gebhart/patrepeval huggingface dataset:
A generic normalization method for proper quantification in untargeted proteomics screening (2018)

ABSTRACT The label-free quantitative mass spectrometry methods, in particular, the SWATH-MS approach, have gained popularity and became a powerful technique for comparison of large datasets. In the present work, it is introduced the use of recombinant proteins as internal standards for untargeted label-free methods. The proposed internal standard strategy reveals a similar intragroup normalization capacity when compared with the most common normalization methods, with the additional advantage of maintaining the overall proteome changes between groups (which are lost using other methods). Therefore, the proposed strategy is able to maintain a good performance even when large qualitative and quantitative differences in sample composition are observed, such as the ones induced by biological regulation (as observed in secretome and other biofluids’ analyses) or by enrichment approaches (such as immunopurifications). Moreover, this approach corresponds to a cost-effective alternative, easier to implement than the current stable-isotope labeling internal standards, therefore being an appealing strategy for large quantitative screening, as clinical cohorts for biomarker discovery.
On‐chip non‐invasive and label‐free cell discrimination by impedance spectroscopy (2008)

These results underline the potential of impedance spectroscopy flow cytometry as a valuable complement to other known cytometers and cell detection systems.
Supplementary Figure 4 from microRNA-205 Regulates HER3 in Human Breast Cancer (2023)

Supplementary Figure 4 from microRNA-205 Regulates HER3 in Human Breast Cancer
Analysis of Glioma Cell Platinum Response by Metacomparison of Two-dimensional Chromatographic Proteome Profiles (2005)

Successful clinical development of cancer treatments is aided by the development of molecular markers that allow the identification of patients likely to respond. In the case of broadly cytotoxic drugs, such as the multinuclear series of platinum chemotherapeutic agents that we are evaluating for the treatment of glioma, one route to marker identification is proteomic profiling. We are using the two-dimensional chromatography system, the ProteomeLab PF2D, to compare proteomic profiles of glioma cells in culture before and after drug treatment. The existing software tools allowed the rapid identification of peaks increased by treatment of a given drug as compared with control untreated cells. To compare across these pairs, we developed new software, called the MetaComparison Tool (MCT). The MCT uses the chromatographic characteristics of peaks as identifiers, an approach that was validated by mass spectrometry of two independent isolations of a peak, from cells that were treated with two different platinum compounds. The MCT made it possible to rapidly query whether a given peak responded to more than one treatment and so allowed the identification of peaks that were specific to a given drug. As a result, this analysis greatly reduced the list of peaks whose isolation and downstream analysis by mass spectrometry is warranted, accelerating the search for protein markers of response.
The SONET edge‐partition problem (2002)

Abstract Motivated by a problem arising in the design of telecommunications networks using the SONET standard, we consider the problem of covering all edges of a graph using subgraphs that contain at most k edges with the objective of minimizing the total number of vertices in the subgraphs. We show that the problem is 𝒩 𝒫 ‐hard when k ≥ 3 and present a linear‐time ‐approximation algorithm. For even k values, we present an approximation scheme with a reduced ratio but with increased complexity. © 2002 Wiley Periodicals, Inc.
Iridium(III)-Catalyzed Direct Arylation of C–H Bonds with Diaryliodonium Salts (2015)

By developing a new Ir(III)-catalyzed C-C cross-coupling, a versatile method for direct arylation of sp(2) and sp(3) C-H bonds in ketoximes, nitrogen-containing heterocycles, various arenes, and olefins has been established. The key to this arylation depends on the appropriate choice of catalyst and the use of diaryliodonium triflate salts as the coupling partners. This transformation has good functional group compatibility and can serve as a powerful synthetic tool for late-stage C-H arylation of complex compounds. Mechanistic studies by density functional theory calculations suggested that the sp(3) C-H activation was realized by a triflate-involved concerted metalation-deprotonation process, and the following oxidation of Ir(III) to Ir(V) is the most favorable when a bistriflimide is contained in the diaryliodonium salt. Calculations indicated that both steps are enabled by initial anion exchange between the reactant complexes.
Micro-endoscope for in vivo widefield high spatial resolution fluorescent imaging (2012)

