gebhart/patrepeval huggingface dataset:
Healthcare-associated respiratory tract infection (2013)

Respiratory tract infections have been identified as the most common healthcare-associated infection in acute hospitals. Patients most at risk are those who are critically ill, in particular patients who are mechanically ventilated. Ventilator-associated pneumonia can have serious consequences for patients, increasing morbidity and mortality rates duration of ventilation and length of stay in intensive care. This article focuses on the prevention of healthcare-associated respiratory tract infections, and discusses strategies that staff can implement to minimise the risk of infection.
Generation and Suppression of 3-/4-Functionalized Benzynes Using Zinc Ate Base (TMP−Zn−ate):  New Approaches to Multisubstituted Benzenes (2007)

We present full details of our new methods for preparing functionalized benzynes with lithium di-alkyl(2,2,6,6-tetramethylpiperidino)zincate (R2Zn(TMP)Li) through deprotonative zincation as a key reaction. In this system, by choosing appropriate ligands for the zincate, either regioselective zincation of functionalized haloaromatics or the generation of substituted benzynes can be controlled in good yields with excellent chemoselectivity, using the same substrate. Zincation with (t)Bu2Zn(TMP)Li followed by electrophilic trapping or zincation with Me2Zn(TMP)Li followed by nucleophilic or diene trapping is shown to be a powerful tool for the chemoselective preparation of 1,2,3-/1,2,4-trisubstituted benzene derivatives. These methods offer far greater generality than previous methods for the synthesis of multifunctionalized benzenes. Computational/theoretical studies of the reaction mechanism of this unique benzyne formation indicated that preferential coordination of the dialkylzinc moiety of zincate to halogen is the reason for the reduced activation energy of the elimination, that is, for the formation of the benzyne. The role of the ligands on Zn in accelerating/decelerating the elimination is also discussed.
Exploring Protein Binding of Uremic Toxins in Patients with Different Stages of Chronic Kidney Disease and during Hemodialysis (2015)

As protein binding of uremic toxins is not well understood, neither in chronic kidney disease (CKD) progression, nor during a hemodialysis (HD) session, we studied protein binding in two cross-sectional studies. Ninety-five CKD 2 to 5 patients and ten stable hemodialysis patients were included. Blood samples were taken either during the routine ambulatory visit (CKD patients) or from blood inlet and outlet line during dialysis (HD patients). Total (CT) and free concentrations were determined of p-cresylglucuronide (pCG), hippuric acid (HA), indole-3-acetic acid (IAA), indoxyl sulfate (IS) and p-cresylsulfate (pCS), and their percentage protein binding (%PB) was calculated. In CKD patients, %PB/CT resulted in a positive correlation (all p < 0.001) with renal function for all five uremic toxins. In HD patients, %PB was increased after 120 min of dialysis for HA and at the dialysis end for the stronger (IAA) and the highly-bound (IS and pCS) solutes. During one passage through the dialyzer at 120 min, %PB was increased for HA (borderline), IAA, IS and pCS. These findings explain why protein-bound solutes are difficult to remove by dialysis: a combination of the fact that (i) only the free fraction can pass the filter and (ii) the equilibrium, as it was pre-dialysis, cannot be restored during the dialysis session, as it is continuously disturbed.
Diffusion of delta doped boron in silicon following oxidation (1993)

Samples from a silicon wafer containing a boron doped delta layer were exposed to plasma oxidation and rapid thermal processing (RTP). It is demonstrated experimentally for the first time that there is no enhanced diffusion resulting from oxidation by plasma anodisation, making it well suited to complement low temperature processing.
Phase controllable Josephson junctions for cryogenic memory (2018)

Abstract Josephson junctions containing ferromagnetic layers have generated interest for application in cryogenic memory. In a junction containing both a magnetically hard fixed layer and soft free layer with carefully chosen thicknesses, the ground-state phase difference of the junction can be controllably switched between 0 and π by changing the relative orientation of the two ferromagnetic layers from antiparallel to parallel. This phase switching has been observed in junctions using Ni fixed layers and NiFe free layers. We present phase-sensitive measurements of such junctions in low-inductance symmetric SQUID loops which simplify analysis relative to our previous work. We confirm controllable 0− π switching in junctions with 2.0 nm Ni fixed layers and 1.25 nm NiFe free layers across multiple devices and using two SQUID designs, expanding the phase diagram of known thicknesses that permit phase control.
Transcriptome Analysis of Gene Expression Provides New Insights into the Effect of Mild Therapeutic Hypothermia on Primary Human Cortical Astrocytes Cultured under Hypoxia (2017)

