gebhart/patrepeval huggingface dataset:
Expression of the Corynebacterium glutamicum panD Gene Encoding l -Aspartate-α-Decarboxylase Leads to Pantothenate Overproduction in Escherichia coli (1999)

The Corynebacterium glutamicum panD gene was identified by functional complementation of an Escherichia coli panD mutant strain. Sequence analysis revealed that the coding region of panD comprises 411 bp and specifies a protein of 136 amino acid residues with a deduced molecular mass of 14.1 kDa. A defined C. glutamicum panD mutant completely lacked L-aspartate-alpha-decarboxylase activity and exhibited beta-alanine auxotrophy. The C. glutamicum panD (panDC. g.) as well as the E. coli panD (panDE.c.) genes were cloned into a bifunctional expression plasmid to allow gene analysis in C. glutamicum as well as in E. coli. The enhanced expression of panDC.g. in C. glutamicum resulted in the formation of two distinct proteins in sodium dodecyl sulfate-polyacrylamide gel electrophoresis, leading to the assumption that the panDC.g. gene product is proteolytically processed into two subunits. By increased expression of panDC.g. in C. glutamicum, the activity of L-aspartate-alpha-decarboxylase was 288-fold increased, whereas the panDE.c. gene resulted only in a 4-fold enhancement. The similar experiment performed in E. coli revealed that panDC.g. achieved a 41-fold increase and that panDE.c. achieved a 3-fold increase of enzyme activity. The effect of the panDC.g. and panDE.c. gene expression in E. coli was studied with a view to pantothenate accumulation. Only by expression of the panDC.g. gene was sufficient beta-alanine produced to abolish its limiting effect on pantothenate production. In cultures expressing the panDE.c. gene, the maximal pantothenate production was still dependent on external beta-alanine supplementation. The enhanced expression of panDC.g. in E. coli yielded the highest amount of pantothenate in the culture medium, with a specific productivity of 140 ng of pantothenate mg (dry weight)-1 h-1.
Significance of T-lymphocytes in wound healing. (1987)

To determine the importance of T-lymphocytes in wound healing, we examined the effect of T-lymphocyte depletion on the healing of surgical wounds. Thirty Balb/c mice were injected intraperitoneally with 1 mg of rat anti-mouse (IgG2b) cytotoxic monoclonal antibody (30H12) against the Thy1.2 (all T) determinant. Twenty-four hours later animals showed a greater than 95% depletion of Thy1.2 cells in peripheral blood and spleen. Thirty control mice received nonspecific rat immunoglobulin (1 mg). Twenty-four hours after treatment mice underwent a 2.5 cm dorsal skin incision with subcutaneous placement of polyvinyl alcohol sponges. Injections were repeated at weekly intervals. Wound healing was assessed at 2, 3, and 4 weeks by the breaking strength of wound strips and by the hydroxyproline content of sponge granulomas (an index of wound reparative collagen deposition). Thy1.2 depletion at death was 95% to 57% in peripheral blood and 86% to 68% in the spleen. Both groups gained weight equally. We found that T cell depletion significantly impairs wound breaking strength and wound collagen deposition at all times studied. The data strongly suggest that T-lymphocytes modulate fibroblast activity during normal wound healing.
The Lactococcal lmrP Gene Encodes a Proton Motive Force- dependent Drug Transporter (1995)

To genetically dissect the drug extrusion systems of Lactococcus lactis, a chromosomal DNA library was made in Escherichia coli and recombinant strains were selected for resistance to high concentrations of ethidium bromide. Recombinant strains were found to be resistant not only to ethidium bromide but also to daunomycin and tetraphenylphosphonium. The drug resistance is conferred by the lmrP gene, which encodes a hydrophobic polypeptide of 408 amino acid residues with 12 putative membrane-spanning segments. Some sequence elements in this novel membrane protein share similarity to regions in the transposon Tn10-encoded tetracycline resistance determinant TetA, the multidrug transporter Bmr from Bacillus subtilis, and the bicyclomycin resistance determinant Bcr from E. coli. Drug resistance associated with lmrP expression correlated with energy-dependent extrusion of the molecules. Drug extrusion was inhibited by ionophores that dissipate the proton motive force but not by the ATPase inhibitor ortho-vanadate. These observations are indicative for a drug-proton antiport system. A lmrP deletion mutant was constructed via homologous recombinant using DNA fragments of the flanking region of the gene. The L. lactis (delta lmrP) strain exhibited residual ethidium extrusion activity, which in contrast to the parent strain was inhibited by ortho-vanadate. The results indicate that in the absence of the functional drug-proton anti-porter LmrP, L. lactis is able to overexpress another, ATP-dependent, drug extrusion system. These findings substantiate earlier studies on the isolation and characterization of drug-resistant mutants of L. lactis (Bolhuis, H., Molenaar, D., Poelarends, G., van Veen, H. W., Poolman, B., Driessen, A. J. M., and Konings, W. N. (1994) J. Bacteriol. 176, 6957-6964).
Discovery of 2-Arylthiazolidine-4-carboxylic Acid Amides as a New Class of Cytotoxic Agents for Prostate Cancer (2005)

