gebhart/patrepeval huggingface dataset:
Color correction of pathological images for different staining-condition slides (2004)

The color of hematoxylin & eosin (H&E) stained tissue image varies with the staining conditions and with the characteristics of the microscope and imaging devices. This color variation affects the diagnostic examination. This paper proposes a color correction method for images of pathological slides prepared under inappropriate staining-condition. In the proposed method, the spectral transmittance obtained by a multispectral digital camera is utilized to estimate the amount of dye for each pixel. Subsequently the amount of dye is adjusted based on the chemical kinetic equation by digital process, so that the dye amount distribution would be equivalent to that of the reference slide, which is prepared under ideal staining conditions. Through the experiments using the H&E stained slides of liver tissue, the color was almost successfully corrected by the proposed method.
ZL Technologies at TREC 2009 Legal Interactive Comparing Exclusionary and Investigative Approaches for Electronic Discovery using the TREC Enron Corpus (2009)

Organizations responding to requests to produce electronically stored information (ESI) for litigation today often conduct information retrieval with a limited amount of data that has first been culled by custodian mailboxes, date ranges, or other factors chosen semi-arbitrarily based on legal negotiations or other exogenous factors. The culling process does not necessarily take into account the composition of the data set; and may, in fact, impede the expediency and cost-effectiveness of the eDiscovery process as ESI not initially identified may need to be collected later in the eDiscovery process. This exclusionary eDiscovery approach has been recommended by search and information retrieval technology providers in the past, in part, based on the state of technology available at the time; however, the technology now exists to perform an inclusive, content-based, investigative eDiscovery across a large document collection without the introduction of semiarbitrary exclusion factors. In this paper, we investigate whether limited document retrieval based on custodian email mailboxes results in lower recall and produces fewer responsive documents than a broader, inclusive search process that covers all potential custodians. In order to compare the two approaches, we designed an experiment with two independent teams conducting electronic discovery using the different approaches. We found that searching across the entire data set resulted in finding significantly more responsive documents and more initial custodians than implementing an approach that relies on custodian-based culling. Specifically, investigative eDiscovery found 516% more relevant documents and 1825% more initial custodians in our study. Based on these results, we believe organizations that employ an exclusionary, culling-based methodology may require subsequent collections, risk under production and sanctions during litigation, and will ultimately expend more resources in responding to eDiscovery production requests with a less comprehensive result.
Supplementary Figure 2 from Runx2 Transcriptional Activation of Indian Hedgehog and a Downstream Bone Metastatic Pathway in Breast Cancer Cells (2023)

Supplementary Figure 2 from Runx2 Transcriptional Activation of Indian Hedgehog and a Downstream Bone Metastatic Pathway in Breast Cancer Cells
Thermodesulfobium acidiphilum sp. nov., a thermoacidophilic, sulfate-reducing, chemoautotrophic bacterium from a thermal site (2016)

An obligately anaerobic, sulfate-reducing micro-organism, strain 3127-1T, was isolated from geothermally heated soil (Oil Site, Uzon Caldera, Kamchatka, Russia). The new isolate was a moderately thermoacidophilic anaerobe able to grow with H2 or formate by respiration of sulfate or thiosulfate. The pH range for growth was 3.7-6.5, with an optimum at 4.8-5.0. The temperature range for growth was 37-65 °C, with an optimum at 55 °C. The G+C content of the genomic DNA was 33.7 mol%. The genome of strain 3127-1T contained two almost identical 16S rRNA genes, differing by a single nucleotide substitution. The closest 16S rRNA gene sequence of a validly published species belonged to Thermodesulfobium narugense Na82T (99.5 % similarity). However, the average nucleotide identity of the genomes of strain 3127-1T and T. narugense Na82T and the predicted DNA-DNA hybridization value (GGDC 2.1 blast+, formula 2) were as low as 86 and 32.5±2.5 %, respectively. This, together with phenotypic data, showed the new isolate to belong to a novel species, for which the name Thermodesulfobium acidiphilum sp. nov. is proposed. The type strain is 3127-1T (=DSM 102892T=VKM B-3043T).
Cardiac drug therapy-considerations in the elderly. (2016)