Hypothermia is increasingly used as a therapeutic measure to treat brain injury. However, the cellular mechanisms underpinning its actions are complex and are not yet fully elucidated. Astrocytes are the most abundant cell type in the brain and are likely to play a critical role. In this study, transcriptional changes and the protein expression profile of human primary cortical astrocytes cultured under hypoxic conditions for 6 h were investigated. Cells were treated either with or without a mild hypothermic intervention 2 h post-insult to mimic the treatment of patients following traumatic brain injury (TBI) and/or stroke. Using human gene expression microarrays, 411 differentially expressed genes were identified following hypothermic treatment of astrocytes following a 2 h hypoxic insult. KEGG pathway analysis indicated that these genes were mainly enriched in the Wnt and p53 signaling pathways, which were inhibited following hypothermic intervention. The expression levels of 168 genes involved in Wnt signaling were validated by quantitative real-time-PCR (qPCR). Among these genes, 10 were up-regulated and 32 were down-regulated with the remainder unchanged. Two of the differentially expressed genes (DEGs), p38 and JNK, were selected for validation at the protein level using cell based ELISA. Hypothermic intervention significantly down-regulated total protein levels for the gene products of p38 and JNK. Moreover, hypothermia significantly up-regulated the phosphorylated (activated) forms of JNK protein, while downregulating phosphorylation of p38 protein. Within the p53 signaling pathway, 35 human apoptosis-related proteins closely associated with Wnt signaling were investigated using a Proteome Profiling Array. Hypothermic intervention significantly down-regulated 18 proteins, while upregulating one protein, survivin. Hypothermia is a complex intervention; this study provides the first detailed longitudinal investigation at the transcript and protein expression levels of the molecular effects of therapeutic hypothermic intervention on hypoxic human primary cortical astrocytes. The identified genes and proteins are targets for detailed functional studies, which may help to develop new treatments for brain injury based on an in-depth mechanistic understanding of the astrocytic response to hypoxia and/or hypothermia.
Inhibition of Reovirus by Mycophenolic Acid Is Associated with the M1 Genome Segment (2004)

Mycophenolic acid (MPA), an inhibitor of IMP dehydrogenase, inhibits reovirus replication and viral RNA and protein production. In mouse L929 cells, antiviral effects were greatest at 30 microg of MPA/ml. At this dosage, MPA inhibited replication of reovirus strain T3D more than 1,000-fold and inhibited replication of reovirus strain T1L nearly 100-fold, compared to non-drug-treated controls. Genetic reassortant analysis indicated the primary determinant of strain-specific differences in sensitivity to MPA mapped to the viral M1 genome segment, which encodes the minor core protein mu2. MPA also inhibited replication of both strains of reovirus in a variety of other cell lines, including Vero monkey kidney and U373 human astrocytoma cells. Addition of exogenous guanosine to MPA-treated reovirus-infected cells restored viral replicative capacity to nearly normal levels. These results suggest the mu2 protein is involved in the uptake and processing of GTP in viral transcription in infected cells and strengthens the evidence that the mu2 protein can function as an NTPase and is likely a transcriptase cofactor.
Research Brief: October 2020: Lost Learning, Lost Earnings (2020)

KEY FINDINGS With coronavirus cases rising across the country, the Test and Trace system already encountering significant difficulties, and growing numbers of school pupils out of school once more in self-isolation, another disrupted school year for many seems inevitable. This study combines an analysis of the Labour Force Survey, the lost learning due to school closures between March and July 2020, and the unequal experiences depending on socio-economic background to estimate the potential impact on earnings and employment later in life.The analysis finds that school closures are likely to have substantial negative labour market impacts for those from less-well off groups, their chances of social mobility, and on the economy in general.
Do TiO2 Nanoparticles Really Taste Better When Cooked in a Microwave Oven? (2012)

