gebhart/patrepeval huggingface dataset:
Developmental omega‐3 supplementation improves motor skills in juvenile‐adult rats (2009)

Long-chain polyunsaturated fatty acids are critical for brain growth spurt during both foetal and postnatal period. They play important roles in the expression of genes regulating cell differentiation and neuronal growth, as well as in the development of synaptic processing of neural cell interaction. Foetus and placenta are dependent on maternal supply for their growth and development, and supplemented infants show significantly greater mental and psychomotor scores. In particular, it has been shown that if mothers take omega-3 supplements, their babies are smarter and better physically coordinated. On these grounds, the aim of the present study was to investigate, in the Sprague-Dawley rat, the effects of perinatal treatment with omega-3 on motor activity, motor coordination, motor learning and memory. From gestational day 8 throughout the lactation period, dams received either an emulsion of 0.05g/kg body weight omega-3 in fruit juice, or an emulsion of 1g/kg body weight omega-3 in fruit juice or just the fruit juice (control). Omega-3 formula was made of 27% docosahexaenoic acid and 53% eicosapentaenoic acid. On the day of birth (postnatal day 1), all pups were weighed, and then randomly culled to eight pups per litter. Pups were weaned at 21 days of age. One male pup per litter from each litter (control, n=6; omega-3 0.05g/kg, n=5; omega-3 1g/kg, n=6) was used. Both control and treated rats were tested for (i) locomotor activity using the open field paradigm, (ii) motor coordination and motor learning using the rotarod/accelerod task and (iii) memory using the passive avoidance paradigm. Rats were tested on postnatal day 21 and re-tested on postnatal day 90. As a result, docosahexaenoic acid and eicosapentaenoic acid supplementation significantly improved motor coordination. In particular, the latency to fall at the first speed was significantly increased in the treated rats as compared to the control animals. This benefit was observed with both doses at each tested age. The rat performance in accelerating rotation speed mode, which provides an indication of motor learning ability, was not modified by the omega-3 supply. Finally, the omega-3 treatment did not influence motor activity in the open field-tested rats, nor the memory ability in the passive avoidance task. In conclusion, perinatal omega-3 supplementation exerts a long lasting beneficial effect on the rotarod performance indicating improvement in balance and motor coordination and, possibly, in the functioning of pathways governing this task.
Proinflammatory role of vasopressin through V1b receptors in hapten-induced experimental colitis in rodents: implication in IBD (2010)

Vasopressin and its receptors modulate several gut functions, but their role in intestinal inflammation is unknown. Our aims were to determine 1) the localization of V1b receptors in human and rodent colon, 2) the role of vasopressin and V1b receptors in experimental colitis using two approaches: V1b⁻(/)⁻ mice and a selective V1b receptor antagonist, SSR149415, and 3) the mechanisms involved. V1b receptors were localized in normal and inflamed colon from humans and rats. Experimental colitis was induced in rats and mice and some groups were treated before or after colitis induction with oral SSR149415 (3-30 mg/kg). Other groups of mice were submitted to dehydration to increase vasopressin plasma levels, prior to colitis induction. Body weight, damage scores, MPO, and TNF-α tissue levels were determined. Finally, colonic segments of wild-type (WT) and V1b⁻(/)⁻ mice were mounted in Ussing chambers and paracellular permeability in response to vasopressin was studied. V1b receptors were expressed in enterocytes and ganglia cells of the enteric nervous system of human and rat intestine. Expression levels were independent from inflammatory status. Colitis was less severe in rodents treated by either preventive or curative SSR149415 and in V1b⁻(/)⁻ mice. 2,4,6-Trinitrobenzene sulfonic acid induced a strong mortality in dehydrated animals that was reversed by preventive SSR149415 or mast cell stabilizer. Vasopressin significantly increased paracellular permeability in WT, but not in V1b⁻(/)⁻ mice. Preincubation of colon tissues with SSR149415 abolished the vasopressin effect. Similarly, vasopressin had no effect in colonic preparations from WT mice pretreated with mast cell stabilizers. Vasopressin, through V1b receptor interaction, has proinflammatory properties linked to mast cell activation and downstream alterations of the colonic epithelial barrier. These findings underline the potential interest of V1b receptor blockers in gut inflammatory diseases.
Transcription-induced Chromatin Remodeling at the c-myc Gene Involves the Local Exchange of Histone H2A.Z (2005)

