Miracle-dz/UniFAR-FTUs huggingface dataset:
Self-catalyzed Cleavage of the Yeast Nucleoporin Nup145p Precursor*

Nup145p is a component of the nuclear pore complex of Saccharomyces cerevisiae and is essential for mRNA export. Nup145p and its apparent vertebrate homologue are the only known nucleoporins to be composed of two functionally independent peptide moieties resulting from the post-translational cleavage of a large precursor molecule. In this study, the proteolytic cleavage site of Nup145p has been mapped upstream of an evolutionary conserved serine residue. Cleavage occurs at the same site when a precursor is artificially expressed in Escherichia coli. A hydroxyl-containing residue is critical for the reaction, although a thiol-containing residue offers an acceptable replacement. In vitro kinetics experiments using a purified precursor molecule demonstrate that the cleavage is self-catalyzed and that the catalytic domain lies within the N-terminal moiety. Taken altogether, our data are consistent with a proteolytic mechanism involving an N>O acyl rearrangement and a subsequent ester intermediate uncovered in other self-processing proteins.
Calibration comparison between SCIAMACHY and MERIS onboard ENVISAT

We present a comparison of the Scanning Imaging Absorption Spectrometer for Atmospheric Chartography (SCIAMACHY) and the Medium Resolution Imaging Spectrometer (MERIS) reflectance calibrations at wavelengths between 442 and 885 nm. Results show that SCIAMACHY underestimates the reflectance by /spl sim/13% at 442 nm reaching up to /spl sim/21% at 885 nm as compared to MERIS. We also find a small nonlinear effect for the lowest reflectance. This effect is more evident for pixels over ocean than over land.
Extending role-based access control model with states

The role-based access control (RBAC) concept is a powerful way of describing access control policy. The goal of this paper is to include the notion of states and state transitions into the RBAC model and to view changes of components of RBAC model as transitions between states of one access control policy. This allows us to better review properties of the access control policy as well as compare the policies.
Climatological coupling of the thermohaline decadal changes in Central Water of the eastern North Atlantic

Data collected at 42oN, 10oW in the intergyre region of the Northeast Atlantic show significant year to year variability in the T-S characteristics of the upper 800m of the water column. Taking salinity values on the sq = 27.1 kg m -3 isopycnal as representative of the Eastern North Atlantic Central Water mass it was found that the variability correlates well with the wind stress at 43oN, 11oW, with cumulative river discharge (which we take as an index of precipitation over the ocean) and with the NAO (which is an index of the strength and position of storm tracks and the state of the evaporation-precipitation balance). The covariation illustrates the close coupling between water mass formation and climate in the North Atlantic, where climate changes affect the deep ventilation by which ENACW is formed and the evaporation-precipitation balance from which the T-S signature results. Hints of a 20 year cycle in the ocean correlate with a 20 year periodicity in the NAO. It remains to be established whether there is a feedback mechanism by which water mass anomalies affect the climate and the intensity and variation of the NAO pattern, and the extent to which upper ocean observations can be used as an indicator of future climate trends.
Two-water-assisted racemization of the succinimide intermediate formed in proteins. A computational model study

Racemization of aspartic acid (Asp) residues in proteins plays an important role in the molecular biology of aging. In the widely accepted mechanism of the Asp racemization, a succinimide (SI) intermediate is the species which actually undergo the direct racemization. In the present study, a two-water-assisted mechanism of the SI racemization was computationally investigated using a model compound in which an aminosuccinyl (Asu) residue is capped with acetyl and NMe groups on the N-and C-termini, respectively. The two water molecules catalyze the enolization of the Hα-Cα-C=O portion in the Asu residue by mediating proton relay from the α-carbon atom to the carboxyl oxygen atom. After the enolization, migration of the water molecules and conformational change lead to the mirror image of the initially formed enol two-water complex, and the racemization is completed by the following ketonization. The overall activation barrier (28.2 kcal·mol-1) corresponds to the enolization and ketonization steps, and falls within the available experimental activation energies (21.4-29.0 kcal·mol-1). Therefore, the two-water-assisted mechanism investigated here is plausible for the in vivo and in vitro racemization reactions of the SI intermediates formed in peptides and proteins.
Microsoft Research Treelet Translation System: IWSLT Evaluation

