gebhart/patrepeval huggingface dataset:
Abstract 98: Myeloid-Specific Deletion of Prolyl Hydroxylase Domain Protein 2 Attenuates Hypertensive Cardiovascular Remodeling (2013)

Background: Hypertension induces cardiovascular hypertrophy and fibrosis. Infiltration of inflammatory cells including macrophages is critically involved in this process. We recently reported that inhibition of prolyl hydroxylase domain protein 2 (PHD2), which hydroxylates proline residue of hypoxia-inducible factor α (HIFα) and thereby induces HIFα degradation, suppressed inflammatory responses in macrophage. We examined whether myeloid-specific PHD2 deletion affects hypertension-induced cardiovascular remodeling. Methods and Results: Myeloid-specific PHD2-deficient mice (MyPHD2KO) were generated by crossing PHD2-floxed mice with LysM-Cre transgenic mice. HIF-1α and 2α proteins were accumulated and mRNA expression of TNFα, IL-6 and IL-1β, M1 macrophage markers, and TGF-β and connective tissue growth factor (CTGF) expression were significantly decreased in peritoneal macrophages from MyPHD2KO mice compared with those from control mice. PHD2-deficient macrophage showed attenuated migration toward MCP-1. Eight to 10 week-old mice were given L-NAME (30mg/kg), an eNOS inhibitor, dissolved in 0.9% NaCl in the drinking water for 14days. Angiotensin II (AngII, 0.8 mg/kg/day) was infused subcutaneously via an osmotic mini-pump for the last 7 days of the experiment. L-NAME/AngII comparably increased systolic blood pressure in control and MyPHD2KO mice. Cardiac interstitial fibrosis (3.4±0.4 vs. 2.3±0.4%, p&lt;0.05), macrophage infiltration and cardiac hypertrophy induced by L-NAEM/AngII were ameliorated in MyPHD2KO mice. Echocardiography revealed that treatment with L-NAME/AngII induced left ventricular hypertrophy and reduction of ejection fraction in control mice, which were not observed in MyPHD2KO mice. L-NAME/AngII-induced expression of TGF-β, CTGF, and Collagen I was decreased in the heart of MyPHD2KO mice. Conclusions: Myeloid specific PHD2 deletion attenuates cardiac hypertrophy and fibrosis induced by L-NAME/AngII, which may be mediated by decreased inflammation- and fibrosis-associated gene expression in macrophage. PHD2 in myeloid lineage plays a critical role in hypertensive cardiovascular remodeling.
Device Characteristics of Pentacene Dual-Gate Organic Thin-Film Transistor (2007)

We fabricated pentacene organic thin-film transistors (OTFTs) with a dual-gate structure, in which 300-nm-thick thermally grown SiO2 and 500-nm-thick parylene were used as a bottom-gate and a top-gate dielectric, respectively. The threshold voltage (Vth) of the dual-gate OTFT changed systematically with the application of voltage bias to the top-gate electrode. When voltage bias from -20 to 20 V was applied to the top-gate electrode, Vth changed from 9.4 to -9.3 V. The range of Vth shift in the dual-gate OTFT with a thin 10 nm pentacene layer was much wider than that with a thick 500 nm pentacene layer. This shift of Vth due to the body effect allows the change from an enhancement- to a depletion-mode transistor, which is beneficial for the fabrication of organic circuits.
Dnmt3a2/Dnmt3L Overexpression in the Dopaminergic System of Mice Increases Exercise Behavior through Signaling Changes in the Hypothalamus (2020)

