gebhart/patrepeval huggingface dataset:
Multiobjective Optimization of Simulated Countercurrent Moving Bed Chromatographic Reactor (SCMCR) for MTBE Synthesis (2002)

The paper addresses the multiobjective optimization of a simulated moving-bed chromatographic reactor (SCMCR). The selection of the operating parameters such as the length and number of columns, switching time, and liquid flow rates in different sections is not straightforward in an SCMCR. In most cases, conflicting requirements and constraints govern the optimal choice of the decision (operating or design) variables. A mathematical model that predicts single-column experimental results well was modified for MTBE synthesis in an SCMCR. Thereafter, a few simple multiobjective optimization problems were solved that included both existing and design-stage SCMCRs using a nondominated sorting genetic algorithm (NSGA). Optimal design and operating conditions for three cases of practical relevance are studied in this work, namely, (a) simultaneous maximization of the purity and yield of MTBE; (b) simultaneous maximization of the purity and yield of MTBE, together with minimization of the total amount of adsorbent/catalyst required; and (c) maximization of the purity of MTBE with simultaneous minimization of the eluent consumption, to illustrate the procedures and interpret the results obtained. Pareto-optimal solutions were obtained in all cases, and moreover, it was found that the performance of the SCMCR could be improved significantly under optimal operating conditions.
Simple and reliable in situ CRISPR-Cas9 nuclease visualization tool is ensuring efficient editing in Streptomyces species (2022)

CRISPR-Cas9 technology has emerged as a promising tool for genetic engineering of Streptomyces strains. However, in practice, numerous technical hurdles have yet to be overcome when developing robust editing procedures. Here, we developed an extension of the CRISPR-Cas toolbox, a simple and reliable cas9 monitoring tool with transcriptional fusion of cas9 nuclease to a beta glucuronidase (gusA) visual reporter gene. The Cas9-SD-GusA tool enables in situ identification of cells expressing Cas9 nuclease following the introduction of the plasmid carrying the CRISPR-Cas9 machinery. Remarkably, when the Cas9-SD-GusA system was applied under optimal conditions, 100% of the colonies displaying GusA activity carried the target genotype. In contrast, it was shown that the cas9 sequence had undergone major recombination events in the colonies that did not exhibit GusA activity, giving rise to "escaper colonies" carrying unedited genotype. Our approach allows a simple detection of "escaper" phenotype and serves as an efficient CRISPR-Cas9 optimisation tool.
Bridged Peptide Macrocycles as Ligands for PDZ Domain Proteins (2005)

[reaction: see text] Conformationally constrained side chain-bridged cyclic peptides were prepared using bis-carboxylic acid ring spacers. These macrocyles were designed to inhibit protein-protein interactions mediated by the third PDZ domain (PDZ3) of a mammalian neuronal protein, PSD-95. Isothermal titration calorimetry (ITC) experiments measured dissociation constants in the low micromolar range. For each compound, the change in entropy (TdeltaS) of binding either is comparable in magnitude to the enthalpy change (deltaH) or is the predominant driving force for association.
Doppler optical coherence tomography for interventional cardiovascular guidance: in vivo feasibility and forward-viewing probe flow phantom demonstration (2010)

We demonstrate the potential of a forward-looking Doppler optical coherence tomography (OCT) probe for color flow imaging in several commonly seen narrowed artery morphologies. As a proof of concept, we present imaging results of a surgically exposed thrombotic occlusion model that was imaged superficially to demonstrate that Doppler OCT can identify flow within the recanalization channels of a blocked artery. We present Doppler OCT images in which the flow is nearly antiparallel to the imaging direction. These images are acquired using a flexible 2.2-mm-diam catheter that used electrostatic actuation to scan up to 30 deg ahead of the distal end. Doppler OCT images of physiologically relevant flow phantoms consisting of small channels and tapered entrance geometries are demonstrated.
Current commercial applications of semiconductor optical amplifiers (2014)

SOAs seem to have finally found their niche. We will review the applications in which semiconductor optical amplifiers are presently used, and will go into the characteristics that make the devices distinctively suited for these purposes. We notice that the modern uses of SOAs are not limited to optical networking, but can also be found in fields as diverse as medical diagnostics and sensing.
Experimental Transmission of the Chronic Wasting Disease Agent to Swine after Oral or Intracranial Inoculation (2017)

