gebhart/patrepeval huggingface dataset:
Evaluation of Computer-Aided Nodule Assessment and Risk Yield (CANARY) in Korean patients for prediction of invasiveness of ground-glass opacity nodule (2021)

Differentiating the invasiveness of ground-glass nodules (GGN) is clinically important, and several institutions have attempted to develop their own solutions by using computed tomography images. The purpose of this study is to evaluate Computer-Aided Analysis of Risk Yield (CANARY), a validated virtual biopsy and risk-stratification machine-learning tool for lung adenocarcinomas, in a Korean patient population. To this end, a total of 380 GGNs from 360 patients who underwent pulmonary resection in a single institution were reviewed. Based on the Score Indicative of Lung Cancer Aggression (SILA), a quantitative indicator of CANARY analysis results, all of the GGNs were classified as "indolent" (atypical adenomatous hyperplasia, adenocarcinomas in situ, or minimally invasive adenocarcinoma) or "invasive" (invasive adenocarcinoma) and compared with the pathology reports. By considering the possibility of uneven class distribution, statistical analysis was performed on the 1) entire cohort and 2) randomly extracted six sets of class-balanced samples. For each trial, the optimal cutoff SILA was obtained from the receiver operating characteristic curve. The classification results were evaluated using several binary classification metrics. Of a total of 380 GGNs, the mean SILA for 65 (17.1%) indolent and 315 (82.9%) invasive lesions were 0.195±0.124 and 0.391±0.208 (p < 0.0001). The area under the curve (AUC) of each trial was 0.814 and 0.809, with an optimal threshold SILA of 0.229 for both. The macro F1-score and geometric mean were found to be 0.675 and 0.745 for the entire cohort, while both scored 0.741 in the class-equalized dataset. From these results, CANARY could be confirmed acceptable in classifying GGN for Korean patients after the cutoff SILA was calibrated. We found that adjusting the cutoff SILA is needed to use CANARY in other countries or races, and geometric mean could be more objective than F1-score or AUC in the binary classification of imbalanced data.
Longitudinal Study of Mammary Epithelial and Fibroblast Co-Cultures Using Optical Coherence Tomography Reveals Morphological Hallmarks of Pre-Malignancy (2012)

The human mammary gland is a complex and heterogeneous organ, where the interactions between mammary epithelial cells (MEC) and stromal fibroblasts are known to regulate normal biology and tumorigenesis. We aimed to longitudinally evaluate morphology and size of organoids in 3D co-cultures of normal (MCF10A) or pre-malignant (MCF10DCIS.com) MEC and hTERT-immortalized fibroblasts from reduction mammoplasty (RMF). This co-culture model, based on an isogenic panel of cell lines, can yield insights to understand breast cancer progression. However, 3D cultures pose challenges for quantitative assessment and imaging, especially when the goal is to measure the same organoid structures over time. Using optical coherence tomography (OCT) as a non-invasive method to longitudinally quantify morphological changes, we found that OCT provides excellent visualization of MEC-fibroblast co-cultures as they form ductal acini and remodel over time. Different concentrations of fibroblasts and MEC reflecting reported physiological ratios [1] were evaluated, and we found that larger, hollower, and more aspherical acini were formed only by pre-malignant MEC (MCF10DCIS.com) in the presence of fibroblasts, whereas in comparable conditions, normal MEC (MCF10A) acini remained smaller and less aspherical. The ratio of fibroblast to MEC was also influential in determining organoid phenotypes, with higher concentrations of fibroblasts producing more aspherical structures in MCF10DCIS.com. These findings suggest that stromal-epithelial interactions between fibroblasts and MEC can be modeled in vitro, with OCT imaging as a convenient means of assaying time dependent changes, with the potential for yielding important biological insights about the differences between benign and pre-malignant cells.
Modular O2 electroreduction activity in triphenylene-based metal–organic frameworks (2018)

Triphenylene ligands hexasubstituted with amino or phenol groups afford two phases of electrically conductive layered two-dimensional metal-organic frameworks upon reaction with various metals. Regardless of the identity of the metal or chelating atom, π-stacking within the MOF layers is essential to achieve high electrical conductivity, redox activity, and catalytic activity.
Novel UV-Activated Colorimetric Oxygen Indicator (2005)

