gebhart/patrepeval huggingface dataset:
Tau as a potential novel therapeutic target in ischemic stroke (2009)

Stroke is associated with high mortality and major disability burdens worldwide, but there are few effective and widely available therapies. Tau plays an important role in promoting microtubule assembly and stabilizing microtubule networks with phosphorylation regulating these functions. Based on the "ischemia-reperfusion theory" of Alzheimer's disease, some previous studies have focused on the relationship of tau and Alzheimer lesions in experimental brain ischemia. Thus, we hypothesize that the alterations in phosphorylation of tau are critical to microtubule dynamics and metabolism, and contribute to the pathophysiologic mechanisms during brain ischemia and/or reperfusion processes. We infer that regulation of phosphorylation of tau may be considered as a potential new therapeutic target in ischemic stroke.
An Illustrated Review of Early Pancreas Development in the Mouse (2007)

Pancreas morphogenesis and cell differentiation are highly conserved among vertebrates during fetal development. The pancreas develops through simple budlike structures on the primitive gut tube to a highly branched organ containing many specialized cell types. This review presents an overview of key molecular components and important signaling sources illustrated by an extensive three-dimensional (3D) imaging of the developing mouse pancreas at single cell resolution. The 3D documentation covers the time window between embryonic days 8.5 and 14.5 in which all the pancreatic cell types become specified and therefore includes gene expression patterns of pancreatic endocrine hormones, exocrine gene products, and essential transcription factors. The 3D perspective provides valuable insight into how a complex organ like the pancreas is formed and a perception of ventral and dorsal pancreatic growth that is otherwise difficult to uncover. We further discuss how this global analysis of the developing pancreas confirms and extends previous studies, and we envisage that this type of analysis can be instrumental for evaluating mutant phenotypes in the future.
Duloxetine Inhibits Effects of MDMA (“Ecstasy") In Vitro and in Humans in a Randomized Placebo-Controlled Laboratory Study (2012)

Clinicaltrials.gov NCT00990067.
Structure of the gene for human uracil—DNA glycosylase and analysis of the promoter function (1994)

The gene for human uracil-DNA glycosylase (UNG) contains 4 exons and has an approximate size of 13 kb. The promoter is very GC rich and lacks a TATA box. Nested deletions of the promoter demonstrated that two SP1 elements and a putative c-MYC element proximal to the transcription initiation region were sufficient to support some 27% of the promoter activity, while a clone that in addition contained the elements E2F/SP1/CCAAT increased expression to almost 90% of the full-length construct. A region upstream of these elements appears to exert a negative control function.
Quantitative Serum Glycomics of Esophageal Adenocarcinoma and Other Esophageal Disease Onsets (2009)

Aberrant glycosylation has been implicated in various types of cancers and changes in glycosylation may be associated with signaling pathways during malignant transformation. Glycomic profiling of blood serum, in which cancer cell proteins or their fragments with altered glycosylation patterns are shed, could reveal the altered glycosylation. We performed glycomic profiling of serum from patients with no known disease (N = 18), patients with high grade dysplasia (HGD, N = 11) and Barrett's esophagus (N = 5), and patients with esophageal adenocarcinoma (EAC, N = 50) in an attempt to delineate distinct differences in glycosylation between these groups. The relative intensities of 98 features were significantly different among the disease onsets; 26 of these correspond to known glycan structures. The changes in the relative intensities of three of the known glycan structures predicted esophageal adenocarcinoma with 94% sensitivity and better than 60% specificity as determined by receiver operating characteristic (ROC) analysis. We have demonstrated that comparative glycomic profiling of EAC reveals a subset of glycans that can be selected as candidate biomarkers. These markers can differentiate disease-free from HGD, disease-free from EAC, and HGD from EAC. The clinical utility of these glycan biomarkers requires further validation.
Endothelial Nitric Oxide Synthase–Dependent Tyrosine Nitration of Prostacyclin Synthase in Diabetes In Vivo (2006)

