gebhart/patrepeval huggingface dataset:
Fluorescence Quenching of (Dimethylamino)naphthalene Dyes Badan and Prodan by Tryptophan in Cytochromes P450 and Micelles (2014)

Fluorescence of 2-(N,N-dimethylamino)-6-propionylnaphthalene dyes Badan and Prodan is quenched by tryptophan in Brij 58 micelles as well as in two cytochrome P450 proteins (CYP102, CYP119) with Badan covalently attached to a cysteine residue. Formation of nonemissive complexes between a dye molecule and tryptophan accounts for about 76% of the fluorescence intensity quenching in micelles, the rest is due to diffusive encounters. In the absence of tryptophan, fluorescence of Badan-labeled cytochromes decays with triexponential kinetics characterized by lifetimes of about 100 ps, 700–800 ps, and 3 ns. Site mutation of a histidine residue in the vicinity of the Badan label by tryptophan results in shortening of all three decay lifetimes. The relative amplitude of the fastest component increases at the expense of the two slower ones. The average quenching rate constants are 4.5 × 10⁸ s–¹ (CYP102) and 3.7 × 10⁸ s–¹ (CYP119), at 288 K. Cyclic voltammetry of Prodan in MeCN shows a reversible reduction peak at −1.85 V vs NHE that becomes chemically irreversible and shifts positively upon addition of water. A quasireversible reduction at −0.88 V was observed in an aqueous buffer (pH 7.3). The excited-state reduction potential of Prodan (and Badan) is estimated to vary from about +0.6 V (vs NHE) in polar aprotic media (MeCN) to approximately +1.6 V in water. Tryptophan quenching of Badan/Prodan fluorescence in CYPs and Brij 58 micelles is exergonic by ≤0.5 V and involves tryptophan oxidation by excited Badan/Prodan, coupled with a fast reaction between the reduced dye and water. Photoreduction is a new quenching mechanism for 2-(N,N-dimethylamino)-6-propionylnaphthalene dyes that are often used as solvatochromic polarity probes, FRET donors and acceptors, as well as reporters of solvation dynamics.
ChemInform Abstract: Ethers from Esters; from Exceptional Transformation to Synthetic Method (2015)

Abstract Review: 90 refs.
Extended methods of molecular dynamic simulations under hydrostatic pressure and/or isostress (2003)

By introducing new cell dynamics to the Parrinello–Rahman method, we propose extended methods for molecular dynamics simulations under hydrostatic pressure and/or isostress. The new method leads straightforwardly to the virial theorem. The obtained equations of motions are invariant under transformations between spatially periodic simulation cells. Molecular dynamics simulations of the crystalline phases of spheres and elongated molecules are conducted.
Abstract 14963: Prevention of Neointimal Hyperplasia After Angioplasty Using NF-kappaB Decoy Oligodeoxynucleotides-Coated Balloon Catheter in Rabbit Restenosis Model (2011)

Restenosis after endovascular intervention is a major limitation of this minimally invasive technique and hampers the procedure's efficacy for treating cardiovascular disease. To overcome this prob...
CAR T Cells Redirected to CD44v6 Control Tumor Growth in Lung and Ovary Adenocarcinoma Bearing Mice (2020)

