gebhart/patrepeval huggingface dataset:
DNA LIBRARIES FOR SEQUENCING THE GENOME OFOSTREOCOCCUS TAURI(CHLOROPHYTA, PRASINOPHYCEAE): THE SMALLEST FREE-LIVING EUKARYOTIC CELL1 (2002)

Ostreococcus tauri is a marine photosynthetic picoeukaryote presenting a minimal cellular organization with one nucleus, one chloroplast, and one mitochondrion. It has the smallest genome described among free-living eukaryotic cells, and we showed by pulsed-field gel electrophoresis (PFGE) that it is divided between 15 bands ranging from 1.2 to 0.15 Mb, giving a total size of 9.7 Mb. A Bacterial Artificial Chromosome (BAC) library was prepared from genomic DNA extracted from a culture of O. tauri. A total of 2457 clones was obtained with an average insert size of around 70 kb, representing an 18-fold coverage of the genome. The library was spotted on high density filters, and several probes of coding sequences were hybridized to both the high density BAC library filters and directly to the dried PFGE gels of the O. tauri genomic DNA. These hybridizations allowed a preliminary organization of the library and the localization of several markers on the chromosomes. Randomly selected fragments were also sequenced, representing 12% of the O. tauri genome. Many sequences showed significant similarities in data banks, mainly with plant and algae sequences. About 1000 coding sequences could be identified. These data confirmed the position of O. tauri in the green lineage and the hypothesis of a very compact organization of its genome.
Prognosis and prediction of response in breast cancer: the current role of the main biological markers (1998)

In the medical literature there are frequently conflicting reports on the utility of biological tumour markers available in the clinical management of breast cancer. In this review we analyse current information on the relationships between the most widely investigated breast cancer biological markers including oestrogen and progesterone receptors, p53, Bcl-2, c-erbB-2, cyclin expression, proliferative activity, DNA ploidy and the urokinase plasminogen activation system, as well as their relevance to prognosis and response to clinical treatment. By biological prognostic indicator, we mean a marker that correlates with survival and disease-free survival; the term predictor marker indicates a marker that is capable of predicting tumour sensitivity or resistance to various therapies. Similarly to other authors' experiences, our analysis suggests that oestrogen receptors are weak prognostic indicators and good predictors of response to endocrine therapy. Furthermore, there are consistent data suggesting that proliferation indices are good indicators of prognosis, and that they are directly related to response to chemotherapy and closely related to response to hormonotherapy. On the contrary, there is no evidence or conflicting data for all of the other biological markers. These should be considered in the context of randomized trials in order to precisely define their prognostic and predictive roles. p53 and c-erbB-2 seem to be the most promising factors, but their use in routine practice still needs validation.
NO production results in suspension-induced muscle atrophy through dislocation of neuronal NOS (2007)

Forkhead box O (Foxo) transcription factors induce muscle atrophy by upregulating the muscle-specific E3 ubiquitin ligases MuRF-1 and atrogin-1/MAFbx, but other than Akt, the upstream regulators of Foxos during muscle atrophy are largely unknown. To examine the involvement of the dystrophin glycoprotein complex (DGC) in regulation of Foxo activities and muscle atrophy, we analyzed the expression of DGC members during tail suspension, a model of unloading-induced muscle atrophy. Among several DGC members, only neuronal NOS (nNOS) quickly dislocated from the sarcolemma to the cytoplasm during tail suspension. Electron paramagnetic resonance spectrometry revealed production of NO in atrophying muscle. nNOS-null mice showed much milder muscle atrophy after tail suspension than did wild-type mice. Importantly, nuclear accumulation of dephosphorylated Foxo3a was not evident in nNOS-null muscle, and neither MuRF-1 nor atrogin-1/MAFbx were upregulated during tail suspension. Furthermore, an nNOS-specific inhibitor, 7-nitroindazole, significantly prevented suspension-induced muscle atrophy. The NF-kappaB pathway was activated in both wild-type and nNOS-null muscle during tail suspension. We also show that nNOS was involved in the mechanism of denervation-induced atrophy. We conclude that nNOS/NO mediates muscle atrophy via regulation of Foxo transcription factors and is a new therapeutic target for disuse-induced muscle atrophy.
Identification of PA2.26 antigen as a novel cell-surface mucin-type glycoprotein that induces plasma membrane extensions and increased motility in keratinocytes (1999)

