gebhart/patrepeval huggingface dataset:
A Model for Learning the Semantics of Pictures (2003)

We propose an approach to learning the semantics of images which allows us to automatically annotate an image with keywords and to retrieve images based on text queries. We do this using a formalism that models the generation of annotated images. We assume that every image is divided into regions, each described by a continuous-valued feature vector. Given a training set of images with annotations, we compute a joint probabilistic model of image features and words which allow us to predict the probability of generating a word given the image regions. This may be used to automatically annotate and retrieve images given a word as a query. Experiments show that our model significantly outperforms the best of the previously reported results on the tasks of automatic image annotation and retrieval. 1
X-Linked Lymphoproliferative Disease (2000)

2B4 is a surface molecule involved in activation of the natural killer (NK) cell-mediated cytotoxicity. It binds a protein termed Src homology 2 domain-containing protein (SH2D1A) or signaling lymphocyte activation molecule (SLAM)-associated protein (SAP), which in turn has been proposed to function as a regulator of the 2B4-associated signal transduction pathway. In this study, we analyzed patients with X-linked lymphoproliferative disease (XLP), a severe inherited immunodeficiency characterized by critical mutations in the SH2D1A gene and by the inability to control Epstein-Barr virus (EBV) infections. We show that, in these patients, 2B4 not only fails to transduce triggering signals, but also mediates a sharp inhibition of the NK-mediated cytolysis. Other receptors involved in NK cell triggering, including CD16, NKp46, NKp44, and NKp30, displayed a normal functional capability. However, their activating function was inhibited upon engagement of 2B4 molecules. CD48, the natural ligand of 2B4, is highly expressed on the surface of EBV(+) B cell lines. Remarkably, NK cells from XLP patients could not kill EBV(+) B cell lines. This failure was found to be the consequence of inhibitory signals generated by the interaction between 2B4 and CD48, as the antibody-mediated disruption of the 2B4-CD48 interaction restored lysis of EBV(+) target cells lacking human histocompatibility leukocyte antigen (HLA) class I molecules. In the case of autologous or allogeneic (HLA class I(+)) EBV(+) lymphoblastoid cell lines, restoration of lysis was achieved only by the simultaneous disruption of 2B4-CD48 and NK receptor-HLA class I interactions. Molecular analysis revealed that 2B4 molecules isolated from either XLP or normal NK cells were identical. As expected, in XLP-NK cells, 2B4 did not associate with SH2D1A, whereas similar to 2B4 molecules isolated from normal NK cells, it did associate with Src homology 2 domain-containing phosphatase 1.
All-trans retinoic acid as adjunct to intensive treatment in younger adult patients with acute myeloid leukemia: results of the randomized AMLSG 07-04 study (2016)

The aim of this clinical trial was to evaluate the impact of all-trans retinoic acid (ATRA) in combination with chemotherapy and to assess the NPM1 status as biomarker for ATRA therapy in younger adult patients (18-60 years) with acute myeloid leukemia (AML). Patients were randomized for intensive chemotherapy with or without open-label ATRA (45 mg/m<sup>2</sup>, days 6-8; 15 mg/m<sup>2</sup>, days 9-21). Two cycles of induction therapy were followed by risk-adapted consolidation with high-dose cytarabine or allogeneic hematopoietic cell transplantation. Due to the open label character of the study, analysis was performed on an intention-to-treat (ITT) and a per-protocol (PP) basis. One thousand one hundred patients were randomized (556, STANDARD; 544, ATRA) with 38 patients treated vice versa. Median follow-up for survival was 5.2 years. ITT analyses revealed no difference between ATRA and STANDARD for the total cohort and for the subset of NPM1-mutated AML with respect to event-free (EFS; p = 0.93, p = 0.17) and overall survival (OS; p = 0.24 and p = 0.32, respectively). Pre-specified PP analyses revealed better EFS in NPM1-mutated AML (p = 0.05) and better OS in the total cohort (p = 0.03). Explorative subgroup analyses on an ITT basis revealed better OS (p = 0.05) in ATRA for genetic low-risk patients according to ELN recommendations. The clinical trial is registered at clinicaltrialsregister.eu (EudraCT Number: 2004-004321-95).
[Proliferative vitreoretinopathy. Activation of the complement system]. (1992)

