gebhart/patrepeval huggingface dataset:
Genetic-Based Biomarkers and Next-Generation Sequencing: The Future of Personalized Care in Colorectal Cancer (2011)

The past 5 years have witnessed extraordinary advances in the field of DNA sequencing technology. What once took years to accomplish with Sanger sequencing can now be accomplished in a matter of days with next-generation sequencing (NGS) technology. This has allowed researchers to sequence individual genomes and match combinations of mutations with specific diseases. As cancer is inherently a disease of the genome, it is not surprising to see NGS technology already being applied to cancer research with promises of greater understanding of carcinogenesis. While the task of deciphering the cancer genomic code remains ongoing, we are already beginning to see the application of genetic-based testing in the area of colorectal cancer. In this article we will provide an overview of current colorectal cancer genetic-based biomarkers, namely mutations and other genetic alterations in cancer genome DNA, discuss recent advances in NGS technology and speculate on future directions for the application of NGS technology to colorectal cancer diagnosis and treatment.
Cloning, heterologous expression, and chromosomal localization of human inositol polyphosphate 1-phosphatase. (1993)

Inositol polyphosphate 1-phosphatase, an enzyme in the phosphatidylinositol signaling pathway, catalyzes the hydrolysis of the 1 position phosphate from inositol 1,3,4-trisphosphate and inositol 1,4-bisphosphate. We used a cDNA that encodes bovine inositol polyphosphate 1-phosphatase as a probe to isolate the human counterpart by low-stringency hybridization. The 1.74-kb human cDNA has 341 bp of 5' untranslated region, 180 bp of 3' untranslated region, poly(A)32, and predicts a protein of 399 amino acids. Human and bovine inositol polyphosphate 1-phosphatases show 84% amino acid sequence identity. Northern blot analysis from a variety of human tissues demonstrates that a 1.9-kb mRNA is ubiquitously expressed with highest levels in pancreas and kidney. Several higher molecular weight mRNAs also are expressed in brain, muscle, heart, and liver. We have confirmed the functional identity of the human cDNA by heterologous expression in NIH 3T3 fibroblasts, COS-7 cells and Escherichia coli. Polymerase chain reaction assay of a panel of human-rodent somatic cell hybrid DNA using human inositol polyphosphate 1-phosphatase-specific DNA primers resulted in amplification of a specific product using chromosome 2 DNA as template. Fluorescence in situ hybridization of metaphase chromosomes localizes the gene to chromosome 2 band q32. The identification of the human inositol polyphosphate 1-phosphatase gene locus provides a target for linkage analysis to identify defects in patients with inherited psychiatric disorders that respond to lithium ions, an inhibitor of the enzyme.
Subspace-based Age-group Classification Using Facial Images under Various Lighting Conditions (2006)

This paper presents a framework of age-group classification using facial images under various lighting conditions. Our method is based on the appearance-based approach that projects images from the original image space into a face-subspace. We propose a two-phased approach (2DLDA+LDA), which is based on 2DPCA and LDA. Our experimental results show that the new 2DLDA+LDA-based approach improves classification accuracy more than the conventional PCA-based and LDA-based approach. Moreover, the effectiveness of eliminating dimensions that do not contain important discriminative information is confirmed. The accuracy rates are 46.3%, 67.8% and 78.1% for age-groups that are in the 5-year, 10-year and 15-year range respectively
Influence of Excess Fat on Cardiac Morphology and Function: Study in Uncomplicated Obesity (2002)

In conclusion, our data showed that obesity, in the absence of glucose intolerance, hypertension, and dyslipidemia, seems to be associated only with an impairment of diastolic function and hyperkinetic systole, and not with left ventricular hypertrophy.
Efficacy of the Ketogenic Diet for Intractable Seizure Disorders: Review of 58 Cases (1992)

