gebhart/patrepeval huggingface dataset:
Restriction Enzyme Digestion, Gel Electrophoresis, and Vacuum Blotting of DNA to Nylon Membranes (2003)

In 1975, Edwin Southern published a paper that revolutionized the molecular analysis of the genomes of organisms (). This procedure enabled the detection of which fragment of DNA (out of the millions that compose the genome of a higher organism) contained sequences related to that of a radioactively labeled probe. It was thus possible to detect and genetically map restriction fragment length polymorphisms (RFLPs, reviewed in ref. ), to know how many copies of a gene were present in an organism, to map the restriction sites around a sequence of interest, and to check if a potentially transgenic organism had really integrated the input gene into its chromosome. Suitable selection of probes, so that they detected sequences that were highly polymorphic (), enabled the identification of individuals from a population, and has led to the use of the method in forensic analysis. The identification of genes, or linked loci, affecting human disease, has also led to applications in clinical research.
Evaluation of mutagenic and genotoxic properties of TPP. (1993)

For evaluation of mutagenic and genotoxic properties of Tołpa Peat Preparation (TPP) four selected short-term tests were employed. TPP has been found to be neither mutagenic nor genotoxic.
Increased Cholesterol Efflux Potential of Sera From ApoA-I Milano Carriers and Transgenic Mice (1999)

The ability of HDL to remove cholesterol from peripheral cells and drive it to the liver for excretion is believed to explain most of the strong inverse correlation between plasma HDL cholesterol levels and coronary heart disease. Carriers of the ApoA-IMilano (A-IM) mutant have a severe hypoalphalipoproteinemia but are not at increased risk for premature of coronary heart disease. To explain this apparent paradox, we compared the capacity of serum from A-IM and control subjects to extract cholesterol from Fu5AH cells. Because the A-IM carriers are all heterozygotes for the mutation, we also compared the cholesterol efflux capacity of serum from transgenic mice expressing A-IM or wild-type ApoA-I (A-IWT), in the absence of murine ApoA-I. In the whole series of human or mouse sera, cholesterol efflux was significantly correlated with several HDL-related parameters; after adjustment for concomitant variables, the only parameter that remained significantly correlated with cholesterol efflux was the serum ApoA-I concentration (r2=0.85 in humans and 0.84 in mice). The same was true when samples from control subjects, A-IM carriers, A-IWT or A-IM mice were analyzed separately. Cholesterol efflux to sera from the A-IM carriers was only reduced slightly compared with control sera (25.0+/-4.2% versus 30.4+/-3.3%), although there was a large reduction (-45%) in the serum ApoA-I concentration in the former. Cholesterol efflux was also lower to sera from A-IM than A-IWT mice (15.6+/-3.8% versus 30. 1+/-7.1%), but less than expected from the 70% reduction in serum ApoA-I concentration. A relative efflux potential of serum was calculated in each group as the slope of the regression line fitting cholesterol efflux to ApoA-I concentrations. Therefore, the relative efflux potential reflects the relative efficiency of ApoA-I in determining cell cholesterol efflux. The relative efflux potential of mouse and human sera was in the following order: A-IM mice>A-IM carriers>A-IWT mice=control subjects, suggesting a gene-dosage effect of the A-IM mutation on the efficiency of serum to extract cholesterol from cells. The high efficiency of A-IM-containing HDL for cell cholesterol uptake would result in an improved reverse cholesterol transport in the A-IM carriers, possibly explaining the low susceptibility to atherosclerosis development.
Crystal Engineering Approach To Forming Cocrystals of Amine Hydrochlorides with Organic Acids. Molecular Complexes of Fluoxetine Hydrochloride with Benzoic, Succinic, and Fumaric Acids (2004)