Elderly individuals constitute a majority of patients encountered in current cardiovascular clinical practice. Management of these patients is a clinical challenge owing to a multitude of factors. Although medications such as statins have been shown to reduce cardiovascular mortality in the general population, evidence supporting the use of these drugs in patients greater than 75 years of age is sparse. Furthermore, aging associated changes in organ function and associated comorbidities influence the pharmacokinetics of multiple medications and can potentiate drug toxicity. In this article, we review the evidence behind the use of common cardiovascular medications in elderly patients and discuss pertinent clinical challenges.
Effect of Mo on Strain Aging Behavior of Low Carbon Steel Sheets with Over Aging (2005)

Aging behavior of low Carbon steel depends on over aging condition and chemical compositions. Over aged samples with Mo after quenching are tensile tested and the effect by Mo on aging parameters are investigated.The following results are obtained: 1) Bake Hardenability of Mo added samples show high value at early stage of over aging than as quenched samples, 2) Tensile strength and Yield strength of the samples with Mo show higher value than those of the sample without Mo for 230 ppm carbon steel, 3) Snoek Peak Height of the samples with Mo show lower value than those of the sample without Mo for 70 ppm carbon steel, but show higher for 230 ppm carbon steel. 4) These phenomena can be explained by assuming the presence of Mo-C-Va cluster which are made during quenching.
Iridium Oxide-Platinum Nanocomposite Coating for Neural Electrode (2018)

Nanostructured coating materials provide high surface areas for effective signal transduction, addressing the challenge of high interfacial impedance and low cathodic charge storage capacity (CSC <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> ) caused by shrinking size of microelectrodes. In order to achieve safe, efficient and durable electrode performances, a novel iridium oxide/platinum (IrO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> /Pt) nanocomposite coating was introduced as a high-performance layer on the Pt substrate to provide extremely large surface, which significantly reduced electrical impedance by 93% and increased the CSC <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> up to 54.14 mC×cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> (15.21 times) compared with that of bare Pt electrodes. In addition, the IrO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> /Pt nanocomposites exhibited great mechanical and electrochemical stability, which was critical and beneficial for effective neural stimulation/recording electrodes for practical applications.
Substantial Evidence for Auxin Secretory Vesicles (2018)

Dear Editor,

In their letter, [Robinson et al., 2018][1] question our recent report on auxin clustered within cells of Arabidopsis root apices. They claim that small molecules such as IAA cannot be visualized using the immunogold EM techniques. However, in 2006, we succeeded in immunolocalizing IAA
Diabetic Retinopathy Reversed by Intravitreous Application of Retinol Binding Protein 3 (2018)

The Joslin Medalists study, enrolling people with type 1 diabetes of &amp;gt;50 years, suggested protective factors exist against diabetic retinopathy (DR), even in the presence of hyperglycemia. Proteomic analysis of retina and vitreous suggested that Retinol Binding Protein 3 (RBP3), secreted by photoreceptors, to be elevated in the Medalists without vs. those with advanced DR. This finding was confirmed by ELISA RBP3 assays in replicating vitreous samples of Medalists and other diabetic patients. In contrast, vitreous VEGF levels increased with DR severity; resulting in decreasing RBP3/VEGF with worsening DR. Transgenic mice overexpressing RBP3 targeted to the photoreceptors prevented diabetes induced retinal capillary permeability and formation of acellular capillaries. To determine whether RBP3 can inhibit DR progression, recombinant human RBP3 (rhRBP3) was injected intravitreously (IVT) in rats with VEGF or after 2 months of diabetes. IVT injection of rhRBP3 inhibited VEGF induced increases in retinal vascular permeability both after a few min or 1 day post-VEGF injections (p=0.009 or p=0.01), respectively. After 2 months of diabetes, IVT rhRBP3 reversed capillary permeability to levels of nondiabetic rats (p=0.007), whereas boiled hRBP3 was ineffective. Surprisingly, IVT rhRBP3 also reduced retinal expression of VEGF and IL-6 in diabetic rats and normalized retinal function, as measured by B wave amplitude of electroretinography. Using cultured retinal endothelial cells and Muller cells, the addition of rhRBP3 inhibited VEGF- or high glucose-induced cell migration, possibly by binding to VEGF receptors. Surprisingly, rhRBP3 also inhibited high glucose-induced expression of VEGF and IL-6 mRNA levels (p=0.05) similar to in vivo studies. Thus, IVT application of RBP3 can intervene to delay, stop and reverse diabetes-induced neuro- and vascular-retinal functional and inflammatory abnormalities, strongly supporting a therapeutic potential for the use of RBP3 for DR. Disclosure H. Yokomizo: None. K. Park: None. A. Clermont: Consultant; Self; Kalvista Pharmaceuticals. Y. Maeda: None. W. Fickweiler: None. A. Ishikado: Employee; Self; Sunstar Inc.. Employee; Spouse/Partner; Sunstar Inc.. Q. Li: None. L.J. Tinsley: None. D.M. Pober: None. I. Wu: None. L.P. Aiello: Consultant; Self; Novo Nordisk Inc., Sanofi Genzyme. Stock/Shareholder; Self; Kalvista Pharmaceuticals, Inc.. Consultant; Self; Kalvista Pharmaceuticals, Inc. H.A. Keenan: Research Support; Self; Sanofi. Employee; Self; Sanofi Genzyme. J. Sun: Other Relationship; Self; Novartis Pharmaceuticals Corporation. Research Support; Self; Genentech, Inc., Optovue, Incorporated, Boston Micromachines Corporation, Adaptive Sensory Technology, Kalvista Pharmaceuticals, Inc.. Other Relationship; Self; Novo Nordisk Inc. G.L. King: Research Support; Self; Sanofi-Aventis.
Shallow water channel tracking using gradient-based mixed norm optimization techniques. (2010)

