gebhart/patrepeval huggingface dataset:
A revised simplex search procedure for stochastic simulation response-surface optimization (1998)

We develop a variant of the Nelder-Mead (NM) simplex search procedure for stochastic simulation optimization that is designed to avoid many of the weaknesses encumbering such direct-search methods-in particular, excessive sensitivity to starting values, premature termination at a local optimum, lack of robustness against noisy responses, and lack of computational efficiency. The revised simplex search (RSS) procedure consists of a three-phase application of the NM method in which: (a) the ending values for one phase become the starting values for the next phase; (b) the size of the initial simplex (respectively, the shrink coefficient) decreases geometrically (respectively, increases linearly) over successive phases; and (c) the final estimated optimum is the best of the ending values for the three phases. To compare RSS versus the NM procedure and RS9 (a simplex search procedure recently proposed by Barton and Ivey (1996)), we summarize a simulation study based on separate factorial experiments and follow-up multiple comparisons tests for four selected performance measures computed on each of six test problems, with three levels of problem dimensionality and noise variability used in each problem. The experimental results provide substantial evidence of RSS's improved performance with only marginally higher computational effort.
Potential mechanisms for renal damage in beta-thalassemia (2013)

Improvement of survival in patients with β-thalassemia has allowed several clinical morbidities to manifest, including renal complications. Patients may experience proximal tubular dysfunctions and abnormalities in glomerular filtration rate. Several risk factors have been proposed. Hypoxia may lead to renal damage with resulting proximal tubular epithelial cell dysfunction and interstitial fibrosis, while anemia induces renal hemodynamic changes. Iron overload secondary to regular transfusion therapy can also result in an increase in oxidative stress and direct cytotoxicity to the kidney. Moreover, the use of certain iron-chelating agents is associated with a transient, nonprogressive increase in serum creatinine levels. However, most available evidence comes from small, cross-sectional studies. Longitudinal follow-up of patients is needed to better understand the mechanisms of renal abnormalities in this patient population.
Essential requirement for both hsf1 and hsf2 transcriptional activity in spermatogenesis and male fertility (2004)

Heat shock factors (Hsfs) are major transactivators of heat shock proteins but are also involved in regulation of other genes active in embryonic development. High expression levels of Hsfs in mouse testis during development suggest a role for these factors in spermatogenesis, a cyclic process of spermatogonia cell-differentiation into mature spermatozoa. In contrast to hsf1(-/-) mice, which exhibit normal spermatogenesis, targeted disruption of hsf2 results in reduced testicular size but only a small impairment in male fertility. We show here that disruption of both hsf1 and hsf2 results in a more severe phenotype associated with male sterility due to severe defects in spermatogenesis. Earliest defects observed are the reduced number of germ cells in juvenile mice and germ cells that enter the meiotic prophase fail to progress beyond the pachytene stage. This was associated with a reduction or absence of transcription of genes critically involved in spermatogenesis. The findings suggest that additive or synergistic transcriptional activity of both hsf1 and hsf2 is required for normal mammalian spermatogenesis and male fertility.
[Plasma levels of probucol in man after single and repeated oral doses (author's transl)]. (1980)

Following administration of a single oral dose of 3 g probucol to healthy volunteers, mean peak plasma concentrations of 3.9 microgram/ml were observed at 24 hours. Successive blood levels measurements showed diphasic elimination, with half-lives of about 1 and 23 days. Plasma levels after a single 250 mg dose in volunteers are also reported. In 51 patients who received probucol 1 g daily for periods of 1 to 12 months, a concentration plateau was obtained within 1 to 3 months of treatment; the mean plasma levels ranged from 18.2 to 39.2 microgram/ml depending on the duration of probucol therapy. In another study carried out on 8 patients who were given the same daily dose during 12 months, the mean probucol plasma level at the end of that period was 18.9 microgram/ml. Repeated administration of probucol to healthy volunteers showed good correlation between dosage and blood levels.
Effect of Ionic Strength on the Binding of Sindbis Virus to Chick Cells (1974)

