Miracle-dz/UniFAR-FTUs huggingface dataset:
Properties of L-methionine gamma-lyase from Pseudomonas ovalis.

The distribution of bacterial L-methionine gamma-lyase (L-methionine methanethiollyase (deaminating) (EC 4.4.1.11) was investigated, and Pseudomonas ovalis (IFO 3738) was found to have the highest activity of enzyme, which was inducibly formed by addition of L-methionine to the medium. L-Methionine gamma-lyase, purified to homogeneity from Ps. ovalis, has a molecular weight of about 173 000 and consists of nonidentical subunits (mol wt: 40 000 and 48 000). The enzyme exhibits absorption maxima at 278 and 420 nm, and a shoulder around 330 nm, which are independent of the pH (6.0 to 10.0), and contains 4 mol of pyridoxal 5'-phosphate per mol of the enzyme. The formyl group of pyridoxal 5'-phosphate is bound in an aldimine linkage to the epsilon-amino group of lysine residues of the protein. The holoenzyme is resolved to the apoenzyme by incubation with hydroxylamine, and reconstituted by addition of pyridoxal 5'-phosphate. The enzyme activity is significantly affected by both carbonyl and sulfhydryl reagents. L-Methionine gamma-lyase catalyzes alpha,gamma- and alpha,beta-elimination reactions of, in addition to L-methionine, several derivatives of L-methionine and L-cysteine, e.g., L-ethionine, DL-methionine sulfone, L-homocysteine, and S-methyl-L-cysteine. The enzyme catalyzes also gamma-replacement reactions of the thiomethyl group of methionine with various alkanethiols (C2-C7), arylthio alcohols (benzenethiol and beta-naphthalenethiol) and the derivatives of ethanethiol (2-mercaptoethanol and cysteamine) to yield the corresponding S-substituted homocysteine. The thiomethyl group of S-methyl-L-cysteine also is replaced by ethanethiol to form S-ethyl-L-cysteine.
Empirical Likelihood-Based ANOVA for Trimmed Means

In this paper, we introduce an alternative to Yuen’s test for the comparison of several population trimmed means. This nonparametric ANOVA type test is based on the empirical likelihood (EL) approach and extends the results for one population trimmed mean from Qin and Tsao (2002). The results of our simulation study indicate that for skewed distributions, with and without variance heterogeneity, Yuen’s test performs better than the new EL ANOVA test for trimmed means with respect to control over the probability of a type I error. This finding is in contrast with our simulation results for the comparison of means, where the EL ANOVA test for means performs better than Welch’s heteroscedastic F test. The analysis of a real data example illustrates the use of Yuen’s test and the new EL ANOVA test for trimmed means for different trimming levels. Based on the results of our study, we recommend the use of Yuen’s test for situations involving the comparison of population trimmed means between groups of interest.
Serum Digoxin Levels After Concomitant Ticarcillin and Clavulanic Acid Administration

Summary Recently it has been recognized that steady-state serum digoxin concentrations may increase or fall to ineffective levels when the glycoside is administered together with several antibiotics. Our study was designed to assess if serum digoxin levels may be modified by the concomitant use of a ticarcillin and clavulanic acid. The study was carried out in 15 hospitalized patients suffering from exacerbation of their chronic bronchitis without liver disease and renal failure. Serum digoxin levels were not significantly modified by the concomitant use of a ticarcillin and clavulanic acid, although peak digoxin serum concentrations were slightly lower. However, the average time to achieve the maximum concentration and area under the curve over 24 h did not change.
Una aproximacion basada en corpus para la deteccion del foco g eografico en el texto A corpus-based approach to geographical focus detection in text

The geographical focus of a document identifies the relevant locations mentioned in text. This paper presents a corpus-based approach to detecting the geographical focus in documents. Despite other approaches focused on using solely geographical information, our proposal employs all the textual information included in the corpus under the assumption that the presence of particular names of persons, events, and even common terms can definitely help to solve this task. In order to validate our hypothesis, a study was carried out on a corpus of georeferenced news that took place between 2008 and 2011. Moreover, this temporal distribution al- lowed to carry out a study on the evolution of the performance of the classifier and the most representative terms for different locations over time.
Functional consequences of compartmentalization of synaptic input

