gebhart/patrepeval huggingface dataset:
Antisense Gene Inhibition by C-5-Substituted Deoxyuridine-Containing Oligodeoxynucleotides (1997)

Antisense oligodeoxynucleotides (ODNs) are capable of inhibiting gene expression via a RNase H mechanism in which the complementary RNA is degraded by RNase H. C-5 propyne dU phosphorothioate ODNs bind selectively and with high affinity to RNA within cells leading to potent antisense inhibition of RNA translation. The effect that increasing steric bulk of C-5-substituted deoxyuridine analogs has on affinity for RNA and ability to inhibit gene expression is discussed. The relative binding affinity was measured by thermal denaturation (Tm) analysis, and antisense activity was determined by inhibition of SV40 T-antigen (TAg) expression in CV1 cells. The results show that antisense activity is not directly correlated to Tm measurements. In vitro analysis (RNase H cleavage, on-rates, and off-rates) and pre-formed ODN/RNA experiments indicate that RNase H activity and intracellular dissociation appear to be major determinants of the antisense potency of the various substituted ODNs. The results of our analysis point to the unique ability of C-5 propyne dU ODNs to selectively bind to RNA within cells and activate cleavage of RNA by RNase H leading to potent inhibition of gene expression.
The DNA sequence of human chromosome 22 (1999)

Knowledge of the complete genomic DNA sequence of an organism allows a systematic approach to defining its genetic components. The genomic sequence provides access to the complete structures of all genes, including those without known function, their control elements, and, by inference, the proteins they encode, as well as all other biologically important sequences. Furthermore, the sequence is a rich and permanent source of information for the design of further biological studies of the organism and for the study of evolution through cross-species sequence comparison. The power of this approach has been amply demonstrated by the determination of the sequences of a number of microbial and model organisms. The next step is to obtain the complete sequence of the entire human genome. Here we report the sequence of the euchromatic part of human chromosome 22. The sequence obtained consists of 12 contiguous segments spanning 33.4 megabases, contains at least 545 genes and 134 pseudogenes, and provides the first view of the complex chromosomal landscapes that will be found in the rest of the genome.
Interface characterization of fully-depleted SOI MOSFET by a subthreshold I-V method (1994)

Interface state densities can dramatically affect the performances of MOSFETs by causing threshold voltage shift and mobility degradation. In SOI structures, due to the complex multi-interface nature and small gate area, the interface state characterization still remains a very challenging problem. Conventional C-V method is not suitable for investigating interfaces in SOI MOS devices, mainly because of the large area needed and the high series resistance in thin-film. Several other measurement techniques based on currents rather than capacitance have been proposed. In this work, an evolved technique for characterizing interface state density in fully-depleted SOI MOSFETs is presented. By measuring subthreshold swing of the SOI MOSFETs, the interface state density can be determined. The distribution of both front- and back-interface state densities in the bandgap can be evaluated by applying a rigorous one-dimensional analytical model for FD-SOI MOSFETs operating in the weak inversion regime. In addition, this technique has been applied successfully to the comparison of interface qualities of various SOI wafers and the study of electrical stress effect. The SOI devices used in this study were n-channel and p-channel MOSFETs fabricated with submicron CMOS technology on both SIMOX and Bonded-and-Etchback SOI (BESOI) wafers.
Molecular genetics of implantation in the mouse (1997)

Embryo implantation is a complex developmental process requiring precise coordination between mother and offspring to ensure success. Implantation failure is clinically relevant to in vitro fertilization programs and to an understanding of diseases of pregnancy like preeclampsia. Basic and clinical research have identified a number of proteins involved in peri-implantation development, but an understanding of the implantation process and its cellular and molecular components is just beginning. This review will focus on the implantation and development of the murine embryo and placenta. The significance of ectopic expression and targeted mutagenesis models to these processes will be discussed.
A consistently successful procedure for in vitro fertilization of golden hamster eggs (1989)