Sindbis virus can adsorb to chicken embryo fibroblasts in two different ways. "Loosely" bound virus can be washed off the cell with buffers of ionic strength 0.2 or greater, whereas "tightly" bound virus remains attached under these conditions. When Sindbis virus is adsorbed to chick cells at 4 C from a buffer of ionic strength 0.17, 40 to 50% of the adsorbed virus is loosely bound, the remainder tightly bound. Infection of chick cells by Sindbis virus has only small effects on the total amount of virus that can be bound to the cells. However, the amount of Sindbis virus that can be tightly bound declines rapidly beginning at 2 to 3 h after infection. By 7 h after infection, the amount of virus that can be tightly bound is only 10 to 20% of the amount bound to uninfected cells. The adsorption (and penetration) of virus at 37 C is most efficient at an ionic strength of 0.15 to 0.17; at this ionic strength most of the adsorbed virus is tightly bound. At higher ionic strengths the virus adsorbs poorly. At lower ionic strengths most of the virus is loosely bound. A second enveloped virus, vesicular stomatitis virus, has been studied for the purposes of comparison; its adsorption behavior differs from that of Sindbis virus.
Investigation of the Reaction Impurities Associated with Methylamphetamine Synthesized Using the Nagai Method (2012)

The synthesis of methylamphetamine hydrochloride from l-ephedrine or d-pseudoephedrine hydrochloride via reduction with hydriodic acid and red phosphorus was investigated. Eighteen batches of methylamphetamine hydrochloride were synthesized in six replicate batches using three different reaction times. This allowed the investigation of the variation of impurities in the final product with reaction time. The results obtained have resolved previously conflicting impurity profile data reported in the literature for this synthesis route. The impurity profile was shown to change with reaction time, and all previously reported impurity components were identified but not in all batches. Additionally, 20 batches of methylamphetamine hydrochloride were synthesized from either from l-ephedrine or d-pseudoephedrine hydrochloride in reactions which were allowed to proceed for 24 h. The impurities present in the resulting batches were investigated, and route-specific impurities present in all batches were identified. Batch-to-batch fluctuations in the resultant chromatographic impurity profile, despite careful synthetic monitoring and control, were also noted.
The Phage Proteomic Tree: a Genome-Based Taxonomy for Phage (2002)

There are approximately 10(31) phage in the biosphere, making them the most abundant biological entities on the planet. Despite their great numbers and ubiquitous presence, very little is known about phage biodiversity, biogeography, or phylogeny. Information is limited, in part, because the current ICTV taxonomical system is based on culturing phage and measuring physical parameters of the free virion. No sequence-based taxonomic systems have previously been established for phage. We present here the "Phage Proteomic Tree," which is based on the overall similarity of 105 completely sequenced phage genomes. The Phage Proteomic Tree places phage relative to both their near neighbors and all other phage included in the analysis. This method groups phage into taxa that predicts several aspects of phage biology and highlights genetic markers that can be used for monitoring phage biodiversity. We propose that the Phage Proteomic Tree be used as the basis of a genome-based taxonomical system for phage.
Ecological Behavior ofLactobacillus reuteri100-23 Is Affected by Mutation of theluxSGene (2005)

The luxS gene of Lactobacillus reuteri 100-23C was amplified by PCR, cloned, and then sequenced. To define a physiological and ecological role for the luxS gene in L. reuteri 100-23C, a luxS mutant was constructed by insertional mutagenesis. The luxS mutant did not produce autoinducers AI-2 or AI-3. Complementation of the luxS mutation by a plasmid construct containing luxS restored AI-2 and AI-3 synthesis. In vitro experiments revealed that neither the growth rate, nor the cell yield, nor cell survival in the stationary phase were compromised in the luxS mutant relative to the wild type and complemented mutant. The ATP content of exponentially growing cells of the luxS mutant was, however, 65% of that of wild-type cells. Biofilms formed by the luxS mutant on plastic surfaces in a bioreactor were thicker than those formed by the wild type. Biofilm thickness was not restored to wild-type values by the addition of purified AI-2 to the culture medium. In vivo experiments, conducted with ex-Lactobacillus-free mice, showed that biofilms formed by the mutant strain on the epithelial surface of the forestomach were approximately twice as thick as those formed by the wild type. The ecological performance of the luxS mutant, when in competition with L. reuteri strain 100-93 in the mouse cecum, was reduced compared to that of a xylA mutant of 100-23C. These results demonstrate that LuxS influences important ecological attributes of L. reuteri 100-23C, the consequences of which are niche specific.
Inducible cell lysis system for the study of natural transformation and environmental fate of DNA released by cell death (1994)