Intra-axonal recordings of stomatogastric nerve axon 1 (SNAX1) indicate that there are synaptic inputs onto the SNAX1 terminals in the stomatogastric ganglion (STG) of the crab Cancer borealis (Nusbaum et al., 1992b). To determine whether this synaptic input only influenced SNAX1 activity within the STG, we identified the SNAX1 soma in the commissural ganglion (CoG). We found that this neuron has a neuropilar arborization in the CoG and also receives synaptic inputs in this ganglion. Based on its soma location, we have renamed this neuron modulatory commissural neuron 1 (MCN1). While intracellular stimulation of MCN1soma and MCN1SNAX has the same excitatory effects on the STG motor patterns, MCN1 receives distinct synaptic inputs in the STG and CoG. Moreover, the synaptic input that MCN1 receives within the STG compartmentalizes its activity. Specifically, the lateral gastric (LG) neuron synaptically inhibits MCN1SNAX-initiated activity within the STG (Nusbaum et al., 1992b), and while LG did not inhibit MCN1soma- initiated activity in the CoG, it did inhibit these MCN1 impulses when they arrived in the STG. As a result, during MCN1soma-elicited gastric mill rhythms, MCN1soma is continually active in the CoG but its effects are rhythmically inhibited in the STG by LG neuron impulse bursts. One functional consequence of this local control of MCN1 within the STG is that the LG neuron thereby controls the timing of the impulse bursts in other gastric mill neurons. Thus, local synaptic input can functionally compartmentalize the activity of a neuron with arbors in distinct regions of the nervous system.
Similarity-based Ordering of Images in Search Engines Klaas Bosteels Supervisor ( s ) :

Search engines such as Google and Yahoo allow internet users to search through huge collections of images. These existing search engines are all text-based, i.e. the searching is based on the comparison of keywords with textual annotations. Content-based image retrieval (CBIR) is a more natural approach in which the searching is based on the actual content of the images. However, CBIR systems are still not capable of searching through collections consisting of millions of images. Therefore they are not suitable yet as a basis for a search engine on the internet. As a solution to that problem, we introduce a hybrid approach that combines text-based image retrieval (TBIR) with CBIR, without sacrificing the scalability of the system. More precisely we propose an extension of TBIR that adds the ability to sort the search results according to their similarity with a given set of examples. Such an extension requires measures that are able to express the similarity between two images. Because similarity is a gradual concept, we use fuzzy set theory to model these measures. Keywords—similarity measures, colour images, fuzzy sets, content-based image retrieval
Software Ecosystems: Trends and Impacts on Software Engineering

Economic and social issues are pointed out as Software Engineering (SE) challenges for the next years, since the field needs to treat issues beyond the technical side. These challenges require analyzing the field of SE from another perspective. In this sense, the study of software ecosystems (SECOs) is an emerging discipline that investigates the relationships among companies in the software industry. Companies work cooperatively and competitively in order to achieve their strategic objectives. They must engage in a new perspective, now also including third parties motivations and movements in the ecosystem, besides their own business viewpoint. Inspired on properties of natural and business ecosystems, SECO covers technical and business aspects of software development as well as partnership among companies. In this paper, we undertake a review on SECOs status as an emerging research topic in SE community. We map what is currently known about SECOs and also analyze them in a three-dimensional perspective in SE, i.e., technical, business and social. We observed that SECOs research is concentrated in eight main areas in which the most relevant ones are open source software, ecosystem modeling, and business issues. This paper also contributes to summarize the body of knowledge and presents a research agenda in SECOs.
Semianalytic Solutions for a Well With a Single Finite-Conductivity Vertical Fracture

In this paper,we developa simple,closedformapproximationfor the Laplaeetransformsolutionfor thecaseof a wellwitha finite conductivityverticalfracturein an infiite-acting reservoir. Our hybrid solution is based on a ooupling of the solution for a Minear Me conductivityvetticalfhwxuremodel(whichdoesnot model radial flow) and the solution for a uniform flwdiinfiinite conductivity vertical fracture (whichdoes model scudoradial f flow). ‘Ilxw solutionsarensadilyobtainedfromthe iterature. Overa.lLweconsideroursolutionto be validfor Cp~. S andwe show that our solutiongives leasthan 1percenterror in bothpD andpD’ for C~>2. We suggest that our hybrid solution is not valid for C@iM and do not recommendits use for CpCO.5 underanycltmtnstanoes. We have verifkd this solution against four different solutions given in the literature. Each comparisonwas excellent which suggestathat our simplifkd solution is more than adequatefor practiwdapplications, In particular,we provideveritlcationfor constantrate and constantpressureproductionfor vah-s of Cp between0.2S and 10,000. We also show that our solution is capableof producingveq accuratederivativefunctions. In addition,by reproducingthe literaturesolutions so well, we also verified that individual flow regimes (formation/fracture b-flow, formationlinearflow,andpaeudoradiaI flow)areall modeledaccumtelyby ournewsolution. INTRODUCTION Ourmotivationfor this paperis to providethe technicalaudience with an aoourate,but computationallysimple,approximationfor the Laphwetransformsolutionfor thecaseof a wellwith a f~tc conductivityvertiealfrsotwein an infiiite-actingte-servoir. Wehavethe followingobjectivesforthiswork
Documenting design patterns in code eases program maintenance

