gebhart/patrepeval huggingface dataset:
Maximum likelihood estimation of the distribution of target registration error (2008)

Estimating the alignment accuracy is an important issue in rigid-body point-based registration algorithms. The registration accuracy depends on the level of the noise perturbing the registering data sets. The noise in the data sets arises from the fiducial (point) localization error (FLE) that may have an identical or inhomogeneous, isotropic or anisotropic distribution at each point in each data set. Target registration error (TRE) has been defined in the literature, as an error measure in terms of FLE, to compute the registration accuracy at a point (target) which is not used in the registration process. In this paper, we mathematically derive a general solution to approximate the distribution of TRE after registration of two data sets in the presence of FLE having any type of distribution. The Maximum Likelihood (ML) algorithm is proposed to estimate the registration parameters and their variances between two data sets. The variances are then used in a closed-form solution, previously presented by these authors, to derive the distribution of TRE at a target location. Based on numerical simulations, it is demonstrated that the derived distribution of TRE, in contrast to the existing methods in the literature, accurately follows the distribution generated by Monte Carlo simulation even when FLE has an inhomogeneous isotropic or anisotropic distribution.
Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing (2009)

T-cell receptor (TCR) genomic loci undergo somatic V(D)J recombination, plus the addition/subtraction of nontemplated bases at recombination junctions, in order to generate the repertoire of structurally diverse T cells necessary for antigen recognition. TCR beta subunits can be unambiguously identified by their hypervariable CDR3 (Complement Determining Region 3) sequence. This is the site of V(D)J recombination encoding the principal site of antigen contact. The complexity and dynamics of the T-cell repertoire remain unknown because the potential repertoire size has made conventional sequence analysis intractable. Here, we use 5'-RACE, Illumina sequencing, and a novel short read assembly strategy to sample CDR3(beta) diversity in human T lymphocytes from peripheral blood. Assembly of 40.5 million short reads identified 33,664 distinct TCR(beta) clonotypes and provides precise measurements of CDR3(beta) length diversity, usage of nontemplated bases, sequence convergence, and preferences for TRBV (T-cell receptor beta variable gene) and TRBJ (T-cell receptor beta joining gene) gene usage and pairing. CDR3 length between conserved residues of TRBV and TRBJ ranged from 21 to 81 nucleotides (nt). TRBV gene usage ranged from 0.01% for TRBV17 to 24.6% for TRBV20-1. TRBJ gene usage ranged from 1.6% for TRBJ2-6 to 17.2% for TRBJ2-1. We identified 1573 examples of convergence where the same amino acid translation was specified by distinct CDR3(beta) nucleotide sequences. Direct sequence-based immunoprofiling will likely prove to be a useful tool for understanding repertoire dynamics in response to immune challenge, without a priori knowledge of antigen.
Identification of a self-association domain in the Ewing's sarcoma protein: a novel function for arginine-glycine-glycine rich motifs? (2010)

The Ewing's sarcoma (EWS) protein is a ubiquitously expressed RNA chaperone. The EWS protein localizes predominantly to the nucleus. Previous reports have suggested that the EWS protein is capable of dimerizing. However, to date this has not been confirmed. Here, using a novel panel of recombinant proteins, we have performed an in vitro biomolecular interaction analysis of the EWS protein. We have demonstrated that all three arginine-glycine-glycine (RGG) motifs are capable of binding directly to the survival motor neuron protein, a Tudor domain containing EWS binding partner. We have also confirmed EWS is capable of self-associating, and we have mapped this binding domain to the RGG motifs. We have also found that self-association may be required for EWS nuclear import. This is the first direct evidence of RGG domains being involved in self-association and has implications on all RGG-containing proteins.
Portable and Error-Free DNA-Based Data Storage (2017)

