gebhart/patrepeval huggingface dataset:
Enhanced production of monocyte chemoattractant protein-1 in rheumatoid arthritis. (1992)

Cells within the synovial tissue may recruit mononuclear phagocytes into the synovial fluid and tissues of arthritic patients. We investigated the production of the chemotactic cytokine monocyte chemoattractant protein-1 (MCP-1) using sera, synovial fluid, synovial tissue, as well as macrophages and fibroblasts isolated from synovial tissues from 80 arthritic patients. MCP-1 levels were significantly higher (P less than 0.05) in synovial fluid from RA patients (mean 25.5 +/- 8.1 ng/ml [SE]) compared to synovial fluid from osteoarthritis (OA) patients (0.92 +/- 0.08), or from patients with other arthritides (2.9 +/- 1.5). MCP-1 levels in RA sera (8.44 +/- 2.33) were significantly greater than MCP-1 in normal sera (0.16 +/- 0.06). The quantities of RA synovial fluid IL-8, which is chemotactic for neutrophils and lymphocytes, and MCP-1 were strongly positively correlated (P less than 0.05). To examine the cellular source of MCP-1, RA synovial tissue macrophages and fibroblasts were isolated. Synovial tissue fibroblasts did not express MCP-1 mRNA, but could be induced to produce MCP-1 by stimulation with either IL-1 beta, tumor necrosis factor-alpha (TNF-alpha), or LPS. In contrast, unlike normal peripheral blood monocytes or alveolar macrophages, RA synovial tissue macrophages constitutively expressed MCP-1 mRNA and antigen. Immunohistochemical analysis of synovial tissue showed that a significantly greater percentage of RA macrophages (50 +/- 8%) as compared to either OA macrophages (5 +/- 2) or normal macrophages (1 +/- 0.3) reacted with anti-MCP-1 antibodies. In addition, the synovial lining layer reacted with MCP-1 in both RA and OA synovial tissues. In contrast, only a minority of synovial fibroblasts (18 +/- 8%) from RA synovium were positive for immunolocalization of MCP-1. These results suggest that synovial production of MCP-1 may play an important role in the recruitment of mononuclear phagocytes during inflammation associated with RA and that synovial tissue macrophages are the dominant source of this cytokine.
Effect of Self-association and Protein Binding on the Photochemical Reactivity of Triarylmethanes. Implications of Noncovalent Interactions on the Competition between Photosensitization Mechanisms Type I and Type II (1999)

We have explored the photochemical behavior of cationic triarylmethane dye monomers and dimers free in solution and noncovalently bound to bovine serum albumin (BSA) and examined how self-association and the formation of host-guest complexes involving biopolymers and photosensitizers affect the competition between the photosensitization type I and type II mechanisms. Our results have clearly indicated that tri-para -substituted triarylmethane dyes bind efficiently to albumin as monomers and dimers and, interestingly, that the formation of dye aggregates in aqueous solutions is actually assisted by the protein. Protein-assisted dye aggregation takes place under conditions of high biopolymer loading (high [dye]/[protein] ratios), as attested by the appearance of a hypsochromically shifted absorption band (H-band) that overlaps with the spectral shoulder of the respective dye monomer. As predicted by the molecular exciton theory, the intersystem crossing efficiency in H-type dimers is expected to be higher than in the respective dye monomers, and photoinduced electron transfer events are intrinsically favored in dye aggregates as a result of the physical contact between donor and acceptor. We have found that when triarylmethanes are noncovalently bound to BSA their photoreactivity undergoes a remarkable enhancement, and that the photooxidation mechanism type I is particularly favored in the macromolecular environment. A comparative examination of the behavior of triarylmethane dyes with that of methylene blue have shown that in the case of methylene blue the binding phenomenon also favor the type I mechanism.
Guanosine gel for sequence‐dependent separation of polymorphic ssDNA (2007)

