gebhart/patrepeval huggingface dataset:
A novel aldose-aldose oxidoreductase for co-production of D-xylonate and xylitol from D-xylose with Saccharomyces cerevisiae (2015)

An open reading frame CC1225 from the Caulobacter crescentus CB15 genome sequence belongs to the Gfo/Idh/MocA protein family and has 47 % amino acid sequence identity with the glucose-fructose oxidoreductase from Zymomonas mobilis (Zm GFOR). We expressed the ORF CC1225 in the yeast Saccharomyces cerevisiae and used a yeast strain expressing the gene coding for Zm GFOR as a reference. Cell extracts of strains overexpressing CC1225 (renamed as Cc aaor) showed some Zm GFOR type of activity, producing D-gluconate and D-sorbitol when a mixture of D-glucose and D-fructose was used as substrate. However, the activity in Cc aaor expressing strain was >100-fold lower compared to strains expressing Zm gfor. Interestingly, C. crescentus AAOR was clearly more efficient than the Zm GFOR in converting in vitro a single sugar substrate D-xylose (10 mM) to xylitol without an added cofactor, whereas this type of activity was very low with Zm GFOR. Furthermore, when cultured in the presence of D-xylose, the S. cerevisiae strain expressing Cc aaor produced nearly equal concentrations of D-xylonate and xylitol (12.5 g D-xylonate l(-1) and 11.5 g D-xylitol l(-1) from 26 g D-xylose l(-1)), whereas the control strain and strain expressing Zm gfor produced only D-xylitol (5 g l(-1)). Deletion of the gene encoding the major aldose reductase, Gre3p, did not affect xylitol production in the strain expressing Cc aaor, but decreased xylitol production in the strain expressing Zm gfor. In addition, expression of Cc aaor together with the D-xylonolactone lactonase encoding the gene xylC from C. crescentus slightly increased the final concentration and initial volumetric production rate of both D-xylonate and D-xylitol. These results suggest that C. crescentus AAOR is a novel type of oxidoreductase able to convert the single aldose substrate D-xylose to both its oxidized and reduced product.
The Long-term Outcomes of Kidney Transplantation from Donation after Circulatory Death during Brain Death Donor Evaluation in a Single Center in Korea (2015)

Nayoon Hur, M.D., Hyojun Park, M.D., Kyowon Lee, M.D., Gyuseong Choi, M.D., Jong Man Kim, M.D., Jae Berm Park, M.D., Choon Hyuck Kwon, M.D., Sung Joo Kim, M.D., Jae-Won Joh, M.D.and Suk-Koo Lee, M.D.. J Korean Soc Transplant 2015;29:216-26. https://doi.org/10.4285/jkstn.2015.29.4.216
Monolithically Integrated, Sampled Grating DBR Laser Transmitter with an Asymmetric Quantum Well Electroabsorption Modulator (2006)

We present the first widely-tunable transmitter that employs intra-step quantum wells for intensity modulation. Fiber coupled output power is >2 dBm with tuning range >40 nm. EAMs show modulation depths >20 dB, slope efficiency >7 dB/V, and 10 bandwidth
Hydroxyapatite for Keratoprosthesis Biointegration (2011)

These results are encouraging for the potential of HAp-coated surfaces for use in keratoprostheses.
Dependence of H2O/CO2Co-Electrolysis Performance of SOEC on Microstructural and Thermodynamic Parameters (2016)

High temperature co-electrolysis of steam and CO2 based on solid oxide electrolysis cell (SOEC) to produce syngas as a feedstock for the well-known Fischer-Tropsch process is the main aim of the present research. Here Ni-8YSZ/8YSZ/LSCF6428-GDC button cells have been fabricated and the effect of the different microstructural parameters like air electrode thicknesses, fuel electrode porosities, adhesion layer and thermodynamic parameters like gas composition, temperature, on the performance of SOEC has been investigated systematically. The SOEC with 10 μm air electrode thickness, functional layer, fuel electrode having 20 vol% PMMA content, addition of YSZ-GDC adhesion layer gives the better performance in overall results and the voltage obtained for this SOEC at current density of 0.8 A.cm−2 is ∼1.25 V at 800°C in 49% N2, 5% H2, 23% CO2 and 23% H2O gas mixture at fuel electrode side. To identify the electrochemical processes occurring at the electrodes of SOEC, distribution function of relaxation time (DRT) analysis of the electrochemical impedance (EIS) data is carried out.
Treating multiple antiaging pathways improves health markers in open label clinical study (2017)