The complement system is a principal constituent of humoral immune reactions. Because of the multitude of biological effects related to complement activation, we analyzed its potential pathophysiological importance in the development of proliferative vitreoretinopathy (PVR). Vitreous aspirates from patients with idiopathic PVR (n = 7) and traumatic PVR (n = 11) were examined for total vitreal protein, complement components C3, C3d, and C1q-fixed immunoglobulins using enzyme-linked immunosorbent assay (ELISA), SDS-Page and Western blotting. Total vitreal protein and C3 components were significantly elevated both in traumatic and idiopathic PVR. Elevated levels of C3d titers in both PVR forms reflect an activation of the complement system. C1q-fixed IgG suggests complement activation via the classic pathway as a result of a humoral antibody-dependent immune reaction.
Preparation of optically active 1,2-diols and .alpha.-hydroxy ketones using glycerol dehydrogenase as catalyst. Limits to enzyme-catalyzed synthesis due to noncompetitive and mixed inhibition by product (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreparation of optically active 1,2-diols and .alpha.-hydroxy ketones using glycerol dehydrogenase as catalyst. Limits to enzyme-catalyzed synthesis due to noncompetitive and mixed inhibition by productLinda G. Lee and George M. WhitesidesCite this: J. Org. Chem. 1986, 51, 1, 25–36Publication Date (Print):January 1, 1986Publication History Published online1 May 2002Published inissue 1 January 1986https://pubs.acs.org/doi/10.1021/jo00351a005https://doi.org/10.1021/jo00351a005research-articleACS PublicationsRequest reuse permissionsArticle Views1449Altmetric-Citations121LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Scanning electron microscopy of cells and tissues under fully hydrated conditions (2004)

A capability for scanning electron microscopy of wet biological specimens is presented. A membrane that is transparent to electrons protects the fully hydrated sample from the vacuum. The result is a hybrid technique combining the ease of use and ability to see into cells of optical microscopy with the higher resolution of electron microscopy. The resolution of low-contrast materials is approximately 100 nm, whereas in high-contrast materials the resolution can reach 10 nm. Standard immunogold techniques and heavy-metal stains can be applied and viewed in the fluid to improve the contrast. Images present a striking combination of whole-cell morphology with a wealth of internal details. A possibility for direct inspection of tissue slices transpires, imaging only the external layer of cells. Simultaneous imaging with photons excited by the electrons incorporates data on material distribution, indicating a potential for multilabeling and specific scintillating markers.
Development of self-powered strain sensor using mechano-luminescent ZnS:Cu and mechano-optoelectronic P3HT (2017)

Aerospace structural systems are prone to structural damage during their use by vibration, impact, material degradation, and other factors. Due to the harsh environments in which aerospace structures operate, aerospace structures are susceptible to various types of damage and often their structural integrity is jeopardized unless damage onset is detected in timely manner. Yet, current state-of-the-art sensor technologies are still limited for structural health monitoring (SHM) of aerospace structures due to their high power consumption, need for large form factor design, and manageable integration into aerospace structures. This study proposes a design of multilayered self-powered strain sensor by coupling mechano-luminescent (ML) property of copper-doped zinc sulfide (ZnS:Cu) and mechano-optoelectronic (MO) property of poly(3-hexylthiophene) (P3HT). One functional layer of the self-powered strain sensor is ZnS:Cu-based elastomeric composites that emit light in response to mechanical deformation. Another functional layer is P3HT-based thin films that generate direct current (DC) under light illumination and DC magnitude changes with applied strain. First, ML light emission characteristics of ZnS:Cu-based composites are studied under cyclic tensile strain with two various maximum strain up to 10% and 15% at various loading frequencies from 5 Hz to 20 Hz. Second, piezo-optical properties of P3HT-based thin films are investigated by acquiring light absorption of the thin films at various strains from 0% to 2% tensile strain. Last, micro-mechanical properties of the P3HT-based thin films are characterized using nanoindentation.
Phase II Study of Alisertib, a Selective Aurora A Kinase Inhibitor, in Relapsed and Refractory Aggressive B- and T-Cell Non-Hodgkin Lymphomas (2013)

