gebhart/patrepeval huggingface dataset:
Dietary Mutagens and the Risk of Breast Cancer (1998)

In this issue of the Journal, Zheng et al. (1) report a positive association between the preference for well-done red meat and risk of postmenopausal breast cancer. Using color photographs of hamburger, bacon, and beefsteak showing increasing levels of doneness (from extremely rare to very well done), women who selected a cooking preference for ‘‘very well done’’ for each of these foods had a risk nearly five times higher than that for women who consistently selected a preference for rare/medium cooking. Overall consumption of red meat itself had only a weak association with risk, and white meats, including chicken, turkey, and fish, were not statistically significant risk factors regardless of cooking method. The specificity of the findings to meat preparation tends to rule out saturated fat as the causative factor and is consistent with the possibility that mutagens, including heterocyclic amines, formed during high-temperature cooking of meats may be mammary carcinogens in humans. The browned and charred surface of meats contains a hash of laboratory carcinogens. Among these are the heterocyclic amines, formed through chemical reactions involving amino acids. The formation of heterocyclic amines requires high temperatures, such as are found in radiative or conductive cooking (e.g., grilling or frying) but not as a rule in indirect convection (e.g., roasting) or boiling (e.g., poaching or steaming) methods (2). These substances are capable of inducing tumors in a number of species (2) and are reportedly among some of the most powerful mutagenic agents, based on the Ames test (3). Heterocyclic amines involving creatinine as a precursor are numerically most important. Among these, 2-amino-1-methyl-6phenylimidazo[4,5-b]pyridine (PhIP) predominates, accounting for approximately one half of the total heterocyclic amine intake in the U.S. diet. Five compounds, i.e., PhIP, 2-amino3,8-dimethylimidazo[4,5-f ]quinoxaline (MeIQx), 2-amino3,4,8-trimethylimidazo[4,5-f]quinoxaline ( DiMeIQx), 2-amino-3-methylimidazo[4,5-f ]quinoline (IQ), and 2-amino9H-pyrido[2,3-b]indole (AaC), make up approximately two thirds of the total intake (4). Based on animal bioassay data, the relative mutagenic potency of these compounds varies by a factor of more than 20, with IQ and DiMeIQx at the high end, PhIP and AaC at the low end, and MeIQx at an intermediate level of potency (4). Thus, the absolute concentration of specific heterocyclic amines in foods must be weighed against their individual potential for genetic damage when they are evaluated as potential human carcinogens. Major dietary sources of these compounds vary from population to population depending on a number of factors, including cultural mores and meat availability. In a study of female registered nurses (5), the major predictor of PhIP in the diet was grilled or broiled chicken, whereas the chief source of DiMeIQx was pan-fried steak.
Development and Application of the Metalloprotease Activity Multiplexed Bead-Based Immunoassay (MAMBI) (2019)

Metalloproteinases (MMPs) are zinc-dependent endopeptidases that cleave various proteins to regulate normal and diseased cellular functions, and as such, they play significant roles in human tissue development, homeostasis, and the pathogenesis of many diseases, including cancers, endometriosis, arthritis, etc. Most MMPs are produced as zymogenic latent enzymes that must be cleaved to activate their catalytic regions, and localized endogenous protein inhibitors further regulate activity. Accordingly, they operate within recursive networks to degrade extracellular matrix proteins and regulate cell signaling by cleaving growth factors and receptors at the cell surface and in the local pericellular environment. Thus, high-resolution information about the concentrations of specific active MMPs, revealing their intricate regulatory networks, may improve disease diagnosis and treatment. Here, we introduce a new and readily mastered method for measuring MMP activities in a multiplex fashion. We integrate aspects of activity-based enzyme labeling with commercial high-throughput, multiplexed protein quantification to yield the metalloproteinase activity multiplexed bead-based immunoassay (MAMBI). Assays of recombinant active MMP-1, -2, -3, -7, -8, -9, -12, and -13 establish the sensitivity and selectivity of MAMBI detection. Levels of active native MMPs are similarly characterized in conditioned cell culture medium, menstrual effluent, and uterine tissue. In a single MAMBI (5 μL), we achieve sensitivities equal to those from leading single-plex MMP activity detection strategies (e.g., 10-15 M for MMP-1). We also demonstrate high-throughput inhibitor screening via the MAMBI approach in complex, patient-derived samples.
Learning-based Motion Artifact Removal Networks (LEARN) for Quantitative $R_2^\ast$ Mapping (2021)

