gebhart/patrepeval huggingface dataset:
Robust trajectory tracking for a reversing tractor trailer (2008)

Abstract Tractor‐trailer reversing is a classical nonlinear control problem in which many of the solutions proposed in the literature perform poorly in the presence of real‐world constraints such as steering angle, rate limits, and lags. In this paper we describe a new method in which an inner loop controls the hitch angle of the trailer, creating a virtual articulated vehicle to which existing control techniques can be applied. We provide an analysis of the stability and convergence properties of this control approach, as well as experimental results that illustrate the robustness of this approach to model estimation errors, low‐level control loop dynamics, and other disturbances introduced by, for example, state estimation errors. © 2008 Wiley Periodicals, Inc.
His-426 of the Pseudomonas aeruginosa exotoxin A is required for ADP-ribosylation of elongation factor II. (1988)

Exotoxin A (ETA) is recognized as the most toxic product associated with the opportunistic pathogen Pseudomonas aeruginosa. Identification of the amino acids in the polypeptide sequence that are required for toxin activity is critical for vaccine development. By defining the nucleotide sequence of the structural gene of a mutant that encodes an enzymatically inactive ETA (CRM 66), we identified an essential amino acid (His-426), which is involved in the ADP-ribosyltransferase activity associated with functional ETA. A monoclonal antibody that inhibits ETA enzymatic activity in vitro fails to react with ETA variants that have a His 426----Tyr substitution. Several mono-ADP-ribosylating toxins, including diphtheria and pertussis toxins, within the primary amino acid sequences carry a histidine residue that is conserved in spacing and in location with respect to other critical residues. Analysis of the three-dimensional structure of ETA revealed that His-426 is not associated with the proposed NAD+ binding site. These findings should be useful for the design and construction of toxin vaccines.
Understanding enzyme immobilisation (2008)

Enzymes are versatile catalysts in the laboratory and on an industrial scale. To broaden their applicability in the laboratory and to ensure their (re)use in manufacturing the stability of enzymes can often require improvement. Immobilisation can address the issue of enzymatic instability. Immobilisation can also help to enable the employment of enzymes in different solvents, at extremes of pH and temperature and exceptionally high substrate concentrations. At the same time substrate-specificity, enantioselectivity and reactivity can be modified. However, most often the molecular and physical-chemical bases of these phenomena have not been elucidated yet. This tutorial review focuses on the understanding of enzyme immobilisation.
Molecular profiling of human prostate tissues: insights into gene expression patterns of prostate development during puberty (2004)

Testosterone production surges during puberty and orchestrates massive growth and reorganization of the prostate gland, and this glandular architecture is maintained thereafter throughout adulthood. Benign prostatic hyperplasia (BPH) and prostate adenocarcinoma (PCA) are common diseases in adulthood that do not develop in the absence of androgens. Our objective was to gain insight into gene expression changes of the prostate gland at puberty, a crucial juncture in prostate development that is androgen dependent. Understanding the role played by androgens in normal prostate development may provide greater insight into androgen involvement in prostatic diseases. Benign prostate tissues obtained from pubertal and adult age group cadaveric organ donors were harvested and profiled using 20,000 element cDNA microarrays. Statistical analysis of the microarray data identified 375 genes that were differentially expressed in pubertal prostates relative to adult prostates including genes such as Nkx3.1, TMEPAI, TGFBR3, FASN, ANKH, TGFBR2, FAAH, S100P, HoxB13, fibronectin, and TSC2 among others. Comparisons of pubertal and BPH expression profiles revealed a subset of genes that shared the expression pattern between the two groups. In addition, we observed that several genes from this list were previously demonstrated to be regulated by androgen and hence could also be potential in vivo targets of androgen action in the pubertal human prostate. Promoter searches revealed the presence of androgen response elements in a cohort of genes including tumor necrosis factor-alpha induced adipose related protein, which was found to be induced by androgen. In summary, this is the first report that provides a comprehensive view of the molecular events that occur during puberty in the human prostate and provides a cohort of genes that could be potential in vivo targets of androgenic action during puberty.
CD109 attenuates TGF-β1 signaling and enhances EGF signaling in SK-MG-1 human glioblastoma cells (2015)

