gebhart/patrepeval huggingface dataset:
Influence of the Lattice Parameter Difference between the Two Cubic Phases Formed in the 4 V Region on the Capacity Fading of Spinel Manganese Oxides (2003)

To develop a better understanding of the capacity-fading mechanisms of spinel lithium manganese oxides, the electrochemical properties, degree of manganese dissolution, and crystal chemistry of a number of singly substituted LiMn2-yMyO4 (M = Li, Al, Ti, Co, and Ni and 0 ≤ y ≤ 0.2) and doubly substituted LiMn2-y-zMyLizO4 (M = Ti, Co, and Ni, 0 ≤ y ≤ 0.1, and 0 ≤ z ≤ 0.1) oxides have been compared with those of LiMn2O4. The cation-substituted spinel manganese oxides show better electrochemical performances than LiMn2O4. Especially, the doubly substituted LiMn1.85Ni0.075Li0.075O4 exhibits excellent cyclability at both ambient and elevated temperatures with a capacity of around 100 mAh/g. It also exhibits remarkable rate capability and excellent capacity retention (>95%) after storage at 60 °C at various depths of discharge (DOD). Although the degree of manganese dissolution does not vary significantly, the spinel manganese oxides show a clear relationship between the percent capacity fade and the lattice parameter difference (Δa) between the two cubic phases formed in the 4 V region. A smaller Δa and the associated negligible volume change (ΔV) appear to minimize the microstrain, maintain good interparticle contact, and lead to superior electrochemical performances. The excellent cyclability and high rate capability of the LiMn2-y-zNiyLizO4 oxides may make them attractive for electric vehicles.
SemanticFusion: Dense 3D semantic mapping with convolutional neural networks (2017)

Ever more robust, accurate and detailed mapping using visual sensing has proven to be an enabling factor for mobile robots across a wide variety of applications. For the next level of robot intelligence and intuitive user interaction, maps need to extend beyond geometry and appearance - they need to contain semantics. We address this challenge by combining Convolutional Neural Networks (CNNs) and a state-of-the-art dense Simultaneous Localization and Mapping (SLAM) system, ElasticFusion, which provides long-term dense correspondences between frames of indoor RGB-D video even during loopy scanning trajectories. These correspondences allow the CNN's semantic predictions from multiple view points to be probabilistically fused into a map. This not only produces a useful semantic 3D map, but we also show on the NYUv2 dataset that fusing multiple predictions leads to an improvement even in the 2D semantic labelling over baseline single frame predictions. We also show that for a smaller reconstruction dataset with larger variation in prediction viewpoint, the improvement over single frame segmentation increases. Our system is efficient enough to allow real-time interactive use at frame-rates of ≈25Hz.
Enzymatic Ligation Reactions of DNA “Words” on Surfaces for DNA Computing (1998)

The enzymatic manipulation of sets of short, 16-base oligonucleotides, or DNA “words”, is demonstrated with applications toward DNA computing on surfaces. The enzyme T4 DNA ligase is used to ligate (join) DNA words on a chemically modified gold thin film. The efficiency of this surface ligation reaction is 80%, as determined by removal of the ligated molecules from the surface followed by gel electrophoresis. This surface ligation reaction is used in two new operations for DNA computing on surfaces. In a “Surface Word Append” operation, the complexity and information density of DNA word strands attached to gold surfaces are increased by appending additional words onto these word strands. The ligation reaction is also utilized as part of a “Two-Word Mark and Destroy” operation in which singly marked two-word DNA strands are selectively removed from the surface in the presence of doubly marked two-word strands. These new operations are essential for manipulation of the large combinatorial sets of linked DNA word strands required for DNA computing.
Reversible alkylation of a methionyl residue near the active site of β-galactosidase (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReversible alkylation of a methionyl residue near the active site of β-galactosidaseFred Naider, Zvi Bohak, and Joseph YarivCite this: Biochemistry 1972, 11, 17, 3202–3208Publication Date (Print):August 15, 1972Publication History Published online1 May 2002Published inissue 15 August 1972https://pubs.acs.org/doi/10.1021/bi00767a010https://doi.org/10.1021/bi00767a010research-articleACS PublicationsRequest reuse permissionsArticle Views274Altmetric-Citations91LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
The CdTe/HgTe superlattice: Proposal for a new infrared material (1979)