Dnmt3a2, a <i>de novo</i> DNA methyltransferase, is induced by neuronal activity and participates in long-term memory formation with the increased expression of synaptic plasticity genes. We wanted to determine if Dnmt3a2 with its partner Dnmt3L may influence motor behavior via the dopaminergic system. To this end, we generated a mouse line, Dnmt3a2/3L<i><sup>Dat</sup></i><sup>/<i>wt</i></sup>, with dopamine transporter (DAT) promotor driven Dnmt3a2/3L overexpression. The mice were studied with behavioral paradigms (e.g., cylinder test, open field, and treadmill), brain slice patch clamp recordings, ex vivo metabolite analysis, and in vivo positron emission tomography (PET) using the dopaminergic tracer 6-[<sup>18</sup>F]FMT. The results showed that spontaneous activity and exercise performance were enhanced in Dnmt3a2/3L<i><sup>Dat</sup></i><sup>/<i>wt</i></sup> mice compared to Dnmt3a2/3L<i><sup>wt</sup></i><sup>/<i>wt</i></sup> controls. Dopaminergic substantia nigra pars compacta neurons of Dnmt3a2/3L<i><sup>Dat</sup></i><sup>/<i>wt</i></sup> animals displayed a higher fire frequency and excitability. However, dopamine concentration was not increased in the striatum, and dopamine metabolite concentration was even significantly decreased. Striatal 6-[<sup>18</sup>F]FMT uptake, reflecting aromatic L-amino acid decarboxylase activity, was the same in Dnmt3a2/3L<i><sup>Dat</sup></i><sup>/<i>wt</i></sup> mice and controls. [<sup>18</sup>F]FDG PET showed that hypothalamic metabolic activity was tightly linked to motor behavior in Dnmt3a2/3L<i><sup>Dat</sup></i><sup>/<i>wt</i></sup> mice. Furthermore, dopamine biosynthesis and motor-related metabolic activity were correlated in the hypothalamus. Our findings suggest that Dnmt3a2/3L, when overexpressed in dopaminergic neurons, modulates motor performance via activation of the nigrostriatal pathway. This does not involve increased dopamine synthesis.
Alignment of genetic and restriction maps of the photosynthesis region of the Rhodopseudomonas capsulata chromosome by a conjugation-mediated marker rescue technique (1983)

The restriction map of a 46-kilobase fragment of the Rhodopseudomonas capsulata chromosome was aligned with the genetic map of the photosynthesis region of that chromosome by a marker rescue technique. Marker rescue was effected by mobilization of vectors bearing fragments of R. capsulata DNA from Escherichia coli to a set of R. capsulata mutants. Plasmids pDPT51 and pDPT55 were constructed to mediate the intergeneric mobilization of pBR322 derivatives, and a mutant of R. capsulata with improved intergeneric recipient activity was isolated. Four previously unmapped genes affecting bacteriochlorophyll synthesis and two genes affecting photochemical reaction center synthesis have been located by marker rescue. Some of the fragments of R. capsulata DNA are capable of vector-independent complementation, implying that promoters are located on these fragments. Other fragments complement only in one orientation of insertion in the vector, implying transcription from promotors on the vectors and thereby fixing the direction of transcription for those fragments. Still other fragments of DNA show rescue only via recombination between homologous plasmid-borne DNA fragments and chromosomal mutations. The physical dimensions of the genetic map are 3.0 megadaltons per map unit, which agrees with previous estimates based on the size of the R. capsulata gene transfer agent.
Achieving Ultimate Narrowband and Ultrapure Blue Organic Light‐Emitting Diodes Based on Polycyclo‐Heteraborin Multi‐Resonance Delayed‐Fluorescence Emitters (2021)

To achieve an ultimate wide color gamut for ultrahigh-definition displays, there is great demand for the development of organic light-emitting diodes (OLEDs) enabling monochromatic, ultrapure blue electroluminescence (EL). Herein, high-efficiency and ultrapure blue OLEDs based on polycyclo-heteraborin multi-resonance thermally activated delayed fluorescence (MR-TADF) materials, BOBO-Z, BOBS-Z, and BSBS-Z, are reported. The key to the design of the present luminophores is the exquisite combination and interplay of multiple boron, nitrogen, oxygen, and sulfur heteroatoms embedded in a fused polycyclic π-system. Comprehensive photophysical and computational investigations of this family of MR-TADF materials reveal that the systematic implementation of chalcogen (oxygen and sulfur) atoms can finely modulate the emission color while maintaining a narrow bandwidth, as well as the spin-flipping rates between the excited singlet and triplet states. Consequently, OLEDs based on BOBO-Z, BOBS-Z, and BSBS-Z demonstrate narrowband and ultrapure blue EL emission, with peaks at 445-463 nm and full width at half maxima of 18-23 nm, leading to Commission Internationale de l'Éclairage-y coordinates in the range of 0.04-0.08. Particularly, for OLEDs incorporating sulfur-doped BOBS-Z and BSBS-Z, notably high maximum external EL quantum efficiencies of 26.9% and 26.8%, respectively, and small efficiency roll-offs are achieved concurrently.
Regulation of endogenous glucose production after a mixed meal in type 2 diabetes (2002)

