gebhart/patrepeval huggingface dataset:
Abstract 27: Therapeutic Targeting of Human Lipid Genes With in vivo CRISPR-Cas9 Genome Editing (2015)

Individuals with naturally occurring loss-of-function PCSK9, APOC3, and ANGPTL3 mutations experience reduced blood low-density lipoprotein cholesterol (LDL-C) levels, reduced blood triglyceride levels, and/or protection against cardiovascular disease. We recently established that genome editing using a Streptococcus pyogenes clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) system, delivered by adenovirus, can efficiently introduce loss-of-function mutations into the endogenous mouse Pcsk9 gene in vivo, resulting in near-complete knockout of Pcsk9 and a 35%-40% reduction in the blood cholesterol level. Thus, the in vivo genome-editing approach may have therapeutic potential for the prevention of cardiovascular disease in humans. To better evaluate the feasibility of the approach in humans, we are performing preclinical studies using a liver-humanized mouse model in which the endogenous mouse hepatocytes have been replaced with human-derived hepatocytes and in which the plasma lipoprotein profile better reflects human physiology, particularly with respect to LDL-C. One disadvantage of the S. pyogenes CRISPR-Cas9 system is that its Cas9 gene is too large to fit in adeno-associated virus (AAV) vectors, which offer significant therapeutic advantages over adenoviruses. We have adapted the smaller Staphylococcus aureus CRISPR-Cas9 system and demonstrated efficient genome editing of the human PCSK9, APOC3, and ANGPTL3 genes in vitro. Additionally, using a minimal liver-specific promoter and a novel human-hepatocyte-optimized AAV capsid protein, we are employing AAV vectors to knock out each of the three genes in both primary human hepatocytes and liver-humanized mice. This is allowing us to interrogate both the efficacy (lowering of LDL-C and/or triglycerides) and safety (degree of off-target mutagenesis) of genome editing in human hepatocytes in vitro and in vivo. These translational studies are providing critical information on the viability of an approach that could ultimately yield a one-shot, long-term therapy that permanently reduces a person’s blood LDL-C and triglyceride levels, thus serving as a “vaccination” against cardiovascular disease.
A Direct Synthesis of 1-Aryl- and 1-Alkenylcyclopropylamines from Aryl and Alkenyl Nitriles (2003)

The reaction of various aromatic nitriles with 1.1 equiv of Ti(Oi-Pr)(4) and 2.2 equiv of EtMgBr followed by addition of a Lewis acid gave 1-aryl cyclopropylamines in 43-76% yields. Under similar conditions, conjugated alkenenitriles afford 1-alkenylcyclopropylamines (42-65%).
Model equations for condensation biosynthesis using stable isotopes and radioisotopes (1992)

Important syntheses in living systems occur by condensation reactions of the type nA----1B (where n is the number of A molecules needed to synthesize 1 molecule of B). Quantitative relationships for estimating the rate of synthesis of B from radioactive and stable isotope tracers are compared. With radioisotope tracers, only a single quantity is detected, the amount of radioactivity in B. In contrast, isotopes of varying mass produce multiple mass isotopomers B that are detected using mass spectrometry. The analysis demonstrates that the rate of synthesis of B is identifiable from stable isotope data but not from radioisotope data. This results because the isotopomer distribution of B at any time after tracer addition is a function of only the multinomial distribution representing the synthesis of B from n molecules of A and two parameters representing the fractional fluxes of isotopically enriched molecules to the sampled compartment of B. The model considers the possibility that the sampled compartment of B may not reach isotopic steady state during the experiment. A graphical method for obtaining initial estimates of the two parameters is presented.
Crystallographic analysis of the interaction between cyclosporin A and the Fab fragment of a monoclonal antibody (1993)

The structure of the complex between cyclosporin A and the Fab fragment of a monoclonal antibody has been established by crystallographic analysis to 2.65 A resolution. The structure has been solved by molecular replacement using a composite Fab model. The current R-factor after refinement is 0.179 between 8 and 2.65 A resolution. The antibody is one among three known structures with long H3 loops. This loop conformation is observed for the first time in the presence of the antigen. Residues from all six hypervariable loops interact with cyclosporin A. However, the 17 residues long loop H3 is the main contributor to the buried combining site area and to the van der Waals contacts made with cyclosporin A, with 52 and 63%, respectively, of the total contribution.
Integrated microfluidic bioprocessor for single-cell gene expression analysis (2008)

