gebhart/patrepeval huggingface dataset:
CO Adsorption on (110)-(1 × 2) Missing-Row Reconstructed Surfaces of Pd, Au, and Pd<sub>3</sub>Au: Electronic Structures and Vibrational Frequencies (2017)

The adsorption of CO molecule on (110)-(1 × 2) missing-row reconstructed surfaces of Pd, Au, and Pd3Au with 87.5% Au segregation in the topmost layers were investigated by first-principles calculations based on density functional theory. On a pure Pd surface, CO is preferencially adsorbed on pseudo-fcc hollow site near the ridge sites. On pure Au and alloy surfaces, generally the ridge sites are the most stable for adsorption. The charge accumulation between the C atom and the surface atoms explains the calculated adsorption energies, with higher charge accumulation yielding a higher binding energy. The interaction of CO with the surfaces and the adsorption energies were also analyzed using the crystal orbital overlap population (COOP) technique and by considering the d-band model. CO vibrational modes were experimentally investigated for comparison. The vibrational frequencies are strongly influenced by the number of nearest neighbors of surface atoms as well as the type of atoms that constitute the nearest neighbors. In general, fewer nearest neighbors for the CO adsorption site results in higher vibrational frequencies. For adsorption sites with a certain number of nearest neighbors, the presence of Pd slightly decreases the vibrational frequencies. This observation is attributed to the broadening and the population of the derived 2π* orbital of CO upon its interaction with the surface.
Dystrophin is a component of the subsynaptic membrane. (1991)

A subsynaptic protein of Mr approximately 300 kD is a major component of Torpedo electric organ postsynaptic membranes and copurifies with the AChR and the 43-kD subsynaptic protein. mAbs against this protein react with neuromuscular synapses in higher vertebrates, but not at synapses in dystrophic muscle. The Torpedo 300-kD protein comigrates in SDS-PAGE with murine dystrophin and reacts with antibodies against murine dystrophin. The sequence of a partial cDNA isolated by screening an expression library with mAbs against the Torpedo 300-kD protein shows striking homology to mammalian dystrophin, and in particular to the b isoform of dystrophin. These results indicate that dystrophin is a component of the postsynaptic membrane at neuromuscular synapses and raise the possibility that loss of dystrophin from synapses in dystrophic muscle may have consequences that contribute to muscular dystrophy.
Escherichia coli iron enterobactin uptake monitored by Mössbauer spectroscopy (1986)

Iron uptake by Escherichia coli under aerobic conditions of iron deficiency is mediated by a highly stable ferric enterobactin [Fe(ent)3-] siderophore complex. Mössbauer spectroscopy has been used to monitor the fate of the iron as 57Fe(ent) was taken up by the cells. Osmotic shock experiments were used to distinguish between the iron present in the periplasmic space and that in the cytoplasm of the cell. Iron delivery by a synthetic analog of enterobactin, 1,3,5-N,N',N''- tris-(2,3-dihydroxybenzoyl)triaminomethylbenzene (MECAM), was also studied. Although Fe-MECAM was transported at the same rate as was Fe(ent) across the outer membrane and was apparently accumulated in the periplasmic space, the subsequent behaviors of Fe(ent) and Fe-MECAM were very different. After more than 30 min, a major fraction of the iron originally absorbed as ferric enterobactin appeared as Fe(II), apparently in the cytoplasm of the cell. However, little iron was delivered to the cytoplasm by the MECAM complex. The differences in specificity of these two stages of iron uptake by E. coli are discussed.
<i>SOX12</i> and <i>NRSN2</i> are candidate genes for 20p13 subtelomeric deletions associated with developmental delay (2013)

20p13 telomeric/subtelomeric deletions are clinically significant but are currently under-investigated. So far only five molecularly delineated cases have been reported in literature and no candidate genes have been sufficiently implicated. Here, we present six new deletion cases identified by chromosomal microarray analysis (CMA). We also review 32 cases combined from literature and databases. We found that most 20p13 deletion patients exhibit significant developmental delay. Dysmorphic features are common but a consistent pattern was not recognized. Reduced cognitive ability was frequent. Based on pathogenic deletions delineated in this study, we mapped the smallest overlapping region and identified two nervous system expressing genes (SOX12 and NRSN2) as candidate genes that may be involved in the developmental defects in 20p13 microdeletion.
The impact of spatial layout of jobs on parallel I/O performance (1999)

