gebhart/patrepeval huggingface dataset:
Breast cancer subtypes and response to docetaxel in node-positive breast cancer: Use of an immunohistochemical definition in the BCIRG 001 trial (2019)

Purpose To investigate the prognostic and predictive significance of subtyping node-positive early breast cancer by immunohistochemistry in a clinical trial of a docetaxel-containing regimen. Methods Pathologic data from a central laboratory were available for 1,350 patients (91%) from the BCIRG 001 trial of docetaxel, doxorubicin, and cyclophosphamide (TAC) versus fluorouracil, doxorubicin, and cyclophosphamide (FAC) for operable node-positive breast cancer. Patients were classified by tumor characteristics as (1) triple negative (estrogen receptor [ER]–negative, progesterone receptor [PR]–negative, HER2/neu [HER2]–negative), (2) HER2 (HER2-positive, ER-negative, PR-negative), (3) luminal B (ER-positive and/or PR-positive and either HER2-positive and/or Ki67high), and (4) luminal A (ER-positive and/or PR-positive and not HER2-positive or Ki67high), and assessed for prognostic significance and response to adjuvant chemotherapy. Results Patients were subdivided into triple negative (14.5%), HER2 (8.5%), luminal B (61.1%), and luminal A (15.9%). Three-year disease-free survival (DFS) rates (P values with luminal B as referent) were 67% (P < .0001), 68% (P = .0008), 82% (referent luminal B), and 91% (P = .0027), respectively, with hazard ratios of 2.22, 2.12, and 0.46. Improved 3-year DFS with TAC was found in the luminal B group (P = .025) and a combined ER-positive/HER2-negative group treated with tamoxifen (P = .041), with a marginal trend in the triple negatives (P = .051) and HER2 (P = .068) subtypes. No DFS advantage was seen in the luminal A population. Conclusion A simple immunopanel can divide breast cancers into biologic subtypes with strong prognostic effects. TAC significantly complements endocrine therapy in patients with luminal B subtype and, in the absence of targeted therapy, is effective in the triple-negative population.
Modulated Noise Communication: Reading UHF RFID tags without a carrier (2023)

This paper demonstrates that UHF RFID tags can be read without a carrier. More specifically, using an alternative reader design that does not emit a carrier, we show that it is possible to read an RFID tag that was designed to be read by a conventional RFID reader that does emit a carrier. Typical RFID tags are designed to modulate a carrier; it turns out that, in addition to modulating a carrier, a backscatter modulator circuit also modulates tag circuit noise, including Johnson noise; Johnson and other noise is present in a tag even if a carrier is not. Modulated Noise Communication (MNC) can be read by an alternative reader design. The reader for modulated noise communication is simpler than a conventional backscatter reader because it does not have to contend with the problem of self-jamming. The absence of a carrier means that the tag needs an alternative power source; this could be an energy harvester such as a photovoltaic cell, or could be a time-multiplexed continuous wave signal from the reader. The use of time multiplexing means that the reader would still inherit the benefits of not needing to counteract self jamming.
Expression and Prognostic Relevance of GAGE1 and XAGE1 Cancer/Testis Antigens in Head and Neck Squamous Cell Carcinoma (2018)

These findings suggest GAGE1 and XAGE1 expressions to be useful as prognostic markers for HNSCC.
Synthesis of Indenyl Ethers by Gold(I)-Catalyzed Intramolecular Carboalkoxylation of Alkynes (2006)

The gold(I)-catalyzed carboalkoxylation of alkynes to form indanone derivatives from readily available ortho-acetylenic benzylic ethers is described. Importantly, the gold(I)-catalyzed rearrangement of enantioenriched benzylic ethers proceeds with chirality transfer, thus providing a practical method for the enantioselective synthesis of indenyl ethers.
Detailed graphical models for source separation and missing data interpolation in audio (2004)

