Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of Mouse Spleen Cells by Subtractive Proteomics*S

Major analytical challenges encountered by shotgun proteome analysis include both the diversity and dynamic range of protein expression. Often new instrumentation can provide breakthroughs in areas where other analytical improvements have not been successful. In the current study, we utilized new instrumentation (LTQ FT) to characterize complex protein samples by shotgun proteomics. Proteomic analyses were performed on murine spleen tissue separated by magnetic beads into distinct CD45− and CD45+ cell populations. Using shotgun protein analysis we identified ∼2,000 proteins per cell group by over 12,000 peptides with mass deviations of less than 4.5 ppm. Datasets obtained by LTQ FT analysis provided a significant increase in the number of proteins identified and greater confidence in those identifications and improved reproducibility in replicate analyses. Because CD45− and not CD45+ cells are able to regenerate functional pancreatic islet cells in a mouse model of type I diabetes, protein expression was further compared by a subtractive proteomic approach in search of an exclusive protein expression profile in CD45− cells. Characterization of the proteins exclusively identified in CD45− cells was performed using gene ontology terms via the Javascript GoMiner. The CD45− cell subset readily revealed proteins involved in development, suggesting the persistence of a fetal stem cell in an adult animal.
An iterative method for secure inter-procedural information flow control

An information flow control policy specifies the manner in which classified information flows from one object to another. A link-time algorithm is presented for an information flow certification mechanism designed for modular programming systems. The mechanism combines a compile-time algorithm developed for object-oriented systems with the link-time algorithm described. The compile-time algorithm partially verifies the security of each procedure independently and generates equations which express potential flows caused by parameter passing. The link-time algorithm completes the certification of the entire program by verifying the interprocedural information flows. It analyzes the equations for all procedures in the program and calculates the least fixed point by using a standard iterative method. <<ETX>>
Initial Experience with Symbios Model 7008 Pacemaker

Le Symbios 7008 est capable de traiter les bradycardies et les tachycardies. Nous rapportons ici notre expérience initiale chez 21 patients chez qui ce boitier a été implanté. Tous présentaient des tachyarythmies supraventriculaires qui ont été arretées par stimulation auriculaire rapide (19 pts) ou séquentielle. Plus de la moitié des patients présentaient aussi des bradyarythmies nécessitant une stimulation et ont done ainsi bénéficié des deux fonctions du boitier. En l'état actuel des choses, l'expérience est favorable.
Cryptococcus neoformans Growth and Protection from Innate Immunity Are Dependent on Expression of a Virulence-Associated DEAD-Box Protein, Vad1

ABSTRACT The fungus Cryptococcus neoformans has emerged as a major cause of meningoencephalitis worldwide. Host response to the fungus involves both innate and adaptive immunity, but fungal genes that modulate these processes are poorly understood. Previous studies demonstrated attenuated virulence of a mutant of a virulence-associated DEAD-box protein (VAD1) in mice, despite normal growth at host temperatures, suggesting modulation of the immune response. In the present study, the Δvad1 mutant demonstrated progressive clearance from lung and was unable to induce pathological lesions or to cause extrapulmonary disease, despite retaining its ability to grow in mouse serum and a J774.16 macrophage cell line. Pulmonary clearance occurred with a minimal cellular infiltrate, marked by reduced CD4 cells, CD11b+ Ly6Chigh monocytes, and F4/80+ macrophages, but the mutant strain retained recruitment of CD8 cells, compared to infections with wild-type fungi. Adaptive cytokine responses were reduced, including Th1, Th2, and Th17 cytokines; however, early gamma interferon (IFN-γ) and tumor necrosis factor alpha (TNF-α) responses were retained while nonprotective interleukin 4 (IL-4) and IL-5 were diminished. Furthermore, the Δvad1 mutant was controlled in lungs despite CD4/CD8 cell depletion. These data, along with improved phagocytosis by macrophages and increases in early/innate IL-1α, IFN-γ, and chemokines elicited in the lungs within 3 days of infection with the Δvad1 mutant, indicate that VAD1 expression reduces innate recognition of C. neoformans, rendering the yeast resistant to elimination by the innate mechanisms of host defense. Thus, our studies define a novel role of the cryptococcal Vad1 protein as a central regulator of cryptococcal virulence and illustrate that Vad1 promotes microbe resistance to innate host defenses.
Web Unique Method (WUM): An Open Source Blackbox Scanner for Detecting Web Vulnerabilities

