gebhart/patrepeval huggingface dataset:
Multitasking Immune Sp185/333 Protein, rSpTransformer-E1, and Its Recombinant Fragments Undergo Secondary Structural Transformation upon Binding Targets (2017)

The purple sea urchin, <i>Strongylocentrotus purpuratus</i>, expresses a diverse immune response protein family called Sp185/333. A recombinant Sp185/333 protein, previously called rSp0032, shows multitasking antipathogen binding ability, suggesting that the protein family mediates a flexible and effective immune response to multiple foreign cells. Bioinformatic analysis predicts that rSp0032 is intrinsically disordered, and its multiple binding characteristic suggests structural flexibility to adopt different conformations depending on the characteristics of the target. To address the flexibility and structural shifting hypothesis, circular dichroism analysis of rSp0032 suggests that it transforms from disordered (random coil) to α helical structure. This structural transformation may be the basis for the strong affinity between rSp0032 and several pathogen-associated molecular patterns. The N-terminal Gly-rich fragment of rSp0032 and the C-terminal His-rich fragment show unique transformations by either intensifying the α helical structure or changing from α helical to β strand depending on the solvents and molecules added to the buffer. Based on these results, we propose a name change from rSp0032 to rSpTransformer-E1 to represent its flexible structural conformations and its E1 element pattern. Given that rSpTransformer-E1 shifts its conformation in the presence of solvents and binding targets and that all Sp185/333 proteins are predicted to be disordered, many or all of these proteins may undergo structural transformation to enable multitasking binding activity toward a wide range of targets. Consequently, we also propose an overarching name change for the entire family from Sp185/333 proteins to SpTransformer proteins.
Aggregation of porcine pancreatic phospholipase A2 and its zymogen induced by submicellar concentration of negatively charged detergents (1983)

The interaction of two sodium n-alkyl sulfates (C10 and C12) with porcine pancreatic phospholipase A2 and its zymogen was studied by various spectroscopic techniques, equilibrium gel filtration, calorimetry, and photochemically induced dynamic nuclear polarization 1H NMR. At very low concentrations of n-alkyl sulfate [up to 0.07 X critical micelle concentration (cmc)] the enzyme (Mr 14 000) is able to build up a complex with the detergent molecules having a molecular weight of about 90 000. This complex consists of 6 enzyme molecules and about 40 n-alkyl sulfate monomers. The formation of the detergent-protein aggregate occurs in a two-step process: First, two detergent molecules strongly bind to a hydrophobic surface region of the protein, previously called interface recognition site [Pieterson, W. A., Vidal, J. C., Volwerk, J. J., & de Haas, G. H. (1974) Biochemistry 13, 1455-1460]. Subsequently, at higher detergent concentrations suddenly 6 enzyme molecules aggregate, probably including about 30 additional detergent monomers. Although the zymogen of the pancreatic phospholipase A2 seems to form comparable high molecular weight aggregates with these detergents, there are spectroscopic differences, and higher detergent concentrations are required. Moreover, as will be shown in the following paper [Hille, J. D. R., Egmond, M. R., Dijkman, R., van Oort, M. G., Sauve, P., & de Haas, G. H. (1983) Biochemistry (following paper in this issue)], only the phospholipase A2 becomes superactivated in these complexes.
Synthesis of Dimethyl-Substituted Polyviologen and Control of Charge Transport in Electrodes for High-Resolution Electrochromic Displays (2017)

Electrochromic (EC) polymers such as polyviologens have been attracting considerable attention as wet-processable electrodes for EC displays, thanks to their brilliant color change accompanied with reversible redox reactions. To establish wider usage, achieving multicolor and high-resolution characteristics is indispensable. In this paper, we demonstrated that the introduction of substituents such as methyl groups into bipyridine units changed the stereostructure of the cation radicals, and thus shifted the color (e.g., ordinary purple to blue). Also, by relaxing excessive π-stacking between the viologen moieties, the response rate was improved by a factor of more than 10. The controlled charge transport throughout the polyviologen layer gave rise to the fabrication of EC displays which are potentially suitable for the thin film transistor (TFT) substrate as the counter electrodes with submillimeter pixels. The findings can be versatilely used for the new design of polyviologens with enhanced electrochemical properties and high-resolution, multicolor EC displays.
A Versatile Terahertz Chemical Microscope and Its Application for the Detection of Histamine (2022)

