gebhart/patrepeval huggingface dataset:
Mitochondrial Malate Dehydrogenase Lowers Leaf Respiration and Alters Photorespiration and Plant Growth in Arabidopsis (2010)

Malate dehydrogenase (MDH) catalyzes a reversible NAD(+)-dependent-dehydrogenase reaction involved in central metabolism and redox homeostasis between organelle compartments. To explore the role of mitochondrial MDH (mMDH) in Arabidopsis (Arabidopsis thaliana), knockout single and double mutants for the highly expressed mMDH1 and lower expressed mMDH2 isoforms were constructed and analyzed. A mmdh1mmdh2 mutant has no detectable mMDH activity but is viable, albeit small and slow growing. Quantitative proteome analysis of mitochondria shows changes in other mitochondrial NAD-linked dehydrogenases, indicating a reorganization of such enzymes in the mitochondrial matrix. The slow-growing mmdh1mmdh2 mutant has elevated leaf respiration rate in the dark and light, without loss of photosynthetic capacity, suggesting that mMDH normally uses NADH to reduce oxaloacetate to malate, which is then exported to the cytosol, rather than to drive mitochondrial respiration. Increased respiratory rate in leaves can account in part for the low net CO(2) assimilation and slow growth rate of mmdh1mmdh2. Loss of mMDH also affects photorespiration, as evidenced by a lower postillumination burst, alterations in CO(2) assimilation/intercellular CO(2) curves at low CO(2), and the light-dependent elevated concentration of photorespiratory metabolites. Complementation of mmdh1mmdh2 with an mMDH cDNA recovered mMDH activity, suppressed respiratory rate, ameliorated changes to photorespiration, and increased plant growth. A previously established inverse correlation between mMDH and ascorbate content in tomato (Solanum lycopersicum) has been consolidated in Arabidopsis and may potentially be linked to decreased galactonolactone dehydrogenase content in mitochondria in the mutant. Overall, a central yet complex role for mMDH emerges in the partitioning of carbon and energy in leaves, providing new directions for bioengineering of plant growth rate and a new insight into the molecular mechanisms linking respiration and photosynthesis in plants.
Correlates of Protection Induced by Vaccination (2010)

This paper attempts to summarize current knowledge about immune responses to vaccines that correlate with protection. Although the immune system is redundant, almost all current vaccines work through antibodies in serum or on mucosa that block infection or bacteremia/viremia and thus provide a correlate of protection. The functional characteristics of antibodies, as well as quantity, are important. Antibody may be highly correlated with protection or synergistic with other functions. Immune memory is a critical correlate: effector memory for short-incubation diseases and central memory for long-incubation diseases. Cellular immunity acts to kill or suppress intracellular pathogens and may also synergize with antibody. For some vaccines, we have no true correlates, but only useful surrogates, for an unknown protective response.
Cytotoxic Agents of Thujopsis dolabrata (L. fil.) SIEB. et ZUCC. (1972)

A cytotoxic agent which inhibits the division of HeLa cells at metaphase stage was isolated from Thujopsis dolabrata (L. fil.) SIEB. et ZUCC. and identified as desoxypodophyllotoxin. Three substances, desoxypodophillic acid, desoxypicropodophyllin and β-peltatin-B-methylether were isolated from the recrystallization mother liquor of desoxypodophyllotoxin after treatment with alkali. Desoxypodophyllotoxin was found to be almost exclusively contained in the leaf and bark of this tree and only in minute quantity in its wood. It was also shown to be contained in T. dolabrata var. hondae MAKINO, Juniperus rigida SIEB. et ZUCC. and J. chinensis L. by thin-layer chromatography and cytotoxicity.
Machine learning approaches to lung cancer prediction from mass spectra (2003)

