gebhart/patrepeval huggingface dataset:
Image Embedded Segmentation: Uniting Supervised and Unsupervised Objectives for Segmenting Histopathological Images (2020)

This paper presents a new regularization method to train a fully convolutional network for semantic tissue segmentation in histopathological images. This method relies on the benefit of unsupervised learning, in the form of image reconstruction, for network training. To this end, it puts forward an idea of defining a new embedding that allows uniting the main supervised task of semantic segmentation and an auxiliary unsupervised task of image reconstruction into a single one and proposes to learn this united task by a single generative model. This embedding generates an output image by superimposing an input image on its segmentation map. Then, the method learns to translate the input image to this embedded output image using a conditional generative adversarial network, which is known as quite effective for image-to-image translations. This proposal is different than the existing approach that uses image reconstruction for the same regularization purpose. The existing approach considers segmentation and image reconstruction as two separate tasks in a multi-task network, defines their losses independently, and combines them in a joint loss function. However, the definition of such a function requires externally determining right contributions of the supervised and unsupervised losses that yield balanced learning between the segmentation and image reconstruction tasks. The proposed approach provides an easier solution to this problem by uniting these two tasks into a single one, which intrinsically combines their losses. We test our approach on three datasets of histopathological images. Our experiments demonstrate that it leads to better segmentation results in these datasets, compared to its counterparts.
Bacteroides fragilis toxin rapidly intoxicates human intestinal epithelial cells (HT29/C1) in vitro (1996)

Enterotoxigenic Bacteroides fragilis strains associated with childhood diarrhea produce a 20-kDa protein toxin (BFT). Purified BFT causes striking morphologic changes in subconfluent human colonic epithelial cells (HT29/C1). In a 3-h HT29/C1 cell assay, the estimated half-maximal effective concentration of BFT was 12.5 pM, and morphologic effects were detectable as early as 30 min and nearly complete by 1.5 h. Concentrations as low as 0.5 pM could also cause intoxication, but morphologic changes were detectable only when the assay was extended to 18 h. The onset of this intoxication was concentration dependent and rapid, occurring within minutes (<7 min at 0.25 nM, <2 min at 2.5 nM). Notably, the onset of intoxication at 37 degrees C became irreversible to washing within 2 min after exposure to BFT. Morphologic changes were completely inhibited by treatment of HT29/C1 cells with BFT at 4 degrees C but could be demonstrated by subsequent warming to temperatures of 15 degrees C or higher after washing. The time required for the association of BFT with HT29/C1 cells at 4 degrees C was inversely correlated with concentration. Inhibitors of endosomal and Golgi trafficking (NH4Cl and brefeldin A) prevented the intoxication of HT29/C1 cells by Clostridium difficile toxin A and cholera toxin, respectively, but not by BFT. Agents altering microtubule structure did not affect the cellular activity of BFT. These data indicate that a purified toxin from B. fragilis strains associated with diarrhea rapidly and irreversibly intoxicates human intestinal epithelial cells (HT29/C1) in a concentration- and temperature-dependent manner and that the process of intoxication may not involve internalization mechanisms utilizing microtubules or sensitive to pH or brefeldin A.
Erythropoietin Produced in a Human Cell Line (Dynepo) Has Significant Differences in Glycosylation Compared with Erythropoietins Produced in CHO Cell Lines (2010)

