gebhart/patrepeval huggingface dataset:
AIbZIP, a novel bZIP gene located on chromosome 1q21.3 that is highly expressed in prostate tumors and of which the expression is up-regulated by androgens in LNCaP human prostate cancer cells. (2002)

Androgens play an important role in the development and physiology of the normal prostate as well as in prostate cancer cell proliferation. Comparison of the mRNA expression profiles of control and R1881-treated cultures of LNCaP human prostate cancer cells using cDNA subtraction led to the identification of a novel transcription factor that we named Androgen-Induced bZIP (AIbZIP) protein. AIbZIP is a 395 aa protein with homology to cyclic AMP-responsive element binding protein/activating transcription factor transcription factors. It contains an NH(2)-terminal activation domain, a central bZIP domain, and a COOH-terminal transmembrane domain. The AIbZIP gene is localized on chromosome 1q21.3 and consists of 10 exons. A major 1.7-kb transcript was detected exclusively in the prostate as well as in breast and prostate cancer cell lines. Androgens up-regulate AIbZIP mRNA and protein levels in a dose-dependent manner. The kinetics of AIbZIP mRNA up-regulation and the results of experiments with cycloheximide suggest that AIbZIP may be a delayed response gene. Immunoreactive AIbZIP protein was primarily detected in the cytoplasm of prostatic luminal epithelial cells. Similarly, full-length AIbZIP-green fluorescent protein fusion proteins were localized in the cytoplasm of LNCaP cells, whereas a truncated form of AIbZIP lacking the putative transmembrane domain was exclusively nuclear. Examination of AIbZIP protein and mRNA expression in a series of transurethral resection of the prostate and needle biopsy specimens indicated that AIbZIP is expressed at higher levels in cancerous prostate cells compared with noncancerous prostate cells. The highly tissue-specific expression profile, androgen regulation, chromosomal localization, and expression profile of AIbZIP in prostate tumors suggest that AIbZIP may play an important role in prostate cancer and in androgen receptor signaling in prostate cells. Future studies will confirm a possible relationship between AIbZIP and prostate cancer.
Combustion Characteristics of a Single-Cylinder Engine Equipped with Gasoline and Ethanol Dual-Fuel Systems (2008)

&lt;div class="htmlview paragraph"&gt;The requirement of reduced emissions and improved fuel economy led the introduction of direct-injection (DI) spark-ignited (SI) engines. Dual-fuel injection system (direct-injection and port-fuel-injection (PFI)) was also used to improve engine performance at high load and speed. Ethanol is one of the several alternative transportation fuels considered for replacing fossil fuels such as gasoline and diesel. Ethanol offers high octane quality but with lower energy density than fossil fuels. This paper presents the combustion characteristics of a single cylinder dual-fuel injection SI engine with the following fueling cases: a) gasoline for PFI and DI, b) PFI gasoline and DI ethanol, and c) PFI ethanol and DI gasoline. For this study, the DI fueling portion varied from 0 to 100 percentage of the total fueling over different engine operational conditions while the engine air-to-fuel ratio remained at a constant level. It was shown in all cases that the IMEP (indicated mean effective pressure) decreases by as much as 11% as DI fueling percentage increases, except in case b) where the IMEP increases by 2% at light load. The combustion burn duration increases significantly at light load as DI fueling percentage increases, but only moderately at WOT (wide open throttle). In addition, the percentage of the ethanol in the total fueling plays a dominant role in affecting the combustion characteristics at light load; but at heavy load (WOT), the DI fueling percentage becomes an important parameter, regardless of the percentage of ethanol content in the fuel.&lt;/div&gt;
Expression profiling of dipeptidyl peptidase 8 and 9 in breast and ovarian carcinoma cell lines (2012)