DNA-based data storage is an emerging nonvolatile memory technology of potentially unprecedented density, durability, and replication efficiency. The basic system implementation steps include synthesizing DNA strings that contain user information and subsequently retrieving them via high-throughput sequencing technologies. Existing architectures enable reading and writing but do not offer random-access and error-free data recovery from low-cost, portable devices, which is crucial for making the storage technology competitive with classical recorders. Here we show for the first time that a portable, random-access platform may be implemented in practice using nanopore sequencers. The novelty of our approach is to design an integrated processing pipeline that encodes data to avoid costly synthesis and sequencing errors, enables random access through addressing, and leverages efficient portable sequencing via new iterative alignment and deletion error-correcting codes. Our work represents the only known random access DNA-based data storage system that uses error-prone nanopore sequencers, while still producing error-free readouts with the highest reported information rate/density. As such, it represents a crucial step towards practical employment of DNA molecules as storage media.
Uniaxial strain upregulates matrix-degrading enzymes produced by human vascular smooth muscle cells (2003)

Arteries remodel in response to environmental changes. We investigated whether mechanical strain modulates production of matrix metalloproteinase (MMP)-2 and -9 by cultured vascular smooth muscle cells (SMC). MMP-2 and MMP-9 expression were tested using human saphenous vein SMC cultured on silicone membranes at rest or subjected to physiological levels (5%) of stationary or cyclical (1 Hz) uniaxial strain. Compared with control, stationary strain significantly increased MMP-2 mRNA levels at all time points, whereas cyclic strain decreased it after 48 h. Both secreted and cell-associated pro-MMP-2 levels were increased by stationary strain at all times (P < 0.01), whereas cyclic strain decreased secreted levels after 48 h (P < 0.02). MMP-9 mRNA levels and pro-MMP-9 protein were increased after 48 h of stationary stretch (P < 0.01) compared with both no strain and cyclic strain. Our study indicates that vascular SMC show a selective response to different types of strain. We suggest that local increases in stationary mechanical strain resulting from stenting, hypertension, or atherosclerosis may lead to enhanced matrix degradation by SMC.
A Novel Multiplex Tetra-Primer ARMS-PCR for the Simultaneous Genotyping of Six Single Nucleotide Polymorphisms Associated with Female Cancers (2013)

This novel multiplex T-ARMS-PCR method is the first reported method allowing one to genotype six SNPs in a single reaction with no post-PCR treatment other than electrophoresis. This method is reliable, fast, and easy to perform.
Proteins as Random Coils. I. Intrinsic Viscosities and Sedimentation Coefficients in Concentrated Guanidine Hydrochloride (1967)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTProteins as Random Coils. I. Intrinsic Viscosities and Sedimentation Coefficients in Concentrated Guanidine HydrochlorideCharles. Tanford, Kazuo. Kawahara, and Savo. LapanjeCite this: J. Am. Chem. Soc. 1967, 89, 4, 729–736Publication Date (Print):February 1, 1967Publication History Published online1 May 2002Published inissue 1 February 1967https://pubs.acs.org/doi/10.1021/ja00980a001https://doi.org/10.1021/ja00980a001research-articleACS PublicationsRequest reuse permissionsArticle Views757Altmetric-Citations441LEARN 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
SiC devices for advanced power and high-temperature applications (2001)

Silicon carbide (SiC) process technology has made rapid progress, resulting in the realization of very promising electronic devices and sensors, enabling advanced solutions in power industry and mobile systems. In particular, for electronics working under harsh environmental conditions, SiC devices reach unprecedented performance. Transfer to production has already started for some applications.
Small peptides induce antibodies with a sequence and structural requirement for binding antigen comparable to antibodies raised against the native protein. (1985)

