Miracle-dz/UniFAR-FTUs huggingface dataset:
Biophysical assay for tethered signaling reactions reveals tether-controlled activity for the phosphatase SHP-1

Tethering of the cytoplasmic tyrosine phosphatase SHP-1 to clustered receptors increases its activity 900-fold. Tethered enzymatic reactions are ubiquitous in signaling networks but are poorly understood. A previously unreported mathematical analysis is established for tethered signaling reactions in surface plasmon resonance (SPR). Applying the method to the phosphatase SHP-1 interacting with a phosphorylated tether corresponding to an immune receptor cytoplasmic tail provides five biophysical/biochemical constants from a single SPR experiment: two binding rates, two catalytic rates, and a reach parameter. Tether binding increases the activity of SHP-1 by 900-fold through a binding-induced allosteric activation (20-fold) and a more significant increase in local substrate concentration (45-fold). The reach parameter indicates that this local substrate concentration is exquisitely sensitive to receptor clustering. We further show that truncation of the tether leads not only to a lower reach but also to lower binding and catalysis. This work establishes a new framework for studying tethered signaling processes and highlights the tether as a control parameter in clustered receptor signaling.
RESTful implementation of geospatial services for Earth and Space Science applications

Abstract In the recent years, Representational State Transfer (REST) has been proposed as the architectural style for the World Wide Web. REST promises of scalability and simple deployment of Web Services seem to be particularly appealing for Earth and Space Science (ESS) applications. In fact, most of the available solutions for geospatial data sharing, applying standard interoperability specifications, require complex service-oriented infrastructures; these are powerful and extensible environments, but they usually result in difficult to deploy and manage for ESS research teams. Thus, ESS researchers would gain great benefit from an easy way of sharing geo-information using the international interoperability standards. The variety and complexity of geo-information sharing services poses several architectural issues; in fact these services encompass sensor planning and observation, coverages and features publication and retrieving, models and simulations running, data citation and annotation. Consequently, the adoption of a specific architectural style must be carefully evaluated against these specific requirements. In this work we analyse the existing geospatial services from an architectural perspective and investigate their possible RESTful implementation. Particular attention is paid to the OGC Web Coverage Service (WCS). Possible benefits and drawbacks, along with open issues and possible solutions are discussed. Our investigation suggests that REST may fit well to the typical ESS research usage cases. However, the architectural choice (e.g. Simple Object Access Protocol (SOAP) vs REST) will depend on a case-by-case analysis. Other important factors must be considered, such as the application context: a valuable example in point are the e-Business and e-Government application scenarios which require message based solutions – like those implemented by SOAP. In any case, there is a clear need for harmonization and reconciliation of these two approaches.
A multicenter trial on interobserver reproducibility in reporting on 99mTc-DMSA planar scintigraphy: a Belgian survey.

UNLABELLED Conflicting opinions have been expressed regarding reproducibility in 99mTc-dimercaptosuccinic acid (DMSA) planar renal image interpretation. The purpose of this investigation was to determine the level of interobserver variability among a large group of Belgian nuclear medicine physicians who evaluated a randomly selected series of DMSA planar scintigraphic examinations performed on children and adults. METHODS All Belgian nuclear medicine centers (n = 82) were invited to participate in a reproducibility study on 99mTc-DMSA scintigraphy. 99mTc-DMSA scans obtained on 10 adults and 40 children were randomly selected from the databases of 2 hospitals. Those participating in this investigation (65 centers = 79%) received a series of computer disks containing 50 99mTc-DMSA studies. To avoid potential problems related to unfamiliar display, the disks were formatted to be interpretable using the participants' own computer systems. Each participant was then free to use his or her usual display (hard copies, contrast enhancement, color scale, gray scale, and so forth). For each kidney, the observers had to choose between the following answers: normal, abnormal, equivocal, and lack of quality. RESULTS Forty-two responses were obtained from a wide variety of institutions and from observers with different levels of experience in interpreting 99mTc-DMSA scintigraphy. Altogether, the following data were obtained: 60.8% normal, 25.2% abnormal, 7.0% equivocal, and 3.2% lack of quality. The median percentage of agreement (overall reproducibility) for the 42 observers was 92%. When the results of all 42 observers were compared, the median agreements on normality and abnormality were 93.5% and 90.5%, respectively. In a small number (n = 4) of kidneys, reproducibility was poor and ranged from 51% to 70%. Except for 2 outliers, all observers had almost the same level of performance. CONCLUSION A large number of Belgian nuclear medicine physicians participated in evaluating a large randomly selected sample of 99mTc-DMSA studies, and excellent interobserver agreement was found.
Mapping of epitopes for monoclonal antibodies against human platelet thrombospondin with electron microscopy and high sensitivity amino acid sequencing

