gebhart/patrepeval huggingface dataset:
Highly Conjugated, Fused-Ring, Quadrupolar Organic Chromophores with Large Two-Photon Absorption Cross-Sections in the Near-Infrared (2020)

The two-photon absorption (2PA) properties are investigated for two series of organic, π-conjugated, fused-ring, quadrupolar A-π-D-π-A chromophores of the type originally developed as nonfullerene acceptors for organic photovoltaics. These molecules are found to exhibit large nondegenerate two-photon absorption (ND2PA) cross-sections (ca. 6-27 × 10<sup>3</sup> GM) in the near-infrared (NIR). In the first series, involving molecules of varying core size, ND2PA spectra and cross-sections characterized by femtosecond ND2PA spectroscopy in chloroform solutions reveal that increases in core size, and thus conjugation length, leads to substantially red-shifted and enhanced 2PA. In a second series, variation of the strength of the terminal acceptor (A) with constant core size (seven rings, indacene-based) led to less dramatic variation in the 2PA properties. Among the two core types studied, compounds in which the donor has a thieno[3,2-<i>b</i>]thiophene center demonstrate larger 2PA cross-sections than their indacene-centered counterparts, due to the greater electron-richness of their cores amplifying intramolecular charge transfer. Excited-state absorption (ESA) contributions to nonlinear absorption measured by open-aperture Z-scans are deduced for some of the compounds by analyzing the spectral overlap between 2PA bands and NIR ESA transitions obtained by ND2PA and transient absorption measurements, respectively. ESA cross-sections extracted from transient absorption and irradiance-dependent open-aperture Z-scans are in reasonable agreement, and their moderate magnitudes (ca. 10<sup>-21</sup> m<sup>2</sup>) suggest that, although ESA contributions are non-negligible, the effective response is predominantly instantaneous 2PA.
Face Recognition with Renewable and Privacy Preserving Binary Templates (2006)

This paper considers generating binary feature vectors from biometric face data such that their privacy can be protected using recently introduced helper data systems. We explain how the binary feature vectors can be derived and investigate their statistical properties. Experimental results for a subset of the FERET and Caltech databases show that there is only a slight degradation in classification results when using the binary rather than the real-valued feature vectors. Finally, the scheme to extract the binary vectors is combined with a helper data scheme leading to renewable and privacy preserving facial templates with acceptable classification results provided that the within-class variation is not too large.
DNA cytosine methylation in brain of patients with Alzheimer's disease (1990)

We developed a novel quantitative assay to test the hypothesis that defects in DNA cytosine methylation might be responsible for the brain chromatin abnormalities and transcriptional alterations observed in patients with Alzheimer's disease (AD). We found no significant difference in percent methylation of CCGG sites from brain DNA of 44 patients with AD compared with 20 normal subjects. These results, however, would not exclude genomic redistribution of methylcytosine in AD, or disturbed methylation of a limited population of critical brain-specific genes.
Automatic segmentation and classification of cardiac cycles using deep learning and a wireless electronic stethoscope (2017)

We present an automatic heart-sound segmentation and classification system using state-of-the-art deep learning techniques and deep neural networks. This system is implemented for use with a wireless electronic stethoscope, known as Stethee <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">®</sup> . The proposed system automatically identifies the endpoints of temporal events associated with specific cardiac cycles, from audio recordings of heart-sounds captured by Stethee <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">®</sup> . The detected events are automatically classified as either a first heart sound (S1), a second heart sound (S2), systole, diastole or unwanted noise. We demonstrate that our proposed system is able to consistently achieve an accuracy of over 95%, across multiple permutations of training and test data. Finally, we carry out clinical trials against an echocardiogram device operated by a trained technician. We show that our proposed system is as accurate as Doppler echocardiography by a technician, in identifying the full cardiac cycle, systole and diastole durations for every analysed patient.
Table S3 from Aurora A Kinase Inhibition Is Synthetic Lethal with Loss of the <i>RB1</i> Tumor Suppressor Gene (2023)

