gebhart/patrepeval huggingface dataset:
Performance analysis of scheduling and dropping policies in vehicular delay-tolerant networks (2010)

Abstract—Vehicular Delay-Tolerant Networking (VDTN) was proposed as a new variant of a delay/disruptive-tolerant network, designed for vehicular networks. These networks are subject to several limitations including short contact durations, connectivity disruptions, network partitions, intermittent connectivity, and long delays. To address these connectivity issues, an asynchronous, store-carry-and-forward paradigm is combined with opportunistic bundle replication, to achieve multi-hop data delivery. Since VDTN networks are resource-constrained, for example in terms of communication bandwidth and storage capacity, a key challenge is to provide scheduling and dropping policies that can improve the overall performance of the network. This paper investigates the efficiency and tradeoffs of several scheduling and dropping policies enforced in a Spray and Wait routing scheme. It has been observed that these policies should give preferential treatment to less replicated bundles for a better network performance in terms of delivery ratio and average delivery delay.
Sterilization of microorganisms by high-voltage pulsed discharge under water. (1988)

Experimental results are described for sterilization of microorganisms by means of high-voltage pulsed discharge under water, in which the sterilization mechanism is quite different from that of the ordinary thermal method. Immobilized yeast cells did not suffer great damage after the treatment by pulsed discharges. On the contra-ry, microorganisms suspended in bulk liquid were killed to a much greater extent than the immobilized yeast cells. Under observation with a scanning electron microscope the treated yeast cells looked like a deflated ballon, perhaps the result of leakage of the cell contents (cytolysis) after irreversible damage to the cell wall or cell membrane by the applied field.
Altered localization of HrpZ in Pseudomonas syringae pv. syringae hrp mutants suggests that different components of the type III secretion pathway control protein translocation across the inner and outer membranes of gram-negative bacteria (1997)

Pseudomonas syringae pv. syringae 61 (Pss61) secretes the HrpZ harpin by a type III protein secretion pathway encoded by a cluster of hrp (hypersensitive response and pathogenicity) and hrc genes. The nine hrc genes represent a subset of hrp genes that are also conserved in the type III virulence protein secretion systems of animal pathogenic Yersinia, Shigella, and Salmonella spp. The hrpJ and hrpU operons contain seven hrc genes (counting hrcQ(A) and hrcQ(B) as one gene), all with additional homologs involved in flagellar biogenesis and secretion, and five of which encode predicted inner membrane proteins. The hrpC and hrpZ operons encode HrcC and HrcJ, respectively, which are associated with the outer membrane. Interposon mutants affected in all of the hrc genes in the hrpJ and hrpU operons and TnphoA-induced hrcC and hrcJ mutants were assayed for altered localization of HrpZ in mid-log-phase cultures by immunoblotting sodium dodecyl sulfate-polyacrylamide gels that were run with various cell fractions. The hrpJ and hrpU operon mutants revealed a novel phenotype of partially reduced accumulation of HrpZ in the total culture (despite wild-type levels of hrpZ operon transcription), all of which was cell bound and equivalent in level to that of cell-bound HrpZ in the wild type. The hrcC and hrcJ mutant cultures accumulated the same total amount of HrpZ as the wild type, but the HrpZ was cell bound. Among all the strains tested, only the hrcC mutant accumulated significant amounts of HrpZ in the periplasm, as indicated by selective release through spheroplasting. Analysis of nonpolar mutations in the hrpU and hrpC operons support the results obtained with polar mutations. These observations indicate that a constant pool of HrpZ is maintained in the cytoplasm of Pss61 despite secretion deficiencies, that the hrpJ and hrpU operons encode an alternative to the Sec (general protein export) pathway for translocation across the inner membrane, that genes in the hrpC operon are necessary for translocation across the outer membrane, and that the Pss61 Hrp system permits study of two genetically distinguishable stages in type III protein secretion.
Eliminating Turbulence in Spatially Intermittent Flows (2010)

Flows through pipes and channels are the most common means to transport fluids in practical applications and equally occur in numerous natural systems. In general, the transfer of fluids is energetically far more efficient if the motion is smooth and laminar because the friction losses are lower. However, even at moderate velocities pipe and channel flows are sensitive to minute disturbances, and in practice most flows are turbulent. Investigating the motion and spatial distribution of vortices, we uncovered an amplification mechanism that constantly feeds energy from the mean shear into turbulent eddies. At intermediate flow rates, a simple control mechanism suffices to intercept this energy transfer by reducing inflection points in the velocity profile. When activated, an immediate collapse of turbulence is observed, and the flow relaminarizes.
Accuracy of detecting irregular cardiac rhythms via telemedicine (2004)

