gebhart/patrepeval huggingface dataset:
Protein-protein interactions. (1996)

Protein-protein interactions are fundamental to many biological processes. This work updates the current knowledge of the nature of these interactions using the 3-dimensional co-ordinates of protein complexes deposited in the Brookhaven Protein Data Bank (PDB). The characterisation of interfaces within a data set of 32 homo-dimers is presented, including the analysis of interface size, shape complementarity, amino acid composition, polarity and segmentation. The interfaces in these complexes were observed to be, in general, circular, hydrophobic patches on the surface of proteins, which were planar, and segmented with respect to the amino acid sequence. Interface properties were also analysed in different types of protein-protein complex, including dimers, trimers, enzyme-inhibitors, and antibody-proteins. These were classified as permanent (where the components only occur and function in a complexed state), and 'optional' (where the components also exist independently). The 'optional' complexes were less hydrophobic, and contained more inter-molecular hydrogen bonds. These complexes also had smaller and less well packed interfaces than those that only exist in the complexed state. Protein-protein interface properties were also used to differentiate the observed interface from other sites on the protein surface. Circular and contiguous patches of amino acid residues were defmed on the surface of protein structures. For all surface patches defined, 6 properties (solvation potential, residue interface propensity, planarity, hydrophobicity, accessible surface area, and protrusion) were calculated, and compared to those of the observed interface. Using this method, homo-dimer interfaces were found to be those patches that were the most planar, hydrophobic, surface accessible and protruding. This method of patch analysis was used in a predictive algorithm, to locate putative interaction sites on the surface of isolated protomers. The algorithm proved successful in the prediction of such sites in homo-dimers and enzyme- inhibitor complexes.
Prostate-specific antigen vaccines for prostate cancer (2002)

Prostate cancer is the most common malignant tumour in men and there are few treatment options available once the tumour becomes refractory to hormonal manipulation. Prostate-specific antigen (PSA) is a secretory glycoprotein that is commonly expressed by prostatic epithelial cells and is found in elevated levels in the serum of men with prostate cancer. The identification of T cell specific epitopes within the coding sequence of PSA has led to the development of various vaccine strategies that target PSA in an attempt to treat established prostate cancer. These strategies have included human leukocyte antigen-restricted PSA peptides, dendritic cells pulsed with PSA, recombinant viruses expressing PSA and combinations of different vectors. In addition to PSA, several other antigens have been described that may be useful for targeting prostate tumours by vaccines. Animal studies have established the feasibility and safety for many of these agents and clinical trials are now in progress to evaluate the immunological and clinical responses of PSA vaccines. Further research in manipulating anti-PSA immunity with cytokines, costimulatory molecules and other immune modulating agents will likely improve the therapeutic effectiveness of PSA vaccines. Clinical trials designed to evaluate the effects of vaccination in different stages of disease and through different routes of administration need to be performed to define the optimal schedule for PSA vaccines in patients with prostate cancer, or for those at high risk of developing the disease.
Cartilage‐derived morphogenetic proteins induce osteogenic gene expression in the C2C12 mesenchymal cell line (2005)

Cartilage-derived morphogenetic protein-1, -2, and -3 (CDMP-1, -2, and -3) are members of the bone morphogenetic protein (BMP) family and have been shown to exhibit a variety of biological activities. In the present study, effects of these CDMPs on the temporal and spatial expression of genes in the pluripotent mesenchymal cell line C2C12 were examined. Cells cultured in the presence of CDMPs lost the characteristic elongated shape of myoblasts. At the molecular level, CDMP treatment did not change the mRNA expression of MyoD, aggrecan, Six1, and tendin. Scleraxis mRNA level was reduced by CDMP treatment. CDMP-1 and -3, but not CDMP-2, stimulated expression of osteogenic markers, such as alkaline phosphatase (AP), osteocalcin (OC), BSP, and type I collagen, in a dose- and time-dependent manner. With few exceptions, the three CDMPs changed, with different potencies, the expression profile of different members of the BMP family in a similar temporal pattern. Except at the late phase of treatment, CDMP treatment did not change the expression of ActR-IA, BMPR-IA, BMPR-IB, BMPR-II, and ALK-7 mRNAs. Based on the current data, the CDMPs appear to be able to stimulate the C2C12 cells to differentiate into the osteoblast pathway.
A service logic program generation method for advanced intelligent network (2002)