We propose a new material which could be useful in a number of infrared optoelectronic devices. The material consists of alternating (100) layers of CdTe and HgTe. The band gap of this superlattice is adjustable from 0 to 1.6 eV depending on the thicknesses of the CdTe and HgTe layers. Details of the band-gap variation and the character of the band-edge states are presented.
Organic Thin‐Film Transistors Fabricated on Resorbable Biomaterial Substrates (2009)

Organic electronics and biodegradable materials have the potential to be integrated to create a new class of electronic devices for the use in biomedical and environmental applications. Organic thin-film field-effect transistors fabricated using a biodegradable material platform exhibit water stable performance and degrade in vitro.
Molecular Beacons: Powerful Tools for Imaging RNA in Living Cells (2011)

Recent advances in RNA functional studies highlights the pivotal role of these molecules in cell physiology. Diverse methods have been implemented to measure the expression levels of various RNA species, using either purified RNA or fixed cells. Despite the fact that fixed cells offer the possibility to observe the spatial distribution of RNA, assays with capability to real-time monitoring RNA transport into living cells are needed to further understand the role of RNA dynamics in cellular functions. Molecular beacons (MBs) are stem-loop hairpin-structured oligonucleotides equipped with a fluorescence quencher at one end and a fluorescent dye (also called reporter or fluorophore) at the opposite end. This structure permits that MB in the absence of their target complementary sequence do not fluoresce. Upon binding to targets, MBs emit fluorescence, due to the spatial separation of the quencher and the reporter. Molecular beacons are promising probes for the development of RNA imaging techniques; nevertheless much work remains to be done in order to obtain a robust technology for imaging various RNA molecules together in real time and in living cells. The present work concentrates on the different requirements needed to use successfully MB for cellular studies, summarizing recent advances in this area.
BioHealthBase: informatics support in the elucidation of influenza virus host–pathogen interactions and virulence (2007)

The BioHealthBase Bioinformatics Resource Center (BRC) (http://www.biohealthbase.org) is a public bioinformatics database and analysis resource for the study of specific biodefense and public health pathogens-Influenza virus, Francisella tularensis, Mycobacterium tuberculosis, Microsporidia species and ricin toxin. The BioHealthBase serves as an extensive integrated repository of data imported from public databases, data derived from various computational algorithms and information curated from the scientific literature. The goal of the BioHealthBase is to facilitate the development of therapeutics, diagnostics and vaccines by integrating all available data in the context of host-pathogen interactions, thus allowing researchers to understand the root causes of virulence and pathogenicity. Genome and protein annotations can be viewed either as formatted text or graphically through a genome browser. 3D visualization capabilities allow researchers to view proteins with key structural and functional features highlighted. Influenza virus host-pathogen interactions at the molecular/cellular and systemic levels are represented. Host immune response to influenza infection is conveyed through the display of experimentally determined antibody and T-cell epitopes curated from the scientific literature or as derived from computational predictions. At the molecular/cellular level, the BioHealthBase BRC has developed biological pathway representations relevant to influenza virus host-pathogen interaction in collaboration with the Reactome database (http://www.reactome.org).
Enantioselective Ring Opening of Epoxides with Cyanide Catalysed by Halohydrin Dehalogenases: A New Approach to Non‐Racemic β‐Hydroxy Nitriles (2006)

