gebhart/patrepeval huggingface dataset:
Post-transcriptional Regulation of Endothelial Nitric-oxide Synthase by an Overlapping Antisense mRNA Transcript (2004)

Endothelial nitric-oxide synthase (eNOS) mRNA levels are abnormal in diseases of the cardiovascular system, but changes in gene expression cannot be accounted for by transcription alone. We found evidence for the existence of an antisense mRNA (sONE) that is derived from a transcription unit (NOS3AS) on the opposite DNA strand from which the human eNOS (NOS3) mRNA is transcribed at human chromosome 7q36. The genes are oriented in a tail-to-tail configuration, and the mRNAs encoding sONE and eNOS are complementary for 662 nucleotides. The mRNA for sONE could be detected in a variety of cell types, both in vivo and in vitro, but not vascular endothelial cells. In contrast, expression of eNOS is highly restricted to vascular endothelium. Most surprisingly, interrogation of transcriptional events across NOS3/NOS3AS genomic regions, using single- and double-stranded probes for nuclear run-off analyses and chromatin immunoprecipitation-based assessments of RNA polymerase II distribution, indicated that NOS3 and NOS3AS gene transcription did not correlate with steady-state mRNA levels. We found strong evidence supporting a role for NOS3AS in the post-transcriptional regulation of NOS3 expression. RNA interference-mediated inhibition of sONE expression in vascular smooth muscle cells increased eNOS expression. Overexpression of sONE in endothelial cells blunted eNOS expression. Finally, the histone deacetylase inhibitor trichostatin A is known to regulate the expression of eNOS via a post-transcriptional mechanism. We found that trichostatin A treatment of vascular endothelial cells increased expression of sONE mRNA levels prior to the observed decrease in eNOS mRNA expression. Taken together, these results indicate that an antisense mRNA (sONE) participates in the post-transcriptional regulation of eNOS and provide a newer model for endothelial cell-specific gene expression.
Evaluation of Immunoglobulin M (IgM) and IgG Enzyme Immunoassays in Serologic Diagnosis of West Nile Virus Infection (2000)

ABSTRACT A unique urban encephalitis epidemic in Romania signaled the emergence of neurological infection due to West Nile (WN) virus as a novel public health threat in Eastern Europe and provided an opportunity to evaluate patterns of immunoglobulin G (IgG) and IgM reactivity in IgM capture and IgG enzyme-linked immunosorbent assays (ELISAs). WN virus infection was diagnosed serologically in 236 of 290 patients from whom acute serum or cerebrospinal fluid (CSF) samples were available. In 37% of serum samples and in 25% of CSF samples collected in the first week of illness, anti-WN virus IgM antibody was detected in the absence of virus-specific IgG. The switch to an IgG antibody response occurred after 4 to 5 days of illness and earlier in CSF than in serum. A specific humoral immune response was detected in the CSF before the serum in some patients for whom paired CSF and serum samples from the same day were available. IgM antibody in convalescent serum samples persisted beyond 2 months after the onset of illness in more than 50% of patients. ELISA optical density values and antibody concentrations were well correlated for both IgM and IgG immunoassays. Anti-WN virus IgM antibody in acute-phase samples did not cross-react significantly with flaviviruses in other antigenic groups.
Increases in Ductal Carcinoma In Situ (DCIS) of the Breast in Relation to Mammography: A Dilemma (1997)

The increased use of screening mammography has resulted in a marked increase in detected cases of ductal carcinoma in situ (DCIS) of the breast since the early 1980s. In 1993, there were an estimated 23,275 newly diagnosed cases of DCIS in the United States, of which 4,676 were in women aged 40-49. DCIS accounted for 14.7% of all newly diagnosed breast cancers in women aged 40-49 in 1993, and perhaps 40% of all mammographically detected breast cancers in this age group are DCIS. Among women aged 40-49, an estimated 1,890 mastectomies and 2,707 lumpectomies (with or without radiation) were performed for DCIS in 1993. There is an urgent need to better understand the relationship of mammographically detected DCIS to invasive and potentially life-threatening breast cancer. Better information about the appropriate treatment of DCIS is also needed to reduce the confusion and uncertainty many women and their physicians currently experience in the face of a DCIS diagnosis. For the present, women considering screening mammography should be told the likelihood of being diagnosed with DCIS and that only some DCIS cases may be clinically significant but almost all will be treated surgically.
Contribution of a Urinary Antigen Assay (Binax NOW) to the Early Diagnosis of Pneumococcal Pneumonia (2004)

