gebhart/patrepeval huggingface dataset:
Relationships Among Virus Spread, Cytopathogenicity, and Virulence as Revealed by the Noncytopathic Mutants of Newcastle Disease Virus (1981)

We have studied protein synthesis in cultured cells infected with the six noncytopathic (nc) mutants of the Australia-Victoria strain (AV-WT) of Newcastle disease virus and their plaque-forming revertants. Virus-specific polypeptides accumulated at 30 to 63% of wild-type levels in nc mutant-infected cells and between 66 and 175% of wild-type levels in revertant-infected cells. An exception was the L polypeptide, which accumulated in nc mutant-infected cells at only 5 to 20% of the levels found in wild-type infection. The reduced accumulation of the L polypeptide did not appear to be due to increased degradation of that polypeptide. A new polypeptide (X) accumulated instead of polypeptide P in cells infected with mutants nc4 or nc16 and in virions released from them. Peptide mapping identified X as an altered form of P. A revertant of mutant nc4 (nc4S1), which forms larger hemadsorbing spots, but still does not form plaques, accumulated P instead of the X polypeptide. Thus, a lesion in P can affect virus spread without affecting cytopathogenicity. Virions of mutant nc7 and two naturally occurring avirulent strains of Newcastle disease virus (NJ LaSota and B1-Hitchner) contained polypeptides (F(7) and F(A), respectively) related to, but migrating more rapidly than, F(0) in sodium dodecyl sulfate-polyacrylamide gels. As previously reported for avirulent strains, a brief treatment of nc7 virions with trypsin converted F(7) to F and increased infectivity. Similarly, culturing nc7-infected cells in the presence of trypsin facilitated fusion from within and viral spread from cell to cell. A plaque-forming revertant of nc7 still accumulated F(7) in virions, indicating that the lesions responsible for the F(7) and noncytopathic phenotypes are genetically separable. The virulent parental strain, AV-WT, exhibited a mean embryo death time of 42 h. Both the larger-spot-forming revertant of nc4 (nc4S1) and the small-plaque-forming revertant of nc7 exhibited a decrease in mean embryo death time (increase in virulence) from 74 to 63 h. A second-step, plaque-forming revertant derived from nc4S1 (nc4S1R1) exhibited a further decrease in mean embryo death time from 63 to 44 h. The results suggest that the F(A)-F(7) and X lesions affect the ability of virus to spread from cell to cell. In addition, these lesions appear to be genetically separable from those responsible for the noncytopathic phenotype. However, both types of lesions cause an extension of mean embryo death time and, thus, may be relevant to virulence in vivo.
Taming Tricky DSBs: ATM on duty (2017)

Ataxia Telangiectasia Mutated (ATM) has been known for decades as the main kinase mediating the DNA Double-Strand Break Response (DDR). Extensive studies have revealed its dual role in locally promoting detection and repair of DSBs as well as in activating global DNA damage checkpoints. However, recent studies pinpoint additional unanticipated functions for ATM in modifying both the local chromatin landscape and the global chromosome organization, more particularly at persistent breaks. Given the emergence of a novel and unexpected class of DSBs prevalently arising in transcriptionally active genes and intrinsically difficult to repair, a specific role of ATM at refractory DSBs could be an important and so far overlooked feature of Ataxia Telangiectasia (A-T) a severe disorder associated with ATM mutations.
Metabolic implication of tigecycline as an efficacious second‐line treatment for sorafenib‐resistant hepatocellular carcinoma (2020)

Sorafenib represents the current standard of care for patients with advanced-stage hepatocellular carcinoma (HCC). However, acquired drug resistance occurs frequently during therapy and is accompanied by rapid tumor regrowth after sorafenib therapy termination. To identify the mechanism of this therapy-limiting growth resumption, we established robust sorafenib resistance HCC cell models that exhibited mitochondrial dysfunction and chemotherapeutic crossresistance. We found a rapid relapse of tumor cell proliferation after sorafenib withdrawal, which was caused by renewal of mitochondrial structures alongside a metabolic switch toward high electron transport system (ETS) activity. The translation-inhibiting antibiotic tigecycline impaired the biogenesis of mitochondrial DNA-encoded ETS subunits and limited the electron acceptor turnover required for glutamine oxidation. Thereby, tigecycline prevented the tumor relapse in vitro and in murine xenografts in vivo. These results offer a promising second-line therapeutic approach for advanced-stage HCC patients with progressive disease undergoing sorafenib therapy or treatment interruption due to severe adverse events.
Energy forward price prediction with a hybrid adaptive model (2009)

This paper presents a forecasting technique for forward electricity/gas prices, one day ahead. This technique combines a Kalman filter (KF) and a generalised autoregressive conditional heteroschedasticity (GARCH) model (often used in financial forecasting). The GARCH model is used to compute next value of a time series. The KF updates parameters of the GARCH model when the new observation is available. This technique is applied to real data from the UK energy markets to evaluate its performance. The results show that the forecasting accuracy is improved significantly by using this hybrid model. The methodology can be also applied to forecasting market clearing prices and electricity/gas loads.
Self-Healing of a Cross-Linked Polymer with Dynamic Covalent Linkages at Mild Temperature and Evaluation at Macroscopic and Molecular Levels (2015)

