gebhart/patrepeval huggingface dataset:
Factors affecting lung function in adult cystic fibrosis patients after lung transplantation. (2018)

<b>Objectives:</b> To evaluate the factors affecting the dynamics of lung function in adult cystic fibrosis (CF) patients one year after lung transplantation (LT). <b>Methods:</b> From March 2012 to February 2017, 21 CF patients (the mean age at surgery was 26±4 yrs, range 19-37) underwent bilateral LT. Lung function (before and after LT), demographic and clinical variables were analyzed. The surgical complications were categorized according to the Clavien-Dindo classification. <b>Results:</b> There was a significant improvement of postoperative lung function in all patients. The FEV1/FVC ratio was above normal, and airway resistance was below a threshold, that indicates the bronchial obstruction was absent. TLC was reduced to normal values, but VC was slightly reduced, and FRC, RV and RV/TLC ratio were increased. Improvement of postoperative pulmonary function was lower in CF patients with chronic infection of <i>Burkholderia cepacia complex</i> (<i>Bcc</i>) than in those without it (ΔFEV<sub>1</sub>: 42.6±15.5 %pred. <i>vs</i> 60.4±17.4 %pred., p=0.05). There were no significant correlations between the FEV<sub>1</sub> dynamics and the recipient sex, nutritional and functional status, genotype, the presence of hypercapnia, and chronic <i>Ps.aeruginosa</i> infection, but there was a significant correlation with the severity of surgical complications and amount of inpatient bed days within a year after LT (R=-0.51, p=0.020 and R=-0.59, p=0.006, respectively). <b>Conclusion:</b> Improvement of FEV<sub>1</sub> one year after LT was lower in CF patients with preoperative chronic <i>Bcc</i> infection and severe surgical complications, and at a longer length of stay in hospital during a year after LT.
Analysis of Sugar Beet Pulp by X-ray Photoelectron Spectroscopy (2004)

Determining the chemical structure and composition of biomass fuels using x-ray photoelectron spectroscopy (XPS) can provide fundamental knowledge of their structures that is useful in understanding and predicting their combustion behavior. Sugar beet pulp is an example of an agricultural residue (byproduct of food and feed production) of potential interest for biomass combustion. The XPS spectra of sugar beet pulp provide both its elemental composition and indications of its bonding. Traditional fuel analyses of this fuel are also provided. These include: ultimate analysis — the elemental composition of the overall fuel (C, H, N, S, and O); chlorine analysis — reported here as part of the ultimate analysis but formally a separate procedure; proximate analysis — the proximate composition of the fuel (moisture, fixed carbon, volatiles, and ash); heating value — the specific heat of combustion. These data are summarized with the XPS spectra.
Improving Invariance and Equivariance Properties of Convolutional Neural Networks (2017)

Convolutional Neural Networks (CNNs) learn highly discriminative representations from data, but how robust and structured are these representations? How does the data shape the internal network representation? We shed light on these questions by empirically measuring the invariance and equivariance properties of a large number of CNNs trained with various types of input transformations. We find that CNNs learn invariance wrt all 9 tested transformation types and that invariance extends to transformations outside the training range. We also measure the distance between CNN representations and show that similar input transformations lead to more similar internal representations. Transforms can be grouped by the way they affect the learned representation. Additionally, we also propose a loss function that aims to improve CNN equivariance.
Toward Improved Performance of All-Organic Nitroxide Radical Batteries with Ionic Liquids: A Theoretical Perspective (2019)

