gebhart/patrepeval huggingface dataset:
Efficacy Trial of the 5-HT2 Antagonist MDL 11,939 in Patients With Generalized Anxiety Disorder (1995)

The purpose of this study was to assess the anxiolytic effect of MDL 11,939, a selective 5-HT2 receptor antagonist, in patients with generalized anxiety disorder. After a 1-week placebo lead-in period, 72 healthy male outpatients meeting DSM-III-R criteria for generalized anxiety disorder were randomized to MDL 11,939, 32 mg thrice daily (N = 37), or placebo (N = 35) for 6 weeks. At the end of treatment, MDL 11,939 showed a 7.2-point (30%) decrease in Hamilton Rating Scale for Anxiety scores compared with a 5.7-point (23%) decrease with placebo, but the difference was not significant (p > 0.05). The incidence of adverse events between treatments was similar. MDL 11,939 was well tolerated but did not demonstrate significant anxiolytic effects in this pilot study.
Adhesion systems in normal breast and in invasive breast carcinoma. (1995)

To analyze the role of various elements of the adhesion system in the organization of the normal mammary gland and in breast carcinoma, we have studied simultaneously the expression of integrins, E- and P-cadherins, and cytoplasmic constituents of adherens junctions. In the normal gland, E-cadherin and alpha-catenin are present in luminal epithelial and myoepithelial cells, whereas integrins are more abundant in acinar epithelial and in myoepithelial cells. We demonstrate here that, in addition, myoepithelial cells express much more vinculin and alpha-actinin than luminal epithelial cells, whereas talin and focal adhesion kinase (pp125FAK) are restricted to the basal cell layer. In invasive carcinoma, E-cadherin is usually present although often in reduced amount; different integrin subunits are expressed either by a fraction or by all of the cells or are absent. However, the cytoplasmic components of adherens junctions, such as alpha-catenin, vinculin, alpha-actinin, talin, and pp125FAK, are expressed at low levels or cannot be detected in the carcinoma cells. Our data suggest that 1), in the normal mammary gland, the myoepithelial cells, being particularly rich in integrins and cytoplasmic components of the adherens junctions, play an important role in the maintenance of tissue integrity; 2), in invasive carcinoma, cell aggregates may be maintained due to varying levels of expression of E-cadherin and/or integrins; and 3), interaction of the transmembrane adhesion molecules with the cytoskeleton in carcinoma may be impaired as revealed by reduced levels of expression of alpha-catenin, vinculin, alpha-actinin, talin, and pp125FAK. Importantly, carcinoma cells, when exposed to stroma during invasion, do not acquire the adhesion apparatus characteristic of normal cells in contact with the extracellular matrix.
Abstract 823: Identification of FISH biomarkers to detect chromosome abnormalities associated with prostate adenocarcinoma in tumor and field effect environment (2010)

Abstract Introduction. The focal nature of prostate cancer (CA) contributes to needle biopsy sampling error with false negative rates of 15-30%. Here we used fluorescence in situ hybridization (FISH) analysis to assess molecular abnormalities in prostate specimens as an aid to CA diagnosis. We also evaluated the feasibility of combined immunofluorescence and FISH to facilitate assessment of chromosomal abnormalities. Experimental Procedure. 33 radical prostatectomy (RP) specimens from patients with adenocarcinoma of the prostate were evaluated by FISH with MYC, LPL, PTEN and centromere 8 probes. For each specimen, a tissue section was scribed by a pathologist to mark the tumor region(s). For 17 of the RP cases, a second section was available with only histologically benign tissue. FISH signals were enumerated in 50-100 cells per section. 26 hyperplasia (BPH) specimens, served as controls. Immunofluorescence (IF) with AMACR antibody was also used in the same assay with FISH. Results. Chromosomal copy number abnormalities were observed in most RP specimens, both within tumor regions and extending beyond histologically evident tumor, while few abnormalities were observed in the BPH specimens, using a cut-off value for FISH positivity based on the mean +/- 2 SD of cells with less than or greater than 2 signals in BPH specimens. A combination of MYC gain, LPL loss, PTEN loss or chromosome 8 aneusomy within the scribed tumor regions identified adenocarcinoma in 82% (27/33) of RP specimens, with a specificity of 81% relative to BPH (χ2 p&amp;lt;0.001). When detected in regions of normal histology, these abnormalities correlated with adenocarcinoma in 47% (8/17 RP specimens, χ2 p=0.05 relative to BPH). IF combined with FISH facilitated selection of the abnormal regions of interest for molecular assessment in the heterogeneous prostate specimens. The IF-staining closely correlated with morphological assessment of tumor by a trained pathologist. Conclusions. This study identified FISH probes for detection of chromosomal abnormalities associated with prostate CA that could potentially serve as a diagnostic aid in biopsy specimens. This study also indicates that chromosome abnormalities are present in RP specimens within regions of normal histology, indicating a substantial tumor field effect. Therefore, a molecular test based on FISH to measure abnormal MYC, LPL, PTEN and centromere 8 copy numbers may allow detection of cancer otherwise missed by histopathological examination and thus improve diagnosis of prostate cancer by reducing sampling error of needle biopsies. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 823.
General relation for the vector magnetic field of a circular current loop: a closer look (2003)

