gebhart/patrepeval huggingface dataset:
sll1961 is a novel regulator of phycobilisome degradation during nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803 (2008)

The sll1961 gene was reported to encode a regulatory factor of photosystem stoichiometry in the cyanobacterium Synechocystis sp. PCC 6803. We here show that the sll1961 gene is also essential for the phycobilisome degradation during nitrogen starvation. The defect in phycobilisome degradation was observed in the sll1961 mutant despite the increased expression of nblA, a gene involved in phycobilisome degradation during nitrogen starvation. Photosystem stoichiometry is not affected by nitrogen starvation in the sll1961 mutant nor in the wild-type. The results indicate the presence of a novel pathway for phycobilisome degradation control independent of nblA expression.
On Spectral Clustering: Analysis and an algorithm (2001)

Despite many empirical successes of spectral clustering methods -- algorithms that cluster points using eigenvectors of matrices derived from the distances between the points -- there are several unresolved issues. First, there is a wide variety of algorithms that use the eigenvectors in slightly different ways. Second, many of these algorithms have no proof that they will actually compute a reasonable clustering. In this paper, we present a simple spectral clustering algorithm that can be implemented using a few lines of Matlab. Using tools from matrix perturbation theory, we analyze the algorithm, and give conditions under which it can be expected to do well. We also show surprisingly good experimental results on a number of challenging clustering problems.
Silica Nanoparticles as Surfactants and Fillers for Latexes Made by Miniemulsion Polymerization (2001)

Polymer dispersions made of a variety of monomers, including styrene, butyl acrylate, and methyl methacrylate, were generated by the miniemulsion process in the presence of a coupling comonomer, a hydrophobe, and silica nanoparticles. Depending on the reaction conditions and the surfactants employed, different hybrid morphologies were obtained, comprising a “hedgehog” structure where the silica surrounds the latex droplet and provides stabilization even without any low molecular weight surfactant. In other parts of the composition diagram noncoupled structures as well as “raspberry” hybrids where whole clusters of silica nanoparticles are completely embedded in the polymer particle can be made. The resulting structures are promising for a number of applications, e.g. the increase of scratch resistance in water-based coatings.
Spray Deposition of Highly Transparent, Low‐Resistance Networks of Silver Nanowires over Large Areas (2011)

A method to produce scalable, low-resistance, high-transparency, percolating networks of silver nanowires by spray coating is presented. By optimizing the spraying parameters, networks with a sheet resistance of R(s) ≈ 50 Ω □(-1) at a transparency of T = 90% can be produced. The critical processing parameter is shown to be the spraying pressure. Optimizing the pressure reduces the droplet size resulting in more uniform networks. High uniformity leads to a low percolation exponent, which is essential for low-resistance, high-transparency films.
Big Data Analytics for Predictive Manufacturing Control - A Case Study from Process Industry (2014)

Nowadays, companies are more than ever forced to dynamically adapt their business process executions to currently existing business situations in order to keep up with increasing market demands in global competition. Companies that are able to analyze the current state of their processes, forecast its most optimal progress and proactively control them based on reliable predictions will be a decisive step ahead competitors. The paper at hand exploits potentials through predictive analytics on big data aiming at event-based predictions and thereby enabling proactive control of business processes. In doing so, the paper particularly focus production processes in analytical process manufacturing industries and outlines-based on a case study at Saarstahl AG, a large German steel producing company-which production-related data is currently collected forming a potential foundation for accurate forecasts. However, without dedicated approaches of big data analytics, the sample company cannot utilize the potential of already available data for a proactive process control. Hence, the article forms a working and discussion basis for further research in big data analytics by proposing a general system architecture.
Infectious Tolerance (2002)

