gebhart/patrepeval huggingface dataset:
The structural basis of molecular genetic deletions. An integration of classical cytogenetic and molecular analyses in pancreatic adenocarcinoma. (1997)

Molecular genetic alterations are known to be important in human carcinoma, but the structural basis of these changes is largely unknown. To examine the basis of these changes, we compared the karyotypic chromosomal abnormalities of primary pancreatic adenocarcinomas with the molecular changes identified in these same cancers. In 14 cancers with abnormal karyotypes, 65% (123 of 188) of the chromosomal arms with molecular loss of heterozygosity (LOH) were associated with karyotypic structural anomalies. Karyotypic changes accounting for these molecular allelic losses included 83 chromosome losses, 18 partial deletions, nine isochromosomes, eight additions, and five translocations. Eight bomozygous deletions were also identified by molecular analyses. Of the three homozygous deletions identified at 9p21, the only karyotypic change was a single case in which one entire copy of chromosome 9 was deleted. Of the four homozygous deletions identified at 18q21.1, one showed a loss of both copies of chromosome 18, two showed a loss of one copy of chromosome 18, and the fourth had two structurally normal copies of chromosome 18. One homozygous deletion was identified at 13q12.3, and the karyotype revealed the loss of one entire copy of chromosome 13. The second copy of chromosome 13 in this carcinoma was structurally normal. These results indicate that chromosomal structural anomalies can account for two-thirds of the LOH in pancreatic adenocarcinomas and that most homozygous deletions are likely to be interstitial chromosomal deletions that are below the detection limit of conventional karyotypic analyses. Some of the molecular deletions detected as LOH on chromosomes with karyotypically normal structure can be explained by chromosomal loss with reduplication of the remaining chromosome.
Human leucocyte aspartylglucosaminidase. Evidence for two different subunits in a more complex native structure (1991)

Human leucocyte aspartylglucosaminidase (AGA: 1-aspartamido-beta-N-acetylglucosamine amidohydrolase, EC 3.5.1.26) was purified to homogeneity by using affinity chromatography, gel filtration, chromatofocusing and reverse-phase h.p.l.c. As shown by SDS/PAGE, the homogeneous purified enzyme preparation consists of four polypeptide chains with molecular masses of 25, 24, 18 and 17 kDa. In the native polyacrylamide gel these polypeptides migrate as one active enzyme complex, and by gel filtration the peak of enzyme activity can be detected in a position of about 65 kDa. Digestion with endoproteinase Lys-C or endoproteinase Asp-N, followed by peptide analysis with reverse-phase h.p.l.c., reveals an identical peptide pattern for the 24 and 25 kDa bands as well as for the 17 and 18 kDa bands. This treatment further demonstrated a totally different peptide pattern for the 24/25 kDa versus the 17/18 kDa subunit. The N-terminal sequences of the 17 kDa and the 18 kDa peptides were identical, as determined by Edman degradation. The N-termini of the 24 kDa and the 25 kDa peptides were blocked. The enzyme was partly resistant to endoglycosidases H and F, but N-glycosidase F transformed the 24/25 kDa band into one 23 kDa band and the 17/18 kDa band into one 16 kDa band. Also, immunological data obtained with antisera produced against these subunits showed that AGA consists of two non-identical polypeptides.
An Antibody Binding Site on Cytochrome C Defined by Hydrogen Exchange and Two-Dimensional NMR (1990)

The interaction of a protein antigen, horse cytochrome c (cyt c), with a monoclonal antibody has been studied by hydrogen-deuterium (H-D) exchange labeling and two-dimensional nuclear magnetic resonance (2D NMR) methods. The H-exchange rate of residues in three discontiguous regions of the cyt c polypeptide backbone was slowed by factors up to 340-fold in the antibody-antigen complex compared with free cyt c. The protected residues, 36 to 38, 59, 60, 64 to 67, 100, and 101, and their hydrogen-bond acceptors, are brought together in the three-dimensional structure to form a contiguous, largely exposed protein surface with an area of about 750 square angstroms. The interaction site determined in this way is consistent with prior epitope mapping studies and includes several residues that were not previously identified. The hydrogen exchange labeling approach can be used to map binding sites on small proteins in antibody-antigen complexes and may be applicable to protein-protein and protein-ligand interactions in general.
PTU-137 ‘Nutrient Sensing in the Human Gut: Investigation of the Co-Localization Rate Between Casr, T1R1 and GPR43 Receptors with Satiety Peptides in the Human Antrum, Terminal Ileum and Ascending Colon.’ (2013)

