gebhart/patrepeval huggingface dataset:
FcγR expression on macrophages is related to severity and chronicity of synovial inflammation and cartilage destruction during experimental immune-complex-mediated arthritis (ICA) (2000)

STATEMENT OF FINDINGS: We investigated the role of Fc gamma receptors (Fc gamma Rs) on synovial macrophages in immune-complex-mediated arthritis (ICA). ICA elicited in knee joints of C57BL/6 mice caused a short-lasting, florid inflammation and reversible loss of proteoglycans (PGs), moderate chondrocyte death, and minor erosion of the cartilage. In contrast, when ICA was induced in knee joints of Fc receptor (FcR) gamma-chain(-/-) C57BL/6 mice, which lack functional Fc gamma RI and RIII, inflammation and cartilage destruction were prevented. When ICA was elicited in DBA/1 mice, a very severe, chronic inflammation was observed, and significantly more chondrocyte death and cartilage erosion than in arthritic C57BL/6 mice. The synovial lining and peritoneal macrophages of naïve DBA/1 mice expressed a significantly higher level of Fc gamma Rs than was seen in C57BL/6 mice. Moreover, elevated and prolonged expression of IL-1 was found after stimulation of these cells with immune complexes. Zymosan or streptococcal cell walls caused comparable inflammation and only mild cartilage destruction in all strains. We conclude that Fc gamma R expression on synovial macrophages may be related to the severity of synovial inflammation and cartilage destruction during ICA.
Multicenter Evaluation of the Cepheid Xpert Methicillin-Resistant Staphylococcus aureus (MRSA) Test as a Rapid Screening Method for Detection of MRSA in Nares (2009)

The first U.S. multicenter clinical trial to assess the performance of the Cepheid Xpert MRSA assay (Xpert MRSA) was conducted. The assay is a qualitative test designed for the rapid detection of methicillin-resistant Staphylococcus aureus (MRSA) directly from nares swabs. This novel test combines integrated nucleic acid extraction and automated real-time PCR for the detection of a MRSA-specific signature sequence. A total of 1,077 nares specimens were collected from seven geographically distinct health care sites across the United States with prevalence rates ranging from 5.2% to 44%. Nares specimens were tested by (i) the Xpert MRSA assay, (ii) direct culture on CHROMagar MRSA medium (direct CM culture), and (iii) broth-enriched culture (Trypticase soy broth with 6.5% sodium chloride) followed by plating onto CHROMagar MRSA medium (broth-enriched CM culture). When direct CM culture was designated the reference method, the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the Xpert MRSA assay were 94.3%, 93.2%, 73.0%, and 98.8%, respectively. When broth-enriched CM culture was used as the reference method, the clinical sensitivity, specificity, PPV, and NPV of the Xpert MRSA assay were 86.3%, 94.9%, 80.5%, and 96.6%, respectively. The BD GeneOhm MRSA (BDGO) assay was performed as a comparative molecular method. No statistical performance differences were observed between the Xpert MRSA and BDGO assays when they were compared to culture methods. From this large-scale, multicenter clinical comparison, we conclude that the Xpert MRSA assay is a simple, rapid, and accurate method for performing active surveillance for MRSA in a variety of health care populations.
Mobile product recognition (2010)

We present a mobile product recognition system for the camera-phone. By snapping a picture of a product with a camera-phone, the user can retrieve online information of the product. The product is recognized by an image-based retrieval system located on a remote server. Our database currently comprises more than one million entries, primarily products packaged in rigid boxes with printed labels, such as CDs, DVDs, and books. We extract low bit-rate descriptors from the query image and compress the location of the descriptors using location histogram coding on the camera-phone. We transmit the compressed query features, instead of a query image, to reduce the transmission delay. We use inverted index compression and fast geometric re-ranking on our database to provide a low delay image recognition response for large scale databases. Experimental timing results on different parts of the mobile product recognition system is reported in this work.
Development of a Semiquantitative Degenerate Real-Time PCR-Based Assay for Estimation of Numbers of Butyryl-Coenzyme A (CoA) CoA Transferase Genes in Complex Bacterial Samples (2007)

We describe a new degenerate real-time PCR approach to simultaneously quantify phylogenetically different butyrate-producing bacteria based on the detection of butyryl-coenzyme A (CoA) CoA transferase genes. This pathway is present in numerically important groups of butyrate producers within the human colon, and thus this assay estimates the butyrate-producing ability of the microbiota.
Induction by lithium ion of multiplication of mouse mammary epithelium in culture. (1979)