There is evidence that reactive nitrogen species are implicated in diabetic vascular complications, but their sources and targets remain largely unidentified. In the present study, we aimed to study the roles of endothelial nitric oxide synthase (eNOS) in diabetes. Exposure of isolated bovine coronary arteries to high glucose (30 mmol/l d-glucose) but not to osmotic control mannitol (30 mmol/l) switched angiotensin II-stimulated prostacyclin (PGI(2))-dependent relaxation into a persistent vasoconstriction that was sensitive to either indomethacin, a cyclooxygenase inhibitor, or SQ29548, a selective thromboxane receptor antagonist. In parallel, high glucose, but not mannitol, significantly increased superoxide and 3-nitrotyrosine in PGI(2) synthase (PGIS). Concurrent administration of polyethylene-glycolated superoxide dismutase (SOD), l-nitroarginine methyl ester, or sepiapterin not only reversed the effects of high glucose on both angiotensin II-induced relaxation and PGI(2) release but also abolished high-glucose-enhanced PGIS nitration, as well as its association with eNOS. Furthermore, diabetes significantly suppressed PGIS activity in parallel with increased superoxide and PGIS nitration in the aortas of diabetic C57BL6 mice but had less effect in diabetic mice either lacking eNOS or overexpressing human SOD (hSOD(+/+)), suggesting an eNOS-dependent PGIS nitration in vivo. We conclude that diabetes increases PGIS nitration in vivo, likely via dysfunctional eNOS.
ISOLATION OF A TUMOR FACTOR RESPONSIBLE FOR ANGIOGENESIS (1971)

Human and animal solid tumors elaborate a factor which is mitogenic to capillary endothelial cells. This factor has been called tumor-angiogenesis factor. The important components of TAF are RNA and protein. It is suggested that blockade of this factor (inhibition of angiogenesis) might arrest solid tumors at a tiny diameter of a few millimeters.
The chemical basis for interfacial activation of monomeric phospholipases A2. Autocatalytic derivatization of the enzyme by acyl transfer from substrate. (1988)

A basic monomeric phospholipase A2 from the venom of the American water moccasin, Agkistrodon piscivorus piscivorus, undergoes Ca2+-dependent, autocatalytic acylation during the course of hydrolysis of both model and natural phospholipid substrates. Acylation occurs at 2 lysine residues, Lys-7 and Lys-10, in the NH2-terminal alpha-helical segment of the enzyme, and when both positions are fully derivatized, the stable bisacylphospholipase A2 becomes a dimer in solution. The acylated enzyme is fully activated toward monomolecular layers of lecithins. Similar studies applied to the monomeric phospholipases A2 from porcine pancreas and from the venom of Agkistrodon contortrix contortrix also showed irreversible activation of the enzymes by substrate with the same kinetic consequences and formation of dimers. Acylation thus enables these enzymes to overcome the lag period observed under such conditions with native monomeric phospholipases, a phenomenon referred to as interfacial activation. Activation of the enzyme by acylation potentiates the phospholipase for interfacial recognition via formation of a dimeric enzyme. The naturally occurring phospholipase A2 dimer from Crotalus atrox venom displays no lag in the hydrolysis of lecithin monolayers nor does it undergo substrate level acylation. These facts support our proposal that dimerization concomitant with acylation is responsible for the large rate enhancements seen in the hydrolysis of aggregated phospholipids by monomeric phospholipases. Our findings demonstrate for the first time a chemical mechanism for interfacial activation of and interfacial recognition by phospholipases A2.
Optic neuritis: chemokine receptor CXCR3 and its ligands (2004)

These data show that the CSF concentration of the CXCR3 ligand CXCL10 is selectively increased in CSF from ON patients, and CXCR3 positive cells are recruited to the subarachnoid space.
Geographic information systems: An introduction (1991)

(1991). Geographic information systems: An introduction. Geocarto International: Vol. 6, No. 1, pp. 46-46.
Human Immunodeficiency Virus Type 1envEvolves toward Ancestral States upon Transmission to a New Host (2006)