Nitroxide radicals have previously been successfully used as electrodes in all-organic radical batteries. However, one drawback of these batteries is significantly reduced redox potentials, in comparison to that of widely used lithium-ion batteries, making their energy-producing capacity rather small for use as a primary battery. In addition, strong propensity of nitroxide radicals to engage in side reactions with traditional electrolytes based on molecular solvents give rise to a series of undesirable and irreversible byproducts, thus significantly reducing the life of nitroxide batteries. Ionic liquids (ILs) have previously demonstrated their ability to reduce the reactivity of radicals through strong intermolecular interactions. In this study, we investigate the use of ILs as electrolytes with the view of increasing redox potentials of nitroxide radicals. A series of imidazolium, phosphonium, and pyrrolidinium-based ILs coupled with widely used anions were chosen to predict redox potentials of the 2,2,6,6-tetramethyl-1-piperidinyloxy nitroxide (TEMPO) radical using state-of-the-art quantum chemical calculations using one and two ion pairs to describe ILs. Some ILs showed a significant increase in the redox potential of this radical to reach as much as 5.5 eV, compared to the previously measured value of 2.2 eV in aqueous media. In particular, ILs were shown to stabilize the aminoxy anion, the reduced form of the nitroxide radical, which has not been achieved previously in traditional solvents. Although a simple model consisting of one and two ion pairs was used in the current study, these findings clearly demonstrate that ILs have a huge potential in improving redox potentials of nitroxide radicals.
A Chemotype That Inhibits Three Unrelated Pathogenic Targets: The Botulinum Neurotoxin Serotype A Light Chain, P. falciparum Malaria, and the Ebola Filovirus (2011)

A 1,7-bis(alkylamino)diazachrysene-based small molecule was previously identified as an inhibitor of the botulinum neurotoxin serotype A light chain metalloprotease. Subsequently, a variety of derivatives of this chemotype were synthesized to develop structure-activity relationships, and all are inhibitors of the BoNT/A LC. Three-dimensional analyses indicated that half of the originally discovered 1,7-DAAC structure superimposed well with 4-amino-7-chloroquinoline-based antimalarial agents. This observation led to the discovery that several of the 1,7-DAAC derivatives are potent in vitro inhibitors of Plasmodium falciparum and, in general, are more efficacious against CQ-resistant strains than against CQ-susceptible strains. In addition, by inhibiting β-hematin formation, the most efficacious 1,7-DAAC-based antimalarials employ a mechanism of action analogous to that of 4,7-ACQ-based antimalarials and are well tolerated by normal cells. One candidate was also effective when administered orally in a rodent-based malaria model. Finally, the 1,7-DAAC-based derivatives were examined for Ebola filovirus inhibition in an assay employing Vero76 cells, and three provided promising antiviral activities and acceptably low toxicities.
Identifying patient-specific neoepitopes for cell-based and vaccine immunotherapy targets in breast cancer patients by HLA typing and predicting MHC presentation from whole genome and RNA sequencing data. (2016)

11606 Background: Anti-HER2 therapies have demonstrated success in improving the outcomes of patients (pts) with HER2-positive breast cancer; however, a high proportion of pts either do not respond to treatment or develop resistance to these agents. We developed an informatics platform that establishes HLA typing and predicts MHC presentation from whole genome sequencing (WGS) and RNA sequencing (RNAseq) data to identify neoepitopes among pts with HER2-positive breast cancer. Our platform provides a foundation for the development of next-generation, pt-specific cancer cell-based and vaccine immunotherapies. Methods: WGS and RNAseq data from The Cancer Genome Atlas (TCGA) were available for 19 HER2-positive breast cancer pts. Neoepitopes were identified by creating all permutations of 9-mer amino acid strings derived from identified single nucleotide variants and were filtered against all possible 9-mer peptide sequences created from every known human gene. In silico HLA typing was determined from WGS and RNAseq data using the HLA forest algorithm. NetMHC 3.4 was used to obtain the predicted binding affinities of neoepitopes to HLA alleles. Results: The numbers of predicted neoepitopes identified by WGS, neoepitopes expressed per RNAseq, and neoepitopes having binding affinity to any of the pts’ MHC class 1 HLA alleles were 10434, 5332, and 560, respectively, equivalent to an average of 9.8 high-quality neoepitopes per sample. The majority of neoepitopes were unique to each pt, with only 1 that was shared between 2 pts. Across all HER2-positive breast cancers, ~6% of neoepitopes occurred in cancer driver genes.Conclusions: We discovered that the majority of neoepitopes among pts with HER2-positive breast cancer were unique to each pt. For pts who do not respond to HER2-targeted agents, high-throughput identification of neoepitopes could serve as the basis for the development of pt-specific, cell-based and vaccine immunotherapies. Regardless of biomarker status or tissue of origin, all cancer pts may benefit from neoepitope-based immunotherapies.
Hybrid intra-cell TDMA/inter-cell CDMA with inter-cell interference suppression for wireless networks (2002)