The main challenge of adoptive therapy with Chimeric Antigen Receptor modified T cells (CAR T) is the application to the field of solid tumors, where the identification of a proper antigen has emerged as one of the major drawbacks to CAR T cell treatment success. CD44 is a glycoprotein involved in cell-cell and cell-matrix interactions. The isoform containing the variant domain 6 of CD44 gene (CD44v6) has been implicated in tumorigenesis, tumor cell invasion and metastasis and represents an attractive target for CAR T cell therapies. Targeting CD44v6 antigen has been shown to control tumor growth in acute myeloid leukemia and multiple myeloma mouse models. While CAR T approach for the treatment of B cell malignancies has shown great success, response rates among patients with solid cancer are less favorable. The purpose of our study was to test the efficacy of CD44v6.CAR T cells, produced in compliance with Good Manufacturing Practice (GMP), in adenocarcinoma tumor models. We generated a bicistronic retroviral vector containing the CD44v6 CAR and the HSV-TK Mut2 suicide gene to enhance the safety of the proposed CAR T cell therapy. CD44v6 transduced CAR T cells were homogeneously positive for ΔLNGFR selection marker, were enriched in T central memory (T<sub>CM</sub>) and T memory stem cells (T<sub>SCM</sub>) and displayed a highly activated phenotype. <i>In vitro</i> assays revealed antigen-specific activation and cytotoxicity of human CD44v6.CAR T cells against CD44v6 expressing tumor cell lines. When infused in immunodeficient tumor bearing mice, human CD44v6.CAR T cells were able to reach, infiltrate and proliferate at tumor sites, finally resulting in tumor growth control. Next, we checked if cells produced in compliance with GMP grade standards retained the same antitumor activity of those produced with research grade materials and protocols. Noteworthy, no differences in the potency of the CAR T obtained with the two manufacturing processes were observed. In conclusion, our preclinical results suggest that CD44v6.CAR T based adoptive therapy could be a promising strategy in solid cancer treatment.
Designing Energy-Efficient Convolutional Neural Networks using Energy-Aware Pruning (2016)

Deep convolutional neural networks (CNNs) are indispensable to state-of-the-art computer vision algorithms. However, they are still rarely deployed on battery-powered mobile devices, such as smartphones and wearable gadgets, where vision algorithms can enable many revolutionary real-world applications. The key limiting factor is the high energy consumption of CNN processing due to its high computational complexity. While there are many previous efforts that try to reduce the CNN model size or amount of computation, we find that they do not necessarily result in lower energy consumption, and therefore do not serve as a good metric for energy cost estimation. 
To close the gap between CNN design and energy consumption optimization, we propose an energy-aware pruning algorithm for CNNs that directly uses energy consumption estimation of a CNN to guide the pruning process. The energy estimation methodology uses parameters extrapolated from actual hardware measurements that target realistic battery-powered system setups. The proposed layer-by-layer pruning algorithm also prunes more aggressively than previously proposed pruning methods by minimizing the error in output feature maps instead of filter weights. For each layer, the weights are first pruned and then locally fine-tuned with a closed-form least-square solution to quickly restore the accuracy. After all layers are pruned, the entire network is further globally fine-tuned using back-propagation. With the proposed pruning method, the energy consumption of AlexNet and GoogLeNet are reduced by 3.7x and 1.6x, respectively, with less than 1% top-5 accuracy loss. Finally, we show that pruning the AlexNet with a reduced number of target classes can greatly decrease the number of weights but the energy reduction is limited. 
Energy modeling tool and energy-aware pruned models available at this http URL
Distinct Inflammatory Mediator Patterns Characterize Infectious and Sterile Systemic Inflammation in Febrile Neutropenic Hematology Patients (2014)

It is possible to separate patients with infectious inflammation from those with sterile inflammation based on inflammatory mediator patterns. This strategy could be developed into a decision-making tool for diverse clinical applications.
Macrocycloadditions Leading to Conformationally Restricted Small Molecules (2009)

The Cu(I)-catalyzed cycloaddition of alkynes and azides (click reaction) provides a robust method for the construction of macrocyclic small\nmolecules via an intramolecular macrocycloaddition. A three-subunit system has been used to explore the tolerance of this macrocycloaddition\nto variations of stereochemistries and substituents.
Hybrid optical processor for pattern recognition and classification using a generalized set of pattern functions (1982)