Recombinant human erythropoietin has been used to treat anemia associated with chronic renal disease. This paper provides a comprehensive comparative analysis of Dynepo and three other commercial erythropoiesis stimulating agents, Eprex, NeoRecormon and Aranesp. We found significant differences in the type, levels and amount of O-acetylation of sialic acids. Sialic acids and O-acetylation present provide protection from clearance from circulation. Aranesp had up to six O-acetyl groups attached to the sialic acids. Eprex and NeoRecormon had only minor amounts of O-acetylation while Dynepo had none. Dynepo had no Neu5Gc, which is potentially immunogenic for humans. Dynepo contained the least amount of disialylated and Aranesp the highest amount of tetrasialylated glycans. NeoRecormon and Eprex contained more trisialylated, but less tetrasialylated glycans than Dynepo and Aranesp. Dynepo had the highest amount of tetraantennary glycans and the lowest amounts of triantennary glycans with a β1-6-GlcNAc linkage. All the samples contained poly-N-acetyl-lactosamine repeats with Dynepo having the least. The major N-acetyl-lactosamine extensions in Dynepo and Aranesp were on biantennary glycans, whereas in NeoRecomon and Eprex they were on triantennary glycans. The sLe(x) epitope was only detected in Dynepo.
Evaporation-enhanced, dynamically-adaptive air (gas)-cooled heat sink for thermal management of high heat dissipation devices (2008)

To address the thermal management challenges associated with high power dissipation devices, we describe a novel hybrid thermal management device, which enables significant enhancement of conventional air-cooled heat sinks using on- demand and spatially controlled droplet/jet impingement evaporative cooling. The device architecture modifies an air (gas)-cooled heat sink by adding a multiplexed, planar MEMS (microelectromechanical system)-based droplet ejector array as a capping surface of the finned structure of a conventional heat sink. Such a minimal modification of the heat sink allows one to exploit high heat flux evaporative cooling by virtue of delivering streams of liquid droplets or jets to the highly thermally conducting, heat spreading surface of the heat sink fins. The phase change associated with liquid droplet evaporation results in significant (-50%) enhancement of the dissipated thermal load, beyond what could be achieved by using air (gas) cooling alone. Finally, among the additional key attractive features of the described technology is its ease of implementation (i.e., modification of commercially available heat sinks), paving the way to power-efficient, low- cost thermal management of high power dissipation devices.
The Structure Of Human Parathyroid Hormone From a Study of Fragments in Solution Using 1H NMR Spectroscopy and Its Biological Implications (1994)

In order to gain insight into the structure of human parathyroid hormone (hPTH), four fragments [hPTH(1-34), hPTH(18-48), hPTH(28-48), and hPTH(53-84)], which cover all regions of the intact hormone, have been investigated by CD and NMR spectroscopy in combination with distance geometry, and restrained molecular dynamics and energy minimization calculations, under a variety of solution conditions. Significantly, all fragments showed little propensity to form stable structures in aqueous solution alone, and it was only on the addition of trifluoroethanol (TFE) that defined structural features were observed. In an extension of earlier work [Klaus et al. (1991) Biochemistry 30, 6936-6942], hPTH(1-34) in 70% trifluoroethanol (TFE) showed two helices that were longer than in 10% TFE, but essentially showed the same characteristics. Although overlap in the 1H NMR spectra prevented the determination of quantitative NOE data for residues 26-30, the combination of the alpha-proton chemical shift data and quantitative NOE data indicated the helices extend from residues 3 to 13 and 15 to 29. No evidence was found for interaction of the two helical regions. The nature and extent of this second helix in the intact hormone were better defined from the data for hPTH(18-48). Under limiting solution conditions, where the fragment assumed its maximum helical content, a well-defined helix was observed between residues 21 and 38 with a possible discontinuity between Leu-28 and Gln-29. There was little evidence of any form of secondary structure between Gly-38 and the terminus of this fragment, Ser-48. In keeping with this result, the shorter fragment, hPTH(28-48), showed little evidence of stable secondary structure on addition of TFE. From the alpha-proton chemical shifts residues 23-27 appeared to sustain helical structure more readily than the rest of molecule under all solution regimes in both hPTH(1-34) and hPTH(18-48). In contrast to the other two longer fragments hPTH(53-84) showed little propensity for helical secondary structure even at the highest TFE concentrations. However, there was evidence that the molecule did adopt a defined three-dimensional structure. Various long-range NOE's were observed in 10% TFE that allowed the calculation of an open tertiary structure consisting of an initial series of turns surrounded by a loop structure of several loose turns.(ABSTRACT TRUNCATED AT 400 WORDS)
Some New Syntheses of Amino- and Alkylaminopyrimidines and -pteridines (1963)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSome New Syntheses of Amino- and Alkylaminopyrimidines and -pteridinesWilliam V. Curran and Robert B. AngierCite this: J. Org. Chem. 1963, 28, 10, 2672–2677Publication Date (Print):October 1, 1963Publication History Published online1 May 2002Published inissue 1 October 1963https://pubs.acs.org/doi/10.1021/jo01045a043https://doi.org/10.1021/jo01045a043research-articleACS PublicationsRequest reuse permissionsArticle Views347Altmetric-Citations19LEARN 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
CD55 is a key complement regulatory protein that counteracts complement-mediated inactivation of Newcastle Disease Virus (2016)

