gebhart/patrepeval huggingface dataset:
A Multisite Performance Study Comparing the Reading of Immunohistochemical Slides on a Computer Monitor With Conventional Manual Microscopy for Estrogen and Progesterone Receptor Analysis (2011)

A multisite study was conducted to assess the performance of the Aperio digital pathology system (Aperio Technologies, Vista, CA) for reading estrogen receptor (ER) and progesterone receptor (PR) slides on a computer monitor. A total of 520 formalin-fixed breast tissue specimens were assayed at 3 clinical sites for ER and PR (260 each). Percentage and average staining intensity of positive nuclei were assessed. At each site, 3 pathologists performed a blinded reading of the glass slides using their microscopes initially and later using digital images on a computer monitor. Comparable percentages of agreements were obtained for manual microscopy (MM) and manual digital slide reading (MDR) (ER, percentage of positive nuclei with cutoffs: MM, 91.3%-99.0%/MDR, 91.3%-100.0%; PR, percentage of positive nuclei with cutoffs: MM, 83.8%-99.0%/MDR, 76.3%-100.0%). Reading ER and PR slides on a computer monitor using the Aperio digital pathology system is equivalent to reading the slides with a conventional light microscope.
Direct Synthesis of Thiolate-Protected Gold Nanoparticles Using Bunte Salts as Ligand Precursors: Investigations of Ligand Shell Formation and Core Growth (2011)

Applications of ligand-protected nanoparticles have increased markedly in recent years, yet their controlled synthesis remains an under-developed field. Nanoparticle syntheses are highly specialized in their execution and often possess significant limitations. For example, the synthesis of thiol-stabilized gold nanoparticles (AuNPs) with core diameters greater than 5.0 nm is difficult to achieve using existing methods. This dissertation describes the development of a synthetic strategy for thiolate-stabilized AuNPs over a wide range of core sizes using alkyl thiosulfates (Bunte salts) as ligand precursors. The use of Bunte salts permits the synthesis of larger AuNPs than can be achieved using thiols by allowing the AuNP cores to grow to larger diameters before the formation of the thiolate ligand shell. Chapter II details the development of a direct synthesis strategy using Bunte salts as ligand precursors that produces AuNPs with diameters up to 20 nm. Chapter III describes an investigation of the ligand shell formation that occurs during these syntheses. The ligand shell formation involves the adsorption of the Bunte salt to the AuNP surface, where it is converted to the thiolate. This conversion requires an excess of sodium borohydride in the synthesis of &gt;5 nm AuNPs, but not for the synthesis of smaller AuNPs. This synthetic strategy was adapted for use in flow reactors to attain simultaneous AuNP synthesis and characterization. Chapter IV demonstrates that thiol-stabilized AuNPs can be synthesized in a microfluidic device with product monitoring provided by UV-vis absorbance spectroscopy. The development of a capillary flow reactor that permits the incorporation of new monitoring techniques is presented in Chapter V. The incorporation of Small-Angle X-ray Scattering (SAXS) analysis provides quantitative in situ determinations of AuNP diameter. The combination of synthetic control and monitoring makes capillary flow reactors powerful tools for optimization of NP syntheses and monitoring NP growth. In Chapter VI, the capillary flow reactor is used in an investigation of AuNP core growth. We also review AuNP growth mechanisms and show how to differentiate these using SAXS and UV-vis analysis. In these studies, AuNP growth is unexpectedly shown to involve a coalescence mechanism. This dissertation includes previously published and co-authored material.
DP drilling extends technology (1982)

Successful operating experience has proven dynamic positioning the basic component required for drilling in water depths to 5000 feet and identifies the area where improved equipment and procedures will be beneficial for more efficient operations. Forty-two wells have been drilled using dynamically positioned (DP) vessels in water depths exceeding 2000 feet. Of the 15 (DP) vessels, all but one are drillships. For 13,000-ft water depth, two deepwater techniques must be developed riser/rig handling capability and formation fraction gradient. Economic demands to develop the deep water will govern when, where and what water depths will be explored; this will dictate the development of the next generation of deepwater drilling units and the technology required to build and operate the units. Next comes production drilling and subsea completions, where dynamic stationing offers many advantages where there is a tangle of subsea wellheads, flowlines, and pipelines. (DP)
Three-Dimensional Repeated Elasto-Plastic Point Contacts, Rolling, and Sliding (2008)

