gebhart/patrepeval huggingface dataset:
About TimeNarrative, Fiction and the Philosophy of Time (2006)

This book brings together ideas about time from narrative theory and philosophy. It argues that literary criticism and narratology have approached narrative primarily as a form of retrospect, and demonstrates through a series of arguments and readings that anticipation and other forms of projection into the future offer new analytical perspectives to narrative criticism and theory. The book offers an account of ‘prolepsis’ or ‘flashforward’ in the contemporary novel that retrieves it from the realm of experimentation and places it at the heart of a contemporary mode of being, both personal and collective, which experiences the present as the object of a future memory. With reference to some of the most important recent developments in the philosophy of time, it aims to define a set of questions about tense and temporal reference in narrative that make it possible to reconsider the function of stories in contemporary culture. The text also reopens traditional questions about the difference between literature and philosophy in relation to knowledge of time. In the context of these questions, it offers analyses of a range of contemporary fiction by writers such as Ali Smith, Ian McEwan, Martin Amis and Graham Swift.
Structure–Activity Map of Ceria Nanoparticles, Nanocubes, and Mesoporous Architectures (2016)

Structure-activity mapping is central to the exploitation and optimisation of nanomaterial catalysts in a variety of technologically important heterogeneous reactions, such as automotive catalysis and water gas shift reactions. Here, we present a catalytic activity map for nanoceria, calculated as a function of shape, size, architecture and defect content, using atom-level models. The activity map reveals that as oxygen is gradually depleted from the nanoceria catalyst, so it becomes energetically more difficult to extract further oxygen. We propose that the oxygen storage capacity (OSC) of ceria corresponds to the level of oxygen depletion where it becomes thermodynamically prohibitive to extract further oxygen from the material (positive free energy). Moreover, because the reaction enthalpy contributes to the free energy, we predict that the OSC is influenced by the particular reaction being performed. Specifically, the more negative the reaction enthalpy, the higher the potential OSC (notwithstanding entropic contributions). The decrease in catalytic activity during an oxidation reaction - emanating from the increase in energy required to extract oxygen - suggests that there exists a ‘window of catalytic operation’, where the activity of the catalyst can be controlled by operating at different points within this window. We show experimentally, how the activity can be modified by engineering the oxygen vacancy concentration and hence the oxygen content of the catalyst to facility tunable activity. In addition to the defect content, we find that size (particle diameter, mesoporous wall thickness) and nanostructuring (particle, cube, mesoporous architecture, morphology and surfaces exposed) are key drivers of catalytic activity. To generate the atom-level models of ceria nanostructures, we use non-equilibrium Molecular Dynamics to simulate the self-assembly of mesoporous ceria from amorphous nano-building blocks, followed by a (simulated) crystallisation step; the latter evolves the crystal structure and microstructural features such as grain-boundaries and dislocations. Our simulated crystallisations emanate wholly from a multitude of ‘random’ atom collisions, which result in the spontaneous evolution of a crystalline seed that nucleates crystallisation of the whole system. The atomistic models generated by ‘simulating synthesis’ are shown to be in quantitative structural agreement with experiment.
Estimation of Chlorophyll-a Concentrations in the Pearl River Estuary Using In Situ Hyperspectral Data: A Case Study (2008)

Taking Pearl River Estuary (PRE), China as an example, we explored the potential of in situ hyperspectral data in estimating chlorophyll-a concentrations of turbid waters. Two cruises were conducted on August 21, 2006 and May 18, 2004 to collect the data of water quality and remote sensing reflectance (Rrs). The field surveys showed that: chlorophyll-a concentration ranged from 2.97μg/L to 49.97μg/L, and turbidity 13.6-128.9 NTU. The Rrs spectra were binned to 10 nm resolution, and then processed to be first-order and second-order derivatives. A linear algorithm is developed to estimate chlorophyll-a concentrations based on second-order derivative at 670 nm; its mean relative error of estimation is less than 58%, and the root mean square error is 6.69 μg/L, which is better than other popular algorithms for turbid waters, i.e., the ratio of Rrs at 700 nm and 670 nm. The Case-I algorithm of blue-green band ratio is also proved to be a failed application in PRE, and so does the algorithm of fluorescence line height (FLH), which is questionable for its application in waters with strong light scattering and absorption. All the above work was done without classification of cloud conditions. This suggests that the second-order derivative at 670 nm could be effective for estimation of chlorophyll-a concentrations in turbid waters, especially in situ .
Models for acoustic propagation over ground theory and experiment (1980)

