gebhart/patrepeval huggingface dataset:
Rapid microwave fixation of human tissues for light microscopic immunoperoxidase identification of diagnostically useful antigens. (1987)

Microwave (MW) energy permits rapid tissue fixation for light and electron microscopy but its effects on antigen preservation have not been fully evaluated. We, therefore, fixed three samples of human skin, uterus, and cervix, and two samples of human colon and breast by MW irradiation (5 to 8 seconds) during simultaneous immersion in a dilute aldehyde mixture (2% formaldehyde and 0.05% glutaraldehyde). For comparison, similar portions of each specimen were fixed in formalin. Specimens were processed routinely and embedded in paraffin for light microscopy. Sections from each specimen were stained with hematoxylin and eosin and, by immunoperoxidase techniques, for epithelial membrane antigen, leukocyte common antigen, S-100 keratin, carcinoembryonic antigen, and factor VIII-related antigen, the latter three with and without preliminary trypsinization. Colon sections were also stained for chromogranin. In all cases, light microscopic morphology was comparable for tissues fixed by the MW method and formalin-fixed specimens, as was immunostaining for epithelial membrane antigen, leukocyte common antigen, S-100 protein, and chromogranin. Formalin-fixed tissues required trypsinization for optimal detection of keratin, carcinoembryonic antigen, and factor VIII-related antigen. In contrast, trypsin-pretreatment was not necessary to demonstrate these antigens in MW-fixed specimens and, in fact, resulted in tissue digestion. We conclude that this MW fixation method provides a means for rapidly fixing tissues for immunoperoxidase staining while preserving excellent light microscopic morphology.
Managing class imbalance of immune cell populations in multi-class instance segmentation of immunofluorescence images of Lupus Nephritis biopsies (2021)

Lupus nephritis (LuN) is a manifestation of systemic lupus erythematosus defined by chronic infiltration of immune cells into the kidneys—particularly lymphocytes and dendritic cells (DCs). Ultimately, our goal is to characterize the cellular communities associated with progression to kidney failure. To accomplish this, we have generated a dataset of fluorescence confocal microscopy images of kidney biopsies from 31 LuN patients that have been stained for two T-lymphocyte populations, B-lymphocytes and two DC populations. We are using convolutional neural networks (CNNs) with a Mask R-CNN architecture to perform instance segmentation on these five classes. This multi-class instance segmentation task is hindered by an inherent class imbalance between lymphocytes and DCs, with DCs being much less prevalent. Here we discuss methods for managing class imbalance to achieve comparable instance segmentation of both DCs and lymphocytes in LuN biopsies. A network trained to identify all 5 classes yielded higher sensitivity to DCs when the training set was filtered to contain images with all 5 cell classes present. Average DC sensitivity on an independent test set improved from 0.54 to 0.63 with filtered training data. DC segmentation improved further when the network was trained specifically for DC classes. Average DC sensitivity reached 0.91 when trained separately from lymphocytes, with average Jaccard index of DCs improving from 0.69±0.2 to 0.76±0.2. Accurate segmentation of all cell types relevant to LuN pathogenesis enabled in-depth spatial analysis of the immune environments that result in renal failure in LuN patients.
Ibm websphere portal v4 developer's handbook (2003)

Deliver additional functions such as personalization and search capabilities Understand portlet development using WebSphere Portal Toolkit Learn about portlet event handling and messaging This IBM Redbook helps you plan and develop portlet applications using the IBM WebSphere Portal Enable and Extend offerings. The information provided in this redbook targets Business-to-Employee (B2E) enterprise applications, but most of the scenarios presented apply to Business-to-Consumer (B2C) applications as well. In this redbook, you will find step-by-step examples and scenarios showing ways to integrate your enterprise applications into an IBM WebSphere Portal environment using the WebSphere Portal APIs provided by the Portal Toolkit to develop portlets; we also discuss extending your portlet capabilities to use other advanced functions such as themes and skins, personalization, search capabilities, content management, national language support, transcoding, Web clipping, etc. Elements of the portlet API are described and sample code is provided. The scenarios included in this redbook can be used to learn about portlet programming and as a basis to develop your own portlet applications. You will also find numerous scenarios describing recommended ways to develop portlets and portlet applications using the APIs provided by the IBM WebSphere Portal Toolkit. A basic knowledge of Java technologies such as servlets, JavaBeans, EJBs, JavaServer Pages (JSPs), as well as XML applications and the terminology used in Web publishing, is assumed.
The design of high availability in the Dawning server consolidation system (2000)

