gebhart/patrepeval huggingface dataset:
TrustedDB (2011)

TrustedDB is an outsourced database prototype that allows clients to execute SQL queries with privacy and under regulatory compliance constraints without having to trust the service provider. TrustedDB achieves this by leveraging server-hosted tamper-proof trusted hardware in critical query processing stages.TrustedDB does not limit the query expressiveness of supported queries. And, despite the cost overhead and performance limitations of trusted hardware, the costs per query are orders of magnitude lower than any (existing or) potential future software-only mechanisms. TrustedDB is built and runs on actual hardware, and its performance and costs are evaluated here.
Drive Against Hotspot Motifs in Primates Implicates the PRDM9 Gene in Meiotic Recombination (2009)

Although present in both humans and chimpanzees, recombination hotspots, at which meiotic crossover events cluster, differ markedly in their genomic location between the species. We report that a 13-base pair sequence motif previously associated with the activity of 40% of human hotspots does not function in chimpanzees and is being removed by self-destructive drive in the human lineage. Multiple lines of evidence suggest that the rapidly evolving zinc-finger protein PRDM9 binds to this motif and that sequence changes in the protein may be responsible for hotspot differences between species. The involvement of PRDM9, which causes histone H3 lysine 4 trimethylation, implies that there is a common mechanism for recombination hotspots in eukaryotes but raises questions about what forces have driven such rapid change.
Heparanase expression is a prognostic indicator for postoperative survival in pancreatic adenocarcinoma (2002)

Pancreatic ductal adenocarcinoma has a median survival of less than 6 months from diagnosis. This is due to the difficulty in early diagnosis, the aggressive biological behaviour of the tumour and a lack of effective therapies for advanced disease. Mammalian heparanase is a heparan-sulphate proteoglycan cleaving enzyme. It helps to degrade the extracellular matrix and basement membranes and is involved in angiogenesis. Degradation of extracellular matrix and basement membranes as well as angiogenesis are key conditions for tumour cell spreading. Therefore, we have analysed the expression of heparanase in human pancreatic cancer tissue and cell lines. Heparanase is expressed in cell lines derived from primary tumours as well as from metastatic sites. By immunohistochemical analysis, it is preferentially expressed at the invading edge of a tumour at both metastatic and primary tumour sites. There is a trend towards heparanase expression in metastasising tumours as compared to locally growing tumours. Postoperative survival correlates inversely with heparanase expression of the tumour reflected by a median survival of 34 and 17 month for heparanase negative and positive tumours, respectively. Our results suggest, that heparanase promotes cancer cell invasion in pancreatic carcinoma and could be used as a prognostic indicator for postoperative survival of patients.
The role of protein nitration in the inhibition of platelet activation by peroxynitrite (2001)

Peroxynitrite at low concentrations (3-10 microM) inhibited agonist-induced platelet aggregation by a mechanism not dependent on the formation of cyclic guanosine monophosphate. Platelets recovered completely from peroxynitrite-induced inhibition within 30 min. Peroxynitrite induced nitration of cytosolic proteins, but this diminished to near basal levels within 60 min of exposure to the oxidant. During this period there was a reduction in tyrosine phosphorylation of specific proteins such as syk, but this was not due to direct nitration of these same proteins. The inhibition of phosphorylation was reversible with platelet proteins recovering the ability to be phosphorylated within 15 min of exposure to peroxynitrite. Conversely, peroxynitrite increased phosphorylation of other proteins, but again these events were not directly linked to nitration. Nitration may affect the phosphorylation of tyrosine residues in a number of proteins, but by an indirect route, possibly by acting on proteins upstream in the signalling cascades. We suggest that low concentrations of peroxynitrite reversibly inhibit platelet aggregation by preventing the phosphorylation of key signalling proteins.
Direct Correlation between Diffusion of Loxosceles reclusa Venom and Extent of Dermal Inflammation (2001)

