gebhart/patrepeval huggingface dataset:
Implementing design patterns as parametric aspects using ParaAJ: The case of the singleton, observer, and decorator design patterns (2015)

Implementation of a design pattern can take many forms according to the programming language being used. Most of the literature presents design patterns in their conventional object-oriented implementations. Several other studies show the implementation in aspect-oriented languages such as AspectJ, EOS, and Caesar. In this work, we compare the implementation of three design patterns: singleton, observer, and decorator design patterns in these languages and also discuss the possibility of implementing them in ParaAJ: an extension to the AspectJ language that implements the idea of parametric aspects. We found that ParaAJ helps in making the implementation of the singleton and observer patterns reusable but it fails to help in the decorator case. The problem with the decorator pattern exists because of the current translation mechanism of ParaAJ׳s aspects to normal AspectJ׳s aspects. This opens the door for further work in ParaAJ to better support the idea of parametric aspects.
RETRACTED: SARS–CoV–2 Spike Impairs DNA Damage Repair and Inhibits V(D)J Recombination In Vitro (2021)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the coronavirus disease 2019 (COVID-19) pandemic, severely affecting public health and the global economy. Adaptive immunity plays a crucial role in fighting against SARS-CoV-2 infection and directly influences the clinical outcomes of patients. Clinical studies have indicated that patients with severe COVID-19 exhibit delayed and weak adaptive immune responses; however, the mechanism by which SARS-CoV-2 impedes adaptive immunity remains unclear. Here, by using an in vitro cell line, we report that the SARS-CoV-2 spike protein significantly inhibits DNA damage repair, which is required for effective V(D)J recombination in adaptive immunity. Mechanistically, we found that the spike protein localizes in the nucleus and inhibits DNA damage repair by impeding key DNA repair protein BRCA1 and 53BP1 recruitment to the damage site. Our findings reveal a potential molecular mechanism by which the spike protein might impede adaptive immunity and underscore the potential side effects of full-length spike-based vaccines.
Characterization of Salivary Immunoglobulin A Responses in Children Heavily Exposed to the Oral Bacterium <i>Streptococcus mutans</i> : Influence of Specific Antigen Recognition in Infection (2005)

The initial infection of children by Streptococcus mutans, the main pathogen of dental caries, depends on the ability of S. mutans to adhere and accumulate on tooth surfaces. These processes involve the adhesin antigen I/II (AgI/II), glucosyltransferases (GTF) and glucan-binding protein B (GbpB), each a target for anticaries vaccines. The salivary immunoglobulin A (IgA) antibody responses to S. mutans antigens (Ags) were characterized in 21 pairs of 5- to 13-month-old children. Pairs were constructed with one early S. mutans-infected and one noninfected child matched by age, racial background, number of teeth, and salivary levels of IgA. Specific salivary IgA antibody response and S. mutans infection levels were then measured during a 1-year follow-up. Robust responses to S. mutans were detected from 6 months of age. Salivary IgA antibody to AgI/II and GTF was commonly detected in salivas of all 42 children. However, GbpB-specific IgA antibody was seldom detected in the subset of infected children (38.1% at baseline). In contrast, most of the subset of noninfected children (76.2%) showed GbpB-reactive IgA antibody during the same period. Frequencies of GbpB responses increased with age, but differences in intensities of GbpB-IgA antibody reactions were sustained between the subsets. At baseline, GbpB-reactive IgA antibody accounted for at least half of the total salivary IgA S. mutans-reactive antibody in 33.3 and 9.5% of noninfected and infected children, respectively. This study provides evidence that a robust natural response to S. mutans Ags can be achieved by 1 year of age and that IgA antibody specificities may be critical in modulating initial S. mutans infection.
Heterogeneity of erbB-2 gene amplification in bladder cancer. (1993)