Regulatory CD4(+)CD25(+) T cells (Treg) are mandatory for maintaining immunologic self-tolerance. We demonstrate that the cell-cell contact-mediated suppression of conventional CD4(+) T cells by human CD25(+) Treg cells is fixation resistant, independent from membrane-bound TGF-beta but requires activation and protein synthesis of CD25(+) Treg cells. Coactivation of CD25(+) Treg cells with Treg cell-depleted CD4(+) T cells results in anergized CD4(+) T cells that in turn inhibit the activation of conventional, freshly isolated CD4(+) T helper (Th) cells. This infectious suppressive activity, transferred from CD25(+) Treg cells via cell contact, is cell contact-independent and partially mediated by soluble transforming growth factor (TGF)-beta. The induction of suppressive properties in conventional CD4(+) Th cells represents a mechanism underlying the phenomenon of infectious tolerance. This explains previously published conflicting data on the role of TGF-beta in CD25(+) Treg cell-induced immunosuppression.
RAS Interaction with PI3K: More Than Just Another Effector Pathway (2011)

RAS PROTEINS ARE SMALL GTPASES KNOWN FOR THEIR INVOLVEMENT IN ONCOGENESIS: around 25% of human tumors present mutations in a member of this family. RAS operates in a complex signaling network with multiple activators and effectors, which allows them to regulate many cellular functions such as cell proliferation, differentiation, apoptosis, and senescence. Phosphatidylinositol 3-kinase (PI3K) is one of the main effector pathways of RAS, regulating cell growth, cell cycle entry, cell survival, cytoskeleton reorganization, and metabolism. However, it is the involvement of this pathway in human tumors that has attracted most attention. PI3K has proven to be necessary for RAS-induced transformation in vitro, and more importantly, mice with mutations in the PI3K catalytic subunit p110α that block its ability to interact with RAS are highly resistant to endogenous oncogenic KRAS-induced lung tumorigenesis and HRAS-induced skin carcinogenesis. These animals also have a delayed development of the lymphatic vasculature. Many PI3K inhibitors have been developed that are now in clinical trials. However, it is a complex pathway with many feedback loops, and interactions with other pathways make the results of its inhibition hard to predict. Combined therapy with another RAS-regulated pathway such as RAF/MEK/ERK may be the most effective way to treat cancer, at least in animal models mimicking the human disease. In this review, we will summarize current knowledge about how RAS regulates one of its best-known effectors, PI3K.
Hepatitis C Virus Subgenomic Replicons in the Human Embryonic Kidney 293 Cell Line (2003)

Hepatitis C virus (HCV) infects liver cells and its replication in other cells is incompletely defined. Human hepatoma Huh-7 cells harboring subgenomic HCV replicons were used in somatic cell fusion experiments with human embryonic kidney 293 cells as a means of examining the permissiveness of 293 cells for HCV subgenomic RNA replication. 293 cells were generally not permissive for replication of Huh-7 cell-adapted replicons. However, upon coculturing of the two cell lines, we selected rare replicon-containing cells, termed 293Rep cells, that resembled parental 293 cells. Direct metabolic labeling of cells with (33)P in the presence of actinomycin D and Northern blotting to detect the negative strand of the replicon demonstrated functional RNA replicons in 293Rep cells. Furthermore, Western blots revealed that 293Rep cells expressed the HCV nonstructural proteins as well as markers of the naïve 293 cells but not Huh-7 cells. Propidium iodide staining and fluorescence-activated cell sorting analysis of 293Rep cells revealed that clone 293Rep17 closely resembled naïve 293 cells. Transfection of total RNA from 293Rep17 into naïve 293 cells produced replicon-containing 293 cell lines with characteristics distinct from those of Huh-7-derived replicon cell lines. Relative to Huh-7 replicons, the 293 cell replicons were less sensitive to inhibition by alpha interferon and substantially more sensitive to inhibition by poly(I)-poly(C) double-stranded RNA. This study established HCV subgenomic replicons in nonhepatic 293 cells and demonstrated their utility in expanding the study of cellular HCV RNA replication.
Evaluating HER2 amplification and overexpression in breast cancer (2001)