<h3>Introduction</h3> Increasing evidence from animal studies show that apical nutrient sensing receptors, expressed in gut enteroendocrine cells, play a key role in the release of satiety peptides<sup>{1,2}</sup>. Early human studies indicate a similar expression pattern of these receptors and role in peptide release<sup>{3}</sup>. In this study the anatomical relationship between amino acid sensing (CaSR), carbohydrate sensing (T1R1), and short chain fatty acid sensing (GPR43) receptors and appetite regulating peptides GLP-1, PYY, 5-HT was investigated in the human gut. <h3>Methods</h3> Healthy full thickness human gut sections were incubated with primary and fluorescent secondary antibodies and they were viewed under the fluoroscopic microscope to investigate co-localization of the CaSR, T1R1 and GPR43 with the GLP1, PYY and 5HT. <h3>Results</h3> The co-localization rate between CaSR and PYY, GLP1 and 5HT was 0%, &lt; 1% and 43% in the antrum, 20%, 12% and 82% in the ileum and 26%, 14% and 91% in the colon, respectively. Co-localization of T1R1 and GLP1 was observed only in the antrum and the colon. GPR43 was not expressed. <h3>Conclusion</h3> CaSR is expressed at protein level and is colocalized with PYY, 5HT and GLP1 in the human antrum, terminal ileum and ascending colon. T1R1 expression at protein level is very limited in all the tested tissues. GPR43 expression was not observed. The results suggest that CaSR is linked to PYY, GLP1 and 5HT release in the human gut, with data being stronger for the 5HT release. <h3>Disclosure of Interest</h3> None Declared <h3>References</h3> Sternini, <i>et al.</i> 2008. Enteroendocrine cells: a site of ‘taste’ in gastro- intestinal chemosensing. Curr Opin Endocrinol Diabetes Obes 15(1): 73–78. Frenchet <i>et al.</i> 2000. The effects of intestinal infusion of long-chain fatty acids on food intake in humans. Gastroenterology 2000; 119: 943–8. Page <i>et al.</i> 2012. Peripheral neural targets in obesity. British Journal of Pharmacology, 1568-RC.R1.
ChemInform Abstract: Synthesis and anti‐HIV Activity of Cyclic Pyrimidine Phosphonomethoxy Nucleosides and Their Prodrugs: A Comparison of Phosphonates and Corresponding Nucleosides (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Comparative assessment of different drought indices across the Mediterranean (2016)

Droughts have become one of the most challenging issues in hydrological sciences due to their major socioeconomic&#13;\nimpacts all over the world. In the context of the everyday water resources management practice, the&#13;\nidentification and evaluation of droughts are mainly based on simplified indices, which are estimated through&#13;\neasily accessible information. In this work, we employ several meteorological indices, i.e. Standardized Precipitation&#13;\nIndex (SPI), Standardized Precipitation and Evapotranspiration Index (SPEI), Reconnaissance Drought Index&#13;\n(RDI), Palmer Drought Z Index, and Palmer Drought Severity Index (PDSI), in order to evaluate the severity and&#13;\nduration of the observed drought events. The main purpose of this study is to underline the difference in the onset&#13;\ntime of drought, the distance between events, and the discrepancies in the magnitude assessment for the same event.&#13;\nVarious temporal aggregation scales, from one month to one year, have been considered in order to investigate the&#13;\nimpacts of the adopted time scale on the drought characteristics. Our analysis focuses to the Mediterranean region,&#13;\nusing data from Southern Italy and Greece.
A novel three-axis AIM vibration sensor for high accuracy condition monitoring (2010)