In this paper we report the design, testing and use of a scannerless probe specifically for minimally invasive imaging of deep tissue in vivo with an epi-fluorescence modality. The probe images a 500 μm diameter field of view through a 710 μm outer diameter probe with a maximum tissue penetration depth of 15 mm specifically configured for eGFP imaging. Example results are given from imaging the pituitary gland of rats and zebrafish hearts with lateral resolution of 2.5 μm.
Aerobic, Chemoselective Oxidation of Alcohols to Carbonyl Compounds Catalyzed by a DABCO‐Copper Complex under Mild Conditions (2007)

Abstract A DABCO‐copper(I) chloride complex (5 mol %) together with TEMPO (5 mol %) in nitromethane as solvent has been used as an efficient catalytic system for the selective oxidation of benzylic and allylic alcohols into the corresponding carbonyl compounds at room temperature where molecular oxygen acts as an ultimate, stoichiometric oxidant and water is the only by‐product. The solid‐state structure determination of the DABCO‐copper complex shows that the copper is in the +II oxidation state with trigonal bipyramidal geometry and exists in a linear polymeric structure due to strong hydrogen bonding.
Design of Planet Carrier of MW Wind Turbine and its Analysis Based on the Finite Element Method (2012)

Research is on a MW wind turbine gearbox,and the planetary transmission mechanism of the gearbox is designed.Building the planet carrier's calculation model through 3D modeling software,using the finite element method to analysis and calculate the stress,displacement and fatigue life of the planet carrier,and to get the size and position where the maximum stress and biggest deformation is produced.The biggest deformation of planet carrier happens in the shaft hole edge of right wall,and the biggest stress occurs in the attaches of the right wall and the bearing.The analysis of the fatigue life of the planet carrier shows that it can bear unlimited multiple cycles at rated load without being destroyed.The result provides theoretical basis for the design in planet carrier and gear transmission of MW Wind Turbine.
LIGHT POLARIZATION FROM FILMS OF LYOTROPIC NEMATIC LIQUID CRYSTALS (1969)

Light polarizing films are produced by controlled evaporation of a lyotropic nematic dichroic liquid crystal upon an oriented base. The molecules align themselves with their short axes parallel in the direction of the surface orientation. This orientation is maintained upon evaporation of the solvent.
Intrinsic Images by Clustering (2012)

Abstract Decomposing an input image into its intrinsic shading and reflectance components is a long‐standing ill‐posed problem. We present a novel algorithm that requires no user strokes and works on a single image. Based on simple assumptions about its reflectance and luminance, we first find clusters of similar reflectance in the image, and build a linear system describing the connections and relations between them. Our assumptions are less restrictive than widely‐adopted Retinex‐based approaches, and can be further relaxed in conflicting situations. The resulting system is robust even in the presence of areas where our assumptions do not hold. We show a wide variety of results, including natural images, objects from the MIT dataset and texture images, along with several applications, proving the versatility of our method.
Bi-transgenic Mice Reveal that K-rasVal12 Augments a p53-independent Apoptosis When Small Intestinal Villus Enterocytes Reenter the Cell Cycle (1997)