CD109 is a glycosylphosphatidylinositol-anchored cell surface protein that is frequently detected in squamous cell carcinomas. CD109 is a negative regulator of TGF-β1 signaling in human keratinocytes, and the N-terminal fragment of CD109 secreted from cells after cleavage by the furin protease is important for modulating TGF-β1 signaling. Previously, we found that CD109 is expressed in human glioblastoma cells; however, the role of CD109 in glioblastoma cells is not established. Here, we describe the effects of CD109 in human glioblastoma cell lines. Three glioblastoma cell lines, SK-MG-1, U251MG and MG178, were tested and CD109 overexpression attenuated TGF-β1 signaling and enhanced EGF signaling in SK-MG-1, but not in U251MG or MG178. The N-terminal CD109 fragment in SK-MG-1 was hyperglycosylated compared with that in MG178 or U251MG. The conditioned medium of CD109-overexpressing SK-MG-1, containing the secreted N-terminal CD109, had a negative effect on TGF-β1 signaling in wild-type SK-MG-1 and MG178, whereas it did not show any effect on EGF signaling. In addition, cell surface CD109 interacts with EGF receptor in SK-MG-1 overexpressing CD109, and exhibited enhanced cell migration and invasion. These findings suggest that CD109 attenuates TGF-β1 signaling and enhances EGF signaling in SK-MG-1 cells and that the membrane-anchored CD109 may play major roles in the EGF signaling pathway.
Enterprise Rollouts with JumpStart (1999)

JumpStart is Sun's solution for installing the Solaris operating system. The Custom JumpStart feature allows the installation process to be automated. However, configuring boot and NFS servers and the appropriate name services for JumpStart is a time-consuming and error-prone process. The scripts that Sun provides do not help this process much. This paper will talk about how to better automate the configuration steps needed to perform JumpStarts over the network, emphasizing speed and accuracy as well as simplicity from an operator's point of view. The infrastructure needed to perform large numbers of simultaneous JumpStarts is also discussed. By automating the actual rollout process, it is possible to JumpStart several hundred machines at once. Techniques for doing so are presented. The improvements presented in this paper allowed one company to improve the speed of their rollouts to 600 Sun workstations by more than an order of magnitude. This greatly decreased user downtime and saved the company hundreds of thousands of dollars. Lastly, possible future improvements to the process are discussed.
Nopaline Ti-plasmid, pTiT37, T-DNA insertions into a flax genome. (1983)

The FT37/1 plant tumor line induced on flax epicotyls by T37, a nopaline strain of Agrobacterium tumefaciens, contains multiple copies of the pTiT37, T-DNA. There are three to four distinct full-length insertions and one tandem insertion. Allowing for the different copy numbers of the inserts, this amounts to seven to eight T-DNA copies per genome unit. The genome unit in this case is the haploid DNA value (7 X 10(8) bp) which predicts a T-DNA copy number of 14-16 per diploid cell. Three novel types of abnormal insertion are also present. FIL (one copy per basic genome) comprises 3.04-4.47 kb of T-DNA derived from the left end, with a normal left border and an abnormal right border. FIR (four copies per basic genome) comprises 5.88-6.47 kb of T-DNA derived from the right end, with a normal right border and an abnormal left border. The third abnormality is represented by fragment "X," a HindIII fragment of 4.90 kb which contains homology with several noncontiguous regions of the T-DNA and which may derive from a tandem insertion. Of the two possible left-border sites (primary and secondary) in which fusion with plant DNA sequences has been observed, only the primary is used.
Expression of Latent HIV Induced by the Potent HDAC Inhibitor Suberoylanilide Hydroxamic Acid (2009)