The underwater acoustic channel is challenging to estimate and track due to channel dynamism, the ill-conditioned nature of the estimation problem, as well as the need to optimize over a complex field. An extension of previous work is presented where the sparse channel coefficients in the delay and delay-Doppler spread domains are estimated using mixed norm convex optimization. The estimation algorithm is extended to track the time-varying channel using a gradient descent approach, trading off optimality for tracking efficiency. A computationally inexpensive approximation of the dynamic gradient is used rather than re-computing the precise gradient every time. Results presented are based on field data collected over 15-m depth and a range of wave heights and distances using the normalized prediction error as the performance metric. Comparison of performance between tracking the delay-only and delay-Doppler coefficients is presented for different weightings on the mixed norm between L1 and L2 measures and over different lags. Performance and computational efficiency of the proposed tracking algorithm are compared to conventional sparse estimation techniques. [Work supported in part by ONR Grants N00014-05-10085 and N00014-07-10184 and in part by Postdoctoral Scholar Program at the Woods Hole Oceanographic Institution, with funding provided by the Doherty Foundation.]
Colloidal stability, cytotoxicity, and cellular uptake of HfO2 nanoparticles (2021)

The colloidal stability, cytotoxicity, and cellular uptake of hafnium oxide (HfO<sub>2</sub> ) nanoparticles (NPs) were investigated in vitro to assess safety and efficacy for use as a deliverable theranostic in nanomedicine. Monoclinic HfO<sub>2</sub> NPs, ~60-90 nm in diameter and ellipsoidal in shape, were directly prepared without calcination by a hydrothermal synthesis at 83% yield. The as-prepared, bare HfO<sub>2</sub> NPs exhibited colloidal stability in cell culture media for at least 10 days without significant agglomeration or settling. The viability (live/dead assay) of human epithelial cells (HeLa) and monocyte-derived macrophages (THP-1) did not fall below 95% of untreated cells after up to 24 h exposure to HfO<sub>2</sub> NPs at concentrations up to 0.80 mg/ml. Similarly, the mitochondrial activity (MTT assay) of HeLa and THP-1 cells did not fall below 80% of untreated cells after up to 24 h exposure to HfO<sub>2</sub> NPs at concentrations up to 0.40 mg/ml. Cellular uptake was confirmed and visualized in both HeLa and THP-1 cells by fluorescence microscopy of HfO<sub>2</sub> NPs labeled with Cy5 and transmission electron microscopy (TEM) of bare HfO<sub>2</sub> NPs. TEM micrographs provided direct observation of macropinocytosis and endosomal compartmentalization within 4 h of exposure. Thus, the HfO<sub>2</sub> NPs in this study exhibited colloidal stability, cytocompatibility, and cellular uptake for potential use as a deliverable theranostic in nanomedicine.
Investigation of liquid ethanol evaporation and combustion in air and oxygen environments inside a 25 kW vertical reactor (2015)

