gebhart/patrepeval huggingface dataset:
A member of a new repeated sequence family which is conserved throughout eucaryotic evolution is found between the human δ and β globin genes (1981)

A new class of human interspersed repeated sequences distinct from the AluI family was found by screening a human gene library with a mouse ribosomal gene non-transcribed spacer probe (rDNA NTS). A member of this sequence family was localized to a 251 bp segment between the human delta and beta globin genes: a region previously judged to be devoid of repeated DNA. The complete nucleotide sequence of this segment revealed a tandem block of 17 TG dinucleotides, a feature hypothesized by others to be a recombination hot spot responsible for gene conversion in the gamma globin locus region. When the genomes of Xenopus, pigeon, slime mold and yeast were examined, reiterated sequences homologous to both the mouse rDNA NTS and human globin repeat were found in every case. The discovery of this extraordinarily conserved repeated sequence family appears to have depended upon not using salmon sperm DNA during hybridization. The use of eucaryotic carrier DNA may bias the search for repeated sequences against any which may be highly conserved during eucaryotic evolution.
Convergence and stability assessment of Newton-Kantorovich reconstruction algorithms for microwave tomography (1998)

For newly developed iterative Newton-Kantorovitch reconstruction techniques, the quality of the final image depends on both experimental and model noise. Experimental noise is inherent to any experimental acquisition scheme, while model noise refers to the accuracy of the numerical model, used in the reconstruction process, to reproduce the experimental setup. This paper provides a systematic assessment of the major sources of experimental and model noise on the quality of the final image. This assessment is conducted from experimental data obtained with a microwave circular scanner operating at 2.33 GHz. Targets to be imaged include realistic biological structures, such as a human forearm, as well as calibrated samples for the sake of accuracy evaluation. The results provide a quantitative estimation of the effect of experimental factors, such as temperature of the immersion medium, frequency, signal-to-noise ratio, and various numerical parameters.
A cladistic analysis of phenotype associations with haplotypes inferred from restriction endonuclease mapping. II. The analysis of natural populations. (1988)

Genes that code for products involved in the physiology of a phenotype are logical candidates for explaining interindividual variation in that phenotype. We present a methodology for discovering associations between genetic variation at such candidate loci (assayed through restriction endonuclease mapping) with phenotypic variation at the population level. We confine our analyses to DNA regions in which recombination is very rare. In this case, the genetic variation at the candidate locus can be organized into a cladogram that represents the evolutionary relationships between the observed haplotypes. Any mutation causing a significant phenotypic effect should be imbedded within the same historical structure defined by the cladogram. We showed, in the first paper of this series, how to use the cladogram to define a nested analysis of variance (NANOVA) that was very efficient at detecting and localizing phenotypically important mutations. However, the NANOVA of haplotype effects could only be applied to populations of homozygous genotypes. In this paper, we apply the quantitative genetic concept of average excess to evaluate the phenotypic effect of a haplotype or group of haplotypes stratified and contrasted according to the nested design defined by the cladogram. We also show how a permutational procedure can be used to make statistical inferences about the nested average excess values in populations containing heterozygous as well as homozygous genotypes. We provide two worked examples that investigate associations between genetic variation at or near the Alcohol dehydrogenase (Adh) locus and Adh activity in Drosophila melanogaster, and associations between genetic variation at or near some apolipoprotein loci and various lipid phenotypes in a human population.
A Genetic Switch: Gene Control and Phage Lambda (1986)

A genetic switch: gene control and phage [lambda] , A genetic switch: gene control and phage [lambda] , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی
Toxicity of neonicotinoid insecticides to honey bees: laboratory tests. (2011)

Toxic effects on Apis mellifera L. of the neonicotinoid insecticides Thiametoxam, Clothianidin, Acetamiprid and Thiacloprid were tested in the laboratory. Commercial formulations, dispersed in sugar syrup and water, at the highest dose level marked on the label were used to carry out oral and indirect contact trials on each pesticide. Clothianidin and Thiametoxam caused higher mortality than the untreated controls and were also tested at decreasing concentrations until mortality was statistically insignificant in comparison with that of the control; the acute oral Lethal Dose50, the acute indirect contact Lethal Concentration50, and the related Hazard Quotient were calculated at 24, 48, and 72 hours from test initiation. On the contrary, Acetamiprid and Thiacloprid caused higher mortality than the untreated controls only in oral toxicity tests when honey bees, which had starved for two hours, were used. Honey bees that died during the trials were analyzed and the quantity of residues of insecticides determined. These quantities resulted much lower than the administered ones.
Quantification of C‐reactive protein in the serum of patients with rheumatoid arthritis using multiple reaction monitoring mass spectrometry and 13C‐labeled peptide standards (2004)

