gebhart/patrepeval huggingface dataset:
Deep Learning-Based Annotation Transfer between Molecular Imaging Modalities: An Automated Workflow for Multimodal Data Integration (2021)

An ever-increasing array of imaging technologies are being used in the study of complex biological samples, each of which provides complementary, occasionally overlapping information at different length scales and spatial resolutions. It is important to understand the information provided by one technique in the context of the other to achieve a more holistic overview of such complex samples. One way to achieve this is to use annotations from one modality to investigate additional modalities. For microscopy-based techniques, these annotations could be manually generated using digital pathology software or automatically generated by machine learning (including deep learning) methods. Here, we present a generic method for using annotations from one microscopy modality to extract information from complementary modalities. We also present a fast, general, multimodal registration workflow [evaluated on multiple mass spectrometry imaging (MSI) modalities, matrix-assisted laser desorption/ionization, desorption electrospray ionization, and rapid evaporative ionization mass spectrometry] for automatic alignment of complex data sets, demonstrating an order of magnitude speed-up compared to previously published work. To demonstrate the power of the annotation transfer and multimodal registration workflows, we combine MSI, histological staining (such as hematoxylin and eosin), and deep learning (automatic annotation of histology images) to investigate a pancreatic cancer mouse model. Neoplastic pancreatic tissue regions, which were histologically indistinguishable from one another, were observed to be metabolically different. We demonstrate the use of the proposed methods to better understand tumor heterogeneity and the tumor microenvironment by transferring machine learning results freely between the two modalities.
ChemInform Abstract: The Structure‐Directed Synthesis of Cyclacene and Polyacene Derivatives (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Full-Color-Tunable Nanophotonic Device Using Electrochromic Tungsten Trioxide Thin Film (2020)

Color generation based on strategically designed plasmonic nanostructures is a promising approach for display applications with unprecedented high-resolution. However, it is disadvantageous in that the optical response is fixed once the structure is determined. Therefore, obtaining high modulation depth with reversible optical properties while maintaining its fixed nanostructure is a great challenge in nanophotonics. In this work, dynamic color tuning and switching using tungsten trioxide (WO<sub>3</sub>), a representative electrochromic material, are demonstrated with reflection-type and transmission-type optical devices. Thin WO<sub>3</sub> films incorporated in simple stacked configurations undergo dynamic color change by the adjustment of their dielectric constant through the electrochromic principle. A large resonance wavelength shift up to 107 nm under an electrochemical bias of 3.2 V could be achieved by the reflection-type device. For the transmission-type device, on/off switchable color pixels with improved purity are demonstrated of which transmittance is modulated by up to 4.04:1.
ChemInform Abstract: 3‐(4‐Piperidinyl)‐ and 3‐(8‐Aza‐bicyclo[3.2.1]oct‐3‐yl)‐2‐phenyl‐1H‐indoles as Bioavailable h5‐HT2A Antagonists. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A Qualitative Evaluation of Service Mesh-based Traffic Management for Mobile Edge Cloud (2022)

Service mesh is getting widely adopted as the cloud-native mechanism for traffic management in microservice-based applications, in particular for generic IT workloads hosted in more centralized cloud environments. Performance-demanding applications continue to drive the decentralization of modern application execution environments, as in the case of mobile edge cloud. This paper presents a systematic and qualitative analysis of state-of-the-art service mesh to evaluate how suitable its design is for addressing the traffic management needs of performance-demanding application workloads hosted in a mobile edge cloud environment. With this analysis, we argue that today's dependability-centric service mesh design fails at addressing the needs of the different types of emerging mobile edge cloud workloads and motivate further research in the directions of performance-efficient architectures, stronger QoS guarantees and higher complexity abstractions of cloud-native traffic management frameworks.
Effects of infant formula, cow milk and human milk on drug metabolizing enzymes (2005)