An integrated microdevice is developed for the analysis of gene expression in single cells. The system captures a single cell, transcribes and amplifies the mRNA, and quantitatively analyzes the products of interest. The key components of the microdevice include integrated nanoliter metering pumps, a 200-nL RT-PCR reactor with a single-cell capture pad, and an affinity capture matrix for the purification and concentration of products that is coupled to a microfabricated capillary electrophoresis separation channel for product analysis. Efficient microchip integration of these processes enables the sensitive and quantitative examination of gene expression variation at the single-cell level. This microdevice is used to measure siRNA knockdown of the GAPDH gene in individual Jurkat cells. Single-cell measurements suggests the presence of 2 distinct populations of cells with moderate (approximately 50%) or complete (approximately 0%) silencing. This stochastic variation in gene expression and silencing within single cells is masked by conventional bulk measurements.
Serum Uric Acid Is Associated With Microalbuminuria in Prehypertension (2006)

Serum uric acid is associated with cardiovascular disease. However, the independent role of uric acid in the development of cardiovascular disease is uncertain. This study examined the cross-sectional association of serum uric acid level with microalbuminuria among 6771 subjects without diabetes or hypertension. Blood pressure was categorized as prehypertension (systolic blood pressure, 120 to 140 mm Hg or diastolic blood pressure, 80 to 90 mm Hg) and normotension (systolic blood pressure, <120 mm Hg and diastolic blood pressure, <80 mm Hg). Microalbuminuria was found in 4.0% of normotensive subjects (n=4819) and in 7.9% of prehypertensive subjects (n=1952). Prehypertensive subjects with microalbuminuria had higher uric acid level than those with normoalbuminuria (men, 387 [68] mmol/L versus 371 [69] mmol/L; P=0.017; women 286 [56] mmol/L versus 262 [54] mmol/L; P=0.006). However, the difference in serum uric acid level according to the presence or absence of microalbuminuria was not found in the normotensive group. Multiple logistic regression models showed that, in the prehypertensive group, after adjustment for other cardiovascular risk factors, the highest uric acid quartile entailed >2 times greater risk for microalbuminuria than the lowest quartile in both men (odds ratio, 2.12; 95% CI, 1.16 to 3.87) and women (odds ratio, 3.36; 95% CI, 1.17 to 9.69). In the normotensive group, serum uric acid quartile did not show the independent association with microalbuminuria. In conclusion, serum uric acid level was strongly associated with microalbuminuria in prehypertensive subjects.
Reversible Sketches: Enabling Monitoring and Analysis Over High-Speed Data Streams (2007)

A key function for network traffic monitoring and analysis is the ability to perform aggregate queries over multiple data streams. Change detection is an important primitive which can be extended to construct many aggregate queries. The recently proposed sketches are among the very few that can detect heavy changes online for high speed links, and thus support various aggregate queries in both temporal and spatial domains. However, it does not preserve the keys (e. g., source IP address) of flows, making it difficult to reconstruct the desired set of anomalous keys. To address this challenge, we propose the reversible sketch data structure along with reverse hashing algorithms to infer the keys of culprit flows. There are two phases. The first operates online, recording the packet stream in a compact representation with negligible extra memory and few extra memory accesses. Our prototype single FPGA board implementation can achieve a throughput of over 16 Gb/s for 40-byte packet streams (the worst case). The second phase identifies heavy changes and their keys from the representation in nearly real time. We evaluate our scheme using traces from large edge routers with OC-12 or higher links. Both the analytical and experimental results show that we are able to achieve online traffic monitoring and accurate change/intrusion detection over massive data streams on high speed links, all in a manner that scales to large key space size. To the best of our knowledge, our system is the first to achieve these properties simultaneously.
LDL particle size distribution. Results from the Framingham Offspring Study. (1992)

