gebhart/patrepeval huggingface dataset:
Molecular Genetic Screening for Urine Detection of Bladder Cancer (2002)

Urine cytology is not used routinely to assess bladder transitional cell carcinoma (TCC) recurrence in the United Kingdom because of the poor correlation between tumour presence and detection of malignant cells. Recently, it has been suggested that microsatellite marker analysis of cells from patient urine provides a significant improvement of urine cytology [1-3]. However, these authors suggest that this technique may have limitations in the detection of superficial lesions which make up the majority of recurrent tumours. We have identified 23 patients with 25 clinically detected endoscopic lesions thought to represent TCC. Nineteen out of 25 biopsies demonstrated pathologically confirmed TCC (15 pTa, 2 pT1 and 2 pT2 tumours), 6 patients had CIS, cystitis glandularis or no detectable lesion, respectively. Ten out of 19 cytology reports available from patients confirmed with recurrent TCC demonstrated the presence of malignant cells (54%). Urine DNA was obtained and analysed using panels of microsatellites spanning multiple chromosomes. Eight patients failed analysis due to insufficient cells for DNA extraction. Up to 106 microsatellites per patient spanning chromosomes 7-13 and 17-22 were successfully analysed, with matched patient blood DNA as a control, using a commercial service (DNASHEF) for ABI 377 automated DNA microsatellite analysis in the remaining patients. Loss of heterozygosity (LOH) was detected at 25/843 loci (2.34%) below rates detected in previous studies of displastic tissues. No LOH was found in 7 tumours (0/106--pTaG3, 0/98--pT3G2, 0/95--pTaG1, 0/89--pTaG1, 0/63--pTaG1 and 0/50--CIS, markers respectively), or in a benign polyp. LOH was detected in 9 TCC patients: on chromosome 9 (4 patients), 17 (2 patients), 18 (3 patients) and 8 (1 patient). The cystitis glandularis patient had LOH on chromosome 18. The relatively low success rate of "molecular cytology" suggests that this technique may not be readily applicable to detection of "superficial" (pTa) bladder tumours on its own. Keywords: Transitional Cell Carcinoma Of The BladderEarly DetectionMicrosatellite AnalysisLoss Of Heterozygosity
Evaluation of Cancer Immunity in Mice (2013)

There have been significant advances in the development and application of novel therapeutic approaches and improved diagnostics for cancer in the past decade. Manipulation and/or assessment of cancer-specific immunity have been central to these advances. Murine models are a standard for the preclinical development of cancer immunotherapeutics. However, critical advances in our understanding of the role of the immune microenvironment and the assessment of cancer-specific immunity have not been fully applied to rodent models. Methods to preserve the function of immune cells after cryopreservation and standard approaches to quantitative immune assays have not been developed. Furthermore, a detailed evaluation of the immune tumor environment, which can impact a clinical response to different agents, is rarely undertaken as models are being contemplated. Rapid translation of immunoncology agents to the clinic will require standardization of immunologic assay methods and a more detailed immunologic characterization of common mouse models. Outlined here are the critical elements in assessing immunity in cancer mouse models and suggestions concerning the standardization of approaches when using these models for the study of immunoncology.
Hypoxia-Induced Pulmonary Vascular Remodeling: Contribution of the Adventitial Fibroblasts (2000)