Background Caffeine, used for treating neonatal apnea, is eliminated 3-fold slower in breastfed infants than in formula-fed infants. Caffeine is metabolized by cytochrome P450 (CYP) 1A and CYP3A4, which are regulated by aryl hydrocarbon receptor (AhR) and pregnane X receptor (PXR) respectively. Here we hypothesized that formula but not human milk induces CYP1A and/or CYP3A4 via their regulatory pathways. Methods Human milk samples from healthy lactating women were collected. Infant formula and cow milk were purchased. Lipid fraction of milk samples was obtained by organic extraction. mRNA and protein expression were measured by RT-PCR and western blotting. Reporter plasmids containing receptor response elements were tested for their activation. Results CYP1A expression and AhR activity were induced by formula and cow milk but not by human milk. The AhR activation by formula was abolished by co-treatment of Ah antagonist. Formula and human milk also had differential effects on AhR activation by dibenz[a,h]anthracene, an AhR agonist. In addition, lipid fraction of formula but not human milk activated AhR. Both formula and human milk showed mild induction of CYP3A4 mRNA and PXR. However, co-transfection of hPXR did not increase PXR activation by milk treatments, suggesting a non PXR-mediated pathway. Conclusion Infant formula but not human milk contains AhR agonist(s) that induces CYP1A expression. Both infant formula and human milk induce CYP3A4 through non PXR-mediated pathway. Clinical Pharmacology & Therapeutics (2005) 77, P46–P46; doi: 10.1016/j.clpt.2004.12.068
Novel genotypes among transductants made with bacteriophage P1 lysates from an F14 merogenote strain of Escherichia coli K-12 (1976)

Among P1 transductants in Escherichia coli K-12 that were selected for the proximal and distal markers from the large F14 merogenote, a variety of unusual genotypes were found. As earlier workers had found, one class of these could transfer the proximal genes (argH, metB) and distal genes (ilvEDAC) of the F14 during conjugation. These F14 genes could be transferred into RecA recipients, indicating that they were carried on an F-merogenote rather than on an Hfr chromosome. The transduced F-merogenotes could transfer other F14 genes (metE, rha) as well. Transfer kinetic analysis showed that all of the latter transduced F-merogenotes that were examined were indistinguishable from the parental F14 in the order of transfer and the genetic distance between proximal and distal markers. This suggests that the whole F14 had been received somehow by the primary transductional recipients, a remarkable possibility since the F14 is much larger than the largest deoxyribonucleic acid segment normally transduced by P1. The mechanism of this phenomenon is not yet known. Many of the transductants did not transfer any of the F14 markers tested. Some of these transductants segregated certain F14 genes, indicating they were carried on self-replicating genetic elements, but others were not cured of F14 markers, even by acridine orange. Cotransductional analysis of this group was consistent with the hypothesis that the F14 markers in some of these strains had integrated into the chromosome in the expected manner, since in these latter the F14 alleles were linked to the expected chromosomal genes. Other strains among the stable transductants had acquired new linkages in that genes previously separated by several minutes could now be cotransduced. These latter included the novel cotransductional linkages of rbs-ilv-argH, rbs-ilv-argH-metB, and ilvD-argH-purD. Such strains might have been formed as a result of insertion into the chromosome of small circles derived from F14.
Accelerated Proteasomal Activity Induced by Pb2+, Ga3+, or Cu2+ Exposure Does Not Induce Degradation of αt-Synuclein (2009)

