gebhart/patrepeval huggingface dataset:
TACC2 Is an Androgen-Responsive Cell Cycle Regulator Promoting Androgen-Mediated and Castration-Resistant Growth of Prostate Cancer (2012)

Despite the existence of effective antiandrogen therapy for prostate cancer, the disease often progresses to castration-resistant states. Elucidation of the molecular mechanisms underlying the resistance for androgen deprivation in terms of the androgen receptor (AR)-regulated pathways is a requisite to manage castration-resistant prostate cancer (CRPC). Using a ChIP-cloning strategy, we identified functional AR binding sites (ARBS) in the genome of prostate cancer cells. We discovered that a centrosome- and microtubule-interacting gene, transforming acidic coiled-coil protein 2 (TACC2), is a novel androgen-regulated gene. We identified a functional AR-binding site (ARBS) including two canonical androgen response elements in the vicinity of TACC2 gene, in which activated hallmarks of histone modification were observed. Androgen-dependent TACC2 induction is regulated by AR, as confirmed by AR knockdown or its pharmacological inhibitor bicalutamide. Using long-term androgen-deprived cells as cellular models of CRPC, we demonstrated that TACC2 is highly expressed and contributes to hormone-refractory proliferation, as small interfering RNA-mediated knockdown of TACC2 reduced cell growth and cell cycle progression. By contrast, in TACC2-overexpressing cells, an acceleration of the cell cycle was observed. In vivo tumor formation study of prostate cancer in castrated immunocompromised mice revealed that TACC2 is a tumor-promoting factor. Notably, the clinical significance of TACC2 was demonstrated by a correlation between high TACC2 expression and poor survival rates. Taken together with the critical roles of TACC2 in the cell cycle and the biology of prostate cancer, we infer that the molecule is a potential therapeutic target in CRPC as well as hormone-sensitive prostate cancer.
Levodopa therapy for Parkinson disease (2016)

Although levodopa is widely recognized as the most effective therapy for Parkinson disease (PD), its introduction 5 decades ago was preceded by several years of uncertainty and equivocal clinical results. The translation of basic neuroscience research by Arvid Carlsson and Oleh Hornykiewicz provided a logical pathway for treating PD with levodopa. Yet the pioneering clinicians who transformed PD therapeutics with this drug--among them Walther Birkmayer, Isamu Sano, Patrick McGeer, George Cotzias, Melvin Yahr, and others--faced many challenges in determining whether the concept and the method for replenishing deficient striatal dopamine was correct. This article reviews highlights in the early development of levodopa therapy. In addition, it provides an overview of emerging drug delivery strategies that show promise for improving levodopa's pharmacologic limitations.
Incorporation of hyaluronic acid into collagen scaffolds for the control of chondrocyte-mediated contraction and chondrogenesis (2007)

Hyaluronic acid (HA), a principal matrix molecule in many tissues, is present in high amounts in articular cartilage. HA contributes in unique ways to the physical behavior of the tissue, and has been shown to have beneficial effects on chondrocyte activity. The goal of this study was to incorporate graduated amounts of HA into type I collagen scaffolds for the control of chondrocyte-mediated contraction and chondrogenesis in vitro. The results demonstrated that the amount of contraction of HA/collagen scaffolds by adult canine articular chondrocytes increased with the HA content of the scaffolds. The greatest amount of chondrogenesis after two weeks was found in the scaffolds which had undergone the most contraction. HA can play a useful role in adjusting the mechanical behavior of tissue engineering scaffolds and chondrogenesis in chondrocyte-seeded scaffolds.
An ice nucleation active gene of Erwinia ananas (1989)

The ice nucleation active gene, inaA, of Erwinia ananas IN-10 has been sequenced. This gene encodes a protein composed of 1322 amino acid residues. The inaA protein contains a 1120-residue segment consisting of 70 repeats of closely related 16 amino acid motifs (R-domain), which is flanked by N- and C-terminal sequences (N- and C-domains, respectively). Its primary structure is similar to, but not identical with, those of Pseudomonas inaW and inaZ gene products. By truncating the inaA gene to various extents, it was found that deletion of the C-domain resulted in complete loss of the ice nucleation activity, whereas removal of the N-domain led to a moderate decrease in the activity. Complete loss of the activity was also observed when the N-domain plus a large part of the P-domain were deleted. It is suggested that the C-domain is required for the assembly of inaA protein to form a functional ice nucleus.
Heterogeneous Catalysts for Biodiesel Production (2007)