We evaluated the accuracy of an electronic stethoscope in the detection of irregular cardiac rhythms. Ten patients with either normal sinus rhythm or atrial fibrillation previously documented by electrocardiogram (ECG) were recruited from a local retirement community. Six senior family medicine resident physicians were asked to assess the cardiac rhythms of the subjects as either regular or irregular, in both a telemedical and an in-person examination. An ECG was obtained simultaneously as the gold standard. Forty-five of the 60 in-person assessments were correct, as were 49 of the 60 telemedicine assessments. The difference was not significant. Physician confidence in telemedical examination did not affect the accuracy of examination. The results of this study suggest that telemedicine-directed auscultation of patients may be just as successful as inperson examination for the detection of cardiac arrhythmias.
Development of a GC‐MS Method for the Simultaneous Analysis of Latent Fingerprint Components<sup>*</sup> (2006)

Latent fingerprint residue is a complex mixture of organic and inorganic compounds. A full understanding of the composition of this mixture and how it changes after deposition is lacking. Three solvent systems were compared for the simultaneous extraction and derivatization with ethyl chloroformate of selected amino and fatty acids from a nonporous substrate (Mylar for subsequent analysis by gas chromatography-mass spectrometry. A solvent system comprised of sodium hydroxide, ethanol, and pyridine was found to be the most effective. This method was applied to the analysis of latent fingerprint residue deposited on Mylar and preliminary data are presented. Twelve amino acids (e.g., serine, glycine, and aspartic acid) and 10 fatty acids (e.g., tetradecanoic, hexadecanoic, and octadecanoic acids) were identified. The potential application of this method to further the understanding of latent fingerprint chemistry has been demonstrated.
DEDD regulates degradation of intermediate filaments during apoptosis (2002)

Apoptosis depends critically on regulated cytoskeletal reorganization events in a cell. We demonstrate that death effector domain containing DNA binding protein (DEDD), a highly conserved and ubiquitous death effector domain containing protein, exists predominantly as mono- or diubiquitinated, and that diubiquitinated DEDD interacts with both the K8/18 intermediate filament network and pro-caspase-3. Early in apoptosis, both cytosolic DEDD and its close homologue DEDD2 formed filaments that colocalized with and depended on K8/18 and active caspase-3. Subsequently, these filamentous structures collapsed into intracellular inclusions that migrated into cytoplasmic blebs and contained DEDD, DEDD2, active caspase-3, and caspase-3-cleaved K18 late in apoptosis. Biochemical studies further confirmed that DEDD coimmunoprecipitated with both K18 and pro-caspase-3, and kinetic analyses placed apoptotic DEDD staining prior to caspase-3 activation and K18 cleavage. In addition, both caspase-3 activation and K18 cleavage was inhibited by expression of DEDDDeltaNLS1-3, a cytosolic form of DEDD that cannot be ubiquitinated. Finally, siRNA mediated DEDD knockdown cells exhibited inhibition of staurosporine-induced DNA degradation. Our data suggest that DEDD represents a novel scaffold protein that directs the effector caspase-3 to certain substrates facilitating their ordered degradation during apoptosis.
CpGIMethPred: computational model for predicting methylation status of CpG islands in human genome (2013)