We evaluated the usefulness of a rapid urinary antigen test (Binax NOW; Binax) to detect Streptococcus pneumoniae for the early diagnosis of community-acquired pneumococcal pneumonia (PP) in 220 nonseverely immunosuppressed adults. We compared results of this test with those of sputum Gram staining. The rapid urinary antigen test showed limited sensitivity (65.9%; 95% confidence interval [CI], 51.4-80.4) but high specificity (100%; 95% CI, 99.7-100) for diagnosing PP. The test was more sensitive for patients with versus those without high-risk pneumonia (94% vs. 63%; P<.001) and for patients without versus those with demonstrative results of a sputum Gram stain (97% vs. 55%; P<.001), and it tended to be more sensitive for patients with versus those without bacteremic PP (92% vs. 74%; P=NS). Rapid urinary antigen testing permitted early diagnosis of PP in 26% more patients than did Gram staining but missed 22% of the rapid diagnoses initially identified by Gram staining. On the basis of our results, a sequential approach is proposed, with reservation of urinary antigen testing for high-risk patients for whom demonstrative results of a sputum Gram stain are unavailable.
N-Acylethanolamines: Formation and Molecular Composition of a New Class of Plant Lipids1 (1998)

Recently, the biosynthesis of an unusual membrane phospholipid, N-acylphosphatidylethanolamine (NAPE), was found to increase in elicitor-treated tobacco (Nicotiana tabacum L.) cells (K.D. Chapman, A. Conyers-Hackson, R.A. Moreau, S. Tripathy [1995] Physiol Plant 95: 120-126). Here we report that before induction of NAPE biosynthesis, N-acylethanolamine (NAE) is released from NAPE in cultured tobacco cells 10 min after treatment with the fungal elicitor xylanase. In radiolabeling experiments [14C]NAE (labeled on the ethanolamine carbons) increased approximately 6-fold in the culture medium, whereas [14C]NAPE associated with cells decreased approximately 5-fold. Two predominant NAE molecular species, N-lauroylethanolamine and N-myristoylethanolamine, were specifically identified by gas chromatography-mass spectrometry in lipids extracted from culture medium, and both increased in concentration after elicitor treatment. NAEs were found to accumulate extracellularly only. A microsomal phospholipase D activity was discovered that formed NAE from NAPE; its activity in vitro was stimulated about 20-fold by mastoparan, suggesting that NAPE hydrolysis is highly regulated, perhaps by G-proteins. Furthermore, an NAE amidohydrolase activity that catalyzed the hydrolysis of NAE in vitro was detected in homogenates of tobacco cells. Collectively, these results characterize structurally a new class of plant lipids and identify the enzymatic machinery involved in its formation and inactivation in elicitor-treated tobacco cells. Recent evidence indicating a signaling role for NAPE metabolism in mammalian cells (H.H.O. Schmid, P.C. Schmid, V. Natarajan [1996] Chem Phys Lipids 80: 133-142) raises the possibility that a similar mechanism may operate in plant cells.
Crystal and molecular structure of a naturally occurring dinucleoside monophosphate. Uridylyl-(3'-5')-adenosine hemihydrate. Conformational rigidity of the nucleotide unit and models for polynucleotide chain folding (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCrystal and molecular structure of a naturally occurring dinucleoside monophosphate. Uridylyl-(3'-5')-adenosine hemihydrate. Conformational rigidity of the nucleotide unit and models for polynucleotide chain foldingJ. Rubin, T. Brennan, and M. SundaralingamCite this: Biochemistry 1972, 11, 16, 3112–3128Publication Date (Print):August 1, 1972Publication History Published online1 May 2002Published inissue 1 August 1972https://pubs.acs.org/doi/10.1021/bi00766a027https://doi.org/10.1021/bi00766a027research-articleACS PublicationsRequest reuse permissionsArticle Views83Altmetric-Citations111LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Phase II trial of 96-hour paclitaxel plus oral estramustine phosphate in metastatic hormone-refractory prostate cancer. (1997)

