gebhart/patrepeval huggingface dataset:
Expression of the gastrin gene in the normal human colon and colorectal adenocarcinoma. (1993)

Gastrin, produced in the G-cells of the gastric antrum and regulating acid secretion in the stomach, also acts as a trophic factor in the gastrointestinal tract. Because of its possible role in colon cell proliferation and differentiation, evidence for its presence in normal colorectal mucosa and adenocarcinoma was sought. Utilizing tumors and matched normal mucosa from 26 patients, mature gastrin and progastrin were studied by immunohistochemistry. In normal colonic mucosal crypts, occasional cells stained concordantly for gastrin, progastrin, and chromogranin A, suggesting that they are of neuroendocrine origin. Adenomatous polyps stained neither for gastrin nor chromogranin A. In 22 of 23 adenocarcinomas, more than 50% of tumor cells stained for gastrin and progastrin. The expected gastrin transcript was demonstrable by polymerase chain reaction and RNase protection in tumors and by polymerase chain reaction in normal mucosa. Its identity was confirmed by sequencing the polymerase chain reaction product. A larger transcript containing Intron II was present in both cancers and normal mucosa but was barely discernible in the gastric antrum. Aberrant expression of gastrin may contribute to deregulated proliferation of many colorectal carcinomas.
Profiling Peptide Adducts of Oxidized N-Acetyldopamine by Electrospray Mass Spectrometry (1997)

Phenolic and catecholamine polymers are common constituents of many biological systems. Cross-linking of polyphenols with other phenols, peptides, proteins and carbohydrates results in the synthesis of complex natural products which are not easily characterized. Electrospray mass spectrometry (ES-MS) and tandem mass spectrometry (ES-MS/MS) were used to identify polymers of oxidized N-acetyldopamine (NADA) and peptide adducts with oxidized NADA. Following incubation with mushroom tyrosinase, NADA adducts of trityrosine were identified. It was not possible to locate the site of NADA binding to this tripeptide. Compounds formed by incubation of N-acetylhistidine and N-acetyllysine with oxidized NADA, previously characterized using classical chemical techniques, were confirmed using ES-MS/MS. The peptide angiotensin (DRVYIHPFHL) was used as a model substrate to determine whether the site(s) to which oxidized NADA bound could be determined. The lot of angiotensin used was contaminated with a peptide of mass 14 u greater than angiotensin, and it was found that the H in position 9 of the contaminant peptide was modified. ES-MS/MS of the angiotensin and the contaminant peptide following incubation with oxidized NADA revealed that the C-terminal aspartic acid was the primary amino acid to which NADA adducts were covalently bound, but other residues were also modified. Femto-molar sensitivity for analysis of complex mixtures of catecholamine-peptide adducts will facilitate structural elucidation of natural products not amenable to characterization using other spectroscopic techniques.
Forward-Backward Error: Automatic Detection of Tracking Failures (2010)

This paper proposes a novel method for tracking failure detection. The detection is based on the Forward-Backward error, i.e. the tracking is performed forward and backward in time and the discrepancies between these two trajectories are measured. We demonstrate that the proposed error enables reliable detection of tracking failures and selection of reliable trajectories in video sequences. We demonstrate that the approach is complementary to commonly used normalized cross-correlation (NCC). Based on the error, we propose a novel object tracker called Median Flow. State-of-the-art performance is achieved on challenging benchmark video sequences which include non-rigid objects.
Do [all]-S,S′-Dioxide Oligothiophenes Show Electronic and Optical Properties of Oligoenes and/or of Oligothiophenes? (2010)

