gebhart/patrepeval huggingface dataset:
Efficient optimization and processing for distributed monitoring and control applications (2012)

In recent years, we have seen an increasing number of applications in networking, sensor networks, cloud computing, and environmental monitoring, that aim to monitor, control, and make decisions over large volumes of dynamic data. In my dissertation, we aim to enable a generic framework for these distributed monitoring and control applications, and address the limitations of prior work such as data stream management systems and adaptive query processing systems. In particular, we make the following contributions: 1) supporting the maintenance of recursive queries over distributed data streams, 2) enabling full-fledged cost-based incremental query re-optimization, and 3) as ongoing work, incorporating the cost estimation of plan switching during query re-optimization. Our solutions are implemented and evaluated using our prototype system Aspen, over a variety of workloads and benchmarks. In addition, our prototype system Aspen enables an end-to-end framework to support control and decision-making over integrated data streams from both the physical world (e.g., sensor streams) and the digital world (e.g., web, streams, databases).
cDNA Sequence of Two Distinct Pituitary Proteins Homologous to Kex2 and Furin Gene Products: Tissue-Specific mRNAs Encoding Candidates for Pro-Hormone Processing Proteinases (1990)

Based on the concept of sequence conservation around the active sites of serine proteinases, polymerase chain reaction applied to mRNA amplification allowed us to obtain a 260-bp probe which was used to screen a mouse pituitary cDNA library. The primers used derived from the cDNA sequence of active sites Ser* and Asn* of human furin. Two cDNA sequences were obtained from a number of positive clones. These code for two similar but distinct structures (mPC1 and mPC2), each being homologous to yeast Kex2 and human furin. In situ hybridization (mPC1) and Northern blots (mPC1 = 3.0 kb and mPC2 = 2.8 and 4.8 kb) demonstrated tissue and cellular specificity of expression, only within endocrine and neuroendocrine cells. These data suggest that mPC1 and mPC2 represent prime candidates for tissue-specific pro-hormone converting proteinases.
Hydrogen sulfide poisoning: Clarification of some controversial issues (1999)

We conclude that: 1) Certain neurotoxic effects of exposure are probably due to a direct toxic effect on the brain, while others are almost certainly a result of hypoxia secondary to H2S-induced respiratory insufficiency; 2) pulmonary edema is a common consequence of poisoning and there is suggestive evidence of hyperactive airway responses in some individuals following brief H2S-induced unconsciousness (knockdown); 3) criteria for acceptable community levels are very different than those governing occupational standards; 4) urinary thiosulfate determinations can be useful for monitoring occupational exposure; and 5) determination of sulfide ion concentrations in blood or major organs can be useful in corroborating a diagnosis of fatal H2S toxicity, but there are many pitfalls in collecting, storing, and analyzing tissue and fluid samples.
Optical coherence tomography in guided surgery of GI cancer (2005)

Optical Coherence Tomography (OCT) is a new high spatial resolution, real-time optical imaging modality, known from prior pilot studies for its high sensitivity to invasive cancer. We reported our results in an OCT feasibility study for accurate determination of the proximal border for esophageal carcinoma and the distal border for rectal carcinoma. The OCT study enrolled 19 patients with rectal adenocarcinoma and 24 patients with distal esophageal carcinoma (14 squamous cell carcinomas, 10 adenocarcinomas). During pre-surgery planning endoscopy we performed in vivo OCT imaging of the tumor border at four dial clock axes (12, 3, 6 and 9 o’clock). The OCT border then was marked by an electrocoagulator, or by a methylene blue tattoo. A cold biopsy (from the esophagus) was performed at visual and OCT borders and compared with visual and OCT readings. 27 post-surgery excised specimens were analyzed. OCT borders matched the histopathology in 94% cases in the rectum and 83.3% in the esophagus. In the cases of a mismatch between the OCT and histology borders, a deep tumor invasion occurred in the muscle layer (esophagus, rectum). Because of its high sensitivity to mucosal cancer, OCT can be used for pre-surgery planning and surgery guidance of the proximal border for esophageal carcinoma and the distal border for rectal carcinoma. However, deep invasion in the rectum or esophageal wall has to be controlled by alternative diagnostic modalities.
Towards a practical specification language (1981)