The development of Herceptin (Trazumatab) makes testing for HER2 status important for choosing optimal therapy in breast cancer. This study addresses the precision, accuracy, and reproducibility of HER2 assays. HER2 was assessed retrospectively by immunohistochemistry (IHC) with Dako 'Herceptest', by IHC with the monoclonal antibody CB11, and by fluorescence in situ hybridization (FISH, PathVysion), in a series of 216 formalin-fixed breast carcinomas including 191 for which quantitative HER2 data from radioimmunohistochemistry (Q-IHC) were available. All tests were scored independently by two observers. Positivity rates varied between Herceptest (12.6%), FISH (19.4%), and CB11 IHC (28.5%). Kappa values showed that IHC-based tests were more susceptible to inter-observer variation (kappa=0.67 and 0.74 for Herceptest and CB11, respectively) than FISH (kappa=0.973). Overall test accuracy (see the Materials and methods section) for CB11 IHC (83.8%) was lower than Herceptest (87.4%) or FISH (93.2%). FISH predicted p185 HER2 overexpression (determined by Q-IHC) better (concordance index C.Ind. 0.90) than CB11 IHC (C.Ind.=0.85) or Herceptest (C.Ind.=0.81). Of 42 cases with gene amplification by FISH, 67% were positive in the Herceptest (2+ or 3+) vs. 83% with CB11. Of 174 cases negative by FISH, 96% were negative in the Herceptest and 68% with CB11. In conclusion, FISH is the most accurate, reproducible, and precise predictor of HER2 overexpression in routine diagnostic laboratories.
Localization and characterization of three different β‐adrenergic receptors expressed in Escherichia coli (1990)

After fusion with the N-proximal portion of the outer membrane protein LamB, three beta-adrenergic receptors, the human beta 1- and beta 2- and turkey beta 1-adrenergic receptor, were expressed in Escherichia coli with retention of their own specific pharmacological properties. Molecular characterization and localization of the three receptors in bacteria and comparison of the behaviour of each hybrid protein are reported. The bacteria were lysed and fractionated on a sucrose gradient. Saturable [125I]iodocyanopindolol binding activity was found associated mainly with the inner membrane fraction, suggesting that the receptor is correctly folded in this membrane. Binding activity was also found in the outer membrane fraction but varied according to the receptor type. Photoaffinity labeling experiments revealed that the receptors exhibit binding activity only after proteolytic removal of the LamB moiety from the fusion protein. The three hybrid proteins, detected in immunoblots by anti-peptide antibodies, were found mainly in the outer membrane fraction. Each of them exhibited different susceptibility to intrinsic bacterial proteolytic enzymes; sites of proteolytic cleavage were localized by the use of anti-peptide antibodies. The functional expression in E. coli of three beta-adrenergic receptors with similar structure but different amino acid sequences suggests that this expression system may be a general feature among similar receptors of the family of G-protein-coupled receptors. The level of expressed binding activity of a given receptor will be within the control of proteolytic degradation processes, depending on the primary sequence of the receptor. Constructions of new hybrid proteins, in combination with expression in protease mutants of E. coli, should help in controlling such processes.
Motion and Virtual Cutting Simulation System for a Five-Axis Virtual Machine Tool (2011)

Machine tools are an indispensable link in high-efficiency high-tech production. However, since five-axis machine tools are very costly and their use requires a high level of knowledge and expertise, a virtual machine tool must be used to simulate five-axis machine tool operation. Configuration code or a mechanism topology matrix must be used to describe a machine tool, and can be used as the framework for design of a virtual machine tool system. The first step is to isolate the basic motions of each element of a virtual machine tool and then establish their coordinate systems. The establishment of a node tree allows coordinate transformation matrices for virtual motion components to be derived, which are then used to simulate movements. The simulation of virtual cutting must take into consideration both accuracy and efficiency. While either a GPU or CPU can be used to perform calculations, there are currently restrictions on GPU memory use which results in relatively lower accuracy. In contrast, a CPU can perform calculations using an adaptive octree with voxels and multithreading to yield sufficient accuracy and efficiency. A five-axis virtual machine tool motion and virtual cutting simulation system was written in C/C++ with OpenGL and OpenMP, and can perform real-time cutting simulations.
Comparative effects of dindamycin and cindamycin metabolites in the hamster model of antibiotic-associated colitis (1981)