The ketogenic diet was developed in the 1920s as a treatment for intractable childhood seizures when few antiepileptic drugs (AEDs) were available. There are still children whose seizures are refractory even to modern therapy, but use of the ketogenic diet appears to be waning. At Johns Hopkins, we continue to believe that the diet is very effective and well accepted by patients and families. To reevaluate our opinion of the efficacy and acceptability of this form of therapy in patients cared for in the 1980s with the newer AEDs, we analyzed the records of 58 consecutive patients who had been started on the diet. Before using the diet, 80% of the patients had multiple seizure types and 88% were treated with multiple AEDs; these children were among our most intractable patients. Despite this, seizure control improved in 67% of patients with the ketogenic diet, and actuarial analysis indicated that 75% of these improved patients continued the diet for at least 18 months. Sixty-four percent had AEDs reduced, 36% became more alert, and 23% had improved behavior. The improvement in these patients with intractable seizures and the length of time that families maintained the regimen indicate that the ketogenic diet continues to have a very useful therapeutic role in selected patients and their families.
A general two-pass method integrating specular and diffuse reflection (1989)

We analyse some recent approaches to the global illumination problem by introducing the corresponding reflection operators, and we demonstrate the advantages of a two-pass method. A generalization of the system introduced by Wallace et al. at Siggraph '87 to integrate diffuse as well as specular effects is presented. It is based on the calculation of extended form-factors, which allows arbitrary geometries to be used in the scene description, as well as refraction effects. We also present a new sampling method for the calculation of form-factors, which is an alternative to the hemi-cube technique introduced by Cohen and Greenberg for radiosity calculations. This method is particularly well suited to the extended form-factors calculation. The problem of interactive display of the picture being created is also addressed by using hardware-assisted projections and image composition to recreate a complete specular view of the scene.
P‐14: Low‐Cost Amoled Televeision with IGNIS Compensating Technology (2008)

Abstract MaxLife™ is a breakthrough backplane solution for AMOLED television. We demonstrate a compensating technology with a prototype that monitors and corrects for the OLED and TFT aging at each pixel for expected lifetimes of 50,000h+. This provides a tremendous boost in realizing low‐cost AMOLED TVs using amorphous or poly‐Silicon backplanes.
Combinatorial Signaling Microenvironments for Studying Stem Cell Fate (2008)

Extracellular matrix (ECM) and growth factor signaling networks are known to interact in a complex manner. Therefore, reductionist approaches that test the cellular response to individual ECM components and growth factors cannot be used to predict the response to more complex mixtures without knowledge of the underlying signaling network. To address this challenge, we have developed a technology platform to experimentally probe the interactions of ECM components and soluble growth factors on stem cell fate. We present a multiwell microarray platform that allows 1200 simultaneous experiments on 240 unique signaling environments. Mixtures of extracellular matrix (fibronectin, laminin, collagen I, collagen III, collagen IV) are arrayed using a robotic spotter and arranged in a multiwell format. Embryonic stem (ES) cells adhere to ECM spots and are cultured in mixtures of soluble factors [wnt3a, activin A, bone morphogenetic protein-4 (BMP-4), and fibroblast growth factor-4 (FGF-4)]. Differentiation along the cardiac lineage is monitored by myosin heavy chain-alpha-green fluorescent protein (MHC alpha-GFP) reporter expression as compared to growth by monitoring nuclear DNA, and both signals are quantified using a confocal microarray scanner. In developing the platform, we characterized the amount of deposited protein, the fluorescent readout of GFP expression and DNA content, and the use of a laser-based scanner as compared to fluorescent microscopy for data acquisition. The effects of growth factors on growth and differentiation are consistent with previously reported literature, and preliminary evidence of interactive signaling is illuminated. This versatile technique is compatible with virtually any set of insoluble and soluble cues, leverages existing software and hardware, and represents a step toward developing the 'systems biology' of stem cells.
Catalysis of Friedel‐Crafts Alkylation by a Montmorillonite Doped with Transition‐Metal Cations (1987)

