gebhart/patrepeval huggingface dataset:
Transcriptional Activation of Secondary Wall Biosynthesis by Rice and Maize NAC and MYB Transcription Factors (2011)

The bulk of grass biomass potentially useful for cellulose-based biofuel production is the remains of secondary wall-containing sclerenchymatous fibers. Hence, it is important to uncover the molecular mechanisms underlying the regulation of secondary wall thickening in grass species. So far, little is known about the transcriptional regulatory switches responsible for the activation of the secondary wall biosynthetic program in grass species. Here, we report the roles of a group of rice and maize NAC and MYB transcription factors in the regulation of secondary wall biosynthesis. The rice and maize secondary wall-associated NACs (namely OsSWNs and ZmSWNs) were able to complement the Arabidopsis snd1 nst1 double mutant defective in secondary wall thickening. When overexpressed in Arabidopsis, OsSWNs and ZmSWNs were sufficient to activate a number of secondary wall-associated transcription factors and secondary wall biosynthetic genes, and concomitantly result in the ectopic deposition of cellulose, xylan and lignin. It was also found that the rice and maize MYB transcription factors, OsMYB46 and ZmMYB46, are functional orthologs of Arabidopsis MYB46/MYB83 and, when overexpressed in Arabidopsis, they were able to activate the entire secondary wall biosynthetic program. Furthermore, the promoters of OsMYB46 and ZmMYB46 contain secondary wall NAC-binding elements (SNBEs), which can be bound and activated by OsSWNs and ZmSWNs. Together, our results indicate that the rice and maize SWNs and MYB46 are master transcriptional activators of the secondary wall biosynthetic program and that OsSWNs and ZmSWNs activate their direct target genes through binding to the SNBE sites.
Role of a Cytotoxic-T-Lymphocyte Epitope-Defined, AlternativegagOpen Reading Frame in the Pathogenesis of a Murine Retrovirus-Induced Immunodeficiency Syndrome (2005)

LP-BM5 murine leukemia virus-infected C57BL/6 mice develop profound immunodeficiency and B-cell lymphomas. The LP-BM5 complex contains a mixture of defective (BM5def) and replication-competent helper viruses among which BM5def is the primary causative agent of disease. The BM5def primary open reading frame (ORF1) encodes the single gag precursor protein (Pr60gag). Our lab has recently demonstrated that a novel immunodominant cytotoxic-T-lymphocyte (CTL) epitope (SYNTGRFPPL) is expressed from a +1-nucleotide translational open reading frame of BM5def during the course of normal retrovirus expression. The SYNTGRFPPL CTL epitope may be generated from either of two initiation methionines present, ORF2a or ORF2b, located downstream of the ORF1 initiation site. This study investigates the role(s) of the alternative ORF2-derived gag protein(s) of BM5def in viral pathogenesis. We have examined the disease-inducing capabilities of mutant viruses in which the translational potential of either the initiating ORF2a or ORF2b AUG has been disrupted. Although these mutated viruses are capable of wild-type ORF1 expression, they are unable to induce disease. Our data strongly suggest the existence of a novel ORF2 product(s) that is required for LP-BM5-induced pathogenesis and have potentially broad implications for other retroviral diseases.
Repression of Fat-Dependent Intestinal Apo A-IV mRNA Abundance by Medium Chain Triacylglycerols and Proteins, and Elevation by Carbohydrates of Fat-Dependent Apo A-IV Transport in Suckling Rat Pups. (1995)