Vascular repair in response to injury or stress (often referred to as remodeling) is a common complication of many cardiovascular abnormalities including pulmonary hypertension, systemic hypertension, atherosclerosis, vein graft remodeling and restenosis following balloon dilatation of the coronary artery. It is not surprising that repair and remodeling occurs frequently in the vasculature in that exposure of blood, vessels to either excessive hemodynamic stress (e.g. hypertension), noxious blood borne agents (e.g. atherogenic lipids), locally released cytokines, or unusual environmental conditions (e.g. hypoxia), requires readily available mechanisms to counteract these adverse stimuli and to preserve structure and function of the vessel wall. The responses, which were presumably evolutionarily developed to repair an injured tissue, often escape self-limiting control and can result, in the case of blood vessels, in lumen narrowing and obstruction to blood flow. Each cell type (i. e. endothelial cells, smooth muscle cells, and fibroblasts) in the vascular wall plays a specific role in the response to injury. However, while the roles of the endothelial cells and smooth muscle cells (SMC) in vascular remodeling have been extensively studied, relatively little attention has been given to the adventitial fibroblasts. Perhaps this is because the fibroblast is a relatively ill-defined cell which, at least compared to the SMC, exhibits few specific cellular markers. Importantly though, it has been well demonstrated that fibroblasts possess the capacity to express several functions such as migration, rapid proliferation, synthesis of connective tissue components, contraction and cytokine production in response to activation or stimulation. The myriad of responses exhibited by the fibroblasts, especially in response to stimulation, suggest that these cells could play a pivotal role in the repair of injury. This fact has been well documented in the setting of wound healing where a hypoxic environment has been demonstrated to be critical in the cellular responses. As such it is not surprising that fibroblasts may play an important role in the vascular response to hypoxia and/or injury. This paper is intended to provide a brief review of the changes that occur in the adventitial fibroblasts in response to vascular stress (especially hypoxia) and the role the activated fibroblasts might play in hypoxia-mediated pulmonary vascular disease.
Modeling swelling effects during coffee extraction with smoothed particle hydrodynamics (2022)

It is commonly assumed that coffee particles swell during filtration, but it has not been clarified how different degrees of swelling affect the extraction. In this article, we propose a grain swelling model to investigate the influences of swelling on both intra-grain and inter-grain transport. The swelling is modeled through a diffusion process of excess water into the grains. The geometric expansion of the grains is connected to the local concentration of excess water through a specified deformation gradient tensor. Diffusion of soluble compounds inside the grains is coupled with the swelling dynamics through a modified diffusion equation. Inter-grain transport is modeled by solving the Navier–Stokes equation and diffusion equations. This model is solved numerically in the framework of smoothed particle hydrodynamics, and it is used to simulate the extraction of a minimal coffee bed setup and to investigate the effect of a small degree of particle swelling (&amp;lt;8% in size) on the extraction kinetics. It is found that under the normal operating parameter regime of espresso filtration, swelling affects the extraction mainly through the change of inter-grain transport. Swelling also alters the diffusion inside the grains, but this process has a secondary effect on the extraction. In general, swelling slightly impedes the extraction rate, but enhances the strength considerably at both fixed brewing time and fixed brewing volume. Our results justify the endeavor in the literatures to clarify the effect of possible swelling on brewing and preparation variables during coffee extraction.
On feedforward control of piezoelectric dual-stage actuator systems (2021)

The feedforward control design problem for a single-axis dual-stage actuator system with piezoelectric actuator at the short-stroke is analyzed in this paper. With such actuator layout, the main question is how to balance the contribution of the individual actuators in a efficient manner, while complying to actuators limitations. A control configuration and a sequential design methodology are proposed to take into account interactions between actuators. In addition, various feedforward controller design strategies that conform to the configuration proposed are presented, such as inversion based feedforward, mass feedforward and standard compliance compensation. Based on observed shortcomings of each feedforward design, a novel mixed compliance compensation feedforward controller is presented. Results are analyzed in terms of their physical interpretations and simulation studies.
Inhibition of Vascular Endothelial Growth Factor Protects against the Development of Oxaliplatin-Induced Sinusoidal Obstruction Syndrome in Wild-Type but Not in CD39-Null Mice (2022)

(1) <i>Background</i>: Sinusoidal obstruction syndrome (SOS) after oxaliplatin-based chemotherapy is associated with unfavorable outcomes after partial hepatectomy for colorectal liver metastases (CLM). Bevacizumab, a monoclonal antibody against <i>vascular endothelial growth factor</i> (VEGF), may prevent SOS development. We investigated the impact of VEGF-inhibition on the development of SOS in a murine model. (2) <i>Methods</i>: Male wild-type and CD39-null mice received oxaliplatin, additional anti-VEGF (OxAV), or controls, and were sacrificed or subjected to major partial hepatectomy (MH). Specimen were used for histological analysis of SOS. Liver damage was assessed by plasma transaminases. The VEGF pathway was elucidated by quantitative PCR of liver tissue and protein analysis of plasma. (3) <i>Results</i>: Mice treated with oxaliplatin developed SOS. Concomitant anti-VEGF facilitated a reduced incidence of SOS, but not in CD39-null mice. SOS was associated with increased plasma VEGF-A and decreased <i>hepatocyte growth factor</i> (HGF). After OxAV treatment, VEGF-R2 was upregulated in wild-type but downregulated in CD39-null mice. Oxaliplatin alone was associated with higher liver damage after MH than in mice with concomitant VEGF-inhibition. (4) <i>Conclusions</i>: We established a murine model of oxaliplatin-induced SOS and provided novel evidence on the protective effect of VEGF-inhibition against the development of SOS that may be associated with changes in the pathway of VEGF and its receptor VEGF-R2.
Particle Removal from Si Substrates in Organic Solvents using Megasonic Energy (2007)