Accumulative plastic deformation due to repeated loading is crucial to the lives of many mechanical components, such as gears, stamping dies, and rails in rail-wheel contacts. This paper presents a three-dimensional numerical model for simulating the repeated rolling or sliding contact of a rigid sphere over an elasto-plastic half-space. This model is a semi-analytical model based on the discrete convolution and fast Fourier transform algorithm. The half-space behaves either elastic-perfectly plastically or kinematic plastically. The analyses using this model result in histories of stress, strain, residual displacement, and plastic strain volume integral (PV) in the half-space. The model is examined through comparisons of the current results with those from the finite element method for a simple indentation test. The results of rolling contact obtained from four different hardening laws are presented when the load exceeds the theoretical shakedown limit. Shakedown and ratchetting behaviors are discussed in terms of the PV variation. The effect of friction coefficient on material responses to repeated sliding contacts is also investigated.
Continuous glucose monitoring and closed‐loop systems (2005)

The glucose monitor remains the main limiting factor in the development of a commercially viable closed-loop system, as presently available monitors fail to demonstrate satisfactory characteristics in terms of reliability and/or accuracy. Regulatory issues are the second limiting factor. Closed-loop systems are likely to be used first by health-care professionals in controlled environments such as intensive care units.
<title>Image/text automatic indexing and retrieval system using context vector approach</title> (1995)

Thousands of documents and images are generated daily both on and off line on the information superhighway and other media. Storage technology has improved rapidly to handle these data but indexing this information is becoming very costly. HNC Software Inc. has developed a technology for automatic indexing and retrieval of free text and images. This technique is demonstrated and is based on the concept of `context vectors' which encode a succinct representation of the associated text and features of sub-image. In this paper, we will describe the Automated Librarian System which was designed for free text indexing and the Image Content Addressable Retrieval System (ICARS) which extends the technique from the text domain into the image domain. Both systems have the ability to automatically assign indices for a new document and/or image based on the content similarities in the database. ICARS also has the capability to retrieve images based on similarity of content using index terms, text description, and user-generated images as a query without performing segmentation or object recognition.
Experimental studies of the active damping of free-rotor gyroscopes (1970)

Covers advancements in spacecraft and tactical and strategic missile systems, including subsystem design and application, mission design and analysis, materials and structures, developments in space sciences, space processing and manufacturing, space operations, and applications of space technologies to other fields.
Origin of the Significant Impact of Ta on the Creep Resistance of FeCrNi Alloys (2020)

Heat resistant FeCrNi alloys are widely used in the petrochemical industry because they exhibit a unique combination of creep and oxidation resistance at temperatures exceeding 900$^\circ$C. Their creep properties are often optimized by micro-additions of carbide forming elements. In the present work, the influence of Ta micro-additions has been experimentally investigated both on as-cast and aged microstructures to understand the origin of the significant impact of this element on the creep resistance. Calculations with thermocal software were also carried out to support experimental data. It is shown that a small addition of Ta is beneficial as it increases the volume fraction of stable MC carbides. We demonstrate also that additions of Ta may have a dramatic effect on the thermal stability of microstructures. This is attributed to a smaller equilibrium volume fraction of M23C6 and more pronounced heterogeneous precipitation at MC/matrix interfaces. The influence on the creep properties in then discussed.
Supplementary Figure 1 from Improved Stool DNA Integrity Method for Early Colorectal Cancer Diagnosis (2023)

&lt;p&gt;Supplementary Figure 1. Fagan Nomogram analysis. A line is drawn connecting the pre-test probability and the point on the middle vertical line corresponding to the likelihood ratio for the test result, represented by a range of test results (boxes). This line is extended to intersect with the right-hand vertical line, which gives the post-test probability. This point is the new estimate of probability that the patient has the disease. A) Nomogram for post-test probability of having a tumor. B) Nomogram for post-test probability of having a tumor or high-risk adenoma.&lt;/p&gt;
Gammaherpesvirus-mediated repression reveals EWSR1 to be a negative regulator of B cell responses (2022)