Input/Output is a big obstacle to effective use of tenflops- scale computing systems, Motivated by earlier parallel I/O meaurements on an Intel TFLOPS machine, we conduct studies to determine the sensitivity of parallel I/O performance on multi-progmmmed mesh-connected machines with respect to number of I/O nodes, number of compute nodes, network link bandwidth, I/O node bandwidth, spatial layout of jobs, and read or write demands of applications.
ChemInform Abstract: Cycloadditions in Synthesis. Part 66. Addition of Molecular Fluorine to Azlactones: General Synthetic Method of erythro‐β‐Fluorinated . alpha.‐Amino Acids (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
<i>In vivo</i> evaluation of protein adsorption to sterically stabilised colloidal carriers (1993)

A diffusion chamber implanted intraperitoneally in the rabbit was employed as an in vivo model to evaluate the interaction of peritoneal proteins with block copolymer (poloxamer and poloxamine)-coated polystyrene microspheres (PS). Using a desorption technique followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, six proteins of 94, 86, 66, 53, 40, and 20 kDa were desorbed from the carrier systems after incubation with peritoneal fluid in vitro. The 40- and 20-kDa proteins dominated the protein profile. A similar pattern was observed when proteins were desorbed from PS microspheres removed after 24-h implantation in chambers in the peritoneal cavity, although the protein profile was dominated by the 94- and 53-kDa proteins. In general, coating of PS with block copolymers reduced the amount of protein bound to the microspheres in vitro and in vivo but did not change the types of proteins bound.
In vitro bone inducing effects of Lentinula edodes (shiitake) water extract on human osteoblastic cell cultures (2013)

The effect of Lentinula edodes water extract (LE) on two osteoblastic cell cultures (HOS 58 and Saos-2) was investigated to determine if this edible medicinal mushroom has osteoinductive properties. Activity of alkaline phosphatase and mineralization were used as indicators for the vitality and maturation of the bone cells. Cultivation of human osteosarcoma cells HOS 58 for five days in presence of a serial dilution of the aqueous extract of L. edodes (0.8 μg/mL-125 μg/mL) resulted in a significant elevation of alkaline phosphatase activity (ALP) of the cells in comparison to untreated cells. Saos-2 cells, incubated with LE (20 μg/mL) and β-glycerol phosphate (2 mM) for 21 days, displayed a 2 fold level of mineralization than cells cultured soley with the positive control, β-glycerophosphate. The obtained results clearly indicate the activity of LE as a bone inducing agent in vitro. Therefore, the shiitake mushroom (L. edodes) deserves attention as a supportive dietary treatment or nutraceutical in the case of diseases accompanied with bone disorder, such as osteoporosis, osteopenia, and late complication of diabetes.
The Approach to Conception for Women with Seminal Plasma Protein Hypersensitivity (2004)

This case report emphasizes that SPH is not associated with sterility. It also indicates that whole seminal plasma graded challenge is not uniformly successful for the treatment of SPH.
A computational tool for automatic selection of total knee replacement implant size using X-ray images (2022)

<b>Purpose:</b> The aim of this study was to outline a fully automatic tool capable of reliably predicting the most suitable total knee replacement implant sizes for patients, using bi-planar X-ray images. By eliminating the need for manual templating or guiding software tools via the adoption of convolutional neural networks, time and resource requirements for pre-operative assessment and surgery could be reduced, the risk of human error minimized, and patients could see improved outcomes. <b>Methods:</b> The tool utilizes a machine learning-based 2D-3D pipeline to generate accurate predictions of subjects' distal femur and proximal tibia bones from X-ray images. It then virtually fits different implant models and sizes to the 3D predictions, calculates the implant to bone root-mean-squared error and maximum over/under hang for each, and advises the best option for the patient. The tool was tested on 78, predominantly White subjects (45 female/33 male), using generic femur component and tibia plate designs scaled to sizes obtained for five commercially available products. The predictions were then compared to the ground truth best options, determined using subjects' MRI data. <b>Results:</b> The tool achieved average femur component size prediction accuracies across the five implant models of 77.95% in terms of global fit (root-mean-squared error), and 71.79% for minimizing over/underhang. These increased to 99.74% and 99.49% with ±1 size permitted. For tibia plates, the average prediction accuracies were 80.51% and 72.82% respectively. These increased to 99.74% and 98.98% for ±1 size. Better prediction accuracies were obtained for implant models with fewer size options, however such models more frequently resulted in a poor fit. <b>Conclusion:</b> A fully automatic tool was developed and found to enable higher prediction accuracies than generally reported for manual templating techniques, as well as similar computational methods.
Robust nanoscopy of a synaptic protein in living mice by organic-fluorophore labeling (2018)