The Microsoft Research translation system is a syntactically informed p hrasal S MT system that u ses a p hrase translation mod el based on d ep end ency treelets and a g lobal reord ering mod el based on the sou rce d ep end ency tree. These mod els are combined w ith sev eral other k now led g e sou rces in a log linear manner. The w eig hts of the ind iv id u al comp onents in the log -linear mod el are set by an au tomatic p arameter-tu ning method . W e g iv e a brief ov erv iew of the comp onents of the system and d iscu ss its p erformance at IW S L T in tw o track s: J ap anese to E ng lish ( su p p lied d ata and tools), and E ng lish to C hinese ( su p p lied d ata and tools). 1 . I n tro d u cti o n The d ep end ency treelet translation system d ev elop ed at MS R is a statistical MT system that tak es ad v antag e of ling u istic tools, namely a sou rce lang u ag e d ep end ency p arser, as w ell as a w ord alig nment comp onent. [1] To train a translation system, w e req u ire a sentencealig ned p arallel corp u s. F irst the sou rce sid e is p arsed to obtain d ep end ency trees. N ex t the corp u s is w ord -alig ned , and the sou rce d ep end encies are p roj ected onto the targ et sentences u sing the w ord alig nments. F rom the alig ned d ep end ency corp u s w e ex tract all treelet translation p airs, and train an ord er mod el and a bi-lex ical d ep end ency mod el. To translate, w e p arse the inp u t sentence, and emp loy a d ecod er to find a combination and ord ering of treelet translation p airs that cov er the sou rce tree and are op timal accord ing to a set of mod els. In a now -common g eneraliz ation of the classic noisy-channel framew ork , w e u se a log -linear combination of mod els [2], as in below :
Electrical sintering of nanoparticle structures

A method for sintering nanoparticles by applying voltage is presented. This electrical sintering method is demonstrated using silver nanoparticle structures ink-jet-printed onto temperature-sensitive photopaper. The conductivity of the printed nanoparticle layer increases by more than five orders of magnitude during the sintering process, with the final conductivity reaching 3.7 × 107 S m−1 at best. Due to a strong positive feedback induced by the voltage boundary condition, the process is very rapid—the major transition occurs within 2 µs. The best obtained conductivity is two orders of magnitude better than for the equivalent structures oven-sintered at the maximum tolerable temperature of the substrate. Additional key advantages of the method include the feasibility for patterning, systematic control of the final conductivity and in situ process monitoring. The method offers a generic tool for electrical functionalization of nanoparticle structures.
Modified Particle filter for object tracking in low frame rate video

Object tracking algorithm using modified Particle filter in low frame rate (LFR) video is proposed in this paper, which the object moving significantly and randomly between consecutive frames in the low frame rate situation. Traditionally, Particle filtering use motion transitions to model the movement of the target. However, in object tracking with low frame rate sequences, it is very difficult to model significant random jumps of subjects. The key notion of our solution is that using the object detection and extraction to locate the tracked object, while not using the dynamical function. We propagate the sample set around the detected regions, which the samples are assumed to be uniformly distributed in the neighborhoods of the detected region. It is similar to the general particle filter to propagate samples. Then we compute the likelihood between the target model and the candidate regions, which are based on color histogram distances. Our extensive experiments show that the proposed algorithm performs robustly in a large variety of tracking scenarios.
Localization of the Wilson disease protein in murine intestine

