gebhart/patrepeval huggingface dataset:
Noninvasive imaging of bone microarchitecture (2011)

The noninvasive quantification of peripheral compartment-specific bone microarchitecture is feasible with high-resolution peripheral quantitative computed tomography (HR-pQCT) and high-resolution magnetic resonance imaging (HR-MRI). In addition to classic morphometric indices, both techniques provide a suitable basis for virtual biomechanical testing using finite element (FE) analyses. Methodical limitations, morphometric parameter definition, and motion artifacts have to be considered to achieve optimal data interpretation from imaging studies. With increasing availability of in vivo high-resolution bone imaging techniques, special emphasis should be put on quality control including multicenter, cross-site validations. Importantly, conclusions from interventional studies investigating the effects of antiosteoporotic drugs on bone microarchitecture should be drawn with care, ideally involving imaging scientists, translational researchers, and clinicians.
Magnetization transfer in MRI: a review (2001)

This review describes magnetization transfer (MT) contrast in magnetic resonance imaging. A qualitative description of how MT works is provided along with experimental evidence that leads to a quantitative model for MT in tissues. The implementation of MT saturation in imaging sequences and the interpretation of the MT-induced signal change in terms of exchange processes and direct effects are presented. Finally, highlights of clinical uses of MT are outlined and future directions for investigation proposed.
Mapping of a Minimal AU-rich Sequence Required for Lipopolysaccharide-induced Binding of a 55-kDa Protein on Tumor Necrosis Factor-α mRNA (1998)

In monocyte/macrophage cells, the translation of tumor necrosis factor-alpha (TNF-alpha) mRNA is tightly controlled. In unstimulated cells, TNF-alpha mRNA is translationally repressed. However, upon stimulation of the cells with various agents (e.g. lipopolysaccharides (LPS) and viruses), this repression is overcome and translation occurs. The key element in this regulation is the AU-rich sequence present in the 3'-untranslated region of TNF-alpha mRNA. Several groups have described the binding of proteins on AU-rich elements (AREs). We have previously reported the binding of two cytosolic protein complexes (1 and 2) to the TNF-alpha mRNA ARE, one of which (complex 2) is observed only following induction of TNF-alpha production by LPS. In this report, we have demonstrated that complex 1 involves a long fragment of the ARE, whereas the formation of the LPS-inducible complex 2 requires a minimal sequence which corresponds to the nonanucleotide UUAUUUAUU. Furthermore, we show that the RNA-binding protein involved in complex 2 has an apparent molecular mass of 55 kDa. Finally, we tested other AREs for their ability to form complex 2. We observed that the ARE derived from granulocyte/macrophage colony-stimulating factor mRNA, which does contain the nonanucleotide, is able to sustain the LPS-induced binding of the 55-kDa protein. However, c-myc mRNA, which does not contain the nonanucleotide, is unable to promote the formation of any LPS-induced complex.
A Controlled Trial of Leuprolide with and without Flutamide in Prostatic Carcinoma (1989)

To test the hypothesis that maximal androgen blockade improves the effectiveness of the treatment of prostatic cancer, we conducted a randomized, double-blind trial in patients with disseminated, previously untreated prostate cancer (stage D2). All 603 men received leuprolide, an analogue of gonadotropin-releasing hormone that inhibits the release of gonadotropins, in combination with either placebo or flutamide, a nonsteroidal antiandrogen that inhibits the binding of androgens to the cell nucleus. As compared with the 300 patients receiving leuprolide and placebo, the 303 patients randomly assigned to receive leuprolide and flutamide had a longer progression-free survival (16.5 vs. 13.9 months; P = 0.039) and an increase in the median length of survival (35.6 vs. 28.3 months; P = 0.035). The differences between the treatments were particularly evident for men with minimal disease and good performance status; however, further studies should be conducted in this subgroup. Symptomatic improvement was greatest during the first 12 weeks of the combined androgen blockade, when leuprolide alone often produces a painful flare in the disease. We conclude that in patients with advanced prostate cancer, treatment with leuprolide and flutamide is superior to treatment with leuprolide alone.
Secretion of Bovine Uterine Proteins in Response to Type I Interferons1 (1995)

