gebhart/patrepeval huggingface dataset:
Molecular Cloning and Characterization of the 120-Kilodalton Protein Gene of Ehrlichia canis and Application of the Recombinant 120-Kilodalton Protein for Serodiagnosis of Canine Ehrlichiosis (2000)

The 120-kDa outer membrane protein (p120) is a potential adhesin of Ehrlichia chaffeensis, and recombinant p120 is very useful for serodiagnosis of human monocytotropic ehrlichiosis. The analogous gene of p120 in Ehrlichia canis was cloned, sequenced, and expressed. Like the E. chaffeensis p120, the E. canis p120 contains tandem repeat units. However, neither the repeat number nor the amino acid sequences in the repeats are identical in the two Ehrlichia species. The repeat units are hydrophilic and by probability analysis are predicted to be surface exposed in both species. The repeat regions of the p120s of the two species have common amino acid sequences that are predicted to be surface exposed. The overall amino acid sequence of the E. canis p120 is 30% homologous to that of E. chaffeensis p120. Protein immunoblotting demonstrated that the recombinant E. canis p120 reacted with convalescent sera from dogs with canine ehrlichiosis. These results indicate that the recombinant p120 is a potential antigen for the serodiagnosis of canine ehrlichiosis.
5-Hydroxytryptamine Type 3 Receptor Modulates Opioid-induced Hyperalgesia and Tolerance in Mice (2011)

Morphine acts via a 5-HT3-dependent mechanism to support multiple maladaptations to the chronic administration of morphine. Furthermore, the use of 5-HT3 receptor antagonists may provide a new avenue to prevent or reverse OIH and tolerance associated with chronic opioid use.
Attenuation of TGF-β signaling suppresses premature senescence in a p21-dependent manner and promotes oncogenic Ras-mediated metastatic transformation in human mammary epithelial cells (2012)

The molecular mechanisms that drive triple-negative, basal-like breast cancer progression are elusive. Few molecular targets have been identified for the prevention or treatment of this disease. Here we developed a series of isogenic basal-like human mammary epithelial cells (HMECs) with altered transforming growth factor-β (TGF-β) sensitivity and different malignancy, resembling a full spectrum of basal-like breast carcinogenesis, and determined the molecular mechanisms that contribute to oncogene-induced transformation of basal-like HMECs when TGF-β signaling is attenuated. We found that expression of a dominant-negative type II receptor (DNRII) of TGF-β abrogated autocrine TGF-β signaling in telomerase-immortalized HMECs and suppressed H-Ras-V12-induced senescence-like growth arrest (SLGA). Furthermore, coexpression of DNRII and H-Ras-V12 rendered HMECs highly tumorigenic and metastatic in vivo in comparison with H-Ras-V12-transformed HMECs that spontaneously escaped H-Ras-V12-induced SLGA. Microarray analysis revealed that p21 was the major player mediating Ras-induced SLGA, and attenuated or loss of p21 expression contributed to the escape from SLGA when autocrine TGF-β signaling was blocked in HMECs. Furthermore, knockdown of p21 also suppressed H-Ras-V12-induced SLGA. Our results identify that autocrine TGF-β signaling is an integral part of the cellular anti-transformation network by suppressing the expression of a host of genes, including p21-regulated genes, that mediate oncogene-induced transformation in basal-like breast cancer.
Characterization of Irreversible Electroporation Ablation in In Vivo Porcine Liver (2011)

Predictable zones of tissue destruction can be achieved for irreversible electroporation. Ablation dimensions are sensitive to multiple parameters, suggesting that precise technique and attention to detail will be particularly important when using this modality.
Functional modes of retinoic acid in mouse osteoblastic clone MC3T3‐E1, proved as a target cell for retinoic acid (1990)

Mouse osteoblastic clone MC3T3-E1 was proved as a target cell for retinoic acid (RA) in bone tissues through the demonstration of RA-receptor gene expression by the northern blot analysis. The effect of RA on the cell growth of MC3T3-E1 was repressive for both subconfluent and confluent growth, whereas RA enhancement of alkaline phosphatase expression was observed at the confluent stage. This implies that RA is a regulatory factor leading osteogenesis of the cells after the confluent stage. RA exhibited simultaneously the stage-dependent effects on EGF-dependent mitogenesis: promotive at the subconfluent, but repressive at the confluent stage.
Stability of Specific Immunoglobulin Secretion by EBV-Transformed Lymphoblastoid Cells and Human-Murine Heterohybridomas (1989)