The production of biodiesel is greatly increasing due to its enviromental benefits. However, production costs are still rather high, compared to petroleum-based diesel fuel. The introduction of a solid heterogeneous catalyst in biodiesel production could reduce its price, becoming competitive with diesel also from a financial point of view. Therefore, great research efforts have been underway recently to find the right catalysts. This paper will be concerned with reviewing acid and basic heterogeneous catalyst performances for biodiesel production, examining both scientific and patent literature.
A Genetic Strategy for Stochastic Gene Activation with Regulated Sparseness (STARS) (2009)

It remains a challenge to establish a straightforward genetic approach for controlling the probability of gene activation or knockout at a desired level. Here, we developed a method termed STARS: stochastic gene activation with genetically regulated sparseness. The stochastic expression was achieved by two cross-linked, mutually-exclusive Cre-mediated recombinations. The stochastic level was further controlled by regulating Cre/lox reaction kinetics through varying the intrachromosomal distance between the lox sites mediating one of the recombinations. In mammalian cell lines stably transfected with a single copy of different STARS transgenes, the activation/knockout of reporter genes was specifically controlled to occur in from 5% to 50% of the cell population. STARS can potentially provide a convenient way for genetic labeling as well as gene expression/knockout in a population of cells with a desired sparseness level.
Effects of strain on boron diffusion in Si and Si1−xGex (1995)

Boron diffusion in in situ doped Si1−xGex and Si, subjected to inert-ambient furnace annealing at 800 °C, was investigated. For Si1−xGex, the effect of biaxial compressive and tensile strain on boron diffusion was studied using Si1−xGex layers with a constant Ge content (x≊0.10 and x≊0.20) grown epitaxially on various relaxed Si1−yGey (0≤y≤0.20) substrates. Boron diffusion is primarily a function of Ge content, x in the Si1−xGex layers, and does not show a strong dependence on macroscopic biaxial strain. For Si, the effect of biaxial tension was investigated using relaxed Si1−yGey layers as substrate templates for epitaxial Si layers. As in Si1−xGex, boron diffusion in Si does not depend strongly on biaxial strain.
Learning-based scan plane identification from fetal head ultrasound images (2012)

Acquisition of a clinically acceptable scan plane is a pre-requisite for ultrasonic measurement of anatomical features from B-mode images. In obstetric ultrasound, measurement of gestational age predictors, such as biparietal diameter and head circumference, is performed at the level of the thalami and cavum septum pelucidi. In an accurate scan plane, the head can be modeled as an ellipse, the thalami looks like a butterfly, the cavum appears like an empty box and the falx is a straight line along the major axis of a symmetric ellipse inclined either parallel to or at small angles to the probe surface. Arriving at the correct probe placement on the mother's belly to obtain an accurate scan plane is a task of considerable challenge especially for a new user of ultrasound. In this work, we present a novel automated learning-based algorithm to identify an acceptable fetal head scan plane. We divide the problem into cranium detection and a template matching to capture the composite "butterfly" structure present inside the head, which mimics the visual cues used by an expert. The algorithm uses the stateof- the-art Active Appearance Models techniques from the image processing and computer vision literature and tie them to presence or absence of the inclusions within the head to automatically compute a score to represent the goodness of a scan plane. This automated technique can be potentially used to train and aid new users of ultrasound.
Aberrant crypts: potential preneoplastic lesions in the murine colon. (1988)