Terahertz waves have gained increasingly more attention because of their unique characteristics and great potential in a variety of fields. In this study, we introduced the recent progress of our versatile terahertz chemical microscope (TCM) in the detection of small biomolecules, ions, cancer cells, and antibody–antigen immunoassaying. We highlight the advantages of our TCM for chemical sensing and biosensing, such as label-free, high-sensitivity, rapid response, non-pretreatment, and minute amount sample consumption, compared with conventional methods. Furthermore, we demonstrated its new application in detection of allergic-related histamine at low concentration in buffer solutions.
Plant aquaporins: their molecular biology, biophysics and significance for plant water relations (1999)

Over the last decade, considerable advances have occurred in understanding the molecular biology and biophysics of water permeation across plant membranes and tissues. Spurred on by the rapid advances in cloning and functional characterization of a superfamily of major intrinsic proteins, some of which function as aquaporins, the biophysics of transport of water and small non-electrolytes across plant membranes is being re-examined based on the proposed function of these membrane-integral proteins in their native membranes. This review focuses on a number of issues that are central to an understanding of aquaporin function: (1) the need to be able to test for water-channel activity in native membranes; (2) the implications of the observed solute/water selectivity of aquaporins; (3) the putative functional roles of aquaporins at the cell, tissue and organ levels in plants; and (4) information that can be obtained from studies of the abundance, diversity and expression patterns of aquaporins. It is clear that to answer many of the critical questions that remain concerning aquaporin function, combined studies using appropriate molecular and biophysical techniques will be required.
An interactive tool for the choice of the assembly methods and its link with the line balancing (1999)

info:eu-repo/semantics/published
Reduction in reverberation time, resulting from a unique acoustic treatment behind the final surface layer of drywall (2013)

When sound energy generated in room strikes a surface, it is partially reflected, transmitted, and absorbed. This is true for each layer of material in a wall, ceiling, or floor. The wave interaction with the surface depends on many factors. The main factors that are typically involved in calculations of reverberation time are the frequencies of concern, the rigidity and density of the surfaces, and the absorption of various objects in the room. This paper presents results that show the importance of considering the composition of the surface (wall, floor, or ceiling) including materials located behind the exposed surfaces. Specifically, it will be demonstrated that a properly installed layer of a loaded vinyl sheeting under the final wall surface layer of drywall will produce a significant reduction in the room reverberation time. With this technique, the preferred reverberation time can be achieved more naturally, while accommodating design constraints such as washable surfaces and minimizing the amount of additional surface treatments required. An additional benefit in the use of the loaded vinyl product behind the surface is a significant improvement in the STC of the wall or ceiling in which it was installed.
ChemInform Abstract: Biosensing with Polydiacetylene Materials: Structures, Optical Properties and Applications (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
On Regret of Parametric Mismatch in Minimum Mean Square Error Estimation (2010)

This paper studies the effect of parametric mismatch in minimum mean square error (MMSE) estimation. In particular, we consider the problem of estimating the input signal from the output of an additive white Gaussian channel whose gain is fixed, but unknown. The input distribution is known, and the estimation process consists of two algorithms. First, a channel estimator blindly estimates the channel gain using past observations. Second, a mismatched MMSE estimator, optimized for the estimated channel gain, estimates the input signal. We analyze the regret, i.e., the additional mean square error, that is raised in this process. We derive upper-bounds on both absolute and relative regrets. Bounds are expressed in terms of the Fisher information. We also study regret for unbiased, efficient channel estimators, and derive a simple trade-off between Fisher information and relative regret. This trade-off shows that the product of a certain function of relative regret and Fisher information equals the signal-to-noise ratio, independent of the input distribution. The trade-off relation implies that higher Fisher information results to smaller expected relative regret.
Practical considerations for using K3 cameras in CDS mode for high-resolution and high-throughput single particle cryo-EM (2020)