Bovine interferon-tau (bIFN-tau) is secreted by the developing conceptus and initiates antiluteolytic events by interacting with uterine membrane receptors. We have identified three endometrial proteins (approximately 8, 16, and 28 kDa; P8, P16, and P28; respectively) that are secreted in response to recombinant (r) bIFN-tau. The objective of this study was to determine whether or not secretion of these proteins was a unique response to IFN-tau during early pregnancy. Three experiments were designed to examine secretion of endometrial proteins as a function of time in culture (0, 3, 6, 12, 18, 24 h), stage of the estrous cycle and pregnancy (Days 15, 18, 0/21), and dose of Type I IFN (0, 0.5, 5, and 25 nM; rbIFN-tau, rbIFN-alpha, and roIFN-tau). Endometrium was cultured for times specified with L-[3H]leusine to generate radiolabeled proteins. Secreted proteins were quantitated by using one-dimensional (1D)-PAGE, fluorography, and densitometry. Secretion of P8, P16, and P28 increased over time (p < 0.0001) in culture and in response to 25 nM rbIFN-tau (p < 0.05). Secretion of P8 in response to rbIFN-tau was higher (p < 0.05). Secretion of P8 in response to rbIFN-tau was higher (p < 0.0005) in endometrium collected from pregnant than nonpregnant heifers, but did not differ across the days examined. Although secretion of P8 was higher (p < 0.0001) in the presence than in the absence of rbIFN-tau, it was not affected by rbIFN-alpha.(ABSTRACT TRUNCATED AT 250 WORDS)
Structure−Activity Relationships of the Melanocortin Tetrapeptide Ac-His-DPhe-Arg-Trp-NH2 at the Mouse Melanocortin Receptors. 1. Modifications at the His Position (2002)

The melanocortin pathway is an important participant in obesity and energy homeostasis. The centrally located melanocortin-3 and melanocortin-4 receptors (MC3R, MC4R) are involved in the metabolic and food intake aspects of energy homeostasis and are stimulated by melanocortin agonists such as alpha-melanocyte stimulation hormone (alpha-MSH). The melanocortin agonists contain the putative message sequence "His-Phe-Arg-Trp", and it has been well documented that inversion of chirality of the Phe to DPhe results in a dramatic increase in melanocortin receptor potency. Herein, we report a tetrapeptide library based on the template Ac-His-DPhe-Arg-Trp-NH(2), consisting of 17 members that have been modified at the His(6) position (alpha-MSH numbering) and pharmacologically characterized for agonist activity at the mouse melanocortin receptors MC1R, MC3R, MC4R, and MC5R. These studies provide further experimental evidence that the His(6) position can determine MC4R versus MC3R agonist selectivity and that chemically nonreactive side chains may be substituted for the imidazole ring (generally needs to be side chain protected in synthetic schemes) in the design of MC4R-selective, small-molecule, non-peptide agonists. Specifically, the tetrapeptide containing the amino-2-naphthylcarboxylic acid (Anc) amino acid at the His position resulted in a potent agonist at the mMC4R (EC(50) = 21 nM), was a weak mMC3R micromolar antagonist (pA(2) = 5.6, K(i) = 2.5 microM), and possessed >4700-fold agonist selectivity for the MC4R versus the MC3R. Substitution of the His(6) amino acid in the tetrapeptide template by the Phe, Anc, 3-(2-thienyl)alanine (2Thi), and 3-(4-pyridinyl)alanine (4-Pal) resulted in equipotency or only up to a 7-fold decrease in potency, compared to the His(6)-containing tetrapeptide at the mMC4R, demonstrating that these amino acid side chains may be substituted for the imidazole in the design of MC4R-selective non-peptide molecules.
Computerized Detection of Pulmonary Nodules on CT Scans (1999)