The involvement of environmental heavy metals in Parkinson's disease (PD) has been suggested by epidemiologic studies; however, the mechanism of this effect is unknown. PD is characterized by the aggregation of alpha-synuclein in Lewy bodies. We previously showed that Pb2+ accelerates proteasomal activity. Therefore, we examined the effect of Pb2+, Ga3+, and Cu2+ on alpha-synuclein in human SH-SY5Y cells. The heavy metals induced an increase in heme-oxygenase-1 levels without significant cell death or ROS generation. The metals inhibited ALA-dehydratase, which is the inhibitory subunit of the proteasome, thereby accelerating proteasomal activity and decreasing protein levels of CDK-1 and PBGD. However, alpha-synuclein protein levels increased after exposure to metals, similar to the effect obtained with the proteasome inhibitor, hemin, suggesting that alpha-synuclein is inaccessible to proteasomal degradation. Indeed, electron microscopy revealed the formation of aggresomes in Pb2+- or hemin-treated cells. Thus, although heavy metals enhance proteasomal activity, alpha-synuclein is protected from degradation, and its protein levels and aggregation are increased.
Screening of BCOR‐CCNB3 sarcoma using immunohistochemistry for CCNB3: A clinicopathological report of three pediatric cases (2015)

BCOR-CCNB3 sarcoma is a recently recognized tumor morphologically and clinically simulating Ewing sarcoma. We herein retrospectively collected clinicopathologic data on BCOR-CCNB3 sarcoma in the Kyoto University Hospital over the last 10 years. Three (20%) bone sarcomas were revealed to be diffusely positive for CCNB3 immunohistochemistry among 15 pediatric cases of undifferentiated sarcoma morphologically similar to Ewing sarcoma, while the other cases showed completely negative staining. The three patients with immunohistochemically CCNB3-positive tumors were all male, aged between 11 and 17, and confirmed to have the BCOR-CCNB3 fusion transcript by RT-PCR. Radiologically, all cases had well-demarcated solid masses with bone destruction. Although the tumors were basically small round cell tumors, less monomorphic histological patterns such as short spindle cells, a myxoid matrix, and hemangiopericytoma-like pattern were also observed in both biopsy and resected specimens. Two patients achieved a complete response after chemotherapy for Ewing sarcoma and osteosarcoma, respectively. These results demonstrated that the application of CCNB3 immunostaining was useful for differentiating BCOR-CCNB3 from a group of 'Ewing-like sarcomas' and may contribute to the evaluation of treatment strategies for bone sarcomas.
The mouse-primed lymphocyte typing test. III. Dissociation of T lymphocyte-stimulating determinants and antibody-defined specificities of the I region-associated Ia antigens. (1980)

The mouse-primed lymphocyte typing (mPLT) assay, based on the sequential reactivation of specific immunocompetent alloantigen-reactive T blast cells in secondary mixed leukocyte culture (MLC) has been utilized to define the major histocompatibility complex (MHC) I region-, or Class II-associated lymphocyte-stimulating (LS) determinants. The test panel of secondary stimulating cells has been expanded to include 28 B10.W lines (mouse strains carrying MHC regions derived from wild mice); thus, nearly 40 "independently derived" MHC haplotypes are now represented. Data obtained by using mPLT cells generated in primary MLC between I-AB or I-EC subregion disparate strain combinations reveal that 1) an absolute correlation between expression of the serologically defined Ia specificities and capacity to induce subsequent secondary MLC does not exist; 2) based on the apparent genetic derivations of the I-AB and I-EC subregions, T lymphocytes most likely recognize either the beta-chain per se or an interaction product of the alpha- plus beta-chains; and 3) multiple restimulations of mPLT cells with cells expressing cross-reactive serologically defined Ia specificities fail to select for cells with increased reactivity against shared specificities. Based on these observations, we conclude that t and B lymphocytes recognize different antigenic moieties expressed on the MHC Class II antigens.
Novel Structures for High Confinement in Sub-Wavelength Regions (2005)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text M. Lipson, J. T. Robinson, Q. Xu, V. Almeida, and H. Lipson, "Novel structures for high confinement in sub-wavelength regions," in Integrated Photonics Research and Applications/Nanophotonics for Information Systems, Technical Digest (Optica Publishing Group, 2005), paper NWB1. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
A Predictive Controller for Modular Multi-level Converters (2018)

