gebhart/patrepeval huggingface dataset:
Significance of the TMPRSS2:ERG gene fusion in prostate cancer (2017)

The transmembrane protease serine 2:v‑ets erythroblastosis virus E26 oncogene homolog (TMPRSS2:ERG) gene fusion is common in prostate cancer, while its functional role is not fully understood. The present study aimed to investigate the significance of the TMPRSS2:ERG gene fusion in human prostate cancers using bioinformatics tools. Comprehensive alteration analysis of TMPRSS2 and ERG in 148 different human cancer studies was performed by cBioPortal, and the mRNA expression level of the ERG gene was evaluated using Oncomine analysis. Furthermore, lentiviral short hairpin (sh)RNA‑mediated knockdown of TMPRSS2:ERG was performed to study the impact of ERG silencing on cell proliferation and cell cycle distribution in prostate cancer cells. The results demonstrated that the TMPRSS2 and ERG genes were mostly altered in prostate cancer, and the most frequent alteration was gene fusion. Oncomine analysis demonstrated that the ERG gene was significantly upregulated in prostate clinical samples compared with the normal prostate gland in four independent datasets, and a positive association was observed between potassium inwardly‑rectifying channel subfamily J member 15, down syndrome critical region gene 4, potassium inwardly‑rectifying channel subfamily J member 6 and ERG gene expression. There were 272 mutations of the ERG gene identified in the cBioPortal database; among the mutations, 2 missense mutations (R367C and P401H) were regarded as functional mutations (functional impact score >1.938). Furthermore, the present study successfully knocked down ERG gene expression through a lentiviral‑mediated gene silencing approach in VCaP prostate cancer cells. The ERG mRNA and protein expression levels were both suppressed significantly, and a cell‑cycle arrest at G0/G1 phase was observed after ERG gene silencing. In conclusion, these bioinformatics analyses provide novel insights for TMPRSS2:ERG fusion gene study in prostate cancer. Target inhibition of ERG expression could significantly cause cell growth arrest in prostate cancer cells, which could be a potentially valuable target for prostate cancer treatment. However, the precise mechanism of these results remains unclear; therefore, further studies are required.
Whole organ decellularization - a tool for bioscaffold fabrication and organ bioengineering (2009)

The use of synthetic and naturally-derived scaffolds for bioengineering of solid organs has been limited due to a lack of an integrated vascular network. Here, we describe fabrication of a bioscaffold system with intact vascular tree. Animal-donor organs and tissues, ranging in size up-to thirty centimeters, were perfused with decellularization solution to selectively remove the cellular component of the tissue and leave an intact extracellular matrix and vascular network. The vascular tree demonstrated sequential fluid flow through a central inlet vessel that branched into an extensive capillary bed and coalesced back into a single outlet vessel. In one example, the liver, we used central inlet vessels to perfuse human and animal liver cells through the bioscaffold to create a functional liver tissue construct in vitro. These results demonstrate a novel yet simple and scalable method to obtain whole organ vascularized bioscaffolds with potential for liver, kidney, pancreas, intestine and other organs' bioengineering. These bioscaffolds can further provide a tool to study cells in their natural three-dimensional environment, which is superior for drug discovery platform compared with cells cultured in two-dimensional petri dishes.
Identification of autotaxin as a neurite retraction‐inducing factor of PC12 cells in cerebrospinal fluid and its possible sources (2005)

Abstract Cerebrospinal fluid (CSF) induced neurite retraction of differentiated PC12 cells; the action was observed in 15 min (a rapid response) and the activity further increased until 6 h (a long-acting response) during exposure of CSF to the cells. The CSF action was sensitive to monoglyceride lipase and diminished by homologous desensitization with lysophosphatidic acid (LPA) and by pretreatment with an LPA receptor antagonist Ki16425. Although fresh CSF contains LPA to some extent, the LPA content in the medium was increased during culture of PC12 cells with CSF. The rapid response was mimicked by exogenous LPA, and a long-acting response was duplicated by a recombinant autotaxin, lysophospholipase D (lyso-PLD). Although the lyso-PLD substrate lysophosphatidylcholine (LPC) was not detected in CSF, lyso-PLD activity and an approximately 120-kDa autotaxin protein were detected in CSF. On the other hand, LPC but not lyso-PLD activity was detected in the conditioned medium of a PC12 cell culture without CSF. Among neural cells examined, leptomeningeal cells expressed the highest lyso-PLD activity and autotaxin protein. These results suggest that leptomeningeal cells may work as one of the sources for autotaxin, which may play a critical role in LPA production and thereby regulate axonal and neurite morphological change.
Automatic Subcortical Segmentation Using a Contextual Model (2008)