An efficient service logic program (SLP) generation method for the advanced intelligent network is discussed. This method first generates the complete and optimum software specifications for SLPs based on INAP (Q.1218) from plain service specifications, and then translates these software specifications into programming languages. The method features the following key techniques: (1) the global state transition knowledge which defines the INAP-based global state transition rules of the advanced intelligent network service execution system; (2) a specification conversion algorithm using the global state transition knowledge; and (3) a specification supplement algorithm to automatically generate partial SLP software specifications for complex operations such as quasi-normal procedures. This method is expected to greatly reduce the manpower required for SLP creation.
Broadband diode-pumped fibre laser (1988)

We report the observation of a strong dependence of the emission spectrum (centre wavelength and linewidth) of Nd : silica fibre lasers on pump wavelength. In a particular fibre, careful selection of the pump wavelength has led to the operation of a broadband fibre laser at 1060 nm with 19 nm FWHM bandwidth. When pumped with a 30 mW diode laser, it exhibits a 1 mW threshold, a 2.5 mW output, and an intrinsic average wavelength temperature stability of about 10 ppm/°C.
Antibodies in Single-Chain Format Against Tumour-Associated Antigens:Present and Future Applications (2010)

The recombinant antibodies in single-chain format (scFv) have found broad applications in both therapeutic and diagnostic fields. Tumour-associated antigens (TAAs) are proteins or other molecular species expressed in a specific tumour type, that can be targeted for diagnostic and immunotherapy purposes. The possibility of obtaining highly selective and efficacious scFvs makes them appropriate tools to target TAAs. The approach utilised for targeting depends on the nature of TAAs and their cell localisation. Tumour antigens displayed on the cell surface can be recognised by scFvs coupled to radioisotopes, toxins and enzymes to be used in cancer diagnosis and therapy. Intracellular tumour antigens can be targeted by scFvs expressed as "intracellular antibodies". This review reports the existing scFv-based formats, hints of their generation and pharmacokinetics, and a description of the most promising TAAs. It also provides an update of in vitro, preclinical and clinical studies using scFvs against TAAs for cancer diagnosis and treatment, with their merits and limits.
Germination Stimulants of Witchweed (Striga asiatica) from Hydrophobic Root Exudate of Sorghum (Sorghum bicolor) (1988)

Hydrophobic exudate from roots of sorghum [ Sorghum bicolor (L.) Moench. # 3 SORVU ‘IS 8768’] contain four p -benzoquinones which in the dihydroquinone form are active as germination stimulants of witchweed [ Striga asiatica (L.) Kuntz. # STRLU]. The three minor p -benzoquinones were partially characterized and found to be structurally similar to sorgoleone, the major p -benzoquinone of this exudate. Herbicidal activity of the hydrophobic exudate was due to concentration- and pH-dependent inhibition of root elongation in some but not all weeds tested. Witchweed has apparently adapted these “defense” compounds of sorghum as host-specific germination stimulants.
Switched-capacitor neural networks (1987)

A neural network implementation is proposed, consisting of switches, capacitors and inverters. A number of potentially attractive features of the implementation are pointed out.
A study of the kinetics of the reaction between thiol compounds and chloroacetamide (1960)