Software design patterns are a promising idea with many advocates. While subjective reports of their usefulness are available, scienti c proof is still missing. We consider the case of programmers using design pattern documentation (in the form of comments in the source program) during maintenance. Is such pattern documentation (PD) helpful for understanding a program more quickly and designing better solutions for given maintenance tasks? We describe a controlled experiment for investigating this question, present its results, and conclude that design pattern documentation can speed up program changes as well as improve their quality.
Development and Assessment of an Impact Apparatus and High-Speed Camera Motion Tracking System to Quantify the Effect of Static Muscle Loads on Fracture Threshold Measures in the Distal Radius

ii CO-AUTHORSHIP . iii ACKNOWLEDGMENTS . iv TABLE OF CONTENTS . v LIST OF TABLES . viii LIST OF FIGURES . xi LIST OF APPENDICES . xvii LIST OF ABREVIATIONS, SYMBOLS AND NOMENCLATURE . xix CHAPTER 1 . 1 1.1 THE WRIST . 1 1.2 DISTAL RADIUS FRACTURES . 1 1.2. 1 FRACTURE INCIDENCE . 1 1.2. 2 ASSOCIATED COSTS . 4 1.2. 3 FRACTURE CLASSIFICATION AND TREATMENT . 5 1.2. 4 COMPLICATIONS . 7 1.3 ANATOMY OF THE WRIST . 7 1.3. 1 BONES OF THE WRIST . 7 1.3. 2 LIGAMENTS OF THE WRIST . 9 1.3. 3 MUSCULOTENDINOUS UNITS OF THE WRIST . 13 1.3. 4 MOTIONS OF THE WRIST . 13 1.4 UPPER EXTREMITY IMPACT BIOMECHANICS . 15 1.4. 1 IN VIVO TESTING . 15 1.4. 2 IN VITRO TESTING . 16 1.5 APPARATUS DESIGN . 20 1.6 INSTRUMENTATION REQUIRED FOR IMPACT ASSESSMENT . 23 1.6. 1 HIGH-SPEED CAMERAS . 23 1.6. 2 STRAIN GAUGES . 24 1.6. 3 LOAD CELL . 27 1.6. 4 FRACTURE DETECTION . 27
Hsp65-Producing Lactococcus lactis Prevents Inflammatory Intestinal Disease in Mice by IL-10- and TLR2-Dependent Pathways

Heat shock proteins (Hsps) are highly expressed at all sites of inflammation. As they are ubiquitous and immunodominant antigens, these molecules represent good candidates for the therapeutic use of oral tolerance in autoimmune and chronic inflammatory diseases. Evidences from human and animal studies indicate that inflammatory bowel disease (IBD) results from uncontrolled inflammatory responses to intestinal microbiota. Hsps are immunodominant proteins expressed by several immune cells and by commensal bacteria. Using an IBD mouse model, we showed that oral pretreatment with genetically modified Lactococcus lactis that produces and releases Mycobacterium Hsp65, completely prevented DSS-induced colitis in C57BL/6 mice. Protection was associated with reduced pro-inflammatory cytokines, such as IFN-γ, IL-6, and TNF-α; increased IL-10 production in colonic tissue; and expansion of CD4+Foxp3+ and CD4+LAP+ regulatory T cells in spleen and mesenteric lymph nodes. This effect was dependent on IL-10 and toll-like receptor 2. Thus, this approach may open alternative options for long-term management of IBD.
Identification of deformation pattern changes caused by enhanced oil recovery (EOR) using InSAR