&lt;p&gt;shRNA suppressor screening data for H446 and MDA-MB-468 cells (tabs 1, 2) and RNA expression level associations with LY3295668 Abs IC50 values from 493 cancer cell lines (tab 3).&lt;/p&gt;
Multipoint model order reduction for systems with delays (2015)

An adaptive frequency sampling algorithm is proposed in this paper to automate the generation of reduced order models for systems with delays which can be represented as frequency dependent state-space matrices. Reflective exploration technique is used to obtain an optimum number of frequency samples for which the reduced state-space matrices per frequency is computed using a common projection matrix and is then interpolated to obtain the frequency response. The algorithm is illustrated using a numerical example.
Crossover Digital Predistorter for the Compensation of Crosstalk and Nonlinearity in MIMO Transmitters (2009)

This paper proposes a novel crossover digital predistorter (CO-DPD) model to compensate for crosstalk and nonlinearity in multiple-input multiple-output (MIMO) radio systems. Crosstalk can take place before or after the power amplifiers, designated herein as nonlinear and linear crosstalk, respectively. This paper demonstrates that, contrary to linear crosstalk, nonlinear crosstalk significantly affects the performance of the digital predistortion algorithm; and, it cannot be embedded and compensated for by the conventional channel matrix inversion algorithm at the receiver side of MIMO links. Based on a parametric study of system-level simulations and measurements, it was found that for a -20-dB nonlinear crosstalk level, the use of a memory multibranch polynomial predistorter, along with the channel matrix inversion algorithm, bounds the adjacent channel power ratio (ACPR) for a wideband code division multiple access (WCDMA) signal to -46 dBc and the error vector magnitude (EVM) for a world interoperability for microwave access (WiMAX) signal to -43 dB in MIMO links. The proposed CO-DPD was investigated and analyzed for the MIMO transmitter with <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</i> = 2, where <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</i> is the number of RF front-ends. Its performance was evaluated through measurements, the experimental results obtained show that, in the presence of -20-dB nonlinear crosstalk, the proposed CO-DPD improve the ACPR of the WCDMA signal by 13 dB to -56.81 dBc from those obtained using a conventional digital predistorter. The same improvement was observed in the EVM measurement of the WiMAX signal, where the EVM decreases from -21.22 dB for the conventional DPD to -49.71 dB for the proposed CO-DPD.
rRNA-based profiling of bacteria in the axilla of healthy males suggests right-left asymmetry in bacterial activity (2011)

The activity of the human armpit microbiota triggers the formation of body odor. We used differential 16S rRNA gene (rDNA)- and rRNA-based terminal-restriction fragment length polymorphism fingerprinting in combination with cloning and sequencing to identify active members of the human armpit microbiota. DNA and RNA were isolated from skin scrub samples taken from both armpits of 10 preconditioned, healthy males. The fingerprint profiles indicated pronounced similarities between the armpit microbiota in the right and the left axillae of an individual test person, but larger differences between the axilla microbiota of different individuals. Using 16S rDNA and rRNA sequence data, the majority of peaks in the armpit profiles were assigned to bacteria affiliated with well-known genera of skin bacteria. The relative abundances of all groups were similar among the rDNA and rRNA samples, suggesting that all groups of armpit bacteria were active. Surprisingly, the relative abundance of sequences affiliated with Peptoniphilus sp. was by far and with statistical significance the highest in the rRNA samples of the right armpits. Thus, bacteria affiliated with Peptoniphilus sp. might have been particularly active in the right axillae of the test persons, possibly owing to the handedness of the test persons, which might cause different environmental conditions in the right axillae.
Structure-Based Design of an Indolicidin Peptide Analogue with Increased Protease Stability, (2003)

