gebhart/patrepeval huggingface dataset:
Adverse Effects of Testosterone Therapy in Adult Men: A Systematic Review and Meta-Analysis (2010)

The adverse effects of testosterone therapy include an increase in hemoglobin and hematocrit and a small decrease in high-density lipoprotein cholesterol. These findings are of unknown clinical significance. Current evidence about the safety of testosterone treatment in men in terms of patient-important outcomes is of low quality and is hampered by the brief study follow-up.
Helicase-dependent amplification: use in OnChip amplification and potential for point-of-care diagnostics (2009)

Isothermal amplification technologies are emerging on the horizon that could have the potential to pose as alternatives to PCR in terms of sensitivity and ease of use. One of the most recent isothermal technologies is helicase-dependent amplification (HDA). This technology uses the helicase's capability to disrupt the hydrogen bonds of a Watson-Crick base pair in order to separate dsDNA. A denaturation step, as is used in PCR, is no longer required. This gives rise to new, less expensive and less complicated designs for point-of-care devices and 'Lab on Chip' systems. Helicase-dependent OnChip-amplification (OnChip-HDA) is a further step into this direction as it integrates the HDA technology with microarray technology and its power of multiplexing. This special report will give an overview on the HDA and OnChip-HDA technology, and its potential for point-of-care diagnostics.
Characterization of peptide binding to the murine MHC class I H-2Kk molecule. Sequencing of the bound peptides and direct binding of synthetic peptides to isolated class I molecules. (1994)

Peptides that are bound by the murine class I MHC molecule H-2Kk have been isolated and sequenced. The initial step in the fractionation was affinity column isolation of the peptide-class I complex from either RDM-4 or x5563 tumor cell lines. Acid denaturation of the complex followed by HPLC fractionation of the peptides allowed us to sequence individual peptides, as well as pools of peptides. To date, a total of 10 sequences have been characterized, and all were 8 mers. The sequences were variable except for glutamic acid in the second position (P2) and isoleucine in the eighth (P8), which were highly conserved. To further study peptide binding to H-2Kk, a competitive binding assay consisting of the immobilized histocompatibility protein and a biotinylated self-peptide for signal generation was developed. A complete set of single-alanine variants for this one self-peptide was tested in the assay, demonstrating that substitution at P2 and P8 markedly decreased the affinity for the class I molecule; alanine at position 3 had an intermediate effect on binding. A comparison of the identified self-peptides for binding to H-2Kk showed that they differed in affinity by more than one order of magnitude. Influenza virus nucleoprotein peptide, SDY EGR LI, associated with the plate-bound class I molecule, and the resulting MHC-peptide complex could trigger TNF release by influenza-primed CTLs. This result demonstrated the functional activity of the plate-bound H-2Kk-peptide complex.
Singlet oxygen production by chloroperoxidase-hydrogen peroxide-halide systems. (1984)

Singlet oxygen production in the chloroperoxidase-hydrogen peroxide-halide system was studied using 1268 nm chemiluminescence. With chloride or bromide ions, singlet oxygen is produced by the mechanism (formula; see text) (formula; see text) where X- is chloride or bromide ion. Under conditions where there is high enzyme activity and when Reaction B is fast relative to Reaction A, singlet oxygen is produced in near stoichiometric amounts. In contrast, when Reaction A is fast relative to Reaction B, oxidized halogen species (chlorine and hypochlorous acid for chloride ion; bromide, tribromide ion, and hypobromous acid for bromide ion) are the principle reaction products. With iodide ion, no 1268 nm chemiluminescence was detected. Past studies have shown that iodine and iodate ion are the major end products of this system.
HAIL: A High-Availability and Integrity Layer for Cloud Storage. (2008)

We introduce HAIL (High-Availability and Integrity Layer), a distributed cryptographic system that permits a set of servers to prove to a client that a stored file is in-tact and retrievable. HAIL strengthens, formally unifies, and streamlines distinct approaches from the cryptographic and distributed-systems communities. Proofs in HAIL are efficiently computable by servers and highly compact— typically tens or hundreds of bytes, irrespective of file size. HAIL cryptographically verifies and reactively reallocates file shares. It is robust against an active, mobile adver-sary, i.e., one that may progressively corrupt the full set of servers. We propose a strong, formal adversarial model for HAIL, and rigorous analysis and parameter choices. We show how HAIL improves on the security and efficiency of existing tools, like Proofs of Retrievability (PORs) deployed on individual servers. We also report on a prototype imple-mentation. 1
Revising the evolutionary computation abstraction (2010)