The combustion characteristics of liquid ethanol in air and oxygen–carbon dioxide environments are investigated numerically inside a vertical reactor. Gambit 2.2 was used to construct the mesh and Fluent 12.1 was used to perform the calculations. Different oxidizer environments were considered including pure air, oxygen-enriched air, in addition to the cases of OF21 (21% O 2 and 79% CO 2 ) and OF29 (29% O 2 and 71% CO 2 ). Comparisons were performed between the different cases and the results were validated against wide range of the experimental data. Nonpremixed combustion model which utilizes probability density function to predict the scalar quantities was incorporated to simulate the combustion process. Two turbulence models, realizable k–ɛ (RKE) model and Reynolds stress model (RSM), were applied and their results were compared. The Euler–Lagrange approach was utilized to solve the discrete phase model. The results showed the ability of the RKE model to predict much closer data to the experimental data than the RSM which over predicts the temperature. For the case of OF21, the flame was lifted and the combustion temperature was reduced as compared to the air combustion case. However, the OF29 combustion case resulted in a very close performance to the case of air combustion.
Characterizing the Adsorption of Proteins on Glass Capillary Surfaces Using Electrospray-Differential Mobility Analysis (2011)

We quantify the adsorption and desorption of a monoclonal immunoglobulin-G antibody, rituxamab (RmAb), on silica capillary surfaces using electrospray-differential mobility analysis (ES-DMA). We first develop a theory to calculate coverages and desorption rate constants from the ES-DMA data for proteins adsorbing on glass capillaries used to electrospray protein solutions. This model is then used to study the adsorption of RmAb on a bare silica capillary surface. A concentration-independent coverage of ≈4.0 mg/m(2) is found for RmAb concentrations ranging from 0.01 to 0.1 mg/mL. A study of RmAb adsorption to bare silica as a function of pH shows maximum adsorption at its isoelectric point (pI of pH 8.5) consistent with literature. The desorption rate constants are determined to be ≈10(-5) s(-1), consistent with previously reported values, thus suggesting that shear forces in the capillary may not have a considerable effect on desorption. We anticipate that this study will allow ES-DMA to be used as a "label-free" tool to study adsorption of oligomeric and multicomponent protein systems onto fused silica as well as other surface modifications.
Machine learning reveals sequence-function relationships in family 7 glycoside hydrolases (2021)

Family 7 glycoside hydrolases (GH7) are among the principal enzymes for cellulose degradation in nature and industrially. These enzymes are often bimodular, including a catalytic domain and carbohydrate-binding module (CBM) attached via a flexible linker, and exhibit an active site that binds cello-oligomers of up to ten glucosyl moieties. GH7 cellulases consist of two major subtypes: cellobiohydrolases (CBH) and endoglucanases (EG). Despite the critical importance of GH7 enzymes, there remain gaps in our understanding of how GH7 sequence and structure relate to function. Here, we employed machine learning to gain data-driven insights into relationships between sequence, structure, and function across the GH7 family. Machine-learning models, trained only on the number of residues in the active-site loops as features, were able to discriminate GH7 CBHs and EGs with up to 99% accuracy, demonstrating that the lengths of loops A4, B2, B3, and B4 strongly correlate with functional subtype across the GH7 family. Classification rules were derived such that specific residues at 42 different sequence positions each predicted the functional subtype with accuracies surpassing 87%. A random forest model trained on residues at 19 positions in the catalytic domain predicted the presence of a CBM with 89.5% accuracy. Our machine learning results recapitulate, as top-performing features, a substantial number of the sequence positions determined by previous experimental studies to play vital roles in GH7 activity. We surmise that the yet-to-be-explored sequence positions among the top-performing features also contribute to GH7 functional variation and may be exploited to understand and manipulate function.
Network Coding Multicast Key-Capacity (2022)