The extent and time course of suppression of endogenous glucose production (EGP) in type 2 diabetes after a mixed meal have been determined using a new tracer methodology. Groups of age-, sex-, and weight-matched normal controls (n = 8) and diet-controlled type 2 diabetic subjects (n = 8) were studied after ingesting a standard mixed meal (550 kcal; 67% carbohydrate, 19% fat, 14% protein). There was an early insulin increment in both groups such that, by 20 min, plasma insulin levels were 266 +/- 54 and 190 +/- 53 pmol/l, respectively. EGP was similar basally [2.55 +/- 0.12 mg x kg(-1) x min(-1) in control subjects vs. 2.92 +/- 0.16 mg x kg(-1) x min(-1) in the patients (P = 0.09)]. After glucose ingestion, EGP declined rapidly in both groups to approximately 50% of basal within 30 min of the meal. Despite the initial rapid decrease, the EGP was significantly greater in the diabetic group at 60 min (1.75 +/- 0.12 vs. 1.05 +/- 0.14 mg x kg(-1) x min(-1); P < 0.01) and did not reach nadir until 210 min (0.96 +/- 0.17 mg x kg(-1) x min(-1)). Between 60 and 240 min, EGP was 47% higher in the diabetic group (0.89 +/- 0.09 vs. 1.31 +/- 0.13 mg x kg(-1) x min(-1), P < 0.02). These data quantitate the initial rapid suppression of EGP after a mixed meal in type 2 diabetes and the contribution of continuing excess glucose production to subsequent hyperglycemia.
Tocilizumab and remdesivir in hospitalized patients with severe COVID-19 pneumonia: a randomized clinical trial (2021)

Tocilizumab plus remdesivir did not shorten time to hospital discharge or "ready for discharge" to day 28 compared with placebo plus remdesivir in patients with severe COVID-19 pneumonia.
Mapping the gas thermodynamic properties of the massive cluster merger MOO J1142+1527 at z = 1.2 (2020)

We present the results of the analysis of the very massive cluster MOO J1142+1527 at a redshift z = 1.2 based on high angular resolution NIKA2 Sunyaev-Zel’dovich (SZ) and Chandra X-ray data. This multi-wavelength analysis enables us to estimate the shape of the temperature profile with unprecedented precision at this redshift and to obtain a map of the gas entropy distribution averaged along the line of sight. The comparison between the cluster morphological properties observed in the NIKA2 and Chandra maps together with the analysis of the entropy map allows us to conclude that MOOJ1142+1527 is an on-going merger hosting a cool-core at the position of the X-ray peak. This work demonstrates how the addition of spatially-resolved SZ observations to low signal-to-noise X-ray data can bring valuable insights on the intracluster medium thermodynamic properties at z &gt; 1.
Low-Temperature Electron–Phonon Interaction\nof Quantum Emitters in Hexagonal Boron Nitride (2019)

Quantum emitters based on atomic defects in layered hexagonal Boron Nitride\n(hBN) have emerged as promising solid state 'artificial atoms' with atom-like\nphotophysical and quantum optoelectronic properties. Similar to other atom-like\nemitters, defect-phonon coupling in hBN governs the characteristic\nsingle-photon emission and provides an opportunity to investigate the atomic\nand electronic structure of emitters as well as the coupling of their spin- and\ncharge-dependent electronic states to phonons. Here, we investigate these\nquestions using photoluminescence excitation (PLE) experiments at T=4K on\nsingle photon emitters in multilayer hBN grown by chemical vapor deposition. By\nscanning up to 250 meV from the zero phonon line (ZPL), we can precisely\nmeasure the emitter's coupling efficiency to different phonon modes. Our\nresults show that excitation mediated by the absorption of one in-plane optical\nphonon increases the emitter absorption probability ten-fold compared to that\nmediated by acoustic or out-of-plane optical phonons. We compare these\nmeasurements against theoretical predictions by first-principles\ndensity-functional theory of four defect candidates, for which we calculate\nprevalent charge states and their spin-dependent coupling to bulk and local\nphonon modes. Our work illuminates the phonon-coupled dynamics in hBN quantum\nemitters at cryogenic temperature, with implications more generally for\nmesoscopic quantum emitter systems in 2D materials and represents possible\napplications in solid-state quantum technologies.\n
Practical experience with wireless networks integration using Mobile IPv6 (2003)