The post-translational modification of histones and the incorporation of core histone variants play key roles in governing gene expression. Many eukaryotic genes regulate their expression by limiting the escape of RNA polymerase from promoter-proximal pause sites. Here we report that elongating RNA polymerase II complexes encounter distinct chromatin landscapes that are marked by methylation of lysine residues Lys(4), Lys(79), and Lys(36) of histone H3. However, neither histone methylation nor acetylation directly regulates the release of elongation complexes stalled at promoter-proximal pause sites of the c-myc gene. In contrast, transcriptional activation is associated with local displacement of the histone variant H2A.Z within the transcribed region and incorporation of the major histone variant H2A. This result indicates that transcribing RNA polymerase II remodels chromatin in part through coincident displacement of H2A.Z-H2B dimers and incorporation of H2A-H2B dimers. In combination, these results suggest a new model in which the incorporation of H2A.Z into nucleosomes down-regulates transcription; at the same time it may act as a cellular memory for transcriptionally poised gene domains.
Study of statistic damage constitutive model for shear failure rock (2011)

Considering the heterogeneity of rock, cohesion for elements throughout the rock is supposed to follow a three parameter Weibull distribution, and the cohesion decreases to zero when the element fails according to Mohr–Coulomb criterion. A damage evolution equation for rock undergoing compression is derived based on the statistic theory and shear force equilibrium equation of the shear failure plane. The derived damage evolution equation is reasonable because it considers the failed elements ability of resisting pressure and frictional shear force. A statistic damage constitutive model is then established and verified by comparing the simulated finite element method results with laboratory triaxial testing results. Numerical results show that the developed model simulates the peak and residual strength of triaxial tests very well.
Maximizing throughput for satellite communication in a hybrid FEC/ARQ scheme using LDPC codes (2005)

A hybrid forward error correction (FEC)/automatic repeat request (ARQ) has been considered as a mechanism for providing reliable communication between NASA orbiters and landers at the planet Mars. On such a link it is proposed to use a family of capacity achieving LDPC channel codes for FEC and go-back-N protocols for ARQ. In this paper, we analyze such a system and derive equations for its performance. We then use these equations to optimize the performance of the link in terms of information throughput subject to limitations on maximum channel baud rate and spacecraft power and select the best channel code and packet size accordingly at different link path lengths. In this optimization, first the frame error rate of the channel code is expressed in terms of a simple exponential function of the transmitted bit signal-to-noise ratio (E <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">b</sub> /N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> ), obtained through curve-fitting. Then the standard throughput equation for the go-back-N protocol in terms of the channel codes frame error rate is derived. Next, using the equations for the throughput and the frame error rate, the received E <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">b</sub> /N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> is calculated as a function of transmitted E <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">b</sub> /N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> . By minimizing this function, the throughput of the system is maximized for a given available spacecraft power. In the course of this optimization, we quantify the advantage afforded by a system that supports a set of possible code rates and bandwidths as opposed to a system that uses a single rate at different link path lengths.
Optimum Injected Current Harmonics to Minimize Peak-to-Average Ratio of LED Current for Electrolytic Capacitor-Less AC–DC Drivers (2010)