This paper presents a general theory for the fields generated by a circular current loop and compares it with existing theories. The existing, general, closed solution for the vector magnetic field may be expressed in a number of seemingly different but equivalent forms. These relations offer alternative closed-form solutions that may find various applications, including the characterization of Helmholtz coils. The paper provides alternative closed forms in both spherical and cylindrical coordinate systems. It employs Gauss's magnetic law to show that the alternative closed form is self-consistent and correct and also shows agreement with well-known solutions. Finally, it develops a new (or not readily found) tabulated mathematical identity.
Mobile Clouds: An Introduction (2013)

In this chapter mobile clouds are defined and discussed. The mobile cloud concept is approached from different perspectives. A generic mobile cloud definition is first presented, followed by other definitions that take into account their cooperative and social aspects. The mobile cloud capabilities for sharing its distributed resources are also discussed. This chapter also discusses how cooperative and cognitive principles are exploited by mobile clouds. Finally, a classification of mobile clouds is provided, including a discussion on the main types of cooperation arising in different types of mobile clouds and their associated scenarios.
Mid-infrared speckle reduction technique for hyperspectral imaging (2022)

Recently, we proposed an active mid-infrared (MIR) hyperspectral imaging system for early detection of plant water stress. A quantum cascade tunable laser powered this stand-off detection system, in which “speckle” in images due to coherent nature of laser radiation. The speckle affects the spatial resolution of the images. In this article, we evaluate several speckle suppression methods suitable for the mid-infrared region. To quantify the reduction of speckle, we compare their spatial contrast. We combined optical techniques and showed their ability to reduce the speckle contrast from its initial value 0.413 down to 0.11, representing a 73% reduction
Haplotypes associated to gene expression in breast cancer: can they lead us to the susceptibility markers? (2018)

Abstract We have undertaken a systematic haplotype analysis of the positional type of biclusters analysing samples collected from 164 breast cancer patients and 86 women with no known history of breast cancer. We present here the haplotypes and LD patterns in more than 80 genes distributed across all chromosomes and how they differ between cases and controls. We aim by this to 1) identify genes with different haplotype distribution or LD patterns between breast cancer patients and controls and 2) to evaluate the intratumoral mRNA expression patterns in breast cancer associated particularly to the cancer susceptibility haplotypes. A significant difference in haplotype distribution between cases and controls was observed for a total of 35 genes including ABCC1, AKT2, NFKB1, TGFBR2 and XRCC4 . In addition we see a negative correlation between LD patterns in cases and controls for neighboring markers in 8 genes such as CDKN1A, EPHX1 and XRCC1 .
LIPID PARTICLE DETECTION BY MEANS DIGITAL HOLOGRAPHY AND LATERAL SHEAR INTERFEROMETRY (2007)