erbB-2 amplification and overexpression have been suggested as potentially useful prognostic markers in bladder cancer. We examined 141 bladder tumor specimens (45 fresh tissue samples and 96 formalin fixed tissue blocks) for erbB-2 amplification using fluorescence in situ hybridization. A dual labeling hybridization using a repetitive pericentromeric probe specific for chromosome 17 and a cosmid probe for the erbB-2 locus was performed to analyze the erbB-2 copy number in relation to chromosome 17 copy number on a cell by cell basis. Amplification (more than twice as many erbB-2 signals as centromere 17 signals per tumor) was found in 10 of 141 tumors. There was considerable heterogeneity in erbB-2 amplification. In a given tumor there was a wide range of erbB-2 copy number in amplified cells. The arrangement of erbB-2 signals in clusters in all amplified cases suggests that erbB-2 amplification occurs intrachromosomally in bladder cancer. Amplification was found only in tumors with aneusomy of chromosome 17 and was more frequent in pT2-T4 tumors than in pTa/T1 tumors. Overexpression was present without amplification in 51 tumors. All tumors with erbB-2 amplification showed erbB-2 overexpression. However, in 5 samples the proportion of cells with amplification was significantly lower than the fraction of cells with overexpression, indicating coexistence of two different mechanisms leading to overexpression in these tumors.
Extracting information about emotions in films (2003)

We present a method being developed to extract information about characters' emotions in films. It is suggested that this information can help describe higher levels of multimedia semantics relating to narrative structures. Our method extracts information from audio description that is provided for the visually-impaired with an increasing number of films. The method is based on a cognitive theory of emotions that links a character's emotional states to the events in their environment. In this paper the method is described along with some preliminary evaluation and discussions about the kinds of novel video retrieval and browsing applications it may support.
Treeing in Polyethylene as a Prelude to Breakdown (1958)

Trees, or fine, branching, microscopic channels extending partly or even wholly through a wall of insulation, represent a characteristic form of latent damage. This phase of dielectric breakdown has been studied in polyethylene. The phenomenon is probably similar in other dielectrics, such as rubber, where it cannot be so readily seen. A method of observing the progressive stages of treeing and final punchout under the microscope is described. The similarity between the appearance in the final stage of needle breakdowns after preliminary treeing and that of the breakdown paths from ordinary tests with alternating, direct, or impulse voltage supports the view that in most breakdowns the eventual failure is preceded by treeing. It is probable that the time interval between the start of a tree and the final breakdown can vary from months to microseconds. At low over-all stress trees may start at points of high local overstress but eventually stop growing. This permits the growth of the other trees before breakdown, so that the presence of many trees in different stages of growth is most likely in insulation after prolonged life tests. At very high stress the first channel may traverse the wall before others form and the whole process from tree start to final punchout may require times only of the order of microseconds. Regardless of the time scale, the phenomenon seems to be basically similar, in that the tree comes before the punchout.
Phylogenetic relationships, evolution, and genetic diversity of the domestic dog (1999)

The spectacular diversity in size, conformation, and pelage that characterizes the domestic dog reflects not only the intensity of artificial selection but ultimately the genetic variability of founding populations. Here we review past molecular genetic data that are relevant to understanding the origin and phylogenetic relationships of the dog. DNA-DNA hybridization data show that the dog family Canidae diverged about 50 million years ago from other carnivore families. In contrast, the extant canids are very closely related and diverged from a common ancestor about 10 million years ago. The evidence supporting a close relationship of dogs with gray wolves is overwhelming. However, dogs are remarkably diverse in mitochondrial and nuclear genes. Mitochondrial DNA analysis suggests a more ancient origin of dogs than has been indicated by the fossil record. In addition, dogs have originated from or interbred with wolves throughout their history at different times and different places. We test the possibility of an independent domestication event in North America by analysis of mtDNA variation in the Xoloitzcuintli. This unusual breed is believed to have been kept isolated for thousands of years and may be one of the most ancient breeds in North America. Our results do not support a New World domestication of dogs nor a close association of the Xoloitzcuintli with other hair-less breeds of dogs. Despite their phenotypic uniformity, the Xoloitzcuintli has a surprisingly high level of mtDNA sequence variation. Other breeds are also genetically diverse, suggesting that dog breeds were often founded with a large number of dogs from outbred populations.
Detection of the molecular abnormality in chronic myeloid leukemia by use of the polymerase chain reaction (1988)