Histone deacetylases (HDACs) act on histones within the nucleosome-bound promoter of human immunodeficiency virus type 1 (HIV-1) to maintain proviral latency. HDAC inhibition leads to promoter expression and the escape of HIV from latency. We evaluated the ability of the potent inhibitor recently licensed for use in oncology, suberoylanilide hydroxamic acid (SAHA; Vorinostat), selective for Class I HDACs, to induce HIV promoter expression in cell lines and virus production from the resting CD4(+) T cells of antiretroviral-treated, aviremic HIV-infected patients. In J89, a Jurkat T cell line infected with a single HIV genome encoding the enhanced green fluorescence protein (EGFP) within the HIV genome, SAHA induced changes at nucleosome 1 of the HIV promoter in chromatin immunoprecipitation (ChIP) assays in concert with EGFP expression. In the resting CD4(+) T cells of antiretroviral-treated, aviremic HIV-infected patients clinically achievable exposures to SAHA induced virus outgrowth ex vivo. These results suggest that potent, selective HDAC inhibitors may allow improved targeting of persistent proviral HIV infection, and define parameters for in vivo studies using SAHA.
Strategies for multilocus linkage analysis in humans. (1984)

The increasing number of DNA polymorphisms characterized in humans will soon allow the construction of fine genetic maps of human chromosomes. This advance calls for a reexamination of current methodologies for linkage analysis by the family method. We have investigated the relative efficiency of two-point and three-point linkage tests for the detection of linkage and the estimation of recombination in a variety of situations. This led us to develop the computer program LINKAGE to perform multilocus linkage analysis. The investigation also enables us to propose a method of location scores for the efficient detection of linkage between a disease locus, or a new genetic marker, and a linkage group previously established from a reference panel of families. The method is illustrated by an application to simulated pedigree data in a situation akin to Duchenne muscular dystrophy. These results show that considerable economy and efficiency can be brought to the mapping endeavor by resorting to appropriate strategies of detecting linkage and by constructing the human genetic map on a common reference panel of families.
Uridine in the Prevention and Treatment of Nrti-Related Mitochondrial Toxicity (2005)

Long-term side effects of antiretroviral therapy are attributed to the mitochondrial (mt) toxicity of nucleoside analogue reverse transcriptase inhibitors (NRTIs) and their ability to deplete mtDNA. Studies in hepatocytes suggest that uridine is able to prevent and treat mtDNA depletion by pyrimidine NRTls [zalcitabine (ddC) and stavudine (d4T)] and to fully abrogate hepatocyte death, elevated lactate production and intracellular steatosis. Uridine was also found to improve the liver and haematopoietic toxicities of zidovudine (AZT), which are unrelated to mtDNA depletion, and to prevent neuronal cell death induced by ddC. Most recently, uridine was found to prevent the onset of a lipoatrophic phenotype (reduced intracellular lipids, increased apoptosis, mtDNA depletion and mt depolarization) in adipocytes incubated long-term with d4T and AZT. Various steps of mt nucleoside utilization may be involved in the protective effect, but competition of uridine metabolites with NRTIs at polymerase y or other enzymes is a plausible explanation. Pharmacokinetic studies suggest that uridine serum levels can be safely increased in humans to achieve concentrations which are protective in vitro (50-200 microM). Uridine was not found to interfere with the antiretroviral activity of NRTIs. Mitocnol, a sugar cane extract which effectively increases uridine in human serum, was beneficial in individual HIV patients with mt toxicity and is now being tested in placebo-controlled randomized trials. Until these data become available, the risk-benefit calculation of using uridine should be individualized. The current safety data justify the closely monitored use of uridine in individuals who suffer from mt toxicity but who cannot be switched to less toxic NRTIs.
Current clinical trials for the treatment of idiopathic pulmonary fibrosis (2009)

Most pulmonary consultants are called upon to discuss IPF management with their patients. The gravity of IPF treatment discussion is immense in view of the data that 3- and 5-year mortality rates are approximately 50% and 80%, respectively. Although IPF occurs in older patients with comorbid diseases, most patients with IPF die as a direct consequence of their lung fibrosis. Here, the results of recently completed IPF trials and the rationale for ongoing studies are succinctly reviewed. There are a number of novel agents in clinical trials that are in the earlier stages of development, and there is new evidence supporting palliative therapies, which may help in managing symptoms of IPF, such as cough, without necessarily altering the course of the disease. The information provided herein should facilitate informed physician-patient dialogue.
Benzalkonium Chloride (1998)