Nutrients regulating intestinal apo A-IV synthesis and secretion in developing rats have not been clearly defined. We examined the effect of ingestion of fats, carbohydrates and proteins on the abundance of intestinal apo A-IV mRNA and the serum concentration of apo A-IV in 14-day-old suckling rat pups fasted overnight. In pups ingesting long-chain fatty acid-fat (soybean oil, triolein: LCT), there was a prompt elevation of the mRNA at 1.5 h after ingestion, although a graded dose of soybean oil did not result in a comparable elevation of the apo A-IV mRNA. In pups on MCT, but not trilaurin, there was a repression of the LCT-dependent elevation of the message. In pups on Intralipid (composed of soybean oil, lecithin and glycerol), mRNA was elevated at 6 h after ingestion. Administration of Intralipid with lactose, glucose, fructose and sucrose induced a rapid elevation of mRNA together with elevation of serum apo A-IV, although administration of casein, whey proteins and soybean proteins resulted in repression of the Intralipid-dependent mRNA elevation. The message correlated weakly to the serum apo A-IV and triacylglycerols and with no correlation to intestinal fat accumulation. These results suggest that metabolic events following the ingestion of milk components modulate intestinal apo A-IV expression in developing rats, possibly through mucosal fatty acid utilization.
A physiological analysis of walking in the American lobster (Homarus americanus) (1975)

The normal, unrestrained, forward walking of the lobster was studied with a closed-circuit television system and a video-tape recorder. A frame-by-frame analysis was undertaken and measurements made of unilateral stepping sequences, contralateral and ipsilateral phase relations between pairs of legs, the movements at the leg joints primarily involved in stepping and their differences in each of the four pereiopods. The order of stepping was expressed in terms of the probability of any leg following any other leg and it was found that while there is a preferred order, there is considerable variation from the dominant pattern. The commonest deviations from the dominant gait are those involving the simplest types of re-ordering of the sequence. Pairs of contralateral legs show a strong tendency to alternate but all phase relations can occur. Similarly, while the ipsilateral legs show preferred phase relations, all possible relations do occur. The four pereiopods from anterior to posterior were found to have respectively, a pulling action, a combined pulling and rowing action, a rowing action and a combined pushing and rowing action. The same parameters of stepping were recorded from animals walking on a transparent, driven treadmill and, as no significant differences were found in comparisons with results from freely moving animals, subsequent results were obtained from animals walking on the treadmill where more detailed study and manipulation could readily be made. The stepping action of the third pereiopod during forwards walking involves major movements about two joints whereas the other pereiopods move about three joints. Detailed study of the intra-leg activity was therefore confined to the third pereiopod where the simpler action considerably simplified the problems involved in collecting and analysing data. Measurements were made of the angles swept out by the joints of the third pereiopod during movement. Electromyograms were recorded from the six muscles primarily responsible for these movements and from movement transducers placed at the joints. The duration of the movements and of the bursts of acitivity in the muscles and the interrelation between different muscle bursts were measured and a computer-aided analysis made to determine the characteristic features of the inter-burst relations during stepping. While there is considerable variability from step to step, the overall activity is relatively phase-constant over a wide range of stepping frequencies. When some of the key parameters of normal walking had been characterized, changes designed to alter the sensory input to the system were imposed.
Dietary Agents in the Chemoprevention of Prostate Cancer (2005)

Nutritional factors have been estimated to contribute 20-60% of cancers around the globe, and almost one-third of deaths are being reported in Western countries. According to estimates by the American Cancer Society, during the year 2005 about 232,090 new cases of prostate cancer will be diagnosed alone in the United States and 30,350 men will die of this disease. The high incidence and long latency period of prostate cancer offer plenty of time to pursue strategies toward prevention and/or treatment to suppress or revert this disease. Epidemiological evidence suggests that plant-based dietary agents decrease the risk of some types of human cancer, including prostate cancer. Intake of 400-600 g/day of fruits and vegetables is associated with reduced risk of several cancers. The use of micronutrients and/or other phenolic agents in the diet or synthetic exogenous supplements to prevent neoplastic transformation of normal cells or to slow the progression of established malignant changes in cancer cells is termed "chemoprevention." Considerable attention has been devoted to identify plant-based dietary agents that may serve as natural inhibitors of prostate carcinogenesis. Much progress has been made in the last decade in this area of investigation through identification of pathways that play important roles in prostate tumorigenesis. This article summarizes epidemiological, clinical, and mechanistic studies and the significance of plant-derived dietary agents such as flavonoids, indoles, isothiocyanates, phenolics, monoterpenes, and complementary and alternative agents in the management of prostate cancer with recommendations for future studies to advance this area of research.
Long-term stability of neural prosthetic control signals from silicon cortical arrays in rhesus macaque motor cortex (2011)