Complete details are described for the first time of the procedures used in the author's laboratory for obtaining in vitro fertilization (IVF) of golden hamster eggs leading to the first cleavage division. These IVF procedures have been developed during the past 20 years and are very reproducible: IVF of at least 75% of eggs is routinely achieved, and on average 65% of inseminated eggs undergo the first cleavage division in vitro. These results can easily be obtained by inexperienced investigators. The ease and reproducibility of the hamster IVF procedures make them very suitable for studies of sperm:egg interaction and associated events. Studies in the author's laboratory have included analysis of sperm fertilizing ability under chemically defined conditions, the presence of sperm acrosome reaction stimulating factors in the egg investments, maturation of oocytes in vitro, the block to polyspermy, and the contribution of egg aging to fertilization anomalies. In addition, the motility of hamster sperm under chemically defined conditions is used in a routine screening protocol for detecting contaminants in the culture milieu. Golden hamster gametes offer several distinct advantages for IVF studies, including the large size of the sperm acrosome, the persistence of the very large sperm tail in the ooplasm for many hours following fertilization, and the translucence of the ooplasm, which facilitates observation of the sperm tail and pronuclei. The female golden hamster exhibits a regular 4 day estrous cycle, with distinctive indications of estrus and proestrus phases. Because of the advantages of using the golden hamster, the procedures described in this report may be useful to other investigators wishing to conduct research using IVF. Essentially the same IVF procedures can be used with monkey and bovine gametes.
The Total Least Squares Problem: Computational Aspects and Analysis. (1992)

Introduction Basic principles of the total least squares problem Extensions of the basic total least squares problem Direct speed Improvement of the total least squares computations Iterative speed Improvement for solving slowly varying total least squares problems Algebraic Connections Between total least squares and least squares problems Sensitivity analysis of total least squares and least squares problems in the presence of errors in all data Statistical properties of the total least squares problem Algebraic connections between total least squares estimation and classical linear regression in Multicollinearity problems Conclusions.
A nonlinear filter system for beautifying facial images with contrast enhancement (2010)

A nonlinear image processing system for beautifying human facial images is proposed using contrast enhancement which effects highlighting and shading. Authors proposed before a nonlinear digital filter bank system, which removes undesirable skin components, such as wrinkles and spots, to make the skin look smoothed and beautified. Also, edge enhancement is utilized in this system to make the features of the face look clear-cut. This system is designed optimally on the basis of human subjective criteria and taste, using interactive evolutionary computing (IEC). Now, contrast enhancement is newly introduced to this system. By enhancing the contrast of the base component of the face image, which is extracted by the nonlinear filter bank, the face looks deeply chiseled from the effect of highlighting and shading. Especially, the dark shade around the outline of the face makes the face look slim and sharp. The degree of contrast enhancement is optimally set by IEC as well as other parameters in the nonlinear filter bank system. The proposed system is verified to be effective in experiments of processing an actual facial image.
adg2‐1 represents a missense mutation in the ADPG pyrophosphorylase large subunit gene of Arabidopsis thaliana (1997)

Arabidopsis mutants affecting ADPG pyrophosphorylase (ADGase) activity can be divided into two complementation groups, adg1 and adg2. Previous biochemical studies of adg2-1 mutant indicated that mutant plants do not accumulate ADGase large subunit protein and that ADGase small subunits assemble as homotetramers. This suggested that the ADG2 gene may encode the large subunit of ADGase. In this paper, it is shown that adg2-1 mutant plants accumulate near wild-type levels of transcripts encoding both the large and small subunits of ADGase. However, by RFLP analysis and complementation of adg2-1 with the ADGase large subunit gene, we show that the adg2-1 mutant does represent a mutation of the ADGase large subunit gene. Sequence analysis of the adg2-1 allele revealed a missense mutation. The results therefore suggest either that the missense mutation affects the stability of the ADGase large subunit protein or that it prevents assembly of the large subunit into holoenzyme.
Dynamic MR imaging of human brain oxygenation during rest and photic stimulation (1992)