article Practical experience with wireless networks integration using Mobile IPv6 Share on Authors: Rajiv Chakravorty University of Cambridge, Cambridge, U.K. University of Cambridge, Cambridge, U.K.View Profile , Pablo Vidales Laboratory for Communication Engineering, Cambridge, U.K. Laboratory for Communication Engineering, Cambridge, U.K.View Profile , Kavitha Subramanian University of Cambridge, Cambridge, U.K. University of Cambridge, Cambridge, U.K.View Profile , Ian Pratt University of Cambridge, Cambridge, U.K. University of Cambridge, Cambridge, U.K.View Profile , Jon Crowcroft University of Cambridge, Cambridge, U.K. University of Cambridge, Cambridge, U.K.View Profile Authors Info & Claims ACM SIGMOBILE Mobile Computing and Communications ReviewVolume 7Issue 4October 2003 pp 47–49https://doi.org/10.1145/965732.965741Published:01 October 2003 10citation926DownloadsMetricsTotal Citations10Total Downloads926Last 12 Months0Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Preliminary Report: Evaluation of Storage Conditions and Cryococktails during Peripheral Blood Mononuclear Cell Cryopreservation (2007)

The use of cryopreserved peripheral blood mononuclear cells (PBMCs) has proven critical in both clinical and biomedical applications. While utilized, in numerous settings, the functionality of frozen PBMCs is often limited, and a disconnect exists between measured viability and outcome. In this study we investigated parameters affecting outcome including storage protocol, freeze media, and assessment assay. PBMCs were isolated from seven healthy donors and cryopreserved in: (1) a media-based cocktail (SAIC), (2) CryoStor 7.5 (CS7.5), and (3) CryoStor 7.5 plus caspase inhibitors (CS7.5 ± Inh). All samples were stored in vapor phase liquid nitrogen (static) with replicates exposed to a thermal cycling regime, which mimicked typical sample handling (cycle). Viability was assessed immediately postthaw by trypan blue. Cryopreservation-induced delayed-onset cell death (CIDOCD) was evaluated postthaw using the Vybrant® Apoptosis Assay (VAA) that differentiated viability, apoptosis, and necrosis by fluorescent microscopy. Analysis of static stored PBMCs in CS7.5 demonstrated improved viability 1 h postthaw (82% –90%) compared to SAIC samples (60%–72%). Both cryococktails performed similarly after 24 h postthaw, yet fewer surviving PBMCs were evident, especially when assessed by VAA (SAIC: 31%; CS7.5: 36%). Replicate PBMC aliquots subjected to temperature cycling did not appear to have altered viability at 1 and 24 h postthaw (trypan blue). However, VAA showed that the SAIC cryococktail yielded improved viability at 1 h postthaw (61% vs. 51.8%, respectively) whereas by 24 h both the SAIC and CS7.5 samples were similar (∼20%). CIDOCD assessment revealed significant levels of both necrosis and apoptosis at 4 h and 8 h across all conditions. The observed decline in viability in the cycled samples was a result of increased apoptosis. Finally, the incorporation of caspase inhibitors did not improve static sample viability, but did significantly reduce the negative effect of temperature cycling. These preliminary investigations demonstrate that CIDOCD plays a significant role in PBMC cryopreservation failure, and that temperature fluctuations influence the overall level. Further, these studies demonstrate the importance of using multiple viability assessment techniques in evaluating PBMC cryococktail performance.
A high-throughput platform for population reformatting and mammalian expression of phage display libraries to enable functional screening as full-length IgG (2017)

