gebhart/patrepeval huggingface dataset:
Frequent somatic mutation of the MTS1/CDK4I (multiple tumor suppressor/cyclin-dependent kinase 4 inhibitor) gene in esophageal squamous cell carcinoma. (1994)

We previously reported frequent loss of heterozygosity on chromosome 9p in esophageal carcinomas and suggested that a tumor suppressor gene located on this chromosomal arm might be involved in development of these cancers. Since recently published studies have shown that a gene mapped on chromosome 9p21, MTS1/CDK4I (multiple tumor suppressor 1/cyclin-dependent kinase 4 inhibitor), is frequently mutated in various types of tumors, we chose to examine esophageal squamous cell carcinomas for mutations in this candidate gene. DNA sequence analyses revealed somatic mutations of MTS1/CDK4I in 14 of 27 tumors examined; 8 were frame-shift mutations and 6 were missense mutations. These results suggested that the MTS1/CDK4I gene is a tumor suppressor the inactivation of which plays an important role during carcinogenesis of the squamous cell type of esophageal carcinoma.
ENLARGEMENT OF GROWTH PLATE CHONDROCYTES MODULATED BY SUSTAINED MECHANICAL LOADING (2002)

Information about the growth rate and chondrocytic response to mechanical loads in rat vertebrae undergoing mechanically modulated growth will be helpful in determining how human vertebral growth might respond to altered loading states during progression or treatment of scoliosis and other growth-related angular skeletal deformities.
Dispenser Printing of Solid Polymer-Ionic Liquid Electrolytes for Lithium Ion Cells (2007)

Microfabrication of on-chip solid state electrochemical cells has provided a robust challenge to industry for the past decade. Previous efforts include RF Sputtering, screen-printing, and laser printing. All have merit in the laboratory but have proven difficult to scale due a combination of equipment cost and proper isolation from water and oxygen. We present a promising method for printing additively all structures necessary for a working lithium polymer battery that is both small enough to fit in a compact glovebox, yet scaleable for industrial production.
Setting the stage for bench-to-bedside movement of anti-HIV RNA inhibitors-gene therapy for AIDS in macaques (2006)

Despite significant progress over the last two decades, treatment of HIV infection remains a tremendous challenge. Although antiretroviral therapy has proved quite effective in most HIV-infected patients, increasing recognition of toxicity and the emergence of multidrug resistant HIV strains has fueled the development of alternative therapeutic approaches. Introduction of genes to inhibit HIV replication into CD4+ T lymphocytes or hematopoietic stem cells represents a potentially attractive but still unproven strategy. Despite the availability of a diverse range of molecular strategies that are able to provide potent inhibition of HIV replication in the laboratory, translation of these in vitro successes to in vivo therapies has been difficult. Fundamental challenges facing AIDS gene therapy at the present time includes the need to increase the efficiency of gene transfer in vivo, to confer upon genetically-modified T cells the ability to have a selective growth advantage in vivo, and the development of additional techniques to decrease the probability of emergence of resistant viruses. As one of the leading animal models for AIDS and for hematopoietic stem cell gene therapy, nonhuman primates are ideally suited to help address many of these basic questions. This review will provide a general overview of RNA-based genetic strategies for inhibition of HIV and SIV replication, criteria to be considered in the selection of promising inhibitory strategies for in vivo use, and key questions that can be addressed in the macaque model.
Adaptive linearization schemes for weakly nonlinear systems using adaptive linear and nonlinear FIR filters (2002)

Three adaptive linearization schemes are proposed. In the first scheme, linearization is performed by canceling nonlinearity at the output of a physical system. In the second, a nonlinear postprocessor is employed to postdistort signals. In the third, a preprocessor is used. The schemes using a postprocessor and a preprocessor are designed for weakly nonlinear systems, whereas the scheme of linearization by cancellation at the output can be applied to problems with stronger nonlinearities. In all three methods, necessary estimates of linear and nonlinear operators are provided by adaptive linear and nonlinear filters. Typical simulation results for a physical system modeled by a Volterra series with a linear term, a quadratic term, and a cubic term are presented and are judged encouraging.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Interaction between weak low frequency magnetic fields and cell membranes (2003)

