gebhart/patrepeval huggingface dataset:
A High Affinity Binding Site for the HIV-1 Nucleocapsid Protein (1997)

The nucleocapsid protein (NC) of HIV-1 is a small zinc finger protein that contributes to multiple steps of the viral life cycle, including the proper encapsidation of HIV RNA. This is accomplished through an interaction between NC and a region at the 5'-end of the RNA, defined as the Psi element. However, the specificity of NC for Psi or for RNA in general is not well understood. To study this problem, we used SELEX to identify high affinity RNA ligands that bind to NC. A 'winner' molecule (SelPsi), as well as a subregion of Psi RNA, were further characterized to understand the interaction between NC and SelPsi and its relationship to the interaction between NC and Psi. The comparison makes predictions about the sequence and structure of a high affinity binding site within the HIV-1 Psi element.
Dendritic cells generated in the presence of GM‐CSF plus IL‐15 prime potent CD8+ Tc1 responses in vivo (2003)

Dendritic cells (DC) comprise a system of professional antigen-presenting cells, which induce the stimulation of very rare antigen-specific naive T cells. DC progenitors can be stimulated to differentiate into immature DC by various growth factors, including GM-CSF and IL-4. Here we show that IL-15, in combination with GM-CSF, is a growth factor for murine DC. Murine bone marrow cells, depleted of T cells, B cells, I-A+ cells and Gr-1+ granulocytes, and cultured in the presence of GM-CSF plus IL-15 (IL-15 DC), yielded DC expressing high levels of CD11c and MHC class II molecules, as well as CD11b. These cells expressed significant levels of CD40, CD80 and CD86, and could stimulate allogeneic CD4+ T cells efficiently. Interestingly, IL-15 DC were far superior to DC generated with GM-CSF plus IL-4 in stimulating allogeneic CD8+ T cells in vitro. Consistent with this, IL-15 DC induced much more potent antigen-specific CD8+ T cell responses with high levels of Th1 cytokines in vivo, compared to DC generated with GM-CSF plus IL-4, or with GM-CSF plus TGF-beta, or with GM-CSF alone. Together, these data suggest that IL-15 promotes the development of DC, which induce potent Th1 and Tc1 responses in vivo. This suggests potential roles for these IL-15 DC cells in the immunotherapy of tumors and infectious diseases.
Heparin is required for cell-free binding of basic fibroblast growth factor to a soluble receptor and for mitogenesis in whole cells. (1992)

Heparin is required for the binding of basic fibroblast growth factor (bFGF) to high-affinity receptors on cells deficient in cell surface heparan sulfate proteoglycan. So that this heparin requirement could be evaluated in the absence of other cell surface molecules, we designed a simple assay based on a genetically engineered soluble form of murine FGF receptor 1 (mFR1) tagged with placental alkaline phosphatase. Using this assay, we showed that FGF-receptor binding has an absolute requirement for heparin. By using a cytokine-dependent lymphoid cell line engineered to express mFR1, we also showed that FGF-induced mitogenic activity is heparin dependent. Furthermore, we tested a series of small heparin oligosaccharides of defined lengths for their abilities to support bFGF-receptor binding and biologic activity. We found that a heparin oligosaccharide with as few as eight sugar residues is sufficient to support these activities. We also demonstrated that heparin facilitates FGF dimerization, a property that may be important for receptor activation.
SATB2 interacts with chromatin‐remodeling molecules in differentiating cortical neurons (2008)

During our search for developmental regulators of neuronal differentiation, we identified special AT-rich sequence-binding protein (SATB)2 that is specifically expressed in the developing rat neocortex and binds to AT-rich DNA elements. Here we investigated whether the regulatory function of SATB2 involves chromatin remodeling at the AT-rich DNA site. In-vitro and in-vivo assays using a DNA affinity pre-incubation specificity test of recognition and chromatin immunoprecipitation showed that SATB2 specifically binds to histone deacetylase 1 and metastasis-associated protein 2, members of the nucleosome-remodeling and histone deacetylase complex. Double immunohistochemistry showed that, in the developing rat neocortex, SATB2 is coexpressed with both proteins. Using a cell culture model, we showed that trichostatin A treatment, which blocks the activities of histone deacetylases, reverses the AT-rich dsDNA-dependent repressor effect of SATB2. These findings suggested that the molecular regulatory function of SATB2 involves modification of the chromatin structure. Semi-quantitative chromatin immunoprecipitation analysis of cortices from SATB2 mutant and wild-type animals indicated that, in the knock-out brains, SATB2 is replaced in the chromatin-remodeling complex by AU-rich element RNA binding protein 1, another AT-rich DNA binding protein also expressed in differentiating cortical neurons. These results suggested that an altered chromatin structure, due to the presence of different AT-rich DNA binding proteins in the chromatin-remodeling complex, may contribute to the developmental abnormalities observed in the SATB2 mutant animals. These findings also raised the interesting possibility that SATB2, along with other AT-rich DNA binding proteins, is involved in mediating epigenetic influences during cortical development.
PLC-type hybrid external cavity laser integratedwith front-monitor photodiode on Si platform (2001)