In this paper, particle removal experiments from silicon wafers in organic solvent using megasonic energy are presented. Nanoparticles are first deposited on Si wafers via controlled-contamination process. The particle removal efficiency as a function of megasonic power is studied both for freshly-deposited and aged particles. Several cleaning recipes are evaluated, by changing the processing conditions and rinsing time/chemistry. When low megasonic power is used, particles are found to cluster and re-deposit on the wafer surface after being detached. This phenomenon could be explained by charging phenomena of particles and silicon surfaces in the specific solvent. A surfactant is added to prevent clustering and re-deposition, leading to a noticeably improvement in particle removal efficiency.
Auto-Tag: Tagging-Data-By-Example in Data Lakes (2021)

As data lakes become increasingly popular in large enterprises today, there is a growing need to tag or classify data assets (e.g., files and databases) in data lakes with additional metadata (e.g., semantic column-types), as the inferred metadata can enable a range of downstream applications like data governance (e.g., GDPR compliance), and dataset search. Given the sheer size of today's enterprise data lakes with petabytes of data and millions of data assets, it is imperative that data assets can be ``auto-tagged'', using lightweight inference algorithms and minimal user input. In this work, we develop Auto-Tag, a corpus-driven approach that automates data-tagging of \textit{custom} data types in enterprise data lakes. Using Auto-Tag, users only need to provide \textit{one} example column to demonstrate the desired data-type to tag. Leveraging an index structure built offline using a lightweight scan of the data lake, which is analogous to pre-training in machine learning, Auto-Tag can infer suitable data patterns to best ``describe'' the underlying ``domain'' of the given column at an interactive speed, which can then be used to tag additional data of the same ``type'' in data lakes. The Auto-Tag approach can adapt to custom data-types, and is shown to be both accurate and efficient. Part of Auto-Tag ships as a ``custom-classification'' feature in a cloud-based data governance and catalog solution \textit{Azure Purview}.
Fast computation of double bounce contributions to physical optics integrals in the near field (2015)

A multilevel algorithm for the fast computation of double bounce (DB) contributions to near field (NF) scattering physical optics (PO) integrals is presented. The algorithm aims at accelerating the computation of the mono-static DB contribution for multiple excitations, i.e., for sources set within a wide range of locations with respect to the scatterer, and over a range of frequencies. The DB-NF fast PO algorithm is an extension of its far field predecessor (A. Boag and E. Michielssen, IEEE Trans. Antennas Propag., 52, 205–212, 2004) and it complements our fast NF algorithm for computing the single bounce PO contribution (A. Gendelman, Y. Brick, and A. Boag, IEEE Trans. Antennas Propag., 62, 4325–4335, 2014).
Low Incidence along with Low mRNA Levels of EGFRvIII in Prostate and Colorectal Cancers Compared to Glioblastoma (2017)