We have examined variables leading to the generation of stable, antigen-specific, human immunoglobulin-secreting cell lines. Peripheral blood B lymphocytes enriched for Thomsen-Friedenreich antigen (T antigen)-specific cells were transformed with Epstein-Barr virus. Lymphoblastoid cells (LC) reactive with T antigen were either expanded without cloning or cloned at limiting dilution and then fused with murine 653 cells. Uncloned LCs from three transformations secreting polyclonal anti-T antibody (7-18 micrograms/ml/10(6) cells/24 hr total immunoglobulin) were subcultured at 100 cells/well, and T antigen-reactive cultures pooled. These cultures quickly lost specific antibody secretion, presumably due to overgrowth by clones of unknown specificity. T antigen-reactive LCs that were cloned three times at limiting dilution secreted 0.2 - 6.1 micrograms/ml/10(6) cells/24 hr but died or stopped secreting specific immunoglobulin after 77 to 155 days in culture. Pooling T antigen-reactive clones after each cloning step did not increase the long term stability compared to unpooled clones (p = 0.2). Fusions between cloned LCs and 653 cells failed to yield viable hybrids in nine of ten attempts with seven different LC lines. In contrast, fusion of uncloned LCs and 653 cells resulted in the generation of viable immunoglobulin-secreting heterohybrids in 22 of 24 fusions. The heterohybridomas produced from fusion of uncloned T antigen-reactive cultures with 653 cells secreted significantly more antibody (frequency of cell lines secreting greater than 2 micrograms/ml/10(6) cells/24 hr, p less than 0.01) and higher titers of antibody (frequency of cell lines secreting greater than four hemagglutination units of T antigen-specific antibody, p less than 0.03) than cloned lymphoblastoid cells. The hybrids maintained specific immunoglobulin secretion for longer in culture than either cloned or uncloned lymphoblastoid cell lines (p less than 0.001).
TEMPORAL WINDOW OF METABOLIC BRAIN VULNERABILITY TO CONCUSSIONS (2007)

This study shows the remarkable negative contribution of reactive oxygen species overproduction and activation of inducible nitric oxide synthase in repeat mTBI. Because these effects were maximal when mTBIs were spaced by 3 days, it can be inferred that occurrence of a second mTBI within the temporal window of brain vulnerability not only causes profound derangement of mitochondrial functions, but also induces sustained oxidative and nitrosative stresses. Both phenomena certainly play a major role in the overall brain tissue damage occurring under these pathological conditions.
Spatial integration and cortical dynamics. (1996)

Cells in adult primary visual cortex are capable of integrating information over much larger portions of the visual field than was originally thought. Moreover, their receptive field properties can be altered by the context within which local features are presented and by changes in visual experience. The substrate for both spatial integration and cortical plasticity is likely to be found in a plexus of long-range horizontal connections, formed by cortical pyramidal cells, which link cells within each cortical area over distances of 6-8 mm. The relationship between horizontal connections and cortical functional architecture suggests a role in visual segmentation and spatial integration. The distribution of lateral interactions within striate cortex was visualized with optical recording, and their functional consequences were explored by using comparable stimuli in human psychophysical experiments and in recordings from alert monkeys. They may represent the substrate for perceptual phenomena such as illusory contours, surface fill-in, and contour saliency. The dynamic nature of receptive field properties and cortical architecture has been seen over time scales ranging from seconds to months. One can induce a remapping of the topography of visual cortex by making focal binocular retinal lesions. Shorter-term plasticity of cortical receptive fields was observed following brief periods of visual stimulation. The mechanisms involved entailed, for the short-term changes, altering the effectiveness of existing cortical connections, and for the long-term changes, sprouting of axon collaterals and synaptogenesis. The mutability of cortical function implies a continual process of calibration and normalization of the perception of visual attributes that is dependent on sensory experience throughout adulthood and might further represent the mechanism of perceptual learning.
Surface Plasmon Resonance Thermodynamic and Kinetic Analysis as a Strategic Tool in Drug Design. Distinct Ways for Phosphopeptides to Plug into Src- and Grb2 SH2 Domains (2005)