Abstract Detector technology plays a pivotal role in high-resolution and high-throughput cryo-EM structure determination. Compared with the first-generation, single-electron counting direct detection camera (Gatan K2), the latest K3 camera is faster, larger, and now offers a correlated-double sampling mode (CDS). Importantly this results in a higher DQE and improved throughput compared to its predecessor. In this study, we focused on optimizing camera data collection parameters for daily use within a cryo-EM facility and explored the balance between throughput and resolution. In total, eight data sets of murine heavy-chain apoferritin were collected at different dose rates and magnifications, using 9-hole image shift data collection strategies. The performance of the camera was characterized by the quality of the resultant 3D reconstructions. Our results demonstrated that the Gatan K3 operating in CDS mode outperformed nonCDS mode in terms of reconstruction resolution in all tested conditions with 8 electrons per pixel per second being the optimal dose rate. At low magnification (64kx) we were able to achieve reconstruction resolutions of 149% of the physical Nyquist limit (1.8 Å with a 1.346 Å physical pixel). Low magnification allows more particles to be collected per image, aiding analysis of heterogeneous samples requiring large data sets. At moderate magnification (105kx, 0.834Å physical pixel size) we achieved a resolution of 1.65 Å within 9 hours of data collection, a condition optimal for achieving high-resolution on well behaved samples. Our results also show that for an optimal sample like apoferritin, one can achieve better than 2.5 Å resolution with 5 minutes of data collection. Together, our studies validate the most efficient ways of imaging protein complexes using the K3 direct detector and will greatly benefit the cryo-EM community.
Temperature dependent critical stress for { 10 1 ¯ 2 } twinning in magnesium micropillars at cryogenic temperatures (2022)

Single-crystal magnesium micropillars (5 µm diameter) have been fabricated using focused ion beam (FIB) milling and loaded in compression along the [21¯1¯0] direction at cryogenic temperature (T = 184 K) at three different strain rates: 10-4, 5 × 10-3 and 10-1 s-1. The stress-strain curves and post-mortem analyses reveal the predominance of {101¯2} twinning. The critical stress required for twinning is detected to be significantly higher compared with that previously reported at higher temperatures for the same strain rates. From the experimental data, the temperature dependence of the strain rate sensitivity and activation volume for twinning is unveiled and observed to be constant and linearly dependent with T, respectively. By considering the activation energy (Q) in terms of stress-dependent dislocation motion using the rate equation proposed by Schoeck, for {101¯2} twinning, Q is determined to be 174 kJ mol-1 for T < 273 K and 72 kJ mol-1 above.
From IEEE 11073 SDC Device Specializations to Assistive Systems: Rule-based Data Analysis for Minimal Invasive Surgery (2019)

Modern surgical devices are full of innovations and provide plenty of functionalities. However, they only perform to their full potential if they are properly configured. Only a small subset of surgical device functionalities is used due to the high complexity of today's device systems and the omnipresent situation that only the circulating nurses can (re-)configure non-sterile devices. Hence, there is a huge need for safe and effective assistance supporting the operating room (OR) staff to continuously work with the potentially best device setting to increase patient's safety and clinical outcome. Therefore, we propose a concept for situation-aware parameter recommendations and automatic (re-)configuration. Free access to adequate data is a prerequisite to extract knowledge for assistive systems and to provide situation awareness during execution. Thus, manufacturer-independent medical device interoperability is a basic requirement. Consequently, we use the new IEEE 11073 Service-oriented Device Connectivity (SDC) standards family, including Device Specializations. As part of the developing committee we introduce the idea and concept behind Device Specializations and highlight their use for assistive systems in the domain of minimal invasive surgery. To ensure safety and effectiveness of the assistive functionalities, our concept enforces deterministic rules providing a predictable and approvable behavior. We demonstrate our concept by the use case of a smart surgical double roller pump using an interpreter-based Rule Execution Engine.
Effect of proton pump inhibitors on the outcomes of peptic ulcer bleeding: comparison of event rates in routine clinical practice and a clinical trial (2013)