The combination of EMP and 96-hour paclitaxel is an active regimen for patients with HRPC. These results further support the therapeutic strategy of combining agents that impair microtubule function by complementary mechanisms.
Dry eye disease: A review of diagnostic approaches and treatments (2014)

Dry eye (DE) is a common ocular disease that results in eye discomfort, visual disturbance and substantially affects the quality of life. It has a multifactorial etiology involving tear film instability, increased osmolarity of the tear film and inflammation of the ocular surface with potential damage to the ocular surface. This review discusses the classification, diagnostic approaches and treatments of DE.
Hydraulic Fracturing - Fracture Flow Capacity vs Well Productivity (1958)

Published in Petroleum Transactions, AIME, Volume 213, 1958, pages 91–95. Abstract In the past few years much consideration has been given to the evaluation of the effect of hydraulic fracturing on the productivity of wells. Generally, these studies included the evaluation of fracturing materials, fracture extension and formation damage due to the use of various fracturing fluids. Only little consideration has been given to the characteristics, and in particular the flow capacity, of the fracture itself and its effect on well productivity. This paper presents the results of laboratory investigations pointed toward the evaluation of the efficiency of various fractures with special emphasis on the flow capacity of these fractures. Data presented in this paper are the results of both an electrical model study and physical testing. Under consideration are (1) effect of overflush, (2) premature production of well after treatment,(3) "tailing-in" with coarse sand near the end of the treatment,(4) effect of propping agent size and concentration, (5) reduction in effective fracture permeability caused by formation caused by formation fines, silt and clays, and (6) effect of various fluids on formation strength and competency. The results of this investigation indicate that the flow capacity of a fracture is affected by any or all of the various parameters mentioned above. The authors believe that a better understanding and utilization of these factors should result in more efficient formation fracturing. Introduction Hydraulic fracturing has become almost a standard practice of many companies for stimulating production from old and new wells. Although most companies utilize this service, techniques of application vary widely between companies and areas. Probably too often when a well in an area responds favorably to a particular technique all future wells in the same area are treated in a similar manner. Possibly a modification of the technique would result in a further production increase. Variables, of which many are extremely difficult to evaluate from field results, hamper the selection of procedure changes.
Directed Evolution of Sortase A Mutants with Altered Substrate Selectivity Profiles (2011)

The ligation of two polypeptides in a chemoselective manner by the bacterial transpeptidase sortase A has become a versatile tool for protein engineering approaches. When sortase-mediated ligation is used for protein semisynthesis, up to four mutations resulting from the strict requirement of the LPxTG sorting motif are introduced into the target protein. Here we report the directed evolution of a mutant sortase A that possesses broad substrate selectivity. A phage-display screen of a mutant sortase library that was randomized in the substrate recognition loop was used to isolate this mutant. The altered substrate selectivity represents a gain-of-function that was exploited for the traceless semisynthesis of histone H3. Our report is a decisive step toward a platform of engineered sortases with distinct ligation properties that will conceivably allow for more versatile assemblies of modified proteins in biotechnological approaches.
Activation of the alternative pathway of complement by monoclonal lambda light chains in membranoproliferative glomerulonephritis. (1992)