Research indicates that aging and health are affected by hundreds of biochemical pathways. Our hypothesis is that a multipath intervention strategy directed at multiple aging pathways may promote overall health. The objective of the study was to test the effects of a multipath antiaging dietary supplement on healthy adults using known markers of health. The design of the dietary supplement intervention clinical study was an open-label field study. Fifteen men and women aged 42 to 79 years took a 10 component dietary supplement SC100+ twice daily for 15 weeks. Markers of overall health and life expectancy were measured at baseline and after 15 weeks of treatment. The markers included blood pressure, heart rate, HDL and Total Cholesterol, Stress levels, Lung capacity, and HbA1c. Paired two-sided Student t-tests were performed to evaluate the significance of the differences between baseline and post treatment. Mean laboratory measurements taken at baseline and after 15 weeks of SC100+ showed: 1) Systolic and diastolic blood pressure were both reduced (SBP -10.1 +/− 6.37 mmHg, p = 0.013 and DBP -4.6 +/− 4.17 mmHg, p = 0.048); 2) Stress as measured by heart rate variability was reduced (−25%, p = 0.017); 3) HDL cholesterol was increased (7.9 +/− 2.9 mg/dL, p = 0.005); and 4) Lung capacity was increased (+16.6%, p = 0.001). There were no significant changes in heart rate, total cholesterol, or HbA1c levels and no reported side effects. Targeting multiple aging pathways has the potential to significantly reduce blood pressure and stress, while significantly increasing HDL Cholesterol levels and lung capacity. Targeting multiple critical aging pathways with a single dietary supplement is a novel alternative strategy to promote overall health. The open label pilot study was registered retrospectively on Feb. 8, 2017 ( NCT03052491 ).
Experimental and numerical investigation of the effect of key joint variables on the static and fatigue performance of bonded metallic single-lap joints (2014)

AbstractIn this paper, numerical and experimental methods are employed to investigate the effect of surface preparation, adhesive type and thickness, and nanoparticle enrichment on the mechanical performance of bonded metallic single-lap joints. Adherents are made of similar materials; namely, steel-on-steel or aluminum-on-aluminum. Investigated surface preparation variables include roughness and scratch orientation. Adhesive-related variables include thickness, type, and nanoparticle enrichment. Four different commercially available adhesives are investigated, some of which are nanoparticle enriched for the purpose of this study. Static and/or fatigue testing as well as damage analysis-based numerical prediction of joint performance, are provided. Scanning Electron Microscope (SEM) is used for macro joint characterization through the micro observation of joint fracture surfaces. Experimental fatigue data correlates reasonably well with the numerical results obtained from damage-coupled cohesive model of the adhesive layer.Keywords: adhesive-bonded jointnanoparticle enrichmentdamage-coupled cohesive modelUSDFLD AcknowledgmentOakland University would like to acknowledge the US Army TARDEC for supporting this work as part of a cooperative contract DAAE-03-C-L110 under the supervision of Sayed Nassar (PI). A significant part of this work was a collaborative sub-contract from Oakland University to Wayne State University, Xin Wu (PI). The authors gratefully acknowledge all the help provided by Moustapha Diab and Kassem Moustafa (of FAJRI-OU) during this manuscript preparation.
Monitoring copopulated conformational states during protein folding events using electrospray ionization-ion mobility spectrometry-mass spectrometry (2007)