Research Article| March 01 1960 A study of the kinetics of the reaction between thiol compounds and chloroacetamide H. Lindley H. Lindley 1Division of Protein Chemistry, C.S.I.R.O. Wool Research Laboratories, Parkville, N. 2, Melbourne, Victoria, Australia Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1960) 74 (3): 577–584. https://doi.org/10.1042/bj0740577 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share MailTo Twitter LinkedIn Cite Icon Cite Get Permissions Citation H. Lindley; A study of the kinetics of the reaction between thiol compounds and chloroacetamide. Biochem J 1 March 1960; 74 (3): 577–584. doi: https://doi.org/10.1042/bj0740577 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. © 1960 CAMBRIDGE UNIVERSITY PRESS1960 Article PDF first page preview Close Modal You do not currently have access to this content.
Two new IgA1-kappa plasma cell leukaemia cell lines (JJN-1 & JJN-2) which proliferate in response to B cell stimulatory factor 2. (1989)

Two new cell lines with the phenotype of terminally differentiated B cells have been derived from the presentation bone marrow of a patient with plasma cell leukaemia. They express the same immunoglobulin (A1-kappa) as the original bone marrow cells. JJN-1 is an hypodiploid, slow-growing line with a plasmacytic morphology, which grows in medium with 15-20% fetal calf serum. When JJN-1 was stimulated with a supernatant ('ESG') containing B cell stimulatory factor 2 (BSF-2/IL-6), a hypotetraploid sub-line, JJN-2, was selectively stimulated. JJN-2 is dependent on ESG for survival. The stimulatory effect of ESG can be completely abrogated by an anti-BSF-2 monoclonal antibody. However, purified BSF-2 alone only produces sub-maximal stimulation of the lines. Both lines show complex karyotypic abnormalities, including 14q- and del(6q). JJN-1 and JJN-2 may be useful for the study of late B cell differentiation and for use as immunogens for the generation of anti-plasma cell monoclonal antibodies.
Transcytosis of Retinol-Binding Protein across Renal Proximal Tubule Cells after Megalin (gp 330)-Mediated Endocytosis (2001)

Plasma retinol-binding protein (RBP) combined with vitamin A (retinol) is partially filtered through the glomerulus and then absorbed by proximal tubule cells, leading to recycling of retinol to the circulation. Recently, it was shown that reabsorption of RBP-retinol complexes by proximal tubule cells is mediated by megalin (gp 330), an apical endocytic receptor. It was proposed that RBP is transported by megalin to lysosomes, where it is degraded, thus liberating retinol, which then combines with newly synthesized RBP to be secreted into the bloodstream. This study shows that passage of RBP through immortalized rat renal proximal tubule (IRPT) cells occurs by transcytosis after megalin-mediated endocytosis, which provides an alternative pathway for recycling of retinol. IRPT cells cultured as polarized monolayers with tight junctions were used on permeable filters in the upper chamber of dual-chambered devices, with megalin expression exclusively on the upper surface. After addition of RBP to the upper chamber and incubation at 37 degrees C, intact RBP was found in fluids that were collected from the lower chamber. In contrast, control substances (mannitol, lysozyme, albumin, and glutathione-S-transferase) were not appreciably transported across IRPT cells, indicating that passage of RBP was by transcytosis and not by paracellular leakage. Confocal microscopy analysis of IRPT cells after addition of RBP to the upper chamber revealed RBP-containing granules at the apical membrane, subapically, and also at basolateral membranes. When RBP was added to IRPT cells together with megalin competitors, the amount of transcytosed RBP was markedly reduced. We also found that some RBP was internalized and degraded by IRPT cells, but this process was not appreciably affected by megalin competitors, indicating that RBP endocytosed by megalin was not transported to lysosomes and degraded but rather transcytosed across IRPT cells.
Phylogenetic comparative analysis of RNA structure on Macintosh computers (1991)

A Macintosh Hypertalk program (Hypercard 'stack') for use in phylogenetic comparative analysis of RNA structure is described. The program identifies covariations and compensatory changes in RNA sequence alignments, for use in the construction of secondary structure models or the identification of tertiary interactions. The results of an analysis are presented either as a list of positions in the alignment which covary, or as a 2-dimensional matrix in which potential helices in the secondary structure appear as diagonal patterns.
Direct Ink‐Jet Printing of Vertical Walls (2002)

