gebhart/patrepeval huggingface dataset:
CNV-seq, a new method to detect copy number variation using high-throughput sequencing (2009)

Simulation of various sequencing methods with coverage between 0.1x to 8x show overall specificity between 91.7 - 99.9%, and sensitivity between 72.2 - 96.5%. We also show the results for assessment of CNV between two individual human genomes.
Novel GaAs FET Phase Detector Operable to Ka Band (2005)

A new type of sampling-phase detector using a GaAs FET was developed. This SPD has approximately a 30 mV/rad detection sensitivity at 26.4 GHz with a 19 dBm 100 MHz reference frequency. Detection sensitivity depends on the FET bias voltage in a very unusual way. This paper describes the configuration of the SPD and experimental results of a 50 GHz phase locked oscillator using an oscillator doubler VCO and the SPD .
Graft-versus-Leukemia Target Antigens in Chronic Myelogenous Leukemia Are Expressed on Myeloid Progenitor Cells (2005)

The expression patterns of CML28 and CML66 are strikingly similar and suggest that antigen expression may play a role in shaping the post-DLI antibody repertoire. The CD34+ restricted pattern of expression of CML28 and CML66 is particularly relevant in light of the notion that DLI likely exerts its curative effect by targeting antigens present in self-renewing malignant progenitor populations in CML.
The L1 Cell Adhesion Molecule Is Induced in Renal Cancer Cells and Correlates with Metastasis in Clear Cell Carcinomas (2005)

We have found a combination of markers that can serve to identify a subgroup of high-risk patients with ccRCC that may require more aggressive therapies.
Pulmonary delivery of nicotine pyruvate: Sensory and pharmacokinetic characteristics. (2010)

The aim of this study was to evaluate pharmacokinetic and subjective responses to a prototype nicotine pyruvate (NP) aerosol generation system. In nine healthy adult daily cigarette smokers, plasma nicotine levels and subjective responses were assessed after double-blind administration of 10 inhalations of: NP (10 μg/puff, 20 μg/puff, and 30 μg/puff); Nicotrol/Nicorette nicotine vapor inhaler (NV) cartridge; and placebo (room air). Plasma nicotine concentrations increased to a significantly greater extent after inhalations of 20 μg/puff or 30 μg/puff NP (by 5.0 ± 3.4 ng/ml and 8.3 ± 3.1 ng/ml) than after placebo and NV conditions. Satisfaction ratings were higher for all NP conditions than for placebo, and harshness/irritation was lower for the NP 20 condition than for the NV control condition. Pulmonary function showed no adverse changes. These results demonstrate that NP inhalations produce rapid increases in plasma nicotine concentrations, provide satisfaction and are well tolerated. At the 20 μg/puff dose, peak nicotine concentrations were higher than with the Nicotrol/Nicorette nicotine vapor inhaler cartridge. Further trials of this promising nicotine inhalation technology are warranted to assess its safety and efficacy in smoking cessation treatment or harm reduction approaches.
Biochemical characterization and intracellular localization of the Menkes disease protein (1996)

Menkes disease is a fatal neurodegenerative disorder of childhood due to the absence or dysfunction of a putative copper-transporting P-type ATPase encoded on the X chromosome. To elucidate the biosynthesis and subcellular localization of this protein, polyclonal antisera were generated against a bacterial fusion protein encoding the 4th to 6th copper-binding domains in the amino terminus of the human Menkes protein. RNA blot analysis revealed abundant Menkes gene expression in several cell lines, and immunoblotting studies utilizing this antiserum readily detected a 178-kDa protein in lysates from these cells. Pulse-chase studies indicate that this protein is synthesized as a single-chain polypeptide which is modified by N-linked glycosylation to a mature endoglycosidase H-resistant form. Sucrose gradient fractionation of HeLa cell lysates followed by immunoblotting of individual fractions with antibodies to proteins of known intracellular location identified the Menkes ATPase in fractions similar to those containing the cation-independent mannose-6-phosphate receptor. Consistent with this observation, confocal immunofluorescence studies of these same cells localized this protein to the trans-Golgi network and a vesicular compartment with no expression in the nucleus or on the plasma membrane. Taken together, these data provide a unique model of copper transport into the secretory pathway of mammalian cells which is compatible with clinical observations in affected patients and with recent data on homologous proteins identified in prokaryotes and yeast.
Rapid Benzene Degradation in Methanogenic Sediments from a Petroleum-Contaminated Aquifer (1998)