The results of a detailed characterization study of a novel UV-activated colorimetric oxygen indicator are described. The indicator uses nanoparticles of titania to photosensitize the reduction of methylene blue by triethanolamine in a polymer encapsulation medium, using UVA light. Upon UV irradiation, the indicator bleaches and remains in this colorless state in the dark, unless and until it is exposed to oxygen, whereupon its original color is restored. The indicator is reusable and irreversible. The rate of color recovery is proportional to the level of oxygen present. A layer of PET (poly(ethylene terephthalate)), of thickness b, placed on top of the indicator film slows down its response, and the 90% recovery time is proportional to b.
BRCA Mutation-Related and Claudin-Low Breast Cancer: Blood Relatives or Stepsisters? (2015)

There is a prominent correlation between the genes under focus herein and BRCA mutation status. BRCAmut tumors bear stem cell characteristics displaying a distinct cell adhesion molecule profile characterized by high expression of CDH1 and CLDN4 according to public gene expression data set analysis, and higher claudin-3 expression as detected by IHC; thus, BRCAmut breast carcinomas are not identical with the previously identified claudin-low subtype of breast cancer.
Synthesis of Toll-Like Receptor-2 Targeting Lipopeptides as Self-Adjuvanting Vaccines (2008)

Effective Th1- and Th2-type immune responses that result in protective immunity against pathogens can be induced by self-adjuvanting lipopeptides containing the lipid moiety dipalmitoyl-S-glyceryl cysteine (Pam2Cys). The potent immunogenicity of these lipopeptides is due to their ability to activate dendritic cells by targeting and signaling through Toll-like receptor-2 (TLR-2). In addition, the simplicity and flexibility in their design as well as their ease of chemical definition and characterisation makes them highly attractive vaccine candidates for humans and animals. We describe in this chapter the techniques involved in the synthesis of an immunocontraceptive lipopeptide vaccine as well as the experimental assays carried out to evaluate its efficiency.
Role of oxidative enzymatic treatments on enzymatic hydrolysis of softwood (2004)

The impact of oxidative modification and partial removal of lignin by laccase-mediator treatments on the enzymatic hydrolysis of steam-pretreated softwood (SPS) was evaluated. Two mediators, N-hydroxy-N-phenylacetamide (NHA) and its acetylated precursor, were oxidized by the laccase from Trametes hirsuta, and their effects on the activity of cellulolytic enzymes and on the hydrolysis yield of SPS were examined. Both simultaneous and sequential combinations of laccase-mediator treatments with commercial cellulases increased the sugar yield in the enzymatic hydrolysis of SPS. The maximal increase was 21% when a sequential treatment was applied. Laccase treatment alone was also shown to improve hydrolysis. NHA oxidized by laccase inhibited significantly the cellulases of Trichoderma reesei, but the presence of the solid substrate protected the activities against oxidative inactivation. Surface analysis of the lignocellulosic substrate before and after the laccase and cellulase treatments revealed an enrichment of lignin and an increase of carboxylic groups on the surface of the hydrolysis residue.
Associations between Mental Health, Alcohol Consumption and Drinking Motives during COVID-19 Second Lockdown in Ireland (2021)

Older adults who drink to cope-mainly with depression symptomatology-are an important at-risk population, in line with predictions from alcohol self-medication frameworks. Future research is needed to incorporate strategies into the public mental health ecosystem.
Economic and Phosphorus-Related Effects of Precision Feeding and Forage Management at a Farm Scale (2007)

