gebhart/patrepeval huggingface dataset:
Influence of Androgen Therapy on Growth Rate of Hypogonadal Adolescent Boys. (1940)

The administration of testosterone propionate in doses of 75 to 125 mg weekly to 8 hypogonadal adolescent boys ranging in age between 9 and 18 years was accompanied by an increase in average growth rate from 1.36 cm per 100 days during the control period to 3.6 cm per 100 days during the period of therapy. Following the cessation of treatment the average growth rate again fell to 1.56 cm per 100 days. This apparent stimulation of growth rate was unaccompanied by X-ray evidence of epiphyseal closure. The exact mechanism of this growth stimulation is not clear. Since all of these individuals exhibited evidence of hypogonadism, it must be pointed out that, on the basis of these observations, there is no justification for the use of testosterone propionate as a growth stimulant in normal adolescence since such therapy might result in permanent damage to the individual.
k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design (2014)

Computational strain design protocols aim at the system-wide identification of intervention strategies for the enhanced production of biochemicals in microorganisms. Existing approaches relying solely on stoichiometry and rudimentary constraint-based regulation overlook the effects of metabolite concentrations and substrate-level enzyme regulation while identifying metabolic interventions. In this paper, we introduce k-OptForce, which integrates the available kinetic descriptions of metabolic steps with stoichiometric models to sharpen the prediction of intervention strategies for improving the bio-production of a chemical of interest. It enables identification of a minimal set of interventions comprised of both enzymatic parameter changes (for reactions with available kinetics) and reaction flux changes (for reactions with only stoichiometric information). Application of k-OptForce to the overproduction of L-serine in E. coli and triacetic acid lactone (TAL) in S. cerevisiae revealed that the identified interventions tend to cause less dramatic rearrangements of the flux distribution so as not to violate concentration bounds. In some cases the incorporation of kinetic information leads to the need for additional interventions as kinetic expressions render stoichiometry-only derived interventions infeasible by violating concentration bounds, whereas in other cases the kinetic expressions impart flux changes that favor the overproduction of the target product thereby requiring fewer direct interventions. A sensitivity analysis on metabolite concentrations shows that the required number of interventions can be significantly affected by changing the imposed bounds on metabolite concentrations. Furthermore, k-OptForce was capable of finding non-intuitive interventions aiming at alleviating the substrate-level inhibition of key enzymes in order to enhance the flux towards the product of interest, which cannot be captured by stoichiometry-alone analysis. This study paves the way for the integrated analysis of kinetic and stoichiometric models and enables elucidating system-wide metabolic interventions while capturing regulatory and kinetic effects.
Optimized cutoffs improve performance of the aspartate aminotransferase to platelet ratio index for predicting significant liver fibrosis in human immunodeficiency virus/hepatitis C virus co‐infection (2008)

APRI with adjusted cutoffs can predict significant liver fibrosis in patients with HIV/HCV co-infection and might obviate the need to perform a biopsy in a considerable percentage of those subjects.
GPRC5D Is a Cell Surface Plasma Cell Marker Whose Expression Is High In Myeloma Cells and Reduced Following Coculture With Osteoclasts (2013)