Loxosceles venom diffuses from the envenomation site. The extent of dermal inflammation mirrors the extent of Loxosceles venom diffusion. This observation implies that the venom itself defines the extent and magnitude of tissue injury following Loxosceles envenomation.
Metabolic engineering of Escherichia coli for the production of cadaverine: A five carbon diamine (2010)

A five carbon linear chain diamine, cadaverine (1,5-diaminopentane), is an important platform chemical having many applications in chemical industry. Bio-based production of cadaverine from renewable feedstock is a promising and sustainable alternative to the petroleum-based chemical synthesis. Here, we report development of a metabolically engineered strain of Escherichia coli that overproduces cadaverine in glucose mineral salts medium. First, cadaverine degradation and utilization pathways were inactivated. Next, L-lysine decarboxylase, which converts L-lysine directly to cadaverine, was amplified by plasmid-based overexpression of the cadA gene under the strong tac promoter. Furthermore, the L-lysine biosynthetic pool was increased by the overexpression of the dapA gene encoding dihydrodipicolinate synthase through the replacement of the native promoter with the strong trc promoter in the genome. The final engineered strain was able to produce 9.61 g L(-1) of cadaverine with a productivity of 0.32 g L(-1) h(-1) by fed-batch cultivation. The strategy reported here should be useful for the bio-based production of cadaverine from renewable resources.
Combined kinase inhibition modulates parkin inactivation (2008)

Mutations in the parkin gene cause autosomal-recessive, juvenile-onset parkinsonism, and parkin dysfunction may also play a role in the pathogenesis of sporadic Parkinson disease (PD). Although its precise function remains largely unknown, parkin seems to play a neuroprotective role. Several studies indicate that changes in parkin solubility induced by post-translational modifications, such as S-nitrosylation or dopamine modification, comprise one mechanism of parkin inactivation associated with disease. Protein phosphorylation events have recently been linked to the molecular mechanism(s) underlying PD, but the role of this post-translational modification for parkin function has remained unclear. Here we report that compound phosphorylation of parkin by both casein kinase I and cyclin-dependent kinase 5 (cdk5) decreases parkin solubility, leading to its aggregation and inactivation. Combined kinase inhibition partially reverses the aggregative properties of several pathogenic point mutants in cultured cells. Enhanced parkin phosphorylation is detected in distinct brain areas of individuals with sporadic PD and correlates with increases in the levels of p25, the activator of cdk5. These findings indicate that casein kinase I and cdk5 may represent novel combinatorial therapeutic targets for treating PD.
The influence of granulocyte macrophage colony-stimulating factor and prior chemotherapy on the immunological response to a vaccine (ALVAC-CEA B7.1) in patients with metastatic carcinoma. (2001)

Granulocyte macrophage colony-stimulating factor (GM-CSF) has been shown to be an effective vaccine adjuvant because it enhances antigen processing and presentation by dendritic cells. ALVAC-CEA B7.1 is a canarypox virus encoding the gene for the tumor-associated antigen carcinoembryonic antigen (CEA) and for a T-cell costimulatory molecule, B7.1. After an initial dose escalation phase, this study evaluated vaccination with 4.5 x 10(8) plaque-forming units ALVAC-CEA B7.1 alone (n = 30) or with GM-CSF (n = 30) in patients with advanced CEA-expressing tumors to determine whether the addition of the adjuvant GM-CSF enhances induction of CEA-specific T-cells. Patients were vaccinated with vaccine intradermally every other week for 8 weeks. GM-CSF was given s.c. for 5 days beginning 2 days before vaccination. Patients with stable or responding disease after four immunizations received monthly boost injections alone or with GM-CSF. Biopsies of vaccine sites were obtained 48 h after vaccination to evaluate leukocytic infiltration and CEA expression. Induction of peripheral blood CEA-specific T-cell precursors was assessed in HLA-A2 positive patients by an ELISPOT assay looking for the production of IFN-gamma. Therapy was well tolerated. All of the patients had evidence of leukocytic infiltration and CEA expression in vaccine biopsy sites. In the patients receiving GM-CSF, leukocytic infiltrates were greater in cell number but were less likely to have a predominant lymphocytic infiltrate compared with patients receiving vaccine in the absence of the cytokine adjuvant. After four vaccinations, CEA-specific T-cell precursors were statistically increased in HLA-A2 positive patients who received vaccine alone. However, the GM-CSF plus vaccine cohort of HLA-A2 positive did not demonstrate a statistically significant increase in their CEA-specific T-cell precursor frequencies compared with baseline results. The number of prior chemotherapy regimens was negatively correlated with the generation of a T-cell response, whereas there was a positive correlation between the number of months from the last chemotherapy regimen and the T-cell response. ALVAC-CEA B7.1 is safe in patients with advanced, recurrent adenocarcinomas that express CEA, is associated with the induction of a CEA-specific T-cell response in patients treated with vaccine alone but not with vaccine and GM-CSF, and can lead to disease stabilization for up to 13 months.
OBSERVATIONS ON ATTEMPTS TO PRODUCE ACUTE DISSEMINATED ENCEPHALOMYELITIS IN MONKEYS (1933)