Structural best management practices were implemented throughout the Cannonsville Reservoir Watershed (CRW) in an effort to reduce P losses to the reservoir. Yet long-term water quality control efforts within CRW are hindered by continuous P build-up in the soils resulting from dairy farm P imports exceeding exports. Addressing the P imbalance problems and maintaining economic viability of the farms requires a system-level redesign of farm management. One possible innovative strategy, precision feed management (PFM), reduces soil-P build-up by limiting feed and fertilizer purchases, and increasing high-quality homegrown forage production. This study applied the integrated farm system model (IFSM) to 2 CRW dairy farms to quantify the benefits of a PFM farm planning strategy in controlling P imbalance problems, and maintaining farm profit-ability and reducing off-farm P losses. The IFSM accurately simulated the 2 farms based on farm data supplied by farm planners; these scenarios were used as the baseline conditions. The IFSM simulations of more accurate feeding of P (based on P required in animal diets) integrated with increased productivity of grass-forage and increased proportion of forage in the diet reduced the P imbalance of 1 farm from 5.3 to 0.5 kg/ ha and from 9.6 to 0.0 kg/ha for the second farm. For both farms, soluble P lost to the environment was reduced by 18%. Feed supplement purchases declined by 7.5 kg/cow per year for dietary mineral P, and by 1.04 and 1.29 t/cow per year for protein concentrates through adoption of the PFM system. Moreover, when a land management practice of converting corn to grass was coupled with the precision feeding of P and improved forage management, IFSM predicted reductions of 5.8 and 9.3 kg/ha of converted land sediment-bound P in erosion loss each year. The model predicted slight purchase increases in corn grain to offset reductions in corn silage production and feeding rates, but no appreciable change in the farm P balance due to land conversion. The model-based studies conducted on a farm-by-farm basis complement farm planning efforts in exploring innovative farming systems. Moreover, the results set a benchmark for potential benefits of PFM strategies, economically and environmentally.
ChemInform Abstract: Nucleosides. Part 47. Syntheses, Reactions, and Properties of 6‐ and 7‐(p‐Bromophenyl)lumazine N‐1‐Nucleosides. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Moment method analysis of infinite stripline-fed tapered slot antenna arrays with a ground plane (1994)

A full-wave method of moments solution for infinite arrays of stripline-fed tapered slot antennas is described. The formulation of the problem is sufficiently general to permit performance evaluation of most of the geometries that have been proposed for stripline-fed antennas as well as of several other types of array antennas. Computed results for some well-known antenna arrays are presented to demonstrate the validity and accuracy of the method. Excellent agreement with published results has been obtained for scattering from corrugated surfaces and grounded dielectric slabs and for the input impedance of dipole and monopole arrays. Catastrophic effects such as scan blindness are accurately predicted. A sample result showing the measured and computed input impedance of a stripline-fed tapered slot antenna array is also presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Studies of MEA Durability in Proton Exchange Membrane Water Electrolysis (2015)

Hydrogen production from proton exchange membrane (PEM) water electrolysis is attractive due to its simple and clean nature. Membrane and electrode assemblies (MEAs) of PEM electrolyzers typically use iridium (Ir) as an anode catalyst and Pt as a cathode catalyst. The durability of MEAs plays an essential role for the electrolyzers’ lifetime and cost. However, unlike the well-established MEA durability protocols of PEM fuel cells, there have been a lack of effective procedures for PEM electrolyzer MEA durability evaluation. The objective of this work is to establish a series of test protocols that can help to rapidly evaluate PEM electrolyzer MEA durability. Three testing approaches have been used in this work, which include high-voltage hold (&gt;1.8 V), voltage cycling (1.4 to 1.8 V or 2.0 V), and constant low-current operations. The electrochemical surface area (ECSA) and polarization curves of the MEAs will be obtained after each test. Two categories of anode catalysts have been evaluated using the above durability test protocols: one is the commercial Ir black and the other is Ir supported on tungsten-doped titanium oxide (Ir/W x Ti 1-x O 2 ) developed at Giner. The supported Ir/W x Ti 1-x O 2 catalyst proves to possess 8-10 x higher mass activity than the Ir black. The MEAs made of these two anode catalysts have been evaluated at a variety of loading, low (0.1 mg/cm 2 ), medium (0.4 mg/cm 2 ) and high (1.0 mg/cm 2 ). Figure 1 shows the durability of these two catalysts after voltage cycling from 1.4 V to 1.8 V: (a) 2 mg/cm 2 Ir from Ir black; (b) 0.4 mg/cm 2 Ir from Ir/W x Ti 1-x O 2. It can be seen that at medium to high Ir loadings, these two catalysts demonstrates minimal performance decay after voltage cycling. The morphology and structure of MEAs after durability tests will be characterized to correlate to their performance and to elucidate their degradation mechanisms. Acknowledgement: The financial support is from the Department of Energy under the Contract Grant DE-SC0007471. Figure 1
Investigations of Thienoacene Molecules for Classical and Entangled Two-Photon Absorption (2018)