A general method for the quantification of proteins in human serum was developed using mass spectrometry (MS) and stable isotope-labeled synthetic peptides as internal standards. Using this approach, C-reactive protein (CRP), a diagnostic marker of rheumatoid arthritis (RA), was detected in serum samples taken from patients with either erosive or nonerosive RA and compared to healthy individuals. Small volumes of serum samples were enriched for low-abundance proteins through the selective removal of human serum albumin (HSA), immunoglobulin G (IgG), and haptoglobin. After depletion of abundant proteins, the complexity of the protein mixture was further simplified using size exclusion chromatography (SEC) to fractionate denatured proteins into discrete molecular weight ranges. Fractions of interest containing CRP, M(r) = 25 000, were pooled, digested with trypsin, and then fixed quantities of the synthetic peptides were added to the mixture. The mixture of tryptic peptides was subsequently analyzed by nanoflow chromatography-tandem MS (nanoLC-MS/MS) using multiple-reaction monitoring (MRM) on a triple quadrupole mass spectrometer (TQ-MS). The ratio of transition ions derived from the endogenous and isotope-labeled peptides provided a quantitative measure of CRP in the original samples as assessed by independent measurement of CRP in the same patient samples using an immunoassay. The use of isotope-labeled synthetic peptides and MRM is a powerful analytical method for the prescreening of candidate protein biomarkers in human serum prior to antibody and immunoassay development.
Cortisol Activity and Cognitive Changes in Psychotic Major Depression (2001)

Psychotic major depression is endocrinologically different from nonpsychotic major depression and produces cognitive changes distinct from those seen in nonpsychotic major depression.
Effects of the ResQPOD on Kinetics, Hemodynamics of Vasopressin, and Survivability in a Porcine Cardiac Arrest Model (2015)

Our data suggest that there is no difference in drug kinetics or clinical outcomes in terms of survivability with or without the ResQPOD.
Specific alteration of the oxidation potential of the electron donor in reaction centers from Rhodobacter sphaeroides. (1994)

The effects of multiple changes in hydrogen bond interactions between the electron donor, a bacteriochlorophyll dimer, and histidine residues in the reaction center from Rhodobacter sphaeroides have been investigated. Site-directed mutations were designed to add or remove hydrogen bonds between the 2-acetyl groups of the dimer and histidine residues at the symmetry-related sites His-L168 and Phe-M197, and between the 9-keto groups and Leu-L131 and Leu-M160. The addition of a hydrogen bond was correlated with an increase in the dimer midpoint potential. Measurements on double and triple mutants showed that changes in the midpoint potential due to alterations at the individual sites were additive. Midpoint potentials ranging from 410 to 765 mV, compared with 505 mV for wild type, were achieved by various combinations of mutations. The optical absorption spectra of the reaction centers showed relatively minor changes in the position of the donor absorption band, indicating that the addition of hydrogen bonds to histidines primarily destabilized the oxidized state of the donor and had little effect on the excited state relative to the ground state. Despite the change in energy of the charge-separated states by up to 260 meV, the mutant reaction centers were still capable of electron transfer to the primary quinone. The increase in midpoint potential was correlated with an increase in the rate of charge recombination from the primary quinone, and a fit of these data using the Marcus equation indicated that the reorganization energy for this reaction is approximately 400 meV higher than the change in free energy in wild type. The mutants were still capable of photosynthetic growth, although at reduced rates relative to the wild type. These results suggest a role for protein-cofactor interactions--in particular, histidine-donor interactions--in establishing the redox potentials needed for electron transfer in biological systems.
Global Color Model Based Object Matching in the Multi-Camera Environment (2006)