Indolicidin is an antimicrobial cationic peptide with broad-spectrum activity isolated from bovine neutrophils. An indolicidin analogue CP-11, ILKKWPWWPWRRK-NH(2), with improved activity against Gram-negative bacteria had increased positive charge and amphipathicity while maintaining the short length of the parent molecule. The structure of CP-11 in the presence of dodecylphosphocholine (DPC) micelles was determined using nuclear magnetic resonance spectroscopy. CP-11 was found to be an amphipathic molecule with a U-shaped backbone bringing the N- and C-termini in close proximity. On the basis of this close proximity, a cyclic disulfide-bonded peptide cycloCP-11, ICLKKWPWWPWRRCK-NH(2), was designed to stabilize the lipid-bound structure and to increase protease resistance. The three-dimensional structure of cycloCP-11 was determined under the same conditions as for the linear peptide and was found to be similar to CP-11. Both CP-11 and cycloCP-11 associated with phospholipid membranes in a similar manner as indicated by circular dichroism and fluorescence spectra. The minimal inhibitory concentrations of CP-11 and cycloCP-11 for a range of bacteria differed by no more than 2-fold, and they were nonhemolytic at concentrations up to 256 microg/mL. Cyclization was found to greatly increase protease stability. The half-life of cycloCP-11 in the presence of trypsin was increased by 4.5-fold from 4 to 18 min. More importantly, the antibacterial activity of cycloCP-11, but not that of CP-11, in the presence of trypsin was completely retained up to 90 min since the major degradation product was equally active. A structural comparison of CP-11 and cycloCP-11 revealed that the higher trypsin resistance of cycloCP-11 may be due to the more compact packing of lysine and tryptophan side chains. These findings suggest that cyclization may serve as an important strategy in the rational design of antimicrobial peptides.
Optical incoherent imaging using annular synthetic aperture with the superposition of phase-shifted optical transfer functions (2022)

The optical incoherent synthetic aperture (SA) has wide applications in astronomy and biomedical optics. Super-resolution imaging can be achieved through SAs with an effective size several times larger than the size of the physical apertures. In this Letter, we propose a new, to the best of our knowledge, method to realize optical incoherent SA imaging. Instead of scanning the entire area of the full SA, we show that similar imaging performance can be achieved by scanning only along its perimeter. At any given time, only a single pair of sub-apertures located at the SA perimeter is open and reflects the incident light toward an image sensor. For each location of the two sub-apertures, two interfering images are captured. The phase difference between the two sub-apertures is zero for one interfering image and π for the other. The image of the object is reconstructed by superposition of all the interfering images from some of the sub-aperture locations and with the two-phase differences, 0 and π , between the two sub-apertures. Optical experiments have been performed using reflective objects, and the results demonstrate similar imaging capabilities as that of direct imaging with the aperture size of the SA. Furthermore, we have compared the proposed SA imaging results with the results of annular and full aperture direct imaging.
[Polypeptide vessel complex and its role in physiology function regulation in aging pathology.] (2019)

In review it is shown data about polypeptide vessel complex, extracted from calf vessel and named Slavinorm® (Vasolin). Slavinorm® had therapeutic effects in cardio-vascular age related pathology in animal models. Slavinorm® prevents atherosclerosis, normalizes lipid metabolism, lipid peroxidation parameters, station of congenital and adaptive immunity, callicrein-kinins system, vessel and trombocitary hemostasis, blood coagulability, fibrinolysis, activates vessel wall reparation. Slavinorm® has positive effects in other age-related diseases (arthritis, pancreatitis, respiratory distress).
Abstract B52: Overcoming phenotypic heterogeneity and plasticity in basal-like breast cancer through targeting adaptive pathway use (2016)