A comprehensive photophysical and spectroscopic (electronic and Raman) study guided by density functional theory, DFT, CIS, and correlated ab initio calculations has been performed on a series of fully oxidized oligothiophenes with variable chain length, and up to four rings. A comparison with the properties of oligoenes and oligothiophenes is proposed. Absorption, fluorescence, lifetimes, flash-photolysis, phosphorescence, two-photon absorption, Raman, resonance Raman, and thermospectroscopy data are collected and interpreted according to the obtained theoretical results. The interest is focused on the ground electronic state and in the low-lying excited electronic states. Full oxygenation of the sulfur atoms of oligothiophenes results in: (i) restricted inter-ring isomerization such as observed from the absorption spectra; (ii) an effective quenching of fluorescence, and (iii) the appearance of dual emission. The emission features are explained by the interference of a dipole-allowed and a dipole-forbidden singlet excited states leading to simultaneous lighting from a local Frenkel and an intramolecular charge transfer photon-releasing configurations. These two excited states contribute to the broadening of the light emission spectrum. These properties highlight the similarity of these samples to that of oligoenes with comparable number of pi-electrons.
Innovations in Delta Differential One-Way Range: From Viking to Mars Science Laboratory (2009)

The Deep Space Network has provided the capability for very-long-baseline interferometry measurements in support of spacecraft navigation since the late 1970s. Both system implementation and the importance of such measurements to flight projects have evolved significantly over the past three decades. Innovations introduced through research and development programs have led to much better performance. This paper provides an overview of the development and use of interferometric tracking techniques in the DSN starting with the Viking era and continuing with a description of the current system and its planned use to support Mars Science Laboratory.
Synthesis and antinociceptive activity of 4-pyridyl and -dihydropyridyl analogues of meperidine and ketobemidone. (1990)

The synthesis and antinociceptive activity of 4-pyridylpiperdines (7 and 10) in which the phenyl group pf meperidine (1) or ketobemidone (3) is replaced by 2'-, 3'- or 4'-pyridyl is described. All were active in a rat writhing test, and the results showed that the point of attachment of the pyridyl ring to the 4-position was an important determinant of the activity; the relative potency order was 3'-pyridyl greater than 4'-pyridyl greater than 2'-pyridyl in each of the two series. The most potent compound (half the potency of meperidine) was 4-ethoxycarbonyl-4-(3'-pyridyl)-l-methylpiperidine (7b). This compound, and the corresponding 4'-isomer (7c), were further elaborated to provide 1'-phenyl, 1',6'-dihydropyridine (11), and 1'-phenyl, methyl or n-butyl. 1',2'-dihydropyridine (12) analogues containing an acyl function on the ring nitrogen. The most active compound in this series was 4-[4'-(1'-phenoxycarbonyl-2'-n-butyl-l',2'-dihydropyridyl)]- 4- ethoxycarbonyl-l-methylpiperdine (12k). Though less potent than the parent pyridyl compound (7c), it induced 70% inhibition in the writhing test at a dose of 8 mg/kg sc. [The ED50 for meperidine was 0.6 mg/kg sc.]
Cognitive workload and visual behavior in elderly drivers with hearing loss (2014)

To examine eye tracking data and compare visual behavior in individuals with normal hearing (NH) and with moderate hearing loss (HL) during two types of driving conditions: normal driving and driving while performing a secondary task. 24 participants with HL and 24 with NH were exposed to normal driving and to driving with a secondary task (observation and recall of 4 visually displayed letters). Eye movement behavior was assessed during normal driving by the following performance indicators: number of glances away from the road; mean duration of glances away from the road; maximum duration of glances away from the road; and percentage of time looking at the road. During driving with the secondary task, eye movement data were assessed in terms of number of glances to the secondary task display, mean duration of glances to the secondary task display, and maximum duration of glances to the secondary task display. The secondary task performance was assessed as well, counting the number of correct letters, the number of skipped letters, and the number of correct letters ignoring order. While driving with the secondary task, drivers with HL looked twice as often in the rear-view mirror than during normal driving and twice as often as drivers with NH regardless of condition. During secondary task, the HL group looked away from the road more frequently but for shorter durations than the NH group. Drivers with HL had fewer correct letters and more skipped letters than drivers with NH. Differences in visual behavior between drivers with NH and with HL are bound to the driving condition. Driving with a secondary task, drivers with HL spend as much time looking away from the road as drivers with NH, however with more frequent and shorter glances away. Secondary task performance is lower for the HL group, suggesting this group is less willing to perform this task. The results also indicate that drivers with HL use fewer but more focused glances away than drivers with NH, they also perform a visual scan of the surrounding traffic environment before looking away towards the secondary task display.
Quantitative Single Cell Analysis and Sorting (1977)