We addressed the problem of discriminating between 24 diseased and 17 healthy specimens on the basis of protein mass spectra. To prepare the data, we performed mass to charge ratio (m/z) normalization, baseline elimination, and conversion of absolute peak height measures to height ratios. After preprocessing, the major difficulty encountered was the extremely large number of variables (1676 m/z values) versus the number of examples (41). Dimensionality reduction was treated as an integral part of the classification process; variable selection was coupled with model construction in a single ten-fold cross-validation loop. We explored different experimental setups involving two peak height representations, two variable selection methods, and six induction algorithms, all on both the original 1676-mass data set and on a prescreened 124-mass data set. Highest predictive accuracies (1-2 off-sample misclassifications) were achieved by a multilayer perceptron and Naïve Bayes, with the latter displaying more consistent performance (hence greater reliability) over varying experimental conditions. We attempted to identify the most discriminant peaks (proteins) on the basis of scores assigned by the two variable selection methods and by neural network based sensitivity analysis. These three scoring schemes consistently ranked four peaks as the most relevant discriminators: 11683, 1403, 17350 and 66107.
Model for color vision and light adaptation (1991)

A multizone color model is described. It has nonlinear receptor gain control, two postreceptor opponent-colors processing stages, and neural compression late in the visual pathway. It is assumed that gain control can be activated by receptor responses from a test light itself (self-adaptation) and (or) by receptor responses from other adapting fields. Apparent brightnesses and visual discriminations are mediated by the first processing stage, and apparent hues and saturations are mediated by the second stage. The model accounts for a wide range of data, including nonlinear hue shifts in the color solid, various apparent brightness effects, visual discriminations for achromatic and chromatic lights under various adaptation conditions, and effects of chromatic adaptation on color appearances.
Molecular Basis of Metastasis (2008)

Metastases are the principal cause of death in patients with cancer. Recent advances bring hope that it will be possible to identify the molecules and processes involved in metastasis, and this new knowledge could lead to effective methods of preventing and treating metastases. This review describes the properties of cells that enable them to surmount physical boundaries, disseminate, and colonize a distant organ.
A Smart Image-Based Cloud Detection System for Intrahour Solar Irradiance Forecasts (2014)

Abstract This study proposes an automatic smart adaptive cloud identification (SACI) system for sky imagery and solar irradiance forecast. The system is deployed using off-the-shelf fish-eye cameras that offer substantial advantages in terms of cost when compared to industry-standard sky imagers. SACI uses a smart image categorization (SIC) algorithm that combines the sky images and solar irradiance measurements to classify sky conditions into three categories: clear, overcast, and partly cloudy. A cloud detection scheme, optimized for each image category, is used to quantify cloud cover from the sky images. SACI is optimized and validated against manually annotated images. Results show that SACI achieves overall classification accuracy higher than 90% and outperforms reference cloud detection methods. Cloud cover retrieved by SACI is used as an input for an artificial neural network (ANN) model that predicts 1-min average global horizontal irradiance (GHI), 5-, 10-, and 15-min ahead of time. The performance of the ANN forecasting model is assessed in terms of common error statistics (mean bias and root-mean-square error) and in terms of forecasting skill over persistence. The model proposed in this work achieves forecasting skills above 14%, 18%, and 19% over the persistence forecast for 5-, 10-, and 15-min forecasts, respectively.
Malignant transformation of leukoplakia three times in period of 11-years--case report. (1995)

Leukoplakia is a commonly occurring precancerous lesion. The following case report describes a patient who had multiple leukoplakia in this mouth. He had three sites of leukoplakia, the left hard palate, the gum of the right maxilla and the gum of the left mandible, all of which underwent malignant transformation during the period of 11-years after diagnosis.
The immobilization of oligonucleotides and their hybridization properties (1988)

Conference Article| April 01 1988 The immobilization of oligonucleotides and their hybridization properties UTA B. VOSS; UTA B. VOSS 1Department of Biochemistry, Charing Cross and Westminster Medical School, Fulham Palace Road, London W6 8RF, U.K. Search for other works by this author on: This Site PubMed Google Scholar ALAN D. B. MALCOLM ALAN D. B. MALCOLM 1Department of Biochemistry, Charing Cross and Westminster Medical School, Fulham Palace Road, London W6 8RF, U.K. Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1988) 16 (2): 216–217. https://doi.org/10.1042/bst0160216 Article history Received: April 10 1987 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation UTA B. VOSS, ALAN D. B. MALCOLM; The immobilization of oligonucleotides and their hybridization properties. Biochem Soc Trans 1 April 1988; 16 (2): 216–217. doi: https://doi.org/10.1042/bst0160216 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 Society Transactions Search Advanced Search Keywords: CMC, I-cyclohexyl-3-[2-morpholinoethy]-carbodi-imide metho-p-toluene sulphonate, NET, 0.9 m-NaCI, 0.09 m-Tris/HCL pH 8.0,6 mm-EDTA This content is only available as a PDF. © 1988 Biochemical Society1988 Article PDF first page preview Close Modal You do not currently have access to this content.
Inhibition of lymphoproliferation by a synthetic peptide with sequence identity to gp41 of human immunodeficiency virus type 1 (1989)