Antisera were raised against the chemically synthesized peptide corresponding to each epitope of three foot-and-mouth disease virus strains. Peptide synthesis was further used to determine which amino acid residues in each epitope are important for the specificity of antisera raised against the whole virus. The specificity of the antibody paratope for its epitope was shown to depend on structure as well as sequence. Anti-virus sera demonstrated a greater specificity for the homologous peptide than did the anti-peptide sera. Two of the three peptides were able to induce neutralizing antibodies against the homologous virus. The specificities of the antibodies present in the anti-peptide sera were also inferred from the reactions of each with related sets of peptides. The cross-reactions observed for the anti-peptide sera were readily explained in terms of the antibody specificities determined to be present. The findings also suggest that the diversity of antibodies raised against small peptides is limited and is determined by the immune system. A similar limited response to the native protein was observed, which may account for the high frequency with which anti-peptide sera react with the native homologous protein.
Chemical and Biological Explorations of the Family of CC-1065 and the Duocarmycin Natural Products (2009)

CC-1065, the duocarmycins and yatakemycin are members of a family of ultrapotent antitumour antibiotics that have been the subject of extensive investigations due to their mode of action and potential in the design of new anticancer therapeutics. The natural products and their analogues exert their effects through a sequence selective alkylation of duplex DNA in the minor groove at the N3 of adenine. An understanding of their structure and its effect on biological activity has been derived through chemical synthesis and has also generated new potential lead compounds. These studies form the first section of the review. The desire to progress these compounds to clinic has also led to studies of bioconjugation and prodrug formation and this is discussed in the second section of the review. The combination of synthesis with key biological experiments is a powerful tool to define the requirements for the development of natural products as potential therapeutic agents. The studies described herein form an excellent paradigm for the study and development of other natural products.
Photomask Repair Using An Advanced Laser Based Repair System (MARS2) (2002)

The ability to deliver high end photomasks free of printable defects is key to the success of the photomask manufacturing process. Although investment in substrate purity, particulate control, and cleaning capability has increased dramatically, they have proven no match for the defects’ ability to destroy an otherwise ideal mask. It is, therefore, essential to continue to have the capability to repair defects in order to deliver high-end photomasks. The vast variety of potential defects, combined with the different mask substrates, has driven the repair capability to not only be very technically driven, but also versatile and quick. Between the major defect categories of clear and opaque defects, opaque defects present the greatest challenge. Traditionally, this challenge lies in the reality that there is no perfect full height defect resulting in no one universal removal process. This is compounded with the fact that on any given photomask, these opaque defects can be greater than a micron, sub micron, very numerous, within tight geometries, or out in an isolated region of the photomask. Furthermore, defects identified as opaque defects have the possibility to be foreign material related, presenting a further challenge. They do not respond to repair in the same manner as the opaque defects. The multitude of issues, combined with the need to repair the defects with high throughput, has driven the need for an advanced opaque repair system. This paper will look into the practical application of a laser-based advanced opaque repair tool. Repair tool capability will show repair performance including substrate damage, transmission effects, and edge placement repeatability. This paper will also present a view of the operations of the repair system including imaging capabilities, and process throughput. This practical review of the advanced opaque repair system will show that technical needs of opaque repair, as well as practical needs of throughput and ease of use, can be achieved within one repair process.
Submersible microbial fuel cell sensor for monitoring microbial activity and BOD in groundwater: Focusing on impact of anodic biofilm on sensor applicability (2011)