The question of whether very weak low frequency magnetic fields can affect biological systems, has attracted attention by many research groups for quite some time. Still, today, the theoretical possibility of such an interaction is often questioned and the site of interaction in the cell is unknown. In the present study, the influence of extremely low frequency (ELF) magnetic fields on the transport of Ca(2+) was studied in a biological system consisting of highly purified plasma membrane vesicles. We tested two quantum mechanical theoretical models that assume that biologically active ions can be bound to a channel protein and influence the opening state of the channel. Vesicles were exposed for 30 min at 32 degrees C and the calcium efflux was studied using radioactive (45)Ca as a tracer. Static magnetic fields ranging from 27 to 37 micro T and time varying magnetic fields with frequencies between 7 and 72 Hz and amplitudes between 13 and 114 micro T (peak) were used. We show that suitable combinations of static and time varying magnetic fields directly interact with the Ca(2+) channel protein in the cell membrane, and we could quantitatively confirm the model proposed by Blanchard.
Grapefruit juice and cimetidine inhibit stereoselective metabolism of nitrendipine in humans (1991)

The effects of grapefruit juice (150 ml at -15, -10, -1/4, +5, and +10 hours) and cimetidine (200 mg at the same times) on the stereoselective pharmacokinetics and effects of 20 mg oral racemic nitrendipine were investigated in a placebo-controlled crossover study in nine healthy men. In all subjects the AUC of racemic nitrendipine was increased by grapefruit juice (mean increase 106%; 95% confidence interval 64% to 158%) and cimetidine treatment (+154%; 95% confidence interval 77% to 265%). Comparable results were obtained for the peak plasma drug concentration and for both parameters of (S)- and (R)-nitrendipine. There were highly significant differences in the area under the concentration-time curve and peak plasma drug concentration between enantiomers within all treatments. Grapefruit juice had no effect on this stereoselectivity, but cimetidine increased the mean S/R ratio of areas under the curve (2.25) by 20% (95% confidence interval 12% to 29%) compared with placebo treatment (1.89). Half-lives and time to reach peak concentration of the enantiomers were not different within and between treatments. There were no consistent effects on blood pressure with all treatments, but in most subjects there was a small temporary increase in heart rate after intake of nitrendipine. Grapefruit juice and cimetidine did not affect these hemodynamic parameters and did not cause additional adverse effects.
p-type gallium nitride by reactive ion-beam molecular beam epitaxy with ion implantation, diffusion, or coevaporation of Mg (1994)

Gallium nitride is one of the most promising materials for ultraviolet and blue light-emitting diodes and lasers. The principal technical problem that limits device applications has been achieving controllable p-type doping. Molecular beam epitaxy assisted by a nitrogen ion beam produced p-type GaN when doped via ion implantation, diffusion, or coevaporation of Mg. Nearly intrinsic p-type material was also produced without intentional doping, exhibiting hole carrier concentrations of 5×1011 cm−3 and hole mobilities of over 400 cm2/V/s at 250 K. This value for the hole mobility is an order of magnitude greater than previously reported.
Adaptive matching for efficiency enhancement of switching mode and nonlinear microwave power amplifiers (2010)

In this paper the application of adaptive matching networks for efficiency enhancement of class-E and class-F power amplifiers will be presented. These networks are capable of synthesizing the optimum impedance at the fundamental frequency as well as the suitable terminations at the harmonics. Additionally they use only transmission lines and capacitors, making them suitable for high power applications. A class-E and a class-F GaN based power amplifiers at 1 GHz will be presented, the class-E amplifier has a maximum output power of 36.8 dBm and a PAE of 73.5 %. Through using adaptive matching the amplifier can achieve a PAE of 60 % at an output power of 28.7 dBm, which gives an efficiency improvement over an 8 dB output range. The class-F amplifier has a maximum output power of 38 dBm and a PAE of 72 %. Through adaptive matching the amplifier can achieve a PAE of 58 % at an output power of 29.5 dBm, which gives an improvement of efficiency over an 8.5 dB output range.
Patented HIV-1 Integrase Inhibitors (1998-2005) (2006)