Abstract Identification of unique cell surface markers on myeloma cells is important for development of targeted therapies and detection of residual disease. GPRC5D is an orphan receptor reportedly expressed at high level in bone marrow (BM) aspirates or biopsies from myeloma patients. Other studies detected GPRC5D in skin and brain but not in other tissues. The aims of the study were to assess GPRC5D gene expression and cell surface localization in myeloma cells, the changes in expression of GPRC5D and other typical myeloma cell markers following coculture of primary myeloma cells with osteoclasts and the consequences of GPRC5D gene silencing on myeloma cell growth. Global gene expression profile (GEP), qRT-PCR and immunohistochemistry revealed exclusive high expression of GPRC5D in normal and myeloma plasma cells but not in B cells, MSCs, osteoclasts or BM mononucleated cells. GPRC5D expression was higher in myeloma plasma cells from newly diagnosed patients (n=698) compared to normal plasma cells (n=26, p&lt;0.0001)). Among molecularly classified groups GPRC5D expression is higher in MS, MF and LB subgroups and lowest in CD2 and MM cell lines. Flow cytometry analysis and immunohistochemistry detected cell surface expression of GPRC5D in myeloma plasma cells while nuclear localization was also detected in certain myeloma cell lines (e.g. H929). Western blots analysis confirmed GPRC5D expression in whole cell lysate and nuclear fraction. We and other demonstrated phonotypical plasticity of myeloma plasma cells capable of altered expression of recognizable plasma cell markers (e.g. CD138, CD45) following coculture with stromal cells (Dezorella et al., 2009) or osteoclasts (Yaccoby, 2005). In coculture of primary CD138-selected myeloma cells with osteoclasts (n=8), CD138 (p&lt;0,004), CD38 (p&lt;0.001) and GPRC5D (p&lt;0.007) were commonly and significantly downregulated, CD45 (p&lt;0.02) was upregulated, and IRF4 expression was unaffected in cocultured myeloma cells compared to the control freshly obtained uncultured myeloma cells assessed by GEP and qRT-PCR. We also observed reduced expression of GPRC5D in MM cells purified from focal lesion compared to interstitial marrow in paired clinical samples (n=176, p&lt;1.21E-09), suggesting that high activity of osteoclasts in osteolytic lesions mediates phenotypical alteration in myeloma cells. Stable knockdown of GPRC5D by 70% in CAG myeloma line using lentiviral particles containing shRNA had no effect on short-term growth of these cells assessed by MTT assay. These data indicate that GPRC5D is a novel cell surface marker for myeloma plasma cells and that its expression is reduced in dedifferentiated myeloma cells. Disclosures: No relevant conflicts of interest to declare.
Post-crizotinib management of effective ceritinib therapy in a patient with ALK-positive non-small cell lung cancer (2016)

Second-line ceritinib treatment, when administered at 450 mg/day with food, is both well tolerated and efficacious in a patient with previously treated lung adenocarcinoma who had discontinued crizotinib due to disease progression and gastrointestinal adverse effects (AEs).
Tumor-Released Microvesicles as Vehicles of Immunosuppression (2007)

Tumor-released microvesicles, or exosomes, which are abundant in the body fluids of patients with cancer, are likely to be involved in tumor progression. We recently showed that microvesicles released by human melanoma and colorectal carcinoma cells can promote the differentiation of monocytes to myeloid-derived suppressor cells which support tumoral growth and immune escape. These findings underscore an important role for these extracellular organelles in remodeling tumor-stromal interactions to promote malignancy.
High throughput flow cytometry (2001)

Flow cytometry has potential throughput of 100,000 samples or more per day starting with the method described. The method is currently best suited to end-point assays. However, combined with high-speed sorting and single- cell assays, the number of assays could approach 1 billion per day.
ANTIVIRAL ACTIVITY OF CULTURED BLUE‐GREEN ALGAE (CYANOPHYTA)1 (1993)

ABSTRACT Lipophilic and hydrophilic extracts from approximately 600 strains of cultured cyanophytes, representing some 300 species, were examined for antiviral activity against three pathogenic viruses. Approximately 10% of the cultures produced substances that caused significant reduction in cytopathic effect normally associated with viral infection. The screening program identified the order Chroococcales as commonly producing antiviral agents.
Synthetic matrix metalloproteinase inhibitors and tissue inhibitor of metalloproteinase (TIMP)-2, but not TIMP-1, inhibit shedding of tumor necrosis factor-alpha receptors in a human colon adenocarcinoma (Colo 205) cell line. (1998)