The bcr-abl translocation characteristic of chronic myeloid leukemia (CML) was detected by the polymerase chain reaction (PCR) modified to use mRNA as the starting material. Amplification of a sequence spanning the bcr-abl junction was obtained by using peripheral blood cells from all of 20 patients with classic CML, one patient with acute lymphoblastic leukemia probably secondary to CML, and two cell lines derived from patients with CML. The presence of bcr exon 3 in the mRNA was determined from the size of the amplified sequence; it was present in 14 and absent in seven patients. One leukemic cell per 1,000 nonleukemic cells could be readily detected, thus indicating the great sensitivity of the method. This technique is of routine value in CML both for diagnosis and for following the course of treatment.
Endo-vacuum Assisted Closure Treatment for Rectal Anastomotic Insufficiency (2008)

Endo-vacuum assisted closure therapy is a novel approach that can be considered in diverted patients with failed colorectal anastomoses. Larger randomized trials that include complete cost-benefit analyses are needed to establish its role in this setting.
SLAM Family Receptors Regulate Immunity with and without SAP-related Adaptors (2004)

Two papers describing mice deficient in signaling lymphocyte activation molecule and 2B4 represent the first accounts of immune phenotypes in animals lacking members of the SLAM family of receptors. The findings provide definitive evidence of the importance of SLAM-related receptors in the regulation of T cell, macrophage, and natural killer cell functions.
Liquid and Supercritical Carbon Dioxide Loading into Chewing Gum Base (2003)

The sorption and loading of liquid and supercritical CO2 into chewing gum base spheres with radii of 0.5 cm was experimentally explored over the temperature and pressure ranges of 25−45 °C and 70−276 bar, respectively. Maximum loading amounts were found to be independent of temperature and to increase with increasing CO2 density. The time required to achieve maximum loading decreased with increasing temperature. A loading as high as 0.094 g of CO2 per gram of gum base was achieved. The sorption process was modeled by unsteady-state radial Fickian diffusion assuming a constant diffusion coefficient at a particular temperature and pressure (CO2 density). Volume changes of the polymer blend spheres under the conditions explored were small and ignored in the modeling. Sorption diffusion coefficients were on the order of 10-10 m2/s and increased with increasing temperature and CO2 density.
Wnt/beta-catenin pathway: modulating anticancer immune response (2017)

Wnt/β-catenin signaling, a highly conserved pathway through evolution, regulates key cellular functions including proliferation, differentiation, migration, genetic stability, apoptosis, and stem cell renewal. The Wnt pathway mediates biological processes by a canonical or noncanonical pathway, depending on the involvement of β-catenin in signal transduction. β-catenin is a core component of the cadherin protein complex, whose stabilization is essential for the activation of Wnt/β-catenin signaling. As multiple aberrations in this pathway occur in numerous cancers, WNT-directed therapy represents an area of significant developmental therapeutics focus. The recently described role of Wnt/β-catenin pathway in regulating immune cell infiltration of the tumor microenvironment renewed the interest, given its potential impact on responses to immunotherapy treatments. This article summarizes the role of Wnt/β-catenin pathway in cancer and ongoing therapeutic strategies involving this pathway.
N-Heterocyclic carbene (NHC)-catalysed atom economical construction of 2,3-disubstituted indoles (2017)

A novel organocatalytic approach, harnessing the unique reactivities of N-heterocyclic carbenes (NHCs), has been revealed for the construction of indoles. The NHC-catalysed atom economical synthesis of a wide range of 2-substituted indole-3-acetic acid derivatives is displayed. Strategic application of the developed method was demonstrated for a short synthesis of a cyclin-dependent kinase (CDK) inhibitor: paullone.
Nucleotide sequence and mutational analysis indicate that two <i>Helicobacter pylori</i> genes encode a P‐type ATPase and a cation‐binding protein associated with copper transport (1995)