The lifetime of an ac-dc LED driver can be increased by eliminating the electrolytic capacitor. Unfortunately, it results in pulsation with twice the line frequency in the driving current. Injection of the third and fifth harmonics into the input current can reduce the peak-to-average ratio of the driving current, which is beneficial for reliable operation of the LEDs. This letter discusses the relationship between the peak-to-average ratio and the injected harmonics, and the optimum injected third and fifth harmonics to minimize the peak-to-average ratio are obtained, while ensuring that the input power factor is higher than 0.9 to meet the regulatory requirement such as the ENERGY STAR. This optimum injected current harmonics is verified by a flyback-based electrolytic capacitor-less LED driver with 25 V, 0.35 A output.
Detecting Vulnerabilities in Web Applications by Clustering Web Pages (2008)

Abstract – In this paper, we propose a new approach to detecting vulnerabilities in Web applications. Majority of current Web application vulnerability scanners rely on detecting vulnerabilities by detecting common error messages or input vectors used in testing. The method we propose in this paper is based on detecting unusual behavior of a Web application. Differences between pages are analyzed by examining page structure, i.e. HTML elements. Variations from standard page structure could indicate raised errors in the Web application and could indicate a vulnerability. Issues that arise in building such a tool will be described here. I.
Long ncRNA expression associates with tissue-specific enhancers (2015)

Long non-coding RNAs (ncRNA) have recently been demonstrated to be expressed from a subset of enhancers and to be required for the distant regulation of gene expression. Several approaches to predict enhancers have been developed based on various chromatin marks and occupancy of enhancer-binding proteins. Despite the rapid advances in the field, no consensus how to define tissue specific enhancers yet exists. Here, we identify 2,695 long ncRNAs annotated by ENCODE (corresponding to 28% of all ENCODE annotated long ncRNAs) that overlap tissue-specific enhancers. We use a recently developed algorithm to predict tissue-specific enhancers, PreSTIGE, that is based on the H3K4me1 mark and tissue specific expression of mRNAs. The expression of the long ncRNAs overlapping enhancers is significantly higher when the enhancer is predicted as active in a specific cell line, suggesting a general interdependency of active enhancers and expression of long ncRNAs. This dependency is not identified using previous enhancer prediction algorithms that do not account for expression of their downstream targets. The predicted enhancers that overlap annotated long ncRNAs generally have a lower ratio of H3K4me1 to H3K4me3, suggesting that enhancers expressing long ncRNAs might be associated with specific epigenetic marks. In conclusion, we demonstrate the tissue-specific predictive power of PreSTIGE and provide evidence for thousands of long ncRNAs that are expressed from active tissue-specific enhancers, suggesting a particularly important functional relationship between long ncRNAs and enhancer activity in determining tissue-specific gene expression.
Diffusion of arsenic in silicon: Validity of the percolation model (1983)

It is shown that the percolation model previously proposed to explain the high concentration diffusion of phosphorus in Si holds also in the case of arsenic. Suitable numerical values of the parameters are derived, and it is shown that the model allows the simulation of arsenic diffusion in a wide range of experimental conditions.
Protective Killed<i>Leptospira borgpetersenii</i>Vaccine Induces Potent Th1 Immunity Comprising Responses by CD4 and γδ T Lymphocytes (2001)

Leptospira borgpetersenii serovar hardjo is the most common cause of bovine leptospirosis and also causes zoonotic infections of humans. A protective killed vaccine against serovar hardjo was shown to induce strong antigen-specific proliferative responses by peripheral blood mononuclear cells (PBMC) from vaccinated cattle by 2 months after the first dose of vaccine. This response was absent from nonvaccinated control cattle. The mean response peaked by 2 months after completion of the two-dose vaccination regimen, and substantial proliferation was measured in in vitro cultures throughout the 7 months of the study period. Variations in magnitude of the response occurred among the vaccinated animals, but by 7 months postvaccination there was a substantial antigen-specific response with PBMC from all vaccinated animals. Up to one-third of the PBMC from vaccinated animals produced gamma interferon (IFN-gamma) after 7 days in culture with antigen, as ascertained by flow cytometric analysis, and significant levels of IFN-gamma were measured in culture supernatants by enzyme-linked immunosorbent assay. Two-color immunofluorescence revealed that one-third of the IFN-gamma-producing cells were gammadelta T cells, with the remaining cells being CD4(+) T cells. The significance of this study is the very potent Th1-type immune response induced and sustained following vaccination with a killed bacterial vaccine adjuvanted with aluminum hydroxide and the involvement of gammadelta T cells in the response. Moreover, induction of this Th1-type cellular immune response is associated with the protection afforded by the bovine leptospiral vaccine against L. borgpetersenii serovar hardjo.
The Rainbow Connection - Why Now is the Time for Smallsat Optical Downlinks (2017)

