gebhart/patrepeval huggingface dataset:
Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics (2021)

The influenza A virus (IAV) neuraminidase (NA) is essential for virion release from cells and decoy receptors and an important target of antiviral drugs and antibodies. Adaptation to a new host sialome and escape from the host immune system are forces driving the selection of mutations in the NA gene. Phylogenetic analysis shows that until 2015, 16 amino acid substitutions in NA became fixed in the virus population after introduction in the human population of the pandemic IAV H1N1 (H1N1pdm09) in 2009. The accumulative effect of these substitutions, in the order in which they appeared, was analyzed using recombinant proteins and viruses in combination with different functional assays. The results indicate that NA activity did not evolve to a single optimum but rather fluctuated within a certain bandwidth. Furthermore, antigenic and enzymatic properties of NA were intertwined, with several residues affecting multiple properties. For example, the substitution K432E in the second sialic acid binding site, next to the catalytic site, was shown to affect catalytic activity, substrate specificity, and the pH optimum for maximum activity. This substitution also altered antigenicity of NA, which may explain its selection. We propose that the entanglement of NA phenotypes may be an important determining factor in the evolution of NA.<b>IMPORTANCE</b> Since its emergence in 2009, the pandemic H1N1 influenza A virus (IAV) has caused significant disease and mortality in humans. IAVs contain two envelope glycoproteins, the receptor-binding hemagglutinin (HA) and the receptor-destroying neuraminidase (NA). NA is essential for virion release from cells and decoy receptors, is an important target of antiviral drugs, and is increasingly being recognized as an important vaccine antigen. Not much is known, however, about the evolution of this protein upon the emergence of the novel pandemic H1N1 virus, with respect to its enzymatic activity and antigenicity. By reconstructing the evolutionary path of NA, we show that antigenic and enzymatic properties of NA are intertwined, with several residues affecting multiple properties. Understanding the entanglement of NA phenotypes will lead to better comprehension of IAV evolution and may help the development of NA-based vaccines.
ChemInform Abstract: PREPARATION OF TERTIARY PHOSPHINE‐OLEFIN COMPLEXES OF PLATINUM(0): A CONVENIENT SYNTHESIS OF ETHYLENEBIS(TRIETHYLPHOSPHINE)PLATINUM(0) (1981)

Abstract Der Diethylplatinkomplex (I) zersetzt sich thermisch in Cyclohexanlösung durch β‐Wasserstoffaktivierung bei anschließender reduktiver Eliminierung von Ethan zum Ethylenkomplex (II).
Real-time ultra-wideband frequency sweeping channel sounder for 3–18 GHz (2017)

This paper presents system concept, calibration and example measurements of a novel ultra-wideband, real-time channel sounder. The sounder operates in the frequency range from 3 GHz to 18 GHz thus providing a Fourier delay resolution of 66.7 ps. The developed sounder measures overlapping sub-bands of 1 GHz bandwidth to cover the whole frequency range. This allows us to use a waveform generator and a digitizer with relatively lower sample rates and significantly lowers the cost compared to sampling the whole band at once. With the transmit power of 40 dBm, the maximum measurable path loss is 132 dB without accounting possible antenna gains. In this work, we also describe the calibration procedure along with the method to patch sub-bands into a combined channel response. This approach is validated by comparing the results from vector network analyzer(VNA) measurements performed in the same static environment. In contrast to VNAs, however, our sounder is real-time and can measure in dynamic environments with maximum Doppler spreads up to 166.7 Hz. Additionally, we present sample results from the first measurement campaign performed in an urban cellular scenario covering 3-18 GHz.
The Impact of Inhaler Device Regimen in Patients with Asthma or COPD (2021)