The research field on intelligent environments that consist of many distributed sensors and robots has been expanding. Intelligent environments require the functions of extracting and tracking the multiple objects seamlessly to achieve appropriate services to users under the multi-camera environments. Some tracking systems often prepare the color models of the objects in advance. It is difficult to adopt these models to the tracking of the objects that change their color appearance according to the pose. However, model based tracking is efficient for the tracking in the crowded environment. And also, the object color models have to be valid for seamless tracking in the multi-camera environments. We propose the color histogram based object model configuration. This model termed global model is efficient for object tracking and matching. The eigen space of color histograms configured from color appearance in several poses of the object is utilized for the configuration of the global model. Color histogram models needed for tracking of the object that changed their appearance can be rebuilt from the global model. As results of the first experiments, the object correspondence among the different cameras was achieved empirically, and it was described that the proposed object model is effective for the seamless tracking by the distributed cameras
Memory interfacing and instruction specification for reconfigurable processors (1999)

As custom computing machines evolve, it is clear that a major bottleneck is the slow interconnection architecture between the logic and memory. This paper describes the architecture of a custom computing machine that overcomes the interconnection bottleneck by closely integrating a fixed-logic processor, a reconfigurable logic array, and memory into a single chip, called OneChip-98. The OneChip-system has a seamless programming model that enables the programmer to easily specify instructions without additional complex instruction decoding hardware. As well, there is a simple scheme for mapping instructions to the corresponding programming bits. To allow the processor and the reconfigurable array to execute concurrently, the programming model utilizes a novel memory-consistency scheme implemented in the hardware. To evaluate the feasibility of the OneChip-architecture, a 32-bit MIPS-like processor and several performance enhancement applications were mapped to the Transmogrifier-2 field programmable system. For two typical applications, the 2-dimensional discrete cosine transform and the 64-tap FIR filter, we were capable of achieving a performance speedup of over 30 times that of a stand-alone state-of-the-art processor.
Antibody–Drug Conjugate (ADC) Clinical Pipeline: A Review (2013)

Biological therapies play an increasing role in cancer treatment, although the number of naked antibodies showing clinical efficacy as single agent remains limited. One way to enhance therapeutic potential of antibodies is to conjugate them to small molecule drugs. This combination is expected to bring together the benefits of highly potent drugs on the one hand and selective binders of specific tumor antigens on the other hand. However, designing an ADC is more complex than a simple meccano game, requiring thoughtful combination of antibody, linker, and drugs in the context of a target and a defined cancer indication. Lessons learned from the first-generation antibody-drug conjugate (ADC) and improvement of the technology guided the design of improved compounds which are now in clinical trials. Brentuximab vedotin (Adcetris(®)), an anti-CD30 antibody conjugated to a potent microtubule inhibitor for the treatment of Hodgkin's lymphoma and anaplastic large cell lymphomas, is the only marketed ADC today. A total of 27 ADC are currently undergoing clinical trials in both hematological malignancies and solid tumor indications. Among them, T-DM1 (trastuzumab emtansine), an ADC comprised of trastuzumab conjugated to DM1, via a non-cleavable linker, is showing very promising results in phase III for the treatment of HER2-positive refractory/relapsed metastatic breast cancer. Other compounds, such as CMC-544, SAR3419, CDX-011, PSMA-ADC, BT-062, and IMGN901 currently in clinical trials, targeting varied antigens and bearing different linker and drugs, contribute to the learning curve of ADC, as do the discontinued ADC. Current challenges include improvement of the therapeutic index, linked to a careful selection of the targets, a better understanding of ADC mechanism of action, the management and understanding of ADC off-target toxicities, as well as the selection of appropriate clinical settings (patient selection, dosing regimen) where these molecules can bring highest clinical benefit.
Crystallization of Polymer‐Derived Silicon Carbonitride at 1873 K under Nitrogen Overpressure (2002)

