gebhart/patrepeval huggingface dataset:
Application of transglutaminase to derivatize proteins: 1. Studies on soluble proteins and preliminary results on wool (2004)

Abstract The use of enzymes in chemical processing is gaining favour due to the reduction of hazardous chemicals and because it is considered to be environmentally safe. The acyl transfer reaction between primary amines and glutamine residues in proteins is catalysed by the enzyme transglutaminase. The efficiency of microbial transglutaminase to attach functional amines and catalyse inter‐ and intra‐molecular crosslinks was investigated using reduced carboxymethylated κ‐casein, gelatin and wool. Model systems used in this research gave evidence of both cross‐linking of the protein and covalent binding of the primary amine o ‐phosphorylethanolamine to the protein. These data agree with earlier publications that show transglutaminase catalyses the formation of covalent cross‐links between the γ‐carboxyamide group of glutamine and the ε‐amino group of lysine and also the incorporation of primary amines into proteins. Preliminary analysis of treated wool indicated the covalent bonding of the functional amine to the protein. Our goal is to increase the value of wool by enzymatic addition of functional groups to the wool fibre. Published in 2004 for SCI by John Wiley &amp; Sons, Ltd.
Olivopontocerebellar Degeneration (1974)

Thirty-three persons in the Schut-Swier kindred at risk for autosomal dominant olivopontocerebellar degeneration have been examined and nine new cases identified. These affected individuals manifested severe cerebellar deficits; abnormalities of cortical, bulbar, and spinal motor neurons; and posterior column dysfunction. Cerebellar biopsy material from two patients revealed extensive progressing loss of Purkinje cells, degeneration of cortical afferents, and variable loss of granule cells. Vermiform tubules that resemble paramyxovirus nucleocapsids were found in association with crystalline inclusions in both biopsy specimens.
A MBE-grown high-efficiency GaAs solar cell with a directly deposited aluminum front contact (1992)

A novel metallization scheme for GaAs p-n solar cells grown by molecular beam epitaxy (MBE) is described. A p/sup +/-GaAs contact layer was grown on top of the AlGaAs window layer, followed by a pure aluminum layer. This MBE-grown aluminum layer serves both as metallization and as self-aligned mask for selective etching down to the AlGaAs window. The solar cell showed an efficiency of about 20%; the I-V characteristics revealed that negligible series resistance was present in the structure. To test the novel p-contact a second sample was grown. Using a transmission-line model (TLM) structure, a metal-semiconductor contact resistance of 1.5*10/sup -2/ Omega -cm/sup 2/ was found.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cytochrome P450 epoxygenases 2C8 and 2C9 are implicated in hypoxia-induced endothelial cell migration and angiogenesis (2005)

Recent studies suggest that cytochrome P450 (CYP) epoxygenase-derived epoxyeicosatrienoic acids (EETs) elicit cell proliferation and promote angiogenesis. The aim of this study was to determine the role of CYP 2C8/9-derived EETs in the process of angiogenesis under hypoxic conditions. In human endothelial cells, hypoxia enhanced the activity of the CYP 2C9 promoter, increased the expression of CYP 2C mRNA and protein and augmented 11,12-EET production. In Transwell assays, the migration of endothelial cells pre-exposed to hypoxia to increase CYP expression was abolished by CYP 2C antisense oligonucleotides as well as by the CYP inhibitor MS-PPOH and the EET antagonist 14,15-epoxyeicosa-5(Z)-enoic acid (EEZE). Similar findings were obtained in porcine coronary artery endothelial cells. CYP 2C9 overexpression in endothelial cells increased the association of PAK-1 with Rac, a response also elicited by the CYP 2C9 product 11,12-EET. Matrix metalloprotease (MMP) activity was increased in CYP-2C9-overexpressing cells and correlated with increased invasion through Matrigel-coated Transwell chambers: an effect sensitive to the CYP 2C9 inhibitor sulfaphenazole as well as to EEZE and the MMP inhibitor GM6001. In in vitro angiogenesis models, the EET antagonist inhibited tube formation induced by CYP 2C9 overexpression as well as that in endothelial cells exposed to hypoxia to increase CYP 2C expression. Furthermore, in the chick chorioallantoic membrane assay, EEZE abolished hypoxia-induced angiogenesis. Taken together, these data indicate that CYP 2C-derived EETs significantly affect the sequence of angiogenic events under hypoxic conditions.
The dynamic range in input power for an optical signal regenerator using cascaded wavelength converters based on cross-gain modulation in semiconductor optical amplifiers (2004)