This paper presents a novel predictive controller for modular multi-level converters (M2LCs). Different from existing model predictive control (MPC) strategies, the control variables are separated into two groups with different control schemes. The load current, controlled through the model predictive direct slope control (MPDSC), is regulated within symmetrical bounds around the reference. And the switching frequency, circulating current and capacitor voltage ripples are minimized by a model predictive multilayer control (MPMC), where each variable is evaluated independently on their own control layer. An advantage of the proposed strategy is to allow operation at low switching frequency by forcing switch transitions to take place only near the bounds and selecting a unique output voltage level with the minimum slope of the load current, relative to the reference. Moreover, a hierarchical screening algorithm is proposed to reduce the number of switching states to be evaluated for each control variable. And a further reduction in the overall computational burden can be achieved by assigning variables to their appropriate control layers. Besides, a novel method of tuning weighting factors is proposed to tune the trade-off among different control variables, which significantly improves the efficiency of the tuning procedure. Simulation results of a single-phase, three-level, 380-VA M2LC, controlled through the proposed strategy under both steady-state and transient conditions are given to demonstrate the validity of the proposed strategy.
API RP2T and RP2FPS: Moving Forward (2008)

Abstract API is developing updates for two key floating/tethered system documents for issuance in 2008. Impactful changes in RP 2T based on learnings from the 2004-2005 hurricane season, over 10 years of experience and technology development and metocean changes have been incorporated. Additional criteria regarding tendon loss/damage and an integrity check for conditions significantly above the 100 year design basis will be discussed. API RP 2FPS is being developed using ISO 19904 as a basis (19904 was built upon the current version of RP 2FPS and updated) and " wrapped?? with US Gulf of Mexico specific additions. This paper will present the key changes/additions in these documents and provide a discussion as to the impact. Introduction From the first floating production systems in the 1970's and early 1980's, semisubmersibles, FPSOs, TLPs, and more recently spars have featured prominently in the industry's vision of how to produce oil in deeper water depths. The first floating production system, a converted semisubmersible, was developed in the North Sea for the Hamilton Brothers' Argyle field (1974). The first FPSO was installed on the Shell Castellon field offshore Spain in 1977. The first production TLP was installed in the Conoco Hutton field (1981) in the North Sea. Since then, there have been many floating production systems successfully installed in locations all around the world. The first API recommended practice to address these structures was RP2T, the Recommended Practice for the Planning, Design, and Construction of Tension Leg Platforms, first issued in 1987. Until recently, RP2T was the only issued API document to address floating production systems. Although RP2T was limited to TLP's, it served as a technical basis for other types of structures, along with various classification society documents and European codes. In 2001 the first edition of RP 2FPS was issued. As the industry has developed more experience with these structures, the body of information available for guidance to designers, builders, and operators has expanded, while the methods and practices have evolved and improved. In response to this evolution, API typically issues updates to incorporate the new information. The impetus for issuing an updated RP2T and a new RP 2FPS at this time includes a number of factors. The technology for both FPS's and TLP's has evolved to include varied concepts and configurations. The engineering tools and practices have greatly improved. And finally, the understanding of the environment, especially in the Gulf of Mexico, has changed significantly following the 2004-2005 hurricane seasons. One other evolution in the API offshore structure recommended practices has been brought about by the progress made in the standards developed by the International Standards Organization (ISO). When the ISO first started to develop offshore structure standards, there was a move within API to eventually replace the API RP's in favor of the international standards.
Integration of multiple knowledge sources in speech recognition using minimum error training (2001)