Two novel conditional broad-host-range cell lysis systems have been developed for the study of natural transformation in bacteria and the environmental fate of DNA released by cell death. Plasmid pDKL02 consists of lysis genes S, R, and Rz from bacteriophage lambda under the control of the Ptac promoter. The addition of inducer to Escherichia coli, Acinetobacter calcoaceticus, or Pseudomonas stutzeri containing plasmid pDKL02 resulted in cell lysis coincident with the release of high amounts of nucleic acids into the surrounding medium. The utility of this lysis system for the study of natural transformation with DNA released from lysed cells was assessed with differentially marked but otherwise isogenic donor-recipient pairs of P. stutzeri JM300 and A. calcoaceticus BD4. Transformation frequencies obtained with lysis-released DNA and DNA purified by conventional methods and assessed by the use of antibiotic resistance (P. stutzeri) or amino acid prototrophy (A. calcoaceticus) for markers were comparable. A second cell lysis plasmid, pDKL01, contains the lysis gene E from bacteriophage phi X174 and causes lysis of E. coli and P. stutzeri bacteria by activating cellular autolysins. Whereas DNA released from pDKL02-containing bacteria persists in the culture broth for days, that from induced pDKL01-containing bacteria is degraded immediately after release. The lysis system involving pDKL02 is thus useful for the study of both the fate of DNA released naturally into the environment by dead cells and gene transfer by natural transformation in the environment in that biochemically unmanipulated DNA containing defined sequences and coding for selective phenotypes can be released into a selected environment at a specific time point. This will allow kinetic measurements that will answer some of the current ecological questions about the fate and biological potential of environmental DNA to be made.
The Implementation of Social Choice Rules: Some General Results on Incentive Compatibility (1979)

Journal Article The Implementation of Social Choice Rules: Some General Results on Incentive Compatibility Get access Partha Dasgupta, Partha Dasgupta London School of Economics Search for other works by this author on: Oxford Academic Google Scholar Peter Hammond, Peter Hammond University of Essex Search for other works by this author on: Oxford Academic Google Scholar Eric Maskin Eric Maskin Massachusetts Institute of Technology Search for other works by this author on: Oxford Academic Google Scholar The Review of Economic Studies, Volume 46, Issue 2, April 1979, Pages 185–216, https://doi.org/10.2307/2297045 Published: 01 April 1979 Article history Received: 01 June 1978 Accepted: 01 November 1978 Published: 01 April 1979
Viral Small T Oncoproteins Transform Cells by Alleviating Hippo-Pathway-Mediated Inhibition of the YAP Proto-oncogene (2014)

Primary human cells can be transformed into tumor cells by a defined set of genetic alterations including telomerase, oncogenic Ras(V12), and the tumor suppressors p53 and pRb. SV40 small T (ST) is required for anchorage-independent growth in vitro and in vivo. Here, we identify the Hippo tumor suppressor pathway as a critical target of ST in cellular transformation. We report that ST uncouples YAP from the inhibitory activity of the Hippo pathway through PAK1-mediated inactivation of NF2. Membrane-tethered activated PAK is sufficient to bypass the requirement for ST in anchorage-independent growth. PAK acts via YAP to mediate the transforming effects of ST. Activation of endogenous YAP is required for ST-mediated transformation and is sufficient to bypass ST in anchorage-independent growth and xenograft tumor formation. Our findings uncover the Hippo tumor suppressor pathway as a final gatekeeper to transformation and tumorigenesis of primary cells.
High-Affinity Zn2+Uptake System ZnuABC Is Required for Bacterial Zinc Homeostasis in Intracellular Environments and Contributes to the Virulence ofSalmonella enterica (2007)