Combination therapy, comprising at least three anti-human immunodeficiency virus (anti-HIV) drugs, has become the standard treatment of AIDS. Since 1996, highly active antiretroviral therapy (HAART) was designed to rapidly control HIV replication. It has had a significant impact on patient health and progression of AIDS in developed countries but its success has not been complete. HAART strategy still suffers from issues of patient compliance, cost, deleterious side effects and emerging drug resistance. Therefore it is logical to look for agents that inhibit different viral targets. In addition to the fusion, reverse transcription and protein formation processes, the HIV replicative cycle offers various other events that can be considered as potential targets for chemotherapeutic intervention. Amongst them integration is a key step and integrase (IN), one of the three viral enzymes, has been rapidly identified as a rational target for many years. To date, four molecules have entered in clinical trials. The present article reviews the increasing number of patents on small molecule HIV-1 integrase inhibitors in the 1998-2005 period, from the pioneer ones (discovery of selective strand transfer inhibitors) to the last patents including the actual molecules under clinical trials.
Learning with ensembles: How overfitting can be useful (1995)

We study the characteristics of learning with ensembles. Solving exactly the simple model of an ensemble of linear students, we find surprisingly rich behaviour. For learning in large ensembles, it is advantageous to use under-regularized students, which actually over-fit the training data. Globally optimal performance can be obtained by choosing the training set sizes of the students appropriately. For smaller ensembles, optimization of the ensemble weights can yield significant improvements in ensemble generalization performance, in particular if the individual students are subject to noise in the training process. Choosing students with a wide range of regularization parameters makes this improvement robust against changes in the unknown level of noise in the training data. 1 INTRODUCTION An ensemble is a collection of a (finite) number of neural networks or other types of predictors that are trained for the same task. A combination of many different predictors can often improve pr...
The Biology of Bone Graft Repair (1983)

Cancellous and cortical autografts histologically have three differences: (1) cancellous grafts are revascularized more rapidly and completely than cortical grafts; (2) creeping substitution of cancellous bone initially involves an appositional bone formation phase, followed by a resorptive phase, whereas cortical grafts undergo a reverse creeping substitution process; (3) cancellous grafts tend to repair completely with time, whereas cortical grafts remain as admixtures of necrotic and viable bone. Physiologic skeletal metabolic factors influence the rate, amount, and completeness of bone repair and graft incorporation. The mechanical strengths of cancellous and cortical grafts are correlated with their respective repair processes: cancellous grafts tend to be strengthened first, whereas cortical grafts are weakened. Bone allografts are influenced by the same immunologic factors as other tissue grafts. Fresh bone allografts may be rejected by the host's immune system. The histoincompatibility antigens of bone allografts are presumably the proteins or glycoproteins on cell surfaces. The matrix proteins may or may not elicit graft rejection. The rejection of a bone allograft is considered to be a cellular rather than a humoral response, although the humoral component may play a part. The degree of the host response to an allograft may be related to the antigen concentration and total dose. The rejection of a bone allograft is histologically expressed by the disruption of vessels, an inflammatory process including lymphocytes, fibrous encapsulation, peripheral graft resorption, callus bridging, nonunions, and fatigue fractures.
Miniaturized Solid-Phase Extraction and Sample Preparation for MALDI MS Using a Microfabricated Integrated Selective Enrichment Target (2006)

A microfabricated proteomic sample preparation and sample presentation device, Integrated Selective Enrichment Target, (ISET), comprising an array of 96 perforated nanovials is described. Each perforated nanovial can be filled with solid-phase extraction media for purification and concentration of peptides prior to matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). The validity of the ISET sample preparation is shown by analysis of low nM-pM standard samples, as well as biological samples. The ISET solid-phase extraction sample preparation was compared to ZipTip and MassPREP PROtarget sample preparation, demonstrating a superior performance with respect to number of detected peptides and signal intensity of detected peptides.
Polystyrene-block-poly(2-cinnamoylethyl methacrylate) Nanofibers—Preparation, Characterization, and Liquid Crystalline Properties (1999)