Helical computed tomography (CT) is the most sensitive imaging modality for detection of pulmonary nodules. However, a single CT examination produces a large quantity of image data. Therefore, a computerized scheme has been developed to automatically detect pulmonary nodules on CT images. This scheme includes both two- and three-dimensional analyses. Within each section, gray-level thresholding methods are used to segment the thorax from the background and then the lungs from the thorax. A rolling ball algorithm is applied to the lung segmentation contours to avoid the loss of juxtapleural nodules. Multiple gray-level thresholds are applied to the volumetric lung regions to identify nodule candidates. These candidates represent both nodules and normal pulmonary structures. For each candidate, two- and three-dimensional geometric and gray-level features are computed. These features are merged with linear discriminant analysis to reduce the number of candidates that correspond to normal structures. This method was applied to a 17-case database. Receiver operating characteristic (ROC) analysis was used to evaluate the automated classifier. Results yielded an area under the ROC curve of 0.93 in the task of classifying candidates detected during thresholding as nodules or nonnodules.
A comparison of the mechanical performance characteristics of seven drug‐eluting stent systems (2008)

Better understanding of mechanical properties of DES shall improve tactile skills of the interventionists during PCI and to improve criteria for DES selection in specific clinical settings.
Drained End Shield Effects on Heat Deposition Rate Distribution in CANDU 6 Reactor End Shield Structure (1994)

The loss of water in the carbon steel balls and water region of the end shield for CANDU 6 reactor could lead to significant temperature gradient through the end shield structure which amy result in the excessive deformation. With an assumed end shield drained scenario, the heat deposition rates were calculated through the end shield associated with the central fuel channel during full power operation as an initial step to thermal stress analysis. The drained case was compared with that of water present normal case in therms of heat deposition rater and the total heating throughout the end shield regions. The compared results show that the heat deposition and the total heating remain almost the same between the two cases. It was found that the change of volume integrated flux in the end shield regions due to the loss of water contribute a negligible effect on the heat deposition in this region.
Human Insulin from Recombinant DNA Technology (1983)

Human insulin produced by recombinant DNA technology is the first commercial health care product derived from this technology. Work on this product was initiated before there were federal guidelines for large-scale recombinant DNA work or commercial development of recombinant DNA products. The steps taken to facilitate acceptance of large-scale work and proof of the identity and safety of such a product are described. While basic studies in recombinant DNA technology will continue to have a profound impact on research in the life sciences, commercial applications may well be controlled by economic conditions and the availability of investment capital.
The Janus kinase 1/2 inhibitor ruxolitinib in COVID-19 with severe systemic hyperinflammation (2020)

A subgroup of patients with severe COVID-19 suffers from progression to acute respiratory distress syndrome and multiorgan failure. These patients present with progressive hyperinflammation governed by proinflammatory cytokines. An interdisciplinary COVID-19 work flow was established to detect patients with imminent or full blown hyperinflammation. Using a newly developed COVID-19 Inflammation Score (CIS), patients were prospectively stratified for targeted inhibition of cytokine signalling by the Janus Kinase 1/2 inhibitor ruxolitinib (Rux). Patients were treated with efficacy/toxicity guided step up dosing up to 14 days. Retrospective analysis of CIS reduction and clinical outcome was performed. Out of 105 patients treated between March 30th and April 15th<sub>,</sub> 2020, 14 patients with a CIS ≥ 10 out of 16 points received Rux over a median of 9 days with a median cumulative dose of 135 mg. A total of 12/14 patients achieved significant reduction of CIS by ≥25% on day 7 with sustained clinical improvement in 11/14 patients without short term red flag warnings of Rux-induced toxicity. Rux treatment for COVID-19 in patients with hyperinflammation is shown to be safe with signals of efficacy in this pilot case series for CRS-intervention to prevent or overcome multiorgan failure. A multicenter phase-II clinical trial has been initiated (NCT04338958).
Signal Regulatory Protein α Is Associated With Tumor-Polarized Macrophages Phenotype Switch and Plays a Pivotal Role in Tumor Progression (2013)

These findings suggest that SIRPα functions as an important modulator of tumor-polarized Mψ in hepatoma, and the reduction of SIRPα is a novel strategy used by tumor cells to benefit their behavior. Therefore, SIRPα could be utilized as a potential target for HCC therapy.
Mutations in the erythrocyte chemokine receptor (Duffy) gene: the molecular basis of the Fya/Fyb antigens and identification of a deletion in the Duffy gene of an apparently healthy individual with the Fy(a – b–) phenotype (1995)