&lt;p&gt;With the rapid infrastructure development and economic growth in China, household car ownership in the country's rural areas has changed dramatically in the past 16 years. The total number of cars owned by households in rural areas is currently 12 times higher than it was 16 years ago. The exploration of the effects of the built environment on household car ownership in China's rural areas is worthwhile. However, few studies have investigated this topic. To fill in the research gap, this work collected 374 household data from rural areas in China to examine the effects of the built environment in Sichuan's rural areas on the number of cars in a household. It considered family structure, socioeconomic characteristics, and individual's perceptions of the built environment, preferences towards the built environment and attitudes towards car ownership (shortened to perceptions, preferences and attitudes from now on). Geographic information system (GIS) technology, combined with on-site measurement, was used for data collection. The multinomial logit model was applied for estimation. Household structure and the built environment (including the perceived built environment and the objective built environment) significantly influence the number of cars in a household. By contrast, preference and attitude attributes have less influence on car ownership. Most of the findings are in line with the literature in the context of Chinese cities. Nevertheless, new results are also found. For example, rural hukou, and building density have significant positive impacts on household car ownership in China's rural areas, which is in contrast with their effects on cities. As the first study on rural areas in China, this research provides some insights for rural planners and policymakers to understand better the relationship between built environment and household car ownership.&lt;/p&gt;
Exploring Artificial Muscles As Actuators for Artificial Hands (1993)

Abstract This article presents a brief overview of current research and findings in developing artificial muscles. Furthermore, possibilities of applying such muscles as actuators in prosthetic hands (i.e. The Sharif Artificial Hand) have been proposed and investigated.
Factors Affecting Fidelity of DNA Synthesis During PCR Amplification of d(C-A)n*d(G-T)n Microsatellite Repeats (1996)

The susceptibility of microsatellite DNA sequences to insertions and deletions in vivo makes them useful for genetic mapping and for detecting genomic instability in tumors. An in vitro manifestation of this instability is the production of undesirable frameshift products during amplification of (dC-dA)n x (dG-dT)n microsatellites in the polymerase chain reaction (PCR). These products differ from the primary product by multiples of 2 nucleotides. We have tested the hypothesis that factors known to affect the fidelity of DNA synthesis may affect (dC-dA)n x (dG-dT)n frameshifting during the PCR. Neither modifications of pH, dNTP concentration, and Mg++ concentration using Amplitaq, nor the use of thermophilic DNA polymerases including UITma, Pfu, Vent and Deep Vent significantly decreased the production of frameshift products during amplification. However, 3'-->5' exonuclease activity in thermophilic DNA polymerases inhibited the accumulation of PCR products containing non-templated 3' terminal nucleotides. Most interestingly, extension temperatures of 37 degrees C during amplification using the thermolabile DNA polymerases Sequenase 1.0, Sequenase 2.0, and 3'-->5' exonuclease-deficient Klenow fragment greatly decreased the production of frameshift products. This method can improve the resolution of heterozygous or mutant (dC-dA)n x (dG-dT)n alleles differing in size by one or two repeat units.
Small Scale Reservation Laws and the Misallocation of Talent (2010)

In this paper we quantify the eects of the Small Scale Reservation Laws in India on the aggregate productivity, aggregate output and welfare of the Indian economy. To this end, we extend the span-of-control model by Lucas (1978) into a multi-sector setting and embed it into the neo-classical growth model. Our main theoretical contribution is to model the occupational choice within this framework. We fully calibrate our model to data from India for the early 2000’s. We nd that lifting the Small Scale Reservation Laws would increase output per worker by 3.2 percent, capital per worker by 7.1 percent and aggregate TFP by 0.8 percent. Within manufacturing, output per worker would increase by 9.8 percent, capital per worker by 12.5 percent and TFP by 3.6 percent. Average rm size in manufacturing would raise from 19 to 69 employees. These are large numbers given that the size of the restricted sector is only 12 percent of manufacturing value added and 3 percent of total GDP. However, this conspicuous type of size-dependent policy cannot account for the large gap in manufacturing TFP existing between the US and India.
The structure of mitogen-activated protein kinase p38 at 2.1-Å resolution (1997)

