gebhart/patrepeval huggingface dataset:
Comparative Risk Analysis of Six Volatile Organic Compounds in California Drinking Water (2002)

The widespread use and storage of volatile organic compounds (VOCs) in the United States has led to releases of these chemicals into the environment, including groundwater sources of drinking water. Many of these VOCs are commonly found in public drinking water supplies across the nation and are considered by state or federal agencies to be potentially carcinogenic to humans. In this paper, we evaluate the detection frequencies, detected concentrations, and relative cancer risks of six VOCs in drinking water sources in California from 1995 to 2001. We find that during this 7-year period, the most frequently detected VOCs in sampled drinking water sources were chloroform (12-14%), PCE (11-13%), and TCE (10-12%). Detection frequencies in water were lower for 1,1-DCE (3-6%), MTBE (1-3%), and benzene (<1%). Mean detected concentrations were also consistently above California's primary maximum contaminant level for some VOCs, including benzene, PCE, and TCE. Although none of the six VOCs necessarily poses a significant public health threat from drinking water exposures, 1,1-DCE and benzene werefound to pose the greatest cancer risk relative to the other VOCs. However, after adjusting for the occurrence of each VOC in drinking water, chloroform and PCE were found to pose the greatest relative cancer risk. Despite media reports about significant MTBE contamination of drinking watersupplies in California, MTBE detections were infrequent and this chemical was found to pose the least cancer risk relative to the other VOCs.
Contextualized Videos: Combining Videos with Environment Models to Support Situational Understanding (2007)

Multiple spatially-related videos are increasingly used in security, communication, and other applications. Since it can be difficult to understand the spatial relationships between multiple videos in complex environments (e.g. to predict a person's path through a building), some visualization techniques, such as video texture projection, have been used to aid spatial understanding. In this paper, we identify and begin to characterize an overall class of visualization techniques that combine video with 3D spatial context. This set of techniques, which we call contextualized videos, forms a design palette which must be well understood so that designers can select and use appropriate techniques that address the requirements of particular spatial video tasks. In this paper, we first identify user tasks in video surveillance that are likely to benefit from contextualized videos and discuss the video, model, and navigation related dimensions of the contextualized video design space. We then describe our contextualized video testbed which allows us to explore this design space and compose various video visualizations for evaluation. Finally, we describe the results of our process to identify promising design patterns through user selection of visualization features from the design space, followed by user interviews.
Antigenic characterization of ehrlichiae: protein immunoblotting of Ehrlichia canis, Ehrlichia sennetsu, and Ehrlichia risticii (1992)

In recent years a febrile illness apparently associated with tick bite in patients in the United States has been attributed to infection by an Ehrlichia species. This implication is based on serologic responses to E. canis, morphologic demonstration of ehrlichiae in clinical materials, and a single isolate distinct from E. canis which was obtained from a human patient by the Centers for Disease Control. Little is known about the antigens of the ehrlichiae. This report expands the breadth of available knowledge concerning the antigenic components and serologic responses to component antigens of E. canis, E. sennetsu, and E. risticii. Protein immunoblotting after sodium dodecyl sulfate-polyacrylamide gel electrophoresis by using density gradient-purified ehrlichiae and homologous antisera demonstrated reproducible and characteristic antigens within each species (for E. sennetsu, 91, 64, 54, 44, 36, 34, 28, 25, and 24 kDa; for E. risticii, 70, 52, 48, 44, 35, 28, 24, 23, and 20 kDa; for E. canis, 110, 64, 52, 42, 33, 28, 24, 23, and 20 kDa). When antisera were reacted with heterologous antigens, cross-reactivity among these species was virtually restricted to the 70-kDa antigen. Furthermore, when serum samples obtained from 10 patients who were convalescing from ehrlichiosis were tested against each antigen, only three serum samples had any reactivities, and these serum samples reacted with only a few of the antigenic bands. These results documented the molecular sizes of electrophoretically separated antigens of the three Ehrlichia species, confirm their serologic relationships, and support the novel nature of the agent(s) of human ehrlichiosis in the United States.
Dispatch of distributed generators under local-information constraints (2014)