Recognition of the value of formal specifications in the design and verification of large software systems is becoming more widespread. Specification languages themselves, however, are difficult to develop in part because of the inherent conflict between the goals of clarity and formalism required by these languages. This paper discusses the role of specification languages, examples of specifications in two currently implemented languages, AFFIRM and SPECIAL, and makes some suggestions towards a more practical specification language.
Improving DNA vaccine potency via modification of professional antigen presenting cells. (2003)

DNA vaccines are potentially important immunotherapeutic agents for combating infectious diseases and cancers. Continuing progress in our understanding of how professional antigen presenting cells (APCs) orchestrate immune responses has provided a framework from which to design effective DNA vaccines. Similarly, manipulation of DNA using advances in molecular biology technology has enabled implementation of novel DNA vaccine strategies. This review summarizes recent vaccine strategies that utilize intercellular and intracellular modification of professional APCs, including those involving plasmid delivery, intracellular processing of antigen and enhancement of APC interaction with T-cells.
Optical gain of optically pumped Al0.1Ga0.9N/GaN double heterostructure at room temperature (1994)

In this letter, we report the measurement of the gain of an optically pumped Al0.1Ga0.9N/GaN double heterostructure (DH) which was prepared on a sapphire substrate by metalorganic vapor phase epitaxy using an AlN buffer layer. At room temperature, the optical gain of stimulated emission from Al0.1Ga0.9N/GaN DH was measured to be 160 cm−1 at pumping power density of 200 kW/cm2.
Basic Fibroblast Growth Factor Levels in the Vitreous of Patients With Proliferative Diabetic Retinopathy (1990)

A two-site enzyme-linked immunosorbent assay was used to quantitate levels of basic fibroblast growth factor in the vitreous from 36 patients undergoing vitrectomy for a variety of retinal conditions, including proliferative diabetic retinopathy, macular pucker, and retinal detachment with and without proliferative vitreoretinopathy. Basic fibroblast growth factor levels ranged from undetectable to 52 ng/mL. In patients with proliferative diabetic retinopathy, basic fibroblast growth factor levels were greater than or equal to 30 ng/mL in 8 of 17 specimens. Of the 8 patients with elevated basic fibroblast growth factor levels, 6 had evidence of active proliferative disease (ie, neovascularization of the disc or iris), whereas in the patients who had undetectable levels only 2 of 9 had evidence of neovascularization of disc and none had neovascularization of the iris. In the rhegmatogenous retinal detachment group, 2 of 10 eyes had elevated basic fibroblast growth factor levels, while none in the macular pucker group had elevated levels. Our study documents increased levels of basic fibroblast growth factor in vitreous specimens from patients with proliferative diabetic retinopathy, particularly those with active proliferative retinopathy. The role of basic fibroblast growth factor in the pathogenesis of various retinal disease entities is discussed.
A review of thrust-vectoring in support of a V/STOL non-moving mechanical propulsion system (2013)

Abstract The advantages associated to Vertical Short-Take-Off and Landing (V/STOL) have been demonstrated since the early days of aviation, with the initial technolology being based on airships and later on helicopters and planes. Its operational advantages are enormous, being it in the field of military, humanitarian and rescue operations, or even in general aviation. Helicopters have limits in their maximum horizontal speed and classic V/STOL airplanes have problems associated with their large weight, due to the implementation of moving elements, when based on tilting rotors or turbojet vector mechanical oriented nozzles. A new alternative is proposed within the European Union Project ACHEON (Aerial Coanda High Efficiency Orienting-jet Nozzle). The project introduces a novel scheme to orient the jet that is free of moving elements. This is based on a Coanda effect nozzle supported in two fluid streams, also incorporating boundary layer plasma actuators to achieve larger deflection angles. Herein we introduce a state-of-the-art review of the concepts that have been proposed in the framework of jet orienting propulsion systems. This review allows to demonstrate the advantages of the new concept in comparison to competing technologies in use at present day, or of competing technologies under development worldwide.
Characterization of the internalization of bacillus Calmette-Guerin by human bladder tumor cells. (1993)