Thermodynamic and kinetic studies of biomolecular interactions give insight into specificity of molecular recognition processes and advance rational drug design. Binding of phosphotyrosine (pY)-containing peptides to Src- and Grb2-SH2 domains was investigated using a surface plasmon resonance (SPR)-based method. This SPR assay yielded thermodynamic binding constants in solution, and the kinetic information contained in the SPR signal allowed kinetic analysis, which demonstrated distinct ways for pY ligands to interact with the SH2 domains. The results for binding to Src SH2 were consistent with sequestration of water molecules in the interface of the pYEEI peptide/Src SH2 complex. The results for a pYVNV peptide binding to Grb2 SH2 suggested a conformational change for Grb2 SH2 upon binding, which is not observed for Src SH2. Binding of a cyclic construct, allowing the pYVNV sequence in the bound conformation, did not have the expected entropy advantage. The results suggest an alternative binding mode for this construct, with the hydrophobic ring-closing part interacting with the protein. In all cases, except for full-length Grb2 protein, the affinity for the immobilized peptide at the SPR sensor and in solution was identical. This study demonstrates that SPR thermodynamic and kinetic analysis is a useful strategic tool in drug design.
Use and Implications of the Harmonic Mean Model on Mixtures for Basic Research and Drug Discovery (2011)

The use of the harmonic mean model for predicting the activities of a given mixture and its constituents has not previously been explored in the context of combinatorial libraries and drug discovery. Herein, the analyses of historical data confirm the harmonic mean as an accurate predictor of mixture activity. The implications of these results are discussed.
Stabilization of Elastin mRNA by TGF-β: Initial Characterization of Signaling Pathway (1997)

Abstract The cytokine transforming growth factor-β (TGF-β) has multiple effects on a wide variety of cell types. These effects include modulation of growth and regulation of gene transcription. In a few instances, TGF-β has also been shown to regulate gene expression posttranscriptionally by altering message stability, but the pathway by which this activity is executed remains largely unknown. In the present work, we demonstrate that TGF-β1 has no effect on transcription of the elastin gene in cultured human fetal lung fibroblasts, but does stabilize elastin messenger RNA (mRNA), leading to a dramatic increase in the steady-state level of elastin mRNA. A corresponding increase in production of tropoelastin accompanies the increase in elastin mRNA. Through the use of specific inhibitors, we demonstrate that phosphatidylcholine (PC)-specific phospholipase C (PLC) and protein kinase C (PKC) are involved in mediating the elastin message stabilization. In contrast, G proteins and extracellularly regulated kinases do not appear to be involved. These results suggest that although the TGF-β signaling pathway leading to message stabilization shares components with that modulating transcription, the message-stabilization pathway also contains diverse other elements.
Antibody therapy for treatment of multiple myeloma. (1999)

Monoclonal antibody therapy has emerged as a viable treatment option for patients with lymphoma and some leukemias. It is now beginning to be investigated for treatment of multiple myeloma. There are relatively few surface antigens on the plasma cells that are suitable for antibody-directed treatment. Possible molecules include HM1.24, CD38, ICAM-1 (CD54), CD40, CD45, CD20, and syndecan 1. There is now some clinical experience with anti-CD38 antibody in lymphoma and myeloma. However, to date, there has been minimal clinical activity observed. Additional antibodies are entering clinical trials. A new approach involves the generation of an anti-CD38 single-chain variable fragment (scFv) construct that acts as the carrier of a toxin gene instead of being conjugated directly to the toxin itself. It is hoped that expression of the toxin by CD38+ plasma cells will promote suicide of the malignant cells without affecting normal cells or generating an immunologic response to the toxin. Ongoing clinical trials are also attempting to target B-cell antigens such as CD20. Although CD20 is present only on 20% of myeloma cells, it may be present on myeloma precursor cells. This treatment has met with success in follicular lymphoma and is now being evaluated in clinical trials in both Europe and the United States for myeloma. Although these clinical trials are in very early stages, researchers are beginning to understand that antibody therapy can be used not only as a carrier molecule of radioisotopes and toxins, but also as molecules that can trigger tumor cells and promote growth arrest or apoptosis.
Psychiatric Disorders Following Traumatic Brain Injury (2009)

A high frequency of postinjury psychiatric disorders was evident up to 5.5 years postinjury, with many novel cases of depression and anxiety. Individuals with TBI should be screened for psychiatric disorders at various time points post-injury without reliance on history of psychiatric problems to predict who is at risk, so that appropriate intervention can be offered.
Subacute Chlamydial Endocarditis (1982)