High availability (HA) cluster systems that support more than a dozen nodes were only discussed in recent years. The new industry trend for server consolidation also drives the research for an integral, scalable, high availability and high manageability cluster system. We present our high availability design in the Dawning Server Consolidation system, including the main architecture as well as the design issues in load balance, dynamic configuration, state consistency, error detection, cluster resource management, dependable communication etc.
Paclitaxel-eluting stents vs vascular brachytherapy for in-stent restenosis within bare-metal stents: the TAXUS V ISR randomized trial. (2006)

ClinicalTrials.gov Identifier: NCT00287573.
Synergistic Combination of Small Molecule Inhibitor and RNA Interference against Antiapoptotic Bcl-2 Protein in Head and Neck Cancer Cells (2013)

B-cell lymphoma 2 (Bcl-2) is an antiapoptotic protein that is overexpressed in head and neck squamous cell carcinomas, which has been implicated in development of radio- and chemoresistance. Small molecule inhibitors such as AT-101 (a BH3-mimetic drug) have been developed to inhibit the antiapoptotic activity of Bcl-2 proteins, which proved effective in restoring radio- and chemo-sensitivity in head and neck cancer cells. However, high doses of AT-101 are associated with gastrointestinal, hepatic, and fertility side effects, which prompted the search for other Bcl-2 inhibitors. Short interfering RNA (siRNA) proved to inhibit antiapoptotic Bcl-2 protein expression and trigger cancer cell death. However, transforming siRNA molecules into a viable therapy remains a challenge due to the lack of efficient and biocompatible carriers. We report the development of degradable star-shaped polymers that proved to condense anti-Bcl-2 siRNA into "smart" pH-sensitive and membrane-destabilizing particles that shuttle their cargo past the endosomal membrane and into the cytoplasm of head and neck cancer cells. Results show that "smart" anti-Bcl-2 particles reduced the mRNA and protein levels of antiapoptotic Bcl-2 protein in UM-SCC-17B cancer cells by 50-60% and 65-75%, respectively. Results also show that combining "smart" anti-Bcl-2 particles with the IC25 of AT-101 (inhibitory concentration responsible for killing 25% of the cells) synergistically inhibits cancer cell proliferation and increases cell apoptosis, which reduce the survival of UM-SCC-17B cancer cells compared to treatment with AT-101 alone. Results indicate the therapeutic benefit of combining siRNA-mediated knockdown of antiapoptotic Bcl-2 protein expression with low doses of AT-101 for inhibiting the growth of head and neck cancer cells.
Chireix Power Combining with Saturated Class-BPower Amplifiers (2004)

This paper describes the realization of a Chireix power combining part of an outphasing system for 2.14 GHz consisting of two saturated class-B power amplifiers and a Chireix power combiner circuit. The Chireix power combining scheme can be used in Chireix outphasing architecture, which is currently together with EER and the Doherty amplifier one of the most prominent research topics in power amplifier linearization / efficiency enhancement area. In an outphasing system, also known as LINC (Linear Amplification of Nonlinear Components), an amplitude and phase modulated signal is separated into two constant envelope signals containing only phase modulation. The original signal waveform can subsequently be reconstructed by varying the phases of the two constant envelope signal branches, thus enabling, ideally, linear amplification of the original signal with system efficiency comparable to the efficiency of the used PAs. In this paper, the design and implementation as well as the measurement results of a microstrip-line Chireixcombiner together with saturated class-B pHEMT power amplifiers for WCDMA downlink band 2.11-2.17 GHz are reported. The measurement results verify that the concept is indeed functional, and significant efficiency improvement over traditional power combining can be attained. At peak envelope power 37.4 dBm system efficiency of 77 % was measured, and at –8 dB back-off, representing the computational average point for WCDMA signal, system efficiency of 43 % was measured.
Accelerated Intravascular Ultrasound Imaging using Deep Reinforcement Learning (2022)