No evidence was found to support the idea that vaccine virus placed in the cisterna magna is capable of producing an acute disseminated encephalomyelitis with perivascular demyelination either in normal or in partially immune monkeys. A testicular extract (Reynals' factor) did not induce vaccine virus to cause an acute disseminated encephalomyelitis in monkeys. Repeated intramuscular injections of brain extracts and brain emulsions into eight monkeys were followed in two instances by an inflammatory reaction, accompanied by demyelination, in the central nervous system. The exact relation of the injections to the disease of the nervous system is not clear. The combined action of vaccine virus and an emulsion of fresh rabbit brain did not lead to the production of an acute disseminated encephalomyelitis in monkeys that had received repeated intramuscular injections of emulsions and alcohol-ether extracts of normal rabbit brains.
Combined ultrasound and photoacoustic imaging to detect and stage deep vein thrombosis: phantom and ex vivo studies (2008)

Treatment of deep venous thrombosis (DVT)--a primary cause of potentially fatal pulmonary embolism (PE)--depends on the age of the thrombus. The existing clinical imaging methods are capable of visualizing a thrombus but cannot determine the age of the blood clot. Therefore, there is a need for an imaging technique to reliably diagnose and adequately stage DVT. To stage DVT (i.e., to determine the age of the thrombus, and therefore, to differentiate acute from chronic DVT), we explored photoacoustic imaging, a technique capable of noninvasive measurements of the optical absorption in tissue. Indeed, optical absorption of the blood clot changes with age, since maturation of DVT is associated with significant cellular and molecular reorganization. The ultrasound and photoacoustic imaging studies were performed using DVT-mimicking phantoms and phantoms with embedded acute and chronic thrombi obtained from an animal model of DVT. The location and structure of the clots were visualized using ultrasound imaging, while the composition, and therefore age, of thrombi were related to the magnitude and spatiotemporal characteristics of the photoacoustic signal. Overall, the results of our study suggest that combined ultrasound and photoacoustic imaging of thrombi may be capable of simultaneous detection and staging of DVT.
Single-stranded DNA ‘blue’ T7 promoter plasmids: a versatile tandem promoter system for cloning and protein engineering (1986)

Chimeric phage-plasmid expression vectors were constructed from pUC18/19 plasmids by cloning a single-stranded DNA (ssDNA) origin of replication from bacteriophage f1 and inserting a bacteriophage T7 promoter within the beta-galactosidase gene. A T7 promoter permits in vivo or in vitro expression of single proteins by the translation of T7 RNA polymerase transcripts. Insertional inactivation of the T7 promoter-containing beta-galactosidase gene permits a simple blue-to-white color cloning assay. Compared with several helper phages that were examined, superinfection with M13K07 resulted in the highest yields of the pTZ plasmids as ssDNA viral particles. These ssDNA promoter plasmids are uniquely suited for protein engineering because they simplify cloning, oligonucleotide directed mutagenesis, verification by enzymatic sequence analysis, and expression of mutant proteins from a single vector. These vectors were utilized to eliminate an efficient transcriptional terminator of T7 RNA polymerase in the cDNA of bovine preproparathyroid hormone by oligonucleotide directed mutagenesis. The mutation changed the codon for phenylalanine-19 in the signal peptide to alanine. In a cell-free system the mutant cDNA transcripts were translated into preproparathyroid hormone, which was converted to proparathyroid hormone in the presence of microsomal membranes.
Identification and Removal of Physiological Artifacts From Electroencephalogram Signals: A Review (2018)