The chemical stability of an amorphous silicon carbonitride ceramic, having the composition 0.57SiC·0.43Si 3 N 4 ·0.49C is studied as a function of nitrogen overpressure at 1873 K. The ceramic suffers a weight loss at p N2 &lt; 3.5 bar (1 bar = 100 kPa), does not show a weight change from 3.5 to 11 bar, and gains weight above 11 bar. The structure of the ceramic changes with pressure: it is crystalline from 1 to 6 bar, amorphous at ∼10 bar, and is crystalline above ∼10 bar. The weight‐loss transition, at 3.5 bar, is in excellent agreement with the prediction from thermodynamic analysis when the activities of carbon, SiC, and Si 3 N 4 are set equal to those of the crystalline forms; this implies that the material crystallizes before decomposition. The amorphous to crystalline transition that occurs at ∼10 bar, and which is accompanied by weight gain, is likely to have taken place by a different mechanism. A nucleation and growth reaction with the atmospheric nitrogen is proposed as the likely mechanism. The supersaturation required to nucleate α‐Si 3 N 4 crystals is calculated to be 30 kJ/mol.
Functional correction of episomal mutations withshort DNA fragments and RNA–DNA oligonucleotides (2002)

Whilst delivery of PEI-complexed SDFs or RDOs to the cell is highly effective, nuclear entry appears to be a limiting factor. SDFs elicited episomal GFP correction across a range of cell lines, whereas RDOs only corrected the reporter in a cell line that overexpresses RAD51.
Clopidogrel inhibits the binding of ADP analogues to the receptor mediating inhibition of platelet adenylate cyclase. (1992)

Clopidogrel, like the homologous thienopyridine derivative ticlopidine, selectively inhibits platelet aggregation induced by ADP. We have previously described two nucleotide-binding sites on platelets related to ADP-mediated platelet responses. The first is a high-affinity binding site for 2-methylthio-ADP (2-MeSADP) that is linked to the inhibition of stimulated adenylate cyclase. The second is the 100-kd exofacial membrane protein aggregin, which is labeled by the reactive ADP analogue 5'-p-fluorosulfonylbenzoyl adenosine (FSBA) that is related to shape change and aggregation. We set out to determine if either of these sites is blocked in vivo by clopidogrel or its active metabolite. Six subjects were given clopidogrel (75 mg/day for 10 days) in a double-blind crossover experiment. All of the subjects developed prolonged bleeding times while taking the drug. The rate of onset of the effect on bleeding time varied among subjects. Platelet aggregation induced by ADP or thrombin was significantly impaired by the drug treatment, but no effect was detected on shape change. The incorporation of [3H]FSBA into aggregin was also unaffected. Inhibition of adenylate cyclase by ADP or by 2-MeSADP was greatly reduced in all subjects, and in the case of 2-MeSADP, there was evidence for a noncompetitive effect. Inhibition of adenylate cyclase by epinephrine was unaffected. In the three subjects for whom binding measurements were made, the number of binding sites for [32P]2-MeSADP was reduced from 534 +/- 44 molecules per platelet during control and placebo periods (11 determinations) to 199 +/- 78 molecules per platelet during drug treatment (three determinations). There was no consistent change in the binding affinity.(ABSTRACT TRUNCATED AT 250 WORDS)
A New Biological Approach To Vital Pulp Therapy (1995)

Molecular biology is providing opportunities to develop new strategies or agents for the treatment of a wide variety of diseases. The availability of large amounts of highly purified proteins produced by recombinant DNA techniques is an obvious example. Recent evidence has implicated proteins belonging to the bone morphogenetic protein (BMP) subgroup of the transforming growth factor beta supergene family in tooth formation and dentinogenesis. It has long been known that bone and dentin contain bone morphogenetic protein activity. Recently, recombinant human BMP-2, -4, and -7 (also known as OP-1), have been shown to induce reparative dentin formation in experimental models of large direct pulp exposures in permanent teeth. The manner in which these agents act appears unique. New reparative dentin replaces the stimulating agents applied directly to the partially amputated pulp. Hence, the new tissue forms contiguous with, largely superficial to, and not at the expense of the remaining vital pulp tissue. This suggests a therapeutic approach permitting the induction of a predetermined and controlled amount of reparative dentin. Additionally, OP-1 has been associated with the formation of reparative dentin after application to a freshly cut but intact layer of dentin. These findings may provide future clinicians with additional options for the treatment of substantially damaged or diseased vital teeth.
Generalizing recognition of an individual dialect in program analysis and transformation (2007)