The proportion of patients treated with i.v. esomeprazole in routine clinical practice who experienced further bleeding following endoscopic treatment for peptic ulcer bleeding was between the rates observed in the esomeprazole group and the placebo group in the RCT.
Specific Interaction between Redox Phospholipid Polymers and Plastoquinone in Photosynthetic Electron Transport Chain (2017)

Redox phospholipid polymers added in culture media are known to be capable of extracting electrons from living photosynthetic cells across bacterial cell membranes with high cytocompatibility. In the present study, we identify the intracellular redox species that transfers electrons to the polymers. The open-circuit electrochemical potential of an electrolyte containing the redox polymer and extracted thylakoid membranes shift to positive (or negative) under light irradiation, when an electron transport inhibitor specific to plastoquinone is added upstream (or downstream) in the photosynthetic electron transport chain. The same trend is also observed for a medium containing living photosynthetic cells of Synechococcus elongatus PCC7942. These results clearly indicate that the phospholipid redox polymers extract photosynthetic electrons mainly from plastoquinone.
MapReduce SVM Game (2015)

Despite technological advances making computing devices faster, smaller, and more prevalent in today's age, data generation and collection has outpaced data processing capabilities. Simply having more compute platforms does not provide a means of addressing challenging problems in the big data era. Rather, alternative processing approaches are needed and the application of machine learning to big data is hugely important. The MapReduce programming paradigm is an alternative to conventional supercomputing approaches, and requires less stringent data passing constrained problem decompositions. Rather, MapReduce relies upon defining a means of partitioning the desired problem so that subsets may be computed independently and recom- bined to yield the net desired result. However, not all machine learning algorithms are amenable to such an approach. Game-theoretic algorithms are often innately distributed, consisting of local interactions between players without requiring a central authority and are iterative by nature rather than requiring extensive retraining. Effectively, a game-theoretic approach to machine learning is well suited for the MapReduce paradigm and provides a novel, alternative new perspective to addressing the big data problem. In this paper we present a variant of our Support Vector Machine (SVM) Game classifier which may be used in a distributed manner, and show an illustrative example of applying this algorithm.
Enol Tosylates as Viable Partners in Pd-Catalyzed Cross-Coupling Reactions (2005)

[reaction: see text] Herein we demonstrate functionalized enol tosylates to be robust substrates that undergo Suzuki-Miyaura, Sonogashira, and Stille cross-coupling reactions to provide stereodefined trisubstituted unsaturated esters.
Procedures for Collecting and Processing Aquatic Invertebrates and Fish for Analysis of Mercury as Part of the National Water-Quality Assessment Program (2008)

Mercury studies conducted as part of the U.S. Geological Survey's National Water-Quality Assessment (NAWQA) Program have included nationwide reconnaissance samplings of hundreds of stream sites, as well as detailed, process-oriented research at selected sites. These reconnaissance and detailed studies are intended to provide a better understanding of methylmercury bioaccumulation in stream ecosystems over a range of environmental settings. This publication describes trace-element-clean techniques used for collection and processing of aquatic invertebrates and fish to be analyzed for total mercury, methylmercury, and stable isotopes as part of NAWQA studies.
Transcriptional Organization of thePseudomonas putida tol-oprLGenes (2002)