A comparison in the hamster model of antibiotic-associated colitis (AAC) between clindamycin and several of its established metabolites of widely differing antibacterial potency revealed significant differences in lethality. The presence of intestinal lesions and of high concentrations of Clostridium difficile toxin was demonstrated in all animals showing evidence of disease. Death is not a consequence of any direct toxicity of the antibiotics. This indirect lethality of the various metabolites was calculated as the dose of compound administered which permitted the production by Cl. difficile of a level of toxin lethal to 50% of the animals (AACD50) No statistical correlation exists between antibacterial potency and AACD50 value. It was also noted that de-N-methylclindamycin sulphoxide, which had low antibacterial potency also had the lowest AACD50. Interestingly, the metabolic reduction of the sulphoxide linkage of this compound to the much more antibacterially potent de-N-methylclindamycin was observed; however, this factor does not provide an explanation for the anomalous AACD50 of the sulphoxide.
Maintenance of Differentiated Phenotype of Cultured Rat Hepatic Lipocytes by Basement Membrane Matrix (1989)

This study examined the role of extracellular matrix in regulating matrix phenotype of hepatic lipocytes, the major source of matrix in liver. Lipocytes (Ito, stellate, or fat-storing cells) were purified from normal rat liver and established in primary culture on either uncoated plastic, plastic coated with individual matrix proteins, or a "complete" gel matrix, a basement membrane-like matrix derived from the Engelbreth-Holm-Swarm (EHS) murine tumor. The ultrastructure of lipocytes cultured on the gel matrix resembled that of cells in normal liver, whereas lipocytes on plastic had dispersed nuclear chromatin and expanded rough endoplasmic reticulum, consistent with active proliferation and secretion. Lipocytes on the gel matrix exhibited no proliferative activity; cells maintained on plastic proliferated and produced type I collagen predominantly. Total collagen secretion by lipocytes on the gel matrix was 29% of that of cells on plastic, and consisted of type III collagen only. This difference extended to proteoglycan production, which was less than 5% of the amount produced by cells in conventional culture on plastic. The effects of the EHS gel were not reproduced by the individual components of the gel (laminin, type IV collagen, and heparan sulfate proteoglycan) or by a type I collagen gel. They were also reversible upon transfer of the cells to conventional culture. In contrast to lipocytes, collagen synthesis by hepatocytes was similar whether cultured on EHS gel or on plastic. These results show that the extracellular matrix can modulate matrix protein production by lipocytes and imply that, in early hepatic inflammation, changes in the hepatic subendothelial matrix may underlie stimulation of lipocyte matrix production and progression of the fibrotic process.
The interaction of light with skin (1994)

The past thirty years have seen many advances in medicine. One of the most significant developments has been in the use of the laser. This instrument has been used in a number of surgical therapies including the removal of vascular lesions and the removal of tattoos. Lasers for the treatment of vascular lesions have progressed from early devices which ablated the skin surrounding the ectatic vessels and thus caused scarring, to devices which use selective thermolysis and leave the texture of the skin unchanged. Two such devices are the flash-lamp pumped pulsed dye laser and the copper vapour laser. This thesis investigates what is known about the processes that occur in the skin following the treatment of vascular lesions with these lasers. The purpura-like response of the pulsed dye laser is due to a stationary coagulum of erythrocytes in the treated vessels. The blanching caused by the copper vapour laser is less well understood. We photograph the treatment process, and quantitatively measure the light remitted from the skin. We conclude that blanching is caused by a combination of vasoconstriction, as proposed by Marini et al. (1992), and destruction of epidermal melanin. It is observed that light coloured vascular lesions blanch faster and require more energy to blanch than dark lesions. These phenomena are related to the smaller size of the ectatic vessels in light coloured lesions. The use of Q-switched ruby lasers for removal of tattoos has long been established. However such devices are expensive and are unable to remove red pigments. This thesis reports on progress made towards the development of a cheaper flash-lamp based system which might be able to remove all pigment colours.
A design for a combined infrared cell/differential single-pass reactor (1979)