A panel of monoclonal antibodies (Mab's) has been raised against human platelet thrombospondin (TSP). One Mab, designated A2.5, inhibits the hemagglutinating activity of TSP and immunoprecipitates the NH2 terminal 25 kD heparin binding domain of TSP (Dixit, V.M., D. M. Haverstick, K. M. O'Rourke, S. W. Hennessy, G. A. Grant, S. A. Santoro, and W. A. Frazier, 1985, Biochemistry, in press). Another Mab, C6.7, blocks the thrombin-stimulated aggregation of live platelets and immunoprecipitates an 18-kD fragment distinct from the heparin binding domain (Dixit, V. M., D. M. Haverstick, K. M. O'Rourke, S. W. Hennessy, G. A. Grant, S. A. Santoro, and W. A. Frazier, 1985, Proc. Natl. Acad. Sci. 82: 3472-3476). To determine the relative locations of the epitopes for these Mabs in the three-dimensional structure of TSP, we have examined TSP-Mab complexes by electron microscopy of rotary- shadowed proteins. The TSP molecule is composed of three 180-kD subunits, each of which consists of a small globular domain (approximately 8 nm diam) and a larger globular domain (approximately 16 nm diam) connected by a thin, flexible strand. The subunit interaction site is on the thin connecting strands, nearer the small globular domains. Mab A2.5 binds to the cluster of three small domains, indicating that this region contains the heparin binding domain and thus represents the NH2 termini of the TSP peptide chains. Mab C6.7 binds to the large globular domains on the side opposite the point at which the connecting strand enters the domain, essentially the maximum possible distance from the A2.5 epitope. Using high sensitivity automated NH2 terminal sequencing of TSP chymotryptic peptides we have ordered these fragments within the TSP peptide chain and have confirmed that the epitope for C6.7 in fact lies near the extreme COOH terminus of the peptide chain. In combination with other data, we have been able to construct a map of the linear order of the identified domains of TSP that indicates that to a large extent, the domains are arranged co- linearly with the peptide chain.
Photoacoustic tomography with a line detector array

Photoacoustic tomography with an array of line-shaped detectors is presented as a method to collect data for three-dimensional (3D) images in a short time. Signals measured with the detectors, which are arranged on a half-cylindrical surface, yield a projection image of the initial pressure distribution and a 3D image if the sample is rotated. The steps leading to a 3D reconstruction as well as an image of a chicken embryo are shown
Cold pressor stress reduces left cradling preference in nulliparous human females

The left cradling preference refers to the finding that women hold their infants more frequently on the left side of their own bodies. Several observational studies showed reduced left cradling during stressful circumstances, such as mother–infant separation, or domestic violence. However, until now no experimental study was conducted to investigate the immediate impact of stress on cradling behaviour. Half of the 64 female subjects participating were randomly assigned to a stressful bilateral cold pressor test. The remaining subjects performed a non-stressful control procedure. Before and after this intervention, cradling behaviour was assessed using a baby-like doll. Subjects showed a left cradling preference prior to the intervention. The cold pressor test increased blood pressure and heart rate significantly. A repeated ANOVA revealed an interaction of intervention (cold pressor vs. control) X assessment period (pre- vs. post-intervention), indicating that cold pressor stress reduces left cradling behaviour in female volunteers. Our data indicate that stress influences cradling preference. This may be of relevance for caregiver–infant interactions.
Run length-based control performance monitors: a comparison between two techniques