Purpose: To introduce two novel learning-based motion artifact removal networks (LEARN) for the estimation of quantitative motion- and $B0$-inhomogeneity-corrected $R_2^\ast$ maps from motion-corrupted multi-Gradient-Recalled Echo (mGRE) MRI data. Methods: We train two convolutional neural networks (CNNs) to correct motion artifacts for high-quality estimation of quantitative $B0$-inhomogeneity-corrected $R_2^\ast$ maps from mGRE sequences. The first CNN, LEARN-IMG, performs motion correction on complex mGRE images, to enable the subsequent computation of high-quality motion-free quantitative $R_2^\ast$ (and any other mGRE-enabled) maps using the standard voxel-wise analysis or machine-learning-based analysis. The second CNN, LEARN-BIO, is trained to directly generate motion- and $B0$-inhomogeneity-corrected quantitative $R_2^\ast$ maps from motion-corrupted magnitude-only mGRE images by taking advantage of the biophysical model describing the mGRE signal decay. We show that both CNNs trained on synthetic MR images are capable of suppressing motion artifacts while preserving details in the predicted quantitative $R_2^\ast$ maps. Significant reduction of motion artifacts on experimental in vivo motion-corrupted data has also been achieved by using our trained models. Conclusion: Both LEARN-IMG and LEARN-BIO can enable the computation of high-quality motion- and $B0$-inhomogeneity-corrected $R_2^\ast$ maps. LEARN-IMG performs motion correction on mGRE images and relies on the subsequent analysis for the estimation of $R_2^\ast$ maps, while LEARN-BIO directly performs motion- and $B0$-inhomogeneity-corrected $R_2^\ast$ estimation. Both LEARN-IMG and LEARN-BIO jointly process all the available gradient echoes, which enables them to exploit spatial patterns available in the data. The high computational speed of LEARN-BIO is an advantage that can lead to a broader clinical application.
Extending a Single-Document Summarizer to Multi-Document: a Hierarchical Approach (2015)

The increasing amount of online content motivated the development of multi-document summarization methods. In this work, we explore straightforward approaches to extend single-document summarization methods to multi-document summarization. The proposed methods are based on the hierarchical combination of single-document summaries, and achieves state of the art results.
Pancreatic Islets Under Attack: Cellular and Molecular Effectors (2007)

Abundant information is available on the involvement of various cellular and molecular mechanisms in beta cell apoptosis. The experimental evidence is controversial and difficult to reconcile, and the mechanisms of evasion of the autoreactive clones from immune surveillance are poorly understood. Multiple apoptotic pathways play a role in destructive insulitis, including perforin/granzyme, Fas/Fas-ligand (FasL), and other members of the necrosis factor superfamily. These pathways present redundant behaviors in both the initial and late stages of beta cell injury, and at the same time, each molecular mechanism is dispensable in the evolution of autoimmune diabetes. There may be a preferential use of perforin/granzyme in CD8(+) T cell-mediated lysis, which participates in onset of autoimmunity, and a predominance of FasL in CD4(+) T cell-mediated insulitis. Several cytokines released in the inflammatory infiltrate induce Fas expression in beta cells, priming them to FasL-mediated apoptosis. In this review, we focus on the possible participation of multiple cell subsets and molecular mechanisms in the pathogenesis of diabetes to the point where inflammation incites an irreversible vicious cycle that perpetuates beta cell death.
Effect of booster shed on ceramic post insulator pollution flashover performance improvement (2016)

To prevent substation post insulator from pollution flashover, apart from PRTV (Permanent Room Temperature Vulcanized) coating on insulator surface, booster shed adoption is also a solution for operation maintenance. In this paper, ceramic post insulators installed with silicone rubber sheds in various configuration are tested by pollution flashover experiment, to find out the optimized configuration of booster sheds. Five test specimens are prepared for this work, including 25mm/kV ceramic insulator installed with 0, 2, 4, 6 silicone rubber booster sheds, contaminated with same pollution degree in solid layer method. As well, insulator coating with PRTV material is prepared in same way for comparison. Pollution flashover tests are performed following IEC/TS 60507. Meanwhile, arc shape variation synchronized with voltage and current change are record by high speed camera. In various configuration, flashover voltage, leakage current and arc development shape show significant characteristic separately. Results show that the booster sheds not only provide additional creepage distance, but also create an alternating hydrophobicity distribution on insulator surface, which is more efficient for pollution flashover performance improvement. Booster shed made of silicone rubber alternates hydrophobicity distribution along ceramic insulator. Accordingly it can enhance the pollution flashover voltage greatly.
Novel Nanocomposite Pt/RuO<sub>2</sub>×xH<sub>2</sub>O/Carbon Nanotube Catalysts for Direct Methanol Fuel Cells. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Estimation and Planning of Exploration Over Grid Map Using A\n Spatiotemporal Model with Incomplete State Observations (2021)