Digital Holography in microscope configuration thanks to the numerical reconstruction procedure is a flexible and useful tool for analysis of biological material. We present the investigation of lipid particles growth in in-vitro mouse cell using a Digital Holographic Microscopy (DHM) employed in combination with Lateral Shear Interferometry (LSI). The optical setup is based on a Mach-Zehnder interferometer in transmission geometry. The sample cell is placed in one interferometer arm while the other one is used as a reference beam. By means of the Rayleigh-Sommerfield integral is possible to retrieve the complex object field and then to calculate the amplitude and phase of the laser light transmitted by the sample. Traditional microscopy allows to obtain amplitude contrast image only, DH, instead, enables to calculate the phase map of the complex wave that is simply related to the optical phase difference (OPD) experienced by the light when it is transmitted through the object. In this way it is possible to obtain phase contrast image that is very useful for biological materials that often present low amplitude contrast for quantitative amplitude image. The main difficulty of this technique is to remove the optical aberrations produced by the optical setup components. Several methods have been proposed, such as subtraction of a reference phase map (without sample) [1] or numerical multiplication of a parametric lens [2], We propose a fast and effective solution of this problem based on LSI. We digitally introduce a lateral shear of one pixel in x and y directions calculating the phase difference Δϕx,y, between the actual phase map and its sheared replica in both directions. Δϕx,y include a linear term due to defocus aberration and the object phase difference. The linear term can be easily eliminated and sample phase map retrieved by numerical integration. This technique allows to obtain the correct phase contrast image removing optical aberration, avoiding unwrapping problems.
Genomes to Proteomes (2009)

This chapter contains sections titled: Introduction Gene Modeling Proteomics: Experimental Design Proteomics Sample Processing Statistical Modeling of Proteomics Data Integrating Proteomic Data with Other High-Throughput Data Summary References
Double-stranded RNA induction asa potential dynamic biomarkerfor DNA-demethylating agents (2022)

Hypomethylating agents (HMAs), such as azacitidine and decitabine, induce cancer cell death by demethylating DNAs to promote the expression of tumor-suppressor genes. HMAs also reactivate the transcription of endogenous double-stranded RNAs (dsRNAs) that trigger the innate immune response and subsequent apoptosis via viral mimicry. However, the expression patterns of endogenous dsRNAs and their relevance in the efficacy of HMAs remain largely uninvestigated. Here, we employ amidine-conjugated spiropyran (Am-SP) to examine the dynamic expression pattern of total dsRNAs regulated by HMAs. By analyzing the bone-marrow aspirates of myelodysplastic syndrome or acute myeloid leukemia patients who received the HMAs, we find a dramatic increase in total dsRNA levels upon treatment only in patients who later benefited from the therapy. We further apply our approach in solid tumor cell lines and show that the degree of dsRNA induction correlates with the effectiveness of decitabine in most cases. Notably, when dsRNA induction is accompanied by increased expression of nc886 RNA, decitabine becomes ineffective. Collectively, our study establishes the potential application of monitoring the total dsRNA levels by a small molecule as an analytical method and a dynamic marker to predict the clinical outcome of the HMA therapy.
Corneal surface reconstruction algorithm that uses Zernike polynomial representation (2004)

We developed an algorithm that directly determines Zernike coefficients for the corneal anterior surface derived from the reflection image of a stimulus with pseudorandom encoding. This algorithm does not need to include calculation of corneal height maps. The numerical performance of the algorithm is good. It has the potential of determining corneal shape with submicrometer accuracy in obtaining Zernike coefficients. When applied to real eye measurements the accuracy of the procedure will be limited by the topographer that is used.
A Noncleavable Retro-Binding Peptide That Spans the Substrate Binding Cleft of Serine Proteases. Atomic Structure of Nazumamide A:  Human Thrombin (1996)

The 2.0 Å resolution crystal structure of the retro-binding natural product nazumamide A (NAZA) complexed with human thrombin is presented. The crystal structure shows that the retro-binding nazumamide A is noncleavable and extends into the prime end of the substrate binding cleft. The data suggest ideas for SAR and combinatorial modification of nazumamide A to create a second generation of nazumamide-like compounds which are potent and specific for human thrombin. This crystal structure indicates that fresh ideas for the generation of novel and specific inhibitors may arise from examining weak binding compounds. Additionally, the crystal structure demonstrates the utility of crystallographic analysis of natural product:protein complexes.
A salicide-bridged trench capacitor with a double-sacrificial-Si/sub 3/N/sub 4/-sidewall (DSS) for high-performance logic-embedded DRAMs (2002)