Murine colons treated with the colon carcinogen azoxymethane (AOM) have been reported to contain aberrant crypts (AC), which are characterized by their larger size and wider pericryptal zones. The methodology used to visualize AC consists of staining the fixed, unsectioned colonic mucosa with methylene blue and transillumination of the luminal surface at a magnification of 40x. The objective of the present studies was to determine if AC demonstrate characteristics to support our hypothesis that they are putative preneoplastic lesions. Studies were designed to determine the time of occurrence of AC (Study I), the induction of AC in response to varying dosages of AOM ranging from 0.0 to 10.0 mg/kg body weight (Study II), and the effect of a high fat diet (20% fat by weight) on the number and size of AC (Study III). In all studies 4-6-week-old female CF1 mice were used. In addition C57BL/6J female mice were used in Study I. The major findings were as follows: (a) the time period required to form AC was approximately 2 weeks following a single AOM injection (5 mg/kg); (b) a dose-dependent increase in the induction of AC was noted in response to AOM from none in the control group to a plateau level of 2.90 +/- 0.38 foci at a dose of 5.0 mg/kg; (c) in comparison to the low fat group, the high fat group had a greater (P less than 0.05) mean number of foci of AC per 5 cm of colon (15.67 +/- 1.32 vs. 11.44 +/- 1.44) and a larger (P less than 0.05) mean size of foci of AC (0.0296 +/- 0.0012 mm vs. 0.0249 +/- 0.0012 mm) after 16 weeks on the respective diets; and (d) preliminary histological appearance of foci of AC revealed mild atypia to unequivocal dysplasia. The findings of the present study are consistent with the hypothesis that AC are putative preneoplastic lesions.
Vasopressin: Applications in Clinical Practice (2004)

Arginine vasopressin is a peptide produced in the posterior pituitary whose primary physiologic role is fluid homeostasis. Recent investigations have demonstrated a therapeutic role for arginine vasopressin in adult cardiac arrest as well as adult and pediatric vasodilatory shock. We review the physiology of arginine vasopressin and examine the supporting data behind the developing clinical applications of this naturally produced peptide.
Optimizing cost and performance for content multihoming (2012)

Many large content publishers use multiple content distribution networks to deliver their content, and many commercial systems have become available to help a broader set of content publishers to benefit from using multiple distribution networks, which we refer to as content multihoming. In this paper, we conduct the first systematic study on optimizing content multihoming, by introducing novel algorithms to optimize both performance and cost for content multihoming. In particular, we design a novel, efficient algorithm to compute assignments of content objects to content distribution networks for content publishers, considering both cost and performance. We also design a novel, lightweight client adaptation algorithm executing at individual content viewers to achieve scalable, fine-grained, fast online adaptation to optimize the quality of experience (QoE) for individual viewers. We prove the optimality of our optimization algorithms and conduct systematic, extensive evaluations, using real charging data, content viewer demands, and performance data, to demonstrate the effectiveness of our algorithms. We show that our content multihoming algorithms reduce publishing cost by up to 40%. Our client algorithm executing in browsers reduces viewer QoE degradation by 51%.
Degumming revisited : Innovations technologiques (1998)

A critical review of the chemistry involved in the degumming process shows that non hydratable phosphatides (NHP) consist of alkaline earth salts of phosphatidic acid and some free phosphatidylethanolamine (PE). Their removal from the oil involves the decomposition of these salts by a degumming acid capable of binding the alkaline earth ions and a subsequent dissociation of the phosphatidic acid formed by raising the pH. The phosphatidate ions thus formed is hydratable and capable of entraining the PE into the gum phase. The review of the various degumming processes shows that the water-degumming process should only be used for the production of lecithin and that the dry degumming process using a degumming acid and bleaching earth, is only economically justified for oils with a low phosphatide content (palm oil, lauric oils, etc). For seed oils having a high NHP-content, the acid refining process is recommended, whereby this process is preferably carried out at the oil mill to allow gum disposal via the meal. Acid refined oil could therefore become an article of trade with the Soft Degumming process as a possible polishing operation to be carried out prior to physical refining. Research into the use of membranes and phospholipase C is recommended.
Abstract 1704: AC electrokinetic isolation of cell free high molecular weight DNA (CF-HMW DNA) from serum (2012)