Studies in cell culture systems have indicated that oncogenic forms of Ras can affect apoptosis. Activating mutations of Ras occur in ∼30% of all human tumors and 50% of colorectal carcinomas. Since these mutations appear at early or intermediate stages in multistep journeys to neoplasia, an effect on apoptosis may help determine whether initiated cells progress towards a more neoplastic state. We have tested the effects of K-rasVal12 on apoptosis in transgenic mice. A lineage-specific promoter was used to direct expression of human K-rasVal12, with or without wild-type (wt) or mutant SV-40 T antigens (TAg), in postmitotic villus enterocytes, the principal cell type of the small intestinal epithelium. Enterocytes can be induced to reenter the cell cycle by TAgWt. Reentry is dependent upon the ability of TAg to bind pRB and is associated with a p53-independent apoptosis. Analyses of K-rasVal12 × TAgWt bi-transgenic animals indicated that K-rasVal12 can enhance this apoptosis threefold but only in cycling cells; increased apoptosis does not occur when K-rasVal12 is expressed alone or with a TAg containing Glu107,108→ Lys107,108 substitutions that block its ability to bind pRB. Analysis of bi-transgenic K-rasVal12 × TAgWt mice homozygous for wild-type or null p53 alleles established that the enhancement of apoptosis occurs through a p53-independent mechanism, is not attributable to augmented proliferation or to an increase in abortive cell cycle reentry (compared to TAgWt mice), and is not associated with detectable changes in the crypt–villus patterns of expression of apoptotic regulators (Bcl-2, Bcl-xL, Bak, and Bax) or mediators of epithelial cell–matrix interactions and survival (e.g., α5β1 integrin and its ligand, fibronectin). Coexpression of K-rasVal12 and TAgWt produces dysplasia. The K-rasVal12-augmented apoptosis is unrelated to this dysplasia; enhanced apoptosis is also observed in cycling nondysplastic enterocytes that produce K-rasVal12 and a TAg with a COOH-terminal truncation. The dysplastic epithelium of K-rasVal12 × TAgWt mice does not develop neoplasms. Our results are consistent with this finding: (a) When expressed in initiated enterocytes with a proliferative abnormality, K-rasVal12 facilitates progression to a dysplastic phenotype; (b) by diminishing cell survival on the villus, the oncoprotein may impede further progression; and (c) additional mutations may be needed to suppress this proapoptotic response to K-rasVal12.
Design Thinking as a Means of Citizen Science for Social Innovation (2021)

Members of the public or community can play a significant role in the development of social innovations. When a social innovation is developed involving a scientific approach and the community, there is the confluence of two fields-citizen science and social innovation. Social innovations can be developed through the employment of design-thinking. In this paper, we advocate design thinking as an approach to marry the two fields for a desired outcome of improved community life in ageing housing estates in Tokyo. The two fields, citizen science and social innovation, are described in brief before the design thinking method is introduced and its utility in engaging citizens for social innovation is explored. The paper provides two case illustrations and the lessons drawn from them. We conclude with pointers for others who desire to employ this approach. When the resultant innovation and design-thinking approach are adopted by the community for future projects, there could be a change in society and possible forward movement for self-help and change.
Heterologous Expression of Genes Mediating Enhanced Fungal Resistance in Transgenic Wheat (2001)

Three cDNAs encoding the antifungal protein Ag-AFP from the fungus Aspergillus giganteus, a barley class II chitinase and a barley type I RIP, all regulated by the constitutive Ubiquitin1 promoter from maize, were expressed in transgenic wheat. In 17 wheat lines, stable integration and inheritance of one of the three transgenes has been demonstrated over four generations. The formation of powdery mildew (Erysiphe graminis f. sp. tritici) or leaf rust (Puccinia recondita f. sp. tritici) colonies was significantly reduced on leaves from afp or chitinase II- but not from rip I-expressing wheat lines compared with non-transgenic controls. The increased resistance of afp and chitinase II lines was dependent on the dose of fungal spores used for inoculation. Heterologous expression of the fungal afp gene and the barley chitinase II gene in wheat demonstrated that colony formation and, thereby, spreading of two important biotrophic fungal diseases is inhibited approximately 40 to 50% at an inoculum density of 80 to 100 spores per cm2.
<title>High-Precision Multipass Reflectometer</title> (1981)