We investigated dynamic range in input light power for optical signal regenerator using cascaded wavelength converters based on cross-gain modulation, We achieved 6 dB dynamic range, and over 11 dB under optimized probe light conditions.
Improved Syva MicroTrak Chlamydia trachomatis direct test method (1988)

Recent changes in the MicroTrak Chlamydia trachomatis Direct Specimen Test (Syva Company, Palo Alto, Calif.) have led to improved product performance. The use of the recommended cervical cytology brush can significantly increase the number of endocervical cells collected, and fixation with methanol increases the intensity of elementary-body staining in many specimens.
Self‐Assembled Peptide Nanoarrays: An Approach to Studying Protein–Protein Interactions (2007)

Hochdichte Peptidanordnungen, die eine Vielzahl unterschiedlicher Aminosäuresequenzen an genau definierten und addressierbaren Stellen derselben DNA-Nanostruktur präsentieren können, wurden erzeugt. Dabei wurde die genetische Information genutzt, die im Nucleinsäureteil eines DNA-markierten Peptids verschlüsselt ist, um die Aminosäuresequenz an der vorbestimmten Stelle zu positionieren. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2007/z603919_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
ATRX histone binding and helicase activities have distinct roles in neuronal differentiation (2022)

ATRX is a chromatin remodeler, which is mutated in ATRX syndrome, a neurodevelopmental disorder. ATRX mutations that alter histone binding or chromatin remodeling activities cluster in the PHD finger or the helicase domain respectively. Using engineered mouse embryonic stem cells that exclusively express ATRX protein with mutations in the PHD finger (PHDmut) or helicase domains (K1584R), we examine how specific ATRX mutations affect neurodifferentiation. ATRX PHDmut and K1584R proteins interact with the DAXX histone chaperone but show reduced localization to pericentromeres. Neurodifferentiation is both delayed and compromised in PHDmut and K1584R, and manifest differently from complete ATRX loss. We observe reduced enrichment of PHDmut protein to ATRX targets, while K1584R accumulates at these sites. Interestingly, ATRX mutations have distinct effects on the genome-wide localization of the polycomb repressive complex 2 (PRC2), with PHDmut and ATRX knockout showing reduced PRC2 binding at polycomb targets and K1584R showing loss at some sites and gains at others. Notably, each mutation associated with unique gene signatures, suggesting distinct pathways leading to impaired neurodifferentiation. Our results indicate that the histone binding and chromatin remodeling functions of ATRX play non-redundant roles in neurodevelopment, and when mutated lead to ATRX syndrome through separate regulatory pathways.
Path Planning: Differential Dynamic Programming and Model Predictive Path Integral Control on VTOL Aircraft (2022)

View Video Presentation: https://doi.org/10.2514/6.2022-0624.vid This paper explores two optimal control approaches, widely used in robotics, to establish their viability as real-time trajectory planners for vehicle configurations envisioned for the emerging aviation sector of Urban Air Mobility (UAM). Differential Dynamic Programming (DDP) enables planning over highly nonlinear dynamics using second-order approximations along a nominal trajectory and displays quadratic convergence to a local solution. Model Predictive Path Integral Control (MPPI) is a stochastic sampling-based algorithm that can optimize for general cost criteria, including potentially highly nonlinear formulations, and supports parallel computation through the use of modern GPU hardware. In this work, DDP was implemented in a model predictive control (MPC) fashion alongside MPPI. The results indicate they are able to successfully transition the aircraft over different flight envelopes and generate trajectories unique to UAM vehicles.
iTARGET: A phase II trial to assess the response to gefitinib in epidermal growth factor receptor (EGFR)-mutated non-small cell lung cancer (NSCLC) tumors (2007)