A planar lightwave circuit (PLC)-type hybrid external cavity laser, integrated with a front-monitor photodiode (PD) on Si has been successfully fabricated. Polymer-embedded grooves are incorporated in the cavity to suppress mode hopping, and the optical power of the laser was stabilised from 18 to 56°C with no mode hopping.
ChemInform Abstract: High Pressure Diels—Alder Approach to Hydroxy‐Substituted 6a‐Cyano‐tetrahydro‐6H‐benzo[c]chromen‐6‐ones: A Route to Δ6‐cis‐Cannabidiol. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
rRNA Transcription in Escherichia coli (2004)

Ribosomal RNA transcription is the rate-limiting step in ribosome synthesis in bacteria and has been investigated intensely for over half a century. Multiple mechanisms ensure that rRNA synthesis rates are appropriate for the cell's particular growth condition. Recently, important advances have been made in our understanding of rRNA transcription initiation in Escherichia coli. These include (a) a model at the atomic level of the network of protein-DNA and protein-protein interactions that recruit RNA polymerase to rRNA promoters, accounting for their extraordinary strength; (b) discovery of the nonredundant roles of two small molecule effectors, ppGpp and the initiating NTP, in regulation of rRNA transcription initiation; and (c) identification of a new component of the transcription machinery, DksA, that is absolutely required for regulation of rRNA promoter activity. Together, these advances provide clues important for our molecular understanding not only of rRNA transcription, but also of transcription in general.
Complexity of MAM-6, an epithelial sialomucin associated with carcinomas. (1989)

The complexity of epithelial sialomucins was investigated by immunoprecipitation and membrane immunofluorescence, using monoclonal antibodies (MAbs) against MAM-6 and other sialomucins. MAbs against MAM-6 immunoprecipitated from a variety of sources either one or two sialylated glycoproteins with apparent molecular weights of over 400,000 under reducing as well as nonreducing conditions. The electrophoretic mobility of each MAM-6 glycoprotein as isolated from serum, milk, and cell lines of different individuals showed considerable variation. The differences in molecular weight of the MAM-6 glycoproteins were also reflected at the level of MAM-6 precursors which are less heavily glycosylated. Therefore, large differences in apparent molecular weight (150,000 and over) are most likely due to a variable protein backbone. We used this molecular polymorphism to prove that 11 MAbs against different sialomucins, obtained from various investigators, precipitated sialomucins generated from common precursor molecules. The pattern of reactivity of the MAbs with carcinoma cell lines was complex. All but the two MAbs, directed against putative carbohydrate epitopes, immunoprecipitated the precursor molecule from each cell line. However, some of them were unable to immunoprecipitate the mature form of MAM-6 from these cell lines. These results indicate that those epitopes are masked, probably due to cell line- or possibly cell type-dependent variations in glycosylation of the epithelial sialomucin. Even within a single cell line mature molecules with different epitopes were observed. The differential reactivity of the MAbs was confirmed by membrane immunofluorescence. These results show that MAM-6 belongs to a family of epithelial sialomucins with a polymorphic protein backbone and extensive variation in glycosylation.
Sensorless current mode control-an observer-based technique for DC-DC converters (2002)