Newcastle disease virus (NDV) is being developed as an oncolytic virus for virotherapy. In this study we analysed the regulation of complement-mediated inactivation of a recombinant NDV in different host cells. NDV grown in human cells was less sensitive to complement-mediated virus inactivation than NDV grown in embryonated chicken eggs. Additionally, NDV produced from HeLa-S3 cells is more resistant to complement than NDV from 293F cells, which correlated with higher expression and incorporation of complement regulatory proteins (CD46, CD55 and CD59) into virions from HeLa-S3 cells. Further analysis of the recombinant NDVs individually expressing the three CD molecules showed that CD55 is the most potent in counteracting complement-mediated virus inactivation. The results provide important information on selecting NDV manufacture substrate to mitigate complement-mediated virus inactivation.
An established CD4+ T lymphoma cell line derived from a patient with so- called Lennert's lymphoma: possible roles of cytokines in histopathogenesis (1988)

A T lymphoma cell line, KT-3, was established from the peripheral blood of a patient with so-called Lennert's lymphoma when the patient developed leukemic lymphoma. The KT-3 cells stain positively for alpha- naphthyl acetate esterase, PAS, and acid phosphatase. The surface phenotype is E rosette-positive, CD1-, CD2+, CD3-, CD4+, CD5+, CD8-, CD11-, CD20-, CD25 (anti-Tac)+, OKla-1+, HNK-1-, J-5-, and My9-, and the surface membrane immunoglobulin is negative, which is almost the same phenotype as the leukemic cells studied when the culture was started. Southern blot analysis showed rearrangement in both beta and gamma T cell receptor genes. Although KT-3 cells proliferate spontaneously and form clusters, they cease proliferating when they are cultured at low cell densities. They proliferate vigorously in response to macrophages, macrophage-derived factor, or recombinant interleukin 2 (rIL-2) added to the culture. Furthermore, they secrete interferon- gamma (IFN-gamma) spontaneously, and the secretion is augmented when they are stimulated with macrophage-derived factor. The macrophage- derived factor enhancing KT-3 cell growth is different from IL-1 alpha, IL-1 beta, IL-2, or IFN-gamma. To our knowledge, this is the first tumor cell line established from a patient with Lennert's lymphoma. The results conclusively confirmed that, at the least, Lennert's lymphoma included CD4+ T lymphoma and also suggested that cytokines or factors secreted by T lymphoma cells and epithelioid histiocytes play an important role in the histopathogenesis of Lennert's lymphoma.
Unlocking the DEAD-box: a key to cryptococcal virulence? (2005)

The DEAD-box RNA helicases are enzymes involved in many critical aspects of RNA metabolism within both eukaryotic and prokaryotic organisms. Several studies have shown that these proteins may have important functions in mediating microbial pathogenesis. A new study in this issue of the JCI identifies the first DEAD-box RNA helicase in the pathogenic fungus Cryptococcus neoformans and proposes novel roles for this family of proteins in the development and progression of cryptococcosis.
Serum Urate as a Predictor of Fetal Outcome in Severe Pre‐Eclampsia (1984)