Methods for blind source separation based only on general properties such as source independence encounter difficulties when the degree of overlap and/or the dimensionality of the observations make the blind inference problem unresolvable. Such situations require additional constraints on the form of the individual sources, motivating the development of models able to capture in detail the consistency and variability of a single source's sound. With single-chain HMMs this requires a very large number of states, making the models marginally practical. Here we present two approaches to factorize the variability in detailed models. First is a coupled subband model, where each source signal is broken into multiple frequency bands, and separate but coupled HMMs are built for each band requiring many fewer states per model. In order to avoid the unnatural state combinations that would arise from independent models for each band, we couple adjacent bands resulting in a grid-like model for the full spectrum. Exact inference of such a model is intractable, but we have derived an efficient approximation based on variational methods.
Human bornavirus research: Back on track! (2019)

Bornavirus infections in man have been a matter of controversial scientific debate for most of the last three decades. Because Borna disease virus 1 (BoDV-1) was known to cause fatal encephalitis and behavioral changes in a broad range of infected animals, it is perhaps not surprising that some virologists and clinicians suspected bornaviruses to also induce behavioral and psychiatric disorders in people. In contrast, the possibility of lethal bornavirus-induced disease of the human central nervous system was not appropriately taken into consideration. As recent research shows, however, for years they have been barking up the wrong tree.
Absence of protease-resistant prion protein in the cerebrospinal fluid of Creutzfeldt-Jakob disease (2001)

Creutzfeldt-Jakob disease (CJD), believed to be caused by a protease-resistant isoform of prion protein (PrP(Sc)), usually manifests itself as a clinically distinctive age-related dementia because of its rapid progression, occasionally accompanied by cerebellar ataxia. Recently, a variant CJD (vCJD) has been described, which has prominent early psychiatric symptoms and an earlier age of death. Although cerebrospinal fluid (CSF) is part of the extracellular fluid of the central nervous system (CNS), the bulk of its proteins are derived from the plasma and there is increasing concern about possible transmission of prion disease by blood. As investigation of CSF has played a significant role in the diagnosis and management of several neurological diseases, it was decided to characterize PrP present in the CSF of CJD individuals. Significant variation was observed in the level of PrP in the CSF from both non-CJD and CJD (including vCJD) patients, and the detected PrP forms are protease-sensitive. Using a conformation-dependent immunoassay, it was further demonstrated that the PrP detected in the CSF from CJD patients was broadly similar in conformation to that found in non-CJD patients. Taken together, the results of this study fail to demonstrate any correlation between the presence of protease-resistant PrP isoform (PrP(Sc)) in the CSF and disease manifestation.
Evolutionary Conservation of the <i>FLOWERING LOCUS C</i> -Mediated Vernalization Response: Evidence From the Sugar Beet ( <i>Beta vulgaris</i> ) (2006)

In many plant species, exposure to a prolonged period of cold during the winter promotes flowering in the spring, a process termed vernalization. In Arabidopsis thaliana, the vernalization requirement of winter-annual ecotypes is caused by the MADS-box gene FLOWERING LOCUS C (FLC), which is a repressor of flowering. During the vernalization process, FLC is downregulated by alteration of its chromatin structure, thereby permitting flowering to occur. In wheat, a vernalization requirement is imposed by a different repressor of flowering, suggesting that some components of the regulatory network controlling the vernalization response differ between monocots and dicots. The extent to which the molecular mechanisms underlying vernalization have been conserved during the diversification of the angiosperms is not well understood. Using phylogenetic analysis, we identified homologs of FLC in species representing the three major eudicot lineages. FLC homologs have not previously been documented outside the plant family Brassicaceae. We show that the sugar beet FLC homolog BvFL1 functions as a repressor of flowering in transgenic Arabidopsis and is downregulated in response to cold in sugar beet. Cold-induced downregulation of an FLC-like floral repressor may be a central feature of the vernalization response in at least half of eudicot species.
Effects of low sample mean values and small sample size on the estimation of the fixed dispersion parameter of Poisson-gamma models: A Bayesian Perspective (2006)