The multipass reflectometer has been shown to be a convenient and precise instrument for the measurement of spectral reflectances in excess of 0.99. This report gives a brief sketch of the initial setup of the reflectometer, its operation, optimization of para-meters, and some limitations to the expected precision. The instrumental precision is set by the uncertainty in the computer fit of a straight line to the measured data. Systematic errors due to nonuniform photosurfaces and the effects of astigmatism have been minimized. We have used this reflectrometer to measure the absolute reflectance of evaporated aluminum films in the uv and visible regions. It has also been used to measure the low-level insertion losses of laser window materials for this same spectral region.
Math exercise generation and smart assessment (2013)

In this paper we concentrate on the field of mathematics education where the aim is to generate exercises going beyond those with answers of simple types (e.g.multiple-choice, Boolean, integer, or file comparison). We present three examples from introductory college mathematics and emphasize the key points that should be taken into account in order to develop a “well-posed” exercise together with its verification. All the presented examples were implemented in the system PASSAROLA.
Synthesis of nanowires via helium and neon focused ion beam induced deposition with the gas field ion microscope (2013)

The ion beam induced nanoscale synthesis of platinum nanowires using the trimethyl (methylcyclopentadienyl)platinum(IV) (MeCpPt(IV)Me3) precursor is investigated using helium and neon ion beams in the gas field ion microscope. The He(+) beam induced deposition resembles material deposited by electron beam induced deposition with very small platinum nanocrystallites suspended in a carbonaceous matrix. The He(+) deposited material composition was estimated to be 16% Pt in a matrix of amorphous carbon with a large room-temperature resistivity (∼3.5 × 10(4)-2.2 × 10(5) μΩ cm) and temperature-dependent transport behavior consistent with a granular material in the weak intergrain tunnel coupling regime. The Ne(+) deposited material has comparable composition (17%), however a much lower room-temperature resistivity (∼600-3.0 × 10(3) μΩ cm) and temperature-dependent electrical behavior representative of strong intergrain coupling. The Ne(+) deposited nanostructure has larger platinum nanoparticles and is rationalized via Monte Carlo ion-solid simulations which show that the neon energy density deposited during growth is much larger due to the smaller ion range and is dominated by nuclear stopping relative to helium which has a larger range and is dominated by electronic stopping.
Advances in photonic quantum information science (2014)

This talk will review recent advances in pair photon sources, multiphoton interference and deterministic entanglement generation commenting on prospects for scalable quantum computation.
Hydrogen bonding in coal liquids and coal liquid distillates: Progress report for the period October 1986-December 1987 (1987)

The aqueous phase extractions have differed in two key ways from the direct trichloroacetic acid titrations described in our previous progress report. First, the titration curves for the aqueous extractions have shown an average of 4 or 5 differently sloped regions, with, as a general rule, poorly defined endpoints. In contrast, one or two endpoints were observed for the direct titrations with TCA. Secondly, the enthlapies associated with the different regions of the extraction experiment titration curves have allowed us to identify different classes of nitogen compounds extracted into the aqueous phase, as well as to identify the presence of phenols in the extracted phase; such has not been the case with the direct titrations/emdash/enthalpies associated with the TGA titrations have not corresponded to species known to exist in the coal liquid. The percent nitrogen extracted into the aqueous phase (which corresponds theoretically to the percent nitrogen in the undiluted coal liquid) can be calculated from the sum of the millimoles of titrant added for the various regions of the titration curve, although problems exist with the interpretation of the results. Results from the extraction experiments show the percent nitrogen of the coal liquid to fall in a range ofmore » 8.2% to 17% of PETC's reported nitrogen value of 0.39 /+-/ 0.02 for the HCl experiments and from 89% to 99% of PETC's reported nitrogen value for the first extraction in the NaOH experiments (additional nitrogen ranging from 50% to 69% of PETC's reported value can be obtained in the 2nd extraction with aqueous NaOH). 2 figs., 4 tabs.« less
ESC Working Group on Cellular Biology of the Heart: position paper for Cardiovascular Research: tissue engineering strategies combined with cell therapies for cardiac repair in ischaemic heart disease and heart failure (2019)