Distributed optimization problems are generally described as the minimization of a global objective function in a system, where each agent can get information only from a neighborhood defined by a network topology. To solve this problem, we present a local strategy based on population dynamics (i.e., the local replicator equation (LRE)), to define functions and tasks assigned to each node in a system represented by a connected graph. To show the application of the proposed strategy, we implement the LRE to solve a problem of economic dispatch of distributed generators with some variations over the original framework. Finally, we present some simulation results obtained with different network topologies to illustrate the optimality and stability of the equilibrium points.
Effect of Silk Protein Processing on Drug Delivery from Silk Films (2013)

Sericin removal from the core fibroin protein of silkworm silk is a critical first step in the use of silk for biomaterial-related applications, but degumming can affect silk biomaterial properties, including molecular weight, viscosity, diffusivity and degradation behavior. Increasing the degumming time (10, 30, 60, and 90 min) decreases the average molecular weight of silk protein in solution, silk solution viscosity, and silk film glass-transition temperature, and increases the rate of degradation of a silk film by protease. Model compounds spanning a range of physical-chemical properties generally show an inverse relationship between degumming time and release rate through a varied degumming time silk coating. Degumming provides a useful control point to manipulate silk's material properties.
Well-width dependence of intersubband absorption in InGaAs/InAlAs multiquantum wells (1990)

The well-width dependence of intersubband absorption in InGaAs/InAlAs multiquantum wells grown by molecular beam epitaxy is investigated. The energies of the absorption peaks decrease from 300 to 100 meV with an increasing well width from 35 to 200 Å. This well-width dependence of the peak energy is in good agreement with theoretical calculations. For a wide quantum well, two sharp absorption peaks were observed, including the transitions from the second to the third subbands.
A new characteristic karyotypic anomaly in lymphoproliferative disorders (1979)

A new characteristic chromosome anomaly t(11;14)(q14;q32?) in lymphoproliferative disorders (LPD) is described in 4 cases. The extra material was found on a "14 chromosome (14q+) and belonged to the long arm of one "11 chromosome in 3 cases and to the long arm of a "14 in the other case. These cases confirm that the distal end of chromosome 14q may function as a "receptor site," according to the hypothesis of Kaiser-McCaw et al. and also tend to indicate that chromosome "14 may not be unique in showing so-called "donor" and "receptor sites," and that other chromosomes, in casu chromosome "11, may behave similarly.
Carbon catabolite repression in Aspergillus nidulans involves deubiquitination (2001)

The best studied role of ubiquitination is to mark proteins for destruction by the proteasome but, in addition, it has recently been shown to promote macromolecular assembly and function, and alter protein function, thus playing a regulatory role distinct from protein degradation. Deubiquinating enzymes, the ubiquitin-processing proteases (ubps) and the ubiquitin carboxy-terminal hydrolases (uchs), remove ubiquitin from ubiquitinated substrates. We show here that the creB gene involved in carbon catabolite repression in Aspergillus nidulans encodes a functional member of the novel subfamily of the ubp family defined by the human homologue UBH1, thus implicating ubiquitination in the process of carbon catabolite repression. Members of the novel subfamily of ubps that include CreB are widespread amongst eukaryotes, with homologues present in mammals, nematodes, Drosophila and Arabidopsis, but mutations in the genes have only been identified in A. nidulans. From phenotypes of the A. nidulans mutants it is probable that this subfamily is involved in complex regulatory pathways. Mutations in the gene encoding the WD40 repeat protein CreC result in an identical phenotype, implicating both genes in this pathway.
Wnt Signaling in Polycystic Kidney Disease (2007)

Wnt signaling cascades activate morphogenetic programs that range from cell migration and proliferation to cell fate determination and stem cell renewal. These pathways enable cells to translate environmental cues into the complex cellular programs that are needed to organize tissues and build organs. Wnt signaling is essential for renal development; however, the specific molecular underpinnings involved are poorly understood. Recent research has revealed an unexpected intersection between Wnt signaling and polycystic kidney disease. Some polycystic kidney disease proteins, such as Inversin and Bardet-Biedl syndrome family members, were found to use components of the Wnt signaling cascade to orient cells along a secondary polarity axis within the plane of the epithelium. These spatial cues may be needed to position nascent tubules with a defined geometry.
Confused, timid, and unstable (2012)