Summary A 2.7 kb fragment of Helicobacter pylori UA802 chromosomal DNA was cloned and sequenced. Three open reading frames (designated ORF1, oRF2 and ORF3, respectively) were predicted from the DNA sequence, of which ORF1 and ORF2 appeared to be located within the same operon. The deduced 611‐amino‐acid sequence of ORF1, a P‐type ATPase (designated hpCopA), had striking homology (29‐38%) with several bacterial P‐type ATPases and contained the potential functional domains conserved in P‐type ATPases from various sources ranging from bacterial to human. A protein of 66 amino acids (designated hpCopP) encoded by ORF2 shared extensive sequence similarity with MerP, a periplasmic mercuric ion‐transporting protein, and contains the heavy metal‐binding motif. Disruption of ORF1 with a chloramphenicol‐resistance cassette (CAT) rendered the H. pylori mutants more susceptible to cupric ion than their parental strains, whereas there is no significant alternation of susceptibility to Ni 2+ , Cd 2+ and Hg 2+ between the mutants and the parental strains. The results obtained indicate that ORF1 and ORF2 comprise a cation‐transporting system which is associated with copper export out of the H. pylori cells.
Analysis of Error Recovery Schemes for Networks on Chips (2005)

In this article, we discuss design constraints to characterize efficient error recovery mechanisms for the NoC design environment. We explore error control mechanisms at the data link and network layers and present the schemes' architectural details. We investigate the energy efficiency, error protection efficiency, and performance impact of various error recovery mechanisms.
Tiling resolution array CGH and high density expression profiling of urothelial carcinomas delineate genomic amplicons and candidate target genes specific for advanced tumors (2008)

The presented data indicates 6p22 as a composite amplicon with more than one possible target gene. The data also suggests that amplification of 6p22 and homozygous deletions of 9p21 may have complementary roles. Furthermore, the analysis of paralogous regions that showed genomic amplification indicated altered expression of YWHA (14-3-3) genes as important events in the development of UC.
Human Papillomavirus Infections in Nonmelanoma Skin Cancers From Renal Transplant Recipients and Nonimmunosuppressed Patients (1996)

The presence of HPV DNA in a large percentage of specimens of nonmelanoma carcinomas of the skin from immunosuppressed patients, as well as from nonimmmunosuppressed patients, renders a papillomavirus infection as a possible factor in the etiology of this disease.
Standard management options for rosacea, part 2: options according to subtype. (2009)

The standard management options were developed by a consensus committee and review panel of 26 experts to assist in providing optimal patient care based on the standard classification and grading systems for rosacea that were developed to perform research; analyze results and compare data from different sources; and provide a common terminology and reference for the diagnosis, treatment, and assessment of results in clinical practice. We discuss the standard management options for rosacea in 2 parts: (1) overview and broad spectrum of care, and (2) management options according to subtype. The menu of options is considered provisional and may be expanded and updated as appropriate. Managing the various potential signs and symptoms of rosacea calls for consideration of a broad spectrum of care, and a more precise selection of therapeutic options may become increasingly possible as the mechanisms of action of therapies are more definitively established.
One electron at a time oxidations and enzymatic paradigms: from metallic to non-metallic redox centers (2000)

Biomimetic models of redox metalloenzymes may serve to elucidate structure and mechanisms of these enzymes and, moreover, new catalysts for synthesis can ensue from these models. A number of metalloenzymes utilize free radicals as a catalytic competent cofactor to promote oxidation reactions. Non metallic redox centers (free radicals) may be an advantageous alternative to metallic centers. Several biomimetic approaches are described concerning two selected enzymes, copper–zinc superoxide dismutase and galactose oxidase. The advantages of organic radical instead of metallic centers in abstracting hydrogen atoms are discussed.
Radiation therapy of the oral cavity: Sequelae and management, part 1 (1979)

This is the first article in a two-part series dealing with the effects and manifestations in the oral cavity of radiation therapy of head and neck tumors. In this section, oral mucous membranes, taste buds, edema and trismus, diet, salivary glands, bone, periodontium, teeth, and composition of oral flora are discussed. Dental management of the dentulous patient is then approached; criteria for preradiation extraction are delineated. In the next issue of Head & Neck Surgery, the final article in this series will discuss preradiation and postradiation extractions and will elaborate on the dental management (fluoride treatments, follow-up, and restorative care) of the dentulous patient. Dental management of the edentulous patient will also be presented.
Cross-linking Measurements of In Vivo Protein Complex Topologies (2011)