To investigate the relevance of zinc in host-pathogen interactions, we have constructed Salmonella enterica mutant strains in which the znuA gene, which encodes the periplasmic component of the ZnuABC high-affinity Zn2+ transporter, was deleted. This mutation does not alter the ability of Salmonella to grow in rich media but drastically reduces its ability to multiply in media deprived of zinc. In agreement with this phenotype, ZnuA accumulates only in bacteria cultivated in environments poor in zinc. In spite of the nearly millimolar intracellular concentration of zinc, we have found that znuA is highly expressed in intracellular salmonellae recovered either from cultivated cells or from the spleens of infected mice. We have also observed that znuA mutants are impaired in their ability to grow in Caco-2 epithelial cells and that bacteria starved for zinc display decreased ability to multiply in phagocytes. A dramatic reduction in the pathogenicity of the znuA mutants was observed in Salmonella-susceptible (BALB/c) or Salmonella-resistant (DBA-2) mice infected intraperitoneally or orally. This study shows that the amount of free metals available for bacterial growth within the infected animal is limited, despite the apparent elevated concentration of free metals within cells and in plasma and suggests that Salmonella exploits the ZnuABC zinc transporter to maximize zinc availability in such conditions. These results shed new light on the complex functions of zinc in vertebrate and bacterial physiology and pave the way for a better comprehension of pathogenic mechanisms in Salmonella infections.
Revising Your Proposal (2012)

This chapter contains sections titled: Why Revision? First Steps in Revision Strategies and Tips in Writing a Revision Final Remarks on Revision
Antisense-Mediated Inhibition of Human Immunodeficiency Virus (HIV) Replication by Use of an HIV Type 1-Based Vector Results in Severely Attenuated Mutants Incapable of Developing Resistance (2004)

We have constructed a human immunodeficiency virus type 1 (HIV-1)-based lentiviral vector expressing a 937-base antisense sequence against the HIV-1 envelope gene. Transduction of CD4(+) T lymphocytes with this vector results in expression of the therapeutic antisense sequence and subsequent inhibition of productive HIV-1 replication. In this report, we examined the effect of antisense-mediated suppression on the potential development of virus escape mutants using a permissive T-cell line cultured under conditions that over serial passages specifically allowed for generation and amplification of mutants selected for by antisense pressure. In the resulting virus clones, we found a significant increase in the number of deletions at the envelope target region (91% compared to 27.5% in wild-type HIV). Deletions were most often greater than 1 kb in length. These data demonstrate for the first time that during antisense-mediated suppression of HIV, mutants develop as a direct result of selective pressure on the HIV genomic RNA. Interestingly, in clones where deletions were not observed, there was a high rate of A-G transitions in mutants at the antisense target region but not outside this region, which is consistent with those mutations that are predicted as a result of antisense-mediated modification of double-stranded RNA by the enzyme double-stranded RNA-specific adenosine deaminase. These clones were not found to be escape mutants, as their replicative ability was severely attenuated, and they did not replicate in the presence of vector.
Identification of Strong Aggregating Regions in Soy Glycinin upon Enzymatic Hydrolysis (2008)