Path planning over spatiotemporal models can be applied to a variety of\napplications such as UAVs searching for spreading wildfire in mountains or\nnetwork of balloons in time-varying atmosphere deployed for inexpensive\ninternet service. A notable aspect in such applications is the dynamically\nchanging environment. However, path planning algorithms often assume static\nenvironments and only consider the vehicle's dynamics exploring the\nenvironment. We present a spatiotemporal model that uses a cross-correlation\noperator to consider spatiotemporal dependence. Also, we present an adaptive\nstate estimator for path planning. Since the state estimation depends on the\nvehicle's path, the path planning needs to consider the trade-off between\nexploration and exploitation. We use a high-level decision-maker to choose an\nexplorative path or an exploitative path. The overall proposed framework\nconsists of an adaptive state estimator, a short-term path planner, and a\nhigh-level decision-maker. We tested the framework with a spatiotemporal model\nsimulation where the state of each grid transits from normal, latent, and fire\nstate. For the mission objective of visiting the grids with fire, the proposed\nframework outperformed the random walk (baseline) and the single-minded\nexploitation (or exploration) path.\n
Synchronization of Medial Temporal Lobe and Prefrontal Rhythms in Human Decision Making (2013)

Optimal decision making requires that we integrate mnemonic information regarding previous decisions with value signals that entail likely rewards and punishments. The fact that memory and value signals appear to be coded by segregated brain regions, the hippocampus in the case of memory and sectors of prefrontal cortex in the case of value, raises the question as to how they are integrated during human decision making. Using magnetoencephalography to study healthy human participants, we show increased theta oscillations over frontal and temporal sensors during nonspatial decisions based on memories from previous trials. Using source reconstruction we found that the medial temporal lobe (MTL), in a location compatible with the anterior hippocampus, and the anterior cingulate cortex in the medial wall of the frontal lobe are the source of this increased theta power. Moreover, we observed a correlation between theta power in the MTL source and behavioral performance in decision making, supporting a role for MTL theta oscillations in decision-making performance. These MTL theta oscillations were synchronized with several prefrontal sources, including lateral superior frontal gyrus, dorsal anterior cingulate gyrus, and medial frontopolar cortex. There was no relationship between the strength of synchronization and the expected value of choices. Our results indicate a mnemonic guidance of human decision making, beyond anticipation of expected reward, is supported by hippocampal-prefrontal theta synchronization.
Catalysis of 3-Pyrrolidinecarboxylic Acid and Related Pyrrolidine Derivatives in Enantioselective <i>anti</i>-Mannich-Type Reactions:  Importance of the 3-Acid Group on Pyrrolidine for Stereocontrol (2007)

The development of enantioselective anti-selective Mannich-type reactions of aldehydes and ketones with imines catalyzed by 3-pyrrolidinecarboxylic acid and related pyrrolidine derivatives is reported in detail. Both (3R,5R)-5-methyl-3-pyrrolidinecarboxylic acid and (R)-3-pyrrolidinecarboxylic acid efficiently catalyzed the reactions of aldehydes with alpha-imino esters under mild conditions and afforded anti-Mannich products with high diastereo- and enantioselectivities (anti/syn up to 99:1, up to >99% ee). For the reactions of ketones with alpha-imino esters, (R)-3-pyrrolidinecarboxylic acid was an efficient catalyst (anti/syn up to >99:1, up to 99% ee). Evaluation of a series of pyrrolidine-based catalysts indicated that the acid group at the beta-position of the pyrrolidine ring of the catalyst played an important role in forwarding the carbon-carbon bond formation and in directing anti-selectivity and enantioselectivity.
Endothelial-like properties of claudin-low breast cancer cells promote tumor vascular permeability and metastasis (2020)