The internet has provided a vast range of benefits to society, and empowering people in a variety of ways. Due to incredible growth of Internet usage in past 2 decades, everyday a number of new Web applications are also becoming a part of World Wide Web. The distributed and open nature of internet attracts hackers to interrupt the smooth services of web applications. Some of the famous web application vulnerabilities are SQL Injection, Cross Site Scripting (XSS) and Cross Site request Forgery (CSRF). We believe that in order to encounter these vulnerabilities; the web application vulnerabilities scanner should have strong detection and prevention rules to ease the problem. At present, a number of web application vulnerabilities scanners have been proposed by research community, such as ZED Attack Proxy (ZAP) by AWASP, Wapiti by sourceforge.net and w3af by w3af.org. However, these scanners cannot challenge all web vulnerabilities. This research proposed and develop a vulnerability scanning tool WUM (web unique method) to detection and prevention of all the major instance vulnerabilities and demonstrates how to detect unauthorized access by finding vulnerabilities. With the efficient use of this tool, the developers are able to find potentially vulnerable web application. WUM generated a high level of accuracy and compatibility, which is elaborated underneath. The result of the experiment shows proposed vulnerability scanner tool WUM which gives less false positive and detect more vulnerabilities in comparison of well-known black box scanners.
Usability: Happier Users Mean Greater Profits

Abstract Historically, usability has been associated with the user interface, and human–computer interaction (HCI) professionals have tended to concentrate their work on it. Usability is, however, much deeper than the user interface. Usability refers to the complex set of choices that ends up allowing the users of the system to accomplish one or more specific tasks easily, efficiently, enjoyably, and with a minimum of errors.
Interaction properties of human TRAMP‐like proteins and their role in pre‐rRNA 5′ETS turnover

In yeast, the Trf4/5‐Air1/2‐Mtr4 polyadenylation (TRAMP) complex acts as a cofactor for the nuclear exosome to promote degradation of various RNAs. However, the corresponding machinery in mammals is less characterized. We analyzed the interactions of the human TRAMP‐like proteins, PAPD5, ZCCHC7, and MTR4, with the nuclear exosome. PAPD5 and ZCCHC7 exhibited mutual interactions in presence of the exosome catalytic subunit RRP6, whereas MTR4 was dispensable for their assembly. Furthermore, the human TRAMP‐like proteins were involved in the RRP6‐catalyzed turnover of pre‐rRNA 5′ETS fragments. These results suggest the significant role for RRP6 in the assembly of TRAMP‐like proteins during nucleolar RNA surveillance.
Evidence for Continuous Processing of Visual Information in a Manual Video-Aiming Task

Research shows that individuals are able to correct for an experimentally-induced and unexpected aiming error (i.e., a cursor jump), even when they do not detect it consciously. Researchers have interpreted these results to be evidence of continuous processing of visual afferent information for movement control. The authors conducted 2 experiments to determine whether they would gain additional support for this proposition by showing that correction for a cursor jump can be initiated outside the central visual field. In addition, the authors wanted to determine whether the normally occurring modulation of the ongoing movement is affected by detection and correction of the cursor jump. Participants performed video-aiming movements in which a 30-mm cursor jump occurred in a small proportion of the trials. The results indicate that correction for the cursor jump was initiated when the cursor was as far as 15° of visual angle from the target. In addition, the authors observed accurate corrections when vision of the cursor was withdrawn soon after the cursor jump. Last, online control processes reducing initial movement variability were not significantly affected by the detection and correction for the cursor jump. The results suggest near continuous monitoring of visual afferent information but a more discrete movement-correction process.
The DNA region of phage BF23 encoding receptor binding protein and receptor blocking lipoprotein lacks homology to the corresponding region of closely related phage T5

