gebhart/patrepeval huggingface dataset:
DNA repair protocols : prokaryotic systems (2000)

DNA repair has assumed a new importance with the discovery that malfunctioning of the DNA repair pathways in humans can lead to many disease states. In DNA Repair Protocols: Prokaryotic Systems, well-versed investigators describe in step-by-step detail a wide range of DNA repair activities, from single act-alone repair proteins to complex repair systems. These practical protocols not only detail the various repair activities found in cells, but also demonstrate the use of DNA repair proteins and systems as reagents in molecular biology and biotechnology. The techniques described here include mutation and polymorphism detection, which are useful in the search for disease genes and drug response genes, as well as for breeding and trait selection in animals and plants. Each readily reproducible protocol is presented by a hands-on expert in sufficient detail to ensure robust experimental results and is supplemented by chapter introductions, as well as notes offering a wealth of interesting and useful information. Compact and highly practical, DNA Repair Protocols: Prokaryotic Systems provides expert guidance to both the DNA repair researcher studying the fundamental aspects of DNA repair and the applied researcher in human genetics and biotechnology
New chips stop buffer overflow attacks (2004)

Chip makers are designing a new generation of microprocessors to stop buffer overflow assaults, exploits that hackers often use to attack and extract data from PCs or servers. AMD's Athlon-64 chips for notebook and desktop computers and its Opteron processors for servers include features that provide buffer-overflow protection. Intel offers buffer-overflow protection in its Itanium chips for servers. A buffer overflow occurs when a program or process tries to store more data in a buffer than it was designed to hold. Operating systems that support the buffer-overflow prevention approach mark certain data in memory with a bit that identifies them as executable or nonexecutable. The AMD chips let users turn off the new security feature for legacy programs not written to work with the technology so that the applications can continue to function.
Projector View Synthesis and Virtual Texturing (2008)

Mitochondrial ATPase of Leishmania donovani was characterized using digitonin-permeabilized promastigotes and the results were compared with those from isolated mitochondria. Maximum mitochondrial ATPase activity was obtained in promastigotes permeabilized with digitonin at a final concentration of 20 microM and the specific activity of the enzyme was 46% and 57% higher than that of homogenized and sonicated promastigotes, respectively. At concentrations above 20 microM digitonin inhibited ATPase activity and the degree of inhibition increased with increasing concentrations of the detergent. The ATPase activity of promastigotes remained DCCD-sensitive when permeabilized with digitonin at concentrations up to 120 microM but the enzyme became increasingly resistant to this inhibitor as digitonin concentrations were increased to 140 microM and more, indicating the loss of functional activity of the enzyme. The pH and temperature optima for mitochondrial ATPase were determined to be 7.5 and 30 degrees C, respectively. Mg2+ ions were essential for ATPase activity but free Mg2+ ions were found to be inhibitory. A Mg2+/ATP ratio of 1:3 supported the optimum ATPase activity. Sulfite and hexanol activated the enzyme but failed to prevent the inhibition by free Mg2+ ions. The results indicate that digitonin-permeabilized promastigotes provide an ideal system for studying the mitochondrial ATPase of L. donovani.
Selection of an escape variant of Borrelia burgdorferi by use of bactericidal monoclonal antibodies to OspB (1992)

Two immunoglobulin G (IgG) monoclonal antibodies (MAbs) to outer surface protein B (CB2 and CB6), affinity purified from mouse ascitic fluid, exhibited concentration-dependent inhibitory and bactericidal properties against Borrelia burgdorferi after a 24-h incubation period in spirochete medium. Fab fragments derived from these MAbs showed the same effects, indicating that they were not caused by agglutination of the organisms by the intact MAbs. The inhibition of spirochete growth in cultures containing MAbs was also detected by spectrophotometric analysis of the media. CB2 did not inhibit the growth of Borrelia hermsii or the BEP4 strain of B. burgdorferi, neither of which is recognized by the MAb. Affinity-purified IgG from hybridoma supernatants had similar effects on B. burgdorferi as the ascitic-fluid-derived IgG did, indicating that the inhibitory and bactericidal properties were not due to nonspecific toxic contaminants. The bactericidal properties of the MAbs were not complement dependent as there was none in the serum-free system. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of B. burgdorferi organisms surviving after exposure to CB2 revealed an escape variant which failed to express OspB. The continued presence of OspA in these escape variants indicates that the lack of OspB was not due to the loss of the plasmid which contains the genes for both of these proteins.
Characterization of the Overproduced NADH Dehydrogenase Fragment of the NADH:Ubiquinone Oxidoreductase (Complex I) from <i>Escherichia coli</i> (1998)