Selecting human immunodeficiency virus (HIV) sequences for inclusion within vaccines has been a difficult problem, as circulating HIV strains evolve relentlessly and become increasingly divergent over time. We report an assessment of this divergence from three perspectives: (i) across different hosts as a function of time of infection, (ii) between donors and recipients in known transmission pairs, and (iii) within individual hosts over time in relation to the initially replicating virus and to the deduced ancestral sequence of the intrahost viral population. Surprisingly, we consistently found less divergence between viruses from different individuals sampled in primary infection than in individuals sampled at more advanced stages of illness. Furthermore, longitudinal analysis of intrahost divergence revealed a 2- to 3-year period of evolution toward a common ancestral sequence at the start of infection, indicating that HIV recovers certain ancestral features when infecting a new host. These results have important implications for the study of HIV population genetics and rational vaccine design, including favoring the inclusion of viral gene sequences taken early in infection.
A novel unrestricted center-biased diamond search algorithm for block motion estimation (1998)

The widespread use of block-based interframe motion estimation for video sequence compression in both MPEG and H.263 standards is due to its effectiveness and simplicity of implementation. Nevertheless, the high computational complexity of the full-search algorithm has motivated a host of suboptimal but faster search strategies. A popular example is the three-step search (TSS) algorithm. However, its uniformly spaced search pattern is not well matched to most real-world video sequences in which the motion vector distribution is nonuniformly biased toward the zero vector. Such an observation inspired the new three-step search (NTSS) which has a center-biased search pattern and supports a halfway-stop technique. It is faster on average, and gives better motion estimation as compared to the well-known TSS. Later, the four-step search (4SS) algorithm was introduced to reduce the average case from 21 to 19 search points, while maintaining a performance similar to NTSS in terms of motion compensation errors. We propose a novel unrestricted center-biased diamond search (UCBDS) algorithm which is more efficient, effective, and robust than the previous techniques. It has a best case scenario of only 13 search points and an average of 15.5 block matches. This makes UCBDS consistently faster than the other suboptimal block-matching techniques. This paper also compares the above methods in which both the processing speed and the accuracy of motion compensation are tested over a wide range of test video sequences.
The ClpP Protease of Streptococcus pneumoniae Modulates Virulence Gene Expression and Protects against Fatal Pneumococcal Challenge (2004)

Streptococcus pneumoniae usually colonizes the nasopharynx of humans asymptomatically but occasionally translocates from this niche to the lungs, the brain, and the blood, causing potentially fatal infections. Spread to other host tissues requires a significant morphological change and the expression of virulence factors, such as capsular polysaccharide, and virulence proteins, such as pneumolysin (Ply), PspA, and CbpA. Modulation of the expression of pneumococcal virulence genes by heat shock and by heat shock proteins ClpL and ClpP, as well as the attenuation of virulence of a clpP mutant in a murine intraperitoneal infection model, was demonstrated previously. In this study, we further investigated the underlying mechanism of virulence attenuation by the clpP mutation. The half-lives of the mRNAs of ply and of the first gene of the serotype 2 capsule synthesis locus [cps2A] in the clpP mutant were more than twofold longer than those of the parent after heat shock, suggesting that the mRNA species were regulated posttranscriptionally by ClpP. In addition, the clpP mutant was defective in colonization of the nasopharynx and survival in the lungs of mice after intranasal challenge. The mutant was also killed faster than the parent in the murine macrophage RAW264.7 cell line, indicating that ClpP is required for colonization and intracellular survival in the host. Furthermore, fractionation studies demonstrated that ClpP was translocated into the cell wall after heat shock, and immunization of mice with ClpP elicited a protective immune response against fatal systemic challenge with S. pneumoniae D39, making ClpP a potential vaccine candidate for pneumococcal disease.
T-Shaped Molecular Building Units in the Porous Structure of Ag(4,4‘-bpy)·NO3 (1996)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTT-Shaped Molecular Building Units in the Porous Structure of Ag(4,4'-bpy)·NO3O. M. Yaghi and Hailian LiView Author Information Department of Chemistry and Biochemistry Goldwater Center for Science and Engineering Arizona State University, Tempe, Arizona 85287-1604 Cite this: J. Am. Chem. Soc. 1996, 118, 1, 295–296Publication Date (Web):January 10, 1996Publication History Received12 October 1995Published online10 January 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/ja953438lhttps://doi.org/10.1021/ja953438lrapid-communicationACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views2934Altmetric-Citations614LEARN 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 (2)»Supporting Information Supporting Information SUBJECTS:Anions,Crystal structure,Crystallography,Metals,Silver Get e-Alerts
Fast-SAGD: Half the Wells and 30% Less Steam (2000)