Abstract Recent reports of CF-HMW DNA in a variety of diseases has led to interest in its use as a prognostic biomarker, a diagnostic or screening tool for cancer. Apoptotic DNA (&amp;lt;200bp) is present in the circulation of normal healthy individuals. In cancer, unregulated cell growth leads to uncontrolled cell death, or necrosis, which produces HMW DNA (&amp;gt;500bp) that is then trafficked into circulation. Dielectrophoresis, or DEP (movement of particles in a non-uniform AC electric field), based electrokinetic techniques have been used for protein biomarker screening, cell separation, and DNA manipulation. Using specific DEP frequencies, analytes are moved to known locations (high or low field region) based on their inherent dielectric properties. The process allows specific nano-sized particles to be highly concentrated into high field regions, while micron-size cells are held weakly in low field regions. With fluidic washing, cells can be removed while nano-sized particles are held in high field regions. This method can effectively act as a CF-HMW DNA enrichment process for biological fluids. Unfortunately, DEP does not work well in (high conductance) physiological buffers, requiring significant dilution of the sample and, as a result, the target analyte concentration. Here, we describe a novel AC electrokinetic (ACE) technique using a custom microelectrode array and AC parameters to isolate and analyze CF-HMW DNA from high conductance serum. DNA from normal serum samples and the A549 cell line were isolated using Qiagen kits to determine initial DNA quantities. Normal sera were spiked with A549 cell line DNA at concentrations from 0 to 500 ng/ml and subjected to a 20 minute ACE protocol. DNA isolation was visualized in situ using SYBR Green I fluorescence and then eluted for use in secondary analyses. Results showed minimal fluorescence from samples without spike whereas A549 DNA spiked samples showed concentration-dependent fluorescence on the microelectrodes. After elution, levels of DNA were quantitated using ALU-sequence based qPCR and K-ras mutational status was confirmed by ABI CastPCR. Future experiments will compare CF-HMW DNA levels from normal and cancer patients across a variety of solid tumors. The ACE technique enables rapid isolation and detection of CF-HMW DNA directly from biological fluids without prior sample prep and has broad utility for diagnosis and monitoring of cancer and other diseases in which CF-HMW DNA may be used as a marker. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1704. doi:1538-7445.AM2012-1704
Characterization of Baseline Intestinal Mucosal Indices of Injury and Inflammation in Men for Use in Rectal Microbicide Trials (HIV Prevention Trials Network-056) (2007)

Objectives: The purpose of this study was to evaluate the biologic stability of mucosal parameters that might be used as endpoints in phase 1 rectal safety studies. Methods: Sixteen male participants were enrolled into 4 groups defined by HIV status, viral load, and sexual activity. Each participant underwent 3 flexible sigmoidoscopies at 2-week intervals with collection of blood, intestinal biopsies, and rectal secretions. Intestinal histology, phenotypic characterization of mucosal mononuclear cells, cytokine messenger RNA (mRNA) profiles (RANTES, interferon-γ [IFNγ], and interleukin-10), and immunoglobulin secretion were assessed. Intraclass correlation (ICC) was calculated to assess endpoint stability. Results: Qualitative histology demonstrated minimal inflammation in >95% of biopsies and remained stable throughout the study period. ICC for the tissue cytokine mRNA measurements and several T-cell phenotypic markers was >0.7, indicating stability over time. Mucosal CD4 lymphopenia was seen in the HIV-positive participants and was more pronounced in those with higher viral loads. Modest differences were observed for cytokine expression (IFNγ) and T-cell phenotype (CD3, CD4, CD8, CD19, CD4/CCR5, and CD4/CD38) between the tissue samples collected at 10 and 30 cm. Conclusions: These data help to provide a rationale for the selection of endpoints for future phase 1 rectal safety studies.
Discovery and Characterization of Two Isoforms of Moronecidin, a Novel Antimicrobial Peptide from Hybrid Striped Bass (2002)