The proton-pumping NADH:ubiquinone oxidoreductase of Escherichia coli is composed of 14 different subunits and contains one FMN and up to nine iron-sulfur clusters as prosthetic groups. By use of salt treatment, the complex can be split into an NADH dehydrogenase fragment, a connecting fragment and a membrane fragment. The water-soluble NADH dehydrogenase fragment has a molecular mass of approximately 170,000 Da and consists of the subunits NuoE, F, and G. The fragment harbors the FMN and probably six iron-sulfur clusters, four of them being observable by EPR spectroscopy. Here, we report that the fully assembled fragment can be overproduced in E. coli when the genes nuoE, F, and G were simultaneously overexpressed with the genes nuoB, C, and D. Furthermore, riboflavin, sodium sulfide, and ferric ammonium citrate have to be added to the culture medium. The fragment was purified from the cytoplasm by means of ammonium sulfate fractionation and chromatographic steps. The preparation contains one noncovalently bound FMN per molecule. Two binuclear (N1b and N1c) and two tetranuclear (N3 and N4) iron-sulfur clusters were detected by EPR in the NADH reduced preparation with spectral characteristics identical with those of the corresponding clusters in complex I. The preparation fulfills all prerequisites for crystallization of the fragment.
The health benefits of omega‐3 polyunsaturated fatty acids: a review of the evidence (2004)

The UK dietary guidelines for cardiovascular disease acknowledge the importance of long-chain omega-3 polyunsaturated fatty acids (PUFA) - a component of fish oils - in reducing heart disease risk. At the time, it was recommended that the average n-3 PUFA intake should be increased from 0.1 to 0.2 g day(-1). However, since the publication of these guidelines, a plethora of evidence relating to the beneficial effects of n-3 PUFAs, in areas other than heart disease, has emerged. The majority of intervention studies, which found associations between various conditions and the intake of fish oils or their derivatives, used n-3 intakes well above the 0.2 g day(-1) recommended by Committee on Medical Aspects of Food Policy (COMA). Furthermore, in 2004, the Food Standards Agency changed its advice on oil-rich fish creating a discrepancy between the levels of n-3 PUFA implied by the new advice and the 1994 COMA guideline. This review will examine published evidence from observational and intervention studies relating to the health effects of n-3 PUFAs, and discuss whether the current UK recommendation for long-chain n-3 PUFA needs to be revisited.
Developmental Exposure to Brominated Diphenyl Ethers Results in Thyroid Hormone Disruption (2002)

The objective of the current study was to characterize the effects of DE-71 (a commercial polybrominated diphenyl ether mixture containing mostly tetra- and penta-bromodiphenyl ethers) on thyroid hormones and hepatic enzyme activity in offspring, following perinatal maternal exposure. Primiparous Long-Evans rats were orally administered DE-71 (0, 1, 10, and 30 mg/kg/day) in corn oil from gestation day (GD) 6 to postnatal day (PND) 21. Serum and liver samples obtained from dams (GD 20 and PND 22), fetuses (GD 20), and offspring (PNDs 4, 14, 36, and 90) were analyzed for circulating total serum thyroxine (T(4)) and triiodothyronine (T(3)), or hepatic microsomal ethoxy- and pentoxy-resorufin-O-deethylase (EROD and PROD), and uridine diphosphoglucuronosyl transferase (UDPGT) activity. There were no significant effects of treatment on maternal body weight gain, litter size, or sex ratio, nor were there any effects on any measures of offspring viability or growth. Serum T(4) was reduced in a dose-dependent manner in fetuses on GD 20 (at least 15%) and offspring on PND 4 and PND 14 (50 and 64% maximal in the 10 and 30 mg/kg/day groups, respectively), but recovered to control levels by PND 36. Reduction in serum T(4) was also noted in GD 20 dams (48% at highest dose), as well as PND 22 dams (44% at highest dose). There was no significant effect of DE 71 on T(3) concentrations at any time in the dams or the offspring. Increased liver to body weight ratios in offspring were consistent with induction of EROD (maximal 95-fold), PROD (maximal 26-fold) or UDPGT (maximal 4.7-fold). Induction of PROD was similar in both dams and offspring; however, EROD and UDPGT induction were much greater in offspring compared to dams (EROD = 3.8-fold; UDPGT = 0.5-fold). These data support the conclusion that DE-71 is an endocrine disrupter in rats during development.
Characterization, treatment and prognosis of retinoblastoma with central nervous system metastasis (2018)

