gebhart/patrepeval huggingface dataset:
Inside Cover: High‐Resolution Electronic Spectroscopy Studies of meta‐Aminobenzoic Acid in the Gas Phase Reveal the Origins of its Solvatochromic Behavior (ChemPhysChem 10/2011) (2011)

Measurements of the ground- and excited-state dipole moments of meta-aminobenzoic acid reveal the existence of push-pull charge reorganization upon UV excitation. The nature of this donor–acceptor interaction is also rotamer-specific, as shown on p. 1808 by D. W. Pratt et al.
Comparison of High-Resolution Ellipsometric and Electroreflectance Spectra of Ge, GaAs, and Si (1974)

Joint-density-of-states third-derivative spectra calculated numerically from high-precision ellipsometric data, are compared to low-field electroreflectance spectra for Ge, GaAs, and Si over the energy range 2.0 – 5.4 eV. Relative magnitudes of interband reduced masses are obtained. The signs of these masses are positive for each critical point observed.
The electrochemical doping reactions of the conducting ladder polymer benzimidazobenzophenanthroline (BBL) (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe electrochemical doping reactions of the conducting ladder polymer benzimidazobenzophenanthroline (BBL)K. Wilbourn and Royce W. MurrayCite this: Macromolecules 1988, 21, 1, 89–96Publication Date (Print):January 1, 1988Publication History Published online1 May 2002Published inissue 1 January 1988https://pubs.acs.org/doi/10.1021/ma00179a019https://doi.org/10.1021/ma00179a019research-articleACS PublicationsRequest reuse permissionsArticle Views1063Altmetric-Citations89LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
MHC class I negative phenotype of disseminated tumor cells in bone marrow is associated with poor survival in R0M0 breast cancer patients (2001)

Changing the major histocompatibility complex (MHC) class I phenotype is a pivotal strategy of tumor cells to circumvent an effective immune response and is associated with tumor progression in cancer patients. Epithelial cells in bone marrow have been detected in various tumor types, but the clinical observation that only a portion of the patients with a positive bone marrow status develops solid bone metastasis suggests a certain molecular equipment of the isolated tumor cells as a prerequisite for metastatic formation. In the present study the prognostic impact of the MHC class I phenotype of disseminated epithelial cells in bone marrow was evaluated in a cohort of 30 curatively resected (R0) patients without distant metastases (M0) (designated R0M0) who had minimal residual disease. Immunocytochemical analysis using the alkaline/anti-alkaline immunogold double staining procedure revealed a heterogeneous MHC class I expression profile [monoclonal antibody (mAb) W6/32] of the epithelial cells (mAb CK2). In 16 patients (53.3%) all epithelial cells were human leukocyte antigen (HLA) class I-positive (CK2+//W6/32+ phenotype). Eight patients (26.7%) showed complete loss of the HLA class I molecules (CK2+//W6/32- phenotype) and in 6 patients (20%) partial loss of HLA class I expression was found (CK2+//W6/32+ and - phenotype). CK2+ cells with the HLA class I negative phenotype (CK2+//W6/32- phenotype and CK2+//W6/32+ and - phenotype) were often derived from poorly differentiated (G3) primary breast carcinomas (p = 0.036) and were associated with short survival of the R0M0 patients (follow-up 15-98 months, log rank p = 0.072). These findings support the necessity to develop immmunotherapeutic strategies leading to the restoration of MHC class I positive phenotype.
Diesel Fuel Aromatic and Cetane Number Effects on Combustion and Emissions From a Prototype 1991 Diesel Engine (1990)

&lt;div class="htmlview paragraph"&gt;A prototype 1991-model diesel engine was tested using EPA transient emissions procedures to determine the effect of fuel properties on combustion characteristics and exhaust emissions. The eleven test fuel set focused primarily on total aromatic content, multi-ring aromatic content, and cetane number, but other fuel variables were also studied. Hydrotreating was used to obtain reductions in fuel sulfur and aromatic content.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Increasing cetane number and reducing aromatic content resulted in lower emissions of hydrocarbons and NOx. Particulate emissions were best predicted by sulfur content, aromatic content and 90% distillation temperature. Multi-ring aromatics showed a greater significance than total aromatics on hydrocarbon and particulate emissions. Combustion parameters were highly dependent on fuel cetane number.&lt;/div&gt;
Heart Hypertrophy and Function Are Improved by Idebenone in Friedreich's Ataxia (2002)