Abstract Catalysts are obtained by exchange of the interstitial cations in the K10 montmorillonite. They are applied to Friedel‐Crafts alkylations with halides, alcohols, and olefins. They are quite effective even with unactivated hydrocarbons. Isomer distribution depends little on the catalyst used. Thermodynamic equilibration does not take place, the reactions appear to be kinetically controlled. Efficiency of the catalysts bears no apparent relation to that of the corresponding Lewis acids under homogeneous conditions, and it depends on the nature of the alkylating agent. Zr( IV ) and Ti( IV ), in general, give the best results.
1993 Revised Classification System for HIV Infection and Expanded Surveillance Case Definition for AIDS Among Adolescents and Adults (1993)

CDC has revised the classification system for HIV infection to emphasize the clinical importance of the CD4+ T-lymphocyte count in the categorization of HIV-related clinical conditions. This classification system replaces the system published by CDC in 1986 [1] and is primarily intended for use in public health practice. Consistent with the 1993 revised classification system, CDC has also expanded the AIDS surveillance case definition to include all HIV-infected persons who have <200 CD4+ T-lymphocytes/µL, or a CD4+ T-lymphocyte percentage of total lymphocytes of <14. This expansion includes the addition of three clinical conditions—pulmonary tuberculosis, recurrent pneumonia, and invasive cervical cancer—and retains the 23 clinical conditions in the AIDS surveillance case definition published in 1987 [2]; it is to be used by all states for AIDS case reporting effective January 1, 1993.
Stereoselective Synthesis of (−)-Cephalotaxine and C-7 Alkylated Analogues (2004)

A total asymmetric synthesis of (-)-cephalotaxine is reported. The chemistry of alpha,beta-unsaturated gamma-lactams was used to access the 1-azaspiro[4.4]nonane skeleton in enantiomerically pure form via a stereocontrolled semipinacolic rearrangement of an alpha-hydroxyiminium ion. This spiro compound was transformed into (-)-cephalotaxine without any racemization or epimerization by following the racemic synthesis reported by Kuehne. We thus performed a total synthesis of (-)-cephalotaxine in 98.7% ee with an overall yield of 9.8% over a 16 steps sequence. This synthetic process was adaptable to the access of some alkylated analogues.
Power and performance evaluation of globally asynchronous locally synchronous processors (2003)

We use a cycle-accurate simulation environment to study the impact of asynchrony in a superscalar processor architecture. Our results show that as expected, going from a synchronous to a globally asynchronous locally synchronous (GALS) design causes a drop in performance, but elimination of the global clock does not lead to drastic power reductions. From a power perspective, GALS designs are inherently less efficient when compared to synchronous architectures. However, the flexibility offered by the independently controllable local clocks enables the effective use of other energy conservation techniques like dynamic voltage scaling. Our results show that for a 5-clock domain GALS processor, the drop in performance ranges between 5-15%, while power consumption is reduced by 10% on the average. Fine-grained voltage scaling reduces the gap between fully synchronous and GALS implementations, allowing for better power efficiency.
Engineering the Pichia stipitis Genome for Fermentation of Hemicellulose Hydrolysates (2014)

Pichia stipitis is a source of genes for engineering xylose metabolism in Saccharomyces cerevisiaea task undertaken in numerous laboratories around the world. Increasing the capacity of P. stipitis for rapid xylose fermentation can greatly improve its usefulness in commercial xylose fermentations. Genetic transformation with URA3 is more efficient than transformation with the modified Sh ble marker. Cultivation conditions can strongly affect expression of fermentative enzymes in P. stipitis. Unlike S. cerevisiae, which regulates fermentation by sensing the presence of glucose, P. stipitis induces fermentative activity in response to oxygen limitation. The coupling of Xyl1 and Xyl2 activities therefore tends to result in the consumption of NADPH and accumulation of NADH. Preliminary data based on expressed sequence tags indicate that transcripts for fatty acid synthase (FAS2) stearoyl-coenzyme A desaturase (OLE1) are induced under oxygen-limiting conditions. Xylanase production by P. stipitis has been recognized, and the organism has also been transformed with heterologous xylanases to increase xylanase activity. A genetic system has been developed that includes the auxotrophic markers URA3 and LEU3 along with modified forms of the phleomycin D1 resistance marker, Sh ble, and the Cre recombinase. Many genes in P. stipitis are found in functionally related clusters. Further metabolic engineering and strain selection are needed to increase the overall fermentation rate and ethanol tolerance of P. stipitis for the commercial bioconversion of hemicellulose hydrolysates.
Proton currents through amiloride-sensitive Na channels in hamster taste cells. Role in acid transduction. (1992)