Cylindrical fibers that are tens of micrometers long and ∼100 nm across are synthesized from a diblock copolymer (see figure). The determination of their persistence length and other size parameters in organic solvents by light-scattering has been heroic. The fibers form liquid crystalline phases in bromoform.
Concordancia endoscópico-histológica de la gastritis crónica en Cali. (1998)

Se realizó un estudio prospectivo con el fin de evaluar la concordancia entre signos endoscópicos y diagnóstico histológico en 216 pacientes con gastritis y metaplasia intestinal. Se estableció un registro codificado de los signos sugestivos de gastritis, que se correlacionaron con los diagnósticos histológicos de las biopsias gástricas. Se seleccionaron aquellas asociaciones que tuvieran una correlación mayor que la esperada por azar. Estas fueron: gastritis atrófica y aumento de visibilidad de vasos en antro, Kappa 0.208 (0.041-0.376); gastritis atrófica y aumento de visibilidad de vasos en cuerpo gástrico, Kappa 0.195 (0.002-0.388); gastritis atrófica y superficie en empedrado en antro, Kappa 0.213 (0.044-0.381); inflamación aguda y pliegues engrosados en antro, Kappa 0.094 (0.018-0.16). Hubo una concordancia pobre entre la mayoría de los signos endoscópicos y los diagnósticos histológicos. El diagnóstico definitivo de la gastritis sólo se debe hacer con base en los estudios histológicos de las biopsias.
The Ensembl Variant Effect Predictor (2016)

The Ensembl Variant Effect Predictor is a powerful toolset for the analysis, annotation, and prioritization of genomic variants in coding and non-coding regions. It provides access to an extensive collection of genomic annotation, with a variety of interfaces to suit different requirements, and simple options for configuring and extending analysis. It is open source, free to use, and supports full reproducibility of results. The Ensembl Variant Effect Predictor can simplify and accelerate variant interpretation in a wide range of study designs.
Cytotoxic T Lymphocyte Antigen 4 (CTLA4) Blockade Accelerates the Acute Rejection of Cardiac Allografts in CD28-deficient Mice: CTLA4 Can Function Independently of CD28 (1998)

Cytotoxic T lymphocyte antigen 4 (CTLA4) appears to negatively regulate T cell activation. One mechanism by which CTLA4 might antagonize T cell function is through inhibition of CD28 signaling by competing for their shared ligands B7-1 and B7-2. In addition, CTLA4 ligation could initiate a signaling cascade that inhibits T cell activation. To address whether CTLA4 could inhibit immune responses in the absence of CD28, rejection of heart allografts was studied in CD28-deficient mice. H-2(q) hearts were transplanted into allogeneic wild-type or CD28-deficient mice (H-2(b)). Graft rejection was delayed in CD28-deficient compared with wild-type mice. Treatment of wild-type recipients with CTLA4-immunoglobulin (Ig), or with anti-B7-1 plus anti-B7-2 mAbs significantly prolonged allograft survival. In contrast, treatment of CD28-deficient mice with CTLA4-Ig, anti-B7-1 plus anti-B7-2 mAbs, or a blocking anti-CTLA4 mAb induced acceleration of allograft rejection. This increased rate of graft rejection was associated with more severe mononuclear cell infiltration and enhanced levels of IFN-gamma and IL-6 transcripts in donor hearts of untreated wild-type and CTLA4-Ig- or anti-CTLA4 mAb-treated CD28-deficient mice. Thus, the negative regulatory role of CTLA4 extends beyond its potential ability to prevent CD28 activation through ligand competition. Even in the absence of CD28, CTLA4 plays an inhibitory role in the regulation of allograft rejection.
Translational Repression and Specific RNA Binding by the Coat Protein of the Pseudomonas Phage PP7 (2001)

PP7 is a single-strand RNA bacteriophage of Pseudomonas aeroginosa and a distant relative to coliphages like MS2 and Qbeta. Here we show that PP7 coat protein is a specific RNA-binding protein, capable of repressing the translation of sequences fused to the translation initiation region of PP7 replicase. Its RNA binding activity is specific since it represses the translational operator of PP7, but does not repress the operators of the MS2 or Qbeta phages. Conditions for the purification of coat protein and for the reconstitution of its RNA binding activity from disaggregated virus-like particles were established. Its dissociation constant for PP7 operator RNA in vitro was determined to be about 1 nm. Using a genetic system in which coat protein represses translation of a replicase-beta-galactosidase fusion protein, amino acid residues important for binding of PP7 RNA were identified.
Neurophysiological Measures of Working Memory and Individual Differences in Cognitive Ability and Cognitive Style (2000)