Friedreich's ataxia (FRDA) is a neuro-degenerative disease causing limb and gait ataxia and hypertrophic cardiomyopathy. It results from a triplet expansion in the first intron of the frataxin gene encoding a mitochondrial protein of yet unknown function. Cells with low frataxin content display generalized deficiency of mitochondrial iron-sulfur cluster-containing proteins, which presumably denotes overproduction of superoxide radicals in these organelles. Idebenone, a short-chain quinone, may act as a potent free radical scavenger protecting mitochondria against oxidative stress. We therefore carried out an open trial of idebenone (oral supplementation; 5mg/kg/day) in a large series of FRDA patients and followed their left ventricular mass and function. Consistent and definitive worsening being observed in the natural course of the disease and cardiac hypertrophy having no chance of spontaneous reversal and to be subject to a placebo effect, the patient's heart status before and after the treatment was used to unambiguously establish the effect of the drug. After six months, heart ultrasound revealed more than 20% reduction of left ventricular mass in about half of the patients (p < 0.001) and no significant change in the other half. Since any measurable reversion of this pathogenic trait is highly significant, this demonstrates the efficiency of idebenone in controlling heart hypertrophy in FRDA. Owing to the absence of side effects of the drug, idebenone (up to 15mg/kg/day) should be prescribed for FRDA patients continuously as early as possible.
Performance Trade-offs Implementing Refactoring Support for Objective-C (2009)

When we started implementing a refactoring tool for real-world C programs, we recognized that preprocessing and parsing in straightforward and accurate ways would result in unacceptably slow analysis times and an overly-complicated parsing system. Instead, we traded some accuracy so we could parse, analyze, and change large, real programs while still making the refactoring experience feel interactive and fast. Our tradeoffs fell into three categories: using different levels of accuracy in different parts of the analysis, recognizing that collected wisdom about C programs didn't hold for Objective-C programs, and finding ways to exploit delays in typical interaction with the tool. Categories and Subject Descriptors D.2.6 (Software Engineer-
Massive Intestinal Bleeding in an Adult with IgA Vasculitis Treated with Intravenous Immunoglobulin (2022)

We report the case of a 29-year-old adult presenting with severe IgA vasculitis, with cutaneous, urologic, and renal manifestations. The late appearance of severe gastrointestinal bleeding dominated the clinical picture, necessitating the administration of tens of units of packed cells and the augmentation of the immunosuppressive protocol. It was not until therapy with intravenous immunoglobulin (IVIG) was introduced that the massive bleeding was controlled. We herein discuss the patient's presentation, the gastrointestinal manifestations of IgA vasculitis, the recommended treatments, and the existent evidence about IVIG therapy.
Superionic Conduction in Substoichiometric LiAl Alloy: AnAb InitioStudy (2009)

Based on the new ab initio molecular dynamics method by Kühne et al. [Phys. Rev. Lett. 98, 066401 (2007)10.1103/PhysRevLett.98.066401], we studied the mechanism of superionic conduction in substoichiometric Li-poor Li_{1+x}Al alloys by performing simulations at different temperatures for an overall simulation time of about 1 ns. The dynamical simulations revealed the microscopic path for the diffusion of Li vacancies. The calculated activation energy (0.11 eV) and the prefactor (D_{0} = 6.9 x 10;{-4} cm;{2}/s) for Li diffusivity via a vacancy-mediated mechanism are in good agreement with experimental NMR data. The calculation of the formation energies of different defects-Li and Al Frenkel pair and Li antisites-revealed that only Li;{+} vacancies and Li_{Al} antisites are present in the stability range of the Zintl phase -0.1 < x < 0.2.
Inheritance of Pod Calcium Concentration in Snap Beans (Phaseolus vulgaris L.) (1998)