Sensorless current mode (SCM) control is an observer method that provides the operating benefits of current mode control without current sensing. SCM has significant advantages over both conventional peak and average current-mode control techniques in noise susceptibility and dynamic range. The method supports both line and bulk load regulation, and reduces control complexity to a single loop. The static and dynamic performance of SCM are analyzed and verified experimentally for DC-DC converters. Performance in continuous and discontinuous modes compares favorably to conventional techniques when noise is not a factor, but is significantly better when noise and wide load ranges are a concern. The SCM method encompasses one-cycle control as a special case; the general SCM method is introduced here as a public domain control technique.
Expression of the plant cyclin‐dependent kinase inhibitor ICK1 affects cell division, plant growth and morphology (2000)

The plant CDK inhibitor ICK1 was identified previously from Arabidopis thaliana with its inhibitory activity characterized in vitro. ICK1 displayed several structural and functional features that are distinct from known animal CDK inhibitors. Despite the initial characterization, there is no information on the functions of any plant CDK inhibitor in plants. To gain insight into ICK1 functions in vivo and the role of cell division during plant growth and development, transgenic plants were generated expressing ICK1 driven by the cauliflower mosaic virus 35S promoter. In comparison to control plants, growth was significantly inhibited in transgenic 35S-ICK1 plants, with some plants weighing <10% of wild-type plants at the 3 week stage. Most organs of 35S-ICK1 plants were smaller. There were also modifications in plant morphology such as shape and serration of leaves and petals. The changes were so drastic that 35S-ICK1 plants with strong phenotype no longer resembled wild-type plants morphologically. Analyses showed that increased ICK1 expression resulted in reduced CDK activity and reduced the number of cells in these plants. Cells in 35S-ICK1 plants were larger than corresponding cells in control plants. These results demonstrate that ICK1 acts as a CDK inhibitor in the plant, and the inhibition of cell division by ICK1 expression has profound effects on plant growth and development. They also suggest that alterations of plant organ shape can be achieved by restriction of cell division.
DPP6 gene variability confers increased risk of developing sporadic amyotrophic lateral sclerosis in Italian patients (2008)

Amyotrophic lateral sclerosis (ALS) is an adult-onset neurodegenerative disease characterized by progressive loss of motor neurons. Approximately 10% of ALS cases are familial, with the remaining being sporadic. Although the aetiology of sporadic ALS (SALS) is largely unknown, familial and epidemiological data indicate that genetic factors may contribute to its pathogenesis.
Bandwidth-efficient BVH layout for incremental hardware traversal (2016)

The memory footprint of bounding volume hierarchies (BVHs) can be significantly reduced using incremental encoding, which enables the coarse quantization of bounding volumes. However, this compression alone does not necessarily yield a comparable improvement in memory bandwidth. While the bounding volumes of the BVH nodes can be aggressively quantized, the size of the child node pointers remains a significant overhead. Moreover, as BVH nodes become comparably small to practical cache line sizes, the BVH is cached less efficiently. In this paper we introduce a novel memory layout and node addressing scheme and map it to a system architecture for fixed-function ray traversal. We evaluate this scheme using an architecture simulator and demonstrate a significant reduction in memory bandwidth, compared to previous approaches.
Scope of Multivalent Ligand Function: Lactose-Bearing Neoglycopolymers By Ring-Opening Metathesis Polymerization (1999)

A lactose-bearing norbornene imide template was poly- merized using (Cy3P)2Cl2Ru=CHPh to produce a lactose-substitut- ed neoglycopolymer. The resulting polymer showed a 100-fold overall increase in inhibitory potency (5-fold increase on a per sac- charide residue basis) compared to monomeric lactose in both a ga- lectin-binding assay and an Erythrina corallodendrum hemagglutination assay.
Reconstruction of the Acoustic Field Using a Conformal Array (2006)

Near-field acoustical holography (NAH) requires the measurement of the near-field pressure field over a conformal and closed surface in order to recover the acoustic field on a nearby surface. We are interested in the reconstruction of the acoustic field over the fuselage of a Boeing 757 airplane when pressure data is available over an array of microphones that are conformal to the fuselage surface. In this case the strict NAH theory does not hold, but still there are techniques used to overcome this difficulty. The best known is patch NAH, which has been used for planar surfaces. In this work we will discuss two new techniques used for surfaces with an arbitrarily shape: patch inverse boundary element methods (IBEM) and patch equivalent sources method (ESM). We will discuss the theoretical justification of the method and show reconstructions for in-flight data taken inside a Boeing 757 airplane.
Design Considerations for High Fan-In Systems: The HiFi Approach. (2005)