7504 Background: Somatic EGFR mutations correlate with increased response and survival in NSCLC patients (pts) treated with gefitinib. We conducted the 1st prospective US trial of 1st-line gefitinib in pts with advanced NSCLC harboring EGFR mutations. Methods: Chemotherapy-naïve pts with stage IIIB with effusion or IV NSCLC, measurable disease, and = 1 characteristic associated with mutations (female (F), adenocarcinoma (AC), never-smoking (NS), East Asian (EA)) underwent direct DNA sequencing of tumor tissue EGFR exons 18–24. Mutation-positive pts received gefitinib (250 mg/d) until progression or unacceptable toxicity. The primary outcome was response rate (RR) by RECIST criteria. Results: We sequenced 98 pts and detected EGFR mutations in 34 (35%); 3 were not assessable. Observed mutations were 18 (53%) exon 19 deletions (del), 9 (26%) L858R, 3 (9%) exon 20 insertions (ins), 2 T790M/L858R, 1 G719A, and 1 L861Q. Characteristics of the 98 screened pts were 69 F, 89 AC, 37 NS, and 5 EA; those of the 34 mutation pts were 20 (59%) F, 31 (91%) AC, 19 (56%) NS and 2 (6%) EA. The best predictor of EGFR mutation was NS. Of the 34 mutation pts, 31 (91%) received gefinitib. Reasons for non-treatment were pt preference (1 exon 19 del) and mutation associated with gefitinib-resistance (1 T790M/L858R, 1 exon 20 ins). Adverse events were mainly grade 1–2 rash and diarrhea; 1 case of grade 4 interstitial lung disease occurred after 2 weeks of therapy. The RR was 58% (95% confidence interval 39–75) and was 78% in L858R pts and 65% in del 19 pts. There were no responses among the G719A, L861Q, T790M/L858R and exon 20 ins pts treated. 12 pts have progressed, 18 remain on therapy. The median progression-free survival (PFS) is currently 11.8 mo and does not differ by mutation type, though follow-up is short (median 6.8 mo, range 1–24). 27 pts are still alive. Of the 31 pts treated, 22 (71%) had high EGFR gene copy number (amplification (3) or high polysomy (19)); RR and PFS did not vary by copy number. Conclusions: 1st-line gefitinib therapy in EGFR mutation-positive NSCLC pts is feasible in a multi-institutional study, well tolerated, and yields a substantial RR and PFS. This strategy should be compared to standard chemotherapy in a genotype-directed randomized trial. No significant financial relationships to disclose.
Two cases of HIV-associated cryptococcosis due to the variety gattii in Rwanda (1993)

Journal Article Two cases of HIV-associated cryptococcosis due to the variety gattii in Rwanda Get access J. Bogaerts, J. Bogaerts 1Department of Microbiology, Centre Hospitalier de Kigali, Rwanda Search for other works by this author on: Oxford Academic PubMed Google Scholar H. Taelman, H. Taelman 2Department of Internal Medicine, Centre Hospitalier de Kigali, Rwanda Search for other works by this author on: Oxford Academic PubMed Google Scholar J. Batungwanayo, J. Batungwanayo 2Department of Internal Medicine, Centre Hospitalier de Kigali, Rwanda Search for other works by this author on: Oxford Academic PubMed Google Scholar P. Van de Perre, P. Van de Perre 3National AIDS Surveillance Programme, Kigali, Rwanda Search for other works by this author on: Oxford Academic PubMed Google Scholar D. Swinne D. Swinne 4Laboratory for Mycology, Institute of Tropical Medicine, Antwerp, Belgium Search for other works by this author on: Oxford Academic PubMed Google Scholar Transactions of The Royal Society of Tropical Medicine and Hygiene, Volume 87, Issue 1, January-February 1993, Pages 63–64, https://doi.org/10.1016/0035-9203(93)90423-N Published: 01 January 1993 Article history Received: 12 March 1992 Revision received: 08 May 1992 Accepted: 18 May 1992 Published: 01 January 1993
Automatic Quantitative Left Ventricular Analysis of Cine MR Images by Using Three-dimensional Information for Contour Detection (2006)

The purpose of this study was to evaluate an automatic boundary detection algorithm of the left ventricle on magnetic resonance (MR) short-axis images with the essential restriction of no manual corrections. The study comprised 13 patients (nine men, four women) and 12 healthy volunteers (11 men, one woman), and institutional review board approval and informed consent were obtained. The outline of the left ventricle was indicated manually on horizontal and vertical long-axis MR images. The calculated intersection points with the short-axis MR images were the basis of the automatic contour detection. Automatically derived volumes correlated highly with manually derived (short axis-based) volumes (R2 = 0.98); ejection fraction (EF) and mass showed a correlation of 0.95 and 0.93, respectively. Automatic contour detection reduced interobserver variability to 0.1 mL for endocardial end-diastolic and end-systolic volumes, 1.1 mL for epicardial end-diastolic and end-systolic volumes, 0.02% for EF, and 1.1 g for mass. Thus, the algorithm enabled highly reproducible left ventricular parameters to be obtained.
Optical Interpretation of the Merit Function in Grey’s Lens Design Program (1974)