PA2.26 antigen was identified as a cell-surface protein induced in epidermal carcinogenesis and skin remodeling processes. PA2.26 is expressed in carcinoma cell lines and cultured fibroblasts but absent in nontumorigenic keratinocytes. In tissues, PA2.26 is present in epithelial cells of the choroid plexus, ependyma, glomerulus and alveolus, in mesothelial cells, and in endothelia of lymphatic vessels. Biochemical characterization of PA2.26 protein and sequence analysis of the isolated cDNA demonstrate that PA2.26 antigen is a mucin-like transmembrane glycoprotein. Confocal and immunoelectron microscopy analysis in cultured cells reveal that PA2. 26 is concentrated in actin-rich microvilli and plasma membrane projections, such as filopodia, lamellipodia and ruffles, where it colocalizes with members of the ERM (ezrin, radixin, moesin) family protein. Ezrin and moesin, but not radixin, can be coimmunoprecipitated together with PA2.26 from cell lysates. Ectopic expression of PA2.26 in immortalized, nontumorigenic, keratinocytes induces an epithelial-fibroblastoid morphological conversion with increased plasma membrane extensions, concomitantly to a major reorganization of the actin cytoskeleton, redistribution of ezrin to cell-surface projections, and enhanced motility. These findings suggest an involvement of PA2.26 in cell migration.
Immunogenicity of the Hu14.18-IL2 Immunocytokine Molecule in Adults With Melanoma and Children With Neuroblastoma (2009)

Patients treated with hu14.18-IL2 developed anti-idiotypic antibodies and anti Fc-IL2 antibodies. No association was seen between development of anti-IC antibodies and clinical toxicity.
Gene Expression Profiling of the Irinotecan Pathway in Colorectal Cancer (2005)

The exact mechanism responsible for large variation of response to chemotherapy remains unclear. This study profiled the gene expression for the entire irinotecan pathway to provide insights into individualized cancer therapy. The RNA expressions of 24 irinotecan pathway genes were measured in paired tumor and normal tissues from 52 patients with Dukes' C colorectal cancer using a real-time quantitative reverse transcription-PCR assay. The relative expression levels across the 24 pathway genes varied considerably, with a 441-fold range from highest to lowest expression levels for the tumor tissues and a 934-fold range for the normal tissues. Interpatient variability was also quite large, with a 33.6 median fold change in the tumor tissue genes and a 30.1 median fold change in the normal tissue genes. Six of the 24 irinotecan pathway genes had dramatically lower expression levels in the tumor samples than did the genes in the normal tissues (median range, 1.28-4.39 folds; P = 0.001-0.029). Eight genes had significantly higher levels (median range, 1.35-2.42 folds; P = 0.001-0.011). Using hierarchical clustering, three gene clusters and three patient groups were observed with high similarity indices by the RNA expressions in colorectal tumors. The three patient groups had no unique clinical pathologic features but could be differentiated by the statistically significant differences in RNA expression level of seven genes. Our study indicates that gene expression profiling could be valuable for predicting tumor response to chemotherapy and for tailoring therapy to individual cancer patients.
HIF1α is a regulator of hematopoietic progenitor and stem cell development in hypoxic sites of the mouse embryo (2013)

Hypoxia affects many physiologic processes during early stages of mammalian ontogeny, particularly placental and vascular development. In the adult, the hypoxic bone marrow microenvironment plays a role in regulating hematopoietic stem cell (HSC) function. HSCs are generated from the major vasculature of the embryo, but whether the hypoxic response affects the generation of these HSCs is as yet unknown. Here we examined whether Hypoxia Inducible Factor1-alpha (HIF1α), a key modulator of the response to hypoxia, is essential for HSC development. We found hypoxic cells in embryonic tissues that generate and expand hematopoietic cells (aorta, placenta and fetal liver), and specifically aortic endothelial and hematopoietic cluster cells. A Cre/loxP conditional knockout (cKO) approach was taken to delete HIF1α in Vascular Endothelial-Cadherin expressing endothelial cells, the precursors to definitive hematopoietic cells. Functional assays show that HSC and hematopoietic progenitor cells (HPCs) are significantly reduced in cKO aorta and placenta. Moreover, decreases in phenotypic aortic hematopoietic cluster cells in cKO embryos indicate that HIF1α is necessary for generation and/or expansion of HPCs and HSCs. cKO adult BM HSCs are also affected under transplantation conditions. Thus, HIF1α is a regulator of HSC generation and function beginning at the earliest embryonic stages.
Exhaust Emissions, Fuel Economy, and Driveability of Vehicles Fueled with Alcohol-Gasoline Blends (1975)