Dynamic FLASH (fast low-angle shot) magnetic resonance (MR) imaging was used to monitor changes in brain oxygenation in the human visual cortex during photic stimulation. The approach exploits the sensitivity of the gradient-echo signal to susceptibility changes induced by varying concentrations of paramagnetic deoxyhemoglobin in the cerebral blood pool. After the onset of binocular photic stimulation (10 Hz, red light, checker-board), there was a distinct increase in the MR signal in the calcarine cortex within 6-9 seconds, indicating a decrease in the total deoxyhemoglobin concentration. After the stimulation was switched off, the MR signal returned to a basal value within a similar period of time. Assuming enhanced blood flow and only a minor increase in oxygen consumption (production of deoxyhemoglobin) during physiologic activation, the results reflect an enhanced supply of diamagnetic oxyhemoglobin and an increase in the partial oxygen pressure in the capillary and venous blood pools. In addition, a decrease in the basal MR signal in the calcarine cortex was observed during the first 60-90 seconds of persistent activation, which may be understood as an autoregulatory adaptation to increased overall brain activity associated with information processing due to continuous perception of visual stimuli.
Analysis of Drug Release Kinetics from Degradable Polymeric Devices (1993)

Drug release kinetics from a degradable polymer undergoing surface erosion have been analysed by mathematical modelling and stimulations. This approach considers drug particles homogeneously dispersed in the matrix, and cases of both a single polymer matrix and a matrix surrounded by a membrane are considered. The influence of different polymer, drug, and membrane parameters on long-term performance has been simulated and provides a theoretical basis for the design of degradable drug delivery devices.
Increased plasma level of platelet-activating factor (PAF) and decreased serum PAF acetylhydrolase (PAFAH) activity in adults with bronchial asthma. (1997)

We evaluated the plasma level of platelet-activating factor (PAF), a chemical mediator that induces various symptoms of bronchial asthma, and the activity of serum PAF acetylhydrolase (PAFAH), an enzyme that specifically inactivates PAF, in adults with bronchial asthma. Measurements were made by radioimmunoassay of samples obtained from 137 adult asthmatic patients (137 cases examined in remission and from among these 41 cases were also measured at the time of an asthmatic attack) 59 adult patients with untreated pulmonary tuberculosis and 106 healthy adult volunteers. It was demonstrated that the plasma PAF level was markedly higher and the serum PAFAH activity markedly lower in the asthmatic patients, both in remission and at the time of asthmatic attack, than in the healthy volunteers. The plasma PAF level was more closely associated with asthma both in remission and at the time of asthmatic attack than with pulmonary tuberculosis, whereas there was no significant difference in the serum PAFAH activity between the two diseases. The low serum PAFAH activity in the asthmatic patients may have been due to saturation as a result of continuous reaction to the increased plasma PAF level in those patients.
Cancer Immunotherapy Based on Mutation-Specific CD4+ T Cells in a Patient with Epithelial Cancer (2014)

Limited evidence exists that humans mount a mutation-specific T cell response to epithelial cancers. We used a whole-exomic-sequencing-based approach to demonstrate that tumor-infiltrating lymphocytes (TIL) from a patient with metastatic cholangiocarcinoma contained CD4+ T helper 1 (T(H)1) cells recognizing a mutation in erbb2 interacting protein (ERBB2IP) expressed by the cancer. After adoptive transfer of TIL containing about 25% mutation-specific polyfunctional T(H)1 cells, the patient achieved a decrease in target lesions with prolonged stabilization of disease. Upon disease progression, the patient was retreated with a >95% pure population of mutation-reactive T(H)1 cells and again experienced tumor regression. These results provide evidence that a CD4+ T cell response against a mutated antigen can be harnessed to mediate regression of a metastatic epithelial cancer.
Human Serum Paraoxonase/Arylesterase’s Retained HydrophobicN-Terminal Leader Sequence Associates With HDLs by Binding Phospholipids (1999)