The solubilization of plasma membrane receptors through proteolytic cleavage of the ligand binding domain at the cell surface is an important mechanism for regulating cytokine function and receptor signaling. The inhibition of the shedding of a variety of receptors by synthetic inhibitors of the matrix metalloproteinases (MMPs) implicates metalloproteinases in this regulatory event. We examined the effects of two naturally occurring tissue inhibitors of metalloproteinases, TIMP-1 and TIMP-2, and several synthetic MMP inhibitors (MMPIs) on the shedding of both tumor necrosis factor alpha receptor type I (TNFalpha-RI; Mr 55,000) and TNFalpha-RII (Mr 75,000) by the Colo 205 human colon adenocarcinoma cell line. Culture of Colo 205 cells for 48 h resulted in the shedding of both TNFalpha-RI and TNFalpha-RII, as determined by ELISA. The shedding of TNFalpha receptors was not affected by TIMP-1 or protease inhibitors aprotinin, pepstatin, or leupeptin but was inhibited in a dose-dependent manner by the following synthetic MMPIs: batimastat and marimastat (BB-94 and BB-2516, respectively, British Biotech, Inc.); CT1418 (Celltech Therapeutics); CGS27023A (Novartis Pharmaceuticals); and RO31-9790 (Roche), with IC50s ranging from 3.2 to 38.0 microM. Similarly, TIMP-2 from two different sources reproducibly inhibited the shedding of both TNFalpha-RI and TNFalpha-RII in a dose-dependent manner (IC50 = 286 +/- 33 nM for TNFalpha-RI shedding and 462 +/- 52 nM for shedding of TNFalpha-RII). The inhibition of TNFalpha-RI shedding was confirmed in the SW626 human ovarian adenocarcinoma cell line. The synthetic MMPIs and TIMP-2, but not TIMP-1, also caused a dose-dependent increase in the number of TNFalpha receptors retained on the surface of Colo 205 cells, as determined by flow cytometry. Inhibition of TNFalpha receptor shedding with TIMP-2 occurs at molar concentrations 10-100 times less than those required with low molecular weight, synthetic MMPIs but at concentrations greater than those required to inhibit collagen degradation. Modulation of TNFalpha receptor shedding by TIMP-2 could have important implications for the pleiotropic effects of TNFalpha in both normal and malignant cells and for the pharmacological activity of synthetic MMPIs.
Vaccination with BLP25 liposome vaccine to treat non-small cell lung and prostate cancers (2005)

The identification of tumor-associated/-specific antigens and an increased understanding of the ways in which antigens are processed and presented has led to a revived interest in cancer vaccines as a therapeutic strategy. BLP25 liposome (L-BLP25) vaccine is a cancer vaccine that targets the exposed core peptide of the MUC1 tumor-associated antigen. Studies in advanced-stage non-small cell lung cancer demonstrate that L-BLP25 vaccine has the potential to extend the survival of patients with Stage IIIB locoregional non-small cell lung cancer and maintain quality of life for longer. L-BLP25 vaccine also shows promise for prostate cancer patients, having the potential to prolong prostate-specific antigen doubling time in men with biochemical failure post prostatectomy. These clinically meaningful results with a relatively nontoxic therapeutic vaccine are very encouraging and suggest potential for L-BLP25 to fulfill an unmet medical need.
Peptidylprolyl Cis / Trans Isomerases (Immunophilins): Biological Diversity - Targets - Functions (2003)

Information recovered from genome sequencing projects, multiple sequence alignments, structural analyses of PPIase and published records were used in deciphering the biological diversity, functions and targets of four groups of proteins encoded by dissimilar sets of sequences whose spatial representations exhibit peptidylprolyl cis/trans isomerase activity (PPIase). In the human genome there are encoded fifteen proteins whose segments have significant homology with the sequence of 12 kDa protein which is the target of the potent immunosuppressive macrolides FK506 or rapamycin. The 12 kDa archetype of the FK506-binding protein (FKBP), known as FKBP-12a, is an abundant intracellular protein whereas other FKBPs possessing from one to four FK506-like binding domains (FKBDs) have nominal masses varying from 13 to 135 kDa. The human genome contains at least sixteen genes encoding proteins comprising one cyclosporin-A (CsA) binding domain (CLD) called cyclophilins whose nominal masses vary from 17 to 324 kDa and multiple coding segments for small cyclophilins (17-19 kDa) whose transcription levels and functions remain unknown. The third group of PPIases encoded in the genome comprises two proteins (hPin1 and hParv14) where hPin1 is an important PPIase for cell cycle. The A. thaliana, C. elegans, D. melanogaster and S. cerevisiae genomes encode a less diverse spectrum of PPIases whereas the prokaryotic genomes contain from none to three cyclophilins, from none to four genes encoding FKBPs, one distant homologue of the Pin1 protein named parvulin and the fourth group of PPIases known as trigger factors. PPIases are discretely distributed to different cellular compartments and interact with a number of targets that control a range of cellular processes. Analyses of the sequence alignments of the two groups of PPIases, namely cyclophilins and FKBPs from diverse phyla, show that in each group their sequences diverge but the amino acid residues which form the PPIase activity site and macrolide binding cavity remain well conserved in the majority of them which suggests that the spatial structures and functions of each group of PPIases remain conserved.
Capacitive coupling for power and data telemetry to implantable biomedical microsystems (2009)