Analytic models which predict the propagation of noise from a point source to a point receiver over an impedance covered terrain have been used in this investigation to predict the sideline noise received from an incoherent line noise source. The point to point propagation models include a direct, a reflected, a ground wave, and sometimes a so-called surface wave. Different authors have given different forms of the solution. The incoherent line simulates traffic noise and is located at the accepted source height having the spectrum of an automobile, a light truck, or a heavy truck. To validate these models, tests were made on 1:5 scale model in a gymnasium covered by carpets that simulate grassy terrain. A carriage carrying a set of nine height-adjustable speakers is moved along a line to simulate traffic noise. Each speaker is pulsed with pure tones, so that the nine speakers reproduce 19 third octave components of the simulated traffic noise spectrum. A set of 16 microphones are used to record receiver field. In general, the agreement between the theoretical prediction the experiment was good except for receivers near the ground when the levels were overpredicted. [Work supported by NCHRP and FHWA.]
Heat Transport Capability of Axial Grooved Heat Pipes. Capillary pumping limit under micro- and normal-gravity condition with asymmetrical heating. (1998)

Heat pipes have capillary pumping limit when they operate under micro-gravity condition or axially top heating mode under normal-gravity. A theoretical model was developed to predict temperature rise in evaporator with asymmetrical heating and the capillary pumping limit. In this model, puddling effect, liquid recession into groove bottom and 3-dimensional heat conduction in the evaporator were taken into consideration. The prediction under micro-and normal-gravity condition agreed well with experimental data. It is found by calculation that the temperature at the evaporator end begin to increase just after all gooves dry out at the evaporator end in case of both symmetrical and asymmetrical heating and the capillary pumping limit is not much affected by heating condition when the thermal conductivity of heat pipe envelope is large.
Structural reappraisal of the limonoid insect antifeedant azadirachtin (1985)

J. N. Bilton, H. B. Broughton, S. V. Ley, Z. Lidert, E. D. Morgan, H. S. Rzepa and R. N. Sheppard, J. Chem. Soc., Chem. Commun., 1985, 968 DOI: 10.1039/C39850000968
A possible regulation of negative factor (Nef) activity of human immunodeficiency virus type 1 by the viral protease (1994)

Negative factor (Nef) protein from human immunodeficiency virus type 1 (HIV-1) is cleaved into two well-defined domains by the HIV-1-encoded protease. The cleavage site is located between Trp57 and Leu58 and is well conserved. The two domains are stable in the presence of protease for more than 48 h. The C-terminal core domain contains a well-conserved well-folded region. The cleavage releases the core domain from the myristoylated membrane anchor domain. As is the case for other HIV proteins, cleavage of Nef could be crucial for correct biological function.
Myc instructs and maintains pancreatic adenocarcinoma phenotype (2019)

SUMMARY Pancreatic ductal adenocarcinoma (PDAC) is characterized by its dismal prognosis and its signature fibroinflammatory phenotype. We show that activation of Myc in PanIN epithelial cells is alone sufficient to instruct and maintain immediate transition of indolent PanINs to PDACs phenotypically identical to the spontaneous human disease. Myc does this by inducing a distinct, tissue-specific ensemble of instructive signals that, together, coordinate changes in multiple, stromal and inflammatory cell types to generate the signature PDAC stroma. We also demonstrate that the Myc PDAC switch is completely reversible and that Myc deactivation immediately triggers meticulous disassembly of both PDAC tumor and stroma. Hence, both the formation and deconstruction of the complex PDAC phenotype may be mediated by a single, reversible molecular switch. SIGNIFICANCE Pancreatic ductal adenocarcinoma (PDAC) has a dismal prognosis and lacks effective therapies. We show that Myc is a single molecular switch that directly and immediately instructs transition from indolent KRas G12D -induced PanIN to the characteristic complex, multi-cell-type fibroinflammatory and immune-cold PDAC phenotype through the release of a distinct, tissuespecific set of instructive signals. The same combination of KRas G12D and Myc drives a very different phenotype in lung, indicating that the principal phenotypes of adenocarcinomas are dictated by tissue of origin not specific oncogenes. We also show that the Myc switch is immediately and completely reversible: blocking Myc function triggers meticulous disassembly of the entire PDAC tumor-stromal edifice demonstrating that phenotypic complexity is not a barrier to effective treatment of cancers.
Synthese von 1,3- und 1,4-phenylenverknüpften bischinonsubstituierten Porphyrin-Dimeren (1987)