Advances in data acquisition and sensor technologies are leading towards the development of “high fan-in ” architectures: widely distributed systems whose edges consist of numerous receptors such as sensor networks, RFID readers, or probes, and whose interior nodes are traditional host computers organized using the principles of cascading streams and successive aggregation. Examples include RFID-enabled supply chain management, largescale environmental monitoring, and various types of network and computing infrastructure monitoring. In this paper, we identify the key characteristics and data management challenges presented by high fan-in systems, and argue for a uniform, query-based approach towards addressing them. We then present our initial design concepts behind HiFi, the system we are building to embody these ideas, and describe a proof-of-concept prototype. 1.
Video Assist: a customizable tool for analyzing video data (2002)

Analyzing real world events captured in video is often a very time consuming and labor intensive process. The paper describes Video Assist, a software tool designed to assist encoding and analyzing actions recorded on video tape. It presents the design rationales underlying its features such as: customizable objects and their attributes, their integration with an outliner and time line diagrams, their directly manipulable interface, and its mechanism for supporting consistent labeling. It reports on the use of this tool in analyzing a software review process meeting recorded on video tape. Using this example, it illustrates how Video Assist implements the phases and the operations of ESDA (Exploratory Sequential Data Analysis) and how they can dramatically simplify the process of analyzing the sequential data in video. It concludes by discussing the current limitations of the tool and the plans for future extension.
Human CD8+ T Cells Recognize the 60-kDa Cysteine-Rich Outer Membrane Protein from Chlamydia trachomatis (2004)

The intracellular bacterial pathogen Chlamydia is sequestered from the host cell cytoplasm by remaining within an inclusion body during its replication cycle. Nevertheless, CD8(+) T cells recognizing Chlamydia Ags in the context of MHC class I molecules are primed during infection. We have recently described derivation of Chlamydia-specific human CD8(+) T cells by using infected dendritic cells as a surrogate system to reflect Chlamydia-specific CD8(+) T cell responses in vivo. These CD8(+) T cell clones recognize chlamydial Ags processed via the conventional class Ia processing pathway, as assessed by treatment of infected APC with lactacystin and brefeldin A, suggesting that the Ags are translocated from the chlamydial inclusion into the host cell cytosol. In this study, outer membrane protein 2 (OmcB) was identified as the Ag recognized by one of these Chlamydia-specific human CD8(+) T cells, and we defined the HLA*A0101-restricted epitope from this Ag. CD8(+) T cell responses to this epitope were present at high frequencies in the peripheral blood of both of two HLA*A0101 donors tested. In vitro chlamydial growth was completely inhibited by the OmcB-specific CD8(+) T cell clone independently of lytic mechanisms. OmcB is a 60-kDa protein that has been postulated to be associated with the Chlamydia outer membrane complex. The subcellular localization of OmcB to the cytosol of infected cells, as determined by conventional MHC class I Ag processing and presentation, suggests the possibility of an additional, cytosolic-associated function for this protein.
A Humanized Tumor Necrosis Factor Receptor 1 (TNFR1)-specific Antagonistic Antibody for Selective Inhibition of Tumor Necrosis Factor (TNF) Action (2008)

Tumor necrosis factor (TNF) is a recognized pathogenic mediator in a number of chronic and acute inflammatory diseases. Antibodies targeting TNF have significantly improved therapy of chronic inflammatory diseases, in particular rheumatoid arthritis. Despite this success, anti-TNF treatment shows clinical efficacy only in part of the patients and is often transient, necessitating the development of alternative reagents to combat TNF action. We here describe humanization and functional properties of a TNFR1-specific, monovalent antibody fragment, designated IZI-06.1, which binds to the cysteine-rich domain 1 of TNFR1 with high affinity and competes ligand binding. IZI-06.1 serves as a receptor-selective inhibitor of proapoptotic and antiapoptotic TNF actions, revealed from complete blockage of TNFR1-dependent apoptosis and interleukin-6 induction in Kym 1 and HeLa cells, respectively, whereas TNFR2-mediated signals remained intact, evident from TNF and interleukin-2-mediated costimulation of interferon-gamma production in T cells. Accordingly, IZI-06.1 is a TNFR1-selective TNF antagonist and holds great promise to be developed into a clinically applicable therapeutic. IZI-06.1 could be a useful therapeutic alternative in all diseases already known to clinically respond to anti-TNF treatment and particularly in those diseases, where anti-TNF treatment has failed because of complete blockade of TNF action.
Evaluation of Early-stage Parkinson's Disease with ~(99m)Tc-TROD AT-1 SPECT DAT Imaging (2005)