The activity of taste cells maintained in the intact hamster tongue was monitored in response to acid stimulation by recording action currents from taste receptor cells with an extracellular "macro" patch pipette: a glass pipette was pressed over the taste pore of fungiform papillae and perfused with citric acid, hydrochloric acid, or NaCl. Because this technique restricted stimulus application to the small surface area of the apical membranes of the taste cells, many nonspecific, and potentially detrimental, effects of acid stimulation could be avoided. Acid stimulation reliably elicited fast transient currents (action currents of average amplitude, 9 pA) which were consistently smaller than those elicited by NaCl (29 pA). The frequency of action currents elicited by acid stimuli increased in a dose-dependent manner with decreasing pH from a threshold of about pH 5.0. Acid-elicited responses were independent of K+, Na+, Cl-, or Ca2+ at physiological (salivary) concentrations, and were unaffected by anthracene-9-carboxylic acid, tetraethylammonium bromide, diisothiocyanate-stilbene-2,2'-disulfonic acid, vanadate, or Cd2+. In contrast, amiloride (< or = 30 microM) fully and reversibly suppressed acid-evoked action currents. At submaximal amiloride concentrations, the frequency and amplitude of the action currents were reduced, indicating a reduction of the taste cell apical conductance concomitant with a decrease in cell excitation. Exposure to low pH elicited, in addition to transient currents, an amiloride-sensitive sustained d.c. current. This current is apparently carried by protons instead of Na+ through amiloride-sensitive channels. When citric acid was applied while the taste bud was stimulated by NaCl, the action currents became smaller and the response resembled that produced by acid alone. Because of the strong interdependence of the acid and salt (NaCl) responses when both stimuli are applied simultaneously, and because of the similarity in the concentration dependence of amiloride block, we conclude that amiloride-sensitive Na+ channels on hamster taste receptor cells are permeable to protons and may play a role in acid (sour) taste.
Engineered herpes simplex virus expressing IL-12 in the treatment of experimental murine brain tumors (2000)

Genetically engineered, neuroattenuated herpes simplex viruses (HSVs) expressing various cytokines can improve survival when used in the treatment of experimental brain tumors. These attenuated viruses have both copies of gamma(1)34.5 deleted. Recently, we demonstrated increased survival of C57BL/6 mice bearing syngeneic GL-261 gliomas when treated with an engineered HSV expressing IL-4, as compared with treatment with the parent construct (gamma(1)34. 5(-)) alone or with a virus expressing IL-10. Herein, we report construction of a conditionally replication-competent mutant expressing both subunits of mIL-12 (M002) and its evaluation in a syngeneic neuroblastoma murine model. IL-12 induces a helper T cell subset type 1 response, which may induce more durable antitumor effects. In vitro studies showed that, when infected with M002, both Vero cells and murine Neuro-2a neuroblastoma cells produced physiologically relevant levels of IL-12 heterodimers, as determined by ELISA. M002 was cytotoxic for Neuro-2a cells and human glioma cell lines U251MG and D54MG. Neurotoxicity studies, as defined by plaque-forming units/LD(50), performed in HSV-1-sensitive A/J strain mice found that M002 was not toxic even at high doses. When evaluated in an intracranial syngeneic neuroblastoma murine model, median survival of M002-treated animals was significantly longer than the median survival of animals treated with R3659, the parent gamma(1)34.5(-) mutant lacking any cytokine gene insert. Immunohistochemical analysis of M002-treated tumors identified a pronounced influx of CD4(+) T cells and macrophages as well as CD8(+) cells when compared with an analysis of R3659-treated tumors. We conclude that M002 produced a survival benefit via oncolytic effects combined with immunologic effects meditated by helper T cells of subset type 1.
A Quantitative Analysis of 3-D Coronary Modeling From Two or More Projection Images (2004)