ABSTRACT Continuous hydrocarbon production and steam/water injection cause compaction and expansion of the reservoir rock, leading to irregular downward and upward ground movements. Detecting such anthropogenic ground movements is of importance, as they may significantly influence the safety and sustainability of hydrocarbon production activities, in particular, enhanced oil recovery (EOR) and even lead to local hazards, e.g. earthquakes and sinkholes. As InSAR (Interferometric Synthetic Aperture Radar) can routinely deliver global ground deformation observations on a weekly basis, with millimetre-level precision, it can be a cost-effective, and less labour intensive tool to monitor surface deformation changes due to hydrocarbon production activities. Aimed at identifying the associated deformation pattern changes, this study focuses on InSAR deformation model optimization, in order to automatically detect irregularities, both spatially and temporally. We apply multiple hypothesis testing to determine the best model based on a library of physically realistic canonical deformation models. We develop a cluster-wise constrained least-squares estimation method for parameter estimation, in order to directly introduce contextual information, such as spatio-temporal correlation, into the mathematical model. Here a cluster represents a group of spatially correlated InSAR measurement points. Our approach is demonstrated over an enhanced oil recovery site using a stack of TerraSAR-X images.
Weighting Adjustments for Panel Nonresponse

1 Summary Although similar to weighting for unit nonresponse in cross-sectional surveys, adjustment for panel non-response needs to incorporate information about nonrespondents collected in the early waves of the panel. We review different weighting adjustments for panel nonresponse and discuss methods for incorporating complex survey design variables into the weighting adjustments. We propose a cross-classified method for panel survey data with complex sampling design by first grouping respondents and nonrespondents with similar estimated response propensities to form response propensity strata and then cross-classifying the response propensity strata with the design variables. Our simulation study shows that when design variables are not related to nonresponse, the cross-classified method yields survey estimates that have bias and root mean squared error similar to the estimates weighted by reciprocals of the response propensities and the response propensity stratification method. When design variables are related to nonresponse, the cross-classified method yields estimates with smaller bias than both the other two methods if design variables are not included as covariates in the response propensity regression, but is comparable in the bias to the other two methods if the response propensity model is correctly specified. We apply these methods to the Galveston Bay Recovery Study, a panel study of trajectories of wellness in a community following a disaster.
Poststroke Sexual Function to the Editor

measured Hamilton Scale; Psychosocial Di- mension of and SF-36 Mental Health. A marked decline in sexual function was reported by 71.5% of the stroke patients at 1 year after stroke (72.7% of women and 70.8% of men who were sexually active before stroke); 48.5% of the stroke patients experienced diminished libido. These data are similar to those in the study conducted by Monga et al, 9 who reported diminished libido and erection disorders in 62% impotence was diagnosed in 48% of men 1 year after stroke and was correlated with Physical Dimension of the Sickness Profile. Libido decline was not correlated with stroke etiology, laterality disability by Barthel or age. Libido decline was statistically correlated with the Hamilton Depression Scale (mean value scale 17 versus 9.4 in patients without libido decline; P (cid:53) 0.001) and the Psychosocial Dimension the (mean 22.2 P 0.009). SF-36 Vitality and SF-36 Mental Health were statistically significantly diminished in stroke patients with reduced libido. We found no statistically significant differences in the Barthel Index and Rankin scale scores in stroke patients with and without sexual dysfunction (mean score value of 95 versus 90, respectively) 1 year after stroke. Thus, psychological factors seem to exert a strong impact on libido decline in stroke patients 1 year after stroke. a impact on impotence, not on sexual dysfunction related to libido decline. Quality of life instruments are useful instruments for studying physical and psychological factors related to poststroke sexual dysfunction.
Decreased Plasma Phosphatidylcholine/Free Cholesterol Ratio as an Indicator of Risk for Ischemic Vascular Disease