Many inhaler devices with varying handling requirements for optimal use are available for the treatment of asthma and chronic obstructive pulmonary disease (COPD). Patients may be prescribed different device types for reliever and maintenance medications, which may lead to confusion and suboptimal device use. We aimed to understand whether simplifying inhaler regimens by employing a single device type in patients who use multiple devices or prescribing a device with which a patient was already experienced could improve clinical and economic outcomes in asthma and COPD management. A targeted literature search was performed and additional articles were identified through hand searching citations within screened publications. A total of 114 articles were included in the final review. Findings suggest that simplifying inhaler regimens by applying the same type of inhaler for concomitant inhaled medications over time minimizes device misuse, leading to improved clinical outcomes and reduced health care use in patients with asthma or COPD. Physicians should consider a patient's suitability for a device and training needs when prescribing an inhaled medication and before changing the medication type or dose, especially when suboptimal treatment outcomes are observed. Further research is required to determine whether consistent use of the same device type is associated with better treatment adherence and persistence in patients with asthma or COPD. Nevertheless, this literature review identified clinical benefits and reduced health care use with simplified inhaler regimens.
Selection of Aerosol Delivery Device (1996)

Nilsestuen, Jon PhD, RRT; Fink, James B. MBA, RRT; Witek, Theodore Jr DrPH, RPFT, RRT; Volpe, James III MEd, RRT Author Information
Nerve Cross-Bridging to Enhance Nerve Regeneration in a Rat Model of Delayed Nerve Repair (2015)

There are currently no available options to promote nerve regeneration through chronically denervated distal nerve stumps. Here we used a rat model of delayed nerve repair asking of prior insertion of side-to-side cross-bridges between a donor tibial (TIB) nerve and a recipient denervated common peroneal (CP) nerve stump ameliorates poor nerve regeneration. First, numbers of retrogradely-labelled TIB neurons that grew axons into the nerve stump within three months, increased with the size of the perineurial windows opened in the TIB and CP nerves. Equal numbers of donor TIB axons regenerated into CP stumps either side of the cross-bridges, not being affected by target neurotrophic effects, or by removing the perineurium to insert 5-9 cross-bridges. Second, CP nerve stumps were coapted three months after inserting 0-9 cross-bridges and the number of 1) CP neurons that regenerated their axons within three months or 2) CP motor nerves that reinnervated the extensor digitorum longus (EDL) muscle within five months was determined by counting and motor unit number estimation (MUNE), respectively. We found that three but not more cross-bridges promoted the regeneration of axons and reinnervation of EDL muscle by all the CP motoneurons as compared to only 33% regenerating their axons when no cross-bridges were inserted. The same 3-fold increase in sensory nerve regeneration was found. In conclusion, side-to-side cross-bridges ameliorate poor regeneration after delayed nerve repair possibly by sustaining the growth-permissive state of denervated nerve stumps. Such autografts may be used in human repair surgery to improve outcomes after unavoidable delays.
Ny-ESO-1 expression and immunogenicity associated with transitional cell carcinoma: correlation with tumor grade. (2001)

NY-ESO-1 mRNA expression in transitional cell carcinoma was investigated by reverse transcription-PCR and immunohistochemistry. NY-ESO-1 mRNA was detected in 20 of 62 (32%) tumor specimens. There was a correlation between NY-ESO-1 expression and tumor grade: 0 of 4 (0%) grade 1 (G1), 6 of 26 (23%) grade 2 (G2), and 14 of 32 (44%) grade 3 (G3) tumors were NY-ESO-1 mRNA positive. Immunohistochemical analysis using NY-ESO-1-specific monoclonal antibody ES121 showed that 2 of 14 NY-ESO-1 mRNA-expressing G3 tumors were positive for NY-ESO-1. No NY-ESO-1 staining was observed in the panel of 30 G1 or G2 tumor specimens, including 6 NY-ESO-1 mRNA-positive cases. Sera from an expanded panel of 124 patients with transitional cell carcinoma were tested for the presence of NY-ESO-1 antibody. Seropositivity was observed in 9 of 72 (12.5%) patients with G3 tumors, whereas none of 52 patients with G1 or G2 tumors produced antibody against NY-ESO-1. In the 9 positive patients with NY-ESO-1 antibody, 4 had muscular invasive tumors, and 5 had carcinoma in situ.
(Carboxydiamine)Pt(ii) complexes of a combretastatin A-4 analogous chalcone: the influence of the diamine ligand on DNA binding and anticancer effects (2011)