Using 2-16% gradient gel electrophoresis, we examined low density lipoprotein (LDL) particle size in relation to plasma lipoproteins in 1,168 women and 1,172 men from the Framingham Offspring Study. In addition, we studied the effect of dietary intake on LDL size in a subset of the population. Seven LDL size peaks were identified, with the largest, LDL 1, being found in the density range 1.019-1.033 g/ml; LDL 2 and LDL 3 in d = 1.033-1.038 g/ml; LDL 4 and LDL5 in d = 1.038-1.050 g/ml; and the smallest, LDL 6 and 7, in d = 1.050-1.063 g/ml. Seventy-seven percent of the population had one major and at least one minor LDL peak. Secondary LDL peaks accounted for 23% of the total LDL relative area, based on laser scanning densitometry. LDL size distribution was skewed toward larger LDL particles in women (prevalence of LDL 1, 30% and of LDL 2, 31%), whereas men exhibited a more symmetric distribution (prevalence of LDL 3, 42%). The prevalence of small (< 255 A), dense (d > 1.038 g/ml) LDL particles 4-7 was 33% in men, 5% in premenopausal women, and 14% in postmenopausal women. In agreement with previous reports, small, dense LDL particles were significantly (p < 0.0001) associated with increased triglyceride and apolipoprotein (apo) B levels and decreased HDL cholesterol and apo A-I levels. In addition, we found a significant (p < 0.0001) association between LDL cholesterol and LDL size. The highest LDL cholesterol levels were found among women with LDL 4 (148 mg/dl) and men with LDL 3-5 (138 mg/dl). In addition, the presence of LDL 3 or 4 as secondary peaks was significantly associated with higher LDL cholesterol levels, while smaller secondary LDL peaks were associated with higher triglyceride levels. We also found that compared with subjects with optimal LDL cholesterol levels (< 130 mg/dl), individuals with high-risk LDL cholesterol levels (> or = 160 mg/dl) had 1) a higher prevalence of LDL 3 and 4 (women only) and a lower prevalence of LDL 1 and 2 (women only) and 2) 11% higher LDL cholesterol to apo B ratios, even when matched for LDL particle size. Furthermore, low saturated fat and cholesterol intakes were significantly associated (p < 0.01) with smaller LDL particles. Therefore, the identification of small, dense LDL particles per se may not be a good indicator of coronary artery disease risk in population studies.(ABSTRACT TRUNCATED AT 400 WORDS)
Detection of Epigenetic Changes in Fecal DNA as a Molecular Screening Test for Colorectal Cancer: A Feasibility Study (2004)

Colorectal cancer is the fourth most common cancer worldwide (1). There has been intense interest in the search for potential tumor markers that can be used in the screening of colorectal cancer. Because of the continuous shedding of intestinal cells into the lumen, genetic alterations found in tumors can also been detected in stool, which offers a golden opportunity for the noninvasive screening of colorectal cancer. Previous studies have demonstrated the feasibility of detecting altered DNA, including BAT26 , APC , K- ras , and p53 mutations, in the feces of colorectal cancer patients (2)(3)(4)(5).

Epigenetic gene silencing by promoter hypermethylation is increasingly recognized to play a crucial role in carcinogenesis (6). In colorectal cancer, several tumor-related genes have been found to have promoter hypermethylation in the CpG islands (7)(8)(9)(10). These epigenetic changes are detected in the early phase of colorectal cancer development before the development of K- ras mutations (11). We tested the feasibility of detecting promoter hypermethylation of multiple tumor-related genes in fecal DNA of patients with colorectal cancer.

We recruited 20 colorectal cancer patients (mean age, 69 years; range, 45–90 years; 7 males). Patients who had familial adenomatous polyposis or hereditary nonpolyposis colon cancer, inflammatory bowel diseases, or previous colon surgery were excluded. Colon tumor biopsies were obtained during colonoscopy. Stool samples were collected before initiation of bowel preparation. The stool specimens were stored in a household freezer and then transferred for long-term storage at −80 °C. Twenty age-matched controls were randomly selected from individuals who participated in a colonoscopy screening program during the same period and had normal colonoscopy results (12). Stool samples were collected before bowel preparation as described for cancer patients, and healthy colon tissues were collected during colonoscopy from these …
Alpha- and beta-adrenergic stimulation induces distinct patterns of immediate early gene expression in neonatal rat myocardial cells. fos/jun expression is associated with sarcomere assembly; Egr-1 induction is primarily an alpha 1-mediated response. (1990)