Adjuvant intravesical Mycobacterium bovis BCG is the treatment of choice for recurrent superficial bladder cancer. Fibronectin (FN) was previously demonstrated to be necessary for the retention of BCG within the bladder and for the expression of antitumor activity. Recent studies have demonstrated that BCG attach and are ingested by bladder epithelial cells, suggesting the existence of a second bacterial attachment mechanism. We report the characterization of the molecules involved in BCG attachment and internalization by the human bladder transitional cell carcinoma cell line T-24. Pretreatment of T-24 cells with monoclonal antibodies to either alpha 5 or beta 1 integrin subunits significantly inhibited both BCG attachment and ingestion. Exogenous FN was observed to enhance both attachment and ingestion of BCG, and anti-FN was observed to inhibit both phenomena. Latex beads precoated with either FN or laminin (LN) but not BSA were ingested by T-24 cells, but only FN-coated beads inhibited BCG attachment and ingestion. Pretreatment of BCG with FN augmented both attachment and ingestion. The role of bacterial FN binding proteins was evaluated. A monoclonal antibody to a 55-kD FN-binding protein was observed to abrogate attachment and ingestion. These results demonstrate that attachment and ingestion of BCG are mediated in part by the alpha 5 beta 1 integrin receptor and are dependent on FN. These studies demonstrate a mechanism of entrance of mycobacteria into epithelial cells and suggest a second role for FN in the adjuvant antitumor effect of BCG.
Immunization with recombinant macaque major histocompatibility complex class I and II and human immunodeficiency virus gp140 inhibits simian–human immunodeficiency virus infection in macaques (2012)

Genetic, epidemiological and experimental evidence suggest that the major histocompatibility complex (MHC) is critical in controlling human immunodeficiency virus (HIV) infection. The objectives of this study were to determine whether novel recombinant Mamu MHC constructs would elicit protection against rectal challenge with heterologous simian-human immunodeficiency virus (SHIV) strain SF162.P4 in rhesus macaques. Mamu class I and II gene products were linked together with HIV gp140, simian immunodeficiency virus (SIV) p27 and heat-shock protein 70 to dextran. The vaccine was administered to two groups, each consisting of nine macaques, either subcutaneously (SC), or rectally and boosted by SC immunization. The controls were untreated or adjuvant-treated animals. Repetitive rectal challenges with up to ten doses of SHIV SF162.P4 showed a significant decrease in the peak and sequential viral RNA concentrations, and three macaques remained uninfected, in the nine SC-immunized animals, compared with infection in all nine controls. Macaques immunized rectally followed by SC boosters showed a less significant decrease in both sequential and peak viral loads compared with the SC-immunized animals, and all were infected following rectal challenge with SHIV SF162.P4. Plasma and mucosal IgG and IgA antibodies to Mamu class I alleles and HIV gp120, as well as to RANTES (regulated upon activation, normal T-cell expressed, and secreted; CCR5) were increased, and showed significant inverse correlations with the peak viral load. These results suggested that allo-immunization with recombinant MHC constructs linked to HIV-SIV antigens merits further investigation in preventing HIV-1 infection.
Role of TFIIIA zinc fingers in vivo: analysis of single-finger function in developing Xenopus embryos. (1993)