A crystal engineering strategy for designing cocrystals of pharmaceuticals is presented. The strategy increases the probability of discovering useful cocrystals and decreases the number of experiments that are needed by selecting API:guest combinations that have the greatest potential of forming energetically and structurally robust interactions. Our approach involves multicomponent cocrystallization of hydrochloride salts, wherein strong hydrogen bond donors are introduced to interact with chloride ions that are underutilized as hydrogen bond acceptors. The strategy is particularly effective in producing cocrystals of amine hydrochlorides with neutral organic acid guests. As an example of the approach, we report the discovery of three cocrystals containing fluoxetine hydrochloride (1), which is the active ingredient in the popular antidepressant Prozac. A 1:1 cocrystal was prepared with 1 and benzoic acid (2), while succinic acid and fumaric acid were each cocrystallized with 1 to provide 2:1 cocrystals of fluoxetine hydrochloride:succinic acid (3) and fluoxetine hydrochloride:fumaric acid (4). The presence of a guest molecule along with fluoxetine hydrochloride in the same crystal structure results in a solid phase with altered physical properties when compared to the known crystalline form of fluoxetine hydrochloride. On the basis of intrinsic dissolution rate experiments, cocrystals 2 and 4 dissolve more slowly than 1, and 3 dissolves more quickly than 1. Powder dissolution experiments demonstrated that the solid present at equilibrium corresponds to the cocrystal for 2 and 4, while 3 completely converted to 1 upon prolonged slurry in water.
Cytokine levels in serum and synovial fluid of patients with juvenile rheumatoid arthritis. (1994)

Our studies indicate that (1) IL-1 alpha, IL-2, IL-2R, and IL-6 levels are increased in serum of patients with JRA with different onset types; (2) elevated levels of IL-1 beta, IL-2R, and IL-6 are found in their SF compared to serum levels; (3) a correlation exists between serum and SF levels only for IL-1 alpha; (4) mean IL-2R levels are elevated with active disease in all onset types and mean IL-6 levels with active polyarticular and pauciarticular onset disease are elevated compared to mean levels of inactive patients; and (5) cytokines may thus play a role as inflammatory mediators in JRA.
Micromechanical Mixer-Filters (“Mixlers”) (2004)

A device comprised of interlinked micromechanical resonators with capacitive mixer transducers has been demonstrated to perform both frequency translation (i.e., mixing) and highly selective low-loss filtering of applied electrical input signals. In particular, successful downconversion of a 200-MHz radio frequency (RF) signal down to a 37-MHz intermediate frequency (IF) and subsequent high-Q bandpass filtering at the IF are demonstrated using this single, passive, micromechanical device, all with less than 13 dB of combined mixing conversion and filter insertion loss. The mixer-filter (or "mixler") RF-to-IF voltage transfer function is shown to depend upon a ratio of local oscillator amplitude and applied bias voltages.
Mn Porphyrin Regulation of Aerobic Glycolysis: Implications on the Activation of Diabetogenic Immune Cells (2013)

MnP treatment promotes metabolic quiescence, impeding diabetogenic autoimmune responses by restricting the metabolic pathways for energy production and affecting anabolic processes necessary for cell proliferation.
Analysis of the site of interaction of CD28 with its counter-receptors CD80 and CD86 and correlation with function (1996)

CD28 and CTLA-4 are homologue members of the Ig superfamily of molecules, containing a single V-like domain, transmembrane, and cytoplasmic regions. Both receptors associate with the counter-receptors CD80 and CD86, but the avidity of interaction for CD28 is about 20-fold lower than for CTLA-4. The interaction between CD28 and its cognate receptors provides a costimulatory signal for optimal T cell activation. Our previous mutational analysis of CD28 defined the highly conserved "MYPPPY" motif in the CDR3-region of the V-like domain as a key site of common and selective recognition. We have extended our analysis to cover all residues in the membrane distal loops of the V region, examining their effect on association with CD80/CD86 in cell adhesion and novel protein-based binding assays, and determining correlation between binding and functional response. Conservative F substitutions at either Y residue in the MYPPPY motif selectively reduced binding to CD86, but mutation of the three amino acids immediately C-terminal to Y 104 equivalently reduced binding to both co-receptors. The conservative F substitution of Y 26 in the CDR1-like region also reduced binding to CD80 and CD86. Other substitutions in the CDR1 loop and mutations spanning the CDR2 and DE loops had no effect. We conclude that the CDR1 and CDR3 regions contribute to a common binding site for CD80/CD86, and that the CDR3 region also carries determinants for selective recognition of these counter-receptors within the MYPPPY motif. Furthermore, for CD28, the strength of functional response, as measured by IL-2 production, directly correlates with binding avidity.
Allantoin ameliorates chemically-induced pancreatic β -cell damage through activation of the imidazoline I3 receptors (2015)