Cortically-controlled prosthetic systems aim to help disabled patients by translating neural signals from the brain into control signals for guiding prosthetic devices. Recent reports have demonstrated reasonably high levels of performance and control of computer cursors and prosthetic limbs, but to achieve true clinical viability, the long-term operation of these systems must be better understood. In particular, the quality and stability of the electrically-recorded neural signals require further characterization. Here, we quantify action potential changes and offline neural decoder performance over 382 days of recording from four intracortical arrays in three animals. Action potential amplitude decreased by 2.4% per month on average over the course of 9.4, 10.4, and 31.7 months in three animals. During most time periods, decoder performance was not well correlated with action potential amplitude (p > 0.05 for three of four arrays). In two arrays from one animal, action potential amplitude declined by an average of 37% over the first 2 months after implant. However, when using simple threshold-crossing events rather than well-isolated action potentials, no corresponding performance loss was observed during this time using an offline decoder. One of these arrays was effectively used for online prosthetic experiments over the following year. Substantial short-term variations in waveforms were quantified using a wireless system for contiguous recording in one animal, and compared within and between days for all three animals. Overall, this study suggests that action potential amplitude declines more slowly than previously supposed, and performance can be maintained over the course of multiple years when decoding from threshold-crossing events rather than isolated action potentials. This suggests that neural prosthetic systems may provide high performance over multiple years in human clinical trials.
The Yorktown Simulation Engine (1982)

The Yorktown Simulation Engine (YSE) is a high speed special purpose parallel processor designed and built at the I.B.M. Thomas J. Watson Research Center to simulate the logical operation of large digital networks. A full YSE configuration simulates networks of up to 2,000,000 gates at a rate exceeding 3 billion gate computations per second, doing more simulation in just eight hours than an IBM 370/168 does in an entire year. This paper reviews gate-level logic simulation and describes the architecture and hardware implementation of the YSE. A companion paper by G. Pfister and E. Kronstadt discusses the YSE software.
The tyrosinase gene codes for an antigen recognized by autologous cytolytic T lymphocytes on HLA-A2 melanomas. (1993)

Lymphocytes of melanoma patients can be restimulated in vitro with autologous tumor cells to generate antitumor cytolytic T lymphocytes (CTL). Previous reports have indicated that, when such CTL are obtained from HLA-A2 melanoma patients, they often display broad reactivity on A2 melanoma cell lines. Such antitumor CTL clones, which appeared to recognize the same antigen, were isolated from two patients. We report here the cloning of a cDNA that directs the expression of the antigen recognized by these CTL. This cDNA corresponds to the transcript of the tyrosinase gene. The gene was found to be active in all tested melanoma samples and in most melanoma cell lines. Among normal cells, only melanocytes appear to express the gene. The tyrosinase antigen presented by HLA-A2 may therefore constitute a useful target for specific immunotherapy of melanoma. But possible adverse effects of antityrosinase immunization, such as the destruction of normal melanocytes and its consequences, will have to be examined before clinical pilot studies can be undertaken.
A member of a family of sulfate-activating enzymes causes murine brachymorphism (1998)

Sulfation is critical to the function of a wide variety of biomolecules. This common modification requires the enzymatic synthesis of an activated sulfate donor, phosphoadenosine-phosphosulfate (PAPS). In higher organisms PAPS synthesis is catalyzed by a bifunctional sulfurylase kinase (SK) polypeptide having both ATP-sulfurylase and adenosine-phosphosulfate kinase activities. We report the identification of a gene family encoding murine SK proteins with these two activities. A family member, SK2, colocalizes with the locus for the autosomal recessive murine phenotype brachymorphism. Brachymorphic mice have normal lifespans, but abnormal hepatic detoxification, bleeding times, and postnatal growth, the latter being attributed to undersulfation of cartilage proteoglycan. A missense mutation in the SK2 coding sequence of bm mice that alters a highly conserved amino acid residue destroys adenosine-phosphosulfate kinase activity and therefore the ability of SK2 to synthesize PAPS. We conclude that a family of SK genes are responsible for sulfate activation in mammals, that a mutation in SK2 causes murine brachymorphism, and that members of this gene family have nonredundant, tissue-specific roles.
GVHD after haploidentical transplantation: a novel, MHC-defined rhesus macaque model identifies CD28− CD8+ T cells as a reservoir of breakthrough T-cell proliferation during costimulation blockade and sirolimus-based immunosuppression (2010)