Automatically segmenting subcortical structures in brain im ages has the potential to greatly accelerate drug trials and population studies of disease. Here we propose an automatic subcortical segmentation algorithm using the auto context model. Unlike many segmentation algorithms that separately compute a shape prior and an image appearance model, we develop a framework based on machine learning to learn a unified appearance and context model. We trained our algorithm to segment the hippocampus and tested it on 83 brain MRIs (of 35 Alzheimer's disease patients, 22 with mild cognitive impairment, and 26 normal healthy controls). Using standard distance and overlap metrics, the auto context model method significantly outperformed simpler learning-based algorithms (using AdaBoost alone) and the FreeSurfer system. In tests on a public domain dataset designed to validate segmentation [1], our new algorithm also greatly improved upon a recently-proposed hybrid discriminative/generative approach [2], which was among the top three that performed comparably in a recent head-to-head competition.
An Anti-gp41 Human Monoclonal Antibody That Enhances HIV-1 Infection in the Absence of Complement (1994)

B lymphocytes from tonsillar tissue of an asymptomatic HIV-1-seropositive subject were transformed with Epstein-Barr virus (EBV) and tested for the production of HIV-1-specific antibodies by ELISA, using purified HIV-1SF2.2F11, a monoclonal antibody derived from a transformed line, is of the IgG1 subclass and recognizes an epitope in the conserved region of the envelope transmembrane glycoprotein gp41, which is expressed on the surface of HIV-infected T cells. The antibody does not mediate the lysis of infected T cells in antibody-dependent cellular cytotoxicity (ADCC) assays and does not neutralize the infectivity of HIV-1SF2 or the homologous isolate HIV-1TT2.2F11 appears to be the first anti-gp41 human monoclonal antibody that enhances the infectivity of an HIV-1 strain (i.e., SF128A) in the absence of complement.
Fairness via source throttling (2010)

Cores in a chip-multiprocessor (CMP) system share multiple hardware resources in the memory subsystem. If resource sharing is unfair, some applications can be delayed significantly while others are unfairly prioritized. Previous research proposed separate fairness mechanisms in each individual resource. Such resource-based fairness mechanisms implemented independently in each resource can make contradictory decisions, leading to low fairness and loss of performance. Therefore, a coordinated mechanism that provides fairness in the entire shared memory system is desirable. This paper proposes a new approach that provides fairness in the entire shared memory system , thereby eliminating the need for and complexity of developing fairness mechanisms for each individual resource. Our technique, Fairness via Source Throttling (FST), estimates the unfairness in the entire shared memory system. If the estimated unfairness is above a threshold set by system software, FST throttles down cores causing unfairness by limiting the number of requests they can inject into the system and the frequency at which they do. As such, our source-based fairness control ensures fairness decisions are made in tandem in the entire memory system. FST also enforces thread priorities/weights, and enables system software to enforce different fairness objectives and fairness-performance tradeoffs in the memory system. Our evaluations show that FST provides the best system fairness and performance compared to four systems with no fairness control and with state-of-the-art fairness mechanisms implemented in both shared caches and memory controllers.
Geo-registration and mosaic of UAV video for quick-response to forest fire disaster (2007)