Abstract The use of small-molecule kinase inhibitors is a promising therapeutic strategy for the management of breast cancer. Positive responses to these agents, however, are often transient, and acquired resistance arises in the course of weeks to months. Recent studies have demonstrated that phenotypic plasticity in cancer cell populations can provide adaptive resistance to small-molecule kinase inhibitors, whereby cancer cells transition to drug-tolerant phenotypic states, reliant on compensatory survival and proliferative signaling pathways. Drug combinations and sequences can prevent this adaptive resistance to targeted therapy, however, nominating effective drug pairs is challenging. In this study, we seek to identify such drug combinations through first identifying single agent therapeutics that reduce phenotypic heterogeneity and enrich distinct cell-states with common pathway reliance. To do so, we focus on phenotypic heterogeneity in tumor-cell lineage-state; using immunofluorescent staining against markers of the luminal, basal, and mesenchymal lineages, we combine high-throughput drug screening with high-content imaging and pursue small-molecule inhibitors that reduce phenotypic heterogeneity and promote the accumulation of particular lineage-states in residual cell populations. We observe pronounced lineage-state heterogeneity in Triple-Negative tumors and Basal-Like breast cancer cell lines, and find that the lineage-state distributions are greatly influenced by numerous therapeutics. MEK and PI3K/mTOR inhibitors in particular induce robust time- and dose-dependent alterations is lineage-state distribution in residual cell populations, selecting for a cell population enriched in, or depleted of a basal lineage-state, respectively. Through gene expression profiling and master-regulator analysis of active transcriptional states in the residual cell populations, we are able to identify compensatory-signaling pathways. We demonstrate that combining MEK and PI3K/mTOR inhibitors with agents targeting these compensatory pathways induces synergistic antiproliferative effects. Citation Format: Tyler Risom, Ellen Langer, Juha Rantala, Mariano Alvarez, Katie Johnson-Camacho, Carl Pelz, Nicholas Wang, Paul Spellman, Andrea Califano, Joe Gray, Rosalie Sears. Overcoming phenotypic heterogeneity and plasticity in basal-like breast cancer through targeting adaptive pathway use. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research; Oct 17-20, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(2_Suppl):Abstract nr B52.
Direct laser measurement of the Lamb shift of23S-23P transitions in helium (1989)

For the first time, Lamb shifts of the 2 $^{3}S_{1}$-2 $^{3}\mathrm{P}_{0}$,1,2 transitions in helium have been measured directly with an LNA laser. The absolute wavelengths have been measured to a precision of 1 part in ${10}^{8}$, or ${10}^{\mathrm{\ensuremath{-}}4}$ ${\mathrm{cm}}^{\mathrm{\ensuremath{-}}1}$. The Lamb shifts have been determined to 6 parts in ${10}^{4}$. Our results agree well with previous, indirect measurements, but represent a fivefold improvement in precision. The experimental results are compared with recent precision calculations. The obtained experimental Lamb shifts are 1 order of magnitude more precise than current theory.
Interactive visual machine learning in spreadsheets (2015)

BrainCel is an interactive visual system for performing general-purpose machine learning in spreadsheets, building on end-user programming and interactive machine learning. BrainCel features multiple coordinated views of the model being built, explaining its current confidence in predictions as well as its coverage of the input domain, thus helping the user to evolve the model and select training examples. Through a study investigating users' learning barriers while building models using BrainCel, we found that our approach successfully complements the Teach and Try system [1] to facilitate more complex modelling activities.
Barbituric Acid as a Substituent at Aryl Methylium Ions (2006)

Activation of different benzophenone derivatives with triflic anhydride for electrophilic aromatic substitution of 5-phenylbarbituric acids leads to regioselective formation of the ortho-substituted product. The resulting triphenylmethylium salt can be isolated when the Michlers ketone is used. More electrophilic cations form cyclic enol ethers such as 1-n-butyl-9,9-diaryl-1,9-dihydro-10-oxa-1,3-diazaphenanthrene-2,4-diones. Alternatively, supramolecular complex formation with 2,6-diacetamido pyridine as well as carbenium ion generation have been studied. Although in dilute acid only protonation of one of the carbonyl oxygens occurs, ring opening of the cyclic enol ether toward the carbenium ion is observed in 96% sulfuric acid.
Fabrication of Aluminum Tubes Filled with Aluminum Alloy Foam by Friction Welding (2015)