Lithium ion at concentrations between 2 and 20 mM simulated the stimulatory effects of insulin on the uptake of alpha-aminoisobutyric acid, synthesis of RNA and DNA, and cell multiplication in mouse mammary gland explants cultured in a chemically defined synthetic medium. Other monovalent cations were virtually ineffective. In most instances the stimulatory effect of lithium ion was somewhat smaller than and additive to that of insulin. However, lithium ion was incapable of substituting for the action of insulin in augmenting milk protein synthesis in mammary explants cultured with other lactogenic hormones, prolactin, and glucocorticoid. The observed similarities of the responses of mammary cells to lithium and insulin suggest that possible importance of cation(s) in the regulation of mammary cell proliferation, which may be a common basis for the action of the two agents. On the other hand, the observed inability of lithium to mimic the lactogenic effect of insulin indicates a specific function of the hormone in the functional differentiation of mammary cells.
A micro‐RNA signature associated with race, tumor size, and target gene activity in human uterine leiomyomas (2007)

Human uterine leiomyomas (ULMs) are the most common neoplasms of women. Many genes are dysregulated in ULMs and some of this dysregulation may be due to abnormal expression of micro-RNAs (miRNAs). In this study, 55 ULMs and matched myometrium were collected from 41 patients for microarray-based global miRNA expression analysis. Of 206 miRNAs examined, 45 miRNAs were significantly up- or down-regulated in ULMs in comparison to the matched myometrium (P < 0.001). The top five dysregulated miRNAs in ULMs are the let-7 family, miR-21, miR-23b, miR-29b, and miR-197. Four polycistronic clusters of miRNAs were either up- or down-regulated, but not in a mixed pattern, indicative of coordinated regulation of these miRNAs. Significance analysis revealed that subsets of miRNAs were strongly associated with tumor sizes and race. By prediction analysis we identified some important tumorigenic genes previously identified in ULMs that may be targeted by the dysregulated miRNAs. HMGA2 was identified as one of target genes of the let-7 family of miRNAs and has been found to be suppressed by let-7 in vitro. This article contains Supplementary material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat.
THE USE OF HYPEREMIA IN THE POSTOPERATIVE TREATMENT OF LESIONS OF THE EXTREMITIES AND THORAX (1915)

In calling attention to the use of hyperemia in lesions of the extremities and the thorax, it is my purpose to refer only to the use of that form of treatment known as suction or cupping. In order to be successful with it, it is necessary for a large portion of the extremity to be contained within the vacuum chamber. To successfully create and maintain a vacuum in so large a chamber as will completely envelop an extremity, it is necessary to attach some form of electrically propelled motor, which should be so adapted as to be thoroughly under control while creating the vacuum. Under such favorable conditions a sufficient vacuum may be maintained for a period which will allow of complete and uniform hyperemia of all of the extremity enclosed within the chamber. This means that the veins become fully engorged with new blood, the tissues bathed in the
Co-Optimization and Analysis of Signal, Power, and Thermal Interconnects in 3-D ICs (2011)

Heat removal and power delivery have become two major reliability concerns in 3-D integrated circuit (IC) technology. To alleviate thermal problem, two possible solutions have been proposed: thermal-through-silicon-vias (T-TSVs) and micro-fluidic channel (MFC)-based cooling. In case of power delivery, a complex power distribution network is required to deliver currents reliably to all parts of the 3-D IC while suppressing the power supply noise to an acceptable level. However, these thermal and power networks pose major challenges in signal routability and congestion. This is because signal, power, and thermal interconnects are all competing for routing space, and the related TSVs interfere with gates and wires in each die. We present a co-optimization methodology for signal, power, and thermal interconnects in 3-D ICs based on design of experiments (DOE) and response surface methodology (RSM). The goal of our holistic approach is to improve signal, thermal, and power noise metrics and to provide fast and accurate design space exploration for early design stage. We also provide an in-depth comparison between T-TSV versus MFC-based cooling method and discuss how to employ DOE and RSM techniques to co-optimize the interconnects. Our DOE-based optimization found the optimal design point with less effort than a gradient search-based optimization.
Molecular G rading o f U rothelial C ell C arcinoma W ith Fibroblast G rowth F actor R eceptor 3 a nd M IB-1 i s S uperior t o Pathologic G rade f or t he P rediction o f C linical O utcome (2003)