Wilson disease is an inherited disorder of human copper metabolism, characterized by gradual accumulation of copper in tissues, predominantly liver and brain. The gene defect lies in the Wilson disease protein ATP7B, a copper transporting ATPase highly active in hepatocytes. In the liver, ATP7B is essential for excretion of excess copper into the bile and for copper loading of ceruloplasmin in the Golgi apparatus. The extrahepatic role of ATP7B is not yet completely understood. We analysed the intestinal expression of ATP7B in mice using RT‐PCR, Western blot and indirect immunofluorescence. We found abundant expression of ATP7B in stomach and small intestine, but not in colon. Using confocal microscopy we demonstrate a Golgi localization of ATP7B in enterocytes. In response to elevated copper, the Wilson disease protein shows an intracellular trafficking pattern in the intestinal polarized cell line CaCo‐2, moving away from the Golgi apparatus to dispersed vesicles. This suggests a role for intestinal ATP7B in sequestration of copper in intracellular vesicles for maintenance of copper homeostasis in the enterocyte. In conclusion, the expression of ATP7B in the small intestine might represent an additional regulatory mechanism to fine‐tune intestinal copper absorption.
Scalable production of adeno‐associated virus type 2 vectors via suspension transfection

Vectors derived from adeno‐associated virus type 2 (AAV2) are promising gene delivery vehicles, but it is still challenging to get the large number of recombinant adeno‐associated virus (rAAV) particles required for large animal and clinical studies. Current transfection technology requires adherent cultures of HEK 293 cells that can only be expanded by preparing multiple culture plates. A single large‐scale suspension culture could replace these multiple culture preparations, but there is currently no effective co‐transfection scheme for generating rAAV from cells in suspension culture. Here, we weaned HEK 293 cells to suspension culture using hydrogel‐coated six‐well culture plates and established an efficient transfection strategy suitable for these cells. Then the cultures were gradually scaled up. We used linear polyethylenimine (PEI) to mediate transfection and obtained high transfection efficiencies ranging from 54% to 99%, thereby allowing efficient generation of rAAV vectors. Up to 1013 rAAV particles and, more importantly, up to 1011 infectious particles were generated from a 2‐L bioreactor culture. The suspension‐transfection strategy of this study facilitates the homogeneous preparation of rAAV at a large scale, and holds further potential as the basis for establishing a manufacturing process in a larger bioreactor. © 2006 Wiley Periodicals, Inc.
Ester Cross-Link Profiling of the Cutin Polymer of Wild-Type and Cutin Synthase Tomato Mutants Highlights Different Mechanisms of Polymerization1

A Synthase impacts ester cross-links of tomato cutin. Cuticle function is closely related to the structure of the cutin polymer. However, the structure and formation of this hydrophobic polyester of glycerol and hydroxy/epoxy fatty acids has not been fully resolved. An apoplastic GDSL-lipase known as CUTIN SYNTHASE1 (CUS1) is required for cutin deposition in tomato (Solanum lycopersicum) fruit exocarp. In vitro, CUS1 catalyzes the self-transesterification of 2-monoacylglycerol of 9(10),16-dihydroxyhexadecanoic acid, the major tomato cutin monomer. This reaction releases glycerol and leads to the formation of oligomers with the secondary hydroxyl group remaining nonesterified. To check this mechanism in planta, a benzyl etherification of nonesterified hydroxyl groups of glycerol and hydroxy fatty acids was performed within cutin. Remarkably, in addition to a significant decrease in cutin deposition, mid-chain hydroxyl esterification of the dihydroxyhexadecanoic acid was affected in tomato RNA interference and ethyl methanesulfonate-cus1 mutants. Furthermore, in these mutants, the esterification of both sn-1,3 and sn-2 positions of glycerol was impacted, and their cutin contained a higher molar glycerol-to-dihydroxyhexadecanoic acid ratio. Therefore, in planta, CUS1 can catalyze the esterification of both primary and secondary alcohol groups of cutin monomers, and another enzymatic or nonenzymatic mechanism of polymerization may coexist with CUS1-catalyzed polymerization. This mechanism is poorly efficient with secondary alcohol groups and produces polyesters with lower molecular size. Confocal Raman imaging of benzyl etherified cutins showed that the polymerization is heterogenous at the fruit surface. Finally, by comparing tomato mutants either affected or not in cutin polymerization, we concluded that the level of cutin cross-linking had no significant impact on water permeance.
The Lifetime Risks and Costs of Nursing Home Use Among the Elderly