In methanogenic sediments from a petroleum-contaminated aquifer, [14C]benzene was converted to 14CH4 and 14CO2 without an apparent lag. Phenol, acetate, and propionate were intermediates in benzene mineralization. These results suggest that alternative electron acceptors need not be available for there to be significant natural attenuation of benzene in some petroleum-contaminated aquifers.
KCNQ potassium channels: drug targets for the treatment of epilepsy and pain (2004)

Epilepsy and neuropathic pain are disorders characterised by excessive neuronal activity. These disorders are currently managed by drugs that are capable of dampening neuronal excitability, including voltage-gated sodium channel blockers, voltage-operated calcium channel modulators and modulators of inhibitory GABAergic neurotransmission. However, these drugs are rarely 100% efficacious and their use is often associated with limiting side effects. Thus, there is a clear medical need for novel agents to treat these diseases. One potential mechanism that has not yet been exploited is potassium (K+) channel opening. A significant (and growing) body of genetic, molecular, physiological and pharmacological evidence now exists to indicate that KCNQ-based currents represent particularly interesting targets for the treatment of diseases such as epilepsy and neuropathic pain. Evidence supporting these K+ channels as novel drug targets will be reviewed in the following article. Worldwide patent activity relating to KCNQ channels and KCNQ-modulating drugs and their uses will also be summarised.
Gene‒diet interaction and plasma lipid responses to dietary intervention (2001)

Strategies for disease prevention can have a major impact on people's health. However, major gaps exist in our knowledge with regard to nutritional adequacy, nutrient-disease interactions, nutrient-gene interactions, and effective strategies for implementation of dietary recommendations which have the potential to decrease the disease burden and to contribute to successful aging of the population. Coronary heart disease is one of the major causes of mortality in the world. We have sound evidence that high levels of low-density lipoprotein cholesterol (LDL-C) and low levels of high-density lipoprotein cholesterol (HDL-C) are associated with increased risk of coronary heart disease. Lipoprotein concentrations are associated with environmental variables such as diet and lifestyle, but genetics also play a significant role. We have examined polymorphisms at candidate loci to determine their usefulness as markers for dietary responses. A G/A polymorphism 75 bp upstream from the gene encoding apolipoprotein AI (APOA1) has been described in ~ 30% of the population. Our studies show that this polymorphism is associated with variability in the HDL-C response to dietary fat, specifically to polyunsaturated fatty acids (PUFA) in the diet. Carriers of the A allele respond to increases in dietary PUFA with elevations in HDL-C levels, probably due to altered interactions of transcription factors with the mutated promoter. Therefore carriers of the A allele can potentially decrease their atherogenic risk by consuming high-PUFA diets. Likewise, we have examined the interaction between other dietary habits, such as alcohol drinking, and variability at the APOE locus, and have demonstrated that the classical associations between APOE polymorphism and LDL-C levels are observed primarily in those subjects who consume alcohol. Moreover, we have found a subgroup of the population, APOE4 carriers, for whom drinking alcohol may exert detrimental effects on lipid metabolism. This knowledge will contribute towards the development of more effective personalized dietary recommendations.
Relevance of in vitro antimicrobial susceptibility of Brucella melitensis to relapse rate in human brucellosis (1986)

The in vitro susceptibility of Brucella melitensis was examined vis-a-vis the clinical outcome in 75 patients with brucellosis. The initial MICs for Brucella isolates from patients who relapsed and from those who did not were similar. Furthermore, the MICs for isolates from patients whose infections relapsed were no different from those for original isolates. Our results clearly showed that neither initial nor subsequent antibiotic susceptibility plays a role in the likelihood of relapse of patients with brucellosis.
Herpes Simplex Virus gE/gI and US9 Proteins Promote Transport of both Capsids and Virion Glycoproteins in Neuronal Axons (2008)