The vasculature serves as the main conduit for breast tumor metastases and is a target of therapeutics in many tumor types. In this study, we aimed to determine if tumor-associated vascular properties could help to explain the differences observed in metastagenicity across the intrinsic subtypes of human breast tumors. Analysis of gene expression signatures from more than 3,000 human breast tumors found that genomic programs that measured vascular quantity, vascular proliferation, and a VEGF/Hypoxia-signature were the most highly expressed in claudin-low and basal-like tumors. The majority of the vascular gene signatures added metastasis-predictive information to immunohistochemistry-defined microvessel density scores and genomically defined-intrinsic subtype classification. Interestingly, pure claudin-low cell lines, and subsets of claudin-low-like cells within established basal-like cancer cell lines, exhibited endothelial/tube-like morphology when cultured on Matrigel. In vivo xenografts found that claudin-low tumors, but not luminal tumors, extensively perfused injected contrast agent through paracellular spaces and non-vascular tumor-lined channels. Taken together, the endothelial-like characteristics of the cancer cells, combined with both the amount and the physiologic state of the vasculature contribute to breast cancer metastatic progression. We hypothesize that the genetic signatures we have identified highlight patients that should respond most favorably to anti-vascular agents.Electronic supplementary materialThe online version of this article (doi:10.1007/s10585-013-9607-4) contains supplementary material, which is available to authorized users.
Current Issues in Blood Substitute Research and Development-1995. (1995)

Abstract : Although a substitute for human red cells has been sought for more than a century, still no product is available to patients. Until the early 1980's, research and development in this area was relegated to rather obscure academic efforts, but AIDS suddenly brought new focus to the effort when its transmission by blood transfusion was shown clearly. Although blood is now extensively tested for the AIDS (HIV) virus, research on red cell substitutes has shown tremendous potential application for these products, and development continues at an unprecedented pace. In fact, a number of products are currently in human clinical trials.
Proteomics and the Human Metabolome Project (2007)

These days, it seems like a new omics word is being invented almost every week [101]. Many of these fanciful terms will never be used by anyone other than the individual who first coined them. Howe...
Sprayability Analysis of Pristine and Enhanced PEDOT:PSS Inks via Electrohydrodynamic Spray Deposition (2022)

Poly (3,4-ethylene dioxythiophene) polystyrene sulfonate (PEDOT:PSS) is a conductive polymer and versatile material to fabricate numerous organic electronic devices. PEDOT:PSS inks were studied and analyzed for their sprayability via Electrohydrodynamic (EHD) printing. Commercially obtained pristine PEDOT:PSS ink could not produce any decent cone-jet mode due to its high surface tension and viscosity. Two different surfactants – acetone and ethanol were then dispersed into PEDOT:PSS at different concentrations to enhance the sprayability of the PEDOT:PSS ink. Both modified PEDOT:PSS inks could produce a cone-jet mode of spraying, which is essential for EHD printing. The flow rates were tested between 10 - 20 μl/hr. These limits were established to prevent the splashing effect at a higher flow rate (&gt;20μl/hr) and inks disintegrating at a lower flow rate 5μl/hr. PEDOT:PSS:Acetone and PEDOT:PSS:Ethanol with 50:50 and 75:25 ratios, respectively, produced the best performance in their respective categories.
Supplementary Table 1 from Expression of Wnt3 Activates Wnt/β-Catenin Pathway and Promotes EMT-like Phenotype in Trastuzumab-Resistant HER2-Overexpressing Breast Cancer Cells (2023)

&lt;p&gt;PDF file - 67K, Primers sequences used for the studies&lt;/p&gt;
Measurement of Helicity-Dependent Photoabsorption Cross Sections on the Neutron from 815 to 1825 MeV (2005)

Helicity-dependent total photoabsorption cross sections on the deuteron have been measured for the first time at ELSA (Bonn) in the photon energy range from 815 to 1825 MeV. Circularly polarized tagged photons impinging on a longitudinally polarized LiD target have been used together with a highly efficient 4pi detector system. The data around 1 GeV are not compatible with predictions from existing multipole analyses. From the measured energy range an experimental contribution to the GDH integral on the neutron of [33.9 +/- 5.5(stat) +/- 4.5(syst)] microb is extracted.
&lt;title&gt;Mask inspection and real-time linewidth measurements&lt;/title&gt; (1996)