We have developed a major histocompatibility complex-defined primate model of graft-versus-host disease (GVHD) and have determined the effect that CD28/CD40-directed costimulation blockade and sirolimus have on this disease. Severe GVHD developed after haploidentical transplantation without prophylaxis, characterized by rapid clinical decline and widespread T-cell infiltration and organ damage. Mechanistic analysis showed activation and possible counter-regulation, with rapid T-cell expansion and accumulation of CD8(+) and CD4(+) granzyme B(+) effector cells and FoxP3(pos)/CD27(high)/CD25(pos)/CD127(low) CD4(+) T cells. CD8(+) cells down-regulated CD127 and BCl-2 and up-regulated Ki-67, consistent with a highly activated, proliferative profile. A cytokine storm also occurred, with GVHD-specific secretion of interleukin-1 receptor antagonist (IL-1Ra), IL-18, and CCL4. Costimulation Blockade and Sirolimus (CoBS) resulted in striking protection against GVHD. At the 30-day primary endpoint, CoBS-treated recipients showed 100% survival compared with no survival in untreated recipients. CoBS treatment resulted in survival, increasing from 11.6 to 62 days (P < .01) with blunting of T-cell expansion and activation. Some CoBS-treated animals did eventually develop GVHD, with both clinical and histopathologic evidence of smoldering disease. The reservoir of CoBS-resistant breakthrough immune activation included secretion of interferon-γ, IL-2, monocyte chemotactic protein-1, and IL-12/IL-23 and proliferation of cytotoxic T-lymphocyte-associated antigen 4 immunoglobulin-resistant CD28(-) CD8(+) T cells, suggesting adjuvant treatments targeting this subpopulation will be needed for full disease control.
Neoplastic cells obtained from Hodgkin's disease function as accessory cells for mitogen-induced human T cell proliferative responses. (1984)

Purified human peripheral blood T cells that have been depleted of Ia-bearing cells and adherent cells do not proliferate in response to concanavalin A. The addition of as few as 1% radiated L428 tumor cells restores the proliferative capacity of the T cells. The L428 cell line is a long-term tissue culture line of Reed-Sternberg cells obtained from a patient with Hodgkin's disease. The proliferation of the T cells plus the L428 cells follows the same kinetics and has the same response to varying doses of mitogen as either unfractionated mononuclear leukocytes or purified T cells plus allogeneic adherent cells. The L428 cells are 30 times more potent as accessory cells than allogeneic adherent cells. The accessory cell function of the L428 cells is not blocked in cultures containing anti-Ia antibody. Neither supernatant from the L428 cell cultures nor human IL 1 replaces the accessory cells. The ability of the L428 cells to restore the proliferative capacity of purified T cells isolated from patients with active Hodgkin's disease was also studied. Patients with early stages of the disease had normal proliferative responses in the presence of the L428 accessory cells. However, the proliferative response of the poor prognosis, advanced-stage patients was reduced as compared to age- and sex-matched controls, supporting a deficit in their T cell function. The L428 tumor cells share many properties such as accessory cell function, morphology, and cell surface markers with the dendritic cells described in animal and human systems.
Chromosomal localization of the human apolipoprotein B gene and detection of homologous RNA in monkey intestine. (1986)