We present a novel micromachining approach for on chip three-axis capacitive high aspect ratio acceleration sensors made from standard silicon wafers. The patented AIM (air gap insulated microstructures) technology with their excellent device properties regarding temperature behavior, capacitive sensitivity and reliability was modified for enabling out-of-plane differential measurements. Therefore electrodes with different heights have been patterned by using one additional masking layer. Using the presented AIM technology, high performance vibration sensors with low temperature sensitivity of typically 40 to 110 ppm/K sensitivity change and ± 0.9 mg/K offset failure at a sensitivity of 10 fF/g (25 fF/g for in-plane sensors), a measurement range of ± 50 g and a bandwidth from DC to 1 kHz were fabricated. The sensors have been packaged hermetically by seal glass bonding.
Behavioral Characterizing of CD24 Knockout Mouse—Cognitive and Emotional Alternations (2021)

CD24 is a small, glycophosphatidylinositol-anchored cell surface protein, mostly investigated with respect to cancer, inflammation, and autoimmune diseases. CD24 knockdown or inhibition has been used to test various biochemical mechanisms and neurological conditions; however, the association between CD24 and behavioral phenotypes has not yet been examined. This study aims to characterize cognitive and emotional functions of CD24 knockout mice (CD24<sup>-/-</sup>) compared with CD24 wild-type mice at three time-points: adolescence, young adulthood, and adulthood. Our results show that CD24<sup>-/-</sup> mice exhibited better cognitive performance and less anxiety-like behavior compared with WT mice, with no effect on depression-like behavior. This phenotype was constant from childhood (2 months old) to adulthood (6 months old). The results from our study suggest that CD24 may influence important behavioral aspects at the whole-organism level, which should be taken into consideration when using CD24 knockout models.
Light extraction study on quantum dots embedded in nanoimprinted silica matrix (2010)

International audience
Out-of-plane Doppler imaging based on ultrafast plane wave imaging (2015)

Retrieving the out-of-plane blood flow velocity vector from two-dimensional transverse acquisitions of large vessels could improve the quantification of flow rate and maximum speed. The in-plane vector flow component can be computed easily using the Doppler frequency shift. The main problem is estimating the angle between the probe imaging plane and the vessel axis to derive the out-of-plane component from in-plane measurements. In this article, we study the case in which the velocity vector can be decomposed on two directions: the out-of-plane direction and the in-plane depth direction. We explore the combination of a technique called intrinsic spectral broadening with ultrafast plane wave imaging to retrieve the out-of-plane component of the flow velocity vector. Using a one-time probe calibration of this intrinsic spectral broadening, out-of-plane angle and flow speed can be recovered easily, thus avoiding approximations of a complex theoretical analysis. For the calibration step, ultrafast plane wave imaging permits a fast calibration procedure for the Doppler intrinsic spectral broadening. In vitro experimental validations are performed on a homogeneous flow phantom and a Poiseuille flow; the absolute speed was retrieved with 6% error. The potential of the technique is demonstrated in vivo on the human carotid artery. Combined with in-plane vector flow approaches, this out-of-plane Doppler imaging method paves the way to threedimensional vector flow imaging using only conventional onedimensional probe technology.
Modulatory effects of cannabinoids on brain neurotransmission (2019)

Recreational and chronic cannabis use has been associated with a range of acute and chronic effects including; anti-nociceptive actions, anxiety, depression, psychotic symptoms and neurocognitive impairments. The mechanisms underlying cannabinoid-based drugs effects are not fully known but given the neuro-modulatory functions of the endocannabinoid system, it seems likely that agonistic activity at the cannabinoid type-1 receptors (CB<sub>1</sub> ) might modulate the functions of other neurotransmitter systems. The present review has summarized the currently available pre-clinical and clinical data on the interactions of CB<sub>1</sub> and cannabinoid type-2 receptors (CB<sub>2</sub> ) with the central neurotransmitters; dopamine, serotonin, noradrenaline, GABA, glutamate and opioids. Acute and chronic exposures to cannabinoids exert pharmacological alterations in the mammalian brain that have profound implications for our understanding of the neuropharmacology of cannabinoid-based drugs and their effects on mental health and the brain. A recent emergence uses of cannabis for medical purpose together with legalization and decriminalization of cannabis and increasing use of highly potent synthetic cannabinoids raise a growing concern over the effects of cannabinoids and their interaction with other neurotransmitters on physical and mental health.
The Fragility of Statistically Significant Findings From Randomized Trials in Sports Surgery: A Systematic Survey (2016)