Chlamydial endocarditis has been infrequently reported. A case of blood-culture—negative endocarditis is described in which there was serological evidence of a<i>Chlamydia psittaci</i>infection. Chlamydiae were also identified in aortic valve vegetations by electron microscopy and immunofluorescent staining. Patients with culture-negative endocarditis should be evaluated for infection with<i>Chlamydia</i>as well as other uncommon pathogens. (<i>JAMA</i>1982;247:655-658)
Molecular diversity in ductal carcinoma in situ (DCIS) and early invasive breast cancer (2010)

Ductal carcinoma in situ (DCIS) is a non-invasive form of breast cancer where cells restricted to the ducts exhibit an atypical phenotype. Some DCIS lesions are believed to rapidly transit to invasive ductal carcinomas (IDCs), while others remain unchanged. Existing classification systems for DCIS fail to identify those lesions that transit to IDC. We studied gene expression patterns of 31 pure DCIS, 36 pure invasive cancers and 42 cases of mixed diagnosis (invasive cancer with an in situ component) using Agilent Whole Human Genome Oligo Microarrays 44k. Six normal breast tissue samples were also included as controls. qRT-PCR was used for validation. All DCIS and invasive samples could be classified into the "intrinsic" molecular subtypes defined for invasive breast cancer. Hierarchical clustering establishes that samples group by intrinsic subtype, and not by diagnosis. We observed heterogeneity in the transcriptomes among DCIS of high histological grade and identified a distinct subgroup containing seven of the 31 DCIS samples with gene expression characteristics more similar to advanced tumours. A set of genes independent of grade, ER-status and HER2-status was identified by logistic regression that univariately classified a sample as belonging to this distinct DCIS subgroup. qRT-PCR of single markers clearly separated this DCIS subgroup from the other DCIS, and contains samples from several histopathological and intrinsic molecular subtypes. The genes that differentiate between these two types of DCIS suggest several processes related to the re-organisation of the microenvironment. This raises interesting possibilities for identification of DCIS lesions both with and without invasive characteristics, which potentially could be used in clinical assessment of a woman's risk of progression, and lead to improved management that would avoid the current over- and under-treatment of patients.
Overview of JPEG-2000 (2000)

JPEG-2000 is an emerging standard for still image compression. This paper provides a brief history of the JPEG-2000 standardization process, an overview of the standard, and some description of the capabilities provided by the standard. Part I of the JPEG-2000 standard specifies the minimum compliant decoder, while Part II describes optional, value-added extensions. Although the standard specifies only the decoder and bitstream syntax, in this paper we describe JPEG-2000 from the point of view of encoding. We take this approach, as we believe it is more amenable to a compact description more easily understood by most readers. 1 Introduction As digital imagery becomes more commonplace and of higher quality, there is the need to manipulate more and more data. Thus, image compression must not only reduce the necessary storage and bandwidth requirements, but also allow extraction for editing, processing, and targeting particular devices and applications. The JPEG-2000 image compression s...
Cleavage of Zearalenone byTrichosporon mycotoxinivoransto a Novel Nonestrogenic Metabolite (2010)

Zearalenone (ZON) is a potent estrogenic mycotoxin produced by several Fusarium species most frequently on maize and therefore can be found in food and animal feed. Since animal production performance is negatively affected by the presence of ZON, its detoxification in contaminated plant material or by-products of bioethanol production would be advantageous. Microbial biotransformation into nontoxic metabolites is one promising approach. In this study the main transformation product of ZON formed by the yeast Trichosporon mycotoxinivorans was identified and characterized by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and LC-diode array detector (DAD) analysis. The metabolite, named ZOM-1, was purified, and its molecular formula, C(18)H(24)O(7), was established by time of flight MS (TOF MS) from the ions observed at m/z 351.1445 [M-H](-) and at m/z 375.1416 [M+Na](+). Employing nuclear magnetic resonance (NMR) spectroscopy, the novel ZON metabolite was finally identified as (5S)-5-({2,4-dihydroxy-6-[(1E)-5-hydroxypent-1-en-1-yl]benzoyl}oxy)hexanoic acid. The structure of ZOM-1 is characterized by an opening of the macrocyclic ring of ZON at the ketone group at C6'. ZOM-1 did not show estrogenic activity in a sensitive yeast bioassay, even at a concentration 1,000-fold higher than that of ZON and did not interact with the human estrogen receptor in an in vitro competitive binding assay.
Deconstructing Global Intellectual Property Rights Regimes over Biodiversity (2006)