A pattern recognition and classification system has been studied which computes the inner products of an input pattern with a generalized set of pattern functions. The system utilizes a filter whose impulse response consists of an amplitude superposition of a set of generalized pattern functions in phase-coded form and has a space-bandwidth product the same as that of a matched filter for one pattern function. Each pattern function in the general set may correspond to a different variation (e.g., scale or rotation) of the object to be detected. Because the amplitude superposition of the phase-coded pattern functions takes place in the digital computer, and the filter is created as a computer-generated hologram, the biasing problem of conventional, multiple exposure (intensity superposition) holograms is significantly reduced. This makes it possible to encode many more pattern functions than was previously possible using multiple exposure techniques. Furthermore, the use of computer-generated holograms eliminates the need to generate a transparency for each pattern function and complex phase code. To facilitate real-time operation a hybrid system was constructed consisting of a liquid crystal light valve for incoherent-to-coherent image conversion, a TV camera and image digitizer for image analysis, and a laser scanner to produce the computer-generated holograms. Both the TV camera/digitizer and the laser scanner systems were interfaced to a digital computer for automatic operation. Experimental results using the hybrid system are presented for pattern recognition of rotated and scaled objects and pattern classification. In the second half of the paper we provide an analysis on the SNR of the processor employing the coded-phase technique, on the diffraction efficiencies of computer-generated filters (amplitude superposition) vs conventional filters (intensity superposition), and on the number of pattern functions required for a certain recognition task.
Experimental investigation of steam pressure coffee extraction in a stove-top coffee maker (2008)

The most common household coffee-brewing method in Italy makes use of a stove-top coffee maker known as moka. This device uses the steam pressure, produced by the water contained in an autoclave-type aluminum kettle heated by an external source, to force upwards water itself through a roasted and ground coffee bed contained in a funnel-shaped filter. Despite its well-established usage, the moka has never been the subject of detailed analysis, which led to a series of unclear descriptions or misinterpretations concerning its functioning, such as the consolidated misbelieve that standard atmosphere boiling point temperature is needed to drive the water out. The detailed measurement of the thermodynamics of the moka, described here, sheds light on its actual behaviour. It is shown that extraction commences at pretty low temperatures and depends on the initial amount of dry air in the kettle.\nRemarks on the time decreasing value of the coffee bed permeability are also drawn. A correct understanding of the extraction phenomenon, together with considerations on the coffee chemistry, serves the purpose of assessing possible ways to improve the quality of moka product.
Supplementary Figure Legends from Folate Receptor Beta Designates Immunosuppressive Tumor-Associated Myeloid Cells That Can Be Reprogrammed with Folate-Targeted Drugs (2023)

&lt;p&gt;Figure legends for supplemental figures&lt;/p&gt;
Lowering of tumoral interstitial fluid pressure by prostaglandin E1 is paralleled by an increased uptake of51Cr-EDTA (2000)

High intra-tumoral fluid pressure (TPIF) may impair uptake of anticancer drugs into tumors, contributing to poor efficiency in treatment of carcinomas. Here, we demonstrate that lowering of TPIF parallels increased transport of 51Cr-EDTA (m.w. 341) into tumor interstitium. Introduction of 15 μg prostaglandin E1 (PGE1) -methyl ester into the s.c. tissue surrounding transplanted rat colonic (PROb) carcinomas or chemically-induced rat mammary carcinomas, lowered TPIF by 30%. Transcapillary transport into the interstitium of PROb tumors quantified by microdialysis increased by 39.6% after PGE1 treatment 40 min prior to administration of 51Cr-EDTA (n=6; p<0.05) compared to vehicle (n=10). In mammary tumors, PGE1 increased transport into the tumors by 86.9% over controls (n=16; p<0.05). Both tumors had well developed stroma containing collagen and hyaluronan. Our data demonstrate that adjuvant treatment with PGE1 lowers TPIF, and enhances transport into the tumors. This principle may be of value as adjuvant therapy in treatment of solid malignancies with currently used anticancer drugs. Int. J. Cancer 86:636–643, 2000. © 2000 Wiley-Liss, Inc.
A Retransmission Scheme for Circuit-Mode Data on Wireless Links (2005)

The cellular radio link is characterized by deep fades leading to long error bursts (lasting hundreds of msec). Data transmission over such links results in large packet error rates (in the range 10/sup -3/ to 10/sup -1/). The authors have designed a radio link protocol (RLP) to achieve high throughput on such links. The RLP is based on frequent, complete or partial feedback of the receiver state. Performance results for the US digital cellular TDMA standard show that the scheme can provide the equivalent of 9.6 kbps service per full-rate TDMA channel above a carrier to interference ratio of 18 dB. >
C. elegans LRP-2 functions in vulval precursor cell polarity (2019)