This work compares two techniques of controller performance monitoring. Both are based on the sequences (or run lengths) of signs of the actuating errors of a single controlled loop variable. One technique defines run length as a state, and transition probabilities between states are then modeled as a Markov chain. The other technique observes the distribution of run lengths. Both techniques were tested with experimental data and found to be equivalent in their ability to detect poor control loop performance.
The RNA chaperone Hfq regulates expression of fimbrial-related genes and virulence of Salmonella enterica serovar Enteritidis.

Salmonella Enteritidis is an intracellular pathogen that causes enteritis and systemic disease in humans and other animals. The RNA chaperone protein Hfq mediates the binding of small noncoding RNAs to target mRNA and assists in post-transcriptional gene regulation in bacteria. In this study, we constructed an hfq deletion mutant in S. Enteritidis SE50336 and analyzed the expression of major fimbrial subunits sefA, bcfA, fimA, safA, stbA, sthA, csgA, csgD, and pegA using quantitative real-time PCR. The gene expression of sefA increased about 14-fold in the hfq mutant, as compared with its expression in the wild-type strain. The expression of fimA and pegA did not change significantly, while the expression of the other fimbrial genes was significantly down-regulated in the hfq mutant. The ability of SE50336Δhfq adhering to Caco-2 cells was also reduced as compared with wild-type adherence. The virulence of the hfq mutant was significantly reduced in a 1-day-old chicken model of S. Enteritidis disease, as determined by quantifying the lethal dose 50% of the bacterial strains. We conclude that Hfq critically contributes to S. Enteritidis virulence, likely partially affected by regulating fimbrial gene expression.
N I ] 1 2 Ju l 2 01 2 Contextual Multi-armed Bandits for the Prevention of Spam in VoIP Networks Technical Report

In this paper we argue that contextual multi-armed bandit algorithms could open avenues for designing self-learning security modules for computer networks and related tasks. The paper has two contributions: a conceptual one and an algorithmical one. The conceptual contribution is to formulate – as an example – the real-world problem of preventing SPIT (Spam in VoIP networks), which is currently not satisfyingly addressed by standard techniques, as a sequential learning problem, namely as a contextual multi-armed bandit. Our second contribution is to present CMABFAS, a new algorithm for general contextual multi-armed bandit learning that specifically targets domains with finite actions. We illustrate how CMABFAS could be used to design a fully self-learning SPIT filter that does not rely on feedback from the end-user (i.e., does not require labeled data) and report first simulation results.
Requirements for Budding of Paramyxovirus Simian Virus 5 Virus-Like Particles

ABSTRACT Enveloped viruses are released from infected cells after coalescence of viral components at cellular membranes and budding of membranes to release particles. For some negative-strand RNA viruses (e.g., vesicular stomatitis virus and Ebola virus), the viral matrix (M) protein contains all of the information needed for budding, since virus-like particles (VLPs) are efficiently released from cells when the M protein is expressed from cDNA. To investigate the requirements for budding of the paramyxovirus simian virus 5 (SV5), its M protein was expressed in mammalian cells, and it was found that SV5 M protein alone could not induce vesicle budding and was not secreted from cells. Coexpression of M protein with the viral hemagglutinin-neuraminidase (HN) or fusion (F) glycoproteins also failed to result in significant VLP release. It was found that M protein in the form of VLPs was only secreted from cells, with an efficiency comparable to authentic virus budding, when M protein was coexpressed with one of the two glycoproteins, HN or F, together with the nucleocapsid (NP) protein. The VLPs appeared similar morphologically to authentic virions by electron microscopy. CsCl density gradient centrifugation indicated that almost all of the NP protein in the cells had assembled into nucleocapsid-like structures. Deletion of the F and HN cytoplasmic tails indicated an important role of these cytoplasmic tails in VLP budding. Furthermore, truncation of the HN cytoplasmic tail was found to be inhibitory toward budding, since it prevented coexpressed wild-type (wt) F protein from directing VLP budding. Conversely, truncation of the F protein cytoplasmic tail was not inhibitory and did not affect the ability of coexpressed wt HN protein to direct the budding of particles. Taken together, these data suggest that multiple viral components, including assembled nucleocapsids, have important roles in the paramyxovirus budding process.
Mind-body interventions for chronic pain in older adults: a structured review.