We isolated a novel 22-residue, C-terminally amidated antimicrobial peptide, moronecidin, from the skin and gill of hybrid striped bass. Two isoforms, differing by only one amino acid, are derived from each parental species, white bass (Morone chrysops) and striped bass (Morone saxatilis). Molecular masses (2543 and 2571 Da), amino acid sequences (FFHHIFRGIVHVGKTIH(K/R)LVTGT), cDNA, and genomic DNA sequences were determined for each isoform. A predicted 79-residue moronecidin prepropeptide consists of three domains: a signal peptide (22 amino acids), a mature peptide (22 amino acids), and a C-terminal prodomain (35 amino acids). The synthetic, amidated white bass moronecidin exhibited broad spectrum antimicrobial activity that was retained at high salt concentration. An alpha-helical structure was confirmed by circular dichroism spectroscopy. The moronecidin gene consists of three introns and four exons. Peptide sequence and gene organization were similar to pleurocidin, an antimicrobial peptide from winter flounder. A TATA box and several consensus-binding motifs for transcription factors were found in the region 5' to the transcriptional start site. Moronecidin gene expression was detected in gill, skin, intestine, spleen, anterior kidney, and blood cells by kinetic reverse transcription (RT)-PCR. Thus, moronecidin is a new alpha-helical, broad spectrum antimicrobial peptide isolated from the skin and gills of hybrid striped bass.
Development of a Third Generation on Board Computer System (1989)

An expert software system to solve the problems associated with user acceptance of onboard computers in heavy trucks has been designed and implemented. The resulting third-generation onboard computer system addresses the major marketplace issues responsible for the relatively poor market penetration. The administrative cost of operating an onboard computer system program has been reduced by up to 70% by automating the data management process and automatically providing fleet management with easy-to-read memos to document the performance of the fleet. The memos are designed for several specific management levels, from the driver through the company president. Memos designed for drivers are generated on an exception basis and utilize a unique coaching approach to help to improve the driver's performance. >
[A case of severe hypotension with catecholamine-resistant septic shock in the perioperative period]. (2012)

We report general anesthesia of a 79-year-old man complicated with septic shock from abdominal artery graft infection. When he entered the operating room, intravenous dopamine, dobutamine, and noradrenaline had been administered and his bood pressure was 50/32 mmHg. General anesthesia was induced with inhalation of oxygen-sevoflurane and rocuronium, and maintained with sevoflurane-oxygen. During the operation, the patient's blood pressure was 40-50/30-35 mmHg, and heart rate decreased gradually to 50 beats x min(-1). Although various vasopressors (dopamine, dobutamine, noradrenaline, adrenaline, ephedrine, phenylephrine, atropine and vasopressin) were administered, they were not effective to improve severe hypotension. After the operation, we started blood purification (PMX-DHP+CHDF), and in consequence blood pressure increased. It was thought that hemodynamics improved remarkably by reducing humoral mediators. In conclusion, it is considered that patients with septic shock should undergo immediate diagnosis and the source control should be performed in the minimum period, because it is possible that any vasopressor become ineffective when hypercytokinemia developes.
Threshold field of phase change memory materials measured using phase change bridge devices (2009)

The threshold switching effect of phase change memory devices is typically parameterized by the threshold voltage at which this breakdown occurs. Using phase change memory bridge devices of variable length, we prove unambiguously that the important parameter for threshold switching is a critical electrical field and not a threshold voltage. By switching phase change bridge devices from the amorphous-as-deposited state, we obtain threshold fields for Ge15Sb85, Ag- and In-doped Sb2Te, Ge2Sb2Te5, and 4 nm thick Sb devices of 8.1, 19, 56, and 94 V/μm, respectively.
Reducing test data volume using LFSR reseeding with seed compression (2003)

A new lossless test vector compression scheme is presented which combines linear feedback shift register (LFSR) reseeding and statistical coding in a powerful way. Test vectors can be encoded as LFSR seeds by solving a system of linear equations. The solution space of the linear equations can be quite large. The proposed method takes advantage of this large solution space to find seeds that can be efficiently encoded using a statistical code. Two architectures for implementing LFSR reseeding with seed compression are described. One configures the scan cells themselves to perform the LFSR functionality while the other uses a new idea of "scan windows" to allow the use of a small separate LFSR whose size is independent of the number of scan cells. The proposed scheme can be used either for applying a fully deterministic test set or for mixed-mode built-in self-test (BIST), and it can be used in conjunction with other variations of LFSR reseeding that have been previously proposed to further improve the encoding efficiency.