During the 1986-1994 Uruguay Round negotiations under the General Agreement on Trade and Tariffs (later World Trade Organization), the Agreement on Trade-Related Aspects of Intellectual Property Rights (TRIPS) was adopted by participating countries. TRIPS has not only allowed intellectual property to be introduced into international trade arenas, but also extended the scope of protection to biodiversity such as plant genetic material, arguing that intellectual property rights (IPRs) would help conserve biodiversity. In this paper, I aim to deconstruct the global IPRs regimes over biodiversity by adopting geographers’ sensitivity to place and scale as an analytical window. By investigating how all the issues regarding IPRs over biodiversity that are raised by diverse disciplines, such as environmental ethics, environmental economics and political economy approach, are scale-related, I demonstrate how biodiversity IPRs, and its introduction into international trade agreements, though separate issues with no inevitable relationship to one another, have been put together for the construction of global IPRs regimes. I argue that the notion on the construction of scale (i.e., rhetorical and discursive construct of globalization) can contribute to revealing how fragile global environmental conservation regimes are.
Amniotic membranes as a biological dressing. (1977)

Amniotic membrane dressings were tested in the treatment of 30 patients. Fifteen of them had burns, 5 had chronic varicose ulcers, and 10 had decubitus ulcers or other open infected wounds. No effort was made to separate the chorion from the amnion. Dressings were changed every 48 hours, and treatment was, in some cases, partially ambulatory. Good results were obtained in the treatment of 2nd- and 3rd-degree burns and of other open, infected wounds, both in the preparation of the patients for autografting and in consequent treatment.
Effects of Immunomodulators on Ecto‐5′‐Nucleotidase Activity on Blood Mononuclear Cells In Vitro (1992)

In this study the effects of immunomodulators on the ecto-5'-nucleotidase (ecto-5'-NT) activity on blood mononuclear cells (BMC) were examined in vitro. Interleukin-4 (IL-4) and interferon-gamma (IFN-gamma) decreased the level of ecto-5'-NT activity on BMC whereas prostaglandin E2 (PGE2) increased the ecto-5'-NT level. All three immunomodulators influenced the ecto-5'-NT activity of isolated monocytes whereas only IL-4 and PGE2 had an effect on the enzyme level on isolated lymphocytes. The effect was dependent upon protein synthesis. The effect was dose dependent: IL-4 was effective at concentrations down to 0.5 U/ml, IFN-gamma down to 40 U/ml and PGE2 at nanomolar concentrations. These data indicate that immunomodulators may also take part in the regulation of ecto-5'-NT activity on BMC in vivo. BMC from 7 patients with different immunodeficiency syndromes showed decreased ecto-5'-NT activity on freshly isolated cells. However, following culture ecto-5'-NT activity was increased above the level found on freshly isolated BMC from healthy persons. On BMC from 3 patients with hypogammaglobulinaemia, the effect of IL-4 on the level of ecto-5'-NT activity was identical to that found on BMC from healthy donors, whereas PGE2 increased ecto-5'-NT activity on BMC from only 1 of the 3 patients investigated. The decreased ecto-5'-NT activity of BMC from patients with immunodeficiency may thus be due to a defective regulation of ecto-5'-NT activity in vivo.
Polytopes, permanents and graphs with large factors (1988)

Randomized algorithms for approximating the number of perfect matchings in a graph are considered. An algorithm that is a natural simplification of one suggested and analyzed previously is introduced and analyzed. One of the key ideas is to view the analysis from a geometric perspective: it is proved that for any graph G the k-slice of the well-known Edmonds matching polytope has magnification 1. For a bipartite graph G=(U, V, E), mod U mod = mod V mod =n, with d edge-disjoint perfect matchings, it is proved that the ratio of the number of almost perfect matchings to the number of perfect matchings is at most n/sup 3n/d/. For any constant alpha >0 this yields a a fully polynomial randomized algorithm for approximating the number of perfect matchings in bipartite graphs with d>or= alpha n. Moreover, for some constant c>0 it is the fastest known approximation algorithm for bipartite graphs with d>or= clog n.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>