Abstract Microwave‐assisted synthesis represents a valuable improvement in the domains of molecular and organic chemistry and was recently extended to inorganic and materials chemistry. A comparison of titanium dioxide nanoparticles synthesised in aqueous solution prepared in a microwave or a conventional oven is presented here. More precisely, three different protocols were used in order to determine the impact of the heating mode on the final product in terms of crystalline structure, particle size and morphology. Therefore, the resultant powders were analysed by Raman spectroscopy as well as X‐ray and electron diffraction and transmission electron microscopy. The results show that microwave treatment significantly reduces the heating time and generally produces smaller nanoparticles. The rutile/anatase/brookite phase distribution is also modified by the heating mode in certain protocols up to the formation of a pure anatase phase, for instance. The impact of microwaves on the solvent and on the inorganic precursors has been demonstrated. A photocatalytic test and time‐resolved microwave conductivity experiments were performed on rather similar samples prepared with the two heating modes in order to probe the improvement of the crystalline quality and its consequences on the photocatalytic activity of the TiO 2 material.
PU21: A novel perceptually uniform encoding for adapting existing quality metrics for HDR (2021)

Standard image quality metrics, such as PSNR or SSIM, cannot be directly computed on linear high dynamic range colour values because such values non-linearly related to our perception of visible differences. In this work, we develop a new encoding function (PU21) to convert absolute high dynamic range (HDR) linear colour values into approximately perceptually uniform (PU) values, which can be used with standard quality metrics. The proposed PU21 function is based on a recent contrast sensitivity model, fitted to the measurements up to 10000cd/m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . Unlike the conventional simplified approach of deriving PU functions based on peak sensitivities, we model realistic coding artefacts to find visibility thresholds for our derivation. Furthermore, the new PU accounts for the effect of glare on image quality. The proposed PU21 improves the accuracy of quality predictions for standard metrics of PSNR, VSI, FSIM, SSIM, and MS-SSIM in their correlation with subjective scores on HDR images included in UPIQ, one of the largest HDR image quality datasets.
Congenital Myasthenia Gravis (1971)

Thymectomy and subsequent short course of corticotropin in high doses did not change the course of persistent and unusually severe congenital myasthenia gravis in a 5-year-old boy. Grossly, the thymus appeared normal in size and consistency for the patient's age. On histopathologic examination several changes consistent with an autoimmune disorder were demonstrable, including lymphoid hyperplasia and large numbers of thymic plasma cells. Electron microscopic studies showed intralobular vascular changes and the presence of thymic myoid cells. Their possible significance is discussed.
Influence of different pulse duration of TEA CO2laser radiation on laser material interaction (1994)

A method was described to change the pulse duration of TEA CO2 lasers. It is possible to shorten a laser pulse in a definite way using a second electrical discharge in the air. Experiments were carried out with constant laser energy and different pulse durations in laser medicine. Firstly it was found that the type of laser tissue interaction is characteristically changed according to pulse duration, and secondly that the carbonization of tissue-characterizing these differences-is connected with the appearance of carbon monoxide in the laser plume produced. Positive results were obtained using short laser pulses for drilling in dentistry.
<title>Ti:sapphire-based ultrafast pump-probe laser source in the violet and ultraviolet</title> (1994)

Frequency conversion of an ultrafast 810 nm Ti:sapphire laser has produced 15 mJ, 165-fs pulses at 405 nm with an energy conversion efficiency of 35%. Upon tripling the fundamental to 270 nm, an energy of 0.8 mJ is obtained. Unconverted 405-nm light is used to generate an ultrafast supercontinuum in water that extends from 200 nm to 600 nm. The system operates at a 5 Hz repetition rate, and is useful for applications in deep ultraviolet pump-probe ultrafast spectroscopy.
Integrated Resonators in an Ultralow Loss Si3N4/SiO2 Platform for Multifunction Applications (2018)