Abstract Halohydrin dehalogenases (HheA, HheB and HheC) were found to efficiently catalyse a carbon‐carbon bond forming reaction between terminal aliphatic epoxides and cyanide, yielding β‐hydroxy nitriles. With all three enzymes nucleophilic ring opening of epoxides proceeds with high regioselectivity to the β‐carbon atom. Activity, enantioselectivity and enantiopreference depend on the type of enzyme and the substrate structure. HheC was found to be the most selective among the tested enzymes. The enantioselectivity toward monosubstituted epoxides varies from moderate to high ( E =5–106), while resolution of 2,2‐disubstituted epoxides proceeds with very high enantioselectivity ( E =141 and 200). The results show that halohydrin dehalogenases may become attractive catalysts for the facile preparation of enantiopure β‐hydroxy nitriles from racemic epoxides.
Functional Role of Kallikrein 6 in Regulating Immune Cell Survival (2011)

KLK6 promotes lymphocyte survival by a mechanism that depends in part on activation of PAR1. These findings point to a novel molecular mechanism regulating lymphocyte survival that is likely to have relevance to a range of immunological responses that depend on apoptosis for immune clearance and maintenance of homeostasis.
Line‐scanned micro Raman spectroscopy using a cooled CCD imaging detector (1990)

Abstract The design of a line‐scanned micro Raman spectrometer is described which uses a cooled, slow‐scan, chargecoupled device imaging detector to obtain sequences of Raman spectra from a ca. 100‐μm long line on a sample. The prototype design has a spatial resolution of &lt;10 μm and a spectral resolution of 4 cm −1 . Applications of the instrument to the analysis of mixed TiO 2 powders and the components of a zircon mineral are reported.
Conserved Repetitive Epitope Recognized by CD4 + Clones From a Malaria-Immunized Volunteer (1989)

T cell clones obtained from a human volunteer immunized with Plasmodium falciparum sporozoites specifically recognized the native circumsporozoite (CS) antigen expressed on P. falciparum sporozoites, as well as bacteria- and yeast-derived recombinant falciparum CS proteins. The response of these CD4+ CD8- cells was species-specific, since the clones did not proliferate or secrete gamma interferon when challenged with sporozoites or recombinant CS proteins of other human, simian, or rodent malarias. The epitope recognized by the sporozoite-specific human T cell clones mapped to the 5' repeat region of the CS protein and was contained in the NANPNVDPNANP sequence.
In vivo nitrogen metabolism in ornithine transcarbamylase deficiency. (1996)

We developed a new technique that monitors metabolic competency in female heterozygotes for ornithine transcarbamylase deficiency (OTCD). The method uses mass spectrometry to measure conversion of (15)NH4Cl to [15N]urea and [5-(15)N]glutamine following an oral load of (15)NH4Cl. We found that heterozygotes converted significantly less NH3 nitrogen to urea, with this difference being particularly obvious for symptomatic carriers, in whom the blood [15N]urea concentration (mM) was significantly less than control values at most time points. The blood concentration of [5-(15)N]-glutamine (microM) was significantly higher in both asymptomatic and symptomatic heterozygotes than it was in the control subjects. The administration of a test dose of sodium phenylbutyrate to the control group did not affect the rate of [15N]urea formation. We conclude: (a) This test effectively monitors in vivo N metabolism and might obviate the need for liver biopsy to measure enzyme activity in OTCD; (b) Asymptomatic OTCD carriers form urea at a normal rate, indicating that ureagenesis can be competent even though enzyme activity is below normal; (c) Although ostensibly asymptomatic OTCD carriers form urea at a normal rate, their nitrogen metabolism is still abnormal, as reflected in their increased production of [5-(15)N]glutamine; and (d) This new test may be important for monitoring the efficacy of novel treatments for OTCD, e.g., liver transplantation and gene therapy.
Stimulatory Effects of Hepatocyte Growth Factor on Hemopoiesis of SCF/c‐kit System‐Deficient Mice (1998)