The Xenopus 5S RNA gene-specific transcription factor IIIA (TFIIIA) has nine consecutive Cys2His2 zinc finger motifs. Studies were conducted in vivo to determine the contribution of each of the nine zinc fingers to the activity of TFIIIA in living cells. Nine separate TFIIIA mutants were expressed in Xenopus embryos following microinjection of their respective in vitro-derived mRNAs. Each mutant contained a single histidine-to-asparagine substitution in the third zinc ligand position of an individual zinc finger. These mutations result in structural disruption of the mutated finger with little or no effect on the other fingers. The activity of mutant proteins in vivo was assessed by measuring transcriptional activation of the endogenous 5S RNA genes. Mutants containing a substitution in zinc finger 1, 2, or 3 activate 5S RNA genes at a level which is reduced relative to that in embryos injected with the message for wild-type TFIIIA. Proteins with a histidine-to-asparagine substitution in zinc finger 5 or 7 activate 5S RNA genes at a level that is roughly equivalent to that of the wild-type protein. Zinc fingers 8 and 9 appear to be critical for the normal function of TFIIIA, since mutations in these fingers result in little or no activation of the endogenous 5S RNA genes. Surprisingly, proteins with a mutation in zinc finger 4 or 6 stimulate 5S RNA transcription at a level that is significantly higher than that mediated by similar concentrations of wild-type TFIIIA. Differences in the amount of newly synthesized 5S RNA in embryos containing the various mutant forms of TFIIIA result from differences in the relative number and/or activity of transcription complexes assembled on the endogenous 5S RNA genes and, in the case of the finger 4 and finger 6 mutants, result from increased transcriptional activation of the normally inactive oocyte-type 5S RNA genes. The remarkably high activity of the finger 6 mutant can be reproduced in vitro when transcription is carried out in the presence of 5S RNA. Disruption of zinc finger 6 results in a form of TFIIIA that exhibits reduced susceptibility to feedback inhibition by 5S RNA and therefore increases the availability of the transcription factor for transcription complex formation.
Vacuum-Assisted Fascial Closure for Patients With Abdominal Trauma (2004)

Patients requiring temporary abdominal closure have a significant in-hospital mortality rate of 33%. Delayed primary closure with vacuum assistance was achieved for 71.9% of the surviving patients. Maintaining a negative or total positive fluid balance of less than 20 L before the last attempted fascial closure improves successful closure rates, as seen in 19 of 22 patients (86.4%). The vacuum-assisted closure technique also enabled successful primary closure for two patients with extreme delay (>8 days). Elevated serum lactate levels are significantly correlated with early and in-hospital mortality. A significant decrease in lactate level during the first 12 hours is associated with achievement of primary closure.
APTIMA PCA3 Molecular Urine Test: Development of a Method to Aid in the Diagnosis of Prostate Cancer (2006)

The APTIMA PCA3 assay combines simple specimen processing with precise assays and existing instruments and could add specificity to the current algorithm for prostate cancer diagnosis.
Gene Expression Profiling in Cervical Cancer: Identification of Novel Markers for Disease Diagnosis and Therapy (2009)

Cervical cancer, a potentially preventable disease, remains the second most common malignancy in women worldwide. Human papillomavirus is the single most important etiological agent in cervical cancer. HPV contributes to neoplastic progression through the action of two viral oncoproteins E6 and E7, which interfere with critical cell cycle pathways, p53, and retinoblastoma. However, evidence suggests that HPV infection alone is insufficient to induce malignant changes and other host genetic variations are important in the development of cervical cancer. Advances in molecular biology and high throughput gene expression profiling technologies have heralded a new era in biomarker discovery and identification of molecular targets related to carcinogenesis. These advancements have improved our understanding of carcinogenesis and will facilitate screening, early detection, management, and personalised targeted therapy. In this chapter, we have described the use of high density microarrays to assess gene expression profiles in cervical cancer. Using this approach we have identified a number of novel genes which are differentially expressed in cervical cancer, including several genes involved in cell cycle regulation. These include p16ink4a, MCM 3 and 5, CDC6, Geminin, Cyclins A-D, TOPO2A, CDCA1, and BIRC5. We have validated expression of mRNA using real-time PCR and protein by immunohistochemistry.
VON WILLEBRAND FACTOR (vWF) PRO-POLYPEPTIDE IS REQUIRED FOR vWF MULTIMER FORMATION (1987)