Today's commercial video streaming services use dynamic rate selection to provide a high-quality user experience. Most services host content on standard HTTP servers in CDNs, so rate selection must occur at the client. We measure three popular video streaming services -- Hulu, Netflix, and Vudu -- and find that accurate client-side bandwidth estimation above the HTTP layer is hard. As a result, rate selection based on inaccurate estimates can trigger a feedback loop, leading to undesirably variable and low-quality video. We call this phenomenon the "downward spiral effect", and we measure it on all three services, present insights into its root causes, and validate initial solutions to prevent it.
Construction and Activity of Phosphorylatable Human Interferon-αB2 and Interferon-αA/D (1994)

The polymerase chain reaction (PCR) was used to introduce a phosphorylation site into human interferon-alpha B2 (Hu-IFN-alpha B2) and the chimeric human interferon-alpha A/D (Hu-IFN-alpha A/D). The phosphorylation sites were created by adding an amino acid consensus sequence for phosphorylation by the cAMP-dependent protein kinase to the carboxyl termini of the IFNs. The resultant modified IFNs (Hu-IFN-alpha B2-P and Hu-IFN-alpha A/D-P) were expressed in Escherichia coli and purified. The purified proteins exhibited antiviral activities similar to that of unmodified Hu-IFN-alpha B2 and Hu-IFN-alpha A/D. The Hu-IFN-alpha B2-P and Hu-IFN-alpha A/D-P can be phosphorylated by the catalytic subunit of the cAMP-dependent protein kinase and [gamma-32P]ATP with retention of biological activities. The introduction of phosphorylation sites into Hu-IFN-alpha B2 and Hu-IFN-alpha A/D provides new reagents for studies of receptor binding, pharmacokinetics, and other studies where labeled IFNs are useful.
Ultrastructural assessment of cellulite morphology: clues to a therapeutic strategy ? (2013)

The histological and ultrastructural findings of cellulite clearly distinguish the condition from simple fat deposition. The remodeling of the fat layer into lobulated packets of lipocytes sequestered by fibrotic septa with a high proportion of elastic fibers would suggest the use of a fiber-based interstitial laser-assisted lipolysis system at an appropriate wavelength which might offer benefits through disruption of the septae through a photomechanical effect and lipolysis of the sequestered lipocytes. This could be followed by a course of near-infrared phototherapy to accelerate clearance of freed lipid and debris and reestablish the vascular system.
A classification scheme for mobilization regions of bacterial plasmids (2003)

Transmissible plasmids can be classified according to their mobilization ability, as being conjugative (self-transmissible) or mobilizable (transmissible only in the presence of additional conjugative functions). Naturally occurring mobilizable plasmids carry the genetic information necessary for relaxosome formation and processing, but lack the functions required for mating pair formation. Mobilizable plasmids have a tremendous impact in horizontal gene transfer in nature, including the spread of antibiotic resistance. However, analysis of their promiscuity and diversity has attracted less attention than that of conjugative plasmids. This review will focus on the analysis of the diversity of mobilizable plasmids. For this purpose, we primarily compared the amino acid sequences of their relaxases and, when pertinent, we compared these enzymes with conjugative plasmid relaxases. In this way, we established phylogenetic relationships among the members of each superfamily. We conducted a database and literature analysis that led us to propose a classification system for small mobilizable plasmids in families and superfamilies according to their mobilization regions. This review outlines the genetic organization of each family of mobilization regions, as well as the most relevant properties and relationships among their constituent encoded proteins. In this respect, the present review constitutes a first approach to the characterization of the global gene pool of mobilization regions of small mobilizable plasmids.
Biomechanical activation of vascular endothelium as a determinant of its functional phenotype (2001)