Chronic wasting disease (CWD) is a naturally occurring, fatal neurodegenerative disease of cervids. The potential for swine to serve as hosts for the agent of CWD is unknown. The purpose of this study was to investigate the susceptibility of swine to the CWD agent following experimental oral or intracranial inoculation. Crossbred piglets were assigned to three groups, intracranially inoculated (<i>n</i> = 20), orally inoculated (<i>n</i> = 19), and noninoculated (<i>n</i> = 9). At approximately the age at which commercial pigs reach market weight, half of the pigs in each group were culled ("market weight" groups). The remaining pigs ("aged" groups) were allowed to incubate for up to 73 months postinoculation (mpi). Tissues collected at necropsy were examined for disease-associated prion protein (PrP<sup>Sc</sup>) by Western blotting (WB), antigen capture enzyme immunoassay (EIA), immunohistochemistry (IHC), and <i>in vitro</i> real-time quaking-induced conversion (RT-QuIC). Brain samples from selected pigs were also bioassayed in mice expressing porcine prion protein. Four intracranially inoculated aged pigs and one orally inoculated aged pig were positive by EIA, IHC, and/or WB. By RT-QuIC, PrP<sup>Sc</sup> was detected in lymphoid and/or brain tissue from one or more pigs in each inoculated group. The bioassay was positive in four out of five pigs assayed. This study demonstrates that pigs can support low-level amplification of CWD prions, although the species barrier to CWD infection is relatively high. However, detection of infectivity in orally inoculated pigs with a mouse bioassay raises the possibility that naturally exposed pigs could act as a reservoir of CWD infectivity.<b>IMPORTANCE</b> We challenged domestic swine with the chronic wasting disease agent by inoculation directly into the brain (intracranially) or by oral gavage (orally). Disease-associated prion protein (PrP<sup>Sc</sup>) was detected in brain and lymphoid tissues from intracranially and orally inoculated pigs as early as 8 months of age (6 months postinoculation). Only one pig developed clinical neurologic signs suggestive of prion disease. The amount of PrP<sup>Sc</sup> in the brains and lymphoid tissues of positive pigs was small, especially in orally inoculated pigs. Regardless, positive results obtained with orally inoculated pigs suggest that it may be possible for swine to serve as a reservoir for prion disease under natural conditions.
Long term conservation of human metabolic phenotypes and link to heritability (2014)

Changes in an individual's human metabolic phenotype (metabotype) over time can be indicative of disorder-related modifications. Studies covering several months to a few years have shown that metabolic profiles are often specific for an individual. This "metabolic individuality" and detected changes may contribute to personalized approaches in human health care. However, it is not clear whether such individual metabotypes persist over longer time periods. Here we investigate the conservation of metabotypes characterized by 212 different metabolites of 818 participants from the Cooperative Health Research in the Region of Augsburg; Germany population, taken within a 7-year time interval. For replication, we used paired samples from 83 non-related individuals from the TwinsUK study. Results indicated that over 40 % of all study participants could be uniquely identified after 7 years based on their metabolic profiles alone. Moreover, 95 % of the study participants showed a high degree of metabotype conservation (>70 %) whereas the remaining 5 % displayed major changes in their metabolic profiles over time. These latter individuals were likely to have undergone important biochemical changes between the two time points. We further show that metabolite conservation was positively associated with heritability (rank correlation 0.74), although there were some notable exceptions. Our results suggest that monitoring changes in metabotypes over several years can trace changes in health status and may provide indications for disease onset. Moreover, our study findings provide a general reference for metabotype conservation over longer time periods that can be used in biomarker discovery studies.
Isolation of antifungally active lactobacilli from Edam cheese (2007)