There has been considerable research conducted on the development of statistical models for predicting motor vehicle crashes on highway facilities. Many of these developments were performed for the likelihood-based or frequentist modeling approach. Over the last few years, there has been a significant increase in the application hierarchical Bayes method for modeling motor vehicle crashes. Whether the inferences are estimates using the likelihood-based or the Bayesian method, the most common probabilistic structure used for modeling this type of data remains the traditional Poisson-gamma (or Negative Binomial) distribution. Crash data collected for highway safety studies often have the unusual attributes of being characterized by low sample mean values and, due to the prohibitive costs of collecting data, small sample sizes. Previous studies have shown that the dispersion parameter of Poisson-gamma models can be seriously mis-estimated when the coefficients are estimated using the maximum likelihood method (MLE) for these extreme conditions. Despite important work done on this topic for the MLE, nobody has so far examined how low sample mean values and small sample sizes affect the posterior mean of the dispersion parameter of Poisson-gamma models estimated using the hierarchical Bayes method. The inverse dispersion parameter (posterior mean) plays an important role in various types of highway safety studies, such as building confidence intervals for comparing the safety performance of different highway design alternatives and the application of the empirical Bayes (EB) method for refining the long-term mean of a highway entity, and is particularly important for practitioners who are not familiar with Bayesian methods. It is therefore vital to determine the conditions in which the inverse dispersion parameter may be mis-estimated for this category of models. To accomplish the objectives of this study, a series of Poisson-gamma distributions are simulated using different values describing the mean, the dispersion parameter, the sample size, and the prior specification. Non-informative and informative prior specifications are tested for determining the magnitude of the biases introduced by low sample mean values and small sample sizes. A series of Poisson-lognormal distributions are also simulated, in the light of recent work done by statisticians on this mixed distribution. The study shows that a dataset characterized by a low sample mean combined with a small sample size can seriously affect the estimation of the posterior mean of the dispersion parameter when a non-informative prior specification is used to characterize the gamma hyper-parameter. The risk of a mis-specified posterior mean can be greatly minimized when an appropriate informative prior distribution is used. Finally, the study shows that Poisson-lognormal models are recommended over Poisson-gamma models whenever crash data characterized by low sample mean values are used for developing crash prediction models.
Bayesian Model-Agnostic Meta-Learning (2018)

Learning to infer Bayesian posterior from a few-shot dataset is an important step towards robust meta-learning due to the model uncertainty inherent in the problem. In this paper, we propose a novel Bayesian model-agnostic meta-learning method. The proposed method combines scalable gradient-based meta-learning with nonparametric variational inference in a principled probabilistic framework. During fast adaptation, the method is capable of learning complex uncertainty structure beyond a point estimate or a simple Gaussian approximation. In addition, a robust Bayesian meta-update mechanism with a new meta-loss prevents overfitting during meta-update. Remaining an efficient gradient-based meta-learner, the method is also model-agnostic and simple to implement. Experiment results show the accuracy and robustness of the proposed method in various tasks: sinusoidal regression, image classification, active learning, and reinforcement learning.
Clinical Courses of Two Pediatric Patients with Acute Megakaryoblastic Leukemia Harboring the CBFA2T3-GLIS2 Fusion Gene (2016)

Acute megakaryoblastic leukemia (AMKL) in children without Down syndrome (DS) has an extremely poor outcome with 3-year survival of less than 40%, whereas AMKL in children with DS has an excellent survival rate. Recently, a novel recurrent translocation involving CBFA2T3 and GLIS2 was identified in about 30% of children with non-DS AMKL, and the fusion gene was reported as a strong poor prognostic factor in pediatric AMKL. We report the difficult clinical courses of pediatric patients with AMKL harboring the CBFA2T3-GLIS2 fusion gene.
Biochemical Characterization of CYP505D6, a Self-Sufficient Cytochrome P450 from the White-Rot Fungus Phanerochaete chrysosporium (2018)