Significant variation for pod Ca concentration among snap bean genotypes was previously observed. To evaluate and better understand the genetics that control calcium concentration of pods in snap bean, two populations of snap beans were evaluated during the summers of 1995 and 1996 at Hancock, Wis. These populations were Ca2 (`Top Crop' × `Evergreen') and Ca3 (`Slimgreen' × `Evergreen'), therefore forming a half-sib structure. The experimental design used in this experiment was an 8 × 8 double lattice repeated each year. No calcium was added to the plants, which were grown in a sandy loam soil with 1% organic matter and 600 ppm Ca. To ensure proper comparison for pod calcium concentration among cultivars, only commercial sieve size number 4 pods (a premium grade, 8.3 to 9.5 mm in diameter) were sampled and used for calcium extractions. After calcium was extracted, readings for calcium concentration of extracts were made using an atomic absorption spectrophotometer. Statistical analyses resulted in distinct differences among genotypes and between years for pod calcium concentration ( P = 0.01) in both populations. No significant year × genotype interactions were observed. To assess the power of selection for pod calcium concentration in snap beans, variance components and heritabilities are estimated and discussed.
Release and regulation of plasminogen activator and plasminogen activator inhibitor type 1 in cultured human decidual cells (1997)

Objective:To investigate the release and regulation of PAs and PAI 1 from cultured human decidual cells. Design: An in vitro culture study Methods: PAs and PAI 1 activities were determined by SDS PAGE followed by fibrin overlay and reverse overlay techniques. Results:uPA and PAI 1 were released from both cultured human decidual glandular and stromal cells. Estradiol and RU486 enhanced uPA and reduced PAI 1 activities in both cultured cells,while progesterone was affected in the opposite way Conclusion:The balance regulated by estradiol and progesterone between PA and PAI 1 in human decidual cells may be involved in maintenance of pregnancy.The contragestational effect of RU486 may be mediated by increase in uPA activity and decrease in PAI 1 activity.
Preparing a Suitable Material Designed for Methane Storage:  A Comprehensive Report (2005)

The preparation of a suitable material designed for methane storage is addressed in the present paper. The main features of methane as an energy source are first recalled, and adsorption is recognized as one of the most efficient ways of storing it. The ideal adsorbent is described next, and it is argued that the best candidates are among microporous carbonaceous materials. Preparation of the most relevant carbon requires appropriate choice of both the precursor and its mode of activation. A discussion leads to the conclusion that anthracites chemically activated with alkaline hydroxides are especially adapted for the intended application, because the highest intrinsic molar capacities ever found so far in the open literature are obtained. However, because of their low density, only low-volume storage capacities are attained with such materials. It is then shown that simple processing allows a significant densification, and, therefore, the formerly accepted target for a viable application of methane as an alternative fuel150 V/V delivered at 25 °Cis finally met and even exceeded. Thus, the present work is a comprehensive report explaining how a recent problem was solved through a systematical approach.
Amorphous Calcium Phosphate (2001)

ACP is a unique calcium phosphate in that it lacks long-range crystalline order. Yet the constancy in the composition of ACP over a wide range of solution conditions suggests a well-defined local structural unit. Although this order within disorder is the most distinguishing feature of ACP, the solution instability of ACP and its ready transformation into crystalline phases such as OCP and apatite may be of greater biological relevance. In particular, the initiating role ACP plays in matrix vesicle mineralization raises the importance of this phase from a mere laboratory curiosity to that of a key intermediate in skeletal calcification.
Differential Effects of Oligosaccharides, Antioxidants, Amino Acids and PUFAs on Heat/Hypoxia-Induced Epithelial Injury in a Caco-2/HT-29 Co-Culture Model (2023)