The combretastatin A-4 analogue m-hydroxychalcone 2 was esterified with a (1-carboxyethane-2,3-diamine)dichloridoplatinum(II) fragment to give complex 6 which was more active against various cancer cell lines (IC50 < 1 µM) than its analogue 3 bearing a 6-aminomethylnicotinate ligand. Complex 6 bound to the same sites of DNA as cisplatin but caused a larger DNA unwinding angle and ten times more interstrand cross-links. Also, DNA lesions due to binding of 6 were only half as efficiently repaired as cisplatin–DNA adducts. Complex 6 also showed a much lower affinity to the platinum detoxifier glutathione.
LTE Downlink 2X2 MIMO with Realistic CSI: Overview and Performance Evaluation (2010)

For downlink multiple input multiple output (MIMO) schemes, there is a tradeoff between downlink MIMO performance and uplink reporting cost. The mobile speed has an impact on this tradeoff since the reporting delays the measurements. This paper presents the major downlink MIMO modes in 3GPP Long Term Evolution (LTE) and their related channel state information (CSI) modes. The impact of realistic CSI is investigated through advanced system simulations, showing that the total performance degradation of realistic CSI reporting is at a surprisingly low 20% compared to full, recent channel knowledge. With realistic CSI reporting, a selected set of promising 2×2 MIMO applications are evaluated at different mobile speeds. The open-loop spatial multiplexing mode offers unexpectedly high cell throughput despite its limited feedback requirement. It performs well for a wide range of speeds, as it provides good robustness to delayed channel knowledge. Bitrates can only be further improved by closed-loop spatial multiplexing in stationary scenarios, where CSI delay does not hamper the precoding gain. These results confirm that there are MIMO modes suitable for both high and low speeds.
Big-Data Visualization (2013)

Almost all fields of study and practice sooner or later will confront the big-data problem. Visualization has proven effective for not only presenting essential information in vast amounts of data but also driving complex analyses. Big-data analytics and discovery present new research opportunities to the computer graphics and visualization community. This special issue highlights the latest advancements in solving the big-data problem through visual means, with four articles on new techniques, systems, or applications.
Supplementary Figures 6-10 from MYC Phosphorylation, Activation, and Tumorigenic Potential in Hepatocellular Carcinoma Are Regulated by HMG-CoA Reductase (2023)

Supplementary Figures 6-10 from MYC Phosphorylation, Activation, and Tumorigenic Potential in Hepatocellular Carcinoma Are Regulated by HMG-CoA Reductase
Magnetic susceptibility and magnetic resonance measurements of the moisture content and hydration condition of a magnetic mixture material (2014)

We developed a magnetic measurement method to measure the moisture content and hydration condition of mortar as a magnetic mixture material. Mortar is a mixture of Portland cement, sand, and water, and these materials exhibit different magnetic properties. The magnetization–magnetic field curves of these components and of mortars with different moisture contents were measured, using a specially developed high-temperature-superconductor superconducting quantum interference device. Using the differences in magnetic characteristics, the moisture content of mortar was measured at the ferromagnetic saturation region over 250 mT. A correlation between magnetic susceptibility and moisture content was successfully established. After Portland cement and water are mixed, hydration begins. At the early stage of the hydration/gel, magnetization strength increased over time. To investigate the magnetization change, we measured the distribution between bound and free water in the mortar in the early stage by magnetic resonance imaging (MRI). The MRI results suggest that the amount of free water in mortar correlates with the change in magnetic susceptibility.
Signamization of resist images (1997)