&lt;div class="htmlview paragraph"&gt;Current national interest in alternative fuels has placed considerable emphasis on alcohols, mainly methanol and its blends with gasoline. Vehicle studies with methanol-gasoline and ethanol-gasoline blends showed that adding alcohol to gasoline without carburetor modifications decreased carbon monoxide emissions, volume-based fuel economy, driveability, and performance. Depending on the carburetor's air-fuel ratio characteristics, hydrocarbon and nitrogen oxide emissions and road octane are either increased, decreased, or not affected.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;These effects can be explained on the basis of changes in stoichiometry, energy content, combustion temperatures, and detonation resistance caused by the addition of alcohol to gasoline.&lt;/div&gt;
The balancing act: endogenous modulation of pain in functional gastrointestinal disorders (2011)

Functional gastrointestinal disorders (FGIDs) are characterised by visceral pain or discomfort with an unknown cause. There is increasing evidence for abnormal processing of sensory input in FGIDs. Modulation of sensory input occurs at all levels of the nervous system, with a dynamic balance between facilitation and inhibition and close integration with the body's wider homoeostatic control. Cognitive, emotional, autonomic and spinal reflex pathways effectively orchestrate supraspinal and spinal pain modulation, as demonstrated in neurophysiological and brain imaging studies. Endogenous pain modulation has been studied in visceral pain conditions and abnormal regulation has been shown in irritable bowel syndrome (IBS) and functional dyspepsia, as well as other chronic pain syndromes. A majority of patients with IBS have diminished pain inhibition or even pain facilitation compared with healthy controls. Brain imaging during specific activation of endogenous pain modulation demonstrates a fairly consistent functional hub of mainly frontal, limbic and brainstem modulatory regions in healthy humans. Patients with IBS have a different pattern of activation and a correlation between the imaging and sensory changes. Because the modulatory balance of inhibition and facilitation appears to be distributed within the same functional network, future imaging studies of modulation mechanisms should include conditions allowing quantification of inhibitory and facilitatory components. An altered modulatory balance may well be a unifying pathophysiological mechanism in FGID as it can be driven by both top-down (ie, CNS pathology) and bottom-up (ie, peripheral immune activation) influences, but further validation in diverse FGID groups over time is required. Therapeutic manipulation of the modulatory system is possible by both pharmacological and non-pharmacological means.
Processing material evaluation and ultra-wideband modeling of through-strata-via (TSV) in 3D integrated circuits and systems (2010)

Since the conventional planar ICs encountered many physical, technological and economic bottlenecks, 3D integration by stacking and connecting function blocks in a vertical fashion is regarded as a viable approach to alleviate such bottlenecks. Through-strata-via (TSV) is one of the most attractive 3D integration solutions, which offers a massive number of short interconnects, high bandwidth, reduced delay and power consumption, heterogeneous integration, small footprint, improved yield, and reduced volume production cost. This paper reports on electrical characterizations and wideband modeling of typical TSV structures up to 100 GHz. The analysis is conducted in both the time domain and frequency domain, unveiling the impacts of processing materials on TSV electrical performance. The accurate broadband modeling approaches and results facilitate and benefit the infant 3D CAD development.
Three-Color FISH Analysis of TMPRSS2/ERG Fusions in Prostate Cancer Indicates That Genomic Microdeletion of Chromosome 21 Is Associated with Rearrangement (2006)