As part of a population survey and a follow-up study of plasma lipid profiles by high temperature gas-liquid chromatography, we have determined the quantities and relative proportions of all major chemical classes and molecular species of llpids of plasma from 1200 subjects at Visit 2 of the Toronto-McMaster Lipid Research Clinic Prevalence Study. We have compared these values between our 24 subjects with ischemic vascular disease and 73 control subjects matched for age, sex, and plasma total cholesterol and triacylglycerols. The phosphatidylcholine/free cholesterol ratio showed the highest association with ischemic vascular disease of any of over 10 other lipid parameters and all the common risk indicators except high density lipoprotein cholesterol. The phosphatidylcholine/free cholesterol ratio had a reiatlve risk ratio of 20/4 (95% confidence limits, 15/9,23/1) and high density llpoproteln cholesterol, a risk ratio of 23/1 (95% confidence limits, 24/0,19/5) for ischemic vascular disease. The average ratio of phosphatidylcholine/free cholesterol for the ischemic vascular disease group was 1.36 and for the controls 1.51, the population average being 1.50. Plasma high density lipoproteln cholesterol had a significant correlation (R = 0.15) with the phosphatidytcholine/ffee cholesterol ratio in the total population sample. The Increased risk for ischemic vascular disease from a tower phosphatidylchollne/free cholesterol ratio may possibly be explained on the basis of decreased fluidity and stability of the lipoproteins due to a relative oversaturatfon with free cholesterol.
Reprogramming towards totipotency is greatly facilitated by synergistic effects of small molecules

ABSTRACT Animal cloning has been achieved in many species by transplanting differentiated cell nuclei to unfertilized oocytes. However, the low efficiencies of cloning have remained an unresolved issue. Here we find that the combination of two small molecules, trichostatin A (TSA) and vitamin C (VC), under culture condition with bovine serum albumin deionized by ion-exchange resins, dramatically improves the cloning efficiency in mice and 15% of cloned embryos develop to term by means of somatic cell nuclear transfer (SCNT). The improvement was not observed by adding the non-treated, rather than deionized, bovine serum. RNA-seq analyses of SCNT embryos at the two-cell stage revealed that the treatment with TSA and VC resulted in the upregulated expression of previously identified reprogramming-resistant genes. Moreover, the expression of early-embryo-specific retroelements was upregulated by the TSA and VC treatment. The enhanced gene expression was relevant to the VC-mediated reduction of histone H3 lysine 9 methylation in SCNT embryos. Our study thus shows a simply applicable method to greatly improve mouse cloning efficiency, and furthers our understanding of how somatic nuclei acquire totipotency. Summary: The optimized culture condition with small molecules is sufficient to allow highly efficient mouse cloning by removing epigenetic barriers to reprogramming.
Generation of Speaker Mixture Voice using Spectrum Morphing

We propose a method for synthesizing a "speaker mixture voice" that has both of two speakers' individualities. We define the "speaker mixture voice" as such that 50 percent of the subjects who listen to the voice would identify either speaker A or speaker B in ABX listening test that instructs them to identify the speaker. To synthesize the speaker mixture voice, we parameterize the spectrum envelope with respect to peaks and valleys, find the correspondence between two spectrum envelopes from independent speakers using DP matching, morph one to the other, and generate waveforms using TD-PSOLA. Listening experiments showed 60 percent out of 56 synthesized voices were recognized as the speaker mixture voices. The primary application of the proposed method would be individualization of the characters in online games where multiple users play a single character as separate individuals at the same time.
Mild parkinsonian signs are associated with increased risk of dementia in a prospective, population‐based study of elders

There is some evidence that mild parkinsonian signs (MPSs) are associated with increased risk of dementia, suggesting that MPS could be an early biomarker for dementia. Our aims, in a new cohort, were to determine whether (1) baseline MPS are a predictor of incident dementia and (2) there is an interaction between MPS and other baseline risk factors for dementia (i.e., the presence of both together greatly elevates the risk of dementia) was the objective. In a prospective, longitudinal study of community‐dwelling elders in northern Manhattan, NY, Parkinsonian signs were rated with an abbreviated Unified Parkinson's Disease Rating Scale. Risk of incident dementia was assessed using Cox proportional hazards models. There were 1,851 participants (mean follow‐up = 3.7 years). Participants with baseline MPS were twice as likely to develop dementia as participants without MPS: 16.3% versus 7.7%, unadjusted hazards ratio (HR) = 2.24 (P< 0.001), adjusted HR = 1.98 (P < 0.001). MPS were divided into three subtypes: adjusted HRaxial dysfunction = 2.45 (P < 0.001), adjusted HRtremor = 2.38 (P = 0.006), and adjusted HRrigidity = 1.16 (P = 0.58). When MPS were treated as a continuous variable, the adjusted HR = 1.15 (P = 0.001). There were no interactions between MPS and other baseline risk factors for dementia, including gender, education, race, family history of dementia, stroke, and apolipoprotein E‐e4. Baseline MPS seems to be a predictor of incident dementia. These motor signs might, therefore, serve as a useful biomarker for emerging dementia. © 2010 Movement Disorder Society