Purpose: Fibroblast growth factor receptor 3 (FGFR3) mutations were recently found at a high frequency in welldifferentiated urothelial cell carcinoma (UCC). We investigated the relationship between FGFR3 status and three molecular markers (MIB-1, P53, and P27 kip1 ) associated with worse prognosis and determined the reproducibility of pathologic grade and molecular variables. Patients and Methods: In this multicenter study, we included 286 patients with primary (first diagnosis) UCC. The histologic slides were reviewed. FGFR3 status was examined by polymerase chain reaction‐single strand conformation polymorphism and sequencing. Expression levels of MIB-1, P53, and P27 kip1 were determined by immunohistochemistry. Mean follow-up was 5.5 years (range, 0.4 to 18.4 years). Results: FGFR3 mutations were detected in 172 (60%) of 286 UCCs. Grade 1 tumors had an FGFR3 mutation in 88% of patient samples and grade 3 tumors in 16% of patient samples. Conversely, aberrant expression patterns of MIB-1, P53, and P27 kip1 were seen in 5%, 2%, and 3% of grade 1 tumors and in 85%, 60%, and 56% of grade 3 tumors, respectively. In multivariate analysis with recurrence rate, progression, and disease-specific survival as end points, the combination of FGFR3 and MIB-1 proved independently significant in all three cases. By using these two molecular markers, three molecular grades (mGs) could be identified: mG1 (mutation; normal expression), favorable prognosis; mG2 (two remaining combinations), intermediate prognosis; and mG3 (no mutation; high expression), poor prognosis. The molecular variables were more reproducible than pathologic grade (85% to 100% v 47% to 61%). Conclusion: The FGFR3 mutation represents the favorable molecular pathway of UCC. Molecular grading provides a new, simple, and highly reproducible tool for clinical decision making in UCC patients. J Clin Oncol 21:1912-1921. © 2003 by American Society of Clinical Oncology.
High-Affinity Binding of the Staphylococcal HarA Protein to Haptoglobin and Hemoglobin Involves a Domain with an Antiparallel Eight-Stranded β-Barrel Fold (2006)

Iron scavenging from the host is essential for the growth of pathogenic bacteria. In this study, we further characterized two staphylococcal cell wall proteins previously shown to bind hemoproteins. HarA and IsdB harbor homologous ligand binding domains, the so called NEAT domain (for "near transporter") present in several surface proteins of gram-positive pathogens. Surface plasmon resonance measurements using glutathione S-transferase (GST)-tagged HarAD1, one of the ligand binding domains of HarA, and GST-tagged full-length IsdB proteins confirmed high-affinity binding to hemoglobin and haptoglobin-hemoglobin complexes with equilibrium dissociation constants (K(D)) of 5 to 50 nM. Haptoglobin binding could be detected only with HarA and was in the low micromolar range. In order to determine the fold of this evolutionarily conserved ligand binding domain, the untagged HarAD1 protein was subjected to nuclear magnetic resonance spectroscopy, which revealed an eight-stranded, purely antiparallel beta-barrel with the strand order (-beta1 -beta2 -beta3 -beta6 -beta5 -beta4 -beta7 -beta8), forming two Greek key motifs. Based on structural-homology searches, the topology of the HarAD1 domain resembles that of the immunoglobulin (Ig) fold family, whose members are involved in protein-protein interactions, but with distinct structural features. Therefore, we consider that the HarAD1/NEAT domain fold is a novel variant of the Ig fold that has not yet been observed in other proteins.
Carboranes as a Tool to Tune Phosphorescence (2015)

Phosphorescent transition-metal complexes (PTMCs) have attracted great interest because of their excellent properties which may lead to promising applications in optoelectronics. In recent years, carboranes have been demonstrated to be a novel and effective tool to tune phosphorescence of PTMCs. This Concept article deals with the advances of carborane-functionalized PTMCs for potential optical applications. The discussions are focused on the design strategies and synthetic procedures leading to carborane-functionalized PTMCs, the influence of carboranes on the optical properties of PTMCs, and the promising optical applications of this interesting class of phosphorescent materials.
Selective elimination of recombinant genes in vivo with a suicide retroviral vector. (1991)