Though based on abstractions of nature, current evolutionary algorithms and artificial life models lack the drive to complexity characteristic of natural evolution. Thus this paper argues that the prevalent fitness-pressure-based abstraction does not capture how natural evolution discovers complexity. Alternatively, this paper proposes that natural evolution can be abstracted as a process that discovers many ways to express the same functionality. That is, all successful organisms must meet the same minimal criteria of survival and reproduction. This abstraction leads to the key idea in this paper: Searching for novel ways of meeting the same minimal criteria, which is an accelerated model of this new abstraction, may be an effective search algorithm. Thus the existing novelty search method, which rewards any new behavior, is extended to enforce minimal criteria. Such minimal criteria novelty search prunes the space of viable behaviors and may often be more efficient than the search for novelty alone. In fact, when compared to the raw search for novelty and traditional fitness-based search in the two maze navigation experiments in this paper, minimal criteria novelty search evolves solutions more consistently. It is possible that refining the evolutionary computation abstraction in this way may lead to solving more ambitious problems and evolving more complex artificial organisms. Copyright 2010 ACM.
Cyclooxygenase‐2 is induced globally in infarcted human brain (1998)

Cyclooxygenase (COX) catalyzes synthesis of prostanoids after liberation of arachidonic acid, an important biochemical sequela of cerebral ischemia that aggravates brain injury. We investigated expression of inducible COX-2 in infarcted human brains (symptom duration, 15 hours to 18 days) and found that COX-2 protein was present in both neuronal and glial cells throughout the brain in accord with infarct topography and duration. These results emphasize the global yet temporally regulated nature of COX-2 induction during focal ischemia in humans, clearly different from the circumscribed acute expression reported in experimental animal models. We speculate that early induction of COX-2 may fuel tissue damage through prostanoids and free radicals, and delayed induction in remote brain areas may promote reconstitutive processes in the face of tissue scarring and remodeling of the surviving neural networks.
Solid phase capturable dideoxynucleotides for multiplex genotyping using mass spectrometry (2002)

We report an approach using solid phase capturable biotinylated dideoxynucleotides (biotin-ddNTPs) in single base extension for multiplex genotyping by mass spectrometry (MS). In this method, oligonucleotide primers that have different molecular weights and that are specific to the polymorphic sites in the DNA template are extended with biotin-ddNTPs by DNA polymerase to generate 3'-biotinylated DNA products. These products are then captured by streptavidin-coated solid phase magnetic beads, while the unextended primers and other components in the reaction are washed away. The pure extension DNA products are subsequently released from the solid phase and analyzed by matrix-assisted laser desorption/ionization time-of-flight MS. The mass of the extension products is determined using a stable oligonucleotide as a common internal mass standard. Since only the pure extension DNA products are introduced to the MS for analysis, the resulting mass spectrum is free of non-extended primer peaks and their associated dimers, which increases the accuracy and scope of multiplexing in single nucleotide polymorphism (SNP) analysis. The solid phase purification approach also facilitates desalting of the captured oligonucleotides, which is essential for accurate mass measurement by MS. We selected four biotin-ddNTPs with distinct molecular weights to generate extension products that have a 2-fold increase in mass difference compared to that with conventional ddNTPs. This increase in mass difference provides improved resolution and accuracy in detecting heterozygotes in the mass spectrum. Using this method, we simultaneously distinguished six nucleotide variations on synthetic DNA templates mimicking mutations in the p53 gene and two disease-associated SNPs in the human hereditary hemochromatosis gene.
A Stepwise Huisgen Cycloaddition Process: Copper(I)-Catalyzed Regioselective “Ligation” of Azides and Terminal Alkynes (2002)