The separation of fluorescent-labeled ssDNA fragments of equal length based on differences in sequence was achieved through the use of guanosine gels (G-gels) formed by guanosine-5'-monophosphate (GMP) in capillary gel electrokinetic chromatography (CGEKC) with LIF detection. Baseline resolution was achieved for homodimers and homopentamers of A, T, and C. G-gel CGEKC provided better resolution than CZE, MEKC, or a sieving gel in CGE. Resolution improved with increasing GMP, indicating that the interaction is linked to structural organization of the G-gel. Fluorescence intensity and anisotropy show that the order of interaction with G-gels is T>C>A. We then investigated four conformationally similar, polymorphic 76-mers with A/G substitutions that are utilized in forensic DNA typing. Resolution was achieved by CGEKC but not CZE or CGE. In CGEKC, the negatively charged G-gels and oligonucleotides electromigrate toward the positive inlet while being driven by EOF to the negative outlet. The net forward velocity is the greatest for oligonucleotides most closely associated with the slower, more cumbersome G-gel network. For the 76-mers, resolution increases with increasing difference in guanosine content between strands and, for a given difference, with increasing total guanosines in the strands.
Estradiol Administration After Trauma-Hemorrhage Improves Cardiovascular and Hepatocellular Functions in Male Animals (2000)

Administration of estrogen appears to be a useful adjunct for restoring cardiovascular and hepatocellular functions after trauma-hemorrhage in male rats.
Binding Interaction of the Heregulinβ egf Domain with ErbB3 and ErbB4 Receptors Assessed by Alanine Scanning Mutagenesis (1998)

Individual residues of the heregulinβ (HRG)<i>egf</i> domain were mutated to alanine and displayed monovalently on phagemid particles as gene III fusion proteins. Wild type HRGβ <i>egf</i> domain displayed on phage was properly folded as evidenced by its ability to bind ErbB3 and ErbB4 receptor-IgG fusion proteins with affinities close to those measured for bacterially produced HRGβ <i>egf</i> domain. Binding to ErbB3 and ErbB4 receptors was affected by mutation of residues throughout the<i>egf</i> domain; including the NH<sub>2</sub> terminus (His<sup>2</sup> and Leu<sup>3</sup>), the two β-turns (Val<sup>15</sup>–Gly<sup>18</sup> and Gly<sup>42</sup>–Gln<sup>46</sup>), and some discontinuous residues (including Leu<sup>3</sup>, Val<sup>4</sup>, Phe<sup>13</sup>, Val<sup>23</sup>, and Leu<sup>33</sup>) that form a patch on the major β-sheet and the COOH-terminal region (Tyr<sup>48</sup> and Met<sup>50</sup>–Phe<sup>53</sup>). Binding affinity was least changed by mutations throughout the Ω-loop and the second strand of the major β-sheet. More mutants had greater affinity loss for ErbB3 compared with ErbB4 implying that it has more stringent binding requirements. Many residues important for HRG binding to its receptors correspond to critical residues for epidermal growth factor (EGF) and transforming growth factor α binding to the EGF receptor. Specificity may be determined in part by bulky groups that prevent binding to the unwanted receptor. All of the mutants tested were able to induce phosphorylation and mitogen-activated protein kinase activation through ErbB4 receptors and were able to modulate a transphosphorylation signal from ErbB3 to ErbB2 in MCF7 cells. An understanding of binding similarities and differences among the EGF family of ligands may facilitate the development of <i>egf</i>-like analogs with broad or narrow specificity.
Antioxidants in Kidney Diseases: The Impact of Bardoxolone Methyl (2012)

Drugs targeting the renin-angiotensin-aldosterone system (RAAS) are the mainstay of therapy to retard the progression of proteinuric chronic kidney disease (CKD) such as diabetic nephropathy. However, diabetic nephropathy is still the first cause of end-stage renal disease. New drugs targeted to the pathogenesis and mechanisms of progression of these diseases beyond RAAS inhibition are needed. There is solid experimental evidence of a key role of oxidative stress and its interrelation with inflammation on renal damage. However, randomized and well-powered trials on these agents in CKD are scarce. We now review the biological bases of oxidative stress and its role in kidney diseases, with focus on diabetic nephropathy, as well as the role of the Keap1-Nrf2 pathway and recent clinical trials targeting this pathway with bardoxolone methyl.
Correlation between KLK6 expression and the clinicopathological features of glioma (2014)

Expression of KLK6 inhibits tumour growth. Decreased KLK6 expression may be a possible risk factor for glioma.
An Iontophoretic Fentanyl Patient-Activated Analgesic Delivery System for Postoperative Pain: A Double-Blind, Placebo-Controlled Trial (2005)