The structure of mitogen-activated protein (MAP) kinase p38 has been solved at 2.1-Å to an R factor of 21.0%, making p38 the second low activity MAP kinase solved to date. Although p38 is topologically similar to the MAP kinase ERK2, the phosphorylation Lip (a regulatory loop near the active site) adopts a different fold in p38. The peptide substrate binding site and the ATP binding site are also different from those of ERK2. The results explain why MAP kinases are specific for different activating enzymes, substrates, and inhibitors. A model presented for substrate and activator interactions has implications for the evolution of protein kinase cascades.
Production and partial characterization of thermostable and calcium-independent alpha-amylase of an extreme thermophile Bacillus thermooleovorans NP54 (2000)

The calcium-independent and thermostable alpha-amylase of B. thermooleovorans NP54 will be extremely useful in starch saccharification since the alpha-amylases used in the starch industry are calcium dependent. The use of this enzyme in starch hydrolysis eliminates the use of calcium in starch liquefaction and subsequent removal by ion exchange.
Long-Term Safety and Effectiveness of Lisdexamfetamine Dimesylate in Adults With Attention-Deficit/Hyperactivity Disorder (2009)

LDX demonstrated a safety profile consistent with long-acting stimulant use and provided continued effectiveness in adults with ADHD for up to 12 months.
Regulation of blood coagulation by the protein C system (1992)

Protein C is a plasma, vitamin K-dependent zymogen of a serine protease that can inhibit blood coagulation. Protein C is regulated by a series of reactions known as the protein C pathway. The importance of this pathway is seen in the occurrence of thrombosis in individuals with deficiencies in elements of the pathway like protein C and protein S. Work on several steps in this pathway has revealed that mechanisms involved in activation of protein C and the expression of its anticoagulant activity have features that allow for the expression of the anticoagulant activity away from sites in which procoagulant reactions occur, but not systemically. Thrombin, the principal procoagulant enzyme at the site of an injury, is converted to an anticoagulant enzyme at distant sites through its interaction with the endothelial cell protein thrombomodulin. Structural and functional studies have revealed the importance of several domain structures in the modulation of thrombin activity. Structural features of both activated protein C and its substrates (coagulation factors V and VIII) are such that they require the localization of enzyme and substrate on the surface of phosphatidyl serine containing membranes for optimum activity.
Association of NCF2, IKZF1, IRF8, IFIH1, and TYK2 with Systemic Lupus Erythematosus (2011)

Systemic lupus erythematosus (SLE) is a complex trait characterised by the production of a range of auto-antibodies and a diverse set of clinical phenotypes. Currently, ~8% of the genetic contribution to SLE in Europeans is known, following publication of several moderate-sized genome-wide (GW) association studies, which identified loci with a strong effect (OR>1.3). In order to identify additional genes contributing to SLE susceptibility, we conducted a replication study in a UK dataset (870 cases, 5,551 controls) of 23 variants that showed moderate-risk for lupus in previous studies. Association analysis in the UK dataset and subsequent meta-analysis with the published data identified five SLE susceptibility genes reaching genome-wide levels of significance (P(comb)<5×10(-8)): NCF2 (P(comb) = 2.87×10(-11)), IKZF1 (P(comb) = 2.33×10(-9)), IRF8 (P(comb) = 1.24×10(-8)), IFIH1 (P(comb) = 1.63×10(-8)), and TYK2 (P(comb) = 3.88×10(-8)). Each of the five new loci identified here can be mapped into interferon signalling pathways, which are known to play a key role in the pathogenesis of SLE. These results increase the number of established susceptibility genes for lupus to ~30 and validate the importance of using large datasets to confirm associations of loci which moderately increase the risk for disease.
Splinkerettes—improved vectorettes for greater efficiency in PCR walking (1995)