The C. elegans vulva is formed from divisions of three vulval precursor cells (VPCs) &#8211; P5.p, P6.p, and P7.p – arranged along the anteroposterior axis in the ventral epithelium (Sulston and Horvitz, 1977). Previous analyses show the orientation of P5.p and P7.p descendants is determined by the interaction of multiple Wnt signals. Specifically, in the absence of all Wnts, the VPCs display a randomized orientation, which is likely the default (Green et al., 2008; Minor et al. 2013). Two separate Wnts from the anchor cell, LIN-44 and MOM-2 acting through receptors LIN-17/Frizzled and LIN-18/Ryk, respectively, regulate P7.p orientation (Ferguson et al., 1987; Sternberg and Horvitz, 1988; Sawa et al., 1996; Inoue et al., 2004; Gleason et al., 2006). In the absence of these signals the orientation of the progeny of P7.p mimic those of P5.p and face toward the posterior of the worm, a phenotype referred to as posterior-reversed vulval lineage (P-Rvl). This posterior orientation is dependent on the instructive signal EGL-20, a Wnt expressed in the tail acting through CAM-1/ROR and VANG-1/Van Gogh, and is referred to as “ground polarity” (Green et al., 2008). Here we examine the role of a low-density lipoprotein receptor, lrp-2, and its role in controlling the orientation of P7.p daughter cells. To investigate this interaction double mutants were constructed with both alleles of lrp-2 and lin-17(n671) (Table 1). Much like cam-1(gm122) and vang-1(ok1142), both alleles of lrp-2 suppress the lin-17(n671) phenotype from 74 to approximately 50% P-Rvl leading us to hypothesize that lrp-2 functions in the same pathway as cam-1 and vang-1. Furthering this hypothesis we have shown that, like cam-1 and vang-1, lrp-2 controls the localization of SYS-1/b-catenin (Minor and Sternberg, 2019). To ensure that this phenotype was a result of loss of lrp-2 function as opposed to background effects we injected a fosmid (WRM0617cA02) containing the full-length sequence of lrp-2 and found that it does rescue the double mutant phenotype of lin-17(n671); lrp-2(gk272) from 55 to 73%. In order to better test this hypothesis a triple mutant was constructed between lin-17(n671), lrp-2(gk272), and cam-1(gm122) (Table 1). This triple mutant displays the same P-Rvl penetrance as both the lin-17(n671); lrp-2(gk272) and lin-17(n671); cam-1(gm122) double mutants confirming that lrp-2 functions in the same pathway as cam-1.
How sensitive are cluster compositions to energetics? A joint beam expansion/thermochemical study of water-methanol-trimethylamine clusters (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHow sensitive are cluster compositions to energetics? A joint beam expansion/thermochemical study of water-methanol-trimethylamine clustersM. Samy El-Shall, George M. Daly, Junling Gao, Michael Meot-Ner, and L. Wayne SieckCite this: J. Phys. Chem. 1992, 96, 2, 507–510Publication Date (Print):January 1, 1992Publication History Published online1 May 2002Published inissue 1 January 1992https://pubs.acs.org/doi/10.1021/j100181a002https://doi.org/10.1021/j100181a002research-articleACS PublicationsRequest reuse permissionsArticle Views76Altmetric-Citations17LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Scanning force microscopy using a simple low-noise interferometer (1989)

A force microscope is described that can be used for high-resolution surface profiling and for observing magnetic domains. The microscope uses a Michelson interferometer to sense the vibration of a cantilever. The interferometer contains some straightforward processing to eliminate laser intensity noise. Some measuring results are presented that illustrate the performance of the microscope.
Assigning probes into a small number of pools separable by electrophoresis (2002)

