gebhart/patrepeval huggingface dataset:
Activity Mapping the Acyl Carrier Protein - Elongating Ketosynthase Interaction in Fatty Acid Biosynthesis (2020)

ABSTRACT Elongating ketosynthases (KSs) catalyze carbon-carbon bond forming reactions during the committed step for each round of chain extension in both fatty acid synthases (FASs) and polyketide synthases (PKSs). A small α-helical acyl carrier protein (ACP) shuttles fatty acyl intermediates between enzyme active sites. To accomplish this task, ACP relies on a series of dynamic interactions with multiple partner enzymes of FAS and associated FAS-dependent pathways. Recent structures of the Escherichia coli FAS ACP, AcpP, in covalent complexes with its two cognate elongating KSs, FabF and FabB, provide high-resolution detail of these interfaces, but a systematic analysis of specific interfacial interactions responsible for stabilizing these complexes has not yet been undertaken. Here, we use site-directed mutagenesis with both in vitro and in vivo activity analyses to quantitatively evaluate these contacting surfaces between AcpP and FabF. We delineate the FabF interface into three interacting regions and demonstrate the effects of point mutants, double mutants, and region delete variants. Results from these analyses reveal a robust and modular FabF interface capable of tolerating seemingly critical interface mutations with only the deletion of entire regions significantly compromising activity. Structure and sequence analysis of FabF orthologs from related type II FAS pathways indicate significant conservation of type II FAS KS interface residues and, overall, support its delineation into interaction regions. These findings strengthen our mechanistic understanding of molecular recognition events between ACPs and FAS enzymes and provide a blueprint for engineering ACP-dependent biosynthetic pathways.
Continuous Synthesis of Nanominerals in Supercritical Water (2018)

The synthesis of minerals should play a crucial role in the development of new and advanced materials. Since 2016, a renewal of interest to enlarge the mineral synthesis towards industrial requirements has been observed, especially thanks to three main recent papers. The innovative process exposed combines a continuous process with the use of supercritical water. In addition to curtail synthesis times, this process offers a control on the particle characteristics (size, crystallinity, structure, etc.) and a capacity to be easily transferable at an industrial scale. This innovative concept is demonstrated with the synthesis of three minerals which are the talc (a phyllomineral), the xonotlite and the tobermorite (two inominerals). This article proposes an overview of the possibilities to synthesize nanominerals in continuous processing for the development of advanced materials with promising industrial applications.
Tau Protein, beta-Amyloid 1-42 and Clusterin CSF Levels in Differential Diagnosis of Parkinsonian Syndrome with Dementia (P04.156) (2013)

OBJECTIVE: Parkinson's disease (PD), PD with dementia (PDD) and Lewy Body Dementia (DLB) are synucleinopathies. Some authors believe that PDD and DLB represent different courses of the same disorder. DLB is also sometimes considered a transition between PD and Alzheimer dementia (AD).
Degradation of recombinant proteins by Chinese hamster ovary host cell proteases is prevented by matriptase‐1 knockout (2018)

An increasing number of nonantibody format proteins are entering clinical development. However, one of the major hurdles for the production of nonantibody glycoproteins is host cell-related proteolytic degradation, which can drastically impact developability and timelines of pipeline projects. Chinese hamster ovary (CHO) cells are the preferred production host for recombinant therapeutic proteins. Using protease inhibitors, transcriptomics, and genetic knockdowns, we have identified, out of the >700 known proteases in rodents, matriptase-1 as the major protease involved in the degradation of recombinant proteins expressed in CHO-K1 cells. Subsequently, matriptase-1 was deleted in CHO-K1 cells using "transcription activator-like effector nucleases" (TALENs) as well as zinc-finger nucleases (ZFNs). This resulted in a superior CHO-K1 matriptase (KO) cell line with strongly reduced or no proteolytic degradation activity toward a panel of recombinantly expressed proteins. The matriptase KO cell line was evaluated in spike-in experiments and showed little or no degradation of proteins incubated in culture supernatant derived from the KO cells. This effect was confirmed when the same proteins were recombinantly expressed in the KO cell line. In summary, the combination of novel cell line engineering tools, next-generation sequencing screening methods, and the recently published Chinese hamster genome has enabled the development of this novel matriptase KO CHO cell line capable of improving expression yields of intact therapeutic proteins.
Fast Spray Deposition of Super Gas Barrier Polyelectrolyte Multilayer Thin Films (2015)