Our results were basically consistent with previous reports in the developing countries, and it could be guidance for clinical treatment, prognosis and prevention of CNS metastases in retinoblastoma.
Case Studies of the Bending Vibration and Whirling Motion of Drill Collars (1989)

ABSTRACT Two principal sources of BHA bending vibration are described: (1) drill collar whirling and (2) linear coupling between WOB fluctuations and bending vibration of an initially curved BHA. These mechanisms are described and their consequences in terms of drill collar wear and connection fatigue are evaluated. Formulas are given for forward and backward whirl rate and for tangential velocity at the borehole wall. Downhole measurements of bending moment are shown to be valuable in detecting and identifying bending vibration events. Downhole data taken from a Shell field test of a downhole vibration measurement system are used to illustrate cases of linearly coupled bending vibration, forward and backward whirl, and bit bounce.
Associated Focal and Segmental Glomerulosclerosis in the Acquired Immunodeficiency Syndrome (1984)

Of the 92 patients with the acquired immunodeficiency syndrome (AIDS) who were seen at our institution over a two-year period, 9 acquired the nephrotic syndrome (urinary protein greater than 3.5 g per 24 hours) and 2 had azotemia with lesser amounts of urinary protein. Five of these 11 patients had a history of intravenous-heroin addiction, but in the remaining six, there were no known predisposing factors for nephropathy. In nine patients (including the six non-addicts) the course of renal disease was marked by rapid progression to severe uremia. Renal tissue examined by biopsy in seven patients and at autopsy in three revealed focal and segmental glomerulosclerosis with intraglomerular deposition of IgM and C3. In the 11th patient, renal biopsy revealed an increase in mesangial matrix and cells, with deposition of IgG and C3 consistent with a mild immune-complex glomerulonephritis, and severe interstitial nephritis. We conclude that focal and segmental glomerulosclerosis may be associated with AIDS and suggest that rapid deterioration to uremia may characterize this renal disease.
Effects of Vestibular-Proprioceptive Stimulation on the Neurobehavioral Development of Preterm Infants: A Pilot Study (1983)

This paper reports the results of an intervention study which assessed the effects of compensatory vestibular-proprioceptive stimulation provided by waterbed flotation on the neurobehavioral development of preterm infants. The subjects, who were randomly assigned to experimental and control groups before they were four days old, consisted of infants who were on ventilators for severe RDS. Twenty infants were tested with a new neurobehavioral assessment procedure when they were between 34 and 35 weeks conceptional age. The examiner, a pediatric neurologist, was unaware of the group status of the subjects he examined. The results showed that infants in the experimental group performed significantly better in attending and pursuing animate and inanimate visual and auditory stimuli, demonstrated more mature spontaneous motor behavior, showed significantly fewer signs of irritability and/or hypertonicity and were more than twice as often in th visually alert, inactive state. The assessment procedure, which can be used for longitudinal evaluation of infants ranging between 24 and 36 weeks conceptional age, shows promise of becoming generally useful as a research instrument. Our preliminary results show that the procedure discriminated between an experimental and control group, that inter-observer reliability was readily established and that test-retest reliability is very high in a number of important areas of neurobehavioral functioning.
Nonlinear Electrokinetic Phenomena in Microfluidic Devices (2022)

Nitrification of high total ammonia nitrogen-strength wastewaters is challenging due to free ammonia (FA) inhibition of nitrification. FA inhibition can potentially be alleviated by temporarily adsorbing ammonium (NH<sub>4</sub><sup>+</sup>) to natural zeolite, such as chabazite, followed by direct zeolite bioregeneration via nitrification. In this research, the effectiveness of chabazite addition for reducing nitrification inhibition during treatment of centrate from anaerobic digestion of swine waste was quantified. A mathematical model was developed that accounts for ion exchange of NH<sub>4</sub><sup>+</sup> and sodium at the chabazite surface, surface diffusion of adsorbed NH<sub>4</sub><sup>+</sup> within the chabazite grains, sequential nitrification of aqueous NH<sub>4</sub><sup>+</sup> to nitrite and nitrate, and inhibition of nitritation and nitratation rates by NH<sub>4</sub><sup>+</sup>. The model was calibrated using results of abiotic ion exchange and nitrification studies. Subsequently, nitrification tests were carried out with synthetic wastewater with a NH<sub>4</sub><sup>+</sup>-N concentration of 1000 mg L<sup>-1</sup>, with and without chabazite. A chabazite dose of 150 g L<sup>-1</sup> decreased the FA concentration to below the inhibitory level and increased the nitrification rate from 0.16 to 0.36 mg-N (g-VSS)<sup>-1</sup> h<sup>-1</sup>. Following calibration, the model could predict the experimental data with no additional fitting parameters or parameter adjustment, in both the presence and absence of chabazite. The results suggest that the mathematical model provides a theoretically sound conceptual understanding of ion exchange assisted nitrification.
Blockade of KCa3.1 Ameliorates Renal Fibrosis Through the TGF-β1/Smad Pathway in Diabetic Mice (2013)