Analysis of the DNA region upstream of the BF23 hrs gene revealed a genetic organisation similar to that of closely related phage T5. A gene encoding a lipoprotein (llp BF23) is located directly upstream of the gene encoding the receptor binding protein (hrs ) but is transcribed in opposite direction. The gene is followed by four open reading frames transcribed in the same direction. The llp BF23 gene product does not show similarity to the corresponding T5 LlpT5 protein, however, like LlpT5 does for FhuA it blocks the BtuB receptor for BF23 infection. While no similarity between BF23 and T5 was observed for the DNA region encoding Llp and the receptor binding protein, the flanking regions were highly similar. Based on our results we conclude that a genetic module, the receptor‐binding/receptor‐blocking module, exists in phages BF23 and T5. Due to exclusion of homologous recombination within this module, it is hereditary only as an intact module: separation of the receptor‐binding gene from the receptor‐blocking gene, which apparently results in reduced fitness of the phage due to inactivation of progeny phage by active receptor proteins in the outer membranes of lysed cells, is thus effectively prevented. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Design Criteria for the Quadratically Interpolated FFT Method ( I ) : Bias due to Interpolation October 13 , 2004

Due to its simplicity and accuracy, quadratic peak interpolation in a zero-padded Fast Fourier Transform (FFT) has been widely used for sinusoidal parameter estimation in audio applications. While general criteria can guide the choice of window type, FFT length, and zero-padding factor, it is sometimes desirable in practice to know more precisely the requirements for achieving a prescribed error bound. The purpose of this series of papers is to investigate the estimation error bias associated with the choice of analysis parameters, and provide precise criteria for designing the optimum estimator. In this first paper, we focus on the bias caused by quadratic interpolation. We numerically determine the maximum error bias in the estimation of the frequency, amplitude and phase for various zero-padding factors, and determine the minimum zero-padding factors needed for achieving prescribed error bounds. The results show, for example, zero-padding factors of {4.1, 2.4, 1.9} are sufficient for achieving a 0.1% frequency-error bound when using {rectangular, Hann or Hamming, Blackman} windows, respectively. Noise robustness of the estimator is also investigated. We confirm the estimator works as well as a ML estimator within a certain S/N ratio range.
Severity of Subcortical Gray Matter Hyperintensity Predicts ECT Response in Geriatric Depression

Objective To determine the effect of subcortical white and gray matter lesions on ECT outcome. Method 41 geriatric psychiatric inpatients underwent an MRI scan during their ECT work-up. Periventricular, deep white matter, and subcortical gray matter hyperintensities were graded. The associations of low versus high hyperintensity ratings and symptom scores, Clinical Global Impression severity (CGS) ratings, Montgomery-Asberg Depression Scale score, and number of treatments were examined using t-tests and repeated measures ANOVA. Results Patients with more severe subcortical gray hyperintensities (SCG) had significantly less improvement as measured by CGS ratings. Conclusions SCG severity may limit the improvement of patients receiving ECT. Further studies are needed to examine differences based on electrode placement and to determine whether patients with severe SCG may require more ECT treatments in an index course.
GATA2 Regulates Body Water Homeostasis through Maintaining Aquaporin 2 Expression in Renal Collecting Ducts

ABSTRACT The transcription factor GATA2 plays pivotal roles in early renal development, but its distribution and physiological functions in adult kidney are largely unknown. We examined the GATA2 expression pattern in the adult kidney by tracing green fluorescent protein (GFP) fluorescence in Gata2GFP/+ mice that recapitulate endogenous GATA2 expression and found a robust GFP expression specifically in the renal medulla. Upon purification of the GFP-positive cells, we found that collecting duct (CD)-specific markers, including aquaporin 2 (Aqp2), an important channel for water reabsorption from urine, were abundantly expressed. To address the physiological function of GATA2 in the CD cells, we generated renal tubular cell-specific Gata2-deficient mice (Gata2-CKO) by crossing Gata2 floxed mice with inducible Pax8-Cre mice. We found that the Gata2-CKO mice showed a significant decrease in Aqp2 expression. The Gata2-CKO mice exhibited high 24-h urine volume and low urine osmolality, two important signs of diabetes insipidus. We introduced biotin-tagged GATA2 into a mouse CD-derived cell line and conducted chromatin pulldown assays, which revealed direct GATA2 binding to conserved GATA motifs in the Aqp2 promoter region. A luciferase reporter assay using an Aqp2 promoter-reporter showed that GATA2 trans activates Aqp2 through the GATA motifs. These results demonstrate that GATA2 regulates the Aqp2 gene expression in CD cells and contributes to the maintenance of the body water homeostasis.
Wound measurement comparing the use of acetate tracings and Visitrak digital planimetry.