We propose a Double-Sacrificial-Si/sub 3/N/sub 4/-Sidewall (DSS) technology to develop a salicide-bridged trench-capacitor cell for high-performance logic-embedded DRAMs. Both the DSS technology and the salicide-bridging are fully compatible with high-performance CMOS processes. With these technologies, a storage node of a Substrate-Plate Trench (SPT) capacitor can be connected to a drain node even over a thick oxide collar during the silicidation.
Some Properties for Distances Based on Neighbourhood Sequences in the Face-Centered Cubic Grid and the Body-Centered Cubic Grid (2006)

Some Properties for Distances Based on Neighbourhood Sequences in the Face-Centered Cubic Grid and the Body-Centered Cubic Grid
Exploring Materials Options for Ultra-High Temperature Supercritical CO2 Applications (2023)

There has been recent interest in exploring revolutionary supercritical CO 2 (sCO 2 ) cycles and a small effort is exploring what materials may be compatible with CO 2 at up to 1200C.Initial exposures were conducted at 1 and 20 bar CO 2 for 1000 h at 1000 and 1200C.As expected, Mo and W specimens that might be used as matrix materials in cermets were rapidly attacked under these conditions.Even alumina-forming FeCrAl alloys showed high mass gains in less than 100 h at 1200C and 500 h at 1000C due to the formation of Fe-rich oxide.Both Fe-and Nibased alloys exposed at 1000C showed higher mass gains than formed in air.Thus, Ni-based alloys appear compatible with sCO 2 up to 800C but less so at higher temperatures.Low mass gains were observed for CVD SiC but MoSi 2 and MoSiAl specimens did not form protective scales under these conditions.
Covalent Nucleophilic Catalysis (2001)

Abstract Covalent nucleophilic catalysis is the involvement of a nucleophile on an enzyme (usually one of the side‐chain groups of an α‐amino acid residue) in forming a covalent (shared) bond with a reactant to generate an intermediate on the reaction pathway leading to the observed product(s).
Single Event Transient Compact Model for FDSOI MOSFETs Taking Bipolar Amplification and Circuit Level Arbitrary Generation Into Account (2019)

Single Event Transients (SET) are ionizing particles induced current pulses which are able to generate soft errors in CMOS circuits. In Silicon-on-Insulator (SOI) technologies, bipolar amplification phenomena is more significant due to presence of the Burried Oxide (BOX), which is detrimental to soft errors sensitivity. State of the art FDSOI SET models account for bipolar amplification through a dynamic pre-factor. This approach is mainly empirical and not compact. In this work, we propose a SET compact model for FDSOI MOSFETs including a physical modeling of bipolar amplification. Results are validated through TCAD simulations. A circuit level approach is proposed considering arbitrary generation within functional SRAM cell. This approach allows more realistic Single Event Upset (SEU) prediction and we show how circuit level generation can influence SEU prediction.
Surface Functionalization of Copper via Oxidative Graft Polymerization of 2,2′-Bithiophene and Immobilization of Silver Nanoparticles for Combating Biocorrosion (2010)

An environmentally benign approach to surface modification was developed to impart copper surface with enhanced resistance to corrosion, bacterial adhesion and biocorrosion. Oxidative graft polymerization of 2,2'-bithiophene from the copper surface with self-assembled 2,2'-bithiophene monolayer, and subsequent reduction of silver ions to silver nanoparticles (Ag NPs) on the surface, give rise to a homogeneous bithiophene polymer (PBT) film with densely coupled Ag NPs on the copper surface (Cu-g-PBT-Ag NP surface). The immobilized Ag NPs were found to significantly inhibit bacterial adhesion and enhance the antibacterial properties of the PBT modified copper surface. The corrosion inhibition performance of the functionalized copper substrates was evaluated by Tafel polarization curves and electrochemical impedance spectroscopy. Arising from the chemical affinity of thiols for the noble and coinage metals, the copper surface functionalized with both PBT brushes and Ag NPs also exhibits long-term stability, and is thus potentially useful for combating the combined problems of corrosion and biocorrosion in harsh marine and aquatic environments.
Expression of functional trk protooncogene in human monocytes. (1993)