The Ca2+-activated K+ channel KCa3.1 mediates cellular signaling processes associated with dysfunction of vasculature. However, the role of KCa3.1 in diabetic nephropathy is unknown. We sought to assess whether KCa3.1 mediates the development of renal fibrosis in two animal models of diabetic nephropathy. Wild-type and KCa3.1−/− mice, and secondly eNOS−/− mice, had diabetes induced with streptozotocin and then were treated with/without a selective inhibitor of KCa3.1 (TRAM34). Our results show that the albumin-to-creatinine ratio significantly decreased in diabetic KCa3.1−/− mice compared with diabetic wild-type mice and in diabetic eNOS−/− mice treated with TRAM34 compared with diabetic mice. The expression of monocyte chemoattractant protein-1 (MCP-1), intercellular adhesion molecule 1 (ICAM1), F4/80, plasminogen activator inhibitor type 1 (PAI-1), and type III and IV collagen significantly decreased (P &lt; 0.01) in kidneys of diabetic KCa3.1−/− mice compared with diabetic wild-type mice. Similarly, TRAM34 reduced the expression of the inflammatory and fibrotic markers described above in diabetic eNOS−/− mice. Furthermore, blocking the KCa3.1 channel in both animal models led to a reduction of transforming growth factor-β1 (TGF-β1) and TGF-β1 type II receptor (TβRII) and phosphorylation of Smad2/3. Our results provide evidence that KCa3.1 mediates renal fibrosis in diabetic nephropathy through the TGF-β1/Smad signaling pathway. Blockade of KCa3.1 may be a novel target for therapeutic intervention in patients with diabetic nephropathy.
Fast Diazaborine Formation of Semicarbazide Enables Facile Labeling of Bacterial Pathogens (2016)

Bioorthogonal conjugation chemistry has enabled the development of tools for the interrogation of complex biological systems. Although a number of bioorthogonal reactions have been documented in literature, they are less ideal for one or several reasons including slow kinetics, low stability of the conjugated product, requirement of toxic catalysts, and side reactions with unintended biomolecules. Herein we report a fast (>10<sup>3</sup> M<sup>-1</sup> s<sup>-1</sup>) and bioorthogonal conjugation reaction that joins semicarbazide to an aryl ketone or aldehyde with an ortho-boronic acid substituent. The boronic acid moiety greatly accelerates the initial formation of a semicarbazone conjugate, which rearranges into a stable diazaborine. The diazaborine formation can be performed in blood serum or cell lysates with minimal interference from biomolecules. We further demonstrate that application of this conjugation chemistry enables facile labeling of bacteria. A synthetic amino acid D-AB3, which presents a 2-acetylphenylboronic acid moiety as its side chain, was found to incorporate into several bacterial species through cell wall remodeling, with particularly high efficiency for Escherichia coli. Subsequent D-AB3 conjugation to a fluorophore-labeled semicarbazide allows robust detection of this bacterial pathogen in blood serum.
An Index of Plasma Refilling in Hemodialysis Patients (1996)