By simply stirring in water, organic azides and terminal alkynes are readily and cleanly converted into 1,4-disubstituted 1,2,3-triazoles through a highly efficient and regioselective copper(I)-catalyzed process (see scheme for an example). Supporting information for this article is available on the WWW under http://www.angewandte.org or from the author. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2002/z19191_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
On the catalytic mechanism of prokaryotic leader peptidase 1 (1992)

The catalytic mechanism of leader peptidase 1 (LP1) of the bacterium Escherichia coli has been investigated by a combination of site-directed mutagenesis, assays of enzyme activity in vivo utilizing a strain of E. coli which has a conditional defect in LP1 activity, and gene cloning. The biological activity of mutant forms of E. coli LP1 demonstrates that this enzyme belongs to a novel class of proteinases. The possibility that LP1 may be an aspartyl proteinase has been excluded on the basis of primary sequence comparison and mutagenesis. Assignment of LP1 to one of the other three recognized classes of proteinases (metalloproteinases, thiol proteinases and the classical serine proteinases) can also be excluded, as it is clearly demonstrated that none of the histidine or cysteine residues within LP1 are required for catalytic activity. The Pseudomonas fluorescens lep gene has been cloned and sequenced and the corresponding amino acid sequence compared with that of E. coli LP1. The E. coli LP1 and P. fluorescens LP1 primary sequences are 50% identical after insertion of gaps. The P. fluorescens LP1 has 39 fewer amino acids, a calculated molecular mass of 31903 Da and functions effectively in vivo in E. coli. None of the cysteine residues and only one of the histidine residues which are present in E. coli LP1 are conserved in sequence position in the P. fluorescens LP1 enzyme. The possibility that LP1 is a novel type of serine proteinase is discussed.
Tobacco as a production platform for biofuel: overexpression of Arabidopsis DGAT and LEC2 genes increases accumulation and shifts the composition of lipids in green biomass (2009)

When grown for energy production instead for smoking, tobacco can generate a large amount of inexpensive biomass more efficiently than almost any other agricultural crop. Tobacco possesses potent oil biosynthesis machinery and can accumulate up to 40% of seed weight in oil. In this work, we explored two metabolic engineering approaches to enhance the oil content in tobacco green tissues for potential biofuel production. First, an Arabidopsis thaliana gene diacylglycerol acyltransferase (DGAT) coding for a key enzyme in triacylglycerol (TAG) biosynthesis, was expressed in tobacco under the control of a strong ribulose-biphosphate carboxylase small subunit promoter. This modification led to up to a 20-fold increase in TAG accumulation in tobacco leaves and translated into an overall of about a twofold increase in extracted fatty acids (FA) up to 5.8% of dry biomass in Nicotiana tabacum cv Wisconsin, and up to 6% in high-sugar tobacco variety NC-55. Modified tobacco plants also contained elevated amounts of phospholipids. This increase in lipids was accompanied by a shift in the FA composition favourable for their utilization as biodiesel. Second, we expressed in tobacco Arabidopsis gene LEAFY COTYLEDON 2 (LEC2), a master regulator of seed maturation and seed oil storage under the control of an inducible Alc promoter. Stimulation of LEC2 expression in mature tobacco plants by acetaldehyde led to the accumulation of up to 6.8% per dry weight of total extracted FA. The obtained data reveal the potential of metabolically modified plant biomass for the production of biofuel.
Electrocardiographic Systems With Reduced Numbers of Leads—Synthesis of the 12-Lead ECG (2013)

Systems with reduced numbers of leads that can synthesize the 12-lead electrocardiogram (ECG) with an insignificant or a small loss of diagnostic information have been proposed. The advantage over standard 12-lead ECG systems is the smaller number of measurement sites (i.e., electrodes) and, consequently, fewer wires. In this paper, we review all the important systems with reduced numbers of leads together with the methodology for synthesizing the leads. The fundamental theoretical background necessary to understand the most important concepts related to the synthesis is included. The presented theoretical and experimental justifications for the synthesis show that it is not necessary to measure a large number of leads directly, because the standard 12-lead ECG and arbitrary additional leads can be synthesized. Various approaches to evaluating the synthesized 12-lead ECG are defined and explained, and a number of systems that synthesize 12-lead ECG are presented as they were introduced in the literature. We cover the developments and improvements from the 1940s to the present day. The systems are classified on the basis of the synthesis method used, the approach to the evaluation of the synthesized ECG (depending on the measurement sites used), and on the number and types of leads employed. Based on a detailed assessment of state-of-the-art systems, open problems and challenges are highlighted, while further developments of electrocardiographic systems are envisaged.
Transient Well Testing of Coalbed Methane Reservoirs with Horizontal Wells (1994)