The standard time division multiple access (TDMA) cellular network is designed so that physically adjacent cells are assigned different frequency bands, or channels, in order to reduce inter-cell interference. A multiple-access scheme is presented in which TDMA is used inside each cell, but different transmitted pulse shapes with low cross-correlations are assigned to adjacent cells. These pulses could be direct-sequence spread-spectrum pulses, which have been proposed for code division multiple access (CDMA) wireless networks. Such a hybrid system combines the high intra-cell capacity of TDMA with the inter-cell and multipath interference rejection capabilities of CDMA. It is concluded that this hybrid scheme offers a potential increase in capacity relative to intra-cell TDMA/inter-cell frequency-division multiple access (FDMA) provided that interference suppression techniques can be used to suppress inter-cell interference. Additional advantages and disadvantages of the scheme are discussed.
Optimization-driven design of compact UWB MIMO antenna (2016)

In the paper, a concept and design of a compact MIMO antenna is presented. In our approach, an improved space filling is obtained by constraining an individual antenna layout and optimizing it for minimum size. The MIMO design is constructed by composing the two of previously designed structures. Because the design problem is heavily constrained both in terms of geometry and electrical performance objectives, surrogate-based optimization techniques are used to accomplish the design process in reasonable timeframe. The final MIMO design features a small size of only 565 mm2 and exhibits good isolation in the entire UWB band.
The sequence and structure of the 3' arm of the first stem-loop of the human immunodeficiency virus type 2 trans-activation responsive region mediate Tat-2 transactivation (1997)

Human immunodeficiency virus type 2 (HIV-2) causes AIDS, but generally after a much longer asymptomatic period than that which follows infection with HIV-1. At the molecular level, HIV-2 is much more closely related to the simian immunodeficiency viruses than to HIV-1 and our previous studies have demonstrated that HIV-2 and HIV-1 enhancer stimulation is mediated by different sets of cellular proteins following T-cell activation. Similar to HIV-1, HIV-2 encodes a transactivating protein, Tat, which appears to be necessary for viral replication and stimulates viral transcriptional initiation and/or elongation. While Tat-1 binds to the RNA of the trans-activation responsive (TAR) region of HIV-1 and HIV-2, cellular factors that bind to the RNA transcript are also necessary for Tat to function in vivo. Since almost all previous investigations of cellular cofactors for Tat had focused on HIV-1, we undertook studies aimed at understanding the interaction between the TAR RNA region of the HIV-2 promoter (TAR-2) and cellular proteins. By using extension inhibition analysis (toeprinting) and RNA electrophoretic mobility shift assays, we demonstrated binding of a nuclear factor(s) in T cells to the base of the promoter-proximal stem-loop structure. Mutational analysis of this region revealed that both the sequence of the 3' arm and the stem structure itself are important for activation of the promoter by Tat-2. In contrast, the structure is necessary for activation of TAR-2 by Tat-1 but the sequence is less important. These results suggest that a cellular factor interacts with the 3' arm of the proximal stem-loop structure of TAR-2 and mediates Tat-2-induced increases in the level of HIV-2 transcripts.
Single MEMS Chip Enabling Dual Spectral‐Range Infrared Micro‐Spectrometer with Optimal Detectors (2021)