DNA methylation is an inheritable chemical modification of cytosine, and represents one of the most important epigenetic events. Computational prediction of the DNA methylation status can be employed to speed up the genome-wide methylation profiling, and to identify the key features that are correlated with various methylation patterns. Here, we develop CpGIMethPred, the support vector machine-based models to predict the methylation status of the CpG islands in the human genome under normal conditions. The features for prediction include those that have been previously demonstrated effective (CpG island specific attributes, DNA sequence composition patterns, DNA structure patterns, distribution patterns of conserved transcription factor binding sites and conserved elements, and histone methylation status) as well as those that have not been extensively explored but are likely to contribute additional information from a biological point of view (nucleosome positioning propensities, gene functions, and histone acetylation status). Statistical tests are performed to identify the features that are significantly correlated with the methylation status of the CpG islands, and principal component analysis is then performed to decorrelate the selected features. Data from the Human Epigenome Project (HEP) are used to train, validate and test the predictive models. Specifically, the models are trained and validated by using the DNA methylation data obtained in the CD4 lymphocytes, and are then tested for generalizability using the DNA methylation data obtained in the other 11 normal tissues and cell types. Our experiments have shown that (1) an eight-dimensional feature space that is selected via the principal component analysis and that combines all categories of information is effective for predicting the CpG island methylation status, (2) by incorporating the information regarding the nucleosome positioning, gene functions, and histone acetylation, the models can achieve higher specificity and accuracy than the existing models while maintaining a comparable sensitivity measure, (3) the histone modification (methylation and acetylation) information contributes significantly to the prediction, without which the performance of the models deteriorate, and, (4) the predictive models generalize well to different tissues and cell types. The developed program CpGIMethPred is freely available at http://users.ece.gatech.edu/~hzheng7/CGIMetPred.zip.
Exosomal microRNA modulates pathways of liver fibrosis by regulating connective tissue growth factor (CTGF) expression in fibrogenic cells during chronic injury. (2013)

Aim To establish the regulation of Connective Tissue Growth Factor (CTGF) expression in hepatic stellate cells (HSC) by delivery of miR‐214 in exosomes. Methods Exosomes isolated from conditioned medium of mouse HSC were characterized by Western blot, dynamic light scattering, zeta potential analysis, and cryo‐TEM. MiR‐214 was detected by RT‐PCR. Donor HSC were treated with GW4869 to inhibit exosome production and recipient HSC were transfected with a luciferase reporter vector under the control of a wild type CTGF 3′‐UTR or a mutant CTGF 3′‐UTR lacking the miR‐214 binding site. Results HSC exosomes were bi‐membrane vesicles, 80–150nm in diameter, negatively charged (−26mV), and positive for CD9. MiR‐ 214 was present in exosomes and its levels were increased by transfection of HSC with pre‐mir‐214. MiR‐214 levels in exosomes but not in cell lysates were reduced by pre‐treatment of the cells with GW4869. Co‐culture of miR214‐transfected donor HSC with CTGF UTR luciferase reporter‐transfected recipient HSC resulted in miR‐214‐dependent and GW4869‐dependent regulation of activity of the wild type, but not mutated, CTGF 3′‐UTR. CTGF 3‐UTR activity in activated recipient HSC was more greatly inhibited in a GW4869‐dependent manner by co‐culture with freshly isolated donor HSC (high endogenous miR‐214 levels) than with highly activated donor HSC (low endogenous miR‐214 levels). Conclusions MiR‐214 is exported exosomally between neighboring HSC, suppressing CTGF production by the cells, After injury, miR‐214 expression is suppressed, resulting in its reduced exosomal delivery and increased CTGF expression in recipient cells. Exosome‐dependent delivery of miRs between neighboring HSC represents a novel mechanism by which fibrotic pathways are regulated during chronic liver injury.
Antibody Agents in Solid Organ Transplantation (2003)

Antibody agents play an important role in the pharmacotherapy of solid organ transplantation. These agents can be either monoclonal or polyclonal, derived from an animal source or genetically engineered utilizing human antibody sequences. This reviewpresents basic pharmacology and therapeutic issues related to the antibody preparations utilized in transplantation including equine and rabbit antithymocyte globulins, muromonab-CD3, daclizumab, and basiliximab. The parameters covered for these agents include mechanism of action, pharmacokinetics, pharmacodynamic monitoring strategies, clinical dosing, adverse effects, and clinical trials. The brief overviewof current clinical data related to these agents focuses on kidney transplantation. The use of these very powerful agents in different patient populations needs to be individualized based on certain risks and these data are presented to help in the decision-making process, especially for renal allograft recipients.
Selection Criteria for Developing Therapy Goals (1983)

Although phonological analysis of disordered speech has become very common since the late 1970s, relatively little has been written about how to use the results of a phonological analysis in planning remediation, particularly in selecting therapy targets. This paper is an attempt to fill part of that gap. After a brief review of suggestions made in the published phonological assessment procedures, several criteria for selecting target processes are presented. Next, there is a discussion of criteria to be used in selecting target sounds. In addition, some
Algo más que espacio: La digitalización en sanidad supone importantes ahorros en costes para el sistema y también beneficios extras (2013)