Extending superresolution fluorescence microscopy to living animals has remained a challenging frontier ever since the first demonstration of STED (stimulated emission depletion) nanoscopy in the mouse visual cortex. The use of fluorescent proteins (FPs) in in vivo STED analyses has been limiting available fluorescence photon budgets and attainable image contrasts, in particular for far-red FPs. This has so far precluded the definition of subtle details in protein arrangements at sufficient signal-to-noise ratio. Furthermore, imaging with longer wavelengths holds promise for reducing photostress. Here, we demonstrate that a strategy based on enzymatic self-labeling of the HaloTag fusion protein by high-performance synthetic fluorophore labels provides a robust avenue to superior in vivo analysis with STED nanoscopy in the far-red spectral range. We illustrate our approach by mapping the nanoscale distributions of the abundant scaffolding protein PSD95 at the postsynaptic membrane of excitatory synapses in living mice. With silicon-rhodamine as the reporter fluorophore, we present imaging with high contrast and low background down to ∼70-nm lateral resolution in the visual cortex at ≤25-µm depth. This approach allowed us to identify and characterize the diversity of PSD95 scaffolds in vivo. Besides small round/ovoid shapes, a substantial fraction of scaffolds exhibited a much more complex spatial organization. This highly inhomogeneous, spatially extended PSD95 distribution within the disk-like postsynaptic density, featuring intricate perforations, has not been highlighted in cell- or tissue-culture experiments. Importantly, covisualization of the corresponding spine morphologies enabled us to contextualize the diverse PSD95 patterns within synapses of different orientations and sizes.
ChemInform Abstract: ((9‐Fluorenylmethyl)oxy)carbonyl Amino Acid Chlorides in Solid‐Phase Peptide Synthesis. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A Pilot Plant Scale Reactor/Separator for Ethanol from Cellulosics. ERIP/DOE Quarterly Reports 7, 8 and Final report (1999)

The objective of this project was to develop and demonstrate a continuous low energy process for the conversion of cellulosics to ethanol. BPI's process involves a proprietary low temperature pretreatment step which allows recycle of the pretreatment chemicals and recovery of a lignin stream. The pretreated biomass is then converted to glucans and xylans enzymatically and these sugars simultaneously fermented to ethanol (SSF) in BPI's Continuous Stirred Reactor Separator (CSRS). The CSRS is a multi stage bio-reactor where the glucans are first converted to ethanol using a high temperature tolerant yeast stran, followed by xylan SSF on the lower stages using a second xylose fermenting yeast strain. Ethanol is simultaneously removed from the bio-reactor stages, speeding the fermentation, and allowing the complete utilization of the biomass.
Quantifying the axonal pathways directly stimulated in therapeutic subcallosal cingulate deep brain stimulation (2018)

Deep brain stimulation (DBS) of the subcallosal cingulate (SCC) is an emerging experimental therapy for treatment-resistant depression. New developments in SCC DBS surgical targeting are focused on identifying specific axonal pathways for stimulation that are estimated from patient-specific computational models. This connectomic-based biophysical modeling strategy has proven successful in improving the clinical response to SCC DBS therapy, but the DBS models used to date have been relatively simplistic, limiting the precision of the pathway activation estimates. Therefore, we used the most detailed patient-specific foundation for DBS modeling currently available (i.e., field-cable modeling) to evaluate SCC DBS in our most recent cohort of six subjects, all of which were responders to the therapy. We quantified activation of four major pathways in the SCC region: forceps minor (FM), cingulum bundle (CB), uncinate fasciculus (UF), and subcortical connections between the frontal pole and the thalamus or ventral striatum (FP). We then used the percentage of activated axons in each pathway as regressors in a linear model to predict the time it took patients to reach a stable response, or TSR. Our analysis suggests that stimulation of the left and right CBs, as well as FM are the most likely therapeutic targets for SCC DBS. In addition, the right CB alone predicted 84% of the variation in the TSR, and the correlation was positive, suggesting that activation of the right CB beyond a critical percentage may actually protract the recovery process.
Research findings and strategies to reduce risks of the bioherbicide, Myrothecium verrucaria. (2005)