Signamization is an automated process to optimize the NA and (sigma) settings of a stepper for a given combination of critical features and CD tolerances, basing on the E-D Forest methodology. It has been applied to a variety of feature combinations using disk and annular illuminations, binary intensity mask and phase-shifting mask. They are based on pre-simulated aerial images. This paper deals with signamization of resist images derived from aerial image data. The aerial image is converted to resist image analytically in real time using the lumped parameter model, which make any pre-simulated aerial images; such as those for binary intensity masks, attenuated phase shifting masks, alternating phase shifting masks, disk illumination. Nikon ring illumination, and Canon ring illumination, usable for any resist system characterized by resist thickness, absorption coefficient (alpha) , and contrast (gamma) , without having to simulate for each particular resist system. The signamization results show that in addition to the optimum NA and (sigma) , there is a (gamma) threshold above which further improvement is unrewarding, a higher (alpha) can improve imaging performance, and that the resist thickness plays an important role only when the reflection swing ratio is large or when it is reduced significantly. When this happens, together with (alpha) becoming very small and (gamma) very large, and resist image approaches that aerial image, showing the validity of the lumped parameter model for signamization and the computer programming.
Tracking entities in the dynamic world (2014)

Identifying records referring to the same real world entity over time enables longitudinal data analysis. However, difficulties arise from the dynamic nature of the world: the entities described by a temporal data set often evolve their states over time. While the state of the art approach to temporal entity matching achieves high accuracy, this approach is computationally expensive and cannot handle large data sets. In this paper, we present an approach that achieves equivalent matching accuracy but takes far less time. Our key insight is "static first, dynamic second." Our approach first runs an evidence-collection pass, grouping records without considering the possibility of entity evolution, as if the world were "static." Then, it merges clusters from the initial grouping by determining whether an entity might evolve from the state described in one cluster to the state described in another cluster. This intuitively reduces a difficult problem, record matching with evolution, to two simpler problems: record matching without evolution, then "evolution detection" among the resulting clusters. Experimental results on several temporal data sets show that our approach provides an order of magnitude improvement in run time over the state-of-the-art approach while producing equivalent matching accuracy.
Single cell qPCR reveals that additional HAND2 and microRNA-1 facilitate the early reprogramming progress of seven-factor-induced human myocytes (2017)

The direct reprogramming of cardiac fibroblasts into induced cardiomyocyte (CM)-like cells (iCMs) holds great promise in restoring heart function. We previously found that human fibroblasts could be reprogrammed toward CM-like cells by 7 reprogramming factors; however, iCM reprogramming in human fibroblasts is both more difficult and more time-intensive than that in mouse cells. In this study, we investigated if additional reprogramming factors could quantitatively and/or qualitatively improve 7-factor-mediated human iCM reprogramming by single-cell quantitative PCR. We first validated 46 pairs of TaqMan® primers/probes that had sufficient efficiency and sensitivity to detect the significant difference of gene expression between individual H9 human embryonic stem cell (ESC)-differentiated CMs (H9CMs) and human fibroblasts. The expression profile of these 46 genes revealed an improved reprogramming in 12-week iCMs compared to 4-week iCMs reprogrammed by 7 factors, indicating a prolonged stochastic phase during human iCM reprogramming. Although none of additional one reprogramming factor yielded a greater number of iCMs, our single-cell qPCR revealed that additional HAND2 or microRNA-1 could facilitate the silencing of fibroblast genes and yield a better degree of reprogramming in more reprogrammed iCMs. Noticeably, the more HAND2 expressed, the higher-level were cardiac genes activated in 7Fs+HAND2-reprogrammed iCMs. In conclusion, HAND2 and microRNA-1 could help 7 factors to facilitate the early progress of iCM-reprogramming from human fibroblasts. Our study provides valuable information to further optimize a method of direct iCM-reprogramming in human cells.
T-cell growth factors and the allograft response (2003)