AIMS This study aimed to compare acetate tracing with the new digital planimetry system Visitrak (Smith + Nephew). It also aimed to compare the percentage change in wound size after four weeks using both methods. BACKGROUND There is a need for development and more widespread use of objective tools in wound management. Wound measurement is an integral part of wound assessment and provides possibly the most objective tool available. To achieve this, practitioners use a variety of methods including acetate tracing and digital planimetry. Studies have demonstrated good inter- and intrarater reliability using both methods. METHODS A retrospective, random selection of wound tracings of superficial leg ulcers was completed until 25 tracings of <10 cm2 and 25 tracings of >10 cm2 were obtained. Wound area was calculated firstly by manually counting squares completely within the wound border and those half or more within the border as 1 cm2. The area was then calculated using the Visitrak system. RESULTS The difference between the acetate and Visitrak for wounds <10 cm2 not significant (P = 0.330). For wounds >10 cm2 the difference between both methods was significant (P = 0.008). After four weeks the number of tracings available was too small for any conclusions to be made. CONCLUSION Wound measurement should become part of routine practice. Acetate offers a good indicator of wound size and digital planimetry can enhance the precision of the measurement. RELEVANCE TO CLINICAL PRACTICE Accurate and objective wound measurement is a vital component of wound management. It is essential that nurses have adequate training and skills in wound measuring to assess wounds correctly and objectively. Findings from this study can be used when deciding which method should be used in a particular setting when outcomes and cost have been considered. Accurate on-going wound measuring contributes to improved quality of patient care, more effective communication between professionals, as a predictor to wound healing, to document progress and assess treatment efficacy.
Realtime Epileptic Seizures Detection and Alert System Using NI LabView

For people who have been are suffering from epileptic seizures, a real time system is developed which is helpful in detecting such cases, is Smart epilepsy detection and alert system is an advanced technology by which we have developed a electronic gadget. Using that kit we can save the life of the person who is really effecting with the condition. It will do the help in both the ways means not only checks the condition but also sends an SMS to the concerned doctor for the patient’s live saving sake. To implement all the above process we have used mainly four modules micro controller KEIL module, ARDUINO module, GSM module to send an SMS, and LABVIEW.
Extracellular matrix molecules and synaptic plasticity: immunomapping of intracellular and secreted Reelin in the adult rat brain

Reelin, a large extracellular matrix glycoprotein, is secreted by several neuron populations in the developing and adult rodent brain. Secreted Reelin triggers a complex signaling pathway by binding lipoprotein and integrin membrane receptors in target cells. Reelin signaling regulates migration and dendritic growth in developing neurons, while it can modulate synaptic plasticity in adult neurons. To identify which adult neural circuits can be modulated by Reelin‐mediated signaling, we systematically mapped the distribution of Reelin in adult rat brain using sensitive immunolabeling techniques. Results show that the distribution of intracellular and secreted Reelin is both very widespread and specific. Some interneuron and projection neuron populations in the cerebral cortex contain Reelin. Numerous striatal neurons are weakly immunoreactive for Reelin and these cells are preferentially located in striosomes. Some thalamic nuclei contain Reelin‐immunoreactive cells. Double‐immunolabeling for GABA and Reelin reveals that the Reelin‐immunoreactive cells in the visual thalamus are the intrinsic thalamic interneurons. High local concentrations of extracellular Reelin selectively outline several dendrite spine‐rich neuropils. Together with previous mRNA data, our observations suggest abundant axoplasmic transport and secretion in pathways such as the retino‐collicular tract, the entorhino‐hippocampal (‘perforant’) path, the lateral olfactory tract or the parallel fiber system of the cerebellum. A preferential secretion of Reelin in these neuropils is consistent with reports of rapid, activity‐induced structural changes in adult brain circuits.
Probing Unconscious Visual Processing with the McCollough Effect