Intravascular ultrasound (IVUS) offers a unique perspective in the treatment of vascular diseases by creating a sequence of ultrasound-slices acquired from within the vessel. However, unlike conventional hand-held ultrasound, the thin catheter only provides room for a small number of physical channels for signal transfer from a transducer-array at the tip. For continued improvement of image quality and frame rate, we present the use of deep reinforcement learning to deal with the current physical information bottleneck. Valuable inspiration has come from the field of magnetic resonance imaging (MRI), where learned acquisition schemes have brought significant acceleration in image acquisition at competing image quality. To efficiently accelerate IVUS imaging, we propose a framework that utilizes deep reinforcement learning for an optimal adaptive acquisition policy on a per-frame basis enabled by actor-critic methods and Gumbel top-K sampling.
Iron induced arthritis in immature rabbits (1970)

Abstract Intramuscularly administered iron dextran in immature rabbits leads to iron deposition in the articular cartilage chondrocyte followed by lacunar enlargement, the appearance of transverse striations in the matrix, abnormal staining characteristics of the middle layer of cartilage, rounding of the surface chondrocytes, fibrillation and fraying of the cartilage matrix, and death and disappearance of the chondrocytes. Iron deposition also occurs in the synovium and leads to mild thickening with no inflammatory cell reaction. In mature rabbits, iron is deposited in the synovium only, and none of the above cartilage changes occur.
Speculative Satire and Postracial Capitalism in Nana Kwame Adjei-Brenyah’s Friday Black (2022)

ABSTRACT This article explores the satire in Nana Kwame Adjei-Brenyah’s Friday Black (2018), specifically focusing on the use of speculative devices to question assumptions about racial progress in the twenty-first century United States. Adjei-Brenyah’s humor unsettles the logic of postracial time and demonstrates how contemporary African American satire disrupts race-neutral discourses that reproduce what Maria Bose calls “postracial capitalism.” Drawing on recent scholarship by Bose, Danielle Fuentes Morgan, Lisa Guerrero, and others, I read Adjei-Brenyah’s dark and hilarious short stories as satires that name and challenge the emerging technologies of racist domination that condemn Black bodies to premature death in contemporary America.
I of the Vortex (2001)

A highly original theory of how the mind-brain works, based on the author's study of single neuronal cells.In I of the Vortex, Rodolfo Llinas, a founding father of modern brain science, presents an original view of the evolution and nature of mind. According to Llinas, the "mindness state" evolved to allow predictive interactions between mobile creatures and their environment. He illustrates the early evolution of mind through a primitive animal called the "sea squirt." The mobile larval form has a brainlike ganglion that receives sensory information about the surrounding environment. As an adult, the sea squirt attaches itself to a stationary object and then digests most of its own brain. This suggests that the nervous system evolved to allow active movement in animals. To move through the environment safely, a creature must anticipate the outcome of each movement on the basis of incoming sensory data. Thus the capacity to predict is most likely the ultimate brain function. One could even say that Self is the centralization of prediction.At the heart of Llinas's theory is the concept of oscillation. Many neurons possess electrical activity, manifested as oscillating variations in the minute voltages across the cell membrane. On the crests of these oscillations occur larger electrical events that are the basis for neuron-to-neuron communication. Like cicadas chirping in unison, a group of neurons oscillating in phase can resonate with a distant group of neurons. This simultaneity of neuronal activity is the neurobiological root of cognition. Although the internal state that we call the mind is guided by the senses, it is also generated by the oscillations within the brain. Thus, in a certain sense, one could say that reality is not all "out there," but is a kind of virtual reality.
Rhesus thymic/liver xenografts in severe combined immunodeficient mice: immunologic reconstitution and intrathymic infection with simian immunodeficiency virus. (1996)