Proteases, particularly serine proteases like dipeptidyl peptidase 4 (DP4) and fibroblast activation protein (FAP), play an important role in cancer invasion and angiogenesis. Aberrant expression of DP4 and FAP is associated with numerous cancers, including breast and epithelial ovarian carcinoma. We investigated the mRNA levels, protein expression and enzyme activity of the structural homologs DP8 and DP9, in addition to DP4 and FAP, in three breast carcinoma (MDA-MB-231, MDA-MB-453, MCF-7), three epithelial ovarian carcinoma (EOC) (OVCA-432, OVCA-429, SKOV3), 293T and HeLa cell lines. In addition, DP2 and prolyl endopeptidase (PEP) mRNA and enzyme levels were measured and compared in each cell line. Ubiquitous but differential expression of DP8 and DP9 mRNA and protein was observed across all cell lines. Relative to EOC, DP8 protein was lower in the breast carcinoma cell lines (p=0.057), suggesting that DP8 may play differing roles in different cancer cell types. A strong, negative, non-reciprocal relationship was identified between DP9 protein and DP4 mRNA (r=-0.903, p=0.002) and protein (r=-0.810, p=0.015). This suggests that DP4 expression plays an important role in the post-transcriptional regulation of DP9 in breast and ovarian cancer cell lines. Overall, this study suggests a potential role for DP8 and DP9 in breast and ovarian cancer and further investigations in this area are required.
Purification and Analysis of Recombinant Proteins (1991)

Covering both new and traditional topics in the purification and analysis of recombinant proteins, this volume demonstrates how to overcome problems in protein research and presents practical methods used in protein work, explaining their theoretical bases. The collection also explores innovative co
Psychometric Properties of the Psychotropic-Related Sexual Dysfunction Questionnaire (PRSexDQ-SALSEX) in Patients with Schizophrenia and Other Psychotic Disorders (2008)

Sexual dysfunction is a disturbing and often underrecognized problem associated with schizophrenia and its treatment. The Psychotropic-Related Sexual Dysfunction (PRSexDQ-SALSEX) is a brief and relatively nonintrusive questionnaire that has shown adequate psychometric properties in patients with depression. This study examined the psychometric properties of the PRSexDQ-SALSEX in a sample of patients with schizophrenia or other psychotic disorders who were experiencing anti-psychotic-induced sexual dysfunction and were switched to olanzapine. The PRSexDQ-SALSEX was very feasible and its internal reliability was satisfactory. In addition, this questionnaire showed a good convergent validity and sensitivity to tracking changes in sexual functioning.
Probing Binding Pocket of Serotonin Transporter by Single Molecular Force Spectroscopy on Living Cells (2011)

The serotonin transporter (SERT) terminates neurotransmission by removing serotonin from the synaptic cleft. In addition, it is the site of action of antidepressants (which block the transporter) and of amphetamines (which induce substrate efflux). The interaction energies involved in binding of such compounds to the transporter are unknown. Here, we used atomic force microscopy (AFM) to probe single molecular interactions between the serotonin transporter and MFZ2-12 (a potent cocaine analog) in living CHOK1 cells. For the AFM measurements, MFZ2-12 was immobilized on AFM tips by using a heterobifunctional cross-linker. By varying the pulling velocity in force distance cycles drug-transporter complexes were ruptured at different force loadings allowing for mapping of the interaction energy landscape. We derived chemical rate constants from these recordings and compared them with those inferred from inhibition of transport and ligand binding: koff values were in good agreement with those derived from uptake experiments; in contrast, the kon values were scaled down when determined by AFM. Our observations generated new insights into the energy landscape of the interaction between SERT and inhibitors. They thus provide a useful framework for molecular dynamics simulations by exploring the range of forces and energies that operate during the binding reaction.
Lipid-coated nanocapillaries for DNA sensing (2012)

We report a simple and efficient way to accomplish the chemical modification of glass nanopores by means of lipid self-assembly. Lipid coating improves the success rate of these glass nanopores as biosensors to detect λ-DNA.
Synthesis of phenylazido‐derivatized substances and photochemical surface modification to immobilize functional groups (1996)