The activity of a self-sufficient cytochrome P450 enzyme, CYP505D6, from the lignin-degrading basidiomycete <i>Phanerochaete chrysosporium</i> was characterized. Recombinant CYP505D6 was produced in <i>Escherichia coli</i> and purified. In the presence of NADPH, CYP505D6 used a series of saturated fatty alcohols with C<sub>9-18</sub> carbon chain lengths as the substrates. Hydroxylation occurred at the ω-1 to ω-6 positions of such substrates with C<sub>9-15</sub> carbon chain lengths, except for 1-dodecanol, which was hydroxylated at the ω-1 to ω-7 positions. Fatty acids were also substrates of CYP505D6. Based on the sequence alignment, the corresponding amino acid of Tyr51, which is located at the entrance to the active-site pocket in CYP102A1, was Val51 in CYP505D6. To understand the diverse hydroxylation mechanism, wild-type CYP505D6 and its V51Y variant and wild-type CYP102A1 and its Y51V variant were generated, and the products of their reaction with dodecanoic acid were analyzed. Compared with wild-type CYP505D6, its V51Y variant generated few products hydroxylated at the ω-4 to ω-6 positions. The products generated by wild-type CYP102A1 were hydroxylated at the ω-1 to ω-4 positions, whereas its Y51V variant generated ω-1 to ω-7 hydroxydodecanoic acids. These observations indicated that Val51 plays an important role in determining the regiospecificity of fatty acid hydroxylation, at least that at the ω-4 to ω-6 positions. Aromatic compounds, such as naphthalene and 1-naphthol, were also hydroxylated by CYP505D6. These findings highlight a unique broad substrate spectrum of CYP505D6, rendering it an attractive candidate enzyme for the biotechnological industry.<b>IMPORTANCE</b><i>Phanerochaete chrysosporium</i> is a white-rot fungus whose metabolism of lignin, aromatic pollutants, and lipids has been most extensively studied. This fungus harbors 154 cytochrome P450-encoding genes in the genome. As evidenced in this study, <i>P. chrysosporium</i> CYP505D6, a fused protein of P450 and its reductase, hydroxylates fatty alcohols (C<sub>9-15</sub>) and fatty acids (C<sub>9-15</sub>) at the ω-1 to ω-7 or ω-1 to ω-6 positions, respectively. Naphthalene and 1-naphthol were also hydroxylated, indicating that the substrate specificity of CYP505D6 is broader than those of the known fused proteins CYP102A1 and CYP505A1. The substrate versatility of CYP505D6 makes this enzyme an attractive candidate for biotechnological applications.
Use of the Kalman filters for the analysis of the mechanical properties of human skin <b><i>in vivo</i></b> (2008)

In this article, we present an inverse method for the identification of the mechanical properties of human skin, a complex multi-layered organ which has been studied in vivo using a suction deformation technique. To identify the required properties, experimental results were compared to finite element solutions of the test, with the assumption that skin behaves as a single isotropic hyperelastic layer. The inverse method used in this article is based on that of the extended Kalman filters principle, with two modifications of this standard formulation for use in skin analysis. The modified formulation was then tested using Finite Element Method (FEM) simulated mechanical data and also with a study of linear and nonlinear theoretical problems. The results of the new formulation were also compared with the Gauss–Newton, recursive least square and Kalman smoother approaches. Finally, the reliability of the method was tested on a case study.
Terahertz plasmon-resonant microship emitters and their possible sensing and spectroscopic applications (2009)

This paper reviews recent advances in emission of terahertz (THz) radiation utilizing two-dimensional plasmons in semiconductor heterostructures and their possible sensing and spectroscopic applications. The device is introduced as a light source into a Fourier-transform THz spectrometer. Water-vapor absorption lines as well as fingerprints of honey and maple syrup of suger-group materials were successfully observed.
ZnSe-facet-passivated InGaAs/InGaAsP/InGaP diodelasers of highCW power and ‘wallplug’ efficiency (1996)

A 2.85 W CW output, front-facet-emitted power and 54% maximum CW power conversion efficiency have been obtained from aluminum-free, InGaAs/InGaAsP/InGaP optimised-facet-coated, wide-stripe (100 µm) diode lasers emitting at 950 nm. Half-wave ZnSe layers, deposited on the laser facets prior to applying low/high reflectivity (LR/HR) dielectric coatings, increase the maximum CW optical power by 50%. The power conversion efficiency decreases by only 25% of its maximum value as the CW power increases from 0.75 to 2.85 W.
Functional genomics identifies negative regulatory nodes controlling phagocyte oxidative burst (2015)