Integrated optical resonators are key building blocks for an ever-increasing range of applications including optical communications, sensing, and navigation. A challenge to today's photonics integration is realizing circuits and functions that require ultralow loss waveguides on-chip while balancing the waveguide loss with device function and footprint. Incorporating Si <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> /SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> waveguides into a photonic circuit requires tradeoffs between waveguide loss, device footprint, and desired device specifications. In this paper, we focus on the design of resonator based circuits in the silicon nitride platform and the balancing of desired properties like quality factor Q, free spectral range, finesse, transmission shape with waveguide design, and footprint. The design, fabrication, and characterization of two resonator-based circuit examples operating at 1550 nm are described in detail. The first design is a thin core, large mode-volume bus-coupled resonator, with a 2.72 GHz free spectral range and a measured intrinsic Q of 60 million and loaded Q on the order of 30 Million, representing the highest reported loaded Q for a large mode volume resonator with a deposited upper cladding. The second circuit is a thicker core, smaller footprint, low loss flat passband third-order resonator filter with an ultrahigh extinction ratio of 80 dB tunable over 100% of the free spectral range and insertion loss under 1.3 dB.
Making Radio Frequency Identification Visible--A Watchdog Tag (2007)

To address the privacy concerns associated with RFID, previous work proposed an approach, where RFID readers do not only broadcast commands to inventory tag populations, but also transmit meta-information that describe the ongoing data collection. It was argued that RFID readers should explicitly declare the scope and purpose of their tag data collection by making this meta-information available to consumers and regulators through a watchdog tag. In this paper, we present the prototype of such a watchdog tag that is capable of decoding and displaying the meta-information broadcasted over the RFID communication channel for the visual inspection by the user. The paper details the design and implementation with discrete components, but also discusses limitations and future improvements. Our watchdog tag operates reliably and therefore, it suggests potential to enhance one's control over the data collected by RFID readers
Crystal structures of MS2 coat protein mutants in complex with wild- type RNA operator fragments (1998)

In MS2 assembly of phage particles results from an interaction between a coat protein dimer and a stem-loop of the RNA genome (the operator hairpin). Amino acid residues Thr45, which is universally conserved among the small RNA phages, and Thr59 are part of the specific RNA binding pocket and interact directly with the RNA; the former through a hydrogen bond, the latter through hydrophobic contacts. The crystal structures of MS2 protein capsids formed by mutants Thr45Ala and Thr59Ser, both with and without the 19 nt wild-type operator hairpin bound, are reported here. The RNA hairpin binds to these mutants in a similar way to its binding to wild-type protein. In a companion paper both mutants are shown to be deficient in RNA binding in an in vivo assay, but in vitro the equilibrium dissociation constant is significantly higher than wild-type for the Thr45Ala mutant. The change in binding affinity of the Thr45Ala mutant is probably a direct consequence of removal of direct hydrogen bonds between the protein and the RNA. The properties of the Thr59Ser mutant are more difficult to explain, but are consistent with a loss of non-polar contact.
Estimation on the Individual Hydrogen-Bond Strength in Molecules with Multiple Hydrogen Bonds (2007)

A simple atom-replacement approach is proposed for estimating the individual contributions of each intermolecular hydrogen bond (HB) in multiple hydrogen-bonded systems. The approach is validated by calculations on the homodimer of formylformamide and then applied to nucleic acid base pairs (adenine-thymine and guanine-cytosine) and some quadruply hydrogen-bonded dimers. With the help of this method, it is easy to distinguish the relative strength of each HB, and identify the main factors contributing to the total binding energies of multiple HBs.
Molecular Profiling of Liver Sinusoidal Endothelial Cells in Comparison to Hepatocytes: Reflection on Which Cell Type Should Be the Target for Gene Therapy (2020)

Human factor VIII (FVIII), which deficiency leads to hemophilia A, is largely synthesized and secreted by the liver sinusoidal endothelial cells (LSECs). However, the characteristics of these cells that secrete FVIII are not well known. We have previously reported that based on genome-wide expression and CpG methylation profiling, LSECs have a distinct molecular profile that distinguishes them from other endothelial cells. Hepatocytes are targeted by gene therapy protocols to treat hemophilia A. However, the hepatocyte is not the natural site for FVIII synthesis and current gene therapy protocols are eliciting immune responses that require immune suppression with corticosteroid therapy in a fairly high proportion of patients over a significant period of time. Cellular stress because of ectopic FVIII expression and codon optimization are discussed as potential underlying mechanisms. Here, we highlight the molecular differences between LSECs and hepatocytes.
Adjacent Cell Marker Lateral Spillover Compensation and Reinforcement for Multiplexed Images (2021)