Phenylazido-derivatized low-molecular-weight substances and copolymers containing hydrocarbon- or fluorocarbon-alkyl group, sulfonato or amino group, and hydroxyl group were prepared. Upon coating and subsequent ultraviolet (UV) light irradiation, convalent fixation of these substances or copolymers took place only at irradiated portions of polymer surfaces, providing a hydrophobic, ionic, or hydrophilic nature. These were verified with electron spectroscopy for chemical analysis (ESCA) spectra and water contact-angle measurement. Endothelial cells adhered on photochemically modified surfaces which have alkyl, sulfonato, or amino groups on their surfaces, whereas little adhesion occurred on a hydroxyl group-bearing hydrogellike surface. When UV light was irradiated through a photomask on the polymer surfaces, patterned and microprocessed surfaces having cell-adhering and nonadhering regions were obtained. The potential application of this photochemical surface processing method in biomedical engineering is discussed. © 1996 John Wiley & Sons, Inc.
Relative importance of elements within the SL3-3 virus enhancer for T-cell specificity (1990)

Elements within the enhancer of T-lymphomagenic SL3-3 virus were examined for their contributions to transcriptional activity in T lymphocytes and non-T cells. A region containing two sequences homologous to the enhancer core consensus sequence and a sequence homologous to the binding site for factor LVb was found to have the largest effect on activity. Evidence was obtained that suggests that the activity of this region was greater in T lymphocytes than in non-T cells and that multiple elements within it were necessary for activity. A second region, containing sequences homologous to the binding site of factor NF-I and the glucocorticoid response element, had about a twofold effect on transcription in both T lymphocytes and non-T cell lines. The twofold effect was seen whether the region containing the cores and LVb site was present or not. These results indicate that the most important region for the specificity of SL3-3 enhancer activity and, presumably, for viral leukemogenicity comprises the core elements and the LVb site. DNA-protein-binding studies demonstrated that one cellular factor, S/A-CBF, bound to both core elements, while a second cellular factor, S-CBF, bound to only one of them. In combination with earlier studies, this indicates that cells contain multiple factors that bind to the critical region.
Effects of Escherichia coli Nus A protein on transcription termination in vitro are not increased or decreased by DNA sequences sufficient for antitermination in vivo (1988)

The ability of Escherichia coli Nus A protein to recognize specific DNA or RNA sequences in vitro was tested by using transcription templates containing a variety of promoters, transcription terminators, and antitermination-conferring regions. We conclude that the effects of Nus A on termination are not qualitatively or quantitatively altered by sequences present in promoters, Rho-dependent terminators, or antitermination-conferring regions. Nus A was also shown to increase termination at the rrnC Rho-independent T1 terminator by a mechanism that is independent of the promoter or sequences involved in antitermination. Altogether, these observations argue against a direct Nus A-nucleic acid interaction affecting termination in vitro. Together with the results described in the accompanying paper [Sigmund, C. D., & Morgan, E. A. (1988) Biochemistry (preceding paper in this issue)], these results suggest that the effects of Nus A on termination in vitro may not be related to the in vivo functions of Nus A.
Phase I Safety, Pharmacokinetic, and Pharmacodynamic Study of the Thrombospondin-1–Mimetic Angiogenesis Inhibitor ABT-510 in Patients With Advanced Cancer (2005)

ABT-510 demonstrated a favorable toxicity profile and linear and time-independent pharmacokinetics with biologically relevant plasma concentrations. The significant number of patients with prolonged stable disease and the convenient method of dosing merit further studies with this angiogenesis inhibitor.
Interprofessional learning in health care programmes (2008)

The objective of this study was to investigate the views of students who had undertaken Interprofessional learning (IPL) in the first three months of health care courses. A generic qualitative approach was adopted and three focus groups were used in 2006 to capture the data. A purposive sample of students was selected at one university in the UK. Thematic analysis led to the identification of four main themes: students' understanding of interprofessional learning; educational issues; feelings of isolation; and influence on future practice. Students thought that IPL should involve interaction between students and enable them to find out more about other professions. Common core lectures were not thought to constitute interprofessional learning The findings confirm what other authors have found, but also provide valuable insight into the students' experiences. They can be used to inform quality management processes and curriculum development.
DNA Aptamers Selected Against the HIV-1trans-Activation-responsive RNA Element Form RNA-DNA Kissing Complexes (1999)