Spray-assisted deposition of layer-by-layer (LbL) assemblies was originally developed to reduce the processing time of multilayer thin films. Despite being faster, spraying largely failed to convert dipping practitioners due to lack of consensus regarding the quality of spray-coated films. In an effort to allay this concern, the barrier property of spray and dip-coated polyethylenimine [PEI]/poly(acrylic acid) [PAA] bilayers (BL) was compared. A 7 BL film deposited using optimized spraying parameters was found to be thicker than a dip-coated film prepared with the same deposition time. This larger thickness generated through suppressed polyelectrolyte desorption can effectively enhance the diffusion path of gas molecules, leading to a better gas barrier. This study marks the first report showing that a multilayer assembly with better properties can be produced with spray-assisted deposition. The ability to quickly deposit higher performance thin films using spraying opens up tremendous opportunity for continuous production on a commercial scale.
Cancer chemoprevention (2016)

Cancer prevention certainly would be the best approach to cancer. Interventions should be effective, with minimal side effects, convenient, and inexpensive. Cancer chemoprevention is defined as the pharmacologic intervention with the process of carcinogenesis to prevent the development of overt malignant neoplasms in healthy individuals with elevated cancer risk. The present list of candidate cancer types for active chemoprevention is still short and includes SERMs (tamoxifen, raloxifene) and an aromatase-inhibitor (exemestane) for chemoprevention of breast cancers, showing significant reduction of cancer occurrence. The same holds true for reduction of the development of invasive cancers by aspirin, NSAIDs, and COX2-inhibitors in selected populations with increased colorectal cancer risk. There is also reduction of prostate cancers by long-term application of 5-alfa-reductase-inhibitors (finasteride, dutasteride) in selected high-risk populations. Many other potentially active anti-neoplastic compounds have been tested but do not meet all the criteria of efficiency, efficacy, and cost-effectiveness.
Neisseria meningitidiselicits a pro-inflammatory response involving IκBζ in a human blood-cerebrospinal fluid barrier model (2014)

Our data show that Nm can initiate a pro-inflammatory response in human CP epithelial cells probably involving TLR2/TLR6 signaling and the transcriptional regulator IκBζ.
A NOVEL METHOD FOR EXACT SOLUTIONS OF ELLIPTICAL CRACKS IN PIEZOELECTRICS (2005)

According to the constitutive relationship in linear piezoceramics, elliptical crack problems in the impermeable case are reconsidered with the hypersingular integral equation method. Unknown displacement and electric potential jumps in the integral equations are approximated with a product of the fundamental density function and polynomials, in which the fundamental density function reflects the singular behavior of electroelastic fields near the crack front and the polynomials can be reduced to a real constant under uniform loading. Ellipsoidal coordinates are cleverly introduced to solve the unknown displacement and electric potential jumps in the integral equations under uniform loading. With the help of these solutions and definitions of electroelastic field intensity factors, exact expressions for mode Ⅰ, mode Ⅱ and mode Ⅲ stress intensity factors as well as the mode Ⅳ electric displacement intensity factor are obtained. The present results under uniform normal loading are the same as the available exact solutions, but those under uniform shear loading have not been found in the literature as yet.
Improved stability of organic light-emitting diode with aluminum cathodes prepared by ion beam assisted deposition (2004)

We have fabricated highly stable organic electroluminescent devices based on spin-coated poly-p-phenylene-vynylene (PPV) thin films. The electrical properties of aluminum cathode, prepared by ion beam assisted deposition, on PPV have been investigated and compared to those by thermal evaporation. Although energetic particles of Al assisted by ArC ion may damage the organic material, I–V–L characteristics are improved by applying thin Al buffer layer. In addition, a dense Al cathode inhibits the permeation of H2O and O2 into PPV film through pinhole defects, and thus retards dark spot growth. It may be deduced from highly packed structure of Al cathode with an increase in the contact area between Al and PPV that reduce the contact resistance. In conclusion, the lifetime of organic light-emitting device (OLED) has been extended effectively by dense Al film through ion beam assisted deposition process.
Discussion: Modeling for Hydraulic Capacity [with RESPOND] (2016)

