also often critical parameters for the diagnosis. In recent years, with a better understanding of the molecular and cytogenetic background of several small cell tumors, more accurate diagnoses have been supported by the clinicopathologic criteria and by a panel of immunohistochemical studies. In this review we will provide an overview of the clinical, radiologic, pathologic, and genetic characteristics of these tumors.