Proteins of the Tol system play a key role in the maintenance of outer membrane integrity and cell morphology in gram-negative bacteria. In Pseudomonas putida, the seven genes, orf1, tolQ, tolR, tolA, tolB, oprL, and orf2, which encode the proteins of this complex, are clustered in a 5.8-kb region of chromosomal DNA. Analysis of polar mutations, reverse transcriptase PCR assays, and transcriptional fusion constructs with a promoterless lacZ gene revealed that the genes are arranged in two operons: orf1 tolQ tolR tolA tolB and oprL orf2. We were also able to find a transcript that was initiated at the orf1 promoter and covered the two operons in a single mRNA. On the basis of the OprL protein level, we surmised that this transcript contributed only about 10 to 15% of the total OprL protein. Primer extension analysis identified the oprL orf2 operon promoter within the tolB gene, and the -10 and -35 regions exhibited some similarity to those of sigma(70)-recognized promoters. The transcription start point of orf1 was located 91 bp upstream of the orf1 start codon, and the -10/-35 region also exhibited sigma(70) -10/-35 recognition sequences. The expression from both promoters in rich and minimal media was constitutive and was very little influenced by the growth phase or iron-deficient conditions. In addition, analyses of the beta-galactosidase activities of different translational fusion constructs revealed that translation of tolA and orf2 genes was dependent on the translation of their corresponding upstream genes (tolR and oprL, respectively).
Fluid Spatial Dynamics of West Nile Virus in the United States: Rapid Spread in a Permissive Host Environment (2015)

How viruses spread in new host and geographic environments is central to understanding the emergence and evolution of novel infectious diseases and for predicting their likely impact. The emergence of the vector-borne West Nile virus (WNV) in North America in 1999 represents a classic example of this process. Using approximately 300 new viral genomes sampled from wild birds, we show that WNV experienced an explosive spread with little geographical or host constraints within birds and relatively low levels of adaptive evolution. From its introduction into the state of New York, WNV spread across the United States, reaching California and Florida within 4 years, a migration that is clearly reflected in our genomic sequence data, and with a general absence of distinct geographical clusters of bird viruses. However, some geographically distinct viral lineages were found to circulate in mosquitoes, likely reflecting their limited long-distance movement compared to avian species.
Myelin specific regulatory T cells expand from naturally occurring regulatory T cells and accumulate in the CNS during EAE (128.8) (2007)

Abstract FoxP3 is a lineage specific marker for regulatory T cells (T-reg). We have generated FoxP3 knock-in mice by introducing a bicistronic GFP reporter into the endogenous FoxP3 locus, allowing us to faithfully track T-reg in vivo. We have also generated a MOG 35-55/IAb-tetramer. The combination of these two technologies enables us to study the in vivo behavior of myelin specific T-reg and effector T cells (T-eff) during EAE. Upon immunization with MOG 35-55, we identified a population of MOG-tetramer-reactive T-reg in the peripheral lymphoid compartment. T-reg trafficked to the CNS where they were readily detected as early as day 10 following immunization. At this stage and till the peak of the disease, an overwhelming number of T-eff also targeted the CNS. Thus, the ratio of T-reg and T-eff at the initiation of disease was 1:15. However at the onset of recovery, this ratio changed in favor of T-reg (T-reg/T-eff close to 1:1. During recovery, 50% of the CNS-derived T-reg were IL-10 producers compared to only 10% in the peripheral immune compartment. FOXP3+ T cells isolated from the CNS are effective in suppressing naive MOG-specific T cells, but fail to control CNS-derived T-eff that secrete IL-6 and TNF. Our data suggest that in order for CD4+FOXP3+ T-reg to effectively control autoimmune reactions in the target organ, it may also be necessary to control tissue inflammation
Size Does Matter: Autonomous Micro-Power Sources (2008)

It is indeed a pleasure to be guest editor of this issue of Interface and have the opportunity to shed some light on the relationship of power and size. Remarkable advances have taken place in the ability to construct electronic devices, sensors, and even mechanical systems at the micro scale.