The efficacy of benzalkonium chloride was evaluated as an irrigating solution for the eradication of Staphylococcus aureus from a contaminated orthopaedic wound. Thirty Sprague Dawley rats were randomized into two groups. A stainless steel wire was placed in a lumbar spinous process, and the wound was inoculated with 10(7) or 10(6) colony forming units of Staphylococcus aureus. The wound was irrigated with 1 L of normal saline or 0.1% benzalkonium chloride solution. The animals were sacrificed, and cultures were obtained. Rats inoculated with 10(7) colony forming units of Staphylococcus aureus and irrigated with benzalkonium chloride had a significant decrease in the total number of positive cultures, deep wound cultures, and stainless steel wire cultures. Rats inoculated with 10(6) colony forming units of Staphylococcus aureus and irrigated with benzalkonium chloride also had a significant decrease in the total number of positive cultures, deep wound cultures, and stainless steel wire cultures. In a parallel noninoculation study, histologic evaluation of tissues did not show toxicity in the rats irrigated with benzalkonium chloride. This study shows that benzalkonium chloride is more effective than normal saline as an irrigating agent for eradicating Staphylococcus aureus from a contaminated orthopaedic wound.
Eye and gaze tracking for interactive graphic display (2002)

This paper describes preliminary results we have obtained in developing a computer vision system based on active IR illumination for real time gaze tracking for interactive graphic display. Unlike most of the existing gaze tracking techniques, which often require assuming a static head to work well and require a cumbersome calibration process for each person, our gaze tracker can perform robust and accurate gaze estimation without calibration and under rather significant head movement. This is made possible by a new gaze calibration procedure that identifies the mapping from pupil parameters to screen coordinates using the Generalized Regression Neural Networks (GRNN). With GRNN, the mapping does not have to be an analytical function and head movement is explicitly accounted for by the gaze mapping function. Furthermore, the mapping function can generalize to other individuals not used in the training. The effectiveness of our gaze tracker is demonstrated by preliminary experiments that involve gaze-contingent interactive graphic display.
[Metabolic characteristics of GS-nS0 myeloma cells producing anti-CD25 monoclonal antibody in serum-free culture]. (2009)

As an immunodepressant, anti-CD25 monoclonal antibody has a huge market with wide prospect and economic value. We developed a low protein serum-free medium for large-scale GS-NS0 myeloma cell culture and anti-CD25 monoclonal antibody production. Further study focused on the characteristics of GS-NSO cell growth, glucose and amino acid metabolism, and antibody production. In the serum-free medium, the maximal viable cell density and antibody concentration reached above 3x10(6) cells/mL and 300 mg/L in batch culture. Compared with the commercial serum-free medium (Excell 620 + 0.2% Primatone), the maximal viable cell density doubled and the maximal antibody concentration increased 46%. Results also showed the specific growth rate decreased when the glucose concentration was lower than 6 mmol/L. And the production of lactate increased when glucose concentration was excessively high (> 30 mmol/L). These results were important to provide technique and theory basis for developing optimized GS-NS0 cell culture and anti-CD25 monoclonal antibody production processes.
Design, Synthesis, and Testing of Polyamine Vectored Iron Chelators (2010)

Iron chelators have been shown to control the growth of cancer cells in culture by sequestering exogenous iron in the media. Thus, the ligands prevent cellular access to the metal. However, because transferrin provides iron to tumor cells in animals, chelators have not been effective antitumor agents. Polyamine chelator conjugates in which the polyamine vectored ligands into cells were far more active than the free chelators themselves. However, the free ligands were not released from the vector once in the cell. The current study focuses on the synthesis and preliminary evaluation of a polyamine chelator conjugate capable of releasing the free ligand intracellularly via a nonspecific esterase.
Thermoresponsive Semicrystalline Poly(ε-caprolactone) Networks: Exploiting Cross-linking with Cinnamoyl Moieties to Design Polymers with Tunable Shape Memory (2012)