Controlling line width error is one of the most challenging tasks in mask production. Current methods for monitoring line width are based on either CD measurements or edge defect detection. Neither method guarantees the detection of line width errors with good sensitivity over the whole mask area. For example, a combination of small edge defect together with CD non-uniformity within the allowed tolerance, can yield a significant line width error, which will not be detected using conventional methods. In this paper we are presenting a new approach for line width error detection. The method, a new feature of Orbot's RT-8000 die-to-database Reticle Inspection System, is a sensitive detector that operates during the inspection of all the reticle's area. The detection is based on a comparison of measured line widths on both the database and the scanned image ofthe reticle. In section 2, the motivation for this new detector is driven. An analysis of various defect types, which are difficult to detected using edge detection approach or CD measurements, is presented. In section 3, the basic concept of the new approach is introduced together with a description of the new detector and it's characteristics. In section 4, the calibration process that took place in order to evaluate the sensitivity of the detector is described. The experimental results of this evaluation are reported in section 5.
Association of Hypoglycemia, Hyperglycemia, and Glucose Variability With Morbidity and Death in the Pediatric Intensive Care Unit (2006)

Hyperglycemia and hypoglycemia were prevalent in the PICU. Hypoglycemia, hyperglycemia, and, in particular, increased glucose variability were associated with increased morbidity (length of stay) and mortality rates.
Supplementary Data from The Folate Pathway Inhibitor Pemetrexed Pleiotropically Enhances Effects of Cancer Immunotherapy (2023)

&lt;p&gt;Figure S1. Efficacy of pemetrexed in Lewis Lung carcinoma model and metabolomic analysis of MC38 tumor bearing mice treated with 50 mg/kg of pemetrexed Figure S2. T cell inflamed phenotype induced by pemetrexed is modestly reduced in tumors upon combination with cisplatin Figure S3. Combination Effects of pemetrexed -/+ anti-PD-L1 in MC38, LLC and Colon26 tumor models Figure S4 (A) Mice bearing Colon26 tumors were treated starting 10 days after tumor implantation with pemetrexed (50 mg/kg, 5 days on, 2 days off, IP) and/or anti-PD-L1 (αPD-L1) (500 ug/mouse, weekly IP), and tumors were isolated after 14 days of treatment and single cell suspensions were subjected to flow cytometry analysis. FACS plots show representative data of intra-tumor CD45+ tumor-infiltrating lymphocyte (TIL) T cell (CD3+) and Myeloid cell (CD11b+) subsets frequencies; and percentage of Ki67+ CD4+ T effector cells based on the gating scheme indicated. (B) Spleens, TDLNs and tumors were isolated and antigen specific T cell responses were measured by IFNγ ELISpot, gp70 Tetramer staining (Tet) and Intracellular cytokine staining. (Left) CD8 T cells isolated from pooled spleens and TDLNs from individual mice were cultured alone (control) with irrelevant BALB/c tumor EMT6 or cognate Colon26 tumor cells overnight and number of IFNγ producing T cells was measured by ELISpot. (Middle) Freshly isolated CD8+ T cells from spleens and TDLNs were assessed for % of gp70 Tet+ cells. (Right) Freshly isolated tumors single cell suspensions were stimulated with PMA/ phorbol myristate acetate (PMA) and ionomycin with monensin for 4 hrs and the % of TNF-alpha positive and gp70 Tet+ CD8 T cells were measured from the Live CD45+, CD3+ T cells by FACS. Figure S5. Concordance between QuantiGene and nCounter gene expression data for in vitro activated T cells treated in the presence or absence of pemetrexed (related to Figure 6F). Supplementary Table 1. Ingenuity pathway analysis (IPA) of MC38 tumors treated with pemetrexed or paclitaxel with or without carboplatin Supplementary Table 2: IPA results for Colon26 experiment in Figure 4 sorted by functional class. Pemetrexed monotherapy in this experiment at this timepoint did not have enough differentially expressed genes to generate IPA results.&lt;/p&gt;
Supplementary Figures 1 and 2 from Concurrent Binding of Anti-EphA3 Antibody and Ephrin-A5 Amplifies EphA3 Signaling and Downstream Responses: Potential as EphA3-Specific Tumor-Targeting Reagents (2023)

Supplementary Figures 1 and 2 from Concurrent Binding of Anti-EphA3 Antibody and Ephrin-A5 Amplifies EphA3 Signaling and Downstream Responses: Potential as EphA3-Specific Tumor-Targeting Reagents