The ability to express recombinant genes in vivo offers potential new treatments for human disease if questions of safety and toxicity can be addressed. Complications of gene transfer could include, for example, overexpression of introduced genes for growth or angiogenic factors or insertional mutagenesis, both of which could cause uncontrolled cell growth. We report the development of a suicide retroviral vector that provides a method to eliminate cells undergoing rapid growth in vivo. A murine amphotropic retroviral vector was constructed in which the gene for herpesvirus thymidine kinase was included to render proliferating cells sensitive to ganciclovir, and the Escherichia coli beta-galactosidase gene served as a reporter. This vector's efficacy was first assessed in vitro, and beta-galactosidase activity was abolished in several cell lines after treatment with ganciclovir. In vivo, a transplantable murine CT26 adenocarcinoma whose cells were transduced with this vector regressed completely after administration of ganciclovir. In contrast, expression in nondividing cells within rabbit arteries transduced by retroviral infection in vivo was unaffected. This suicide vector therefore eliminates transformed cells but allows survival of normal nondividing cells that express its specific recombinant genes in vivo, and may thus improve the safety and efficacy of gene transfer into living organisms.
Randomized Trial of Letrozole Following Tamoxifen as Extended Adjuvant Therapy in Receptor-Positive Breast Cancer: Updated Findings from NCIC CTG MA.17 (2005)

Letrozole after tamoxifen is well-tolerated and improves both disease-free and distant disease-free survival but not overall survival, except in node-positive patients.
Induction of HL-60 cell differentiation by 3-deaza-(+/-)-aristeromycin, an inhibitor of S-adenosylhomocysteine hydrolase. (1986)

The metabolically stable inhibitor of S-adenosylhomocysteine hydrolase (AdoHcyase), 3-deaza-(+/-)-aristeromycin (dzAri) has recently been shown to induce differentiation in HL-60 cells. The present study was undertaken to characterize the cytostatic, cytotoxic, and differentiation inducing properties of dzAri in HL-60 cells and to investigate biochemical consequences of AdoHcyase inhibition. A dye exclusion test and a clonogenic assay were used to test cytotoxic and cytostatic properties. dzAri had reversible cytostatic effects on HL-60 cells at concentrations lower than 10 microM and partially reversible cytotoxic effects above 10 microM. The induction of differentiation was dependent upon concentration and time of exposure, with maximal effect after 6 days incubation with 5-10 microM dzAri. Washout experiments demonstrated that the cells were not committed to differentiation after 48 h of incubation with dzAri. The AdoHcyase of HL-60 cells was inhibited with a Ki of 20 nM. The concentration of S-adenosylhomocysteine increased dose dependently 48 h after incubation with 0.1-100 microM dzAri. The incorporation of [3H]methyl from [methyl-3H]methionine into 5-methylcytosine of DNA was reduced by 26% at 5 microM dzAri. The findings indicate that continuous presence of dzAri is necessary to induce differentiation and inhibit proliferation in HL-60 cells. The inhibition of AdoHcyase perturbs levels of transmethylation metabolites and the incorporation of [3H]methyl into 5-methyl-cytosine of DNA.
Nucleic acid related compounds. 24. Transformation of tubercidin 2′,3′-O-orthoacetate into halo, deoxy, epoxide, and unsaturated sugar nucleosides (1977)

Treatment of tubercidin (4-amino-7-β-D-ribofuranosylpyrrolo[2,3-d]pyrimidine) (1) with methyl orthoacetate gave the 2 ′ ,3 ′ -O-orthoester, 2. Pivalic acid chloride in refluxing pyridine converted 2 into a mixture containing 4-N-pivalamido-7-(3-chloro-3-deoxy-2-O-acetyl-5-O-pivalyl-β-D-xylofuranosyl)pyrrolo[2,3-d)pyrimidine (3a) and the corresponding 2 ′ -O-(4,4-dimethyl-3-pivaloxypent-2-enoyl) (DMPP) compound (3b) via acetoxonium ion intermediates. Treatment of 2 with sodium iodide/pivalyl chloride/pyridine gave the iodo analog (3c) of DMPP derivative 3b plus the 3′,4′-unsaturated nucleoside (5a). Treatment of 3a–c with methanolic sodium methoxide gave the ribo-epoxide 4, which underwent N 1 → 3′ intramolecular cyclization readily. Dehalogenation of 3 and deprotection gave 3′-deoxytubercidin (8). Deblocking of 5a gave 5b which was hydrogenated to give 8 plus its 4 ′ -epimer 9. Heating of 3c or 5a produced 4-N-pivalamido-7-(5-pivaloxymethylfuran-2-yl)pyrrolo[2,3-d]pyrimidine (10a). Deblocking of 10a gave 10d which was hydrogenated to give racemic 4-amino-7-(2,3-dideoxy-β-D,L-glycero-pentofuranosyl)pyrrolo[2,3-d]pyrimidine (7,11). The 2′,3′-unsaturated nucleoside (6) was obtained and hydrogenated to produce 2′,3′-dideoxytubercidin (7). Spectroscopic identification of products, epoxide instability, and comparison with other procedures are discussed.
Stable self-seeding of R-SOAs for WDM-PONs (2011)