Peptides were synthesized that contained sequences from two regions (env amino acids [aa] 581 to 597 and 655 to 671) of the transmembrane protein gp41 and one region of the external envelope glycoprotein gp120 (aa 457 to 464) of human immunodeficiency virus type 1. Selection of these sequences was based on their homology to the highly conserved and immunosuppressive sequence contained within the transmembrane proteins p15E and gp21 of animal and human retroviruses, respectively. Peptide aa581-597 was found to specifically inhibit human and murine lymphoproliferation, whereas peptides aa655-671 and aa457-464 had no activity. These results suggest a mechanism by which human immunodeficiency virus type 1 gp41 exerts a direct immunosuppressive effect in vivo, analogous to that postulated for p15E and gp21, which could contribute to the immune dysfunction observed in patients suffering from acquired immunodeficiency syndrome. It is of particular interest that the sequence aa 584 to 609, shown to contain B- and T-helper-cell epitopes, overlaps with the sequence aa 581 to 597 that is shown here to inhibit lymphoproliferation. The potential implications of this overlap of immunologic activities are discussed.
Si 3 N 4 / AlGaN/GaN –metal–insulator–semiconductor heterostructure field–effect transistors (2001)

We report on a metal–insulator–semiconductor heterostructure field-effect transistor (MISHFET) using Si3N4 film simultaneously for channel passivation and as a gate insulator. This design results in increased radio-frequency (rf) powers by reduction of the current collapse and it reduces the gate leakage currents by four orders of magnitude. A MISHFET room temperature gate current of about 90 pA/mm increases to only 1000 pA/mm at ambient temperature as high as 300 °C. Pulsed measurements show that unlike metal–oxide–semiconductor HFETs and regular HFETs, in a Si3N4 MISHFET, the gate voltage amplitude required for current collapse is much higher than the threshold voltage. Therefore, it exhibits significantly reduced rf current collapse.
RANK/RANKL signaling inhibition may improve the effectiveness of checkpoint blockade in cancer treatment (2018)

Binding between the receptor activator of nuclear factor-kB (RANK) and its ligand (RANKL) triggers recruitment of TNF receptor associated factor (TRAF) adaptor proteins and activation of downstream pathways. RANK/RANKL signaling is controlled by a decoy receptor called osteoprotegerin (OPG) which interacts with RANKL. Additional networks regulating RANK/RANKL signaling are active in a context specific manner. RANK/RANKL signaling is essential for the differentiation of bone-resorbing osteoclasts, and is deregulated in pathological processes such as postmenopausal osteoporosis or cancer induced bone destruction. Cells expressing RANK and RANKL are commonly found in the tumor microenvironment. The RANKL/RANK pathway is often overexpressed in tumors of the breast, prostate, endometrium, cervix, stomach, oesophagus and bladder, thyroid and correlated with poor prognosis. RANK signaling plays an important role in the innate and adaptive immune response as it generates regulatory T (Treg) cells and increases production of cytokines. RANK expression induces chemoresistance in vitro through the activation of multiple signal transduction pathways. RANKL blockade improves the efficacy of anti-CTLA-4 monoclonal antibodies against solid tumors and experimental metastases. As RANK inhibition enhances the immune response there is an increasing interest in combining it with immune therapy in an attempt to sensitize immune resistant tumors to immune therapies. Several studies are ongoing to assess this concept. The role of RANK/RANKL inhibition should be further pursued as an immunomodulatory strategy in combination with other treatment modalities.
Transforms for high-rate distributed source coding (2004)

