gebhart/patrepeval huggingface dataset:
Sortase enzymes in Gram‐positive bacteria (2011)

In Gram-positive bacteria proteins are displayed on the cell surface using sortase enzymes. These cysteine transpeptidases join proteins bearing an appropriate sorting signal to strategically positioned amino groups on the cell surface. Working alone, or in concert with other enzymes, sortases either attach proteins to the cross-bridge peptide of the cell wall or they link proteins together to form pili. Because surface proteins play a fundamental role in microbial physiology and are frequently virulence factors, sortase enzymes have been intensely studied since their discovery a little more than a decade ago. Based on their primary sequences and functions sortases can be partitioned into distinct families called class A to F enzymes. Most bacteria elaborate their surfaces using more than one type of sortase that function non-redundantly by recognizing unique sorting signals within their protein substrates. Here we review what is known about the functions of these enzymes and the molecular basis of catalysis. Particular emphasis is placed on 'pilin' specific class C sortases that construct structurally complex pili. Exciting new data have revealed that these enzymes are amazingly promiscuous in the substrates that they can employ and that there is a startling degree of diversity in their mechanism of action. We also review recent data that suggest that sortases are targeted to specific sites on the cell surface where they work with other sortases and accessory factors to properly function.
Study of the micelle formation of sodium deoxycholate. Concentration dependence of carbon-13 nuclear magnetic resonance chemical shift (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStudy of the micelle formation of sodium deoxycholate. Concentration dependence of carbon-13 nuclear magnetic resonance chemical shiftYoshio Murata, Gohsuke Sugihara, Kohsuke Fukushima, Mitsuru Tanaka, and Kazuhiro MatsushitaCite this: J. Phys. Chem. 1982, 86, 24, 4690–4694Publication Date (Print):November 1, 1982Publication History Published online1 May 2002Published inissue 1 November 1982https://pubs.acs.org/doi/10.1021/j100221a010https://doi.org/10.1021/j100221a010research-articleACS PublicationsRequest reuse permissionsArticle Views400Altmetric-Citations36LEARN 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 options Get e-Alerts
Empirical Evaluation of Rectified Activations in Convolutional Network (2015)

In this paper we investigate the performance of different types of rectified activation functions in convolutional neural network: standard rectified linear unit (ReLU), leaky rectified linear unit (Leaky ReLU), parametric rectified linear unit (PReLU) and a new randomized leaky rectified linear units (RReLU). We evaluate these activation function on standard image classification task. Our experiments suggest that incorporating a non-zero slope for negative part in rectified activation units could consistently improve the results. Thus our findings are negative on the common belief that sparsity is the key of good performance in ReLU. Moreover, on small scale dataset, using deterministic negative slope or learning it are both prone to overfitting. They are not as effective as using their randomized counterpart. By using RReLU, we achieved 75.68\% accuracy on CIFAR-100 test set without multiple test or ensemble.
Vi Antigen from Salmonella typhosa and Immunity Against Typhoid Fever I. Isolation and Immunologic Properties in Animals (1974)

The role of Vi antigen in human immunity against typhoid fever has been debated for decades. Circumstantial evidence indicates that Vi antigen may play a role in pathogenicity and immunity. A Vi preparation was isolated from Salmonella typhosa, the causative organism in human typhoid fever, by a mild precipitation method. It was significantly more potent in animal studies than preparations from Citrobacter used in the past for human study and less toxic than conventional typhoid vaccines. With this antigen, the role of Vi antigen in human protection is now being investigated.
Semantic Interoperability Integrating and Augmenting Legacy Applications with OWL Ontologies (2008)

This paper describes an approach to software interoperability based on knowledge representation technologies developed in support of the emerging semantic Web. In particular, we are interested in the interoperation of an arbitrary set (two or more) of "legacy" applications that operate in a common domain, but that were not originally designed to support each other or to share information. To do this, we develop a means to create a general meta-model of the common domain of discourse that contains, organizes and correlates the essential information that each of the applications needs to function as well as any additional information particular to the composed system. This model becomes the basis of communications between the cooperating systems. Each legacy application is able to obtain input data from the model and export output information to augment or update the model in a form that allows cooperating systems to operate on the updated information. We represent the meta-model in RDF/XML which, we believe, provides several important advantages. RDF is a knowledge representation language that allows information to be described as a set of factual sentences. When these sentences are constrained by and consistent with an OWL ontology, this enables the use of an existing, robust collection of automatic reasoners and other logical tools to classify, evaluate, query, apply rules and otherwise operate on the model itself, independently of the cooperating applications. We describe a "layered" set of OWL ontologies that serve as domain models for a number of legacy operations analysis simulations, aeronautical engineering design tools and software prototypes that are used to support the integrated design and development of aeronautical systems. We describe an approach to the development of the ontologies that references, and imports concepts from well known foundational ontologies, including DOLCE, GML and PSL. We then describe an example that illustrates a methodology for creating the meta-model as an "operational scenario" that indicates the benefits to interoperability of this approach. Finally we discuss the use of SPARQL queries and SWRL rules that effectively expands the functionality of the system and greatly improves the analysis of the output of the system of cooperating simulations and tools.
Genetic Recombination between Human Immunodeficiency Virus Type 1 (HIV-1) and HIV-2, Two Distinct Human Lentiviruses (2007)