Abstract Portable spectrometers enable rapid and low‐cost material analysis in a ubiquitous manner by measuring their molecular absorption spectrum. To measure a wide variety of materials, it is essential to have a broad spectral range of operation with acceptable sensitivity. Recently, the miniaturization of Fourier transform infrared spectrometers has been realized using the micro‐electro‐mechanical systems technology. In this work, two identical Michelson interferometers are monolithically integrated on a silicon chip, in a parallel architecture, and their mirrors are driven by a single comb‐drive actuator. The interferometers are fed by a broadband white light and their outputs are coupled to different photodetectors optimally selected for different spectral ranges. This enables an extended wavelength range of operation covering the near‐infrared from 1.4 to 2.6 µm and the mid‐infrared from 2.6 to 4.6 µm, simultaneously. Experimental results are obtained by using multimode optical fibers for light coupling between the components. The signal‐to‐noise ratio is measured and compared to theoretical expectations, showing good agreement. The spectral range of operation of the realized spectrometer is 1.4–4.6 µm (7142–2173 cm ‐1 ) with a spectral resolution of 31.5 cm ‐1 . Finally, the spectrometer is used to acquire the transmission spectrum of polystyrene thin film and TS5 reference material.
On the Relationship Between the Block Error and Channel-State Markov Models in Transmissions Over Slow-Fading Channels (2004)

Block-error processes in transmissions over slow-fading channels can be accurately modeled by a two-state Markov chain [the block Markov model (BMM)]. Another line of research has focused on the use of a channel-state Markov model (CSMM) to analyze block transmissions. Although both techniques provide results that agree well with observations, the relationship between both Markov models has not been recognized in the previous literature. In this letter, we show that the BMM for slow-fading channels can be directly derived from the CSMM. In addition, we introduce a greatly simplified channel-modeling methodology. In the new methodology, the BMM is the primary channel characterization tool, and the CSMM becomes essentially an estimation technique that provides parameters for the BMM. Results of packet transmissions in slow-fading channels show that our approach provides significant improvements in both accuracy and simplicity over previously proposed techniques.
CCDC 1985478: Experimental Crystal Structure Determination (2021)

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
Lipid components that reduce protein solubility of soy protein isolates (1995)

Abstract A lipid fraction from a commercial soy protein isolate (SPI), previously found to be detrimental to SPI solubility, was analyzed by size‐exclusion liquid chromatography, by high‐performance liquid chromatography (HPLC), and for chemical composition. The molecular weight of most of this material was greater than 1,100 daltons. This lipid fraction was water‐soluble yet required a strong nonpolar solvent mixture to elute it from a C 18 HPLC column. The lipid material was alkaline (pH 8.7) and composed of 3.0% nitrogen, 1.6% phosphorus, 17.5% nonvolatile crude fatty acids primarily hydroxylated), 10.4% long‐chain bases, 9.9% hexuronic acid, 3.2% hexosamine, and 6.6% total sugar. The molecular weight, chemical composition, and physical characteristics (solubility characteristics, surfactant characteristics, and appearance) of this material were all similar to those reported for phytoglycolipid.
Invariant Delineation of Nuclear Architecture in Glioblastoma Multiforme for Clinical and Molecular Association (2012)

Automated analysis of whole mount tissue sections can provide insights into tumor subtypes and the underlying molecular basis of neoplasm. However, since tumor sections are collected from different laboratories, inherent technical and biological variations impede analysis for very large datasets such as The Cancer Genome Atlas (TCGA). Our objective is to characterize tumor histopathology, through the delineation of the nuclear regions, from hematoxylin and eosin (H&E) stained tissue sections. Such a representation can then be mined for intrinsic subtypes across a large dataset for prediction and molecular association. Furthermore, nuclear segmentation is formulated within a multi-reference graph framework with geodesic constraints, which enables computation of multidimensional representations, on a cell-by-cell basis, for functional enrichment and bioinformatics analysis. Here, we present a novel method, multi-reference graph cut (MRGC), for nuclear segmentation that overcomes technical variations associated with sample preparation by incorporating prior knowledge from manually annotated reference images and local image features. The proposed approach has been validated on manually annotated samples and then applied to a dataset of 377 Glioblastoma Multiforme (GBM) whole slide images from 146 patients. For the GBM cohort, multidimensional representation of the nuclear features and their organization have identified 1) statistically significant subtypes based on several morphometric indexes, 2) whether each subtype can be predictive or not, and 3) that the molecular correlates of predictive subtypes are consistent with the literature. Data and intermediaries for a number of tumor types (GBM, low grade glial, and kidney renal clear carcinoma) are available at: http://tcga.lbl.gov for correlation with TCGA molecular data. The website also provides an interface for panning and zooming of whole mount tissue sections with/without overlaid segmentation results for quality control.
Light enhancement and formation of photonic band gaps in aperiodic waveguide structures (2006)