One of the striking features of vascular endothelium, the single-cell-thick lining of the cardiovascular system, is its phenotypic plasticity. Various pathophysiologic factors, such as cytokines, growth factors, hormones, and metabolic products, can modulate its functional phenotype in health and disease. In addition to these humoral stimuli, endothelial cells respond to their biomechanical environment, although the functional implications of this biomechanical paradigm of activation have not been fully explored. Here we describe a high-throughput genomic analysis of modulation of gene expression observed in cultured human endothelial cells exposed to two well defined biomechanical stimuli-a steady laminar shear stress and a turbulent shear stress of equivalent spatial and temporal average intensity. Comparison of the transcriptional activity of 11,397 unique genes revealed distinctive patterns of up- and down-regulation associated with each type of stimulus. Cluster analyses of transcriptional profiling data were coupled with other molecular and cell biological techniques to examine whether these global patterns of biomechanical activation are translated into distinct functional phenotypes. Confocal immunofluorescence microscopy of structural and contractile proteins revealed the formation of a complex apical cytoskeleton in response to laminar shear stress. Cell cycle analysis documented different effects of laminar and turbulent shear stresses on cell proliferation. Thus, endothelial cells have the capacity to discriminate among specific biomechanical forces and to translate these input stimuli into distinctive phenotypes. The demonstration that hemodynamically derived stimuli can be strong modulators of endothelial gene expression has important implications for our understanding of the mechanisms of vascular homeostasis and atherogenesis.
Transformation Between Continuous and Discrete Representations of Images: A Perceptual Approach (1985)

The transformation of image signals between the continuous domain of the real world and the discrete domain of modern data processing can have a significant effect on quality and efficiency. Analysis based on perceptual rather than mathematical considerations has been carried out. A series of experiments based on the analysis has shown that substantial improvement over usual techniques can be achieved by the use of a cascade of a presharpening filter combined with Gaussian presampling and interpolation filters. The resulting ``sharpened Gaussian'' filter, although not exactly circularly symmetrical, gives a high degree of isotropy. Each element in the cascade is separable, so that computational efficiency is high. A favorable tradeoff is achieved among sharpness, smoothness, and the effects of aliasing. Subjective testing, in comparison with other commonly used filters, has shown the clear superiority of this filter.
cDNA and protein structure for the .alpha. subunit of human liver alcohol dehydrogenase (1986)

Two cDNA clones for human liver alcohol dehydrogenase (ADH) were identified, together covering 1450 nucleotides that contain the cDNA sequence of the ADH1 locus and include a coding region of 1122 nucleotides for the alpha subunit of the enzyme. In parallel, direct peptide analyses of the carboxymethylated protein also established most of the amino acid sequence. Nucleotide and peptide data were in complete agreement and show exchanges at 24 positions in the alpha relative to the beta subunit. One of the cDNA clones had a 139-nucleotide internal deletion at a position of possible interest in relation to mRNA processing, ancestral connections, or DNA replication. The structure of the alpha subunit is homologous to that of the beta and gamma subunits but has many exchanges, also of functionally important residues, explaining the different enzymatic properties. In total, 35 of 374 amino acid residues differ between the class I isozymes, and the substitutions add an extra SH group in the alpha subunit. Only in the beta-pleated sheet region of the coenzyme-binding domain is almost complete lack of substitutions noted, illustrating the importance of this region. In contrast, the active site region is far less conserved. However, similar exchanges of functional significance have also been found in distantly related alcohol and polyol dehydrogenases.
Evaluation of UPlink–RSV (2007)