Upon hydrolysis with chymotrypsin, soy glycinin has a strong tendency to aggregate. The regions of glycinin from which the aggregating peptides originate were identified by accumulative-quantitative peptide mapping. To this end, the aggregating peptides were further hydrolyzed with trypsin to obtain peptides of which the sequence can be identified using RP-HPLC-MS/MS. This resulted in a hydrolysate in which 90% of the proteinaceous material was dissolved. The soluble fraction was analyzed using the method of accumulative-quantitative peptide mapping: fractionation using ion exchange chromatography, followed by identification of peptides by RP-HPLC-MS/MS, quantification based on the absorbance at 214 nm, and finally peptide mapping. For the peptide mapping the proportions in which each of the five glycinin subunits are present, as determined by Edman degradation, were taken into account. The results showed that mainly the basic polypeptide and a part of the acidic polypeptide, close to the location of the disulfide bridge between the basic and acidic polypeptides, are present in the aggregating peptide fraction. On the basis of the results obtained, an aggregation mechanism was proposed. The hydrophilic acidic polypeptides shield the hydrophobic basic polypeptides, and the former are preferentially degraded upon hydrolysis. This results in a net increase in hydrophobicity of the remaining material, which mainly consists of the basic polypeptide fragments. This increase in hydrophobicity is proposed to be the driving force in the aggregation of chymotrypsin-derived peptides of glycinin.
Stability in single longitudinal mode operation in GaInAsP/InP phase-adjusted DFB lasers (1987)

A single longitudinal mode (SLM) operating condition for phase-adjusted (PA) DFB lasers has been made clear both experimentally and theoretically. As expected, we got a high SLM operation yield of 80 percent in a moderate coupled case up to a light output power of 10 mW. However, in the strongly coupled cases, the two-mode operation with the TE0 mode and the TE + 1 mode occurred frequently. To explain the two-mode operation and to optimize the PA-DFB laser structure, we have developed a theory. Taking the spatial hole burning along the laser axis into account, we succeeded in explaining the longitudinal mode behavior. From our theory, moderate coupling ( <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">kL = 1.25</tex> ) was found to be optimum to maintain the large threshold gain difference above threshold.
Controlling Chemical Turbulence by Global Delayed Feedback: Pattern Formation in Catalytic CO Oxidation on Pt(110) (2001)

Control of spatiotemporal chaos is one of the central problems of nonlinear dynamics. We report on suppression of chemical turbulence by global delayed feedback using, as an example, catalytic carbon monoxide oxidation on a platinum (110) single-crystal surface and carbon monoxide partial pressure as the controlled feedback variable. When feedback intensity was increased, spiral-wave turbulence was transformed into new intermittent chaotic regimes with cascades of reproducing and annihilating local structures on the background of uniform oscillations. The global feedback further led to the development of cluster patterns and standing waves and to the stabilization of uniform oscillations. These findings are reproduced by theoretical simulations.
Pituitary Adenylate Cyclase-Activating Polypeptide Induces Postsynaptically Expressed Potentiation in the Intra-amygdala Circuit (2012)

Pituitary adenylate cyclase-activating polypeptide (PACAP) is a pleiotropic neuropeptide expressed in the brain, where it may act as a neuromodulator or neurotransmitter contributing to different behavioral processes and stress responses. PACAP is highly expressed in the amygdala, a subcortical brain area involved in both innate and learned fear, suggesting a role for PACAP-mediated signaling in fear-related behaviors. It remains unknown, however, whether and how PACAP affects neuronal and synaptic functions in the amygdala. In this study, we focused on neurons in the lateral division of the central nucleus (CeL), where PACAP-positive presynaptic terminals were predominantly found within the amygdala. In our experiments on rat brain slices, exogenous application of PACAP did not affect either resting membrane potential or membrane excitability of CeL neurons. PACAP enhanced, however, excitatory synaptic transmission in projections from the basolateral nucleus (BLA) to the CeL, while inhibitory transmission in the same pathway was unaffected. PACAP-induced potentiation of glutamatergic synaptic responses persisted after the washout of PACAP and was blocked by the VPAC1 receptor antagonist, suggesting that VPAC1 receptors might mediate synaptic effects of PACAP in the CeL. Moreover, potentiation of synaptic transmission by PACAP was dependent on postsynaptic activation of protein kinase A and calcium/calmodulin-dependent protein kinase II, as well as synaptic targeting of GluR1 subunit-containing AMPA receptors. Thus, PACAP may upregulate excitatory neurotransmission in the BLA–CeL pathway postsynaptically, consistent with the known roles of PACAP in control of fear-related behaviors.