During hemodialysis therapy, a large amount of water is removed from the patient's blood in a short time; however, blood pressure remains stable in most patients. As water is removed, the circulating serum proteins become more concentrated, resulting in a marked increase in the driving force which pulls water from the extravascular space into the blood vessels, by a process called plasma refilling. However, since a method for studying plasma refilling has not previously been proposed, it is not known what determines the plasma refilling capacity of hemodialysis patients. To evaluate the plasma refilling capacity of patients, we propose here a method for calculating an index of plasma refilling capacity, which we have called the plasma-refilling coefficient (Kr). In 14 patients receiving maintenance hemodialysis therapy, total serum protein was measured before hemodialysis, and hematocrits were measured hourly during hemodialysis. From the changes in the hematocrits, we estimated the changes in the circulating plasma volume and in the intracapillary oncotic pressure at each time point. The water removal rate was also measured hourly. From these values, we calculated Kr. An averaged volume of 2,692 +/- 219 ml of water was removed from each patient resulting in a decrease in the estimated circulating blood volume, while the hematocrit and the estimated intracapillary oncotic pressure increased gradually. Kr calculated after 1 h of hemodialysis varied widely between patients, 140.3-1,744.2 ml/mm Hg/h, and decreased gradually as water removal continued. The average Kr of 14 patients was 698.9 +/- 15.2 ml/mm Hg/h at the beginning of water removal, and it decreased to 405.3 +/- 75.4, 203.9 +/- 39.5, 130.2 +/- 20.5 and 93.9 +/- 14.3 each hour thereafter. The index of plasma refilling proposed in this paper is useful for examining capillary water permeability and the degree of plasma refilling in hemodialysis patients.
Temporal Profile of in situ DNA Fragmentation after Transient Middle Cerebral Artery Occlusion in the Rat (1995)

We measured the temporal profile and anatomic distribution of cells exhibiting DNA fragmentation at various durations of reperfusion after middle cerebral artery (MCA) occlusion in the rat. Focal cerebral ischemia was induced in male Wistar rats (n = 62) using an intraluminal monofilament blockade of the MCA. After 2 h of MCA occlusion, the animals were killed at different durations of reperfusion (0.5, 3, 6, 9, and 12 h and 1, 2, 4, 7, 14, 21, and 28 days, n = 4 per time point). Sham-operated rats (n = 4) and normal rats not subjected to any surgical procedure (n = 4) were used as controls. Coronal brain sections (5 microns) were analyzed, using an in situ ApopTag kit, hematoxylin and eosin, and immunohistochemical double-staining methods. Six rats subjected to 2 h of MCA occlusion were killed at 24 h for measurement of DNA fragmentation by gel electrophoresis. Our data indicate that within a coronal section, DNA fragmentation was present in zero to three cells in each hemisphere of normal and sham-operated rats as well as in the contralateral hemisphere of ischemic rats. The number of cells exhibiting DNA fragmentation increased as early as 0.5 h (8 +/- 6), peaked at 24-48 h (213 +/- 59), and persisted for 4 weeks (10 +/- 2) after onset of reperfusion (p < 0.01). Groups of cells exhibiting DNA fragmentation (> 95% neurons) were located primarily in the inner boundary zone of the infarct. With use of gel electrophoresis, purified DNA obtained from the ischemic tissue exhibited the characteristic nucleosome ladder pattern associated with apoptosis.(ABSTRACT TRUNCATED AT 250 WORDS)
Glutamate receptor activation can trigger electrical activity in human glioma cells (1998)

Cells from major types of gliomas, i.e. oligodendrogliomas and glioblastomas, are able to generate action potentials upon a current injection similar to neurons (Patt et al. (1996) Neuroscience, 71, 601-611; Labrakakis et al. (1997b) J. Neuropath. Exp. Neurol., 56, 243-254. Here, we report that activation of ionotropic glutamate receptors by the selective agonist, kainate, or by glutamate itself, depolarized the tumour cells in culture and living slices from tumour tissue, and can elicit volleys of action potentials, as recorded with the patch-clamp technique. Sixty-six percent of the glioblastoma cells, 44% of the astocytoma and 86% of the oligodendroglioma cells responded to glutamate and the specific agonist of AMPA/kainate receptors, kainate. The involvement of non-NMDA (N-methyl-D-aspartate) receptors is further supported by the observation that both kainate and glutamate currents were blocked by CNQX (6-cyano-7-nitroquinoxaline-2,3-dione). The receptor activation was accompanied by an increase in cytosolic Ca2+, as recorded with a fura-2 microfluorometric system. The Ca2+ elevation was mediated by the activation of Ca2+ channels due to membrane depolarization. The presence of voltage-gated Ca2+ channels was confirmed by patch-clamp experiments. Taken together, these findings imply that the electrophysiological properties of glioma cells are more reminiscent of those of neurons than of glial cells.
The near infrared absorption properties of W18O49 (2012)

The urchin-like W18O49 nanoparticles showed high transparency in the visible region, strong absorption of near-infrared light and instantaneous conversion of the absorbed photo-energy to local heat.