Immunopathological evidence suggests that activation of the alternative pathway of complement (AP) is involved in membranoproliferative glomerulonephritis (MPGN) and in immunoglobulin A nephropathy. In this report we describe an AP dysfunction-associated factor that was isolated from the serum and urine of a patient with hypocomplementemic MPGN. Extensive glomerular deposits of C3, properdin, and of the terminal complement components were observed in the kidney of the patient. In her serum the AP hemolytic activity was virtually absent. When mixed with fresh normal serum, the patient's serum induced a 96% C3 conversion during a 30-min incubation at +37 degrees C. This activity was found to be due to a circulating factor that by immunochemical characterization proved to be a 46-kD monoclonal immunoglobulin lambda light (L) chain dimer (lambda L). Purified lambda L, but not control lambda or kappa L chains from patients with L chain disease, activated the AP in a dose- and ionic strength-dependent manner. Functionally, lambda L was differentiated from C3 nephritic factor (an autoantibody against the AP C3 convertase, C3bBb) by its inability to bind to and stabilize the C3bBb enzyme. Instead, lambda L was observed to interact directly with the AP control factor H. Thus, lambda L represents a novel type of immunoglobulin-related AP-activating factor with the capacity to initiate alternative complement pathway activation in the fluid phase.
Fabrication of ridge waveguides: a new solgel route (1998)

Passive ridge waveguides can be deposited on silicon by a solvent-assisted lithographic process incorporating simple mask technology and photosensitive solgel-derived glasses. Thick films (~4 mum) are dip coated in one step, and channel waveguides and power splitters are imprinted in them by UV light through appropriate masks. Unexposed regions of the glass are removed by soaking of the films in n-propanol. The remaining ridges are then treated at 200 degrees C and planarized with a solgel cladding layer. Circular mode profiles are observed from ridge guides covered with the cladding. The waveguides are characterized with scanning electron microscopy, atomic force microscopy, surface profilometry, ellipsometry, and fiber end coupling. Overall, the procedure is simple and reproducible and leads to waveguides with low loss, of the order of 0.13 dB/cm.
ECG-synchronized cardiac MR imaging: method and evaluation. (1985)

An electrocardiographic (ECG) sensing and gating device compatible with a 0.35-tesla (T) magnetic resonance (MR) imager has been developed and used to produce 802 MR images of the heart in 30 patients. The instrument consists of an isolated acquisition module, an electrically floating preamplifier, and a monitor gating module. Two spin-echo images were acquired for each of five, 0.7-cm thick, transaxial sections from the base to the apex of the heart during each ECG-synchronized imaging run. Image quality was assessed in a blind study by two investigators, on a scale from 0 to 3, as diagnostic [2-3] or nondiagnostic [0-1]. There was agreement in 91.4% of their assessments of diagnostic images (68.1% of the images studied). Resolution of heart anatomy on the MR images was adversely affected by prolonged spin-echo time delay, imaging in late diastole, image acquisition at the cardiac apex, irregular triggering, and artifacts. The synchronization of gradient pulses to the ECG at 0.35 T appears safe for patients, permits diagnostic resolution of images, allows image acquisition at distinct points during the cardiac cycle, and enables monitoring of patients during imaging.
Neuropathology of Pick’s disease (2001)

The author reviews the gross, microscopic, and biochemical pathology associated with classic Pick's disease, as defined by Constantinidis' Type A Pick's disease. This is contrasted with other Pick's disease subtypes, including Constantinidis' Type B (corticobasal degeneration) and Type C (dementia lacking distinctive histology).
The chemistry of several novel bioconversion lignins (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe chemistry of several novel bioconversion ligninsWolfgang G. Glasser, Charlotte A. Barnett, Peter C. Muller, and Kyosti V. SarkanenCite this: J. Agric. Food Chem. 1983, 31, 5, 921–930Publication Date (Print):September 1, 1983Publication History Published online1 May 2002Published inissue 1 September 1983https://pubs.acs.org/doi/10.1021/jf00119a001https://doi.org/10.1021/jf00119a001research-articleACS PublicationsRequest reuse permissionsArticle Views670Altmetric-Citations87LEARN 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
Tradeoff between PAPR reduction and decoding complexity in transformed OFDM systems (2005)