The erythrocyte chemokine receptor, a receptor for Plasmodium vivax, carries the antigens of the Duffy blood group system. Sequence analysis of reticulocyte RNA from individuals of known Duffy phenotype showed that the Fya antigen differs from the Fyb antigen as a result of a single nucleotide difference (A131 or G) encoding amino acid Gly44 (Fya) or Asp (Fyb) in the N-terminal extracellular domain of the glycoprotein. Evidence is presented for two different genetic backgrounds giving rise to the Fy(a-b-) phenotype. The most likely genetic mechanism in most individuals of the Fy(a-b-) phenotype is down-regulation of Duffy glycoprotein mRNA. However, the Duffy gene from a very rare Caucasian individual (AZ) with the Fy(a-b-) phenotype has a 14 base-pair deletion (nucleotides 287-301) resulting in a frameshift which introduces a stop codon and produces a putative truncated 118 amino acid protein. The occurrence of this mutation in an apparently healthy individual raises questions about the functional importance of the Duffy glycoprotein not only in normal erythrocytes but also in all human cells and tissues.
Quantization of cepstral parameters for speech recognition over the World Wide Web (1999)

We examine alternative architectures for a client-server model of speech-enabled applications over the World Wide Web (WWW). We compare a server-only processing model where the client encodes and transmits the speech signal to the server, to a model where the recognition front end runs locally at the client and encodes and transmits the cepstral coefficients to the recognition server over the Internet. We follow a novel encoding paradigm, trying to maximize recognition performance instead of perceptual reproduction, and we find that by transmitting the cepstral coefficients we can achieve significantly higher recognition performance at a fraction of the bit rate required when encoding the speech signal directly. We find that the required bit rate to achieve the recognition performance of high-quality unquantized speech is just 2000 bits per second.
Role of Integrins in the Attachment of Metastatic Follicular Thyroid Carcinoma Cell Lines to Bone (1998)

One of the principle targets for metastasis of follicular thyroid carcinoma (FTC) is the skeleton. Because no data are available on the role of the integrin adhesion molecule family in the attachment of FTC to bone, we studied the attachment characteristics of three FTC cell lines to bone and the role of integrins. Three cell lines were used from the same patient, one (FTC-133) from the primary tumor and two (FTC-236 and FTC-238) from metastases. Attachment of FTC cell lines to bone was assessed on conditioned medium of an osteoblastic cell line, coated onto plastic, as an in vitro model of bone matrix. The synthetic RGD (Arg-Gly-Asp) peptide GRGDS impaired attachment of the FTC cell lines to bone matrix, demonstrating the role of integrins in the attachment of FTC to bone. Attachment of FTC-133 to bone matrix was blocked completely by GRGDS, whereas attachment of FTC-236 and FTC-238 could not be impaired completely. Semiquantitative polymerase chain reaction (PCR) of cDNA from the cell lines indicated stronger expression of alpha5 integrin mRNA in FTC-133 than in the other cell lines. In line with this, attachment of FTC-133 to bone matrix could be inhibited almost completely by anti alpha5 and beta1 integrin antibodies, indicating the importance of the fibronectin receptor in the attachment of FTC-133 to bone. Binding of FTC-236 and FTC-238 to bone matrix could not be inhibited completely by anti-integrin antibodies, suggesting an additional role of nonintegrin adhesion molecules in the attachment of FTC-236 and FTC-238 to bone. The synthetic bone sialoprotein cyclic peptide, CNB, revealed antiadhesive effects in the binding of FTC to bone. In conclusion, integrins play an important role in the attachment of metastatic FTC to bone. Differences in the functional involvement of integrins in the attachment to bone are observed between the three cell lines studied. From the present results, antiadhesive interventions with synthetic RGD peptides in FTC may be designed.
The effect of logic block complexity on area of programmable gate arrays (1989)