Dn two to key decreases Modeling account finding ways: the for (1) is for pipe roughness that it Hydraulic increases diameter. growth growth Capacity of the As roughness equivalent stated adjust (Boxall by the elements the roughness sand et authors, al, grain in April coefficients pipes most roughness 2004) affects methods the alone authors' pipes and used and (2) in key finding is that growth of roughness elements in pipes affects pipes in two ways: (1) it increases the equivalent sand grain roughness and (2) decreases the pipe diameter. As stated by the authors, most methods used to account for roughness growth adjust the roughness coefficients alone and do not also decrease the pipe diameter. The authors are indeed correct in stating that both should be adjusted; however, how this effect is quantified should be examined.
Enable Super-resolution Parameter Estimation for Mm-wave Channel Sounding (2019)

This paper investigates the capability of millimeter-wave (mmWave) channel sounders with phased arrays to perform super-resolution parameter estimation, i.e., determine the parameters of multipath components (MPC), such as direction of arrival and delay, with resolution better than the Fourier resolution of the setup. We analyze the question both generally, and with respect to a particular novel multi-beam mmWave channel sounder that is capable of performing multiple-input-multiple-output (MIMO) measurements in dynamic environments. We firstly propose a novel two-step calibration procedure that provides higher-accuracy calibration data that are required for Rimax or SAGE. Secondly, we investigate the impact of center misalignment and residual phase noise on the performance of the parameter estimator. Finally we experimentally verify the calibration results and demonstrate the capability of our sounder to perform super-resolution parameter estimation.
Supplementary Figures 1-9 from ALK Mutations Conferring Differential Resistance to Structurally Diverse ALK Inhibitors (2023)

&lt;p&gt;PDF file - 2MB&lt;/p&gt;
Variable regions on the genome of Malawi isolates of African swine fever virus (1990)

Restriction enzyme site mapping showed that most BamHI and all ClaI sites were conserved on the genomes of 17 African swine fever virus isolates from separate disease outbreaks that occurred between 1982 and 1989 in Malawi. However, frequent variation between virus genomes did occur due to addition or deletion of DNA sequences at various positions along the genome and 11 virus genotypes could thus be distinguished among the 17 isolates analysed. Length variations occurred at 10 different loci on the virus genome. These variable regions were located between the left DNA terminus and a position up to 48 kb from that terminus, in the centre of the genome 90 to 93 kb from the left DNA terminus and between the right DNA terminus and a position 22 kb from that terminus. Length variations in most of these regions were small (&lt; 1 kb) but variations of about 4 kb occurred in a region up to 20 kb from the left DNA terminus.
Impact of BCL2 and p53 on postmastectomy radiotherapy response in high-risk breast cancer. A subgroup analysis of DBCG82 b&c (2008)

p53 was not associated with survival after radiotherapy in high-risk breast cancer, but BCL2 might be.
Dehydropyrrolizidine Alkaloids in Boneset (Eupatorium perfoliatum L.) and Three Related Species (2018)

Dehydropyrrolizidine alkaloids (DHPA) have been associated with hepatic veno-occlusive disease. In addition to acute hepatotoxicity, long-term, low-level, or intermittent exposures may contribute to chronic diseases. Eupatorium perfoliatum is a medicinal herb referred to as 'boneset'. The presence of DHPA has been reliably reported in some Eupatorium species, but reports on E. perfoliatum have been contradictory. Although not a big seller in mass markets, boneset is used by medical herbalists in the U.S. A number of boneset samples were acquired for analysis. The herb, alcoholic tinctures, hot water infusions, and decoctions made from a subset of those samples were analyzed. Eupatorium perfoliatum and three closely-related species were subjected to extraction and HPLC-esi(+)MS and MS/MS. Dehydropyrrolizidine alkaloids were identified from their MS data and comparison with standards. Forty collections of E. perfoliatum were tested and shown to contain DHPA, dominated by lycopsamine and intermedine, their N-oxides and acetylated derivatives. Concentrations varied from 0.0002 – 0.07% (w/w). Alcoholic tinctures, hot water infusions, and decoctions also had high concentrations of the alkaloids. Contamination of some E. perfoliatum samples with related species was suggested by the co-presence of retronecine- and heliotridine-based dehydropyrrolizidine alkaloids. It is unknown whether sampling issues, the existence of low and high alkaloid chemotypes, or hybridization contribute to the wide variation in dehydropyrrolizidine alkaloid content observed. Nonetheless, this study definitively demonstrates that E. perfoliatum contains DHPA and provides a reason for caution until further research can better define the toxicity and carcinogenicity of the DHPAs of boneset.
Porous NaTi2 (  PO 4 ) 3 Glass Ceramics (1990)