Human immunodeficiency virus type 1 (HIV-1) and HIV-2 are genetically distinct viruses that each can cause AIDS. Approximately 1 million people are infected with both HIV-1 and HIV-2. Additionally, these two viruses use the same receptor and coreceptors and can therefore infect the same target cell populations. To explore potential genetic interactions, we first examined whether RNAs from HIV-1 and HIV-2 can be copackaged into the same virion. We used modified near-full-length viruses that each contained a green fluorescent protein gene (gfp) with a different inactivating mutation. Thus, a functional gfp could be reconstituted via recombination, which was used to detect the copackaging of HIV-1 and HIV-2 RNAs. The GFP-positive (GFP(+)) phenotype was detected in approximately 0.2% of the infection events, which was 35-fold lower than the intrasubtype HIV-1 rates. We isolated and characterized 54 GFP(+) single-cell clones and determined that all of them contained proviruses with reconstituted gfp. We then mapped the general structures of the recombinant viruses and characterized the recombination junctions by DNA sequencing. We observed several different recombination patterns, including those that had crossovers only in gfp. The most common hybrid genomes had heterologous long terminal repeats. Although infrequent, crossovers in the viral sequences were also identified. Taken together, our study demonstrates that HIV-1 and HIV-2 can recombine, albeit at low frequencies. These observations indicate that multiple factors are likely to restrict the generation of viable hybrid HIV-1 and HIV-2 viruses. However, considering the large coinfected human population and the high viral load in patients, these rare events could provide the basis for the generation of novel human immunodeficiency viruses.
Explicit chemical speciation by microsecond pulsed glow discharge time-of-flight mass spectrometry: concurrent acquisition of structural, molecular and elemental information (2000)

A microsecond pulsed glow discharge (µs-pulsed GD) was used for elemental, structural and molecular analysis. This plasma was generated repeatedly at 100 Hz with a 1 kV electrical pulse lasting 20 µs. Samples were continuously introduced into the µs-pulsed discharge and allowed to interact with the plasma. Depending on the extent of this interaction, which is controllable at the discretion of the user, the samples may undergo soft chemical ionization yielding molecular ions or may be completely atomized and ionized yielding elemental information. The operator could choose the above interaction zones or anything in between, which provides structural information through an electron ionization type fragmentation pattern. Detection of plasma produced ions was done by time-of-flight mass spectrometry (TOF-MS), which is most suitable for complete mass spectrometric analysis of time-gated transient events. Using ion energetic information and the so-called ‘thermometer molecules', the magnitude of ionization energy available in the discharge was calculated. At 60 µs after the plasma ignition the plasma had an equivalent ionization energy of about 17 eV. The plasma energy decreased as a function of time. At about 300 µs the plasma reached a relatively constant ionization energy of 8–9 eV, which lasted for nearly 200 µs. Toluene, p-xylene, ethylbenzene and tungsten hexacarbonyl are among the molecules analyzed using time-gated µs-pulsed GD-TOF-MS.
Conserved WCPL and CX4C Domains Mediate Several Mating Adhesin Interactions inSaccharomyces cerevisiae (2009)

Several adhesins are induced by pheromones during mating in Saccharomyces cerevisiae, including Aga1p, Aga2p, Sag1p (Agalpha1p), and Fig2p. These four proteins all participate in or influence a well-studied agglutinin interaction mediated by Aga1p-Aga2p complexes and Sag1p; however, they also play redundant and essential roles in mating via an unknown mechanism. Aga1p and Fig2p both contain repeated, conserved WCPL and CX(4)C domains. This study was directed toward understanding the mechanism underlying the collective requirement of agglutinins and Fig2p for mating. Apart from the well-known agglutinin interaction between Aga2p and Sag1p, three more pairs of interactions in cells of opposite mating type were revealed by this study, including bilateral heterotypic interactions between Aga1p and Fig2p and a homotypic interaction between Fig2p and Fig2p. These four pairs of adhesin interactions are collectively required for maximum mating efficiency and normal zygote morphogenesis. GPI-less, epitope-tagged forms of Aga1p and Fig2p can be co-immunoprecipitated from the culture medium of mating cells in a manner dependent on the WCPL and CX(4)C domains in the R1 repeat of Aga1p. Using site-directed mutagenesis, the conserved residues in Aga1p that interact with Fig2p were identified. Aga1p is involved in two distinct adhesive functions that are independent of each other, which raises the possibility for combinatorial interactions of this protein with its different adhesion receptors, Sag1 and Fig2p, a property of many higher eukaryotic adhesins.
Quantitative studies of radiation transformation with the A31-11 mouse BALB/3T3 cell line. (1979)