In vitro selection was performed in a DNA library, made of oligonucleotides with a 30-nucleotide random sequence, to identify ligands of the human immunodeficiency virus type-1 trans-activation-responsive (TAR) RNA element. Aptamers, extracted after 15 rounds of selection-amplification, either from a classical library of sequences or from virtual combinatorial libraries, displayed an imperfect stem-loop structure and presented a consensus motif 5'ACTCCCAT in the apical loop. The six central bases of the consensus were complementary to the TAR apical region, giving rise to the formation of RNA-DNA kissing complexes, without disrupting the secondary structure of TAR. The RNA-DNA kissing complex was a poor substrate for Escherichia coli RNase H, likely due to steric and conformational constraints of the DNA/RNA heteroduplex. 2'-O-Methyl derivatives of a selected aptamer were binders of lower efficiency than the parent aptamer in contrast to regular sense/antisense hybrids, indicating that the RNA/DNA loop-loop region adopted a non-canonical heteroduplex structure. These results, which allowed the identification of a new type of complex, DNA-RNA kissing complex, demonstrate the interest of in vitro selection for identifying non-antisense oligonucleotide ligands of RNA structures that are of potential value for artificially modulating gene expression.
Combined detection of serum tumor markers for differential diagnosis of solid lesions located at the pancreatic head. (2007)

Combined measurement of serum tumor markers CA19-9, CA242, CA50 and CEA is valuable in differential diagnosis of solid lesions located at the pancreatic head, and CA19-9 has the best diagnostic ability. Combined measurements can increase the specificity of diagnosis. Evaluation with the ROC curve is better than the sensitivity or specificity alone and the results are more integrated and objective.
Recurrent ischemia in the canine heart causes recurrent bursts of free radical production that have a cumulative effect on contractile function. A pathophysiological basis for chronic myocardial "stunning". (1995)

Open-chest dogs (total number used, 117) underwent 10 5-min coronary occlusions (O) interspersed with 10 min of reperfusion (R). When systolic thickening fraction was measured 9 min after each R, the first O-R cycle was found to cause the largest decrement, with only a slight additional loss during the next four cycles and no further loss during the last five cycles (group IV), suggesting that the first few episodes of ischemia preconditioned the myocardium against the stunning induced by the last five episodes. However, different results were obtained when the total deficit of wall thickening during the final 4-h R interval was measured. The total deficit was similar after one and three 5-min O (groups V and VI, respectively), indicating that the first ischemic episode did precondition against the next two episodes; however, it was approximately 2.5-fold greater after 10 O (group IV) than after 3, indicating that the first 3 episodes failed to precondition against the next 7. Thus, at some point between the 4th and 10th O, the preconditioning effect was lost and recurrent ischemic episodes started to have a cumulative effect. Measurements of free radicals with alpha-phenyl N-tert-butyl nitrone (PBN) demonstrated a burst of free radical generation immediately after the 1st, 5th, and 10th R (group VIII). The total cumulative release of PBN adducts during the initial 5 min of reflow was 58% less after the 5th R than after the 1st (P < 0.05) but did not differ significantly between the 1st and 10th R. When administered throughout the 10 O-R cycles, the .OH scavenger mercaptopropionyl glycine significantly enhanced the recovery of function (group I) and markedly suppressed the formation of free radicals (group VII). However, the beneficial effects of mercaptopropionyl glycine were completely, or largely, lost if the drug was discontinued after the first five (group II) or eight (group III) O-R cycles, respectively, implying that (a) the oxidative stress associated with the last five, or even two, cycles was sufficient to cause severe postischemic dysfunction, and (b) the cumulative injury caused by repetitive ischemic episodes is mediated by recurrent oxidative stress. This study provides direct in vivo evidence that oxygen radicals play an important role in the pathogenesis of myocardial stunning after repetitive ischemia, and implicates .OH as a primary culprit. Taken together, the data indicate that recurrent brief ischemic episodes result in recurrent bouts of oxyradical-mediated injury that have a cumulative effect on contractility, a situation that could lead to protracted or even chronic myocardial stunning.
Learning in neural networks: VLSI implementation strategies (1996)