The novel AAK inhibitor alisertib seems clinically active in both B- and T-cell aggressive lymphomas. On the basis of these results, confirmatory single-agent and combination studies have been initiated.
Induction of macrophage-mediated tumor cytotoxicity by a hamster monoclonal antibody with specificity for lipopolysaccharide receptor. (1990)

Experiments have been carried out to assess the immunostimulatory activity of a hamster IgM mAb (mAb5D3) with specificity for an 80-kDa LPS-binding protein expressed on murine macrophages and monocytes. The addition of mAb5D3 to cultures of murine bone marrow-derived macrophages activated these cells to become tumoricidal for mastocytoma cells in vitro. The activity of mAb5D3 was enhanced in the presence of IFN-gamma. Neither mAb5D3 nor LPS were able to activate macrophages from the LPS-hyporesponsive C3H/HeJ mouse, although these cells responded normally to heat-killed Listeria monocytogenes. The results of several experiments establish that the observed LPS-like activity of mAb5D3 was not due to contaminating endotoxin: 1) the activity of mAb5D3 but not LPS was heat labile at 100 degrees C; 2) the activity of LPS but not mAb5D3, was inhibited by addition of polymyxin B; and 3) quantitative estimates of endotoxin contamination by Limulus amoebocyte lysate reactivity. These experiments thus demonstrate that mAb5D3 can serve as an agonist for LPS-dependent macrophage responses and, when considered with those of our companion paper showing specificity of mAb5D3 for the 80-kDa LPS-binding protein, provide strong support for the concept that the 80-kDa LPS-binding protein previously identified serves as a functional receptor for LPS on murine macrophages.
Interactions of the quorum sensing regulator QscR: interaction with itself and the other regulators of Pseudomonas aeruginosa LasR and RhlR (2003)

Pseudomonas aeruginosa controls the production of many exoproteins and secondary metabolites via a hierarchical quorum sensing (QS) regulatory cascade involving the LuxR-like proteins LasR, RhlR and their cognate signal molecules N-(3-oxododecanoyl)-l-homoserine lactone (3O-C12-HSL) and N-(butanoyl)-l-homoserine lactone (C4-HSL). The finding of a third LuxR-type protein in P. aeruginosa, QscR, adds further complexity to this regulatory network. It has been shown previously that QscR represses transcription of three QS-controlled gene clusters, phz (phenazine), hcn (hydrogen cyanide) and qsc105 (Chugani, Whiteley, Lee, D'Argenio, Manoil, and Greenberg, 2001, Proc Natl Acad Sci USA 98: 2752-2757). In this study, we identify two novel QscR targets these are lasB, encoding the extracellular elastase, and the second phenazine gene cluster, both of which are downregulated by QscR. In addition, we show that QscR synthesis is regulated by the two-component response regulator GacA. Taking advantage of the in vivo fluorescence anisotropy technology that we have developed, we show that QscR can be found in several different types of association. Indeed, we identify QscR multimers in the absence of any acyl-HSL, lower order QscR oligomers associated either with C4-HSL or 3O-C12-HSL and QscR-containing heterodimers with LasR or RhlR. The formation of heterodimers between QscR and LasR or RhlR, in the absence of acyl-HSLs, is a very exciting, new result that should improve our understanding of the QscR network and its relationship to the production of P. aeruginosa virulence factors.
Autophagy and misfolded proteins in neurodegeneration (2010)