We show how to computationally find the probes and assign them into pools for a whole genome such that (i) each gene has a specific probe suitable for amplification and hybridization, and (ii) the expression level measurement can be done in a minimal number of pools separable by electrophoresis in order to minimize the total experiment cost of the measurement. Our main result is a polynomial-time approximation algorithm for assigning the probes into pools. We demonstrate the feasibility of the procedure by selecting probes for the yeast genome and assigning them into less than 100 pools. The probe sequences and their assignment into pools are available for academic research on request from the authors.
Measurement of the top quark pair production cross section in pp collisions at $\sqrt{s}=7$ TeV in the ${\ell}+\tau$ channel and of the top quark branching ratios into channels with leptons and quarks with the ATLAS detector (2012)

A measurement of the inclusive cross section for top quark pair production in pp collisions using events with an isolated lepton (muon or electron) and a $\\tau$ lepton decaying to hadrons ($\\tau_{\\mathrm{had}}$) is reported. Measurements of the branching ratios of top quark decays into leptons and jets using events with $t \\overline{t}$ (top antitop) pairs are also reported. Events were recorded with the ATLAS detector at the LHC in pp collisions at a center-of-mass energy of 7 TeV. The collected data sample corresponds to an integrated luminosity of 4.6 ${\\mathrm{fb}}^{-1}$. The inclusive cross section measured using events with an isolated lepton and a $\\tau_{\\mathrm{had}}$ is $\\sigma_{t\\bar{t}} = 183\\pm 9 (stat.) \\pm 23 (syst.) \\pm 3 (lumi.) \\mathrm{pb.}$ The measured top quark branching ratios agree with the Standard Model predictions within the measurement uncertainties of a few percent.
Light to moderate coffee consumption is associated with lower risk of death: a UK Biobank study (2022)

Coffee consumption of up to three cups per day was associated with favourable CV outcomes. Regular coffee consumption was also associated with a likely healthy pattern of CMR metrics in keeping with the reverse of age-related cardiac alterations.
3D bioprinting and its potential impact on cardiac failure treatment: An industry perspective (2020)

3D printing technologies are emerging as a disruptive innovation for the treatment of patients in cardiac failure. The ability to create custom devices, at the point of care, will affect both the diagnosis and treatment of cardiac diseases. The introduction of bioinks containing cells and biomaterials and the development of new computer assisted design and computer assisted manufacturing systems have ushered in a new technology known as 3D bioprinting. Small scale 3D bioprinting has successfully created cardiac tissue microphysiological systems. 3D bioprinting provides an opportunity to evaluate the assembly of specific parts of the heart and most notably heart valves. With the continuous development of instrumentation and bioinks and a complete understanding of cardiac tissue development, it is proposed that 3D bioprinting may permit the assembly of a heart described as a total biofabricated heart.
Silicon nano-membranes for efficient large angle optical beam steering (2009)

In this paper, we present a silicon nano-membrane-based phased array structure for large angle optical beam steering. The new array structure allows for over ±60° optical beam scanning with minimal degradation in the side-lobe-level and diffraction efficiency.
Addressing the implementation gap in advanced therapeutics for spinal muscular atrophy in the era of newborn screening programs (2022)

Spinal muscular atrophy (SMA) is a rare genetic disease that results in progressive neuromuscular weakness. Without therapy, the most common form of the disease, type 1, typically results in death or chronic respiratory failure in the first 2 years of life. Thanks to the recent introduction of newborn screening programs and the discovery of three disease-modifying therapies in the last decade, the outcomes of children with SMA have dramatically improved. Patients are able to achieve many, if not all, of the typical neuromotor milestones, such as sitting, standing and walking, as well as safe oral intake. As the natural history of treated patients is continuously evolving, children with SMA continue to require complex and multidisciplinary care, posing implementation and sustainability challenges. Accordingly, there is a significant need for the application and evaluation of implementation science to address the steps involved in the diagnosis and treatment of patients with SMA, ensuring that all pertinent stakeholders and systems are working effectively to deliver timely and appropriate care. In this manuscript, we discuss the current challenges and gaps in the care for children with SMA, as well as how implementation science can advance this field. In addition, we provide an adapted implementation science framework that includes the main domains and subdomains involved in the care of patients with SMA.