Electroencephalogram (EEG), boasting the advantages of portability, low cost, and hightemporal resolution, is a non-invasive brain-imaging modality that can be used to measure different brain states. However, EEG recordings are always contaminated with artifacts from different sources other than neurons, which renders EEG data analysis more difficult, and which potentially results in misleading findings. Therefore, it is essential for many medical and practical applications to remove these artifacts in the preprocessing stage before analyzing EEG data. In the last thirty years, various methods have been developed to remove different types of artifacts from contaminated EEG data; still though, there is no standard method that can be used optimally, and therefore, the research remains attractive as well as challenging. This paper presents an extensive overview of the existing methods for ocular, muscle, and cardiac artifact identification and removal with their comparative advantages and limitations. We also reviewed the schemes developed for validating the performances of algorithms with simulated and real EEG data. In future studies, researchers should focus not only on the combining of different methods with multiple processing stages for efficient removal of artifactual interferences but also on the development of standard criteria for validation of recorded EEG signals.
A Tight Linear Time (1/2)-Approximation for Unconstrained Submodular Maximization (2012)

We consider the Unconstrained Submodular Maximization problem in which we are given a non-negative submodular function f : 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</sup> → ℝ <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> , and the objective is to find a subset S ⊆ N maximizing f(S). This is one of the most basic submodular optimization problems, having a wide range of applications. Some well known problems captured by Unconstrained Submodular Maximization include MaxCut, Max-DiCut, and variants of Max-SAT and maximum facility location. We present a simple randomized linear time algorithm achieving a tight approximation guarantee of 1/2, thus matching the known hardness result of Feige et al. [11]. Our algorithm is based on an adaptation of the greedy approach which exploits certain symmetry properties of the problem. Our method might seem counterintuitive, since it is known that the greedy algorithm fails to achieve any bounded approximation factor for the problem.
Extension of acoustic levitation to include the study of micron-size particles in a more compressible host liquid (1982)

We discuss the development of a new technique for measuring the mechanical properties, namely density, compressibility, and sound velocity, of biological materials. The technique makes use of acoustic levitation, a phenomenon resulting from the balance of the gravitational force and a time averaged radiation pressure force acting on an object subjected to a sufficiently energetic sound field. The levitation technique is especially suited for studying biological materials, because it requires only very small samples (&amp;lt;1 μ1) and it employs a host liquid which acts as a container whose properties can be controlled to accommodate the material under consideration. Previous applications of acoustic levitation have been concerned with single millimeter diameter size droplets in a less compressible host liquid. Through this study, application of this technique has been extended to include levitation of samples consisting of a large number of micron-size particles in a more compressible host liquid. Application of the technique to this new class of materials required the development of a new apparatus, as well as greater attention to phenomena previously neglected in the theory describing the forces acting on a compressible sphere in a standing wave field. The technique was used to measure the compressibility of red blood cells in several different host environments. Results from the normal red blood cell compressibility measurements were in good agreement with those obtained using a more traditional technique.
A hitless reconfigurable add-drop multiplexer for WDM networks utilizing planar waveguides, thermo-optic switches and UV-induced gratings (2002)

Summary form only given. We describe a reconfigurable add-drop multiplexer that can insert or remove a single channel per stage without disrupting service on the remaining channels. The device was fabricated in Ge-doped SiO/sub 2/ channel waveguides with a delta of 1.2 percent on silicon substrates. The device design consists of two null path Mach-Zehnder thermo-optic switches on either side of an inner Mach-Zehnder grating filter.
Capacitive micromachined ultrasonic transducers for medical imaging and therapy (2011)