The recent description of novel recurrent gene fusions in approximately 80% of prostate cancer (PCa) cases has generated increased interest in the search for new translocations in other epithelial cancers and emphasizes the importance of understanding the origins and biologic implications of these genomic rearrangements. Analysis of 15 PCa cases by reverse transcription-polymerase chain reaction was used to detect six ERG-related gene fusion transcripts with TMPRSS2. No TMPRSS2/ETV1 chimeric fusion was detected in this series. Three-color fluorescence in situ hybridization confirms that TMPRSS2/ERG fusion may be accompanied by a small hemizygous sequence deletion on chromosome 21 between ERG and TMPRSS2 genes. Analysis of genomic architecture in the region of genomic rearrangement suggests that tracts of microhomology could facilitate TMPRSS2/ERG fusion events.
An Introduction to the Stream Control Transmission Protocol (SCTP) (2002)

This document provides a high level introduction to the capabilities supported by the Stream Control Transmission Protocol (SCTP). It is intended as a guide for potential users of SCTP as a general purpose transport protocol.
Li[sub x]Cu[sub 6]Sn[sub 5] (0<x<13): An Intermetallic Insertion Electrode for Rechargeable Lithium Batteries (1999)

It has been discovered that lithium can be inserted into the intermetallic compound in a two‐phase reaction to yield the product . This finding has important implications for designing new intermetallic insertion electrodes (anodes) for rechargeable lithium batteries. The theoretical capacity of derived from the eta‐phase, , with a structure is for , which corresponds to a fully lithiated composition ; this capacity is close to the theoretical capacity of lithiated graphite . The reaction occurs at approximately vs. lithium metal. The best cycling efficiency is obtained when the end voltage is restricted to above the potential of lithium metal. A mechanism is proposed for the insertion of lithium into . ©1999 The Electrochemical Society
Centromere formation in mouse cells cotransformed with human DNA and a dominant marker gene. (1991)

A 13,863-base-pair (bp) putative centromeric DNA fragment has been isolated from a human genomic library by using a probe obtained from metaphase chromosomes of human colon carcinoma cells. The abundance of this DNA was estimated to be 16-32 copies per genome. Cotransfection of mouse cells with this sequence and a selectable marker gene (aminoglycoside 3'-phosphotransferase type II, APH-II) resulted in a transformed cell line carrying an additional centromere in a dicentric chromosome. This centromere was capable of binding an anti-centromere antibody. In situ hybridization demonstrated that the human DNA sequence as well as the APH-II gene and vector DNA sequences were located only in the additional centromere of the dicentric chromosome. The extra centromere separated from the dicentric chromosome, forming a stable minichromosome. This functional centromere linked to a dominant selectable marker may be a step toward the construction of an artificial mammalian chromosome.
Dark Classics in Chemical Neuroscience: Mescaline (2018)

Archeological studies in the United States, Mexico, and Peru suggest that mescaline, as a cactus constituent, has been used for more than 6000 years. Although it is a widespread cactus alkaloid, it is present in high concentrations in few species, notably the North American peyote ( Lophophora williamsii) and the South American wachuma ( Trichocereus pachanoi, T. peruvianus, and T. bridgesii). Spanish 16th century chroniclers considered these cacti "diabolic", leading to their prohibition, but their use persisted to our days and has been spreading for the last 150 years. In the late 1800s, peyote attracted scientific attention; mescaline was isolated, and its role in the psychedelic effects of peyote tops or "mescal buttons" was demonstrated. Its structure was established by synthesis in 1929, and alternative routes were developed, providing larger amounts for pharmacological and biosynthetic research. Although its effects are attributed mainly to its action as a 5-HT<sub>2A</sub> serotonin receptor agonist, mescaline binds in a similar concentration range to 5-HT<sub>1A</sub> and α<sub>2A</sub> receptors. It is largely excreted unchanged in human urine, and its metabolic products are apparently unrelated to its psychedelic properties. Its low potency is probably responsible for its relative neglect by recreational substance users, as the successful search for structure-activity relationships in the hallucinogen field focused largely on finding more potent analogues. Renewed interest in the possible therapeutic applications of psychedelic drugs may hopefully lead to novel insights regarding the commonalities and differences between the actions of individual classic hallucinogens.
Production of arabitol by yeasts: current status and future prospects (2015)