STUDY DESIGN We conducted a structured review of eight mind-body interventions for older adults with chronic nonmalignant pain. OBJECTIVES To evaluate the feasibility, safety, and evidence for pain reduction in older adults with chronic nonmalignant pain in the following mind-body therapies: biofeedback, progressive muscle relaxation, meditation, guided imagery, hypnosis, tai chi, qi gong, and yoga. METHODS Relevant studies in the MEDLINE, PsycINFO, AMED, and CINAHL databases were located. A manual search of references from retrieved articles was also conducted. Of 381 articles retrieved through search strategies, 20 trials that included older adults with chronic pain were reviewed. RESULTS Fourteen articles included participants aged 50 years and above, while only two of these focused specifically on persons aged >or=65 years. An additional six articles included persons aged >or=50 years. Fourteen articles were controlled trials. There is some support for the efficacy of progressive muscle relaxation plus guided imagery for osteoarthritis pain. There is limited support for meditation and tai chi for improving function or coping in older adults with low back pain or osteoarthritis. In an uncontrolled biofeedback trial that stratified by age group, both older and younger adults had significant reductions in pain following the intervention. Several studies included older adults, but did not analyze benefits by age. Tai chi, yoga, hypnosis, and progressive muscle relaxation were significantly associated with pain reduction in these studies. CONCLUSION The eight mind-body interventions reviewed are feasible in an older population. They are likely safe, but many of the therapies included modifications tailored for older adults. There is not yet sufficient evidence to conclude that these eight mind-body interventions reduce chronic nonmalignant pain in older adults. Further research should focus on larger, clinical trials of mind-body interventions to answer this question.
SNARE complexes of different composition jointly mediate membrane fusion in Arabidopsis cytokinesis

The partitioning membrane of dividing plant cells is made by homotypic fusion of trans-Golgi network–derived membrane vesicles delivered to the division plane. The cytokinesis-specific syntaxin of Arabidopsis forms two different types of SNARE complexes, which can functionally replace each other in membrane fusion during cytokinesis.
Robust visual servoing: bounding the task function tracking errors

This article deals with the well known problem of robust visual servoing (VS), which is formulated by the use of the general task function approach. Robustness is provided with respect to calibration parametric errors not only in terms of stability, but also in terms of tracking errors boundness. As a result, the proposed approach allows the user to choose a bound on the tracking error so as to guarantee the visibility of the target during the task execution. Most importantly, the error boundness is obtained while avoiding the use of large gains. Rather, one uses bounded gains, together with the modulation of the desired velocity along the desired path. An application of this general approach is developed and experimentally validated.
Shadow removal and contrast enhancement in optical coherence tomography images of the human optic nerve head.