The germinal center (GC) plays a central role in the generation of antigen-specific B cells and antibodies. Tight regulation of the GC is essential due to the inherent risks of tumorigenesis and autoimmunity posed by inappropriate GC B cell processes. Gammaherpesviruses such as Epstein-Barr virus (EBV) and murine gammaherpesvirus 68 (MHV68) utilize numerous armaments to drive infected naïve B cells, independent of antigen, through GC reactions to expand the latently infected B cell population and establish a stable latency reservoir. We previously demonstrated that the MHV68 microRNA (miRNA) <i>mghv-miR-M1-7-5p</i> represses host <i>EWSR1</i> (Ewing sarcoma breakpoint region 1) to promote B cell infection. EWSR1 is a transcription and splicing regulator that is recognized for its involvement as a fusion protein in Ewing sarcoma. A function for EWSR1 in B cell responses has not been previously reported. Here, we demonstrate that 1) B cell-specific deletion of EWSR1 had no effect on generation of mature B cell subsets or basal immunoglobulin levels in naïve mice, 2) repression or ablation of EWSR1 in B cells promoted expansion of MHV68 latently infected GC B cells, and 3) B cell-specific deletion of EWSR1 during a normal immune response to nonviral antigen resulted in significantly elevated numbers of antigen-specific GC B cells, plasma cells, and circulating antibodies. Notably, EWSR1 deficiency did not affect the proliferation or survival of GC B cells but instead resulted in the generation of increased numbers of precursor GC B cells. Cumulatively, these findings demonstrate that EWSR1 is a negative regulator of B cell responses.
Transitions from high to low molecular weight isoforms of CD45 (T200) involve rapid activation of alternate mRNA splicing and slow turnover of surface CD45R. (1989)

The expression of CD45 isoforms and of CDw29 has been analyzed as a function of time by correlating cell surface phenotype with mRNA synthesis. After activation, T cells lose CD45R and acquire a high density of CD45 p180 and of CDw29. Throughout this transition the density of CD45 common determinants steadily increases, resulting in a net gain of surface CD45. The gradual loss of CD45R could reflect a rapid switch in CD45 mRNA splicing patterns followed by a slow loss of surface CD45R. Alternatively it could reflect a delayed activation of splicing to produce the 4.8-kb CD45 mRNA, or long lived 5.4-kb CD45 mRNA. Analysis of CD45 mRNA indicated that at 24 h postactivation, 5.4-kb CD45 mRNA is lost and only 4.8-kb mRNA is detectable. The amount of 4.8-kb mRNA increases until day 3 and then decreases somewhat. Thus our results support the interpretation that transitions in CD45 isoform mRNA expression occur within the first 24 h after activation and that the persistence of CD45R+ T cells until day 3 to 4 of culture results from slow turnover of surface CD45R glycoprotein.
Abstract PO-101: Characterization of longitudinally collected fine needle aspiration biopsies of pancreatic ductal adenocarcinoma upon endoscopic ultrasound guided radiofrequency ablation (2021)