Investigations of the optical effects in thienoacene chromophores with different central atoms were performed. These chromophores provide a basis for the comparison of the linear, two-photon, and entangled two-photon properties in organic molecules with varying degrees of dipolar or quadrupolar character. Linear absorption and emission as well as time-dependent density functional theory calculations were performed for the chromophores investigated. Measurements of the classical two-photon absorption (TPA), entangled two-photon absorption (ETPA), as well as entangled two-photon fluorescence were experimentally performed for the four chromophores. Electronic structure calculations were utilized to provide estimates of the classical two-photon absorption coefficients. The results of the measured entangled two-photon cross sections were compared with theoretical estimates for the molecules investigated. It is found that the dipole (transition or permanent) pathway can have an effect on the trends in the entangled photon absorption process in dipolar organic chromophores. This study helps predict the properties of the entangled two-photon effect in chromophores with different dipolar and quadrupolar character.
DEVELOPPEMENT D'UN PROCEDE INTEGRE DE FERMENTATION ANAEROBIECOUPLEE A LA PERVAPORATION POUR LA PRODUCTION DE N-BUTANOL (2017)

International audience
Kinetics in Parasite Abundance in Susceptible and Resistant Mice Infected with an Avirulent Strain of Toxoplasma gondii by Using Quantitative Competitive PCR (1997)

The kinetics of changes in Toxoplasma gondii abundance were evaluated with a quantitative competitive (QC)-polymerase chain reaction (PCR) assay at various sites in both C57BL/6 and BALB/c mice. Higher mortality was apparent in C57BL/6 mice than in BALB/c mice when infected with a high dose of cysts. There were significant differences in cyst number when infected with a low dose of cysts, although there was no significant difference in mortality between the 2 mouse strains. One day after infection with a low dose of an avirulent Fukaya strain, T. gondii was detected in peripheral blood, mesenteric lymph nodes, spleen, lungs, and brain. Two weeks after infection, the number of T. gondii in the brain greatly increased in C57BL/6 mice but not in BALB/c mice. Thus, it would appear that the first to second week after infection is a critical period in determining T. gondii abundance. QC PCR allows the detection of low numbers of T. gondii at an early stage of infection in the murine model. This is useful for the early diagnosis of toxoplasmosis and to understand reactivation of toxoplasmosis.
Influences of Global Warming on Wave Dissipating Blocks (2019)

Presented at: Coastal Structures Conference 2019, Hannover, Germany, September 30th – October 2nd, 2019
Next generation sequencing based detection of 15 target genes mutations in papillary thyroid carcinoma (2020)

Abstract Objectives Next generation sequencing (NGS) method provided a valuable tool for a comprehensive understanding of papillary thyroid carcinoma (PTC) biology. We explored the application of NGS based detection for a panel of 15 target genes mutations and analyzed the gene spectrum in PTC. Methods A total of 211 formalin‐fixed, paraffin‐embedded (FFPE) tissue specimens from surgically removed PTC samples were collected and detected with 15 target genes by NGS. Results In general, 181 mutations of all types of 15 target genes were detected in 164 samples (77.73% of 211 samples). There were 22.27% samples with no mutation, and 70.14% samples carried mutations in single gene. A total of 7.11% samples simultaneously harboured two gene mutations and 0.47% sample carried triple different gene mutations. The BRAF mutation was the most common mutation type, followed by TERT, RET fusion, TP53, PIK3CA, GNAS, NTRK1 fusion, CTNNB1, NRAS, and HRAS. TSHR, AKT1, PETN, KRAS, and PAX8 mutations were negative among PTC patients. All point mutations found in PTC samples were heterozygous mutations with allelic frequency ranged from 1.12% to 48.04% of alleles. The fusion mutations showed the percent of reads ranged from 2.30% to 55.54%. For samples with carried two mutations, the allelic frequency of mutations was similar. However, for the sample harboured triple gene mutations, the allelic frequency of NRAS mutation was similar to TERT mutation (33.62%‐39.67%) and TP53 mutation showed much lower abundance (4.13%). Conclusions NGS‐based detection method showed advantages in detecting multiple gene mutations simultaneously, economically and efficiently, and providing quantitative assessment of mutation frequency using targeted sequencing panel. It can improve the accuracy of diagnosis and prognostication and is useful for providing personalized treatments for PTC patients.
Dependence of the Reactivity of Acridine on Its Substituents: A Computational and Kinetic Study (2011)