Objective. Allantoin is the primary active compound in yams (Dioscorea spp.). Recently, allantoin has been demonstrated to activate imidazoline 3 (I3) receptors located in pancreatic tissues. Thus, the present study aimed to investigate the role of allantoin in the effect to improve damage induced in pancreatic β-cells by streptozotocin (STZ) via the I3 receptors. Research Design and Methods. The effect of allantoin on STZ-induced apoptosis in pancreatic β-cells was examined using the ApoTox-Glo triplex assay, live/dead cell double staining assay, flow cytometric analysis, and Western blottings. The potential mechanism was investigated using KU14R: an I3 receptor antagonist, and U73122: a phospholipase C (PLC) inhibitor. The effects of allantoin on serum glucose and insulin secretion were measured in STZ-treated rats. Results. Allantoin attenuated apoptosis and cytotoxicity and increased the viability of STZ-induced β-cells in a dose-dependent manner; this effect was suppressed by KU14R and U73112. Allantoin decreased the level of caspase-3 and increased the level of phosphorylated B-cell lymphoma 2 (Bcl-2) expression detected by Western blotting. The improvement in β-cells viability was confirmed using flow cytometry analysis. Daily injection of allantoin for 8 days in STZ-treated rats significantly lowered plasma glucose and increased plasma insulin levels. This action was inhibited by treatment with KU14R. Conclusion. Allantoin ameliorates the damage of β-cells induced by STZ. The blockade by pharmacological inhibitors indicated that allantoin can activate the I3 receptors through a PLC-related pathway to decrease this damage. Therefore, allantoin and related analogs may be effective in the therapy for β-cell damage.
PROTEIN IMPORT INTO MITOCHONDRIA (1997)

Mitochondria import many hundreds of different proteins that are encoded by nuclear genes. These proteins are targeted to the mitochondria, translocated through the mitochondrial membranes, and sorted to the different mitochondrial subcompartments. Separate translocases in the mitochondrial outer membrane (TOM complex) and in the inner membrane (TIM complex) facilitate recognition of preproteins and transport across the two membranes. Factors in the cytosol assist in targeting of preproteins. Protein components in the matrix partake in energetically driving translocation in a reaction that depends on the membrane potential and matrix-ATP. Molecular chaperones in the matrix exert multiple functions in translocation, sorting, folding, and assembly of newly imported proteins.
Antagomirbase: A putative antagomir database (2011)

The database is available for free at http://bioinfopresidencycollegekolkata.edu.in/antagomirs.html.
Modulation of C-Reactive Protein–Mediated Monocyte Chemoattractant Protein-1 Induction in Human Endothelial Cells by Anti-Atherosclerosis Drugs (2001)

These results further strengthen the role of CRP in the pathogenesis of vascular inflammation and, likely, atherosclerosis and provide a crucial insight into a novel mechanism of action of anti-atherosclerosis drugs such as simvastatin and fenofibrate.
Cardiac PET/CT for the Evaluation of Known or Suspected Coronary Artery Disease (2011)

Positron emission tomography (PET) is increasingly being applied in the evaluation of myocardial perfusion. Cardiac PET can be performed with an increasing variety of cyclotron- and generator-produced radiotracers. Compared with single photon emission computed tomography, PET offers lower radiation exposure, fewer artifacts, improved spatial resolution, and, most important, improved diagnostic performance. With its capacity to quantify rest-peak stress left ventricular systolic function as well as coronary flow reserve, PET is superior to other methods for the detection of multivessel coronary artery disease and, potentially, for risk stratification. Coronary artery calcium scoring may be included for further risk stratification in patients with normal perfusion imaging findings. Furthermore, PET allows quantification of absolute myocardial perfusion, which also carries substantial prognostic value. Hybrid PET-computed tomography scanners allow functional evaluation of myocardial perfusion combined with anatomic characterization of the epicardial coronary arteries, thereby offering great potential for both diagnosis and management. Additional studies to further validate the prognostic value and cost effectiveness of PET are warranted.
Quantification of HER2/neu Gene Amplification by Competitive PCR Using Fluorescent Melting Curve Analysis (2001)