The present study was designed to determine if alpha- and beta-adrenergic stimulation of neonatal rat myocardial cells might induce common and/or distinct members of the immediate early gene program and to assess whether their induction might correlate with the differential effects of these adrenergic agonists on cardiac gene expression, sarcomere assembly, and several features of myocardial cell hypertrophy. Alpha- and beta-adrenergic stimulation of neonatal rat myocardial cells both produce an increase in the assembly of an individual contractile protein (myosin light chain-2) into organized sarcomeric units and also rapidly induce mRNAs for the immediate early genes c-fos and c-jun, thereby suggesting a potential role for these protooncogenes in sarcomerogenesis. alpha-Adrenergic stimulation results in the co-induction of mRNAs encoding a zinc finger protein gene (Egr-1). However, beta-adrenergic stimulation does not produce a significant increase in the levels of Egr-1 mRNA, providing the first evidence in any cell system that c-fos and Egr-1 expression can regulated separately. Studies with norepinephrine in combination with various adrenergic receptor antagonists revealed that the induction of Egr-1 is primarily an alpha 1-mediated, pertussis toxin-insensitive response. These studies provide the first evidence for the induction of immediate early genes following adrenergic stimulation of myocardial cells and demonstrate alpha- and beta-adrenergic stimulation can rapidly activate the expression of common and distinct subsets of these transcriptional regulators. Since alpha- and beta-adrenergic agonists have differential effects on cardiac gene expression and on the acquisition of several features of myocardial cell hypertrophy, the induction of Egr-1 provides a potential mechanism for the induction of genes that are exclusively induced during alpha-adrenergic-mediated myocardial cell hypertrophy.
Virtual Mechanics Simulation and Animation of Rigid Body Systems with AERO (1995)

AERO is an animation system using physically based modelling. It allows the creation of virtual environrnents from scenes with simple three-dimensional geometrical objects (sphere, cylinder, box, point, plane). Objects can be linked to each other by a variety of methods (rod, spring, damper, joint). Realistic object movements are achieved by a simulation procedure, where forces can be applied to the objects in addition to gravity, friction, and air resistance. Wire frame animations can be generated in real time, depending on scene complexity and computer system performance. AERO generates scene description sequences, which can be used as input for ray tracing programs to generate photorealistic animations. AERO also enables stereo graphics output, camera control, and the mounting of the camera to an object in the scene.
Centenary of the first triaxial test – recalculation of the results of Kármán (2010)

Hundred years ago Tódor Kármán (Theodore von Kármán1) published his results on triaxial tests of brittle rocks. First it was published in Hungarian in the Journal of Hungarian Engineers andArchitects in 1910 (Kármán, 1910) and a year later it was published in German (von Kármán, 1911), as well.
Primed In Situ (PRINS) Labeling of RNA (2003)

It has been possible for a number of years to detect RNA in situ in fixed cells or whole tissue-sections by the use of cloned probes (, , , ). The probes are labeled either with radioactive nucleotides or modified nonradioactive nucleotides, such as biotinylated dUTP, which can be visualized by fluoresceinconjugated avidin. RNA-studies by this strategy have the advantage of being very sensitive, and give a quantitative impression of the variations in RNA contents in the cells/tissue sections studied. However, it is not possible to study closely related RNA populations by these methods because the probes used are generally long and do not allow the detection of small differences, such as single base mutations or minor splicing-errors. Such a detection is made possible by the recently described “in situ transcription” (IST) method involving the direct synthesis of a first strand cDNA in situ (, , , ). In this method, labeling is achieved by annealing unlabeled short oligonucleotides to the target RNA and using these as primers for chain elongation in a reaction catalyzed by AMV-reverse-transcriptase in the presence of radioactive nucleotides.
Inhibition of enzymes of estrogen and androgen biosynthesis by esters of 4-pyridylacetic acid (1990)

A variety of esters of 4-pyridylacetic acid have been prepared by base mediated exchange from the methyl ester. Several of the esters of alcohols that contained a cyclohexyl ring were potent inhibitors of human placental aromatase and of the rat testicular 17 alpha-hydroxylase/C17-20lyase complex. The most potent agents found against both enzyme complexes were the borneyl, isopinocampheyl, and 1-adamantyl esters. These were over 100 times more potent than aminoglutethimide against aromatase and of greater potency than ketoconazole against hydroxylase/lyase. Potency against either enzyme complex was reduced if the ester function was borne on the cyclohexyl ring in an axial rather than an equatorial position. Some differential selectivity could be introduced since whereas methyl substitution adjacent to the carbonyl group reduced the inhibition of aromatase, it increased that against hydroxylase/lyase.
Recombinant virus vaccination against "self" antigens using anchor-fixed immunogens. (1999)