We extend high-rate quantization theory to distributed source coding for the case in which the rate is the conditional entropy of the quantization index given the side information. This theory is applied to orthonormal block transforms for distributed source coding. A formula for the optimal rate allocation and an approximation to the optimal transform are derived. We implement a transform-domain Wyner-Ziv video coder that encodes frames independently but decodes them conditionally. Experimental results show a rate-distortion improvement with respect to the pixel-domain coder by using the discrete cosine transform.
Chronic Exposure to Exogenous Nitric Oxide May Suppress Its Endogenous Release and Efficacy (1991)

Summary: The aim of the study was to investigate the effects of semichronic treatment with molsidomine, an exogenous nitric oxide (NO) donor, on the biosynthesis of and the responses to this gas in large arteries. For this purpose, groups of 10 rabbits were fed either a control diet or a diet containing 200 ppm of molsidomine. Sixteen weeks later, rings of the isolated aorta of the latter rabbits appeared to be less sensitive to the dilating effects of acetylcholine, SIN-1, and NO. As complete relaxation was still attained with SIN-1, and as the shift for NO was of a similar magnitude, part of the attenuation is explained by a diminished sensitivity of the smooth muscle cells to NO, rather than a suppression of the release of NO from SIN-1. In addition, the biosynthesis of NO in segments treated with exogenous NO was depressed, as indicated by bioassay of the NO released upon stimulation of the endothelial cells with acetylcholine. These results indicate that exposure to large quantities of NO may lead to downregulation of the endogenous biosynthesis in the generator cells and a diminished responsiveness of the effector cells.
Research Briefs Vol 109 No 11/12 (2013) (2013)

The earliest terrestrial animal in GondwanaGondwanascorpio emzantsiensis is a new genus and species of scorpion from 360-million-year-old (Late Devonian) deposits near Grahamstown, Eastern Cape, South Africa, and has been described by Robert Gess from the University of the Witwatersrand.This finding adds to the sparse record of Late Devonian scorpion fauna and provides the first evidence of Palaeozoic scorpions from Gondwana.The find is also the first record of a scorpion occurring at high latitudes.G. emzantsiensis' close resemblance to contemporary taxa from Laurasia and China is consistent with evidence for increasingly uniform terrestrial ecosystems by the end of the Devonian period, characterised by cosmopolitan plant genera such as the progymnosperm tree Archaeopteris.This uniformity may in part reflect increasing proximity between Laurasia and Gondwana towards the end of the Devonian.The discovery of G. emzantsiensis also provides the earliest record of a terrestrial animal in Gondwana.
The cAMP-regulated transcription factor CREB interactswith a component of the TFIID complex. (1994)

cAMP regulates the expression of a number of genes through the protein kinase A-mediated phosphorylation of CREB at Ser-133. The effects of Ser-133 phosphorylation appear to be primarily transmitted through a modulatory kinase-inducible domain in CREB that functions cooperatively with a 120-amino acid glutamine-rich region (Q2) to stimulate transcription. Indeed, the kinase-inducible domain activity alone is not sufficient to sustain a transcriptional response as illustrated by the CREM family of repressors, which contain the kinase-inducible domain but lack the Q2 region. Here we demonstrate that Q2 functions as a potent constitutive activator in vitro. The transcription factor TFIID fraction supports transcriptional activation by Q2, although the "TATA" binding protein alone does not, suggesting that other components of the TFIID complex mediate the response to CREB Q2. In fact, Q2 associates with the TATA binding protein-associated factor dTAFII110. As the transcriptionally inactive CREM alpha and beta proteins lack sequences in Q2 that are necessary for binding dTAFII110, our results suggest that these proteins may repress transcription because they are unable to interact with the basal transcription complex.
The vrille Gene of Drosophila Is a Maternal Enhancer of decapentaplegic and Encodes a New Member of the bZIP Family of Transcription Factors (1997)