Following reactivation from latency, alphaherpesviruses replicate in sensory neurons and assemble capsids that are transported in the anterograde direction toward axon termini for spread to epithelial tissues. Two models currently describe this transport. The Separate model suggests that capsids are transported in axons independently from viral envelope glycoproteins. The Married model holds that fully assembled enveloped virions are transported in axons. The herpes simplex virus (HSV) membrane glycoprotein heterodimer gE/gI and the US9 protein are important for virus anterograde spread in the nervous systems of animal models. It was not clear whether gE/gI and US9 contribute to the axonal transport of HSV capsids, the transport of membrane proteins, or both. Here, we report that the efficient axonal transport of HSV requires both gE/gI and US9. The transport of both capsids and glycoproteins was dramatically reduced, especially in more distal regions of axons, with gE(-), gI(-), and US9-null mutants. An HSV mutant lacking just the gE cytoplasmic (CT) domain displayed an intermediate reduction in capsid and glycoprotein transport. We concluded that HSV gE/gI and US9 promote the separate transport of both capsids and glycoproteins. gE/gI was transported in association with other HSV glycoproteins, gB and gD, but not with capsids. In contrast, US9 colocalized with capsids and not with membrane glycoproteins. Our observations suggest that gE/gI and US9 function in the neuron cell body to promote the loading of capsids and glycoprotein-containing vesicles onto microtubule motors that ferry HSV structural components toward axon tips.
Immunohistochemical Determination of P53 Protein Nuclear Accumulation in Prostatic Adenocarcinoma (1994)

Abnormalities of the TP53 gene are currently the most common genetic alterations associated with human malignancy. The study of altered patterns of p53 protein expression in primary prostate cancer has to date yielded a much lower incidence of alteration compared to bladder, colon, lung and breast cancer. However, the analysis of prostate cancer metastases has been limited. The objective of our study was to determine the prevalence of p53 nuclear accumulation in primary, metastatic and hormone refractory prostatic adenocarcinoma, and to characterize its relationship with conventional clinicopathological variables. We used 2 antibodies (mouse monoclonal PAb 1801 and rabbit polyclonal CM-1) and an immunohistochemical method in 93 paraffin embedded tumors (48 primary tumors, 29 lymph node metastases and 16 bone metastases) to assess p53 nuclear accumulation. Overall, p53 nuclear accumulation was observed in 19 tumors (20%), including 17 with PAb 1801 and CM-1 immunoreactivities, and 2 with CM-1 immunoreactivity only. The pattern of p53 immunoreactivity was heterogeneous in most tumors, with only 3 cases exhibiting homogeneous staining. Primary, lymph node and bone metastases exhibited p53 nuclear staining in 9 of 48 (19%), 2 of 29 (7%) and 8 of 16 (50%) cases, respectively (p = 0.003). In 6 of 10 primary hormone refractory tumors (60%) and in 3 of 38 primary hormone naive tumors (8%) p53 nuclear immunoreactivity was expressed (p = 0.002). P53 nuclear accumulation was significantly more common in higher grade primary tumors (p = 0.007). Our results suggest that p53 nuclear accumulation is relatively uncommon in prostate cancer. However, p53 nuclear accumulation appears to be associated with advanced stages of disease, as illustrated by its relatively higher occurrence in hormone refractory tumors and bone metastases. Furthermore, the significantly greater prevalence of p53 accumulation in bone metastases is currently the highest reported for prostate cancer.
An introduction to multisensor data fusion (1997)

Multisensor data fusion is an emerging technology applied to Department of Defense (DoD) areas such as automated target recognition, battlefield surveillance, and guidance and control of autonomous vehicles, and to non-DoD applications such as monitoring of complex machinery, medical diagnosis, and smart buildings. Techniques for multisensor data fusion are drawn from a wide range of areas including artificial intelligence, pattern recognition, statistical estimation and other areas. This paper provides a tutorial on data fusion, introducing data fusion applications, process models, and identification of applicable techniques. Comments are made on the state-of-the-art in data fusion.
Band diagram and carrier conduction mechanism in ZrO/sub 2//Zr-silicate/Si MIS structure fabricated by pulsed-laser-ablation deposition (2002)

On the basis of the experimental results of XPS analysis and the carrier separation, the band diagram and carrier transport mechanism in ZrO/sub 2/ dielectrics were clarified for the first time. ZrO/sub 2/-MIS structure consists of ZrO/sub 2/ layer and the interfacial Zr-silicate layer. The carrier conduction in ZrO/sub 2/ layer is dominant in the ZrO/sub 2//Zr-silicate/Si MIS structure. It was found that the hole conduction mechanism is different from electron conduction mechanism in ZrO/sub 2/ gate dielectrics.
Tags for the Identification of Languages (2001)