On etudie la fabrication de vitroceramique poreuses obtenues par cristallisation d'un verre de composition (% molaire): 6Na 2 O•39CaO•24TiO 2 •31P 2 O 5 et lessivage acide des vitroceramiques denses resultantes
Mode-Selective Optical Kerr Effect Spectroscopy (2004)

We demonstrate that by using two pump pulses with independently controllable polarizations, intensity, and timing, different contributions to the optical Kerr effect (OKE) signal in liquids can be enhanced and suppressed. When both pump pulses have the same polarization, intramolecular vibrations can be enhanced or suppressed without affecting the reorientational diffusion contribution to the signal significantly. Similar control can be exerted over intramolecular vibrations when the pump pulses are perpendicularly polarized, and under these conditions it is also possible to suppress the reorientational diffusion component of the signal completely. When two intramolecular vibrational modes are present in the signal, it is possible to enhance one while completely suppressing the other if the pump polarizations and timing are chosen appropriately. This technique should be a useful means for enhancing contrast in OKE microscopy.
A 4×12.5 Gb/s CWDM Si photonics link using integrated hybrid silicon lasers (2011)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text B. Koch, A. Alduino, L. Liao, R. Jones, M. Morse, B. Kim, W. Lo, J. Basak, H. Liu, H. Rong, M. Sysak, C. Krause, R. Saba, D. Lazar, L. Horwitz, R. Bar, S. Litski, A. Liu, K. Sullivan, O. Dosunmu, N. Na, T. Yin, F. Haubensack, I. Hsieh, J. Heck, R. Beatty, J. Bovington, and M. Paniccia, "A 4×12.5 Gb/s CWDM Si photonics link using integrated hybrid silicon lasers," in CLEO:2011 - Laser Applications to Photonic Applications, OSA Technical Digest (CD) (Optica Publishing Group, 2011), paper CThP5. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Recurrent Super-Resolution Method for Enhancing Low Quality Thermal Facial Data (2022)

The process of obtaining high-resolution images from single or multiple low-resolution images of the same scene is of great interest for real-world image and signal processing applications. This study is about exploring the potential usage of deep learning based image super-resolution algorithms on thermal data for producing high quality thermal imaging results for in-cabin vehicular driver monitoring systems. In this work we have proposed and developed a novel multi-image super-resolution recurrent neural network to enhance the resolution and improve the quality of low-resolution thermal imaging data captured from uncooled thermal cameras. The end-to-end fully convolutional neural network is trained from scratch on newly acquired thermal data of 30 different subjects in indoor environmental conditions. The effectiveness of the thermally tuned super-resolution network is validated quantitatively as well as qualitatively on test data of 6 distinct subjects. The network was able to achieve a mean peak signal to noise ratio of 39.24 on the validation dataset for 4x super-resolution, outperforming bicubic interpolation both quantitatively and qualitatively.
13C/15N‐Enriched l‐Dopa as a Triple‐Resonance NMR Probe to Monitor Neurotransmitter Dopamine in the Brain and Liver Extracts of Mice (2015)

In an attempt to monitor μm-level trace constituents, we applied here (1)H-{(13)C-(15)N} triple-resonance nuclear magnetic resonance (NMR) to (13)C/(15)N-enriched l-Dopa as the inevitable precursor of the neurotransmitter dopamine in the brain. The perfect selectivity (to render endogenous components silent) and μm-level sensitivity (700 MHz spectrometer equipped with a cryogenic probe) of triple-resonance allowed the unambiguous and quantitative metabolic and pharmacokinetic analyses of administered l-Dopa/dopamine in the brain and liver of mice. The level of dopamine generated in the brain (within the range 7-76 μm, which covers the typical stimulated level of ∼30 μm) could be clearly monitored ex vivo, but was slightly short of the detection limit of a 7 T MR machine for small animals. This work suggests that μm-level trace constituents are potential targets of ex vivo monitoring as long as they contain N atom(s) and their appropriate (13)C/(15)N-enrichment is synthetically accessible.
The Metabolic and Mitogenic Effects of Both Insulin and Insulin-like Growth Factor Are Enhanced by Transfection of Insulin Receptors into NIH3T3 Fibroblasts (1989)