Abstract Background: Most patients with pancreatic ductal adenocarcinoma (PDAC) are metastatic at presentation with dismal prognosis warranting improved systemic therapy options. Longitudinal sampling for assessment of treatment response poses a challenge for validating novel therapies. In this proof-of-principle study, we evaluate the role of endoscopic ultrasound (EUS)-guided serial fine-needle aspiration biopsies (FNABs) to study the mechanism of action of radiofrequency ablation (RFA). Methods: Patients with stage III inoperable PDAC with prior exposure to gemcitabine were selected into ARDEO (ethically approved Phase-II prospective clinical study of EUS-RFA). Post examination, targeted RF was delivered thrice and sequential FNABs of tumor were taken before and after treatment. Transcriptomic profiling of 6 FNABs from 2 patients was performed using a custom NanoString gene panel (144 genes) consisting of cancer and cancer-associated fibroblast (CAFs) subtypes along with immune changes. CAF culture was established from one FNAB and characterised by immunofluorescence and immunoblotting. Results: RFA treatments were well tolerated without any complications and both patients had stable disease immediately after EUS-RFA. Two-course RFA led to upregulation of CD1E gene (participates in antigen presentation) in both, patient 1 and 2 (4.5 and 3.9-fold) compared to baseline. Patient 1 showed increased expression of T cell genes (CD4 – 8.7-fold, CD8 – 35.7-fold), cytolytic function (6.4-fold) and inflammatory response (8-fold) post-RFA. Greater than 2-fold upregulation of CD274 (PDL1), IDO1, PDCD1 and TNFRSF18 (GITR) was observed post 2nd RFA in both the patients. Further, two-course RFA led to increased PDGFRa (4.5 and 9-fold) in both patients along with enrichment of pCAF subtypes B and C in patient 1 and subtypes A, B and D in patient 2. Immunofluorescence staining revealed expression of PDGFRa, aSMA, VIM, POSTN and MYH11 on patient2-derived CAFs post 1st RFA; validated by immunoblotting. Finally, RFA led to downregulation of classical PDA subtype in both patients. Conclusions: This feasibility study validates longitudinal sampling by EUS-FNABs as an appropriate research tool to study tumor microenvironmental changes associated with local pancreatic immunomodulatory techniques like RFA. Citation Format: Krisha Desai, Patrick Varun Lawrence, Christopher Wadsworth, Nagina Mangal, Nagy Habib, Anguraj Sadanandam, Mikael Sodergren. Characterization of longitudinally collected fine needle aspiration biopsies of pancreatic ductal adenocarcinoma upon endoscopic ultrasound guided radiofrequency ablation [abstract]. In: Proceedings of the AACR Virtual Special Conference on Pancreatic Cancer; 2021 Sep 29-30. Philadelphia (PA): AACR; Cancer Res 2021;81(22 Suppl):Abstract nr PO-101.
Drug discovery in Parkinson's disease: update and developments in the use of cellular models (2011)

Parkinson's disease (PD) is the second most common neurodegenerative disorder and is characterized by the degeneration of dopaminergic (DA) neurons within the substantia nigra. Dopamine replacement drugs remain the most effective PD treatment but only provide temporary symptomatic relief. New therapies are urgently needed, but the search for a disease-modifying treatment and a definitive understanding of the underlying mechanisms of PD has been limited by the lack of physiologically relevant models that recapitulate the disease phenotype. The use of immortalized cell lines as <i>in vitro</i> model systems for drug discovery has met with limited success, since efficacy and safety too often fail to translate successfully in human clinical trials. Drug discoverers are shifting their focus to more physiologically relevant cellular models, including primary neurons and stem cells. The recent discovery of induced pluripotent stem (iPS) cell technology presents an exciting opportunity to derive human DA neurons from patients with sporadic and familial forms of PD. We anticipate that these human DA models will recapitulate key features of the PD phenotype. In parallel, high-content screening platforms, which extract information on multiple cellular features within individual neurons, provide a network-based approach that can resolve temporal and spatial relationships underlying mechanisms of neurodegeneration and drug perturbations. These emerging technologies have the potential to establish highly predictive cellular models that could bring about a desperately needed revolution in PD drug discovery.
RhoB antibody alters retinal vascularization in models of murine retinopathy (2018)

Neovascularization in cancer or retinopathy is driven by pathological changes that foster abnormal sprouting of endothelial cells. Mouse genetic studies indicate that the stress-induced small GTPase RhoB is dispensable for normal physiology but required for pathogenic angiogenesis. In diabetic retinopathy, retinopathy of prematurity (ROP) or age-related wet macular degeneration (AMD), progressive pathologic anatomic changes and ischemia foster neovascularization are characterized by abnormal sprouting of endothelial cells. This process is driven by the angiogenic growth factor VEGF, which induces and supports the formation of new blood vessels. While injectable biologics targeting VEGF have been used to treat these pathological conditions, many patients respond poorly, prompting interest in other types of mechanism-based therapy. Here we report the preclinical efficacy of a monoclonal antibody that specifically targets RhoB, a signaling molecule that is genetically dispensable for normal physiology but required for pathogenic retinal angiogenesis. In murine models of proliferative retinal angiogenesis or oxygen-induced retinopathy, administering a monoclonal RhoB antibody (7F7) was sufficient to block neoangiogenesis or avascular pathology, respectively. Our findings offer preclinical proof of concept for antibody targeting of RhoB to limit diabetic retinopathy, ROP or wet AMD and perhaps other diseases of neovasculogenesis such as hemangioma or hemangiosarcoma nonresponsive to existing therapies.
Temporal trends and clonal diversity of penicillin non-susceptible pneumococci from meningitis cases from 1996 to 2012, in Salvador, Brazil (2015)