ABSTRACT Natural gas production from coalbeds using horizontal wells may be of interest to producers in the future. Since sedimentary gas reserves are limited, the unconventional gas reservoirs could be an alternative resource to meet the demand for natural gas. Naturally fractured coalbeds with their dual porosity character can produce at much higher rates with horizontal wells. The presented paper shows an analytical solution for transient pressure response of a horizontal well in a coalbed reservoir. Effects of wellbore storage and skin on the solution are illustrated. The solution is developed for a semi-infinite, anisotropic coalbed reservoir assuming single phase gas flow. The solution can be used to generate type curves for particular reservoir geometry and subsequent determination of reservoir parameters. The paper illustrates the application of type curve matching for a typical case through an example on computer generated data.
Pressure wave‐field deghosting for non‐horizontal streamers (2008)

This abstract discusses a receiver deghosting method for seismic pressure wave‐fields that have been recorded at arbitrary depth. For horizontal streamers, the deghosted pressure wave‐field can be directly constructed from the scattered pressure wave‐field in the spectral domain. For non‐horizontal streamers, a system of equations is solved using a preconditioned conjugate gradient method. The mathematical derivation of the method is shown, and implementation issues are discussed. The effectiveness of the method is demonstrated using two synthetic examples.
Molecular Cloning, Sequencing, and Expression of the Gene Encoding Alkaline Ceramidase from Pseudomonas aeruginosa (1999)

We previously reported the purification and characterization of a novel type of alkaline ceramidase from Pseudomonas aeruginosa strain AN17 (Okino, N., Tani, M., Imayama, S., and Ito, M. (1998) J. Biol. Chem. 273, 14368-14373). Here, we report the molecular cloning, sequencing, and expression of the gene encoding the ceramidase of this strain. Specific oligonucleotide primers were synthesized using the peptide sequences of the purified ceramidase obtained by digestion with lysylendopeptidase and used for polymerase chain reaction. DNA fragments thus amplified were used as probes to clone the gene encoding the ceramidase from a genomic library of strain AN17. The open reading frame of 2,010 nucleotides encoded a polypeptide of 670 amino acids including a signal sequence of 24 residues, 64 residues of which matched the amino acid sequence determined for the purified enzyme. The molecular weight of the mature enzyme was estimated to be 70,767 from the deduced amino acid sequence. Expression of the ceramidase gene in Escherichia coli, resulted in production of a soluble enzyme with the identical N-terminal amino acid sequence. Recombinant ceramidase was purified to homogeneity from the lysate of E. coli cells and confirmed to be identical to the Pseudomonas enzyme in its specificity and other enzymatic properties. No significant sequence similarities were found in other known functional proteins including human acid ceramidase. However, we found a sequence homologous to the ceramidase in hypothetical proteins encoded in Mycobacterium tuberculosis, Dictyostelium discoideum, and Arabidopsis thaliana. The homologue of the ceramidase gene was thus cloned from an M. tuberculosis cosmid and expressed in E. coli, and the gene was demonstrated to encode an alkaline ceramidase. This is the first report for the cloning of an alkaline ceramidase.
Pt-Catalyzed Cyclization/1,2-Migration for the Synthesis of Indolizines, Pyrrolones, and Indolizinones (2007)

Indolizine, pyrrolone, and indolizinone heterocycles are easily accessed via the Pt(II)-catalyzed cycloisomerization or a tandem cyclization/1,2-migration of pyridine propargylic alcohols and derivatives. This method provides an efficient synthesis of highly functionalized heterocycles from readily available substrates. [reaction: see text]
Acrylamide in Foods:  Occurrence, Sources, and Modeling (2002)