Alle bisher synthetisierten Modellverbindungen für das photosynthetische Reaktionszentrum (RC) variierten den Abstand zwischen Donor- und Acceptoreinheit. Da aber, wie die Strukturbestimmung des RCs ergab, auch die Orientierung der Makrocyclen zueinander wichtig ist, wurden erstmals Modelle mit verschiedenen fixierten Winkeln zwischen den Porphyrineinheiten synthetisiert: das lineare 1 und ein giebelartiges Analogon. Lösungen beider Verbindungen in Toluol zeigen bei 418 nm-Anregung keine Fluoreszenz.
Evaluation of tolerance to Phytophthora capsici-the causal agent of foot rot disease in black pepper (2019)

Vietnam is the leading black pepper export country in the world. However, the production of pepper may be affected by natural disasters, pests such as Phytophthora capsici. The Phytophthora capsica disease has caused a significant decline in pepper yields. The disease is characterized with a high mortality rate (up to 100%) and rapid outbreak and thus is very challenging to control. In the present study, eight strains of P. capsici were isolated from 100 samples of leaf, stem, root and soil that were collected from pepper-growing areas of Dong Nai, Binh Duong and Ba Ria - Vung Tau provinces. These isolates' straits had capacity to cause foot rot on pepper leaf after two days of inoculation. Among them, the isolates with the highest pathogenicity are BR-L1, DN-D1 and DN-D2. In order to determine the resistance level to P. capsici of commonly grown pepper varieties (Vinh Linh, Se, Xanh, Trau and Kuching), the pepper leaves were in vitro infected with P. capsici BR-L1 spores in laboratory and greenhouse conditions. Trau variety showed the highest resistance level to P. capsici with the as indicated by (P &lt; 0.01) disease ratio (74.1%) and disease index (73.7%) after 6 days in laboratory condition and the corresponding numbers of 17.3% and 15.8% after 12 days in greenhouse condition.
Pymol script: listselection.py (2014)

From the description on Pymolwiki: <em>This script will:</em> <em>- list multiple residues once</em> <em>- include water and hetatoms</em> <em>- account for different chains/objects</em> <em>- produce a screen/printed output</em> Full description, examples and usage notes: http://www.pymolwiki.org/index.php/ListSelection2
Targeting diseased tissues by pHLIP insertion at low cell surface pH (2014)

The discovery of the pH Low Insertion Peptides (pHLIPs®) provides an opportunity to develop imaging and drug delivery agents targeting extracellular acidity. Extracellular acidity is associated with many pathological states, such as those in cancer, ischemic stroke, neurotrauma, infection, lacerations, and others. The metabolism of cells in injured or diseased tissues often results in the acidification of the extracellular environment, so acidosis might be useful as a general marker for the imaging and treatment of diseased states if an effective targeting method can be developed. The molecular mechanism of a pHLIP peptide is based on pH-dependent membrane-associated folding. pHLIPs, being moderately hydrophobic peptides, have high affinities for cellular membranes at normal pH, but fold and insert across membranes at low pH, allowing them to sense pH at the surfaces of cells in diseased tissues, where it is the lowest. Here we discuss the main principles of pHLIP interactions with membrane lipid bilayers at neutral and low pHs, the possibility of tuning the folding and insertion pH by peptide sequence variation, and potential applications of pHLIPs for imaging, therapy and image-guided interventions.
Integration of ATAC-seq and RNA-seq identifies human alpha cell and beta cell signature genes (2016)