Arabitol belongs to the pentitol family and is used in the food industry as a sweetener and in the production of human therapeutics as an anticariogenic agent and an adipose tissue reducer. It can also be utilized as a substrate for chemical products such as arabinoic and xylonic acids, propylene, ethylene glycol, xylitol and others. It is included on the list of 12 building block C3-C6 compounds, designated for further biotechnological research. This polyol can be produced by yeasts in the processes of bioconversion or biotransformation of waste materials from agriculture, the forest industry (l-arabinose, glucose) and the biodiesel industry (glycerol). The present review discusses research on native yeasts from the genera Candida, Pichia, Debaryomyces and Zygosaccharomyces as well as genetically modified strains of Saccharomyces cerevisiae which are able to utilize biomass hydrolysates to effectively produce L- or D-arabitol. The metabolic pathways of these yeasts leading from sugars and glycerol to arabitol are presented. Although the number of reports concerning microbial production of arabitol is rather limited, the research on this topic has been growing for the last several years, with researchers looking for new micro-organisms, substrates and technologies.
Effects of Sample Thickness on the Optical Properties of Surface Plasmon-Coupled Emission (2004)

In recent reports, we demonstrated coupling of excited fluorophores with thin silver or gold films resulting in directional surface plasmon-coupled emission (SPCE) through the silver film and into the glass substrate. In the present report, we describe the spectral and spatial properties of SPCE from sulforhomamine 101 in polyvinyl alcohol (PVA) films of various thicknesses on 50-nm silver films. The PVA thickness varied from about 30 to 750 nm. In thin PVA films with a thickness less than 160 nm, SPCE occurred at a single angle in the glass substrate and displayed only p polarization. As the PVA thickness increased to 300 nm, we observed SPCE at two angles, with different s or p polarization for each angle. For PVA films from 500 to 750 nm thick, we observed SPCE at three or four angles, with alternating s and p polarizations. The multiple rings of SPCE and the unusual s-polarized emission are consistent with the expected waveguide modes in the silver-PVA composite film. However, in contrast to our expectations, the average lifetimes of SPCE were not substantially changed from the PVA films. The observation of SPCE at multiple angles and with different polarization opens new opportunities for the use of SPCE to study anisotropic systems or to develop unique sensing devices.
HEVC for high dynamic range services (2015)

Displays capable of showing a greater range of luminance values can render content containing high dynamic range information in a way such that the viewers have a more immersive experience. This paper introduces the design aspects of a high dynamic range (HDR) system, and examines the performance of the HDR processing chain in terms of compression efficiency. Specifically it examines the relation between recently introduced Society of Motion Picture and Television Engineers (SMPTE) ST 2084 transfer function and the High Efficiency Video Coding (HEVC) standard. SMPTE ST 2084 is designed to cover the full range of an HDR signal from 0 to 10,000 nits, however in many situations the valid signal range of actual video might be smaller than SMPTE ST 2084 supported range. The above restricted signal range results in restricted range of code values for input video data and adversely impacts compression efficiency. In this paper, we propose a code value remapping method that extends the restricted range code values into the full range code values so that the existing standards such as HEVC may better compress the video content. The paper also identifies related non-normative encoder-only changes that are required for remapping method for a fair comparison with anchor. Results are presented comparing the efficiency of the current approach versus the proposed remapping method for HM-16.2.
Synthesis and coding of continuous speech with the nonlinear oscillator model (2002)

The nonlinear oscillator model for speech signals has been previously applied to time-scale modification of speech. We report on the application of the model to speech synthesis and waveform coding. For speech synthesis, a new radial basis function representation of the oscillator feedback nonlinearity is introduced. The local approximation properties of this representation have been investigated and it is shown how it can be adapted to continuous speech on a frame-by-frame basis. For speech coding, synchronization of the nonlinear oscillator model to the original waveform is demonstrated and applied in the design of a new backward-adaptive speech coding system.
Cloning and functional expression of a brain G‐protein‐coupled ATP receptor (1993)

A cDNA encoding a novel member of the G-protein-coupled receptor (GCR) superfamily, an ATP receptor, has been isolated from an embryonic chick whole brain cDNA library by hybridization screening. The encoded protein has a sequence of 362 amino acids (41 kDa) and shares no more than 27% amino acid identity with any known GCR. When expressed as a complementary RNA (cRNA) in Xenopus oocytes a slowly-developing inward current was observed in response to application of ATP. The pharmacology of this expressed protein defines it as a P2Y purinoceptor.