The von Willebrand factor (vWF) is a multimeric plasma glycoprotein synthesized in vascular endothelial cells as a pre-pro-polypeptide with a highly repetitive domain structure, symbolized by the formula: (H)-D1-D2-D'-D3-A1-A2-A3-D4-B1-B2-B3-C1-C2-(0H). A heterologous expression system, consisting of a monkey kidney cell line (C0S-1), transfected with full-length vWF cDNA, is shown to mimic the constitutively, secretory pathway of vWF in endothelial cells. The assembly of pro-vWF into multimers and the proteolytic processing of these structures is found to oro-ceed along the following, consecutive steps. Pro-vWF subunits associate to form dimers, a process that does not involve the pro-polypeptide of pro-vWF. This observation is derived from transfection of C0S-1 cells with vWF cDNA, lacking the genetic information encoding the pro-polypeptide, composed of the domains D1 and D2. Pro-vWF dimers are linked intracellularly to form a regular series of multimeric structures that are secreted and cannot be distinguished from those released constitutively by endothelial cells. The presence of the pro-polypeptide, embedded in pro-vWF, is obligatory for multimerization since the deletion mutant lacking the D1 and D2 domains fails to assemble beyond the dimer stage. It is argued that the D domains are involved in interchain interactions.
Effect of Mechanical Forces on Growth and Matrix Protein Synthesis in the In Vitro Pulmonary Artery (1995)

The effect of mechanical stimuli on pulmonary artery growth and matrix tissue synthesis (and how individual cell types in the vessel wall respond to such stimuli) is incompletely characterized. Rabbit pulmonary arteries were placed in tissue culture medium and subjected to varying magnitudes of stretch or hydrostatic pressure (separately) for 4 days. The rate of protein synthesis in smooth muscle cells (by quantitative autoradiography) was positively related to the magnitude of stretch, as were the percentage of procollagen type I-positive cells and the rate of cell replication. In adventitial fibroblasts, stretch increased the rate of replication but not of protein synthesis. Hydrostatic pressure had little or no effect on the variables measured in either smooth muscle cells or fibroblasts. Stretch also increased the rate of elastin and collagen synthesis in the whole pulmonary artery segment, and after 4 days of stretch, the contents of actin and elastin were increased. Removal of the endothelium did not affect stretch-induced protein, collagen, or elastin synthesis but augmented stretch-induced smooth muscle replication. These data suggest that in the intact pulmonary artery, stretch, but not pressure, can stimulate hypertrophy and hyperplasia in smooth muscle cells and hyperplasia in fibroblasts. Matrix protein synthesis and accumulation are also increased by stretch. Neither stretch-mediated growth nor matrix protein synthesis required endothelium in this model.
Polaris, a Protein Involved in Left-Right Axis Patterning, Localizes to Basal Bodies and Cilia (2001)

Mutations in Tg737 cause a wide spectrum of phenotypes, including random left-right axis specification, polycystic kidney disease, liver and pancreatic defects, hydrocephalus, and skeletal patterning abnormalities. To further assess the biological function of Tg737 and its role in the mutant pathology, we identified the cell population expressing Tg737 and determined the subcellular localization of its protein product called Polaris. Tg737 expression is associated with cells possessing either motile or immotile cilia and sperm. Similarly, Polaris concentrated just below the apical membrane in the region of the basal bodies and within the cilia or flagellar axoneme. The data suggest that Polaris functions in a ciliogenic pathway or in cilia maintenance, a role supported by the loss of cilia on the ependymal cell layer in ventricles of Tg737(orpk) brains and by the lack of node cilia in Tg737(Delta2-3betaGal) mutants.
Distributed Data Mining with Differential Privacy (2011)

With recent advances in communication and data storage technology, an explosive amount of information is being collected and stored in the Internet. Even though such vast amount of information presents great opportunities for knowledge discovery, organizations might not want to share their data due to legal or competitive reasons. This posts the challenge of mining knowledge while preserving privacy. Current efficient privacy-preserving data mining algorithms are based on an assumption that it is acceptable to release all the intermediate results during the data mining operations. However, it has been shown that such intermediate results can still leak private information. In this work, we use differential privacy to quantitatively limit such information leak. Differential privacy is a newly emerged privacy definition that is capable of providing strong measurable privacy guarantees. We propose Secure group Differential private Query (SDQ), a new algorithm that combines techniques from differential privacy and secure multiparty computation. Using decision tree induction as a case study, we show that SDQ can achieve stronger privacy than current efficient secure multiparty computation approach, and better accuracy than current differential privacy approach while maintaining efficiency.