Journal Article Splinkerettes—improved vectorettes for greater efficiency in PCR walking Get access Rebecca S. Devon, Rebecca S. Devon * MRC Human Genetics Unit, Western General HospitalCrewe Road, Edinburgh EH4 2XU, UK * To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar David J. Porteous, David J. Porteous MRC Human Genetics Unit, Western General HospitalCrewe Road, Edinburgh EH4 2XU, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar Anthony J. Brookes Anthony J. Brookes MRC Human Genetics Unit, Western General HospitalCrewe Road, Edinburgh EH4 2XU, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 23, Issue 9, 11 May 1995, Pages 1644–1645, https://doi.org/10.1093/nar/23.9.1644 Published: 11 May 1995 Article history Received: 03 October 1994 Revision received: 25 November 1994 Accepted: 25 November 1994 Published: 11 May 1995
Proteomics in Early Detection of Cancer (2001)

Early detection is critical in cancer control and prevention. Biomarkers help in this process by providing valuable information about a the status of a cell at any given point in time. As a cell transforms from nondiseased to neoplastic, distinct changes occur that could be potentially detected through the identification of the appropriate biomarkers. Biomarker research has benefited from advances in technology such as proteomics. We discuss here ongoing research in this field, focusing on proteomic technologies. The advances in two-dimensional electrophoresis and mass spectrometry are discussed in light of their contribution to biomarker research. Chip-based techniques, such as surface-enhanced laser desorption, and ionization and emerging methods, such as tissue and antibody arrays, are also discussed. The development of bioinformatic tools that have and are being developed in parallel to proteomics is also addressed. This report brings into focus the efforts of the Early Detection Research Network at the National Cancer Institute in harnessing scientific expertise from leading institutions to identify and validate biomarkers for early detection and risk assessment.
PERSPECTIVE ARTICLE: Growth factors and cytokines in wound healing (2008)

Wound healing is an evolutionarily conserved, complex, multicellular process that, in skin, aims at barrier restoration. This process involves the coordinated efforts of several cell types including keratinocytes, fibroblasts, endothelial cells, macrophages, and platelets. The migration, infiltration, proliferation, and differentiation of these cells will culminate in an inflammatory response, the formation of new tissue and ultimately wound closure. This complex process is executed and regulated by an equally complex signaling network involving numerous growth factors, cytokines and chemokines. Of particular importance is the epidermal growth factor (EGF) family, transforming growth factor beta (TGF-beta) family, fibroblast growth factor (FGF) family, vascular endothelial growth factor (VEGF), granulocyte macrophage colony stimulating factor (GM-CSF), platelet-derived growth factor (PDGF), connective tissue growth factor (CTGF), interleukin (IL) family, and tumor necrosis factor-alpha family. Currently, patients are treated by three growth factors: PDGF-BB, bFGF, and GM-CSF. Only PDGF-BB has successfully completed randomized clinical trials in the Unites States. With gene therapy now in clinical trial and the discovery of biodegradable polymers, fibrin mesh, and human collagen serving as potential delivery systems other growth factors may soon be available to patients. This review will focus on the specific roles of these growth factors and cytokines during the wound healing process.
Neuroendocrine cells in tumour growth of the prostate. (1999)

The prognostic significance of neuroendocrine differentiation in prostatic malignancy is controversial, but the results of recent studies with markers such as chromogranin A and neurone-specific enolase suggest that neuroendocrine differentiation, as reflected by increased tissue expression or blood concentrations of these neuroendocrine secretory products, is associated with a poor prognosis, tumour progression, and androgen independence. As all malignant neuroendocrine cells are devoid of androgen receptors and the expression of neuroendocrine cells is not suppressed by androgen ablation, clonal propagation of androgen receptor-negative neuroendocrine cells may have an important role in the development of androgen-independent prostatic carcinoma. This has significant implications for the treatment of prostate cancer, because several of the hormones that are secreted by neuroendocrine differentiated, malignant prostatic cells are potential candidates for use in drug treatment. A limited number of hormones have been tested in this context, in particular somatostatin, bombesin, and serotonin. As there is currently no successful treatment for differentiated prostate cancer, new therapeutic procedures and trials need to be developed to test drugs based on neuroendocrine hormones or their antagonists.