We present a novel method for generalizing the recognition capability of a tool from one dialect of a language to other dialects. The framework defines a novel base-dialect-specific map layer for representing program geography as recognised/unrecognised program zones in terms of an annotated preprocessor token stream. Error call stacks generated in the front-end syntax-analysis are also stored in the map for invoking programmable, error handling and repair transformations to obtain recognizable constructs from un-recognized ones. An iterative process is followed, wherein for each transformation, reversion-identifying edits are also stored in the map to provide a handle on (and preserved semantics of) the unchanged, original form.
Experimental investigation of high Si/Al selectivity during anisotropic etching in tetra-methyl ammonium hydroxide (1998)

This work contributes to the understanding of anisotropic etching of silicon, for microsystems technology, by studying Si/Al selectivity during anisotropic etching of silicon in tetra-methyl ammonium hydroxide (TMAH). By under-etch experiments using a wagon-wheel mask pattern, Si/Al selectivity is studied in relation to trends in etch anisotropy, etched surface morphology, and variations of under-etch behavior with mask-edge angle. TMAH at 5 wt % is used, with or without the additives: dissolved silicon and ammonium persulfate. High Si/Al selectivity is accompanied by obvious changes in the roughness, flatness, and etch rate of the {100} cavity bottoms, by large changes in anisotropy as seen in under-etch rate curves, by lower ratio of {101} to {100} etch rates, and by more regular 〈101〉-oriented steps on non-{111} cavity sidewalls. The conditions are consistent with a low rate of attack of 〈101〉-directed periodic bond chains in the Si lattice.
Acid-base equilibria of some 7-dimethylamino-3-phenoxazone derivatives (1982)

The acid-base equilibria of some phenoxazine dyes in aqueous-ethanolic solutions were studied spectrophotometrically. The compounds examined were prepared in reagent grade purity, their main spectral characteristics in UV and VIS reagion were found and their dissociation constants were determined in 41% (m/m) ethanol. For the analytically most interesting derivative, gallocyanine methyl ester ( IV ), the p K values were measured also in solutions with different proportions of ethanol. The colour changes accompanying the protolytic reactions and the factors governing the phenomena are discussed.
Strikingly higher interleukin (IL)-1α, IL-1β and soluble interleukin-1 receptor antagonist (sIL-1RA) but similar IL-2, sIL-2R, IL-3, IL-4, IL-6, sIL-6R, IL-10, tumour necrosis factor (TNF)-α, transforming growth factor (TGF)-β2 and interferon IFN-γ urine levels in healthy females compared to healthy males: protection against urinary tract injury? (2005)

The aim of this prospective study was to examine gender-related differences of cytokines in the plasma and urine of healthy individuals that might provide a clue concerning the lower rate of chronic renal diseases in females. Soluble interleukin-1 receptor antagonist (sIL-1RA), interleukin (IL)-1alpha, IL-1beta, IL-2, sIL-2R, IL-3, IL-4, IL-6, sIL-6R, IL-10, tumor necrosis factor (TNF)-alpha, transforming growth factor (TGF)-beta(2) and interferon (IFN)-gamma were determined using standard enzyme-linked immunosorbent assay (ELISA). Cytokine levels were determined in simultaneously obtained plasma and urine samples of 18 male and 28 female healthy members of our laboratory staff. Urine cytokine levels were studied three times at 1-month intervals. All individuals had a negative urine nitrite test and showed no symptoms of urinary tract infection (UTI). Plasma levels of all studied cytokines were similar in males and females (P = n.s.). However, females had significantly higher urine IL-1alpha (P < 0.0001; P < 0.0001; P < 0.0001) and sIL-1RA (P = 0.0001; P = 0.0003; P = 0.0002) than males at three and higher IL-1beta at one of the three investigations (P = 0.098; P = 0.003; P = 0.073). Urine levels of the other cytokines were similar in males and females. Higher urine levels of IL-1alpha, IL-1beta and sIL-1RA in females may result from stimulation of cells in the urinary tract. Increased sIL-1RA might block T lymphocyte activation. The elevated cytokines may play a role in the protection of the female urinary tract from certain renal diseases, such as pyelonephritis and other inflammatory and sclerotic kidney diseases.