Insulin and insulin-like growth factor (IGF-I) have 50% sequence homology and regulate similar cellular functions. Their membrane receptors also share 84% homology in a tyrosine kinase domain essential to transmembrane signaling and may thus share common postreceptor paths. To probe action mechanisms for these related hormones, we examined the receptor and postreceptor overlap of responses stimulated by insulin and IGF-I. NIH3T3 mouse fibroblasts have few endogenous insulin receptors and are insensitive to insulin; they have IGF-I receptors and are responsive to IGF-I. Stable transfection of these cells with cDNA for the human insulin receptor yielded a cell line (3T3/HIR) expressing greater than 6 x 10(6) receptors/cell that was highly sensitive and responsive to insulin for stimulation of deoxy[14C]glucose uptake and [3H]thymidine incorporation. The cells also showed increased responses to IGF-I, although the sensitivity was less than that for insulin. The receptor specificity of such responses was examined with a monoclonal antibody MA10 that bound to insulin receptors, but elicited no responses. When 3T3/HIR cells were preincubated with MA10, subsequent insulin- or IGF-I-stimulated deoxy[14C]glucose uptake was markedly inhibited. Likewise, the presence of MA10 caused a 10-fold increase in the concentration of insulin needed to stimulate half-maximal incorporation of [3H]thymidine and also led to diminished IGF-I-stimulated responses. These results showed that the transfected human insulin receptors coupled readily with existing effector pathways in the mouse fibroblasts and mediated metabolic and mitogenic responses to both insulin and IGF-I. Such findings indicate that insulin and IGF-I regulate common cellular functions using both overlapping receptor and postreceptor signaling pathways.
Dual inhibition of tumour necrosis factor and interleukin-17A with ABT-122: open-label long-term extension studies in rheumatoid arthritis or psoriatic arthritis (2018)

ClinicalTrials.gov, http://clinicaltrials.gov, NCT02433340 and NCT02429895.
Agent-based Mission Modeling and Simulation (2006)

Abstract A simulation environment for agents is presented, enabling agent-based modeling and simulation of people, systems and robots in space exploration missions. The environment allows the analysis and design of mission operation work procedures, communications and interactions between people and systems, co-located or distributed on Earth and in space. The MODAT (Mission Operations Design and Analysis Toolkit) is the integration of NASA Ames’ Brahms multiagent modeling and simulation environment, the Mission Simulation Toolkit (MST), a 3-D Visualization and Surface Reconstruction (Viz), plus JPL’s Virtual Mission Operations Framework (VMOF) into an agent-based end-to-end mission modeling and simulation environment. This paper describes a work in progress. Introduction Simulation-based design tools enabling mission designers to simulate and analyze systems-of-systems impact are critical to the success of Exploration Missions. Innovations affecting human-robot work processes must be evaluated before designs are implemented. In our End-to-end Mission Modeling and Simulation (EMMSE) project, funded by NASA’s Exploration Systems Mission Directorate, the objective is to develop an agent-based mixed fidelity end-to-end mission simulation capability to baseline, verify and validate human and robot mission operations. An end-to-end mission modeling and simulation environment provides a holistic approach to mission design and analysis of human-robot teams that was heretofore not possible. Multiple “what if” scenarios can be tested and the impact of ground/crew and human/robot interactions analyzed at a systems level. Mission operations designers can simulate the least costly and most efficient mission operations. In this paper we discuss the integration of NASA Ames’ Brahms multiagent MS the VMOF simulates the spacecraft and telemetry systems, uplink and downlink and command sequences. We will develop an agent for mission planning and scheduling (in the simulation environment) that interfaces with an adaptation of MAPGEN [Ai-Chang, et al. 2004]. This provides mission designers with the ability to simulate mixed-initiative planning operations with humans in the