By serving as host recipients of xenografts from both humans and animals, severe combined immunodeficient (SCID) mice have become valuable to many laboratories interested in examining the pathophysiology of different diseases. To gain insight into the usefulness of the SCID mutation in retrovirus research, rhesus monkey fetal hematolymphoid tissues (liver and thymus) were used to construct a SCID-rhesus chimeric mouse (SCID-rh) and were engrafted in the renal capsule. The size and maturation of the thymic engrafts were monitored grossly, histologically, and immunologically. SCID mice were tolerant to rhesus tissues, and thymic engrafts contained thymocytes at different stages of maturation and differentiation that had morphologic features similar to age-matched rhesus thymus. Mature single positive CD2+, CD4+, and CD8+ T lymphocytes that were phenotypically similar to rhesus T lymphocytes were present at low levels (2% to 5%) in the peripheral blood and at moderately higher levels (7% to 15%) in the spleens of SCID-rh mice obtained between 12 and 15 weeks after thymus/liver engraftment. Within 3 weeks after engraftment, > 85% of the thymocytes in the thymic engrafts were immature double positive CD4+CD8+ T cells. The highest number of positive cells were seen in thymic engrafts obtained at 12 to 18 weeks. During these weeks, > 90% of the cells were double positive (CD2+CD4+, CD2+CD8+, and CD4+CD8+). After infection of the engrafted thymus tissue with simian immonodeficiency virus (SIVmac239), PCR analysis revealed successful viral infection of engrafts at 2 and 4 weeks after infection. No significant histopathologic and flow cytometric changes were observed in the thymic engrafts at 2 and 4 weeks after infection. An unrelated lesion of thymic lymphomas involving the SCID host thymus was seen in 12% of the mice. The data presented herein suggest that the SCID-rh is a valuable model for specific studies related to thymus-retrovirus interaction and that it could be used for further studies. The results are discussed in relation to current knowledge of thymus involvement during simian and human immunodeficiency virus infection.
Quantitative Analysis of Etching Damage in the Highly-Selective Oxide Etching (2005)

The damage produced by the oxide dry etching process was quantified by the Time of Flight-Low Energy Ion Scattering Spectroscopy, paying special attention to the crystalline degradation and to the contamination. The highly selective oxide dry etching process, in which CO gas is added to the C4F8 gas produced a damaged layer of more than 10.0 nm thickness. This layer contains abundant Si-C and Si-O bonds. These make it difficult to remove the damaged layer by post treatment, and suppress the lifetime recovery. In case of conventional contact hole etching process using CF/sub 4/ / CHF/sub 3/ gas, the damaged layer contains less Si-C, Si-O bonds although the layer thickness is more than 10nm.
Mitigation of spectral mis-registration effects in imaging spectrometers via cubic spline interpolation (2008)

The effects of spectral curvature (smile) on the co-registration of measured radiance spectra were analyzed for a dispersive imaging spectrometer. The spectra measured by the imaging spectrometer with spectral curvature were re-sampled using cubic spline Interpolation to mitigate the mis-registration of spectral radiance measurement. After correction, the co-registration of measured radiance spectra is distinctly improved.
TR-700 in vitro activity against and resistance mutation frequencies among Gram-positive pathogens (2009)

TR-700 exhibited enhanced activity against linezolid-non-susceptible and wild-type control strains of Gram-positive cocci. A significant number (nearly 90%) of linezolid-non-susceptible strains were inhibited by potentially achievable levels (< or = 4 mg/L) of TR-700. All strains with the emerging cfr-mediated resistance determinant had TR-700 MIC results at < or = 8 mg/L.
Halogenated silicon(iv) phthalocyanines with axial poly(ethylene glycol) chains. Synthesis, spectroscopic properties, complexation with bovine serum albumin and in vitro photodynamic activitiesDedicated to Prof. Malcolm L. H. Green on the occasion of his retirement, with our warmest congratulations. (2004)