This document describes a language tag for use in cases where it is desired to indicate the language used in an information object, how to register values for use in this language tag, and a construct for matching such language tags. One means of indicating the language used is by labeling the information content with an identifier for the language that is used in this information content.
English-to-Czech factored machine translation (2007)

This paper describes experiments with English-to-Czech phrase-based machine translation. Additional annotation of input and output tokens (multiple factors) is used to explicitly model morphology. We vary the translation scenario (the setup of multiple factors) and the amount of information in the morphological tags. Experimental results demonstrate significant improvement of translation quality in terms of BLEU.
Engineered Enteroendocrine Cells Secrete Insulin in Response to Glucose and Reverse Hyperglycemia in Diabetic Mice (2007)

Type 1 diabetes is a metabolic disorder caused by loss of insulin-producing pancreatic beta-cells. Expression of insulin in non-beta-cells to create beta-cell surrogates has been tried to treat type 1 diabetes. Enteroendocrine K cells have characteristics similar to pancreatic beta-cells, such as a glucose-sensing system and insulin-processing proteases. In this study, we genetically engineered an enteroendocrine cell line (STC-1) to express insulin under the control of the glucose-dependent insulinotropic polypeptide promoter. We screened clones and chose one, Gi-INS-7, based on its high production of insulin. Gi-INS-7 cells expressed glucose transporter 2 (GLUT2) and glucokinase (GK) and secreted insulin in response to elevated glucose levels in vitro. To determine whether Gi-INS-7 cells can control blood glucose levels in diabetic mice, we transplanted these cells under the kidney capsule of streptozotocin (STZ)-induced diabetic mice and found that blood glucose levels became normal within 2 weeks of transplantation. In addition, glucose tolerance tests in mice that became normoglycemic after transplantation with Gi-INS-7 cells showed that exogenous glucose was cleared appropriately. These results suggest that engineered K cells may be promising surrogate beta-cells for possible therapeutic use for the treatment of type 1 diabetes.
An Embedded 4-Channel Real-Time Multimedia Coding System (2006)

With the growing of multimedia applications, requirement for embedded multimedia systems becomes popular In this paper we design and implement an embedded 4-channel real-time video and audio coding system (VACS). To achieve real-time coding of 4-channel video and audio, we optimize the coding software at algorithm, system and code level. Experimental results of VACS indicate that it works efficiently. Furthermore, since the hardware framework of VACS is based on programmable devices (DSP and FPGA), consequently by realizing diverse multimedia processing algorithms, VACS can also satisfy the requirement of some other embedded multimedia applications
Iterative Turbo Multipath Interference Cancellation for WCDMA Systems with Non-Uniform Modulations (2005)

In this paper we consider the use of non-uniform QAM constellations (quadrature amplitude modulation) for the transmission of multicast and broadcast services in the downlink connection of a WCDMA (wideband code division multiplexing) system. The objective is to increase the efficiency of the transmission by splitting the information in classes with different importance and mapping the bit streams of these classes to more or less protected positions of the modulation symbols. With this strategy, the most important information streams can be received by all users while the less relevant information will only be extracted by users with good propagation conditions. It is shown that the multipath interference introduced by the channel induces a severe performance loss for these modulations. A low complexity iterative turbo multipath interference canceller (MPIC) that uses feedback information from the turbo-decoder is proposed for suppressing this interference. Computer simulation results are presented, showing that a considerable performance gain can be obtained with the use of the iterative MPIC.
A preliminary pharmacogenetic investigation of adverse events from topiramate in heavy drinkers. (2009)

Topiramate, an anticonvulsant medication, is an efficacious treatment for alcohol dependence. To date, little is known about genetic moderators of side effects from topiramate. The objective of this study was to examine 3 single nucleotide polymorphisms (SNPs) of the glutamate receptor GluR5 gene (GRIK1) as predictors of topiramate-induced side effects in the context of a laboratory study of topiramate. Heavy drinkers (n=51, 19 women and 32 men), 75% of whom met criteria for an alcohol use disorder, completed a 5-week dose escalation schedule to a target dose of either 200 or 300 mg or matched placebo. The combined medication groups were compared with placebo-treated individuals for side effects at target dose. Analyses revealed that an SNP in intron 9 of the GRIK1 gene (rs2832407) was associated with the severity of topiramate-induced side effects and with serum levels of topiramate. Genes underlying glutamatergic neurotransmission, such as the GRIK1 gene, may help predict heterogeneity in topiramate-induced side effects. Future studies in larger samples are needed to more fully establish these preliminary findings.
Isolation of autophagic vacuoles from rat liver: morphological and biochemical characterization. (1982)