In this study, we report that W/W mutant mice, which have severe macrocytic anemia caused by a deficit of extracellular domain in c-kit molecules and therefore die perinatally, have hemopoietic stem cells (HSCs) and mature hematolymphoid cells in the bone marrow (BM), thymus, and spleen, although there are significant decreases in cell counts. Moreover, the mitogen-induced proliferative response, mixed lymphocyte reaction, and anti-SRBC plaque formation of spleen cells in W/W mice are similar to those in age-matched +/? littermates and normal mice, suggesting that the SCF/c-kit system is necessary for cell proliferation but not essential for HSCs to differentiate. We next examine the stimulatory effects of hepatocyte growth factor (HGF) on hemopoiesis in W/W mice. HGF has a stimulatory effect on the colony formation (CFU-C) of W/W BM cells when cultured using either a methylcellulose assay (containing cytokines) or a long-term culture (LTC) assay. A similar stimulatory effect of HGF is observed in the other W or SI locus-mutant mice (W/Wv and SI/SId mice), which show less severe anemia than W/W. The numbers of nonadherent cells and cobblestone colonies significantly increase in the LTCs using their BM cells. In addition, in vivo administration of HGF shows a transient increase in the CFU-C counts in BM cells and peripheral blood cells. RBC, WBC, and platelet counts also increased. These results suggest that the SCF/c-kit system is not essential to hemopoiesis but that a compensatory system such as the HGF/c-met system functions in the SCF/c-kit system-deficient mice.
Cell Surface Protein Disulfide-Isomerase Is Involved in the Shedding of Human Thyrotropin Receptor Ectodomain (1996)

In human thyroid glands the TSH receptor undergoes a cleavage reaction which yields to an extracellular alpha subunit and a membrane spanning beta subunit linked together by disulfide bridges. A similar reaction is observed in transfected L cells although some uncleaved monomers persist in these cells. We have recently shown that the alpha subunit of the TSH receptor undergoes partial shedding in human thyroid cells and heterologous cells permanently transfected with an expression vector encoding the receptor. This shedding is a two-step process. The first step consists in the cleavage of the proreceptor at the cell surface probably by a matrix metalloprotease and the second step in the reduction of the disulfide bridge(s) (Couet, J., Sar, S., Jolivet, A., Vu Hai, M. T., Milgrom, E., & Misrahi, M. 1996, J. Biol. Chem. 271, 4545-4552). We have used the transfected L cells to study the second step involved in sTSHR shedding. The membrane impermeant sulfhydryl reagent DTNB (5,5'-dithiobis(2-nitrobenzoic acid) allowed us to confirm that the reduction of the TSH receptor disulfide bonds occurred at the cell surface. The antibiotic bacitracin even at low concentrations also elicited a marked inhibition of TSH receptor shedding. This led us to implicate the enzyme protein disulfide isomerase (PDI, EC 5.3.4.1) in this process. We thus tested the inhibitory activity of specific monoclonal antibodies raised against PDI. All antibodies elicited a marked inhibition of sTSHR shedding. This confirmed that cell surface PDI is involved in the shedding of the TSH receptor ectodomain. The shed alpha subunit may be at the origin of circulating TSH receptor ectodomain detected in human blood.
Post-translational modifications in proteins: resources, tools and prediction methods (2021)

Posttranslational modifications (PTMs) refer to amino acid side chain modification in some proteins after their biosynthesis. There are more than 400 different types of PTMs affecting many aspects of protein functions. Such modifications happen as crucial molecular regulatory mechanisms to regulate diverse cellular processes. These processes have a significant impact on the structure and function of proteins. Disruption in PTMs can lead to the dysfunction of vital biological processes and hence to various diseases. High-throughput experimental methods for discovery of PTMs are very laborious and time-consuming. Therefore, there is an urgent need for computational methods and powerful tools to predict PTMs. There are vast amounts of PTMs data, which are publicly accessible through many online databases. In this survey, we comprehensively reviewed the major online databases and related tools. The current challenges of computational methods were reviewed in detail as well.
A Systematic Review of Serum Biomarkers Anti-Cyclic Citrullinated Peptide and Rheumatoid Factor as Tests for Rheumatoid Arthritis (2011)