A cloned mouse embryo-derived fibroblast cell line was used to study morphological transformation induced by X-rays and 254-nm ultraviolet light (UV). The transformation frequency increased exponentially with increasing dose from 10 to 400 rads for X-rays and 1.0 to 7.5 J/sq m for UV exposure. Split-dose X-ray exposures led to an enhancement in transformation at total doses below 100 rads and a reduction at doses of 300 to 400 rads. The induced transformation frequency varied among serum lots and was very dependent upon the initial cell density. Spontaneous transformants were observed in 10 of 22 consecutive experiments; the spontaneous transformation frequency was generally about 1 to 2 X 10(-5) as compared to induced frequencies which ranged up to 3 X 10(-3) for X-rays and 7.5 X 10(-4) for UV exposure. Further results indicate that this cell line has several potential advantages over the mouse 10T1/2 line for studies with relatively weak in vitro carcinogens such as radiation. These include (a) a reduced overall expression time for the appearance of transformed foci (4 weeks); (b) a high cloning efficiency (50 to 60%); and (c) the fact that about 20 times as many viable cells may be plated per dish for optimal results, allowing transformation frequencies as low as 10(-5) to be measured easily. On the other hand, there was more variability in the results among experiments with the 3T3 cell line.
Scalable Stirred-Suspension Bioreactor Culture of Human Pluripotent Stem Cells (2009)

Advances in stem cell biology have afforded promising results for the generation of various cell types for therapies against devastating diseases. However, a prerequisite for realizing the therapeutic potential of stem cells is the development of bioprocesses for the production of stem cell progeny in quantities that satisfy clinical demands. Recent reports on the expansion and directed differentiation of human embryonic stem cells (hESCs) in scalable stirred-suspension bioreactors (SSBs) demonstrated that large-scale production of therapeutically useful hESC progeny is feasible with current state-of-the-art culture technologies. Stem cells have been cultured in SSBs as aggregates, in microcarrier suspension and after encapsulation. The various modes in which SSBs can be employed for the cultivation of hESCs and human induced pluripotent stem cells (hiPSCs) are described. To that end, this is the first account of hiPSC cultivation in a microcarrier stirred-suspension system. Given that cultured stem cells and their differentiated progeny are the actual products used in tissue engineering and cell therapies, the impact of bioreactor's operating conditions on stem cell self-renewal and commitment should be considered. The effects of variables specific to SSB operation on stem cell physiology are discussed. Finally, major challenges are presented which remain to be addressed before the mainstream use of SSBs for the large-scale culture of hESCs and hiPSCs.
Study of Ta-2.5W Welding Processing Test (2007)

Ta-2.5W is a heavy metal with characteristic of difficult meltability.It is oxidized easily and tends to appear cold crack and hot crack while being welded.Through studying the series of welding,heat treatment,tensile test,high temperature static state soak test and crystalline phase analysis,the special welding processing and welding performance were grasped.
Increased Production of Immature Myeloid Cells in Cancer Patients: A Mechanism of Immunosuppression in Cancer (2001)

Defective dendritic cell (DC) function caused by abnormal differentiation of these cells is an important mechanism of tumor escape from immune system control. Previously, we have demonstrated that the number and function of DC were dramatically reduced in cancer patients. This effect was closely associated with accumulation of immature cells (ImC) in peripheral blood. In this study, we investigated the nature and functional role of those ImC. Using flow cytometry, electron microscopy, colony formation assays, and cell differentiation in the presence of different cell growth factors, we have determined that the population of ImC is composed of a small percentage (<2%) of hemopoietic progenitor cells, with all other cells being represented by MHC class I-positive myeloid cells. About one-third of ImC were immature macrophages and DC, and the remaining cells were immature myeloid cells at earlier stages of differentiation. These cells were differentiated into mature DC in the presence of 1 microM all-trans-retinoic acid. Removal of ImC from DC fractions completely restored the ability of the DC to stimulate allogeneic T cells. In two different experimental systems ImC inhibited Ag-specific T cell responses. Thus, immature myeloid cells generated in large numbers in cancer patients are able to directly inhibit Ag-specific T cell responses. This may represent a new mechanism of immune suppression in cancer and may suggest a new approach to cancer treatment.
Administration of a Replication-Deficient Adeno-Associated Virus Gene Transfer Vector Expressing the Human CLN2 cDNA to the Brain of Children with Late Infantile Neuronal Ceroid Lipofuscinosis (2004)