A ray and wavefront analysis is the basis of an interpretation of the aberration balancing merit function in Grey's lens design program. From each of several field angles, this program traces a coarse grid of rays through an axially symmetric optical system. A polynomial in a region around each ray describes the wave error. This polynomial includes terms (through second order) in aperture, field angle, and wavelength variables. The coefficients of the terms in the polynomial are calculated from real and differential ray trace data. The merit function is the variance of the wave error, obtained by squaring and integrating the polynomials over appropriate ranges of the variables. Distortion is removed from the wave error polynomials and is included in the merit function in a unique manner.
Effect of reaction conditions on hydrocracking in slurry bed (2006)

The effect of partial hydrogen pressure within 3MPa~28MPa on cracking of butylbenzene and tert-butylbenzene were examined in a batch reactor.Pressure has different effects depending on the molecular structure of reactants.With the raising of partial hydrogen pressure,the cracking reaction of tert-butylbenzene is prompted,while the conversion of butylbenzene is restricted.In any case,the break of C—C bonds between the aromatic ring and the whole branch chain are promoted with the increasing of partial hydrogen pressure.Based on the above result,the effect of initial hydrogen pressure on slurry bed hydrocracking of Lungu and Karamay atmospheric residues was studied.With the raising of initial hydrogen pressure,the reactions of hydrocracking and the formation of toluene insoluble fraction are promoted simultaneously.Effects of reaction temperature and time are also discussed.
ASSESSING REPOSITORY TECHNOLOGY: WHERE DO WE GO FROM HERE? (1992)

Three sample information retrieval systems, archie, autoLib, and WAIS, are compared as to their expressiveness and usefulness — first, in the general context of information retrieval, and then as prospective software reuse repositories. While the representational capabilities of these systems are limited, they provide a useful foundation for future repository efforts, particularly from the perspective of repository distribution and coherent user interface design.
Hybride Nanocomposites aus Ruß, Nanoclay und NR/BR (2013)

The influence of partial replacement of carbon black (CB) by nanoclay on the curing kinetics of natural rubber/butadiene rubber-based hybrid nanocomposites was studied. The successive replacement of CB by organically modified nanoclays significantly influenced the curing behaviour of the compound: The crosslinking reaction is facilitated by the presence of nanoclay in these hybrid nanocomposites, as indicated by a decrease in activation energy. Furthermore, the modified nanoclays form a filler-filler network as indicated by viscosity and Payne effect measurements.
Decentralized neural network control of a class of large-scale systems with unknown interconnections (2004)

A novel decentralized neural network (DNN) controller is proposed for a class of large-scale nonlinear systems with unknown interconnections. The objective is to design a DNN for a class of large-scale systems which do not satisfy the matching condition requirement. The NNs are used to approximate the unknown subsystem dynamics and the interconnections. The DNN is designed using the back stepping methodology with only local signals for feedback. All of the signals in the closed loop (system states and weights estimation errors) are guaranteed to be uniformly ultimately bounded and eventually converge to a compact set.
Performance analysis of variable bit rate multiclass services in the downlink of a dynamic complete partitioning round-robin carrier-hopping multirate multi-carrier DS-CDMA system (2005)

Analytical formulations of the outage probability in terms of bit error rate specification using Chernoff bound and central limit Gaussian approximation for variable bit rate (VBR) multiclass services in the downlink of a dynamic complete partitioning (DCP) round-robin carrier-hopping multirate multi-carrier (MC) DS-CDMA cellular system is presented. The analytical framework is formulated for the general case in which different traffic classes have different spreading gains in each of the subcarriers. The analytical work leads to the determination of the capacity region of a dynamic complete partitioning round-robin carrier-hopping multirate MC-DS-CDMA system for VBR traffic. Numerical results show that the system capacity with DCP can be larger than that with complete sharing (CS) of the subcarriers.
Infrared nanospectroscopy reveals the molecular interaction fingerprint of an aggregation inhibitor with single Aβ42 oligomers (2021)