Aluminum foam is usually used as the core of composite materials by combining it with dense materials, such as in Al foam core sandwich panels and Al-foam-filled tubes, owing to its low tensile and bending strengths. In this study, all-Al foam-filled tubes consisting of ADC12 Al-Si-Cu die-cast aluminum alloy foam and a dense A1050 commercially pure Al tube with metal bonding were fabricated by friction welding. First, it was found that the ADC12 precursor was firmly bonded throughout the inner wall of the A1050 tube without a gap between the precursor and the tube by friction welding. No deformation of the tube or foaming of the precursor was observed during the friction welding. Next, it was shown that by heat treatment of an ADC12-precursor-bonded A1050 tube, gases generated by the decomposition of the blowing agent expand the softened ADC12 to produce the ADC12 foam interior of the dense A1050 tube. A holding time during the foaming process of approximately <i>t</i><sub>H</sub> = 8.5 min with a holding temperature of 948 K was found to be suitable for obtaining a sound ADC12-foam-filled A1050 tube with sufficient foaming, almost uniform pore structures over the entire specimen, and no deformation or reduction in the thickness of the tube.
Quantitative Analysis of Cellular Antigen and Determination of the Half‐Life of Hsp90‐peptide complexes in vivo (2008)

Heat shock proteins (HSPs) are ubiquitous, highly‐abundant components of cells, functioning as molecular chaperones for nascent or denatured proteins, as well as short protein fragments. HSPs can be biochemically purified in complexes with short polypeptides (8–20 AA) that include the precursors to MHC Class I‐binding octa/nonamers. Chaperones protect these peptides on their journey to MHC‐I for direct presentation, and HSP‐peptide complexes specifically activate the immune system through delivery of the antigenic peptides to antigen‐presenting cells (APC) for cross‐presentation. To study the cell biology of HSP‐peptide formation we developed a novel cell line, PIK23, which employs a modified version of ovalbumin (KOVAK) under the control of an inducible promoter system. Using this cell line we have identified MHC‐I binding peptide precursors associated with gp96 and Hsp90. In the present study we have quantified the peptides bound to biochemically‐purified Hsp90 and found: (1) Hsp90‐chaperoned KOVAK peptides are abundant even in cells synthesizing minute quantities of antigen, (2) these peptides increase in proportion to antigen synthesis, (3) these peptides represent a mixture of proteasomal products, and (4) the half‐life of Hsp90‐peptide association is ~12 hours. These findings shed new light into the mechanics of Hsp90's chaperone role in direct and cross presentation of antigen.
Selective Androgen Receptor Modulator RAD140 Inhibits the Growth of Androgen/Estrogen Receptor–Positive Breast Cancer Models with a Distinct Mechanism of Action (2017)

<b>Purpose:</b> Steroidal androgens suppress androgen receptor and estrogen receptor positive (AR/ER<sup>+</sup>) breast cancer cells and were used to treat breast cancer, eliciting favorable response. The current study evaluates the activity and efficacy of the oral selective AR modulator RAD140 in <i>in vivo</i> and <i>in vitro</i> models of AR/ER<sup>+</sup> breast cancer.<b>Experimental Design:</b> A series of <i>in vitro</i> assays were used to determine the affinity of RAD140 to 4 nuclear receptors and evaluate its tissue-selective AR activity. The efficacy and pharmacodynamics of RAD140 as monotherapy or in combination with palbociclib were evaluated in AR/ER<sup>+</sup> breast cancer xenograft models.<b>Results:</b> RAD140 bound AR with high affinity and specificity and activated AR in breast cancer but not prostate cancer cells. Oral administration of RAD140 substantially inhibited the growth of AR/ER<sup>+</sup> breast cancer patient-derived xenografts (PDX). Activation of AR and suppression of ER pathway, including the <i>ESR1</i> gene, were seen with RAD140 treatment. Coadministration of RAD140 and palbociclib showed improved efficacy in the AR/ER<sup>+</sup> PDX models. In line with efficacy, a subset of AR-repressed genes associated with DNA replication was suppressed with RAD140 treatment, an effect apparently enhanced by concurrent administration of palbociclib.<b>Conclusions:</b> RAD140 is a potent AR agonist in breast cancer cells with a distinct mechanism of action, including the AR-mediated repression of <i>ESR1</i> It inhibits the growth of multiple AR/ER<sup>+</sup> breast cancer PDX models as a single agent, and in combination with palbociclib. The preclinical data presented here support further clinical investigation of RAD140 in AR/ER<sup>+</sup> breast cancer patients. <i>Clin Cancer Res; 23(24); 7608-20. ©2017 AACR</i>.