The phagocyte oxidative burst, mediated by Nox2 NADPH oxidase-derived reactive oxygen species, confers host defense against a broad spectrum of bacterial and fungal pathogens. Loss-of-function mutations that impair function of the Nox2 complex result in a life-threatening immunodeficiency, and genetic variants of Nox2 subunits have been implicated in pathogenesis of inflammatory bowel disease (IBD). Thus, alterations in the oxidative burst can profoundly impact host defense, yet little is known about regulatory mechanisms that fine-tune this response. Here we report the discovery of regulatory nodes controlling oxidative burst by functional screening of genes within loci linked to human inflammatory disease. Implementing a multi-omics approach, we define transcriptional, metabolic and ubiquitin-cycling nodes controlled by Rbpj, Pfkl and Rnf145, respectively. Furthermore, we implicate Rnf145 in proteostasis of the Nox2 complex by endoplasmic reticulum-associated degradation. Consequently, ablation of Rnf145 in murine macrophages enhances bacterial clearance, and rescues the oxidative burst defects associated with Ncf4 haploinsufficiency.
Development of a culturally and linguistically sensitive virtual reality educational platform to improve vaccine acceptance within a refugee population: the SHIFA community engagement-public health innovation programme (2021)

We describe using community co-design to create a culturally and linguistically sensitive VR experience promoting vaccination within a refugee community. Our approach to VR development incorporated community members at each step of the process. Our methodology is potentially applicable to other populations where cultural sensitivities and language are common health education barriers.
Iron-catalyzed gasification of char in carbon dioxide (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIron-catalyzed gasification of char in carbon dioxideEdward Furimsky, Paul Sears, and Toshimitsu SuzukiCite this: Energy Fuels 1988, 2, 5, 634–639Publication Date (Print):September 1, 1988Publication History Published online1 May 2002Published inissue 1 September 1988https://pubs.acs.org/doi/10.1021/ef00011a005https://doi.org/10.1021/ef00011a005research-articleACS PublicationsRequest reuse permissionsArticle Views256Altmetric-Citations39LEARN 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
Gel Electrophoresis: One‐dimensional (2001)

Abstract Gel electrophoresis in a single direction of migration is termed ‘one‐dimensional’. It is presently the most widely used mode of gel electrophoretic separation.
SAW characteristics of diamond-like carbon thin films on various piezoelectric substrates (2002)

We studied SAW characteristics of DLC thin films sputter deposited on various substrates, such as Si, quartz, and LiTaO/sub 3/. The film properties as well as SAW characteristics showed quite a large dependence on the kind of substrates on which the film was deposited. To examine their SAW properties, 1-port SAW resonators and 2IDT-type SAW filters were fabricated. The ZnO/IDT/DLC/Si(100) multilayer structure showed the 1st mode SAW velocity at kH/sub DLC/=0.262 and kH/sub ZnO/=0.837 was 5614 m/sec. On the contrary, DLC films on quartz and LiTaO/sub 3/ were observed to decrease SAW velocity. This contradictory result might be due to different properties of the DLC film according to the substrate on which it was deposited.
The tryptophan connection: cyclic peptide natural products linked<i>via</i>the tryptophan side chain (2021)

Covering: from 1938 up to March 2021The electron-rich indole side chain of tryptophan is a versatile substrate for peptide modification. Upon the action of various cyclases, the tryptophan side chain may be linked to a nearby amino acid residue, opening the door to a diverse range of cyclic peptide natural products. These compounds exhibit a wide array of biological activity and possess fascinating molecular architectures, which have made them popular targets for total synthesis studies. This review examines the isolation and bioactivity of tryptophan-linked cyclic peptide natural products, along with a discussion of their first total synthesis, and biosynthesis where this has been studied.