Capacitive micromachined ultrasonic transducers (CMUTs) have been subject to extensive research for the last two decades. Although they were initially developed for air-coupled applications, today their main application space is medical imaging and therapy. This paper first presents a brief description of CMUTs, their basic structure, and operating principles. Our progression of developing several generations of fabrication processes is discussed with an emphasis on the advantages and disadvantages of each process. Monolithic and hybrid approaches for integrating CMUTs with supporting integrated circuits are surveyed. Several prototype transducer arrays with integrated frontend electronic circuits we developed and their use for 2-D and 3-D, anatomical and functional imaging, and ablative therapies are described. The presented results prove the CMUT as a MEMS technology for many medical diagnostic and therapeutic applications.
Excretion of ammonium by a nifL mutant of Azotobacter vinelandii fixing nitrogen (1992)

A mutation in the gene upstream of nifA in Azotobacter vinelandii was introduced into the chromosome to replace the corresponding wild-type region. The resulting mutant, MV376, produced nitrogenase constitutively in the presence of 15 mM ammonium. When introduced into a nifH-lacZ fusion strain, the mutation permitted beta-galactosidase production in the presence of ammonium. The gene upstream of nifA is therefore designated nifL because of its similarity to the Klebsiella pneumoniae nifL gene in proximity to nifA, in mutant phenotype, and in amino acid sequence of the gene product. The A. vinelandii nifL mutant MV376 excreted significant quantities of ammonium (approximately 10 mM) during diazotrophic growth. In contrast, ammonium excretion during diazotrophy was much lower in a K. pneumoniae nifL deletion mutant (maximum, 0.15 mM) but significantly higher than in NifL+ K. pneumoniae. The expression of the A. vinelandii nifA gene, unlike that of K. pneumoniae, was not repressed by ammonium.
Clinical impact of glycated albumin as another glycemic control marker (2010)

It is known that glycation among various proteins is increased in diabetic patients compared with non-diabetic subjects. Currently, among these glycated proteins, glycated hemoglobin (HbA(1C)) is used as the gold standard index of glycemic control in clinical practice for diabetes treatment. However, HbA(1C) does not accurately reflect the actual status of glycemic control in some conditions where plasma glucose changes during short term, and in patients who have diseases such as anemia and variant hemoglobin. In comparison, another index of glycemic control, glycated albumin (GA), more accurately reflects changes in plasma glucose during short term and also postprandial plasma glucose. Although GA is not influenced by disorders of hemoglobin metabolism, it is affected by disorders of albumin metabolism. This review summarizes diseases and pathological conditions where GA measurement is useful. These include the status of glycemic control changes during short term, diseases which cause postprandial hyperglycemia, iron deficiency anemia, pregnancy, chronic liver disease (liver cirrhosis), chronic renal failure (diabetic nephropathy), and variant hemoglobin.
A breathtaking headache (2004)

Extrameningeal complications of meningococcal septicaemia occur in about 11-19% of cases, and include myocarditis, acute renal failure, arthritis, pneumonia, skin gangrene, conjunctivitis, endocarditis,
Growth Inhibition by Glyphosate and Reversal of Its Action by Phenylalanine and Tyrosine (1979)

The broad spectrum herbicide glyphosate inhibited growth of a bacterium (E. coli), an alga (Chlamydomonas reinhardi), plant cell cultures (carrot and soybean) and roots of whole plants (Arabidopsis thaliana). Inhibition was transitory, except in plant roots, suggesting breakdown of the herbicide by the test organism. Phenylalanine and tyrosine acted synergistically to reverse the growth inhibition. Addition of these alone, other amino acids and/or divalent metal ions (Fe2+, Co2+ , Zn2+) had no effect. The data are discussed in relation to a possible mode of action of glyphosate.