OBJECTIVE: Although glucagon-secreting α-cells and insulin-secreting β-cells have opposing functions in regulating plasma glucose levels, the two cell types share a common developmental origin and exhibit overlapping transcriptomes and epigenomes. Notably, destruction of β-cells can stimulate repopulation via transdifferentiation of α-cells, at least in mice, suggesting plasticity between these cell fates. Furthermore, dysfunction of both α- and β-cells contributes to the pathophysiology of type 1 and type 2 diabetes, and β-cell de-differentiation has been proposed to contribute to type 2 diabetes. Our objective was to delineate the molecular properties that maintain islet cell type specification yet allow for cellular plasticity. We hypothesized that correlating cell type-specific transcriptomes with an atlas of open chromatin will identify novel genes and transcriptional regulatory elements such as enhancers involved in α- and β-cell specification and plasticity. METHODS: We sorted human α- and β-cells and performed the “Assay for Transposase-Accessible Chromatin with high throughput sequencing” (ATAC-seq) and mRNA-seq, followed by integrative analysis to identify cell type-selective gene regulatory regions. RESULTS: We identified numerous transcripts with either α-cell- or β-cell-selective expression and discovered the cell type-selective open chromatin regions that correlate with these gene activation patterns. We confirmed cell type-selective expression on the protein level for two of the top hits from our screen. The “group specific protein” (GC; or vitamin D binding protein) was restricted to α-cells, while CHODL (chondrolectin) immunoreactivity was only present in β-cells. Furthermore, α-cell- and β-cell-selective ATAC-seq peaks were identified to overlap with known binding sites for islet transcription factors, as well as with single nucleotide polymorphisms (SNPs) previously identified as risk loci for type 2 diabetes. CONCLUSIONS: We have determined the genetic landscape of human α- and β-cells based on chromatin accessibility and transcript levels, which allowed for detection of novel α- and β-cell signature genes not previously known to be expressed in islets. Using fine-mapping of open chromatin, we have identified thousands of potential cis-regulatory elements that operate in an endocrine cell type-specific fashion.
Tunnel junctions for two-color nitride light emitting diodes and laser diodes grown by plasma assisted molecular beam epitaxy (2018)

One of the most challenging issues to address in nitride based devices like light emitting diodes (LEDs) and laser diodes (LDs) is poor conductivity of p-type region. Additionally, high resistance of the p-type contact, that is very difficult to reduce, determines performance and influences design of InGaN LEDs and LDs. Recently, there has been increasing attention given to the interband tunnel junctions (TJ) for effective carrier conversion between n-type and p-type material region in nitride LEDs and LDs. It was clearly demonstrated that TJ resistance for wide bandgap semiconductors can be effectively suppressed by making use of the piezoelectric fields in the region of the junction [1]. Low resistance TJ were investigated and realized using GaN/InGaN/GaN heterostructures. The MBE technology seems to be more efficient than MOVPE for practical realization of the devices with TJ. For MOVPE it is difficult to activate the p-type conductivity in the (In)GaN:Mg layers which are deeply buried below n-type layers due to the fact that diffusion of hydrogen is completely blocked through n-type layers. Therefore several attempts for hybrid MOVPE/MBE growth was performed and TJ LEDs [2], TJ LDs [3] and TJ VCSELs [4] were shown where active p-i-n region was grown by MOVPE and p-n TJ by MBE. However, the presence of the impurities in the MOVPE p-type surface used for MBE regrowth can deteriorate/limit performance of devices grown by hybrid method.
Adipocyte-induced transdifferentiation of osteoblasts and its potential role in age-related bone loss (2021)

Our preliminary findings have lead us to propose bone marrow adipocyte secretions as new contributors to bone loss. Indeed, using a coculture model based on human bone marrow stromal cells, we previously showed that soluble factors secreted by adipocytes induced the conversion of osteoblasts towards an adipocyte-like phenotype. In this study, microarray gene expression profiling showed profound transcriptomic changes in osteoblasts following coculture and confirmed the enrichment of the adipocyte gene signature. Double immunofluorescence microscopic analyses demonstrated the coexpression of adipogenic and osteoblastic specific markers in individual cells, providing evidence for a transdifferentiation event. At the molecular level, this conversion was associated with upregulated expression levels of reprogramming genes and a decrease in the DNA methylation level. In line with these in vitro results, preliminary immunohistochemical analysis of bone sections revealed adipogenic marker expression in osteoblasts from elderly subjects. Altogether, these data suggest that osteoblast transdifferentiation could contribute to decreased bone mass upon ageing.
The biology and mechanism of action of suppressor of cytokine signaling 3 (2012)