The induction of autophagy caused by vinblastine (VBL) has been found to be concomitant with a stimulation of proteolysis in a mitochondrial-lysosomal (ML) fraction from the rat liver (Marzella and Glaumann, 1980, Lab. Invest., 42: 8-17. Marzella and Glaumann, 1980, Lab. Invest., 42:18-27). In this fraction the enhanced proteolysis is associated with a threefold increase in the relative fractional volume of autophagic vacuoles (AVs). In an attempt to isolate the AVs, we subfractionated the ML suspension at different intervals after the induction of autophagy by VBL by centrifugation on a discontinuous Metrizamide gradient ranging from 50% to 15%. The material banding at the 24 to 20% and the 20 to 15% interphases was collected. Morphological analysis reveals that 3 h after induction of autophagy these fractions consist predominantly (approximately 90%) of intact autophagic vacuoles. These autophagic vacuoles contain cytosol, mitochondria, portions of endoplasmic reticulum, and occasional very low density lipoprotein, particles either free or in Golgi apparatus derivatives, in particular secretory granules. The sequestered materials show ultrastructural signs of ongoing degradation. In addition to containing typical autophagic vacuoles, the isolated fractions consist of lysosomes lacking morphologically recognizable cellular components. Contamination from nonlysosomal material is only a few percent as judged from morphometric analysis. Typical lysosomal "marker" enzymes are enriched 15-fold, whereas the proteolytic activity is enriched 10- to 20-fold in the isolated AV fraction as compared to the homogenate. Initially, the yield of nonlysosomal mitochondrial and microsomal enzyme activities increases in parallel with the induction of autophagy but, later on, decreases with advanced degradation of the sequestered cell organelles. Therefore, in the case of AVs the presence of nonlysosomal marker enzymes cannot be used for calculation of fraction purity, since newly sequestered organelles are enzymatically active. Isolated autophagic vacuoles show proteolytic activity when incubated in vitro. The comparatively high phospholipid/protein ratio (0.5) of the AV fraction suggests that phospholipids are degraded more slow than proteins. Is it concluded that AVs can be isolated into a pure fraction and are the subcellular site of enhanced protein degradation in the rat liver after induction of autophagy.
Identification of Constitutively Active Interleukin 33 (IL-33) Splice Variant (2011)

IL-33/IL-1F11 is a new member of the IL-1 family ligand and provokes T helper-type immune responses. IL-33 is the ligand of ST2 and IL-1 receptor accessory protein (IL-1RAcP) that triggers nuclear factor-κ light chain enhancer of activated B cells (NF-κB) and MAPK signaling. We discovered a novel short splice variant of IL-33 that was termed spIL-33. The new spIL-33 lacks exon 3 containing a proposed caspase-1 cleavage site. We isolated spIL-33 cDNA from the Huh7 human hepatocarcinoma cell line and expressed the recombinant spIL-33 protein in Escherichia coli. The recombinant spIL-33 and pro-IL-33 were not cleaved by caspase-1, unlike IL-18 (IL-1F4). The recombinant spIL-33 was constitutively active, and spIL-33-induced inflammatory cytokine production was caspase-1-independent in HMC-1 and Raw 264.7 cells. The recombinant spIL-33 induced the phosphorylation of IL-1 receptor-associated kinase (IRAK1), NF-κB, p38 MAPK, p44/42 MAPK, and JNK in a time- and dose-dependent manner. Anti-ST2 monoclonal antibody specifically blocked the spIL-33-induced cytokine production. In this study, we identified and characterized a new IL-33 splice variant, which was a constitutively active IL-33 isoform. The existence of constitutively active spIL-33 suggests that the biological activity of IL-33 could be triggered by diverse stimulations during immune responses. Further investigation of the spIL-33 expression pattern may contribute to understanding the involvement of IL-33 in inflammatory disorders.