Identification and measurement of in vivo protein interactions pose critical challenges in the goal to understand biological systems. The measurement of structures and topologies of proteins and protein complexes as they exist in cells is particularly challenging, yet critically important to improve understanding of biological function because proteins exert their intended function only through the structures and interactions they exhibit in vivo. In the present study, protein interactions in E. coli cells were identified in our unbiased cross-linking approach, yielding the first in vivo topological data on many interactions and the largest set of identified in vivo cross-linked peptides produced to date. These data show excellent agreement with protein and complex crystal structures where available. Furthermore, our unbiased data provide novel in vivo topological information that can impact understanding of biological function, even for cases where high resolution structures are not yet available.
Ein integriertes chemisches Verfahren: Eintopfaromatisierung von cyclischen Enonen durch Doppeleliminierung (1999)

Eine Vielzahl von aromatischen Kohlenwasserstoffen mit mehreren Alkylsubstituenten läßt sich unter vollständiger Regiokontrolle in einer Eintopfreaktion aus Cyclohexenon und dessen aromatischen Analoga herstellen [Gl. (1)]. Die vorgestellte Methode kann auch auf die Synthese von polycyclischen aromatischen Kohlenwasserstoffen ausgedehnt werden. Die Nachteile der Friedel-Crafts-Reaktion treten nicht auf, da die Reaktion unter basischen Bedingungen stattfindet.
Synthesis and characterization of a novel UHMWPE interpenetrating polymer network. (1999)

A novel, biomimetic, interpenetrating polymer network (IPN) between poly-L-lysine (PLL) and ultra high molecular weight polyethylene (UHMWPE) has been synthesized in an attempt to decrease wear in joint prostheses. A biomaterial with a gradient IPN of cationic PLL and UHMWPE has been synthesized, in the surface of bulk UHMWPE, to recruit the poly-anion, hyaluronic acid, from the synovial fluid. It is hypothesized that the hyaluronic acid molecules and their associated hydration layer will improve lubrication between the articulating surfaces, thus lowering both friction and wear. The synthesis involves four steps. Silylation of the PLL-HBr to PLL-SiMe3 utilizing bis(trimethylsiyl)acetamide (BSA). Swelling of the UHMWPE in a solution of PLL-SiMe3/xylenes at 60 degrees C with ultrasonics. Crosslinking of the PLL-SiMe3 within the UHMWPE with 1,8-diisocyanatooctane (a.k.a. OMDI). Finally, de-swelling and drying of the IPN under vacuum at 50 C. Visual observations show an adhered film on the IPN surface. Reflective FTIR spectra contain the characteristic peaks associated with UHMWPE. Two additional peaks, at 3410 and 1690 cm-1, are associated with PLL. SEM shows a morphology dominated by PLL spheres with diameters ranging from < 1 micron up to 3 micron. This shows that the PLL-SiMe3 has been crosslinked by the OMDI and was not rinsed away by either xylenes or sonicated water rinses. High contact angle of the PLL in contact with the UHMWPE demonstrate that the PLL has been de-silylated and returned to its hydrophilic nature. The spheres attached to the surface of the UHMWPE indicate that PLL has infiltrated the UHMWPE physical network and is entangled there. XPS confirms the presence of nitrogen by a 3-5 atomic percent signal in the outer 100 A of the IPN surface.
Separately reconstructing the structural and functional parameters of a fluorescent inclusion embedded in a turbid medium (2006)

We report a novel imaging technique for fluorescence diffuse optical tomography (FDOT). Unlike conventional FDOT, this technique separates the imaging procedure into two steps to respectively reconstruct the structural information (such as the center position and the radius), and the functional information (such as the fluorophore concentration and/or lifetime) of a fluorescing target embedded in a turbid medium. The structural parameters of the target were estimated from the amplitude ratio and phase difference of fluorescence signals received at different detectors, because the amplitude ratio and phase difference were found independent of, or weakly related to, the functional parameters. Based on the estimated structural parameters, a dual-zone mesh technique was utilized to reconstruct the fluorophore concentration. Results of simulations and phantom experiments showed that the structural parameters could be accurately recovered, without knowing the functional information, and that the reconstruction accuracy of the functional parameter was greater than 80%.