Fully-parallel hardware neural network implementations may be applied to high-speed recognition, classification, and mapping tasks in areas such as vision, or can be used as low-cost self-contained units for tasks such as error detection in mechanical systems (e.g. autos). Learning is required not only to satisfy application requirements, but also to overcome hardware-imposed limitations such as reduced dynamic range of connections.
A bioresponsive hydrogel tuned to chondrogenesis of human mesenchymal stem cells (2011)

Cartilage tissue engineering aims to replace damaged or diseased tissue with a functional regenerate that restores joint function. Scaffolds are used to deliver cells and facilitate tissue development, but they can also interfere with the structural assembly of the cartilage matrix. Biodegradable scaffolds have been proposed as a means to improve matrix deposition and the biomechanical properties of neocartilage. The challenge is designing scaffolds with appropriate degradation rates, ideally such that scaffold degradation is proportional to matrix deposition. In this study, we developed a bioresponsive hydrogel with cell-mediated degradation aligned to the chondrogenic differentiation of human mesenchymal stem cells (hMSCs). We identified matrix metalloproteinase 7 (MMP7) as an enzyme with a temporal expression pattern that corresponded with cartilage development. By embedding MMP7 peptide substrates within a poly(ethylene glycol) diacrylate backbone, we built MMP7-sensitive hydrogels with distinct degradation rates. When MMP7-sensitive scaffolds were compared with nondegradable scaffolds in vitro, photoencapsulated hMSCs produced neocartilage constructs with more extensive collagenous matrices, as demonstrated through immunohistochemistry and biochemical quantification of matrix molecules. Furthermore, these changes translated into an increased dynamic compressive modulus. This work presents a practical strategy for designing biomaterials uniquely tuned to individual biological processes.
Discovery of acoustic emission based biomarker for quantitative assessment of knee joint ageing and degeneration (2011)

Based on the study of 34 healthy and 19 osteoarthritic knees in three different age groups (early, middle and late adulthood), this thesis reports the discovery of the potential of knee acoustic emission (AE) as a biomarker for quantitative assessment of joint ageing and degeneration. Signal processing and statistical analysis were conducted on the joint angle signals acquired using electronic goniometers attached to the lateral side of the legs during repeated sit- stand-sit movements. A four-phase movement model derived from joint angle measurement is proposed for statistical analysis, and it consists of the ascending- acceleration and ascending-deceleration phases in the sit-to- stand movement, followed by the descending-acceleration and descending-deceleration phases in the stand-to-sit movement. Through the quantitative assessment of joint angle signals based on the four-phase model established, statistical differences of different knee conditions related to age and degeneration were discovered based on cycle-by- cycle variations and movement symmetry.&#13;\nFor AE burst signals acquired from piezo-electric sensors&#13;\nattached to the knee joints during repeated sit-stand-sit movements, the statistical analysis started from the quantity of AE events in the proposed four movement phases and extended to waveform features extracted from AE signals. While the quantity of AE events was found to follow certain statistical trends related to age and degeneration in each movement phase, detail statistical analysis of AE waveform features yielded the peak amplitude value and average signal level of each AE burst as two most significant features. An image based knee AE feature profile is presented based on 2D colour histograms formed by the peak amplitude value and average signal level in four movement phases. It provides not only a visual trend related to knee age and degeneration, but also enables visual assessment of the
Preclinical Analysis of Irreversible Electroporation on Rat Liver Tissues Using a Microfabricated Electroporator (2010)

A microfabricated electroporator (MFE) for the irreversible electroporation (IRE) of tissues has been developed by miniaturizing a clinical electroporator with a two-needle array while keeping the same electric field strength distribution. Since IRE was brought to special attention as one of the local tissue ablation techniques to treat tumors, many preclinical studies have been conducted to investigate the efficacy of IRE on animal tissues. However, some technical difficulties have been frequently encountered due to the macroscale dimension of clinical electroporators, particularly in experiments on small animal models such as the mouse or rat. Here, the MFE was proposed to solve the associated problems, resulting in time- and cost-effective experimental procedures. With the developed MFE, the effect of IRE on rat liver tissues was analyzed with time by immunohistological stainings and electrical measurement, and the experimental results were compared with those operated with the corresponding real-scale clinical electroporator.