<b>Background:</b> The presence as well as the potential role of EGFR<sup>vIII</sup> in tumors other than glioblastoma still remains a controversial subject with many contradictory data published. Previous analyses, however, did not consider the level of <i>EGFR<sup>vIII</sup></i> mRNA expression in different tumor types. <b>Methods:</b> Appropriately designed protocol for Real-time quantitative reverse-transcription PCR (Real-time qRT-PCR) was applied to analyze <i>EGFR<sup>vIII</sup></i> and <i>EGFR<sup>WT</sup></i> mRNA expression in 155 tumor specimens. Additionally, Western Blot (WB) analysis was performed for selected samples. Stable cell lines showing EGFR<sup>vIII</sup> expression (CAS-1 and DK-MG) were analyzed by means of WB, immunocytochemistry (ICC) and fluorescence <i>in situ</i> hybridization (FISH). <b>Results:</b> Our analyses revealed <i>EGFR<sup>vIII</sup></i> expression in 27.59% of glioblastomas (8/29), 8.11% of colorectal cancers (3/37), 6.52% of prostate cancers (3/46) and none of breast cancers (0/43). Despite the average relative expression of <i>EGFR<sup>vIII</sup></i> varying greatly among tumors of different tissues (approximately 800-fold) or even within the same tissue group (up to 8000-fold for GB), even the marginal expression of <i>EGFR<sup>vIII</sup></i> mRNA can be detrimental to cancer progression, as determined by the analysis of stable cell lines endogenously expressing the oncogene. <b>Conclusion:</b> EGFR<sup>vIII</sup> plays an unquestionable role in glioblastomas with high expression of this oncogene. Our data suggests that EGFR<sup>vIII</sup> importance should not be underestimated even in tumors with relatively low expression of this oncogene.
Online measurement system for fault location in railways overhead lines (2013)

Fault location in railways overhead lines is still an open problem because the technique actually applied may requires several tens of minutes to reach the goal. The paper proposes an online measurement system for fault location and, thanks to the support of “Rete Ferroviaria Italiana SpA”, the results of tests performed on a real railway.
Robust Image Population Based Stain Color Normalization: How Many Reference Slides Are Enough? (2022)

Histopathologic evaluation of Hematoxylin & Eosin (H&E) stained slides is essential for disease diagnosis, revealing tissue morphology, structure, and cellular composition. Variations in staining protocols and equipment result in images with color nonconformity. Although pathologists compensate for color variations, these disparities introduce inaccuracies in computational whole slide image (WSI) analysis, accentuating data domain shift and degrading generalization. Current state-of-the-art normalization methods employ a single WSI as reference, but selecting a single WSI representative of a complete WSI-cohort is infeasible, inadvertently introducing normalization bias. We seek the optimal number of slides to construct a more representative reference based on composite/aggregate of multiple H&E density histograms and stain-vectors, obtained from a randomly selected WSI population (WSI-Cohort-Subset). We utilized 1,864 IvyGAP WSIs as a WSI-cohort, and built 200 WSI-Cohort-Subsets varying in size (from 1 to 200 WSI-pairs) using randomly selected WSIs. The WSI-pairs' mean Wasserstein Distances and WSI-Cohort-Subsets' standard deviations were calculated. The Pareto Principle defined the optimal WSI-Cohort-Subset size. The WSI-cohort underwent structure-preserving color normalization using the optimal WSI-Cohort-Subset histogram and stain-vector aggregates. Numerous normalization permutations support WSI-Cohort-Subset aggregates as representative of a WSI-cohort through WSI-cohort CIELAB color space swift convergence, as a result of the law of large numbers and shown as a power law distribution. We show normalization at the optimal (Pareto Principle) WSI-Cohort-Subset size and corresponding CIELAB convergence: a) Quantitatively, using 500 WSI-cohorts; b) Quantitatively, using 8,100 WSI-regions; c) Qualitatively, using 30 cellular tumor normalization permutations. Aggregate-based stain normalization may contribute in increasing computational pathology robustness, reproducibility, and integrity.
Processes controlling the rate of In/sub 2/O/sub 3/ thin film gas sensor's response (2005)

The kinetics of gas response to reducing and oxidizing gases of In/sub 2/O/sub 3/-based thin film gas sensors is analyzed in this report. The influence of operating temperature, air humidity and film thickness (d from 20 to 400 nm) on both the E/sub act/ and time constants of gas response is reviewed. Model conceptions allowing to explain specific character of In/sub 2/O/sub 3/ interaction with reducing and oxidizing gases are proposed.
Modeling and Analysis of Capacitive Relaxation Quenching in a Single Photon Avalanche Diode (SPAD) Applied to a CMOS Image Sensor (2020)