This paper proposes a new method for power telemetry and wireless data transfer to biomedical implants. Confinement of the transferred energy within a predefined area, hence not influencing the neighboring sensitive circuitry on the microsystem, and also allowing for more than one telemetry link on the same platform and even operating at the same carrier frequency are among the advantages of the proposed method over the traditional approaches for power and data telemetry.
A novel suicide substrate for DNA topoisomerases and site-specific recombinases (1995)

DNA topoisomerases and DNA site-specific recombinases are biologically important enzymes involved in a diverse set of cellular processes. We show that replacement of a phosphodiester linkage by a 5'-bridging phosphorothioate linkage creates an efficient suicide substrate for calf thymus topoisomerase I and lambda integrase protein (Int). Although the bridging phosphorothioate linkage is cleaved by these enzymes, the 5'-sulfhydryl which is generated is not competent for subsequent ligation reactions. We use the irreversibility of Int-promoted cleavage to explore conditions and factors that contribute to various steps of lambda integrative recombination. The phosphorothioate substrates offer advantages over conventional suicide substrates, may be potent tools for inhibition of the relevant cellular enzymes and represent a unique tool for the study of many other phosphoryl transfer reactions.
Classical Pathway Evaluation (1994)

This unit describes several assay methods that can be used to determine the functional status of the classical pathway of complement and to quantitate its component proteins. The classical pathway includes C1qrs, C2, C4, C3, C5, C6, C7, C8, and C9, listed in the order in which they interact. Two CH(50) assay procedures are presented that test total classical pathway function; one is carried out in test tubes, whereas the alternate protocol describes a variation that is carried out in 96-well microtiter plates. Three support protocols describe preparing serum and erythrocyte-antibody complexes (EA) for use in CH(50) assays,and titrating of hemolysin for use in EA preparation. As an alternative to functional assays, radial immunodiffusion (RID) methods are also presented. These can be used to measure the concentrations of most circulating complement proteins and to evaluate the functional status of C1-esterase inhibitor. A fourth support protocol provides a method to determine antibody concentrations for RID assays.
Visual attention based image browsing on mobile devices (2003)

Images have become more and more common in mobile communications. People now can easily take and exchange pictures on the move using their mobile devices and digital cameras. However, a crucial challenge is to provide a better user experience for browsing large images on limited and heterogeneous screen sizes of mobile devices. In this paper, we propose a novel image viewing technique based on an adaptive attention shifting model. A presentation technique named rapid serial visual presentation (RSVP), borrowed from the UI community, is used to simulate the attention shifting process. We show a prototype image viewer developed for pocket PC and conduct some evaluations to demonstrate the effectiveness of our approach.
High-speed 3D shape measurement by GOBO projection of aperiodic sinusoidal fringes: a performance analysis (2018)

In order to increase the measurement speed of pattern projection-based 3D sensors, we have developed a GOBO slide-based pattern projector (GOes Before Optics) which allows for pattern projection at several 10,000 fps. After first experimental configurations have been mainly set up based on empirical study, in this contribution, we investigate the capabilities of a GOBO projection-based 3D sensor on a theoretical level. We discuss and optimize the parameters which influence the completeness and accuracy of the 3D result, and we experimentally verify the theoretical results by means of a GOBO projection-based 3D sensor operating in the near infrared.
A practical 3D bearing-only SLAM algorithm (2005)