The overall goal of this study was to synthesize semicrystalline poly(ε-caprolactone) (PCL) copolymer networks with stimuli-responsive shape memory behavior. Herein, we investigate the influence of a cinnamoyl moiety to design shape memory polymer networks with tunable transition temperatures. The effect of various copolymer architectures (random or ABA triblock), the molecular weight of the crystalline domains, PCL diol, (M(w) 1250 or 2000 g mol(-1)) and its composition in the triblock (50 or 80 mol %) were also investigated. The polymer microstructures were confirmed by NMR, DSC, WAXS and UV-vis spectroscopic techniques. The thermal and mechanical properties and the cross-linking density of the networks were characterized by DSC, tensile testing and solvent swelling, respectively. Detailed thermomechanical investigations conducted using DMA showed that shape memory behavior was obtained only in the ABA triblock copolymers. The best shape memory fixity, R(f) of ~99% and shape recovery, R(r) of ~99% was obtained when PCL diol with M(w) 2000 g mol(-1) was incorporated in the triblock copolymer at a concentration of 50 mol %. The series of triblock copolymers with PCL at 50 mol % also showed mechanical properties with tunable shape memory transition temperatures, ranging from 54 °C to close to body temperature. Our work establishes a general design concept for inducing a shape memory effect into any semicrystalline polyester network. More specifically, it can be applied to systems which have the highest transition temperature closest to the application temperature. An advantage of our novel copolymers is their ability to be cross-linked with UV radiation without any initiator or chemical cross-linker. Possible applications are envisioned in the area of endovascular treatment of ischemic stroke and cerebrovascular aneurysms, and for femoral stents.
SeqMap: mapping massive amount of oligonucleotides to the genome (2008)

SeqMap is a tool for mapping large amount of short sequences to the genome. It is designed for finding all the places in a reference genome where each sequence may come from. This task is essential to the analysis of data from ultra high-throughput sequencing machines. With a carefully designed index-filtering algorithm and an efficient implementation, SeqMap can map tens of millions of short sequences to a genome of several billions of nucleotides. Multiple substitutions and insertions/deletions of the nucleotide bases in the sequences can be tolerated and therefore detected. SeqMap supports FASTA input format and various output formats, and provides command line options for tuning almost every aspect of the mapping process. A typical mapping can be done in a few hours on a desktop PC. Parallel use of SeqMap on a cluster is also very straightforward.
In vitro immunologic and virologic effects of interleukin 15 on peripheral blood mononuclear cells from normal donors and human immunodeficiency virus type 1-infected patients (1997)

Interleukin 15 (IL-15) is a cytokine that shares receptor subunits and functional activity, such as T-cell and B-cell stimulation, with IL-2. The effect of IL-2 on immune function and human immunodeficiency virus (HIV) viral load in HIV-infected patients is being actively studied. Thus, we examined how IL-15 compares with IL-2 in several in vitro immunologic and virologic assays in order to explore whether a rationale exists for pursuing initial clinical therapeutic trials with IL-15. The effects of IL-15 on induction of lymphokine-activated killer (LAK) cells, gamma interferon (IFN-gamma) production from HIV-positive peripheral blood mononuclear cells (PBMCs), and HIV production from PBMCs were studied. Induction of LAK cells by IL-15 was found in eight of eight HIV-positive donors. Incubation of PBMCs from some donors with IL-15 (1, 10, 50, and 100 ng/ml) induced production of IFN-gamma. The effect of IL-15 was compared with that of IL-2 on HIV replication in PBMCs from five HIV-positive patients and four HIV-negative donors whose PBMCs were infected in vitro with HIV. Levels of HIV p24 antigen were moderately lower in the presence of 10 ng of IL-15 per ml than with 10 ng of IL-2 per ml, but they were similar for 100 and 500 ng of each cytokine per ml. In summary, IL-15 can induce LAK cell activity in HIV-seropositive patients and can stimulate IFN-gamma production from PBMCs of some donors. IL-15 stimulates levels of HIV production from PBMCs which are similar to or moderately lower than those obtained with IL-2, depending on cytokine concentration.
Effectiveness of a Clozapine–Aripiprazole Combination in Tourette Syndrome and Bipolar Spectrum Disorder (2013)

Antipsychotic combination is a common strategy used in both bipolar disorder and schizophrenia, although just a few trials are available exploring its effectiveness. We report herein the case of a patient suffering from severe Tourette syndrome (TS) and bipolar spectrum disorder who benefited from a combination of clozapine and aripiprazole.