Aim: To investigate the potential usefulness of 99mTc-TRODAT-1 imaging in the evaluation of patients with early-stage Parkinson's disease and correlate the findings to the severity of the disease. Methods: 62 patients with early-stage idiopathic Parkinson's disease were recruited (for all patients, the Parkinson's disease was stage 2 or less as assessed by the Hoehn and Yahr scale), 12 advanced Parkinson patients ( stage 4 by the Hoehn and Yahr scale ), 10 patients with parkinsonism, 19 patients with essential tremor, and 10 age-matched healthy volunteers served as controls. Brain SPECT imaging was performed 2 hours after injection of 99mTc-TRODAT-1 . Regions of interest were drawn over the striatum and the cerebellum, and the ratios of striatum-to-cerebellum ( ST/CB) were calculated. The correlations among DAT binding in striatum and Hoehn and Yahr scale and UPDRS motor scores were determined in the parkinsonian patients. Results: A reduction of specific striatal uptake of 99mTc-TRODAT-l was found in Parkinson's disease patients. The mean values of specific uptake contralateral to the more affected limbs were significantly decreased compared with the ipsilateral sides in patients with early stage Parkinson' s disease. The DAT binding uptake in striatum of all parkinsonian patients showed significantly negative correlation to HY stage, but did not show any relation to UPDRS motor scores. Conclusion: For clinical practice, 99m Tc-TRODAT-1 DAT SPECT imaging is helpful for the early detection of Parkinson's disease.
Presence of previously undescribed bacterial taxa in non-axenic Chlorella cultures (2008)

We determined the bacterial community profile in non-axenic cultures of Chlorella (Chlorophyceae, Chlorophyta) isolated from soil. The bacterial composition at the phylum level was different from that of whole soil bacteria, but it was similar to that reported for non-axenic cultures of marine microalgae such as diatoms (Bacillariophyceae, Heterokontophyta). Expected novel bacteria, i.e. those which do not have close relatives among described species, were maintained in the cultures, and these bacteria were chiefly composed of members of the phylum Bacteroidetes. They may have been 'as-yet-uncultured' but in practice unintentionally been cultured in microalgal cultures. They could serve as good bioresources in various fields of biological and ecological studies.
Prognostic significance of differentially expressed miRNAs in esophageal cancer (2010)

Altered microRNA (miRNA) expression has been found to promote carcinogenesis, but little is known about the role of miRNAs in esophageal cancer. In this study, we selected 10 miRNAs and analyzed their expression in 10 esophageal cancer cell lines and 158 tissue specimens using Northern blotting and in situ hybridization, respectively. We found that Let-7g, miR-21 and miR-195p were expressed in all 10 cell lines, miR-9 and miR-20a were not expressed in any of the cell lines, and miR-16-2, miR-30e, miR-34a, miR-126 and miR-200a were expressed in some of the cell lines but not others. In addition, transient transfection of miR-34a inhibited c-Met and cyclin D1 expression and esophageal cancer cell proliferation, whereas miR-16-2 suppressed RAR-β(2) expression and increased tumor cell proliferation. Furthermore, we found that miR-126 expression was associated with tumor cell dedifferentiation and lymph node metastasis, miR-16-2 was associated with lymph node metastasis, and miR-195p was associated with higher pathologic disease stages in patients with esophageal adenocarcinoma. Kaplan-Meier analysis showed that miR-16-2 expression and miR-30e expression were associated with shorter overall and disease-free survival in all esophageal cancer patients. In addition, miR-16-2, miR-30e and miR-200a expression were associated with shorter overall and disease-free survival in patients with esophageal adenocarcinoma; however, miR-16-2, miR-30e and miR-200a expression were not associated with overall or disease-free survival in squamous cell carcinoma patients. Our data indicate that further evaluation of miR-30e and miR-16-2 as prognostic biomarkers is warranted in patients with esophageal adenocarcinoma. In addition, the role of miR-34a in esophageal cancer also warrants further study.