Abstract Numerical simulation that provides history match of a SAGD pilot in a Cold Lake type reservoir may be expanded to include steaming of an offset well. In this theoretical configuration, the offset well is equidepth and parallel to, but 50 metres away, from the SAGD producer. After three years of SAGD operation, steam stimulation of the offset well with concomitant increased steaming of the SAGD injector provides early steam communication between the SAGD steam chest and the offset well. The result is markedly increased rate of production of bitumen and reduced steam-oil ratio. Mindful of such results, laboratory work is being undertaken to verify, and understand these results. We also encourage field-pilot testing of this process.
Flow-injection analysis and real-time detection of RNA bases by surface-enhanced Raman spectroscopy (1990)

Surface-enhanced Raman scattering (SERS) spectroscopy has been successfully interfaced with a flow injection analysis system to detect RNA bases in real time. Four of the major base components of RNA, uracil, cytosine, adenine, and guanine, were introduced into the flow injection system and were mixed with a Ag sol prior to SERS measurements. Several experimental parameters including pH, temperature, flow rate, and tubing materials were examined, and their impact on the SERS spectra is presented here. The feasibility of interfacing flow injection based SERS detection methods with liquid or high-performance liquid chromatography for the detection of individual components in a complex mixture is also assessed.
Exhaled breath analysis for lung cancer. (2013)

Early diagnosis of lung cancer results in improved survival compared to diagnosis with more advanced disease. Early disease is not reliably indicated by symptoms. Because investigations such as bronchoscopy and needle biopsy have associated risks and substantial costs, they are not suitable for population screening. Hence new easily applicable tests, which can be used to screen individuals at risk, are required. Biomarker testing in exhaled breath samples is a simple, relatively inexpensive, non-invasive approach. Exhaled breath contains volatile and non-volatile organic compounds produced as end-products of metabolic processes and the composition of such compounds varies between healthy subjects and subjects with lung cancer. Many studies have analysed the patterns of these compounds in exhaled breath. In addition studies have also reported that the exhaled breath condensate (EBC) can reveal gene mutations or DNA abnormalities in patients with lung cancer. This review has summarised the scientific evidence demonstrating that lung cancer has distinct chemical profiles in exhaled breath and characteristic genetic changes in EBC. It is not yet possible to accurately identify individuals with lung cancer in at risk populations by any of these techniques. However, analysis of both volatile organic compounds in exhaled breath and of EBC have great potential to become clinically useful diagnostic and screening tools for early stage lung cancer detection.
Role of CCR8 and Other Chemokine Pathways in the Migration of Monocyte-derived Dendritic Cells to Lymph Nodes (2004)