Most statistically significant RCTs in sports medicine and arthroscopic surgery are not robust because their statistical significance can be reversed by changing the outcome status on only a few patients in 1 treatment group. Future work is required to determine whether routine reporting of the Fragility Index enhances clinicians' ability to detect trial results that should be viewed cautiously.
Potassium-Modified ZSM-5 Catalysts for Methyl Acrylate Formation from Methyl Lactate: The Impact of the Intrinsic Properties on Their Stability and Selectivity (2022)

Methyl lactate (ML) conversion to methyl acrylate is studied in the gaseous phase over ZSM-5 zeolite catalysts. High acrylate selectivity and catalyst service time were achieved using the K-ZSM-5 catalyst with low content of Brønsted acid sites (below 1 μmol g–1) and an overall K-to-Al atom ratio of unity. Feeding of ML in methanol containing 5 to 25 vol % of water improves catalyst stability. As such, up to 80% acrylate yield at complete ML conversion, along with minor deactivation after days-on-stream and fully recoverable catalysis, is presented.
Characterization and optimization of charge trapping in high-k dielectrics (2013)

Continued scaling of semiconductor devices in logic and memory applications requires the introduction of high-k (HK) dielectrics to enhance the capacitance density while maintaining a low leakage. Of particular concern in DRAM memory applications is the so called `dielectric relaxation current', which is significantly enhanced with HfO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> dielectrics as compared to SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> . In this paper, it is shown that these relaxation currents arise from electron trapping/detrapping by/from oxygen vacancy defects in the HfO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> dielectric from/to the contact electrodes. This understanding is utilized to minimize `dielectric relaxation currents' by optimizing the defect structure in the HK dielectric. By creating trap-free dielectric films with N or La doping, we show that substantial reductions in the relaxation currents can be achieved. For the first time, it is demonstrated that a HK dielectric stack formed as a result of these treatments can have reduced relaxation currents similar to SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> , thus providing a pathway to solving a fundamental paradigm associated with HK dielectrics that has persisted for several years.
Imaging α-synuclein pathologies in animal models and patients with Parkinson’s and related diseases (2020)

SUMMARY Deposition of α-synuclein fibrils is implicated in Parkinson’s disease (PD) and dementia with Lewy bodies (DLB), while in vivo detection of α-synuclein pathologies in these illnesses has been challenging. Here, we have developed a small-molecule ligand, C05-05, for visualizing α-synuclein deposits in the brains of living subjects. In vivo optical and positron emission tomography (PET) imaging of mouse and marmoset models demonstrated that C05-05 captured a dynamic propagation of fibrillogenesis along neural pathways followed by disruptions of these structures. High-affinity binding of 18 F-C05-05 to α-synuclein aggregates in human brain tissues was also proven by in vitro assays. Notably, PET-detectable 18 F-C05-05 signals were intensified in the midbrains of PD and DLB patients as compared to healthy controls, providing the first demonstration of visualizing α-synuclein pathologies in these illnesses. Collectively, we propose a new imaging technology offering neuropathology-based translational assessments of PD and allied disorders towards diagnostic and therapeutic research and development.
Effective Schottky Barrier lowering for contact resistivity reduction using silicides as diffusion sources (2010)

In this work we present a potential solution for forming ultra-shallow junctions with extremely low contact resistivities in which dopants are implanted into silicides and diffused to the semiconductor interface using low temperature anneals. Conventional silicide process requires a fine tuning of silicide thickness and deep source/drain doping profile to achieve low contact resistance and low source/drain diffusion sheet resistance. With the silicide implantation approach, we show that they can be engineered independently, providing a larger design space for the reduction of total external resistance.
Expression of Pre-S-Encoded Proteins in Sera of Individuals Chronically Infected with Hepatitis D Virus (1988)

The sera of 16 individuals chronically infected with the hepatitis D virus were analyzed for hepatitis B virus (HBV) markers. The majority of these patients had a non-replicative form of viral type B hepatitis as indicated by negative tests for HBeAg and HBV-DNA. Pre-S-encoded proteins were detected in 13/16 sera. Sera that were negative for polymerized serum albumin did also not contain pre-S1-encoded proteins. The presence of pre-S-encoded proteins is probably predominantly associated with 22-nm HBsAg forms present in large amounts in sera of individuals with chronic type D hepatitis.
Ultra-Flat Bands In Photonic Crystals (2005)