The accumulation of misfolded proteins in insoluble aggregates within the neuronal cytoplasm is one of the common pathological hallmarks of most adult-onset human neurodegenerative diseases. The clearance of these misfolded proteins may represent a promising therapeutic strategy in these diseases. The two main routes for intracellular protein degradation are the ubiquitin-proteasome and the autophagy-lysosome pathways. In this review, we will focus on the autophagic pathway, by providing some examples of how impairment at different steps in this degradation pathway is related to different neurodegenerative diseases. We will also consider that upregulating autophagy may be useful in the treatment of some of these diseases. Finally, we discuss how antioxidants, which have been considered to be beneficial in neurodegenerative diseases, can block autophagy, thus potentially compromising their therapeutic potential.
The Added Mass by Schwarz-Christoffel Transformation (1981)

The hydrodynamic added mass of two dimensional cylinders oscillating vertically at high frequencies in the free surface is of interest to ship vibration problems. Conformal transformation is one of the methods commonly in use for computing the inertia coefficient. Especially, Schwarz-Christoffel transformation has been employed to evaluate the inertia coefficient for the cylinders of straight frames and chines. In this paper, the inertia coefficient for the cylinders with round corners in vertical oscillation at high frequencies are evaluated by employing the Schwarz-Christoffel transformation for the concave corner. The results of calculation by employing the Schwarz-Christoffel transformation are found to be well within the expected range of values compared to Lewis form and the results obtained by source distribution method.
A Mild Preparation of Protected Phosphate Esters From Alcohols (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA Mild Preparation of Protected Phosphate Esters From AlcoholsVibha B. Oza and Robert C. CorcoranCite this: J. Org. Chem. 1995, 60, 12, 3680–3684Publication Date (Print):June 1, 1995Publication History Published online1 May 2002Published inissue 1 June 1995https://pubs.acs.org/doi/10.1021/jo00117a018https://doi.org/10.1021/jo00117a018research-articleACS PublicationsRequest reuse permissionsArticle Views2405Altmetric-Citations33LEARN 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-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Cellular localization of soybean storage protein mRNA in transformed tobacco seeds (1988)

We transformed tobacco plants with a soybean beta-conglycinin gene that encodes the 1.7-kilobase beta-subunit mRNA. We showed that the beta-conglycinin mRNA accumulates and decays during tobacco seed development and that beta-conglycinin mRNA is undetectable in the tobacco leaf. We utilized in situ hybridization to localize beta-conglycinin mRNA within the tobacco seed. beta-Conglycinin mRNA is not detectable within the endosperm but is localized within specific embryonic cell types. The highest concentration of beta-conglycinin mRNA is found in cotyledon storage parenchyma cells. We conclude that sequences required for embryo expression, temporal control, and cell specificity are linked to the beta-conglycinin gene, and that factors regulating beta-conglycinin gene expression are compartmentalized within analogous soybean and tobacco seed regions.
Library Preparation and Multiplex Capture for Massive Parallel Sequencing Applications Made Efficient and Easy (2012)

During the recent years, rapid development of sequencing technologies and a competitive market has enabled researchers to perform massive sequencing projects at a reasonable cost. As the price for the actual sequencing reactions drops, enabling more samples to be sequenced, the relative price for preparing libraries gets larger and the practical laboratory work becomes complex and tedious. We present a cost-effective strategy for simplified library preparation compatible with both whole genome- and targeted sequencing experiments. An optimized enzyme composition and reaction buffer reduces the number of required clean-up steps and allows for usage of bulk enzymes which makes the whole process cheap, efficient and simple. We also present a two-tagging strategy, which allows for multiplex sequencing of targeted regions. To prove our concept, we have prepared libraries for low-pass sequencing from 100 ng DNA, performed 2-, 4- and 8-plex exome capture and a 96-plex capture of a 500 kb region. In all samples we see a high concordance (>99.4%) of SNP calls when comparing to commercially available SNP-chip platforms.
Performance evaluation of exclusive cache hierarchies (2004)