Late infantile neuronal ceroid lipofuscinosis (LINCL) is a fatal childhood neurodegenerative lysosomal storage disease with no known therapy. There are estimated to be 200 to 300 children in the United States at any one time with the disease. LINCL is a genetic disease resulting from a deficiency of tripeptidyl peptidase I (TPP-I), a proteolytic enzyme encoded by CLN2, the gene that is mutated in individuals with LINCL. The subjects are chronically ill, with a progressive CNS disorder that invariably results in death, typically by age 8 to 12 years. The strategy of this clinical study is based on the concept that persistent expression in the CNS of the normal CLN2 cDNA with production of sufficient amounts of TPP-I should prevent further loss of neurons, and hence limit disease progression. To assess this concept, an adeno-associated virus vector (AAV2CUh-CLN2) will be used to transfer to and express the human CLN2 cDNA in the brain of children with LINCL. The vector consists of the AAV2 capsid enclosing the 4278-base single-stranded genome consisting of the two inverted terminal repeats of AAV serotype 2 and an expression cassette composed of the human cytomegalovirus (CMV) enhancer, the chicken beta-actin promoter/splice donor and 5' end of the intron, the 3' end of the rabbit P-globin intron and splice acceptor, the human CLN2 cDNA with an optimized Kozak translation initiation signal, and the polyadenylation/transcription stop codon from rabbit 3-globin. The proposed study will include 10 individuals and will be divided into two parts. Group A, to be studied first, will include four individuals with the severe form of the disease. Group B of the trial will include six individuals with a moderate form of the disease. After direct intracranial administration of the vector, there will be neurological assessment based on the LINCL clinical rating scale and magnetic resonance imaging/magnetic resonance spectroscopy assessment of the brain in regions of vector administration. The data generated will help evaluate two hypotheses: (1) that it is safe to carry out direct intracranial administration of the AAV2cuhCLN2 vector to the CNS of individuals with LINCL, and (2) that administration of the AAV2cuhCLN2 vector will slow down or halt the progression of the disease in the central nervous system.
Selective Electrical Stimulation of Peripheral Nerve Fibers: Accommodation Based Methods (2004)

project was motivated by the idea of using and adapting accommodation-based methods for selective electrical stimulation of motor fibers to the study of the human nociceptive system. This has not been without difficulties, but it has still been a rewarding process, as it has provided the opportunity to study interesting biophysical mechanisms and to enhance the understanding of accommodation based methods. Throughout this project, I am indebted to all the co-workers and friends at the Center of Sensory Motor Interaction and at the Faculty of Dentistry, University of Toronto that I have had the fortune to work with and learn from. I wish to express my sincerest gratitude to my supervisor Associate Prof. Ole K. Andersen and Professor Lars Arendt-Nielsen, the head of Center for Sensory Motor Interaction, for their never failing interest and enthusiasm. I will also like to express my deepest gratitude to my hosts at the Faculty of Dentistry, University of Toronto, Professor Barry J. Sessle and Professor James W. Hu. Furthermore, I will like to thank Dr. Alexandra Vuckovic for graciously offering her volume conductor
A Randomized, Placebo-Controlled, Clinical Trial of High-Dose Supplementation With Vitamins C and E, Beta Carotene, and Zinc for Age-Related Macular Degeneration and Vision Loss (2001)

Persons older than 55 years should have dilated eye examinations to determine their risk of developing advanced AMD. Those with extensive intermediate size drusen, at least 1 large druse, noncentral geographic atrophy in 1 or both eyes, or advanced AMD or vision loss due to AMD in 1 eye, and without contraindications such as smoking, should consider taking a supplement of antioxidants plus zinc such as that used in this study.
High-resolution, lensless endoscope based on digital scanning through a multimode optical fiber (2013)

We propose and experimentally demonstrate an ultra-thin rigid endoscope (450 μm diameter) based on a passive multimode optical fiber. We use digital phase conjugation to overcome the modal scrambling of the fiber to tightly focus and scan the laser light at its distal end. By exploiting the maximum number of modes available, sub-micron resolution, high quality fluorescence images of neuronal cells were acquired. The imaging system is evaluated in terms of fluorescence collection efficiency, resolution and field of view. The small diameter of the proposed endoscope, along with its high quality images offer an opportunity for minimally invasive medical endoscopic imaging and diagnosis based on cellular phenotype via direct tissue penetration.