UAV Video is rapidly emerging as a widely used source of imagery for many applications in recent years. This paper presents our research on the UAV video processing system for the purpose of fire surveillance, which include: (1) UAV video stream processing. This step involves three aspects: decoding, re-sampling and matching. Microsoft(R) DirectX(R) technology is used to decode highly compressed video stream and re-sampled them into still video frame based on the time base and rate of UAV navigation sensor. One feature-based image-matching algorithm is developed to quickly obtain Tie points for latter calibration operation. (2) UAV system orientation. This step also involves three aspects: Camera IOP, Boresight Alignment and bundle adjustment. TSAI's two-stage technique is used to obtain initial camera focus length <i>f</i>, distortion coefficients <i>k</i><sub>1</sub> and six Exterior Of Parameter (EOP) for one selected video image. Meanwhile, the Boresight Matrix is deduced by the comparison of GPS/INS derived parameters with solved EOPs. Further more, all parameters including EOPs of all re-sampled video images and camera IOP are optimally estimated based on developed bundle adjustment algorithm. (3) UAV Video geo-registration and mosaic. All re-sampled video frames are geo-registered into uniform geo-reference coordinate frame vice Classic photogrammetric orthorectification model and merge with each other with developed mosaic algorithm. The results demonstrated that the geo-accuracy of mosaic image generated from UAV video can achieve 1-2 pixels in planimetry and its combination with GIS-supported data for fast response to time-critical event, e.g., forest fire, is descried.
Kallikrein-related peptidase 6 regulates epithelial-to-mesenchymal transition and serves as prognostic biomarker for head and neck squamous cell carcinoma patients (2015)

In summary, detection of low KLK6 expression in primary tumors represents a promising tool to stratify HNSCC patients with high risk for treatment failure. These patients might benefit from restoration of KLK6 expression or pharmacological targeting of signaling pathways implicated in EMT.
Efficacy and tolerability of memantine in patients with dementia syndrome. A double-blind, placebo controlled trial. (1991)

The efficacy and tolerability of memantine (1-amino-3,5-dimethyl-adamantane hydrochloride, Akatinol Memantine; CAS 41100-52-1) was investigated in a double-blind, randomized clinical study versus placebo in 66 patients aged between 65 and 80 years predominantly suffering from mild to moderate vascular dementia. The target variables assessed were the baseline differences of the Sandoz Clinical Assessment Geriatric scale (SCAG) and Syndrom-Kurz-Test (SKT) total scores and the total time required in the subtests of Activity of Daily Living tests (ADL). Additional parameters assessed were the physician's global impression, the Mini Mental State Evaluation (MMSE), the Tapping and Trace tests for fine motor rating and the quality in performing the ADL tests. Adverse drug effects were recorded by DOTES/TWIS. 59 of the 66 patients included in the study terminated the trial (29 in the placebo and 30 in the memantine group). For the baseline differences of the SCAG total score a statistically significant improvement was observed already after 14 days of memantine treatment as compared to placebo. After 42 days this difference was still more pronounced and highly significant. Significant improvements after 14 and 42 days of memantine treatment could also be demonstrated for the SCAG subscales cognitive disturbances, lack of drive, emotional disturbances, social behaviour and somatic disturbances. Additionally, the efficacy of the drug could be confirmed by the SKT and ADL tests. Particularly striking in the ADL tests was the considerable improvement achieved in the quality of performing the tasks under memantine treatment.(ABSTRACT TRUNCATED AT 250 WORDS)
Structure of two pectate lyase genes from Erwinia chrysanthemi EC16 and their high-level expression in Escherichia coli (1986)

The pelB and pelE genes from Erwinia chrysanthemi EC16, which encode different pectate lyase enzymes, were sequenced and expressed at a high level in Escherichia coli. The genes possessed little similarity to each other in 5' signal regions, signal peptide sequences, coding sequences, or 3' noncoding regions. Both genes contained their own promoters as well as sequences 3' to the coding regions with considerable secondary structure which may function as rho-independent transcriptional termination signals. High-level expression plasmids were constructed with both genes, which led to 20% or more of E. coli cellular protein. The pectate lyases were secreted efficiently to the periplasm and, to a lesser extent, the culture medium. The mature proteins in E. coli periplasmic fractions were obtained in milligram amounts and high purity with a single-column affinity purification method. E. coli cells which produced high amounts of the pelE protein macerated potato tuber tissue as efficiently as E. chrysanthemi EC16 cells but cells producing high amounts of the pelB protein were less effective. Thus, the pelE gene product is an important pathogenicity factor which solely enables E. coli to cause a soft-rot disease on potato tuber tissue under laboratory conditions.
Cloning and expression of a cDNA for the human prostanoid FP receptor. (1994)