Phage display antibody libraries are a rich resource for discovery of potential therapeutic antibodies. Single-chain variable fragment (scFv) libraries are the most common format due to the efficient display of scFv by phage particles and the ease by which soluble scFv antibodies can be expressed for high-throughput screening. Typically, a cascade of screening and triaging activities are performed, beginning with the assessment of large numbers of E. coli-expressed scFv, and progressing through additional assays with individual reformatting of the most promising scFv to full-length IgG. However, use of high-throughput screening of scFv for the discovery of full-length IgG is not ideal because of the differences between these molecules. Furthermore, the reformatting step represents a bottle neck in the process because each antibody has to be handled individually to preserve the unique VH and VL pairing. These problems could be resolved if populations of scFv could be reformatted to full-length IgG before screening without disrupting the variable region pairing. Here, we describe a novel strategy that allows the reformatting of diverse populations of scFv from phage selections to full-length IgG in a batch format. The reformatting process maintains the diversity and variable region pairing with high fidelity, and the resulted IgG pool enables high-throughput expression of IgG in mammalian cells and cell-based functional screening. The improved process led to the discovery of potent candidates that are comparable or better than those obtained by traditional methods. This strategy should also be readily applicable to Fab-based phage libraries. Our approach, Screening in Product Format (SiPF), represents a substantial improvement in the field of antibody discovery using phage display.
ImprovedO/SExchange Reagents (1984)

Les disulfures-2,4 de diarylthio-2,4 dithiadiphosphetannes-1,3,2,4, permettent de realiser l'echange O/S dans des acides et amides carboxyliques. Obtention de dithioesters, thioamides, thiolactames
Variable-sensitivity photodetector that uses a metal–semiconductor–metal structure for optical neural networks (1991)

A novel type of photodetector called a variable-sensitivity photodetector has been developed for optical implementation of neural networks. It utilizes a metal-semiconductor-metal structure whose quantum efficiency can be modulated by an applied bias voltage. A linear dependence of the sensitivity on the bias voltage was obtained with the bipolar current flow. This device operated as a multiplier of the incident light intensity and the bias voltage. It is shown that this device is suitable for achieving dynamic synaptic interconnections. A 4 x 4 array device was fabricated and demonstrated.
Is it worth ‘flipping’ your favourite journal to open access? An opinion (2022)

In the course of 2019, a new open access journal called Magnetic Resonance was launched by the Groupement Ampère in Zurich. The journal is produced by a small publisher in Göttingen, Germany, that has gathered experience with a palette of journals run by the European Geosciences Union (EGU). The initial idea of Magnetic Resonance was to create a so-called “gold” open access journal: one can freely download all papers, including preliminary and revised versions, reviewers’ critiques and authors’ replies, while the authors’ institutions pay reasonable Article Processing Charges (APCs). The new journal is independent of learned societies like the Royal Society of Chemistry (RSC) and the American Chemical Society (ACS), and it is not exposed to profit-oriented business models of commercial publishers like RLX/Elsevier, Springer/Nature, Cell Press, and Wiley. After about 2 years, it seems appropriate to publish a few remarks about our experience of the strengths and weaknesses of open access publishing. Our discussion draws on a detailed analysis of the Ethics Committee of the French CNRS, and on a debate organized by the Royal Dutch Academy of Science.
A comparative assessment of clinical whole exome and transcriptome profiling across sequencing centers: implications for precision cancer medicine (2016)

Advances in next generation sequencing technologies provide approaches to comprehensively determine genomic alterations within a tumor that occur as a cause or consequence of neoplastic growth. Though providers offering various cancer genomics assays have multiplied, the level of reproducibility in terms of the technical sensitivity and the conclusions resulting from the data analyses have not been assessed.We sought to determine the reproducibility of ascertaining tumor genome aberrations using whole exome sequencing (WES) and RNAseq. Samples of the same metastatic tumors were independently processed and subjected to WES of tumor and constitutional DNA, and RNAseq of RNA, at two sequencing centers. Overall, the sequencing results were highly comparable. Concordant mutation calls ranged from 88% to 93% of all variants including 100% agreement across 154 cancer-associated genes. Regions of copy losses and gains were uniformly identified and called by each sequencing center and chromosomal plots showed nearly identical patterns. Transcript abundance levels also exhibited a high degree of concordance (r2 ≥ 0.78;Pearson). Biologically-relevant gene fusion events were concordantly called. Exome sequencing of germline DNA samples provided a minimum of 30X coverage depth across 56 genes where incidental findings are recommended to be reported. One possible pathogenic variant in the APC gene was identified by both sequencing centers.The findings from this study demonstrate that results of somatic and germline sequencing are highly concordant across sequencing centers that have substantial experience in the technological requirements for preparing, sequencing and annotating DNA and RNA from human biospecimens.