Studying the influence of chemokine receptors (CCRs) on monocyte fate may reveal information about which subpopulations of monocytes convert to dendritic cells (DCs) and the migration pathways that they use. First, we examined whether prominent CCRs on different monocyte subsets, CCR2 or CX3CR1, mediated migration events upstream of the accumulation of monocyte-derived DCs in lymph nodes (LNs). Monocytes were labeled and traced by uptake of latex microspheres in skin. Unexpectedly, neither CCR2 nor CX3CR1 were required. However, absence of CCR2 led to an increased labeling of the minor Gr-1int monocyte population, and the number of latex+ DCs that emigrated to LNs was correspondingly increased. Characterization of Gr-1int monocytes revealed that they selectively expressed CCR7 and CCR8 mRNA in blood. CCR7 and CCR8 pathways were used by monocyte-derived DCs during mobilization from skin to LNs. The role of CCR8 in emigration from tissues also applied to human monocyte-derived cells in a model of transendothelial trafficking. Collectively, the data suggest that Gr-1int monocytes may be most disposed to become a lymphatic-migrating DCs. When these monocyte-derived DCs exit skin to emigrate to LNs, they use not only CCR7 but also CCR8, which was not previously recognized to participate in migration to LNs.
A Simple Sequentially Rejective Multiple Test Procedure (1979)

This paper presents a simple and widely ap- plicable multiple test procedure of the sequentially rejective type, i.e. hypotheses are rejected one at a tine until no further rejections can be done. It is shown that the test has a prescribed level of significance protection against error of the first kind for any combination of true hypotheses. The power properties of the test and a number of possible applications are also discussed.
Chromosome 3 Anomalies Investigated by Genome Wide SNP Analysis of Benign, Low Malignant Potential and Low Grade Ovarian Serous Tumours (2011)

Ovarian carcinomas exhibit extensive heterogeneity, and their etiology remains unknown. Histological and genetic evidence has led to the proposal that low grade ovarian serous carcinomas (LGOSC) have a different etiology than high grade carcinomas (HGOSC), arising from serous tumours of low malignant potential (LMP). Common regions of chromosome (chr) 3 loss have been observed in all types of serous ovarian tumours, including benign, suggesting that these regions contain genes important in the development of all ovarian serous carcinomas. A high-density genome-wide genotyping bead array technology, which assayed >600,000 markers, was applied to a panel of serous benign and LMP tumours and a small set of LGOSC, to characterize somatic events associated with the most indolent forms of ovarian disease. The genomic patterns inferred were related to TP53, KRAS and BRAF mutations. An increasing frequency of genomic anomalies was observed with pathology of disease: 3/22 (13.6%) benign cases, 40/53 (75.5%) LMP cases and 10/11 (90.9%) LGOSC cases. Low frequencies of chr3 anomalies occurred in all tumour types. Runs of homozygosity were most commonly observed on chr3, with the 3p12-p11 candidate tumour suppressor region the most frequently homozygous region in the genome. An LMP harboured a homozygous deletion on chr6 which created a GOPC-ROS1 fusion gene, previously reported as oncogenic in other cancer types. Somatic TP53, KRAS and BRAF mutations were not observed in benign tumours. KRAS-mutation positive LMP cases displayed significantly more chromosomal aberrations than BRAF-mutation positive or KRAS and BRAF mutation negative cases. Gain of 12p, which harbours the KRAS gene, was particularly evident. A pathology review reclassified all TP53-mutation positive LGOSC cases, some of which acquired a HGOSC status. Taken together, our results support the view that LGOSC could arise from serous benign and LMP tumours, but does not exclude the possibility that HGOSC may derive from LMP tumours.
Fast optimal pose estimation for matching in two dimensions (1995)

The problem of searching for the occurrence of a model in a scene is a familiar one in object recognition, and has been extensively researched. The model may be present at any pose (i.e. may be translated, scaled and rotated), and may be obscured by clutter in the scene. We consider the search to take place after the model and the scene have been converted to sets of features. The search is then for a pose of the model which produces a close juxtaposition of a significant subset of its features to a subset of the scene features. In this process, trial sets of matches of pairs of model and scene features are assembled, and their geometrical consistency is tested. It is desirable, then, to find a procedure that will check two or more match pairs, produce a meaningful error estimate, will economically handle many match pairs and the incremental addition of new pairs to the set, will incorporate a realistic error function for a useful range of features, and will estimate an optimal pose for a given match set. The paper describes such a procedure for edge features in two dimensions.