The capacity to deliberately control attention in order to hold and manipulate information in working memory is critical to higher cognitive functions. This suggests that between-subject differences in general cognitive ability might be related to observable differences in the activity of brain systems that support working memory and attention control. To test this notion, electroencephalograms were recorded from 80 healthy young adults during spatial working memory tasks. Measures of task-related neurophysiological and behavioral variables were derived from these data and compared to scores on a test battery commonly used to assess general cognitive ability (the WAIS-R). Subjects who scored high on the psychometric test also tended to respond faster in the experimental tasks without any loss of accuracy. The amplitude of the late positive component of the event-related potential was larger in high-ability subjects, and the frontal midline theta component of the EEG signal was also selectively enhanced in this group under conditions of sustained performance and high working memory load. These results suggest that subjects who scored high on the WAIS-R were better able to focus and sustain attention to task performance. Changes in the EEG alpha rhythm in response to manipulations of task practice and load were also examined and compared between frontal and parietal regions. The results indicated that high-ability subjects developed strategies that made relatively greater use of parietal regions, whereas low-ability subjects relied more exclusively on frontal regions. Other analyses indicated that hemispheric asymmetries in alpha band measures distinguish between individuals with relatively high verbal aptitude and those with relatively high nonverbal aptitude. In particular, subjects with a verbal cognitive style tended to make greater use of the left parietal region during task performance, and subjects with a nonverbal style tended to make greater use of the right parietal region. These results help clarify relationships between task-related brain activity and individual differences in cognitive ability and style.
Role of AlF[sub 3] Coating on LiCoO[sub 2] Particles during Cycling to Cutoff Voltage above 4.5 V (2009)

Cell tests demonstrated that the use of an AlF3 coating enabled a LiCoO2 electrode to deliver a higher discharge capacity (208 mAh g(-1)) at an upper cutoff voltage of 4.54 V. About 94% of the initial capacity was retained after 50 cycles, while the capacity retention of pristine LiCoO2 was only 60% at 4.5 V. The improved electrochemical performance with the AlF3 coating was attributed to the delay of structural degradation of LiCoO2 during cycling. A structural analysis of the cycled LiCoO2 electrode revealed that the pristine LiCoO2 transforms to a cubic spinel phase via an intermediate phase triggered by progressive chemical leaching of Co during cycling. The AlF3 coating protected LiCoO2 from the chemical attack by HF and thus helped to delay the eventual phase transformation to a spinel phase. By delaying this transformation, the AlF3 coating was able to reduce the charge-transfer resistance and maintain the structural stability when cycled above 4.5 V. (C) 2009 The Electrochemical Society. [DOI: 10.1149/1.3236501] All rights reserved.
Donor level of bond-center hydrogen in germanium (2004)

We apply Laplace deep-level transient spectroscopy (LDLTS) in situ after low-temperature proton implantation into crystalline $n$-type germanium and identify a deep metastable donor center. The activation energy of the donor emission is $\ensuremath{\sim}110\phantom{\rule{0.3em}{0ex}}\text{meV}$ when extrapolated to zero electric field. We obtain the split patterns of the emission signal for uniaxial stress applied along three major crystal directions $⟨100⟩$, $⟨110⟩$, and $⟨111⟩$, and conclude that the symmetry of the center is trigonal. We compare the annealing characteristics with those of bond-center hydrogen in silicon and with those of a trigonal center in germanium previously identified as bond-center hydrogen by in situ local-mode infrared absorption spectroscopy. From this comparison it is concluded that the observed donor emission originates from bond-center hydrogen. Infrared absorption also revealed another trigonal center tentatively ascribed to hydrogen occupying an antibonding configuration. A search for a corresponding deep level (as a hole or electron trap) failed, indicating that such level must be near midgap or resonant with (close to) the valence band.