Maternal serum urate levels were studied in 50 normal pregnancies and 72 cases of severe pre-eclampsia. Markedly elevated levels of serum urate were found in severe pre-eclampsia, compared with normal pregnancy. In severe pre-eclampsia significantly higher levels were found prior to parturition in cases of growth retardation and perinatal distress, compared with patients whose newborns were of normal size and condition. Particularly high serum urate levels were found early in the third trimester in cases of perinatal death. A slight but significant correlation was found between the weight centile of the newborn and the last maternal urate level before parturition. A rapidly rising urate level reliably predicted perinatal distress. The last maternal serum urate before parturition was correlated with the hemoglobin and erythrocyte volume fraction values in the same blood sample.
Photoreceptor degeneration induced by the expression of simian virus 40 large tumor antigen in the retina of transgenic mice. (1992)

Expression of the viral oncogene encoding the simian virus 40 (SV40) large tumor antigen (T antigen) typically promotes tumorigenesis in mammalian cells. To generate transgenic mice that express T antigen in rod photoreceptors, a chimeric construct consisting of a mouse opsin promoter fragment fused to the coding region of SV40 T antigen was generated. Expression of T antigen in the transgenic retina began at early stages of postnatal development concomitant with expression of endogenous opsin. Instead of inducing hyperplasia or tumor formation, T-antigen expression caused a rapidly progressing photoreceptor degeneration. The degeneration was accompanied by sustained DNA synthesis in photoreceptor cells, as evidenced by incorporation of [3H]thymidine and by the appearance of mitotic figures at postnatal day 10, a stage when nontransgenic photoreceptor cells are postmitotic and quiescent. Although transgenic photoreceptor cells undergo S phase and enter mitosis, the consequences of T-antigen expression are not proliferation and tumorigenesis but proliferation and cell death.
Robust Data-Driven Modeling Approach for Real-Time Final Product Quality Prediction in Batch Process Operation (2011)

Making on-specification products is a primary goal, and also a challenge in chemical batch process operation. Due to the uncertainty of raw materials and instability of operating conditions, it may not produce the desired on-spec final product. It would be helpful if one can predict the product quality during each operation, so that one can make adjustments to process conditions in order to make on-spec product. This paper addresses the issue of real-time prediction of final product quality during a batch operation. First, a data-driven modeling approach is presented. This multimodel approach uses available process information up to the current points to capture their time-varying relationships with the final product quality during the course of operation, so that the prognosis of product quality can be obtained in real-time. Then, due to its data-driven nature, the focus is given on how to make the models robust in order to eliminate the effect of noise, especially, outliers in the data. A model-based outlier detection method is presented. The proposed approach is applied to a generic chemical batch case study, with its prediction performance being evaluated.
Growth of GaN Nanorods by a Hydride Vapor Phase Epitaxy Method (2002)

Straight and well-aligned GaN nanorods have been obtained by horizontal hydride vapor phase epitaxy (HVPE) at a relatively low temperature (∼ 480 °C). This catalyst- and template- independent method involves the controllable growth of GaN nanorods on a sapphire substrate, with the rods preferentially oriented along the crystal c-axis. The Figure shows a cross-sectional SEM image of the GaN nanorods.
Potential Impact of Exempt Vehicles on HOV Lanes (2005)