A cDNA clone coding for a functional human prostanoid IP receptor has been isolated from a lung cDNA library. The human IP receptor consists of 386 amino acid residues with a predicted molecular mass of 40,961, and has the seven putative transmembrane domains characteristic of G-protein-coupled receptors. Challenge of Xenopus oocytes co-expressing the IP receptor and the cystic fibrosis transmembrane conductance regulator (cAMP-activated Cl- channel) with the stable prostacyclin analog iloprost resulted in specific inward Cl- currents, demonstrating that the cDNA encoded a functional IP prostanoid receptor coupled to elevation in cAMP. Radioreceptor binding studies using membranes prepared from mammalian COS cells transfected with the IP receptor cDNA showed that the rank order of potency for prostaglandins and prostaglandin analogs in competition for [3H]iloprost specific binding sites was as predicted for the IP receptor, with iloprost >> carbacyclin >> prostaglandin (PG) E2 > PGF 2 alpha = PGD2 = U46619. Northern blot analysis showed that IP mRNA was most abundantly expressed in kidney, with lesser amounts detected in lung and liver. In summary, we have cloned and expressed a cDNA for the human prostanoid IP receptor that is functionally coupled to a signaling pathway involving stimulation of intracellular cAMP production.
Catalytic asymmetric fluorinations (2006)

The appearance of structurally diverse fluorinating reagents displaying a large spectrum of reactivity has been critical to the development of the catalytic asymmetric fluorination processes known to date. In this article, we discuss how this area of research emerged and which strategies have allowed for the successful development of both nucleophilic and electrophilic catalytic enantioselective fluorinations. We also present the fundamental understanding of catalytic activity and enantioselectivity for the most efficient processes and highlight the first synthetic application with the preparation of a complex fluorinated target.
Deposition of copper films by an alternate supply of CuCl and Zn (1997)

Deposition of copper thin films by an alternate supply of CuCl and Zn was examined. Due to a reversible dissolution of Zn into the Cu film, no self-limiting growth characteristic for the atomic layer epitaxy method could be achieved. The resulting films contained about 3 at. % zinc while chlorine residue contents were below 0.5 at. %. The films were polycrystalline consisting of rather coarse grains.
CNS Changes in DRPLA with Dementia and Personality Changes: CT, MR and SPECT Findings (1993)

CNS changes in a case of DRPLA associated with dementia and personality changes were observed by CT, MR and SPECT. Brain CT and MR of the patient revealed progressive cortical atrophy which was recognized in parallel with the clinical course of the progression of dementia and personality changes. SPECT using 123I-iodoamphetamine (IMP) disclosed a diffuse low perfusion of the cerebral cortex, especially in the frontal and temporal lobes. These findings suggest that the dementia and personality changes in this case might be concerned with a dysfunction of the cerebral cortex.
Hantzsch-type dihydropyridine hypotensive agents (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHantzsch-type dihydropyridine hypotensive agentsBernard Loev, Marjorie M. Goodman, Kenneth M. Snader, Ralph Tedeschi, and Edward MackoCite this: J. Med. Chem. 1974, 17, 9, 956–965Publication Date (Print):September 1, 1974Publication History Published online1 May 2002Published inissue 1 September 1974https://pubs.acs.org/doi/10.1021/jm00255a010https://doi.org/10.1021/jm00255a010research-articleACS PublicationsRequest reuse permissionsArticle Views2652Altmetric-Citations301LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Serodiagnosis of scrub typhus with antigens immobilized on nitrocellulose sheet (1989)