Direct jet printing can assemble ceramic powder into a three dimensional shape by firing droplets of ink through a nozzle to build a multiple layered structure. As with stereolithography and selective laser sintering, the surface texture is expected to witness the layered assembly. The ability to create vertical walls by direct ink‐jet printing was explored using a test piece based on a maze. The structure and topography are discussed in terms of droplet spreading and drying.
A Mouse Model of Burn Wounding and Sepsis (2003)

Despite major advances in the treatment of critically injured burn patients, sepsis remains a major obstacle to recovery (1-4). In fact, sepsis is a leading cause of morbidity and mortality in this patient population (5-6). Those who survive the initial injury become increasingly susceptible to septic complications during the second week of hospitalization. The majority of these patients show a severe depression of their innate immunity as evidenced by T-cell suppression and functional deficits in neutrophils and monocytes (7-14).
Pro-inflammatory cytokine inhibition in the primate using microencapsulated antisense oligomers to NF-κB (2007)

Microencapsulated ASO to NF-kappaB is more effective than ASO in solution in pro-inflammatory cytokine inhibition in non-human primates.
Role of the carboxyl-terminal region of arrestin in binding to phosphorylated rhodopsin (1991)

The structural and functional properties of arrestin were studied by subjecting the protein to limited proteolysis. Limited proteolysis by trypsin cleaves arrestin (48 kDa), producing 20-25-kDa fragments. Prior to this stage of proteolysis, trypsin produced 46.6-, 45.4-, and 42-kDa fragments. Structural analysis of the proteolytic fragments demonstrated major cleavage at the carboxyl terminus, indicating that the carboxyl terminus is highly exposed. We found that forms of arrestin truncated at their carboxyl terminus maintained their functional properties and bound to phosphorylated rhodopsin. Native arrestin binds only to photoexcited phosphorylated rhodopsin, whereas the truncated arrestin binds to phosphorylated rhodopsin independent of its exposure to light. The truncated forms of arrestin were separated from native arrestin by a chromatographic procedure and subsequently characterized in functional studies. The binding of the truncated forms of arrestin to phosphorylated photoexcited rhodopsin is more tight than the binding of native arrestin as determined by a direct binding assay and the phosphodiesterase assay. We suggest that the acidic carboxyl-terminal region of arrestin may act as a regulator for light-dependent binding to phosphorylated rhodopsin.
Prevention of wound infection in elective colorectal surgery by local application of a gentamicin-containing collagen sponge. (1997)

Preoperative antibiotic prophylaxis is known to significantly reduce the incidence of postoperative wound infection in elective colorectal surgery, and is a recognized part of surgical management. Antibiotics are usually given systemically or orally, or by a combination of the two routes. Local antibiotic delivery to the wound site using an implanted, reabsorbable, gentamicin-containing collagen sponge is a novel concept. We compared postoperative wound infection rates in 221 colorectal surgery patients randomized to receive systemic gentamicin/metronidazole with (Group I, n = 107) or without (Group II, n = 114) the gentamicin-collagen sponge. The two patient groups were identical on the basis of demographics and operations undergone. The postoperative wound infection rate was significantly lower in Group I patients than Group II 5.6% (6/107) and 18.4% (21/ 114), respectively (p < 0.01). The mean duration of hospital stay was 13.8 days in Group I and 16.3 days in Group II, which did not represent a statistically significant difference. The gentamicin collagen sponge was well tolerated and no adverse events were reported that were attributable to its use. This new method for delivering gentamicin directly to the operative site may represent a significant method for reducing postoperative wound infection rates to levels lower than those currently achieved with systemic antibiotics alone.
Renalase (2014)

The consistent association of renalase single nucleotide polymorphisms and the development of type 1 diabetes is a great interest particularly because we now understand that renalase functions as a cytokine. Future work on renalase should focus on exploring the identity of its receptor(s), and its potential role as an immune modulator.
Dynamic splitting of large intensity-modulated fields (2000)