Memory hierarchy performance, specifically cache memory capacity, is a constraining factor in the performance of modern computers. This paper presents the results of two-level cache memory simulations and examines the impact of exclusive caching on system performance. Exclusive caching enables higher capacity with the same cache area by eliminating redundant copies. The experiments presented compare an exclusive cache hierarchy with an inclusive cache hierarchy utilizing similar L1 and L2 parameters. Experiments indicate that significant performance advantages can be gained for some benchmark through the use of an exclusive organization. The performance differences are illustrated using the L2 cache misses and execution time metrics. The most significant improvement shown is a 16% reduction in execution time, with an average reduction of 8% for the smallest cache configuration tested. With equal size victim buffer and victim cache for exclusive and inclusive cache hierarchies respectively, some benchmarks show increased execution time for exclusive caches because a victim cache can reduce conflict misses significantly while a victim buffer can introduce worst-case penalties. Considering the inconsistent performance improvement, the increased complexity of an exclusive cache hierarchy needs to be justified based upon the specifics of the application and system.
<title>Method for comparing content based image retrieval methods</title> (2003)

We assume that the goal of content based image retrieval is to find images which are both semantically and visually relevant to users based on image descriptors. These descriptors are often provided by an example image--the query by example paradigm. In this work we develop a very simple method for evaluating such systems based on large collections of images with associated text. Examples of such collections include the Corel image collection, annotated museum collections, news photos with captions, and web images with associated text based on heuristic reasoning on the structure of typical web pages (such as used by Google(tm)). The advantage of using such data is that it is plentiful, and the method we propose can be automatically applied to hundreds of thousands of queries. However, it is critical that such a method be verified against human usage, and to do this we evaluate over 6000 query/result pairs. Our results strongly suggest that at least in the case of the Corel image collection, the automated measure is a good proxy for human evaluation. Importantly, our human evaluation data can be reused for the evaluation of any content based image retrieval system and/or the verification of additional proxy measures.
Percept-choice sequences driven by interrupted ambiguous stimuli: A low-level neural model (2007)

Existing neural explanations of spontaneous percept switching under steady viewing of an ambiguous stimulus do not fit the fact that stimulus interruptions cause the same percept to reappear across many ON/OFF cycles. We present a simple neural model that explains the observed behavior and predicts several more complicated percept sequences, without invoking any "high-level" decision making or memory. Percept choice at stimulus onset, which differs fundamentally from standard percept switching, depends crucially on a hitherto neglected interaction between local "shunting" adaptation and a near-threshold neural baseline. Stimulus ON/OFF timing then controls the generation of repeating, alternating, or more complex choice sequences. Our model also explains "priming" versus "habituation" effects on percept choice, reinterprets recent neurophysiological data, and predicts the emergence of hysteresis at the level of percept sequences, with occasional noise-induced sequence "hopping."
Arrays of distributed-Bragg-reflector waveguide lasers at 1536 nm in Yb/Er codoped phosphate glass (1999)

We have demonstrated an array of monolithic, single-frequency-distributed-Bragg-reflector (DBR), waveguide lasers operating near 1536 nm wavelengths. The lasers were fabricated by forming waveguides in Yb/Er-codoped phosphate glass by ion exchange. The slope efficiency for each laser as a function of launched pump power is 26% and the thresholds occur at 50 mW of launched pump power. An output power of 80 mW was achieved with 350 mW of coupled pump power. Each laser exhibits stable operation on a single longitudinal mode and all have linewidths less than 500 kHz. A comb of waveguides with varying effective indices allows the selection of wavelength using a single-period grating.