To improve the selectivity and antiproliferative activity of previously reported serine amide phosphates (SAPs), we designed a new series of 4-thiazolidinone amides, in which the 4-thiazolidinone moiety was introduced as a phosphate mimic. However, these 4-thiazolidinone derivatives demonstrated less cytotoxicity in prostate cancer cells despite improved selectivity over RH7777 cells. To further optimize the thiazolidinone analogues in terms of cytotoxicity and selectivity, we made closely related structural modifications, which led us to the discovery of a new class of 2-arylthiazolidine-4-carboxylic acid amides. These compounds were potent cytotoxic agents with IC(50) values in the low micromolar concentration range and demonstrated enhanced selectivity in receptor-negative cells compared to SAPs and 4-thiazolidinone amides.
Oggetto: An Object Oriented Database Layered on a Triple Store (1992)

Interest in object oriented database (OODB) systems continues to grow. This paper describes the implementation of an OODB by layering over a triple store. The OODB thus implemented allows experimentation with an object-oriented query language. It is shown how this system, Oggetto, is capable of handling, the four tasks outlined in ref. 2.
Temporal Data Clustering via Weighted Clustering Ensemble with Different Representations (2010)

Temporal data clustering provides underpinning techniques for discovering the intrinsic structure and condensing information over temporal data. In this paper, we present a temporal data clustering framework via a weighted clustering ensemble of multiple partitions produced by initial clustering analysis on different temporal data representations. In our approach, we propose a novel weighted consensus function guided by clustering validation criteria to reconcile initial partitions to candidate consensus partitions from different perspectives, and then, introduce an agreement function to further reconcile those candidate consensus partitions to a final partition. As a result, the proposed weighted clustering ensemble algorithm provides an effective enabling technique for the joint use of different representations, which cuts the information loss in a single representation and exploits various information sources underlying temporal data. In addition, our approach tends to capture the intrinsic structure of a data set, e.g., the number of clusters. Our approach has been evaluated with benchmark time series, motion trajectory, and time-series data stream clustering tasks. Simulation results demonstrate that our approach yields favorite results for a variety of temporal data clustering tasks. As our weighted cluster ensemble algorithm can combine any input partitions to generate a clustering ensemble, we also investigate its limitation by formal analysis and empirical studies.
-Hydroxybutyrate accumulation in Arabidopsis and tobacco plants is a general response to abiotic stress: putative regulation by redox balance and glyoxylate reductase isoforms (2008)

Enzymes that reduce the aldehyde chemical grouping (i.e. H-C=O) to its corresponding alcohol are probably crucial in maintaining plant health during stress. Succinic semialdehyde (SSA) is a mitochondrially-generated intermediate in the metabolism of gamma-aminobutyrate (GABA), which accumulates in response to a variety of biotic and abiotic stresses. SSA can be reduced to gamma-hydroxybutyrate (GHB) under oxygen deficiency and high light conditions. Recent evidence indicates that distinct cytosolic and plastidial glyoxylate reductase isoforms from Arabidopsis (designated herein after as AtGR1 and AtGR2, respectively) catalyse the in vitro conversion of SSA to GHB, as well as glyoxylate to glycolate, via NADPH-dependent reactions. In the present report, the responses of GHB and related amino acids, as well as NADP(+) and NADPH, were monitored in leaves from Arabidopsis or tobacco plants subjected to various abiotic stresses (i.e. Arabidopsis during exposure to salinity, drought, submergence, cold, or heat; tobacco during exposure to, and recovery from, submergence). Time-course experiments revealed that GHB accumulated in both Arabidopsis and tobacco plants subjected to stress, and that this accumulation was generally accompanied by higher GABA and alanine levels, higher NADPH/NADP(+) ratio, and lower glutamate levels. Furthermore, the analysis of gene expression in Arabidopsis revealed that the relative abundance of GR1 (salinity, drought, submergence, cold, and heat) and GR2 (cold and heat) transcripts was enhanced by the stress tested. Thus, GHB accumulation in plants is a general response to abiotic stress and appears to be regulated by both biochemical and transcriptional processes.
CD34-Positive Cells Exhibit Increased Potency and Safety for Therapeutic Neovascularization After Myocardial Infarction Compared With Total Mononuclear Cells (2006)