En el pasado mes de abril, el Grove House Practice ha sacado a la luz algunas de sus experiencias al ser el objeto del programa piloto de digitalizacion en el St Helens & Knowsley Teaching Hospitals, situados en las inmediaciones de Liverpool. El objetivo consistia en digitalizar toda la documentacion generada por los medicos en la actualidad remontandose hasta el inicio del primer sistema de seguros sociales instaurado por Lloyd George en 1911.Desde el ano 2000, los medicos podian generar la documentacion en sistemas electronicos, pero mantienen la obligacion legal de seguir generando copias en papel y conservarlas dentro de sobres, cuyo formato caracteristico data de la epoca del propio Lloyd George, para atender las reclamaciones por parte de aseguradoras, juzgados e incluso con fines estadisticos para seguir el movimiento de los pacientes de un area a otra.
Endogenously Synthesized (−)-<i>proto</i>-Quercitol and Glycine Betaine Are Principal Compatible Solutes of<i>Schizochytrium</i>sp. Strain S8 (ATCC 20889) and Three New Isolates of Phylogenetically Related Thraustochytrids (2007)

ABSTRACT We report that endogenously synthesized (−)- prot o-quercitol (1 d -1,3,4/2,5-cyclohexanepentol) and glycine betaine were the principal compatible solutes of Schizochytrium sp. strain S8 (ATCC 20889) and three new osmotolerant isolates of thraustochytrids (strains T65, T66, and T67). The compatible solutes were identified and quantified by use of nuclear magnetic resonance spectroscopy, and their identity was confirmed by mass spectroscopy and measurement of the specific optical rotation. The cellular content of compatible solutes increased with increasing NaCl concentration of a defined medium. (−)- proto -Quercitol was the dominating solute at all NaCl concentrations tested (0.25 to 1.0 M), e.g., cells of S8 and T66 stressed with 1.0 M NaCl accumulated about 500 μmol (−)- proto -quercitol and 100 μmol glycine betaine per g dry weight. To our knowledge, (−)- proto -quercitol has previously been found only in eucalyptus. The 18S rRNA gene sequences of the four (−)- proto -quercitol-producing strains showed 99% identity, and they displayed the same fatty acid profile. The only polyunsaturated fatty acids accumulated were docosahexaenoic acid (78%) and docosapentaenoic acid (22%). A less osmotolerant isolate (strain T29), which was closely phylogenetically related to Thraustochytrium aureum (ATCC 34304), did not contain (−)- proto -quercitol or glycine betaine. Thus, the level of osmotolerance and the osmolyte systems vary among thraustochytrids.
Human hepatoma cell line plasminogen activator. (1983)

A human hepatoma cell line, Hep G2, which synthesizes and secretes several components of the fibrinolytic system, was examined for the capacity to produce plasminogen activator (PA). PA activity was found to accumulate in medium conditioned by the cells but was not detected in cell extracts. Analysis of Hep G2 conditioned medium by SDS-polyacrylamide gel electrophoresis revealed multiple PAs of Mr 100,000, 60,000, and 52,000 daltons. In addition, a heterogeneous band of activity was present between the 100,000 and 60,000 dalton PAs. All detectable PA activity in conditioned medium fractionated at a single position after isoelectric focusing. The isoelectric point of this material (pI 8.6) was identical to that of purified urokinase. Anti-urokinase IgG, but not anti-tissue activator IgG, neutralized the activity of these PAs. Treatment of conditioned medium with 25 mM diisopropylfluorophosphate for 5 hr at 37 degrees C inactivated the 52,000 and 60,000 dalton PAs but had no effect on the 100,000 dalton PA or the heterogeneous zone of activity. The possibility that the absence of detectable PA activity in the cell extracts resulted from the presence of fibrinolytic inhibitors was considered. Addition of cell extract to purified urokinase resulted in a concentration-dependent reduction of urokinase-mediated fibrinolytic activity, consistent with the presence of such inhibitors. Acidification of the cell extracts to inactivate the inhibitor(s) revealed the presence of a latent, cell-associated PA activity. Thus, in addition to the other major components of the fibrinolytic system, Hep G2 cells produce multiple forms of a urokinase-like PA. Detection of these PAs may be obscured by the presence of cellular inhibitors.
Nucleolar function and size in cancer cells. (1998)