Multiplex imaging technologies are now routinely capable of measuring more than 40 antibody-labeled parameters in single cells. However, lateral spillage of signals in densely packed tissues presents an obstacle to the assignment of high-dimensional spatial features to individual cells for accurate cell-type annotation. We devised a method to correct for lateral spillage of cell surface markers between adjacent cells termed REinforcement Dynamic Spillover EliminAtion (REDSEA). The use of REDSEA decreased contaminating signals from neighboring cells. It improved the recovery of marker signals across both isotopic (i.e., Multiplexed Ion Beam Imaging) and immunofluorescent (i.e., Cyclic Immunofluorescence) multiplexed images resulting in a marked improvement in cell-type classification.
Loss of protein tyrosine phosphatase N2 potentiates epidermal growth factor suppression of intestinal epithelial chloride secretion (2010)

The Crohn's disease candidate gene, protein tyrosine phosphatase nonreceptor type 2 (PTPN2), has been shown to regulate epidermal growth factor (EGF)-induced phosphatidylinositol 3-kinase (PI3K) activation in fibroblasts. In intestinal epithelial cells (IECs), EGF-induced EGF receptor (EGFR) activation and recruitment of PI3K play a key role in regulating many cellular functions including Ca(2+)-dependent Cl(-) secretion. Moreover, EGFR also serves as a conduit for signaling by other non-growth factor receptor ligands such as the proinflammatory cytokine, IFN-γ. Here we investigated a possible role for PTPN2 in the regulation of EGFR signaling and Ca(2+)-dependent Cl(-) secretion in IECs. PTPN2 knockdown enhanced EGF-induced EGFR tyrosine phosphorylation in T(84) cells. In particular, PTPN2 knockdown promoted EGF-induced phosphorylation of EGFR residues Tyr-992 and Tyr-1068 and led subsequently to increased association of the catalytic PI3K subunit, p110, with EGFR and elevated phosphorylation of the downstream marker, Akt. As a functional consequence, loss of PTPN2 potentiated EGF-induced inhibition of carbachol-stimulated Ca(2+)-dependent Cl(-) secretion. In contrast, PTPN2 knockdown affected neither IFN-γ-induced EGFR transactivation nor EGF- or IFN-γ-induced phosphorylation of ERK1/2. In summary, our data establish a role for PTPN2 in the regulation of EGFR signaling in IECs in response to EGF but not IFN-γ. Knockdown of PTPN2 directs EGFR signaling toward increased PI3K activation and increased suppression of epithelial chloride secretory responses. Moreover, our findings suggest that PTPN2 dysfunction in IECs leads to altered control of intestinal epithelial functions regulated by EGFR.
The Integration of Spontaneous Intracellular Ca2+ Cycling and Surface Membrane Ion Channel Activation Entrains Normal Automaticity in Cells of the Heart's Pacemaker (2006)

Although the ensemble of voltage- and time-dependent rhythms of surface membrane ion channels, the membrane "Clock", is the immediate cause of a sinoatrial nodal cell (SANC) action potential (AP), it does not necessarily follow that this ion channel ensemble is the formal cause of spontaneous, rhythmic APs. SANC also generates intracellular oscillatory spontaneous Ca(2+) releases that ignite excitation (SCaRIE) of the surface membrane via Na(+)/Ca(2+) exchanger activation. The idea that a rhythmic intracellular Ca(2+) Clock might keep time for normal automaticity of SANC, however, has not been assimilated into mainstream pacemaker dogma. Recent experimental evidence, derived from simultaneous, confocal imaging of submembrane Ca(2+) and membrane potential of SANC, and supported by numerical modeling, indicates that normal automaticity of SANC is entrained and stabilized by the tight integration of the SR Ca(2+) Clock that generates rhythmic SCaRIE, and the surface membrane Clock that responds to SCaRIE to immediately produce APs of an adequate shape. Thus, tightly controlled, rhythmic SCaRIE does not merely fine tune SANC AP firing, but is the formal cause of the basal and reserve rhythms, insuring pacemaker stability by rhythmically integrating multiple Ca(2+)-dependent functions, and effects normal automaticity by rhythmic ignition of the surface membrane Clock.