CD34+ cells exhibit superior efficacy for preserving myocardial integrity and function after MI than unselected circulating MNCs.
Hydrogel dual delivered celecoxib and anti-PD-1 synergistically improve antitumor immunity (2015)

Two major challenges facing cancer immunotherapy are the relatively low therapeutic efficacy and the potential side effects. New drug delivery system and efficient drug combination are required to overcome these challenges. We utilize an alginate hydrogel system to locally deliver 2 FDA-approved drugs, celecoxib and programmed death 1 (PD-1) monoclonal antibody (mAb), to treat tumor-bearing mice. In two cancer models, B16-F10 melanoma and 4T1 metastatic breast cancer, the alginate hydrogel delivery system significantly improves the antitumor activities of celecoxib (CXB), PD-1 mAb, or both combined. These effects are associated with the sustained high concentrations of the drugs in peripheral circulation and within tumor regions. Strikingly, the simultaneous dual local delivery of celecoxib and PD-1 from this hydrogel system synergistically enhanced the presence of CD4<sup>+</sup>inteferon (IFN)-γ<sup>+</sup> and CD8<sup>+</sup>IFN-γ<sup>+</sup> T cells within the tumor as well as in the immune system. These effects are accompanied with reduced CD4<sup>+</sup>FoxP3<sup>+</sup> regulatory T cells (Tregs) and myeloid derived suppressor cells (MDSCs) in the tumor, reflecting a weakened immuosuppressive response. Furthermore, this combinatorial therapy increases the expression of two anti-angiogenic chemokines C-X-C motif ligand (CXCL) 9 and CXCL10, and suppresses the intratumoral production of interleukin (IL)-1, IL-6, and cycloxygenase-2 (COX2), suggesting a dampened pro-tumor angiogenic and inflammatory microenvironment. This alginate-hydrogel-mediated, combinatorial therapy of celecoxib and PD-1 mAb provides a potential valuable regimen for treating human cancer.
Exploring the privacy implications of addressable advertising and viewer profiling (2006)

Collecting consumer viewing habits will come back to bite advertisers who do not understand or appreciate how consumers feel about privacy infringement.
Analysis of fluorescence energy transfer in duplex and branched DNA molecules (1990)

Nonradiative fluorescence energy transfer (FET) is thought to be a highly sensitive measure of distance, occurring through a dipole coupling (Forster) mechanism in which the efficiency of FET depends on the inverse sixth power of the distance between fluorophores. The current work assesses the utility of FET for measuring distances in duplex and branched DNA molecules. The apparent efficiencies of FET between donor (fluorescein) and acceptor (eosin) fluorophores attached to opposite ends of oligonucleotide duplexes of varying length were determined; the results suggest that FET is a useful qualitative indicator of distance in DNA molecules. However, the apparent FET efficiency values cannot be fit to the Forster equation without the specification of highly extended DNA-to-fluorophore tethers and motionally restricted fluorophores, conditions that are unlikely to coexist. Three other lines of evidence further suggest that factors in addition to Forster transfer contribute to apparent FET in DNA: (1) The efficiency of FET appears to depend on the base sequence in some instances. (2) Donor fluorescence changes with the extent of thermally induced DNA melting in a sequence-dependent fashion, indicating dye-DNA interactions. (3) The distances between the ends of various pairwise combinations of arms of a DNA four-way junction do not vary as much as expected from previous work. Thus, the occurrence of any nondipolar effects on energy transfer in oligonucleotide systems must be defined before distances in DNA molecules can be quantified by using FET.
Prevention of graft-versus-host disease by peptides binding to class II major histocompatibility complex molecules (1994)