Morbidity and mortality from ischaemic heart disease (IHD) and heart failure (HF) remain significant in Europe and are increasing worldwide. Patients with IHD or HF might benefit from novel therapeutic strategies, such as cell-based therapies. We recently discussed the therapeutic potential of cell-based therapies and provided recommendations on how to improve the therapeutic translation of these novel strategies for effective cardiac regeneration and repair. Despite major advances in optimizing these strategies with respect to cell source and delivery method, the clinical outcome of cell-based therapy remains unsatisfactory. Major obstacles are the low engraftment and survival rate of transplanted cells in the harmful microenvironment of the host tissue, and the paucity or even lack of endogenous cells with repair capacity. Therefore, new ways of delivering cells and their derivatives are required in order to empower cell-based cardiac repair and regeneration in patients with IHD or HF. Strategies using tissue engineering (TE) combine cells with matrix materials to enhance cell retention or cell delivery in the transplanted area, and have recently received much attention for this purpose. Here, we summarize knowledge on novel approaches emerging from the TE scenario. In particular, we will discuss how combinations of cell/bio-materials (e.g. hydrogels, cell sheets, prefabricated matrices, microspheres, and injectable matrices) combinations might enhance cell retention or cell delivery in the transplantation areas, thereby increase the success rate of cell therapies for IHD and HF. We will not focus on the use of classical engineering approaches, employing fully synthetic materials, because of their unsatisfactory material properties which render them not clinically applicable. The overall aim of this Position Paper from the ESC Working Group Cellular Biology of the Heart is to provide recommendations on how to proceed in research with these novel TE strategies combined with cell-based therapies to boost cardiac repair in the clinical settings of IHD and HF.
Functional Limb Salvage in the Diabetic Patient: The Use of a Collagen Bilayer Matrix and Risk Factors for Amputation (2010)

Use of a collagen bilayer matrix appears to be a viable option for reconstruction and stable closure in the diabetic patient at low risk for amputation, with risk based on available blood supply and evidence of infection. In the diabetic patient at high risk for amputation, however, the rate of salvage may not be improved with the use of Integra.
Biometric binary string generation with detection rate optimized bit allocation (2008)

Extracting binary strings from real-valued templates has been a fundamental issue in many biometric template protection systems. In this paper, we present an optimal bit allocation method (OBA). By means of it, a binary string at a pre-defined length with maximized overall detection rate is generated. Experiments with the binary strings and a Hamming distance classifier on FRGC and FERET databases show promising performance in terms of FAR and FRR.
Anti-CD3 antibody MacroGenics Inc. (2006)

A non-FcR-binding anti-CD3 monoclonal antibody, hOKT3gamma1 (Ala-Ala), originally developed by Columbia University, is being developed by MacroGenics for the potential treatment of type 1 diabetes and autoimmune diseases. Phase I/II trials in patients with diabetes have been completed, and a phase II clinical trial in psoriatic arthritis was initiated in October 2005. A Phase II trial that will evaluate a multi-course study of the drug in patients with new-onset diabetes began in March 2006. MacroGenics is currently seeking to outlicense the project to a strategic partner.
Multi-photon activation of fluorescent proteins using visible wavelength for high-resolution imaging (2022)

We experimentally demonstrated the photo-activation of reversibly photo-switchable fluorescent proteins by visible-wavelength two-photon excitation and applied the activation technique in confocal imaging of biological cells. Higher spatial resolution than conventional confocal microscopy was confirmed.
Human Subinsular Asymmetry Studied by Diffusion Tensor Imaging and Fiber Tracking (2007)

Because the left hemisphere hosts language functions in most right-handers, the significant leftward asymmetry observed within the arcuate fasciculus, the subinsular part of the UF and IOF may be related to the hemispheric specialization for language.
Data Supplement from Sun Exposure and Melanoma Survival: A GEM Study (2023)

&lt;p&gt;Supplementary Table S2. Early life sun exposure and its association with melanoma survival, adjusting for Breslow thickness.&lt;/p&gt;