The antifungal activity of 322 lactobacilli strains isolated from Edam cheese at different stages of the ripening process was tested against Fusarium proliferatum M 5689 using a dual overlay spot assay. Approximately 21% of the isolates showed a certain level of inhibitory activity.Seven strains with the strongest antifungal activity were examined by the milk agar plate method with three different mould strains isolated from spoiled dairy products as target microorganisms and were compared with the antifungal effectiveness of standard antifungal strains Lactobacillus rhamnosus VT1 and Lb. plantarum DC 1246.The newly isolated lactobacilli strains exhibited the strongest inhibition against F. proliferatum M 5689, followed by Penicillium sp. DMF 0006 and Aspergillus niger DMF 0801. The level of mould growth inhibition of several new isolates, namely Lb. paracasei ST 68, Lb. fermentum ST 40 and Lb. fermentum ST 41, was comparable to or slightly higher than that of standard strains. By use of both phenotypic and genotypic methods (REP-PCR, 16S rDNA), four out of seven antifungally active isolates were identified, one as Lb. paracasei and three as Lb. fermentum. Lb. paracasei ST 68 was chosen for further testing as antifungal protective adjunct for Edam cheese production.
Electropolishing of Niobium in Sulfuric Acid-methanol Electrolyte (2009)

Abstract not Available.
Correlational Dueling Bandits with Application to Clinical Treatment in Large Decision Spaces (2017)

We consider sequential decision making under uncertainty, the optimization over large decision space with noisy comparative feedback. This problem can be formulated as a K-armed Dueling Bandits problem where K is the total number of decisions. When K is very large, existing dueling bandits algorithms suffer huge cumulative regret before converging on the optimal arm. This paper studies the dueling bandits problem with a large number of dependent arms. Our problem is motivated by a clinical decision making process in large decision space. We propose an efficient algorithm CorrDuel for the problem which makes decisions to simultaneously deliver effective therapy and explore the decision space. Many sequential decision making problems with large and structured decision space could be facilitated by our algorithm. After evaluated the fast convergence of CorrDuel in analysis and simulation experiments, we applied it on a live clinical trial of therapeutic spinal cord stimulation. It is the first applied algorithm towards spinal cord injury treatments and experimental results show the effectiveness and efficiency of our algorithm.
Performance Assessment for Pump-and-Treat Closure or Transition (2015)

A structured performance assessment approach is useful to evaluate pump-and-treat (P&T) groundwater remediation, which has been applied at numerous sites. Consistent with the U.S. Environmental Protection Agency’s Groundwater Road Map, performance assessment during remedy implementation may be needed, and should consider remedy optimization, transition to alternative remedies, or remedy closure. In addition, a recent National Research Council study examined groundwater remediation at complex contaminated sites and concluded that it may be beneficial to evaluate remedy performance and the potential need for transition to alternative approaches at these sites. The intent of this document is to provide a structured approach for assessing P&T performance to support a decision to optimize, transition, or close a P&T remedy. The process presented in this document for gathering information and performing evaluations to support P&T remedy decisions includes use of decision elements to distinguish between potential outcomes of a remedy decision. Case studies are used to augment descriptions of decision elements and to illustrate each type of outcome identified in the performance assessment approach. The document provides references to resources for tools and other guidance relevant to conducting the P&T assessment.
Demonstration of Training and Process Support Capabilities for Bridging the Gap between Systems Engineering and Cognitive Engineering (2007)

The systems engineering and cognitive engineering communities both offer processes and methods that must be jointly used to design tools and technologies that can effectively and efficiently support task performance. Unfortunately, these groups have not effectively integrated their approaches. To begin to bridge the gap between systems engineers and cognitive engineers, we have developed The Resource for Applied Cognitive Engineering and Systems Engineering (TRACE-SE). TRACE-SE is a web-based tool designed for both cognitive and systems engineers to provide the information needed to create and support awareness and understanding of the processes and methods used by both the cognitive and systems engineering communities and to facilitate communication between these two groups. Using the TRACE-SE tool, both communities will better understand how to use their respective processes in order to develop systems that support superior decision making, improved safety, and greater operator productivity.
Mo2Ga2C: a new ternary nanolaminated carbide (2015)

We report the discovery of a new hexagonal Mo2Ga2C phase, wherein two Ga layers – instead of one – are stacked in a simple hexagonal arrangement in between Mo2C layers. It is reasonable to assume this compound is the first of a larger family.
Simultaneous Measurement of Radiation Pattern by Modulated Scattering Element Array (2006)