Allograft rejection-like tolerance is a T-cell–mediated event. Acquisition of transplant tolerance, however, is a learned process, and T cells need to engage actively in alloantigens to learn to tolerate the graft. T-cell growth factors play an important role in regulating multiple aspects of the allograft response. It is true that T-cell growth factors can drive clonal expansion and functional maturation of alloreactive T cells; therefore, targeting growth factors and their receptor components remains one of the key aspects in transplantation. There is compelling evidence that growth factors also regulate the induction of peripheral allograft tolerance through programming activated T cells for apoptosis and guiding the development of regulatory T cells. Thus, understanding precisely the role of T-cell growth factors in regulating T-cell homeostasis and in developing active immune regulation is critically important in transplant tolerance.
Transition-Metal Mediated Transformations of Tetrafluoroethylene intoVarious Polyfluorinated Organic Compounds (2016)

This account describes our studies on the transition-metal mediated transformation of tetrafluoroethylene into a variety of polyfluorinated organic compounds. We have divided our account into three main parts. First, we describe a series of palladium-catalyzed cross-coupling reactions that involve a C-F bond cleavage of tetrafluoroethylene as a key elementary reaction step. Also described are reactions that enable the construction of tetrafluoroethylene-bridging structures, such as R-CF2CF2-R’ and R-CF2CF2-H, from tetrafluoroethylene using either copper(I) or nickel(0) species. This account emphasizes the merits of a derivatization of readily available perfluorinated compounds to valuable highly fluorinated organic compounds.
Twists and Turns in Glassy, Liquid Crystalline Polymer Networks (2015)

Three-dimensional shape control is an enabler of dexterous motion in nature. Herein, we report on the thermally initiated out-of-plane (torsional) responses observed in a series of glassy, liquid crystalline polymer networks prepared with a range of cross-link densities. The three-dimensional shape of these materials is strongly dictated by both cross-link density as well as the preparation conditions (polymerization temperature). All of the materials examined herein undergo torsional inversion of the handedness with increasing temperature. The temperature at which the material flattens (crossover between handedness inversion) can be positioned by the polymerization temperature. Monoliths prepared with either multimaterial composition or multidirector orientations are shown to exhibit spatial variation in shape adaptivity.
FSO links using high sensitivity gigabit combinational sensors and an adaptive high-throughput error-correction protocol (2018)

For terrestrial free space optical (FSO) communication applications, large area photodetectors not only allow for more efficient power coupling but also ease the effects of atmospheric turbulence. When fabricated in array form, these devices have the added capability of operating as both data reception sensors and position sensitive detectors (PSD). Concentric five element impact ionization engineered (I2E) avalanche photodetector (APD) arrays have been developed to operate as combinational sensors at gigabit data rates. While the excellent sensitivity performance of these detectors allows for enhanced link range in calm atmospheric conditions, link availability with a high quality of service for an FSO system is strongly impacted by its ability to dynamically counter-act atmospheric fading with varying temporal scale. In this paper we present initial results using a combinational sensor in tandem with an advanced FSO modem which utilizes low-density parity check coding (LDPC) in an incremental redundancy (IR) hybrid automatic repeat request (HARQ) protocol. System performance enhancements as function of varying atmospheric scintillation will be discussed.
Comparison of the Resistance Spot Weldability of AA5754 and AA6022 Aluminum to Steels (2020)

In this paper, a traditional resistance spot welding (RSW) process in combination with a GM-patented Multi-Ring Domed (MRD) electrode was used to join two types of aluminum alloys, AA5754-O and AA6022-T4, to interstitial-free low carbon steel (LCS). Parallel studies were carried out for AA5754-LCS and AA6022-LCS resistance spot welds to investigate the effects of aluminum contact resistance on the weld profile, interfacial microstructure, defect distribution, and coach peel performance. The results indicated AA5754-O develops a higher contact resistance when ex-posed to atmospheric conditions. This resulted in a degradation of the RSW process due to increased internal expulsion of the molten aluminum nugget and concurrent reduction in aluminum nugget size that contributed to a loss in joint mechanical performance. By contrast, AA6022-T4 exhibited a lower contact resistance, which minimized internal expulsion and promoted the retention of larger aluminum nuggets. The larger AA6022 weld nuggets exhibited improved mechanical performance in comparison to the smaller 5754 nuggets.