A new series of unsubstituted and halogenated silicon(IV) phthalocyanines with two axial poly(ethylene glycol) (PEG) chains having an average molecular weight of 550 or 750 (PEG550 or PEG750) have been synthesised by treating the corresponding silicon phthalocyanine dichloride with PEG methyl ether in the presence of NaH. The compounds have been unambiguously characterised with 1H NMR and MALDI-TOF mass spectrometry. With two bulky polymeric substituents, the compounds are essentially non-aggregated in common organic solvents. The longer PEG750 chain enhances the hydrophilicity of the phthalocyanine ring and is more effective to prevent aggregation and fluorescence quenching by Cu(OAc)2. Substitution with heavier halogen atoms on the periphery of the ring leads to a reduction in fluorescence emission and an increase in singlet oxygen quantum yield, as a result of heavy atom effect. The compounds Si(PcX8)(PEG750)2 [X = H (4b), Cl (4c), Br (4d)] are photocytotoxic towards HepG2 human hepatocarcinoma cells and J774 mouse mammary tumour cells. Although halogenation results in an increase in singlet oxygen quantum yield, the general photocytotoxicity follows the order 4b > 4d > 4c. This can be attributed to the opposite effect of aggregation, which follows the order 4a < 4b < 4c in the growth medium. The interactions of 4b–d with bovine serum albumin (BSA) have also been investigated by a fluorescence quenching method and a non-covalent conjugate of 4b and BSA has been prepared. Conjugation with BSA leads to a higher photocytotoxicity against J774 cells, which have a BSA-loving macrophage origin.
Protonation States and pH Titration in the Photocycle of Photoactive Yellow Protein (2000)

Photoactive yellow protein (PYP) undergoes a light-driven cycle of color and protonation states that is part of a mechanism of bacterial phototaxis. This article concerns functionally important protonation states of PYP and the interactions that stabilize them, and changes in the protonation state during the photocycle. In particular, the chromophore pK(a) is known to be shifted down so that the chromophore is negatively charged in the ground state (dark state) even though it is buried in the protein, while nearby Glu46 has an unusually high pK(a). The photocycle involves changes of one or both of these protonation states. Calculations of pK(a) values and protonation states using a semi-macroscopic electrostatic model are presented for the wild-type and three mutants, in both the ground state and the bleached (I(2)) intermediate state. Calculations allowing multiple H-bonding arrangements around the chromophore also have been carried out. In addition, ground-state pK(a) values of the chromophore have been measured by UV-visible spectroscopy for the wild-type and the same three mutants. Because of the unusual protonation states and strong electrostatic interactions, PYP represents a severe test of the ability of theoretical models to yield correct calculations of electrostatic interactions in proteins. Good agreement between experiment and theory can be obtained for the ground state provided the protein interior is assumed to have a relatively low dielectric constant, but only partial agreement between theory and experiment is obtained for the bleached state. We also present a reinterpretation of previously published data on the pH-dependence of the recovery of the ground state from the bleached state. The new analysis implies a pK(a) value of 6.37 for Glu46 in the bleached state, which is consistent with other available experimental data, including data that only became available after this analysis. The new analysis suggests that signal transduction is modulated by the titration properties of the bleached state, which are in turn determined by electrostatic interactions. Overall, the results of this study provide a quantitative picture of the interactions responsible for the unusual protonation states of the chromophore and Glu46, and of protonation changes upon bleaching.
A MILP Model for the Design Optimization of Energy Communities (2022)

Energy communities are considered a key element in the transition towards more sustainable energy systems.Indeed, the final consumers are encouraged to form communities to share the locally produced renewable electricity.In such a prospective, this work proposes a novel Mixed Integer Linear Programming formulation for the design optimization of energy communities: given a set of buildings/prosumers of a district, the model allows optimizing the number of energy communities and the selection of prosumers/buildings to be included in each community with the objective of maximizing the economic or energy benefit for the whole district.The proposed model is applied to a case study of a district with 40 prosumers and results are critically analyzed.