This systematic review assesses the current status of anti-cyclic citrullinated peptide (anti-CCP) and rheumatoid factor (RF) tests in the diagnosis and prognosis of rheumatoid arthritis (RA). We reviewed publications on tests and biomarkers for early diagnosis of RA from English-language MEDLINE-indexed journals and non-MEDLINE-indexed sources. 85 publications were identified and reviewed, including 68 studies from MEDLINE and 17 non-MEDLINE sources. Anti-CCP2 assays provide improved sensitivity over anti-CCP assays and RF, but anti-CCP2 and RF assays in combination demonstrate a positive predictive value (PPV) nearing 100%, greater than the PPV of either of the tests alone. The combination also appears to be able to distinguish between patients whose disease course is expected to be more severe and both tests are incorporated in the 2010 ACR Rheumatoid Arthritis Classification Criteria. While the clinical value of anti-CCP tests has been established, differences in cut-off values, sensitivities and specificities exist between first-, second- and third-generation tests and harmonization efforts are under way. Anti-CCP and RF are clinically valuable biomarkers for the diagnosis and prognosis of RA patients. The combination of the two biomarkers in conjunction with other clinical measures is an important tool for the diagnosis and management of RA patients.
A dramatic conformational rearrangement is necessary for the activation of DNR from Pseudomonas aeruginosa. Crystal structure of wild‐type DNR (2009)

The opportunistic pathogen Pseudomonas aeruginosa can grow in low oxygen, because it is capable of anaerobic respiration using nitrate as a terminal electron acceptor (denitrification). An intermediate of the denitrification pathway is nitric oxide, a compound that may become cytotoxic at high concentration. The intracellular levels of nitric oxide are tightly controlled by regulating the expression of the enzymes responsible for its synthesis and degradation (nitrite and nitric oxide reductases). In this article, we present the crystallographic structure of the wild-type dissimilative nitrate respiration regulator (DNR), a master regulator controlling expression of the denitrification machinery and a putative target for new therapeutic strategies. Comparison with other structures among the CRP-FNR class of regulators reveals that DNR has crystallized in a conformation that has never been observed before. In particular, the sensing domain of DNR has undergone a rotation of more than 50 degrees with respect to the other structures. This suggests that DNR may undergo an unexpected and very large conformational rearrangement on activation.
Light scattering from optical fibers with arbitrary refractive-index distributions (1975)

A scattering theory is presented, which is capable of predicting the light-distribution pattern that arises when a clad optical fiber of arbitrary core refractive-index distribution is illuminated by a laser beam perpendicular to its axis. Theoretical predictions are compared to experimental results in the backscattering direction, with excellent agreement for fibers of practical interest having core and cladding diameters on the order to 50 and 150 μm, respectively. Considerable sensitivity to parameter variations has been observed and implications for diameter and refractive-index distribution determinations are discussed.
Selective chemical autoligation on a double-stranded DNA template (1994)

We show that a double-stranded DNA segment serves as an effective template for spontaneously coupling short pyrimidine oligonucleotides containing terminal -P(O)(O-)S- and BrCH2C(O)NH- groups. The efficiency of this autoligation depends markedly on proper base-pairing between the probe oligomers and the double-stranded target. This chemistry should be useful in designing highly selective probes for double-stranded polynucleotide segments.
The interactive chef (2002)

In this paper, we describe the Interactive Chef (IChef), an intelligent system that attempts to emulate a human cooking assistant. The user navigates through a recipe using voice, while IChef reads aloud each step. IChef is designed to be aware of the present context and exploit this knowledge by answering questions about ingredients or techniques posed by the user in natural spoken language.
Statistical mechanics of the maximum-likelihood density estimation (1994)

Estimating the density of data generated by Gaussian mixtures, using the maximum-likelihood criterion, is investigated. Solving the statistical mechanics of this problem we evaluate the quality of the estimation as a function of the number of data points, P=\ensuremath{\alpha}N, N being the dimensionality of the points, in the limit of large N. Below a critical value of \ensuremath{\alpha}, the estimated density consists of Gaussian centers that have zero overlap with the structure of the true mixture. We show numerically that estimating the centers by slowly reducing the estimated Gaussian width yields a good agreement with the theory even in the presence of many local minima.