Studies were conducted on a Myrothecium verrucaria (MV) fungal isolate from sicklepod (Senna obtusifolia L.) that exhibits bioherbicidal activity against kudzu [Pueraria lobata (Willd.) Ohwi] and several other weeds. Treatments of MV plus the surfactant SilWet L-77 caused 100% mortality or control to kudzu seedlings under greenhouse conditions, and 90 to 100% control of older kudzu plants in naturally-infested and experimental kudzu plots, respectively. MV caused greater reductions of kudzu plant biomass production at 30°C, compared to 20 or 40°C in environmental chamber experiments. Responses of various non-target, young, woody plant species from several plant families to MV ranged from non-susceptible to moderately-susceptible. Bioassays of MV on seed germination and early growth of sicklepod and hemp sesbania demonstrated that hemp sesbania was more sensitive than sicklepod. Although MV possess desirable bioherbicidal traits such as high efficacy and the ability to control several species of weeds, this isolate also produces unwanted mycotoxins, i.e., trichothecenes. Data on this research is presented, as well as discussion of some future approaches to reduce or eliminate these mycotoxins in order to develop a safe and efficacious bioherbicide. Media Summary Myrothecium verrucaria is a fungal phytopathogen with significant bioherbicidal activity on several economically important weeds, but it also produces undesirable mycotoxins. Research data and general strategies for reducing the mycotoxin levels in this bioherbicide are presented.
Breaking lignin: blue and yellow laccases for a green chemistry (2015)

Lignin is an amorphous polymer with a molecular mass around 10 kDa that presents a three-dimensional structure disordered and branched, insoluble in water and most common solvents. During the industrial processes, lignin must be degraded and effectively removed. Enzymatic hydrolysis could be an environmentally friendly alternative to chemical methods to perform lignin degradation. The identification of enzymes able to efficiently fragmenting lignin, i.e., an "enzymatic tool box", is of utmost importance. On this side, laccase represents an enzymatic class of main relevance.&#13;\nLaccases are attracting great scientific interest because of their very basic requirements and huge catalytic capabilities: this renders it one of the ‘‘greenest’’ enzymes [1]. &#13;\nIn order to identify interesting lignin degrading biocatalysts, in this study we evaluated the main biochemical properties of a number of commercial and recombinant laccases under identical experimental conditions. The kinetic properties of laccases has been determined on 3 substrates: ABTS, catechol and 2,6-dimethoxyphenol (2,6-DMP). The microbial Bacillus licheniformis laccase (BALL) showed the highest specific activity and catalytic efficiency on ABTS, while the recombinant OB1 from Basidiomycete PM-1 showed the highest affinity for this compound [2]. The stability on pH, temperature, detergents and DMSO of the different laccases was also assessed. &#13;\nFinally, a change in MW distribution after incubation of lignin with the laccase from Trametes versicolor was observed in gel permeation chromatography.&#13;\n&#13;\nThis work was done as part of the ValorPlus project that has received funding from the European Union's Seventh Framework Programme for research, technological development and demonstration under grant agreement no FP7-KBBE-2013-7-613802.&#13;\n&#13;\n[1] L. Pollegioni, F. Tonin, E. Rosini, FEBS J. 282 (7) (2015) 1190-1213&#13;\n[2] F. Tonin, R. Melis, A. Cordes, A. Sanchez-Amat, L. Pollegioni, E. Rosini, Submitted
Identification of the Active-site Arginine in Rat Neutral Endopeptidase 24.11 (Enkephalinase) as Arginine 102 and Analysis of a Glutamine 102 Mutant (1989)