Many small satellite missions are data constrained, with payloads generating more data than can be sent to Earth over radio downlinks. To address this, we have developed a novel optical downlink system, comprising a space and ground terminal. The space terminal projects a 1 W laser beam with wavelength 785 nm, on-off modulated at 1 Gbps. It aims this at the ground station using a MEMS steering mirror, guided by an integral star tracker and rate sensors. The ground station is a 22” reflecting telescope with a fine steering mirror at the focal plane and a silicon avalanche photodiode detector. The use of a semiconductor tapered power amplifier, in place of a traditional doped fiber amplifier, makes this compact and low power. We believe this technology will allow even smaller spacecraft to carry data-intensive payloads.
Characterization of hNek6 Interactome Reveals an Important Role for Its Short N-Terminal Domain and Colocalization with Proteins at the Centrosome (2010)

Physical protein-protein interactions are fundamental to all biological processes and are organized in complex networks. One branch of the kinome network is the evolutionarily conserved NIMA-related serine/threonine kinases (Neks). Most of the 11 mammalian Neks studied so far are related to cell cycle regulation, and due to association with diverse human pathologies, Neks are promising chemotherapeutic targets. Human Nek6 was associated to carcinogenesis, but its interacting partners and signaling pathways remain elusive. Here we introduce hNek6 as a highly connected member in the human kinase interactome. In a more global context, we performed a broad data bank comparison based on degree distribution analysis and found that the human kinome is enriched in hubs. Our networks include a broad set of novel hNek6 interactors as identified by our yeast two-hybrid screens classified into 18 functional categories. All of the tested interactions were confirmed, and the majority of tested substrates were phosphorylated in vitro by hNek6. Notably, we found that hNek6 N-terminal is important to mediate the interactions with its partners. Some novel interactors also colocalized with hNek6 and γ-tubulin in human cells, pointing to a possible centrosomal interaction. The interacting proteins link hNek6 to novel pathways, for example, Notch signaling and actin cytoskeleton regulation, or give new insights on how hNek6 may regulate previously proposed pathways such as cell cycle regulation, DNA repair response, and NF-κB signaling. Our findings open new perspectives in the study of hNek6 role in cancer by analyzing its novel interactions in specific pathways in tumor cells, which may provide important implications for drug design and cancer therapy.
Professional's Guide to Robust Spreadsheets: Using Examples in Lotus 1-2-3 and Microsoft Excel (1996)

From the Publisher:
This is the first book that gives professionals the specialized tools and techniques they need to write more effective worksheets.Thousands of managers, accountants, and other business professionals are called upon to design and implement large spreadsheets that must be used by multiple users over long periods of time. Learn better ways to get input from users, prevent errors and incorrect calculations -- and make sure your spreadsheets actually support decision-making, instead of just delivering incoherent piles of numbers. Discover macro techniques that help you streamline both development and usage of spreadsheets. Learn systematic quality control techniques that are invaluable in the corporate environment.Professional spreadsheet users.
Regulation of the expression of human C[epsilon] germline transcript (1993)