This article presents a bearing only 3D SLAM algorithm which has the same complexity and optimality as the usual extended Kalman filter used in classical SLAM. We especially focus on the landmark initialization process, which relies on visual point features tracked in the sequence of acquired images: a probabilistic approach to estimate their parameters is presented. This induces a particular structure of the filter architecture, in which are memorized a set of past robot poses. Simulations are made to compare the influence of some parameters required by our approach, and results with an indoor robot and an airship are presented.
A Survey on Network Codes for Distributed Storage (2011)

Distributed storage systems often introduce redundancy to increase reliability. When coding is used, the repair problem arises: if a node storing encoded information fails, in order to maintain the same level of reliability we need to create encoded information at a new node. This amounts to a partial recovery of the code, whereas conventional erasure coding focuses on the complete recovery of the information from a subset of encoded packets. The consideration of the repair network traffic gives rise to new design challenges. Recently, network coding techniques have been instrumental in addressing these challenges, establishing that maintenance bandwidth can be reduced by orders of magnitude compared to standard erasure codes. This paper provides an overview of the research results on this topic.
Genetic characterization of psp encoding the DING protein in Pseudomonas fluorescens SBW25 (2007)

Psp gene is expressed under conditions of Pi limitation. It is an exoprotein secreted mainly via the Hxc type II secretion system, whose expression is elevated on plant surfaces. We propose that Psp is involved in extracellular scavenging of phosphates, which are subsequently taken up by the cell-bound Pst transport system.
Techniques for integrating parallelizing transformations and compiler-based scheduling methods (1992)

Although the tasks of applying transformations and scheduling instructions are typically implemented in separate phases of a parallelizing compiler, interactions between these phases occur. The authors discuss these interdependencies and demonstrate that the separate phase approach can result in the application of a sequence of transformations that is not effective. The techniques presented for integrating these tasks utilize an iterative approach to applying program transformations and scheduling instructions for execution on a multiprocessor. These integrated techniques employ a demand driven approach to applying transformations; by iterating between the scheduling and transforming tasks, transformations are applied to the program only if and where they are needed. The authors also introduce an automatic transformation application and selection algorithm that provides further control over the application of transformations. >
Application of two-wavelength optical heterodyne alignment system in XS-1 (1999)

This article presents the alignment performance of the two- wavelength optical heterodyne alignment system in the x-ray stepper XS-1. The alignment accuracy obtained by the double- exposure method with a single mask and a Si trench wafer was better than 20 nm. The dependence of the alignment accuracy on Si trench depth indicated that the two wavelengths compliment each other and ensure a 3(sigma) of less than 20 nm. The alignment capabilities for other processed test wafers were also investigated by mix-and-match exposure. For etched SiO<SUB>2</SUB> and poly-Si film on a Si trench, an accuracy below 20 nm was obtained. For AlSiCu film sputtered on etched SiO<SUB>2</SUB>, there appeared systematic alignment offsets depended on die position, which are thought to be due to a wafer-induced shift. The systematic offset errors were eliminated by the use of send-ahead wafer and corrections for individual offsets on each die, and thus the alignment accuracy was improved to 20-40 nm for each alignment axis. The two-wavelength heterodyne alignment system of the XS-1 has sufficient potential for 130-nm lithography and below.
Imaging interferometric microscopy (2003)

We introduce and demonstrate a new microscopy concept: imaging interferometric microscopy (IIM), which is related to holography, synthetic-aperture imaging, and off-axis-dark-field illumination techniques. IIM is a wavelength-division multiplex approach to image formation that combines multiple images covering different spatial-frequency regions to form a composite image with a resolution much greater than that permitted by the same optical system using conventional techniques. This new type of microscopy involves both off-axis coherent illumination and reinjection of appropriate zero-order reference beams. Images demonstrate high resolution, comparable with that of a high-numerical-aperture (NA) objective, while they retain the long working distance, the large depth of field, and the large field of view of a low-NA objective. A Fourier-optics model of IIM is in good agreement with the experiment.