We report here the genetical and molecular characterization of a new Drosophila zygotic lethal locus, vrille (vri). Vri alleles act not only as dominant maternal enhancers of embryonic dorsoventral patterning defects caused by easter and decapentaplegic (dpp) mutations, but also as dominant zygotic enhancers of dpp alleles for phenotypes in wing. The vri gene encodes a new member of the bZIP family of transcription factors closely related to gene 9 of Xenopus laevis, induced by thyroid hormone during the tadpole tail resorption program, and NF-IL3A, a human T cell transcription factor that transactivates the interleukin-3 promoter. NF-IL3A shares 93% similarity and 60% identity with Vri for a stretch of 68 amino acids that includes the bZIP domain. Although all the alleles tested behave like antimorphs, the dominant enhancement is also seen with a nonsense mutation allele that prevents translation of the bZIP domain. Because of the strong domainant enhancement of dpp phenotypes by vri alleles in both embryo and wing, and also the similarity between the wing vein phenotypes caused by the vri and shortvein dpp alleles, we postulate that vri interacts either directly or indirectly with certain components of the dpp (a TGF beta homologue) signal transduction pathway.
The Cambridge Structural Database: a quarter of a million crystal structures and rising (2002)

The Cambridge Structural Database (CSD) now contains data for more than a quarter of a million small-molecule crystal structures. The information content of the CSD, together with methods for data acquisition, processing and validation, are summarized, with particular emphasis on the chemical information added by CSD editors. Nearly 80% of new structural data arrives electronically, mostly in CIF format, and the CCDC acts as the official crystal structure data depository for 51 major journals. The CCDC now maintains both a CIF archive (more than 73,000 CIFs dating from 1996), as well as the distributed binary CSD archive; the availability of data in both archives is discussed. A statistical survey of the CSD is also presented and projections concerning future accession rates indicate that the CSD will contain at least 500,000 crystal structures by the year 2010.
Molecular Mechanism of DNA Deadenylation by the Neurological Disease Protein Aprataxin (2008)

The human neurological disease known as ataxia with oculomotor apraxia 1 is caused by mutations in the APTX gene that encodes Aprataxin (APTX) protein. APTX is a member of the histidine triad superfamily of nucleotide hydrolases and transferases but is distinct from other family members in that it acts upon DNA. The target of APTX is 5'-adenylates at DNA nicks or breaks that result from abortive DNA ligation reactions. In this work, we show that APTX acts as a nick sensor, which provides a mechanism to assess the adenylation status of unsealed nicks. When an adenylated nick is encountered by APTX, base pairing at the 5' terminus of the nick is disrupted as the adenylate is accepted into the active site of the enzyme. Adenylate removal occurs by a two-step process that proceeds through a transient AMP-APTX covalent intermediate. These results pinpoint APTX as the first protein to adopt canonical histidine triad-type reaction chemistry for the repair of DNA.
Automatic Classification of Cellular Expression by Nonlinear Stochastic Embedding (ACCENSE) (2013)

Mass cytometry enables an unprecedented number of parameters to be measured in individual cells at a high throughput, but the large dimensionality of the resulting data severely limits approaches relying on manual "gating." Clustering cells based on phenotypic similarity comes at a loss of single-cell resolution and often the number of subpopulations is unknown a priori. Here we describe ACCENSE, a tool that combines nonlinear dimensionality reduction with density-based partitioning, and displays multivariate cellular phenotypes on a 2D plot. We apply ACCENSE to 35-parameter mass cytometry data from CD8(+) T cells derived from specific pathogen-free and germ-free mice, and stratify cells into phenotypic subpopulations. Our results show significant heterogeneity within the known CD8(+) T-cell subpopulations, and of particular note is that we find a large novel subpopulation in both specific pathogen-free and germ-free mice that has not been described previously. This subpopulation possesses a phenotypic signature that is distinct from conventional naive and memory subpopulations when analyzed by ACCENSE, but is not distinguishable on a biaxial plot of standard markers. We are able to automatically identify cellular subpopulations based on all proteins analyzed, thus aiding the full utilization of powerful new single-cell technologies such as mass cytometry.
Microcellular foams via phase separation (1986)

A study of wide variety of processes for making plastic foams shows that phase separation processes for polymers from solutions offer the most viable methods for obtaining rigid plastic foams which meet the physical requirements for fusion target designs. Four general phase separation methods have been shown to give polymer foams with densities less than 0.1 g/cm3 and cell sizes of 30 μm or less. These methods involve the utilization of nonsolvent, chemical or thermal cooling processes to achieve a controlled phase separation. Two distinct phases are obtained where either the polymer phase is a continuous phase or two bicontinuous phases are obtained where both the polymer and solvent are interpenetrating, continuous, labyrinthine phases. Subsequent removal of the solvent gives the final foam structure.