In serum, human paraoxonase/arylesterase (PON1) is found exclusively associated with high density lipoprotein (HDL) and contributes to its antiatherogenic properties by inhibiting low density lipoprotein (LDL) oxidation. Difficulties in purifying PON1 from apolipoprotein A-I (apoA-I) suggested that PON1's association with HDL may occur through a direct binding between these 2 proteins. An unusual property of PON1 is that the mature protein retains its hydrophobic N-terminal signal sequence. By expressing in vitro a mutant PON1 with a cleavable N-terminus, we demonstrate that PON1 associates with lipoproteins through its N-terminus by binding phospholipids directly rather than binding apoA-I. Nonetheless, apoA-I stabilized arylesterase activity more than did phospholipid alone, apoA-II, or apoE. Consequently, we studied the role of apoA-I in PON1 expression and HDL association in mice genetically deficient in apoA-I. Though present in HDL fractions at decreased levels, PON1 arylesterase activity was less stable than in control mice. Furthermore, PON1 could be competitively removed from HDL by phospholipids, suggesting that PON1's retained N-terminal peptide allows transfer of the enzyme between phospholipid surfaces. Thus, our data suggest that PON1 is stabilized by apoA-I, and its binding to HDL and physiological distribution are dependent on the direct binding of the retained hydrophobic N-terminus to phospholipids optimally presented in association with apoA-I.
Dysferlin-mediated membrane repair protects the heart from stress-induced left ventricular injury (2007)

Dilated cardiomyopathy is a life-threatening syndrome that can arise from a myriad of causes, but predisposition toward this malady is inherited in many cases. A number of inherited forms of dilated cardiomyopathy arise from mutations in genes that encode proteins involved in linking the cytoskeleton to the extracellular matrix, and disruption of this link renders the cell membrane more susceptible to injury. Membrane repair is an important cellular mechanism that animal cells have developed to survive membrane disruption. We have previously shown that dysferlin deficiency leads to defective membrane resealing in skeletal muscle and muscle necrosis; however, the function of dysferlin in the heart remains to be determined. Here, we demonstrate that dysferlin is also involved in cardiomyocyte membrane repair and that dysferlin deficiency leads to cardiomyopathy. In particular, stress exercise disturbs left ventricular function in dysferlin-null mice and increases Evans blue dye uptake in dysferlin-deficient cardiomyocytes. Furthermore, a combined deficiency of dystrophin and dysferlin leads to early onset cardiomyopathy. Our results suggest that dysferlin-mediated membrane repair is important for maintaining membrane integrity of cardiomyocytes, particularly under conditions of mechanical stress. Thus, our study establishes what we believe is a novel mechanism underlying the cardiomyopathy that results from a defective membrane repair in the absence of dysferlin.
Review: Anti-infectives Developments in viral hepatitis during 1994 (1995)

The hepatitis vi ruses are a diverse collection which, for the most part, have little in common except their name and the disease they cause in a susceptible host. This article outlines what is currently known about each of the hepatitis viruses A - E and summarises the methods which are available for treatment. The most recent developments that have been published in the patent literature during 1994 are also outlined. Emphasis is placed on hepatitis B and C as these are currently perceived to be the largest areas of unmet need for antiviral therapy.
Development Of The Depth-Fused Multi-Focal-Plane Display Technology (2014)