An iontophoretic fentanyl HCl patient-activated transdermal system (fentanyl HCl PATS) is under development for the treatment of acute postoperative pain. The fentanyl HCl PATS is a needle-free, credit card-sized, preprogrammed system that is applied to the patient's upper outer arm or chest. The fentanyl HCl PATS was demonstrated to be superior to placebo in a previous trial; however, the randomization scheme used and the lack of control of entry pain level may have contributed to the lack of robust findings. We compared the fentanyl HCl PATS with placebo for acute postoperative pain management in a larger trial that addressed the limitations of the previous study. Adult patients admitted to the postanesthesia care unit after major surgery were titrated to comfort with opioids and randomized 1:1 to receive the fentanyl HCl PATS 40 microg or placebo for 24 hours. Supplemental IV fentanyl was available to patients upon request in both treatment groups for the first 3 hours after enrollment. The primary efficacy end-point was the percentage of patients who discontinued participation in the study because of inadequate analgesia. Pain intensity scores, patient global assessments (PGA), and investigator global assessments (IGA) were collected. Four-hundred-eighty-four patients (PATS, n = 244; placebo, n = 240) were enrolled. Fewer patients receiving the fentanyl HCl PATS discontinued because of inadequate analgesia compared with placebo (28.7% versus 60.0%; P < 0.0001). Mean last pain intensity scores were 3.5 and 5.4 for the fentanyl HCl PATS and placebo groups, respectively. Patients (73.4%, PGA) and investigators (72.1%, IGA) considered the fentanyl HCl PATS a good or excellent method of pain control. Treatment-related adverse events were similar between groups. This study demonstrated the superiority of the iontophoretic fentanyl HCl PATS over placebo for acute postoperative pain management.
Syntheses, Structures, and Porous/Luminescent Properties of Silver 3-Alkyl-1,2,4-Triazolate Frameworks with Rare 3-Connected Topologies (2011)

Self-assembly of silver(I) ion with 3-alkyl-1,2,4-triazoles in different solvents yielded four new metal azolate frameworks (MAFs), namely, [Ag(mtz)] (1, Hmtz = 3-methyl-1,2,4-triazole), [Ag(etz)] (2, Hetz = 3-ethyl-1,2,4-triazole), [Ag4(etz)4]·H2O (3·H2O), and [Ag4(ptz)4] (4, Hptz = 3-propyl-1,2,4-triazole). Single-crystal X-ray diffraction revealed that Ag(I) ions and triazolates in these MAFs are all three-coordinated to give rare 3-connected framework topologies. Although 1 and 2 possess the same uniform (10,3)-d (utp) topology, variation of the alkyl groups renders substantially different coordination structures. On the other hand, 3·H2O and 4, also bearing different alkyl substituents, are isomorphours, and can be simplified as the same uninodal sqc5603 topology (point and vertex symbols are 82.10 and 8.82.12, respectively). Due to the relatively short alkyl length, the coordination framework of 3·H2O contains one-dimensional narrow channels. According to thermogravimetry and single-crystal X-ray diffraction, 3·H2O can be dehydrated without framework collapse. Although guest-free 3 does not adsorb N2 at 77 K, 3·H2O can undergo guest exchange, and 3 can adsorb solvent vapor, to give CH2Cl2- and CH3CN-included crystals. Comparing the single-crystal structures of 3·H2O, 3, 3·CH2Cl2, and 3·CH3CN reveals the framework flexibility of 3. These materials also show interesting structure- and guest-dependent photoluminescent properties.
Feature extraction for biometric recognition with photoplethysmography signals (2013)

Photoplethysmography (PPG) signals stand out due to features such as readily accessible, high reliability and confidentiality, the ease of use etc. among bio-signals. The feasibility studies carried out on the PPG signals demonstrated that PPG signals contained important features for human recognition and were the availability of biometric identification systems. In this study, twenty new features were extracted from PPG signal as a preliminary study intended to biometric recognition. PPG signals with 10 seconds were recorded from five healthy people using SDPPG (second derivative PPG) data acquisition card. To remove the noise from received raw PPG signals, a FIR low pass filtering with 200 points and 10 Hz cut-off frequency was designed. These twenty new features were obtained from filtered PPG signal and its second derivative. PPG signal with 10 seconds contains eight periods and twenty characteristic features in each person must not change within an individual over a period. This feature symbolizes the consistency in the identification of a person. To test the performance of biometric recognition system, the k-NN (k-nearest neighbor) classifier was used and achieved 95% of recognition success rate using 10-fold cross validation with twenty new features. The obtained results showed that the developed biometric recognition system based on PPG signal were very promising.
Deep Neural Networks for Acoustic Modeling in Speech Recognition: The Shared Views of Four Research Groups (2012)