The McCollough effect, an orientation-contingent color aftereffect, has been known for over 30 years and, like other aftereffects, has been taken as a means of probing the brain's operations psychophysically. In this paper, we review psychophysical, neuropsychological, and neuroimaging studies of the McCollough effect. Much of the evidence suggests that the McCollough effect depends on neural mechanisms that are located early in the cortical visual pathways, probably in V1. We also review evidence showing that the aftereffect can be induced without conscious perception of the induction patterns. Based on these two lines of evidence, it is argued that our conscious visual experience of the world arises in the cortical visual system beyond V1.
Flow cytometric determination of spermatozoa binding monoclonal antibodies does not improve the prediction of fertility potential

Summary. In a previous publication the determination of binding of several monoclonal antibodies to human spermatozoa by flow cytometry was described in 223 patients. In normozoo‐spermic samples the percentage of spermatozoa binding antibodies was higher than in samples with oligozoospermia. However, only weak correlations were found between the percentage of antibody binding spermatozoa and sperm count, motility and morphology. Thus the antibody binding may represent a property different from the classical parameters and might improve the prediction of fertility in the patients. A questionnaire was sent to all the patients inquiring about a conception in their female partners. One hundred and twenty one out of the 223 patients replied, 103 of whom we were able to evaluate. Forty five of them had induced a pregnancy in their partners. The mean values of sperm count, motility and morphological normal cells, as well as the percentages of cells that bound antibodies, were significantly higher in the group of men whose partners became pregnant, than in those who had not achieved conception. The differences, however, were only marginal. We conclude from our results that the determination of the percentage of spermatozoa binding the monoclonal antibodies used in our study is not likely to improve the prediction of conception probability.
Automatic semantic interpretation of anatomic spatial relationships in clinical text

A set of semantic interpretation rules to link the syntax and semantics of locative relationships among anatomic entities was developed and implemented in a natural language processing system. Two experiments assessed the ability of the system to identify and characterize physico-spatial relationships in coronary angiography reports. Branching relationships were by far the most common observed (75%), followed by PATH (20%) and PART/WHOLE relationships. Recall and precision scores were 0.78 and 0.67 overall, suggesting the viability of this approach in semantic processing of clinical text.
Stability of Stochastic Nonlinear Systems With State-Dependent Switching

In this paper, the problem of stability on stochastic systems with state-dependent switching is investigated. To analyze properties of the switched system by means of Itô's formula and Dynkin's formula, it is critical to show switching instants being stopping times. When the given active-region set can be replaced by its interior, the local solution of the switched system is constructed by defining a series of stopping times as switching instants, and the criteria on global existence and stability of solution are presented by Lyapunov approach. For the case where the active-region set can not be replaced by its interior, the switched systems do not necessarily have solutions, thereby quasi-solution to the underlying problem is constructed and the boundedness criterion is proposed. The significance of this paper is that all the results presented depend on some easily-verified assumptions that are as elegant as those in the deterministic case, and the proofs themselves provide design procedures for switching controls.
Molecular evolution Positive natural selection has driven the evolution of the Hsp 70 s in Diguetia spiders

Hsp70s are a ubiquitous family of highly conserved proteins. Hsp70s are chaperones and have important roles in both protein folding and thermotolerance. It has been widely assumed that Hsp70 sequence evolution is governed by the strong functional constraints imposed by its crucial cellular functions. In this study of cytosolic heatinducible Hsp70s from three spider families, we have found clear evidence of positive natural selection altering Hsp70s in desert-dwelling and heat-loving Diguetidae spiders. These spiders are a small family restricted to deserts. They display heat-tolerant behaviours not seen in their closest relatives, the Pholcidae and Plectreuridae.