We present an analysis of carrier dynamics of the single-photon detection process, i.e., from Geiger mode pulse generation to its quenching, in a single-photon avalanche diode (SPAD). The device is modeled by a parallel circuit of a SPAD and a capacitance representing both space charge accumulation inside the SPAD and parasitic components. The carrier dynamics inside the SPAD is described by time-dependent bipolar-coupled continuity equations (BCE). Numerical solutions of BCE show that the entire process completes within a few hundreds of picoseconds. More importantly, we find that the total amount of charges stored on the series capacitance gives rise to a voltage swing of the internal bias of SPAD twice of the excess bias voltage with respect to the breakdown voltage. This, in turn, gives a design methodology to control precisely generated charges and enables one to use SPADs as conventional photodiodes (PDs) in a four transistor pixel of a complementary metal-oxide-semiconductor (CMOS) image sensor (CIS) with short exposure time and without carrier overflow. Such operation is demonstrated by experiments with a 6 µm size 400 × 400 pixels SPAD-based CIS designed with this methodology.
ChemInform Abstract: An Oxidation of Benzyl Methyl Ethers with NBS that Selectively Affords Either Aromatic Aldehydes or Aromatic Methyl Esters. (2010)

Abstract Irradiation of benzylic methyl ethers in the presence of 2 equiv.
Unconditional care in academic emergency departments (2020)

Recent news stories have explicitly stated that patients with symptoms of COVID-19 were "turned away" from emergency departments. This commentary addresses these serious allegations, with an attempt to provide the perspective of academic emergency departments (EDs) around the Nation. The overarching point we wish to make is that academic EDs never deny emergency care to any person.
Low plasma carnosinase activity promotes carnosinemia after carnosine ingestion in humans (2012)

A polymorphism in the carnosine dipeptidase-1 gene (CNDP1), resulting in decreased plasma carnosinase activity, is associated with a reduced risk for diabetic nephropathy. Because carnosine, a natural scavenger/suppressor of ROS, advanced glycation end products, and reactive aldehydes, is readily degraded in blood by the highly active carnosinase enzyme, it has been postulated that low serum carnosinase activity might be advantageous to reduce diabetic complications. The aim of this study was to examine whether low carnosinase activity promotes circulating carnosine levels after carnosine supplementation in humans. Blood and urine were sampled in 25 healthy subjects after acute supplementation with 60 mg/kg body wt carnosine. Precooled EDTA-containing tubes were used for blood withdrawal, and plasma samples were immediately deproteinized and analyzed for carnosine and β-alanine by HPLC. CNDP1 genotype, baseline plasma carnosinase activity, and protein content were assessed. Upon carnosine ingestion, 8 of the 25 subjects (responders) displayed a measurable increase in plasma carnosine up to 1 h after supplementation. Subjects with no measurable increment in plasma carnosine (nonresponders) had ∼2-fold higher plasma carnosinase protein content and ∼1.5-fold higher activity compared with responders. Urinary carnosine recovery was 2.6-fold higher in responders versus nonresponders and was negatively dependent on both the activity and protein content of the plasma carnosinase enzyme. In conclusion, low plasma carnosinase activity promotes the presence of circulating carnosine upon an oral challenge. These data may further clarify the link among CNDP1 genotype, carnosinase, and diabetic nephropathy.
Open Air Plasma Deposition of Superhydrophilic Titania Coatings (2019)

Abstract A method for the deposition and functionalization of a nanostructured organotitanate thin film, which imparts superhydrophilicity to a surface with a one‐step, open‐air process, is described. Extreme wetting ( Θ &lt; 5°) is achieved through synergistic contributions from both nanoscale roughness, visible light absorption caused by nonmetal dopants, and oxygen vacancies and surface activation by reactive plasma species. To test the efficacy of this material as an antifog coating, glass is coated and subjected to aggressive changes in humidity. Under both fogging and defrosting conditions, the superhydrophilic coating achieves a high degree of transparency, showing nearly two orders of magnitude improvement over the bare glass. The measured adhesion of the superhydrophilic coating is 5.9 J m −2 , nearly double that of the solution‐processed control. The reliability of the coating is further validated by demonstrating scratch‐resistance. Additionally, the incorporation of organic matter into the molecular structure of the coating disrupts long‐range crystallinity from developing. This structural and subsequent chemical analysis of the coating reveals that inorganic and organic species are intimately connected at the nanoscale via alkyl and alkoxy bridges. The amorphous organotitanate material is distinct from conventional TiO 2 , which requires high temperature crystallization and extensive UV irradiation to display similar superhydrophilic qualities.