The aims of this paper are to describe a method of splitting large intensity-modulated fields that cannot be delivered as a single field and to verify the accuracy of our method. Some multi-leaf collimators may be operated in the dynamic mode to deliver intensity-modulated radiation treatments (IMRT) using the 'sliding window' technique. In this technique each pair of leaves sweeps over the treatment field while the beam is on. However, there are limitations on the width of the field that can be treated due to the limited length of the leaves. For instance, the leaf length of the Varian MLC is 14.5 cm. Since each leaf pair must travel from the left boundary to the right boundary of the beam aperture, the maximum width of the field aperture that can be accommodated in one sweep of leaves is also limited to 14.5 cm, in fact to a slightly smaller value. It has been shown that IMRT is more efficient when used to plan and deliver the large and boost fields simultaneously. In such situations, the fields must be large enough to cover simultaneously the volumes of the gross tumour, microscopic disease and electively treated regions. Such field sizes are often larger than 14.5 cm wide. In this paper, we present a dynamic 'feathering' technique to split the large intensity-modulated fields into smaller fields. In this technique, the component beams overlap each other by a small amount, and the intensity in the overlap region gradually decreases for one field component and increases for the other. The sum of intensities remains the same as for the original field. This method eliminates the field matching problems associated with the conventional step 'break' for static fields. The splitting process is integrated into the IMRT treatment procedure and the entire planning process is automated. Comparison of dose distributions calculated and measured in a phantom showed good agreement. Such a method can be applied to the 'step and shoot' technique as well. IMRT fields of widths up to 25 cm can be delivered by splitting only once, which is adequate for most treatments.
Tau Aggregation Inhibitor Therapy: An Exploratory Phase 2 Study in Mild or Moderate Alzheimer's Disease (2015)

Background: As tau aggregation pathology correlates with clinical dementia in Alzheimer's disease (AD), a tau aggregation inhibitor (TAI) could have therapeutic utility. Methylthioninium (MT) acts as a selective TAI in vitro and reduces tau pathology
Shapeshifter: Dynamically changing pipeline width and speed to address process variations (2008)

Process variations are a manufacturing phenomenon that result in some parameters of the transistors in a real chip to be different from those specified in the design. One impact of these variations is that the affected circuits may perform faster or slower than the design target. Unfortunately, only a small fraction of chips speed up whereas the vast majority incur slow downs. While die-to-die variations have been addressed by clock binning, within-die variations are increasing in importance with scaling. Clock binning in the presence of within-die variations results in slow clock speeds for dies with many components that can operate at higher clock speeds. A recent paper addressing within-die variations proposes variable-latency functional units and register file so that the fast instances of these components take fewer clock cycles to operate than the slower instances. However, in pipeline stages where the instances are interdependent, the fast instances would be held up by the slow instances. Also, variable latency may complicate timing-critical instruction scheduling. Instead of varying the number of clock cycles, we advocate varying the clock speed. Our scheme, called Shapeshifter, maintains high clock speeds during low-ILP program phases by using a narrower pipeline of only the faster instances, and reduces the clock speed only in the high-ILP phases which use all the instances. Shapeshifter simply turns off the slow instances, removing them from any interdependence among all the instances. Also, Shapeshifter requires minimal additions to the pipeline because almost all pipelines already support varying the clock speed for power management purposes. Using simulations, we show that Shapeshifter performs better than clock binning and the variable-latency approach.
Regulation of Functionally Active P2Y12 ADP Receptors by Thrombin in Human Smooth Muscle Cells and the Presence of P2Y12 in Carotid Artery Lesions (2010)

These data suggest that the P2Y12 receptor not only is central to ADP-induced platelet activation but also may mediate platelet-independent responses, specifically under conditions of enhanced thrombin formation, such as local vessel injury and atherosclerotic plaque rupture.
Functionally graded materials and new prospects for thermoelectricity use (2002)

Investigation results of state of the art and prospects of the theory, technology and practical use of thermoelectric FGM development have been presented. Computer technologies for the optimal predicted inhomogeneities determination have been considered. Data on the limiting possibilities of thermoelectric conversion efficiency improvement by means of FGM use as well as the data on the FGM technologies have been given. New possibilities of thermoelectric use have been considered.