Use of relative peak areas allows gene copy numbers to be quantified against an internal competitive control in < 1 h.
Structure-Guided Design of Potent and Selective Pyrimidylpyrrole Inhibitors of Extracellular Signal-Regulated Kinase (ERK) Using Conformational Control (2009)

The Ras/Raf/MEK/ERK signal transduction, an oncogenic pathway implicated in a variety of human cancers, is a key target in anticancer drug design. A novel series of pyrimidylpyrrole ERK inhibitors has been identified. Discovery of a conformational change for lead compound 2, when bound to ERK2 relative to antitarget GSK3, enabled structure-guided selectivity optimization, which led to the discovery of 11e, a potent, selective, and orally bioavailable inhibitor of ERK.
Urinary Levels of the Renal Tubular Enzyme N-Acetyl- β -D-Glucosaminidase in Unilateral Obstructive Uropathy (1994)

Elevated urinary levels of the renal tubular enzyme, N-acetyl-beta-D-glucosaminidase (NAG), have been shown to be associated with reversible tubular damage and, therefore, may serve as an indicator of tubular damage in the setting of presumed obstruction uropathy. This study compares urinary NAG levels in children with apparent upper tract obstruction with normal children to assess the sensitivity of this assay for the detection of possible renal tubular damage. The study included 40 children 3 weeks to 16 years old with unilateral ureteropelvic junction obstruction (30) or primary obstructive megaureter (10). Urine was obtained from the bladder in all children and from the renal pelvis or ureter in 30 patients at surgery. Pelvic and ureteral urinary NAG levels were consistently higher than bladder levels. In patients with ureteropelvic junction obstruction NAG levels were 7 times higher than normal (76 units per mg., p < 0.0001) and 3 times higher than normal in patients with obstructive megaureter (29 units per mg., p < 0.001). The mean bladder urinary NAG levels in patients with ureteropelvic junction obstruction (17.6 units per mg. creatinine, standard error of mean 2.01, p < 0.001) and megaureters (19.2 units per mg. creatinine, standard error of mean 3.6, p < 0.049) were elevated above control patients (10.6 units per mg. creatinine, standard error of mean 1.02). Elevated urinary NAG levels in the renal pelvis, ureter and bladder may be helpful in identifying upper tract obstruction, which if left untreated, might cause progressive renal deterioration.
Preparation and physical properties of biodegradable polybutylene succinate/polybutylene adipate-co-terephthalate blend monofilament by melt spinning (2010)

In order to improve the breaking strength and elongation of Polybutylene succinate (PBS) monofilament, the monofilament was produced by blending PBS and Polybutlyne adipate-co-terephthalate (PBAT). The PBS/PBAT blend monofilament was prepared by the melt spinning system, and the weight ratios of the compositions of PBS/PBAT was 100/0, 95/5, 90/10 and 85/15, respectively. The breaking strength, elongation, softness and crystallization of PBS/PBAT blend monofilament were analyzed by using a tensionmeter, softness measurement, X-ray diffractometer in the both dry and wet conditions. The PBS/PBAT blend monofilaments were spun in the take-up velocity of 1.19m/sec under the drawing ratio of 6.8:1 condition. The production volumes of PBS/PBAT blend monofilaments showed 20% less than that of Nylon. The breaking strength of PBS/PBAT blend monofilaments were decreased as PBAT contents increased, while elongation and softness were increased. In case of PBAT content were over 5%, the breaking strength, elongation and softness of PBS/PBAT blend monofilaments were not shown to increase in spite of increasing in PBAT contents. Based on these results, it was possible to make the monofilaments with the maximized physical properties when the PBAT contents at 5%.
Conditional Deletion of Gremlin Causes a Transient Increase in Bone Formation and Bone Mass (2007)