The precise mechanism of protein folding remains elusive and there is a deficiency of biophysical techniques that are capable of monitoring the individual behavior of copopulated protein conformers during the folding process. Herein, an ion mobility spectrometry (IMS) device integrated with electrospray ionization mass spectrometry (ESI-MS) has been used to successfully separate and analyze protein conformers differing in cross section and/or charge state. In an initial test, an ensemble of folded and partially folded conformers of the protein cytochrome c was separated. A detailed study undertaken on the amyloidogenic protein beta(2)-microglobulin (beta(2)m), which forms fibrils by protein unfolding followed by self-aggregation and is responsible for the disease dialysis-related amyloidosis, has generated important insights into its folding landscape. Initially, a systematic titration of beta(2)m over the pH range 2 to 7 using ESI-IMS-MS allowed individual conformers to be monitored and quantified throughout the acid denaturation process. Furthermore, a comparison of wild-type beta(2)m with single and double amino acid variants with a range of folding stabilities and propensities for amyloid fibril formation has provided illuminating evidence of the role of different conformers in protein stability and amyloidogenic aggregation. The ESI-IMS-MS data presented here not only demonstrate an important and informative further dimension to ESI-MS, but also illustrate the potential of the ESI-IMS-MS technique for unravelling protein folding enigmas in general and studying protein misfolding diseases in particular.
Endophenazines A—D, New Phenazine Antibiotics from the Athropod Associated Endosymbiont Streptomyces anulatus. Part 2. Structure Elucidation. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Base‐Free Hydrogenation of Carbon Dioxide to Methyl Formate with a Molecular Ruthenium‐Phosphine Catalyst (2019)

Abstract Herein, a molecular ruthenium‐phosphine catalyst system for the effective base‐free methyl formate production from carbon dioxide is described. In detail, the novel [Ru(N‐triphos Cy )(tmm)] complex, bearing sterically demanding cyclohexyl groups in the triphos‐ligand structure, enabled in combination with the Lewis acid Al(OTf) 3 the selective transformation of carbon dioxide to methyl formate with unprecedented activity. From a mechanistic perspective, in the initial step formic acid is formed, undergoing a consecutive Lewis acid promoted esterification with methanol to methyl formate. This selective transformation with carbon dioxide paves the way to versatile processes for important C 1 building blocks.
Phosphonates and Phosphinates: Novel Leaving Groups for Benzisothiazolone Inhibitors of Human Leukocyte Elastase (1995)

A novel class of alkyl and aryl phosphonate and phosphinate acid-based leaving groups has been developed for utilization in the synthesis of benzoisothiazolone (BIT) inhibitors of human leukocyte elastase (HLE). A number of BITs were synthesized with phosphonate and phosphinate acid-based leaving groups and were found to be potent inhibitors of HLE. Compound 3c with a diethyl phosphonate leaving group is the most potent inhibitor synthesized in this series with Ki* = 0.035 nM and ED50 = 2.0 mg/kg.
ChemInform Abstract: A Practical Synthesis of Enantiopure Ethyl cis‐2‐Amino‐1‐cyclohexanecarboxylate via Asymmetric Reductive Amination Methodology. (1997)

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.
Source localization using a maximum likelihood/semidefinite programming hybrid (2008)

This paper considers source localization using Received Signal Strength (RSS) values at sensor locations, under the assumption of lognormal shadowing. It is known that such localization can be sensitive to path loss parameter estimates. We derive a cost function whose global minimum provides the ML estimate of the source localization. It turns out that this cost function is manifested with multiple local minima, leading to potentially poor gradient descent performance. The contribution of this paper are two fold. First, we show that in the noise free case the local minima are insensitive to the path loss parameter value. Traditional nonlinear stability theory suggests that this would imply an insensitivity of the ML algorithm to the value of the path loss parameter. Second, we propose a SDP based algorithm to initialize the ML minimization algorithm, that provides good performance, by avoiding local minima.
Bacillus anthracisEdema Toxin Impairs Neutrophil Actin-Based Motility (2009)