Neutral endopeptidase 24.11 contains an active-site arginine residue involved in binding the free carboxylate of substrate peptides and inhibitors. This arginine reacts rapidly with [14C]phenylglyoxal, and its reaction is selectively blocked by the presence of either the substrate Met5-enkephalin, the competitive inhibitor phenylalanylalanine, or the transition state analog phosphoramidon. The phenylglyoxal-modified peptide was isolated by a procedure involving limited digestion by trypsin, separation of the tryptic peptides by high pressure liquid chromatography (HPLC), further digestion of the modified peptide by pepsin, and a final purification by HPLC. By this procedure arginine 102 was identified as the active-site arginine. Verification of this finding came from the use of site-directed mutagenesis in which this arginine was replaced by glutamine. Both the mutant and wild-type enzyme reacted equally well with an amide containing substrate, glutaryl-Ala-Ala-Phe-4-methoxy-2-naphthylamide. However, reaction of the mutant enzyme with a substrate containing a free COOH-terminal carboxylate, 5-dimethylaminonaphthalene-1-sulfonyl-D-Ala-Gly-(NO2)Phe-Gly, was barely detectable with the mutant enzyme. Similarly the mutant enzyme showed a loss of selectivity in inhibition by D-Ala2-Met5-enkephalin compared to the corresponding amide but exhibited no difference in the maximal velocity for hydrolysis of D-Ala2-Met5-enkephalin and its amide.
Influence of different magnetites on properties of magnetic <i>Pseudomonas aeruginosa</i> immobilizates used for biosurfactant production (2009)

During the last decades, whole-cell immobilization has been used successfully in many bioprocesses. In particular, it is aimed at implementing continuous production processes, reaching higher production rates, and reusing the biocatalyst. In some cases, effective retention of immobilizates in the bioprocess is not feasible by membranes or sieves due to pore plugging or undesired losses of immobilizates. In the present publication, it is reported about the investigation of magnetic immobilizates of Pseudomonas aeruginosa for application in continuous biosurfactant production of rhamnolipids by foam fractionation and retention of entrained immobilizates by high-gradient magnetic separation from foam. Different materials and methods were tested with respect to important parameters, such as stability, diffusion properties or magnetic separation. Good magnetic separation of immobilizates was achieved at 5% (w/w) magnetite loading. Best results in terms of homogeneous embedding, good diffusion properties, and stability enhancement vis-à-vis pure alginate beads was achieved with alginate beads with embedded Bayoxide magnetite or MagPrep silica particles. Although polyurethane immobilizates showed higher stabilities compared with alginate beads, rhamnolipid diffusion in immobilizates was superior in magnetic alginate beads. Regarding bead production, smaller immobilizates were achieved with suspension polymerization compared to droplet extrusion by the JetCutting technology. In total, magnetic immobilizates are a promising tool for an easier handling of biocatalysts in a continuous biological production process, but they have to be adapted to the current production task.
High temperature fuel cell, which is an electrochemical energy converter, comprises a ferritic component and a nickel component and an intermediate barrier layer, which consists of e.g. cerium oxide (2006)

TECHNOLOGY FOCUS - INORGANIC CHEMISTRY - Preferred Components: The barrier layer consists of cerium dioxide. The barrier layer is endowed with yttrium, gadolinium, niobium or samarium. The barrier layer covers at least on one side of the ferritic component, as thin, preferably thick film. The barrier layer is not thicker than 10 mu m, preferably thinner than 2 mu m. The ferritic component is a porous metallic substrate and the nickel component is an anode. The ferritic component is an inter-connector and the nickel component is a nickel network. The barrier layer consists of: (calcium, strontium, barium)1-3x/2 (yttrium, lanthanide (ln))x titanium oxide (where Xy is 0-0.1 and/or Xln is 0-0.67); chromium oxide and/or chromium(II, III) oxide, manganese(II, III) oxide; iron(II) oxide and/or iron(II, III) oxide; cerium1-x-y (yttrium, lanthanide)x (titanium, niobium)yO2 (where x is 0-0.5 and y is 0-0.2); lanthanide1-x(strontium, calcium)x (magnesium oxide (mgO3)) aluminum oxide (AlO3), chromium oxide (CrO3) (where x is 0.1-0.5).