Abstract Aromatic nucleophilic substitution on the C9 carbon of acridine plays an important role in multiple biological and medicinal applications. The rate of the key reaction is strongly dependent on the environment and acridine substituents. In this study, the factors influencing the reaction mechanism were studied theoretically and verified experimentally for simplified systems. Density functional theory was used for the computations. The activation energy of a model derivative was determined experimentally from a kinetic study. Also, the relative reactivities of selected compounds were verified by a competition experiment. The theoretical predictions correlate well with the observations. The computed reaction path confirms that the thiol group attacks the aromatic core activated by the nitrogen heteroatom and replaces halogen or amino substituents via a well‐defined Meisenheimer transition state. The reaction barrier is strongly influenced by both the solvent and substituents on the aromatic system. A multistep mechanism is proposed for the reaction of aminoacridine in which the aqueous solvent participates in the reaction. Strong correlations between reaction energies and geometrical parameters were observed and can be used to rationalize the design of acridine drugs as well as to avoid lengthy computations of the transition states.
<title>Ultra-low-power imaging systems using CMOS image sensor technology</title> (1994)

The need for miniaturization in advanced science sensor systems has led to the development of a new image sensor technology, the active pixel image sensors (APS). The development of CMOS APS technology allows the integration of timing and control electronics, imaging detector arrays, signal chains and analog-to-digital conversion on a single integrated circuit. The impact on the imaging system is to reduce power by approximately 1000X over existing systems--from tens of watts to tens of milliwatts. This paper will describe the development of this technology and its application to future space science sensor systems.
ChemInform Abstract: Regio‐ and Stereoselective Fe(III)‐ and Pd(0)‐Mediated Ring Openings of 3‐Aza‐2‐oxabicyclo[2.2.1]hept‐5‐ene Systems. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Hyaluronan receptors involved in cytokine induction in monocytes (2008)

During inflammation, lower molecular weight fragments of hyaluronan accumulate, and this is known to be inflammatory and immune-stimulatory. In diseases such as inflammatory bowel disease, inflammatory cells bind to hyaluronan; however, the cellular response and molecular mechanism of hyaluronan-hyaluronan receptor interactions in mononuclear cells are not well understood. The expression of hyaluronan receptors in peripheral blood mononuclear cells (PBMC) was examined. PBMC were stimulated with lower and higher molecular weight hyaluronan (molecular weight 100-150 kDa and 2700 kDa) and the induction of proinflammatory cytokines (interleukin-6 (IL-6) and monocyte chemoattractant protein (MCP-1)) was compared by enzyme-linked immunoabsorbant assay (ELISA). Cells were coincubated with various signaling pathway inhibitors. In addition, neutralizing antibodies against CD44 and TLR4 were added and the effects on PBMC were investigated. Finally, mononuclear cells from CD44-null and toll-like receptor 4 (TLR4) mutant mice were both stimulated with lower molecular weight hyaluronan. Among the hyaluronan receptors, TLR4 and CD44 were markedly expressed on PBMC. Hyaluronan-stimulated PBMC enhanced the attachment to the extracellular matrix. Lower molecular weight hyaluronan induced IL-6 and MCP-1 production in PBMC, but high-molecular-weight hyaluronan did not induce IL-6 and MCP-1 production. An anti-CD44 antibody attenuated the induction of both IL-6 and MCP-1 in lower molecular weight hyaluronan-stimulated PBMC. In both TLR4 mutant and CD44-null mice, the induction of IL-6 by lower molecular weight hyaluronan stimulation was decreased. SB203580 completely abolished IL-6 production in both TLR4 mutant and CD44-null mononuclear cells, while PD98059 abolished IL-6 production in CD44-null mononuclear cells. Hyaluronan receptors, CD44 and TLR4, play distinct roles in cytokine induction in hyaluronan-stimulated mononuclear cells.
注解C++リファレンス・マニュアル : ANSI base document (1993)

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