It is known that in an OFDM system using Hadamard transform or phase alteration before the IDFT operation can reduce the peak-to-average power ratio (PAPR). Both these techniques can be viewed as constellation preceding for PAPR reduction. In general, using non-diagonal transforms, like Hadamard transform, increases the ML decoding complexity. In this paper we propose the use of block-IDFT matrices and show that appropriate block-IDFT matrices give lower PAPR as well as lower decoding complexity compared to using Hadamard transform. Moreover, we present a detailed study of the tradeoff between PAPR reduction and the ML decoding complexity when using block-IDFT matrices with various sizes of the blocks
The audio-graphical interface to a personal integrated telecommunications system (1984)

Thesis (M.S.V.S.)--Massachusetts Institute of Technology, Dept. of Architecture, 1984.
Discovery of 2-[(2,4-Dichlorophenyl)amino]- N -[(tetrahydro- 2 H -pyran-4-yl)methyl]-4-(trifluoromethyl)- 5-pyrimidinecarboxamide, a Selective CB2 Receptor Agonist for the Treatment of Inflammatory Pain (2007)

Selective CB2 receptor agonists are promising potential therapeutic agents for the treatment of inflammatory and neuropathic pain. A focused screen identified a pyrimidine ester as a partial agonist at the CB2 receptor with micromolar potency. Subsequent lead optimization identified 35, GW842166X, as the optimal compound in the series. 35 has an oral ED50 of 0.1 mg/kg in the rat FCA model of inflammatory pain and was selected as a clinical candidate for this indication.
Nonpeptidic Inhibitors of Human Leukocyte Elastase. 2. Design, Synthesis, and in vitro Activity of a Series of 3-Amino-6-aryl-2-oxopyridyl Trifluoromethyl Ketones (1994)

A series of potent nonpeptidic inhibitors of the enzyme human leukocyte elastase (HLE) is reported. These inhibitors contain a 3-amino-2-pyridone ring as a central template in which the pyridone carbonyl and 3-position NH group are thought to form important hydrogen bonding interactions with the Val-216 residue of HLE. Substitution of the 6-position of the pyridone ring by various alkyl and aryl groups was found to afford increases in the in vitro potency of these inhibitors. A 6-position phenyl group, compound 10f, was found to result in a large increase in binding affinity, which was not obtained when the phenyl group was placed in either the 4- or 5-position of the molecule. Compound 10f was found to have good selectivity for HLE over other proteolytic enzymes, with the exception of bovine pancreatic chymotrypsin (BPC). Substitution of the 6-phenyl group in these molecules was found to decrease binding affinity for BPC without adversely affecting affinity for HLE.
Phosphorylation of SMC1 by ATR is required for desferrioxamine (DFO)-induced apoptosis (2011)

DNA damage signaling pathways are initiated in response to chemical reagents and radiation damage, as well as in response to hypoxia. It is implicated that structural maintenance of chromosomes 1 (SMC1) is not only a component of the cohesion complex but also facilitates the activation of DNA damage checkpoint proteins. Here, we studied the mechanism of DNA damage checkpoint activated by ATR-SMC1 pathway when cells are treated with desferrioxamine (DFO), a hypoxia-mimetic reagent. We show that DFO treatment induces phosphorylation of SMC1 at Ser966, NBS1 at Ser343, Chk1 at Ser317, Chk2 at Thr68, and p53 at Ser15. Among these sites, phosphorylation of SMC1, NBS1, and Chk1 by DFO are mediated by ATR as it is greatly reduced in both ATR-deficient human fibroblasts and HCT116 human colon cancer cells in which ATR is heterozygously mutated, whereas these proteins are phosphorylated in cells deficient for ATM and DNA-PKcs. DFO-induced apoptosis is decreased in ATR-mutant HCT116 cells, although p53 is normally activated in those cells. Expression of SMC1 S966A in which Ser966 is substituted to Ala attenuates apoptosis and phosphorylation of Chk1 at Ser317 after DFO treatment, although levels of HIF1α are not significantly changed. These results suggest that DFO induces apoptosis through the ATR-SMC1 arm of the pathway.