This study was designed to develop a simple method for serodiagnosis of scrub typhus. The basis of the method is detection of anti-Rickettsia tsutsugamushi antibody in patient serum by reaction with antigens dot blotted on a nitrocellulose sheet (NCS). The final evaluation of the reaction is performed by observing the color intensity which develops as a result of sequential treatments of the NCS with peroxidase-conjugated anti-human immunoglobulin G or immunoglobulin M antibody and with the substrate of the enzyme. After various trials, we found that the best results were obtained by using a purified antigen which adhered to an NCS at 0.2 to 2 micrograms of protein per dot and a test serum diluted 1,000- to 4,000-fold. Under these conditions, almost all antibody-positive sera showed a distinct color at the dot on the NCS, so that a positive reaction could be distinguished by the naked eye from a negative reaction with antibody-negative sera, which developed only a faint color. A comparison of the results of screening of antibody-positive and -negative sera by this method and the immunofluorescence test showed that both methods produced similar results. From these results, it is concluded that this dot immunoassay can be useful for the serodiagnosis of scrub typhus.
Molecular Cloning and Functional Characterization of a Lepidopteran Insect β4-N-Acetylgalactosaminyltransferase with Broad Substrate Specificity, a Functional Role in Glycoprotein Biosynthesis, and a Potential Functional Role in Glycolipid Biosynthesis (2004)

A degenerate PCR approach was used to isolate a lepidopteran insect cDNA encoding a beta4-galactosyl-transferase family member. The isolation and initial identification of this cDNA was based on bioinformatics, but its identification as a beta4-galactosyltransferase family member was experimentally confirmed. The newly identified beta4-galactosyltransferase family member had unusually broad donor and acceptor substrate specificities in vitro, as transferred galactose, N-acetylglucosamine, and N-acetylgalactosamine to carbohydrate, glycoprotein, and glycolipid acceptors. However, the enzyme preferentially utilized N-acetylgalactosamine as the donor for all three acceptors, and its derived amino acid sequence was closely related to a known N-acetylgalactosaminyltransferase. These data suggested that the newly isolated cDNA encodes a beta4-N-acetylgalactosaminyltransferase that functions in insect cell glycoprotein biosynthesis, glycolipid biosynthesis, or both. The remainder of this study focused on the role of this enzyme in N-glycoprotein biosynthesis. The results showed that the purified enzyme transferred N-acetylgalactosamine, but no detectable galactose or N-acetylglucosamine, to a synthetic N-glycan in vitro. The structure of the reaction product was confirmed by chromatographic, mass spectroscopic, and nuclear magnetic resonance analyses. Co-expression of the new cDNA product in insect cells with an N-glycoprotein reporter showed that it transferred N-acetylgalactosamine, but no detectable galactose or N-acetylglucosamine, to this N-glycoprotein in vivo. Confocal microscopy showed that a GFP-tagged version of the enzyme was localized in the insect cell Golgi apparatus. In summary, this study demonstrated that lepidopteran insect cells encode and express a beta4-N-acetylgalactosaminyltransferase that functions in N-glycoprotein biosynthesis and perhaps in glycolipid biosynthesis, as well. The isolation and characterization of this gene and its product contribute to our basic understanding of insect protein N-glycosylation pathways and to the growing body of evidence that insects can produce glycoproteins with complex N-glycans.
Absorption enhancement using photonic crystals for silicon thin film solar cells (2009)

We propose a design that increases significantly the absorption of a thin layer of absorbing material such as amorphous silicon. This is achieved by patterning a one-dimensional photonic crystal (1DPC) in this layer. Indeed, by coupling the incident light into slow Bloch modes of the 1DPC, we can control the photon lifetime and then, enhance the absorption integrated over the whole solar spectrum. Optimal parameters of the 1DPC maximize the integrated absorption in the wavelength range of interest, up to 45% in both S and P polarization states instead of 33% for the unpatterned, 100 nm thick amorphous silicon layer. Moreover, the absorption is tolerant with respect to fabrication errors, and remains relatively stable if the angle of incidence is changed.