We have have studied the relationship between nucleolar function and size and cell doubling time in cancer cells. Seven human cancer cell lines characterized by different proliferation rates were used. Nucleolar functional activity was evaluated by measuring RNA polymerase I activity and expression of RNA polymerase I upstream binding factor (UBF), DNA topoisomerase I, and fibrillarin, three proteins involved in synthesis and processing of rRNA. Transcriptional activity of RNA polymerase I was strictly related to cell doubling time (r = -0.97; P < 0.001). The quantitative distribution of UBF, DNA topoisomerase I, and fibrillarin was evaluated on Western blots using specific monoclonal antibodies by densitometric analysis of autoradiographic signals. It was found to be directly related to RNA polymerase I transcriptional activity (r = 0.89, P = 0.008 for UBF; r = 0.95, P = 0.001 for DNA topoisomerase I; and r = 0.91, P = 0.004 for fibrillarin) and inversely related to cell doubling time (r = -0.87, P = 0.011 for UBF; r = -0.97, P < 0.001 for DNA topoisomerase I; and r = -0.91, P = 0.005 for fibrillarin). The nucleolar areas were measured by automated image analysis on toluidine blue-stained cells. The values of the stained nucleolar structures per cell were directly related to RNA polymerase I transcriptional activity (r = 0.94, P = 0.001) and inversely related to cell doubling time (r = -0.98, P < 0.001). The same area values of the nucleolar structures stained by toluidine blue were also closely related to the amount of UBF (r = 0.92, P = 0.003), DNA topoisomerase I (r = 0.98, P < 0.001), and fibrillarin (r = 0.95, P = 0.001), and to the in situ quantitative distribution of AgNOR proteins (r = 0.98, P < 0.001). Our results demonstrated that in cancer cells rRNA transcriptional activity and nucleolar size are inversely related to cell doubling time. Quantitative distribution of nucleolar structures within the cell represents a cytohistological parameter of the rapidity of cell proliferation.
Development and commercialization of a genetic marker for marbling of beef in cattle: a case study. (2002)

This chapter describes a case study on the identification of genetic markers for marbling in beef, the uses and patenting of the DNA tests used to identify the markers, their marketing and the implications of these tests to the beef industry.
Heterogeneous endolysins in <i>Listeria monocytogenes</i> bacteriophages: a new class of enzymes and evidence for conserved holin genes within the siphoviral lysis cassettes (1995)

Listeria monocytogenes bacteriophages A118, A500 and A511 are members of three distinct phage groups with characteristic host ranges. Their endolysin (ply) genes were cloned and expressed in Escherichia coli as demonstrated by the conferred lytic phenotype when colonies of recombinant cells were overlaid with a lawn of Listeria cells. The nucleotide sequences of the cloned DNA fragments were determined and the individual enzymes (PLY118, 30.8 kDa; PLY500, 33.4 kDa; PLY511, 36.5 kDa) were shown to have varying degrees of homology within their N-terminal or C-terminal domains. Transcriptional analysis revealed them to be 'late' genes with transcription beginning 15-20 min post-infection. The enzymes were overexpressed and partially purified and their individual specificities examined. When applied exogenously, the lysins induced rapid lysis of Listeria strains from all species but generally did not affect other bacteria. Using hydrolysis of purified listerial cell walls, PLY511 was characterized as an N-acetylmuramoyl-L-alanine amidase (EC 3.5.1.28) and shows homology in its N-terminal domain to other enzymes of this type. In contrast, PLY118 and PLY500 were shown to represent a new class of cell wall lytic enzymes which cleave between the L-alanine and D-glutamate residues of listerial peptidoglycan; these were designated as L-alanoyl-D-glutamate peptidases. These two enzymes share homology in the N-terminal domain which we propose determines hydrolytic specificity. Highly conserved holin (hol) gene sequences are present upstream of ply118 and ply500. They encode proteins of structural similarity to the product of phage lambda gene S, and are predicted to be membrane proteins which form pores to allow access of the lysins to their peptidoglycan substrates. This arrangement of conserved holin genes with downstream lysin genes among the siphoviral lysis cassettes explains why the cytoplasmic endolysins alone are not lethal, since they require a specific transport function across the cell membrane.