A method is introduced to examine the geometrical accuracy of the three-dimensional (3-D) representation of coronary arteries from multiple (two and more) calibrated two-dimensional (2-D) angiographic projections. When involving more then two projections, (multiprojection modeling) a novel procedure is presented that consists of fully automated centerline and width determination in all available projections based on the information provided by the semi-automated centerline detection in two initial calibrated projections. The accuracy of the 3-D coronary modeling approach is determined by a quantitative examination of the 3-D centerline point position and the 3-D cross sectional area of the reconstructed objects. The measurements are based on the analysis of calibrated phantom and calibrated coronary 2-D projection data. From this analysis a confidence region (alpha degrees approximately equal to [35 degrees - 145 degrees]) for the angular distance of two initial projection images is determined for which the modeling procedure is sufficiently accurate for the applied system. Within this angular border range the centerline position error is less then 0.8 mm, in terms of the Euclidean distance to a predefined ground truth. When involving more projections using our new procedure, experiments show that when the initial pair of projection images has an angular distance in the range alpha degrees approximately equal to [35 degrees - 145 degrees], the centerlines in all other projections (gamma = 0 degrees - 180 degrees) were indicated very precisely without any additional centering procedure. When involving additional projection images in the modeling procedure a more realistic shape of the structure can be provided. In case of the concave segment, however, the involvement of multiple projections does not necessarily provide a more realistic shape of the reconstructed structure.
Arterial Uptake of Biodegradable Nanoparticles: Effect of Surface Modifications (1998)

Restenosis is the reobstruction of an artery following interventional procedures such as balloon angioplasty or stenting. Local pharmacotherapeutic approaches using controlled release systems are under investigation to inhibit the regional pathophysiologic process of restenosis. We have been investigating biodegradable nanoparticles (100 +/- 39 nm in diameter, mean +/- sd) for the local intra-arterial drug delivery. The purpose of this study was to investigate nanoparticle surface modifications (see Table 1) to enhance their arterial uptake. The PLGA (polylactic polyglycolic acid copolymer) nanoparticles were formulated by an oil-in-water emulsion solvent evaporation technique using a 2-aminochromone (U-86983, Upjohn and Pharmacia) (U-86) as a model antiproliferative agent. The various formulations of nanoparticles were evaluated for the arterial wall uptake by using an ex-vivo dog femoral artery model. The selected formulations were then tested in vivo in acute dog femoral artery and pig coronary artery models. The nanoparticles surface modified with a cationic compound, didodecyldimethylammonium bromide (DMAB), demonstrated 7-10-fold greater arterial U-86 levels compared to the unmodified nanoparticles in different ex-vivo and in-vivo studies. The mean U-86 levels were 10.7 +/- 1.7 microg/10 mg (dog) and 6.6 +/- 0.6 microg/10 mg (pig) in the artery segments ( approximately 2 cm) which were infused with the nanoparticles. The pig coronary studies further demonstrated that the infusion of nanoparticles with higher U-86 loading reduced the arterial U-86 levels, whereas increasing the nanoparticle concentration in the infusion solutions increased the arterial U-86 levels. The biodistribution studies in pigs following coronary arterial administration of nanoparticles demonstrated disposition of U-86 in the myocardium and distally in the liver and the lung. The mechanism of enhanced arterial uptake of the DMAB surface modified nanoparticles seems to be due to the alteration in the nanoparticle surface charge. The unmodified nanoparticles had a zeta potential of -27.8 +/- 0.5 mV (mean +/- sem, n = 5), whereas the DMAB modified nanoparticles demonstrated a zeta potential of +22.1 +/- 3.2 mV (mean +/- sem, n = 5). The adsorption of DMAB to the nanoparticle surface followed the Freundlich isotherm with binding capacity k = 28.1 microg/mg and affinity constant p = 2. 33. In conclusion, surface modified nanoparticles have potential applications for intra-arterial drug delivery to localize therapeutic agents in the arterial wall to inhibit restenosis.