Modern automatic speech recognition systems employ two statistical models: a language model and an acoustic model. These two models are estimated independently of each other, most often using a maximum likelihood criterion. They are then combined to compute the a posteriori probability of a word sequence given an acoustic signal. During combination, a static tunable parameter is used to scale the score of one of the models relative to the other. 
In this work a general formulation is presented for combining scores from several models—knowledge sources—into a single log-linear model to compute sentence probabilities. The parameters of the new model are the weights of the log-linear combination. The combination can be performed either statically, with constant weights, as is the case in the traditional way the acoustic and language models are combined, or dynamically, where the parameters may vary for different segments of a hypothesis. In the dynamic combination the weights aim to capture the dynamic change of confidence on each of the models combined. In order to achieve robust estimation of the parameters, each segment is automatically assigned to one of a small number of categories, or classes, and a single set of parameters is used for each segment class. Different techniques are described to estimate the parameters in order to achieve minimum word error rate. 
Three applications of this approach are presented: (1) The combination of several acoustic models trained using speech from resource-rich languages in order to obtain a recognition system for a language with little acoustic training data. The segments for which a set of parameters is defined correspond to hypothesized phones and the classes for the dynamic combination are chosen using phonological knowledge. (2) The dynamic combination of the baseline acoustic and language models. Different ways are investigated for clustering word links in a recognition lattice, and the language model weight and insertion penalty parameters are estimated for each cluster. Features previously used to predict confidence (correctness) of the recognized words are utilized here to define the link clusters. This way of dynamically modifying the language model weight may be interpreted as acoustic sensitive language modeling. (3) The integration in the model of side-information, available during a first pass recognition. The new model is used to rescore the hypotheses.
The Importance of a β‐Glucan Receptor in the Nonopsonic Entry of NontypeableHaemophilus influenzaeinto Human Monocytic and Epithelial Cells (2001)

Previous reports showed that nontypeable Haemophilus influenzae (NTHi) reside in macrophage-like cells in human adenoid tissue. This study investigated the ability of nonopsonized NTHi and encapsulated H. influenzae type b (Hib) to enter human monocytic and epithelial cells. The number of intracellular bacteria was determined by a viability assay and flow cytometry. To characterize the mechanisms responsible for the internalization of NTHi, different inhibitors of surface molecules, receptor turnover, and the cytoskeleton were used. Hib were found in monocytic cells at very low numbers (<100 bacteria/2x105 cells). In contrast, a great variation in intracellular numbers was detected between the different NTHi isolates (range, 0.0007%-0.28% of the inoculum for monocytes and 0.053%-3.5% for epithelial cells). NTHi entered human monocytic and epithelial cells via a receptor-mediated endocytosis involving mainly a beta-glucan receptor that could be blocked by laminarin.
Therapeutic Drug-Monitoring of Methotrexate-Polyglutamates in Rheumatoid Arthritis (2014)

markdownabstract__Abstract__

Rheumatoid Arthritis (RA) is a chronic autoimmune disease, characterized by the swelling
of joints, uncontrolled proliferation of synovial tissue and multisystem co-morbidities. RA
mainly affects the joints of the hands, feet, knees, wrist and elbows, with joint damage
occurring early in the disease course. RA affects an estimated 1% of the general population
and women have a higher risk of developing RA than men. Despite the fact that treatment
strategy has changed considerably over the years, reflected by a much improved disease
outcome, there is still no cure for RA.
Early initiation of therapy is effective in prevention of joint damage and results in
milder medication regimes while maintaining disease remission. Early in the disease,
the inflammation is less self-perpetuating and easier to suppress, therefore it is important
to start treatment as early as possible in order to optimize outcome, minimize medical costs,
improve quality of life, and improve medical decision making.
Post-silicon debug using programmable logic cores (2006)

Producing a functionally correct integrated circuit is becoming increasingly difficult. No matter how careful a designer is, there will always be integrated circuits that are fabricated, but do not operate as expected. Providing a means to effectively debug these integrated circuits is vital to help pin-point problems and reduce the number of re-spins required to create a correctly-functioning chip. In this paper, we show that programmable logic cores (PLCs) and flexible networks can provide this debugging capability. We present an architecture and example implementation. We show that the area overhead of this proposed architecture would be well below 10% for many target ICs.