This cell allows IR spectra and kinetic data to be obtained simultaneously under well defined reaction conditions. Details are given concerning the construction of the cell, and a description of the total reactor system is also provided.
Presentation of a T Cell Receptor Antagonist Peptide by Immunoglobulins Ablates Activation of  T Cells by a Synthetic Peptide or Proteins Requiring Endocytic Processing (1997)

T cell receptor (TCR) antagonism is being considered for inactivation of aggressive T cells and reversal of T cell-mediated autoimmune diseases. TCR antagonist peptides silence aggressive T cells and reverse experimental allergic encephalomyelitis induced with free peptides. However, it is not clear whether free antagonist peptides could reverse natural disease where the antigen is presumably available for endocytic processing and peptides gain access to newly synthesized class II MHC molecules. Using an efficient endocytic presentation system, we demonstrate that a proteolipid protein (PLP) TCR antagonist peptide (PLP-LR) presented on an Ig molecule (Ig-PLP-LR) abrogates the activation of T cells stimulated with free encephalitogenic PLP peptide (PLP1), native PLP, or an Ig containing PLP1 peptide (Ig-PLP1). Free PLP-LR abolishes T cell activation when the stimulator is free PLP1 peptide, but has no measurable effect when the stimulator is the native PLP or Ig-PLP1. In vivo, Ig-PLP1 induces a T cell response to PLP1 peptide. However, when coadministered with Ig-PLP-LR, the response to PLP1 peptide is markedly reduced whereas the response to PLP-LR is normal. Free PLP-LR coadministered with Ig-PLP1 has no effect on the T cell response to PLP1. These findings indicate that endocytic presentation of an antagonist peptide by Ig outcompete both external and endocytic agonist peptides whereas free antagonist hinders external but not endocytic agonist peptide. Direct contact with antagonist ligand and/or trans-regulation by PLP-LR-specific T cells may be the operative mechanism for Ig-PLP-LR-mediated downregulation of PLP1-specific T cells in vivo. Efficient endocytic presentation of antagonist peptides, which is the fundamental event for either mechanism, may be critical for reversal of spontaneous T cell-mediated autoimmune diseases where incessant endocytic antigen processing could be responsible for T cell aggressivity.
The primary structure of Clostridium septicum alpha-toxin exhibits similarity with that of Aeromonas hydrophila aerolysin (1995)

The gene for Clostridium septicum alpha-toxin was cloned and expressed in Escherichia coli from C. septicum BX96. The toxin was determined to be 443 amino acids in length, with a 31-residue signal peptide that was removed from the toxin during secretion. No extended hydrophobic regions were observed in the mature toxin sequence. Expression of alpha-toxin in E. coli BL21 resulted in the production of ATpro, which was identical to native toxin from C. septicum with respect to activity and activation. The proteolytic activation site for alpha-toxin was determined to be on the carboxy-terminal side of arginine 398, which lies within the sequence KKRRGKR-398SVD. Previous work showing similarities in activation and mechanism between alpha-toxin and Aeromonas hydrophila aerolysin was extended to the primary structures of both toxins. The DNA-derived primary sequence of alpha-toxin exhibited 27% identity and 72% similarity over a 387-residue region with the primary structure of the A. hydrophila aerolysin toxin, a level of similarity heretofore unobserved between toxins produced by a gram-positive organism and a gram-negative organism.
Synthesis, Stability, and Surface Plasmonic Properties of Rhodium Multipods, and Their Use as Substrates for Surface‐Enhanced Raman Scattering (2006)

Multipodal Rh nanocrystals (see HRTEM image of a tripod) prepared through a polyol synthesis display surface plasmon resonance bands in the visible region. Surface-enhanced Raman scattering from 4-mercaptopyridine adsorbed on Rh multipods is 19-times stronger than that from Rh nanocubes. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2006/z503174_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.