Our results show sustained reductions in pneumococcal meningitis cases in the Metropolitan region of Salvador from 1996 to 2012. This might reflect a beneficial impact of conjugate vaccines. Continued surveillance and further studies need to be conducted to better understanding on PCV10 vaccine impact.
Small Low Mass Advanced PBR's for Bi-Modal Operation (1994)

A preliminary assessment is made of a low mass bi‐modal reactor for use as a propulsion unit and as a heat source for generating electricity. This reactor is based on the particle bed reactor (PBR) concept. It will be able to generate both thrust and electricity simultaneously. This assessment indicates that the reactor can generate approximately 6.8 (4) N of thrust using hydrogen as a coolant, and 100 KWe using a closed Brayton cycle (CBC) power conversion system. Two cooling paths pass through the reactor allowing simultaneous operation of both modes. The development of all the components for this reactor are within the experience base of the NTP project.
E-080 4D-Flow MRI quantifies hemodynamics in large and giant intracranial aneurysms (2012)

Purpose Unruptured intracranial aneurysms (IA) are potentially life threatening conditions. Rupture risk based on specific data regarding interval growth or destabilization is lacking. We studied the feasibility of 4D-Flow MRI to analyze 3D flow patterns (vorticity) and aneurysm wall shear stress (WSS) in large and giant IAs. Materials and Methods Seven patients (4F:3M, age=3.6±15.4 years) with large IAs (mean diameter=2.6±0.9 cm) were studied. IAs were located near the ICA bifurcation (n=5) or basilar artery (n=2) with saccular, spherical, or fusiform morphology. 4D flow MRI (3T TRIO &amp; 1.5T Avanto, Siemens, Germany, voxel =0.99–1.8×0.78–1.46×1.2–1.4 mm, TE/TR=2.9–3.3/5.5–6 ms, temporal-res=44–48 ms, 3-directional velocity encoding with venc =70–80 cm/s) data were analyzed using Matlab-based tools and 3D blood flow visualization software. The WSS pattern along the aneurysm wall was calculated by cubic spline interpolation of the velocity gradient along the aneurysm contour as described previously. The vorticity defined as Vort =abs(ζ x ,ζ y ,ζ z ) (with ζ x = δw / δy –δv / δz , ζ y =δu/δz – δw/δx, ζ z =δv/δx – δu/δy and u , v , w being the velocity vector components 2 ) was calculated within the plane transecting the aneurysm. Results 3D spatial and 3-directional velocity encoding allowed for the 3D visualization of complex intracranial flow patterns. Flow patterns in the aneurysms could be classified in two morphological groups. Narrow high-flow channels in combination with large central low flow regions were identified in five saccular/spherical IAs. Slow flow with less defined flow channels were noted in two fusiform IAs. The distribution of WSS was significantly more heterogeneous and increased and vorticity in the plane through the IA center was significantly higher for saccular/spherical vs fusiform IAs (WSS=0.63N/m2±0.33 N/m2 vs 0.038 N/m 2 ±0.016; Vorticity =0.073±0.028 vs 0.018±0.005; p&lt;0.01). Conclusion Our feasibility study shows the potential of 4D flow MRI to identify differences in flow characteristics such as vorticity and WSS patterns in two IA morphology groups which may improve risk stratification and treatment planning. Competing interests None. Abstract E-080 Figure 1 Abstract E-080 Figure 2
Perspectives on the development of genetically modified arthropodnatural enemies for agricultural pest management programmes. (2007)

Abstract The history of genetic improvement of arthropod natural enemies is reviewed briefly and I describe the successful genetic improvement and deployment in California almond orchards of a pesticide-resistant predatory mite. Lessons learned from our efforts to deploy this and other natural enemies in alfalfa [lucerne], citrus and walnuts from several genetic improvement projects conducted over the past 30 years are described, because they may provide useful lessons for future projects. Gaps in our knowledge are identified, especially in deploying such genetically modified natural enemies, and recommendations are made regarding how to plan such projects. Finally, issues of risk and regulation are discussed based on our experiences with a short-term field trial of a transgenic predatory mite in Florida.