Significant efforts have been devoted in the last twenty years to developing compounds that can interfere with the aggregation pathways of proteins related to misfolding disorders, including Alzheimer's and Parkinson's diseases. However, no disease-modifying drug has become available for clinical use to date for these conditions. One of the main reasons for this failure is the incomplete knowledge of the molecular mechanisms underlying the process by which small molecules interact with protein aggregates and interfere with their aggregation pathways. Here, we leverage the single molecule morphological and chemical sensitivity of infrared nanospectroscopy to provide the first direct measurement of the structure and interaction between single Aβ42 oligomeric and fibrillar species and an aggregation inhibitor, bexarotene, which is able to prevent Aβ42 aggregation in vitro and reverses its neurotoxicity in cell and animal models of Alzheimer's disease. Our results demonstrate that the carboxyl group of this compound interacts with Aβ42 aggregates through a single hydrogen bond. These results establish infrared nanospectroscopy as a powerful tool in structure-based drug discovery for protein misfolding diseases.
Making oral history accessible over the World Wide Web (1998)

This article describes a multimedia, WWW-based oral history collection constructed from off-the-shelf or publicly available software. The source materials for the collection include audio tapes of interviews and summary transcripts of each interview, as well as photographs illustrating episodes mentioned in the tapes. Sections of the transcripts are manually matched to associated segments of the tapes, and the tapes are digitized. Users search a full-text retrieval system based on the text transcripts to retrieve relevant transcript sections and their associated audio recordings and photographs. It is also possible to search for photographs by ma tching text queries against text descriptions of the photographs in the collection, where the located photographs link back to their respective interview transcript and audio recording.
Purification of topoisomerase II from amsacrine-resistant P388 leukemia cells. Evidence for two forms of the enzyme. (1987)

Topoisomerase II was purified from an amsacrine-resistant mutant of P388 leukemia. A procedure has been developed which allows the rapid purification of nearly homogeneous enzyme in quantities sufficient for enzyme studies or production of specific antisera. The purified topoisomerase II migrated on sodium dodecyl sulfate-polyacrylamide gel electrophoresis as two bands with apparent molecular masses of 180 (p180) and 170 kDa (p170); both proteins unknotted P4 DNA in an ATP-dependent manner and displayed amsacrine-stimulated covalent attachment to DNA. Staphylococcus V8 protease cleavage patterns of p170 and p180 showed distinct differences. Specific polyclonal antibodies to either p170 or p180 recognized very selectively the form of the enzyme used to generate the antibodies. Immunoblotting with these specific antibodies showed that both p180 and p170 were present in cells lysed immediately in boiling sodium dodecyl sulfate. Comparison of the purified topoisomerase II from amsacrine-resistant P388 with that from amsacrine-sensitive P388 demonstrated that each cell type contained both p180 and p170; however, the relative amounts of the two proteins were consistently different in the two cell types. The data strongly suggest that p170 is not a proteolytic fragment of p180. Thus, P388 cells appear to contain two distinct forms of topoisomerase II.
Solution-Processed White Light-Emitting Diode Utilizing Hybrid Polymer and Red–Green–Blue Quantum Dots (2012)

A hybrid polymer-quantum dots (QDs) white light-emitting diode (WLEDs) device with a multi-layer structure by all solution processing is simply fabricated by using a spin coating technique. From transmission electron microscopy (TEM) study, red–green–blue (RGB) CdSe/ZnS QDs are mainly distributed along with the circumference of poly(N-vinylcarbazole) (PVK) surfaces, resulting in core–shell hybrid polymer-QDs of [RGB CdSe/ZnS QDs]/PVK. The Al/Cs2CO3/[RGB CdSe/ZnS QDs+PVK]/poly[(N,N '-bis(4-butylphenyl)-N,N '-bis(phenyl)benzidine)] (poly-TPD)/poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS)/indium–tin-oxide (ITO)/glass WLEDs shows electroluminescence (EL) centered at around 474, 544, and 629 nm with CIE coordinates, (0.44,0.32) at the forward bias +11 V, which clearly reveals that CdSe/ZnS QDs existing at the interface between PVK plays as a recombination center of exciton.