Gremlin is a glycoprotein that binds bone morphogenetic proteins (BMPs) 2, 4, and 7, antagonizing their actions. Gremlin opposes BMP effects on osteoblastic differentiation and function in vitro and in vivo, and its overexpression causes osteopenia. To define the function of gremlin in the skeleton, we generated gremlin 1 (grem1) conditional null mice by mating mice where grem1 was flanked by lox(P) sequences with mice expressing the Cre recombinase under the control of the osteocalcin promoter. grem1 null male mice displayed increased trabecular bone volume due to enhanced osteoblastic activity, because mineral apposition and bone formation rates were increased. Osteoblast number and bone resorption were not altered. Marrow stromal cells from grem1 conditional null mice expressed higher levels of alkaline phosphatase activity. Gremlin down-regulation by RNA interference in ST-2 stromal and MC3T3 osteoblastic cells increased the BMP-2 stimulatory effect on alkaline phosphatase activity, on Smad 1/5/8 phosphorylation, and on the transactivation of the BMP/Smad reporter construct 12xSBE-Oc-pGL3. Gremlin down-regulation also enhanced osteocalcin and Runx-2 expression, Wnt 3a signaling, and activity in ST-2 cells. In conclusion, deletion of grem1 in the bone microenvironment results in sensitization of BMP signaling and activity and enhanced bone formation in vivo.
Procalcitonin as a Biomarker in Respiratory Tract Infection (2011)

Serum procalcitonin (PCT) levels rapidly increase in patients with invasive bacterial disease. PCT levels increase faster than do C-reactive protein levels. Furthermore, a rapid decrease in the PCT level is supporting evidence that the source of the bacterial infection is responding to clinical management. In patients with community-acquired bacterial pneumonia, sequential PCT levels are useful as a guide to shorter courses of antimicrobial therapy. With use of emerging multiplex real-time polymerase chain reaction platforms for the detection of viral and bacterial respiratory pathogens, it should be possible to critically assess whether an elevated serum PCT level is a valid biomarker of invasive bacterial infection.
Two-year follow-up of conductive keratoplasty for the treatment of hyperopic astigmatism (2006)

Conductive keratoplasty for low hyperopic astigmatism was a safe, effective, and stable procedure. Nomogram adjustments and careful patient selection should contribute to higher levels of predictability when treating hyperopic astigmatism.
Generation of T Cells from Human Embryonic Stem Cell-Derived Hematopoietic Zones (2009)

Human embryonic stem cells (hESC) are pluripotent stem cells. A major challenge in the field of hESC is the establishment of specific differentiation protocols that drives hESC down a particular lineage fate. So far, attempts to generate T cells from hESC in vitro were unsuccessful. In this study, we show that T cells can be generated in vitro from hESC-derived hematopoietic precursor cells present in hematopoietic zones (HZs). These zones are morphologically similar to blood islands during embryonic development, and are formed when hESC are cultured on OP9 stromal cells. Upon subsequent transfer of these HZs on OP9 cells expressing high levels of Delta-like 1 and in the presence of growth factors, cells expand and differentiate to T cells. Furthermore, we show that T cells derive exclusively from a CD34(high)CD43(low) population, further substantiating the notion that hESC-derived CD34(high)CD43(low) cells are formed in HZs and are the only population containing multipotent hematopoietic precursor cells. Differentiation to T cells sequentially passes through the physiological intermediates: CD34(+)CD7(+) T/NK committed, CD7(+)CD4(+)CD8(-) immature single positive, CD4(+)CD8(+) double positive, and finally CD3(+)CD1(-)CD27(+) mature T cell stages. TCRalphabeta(+) and TCRgammadelta(+) T cells are generated. Mature T cells are polyclonal, proliferate, and secrete cytokines in response to mitogens. This protocol for the de novo generation of T cells from hESC could be clinically and scientifically relevant.
A compaction method for full chip VLSI layouts (1993)

An algorithm independent layout compaction method for full chip layouts is proposed. The partitioning compaction method cuts up a large layout, compacts each block independently and then merges them to give the final compacted layout. A 16-bit CPU core (28.8K transistors) layout was compacted on a standard workstation using this method.