The authors explore the tradeoff between the area of a programmable gate array (PGA) and the functionality of its logic block. A set of industrial circuits is implemented as PGAs using tools for technology mapping, placement, and routing. A simple model allows the exploration of a range of programming technologies and accounts for the area required by wiring. Experiments indicate that for combinational logic blocks implemented using lookup tables, the best number of inputs to use is between three and four, and that a D flip-flop should always be included in the logic block. These results are independent of the programming technology
Targeting CD47-SIRPα interactions for potentiating therapeutic antibody-mediated tumor cell destruction by phagocytes (2014)

The primary aim of the studies described in this thesis was to investigate the role of CD47-SIRPα interactions in therapeutic antibody-dependent tumor cell destruction by human phagocytes and also explore the killing mechanism(s) by which human phagocytes, and in particular human neutrophils, mediate therapeutic antibody-dependent cytotoxicity towards cancer cells.
Structuring research methods and data with the research object model: genomics workflows as a case study (2014)

The Research Object is available at http://www.myexperiment.org/packs/428 The Wf4Ever Research Object Model is available at http://wf4ever.github.io/ro.
Neural Cell Adhesion Molecule: Structure, Immunoglobulin-Like Domains, Cell Surface Modulation, and Alternative RNA Splicing (1987)

The neural cell adhesion molecule, N-CAM, appears on early embryonic cells and is important in the formation of cell collectives and their boundaries at sites of morphogenesis. Later in development it is found on various differentiated tissues and is a major CAM mediating adhesion among neurons and between neurons and muscle. To provide a molecular basis for understanding N-CAM function, the complete amino acid sequences of the three major polypeptides of N-CAM and most of the noncoding sequences of their messenger RNA's were determined from the analysis of complementary DNA clones and were verified by amino acid sequences of selected CNBr fragments and proteolytic fragments. The extracellular region of each N-CAM polypeptide includes five contiguous segments that are homologous in sequence to each other and to members of the immunoglobulin superfamily, suggesting that interactions among immunoglobulin-like domains form the basis for N-CAM homophilic binding. Although different in their membrane-associated and cytoplasmic domains, the amino acid sequences of the three polypeptides appear to be identical throughout this extracellular region (682 amino acids) where the binding site is located. Variations in N-CAM activity thus do not occur by changes in the amino acid sequence that alter the specificity of binding. Instead, regulation is achieved by cell surface modulation events that alter N-CAM affinity, prevalence, mobility, and distribution on the surface. A major mechanism for modulation is alternative RNA splicing resulting in N-CAM's with different cytoplasmic domains that differentially interact with the cell membrane. Such regulatory mechanisms may link N-CAM binding function with other primary cellular processes during the embryonic development of pattern.
Avian thymic accessory cells. (1984)

On the basis of morphologic criteria and ingestion of latex particles, two basic types of accessory cells can be identified from quail and chick thymuses, dendritic cells, and macrophages. By using embryonic grafting techniques, we show that cells of this lineage enter the thymus during the initial colonization of the epithelial thymic rudiment by hemopoietic cells, and within a few days differentiate into cells exhibiting properties of glass adherence, Ia expression, and formation of rosettes with thymocytes. It appears that the precursors of this lineage undergo extensive, but finite, proliferation and are eventually replaced by further influx of the accessory cell lineage. In chimeric grafts, quail thymocytes were seen forming rosettes with chick accessory cells, and vice versa, indicating, as in the interaction between the epithelial cells and thymocytes, that the molecules involved in thymocyte-accessory cell association can interact across species barriers in our system.
Leakage currents in thin ferroelectric films (2012)

The basic mechanisms of leakage current components of thin lead zirconate titanate (PZT) ferroelectric films grown by the sol-gel method have been studied. Characteristic regions of current-voltage characteristics with different charge transport mechanisms have been determined. It has been shown that there is an intermediate region which separates such regions. In one of them, the leakage current depends on properties of the contact of electrodes with PZT film at low voltages; in the other, the leakage current is controlled by intrinsic properties of the PZT film bulk, and the basic mechanism of charge transport is Poole-Frenkel emission. In the intermediate region, a stepwise change in the current has been observed, which is caused by relaxing breakdown of the Schottky barrier. Time dependences of the leakage currents have been determined. It has been shown that the leakage current decreases with increasing delay time before the Schottky barrier breakdown, and the dependence becomes opposite in character after the breakdown.