(1) Exposure of intestinal epithelial cells to heat and hypoxia causes a (heat) stress response, resulting in the breakdown of epithelial integrity. There are indications that several categories of nutritional components have beneficial effects on maintaining the intestinal epithelial integrity under stress conditions. This study evaluated the effect of nine nutritional components, including non-digestible oligosaccharides (galacto-oligosaccharides (GOS), fructo-oligosaccharides (FOS), chitosan oligosaccharides (COS)), antioxidants (α-lipoic acid (ALA), resveratrol (RES)), amino acids (l-glutamine (Glu), l-arginine (Arg)) and polyunsaturated fatty acids (PUFAs) (docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA)), on heat/hypoxia-induced epithelial injury. (2) Two human colonic cell lines, Caco-2 and HT-29, were co-cultured and pre-treated with the nutritional components for 48 h. After pre-treatment, the cells were exposed to heat/hypoxia (42 °C, 5% O<sub>2</sub>) for 2 h. Epithelial integrity was evaluated by measuring trans-epithelial electrical resistance (TEER), paracellular Lucifer Yellow (LY) permeability, and tight junction (TJ) protein expression. Heat stress and oxidative stress levels were evaluated by determining heat-shock protein-70 (HSP-70) expression and the concentration of the lipid peroxidation product malondialdehyde (MDA). (3) GOS, FOS, COS, ALA, RES, Arg, and EPA presented protective effects on epithelial damage in heat/hypoxia-exposed Caco-2/HT-29 cells by preventing the decrease in TEER, the increase in LY permeability, and/or decrease in TJ proteins zonula occludens-1 (ZO-1) and claudin-3 expression. COS, RES, and EPA demonstrated anti-oxidative stress effects by suppressing the heat/hypoxia-induced MDA production, while Arg further elevated the heat/hypoxia-induced increase in HSP-70 expression. (4) This study indicates that various nutritional components have the potential to counteract heat/hypoxia-induced intestinal injury and might be interesting candidates for future in vivo studies and clinical trials in gastrointestinal disorders related to heat stress and hypoxia.
Activities and Structure-Function Analysis of Fission Yeast Inositol Pyrophosphate (IPP) Kinase-Pyrophosphatase Asp1 and Its Impact on Regulation of pho1 Gene Expression (2022)

Inositol pyrophosphates (IPPs) are signaling molecules that regulate cellular phosphate homeostasis in diverse eukaryal taxa. In fission yeast, mutations that increase 1,5-IP<sub>8</sub> derepress the <i>PHO</i> regulon while mutations that ablate IP<sub>8</sub> synthesis are <i>PHO</i> hyper-repressive. Fission yeast Asp1, the principal agent of 1,5-IP<sub>8</sub> dynamics, is a bifunctional enzyme composed of an N-terminal IPP kinase domain and a C-terminal IPP pyrophosphatase domain. Here we conducted a biochemical characterization and mutational analysis of the autonomous Asp1 kinase domain (aa 1-385). Reaction of Asp1 kinase with IP<sub>6</sub> and ATP resulted in both IP<sub>6</sub> phosphorylation to 1-IP<sub>7</sub> and hydrolysis of the ATP γ-phosphate, with near-equal partitioning between productive 1-IP<sub>7</sub> synthesis and unproductive ATP hydrolysis under optimal kinase conditions. By contrast, reaction of Asp1 kinase with 5-IP<sub>7</sub> is 22-fold faster than with IP<sub>6</sub> and is strongly biased in favor of IP<sub>8</sub> synthesis versus ATP hydrolysis. Alanine scanning identified essential constituents of the active site. We deployed the Ala mutants to show that derepression of <i>pho1</i> expression correlated with Asp1's kinase activity. In the case of full-length Asp1, the activity of the C-terminal pyrophosphatase domain stifled net phosphorylation of the 1-position during reaction of Asp1 with ATP and either IP<sub>6</sub> or 5-IP<sub>7</sub>. We report that inorganic phosphate is a concentration-dependent enabler of net IP<sub>8</sub> synthesis by full-length Asp1 <i>in vitro</i>, by virtue of its antagonism of IP<sub>8</sub> turnover. <b>IMPORTANCE</b> Expression of the fission yeast phosphate regulon is sensitive to the intracellular level of the inositol pyrophosphate (IPP) signaling molecule 1,5-IP<sub>8</sub>. IP<sub>8</sub> dynamics are determined by Asp1, a bifunctional enzyme comprising N-terminal IPP 1-kinase and C-terminal IPP 1-pyrophosphatase domains that catalyze IP<sub>8</sub> synthesis and catabolism, respectively. Here, we interrogated the activities and specificities of the Asp1 kinase domain and full length Asp1. We find that reaction of Asp1 kinase with 5-IP<sub>7</sub> is 22-fold faster than with IP<sub>6</sub> and is strongly biased in favor of IP<sub>8</sub> synthesis versus the significant unproductive ATP hydrolysis seen during its reaction with IP<sub>6</sub>. We report that full-length Asp1 catalyzes futile cycles of 1-phosphate phosphorylation by its kinase component and 1-pyrophosphate hydrolysis by its pyrophosphatase component that result in unproductive net consumption of the ATP substrate. Net synthesis of 1,5-IP<sub>8</sub> is enabled by physiological concentrations of inorganic phosphate that selectively antagonize IP<sub>8</sub> turnover.
Efficient regeneration of NADPH using an engineered phosphite dehydrogenase (2006)