Conventional stereoscopic displays present a pair of stereoscopic images on a single and fixed image plane. In consequence, these displays lack the capability of correctly rendering focus cues (i.e. accommodation and retinal blur) and may induce the discrepancy between accommodation and convergence. A number of visual artifacts associated with incorrect focus cues in stereoscopic displays have been reported, limiting the applicability of these displays for demanding applications and daily usage. Depth-fused multi-focal-plane display was proposed to create a fixed-viewpoint volumetric display capable of rendering correct or nearly-correct focus cues in a stereoscopic display through a small number of discretely placed focal planes. It effectively addresses the negative effects of conventional stereoscopic displays on depth perception accuracy and visual fatigue. In this dissertation, the fundamental design methods and considerations of depth-fused displays were refined and extended based on previous works and a high-resolution optical see-through multi-focal-plane head-mounted display enabled by state-of-the-art freeform optics was developed. The prototype system is capable of rendering nearly-correct focus cues for a large volume of 3D space extending into a depth range from 0 to 3 diopters at flicker-free speed. By incorporating freeform optics, the prototype not only achieves high quality imagery across a large 3D volume for the virtual display path but it also maintains better than 0.5 arcminutes visual resolution of the see-through view. The optical design, implementation and experimental validation of the display are presented and discussed in detail.
A Bayesian hybrid method for context-sensitive spelling correction (1996)

Two classes of methods have been shown to be useful for resolving lexical ambiguity. The first relies on the presence of particular words within some distance of the ambiguous target word; the second uses the pattern of words and part-of-speech tags around the target word. These methods have complementary coverage: the former captures the lexical ``atmosphere'' (discourse topic, tense, etc.), while the latter captures local syntax. Yarowsky has exploited this complementarity by combining the two methods using decision lists. The idea is to pool the evidence provided by the component methods, and to then solve a target problem by applying the single strongest piece of evidence, whatever type it happens to be. This paper takes Yarowsky's work as a starting point, applying decision lists to the problem of context-sensitive spelling correction. Decision lists are found, by and large, to outperform either component method. However, it is found that further improvements can be obtained by taking into account not just the single strongest piece of evidence, but ALL the available evidence. A new hybrid method, based on Bayesian classifiers, is presented for doing this, and its performance improvements are demonstrated.
Variable-depth Streamer Acquisition - Broadband Data for Imaging and Inversion (2011)

This paper starts by describing a new deghosting algorithm, based on computing a migration together with a mirror migration, and performing a joint deconvolution of these two images. It is true amplitude, being able to extract the true deghosted reflectivity, that is the reflectivity that would have been obtained should the water surface be not reflecting. The paper then describes how this new method allows to deghost acquisitions based on pre-stack notch diversity, such as the slant streamer technique. We revisit this acquisition technique in two ways: firstly, we optimize the depth profile of the streamer to ensure diversity for all reflectors depths, leading to variable-depth streamer rather than slant streamer. Secondly, recognizing that the stack performs an imperfect deghosting, leaving a residual ghost, we perform the residual deghosting with our new deghosting technique. This variable-depth streamer acquisition and processing has been tested on several locations. Here, we show results from a West Africa acquisition, where a 2.5-150 Hz bandwidth was achieved. This broad bandwidth translates into improved results for the acoustic impedance inversion.
Cellular Adaptation in Migraineurs with Chronic Daily Headache (1993)

Ergotamine and analgesic misuse are now recognized as causes of chronic daily headache and the condition responds well to drug withdrawal with reduced headache frequency. In this study, we have investigated whether medication misuse is associated with an alteration in membrane transduction which is sensitive to drug withdrawal. This was carried out by assay of the thrombin-stimulated generation of inositol phosphates in platelets from 12 migraine patients with chronic daily headache and analgesic misuse, 7 migraine patients with chronic daily headache and ergotamine misuse and 7 control subjects. After drug withdrawal, a significant decrease in headache frequency was seen at one month in both patient groups. Withdrawal of analgesics produced a significant decrease in thrombin-stimulated inositol phosphate production at one month; this was further decreased a month later with a reduction in Bmax of 60% and no significant change in KD. A similar pattern was obtained in ergot misuse patients, with the KD value decreasing by 56% one month after drug withdrawal. These results provide evidence of an adaptation in transduction with misuse of analgesics and ergotamine which correlates with headache frequency.