Inhalation anthrax results in high-grade bacteremia and is accompanied by a delay in the rise of the peripheral polymorphonuclear neutrophil (PMN) count and a paucity of PMNs in the infected pleural fluid and mediastinum. Edema toxin (ET) is one of the major Bacillus anthracis virulence factors and consists of the adenylate cyclase edema factor (EF) and protective antigen (PA). Relatively low concentrations of ET (100 to 500 ng/ml of PA and EF) significantly impair human PMN chemokinesis, chemotaxis, and ability to polarize. These changes are accompanied by a reduction in chemoattractant-stimulated PMN actin assembly. ET also causes a significant decrease in Listeria monocytogenes intracellular actin-based motility within HeLa cells. These defects in actin assembly are accompanied by a >50-fold increase in intracellular cyclic AMP and a >4-fold increase in the phosphorylation of protein kinase A. We have previously shown that anthrax lethal toxin (LT) also impairs neutrophil actin-based motility (R. L. During, W. Li, B. Hao, J. M. Koenig, D. S. Stephens, C. P. Quinn, and F. S. Southwick, J. Infect. Dis. 192:837-845, 2005), and we now find that LT combined with ET causes an additive inhibition of PMN chemokinesis, polarization, chemotaxis, and FMLP (N-formyl-met-leu-phe)-induced actin assembly. We conclude that ET alone or combined with LT impairs PMN actin assembly, resulting in paralysis of PMN chemotaxis.
Characterization on the impact of different clarifiers on the white wine colloids using Asymmetrical Flow Field-Flow Fractionation (2022)

Clarifiers are substances used during the winemaking process to enhance clarity and stability in the wines. The different clarifiers may alter removal capacities differently. In this study, the removal efficiency of seven common fining agents, divided into three groups (mineral clarifiers, synthetic polymeric clarifiers, and vegetable protein clarifiers), was analyzed with Asymmetrical Flow Field-Flow fractionation (AF4). Besides, the relationship between the removal capacity and different molecular and macromolecular properties has been evaluated. The results showed extensive removal of colloidal and macromolecular matter by the bentonites with potential impact on characteristic properties of the wine. The vegetable clarifiers showed a more profiled reduction, potentially preserving characteristics of the wine. The synthetic polymers showed a more limited removal efficiency but with a high affinity to remove colloidal phenols. The use of AF4-UV-MALS-dRI allowed the characterization of the wines after different clarification treatments, showing to be an analytical technique with a potential impact on the wine industry.
Factors That May Influence Social Communication Questionnaire (SCQ) Scores: An Examination of the Spanish and English SCQ in School-Aged Students (2021)

This study examined child and family factors that may influence the Social Communication Questionnaire (SCQ) in English- and Spanish-speaking samples. A total of 199 English- or Spanish-speaking mothers completed the SCQ. Results indicated that Spanish-speaking mothers with limited educational attainment were more likely to report higher scores on the SCQ than those with higher educational attainment. Moreover, differences in response patterns were also observed between Spanish- and English-speaking mothers. That is, SCQ scores tended to be influenced by maternal education in the Spanish-speaking sample and by teachers’ reports of behavior/emotional problems in the English-speaking sample. These findings suggest that when using the SCQ, researchers, clinicians, and school providers need to be mindful that a high score on the SCQ does not necessarily indicate autism symptoms or characteristics. Rather, high SCQ scores might represent factors unrelated to autism symptoms, such as child and family characteristics.Impact StatementThe Social Communication Questionnaire (SCQ), an autism spectrum disorder screener, was administered to English- or Spanish-speaking mothers of school-aged children. Results from this study showed that the SCQ scores should be interpreted with caution when used with diverse students and students with emotional and behavior problems.Supplemental data for this article is available online at https://doi.org/10.1080/2372966X.2021.1927830 .
CCDC 711327: Experimental Crystal Structure Determination (2009)

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
A Formal Total Synthesis of (+)‐Methyl Trachyloban‐18‐oate and (+)‐Methyl 16‐Oxo‐17‐norkauran‐18‐oate: Regio‐ and Diastereoselective Preparation of Methyl (13S)‐13‐Hydroxyisoatisiren‐18‐oate from (−)‐Abietic Acid (1996)

Abstract A novel preparation of methyl (13 S )‐13‐hydroxyisoatisiren‐18‐oate ( 4 ), a key‐intermediate in a synthesis of (+)‐methyl trachyloban‐18‐oate ((+)‐ 1 ), from (−)‐abietic acid, is described. Since (−)‐ 1 has been previously converted into (−)‐methyl 16‐oxo‐17‐norkauran‐18‐oate ((−)‐ 16 ), our preparation of 4 constitutes also a formal total synthesis, from (−)‐abietic acid, of (+)‐ 16 . Key steps in this approach were the allene photoaddition to podocarp‐8(14)‐en‐13‐one ( 5 ) and the conversion of the endo ‐toluene‐4‐sulfonate 11 into the exo ‐benzoate 12b .
CloneRetriever: retrieval of rare clones from heterogeneous cell populations (2019)