Most current speech recognition systems use hidden Markov models (HMMs) to deal with the temporal variability of speech and Gaussian mixture models (GMMs) to determine how well each state of each HMM fits a frame or a short window of frames of coefficients that represents the acoustic input. An alternative way to evaluate the fit is to use a feed-forward neural network that takes several frames of coefficients as input and produces posterior probabilities over HMM states as output. Deep neural networks (DNNs) that have many hidden layers and are trained using new methods have been shown to outperform GMMs on a variety of speech recognition benchmarks, sometimes by a large margin. This article provides an overview of this progress and represents the shared views of four research groups that have had recent successes in using DNNs for acoustic modeling in speech recognition.
A mutant alpha subunit of Gi2 induces neoplastic transformation of Rat-1 cells. (1991)

In a recently discovered class of oncogenes, GTPase-inhibiting mutations constitutively activate alpha subunits of signal-transducing guanine nucleotide-binding proteins (G proteins). Somatic mutations in a subclass of endocrine tumors are found in the arginine-179 codon of the alpha subunit of Gi2 (alpha i2), creating the putative gip2 oncogene. We have tested the ability of gip2 to mediate neoplastic transformation of Rat-1 and NIH 3T3 fibroblasts in tissue culture. Expression of a mutant alpha i2 cDNA encoding cysteine in place of arginine-179 (alpha i2-R179C) caused Rat-1 cells to grow to a higher density in monolayer culture, to lose anchorage dependence, and to form tumors when injected subcutaneously into nude mice. In contrast, expression of alpha i2-R179C failed to alter growth or tumorigenicity of NIH 3T3 cells. We conclude that gip2 is an oncogene, by the criterion that it induces neoplastic transformation of Rat-1 cells. Failure of gip2 to transform NIH 3T3 cells is in keeping with clinical indications that gip2 is a tissue-selective oncogene.
Plant polysaccharide PSK: cytostatic effects on growth and invasion; modulating effect on the expression of HLA and adhesion molecules on human gastric and colonic tumor cell surface. (2001)

PSK is a plant polysaccharide widely used for cancer immunotherapy in Japan and other Asian countries. It is considered that its antitumor effect is derived from its immunomodulating activity on the tumor-bearing host. The present study was designed to assess the direct action of PSK on in vitro proliferation and invasion of human KATO-3 gastric and Colo205 colonic cancer cell lines, and the expression of surface molecules such as HLA and adhesion molecules on these cells. The in vitro growth of KATO-3 cells was significantly inhibited by 100 micrograms/ml of PSK 48 hrs after culture initiation, and that of Colo205 was significantly inhibited by 10 and 100 micrograms/ml of PSK 24 hrs after culture initiation. The effect of PSK on the in vitro invasion of the tumor cells, assessed with a Matrigel invasion chamber, revealed that invasion of KATO-3 and Colo205 cells was inhibited by more than 10 micrograms/ml and more than 5 micrograms/ml of PSK, respectively. KATO-3 cells expressed HLA-ABC, HLA-A2/A28, HLA-DR very weakly, at almost baseline levels, but HLA-B27, B2-microglobulin and HLA-DQ were expressed at various levels. After treatment of KATO-3 cells with PSK, the expression of HLA-B27 and beta 2-microglobulin was significantly enhanced. Colo205 cells expressed all class-I antigens tested in this study at different levels, but class-II antigens at almost baseline levels. PSK also enhanced the expression of class-I antigens on Colo205 cells. ICAM-1 was expressed on KATO-3, but not on Colo205. The expression of ICAM-1 was enhanced to a greater extent by treatment with 10 micrograms/ml than with 100 micrograms/ml of PSK. Adenocarcinoma antigen AC-81 was strongly expressed on both cell lines, but PSK-treatment significantly enhanced its expression. These results suggested that enhancement of HLA class-I expression on tumor cells after PSK treatment may be one of the mechanisms responsible for the induction of anti-tumor immunity by PSK.
TP53 copy number expansion is associated with the evolution of increased body size and an enhanced DNA damage response in elephants (2015)