In this paper, we estimate the risk of an individual of entering a nursing home throughout the aging process. We then estimate the expected lifetime costs of nursing home use both for an individual and for society as a whole. The model is based on double-decrement life-table analysis. Data are taken from a 1977 survey of 4,400 Medicare beneficiaries. At age 65, the upper bound for the lifetime risk of entering a nursing home is 43.1%. The risk of entering a nursing home increases with age until around age 80. At about age 85, the risk begins to decline significantly. At almost all ages, the lifetime risk of entry for females is twice that of males. The expected lifetime costs of nursing home care across all ages are between $10,500 and $13,600. These costs are distributed very unequally. Only 13% of the elderly account for 90% of all nursing home expenditures. Given current life expectancy, the expected annual cost per person over age 65 is between $532 and $760. In the year 2000, the expected annual average costs of nursing home care per elderly person will range from $450 to $650. The decline in the average annual cost per person reflects shifts in the age structure and increased life expectancy. These figures need not represent an unmanageable burden on society's resources. Figures presented here help establish the feasibility and desirability of long-term care risk-sharing arrangements among the elderly, like long-term care insurance, life care communities, and other models.
Social media enhanced studying and learning in higher education

Social media services have recently become well known especially among young people [1]. In social networking sites a user can participate intensively in activities in the service. To support collaborative study at Tampere University of Technology (TUT) and also to provide social networking tools for students especially at the beginning their studies, the development TUT's own social network site was begun in spring 2008. To make the system popular among students, developers and researchers at the Department of Mathematics and Hypermedia Laboratory at TUT designed interventions for fall 2009 when the semester began and new students started their studies. The earlier research [2] revealed numerous motivating aspects that should be somehow included in a study oriented social networking site. This paper will describe the research results of interventions to motivate students to use a social networking site in the context of studies. The results will show that such an environment with social aspects connected to studying and study life on various levels is a means of enhancing studies and basically a necessary tool, especially for students in the early phase of their studies in a new university. The motivation should be further encouraged by the system itself when it relies on students' own voluntary activity. Moreover, the intensive actions of developers, researchers and administrators can be used as tools in directing network activity development.
Integrated optical switches in silicon based on SiGe-waveguides

The realization of switches in silicon base on monomode Ge-indiffused SiGe waveguides is reported. At a wavelength of 1.3 mu m a Mach-Zehnder interferometer switch with a modulation depth of -10 dB at a current of 150 mA is obtained. This is the lowest value reported so far for single-mode optical switches in silicon. <<ETX>>
Detection of toxigenic Clostridium difficile in stool samples by real-time polymerase chain reaction for the diagnosis of C. difficile-associated diarrhea.

BACKGROUND Clostridium difficile-associated diarrhea (CDAD) is the major cause of health care-associated infectious diarrhea. Current laboratory testing lacks a single assay that is sensitive, specific, and rapid. The purpose of this work was to design and validate a sensitive and specific real-time polymerase chain reaction (PCR) diagnostic test for CDAD. METHODS This observational validation study of a new real-time PCR assay occurred from July 2004 through April 2006 and involved the testing of 1368 stool samples. As the final validation portion of the investigation, 350 inpatients were prospectively interviewed for clinical findings for 365 episodes of diarrheal illness. Test results and clinical criteria were used to assess the performance of 4 assays. RESULTS Using clinical criteria requiring at least 3 loose stools in 1 day as part of the reference standard for a positive test result supporting CDAD, the sensitivity, specificity, and positive and negative predictive values were 73.3%, 97.6%, 73.3%, and 97.6%, respectively, for enzyme immunoassay; 93.3%, 97.4%, 75.7%, and 99.4%, respectively, for real-time PCR; 76.7%, 97.1%, 69.7%, and 97.9%, respectively, for cell culture cytotoxin assay; and 100.0%, 95.9%, 68.2%, and 100.0%, respectively, for anaerobic culture (for toxigenic C. difficile strains). The real-time PCR and anaerobic culture assays were significantly more sensitive than the enzyme immunoassay (P<.01 to P<.05). CONCLUSIONS With an assay turnaround time of <4 h, real-time PCR is a more sensitive and equally rapid test, compared with enzyme immunoassay, and is a feasible laboratory option to replace enzyme immunoassay for toxigenic C. difficile detection in clinical practice, as well as for use during the development of new therapeutic agents.
Measuring Values of Extramarket Goods: Are Indirect Measures Biased?