There is increasing evidence that neurotrophins, including nerve growth factor (NGF), exert specific effects on cells of the immune system in addition to their neurotrophic actions. This report shows that human monocytes express the trk protooncogene, encoding the signal-transducing receptor unit for NGF. This receptor is functional, since interaction of NGF with monocytes triggered a respiratory burst, the major component of monocyte cytotoxic activity. During in vitro differentiation of human blood monocytes to macrophages trk expression decreased, suggesting a maturation-dependent trk expression decreased, suggesting a maturation-dependent trk regulation. Treatment of monocytes with Staphylococcus aureus Cowan I, a potent activator of monocytes, stimulated trk mRNA synthesis in a time-dependent way, implying a modulatory role for NGF in immune functions. The finding that dibutyryl cAMP elicited a time-dependent trk induction in monocytes as well as in phorbol ester-differentiated promonocytic U937 cells indicates that adenylate cyclase is involved in monocytic trk regulation. These results suggest that NGF, in addition to its neurotrophic function, is an immunoregulatory cytokine acting on monocytes.
Colonic transit time relates to bacterial metabolism and mucosal turnover in the human gut (2016)

Little is known about how colonic transit time relates to human colonic metabolism, and its importance for host health, although stool consistency, a proxy for colonic transit time, has recently been negatively associated with gut microbial richness. To address the relationships between colonic transit time and the gut microbial composition and metabolism, we assessed the colonic transit time of 98 subjects using radiopaque markers, and profiled their gut microbiota by16S rRNA gene sequencingand their urine metabolome by ultra performance liquid chromatography mass spectrometry. Based on correlation analyses,we show that colonic transit time is associated with overall gutmicrobial composition, diversity and metabolism. A relatively prolonged colonic transit time associates with high microbial species richness and a shift in colonic metabolismfrom carbohydrate fermentation to protein catabolism as reflected by microbial metabolites in urine. This results in a number of potentially deleterious protein-derived metabolites. Additionally, longer colonic transit time correlates with metabolites likely reflecting reduced renewal of the colonic mucosa. Together, this suggests that a high gut microbial richness does not per seimply a healthy gut microbiota, and contributes to the understanding of the pathophysiologyof diseases where increased transit time is a risk factor.Finally, our findings highlight the colonic transit time as an important physiological variable, which should be considered in gut microbiota and metabolomics studies
Wheelchair Securement for Urban Transit Vehicles: It’s Time to Address the Other Side of the Problem (2006)

Travel is an integral part of life in today’s society and wheelchair securement is an essential part of safe travel. Advances in wheelchair securement are facing a challenge in that different types of securement are appropriate for different types of transportation but it’s impractical to expect any given wheelchair to work with all of them. The signing of the Americans with Disabilities Act spurred the development and implementation of accessible transportation. This included technologies for the securement of wheelchairs in buses, paratransit vehicles, and personal vehicles. Although several types of securement systems were developed early on, belt-type systems were almost universally adopted because of their low cost and flexibility. Standards have been developed for belt-type securement and they are being worked on for both docking and rear facing securement as well. The dilemma is that each of these systems requires different features for the wheelchair to be secured: belt-systems require one type of attachment bracket, transit docking another, personal van docking yet another, and rear facing requires none. Rather than trying to standardize the securement industry, wheelchairs should be built to accommodate various securement systems by using a system analogous to that used for trailer hitches on automobiles. Incentives should be developed so that manufacturers will incorporate attachment points in their products for either a factory or an aftermarket interface receiver. On installation of the receiver, the user could then easily change between a bracket for belts, an interface for their personal van, or any other type of securement system to be used.
Efficient Range-based Query Processing on the Hadoop Distributed File System (2013)

There was a common belief that the performance of query in a data warehousing system built on top of Hadoop Distributed File System (HDFS) does not meet the performance in traditional data warehousing systems. Therefore, in the past five years, there has been considerable effort to improve the query performance on data warehousing systems running on the HDFS. The main goal of this work is to develop the mechanisms to support an efficient processing of range-based queries over large size of data stored in the HDFS. In particular, we present the data storage scheme which logically partitions each HDFS block based on the user-specified columns.