The in situ regeneration of reduced nicotinamide cofactors (NAD(P)H) is necessary for practical synthesis of many important chemicals. Here, we report the engineering of a highly stable and active mutant phosphite dehydrogenase (12x-A176R PTDH) from Pseudomonas stutzeri and evaluation of its potential as an effective NADPH regeneration system in an enzyme membrane reactor. Two practically important enzymatic reactions including xylose reductase-catalyzed xylitol synthesis and alcohol dehydrogenase-catalyzed (R)-phenylethanol synthesis were used as model systems, and the mutant PTDH was directly compared to the commercially available NADP(+)-specific Pseudomonas sp. 101 formate dehydrogenase (mut Pse-FDH) that is widely used for NADPH regeneration. In both model reactions, the two regeneration enzymes showed similar rates of enzyme activity loss; however, the mutant PTDH showed higher substrate conversion and higher total turnover numbers for NADP(+) than mut Pse-FDH. The space-time yields of the product with the mutant PTDH were also up to fourfold higher than those with mut Pse-FDH. In particular, a space-time yield of 230 g L(-1) d(-1) xylitol was obtained with the mutant PTDH using a charged nanofiltration membrane, representing the highest productivity compared to other existing biological processes for xylitol synthesis based on yeast D-xylose converting strains or similar in vitro enzyme membrane reactor systems.
Absolute Proteome Quantification in the Gas-Fermenting Acetogen Clostridium autoethanogenum (2022)

Microbes that can recycle one-carbon (C<sub>1</sub>) greenhouse gases into fuels and chemicals are vital for the biosustainability of future industries. Acetogens are the most efficient known microbes for fixing carbon oxides CO<sub>2</sub> and CO. Understanding proteome allocation is important for metabolic engineering as it dictates metabolic fitness. Here, we use absolute proteomics to quantify intracellular concentrations for >1,000 proteins in the model acetogen Clostridium autoethanogenum grown autotrophically on three gas mixtures (CO, CO+H<sub>2</sub>, or CO+CO<sub>2</sub>+H<sub>2</sub>). We detect the prioritization of proteome allocation for C<sub>1</sub> fixation and the significant expression of proteins involved in the production of acetate and ethanol as well as proteins with unclear functions. The data also revealed which isoenzymes are likely relevant <i>in vivo</i> for CO oxidation, H<sub>2</sub> metabolism, and ethanol production. The integration of proteomic and metabolic flux data demonstrated that enzymes catalyze high fluxes with high concentrations and high <i>in vivo</i> catalytic rates. We show that flux adjustments were dominantly accompanied by changing enzyme catalytic rates rather than concentrations. <b>IMPORTANCE</b> Acetogen bacteria are important for maintaining biosustainability as they can recycle gaseous C<sub>1</sub> waste feedstocks (e.g., industrial waste gases and syngas from gasified biomass or municipal solid waste) into fuels and chemicals. Notably, the acetogen <i>Clostridium autoethanogenum</i> is being used as a cell factory in industrial-scale gas fermentation. Here, we perform reliable absolute proteome quantification for the first time in an acetogen. This is important as our work advances both rational metabolic engineering of acetogen cell factories and accurate <i>in silico</i> reconstruction of their phenotypes. Furthermore, this absolute proteomics data set serves as a reference toward a better systems-level understanding of the ancient metabolism of acetogens.
Comparison of joint space versus task force load distribution optimization for a multiarm manipulator system (1989)

It is often proposed that the redundancy in choosing a force distribution for multiple arms grasping a single object should be handled by minimizing a quadratic performance index. The performance index may be formulated in terms of joint torques or in terms of the Cartesian space force/torque applied to the body by the grippers. The former seeks to minimize power consumption while the latter minimizes body stresses. Because the cost functions are related to each other by a joint angle dependent transformation on the weight matrix, it might be argued that either method tends to reduce power consumption, but clearly the joint space minimization is optimal. A comparison of these two options is presented with consideration given to computational cost and power consumption. Simulation results using a two arm robot system are presented to show the savings realized by employing the joint space optimization. These savings are offset by additional complexity, computation time and in some cases processor power consumption.