A cDNA clone of the human apolipoprotein B-100 was used as a hybridization probe to detect homologous sequences in both flow-sorted and in situ metaphase chromosomes. The results indicate that the gene encoding this protein is on the distal end of the short arm of chromosome 2 (2p23-2p24). RNA isolated from monkey small intestine contained sequences (6.5 and 18 kilobases) homologous to the cDNA of apolipoprotein B-100. These results are consistent with the hypothesis that one gene codes for both the intestinal (B-48) and the hepatic (B-100) forms.
Inflammatory Biomarkers, Death, and Recurrent Nonfatal Coronary Events After an Acute Coronary Syndrome in the MIRACL Study (2013)

In acute coronary syndromes, the CRP inflammatory axis relates to the risk of death and may reflect myocardial injury. VCAM and tPA may have greater specificity for processes reflecting inflammation and thrombosis in the epicardial arteries, which determine recurrent coronary events.
RESPONSIVITY TO NALOXONE DURING MORPHINE DEPENDENCE (1976)

This report compensates for what we believe is a shortage of impartial, basic, one-stop readings on the main drone points. It represents the culmination of what we have learned and taught over the past two years, presented in an accessible, straightforward way. Our hope is that the reader will gain a basic, comprehensive understanding of the key issues and, more importantly, a desire to keep learning about them.\nUnderstanding the drone is prerequisite to developing the right policies and attitudes to govern its use. And to understand the drone, it’s important to know its history, how it works, and how it’s ...
Synthesis of Robust Surface-Charged Nanoparticles Based on Cyclopropenium Ions (2015)

We investigate synthetic strategies of cationic surface-charged nanoparticles using cyclopropenium-based (CP) monomers and block copolyelectrolytes (BCPEs) via surfactant-free emulsion polymerization. The monomers and BCPEs themselves were found to stabilize oil-in-water emulsions. With these systems, the hydrodynamic diameters of the resultant particles can be reliably tuned from 30 to 100 nm, simply by varying the amount of CP monomer added. As CP is a remarkably stable carbocation, the nanoparticles retain their charge over a wide pH range. Furthermore, we found that the nanoparticle interior can be covalently functionalized with fluorescent dyes. The ability to easily synthesize sub-100 nm surface-charged particles with narrow polydispersity in one-pot can lead to applications as additives, gene-delivery vectors, and chromatographic separation, among others. Here, we demonstrate the versatility of CP-based monomers and BCPEs for the synthesis of surface-charged nanoparticles and the modulation of synthetic parameters to tune nanoparticle size and surface functionality.
Solution structure of a new hypothalamic neuropeptide, human hypocretin‐2/orexin‐B (1999)

Orexin-A and orexin-B (also called hypocretin-1 and hypocretin-2, respectively) are novel hypothalamic neuropeptides encoded by a single mRNA transcript; they stimulate food intake. We have determined the three-dimensional solution structure of human hypocretin-2/orexin-B using two-dimensional 1H-NMR data and dynamical simulated annealing calculations. On the basis of NOEs, 3JHNalpha coupling constants and hydrogen-deuterium exchange rates together with chemical shift indices, human hypocretin-2/orexin-B was deduced to consist of two alpha-helices connected with a short linker in both H2O and 30% trifluoroethanol solutions. The helical axis of helix I is oriented about 60-80 degrees relative to helix II. Hybrid distance geometry and simulated-annealing protocols were used to generate an ensemble of 30 structures with no constraint violations greater than 0.03 nm for distances and 3 degrees for angles. In addition, human hypocretin-2/orexin-B shares a similar secondary-structural motif with human neuropeptide Y. This result can form the basis for further study on ligand-receptor recognition of human orexin receptors.
Exploring the ‘RPRL’ Motif of Apelin‐13 through Molecular Simulation and Biological Evaluation of Cyclic Peptide Analogues (2010)

Apelin-13 is a vasoactive peptide and one of the most potent endogenous inotropic agents identified to date. We report the design and evaluation, through extensive replica-exchange molecular dynamics and competition binding experiments, of head-to-tail cyclised analogues. This combined in silico and in vitro approach reveals that peptides promoting a β-turn at the RPRL motif show affinity for the APJ receptor, a class A G-protein-coupled receptor (GPCR) and co-receptor for HIV cellular entry.