A sensor, based on a submersible microbial fuel cell (SUMFC), was developed for in situ monitoring of microbial activity and biochemical oxygen demand (BOD) in groundwater. Presence or absence of a biofilm on the anode was a decisive factor for the applicability of the sensor. Fresh anode was required for application of the sensor for microbial activity measurement, while biofilm-colonized anode was needed for utilizing the sensor for BOD content measurement. The current density of SUMFC sensor equipped with a biofilm-colonized anode showed linear relationship with BOD content, to up to 250 mg/L (∼233 ± 1 mA/m(2)), with a response time of <0.67 h. This sensor could, however, not measure microbial activity, as indicated by the indifferent current produced at varying active microorganisms concentration, which was expressed as microbial adenosine-triphosphate (ATP) concentration. On the contrary, the current density (0.6 ± 0.1 to 12.4 ± 0.1 mA/m(2)) of the SUMFC sensor equipped with a fresh anode showed linear relationship, with active microorganism concentrations from 0 to 6.52 nmol-ATP/L, while no correlation between the current and BOD was observed. It was found that temperature, pH, conductivity, and inorganic solid content were significantly affecting the sensitivity of the sensor. Lastly, the sensor was tested with real contaminated groundwater, where the microbial activity and BOD content could be detected in <3.1 h. The microbial activity and BOD concentration measured by SUMFC sensor fitted well with the one measured by the standard methods, with deviations ranging from 15% to 22% and 6% to 16%, respectively. The SUMFC sensor provides a new way for in situ and quantitative monitoring contaminants content and biological activity during bioremediation process in variety of anoxic aquifers.
JOLT: a highly directive, very intensive, impulse-like radiator (2004)

Ultrawideband (UWB) systems that radiate very high-level transient waveforms and exhibit operating bandwidths of over two decades are now in demand for a number of applications. Such systems are known to radiate impulse-like waveforms with rise times around 100 ps and peak electric field values of tens of kilovolts per meter. Such waveforms, if properly radiated, will exhibit an operating spectrum of over two decades, making them ideal for applications such as concealed object detection, countermine, transient radar, and communications. In this paper, we describe a large, high-voltage transient system built at the Air Force Research Laboratory, Kirtland AFB, NM, from 1997 to 1999. The pulsed power system centers around a very compact resonant transformer capable of generating over 1 MV at a pulse-repetition frequency of /spl sim/ 600 Hz. This is switched, via an integrated transfer capacitor and an oil peaking switch onto an 85-/spl Omega/ half-impulse radiating antenna. This unique system will deliver a far radiated field with a full-width at half-maximum on the order of 100 ps, and a field-range product (rE/sub far/) of /spl sim/ 5.3 MV, exceeding all previously reported results by a factor of several.
Mechanisms of radiation damage in beam‐sensitive specimens, for TEM accelerating voltages between 10 and 300 kV (2012)

Ionization damage (radiolysis) and knock-on displacement are compared in terms of scattering cross section and stopping power, for thin organic specimens exposed to the electrons in a TEM. Based on stopping power, which includes secondary processes, radiolysis is found to be predominant for all incident energies (10-300 keV), even in materials containing hydrogen. For conducting inorganic specimens, knock-on displacement is the only damage mechanism but an electron dose exceeding 1000 C cm(-2) is usually required. Ways of experimentally determining the damage mechanism (with a view to minimizing damage) are discussed.
Biological roles and mechanistic actions of co-repressor complexes (2002)

Transcriptional repression, which plays a crucial role in diverse biological processes, is mediated in part by non-DNA-binding co-repressors. The closely related co-repressor proteins N-CoR and SMRT, although originally identified on the basis of their ability to associate with and confer transcriptional repression through nuclear receptors, have been shown to be recruited to many classes of transcription factor and are in fact components of multiple protein complexes containing histone deacetylase proteins. This association with histone deacetylase activity provides an important component of the mechanism that allows DNA-binding proteins interacting with N-CoR or SMRT to repress transcription of specific target genes. Both N-CoR and SMRT are important targets for cell signaling pathways, which influence their expression levels, subcellular localization and association with other proteins. Recently, the biological importance of these proteins has been revealed by studies of genetically engineered mice and human diseases such as acute promyelocytic leukemia (APL) and resistance to thyroid hormone (RTH).
The Incidence of Zoster after Immunization with Live Attenuated Varicella Vaccine (1991)

In children with leukemia who receive the live attenuated varicella vaccine, the subsequent incidence of zoster is lower than in children who have natural varicella infections.
Preferential proliferation of natural killer cells among peripheral blood mononuclear cells cocultured with B lymphoblastoid cell lines. (1987)