Novel design of complex waveguide structures that guide light due to the excitation of multiple resonant transmission states induced by aperiodic Thue-Morse environment is presented. We illustrate bandgaps and localization states formed into these structures.
Monoclonal Antibodies for Prevention and Treatment of COVID-19 (2020)

James M. Sanders, PhD, PharmD; Marguerite L. Monogue, PharmD; Tomasz Z. Jodlowski, PharmD; James B. Cutrell, MD
C—H Bond Functionalization in Complex Organic Synthesis (2004)

Activation and functionalization of unactivated sp3 C-H bonds have been demonstrated in complex substrates containing multiple reactive groups. These reactions were designed as key steps in syntheses of natural products (rhazinilam, teleocidins) as well as in direct hydroxylation of α-amino acids. Both stoichiometric and catalytic C-H bond functionalization methods are discussed in this chapter.
Simulation based generation of X-parameters using the harmonic balance first moment (2016)

As the complexity of radio frequency circuits increases, the generation of macromodels for circuit blocks that can be used in system simulations has become increasingly useful and even necessary. Recently X-parameters1 have been proposed as an extension to the concept of S-Parameters in order to create a macromodel that captures some of the key nonlinearities in the circuit. In this paper, an efficient semi-analytical approach for the computation of X-parameters is presented. More specifically, a clear relation between the X-parameters and the circuit moments is developed, which in turn facilitates the application of moments to further improve the efficiency of X-parameter generation.
Investigation of Flux Weakening Capability of an Unconventional 9-Phase PM Motor with Different Winding Configurations (2019)

In this paper, two different winding configurations and phase angle displacements of an unconventional nine-phase permanent magnet (PM) motor have been investigated in terms of flux weakening capabilities. The focus has been on a 117-slot 36-pole unbalanced and asymmetric winding motor since these motors have certain benefits. In addition, it is not possible to create a balanced winding structure for this motor due to the selected slot-pole combination. Performance of the designed motors have been verified experimentally and flux weakening capabilities have been investigated using 2 Dimensional finite element analysis (2D FEA) and test results. It is shown that the flux weakening capabilities of the proposed 9-phase PM motors with two winding options yield similar results compared to a conventional balanced multi-phase PM motors.
Deoxyspergualin therapy in autoimmune MRL/1pr mice suffering advanced lupus-like disease. (1990)

The present study was designed to evaluate the therapeutic activity of a novel immunosuppressive agent, deoxyspergualin (DSG, NKT-01) in male MRL/MpJ-lpr/lpr (MRL/lpr) mice suffering advanced systemic lupus erythematosus (SLE)-like lesions. Treatment with DSG in the early phase of the disease at doses of 1.5 and 3 mg/kg strongly suppressed the development of SLE-like lesions. When DSG was administered from week 21 through 29 to MRL/lpr mice in advanced phases of the disease, a daily iv dose of 3 mg/kg (5 days/week) markedly reduced the symptoms, whereas a dose of 1.5 mg/kg did not. Moreover, DSG treatment at a dose of 3mg/kg, started at the time when the blood urea nitrogen levels were over 50 mg/deciliter, significantly prevented deterioration of the hyperuremia. Taking these findings into consideration, DSG was found to be a promising agent for curing such established autoimmune disease.
A Supramolecular Array of Fullerenes by Quadruple Hydrogen Bonding (2002)

Kugeln und Ketten: Bei dem durch Wasserstoffbrücken verknüpften Fulleren-System 1 bleibt die chemische Integrität der Monomereinheiten im hochdynamischen polymeren Zustand vollständig erhalten, auch im Hinblick auf das Redoxverhalten sowie auf UV/Vis-Charakteristika, weshalb 1 Potential zum Aufbau supramolekularer elektronischer Bauelemente hat. Supporting information for this article is available on the WWW under http://www.angewandte.com or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.