Self-seeding of R-SOAs is a polarization dependent process resulting in unstable operations. We experimentally demonstrate a passive stabilization technique enabling class carrier availability in 1.25 Gb/s WDM-PONs.
The IGF system in metabolism regulation. (1995)

Insulin-like growth factors (IGF-I and IGF-II) are produced in most tissues, particularly liver. Via endocrine and paracrine or autocrine mechanisms, they play an essential role in cell proliferation and differentiation and complement the metabolic effects of insulin. Similarities between the effects of insulin and IGF in vitro are largely due to cross-reaction, owing to their structural homology as well as that of their receptors. At physiological concentrations, insulin is not mitogenic. Compared with insulin, IGFs have negligible metabolic effects on hepatocytes or adipocytes. However, the presence of the IGF-I receptor in muscle accounts for IGF physiological effects in vivo on glucose uptake and glycogen synthesis. Moreover, recombinant IGF-I administered subcutaneously to healthy subjects or patients with Type 2 diabetes causes a drop in plasma levels of triglycerides and VLDL as well as cholesterol and LDL, but not HDL, and also increases insulin sensitivity. All these responses reflect IGF-I inhibition of insulin and GH secretion. In biological media, IGF-I and IGF-II are reversibly associated with specific high-affinity (10(9)-10(11) M-1) binding proteins (IGFBP-1 to -6) differing in expression according to tissue of origin and playing a variety of roles in IGF transport and half-lives, delivery of IGFs to their target cells and modulation of IGF interactions with their receptors. In the blood, where IGF concentrations are 1,000 times those of insulin, IGFBP-3 (the major form) binds at least 80% of IGFs as 140-kDa complexes which do not cross the capillary endothelium and therefore prevent the insulin-like action of IGFs. Nevertheless, these circulating IGF reserves may be mobilized in response to metabolic needs via limited proteolysis of IGFBP-3 by serine proteases. In the case of IGFBP-1, whose hepatic synthesis is negatively regulated by insulin, plasma concentrations are subject to extensive nycthemeral variation, rising with fasting and dropping after feeding, which may be involved in controlling the access of free IGF-I to its cellular receptors and hence IGF-I-regulated glucose and amino acid uptake. Therapeutic applications of recombinant human IGF-I, currently under trial in the treatment of growth retardation resulting from GH receptor abnormalities, hypercatabolic states and would repair, may also be envisaged for cases of insulin resistance, particularly type 2 diabetes.
Assessment of Stanniocalcin-1 mRNA as a molecular marker for micrometastases of various human cancers. (2000)

We assessed Stanniocalcin-1 (STC-1) mRNA expression in human normal tissues, various types of human cancer cell lines, and cancer tissues obtained during surgery. Using a reverse transcriptase-polymerase chain reaction (RT-PCR) assay developed to detect STC-1 mRNA, the transcripts were detected in 20 out of 21 cancer cell lines and in all tumor tissues from various types of cancer. Semi-quantitative analyses with multiplex RT-PCR showed that STC-1 mRNA tended to be enhanced in cancer tissues of hepatocellular carcinoma and colorectal cancer compared to background cancer-free tissues. Analysis of blood samples obtained from 11 patients with hepatocellular carcinoma before, after and during hepatectomy showed STC-1 mRNA expression in 8 out of 11 patients at least one time. Normal donor blood samples (n=31) were all-negative for STC-1 mRNA expression. Our results indicate that STC-1 mRNA might be a useful molecular marker for detection of tumor cells in blood from patients with various types of malignancies.
Effects of testosterone on body composition, bone metabolism and serum lipid profile in middle‐aged men: a meta‐analysis (2005)

The present analysis provides an estimate of the average treatment effects of testosterone therapy in middle-aged men. Our findings are sufficiently strong to justify further interventional studies focused on alternative targets of androgenic treatment carrying more stringent clinical implications, in particular the cardiovascular, metabolic and neurological systems.