Suppressors of cytokine signaling 3 (SOCS3) has been shown to be an important and non-redundant feedback inhibitor of several cytokines including leukemia inhibitory factor, IL-6, IL-11, Ciliary neurotrophic factor (CNTF), leptin, and granulocyte colony-stimulating factor (G-CSF). Loss of SOCS3 in vivo has profound effects on placental development, inflammation, fat-induced weight gain, and insulin sensitivity. SOCS3 expression is induced by Janus kinase (JAK)/signal transducers and activators of transcription (STAT) signaling and it then binds to specific cytokine receptors (including gp130, G-CSF, and leptin receptors). SOCS3 then inhibits JAK/STAT signaling in two distinct ways. First, SOCS3 is able to directly inhibit the catalytic activity of JAK1, JAK2, or TYK2 while remaining bound to the cytokine receptor. Second, SOCS3 recruits elongins B/C and Cullin5 to generate an E3 ligase that ubiquitinates both JAK and cytokine receptor targeting them for proteasomal degradation. Detailed in vivo studies have revealed that SOCS3 action not only limits the duration of cytokine signaling to prevent overactivity but it is also important in maintaining the specificity of cytokine signaling.
Humeral fractures after shoulder arthroplasty. (1995)

Nine humeral fractures occurred subsequent to 499 shoulder arthroplasties that had been performed between December 1978 and November 1987 at the Mayo Clinic. The time from the arthroplasty to the fracture averaged thirty-nine months (range, eight to 101 months). Seven patients were women and two were men, and the average age was seventy years (range, forty-five to eighty-five years). The arthroplasties were performed for rheumatoid arthritis in five patients and for the sequelae of trauma in four. Six patients had advanced osteopenia, and two had had an ipsilateral total elbow arthroplasty. Six of the fractures were centered at the tip of the prosthesis; one fracture (type A) extended proximally, and five (type B) did not. The three remaining fractures (type C) involved the humeral shaft distal to the implant and extended into the distal humeral metaphysis. Four fractures healed with non-operative treatment. Two fractures that had unacceptable alignment were treated successfully with operative intervention. Three fractures that were treated with immobilization in a splint failed to heal; two of those fractures eventually united after a revision of the prosthesis and bone-grafting was performed, and one fracture remained ununited. Radial nerve palsy developed postoperatively in two patients, and it resolved within three months. Five patients had poor active motion before the fracture, and two of them had even less motion after the fracture was treated. Our experience suggests that long oblique and spiral fractures can be successfully treated non-operatively, provided that the skeletal alignment is acceptable.(ABSTRACT TRUNCATED AT 250 WORDS)
Loss of function mutations inHARScause a spectrum of inherited peripheral neuropathies (2015)

Inherited peripheral neuropathies are a genetically heterogeneous group of disorders characterized by distal muscle weakness and sensory loss. Mutations in genes encoding aminoacyl-tRNA synthetases have been implicated in peripheral neuropathies, suggesting that these tRNA charging enzymes are uniquely important for the peripheral nerve. Recently, a mutation in histidyl-tRNA synthetase (HARS) was identified in a single patient with a late-onset, sensory-predominant peripheral neuropathy; however, the genetic evidence was lacking, making the significance of the finding unclear. Here, we present clinical, genetic, and functional data that implicate HARS mutations in inherited peripheral neuropathies. The associated phenotypic spectrum is broad and encompasses axonal and demyelinating motor and sensory neuropathies, including four young patients presenting with pure motor axonal neuropathy. Genome-wide linkage studies in combination with whole-exome and conventional sequencing revealed four distinct and previously unreported heterozygous HARS mutations segregating with autosomal dominant peripheral neuropathy in four unrelated families (p.Thr132Ile, p.Pro134His, p.Asp175Glu and p.Asp364Tyr). All mutations cause a loss of function in yeast complementation assays, and p.Asp364Tyr is dominantly neurotoxic in a Caenorhabditis elegans model. This study demonstrates the role of HARS mutations in peripheral neuropathy and expands the genetic and clinical spectrum of aminoacyl-tRNA synthetase-related human disease.