In this report, we show that in vitro stimulation of human peripheral blood mononuclear cells (PBMC) with B lymphoblastoid cell lines results in preferential proliferation of cells with the phenotypic, genotypic and functional characteristics of natural killer (NK) cells. This culture system offers a useful method for obtaining large numbers of pure NK cells on which biochemical, molecular and functional studies can be performed. Using this culture system, and average 25-fold increase in NK cell number is obtained, whereas the number of T cells is increased only 3-fold. At early times, activation of both T and NK cells occurs, as detected by the presence of activation antigens on both cell types, but actual proliferation of NK cells starts on day 6 of culture. Elimination of CD3(+)/CD5(+) T cells from the cultured cells gives homogeneous preparations of large numbers of CD16(+)/NKH-1(+) cells that have the morphology of large granular lymphocytes, are powerful effectors of both spontaneous and antibody-dependent cell-mediated cytotoxicity, and rapidly proliferate in the presence of recombinant interleukin 2 (rIL-2). As fresh NK cells, NK cell-enriched preparations from 10-day cultures of Daudi-stimulated PBMC do not show rearrangement of the gene for the beta-chain of the T cell antigen receptor; the 1.3-kb functional transcript of the beta-chain gene was not expressed in NK cells, but the 1.0-kb truncated transcript was present in all preparations. Our data indicate that proliferation of both T and NK cells is dependent upon IL-2 production in the culture, because an anti-IL-2 antiserum completely suppresses proliferation. Because T cells, and in particular CD4(+) T cells, are required for preferential proliferation of NK cells, the NK cell stimulation induced by the B cell line is probably in part indirect, and due to induction of IL-2 production by allogeneic stimulation of CD4(+) cells. However, the B cell lines also need to interact directly with NK cells because neither allogeneic PBMC nor high doses of rIL-2 are sufficient to induce preferential proliferation of NK cells.
Stimulation of T cells by antigenic peptide complexed with isolated chains of major histocompatibility complex class II molecules. (1993)

Major histocompatibility complex (MHC) class II molecules are heterodimeric glycoproteins with one alpha and one beta polypeptide chain of similar molecular size. In this report, we describe the binding of an acetylated N-terminal peptide of myelin basic protein, [Ala4]MBP-(1-14), to purified individual alpha and beta chains of murine I-Ak molecules. Purified complexes of isolated single chains and antigenic peptide bind to cloned T cells restricted by I-Ak and [Ala4]MBP-(1-14) tetradecapeptide. The binding is blocked by alpha/beta anti-T-cell receptor (TCR) monoclonal antibody. Cell triggering as measured by an increase in extracellular acidification rate is observed when cloned T cells are exposed to purified complexes of isolated chains and antigenic peptide. This increase in the extracellular acidification rate is antigen specific and MHC-restricted, as chains alone or irrelevant chain-peptide complexes do not trigger an increase in the metabolic acidification rate. These results together demonstrate that in vitro cloned T cells are triggered by complexes of specific antigenic peptides and isolated individual chains of their cognate MHC proteins.
Level set contour extraction based on data-adaptive Gaussian smoother (2012)

This paper presents a new object contour extraction method, which combines the level set evolution with the data-adaptive Gaussian smoother. It analyzes image under the framework of local data-adaptived Gaussian smoother and uses the local adaptive Gaussian kernels to represent salient features underlying image. The Gaussian filter, used in conventional level set method to compute the edge indicator, is replaced by the data-adaptive Gaussian smoother. The level set evolution method is implemented on the feature image obtained by convolving the data-adaptive Gaussian smoother with the original image. The proposed level set contour extraction method based on adaptive Gaussian smoother (LSAG), has been tested on both synthetic and real images. Comparisons with other methods, such as level set evolution without re-initialization (LSWR), demonstrate that the proposed LSAG method has advantages in extracting contours of the noise and weak contrast image and level set evolution speed.