PURPOSE To improve the quality of optical coherence tomography (OCT) images of the optic nerve head (ONH). METHODS Two algorithms were developed, one to compensate for light attenuation and the other to enhance contrast in OCT images. The former was borrowed from developments in ultrasound imaging and was proven suitable with either time- or spectral-domain OCT. The latter was based on direct application of pixel intensity exponentiation. The performances of these two algorithms were tested on spectral-domain OCT images of four adult ONHs. RESULTS Application of the compensation algorithm significantly reduced the intralayer contrast (from 0.74 ± 0.16 to 0.17 ± 0.12; P < 0.001), indicating successful blood vessel shadow removal. Furthermore, compensation dramatically improved the visibility of deeper ONH tissues, such as the peripapillary sclera and lamina cribrosa. Application of the contrast-enhancement algorithm significantly increased the interlayer contrast (from 0.48 ± 0.22 to a maximum of 0.89 ± 0.05; P < 0.001) and thus allowed a better differentiation of tissue boundaries. Contrast enhancement was robust only when compensation was considered. CONCLUSIONS The proposed algorithms are simple and can significantly improve the quality of ONH images clinically captured with OCT. This study has important implications, as it will help improve our ability to perform automated segmentation of the ONH; quantify the morphometry and biomechanics of ONH tissues in vivo; and identify potential risk indicators for glaucoma.
Measuring XML schema standard quality change through versioning

Quality measurements of XML schemas are difficult to perform objectively, providing all aspects of quality demands. However, an approximate evaluation of XML schema's quality and validation, whether a higher version of an XML schema standard is in fact an improvement, is useful information for XML schema users. The paper addresses who are the users of XML schemas, what aspects of XML schemas are vital to its quality and how to measure those aspects. We present 3 quality aspects in more detail: (1) structure type, (2) re-use possibilities and (3) balance of building blocks. A table of all included variables, that were measured, is provided. Based on results of over 200 XML schemas, quality assessment are given, including data standardization methods. Measurement results of XML schema's versions are compared, providing insight into quality growth (or decline) through versioning.
A longitudinal study of the hyaluronan level in the serum of patients with malignant mesothelioma under treatment. Hyaluronan as an indicator of progressive disease

The serum hyaluronan levels of 37 patients with malignant mesothelioma were followed during the course of treatment (high doses of methotrexate were given to 32 of these patients). The patients could be divided into the following two groups: (1) those with progressive disease (n = 17) or (2) those showing improvement during therapy (complete remission [n = 2], partial remission, or no change [n = 18]). On admission to the hospital, the patients with progressive disease showed significantly higher initial serum hyaluronan levels (median value, 250 μg/l) than those in the second group (median value, 97 μg/l) (P < 0.005, Wilcoxon). Serum hyaluronan as a predictor of progressive disease has a sensitivity of 65% and a specificity of 85%. There was a significant increase in serum hyaluronan levels during treatment in patients with progression (P < 0.01). In three patients with initially high levels there was a clear decrease in parallel with the reduction in tumor burden. In the remaining patients of the responder group, the values were constantly low. There was no significant correlation between the hyaluronan level and any other laboratory test performed on blood samples. Pleural fluid was removed for medical reasons from 13 patients. Neither the presence of pleural fluid nor its hyaluronan level were correlated to the progression of the disease. However, there was an interesting negative correlation between serum and pleural hyaluronan levels, indicating that an elevated serum hyaluronan level does not reflect high production in the pleural cavity.
The Release of Immunosuppressive Factor(s) in Young Males Following Exercise

It has been shown that a suppressive protein, acting as an immune suppressor, is generated in animals and humans under particular stresses. However, studies related to immunosuppressive factors in response to the stress resulting from acute exercise are limited. This study compares the effects of pre- and post-exercise human serum on concanavalin A stimulated lymphocyte proliferation of mice. In the present study, blood samples in eight male undergraduates (age 21 ± 0.7 years) were taken before and immediately after ten sets of exercise consisting of 15 free and 30 10-kg loaded squat jumps in each set. The suppression of lymphocyte proliferation was analysed with high pressure liquid chromatography. It was noted from the result of gel chromatography columns that the post-exercise values of the suppression of lymphocyte proliferation, in comparison to corresponding pre-exercise values, were generally greater with significant differences observed in 7.5th–9th min post-exercise eluates (P < 0.05). Such findings suggest that intense eccentric type exercise may lead to generation of immunosuppressive factor(s) in young males.