We create one-dimensional extended ultra-flat bands with relative frequency widths below 1% in two-dimensional photonic crystals. Caused by an interior saddle point, these flat bands lead to an enhanced density of states and improved self-collimation.
Recombinant Spider Silk Gels Derived from Aqueous–Organic Solvents as Depots for Drugs (2021)

Hydrogels are widely used in various biomedical applications, as they cannot only serve as materials for biofabrication but also as depots for the administration of drugs. However, the possibilities of formulation of water-insoluble drugs in hydrogels are rather limited. Herein, we assembled recombinant spider silk gels using a new processing route with aqueous-organic co-solvents, and the properties of these gels could be controlled by the choice of the co-solvent. The presence of the organic co-solvent further enabled the incorporation of hydrophobic drugs as exemplarily shown for 6-mercaptopurine. The developed gels showed shear-thinning behaviour and could be easily injected to serve, for example, as drug depots, and they could even be 3D printed to serve as scaffolds for biofabrication. With this new processing route, the formulation of water-insoluble drugs in spider silk-based depots is possible, circumventing common pharmaceutical solubility issues.
Pattern separation or Pattern Resolution - A critical look at DG and neurogenesis function. (2012)

Abstract not provided.
Structures of enzymatically modified products of arbekacin by methicillin-resistant Staphylococcus aureus. (1993)

Only a limited number of strains of methicillin-resistant Staphylococcus aureus (MRSA) moderately resistant to arbekacin (ABK) have been isolated clinically. Three inactivated products of ABK have been obtained by reaction with excess amounts of a crude enzyme preparation extracted from an ABK-resistant MRSA strain (MIC, 25 micrograms/ml). The 2"-O-phosphate was the major product together with small amounts of the 6'-N-acetate and the double modification product. The structures of these modification products were determined by MS and NMR spectral analyses.
Editorial Comment (2008)

No AccessJournal of UrologyAdult Urology1 Feb 2009Editorial Comment Brian Shuch and Arie Belldegrun Brian ShuchBrian Shuch More articles by this author and Arie BelldegrunArie Belldegrun More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2008.10.098AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Editorial Comment." The Journal of Urology, 181(2), p. 523 References 1 : Performance status and cytoreductive nephrectomy: redefining management in patients with poor performance. Cancer2008; 113: 1324. Google Scholar Department of Urology, University of California, Los Angeles, Los Angeles, California© 2009 by American Urological AssociationFiguresReferencesRelatedDetails Volume 181Issue 2February 2009Page: 523 Advertisement Copyright & Permissions© 2009 by American Urological AssociationMetricsAuthor Information Brian Shuch More articles by this author Arie Belldegrun More articles by this author Expand All Advertisement PDF downloadLoading ...
Extracellular Vesicles Produced by Cryptococcus neoformans Contain Protein Components Associated with Virulence (2007)

Cryptococcus neoformans produces vesicles containing its major virulence factor, the capsular polysaccharide glucuronoxylomannan (GXM). These vesicles cross the cell wall to reach the extracellular space, where the polysaccharide is supposedly used for capsule growth or delivered into host tissues. In the present study, we characterized vesicle morphology and protein composition by a combination of techniques including electron microscopy, proteomics, enzymatic activity, and serological reactivity. Secretory vesicles in C. neoformans appear to be correlated with exosome-like compartments derived from multivesicular bodies. Extracellular vesicles manifested various sizes and morphologies, including electron-lucid membrane bodies and electron-dense vesicles. Seventy-six proteins were identified by proteomic analysis, including several related to virulence and protection against oxidative stress. Biochemical tests indicated laccase and urease activities in vesicles. In addition, different vesicle proteins were recognized by sera from patients with cryptococcosis. These results reveal an efficient and general mechanism of secretion of pathogenesis-related molecules in C. neoformans, suggesting that extracellular vesicles function as "virulence bags" that deliver a concentrated payload of fungal products to host effector cells and tissues.