This report explores the use of high-occupancy vehicle (HOV) lanes by exempt vehicles, including Inherently Low-Emission Vehicles (ILEV), environmentally friendly vehicles, law enforcement and emergency vehicles, and designated public transportation vehicles. Potential issues and approaches for allowing these types of exempt vehicles to use HOV lanes are examined. This information could be of use to state departments of transportation and other agencies in considering possible HOV exemption policies, and in monitoring and evaluating the use of HOV lanes by exempt vehicles. As authorized in recent federal legislation, at least 10 states have approved legislation allowing ILEVs to use HOV lanes without meeting the minimum occupancy requirement. Additional legislation in five states includes hybrid vehicles in the HOV lane exemption, if allowed by federal laws or federal agency regulations. Contrary to federal law, Virginia already allows hybrid vehicles to use HOV lanes in the state. The available information examined in this report indicates that the use of HOV lanes by ILEVs is low. However, based on monitoring hybrid vehicle use of the HOV lanes in northern Virginia there is evidence that hybrids are contributing to congestion problems on some facilities. Clearly marked law enforcement and emergency services vehicles, equipped with rooftop emergency lights and sirens, and designated public transportation vehicles are allowed to use most HOV facilities. There does not appear to be any major issues with the use of HOV lanes by these types of vehicle. However, there do appear to be issues in some areas with the unauthorized use of HOV lanes by law enforcement and emergency services personnel traveling in their personal vehicles or in unmarked agency vehicles while not on duty.\n
Optimising calcium phosphate cement formulations to widen clinical applications (2011)

The demand for reconstructive orthopaedic implants continues expanding at a reasonable pace as the incidence of fracture injuries and infectious diseases rises. There has been an increase in the clinical need for more effective synthetic bone graft materials due to the drawbacks of autogenous grafts. Since the 1980’s calcium phosphate cements (CPC’s) have attracted a great deal of interest due to their chemical similarities to natural bone; chemical, physical and mechanical characteristics have been investigated and manipulated to maximise osteoconductivity and osteointegration of these CPC’s since the start of their commercialisation. Here in this thesis, a series of investigation are complied to demonstrate novel and inventive approaches to expand the application of CPC’s: (1) limiting the liquid phase in the setting reaction of a brushite cement to produce monetite (dehydrated brushite) based cement, with increased solubility to overcome the problems faced by long term stability of hydroxyapatite (HA) cements; (2) manipulating the cement formulation to produce a cement that can set on a change in temperature, upon implantation, increasing handling time during surgeries; (3) incorporating therapeutic molecules to eliminate secondary surgeries following infectious diseases; (4) to enhance osteointegration of CPC’s by synchronising the degradation to natural bone formation. Results exhibit compressive strength appropriate for the application of cranioplasty; long term ageing studies demonstrates that the novel cement formulations do not hydrolyse to HA, eliminating the risk of catastrophic brittle failure that is commonly associated with CPC’s.
Adaptive Neurons For Artificial Neural Networks (1990)

Training time decreases dramatically. In improved mathematical model of neural-network processor, temperature of neurons (in addition to connection strengths, also called weights, of synapses) varied during supervised-learning phase of operation according to mathematical formalism and not heuristic rule. Evidence that biological neural networks also process information at neuronal level.
High-frequency effects in carbon nanotube interconnects and implications for on-chip inductor design (2008)

This paper presents a rigorous investigation of high-frequency effects in carbon nanotube interconnects and their implications for the design and performance analysis of high-quality on-chip inductors. An accurate method is developed to calculate the frequency-dependent resistance and inductance of both single-walled (SWCNT) and multi-walled carbon nanotube (MWCNT) bundle interconnects. Our analysis reveals for the first time that skin effect (current redistribution) in CNT bundles is negligible compared to that in conventional metal conductors, which make them a very attractive and promising material for high-frequency applications, including on-chip inductor design in high-performance RF/mixed-signal circuits. It is subsequently shown that CNT based inductors can achieve nearly 4times higher Q factor than Cu based inductors.
Volume clipping via per-fragment operations in texture-based volume visualization (2002)

We propose new clipping methods that are capable of using complex geometries for volume clipping. The clipping tests exploit per-fragment operations on the graphics hardware to achieve high frame rates. In combination with texture-based volume rendering, these techniques enable the user to interactively select and explore regions of the data set. We present depth-based clipping techniques that analyze the depth structure of the boundary representation of the clip geometry to decide which parts of the volume have to be clipped. In another approach, a voxelized clip object is used to identify the clipped regions.