To study the induction of anti-"self" CD8+ T-cell reactivity against the tumor antigen gp100, we used a mouse transgenic for a chimeric HLA-A*0201/H-2 Kb molecule (A2/Kb). We immunized the mice with a recombinant vaccinia virus encoding a form of gp100 that had been modified at position 210 (from a threonine to a methionine) to increase epitope binding to the restricting class I molecule. Immunogens containing the "anchor-fixed" modification elicited anti-self CD8+ T cells specific for the wild-type gp100(209-217) peptide pulsed onto target cells. More important, these cells specifically recognized the naturally presented epitope on the surface of an A2/Kb-expressing murine melanoma, B16. These data indicate that anchor-fixing epitopes could enhance the function of recombinant virus-based immunogens.
Channel‐Length‐Dependent Field‐Effect Mobility and Carrier Concentration of Reduced Graphene Oxide Thin‐Film Transistors (2010)

Reduced graphene oxide thin-film transistors exhibit unique channel-length-dependent field-effect mobilities and carrier concentrations due to their structural and electronic properties. Increase in these characteristics with decreasing channel length is a consequence of the hopping transport from nanosheet to nanosheet and pinning of the Fermi energy at source and drain electrodes.
Role of bactericidal permeability-increasing protein in the treatment of gram-negative pneumonia. (1993)

rBPI23 may be a novel therapeutic agent in the management of gram-negative sepsis.
Thin-film GaAs epitaxial lift-off solar cells for space applications (2005)

In the present work the space compatibility of thin-film GaAs solar cells is studied. These cells are separated from their GaAs substrate by the epitaxial lift-off (ELO) technique and mounted behind a CMG cover glass which at the same time serves as a stable carrier for the thin film cells. In the present initial stage of development these cells have an average efficiency of about 15·4% under AM0 illumination due to not yet optimized grid contacts and anti-reflection coatings. Inspection after irradiation by 1 MeV electrons, thermal vacuum and thermal cycling experiments reveal that degradation of the cells is largely due to delamination and micro-cracking. Based on these results, glass dehydration and adhesive degassing procedures are implemented in the ELO cell processing. As a consequence, even in this premature phase, newly produced cells show a radiation hardness comparable to or better than that of commercially available GaAs cells on Ge substrates and are virtually unaffected by severe thermal cycling. Copyright © 2005 John Wiley & Sons, Ltd.
Mapping the σ 70 subunit contact sites on Escherichia coli RNA polymerase with a σ 70 -conjugated chemical protease (1998)

The core enzyme of Escherichia coli RNA polymerase acquires essential promoter recognition and transcription initiation activities by binding one of several sigma subunits. To characterize the proximity between sigma70, the major sigma for transcription of the growth-related genes, and the core enzyme subunits (alpha2 beta beta'), we analyzed the protein-cutting patterns produced by a set of covalently tethered FeEDTA probes [FeBABE: Fe (S)-1-(p-bromoacetamidobenzyl)EDTA]. The probes were positioned in or near conserved regions of sigma70 by using seven mutants, each carrying a single cysteine residue at position 132, 376, 396, 422, 496, 517, or 581. Each FeBABE-conjugated sigma70 was bound to the core enzyme, which led to cleavage of nearby sites on the beta and beta' subunits (but not alpha). Unlike the results of random cleavage [Greiner, D. P., Hughes, K. A., Gunasekera, A. H. & Meares, C. F. (1996) Proc. Natl. Acad. Sci. USA 93, 71-75], the cut sites from different probe-modified sigma70 proteins are clustered in distinct regions of the subunits. On the beta subunit, cleavage is observed in two regions, one between residues 383 and 554, including the conserved C and Rif regions; and the other between 854 and 1022, including conserved region G, regions of ppGpp sensitivity, and one of the segments forming the catalytic center of RNA polymerase. On the beta' subunit, the cleavage was identified within the sequence 228-461, including beta' conserved regions C and D (which comprise part of the catalytic center).