Abstract Background Many biological processes, such as cancer metastasis, organismal development, and development of resistance to cytotoxic therapy, rely on the emergence of rare sub-clones from a larger population. Understanding how the genetic and epigenetic features of diverse clones affect clonal fitness provides insight into molecular mechanisms underlying selective processes. However, identifying causal drivers of clonal fitness remains challenging. Population-level analysis has limited resolution to characterize clones prior to selection, while high-resolution single-cell methods are destructive and challenging to scale across large populations, limiting further functional analysis of relevant clones. Results Here, we develop CloneRetriever, a methodology for tracking and retrieving rare clones throughout their response to selection. CloneRetriever utilizes a CRISPR sgRNA-barcode library that allows isolation of viable cells from specific clones within the barcoded population using a sequence-specific retrieval reporter. We demonstrated that CloneRetriever can measure clonal fitness of cancer cell models in vitro and retrieve targeted clones at abundance as low as 1 in 1,883 in a heterogeneous cell population. Conclusions CloneRetriever provides a means to track and access specific and rare clones of interest across dynamic changes in population structure to comprehensively explore the basis of these changes.
Multi-oracle interactive protocols with space bounded verifiers (2003)

It is proved that both in the multiprover model of M. Ben-or et al. (Proc. 20th Symp. Theory Comput., 1988, p.113-131) and in the the noisy oracle model of U. Feige et al. (Proc. CRYPTO 88) a finite-state verifier can accept any recursive language. The power of verifiers with simultaneous time bounds and space bounds is considered as well.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Effect of Filler–Polymer Interface on Elastic Properties of Polymer Nanocomposites: A Molecular Dynamics Study (2017)

ABSTRACT A coarse-grained model has been built to study the effect of the interfacial interaction between spherical filler particles and polymer on the mechanical properties of polymer nanocomposites. The polymer is modeled as bead-spring chains, and nano-fillers grafted with coupling agent are embedded into the polymer matrix. The potential parameters for polymer and filler are optimized to maximally match styrene-butadiene rubber reinforced with silica particles. The results indicated that, to play a noticeable role in mechanical reinforcement, a critical value exists for the grafting density of the filler–polymer coupling agent. After reaching the critical value, the increase of grafting density can substantially enhance mechanical properties. It is also observed that the increase of grafting density does not necessarily increase the amount of independent polymer chains connected to fillers. Instead, a significant amount of increased grafting sites serve to further strengthen already connected polymer and filler, indicating that mechanical reinforcement can occur through the locally strengthened confinement at the filler–polymer interface. These understandings based on microstructure visualization shed light on the development of new filler polymer interfaces with better mechanical properties.
Pathological Tau Promotes Neuronal Damage by Impairing Ribosomal Function and Decreasing Protein Synthesis (2016)

One of the most common symptoms of Alzheimer's disease (AD) and related tauopathies is memory loss. The exact mechanisms leading to memory loss in tauopathies are not yet known; however, decreased translation due to ribosomal dysfunction has been implicated as a part of this process. Here we use a proteomics approach that incorporates subcellular fractionation and coimmunoprecipitation of tau from human AD and non-demented control brains to identify novel interactions between tau and the endoplasmic reticulum (ER). We show that ribosomes associate more closely with tau in AD than with tau in control brains, and that this abnormal association leads to a decrease in RNA translation. The aberrant tau-ribosome association also impaired synthesis of the synaptic protein PSD-95, suggesting that this phenomenon contributes to synaptic dysfunction. These findings provide novel information about tau-protein interactions in human brains, and they describe, for the first time, a dysfunctional consequence of tau-ribosome associations that directly alters protein synthesis. Significance statement: Despite the identification of abnormal tau-ribosomal interactions in tauopathies >25 years ago, the consequences of this association remained elusive until now. Here, we show that pathological tau associates closely with ribosomes in AD brains, and that this interaction impairs protein synthesis. The overall result is a stark reduction of nascent proteins, including those that participate in synaptic plasticity, which is crucial for learning and memory. These data mechanistically link a common pathologic sign, such as the appearance of pathological tau inside brain cells, with cognitive impairments evident in virtually all tauopathies.