A prototype rapid antigen test for the on-site detection of respiratory syncytial virus (RSV) infection was developed and evaluated. The platform uses instrumented assay analysis, eliminating potential operator bias in the interpretation of the test result that may occur with visually interpreted rapid antigen assays. The device was tested as the first point-of-care (POC) infectious disease application of novel reporter up-converting phosphor technology (UPT) using a specifically designed portable UPT reader (UPlink). Assays were performed by mixing nasopharyngeal specimen with RSV-specific UPT reporter particles and addition of the mixture to a disposable cassette containing a lateral flow (LF) strip with RSV capture antibodies. UPT reporters bound on the specific capture zone were analyzed with the UPlink reader. Reproducibility testing of the UPlink-RSV (UPR) test by naïve users confirmed the potential of UPlink for POC applications where testing is not always performed by highly trained medical staff. The performance of UPR was further evaluated with clinical nasopharyngeal specimens. A prospective study at an independent test site demonstrated clinical parameters of 90% sensitivity and 98.3% specificity with an overall correlation of 96.2% as compared to viral culture with RT-PCR verification. These results are in agreement with in-house retrospective studies and results obtained with other available commercial rapid antigen assays.
Treatment of advanced and metastatic pancreatic cancer (1998)

The majority of adenocarcinoma of the pancreas are non-resectable at diagnosis due to locally advanced or metastatic disease. There will be an estimated 28,900 new cases of pancreatic cancer diagnosed in the United States in 1998. In data collected from 1986-1993, the five year survival of all stages combined was 4%. Realizing that most patients present with advanced disease, and there are no acceptable screening methods to detect early stage disease, efforts to develop active anti-cancer agents with minimal toxicity are essential in order to improve the quality of life and survival. Several 5-fluorouracil based regimens have been tried without a significant impact on palliation or survival. Recently, the anti-metabolite gemcitabine has been approved for use in individuals with locally advanced and metastatic disease, primarily on the basis of improved functional status. Many cytotoxic agents have proven ineffective in the treatment of this disease. There are several ongoing studies investigating the role of new cytotoxic and biologic agents.
Cell lysis methods for high‐throughput screening or miniaturized assays (2009)

The widely and routinely used cell lysis techniques are still being evolved to address the technical needs of micro-scale sample processing, for example in high-throughput screening or miniaturized assays. This review focuses on several recently emerged mechanical, physical and biological methods designed for lysing cells on small scales for screening or analysis.
Isolated dog hearts prepared in cold Tyrode solution and reperfused with arterial blood are functionally and ultrastructurally normal. (1988)

Isolated dog whole heart preparations run by means of cross-circulation with support dogs were prepared in two different ways. In one way the donors' hearts were quickly removed, and cannulation of their major vessels, insertion of a latex balloon into the left ventricle, etc. were all done in cold Tyrode solution in the condition of heart-anoxia within 30 min and then reperfused with arterial blood of support dogs (Group A). In the other, cannulation of the major vessels of the donors' hearts were done in the state of "beating heart" (Group B). In these two kinds of preparations we compared basal cardio-coronary measurements (coronary blood flow, left ventricular pressure (LVP), its first derivative (LV dP/dt) and myocardial oxygen consumption (MVO2) and ultrastructure of the myocardium at various periods of the experiments. There were no significant differences in these cardio-coronary measurements and ultrastructural findings. Furthermore, Group A preparations kept stable levels of cardio-coronary measurements for 5 hr or more and responded normally to isoproterenol. Therefore, isolated, blood-perfused dog whole hearts prepared in cold Tyrode solution and reperfused by means of the cross-circulation method would be useful for physiological, pharmacological and biochemical studies.
Estrogen receptor-beta messenger RNA expression in human breast tumor biopsies: relationship to steroid receptor status and regulation by progestins. (1999)

When the level of estrogen receptor (ER)-beta mRNA in tumors, determined by reverse transcription-PCR, was assessed according to either ER status or PR status alone, determined by ligand binding assays, the level of ER-beta mRNA was significantly lower in PR+ tumors compared with PR- tumors (P = 0.036), and no association with ER status was found. Subgroup analysis showed that ER-beta mRNA expression in ER+/PR+ breast tumors was significantly less than in ER+/PR- (P = 0.009), ER-/PR+ (P = 0.029), and ER-/PR- (P = 0.023) groups. Interestingly, the ER-beta mRNA expression was specifically decreased by progestin in T47D breast cancer cells. The data suggest the possibility that expression of ER-beta in human breast tumors is a marker of endocrine therapy responsiveness.