Transcriptional regulation for Ig H chain germline transcripts induced by cytokines is a topic of recent interest for the understanding of the mechanism of class switch recombination. Among human B cell lines examined, the authors have found that a human IgM-producing B cell line, DND39 (EBV negative) expressed germ-line transcripts of [epsilon] constant gene (C[epsilon]) when stimulated with lL-4. In this study, the regulatory element responsible for the expression of lL-4-induced human C[epsilon] germ-line transcript was determined using DND39 cells. To identify the lL-4 responsive promotor/enhancer element, deletion analysis of the upstream region of the germ-line exon (l[epsilon]) of the C[epsilon] germ-line transcript which is located 5' to the switch region, was performed by using a luciferase gene as a reporter. Deletion analysis showed that a DNA fragment which lies between [minus]215 and [minus]154 bp upstream from the most 3' transcriptional initiation site of human l[epsilon] gene is fully responsible for the induction of germ-line transcripts by IL-4. According to a mutational analysis, the DNA fragment between [minus]163 and [minus]152 bp was identified to be a novel IL-4 responsive element in a human C[epsilon] gene. Electrophoretic gel mobility shift assay showed the presence of IL-4-induced nuclear factor that specifically boundmore » to this IL-4 responsive element. This novel IL-4 responsive element and an IL-4-induced DNA binding protein may play an important role for the induction of C[epsilon] germ-line transcript as well as class switching to IgE. 54 refs., 7 figs.« less
An extended bacterial reductive pyrimidine degradation pathway that enables nitrogen release from β-alanine (2019)

The reductive pyrimidine catabolic pathway is the most widespread pathway for pyrimidine degradation in bacteria, enabling assimilation of nitrogen for growth. This pathway, which has been studied in several bacteria including Escherichia coli B, releases only one utilizable nitrogen atom from each molecule of uracil, whereas the other nitrogen atom remains trapped in the end product β-alanine. Here, we report the biochemical characterization of a β-alanine:2-oxoglutarate aminotransferase (PydD) and an NAD(P)H-dependent malonic semialdehyde reductase (PydE) from a pyrimidine degradation gene cluster in the bacterium Lysinibacillus massiliensis. Together, these two enzymes converted β-alanine into 3-hydroxypropionate (3-HP) and generated glutamate, thereby making the second nitrogen from the pyrimidine ring available for assimilation. Using bioinformatics analyses, we found that PydDE homologs are associated with reductive pyrimidine pathway genes in many Gram-positive bacteria in the classes Bacilli and Clostridia. We demonstrate that Bacillus smithii grows in a defined medium with uracil or uridine as its sole nitrogen source and detected the accumulation of 3-HP as a waste product. Our findings extend the reductive pyrimidine catabolic pathway and expand the diversity of enzymes involved in bacterial pyrimidine degradation. The reductive pyrimidine catabolic pathway is the most widespread pathway for pyrimidine degradation in bacteria, enabling assimilation of nitrogen for growth. This pathway, which has been studied in several bacteria including Escherichia coli B, releases only one utilizable nitrogen atom from each molecule of uracil, whereas the other nitrogen atom remains trapped in the end product β-alanine. Here, we report the biochemical characterization of a β-alanine:2-oxoglutarate aminotransferase (PydD) and an NAD(P)H-dependent malonic semialdehyde reductase (PydE) from a pyrimidine degradation gene cluster in the bacterium Lysinibacillus massiliensis. Together, these two enzymes converted β-alanine into 3-hydroxypropionate (3-HP) and generated glutamate, thereby making the second nitrogen from the pyrimidine ring available for assimilation. Using bioinformatics analyses, we found that PydDE homologs are associated with reductive pyrimidine pathway genes in many Gram-positive bacteria in the classes Bacilli and Clostridia. We demonstrate that Bacillus smithii grows in a defined medium with uracil or uridine as its sole nitrogen source and detected the accumulation of 3-HP as a waste product. Our findings extend the reductive pyrimidine catabolic pathway and expand the diversity of enzymes involved in bacterial pyrimidine degradation.