Graft-versus-host disease across minor histocompatibility barriers was induced in two different models by transplanting allogeneic bone marrow and spleen cells into irradiated H-2-compatible recipient mice. In this report, we show that administration of peptides with high binding affinity for the respective class II major histocompatibility complex molecules after transplantation is capable of preventing the development of graft-versus-host disease in two different murine models. The peptides used were myelin basic protein residues 1 through 11 with alanine at position 4 (Ac 1-11[4A]) for I-Au (A alpha uA beta u), and the antigenic core sequence 323 through 339 of ovalbumin with lysine and methionine extension (KM core) for I-As (A alpha sA beta s). In both systems, the mechanism of prevention was found to be major histocompatibility complex-associated, because nonbinding control peptides did not have any effect. Engraftment of allogeneic bone marrow cells was shown by polymerase chain reaction analysis of DNA polymorphisms in a microsatellite region within the murine interleukin-5 gene.
Novel Application of Crystalline Indium-Gallium-Zinc-Oxide Technology to LSI: Dynamically Reconfigurable Programmable Logic Device Based on Multi-Context Architecture (2013)

A pass gate (PG) configured with a configuration memory (CM) composed of a c-axis aligned crystalline In-Ga-Zn-O (CAAC-IGZO) FET and a pass transistor composed of an NMOS FET is applied to a multi-context routing switch (MC-RS) of a dynamically reconfigurable programmable logic device (DRPLD) based on multi-context architecture (MC-DRPLD). The proposed PG (OS PG) requires fewer transistors than a conventional PG configured with an SRAM cell served as a CM (SRAM PG). A MC-RS configured with the OS PG (OS MC-RS) has enabled its layout area to be 40% less than that of a MC-RS configured with the SRAM PG (SRAM MC-RS). Further, the delays of the MC-RSs with 2 to 16 contexts have been reduced by 24% to 37%. The MC-DRPLD including the OS MC-RS can switch contexts in one clock (50 nsec) at a clock frequency of 20 MHz, which enables dynamic reconfiguration at high speed.
Effect of Local Environment on Molecular Conduction:  Isolated Molecule versus Self-Assembled Monolayer (2004)

Developing a fundamental understanding of molecular conduction in different device environments is essential to the advance of molecular electronics. We show through a quantitative comparison of two types of junctions with the same molecule - one based on an isolated individual molecule and the other on a self-assembled monolayer - that intrinsic differences in the conduction per molecule as large as several orders of magnitude can exist simply as a function of the presence or absence of neighboring molecules. This behavior can be understood on the basis of thermal and electrostatic effects that depend critically on the local molecular environment. These results will help to unify data obtained from disparate device structures and to provide an improved basis for designing future molecular electronic devices.
Total synthesis of human beta-lipotropin. (1983)

The total synthesis of human beta-lipotropin has been accomplished by the new segment-coupling method in aqueous solution. The peptides Ac-Arg-beta-lipotropin-(61-89) (I) and [GlyS60]-beta-lipotropin-(1-60) (II) were synthesized by the solid-phase method. Reaction of peptide I with citraconic anhydride followed by brief digestion with trypsin to remove the acetylarginyl group, gave Ia. Reaction of peptide II with citraconic anhydride gave the citraconyl peptide IIa. Ia and IIa were coupled together in 50% dimethylformamide by reaction with silver nitrate/N-hydroxysuccinimide. After removal of the citraconyl groups in 25% acetic acid, a 10% yield of synthetic beta-lipotropin could be isolated. The synthetic product was shown to be identical to native human beta-lipotropin by paper electrophoresis, isoelectric focusing, HPLC, lipolytic activity in isolated rabbit fat cells, and radioimmunoassay.
Classifying emotions in rehabilitation robotics based on facial skin temperature (2014)