Acrylamide in food products-chiefly in commercially available potato chips, potato fries, cereals, and bread-was determined by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Samples were homogenized with water/dichloromethane, centrifuged, and filtered through a 5 kDa filter. The filtrate was cleaned up on mixed mode, anion and cation exchange (Oasis MAX and MCX) and carbon (Envirocarb) cartridges. Analysis was done by isotope dilution ([D(3)]- or [(13)C(3)]acrylamide) electrospray LC-MS/MS using a 2 x 150 mm (or 2 x 100 mm) Thermo HyperCarb column eluted with 1 mM ammonium formate in 15% (or 10% for the 2 x 100 mm column) methanol. Thirty samples of foods were analyzed. Concentrations of acrylamide varied from 14 ng/g (bread) to 3700 ng/g (potato chips). Acrylamide was formed during model reactions involving heating of mixtures of amino acids and glucose in ratios similar to those found in potatoes. In model reactions between amino acids and glucose, asparagine was found to be the main precursor of acrylamide. Thus, in the reaction between nitrogen-15 (amido)-labeled asparagine and glucose, corresponding (15)N-labeled acrylamide was formed. The yield of the model reaction is approximately 0.1%.
Induction and function of vascular adhesion protein-1 at sites of inflammation. (1993)

Emigration of leukocytes from the blood into the tissues is critical in controlling lymphocyte patrolling in different lymphatic organs and in leukocyte accumulation at sites of inflammation. During the first stage of the extravasation process, leukocytes bind to the endothelial lining of vessels. At the molecular level, several adhesion molecules on leukocytes and endothelial cells function as receptor-ligand pairs in mediating this dynamic interaction. Recently, we have identified a novel human endothelial cell molecule, vascular adhesion protein 1 (VAP-1), that mediates lymphocyte binding (Salmi, M., and S. Jalkanen. 1992. Science [Wash. DC] 257:1407). VAP-1 was initially characterized by mAb 1B2 which inhibits lymphocyte adhesion to high endothelial venules (HEV) and to purified VAP-1 protein. Here we report the location and function of VAP-1 in normal and inflamed tissues in humans. VAP-1 is abundant in HEV of lymphatic organs belonging to the peripheral lymph node system, but considerably less is expressed in vessels of mucosa-associated lymphatic tissues. A subset of venules in most normal nonlymphatic tissues like skin, brain, kidney, liver, and heart is also VAP-1 positive. In addition to vessels, VAP-1 is distributed on a few other cell types, most notably in dendritic-like cells of germinal centers. At sites of inflammation, such as in inflammatory bowel diseases and chronic dermatoses, expression of VAP-1 is clearly increased. The induced VAP-1 is functional, since mAb 1B2 inhibits lymphocyte binding to inflamed lamina propria venules by approximately 60%. Thus VAP-1 is an endothelial adhesion molecule that under normal conditions is expressed mainly in HEV of lymphatic tissues. However, expression of functional VAP-1 in vivo is upregulated during an inflammatory reaction at other sites as well. Inducibility of VAP-1 suggests that it may play a significant role, not only in recirculation of lymphocytes, but also in controlling entry of leukocytes into sites of inflammation.
Ethylene gas: perception, signaling and response (1998)

During the last decade a genetic approach based on the Arabidopsis 'triple response' to the hormone ethylene has allowed the identification of numerous components of the signal transduction pathway. Cloning of the genes and biochemical analysis of the proteins that they encode are uncovering the molecular mechanisms that allow a plant cell to perceive and respond to this gaseous regulator of plant growth/stress responses.
[Diabetic nephropathy and pregnancy]. (1997)

With a percentage of 20% diabetic nephropathy represents one of the most common causes of end-stage renal failure. During pregnancy it is associated with an increased perinatal morbidity as a striking result of the consistently high rate of 50% preterm deliveries mainly due to the frequent development of pre-eclampsia ranging between 35-55%. Perinatal mortality (0-11%) seems to be less increased in recent years. Simple and reliable screening methods by means of test-strips are available in order to detect microalbuminuria, which characterizes incipient diabetic nephropathy (stage III). Strict maternal metabolic control achieving normoglycemic blood glucose levels represents the basic of treatment. Furthermore, an adequate diet and control of blood pressure are fundamental issues of sufficient therapy. Currently, there are no data available to assess definitely the influence of pregnancy on the clinical course of diabetic nephropathy.