SUMMARY A major constraint on the evolution of large body sizes in animals is an increased risk of developing cancer. There is no correlation, however, between body size and cancer risk. This lack of correlation is often referred to as ‘Peto’s Paradox’. Here we show that the elephant genome encodes 20 copies of the tumor suppressor gene TP53 and that the increase in TP53 copy number occurred coincident with the evolution of large body sizes, the evolution of extreme sensitivity to genotoxic stress, and a hyperactive TP53 signaling pathway in the elephant (Proboscidean) lineage. Furthermore we show that several of the TP53 retrogenes ( TP53RTGs ) are transcribed and likely translated. While TP53RTGs do not appear to directly function as transcription factors, they do contribute to the enhanced sensitivity of elephant cells to DNA damage and the induction of apoptosis by regulating activity of the TP53 signaling pathway. These results suggest that an increase in the copy number of TP53 may have played a direct role in the evolution of very large body sizes and the resolution of Peto’s paradox in Proboscideans.
Molecular Cloning and Characterization of Complementary Deoxyribonucleic Acids Corresponding to Bovine Trophoblast Protein-1: A Comparison with Ovine Trophoblast Protein-1 and Bovine Interferon-αII (1989)

Bovine trophoblast protein-1 (bTP-1) is a secreted glycoprotein that consists of several forms differing slightly in mol wt and isoelectric point. It is produced by bovine conceptuses after about day 15 of pregnancy and is believed to play a key role in signalling the presence of an embryo to the mother. In this study, a series of recombinant cDNA clones corresponding to the mRNA for bTP-1 have been isolated from cDNA libraries representing day 18-19 bovine conceptus poly(A) + mRNA. Base sequencing of several cDNAs indicated that multiple mRNAs for bTP-1 exist. Northern blotting and primer extension experiments showed that the mRNAs average about 1 kilobase in length. One apparently full-length cDNA clone consisted of 1035 bases up to the beginning of the poly(A) tail. It contained an open reading frame of 195 codons which began at a position 79 bases from the 5' end. Its entire sequence was 85% identical to that of a cDNA for the immunologically related ovine trophoblast protein-1 (oTP-1) and about 79% identical to that for a bovine interferona u (IFNa M ). The highest conservation of sequence (>90%) was noted in the 3'-untranslated sequences of the bTP-1 and oTP-1 cDNAs. The deduced amino acid sequence of bTP-1 shared 80% identity with oTP-1, between 45-55% with human, rodent, porcine, and bovine IFNs of the a ( subfamily and about 70% with a bovine IFNa M . A single potential site for A/-glycosylation was noted at Asn 78 . These results show that bTP-1, like its ovine counterpart oTP-1, is structurally related to the IFNas. We suggest that
Genome-Wide Serum microRNA Expression Profiling Identifies Serum Biomarkers for Alzheimer's Disease (2014)

Recent findings that human serum contains stably expressed microRNAs (miRNAs) have revealed a great potential of serum miRNA signature as disease fingerprints to diagnosis. Here we used genome-wide serum miRNA expression analysis to investigate the value of serum miRNAs as biomarkers for the diagnosis of Alzheimer's disease (AD). Illumina HiSeq 2000 sequencing followed by individual quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) assays was used to test the difference in levels of serum miRNAs between 50 AD patients and 50 controls in the screening stages. The detected serum miRNAs then were validated by qRT-PCR in 158 patients and 155 controls. MiR-98-5p, miR-885-5p, miR-483-3p, miR-342-3p, miR-191-5p, and miR-let-7d-5p displayed significantly different expression levels in AD patients compared with controls. Among the 6 miRNAs, miR-342-3p has the best sensitivity (81.5%) and specificity (70.1%) and was correlated to Mini-Mental State Examination score. This study identified six serum miRNAs that distinguish AD patients from healthy controls with high sensitivity and specificity. Serum miRNA panel (or miR-342-3p alone) may serve as a novel, noninvasive biomarker for AD.
PC-notebook based mobile networking: algorithms, architectures and implementation (2002)

The integration of multimedia adaptive wireless networking capabilities in a PC-notebook platform are investigated. To support mobile networking, while providing compatibility with the wired infrastructure, new functions are required for topology creation using multihop protocols. To support mobility in a wireless environment, power control and bandwidth allocation are required in conjunction with adaptive wireless modems and rate-adaptive video codecs. A prototype implementation of a wireless node with these capabilities reveals several performance and complexity limitations with current technology. In particular the DOS operating system, the PC shared bus architecture and traditional partitioning of the network and modem functions lead to severe performance losses that are detrimental in wireless networking. For mobile wireless nodes, these limitations are unacceptable. Several ideas are presented for re-architecting the PC-notebook for wireless networking nodes that can substantially improve bandwidth efficiency while overcoming the complexity and power limitations of current technology.