Rehabilitation robotic plays an important role in therapeutic exercises by combining robots with computer serious games into an attractive therapeutic platform. However, measuring the degree of engagement of the user is not a trivial task. The difficulty of applying question-based techniques, particularly for patients who have the speech capacity compromised due to cerebrovascular accidents, has inspired us to investigate noninvasive and nonverbal techniques aiming to classifying emotions. For this purpose, a supervised artificial neural network interprets facial infrared thermal images of individuals performing rehabilitation robotic therapy integrated with games. A database containing images of 8 users was generated by combining evoked and spontaneous emotional reactions. In total, 2445 facial thermal images with an average of 100 images per person for three categories of emotions (neutral, motivated, overstressed) were classified. Based on confusion matrix analysis, the experimental results correlated very well with manual estimates, producing an overall performance of 92.6%.
Effects of the nitric oxide synthase inhibitor NG‐nitro‐L‐arginine on the erectile response to cavernous nerve stimulation in the rabbit (1991)

Using a rabbit model, the involvement of the L-arginine/nitric oxide pathway in penile erection was investigated. The mean basal intracavernous pressure was 21 cm H2O. Cavernous nerve stimulation (4-8 V, 20-30 Hz) increased the pressure to approximately 130 cm H2O. This response was highly reproducible and usually associated with full penile erection. The pressure increase could be quantified in terms of: (1) the slope of the initial, ascending part of the pressure increase; (2) delta P, which was defined as the maximal pressure obtained by the stimulation minus the basal pressure before the stimulation; (3) T90, which was defined as the time to reach 90 per cent of delta P. Intrapenile administration of the L-arginine/nitric oxide synthesis inhibitor NG-nitro-L-arginine had no effect on systemic arterial blood pressure. However, NG-nitro-L-arginine (0.22 and 2.19 mg), administered via the same route, abolished the erectile response induced by cavernous nerve stimulation; T90 increased and slope and delta P decreased significantly. NG-nitro-D-arginine (2.19), on the other hand, had no inhibitory effect. L-arginine (21.07 mg), given either directly or after NG-nitro-L-arginine had no consistent effect on the functional response to cavernous nerve stimulation. The results suggest that pharmacologically induced effects on intracavernous pressure in the rabbit can be described quantitatively, and that this model may be useful to study the mechanisms controlling penile erection in vivo. The pronounced inhibitory action of NG-nitro-L-arginine demonstrates the important role of the arginine/nitric oxide pathway in mediating relaxation of penile smooth muscles necessary for erection.
Vitamin D Analogs as Anti-Carcinogenic Agents (2006)

Deltanoids are the class of compounds comprising all natural and synthetic vitamin D molecules. The anti-proliferative, pro-differentiation, and pro-apoptotic properties of deltanoids have garnered interest in the fields of cancer chemoprevention and chemotherapy. The naturally occurring, biologically active form of vitamin D, 1,25(OH)2D3, causes hypercalcemia at pharmacologically relevant doses which forms a major obstacle in the clinical development of this compound. Design of new deltanoids has shown promise in separating the beneficial effects from the toxic effects. The Vitamin D receptor (VDR) is a major target for deltanoid design, and the structural features of deltanoid binding have been described. Effective compounds must also exhibit beneficial pharmacokinetic properties in vivo, and the plasma vitamin D binding protein (DBP) is likely to play an important role in the success of deltanoids in the clinic. Further, dual strategies of avoiding vitamin D toxicity through altering the dosing schedule and using less toxic deltanoids are in development. The three main categories of structural modification to the vitamin D backbone include the C,D-ring, the A-ring, and the C,D-ring side chain, and the ways each area has impacted efficacy and toxicity have been described through structure-activity relationships (SARs). Lastly, there is evidence that deltanoids can enhance the activity of other chemopreventive agents. The use of a cocktail approach will be discussed as a potential avenue for deltanoids in chemoprevention and chemotherapy.
Coherent pulse synthesis: towards sub-cycle optical waveforms (2015)

The generation of sub-optical-cycle, carrier–envelope phase-stable light pulses is one of the frontiers of ultrafast optics. The two key ingredients for sub-cycle pulse generation are bandwidths substantially exceeding one octave and accurate control of the spectral phase. These requirements are very challenging to satisfy with a single laser beam, and thus intense research activity is currently devoted to the coherent synthesis of pulses generated by separate sources. In this review we discuss the conceptual schemes and experimental tools that can be employed for the generation, amplification, control, and combination of separate light pulses. The main techniques for the spectrotemporal characterization of the synthesized fields are also described. We discuss recent implementations of coherent waveform synthesis: from the first demonstration of a single-cycle optical pulse by the addition of two pulse trains derived from a fiber laser, to the coherent combination of the outputs from optical parametric chirped-pulse amplifiers.