For a multi-source multi-terminal noiseless network, the key-dissemination problem involves the task of multicasting a secret key K from the network sources to its terminals. As in secure multicast network-coding, in the key-dissemination problem the source nodes have access to independent randomness and, as the network is noiseless, the resulting key K is a function of the sources’ information. However, different from traditional forms of multicast, in key-dissemination the key K need not consist of source messages, but rather may be any function of the information generated at the sources, as long as it is shared by all terminals. Allowing the shared key K to be a mixture of source information grants a flexibility to the communication process which gives rise to the potential of increased key-rates when compared to traditional secure multicast. The multicast key-capacity is the supremum of achievable key-rates, subject to the security requirement that the shared key is not revealed to an eavesdropper with predefined eavesdropping capabilities. The key-dissemination problem (termed also, secret key-agreement) has seen significant studies over the past decades in memoryless network structures. In this work, we initiate the study of key-dissemination in the context of noiseless networks, i.e., network coding. In this context, we study similarities and differences between traditional secure-multicast and the more lenient task of key-dissemination.
Application of IR-Sensors in Container Glass Forming Process (2008)

This paper describes the functionality of equipment measuring the infrared (IR) radiation emitted from each single glass container directly after the forming processes in glass production plants. The IR images from the hot containers show the glass distribution, cooling behavior of the article, but also glass faults in an early stage after forming. Combination of this technique with statistical methods enables process control and the IR imaging method supports operators to improve the settings of the forming machines or gobbing process and monitors the performance of the swabbing process. Examples are shown for the application of these IR imaging sensors in an industrial environment for Hot End Quality Inspection, Process Monitoring, Process Control and Process Optimization.
Electrically Modulated Nonlinear Terahertz Metamaterials (2017)

We present an electrically modulated nonlinear metamaterial at terahertz frequencies. The device consists of a planar array of split-ring resonators (SRRs) fabricated on n-type GaAs. Increasing the incident THz field strength induces carriers in the GaAs substrate, shorting the SRR capacitive gap and modulating the MM resonance. The application of a 15V bias to the MM reduces the net field modulation by ~60%.
Operation Controlling Technique in Hot Metal Pretreatment Furnace (1988)

A new technology for hot metal pretreatment with the modified BOF has been developed at Kobe Works. This technology has been successfully applied to mass production of high-grade steel since November 1983. The furnace for hot metal pretreatment has an 80 t capacity and is equipped with two lances for flux injection and oxygen top blowing. Hot metal is desiliconized and dephosphorized with oxygen and lime-iron oxide based flux in the first stage of refining, and desulphurization with soda ash injection is followed without deslagging.
Electron paramagnetic centers in donor-dopedCaTiO3single crystals (2000)

Electron spin resonance signals observed in donor-doped ${\mathrm{CaTiO}}_{3}$ single crystals $({\mathrm{Ca}}_{1\ensuremath{-}x}{\mathrm{Y}}_{x}{\mathrm{TiO}}_{3}$ or ${\mathrm{CaTi}}_{1\ensuremath{-}x}{\mathrm{Nb}}_{x}{\mathrm{O}}_{3})$ were analyzed and the results were discussed from a viewpoint of carrier generation. Several types of signals were observed in insulating samples, and they were tentatively assigned to some acceptors such as Al impurity and the defects relating oxygen excess. Two types of signals with sharp and broad features, both of which are assignable to electron-trapped-type centers, were observed in conductive samples. The origins of the sharp and broad signals were attributed to electrons tightly trapped on ${\mathrm{Ti}}^{4+}$ ions and electrons loosely localized around donors, respectively, from analysis of angular and temperature dependence of the signals. The concentrations of the centers for the sharp and broad signals were estimated at \ensuremath{\sim}3 K to be $\ensuremath{\sim}3\ifmmode\times\else\texttimes\fi{}{10}^{18} {\mathrm{cm}}^{\ensuremath{-}3}$ in the ${\mathrm{H}}_{2}$-reduced samples with ${x=10}^{\ensuremath{-}4}$ and $\ensuremath{\sim}3\ifmmode\times\else\texttimes\fi{}{10}^{19} {\mathrm{cm}}^{\ensuremath{-}3}$ in the as-prepared samples with ${x=10}^{\ensuremath{-}2},$ respectively. Although no obvious correlation between electroconductive behavior and signal intensity was observed for the sharp signals, intensities of the broad signal increased as the electroconductive behavior turned from metallic to semiconducting below \ensuremath{\sim}25 K. Therefore, it was found that the electrons responsible for the broad signals convert into conduction electrons when they are thermally released at high temperatures, and their concentration is high enough to influence the electroconductive behavior.