The well known travel cost method (TC)has been widely applied to outdoor recreation. A second approach has been referred to in the past as the Davis method, the questionnaire approach, and contingent valuation. It will here be termed hypothetical valuation (HV), since it involves creating a hypothetical situation designed to elicit willingness to pay for or willingness to accept compensation for a recreational or other extramarket good (or bad). TC and HV are termed "indirect methods", since they do not depend on the direct information about prices and quantities that economists would prefer to use where available to value goods and services.
Expression of inducible nitric oxide synthase in human heart failure.

BACKGROUND There is increasing evidence that alterations in nitric oxide synthesis are of pathophysiological importance in heart failure. A number of studies have shown altered nitric oxide production by the endothelial constitutive isoform of nitric oxide synthase (NOS), but there is very little information on the role of the inducible isoform. METHODS AND RESULTS We analyzed inducible NOS (iNOS) expression in ventricular myocardium taken from 11 control subjects (who had died suddenly from noncardiac causes), from 10 donor hearts before implantation, and from 51 patients with heart failure (24 with dilated cardiomyopathy [DCM], 17 with ischemic heart disease [IHD], and 10 with valvular heart disease [VHD]). Reverse transcription-polymerase chain reaction was used to confirm the presence of intact mRNA and to detect expression of iNOS and atrial natriuretic peptide (ANP). ANP was used as a molecular phenotypic marker of ventricular failure. iNOS was expressed in 36 of 51 biopsies (71%) from patients with heart failure and in none of the control patients (P<.0001). iNOS expression could also be detected in 50% of the donor hearts. All samples that expressed iNOS also expressed ANP. iNOS gene expression occurred in 67% of patients with DCM, 59% of patients with IHD, and 100% of patients with VHD. To determine whether iNOS protein was expressed in failing ventricles, immunohistochemistry was performed on three donor hearts and nine failing hearts with iNOS mRNA expression. Staining for iNOS was almost undetectable in the donor myocardium and in control sections, but all failing hearts showed diffuse cytoplasmic staining in cardiac myocytes. Expression of iNOS could be observed in all four chambers. Western blot analysis with the same primary antibody showed a specific positive band for iNOS protein in the heart failure specimens; minimal iNOS protein expression was seen in donor heart samples. CONCLUSIONS iNOS expression occurs in failing human cardiac myocytes and may be involved in the pathophysiology of DCM, IHD, and VHD.
Electric Load Forecasting Based on Statistical Robust Methods

In this paper, the stochastic characteristics of the electric consumption in France are analyzed. It is shown that the load time series exhibit lasting abrupt changes in the stochastic pattern, termed breaks. The goal is to propose an efficient and robust load forecasting method for prediction up to a day-ahead. To this end, two new robust procedures for outlier identification and suppression are developed. They are termed the multivariate ratio-of-medians-based estimator (RME) and the multivariate minimum-Hellinger-distance-based estimator (MHDE). The performance of the proposed methods has been evaluated on the French electric load time series in terms of execution times, ability to detect and suppress outliers, and forecasting accuracy. Their performances are compared with those of the robust methods proposed in the literature to estimate the parameters of SARIMA models and of the multiplicative double seasonal exponential smoothing. A new robust version of the latter is proposed as well. It is found that the RME approach outperforms all the other methods for “normal days” and presents several interesting properties such as good robustness, fast execution, simplicity, and easy online implementation. Finally, to deal with heteroscedasticity, we propose a simple novel multivariate modeling that improves the quality of the forecast.