A simultaneous measurement method using the modulated scattering element array is proposed to measure the electromagnetic radiation which is instant and irregular. Each modulated scattering element (MSE) is excited by a local signal with different frequency, so that the received IF signal contains different frequency components which indicates the relative magnitude of the RF signal at positions of the MSEs, and all of the IF components are measured simultaneously by the broadband microwave receiver. Radiation pattern of a 2-element quarter wavelength monopole array is measured for evaluating the performance of the measurement method. It is found that good agreement of the measurement results is obtained between the present measurement and the conventional method.
Lignoceric acid is oxidized in the peroxisome: implications for the Zellweger cerebro-hepato-renal syndrome and adrenoleukodystrophy. (1984)

The deficient oxidation and accumulation of very-long-chain fatty acids in the Zellweger cerebro-hepato-renal syndrome (CHRS) and X chromosome-linked adrenoleukodystrophy (ALD), coupled with the observation that peroxisomes are lacking in CHRS, prompted us to investigate the subcellular localization of the catabolism of lignoceric acid (C24:0). Peroxisomal and mitochondrial-rich fractions were separated from rat liver crude mitochondria by sucrose density gradient centrifugation. Enzyme activity for the oxidation of [1-14C]palmitic acid to water-soluble acetate was 2- to 3-fold higher in the mitochondrial than in the peroxisomal-rich fraction whereas [1-14C]lignoceric acid was oxidized at a 2- to 3-fold higher rate in the peroxisomal than in the mitochondrial fraction. Moreover, unlike palmitic acid oxidation, lignoceric acid oxidation was not inhibited by potassium cyanide in either rat liver fractions or human skin cultured fibroblasts, showing that lignoceric acid is mainly and possibly exclusively oxidized in peroxisomes. We also conducted studies to clarify the striking phenotypic differences between CHRS and the childhood form of ALD. In contrast to CHRS, we found normal hepatocellular peroxisomes in the liver biopsy of a childhood ALD patient. In addition, in the presence of potassium cyanide, the oxidation of palmitic acid in cultured skin fibroblasts was inhibited by 62% in control and X chromosome-linked ALD patients compared with 88% in CHRS and neonatal ALD. This differential effect may be related to differences in peroxisomal morphology in those disorders.
Transplantation of Human Umbilical Cord Blood Cells in Macrophage-Depleted SCID Mice: Evidence for Accessory Cell Involvement in Expansion of Immature CD34+CD38−Cells (1998)

In vivo expansion and multilineage outgrowth of human immature hematopoietic cell subsets from umbilical cord blood (UCB) were studied by transplantation into hereditary immunodeficient (SCID) mice. The mice were preconditioned with Cl2MDP-liposomes to deplete macrophages and 3.5 Gy total body irradiation (TBI). As measured by immunophenotyping, this procedure resulted in high levels of human CD45+ cells in SCID mouse bone marrow (BM) 5 weeks after transplantation, similar to the levels of human cells observed in NOD/SCID mice preconditioned with TBI. Grafts containing approximately 107 unfractionated cells, approximately 105purified CD34+ cells, or 5 × 103 purified CD34+CD38− cells yielded equivalent numbers of human CD45+ cells in the SCID mouse BM, which contained human CD34+ cells, monocytes, granulocytes, erythroid cells, and B lymphocytes at different stages of maturation. Low numbers of human GpA+ erythroid cells and CD41+ platelets were observed in the peripheral blood of engrafted mice. CD34+CD38+ cells (5 × 104/mouse) failed to engraft, whereas CD34− cells (107/mouse) displayed only low levels of chimerism, mainly due to mature T lymphocytes. Transplantation of graded numbers of UCB cells resulted in a proportional increase of the percentages of CD45+ and CD34+ cells produced in SCID mouse BM. In contrast, the number of immature, CD34+CD38− cells produced in vivo showed a second-order relation to CD34+graft size, and mice engrafted with purified CD34+CD38− grafts produced 10-fold fewer CD34+ cells without detectable CD34+CD38− cells than mice transplanted with equivalent numbers of unfractionated or purified CD34+ cells. These results indicate that SCID repopulating CD34+CD38− cells require CD34+CD38+ accessory cell support for survival and expansion of immature cells, but not for production of mature multilineage progeny in SCID mouse BM. These accessory cells are present in the purified, nonrepopulating CD34+CD38+ subset as was directly proven by the ability of this fraction to restore the maintenance and expansion of immature CD34+CD38− cells in vivo when cotransplanted with purified CD34+CD38−grafts. The possibility to distinguish between maintenance and outgrowth of immature repopulating cells in SCID mice will facilitate further studies on the regulatory functions of accessory cells, growth factors, and other stimuli. Such information will be essential to design efficient stem cell expansion procedures for clinical use.
Altered GABAA-Benzodiazepine Receptor Number and Pharmacology in the Adult Guinea Pig Cerebral Cortex After Chronic Prenatal Ethanol Exposure (1999)

Background : The effects of chronic prenatal ethanol exposure on GABAA-benzodiazepine receptor number and binding pharmacology were examined in the cerebral cortex of the postnatal guinea pig. Methods : [3H]Flunitrazepam binding to GABAA-benzodiazepine receptors was measured in a cerebral cortical cell membrane preparation obtained at postnatal days 11 (preweaning), 21 (postweaning), and 61 (adulthood). Zolpidem, a GABAA-benzodiazepine type 1 receptor-selective ligand, was used in a [3H]flunitrazepam compctition study. 3α-Hydroxy-5α-pregnan-20-one (allopregnanolone) potentiation of [3H]muscimol and [3H]flunitrazepam binding, and GABA potentiation of [3H]flunitrazepam binding were measured in these same animals. Results : At postnatal day 61, but not at the younger ages studied, the following was observed: (1) [3H]Flunitrazepam binding exhibited an increased receptor number (Bmax) and decreased affinity (increased KD) in the ethanol-treated offspring compared with isocaloric-sucrose (with pair-feeding) and water-treated controls; and (2) the relative proportion of GABAA-benzodiazepine receptors that had high-affinity binding sites for zolpidem was decreased in the ethanol-treated offspring by 31% and 38% compared with the isocaloric-sucrose/pair-fed and water-treated controls, respectively. Chronic prenatal ethanol exposure did not alter the efficiency of coupling between GABA, benzodiazepine, and neurosteroid binding sites at any postnatal ages studied. Conclusions : These results suggest that, in the cerebral cortex of the adult guinea pig, chronic prenatal exposure to ethanol results in increased GABAA-benzodiazepine receptor number, decreased affinity for flunitrazepam, and decreased relative proportion of the GABAA-benzodiazepine type 1 receptor.
River depletion resulting from pumping a well near a river (1954)

A well adjacent to a river will take a portion of its supply from the river A theoretical formula is developed which permits the draft on the river to be computed in terms of the distance of the well from the river, the properties of the aquifer, and time. The formula applies where the river can be considered to flow in a straight course which extends for a considerable distance both upstream and downstream from the well location.
Existence of a Common Glycoprotein Homologous to <italic>S</italic>-Glycoproteins in Two Self-incompatible Homozygotes of <italic>Brassica campestris</italic> (1988)

S-Glycoproteins (S-locus-specific glycoproteins) in Brassica species are present only in stigmas and thought to play an important role in self-incompatibility system. The stigma extract contains also several other glycoproteins reacting with the antiserum to S-glycoproteins, among which some glycoproteins from S8S8- and S9S9-homozygotes have the same pI value. Both of the glycoproteins which were tentatively termed NS8- and NS8S9-glycoproteins, respectively, were isolated and analyzed. Those were revealed to be identical. Its amino acid sequence was homologous with the S-glycoproteins in Brassica species. The NS-glycoproteins were expressed at the same time and only in stigma as S-glycoproteins.
Profiling of Autoantibodies in IgA Nephropathy, an Integrative Antibiomics Approach (2011)

IgAN is associated with elevated IgG autoAbs to multiple proteins in the kidney. This first analysis of the repertoire of autoAbs in IgAN identifies novel, immunogenic protein targets that are highly expressed in the kidney glomerulus and tubules that may bear relevance in the pathogenesis and progression of IgAN.