A lot of self-healing materials using dynamic bonding systems have been reported, while the focus is mainly on the macroscopic self-healing behavior such as visually recognizable healing. Because the healing originates from microscopic chemical reactions of the dynamic bonds, evaluation of the reactions in the materials is necessary for elucidation of the healing mechanisms and development of the healing ability. Herein, we demonstrated self-healing of a cross-linked polymer with diarylbibenzofuranone (DABBF)-based dynamic covalent linkages at mild temperature and investigated the healing behavior from both macroscopic and microscopic viewpoints. The macroscopic behavior was inspected by mechanical tests, and the linkage reaction (equilibrium) was evaluated by electron paramagnetic resonance measurements. These assessments revealed that the healing is strongly dependent on temperature, which is attributable to synergism between changes in the chain mobility and in the equilibrium of the incorporated linkages. These findings would be applicable to other dynamic bonding systems.
Plasmodium falciparum Variant Surface Antigen Expression Patterns during Malaria (2005)

The variant surface antigens expressed on Plasmodium falciparum-infected erythrocytes are potentially important targets of immunity to malaria and are encoded, at least in part, by a family of var genes, about 60 of which are present within every parasite genome. Here we use semi-conserved regions within short var gene sequence "tags" to make direct comparisons of var gene expression in 12 clinical parasite isolates from Kenyan children. A total of 1,746 var clones were sequenced from genomic and cDNA and assigned to one of six sequence groups using specific sequence features. The results show the following. (1) The relative numbers of genomic clones falling in each of the sequence groups was similar between parasite isolates and corresponded well with the numbers of genes found in the genome of a single, fully sequenced parasite isolate. In contrast, the relative numbers of cDNA clones falling in each group varied considerably between isolates. (2) Expression of sequences belonging to a relatively conserved group was negatively associated with the repertoire of variant surface antigen antibodies carried by the infected child at the time of disease, whereas expression of sequences belonging to another group was associated with the parasite "rosetting" phenotype, a well established virulence determinant. Our results suggest that information on the state of the host-parasite relationship in vivo can be provided by measurements of the differential expression of different var groups, and need only be defined by short stretches of sequence data.
Multiple clustered instance learning for histopathology cancer image classification, segmentation and clustering (2012)

Cancer tissues in histopathology images exhibit abnormal patterns; it is of great clinical importance to label a histopathology image as having cancerous regions or not and perform the corresponding image segmentation. However, the detailed annotation of cancer cells is often an ambiguous and challenging task. In this paper, we propose a new learning method, multiple clustered instance learning (MCIL), to classify, segment and cluster cancer cells in colon histopathology images. The proposed MCIL method simultaneously performs image-level classification (cancer vs. non-cancer image), pixel-level segmentation (cancer vs. non-cancer tissue), and patch-level clustering (cancer subclasses). We embed the clustering concept into the multiple instance learning (MIL) setting and derive a principled solution to perform the above three tasks in an integrated framework. Experimental results demonstrate the efficiency and effectiveness of MCIL in analyzing colon cancers.
Anti-invasive Activity of Lawsonia inermis Branch and Its Potential Target Protein (2018)

The methanolic extract from the branch of Lawsonia inermis was found to inhibit the invasion of HT1080 cells strongly. The extract and its EtOAc- and 1-BuOH-soluble fractions strongly inhibited the enzyme activities and the secretions of MMPs from HT1080 cells. We, therefore, tried to examine and estimate the active constituents among the constituents isolated. However, there are no active compound among the isolated compounds. Next, we tried to identify the selective binding protein of whole constituents of their extracts. As a result, ribosomal protein S18 (RPs S18, human), 60S ribosomal protein L18 isoform 1 (60S RPs L18 i1, human) and eukaryotic elongation factor 2 (eEF2, human) were detected as their selective binding and potential target proteins. To confirm that the proteins are target proteins or not, we examined the effects of their proteins on synthesis of MMPs using siRNA method. With the treatment of siRNA for RPs S18, 60S RPs L18 i1 and eEF2 proteins, the MMP-2 protein synthesis were downregulated in HT1080 cells. MMP-9 productions were also downregulated with the treatment of siRNA for RPs S18 and eEF2. From the results, we reached a conclusion that the extract was considered to have the potential to inhibit the production of MMPs proteins via inhibition of RPs S18 and eEF2 proteins, leading to inhibit the invasion in HT1080 cells.
Detection of Electrolytically Generated Transient Free Radicals by Electron Spin Resonance (1959)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation August H. Maki, David H. Geske; Detection of Electrolytically Generated Transient Free Radicals by Electron Spin Resonance. J. Chem. Phys. 1 May 1959; 30 (5): 1356–1357. https://doi.org/10.1063/1.1730187 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAIP Publishing PortfolioThe Journal of Chemical Physics Search Advanced Search |Citation Search
VALUE OF THE IN VITRO OR IN VIVO MONOETHYLGLYCINEXYLIDIDE TEST FOR PREDICTING LIVER GRAFT FUNCTION1 (1997)

MEGX formation in liver biopsy specimens in vitro properly reflects metabolic function of the particular liver. Therefore, liver biopsies may be a valuable tool to help predict liver function in vivo. However, the MEGX test alone is not sufficient to provide the gold standard to determine liver function in donor and transplantation livers.
Photoluminescence Studies and Solar-Cell Application of CuInSe2 Thin Films Prepared using Selenization Techniques (1993)

Photoluminescence measurements were carried out on CuInSe 2 thin films prepared using the selenization technique with solid- or vapor-phase selenium, and the correlation between photoluminescence spectra and cell performance was studied. In our previous studies, several peaks were observed in the wavelength region below 1400 nm in the photoluminescence spectra of low-photovoltaic CuInSe 2 thin films. In contrast, in the spectra of high-photovoltaic films, a strong peak was observed at 1420 nm, and there were no additional peaks below 1400 nm. From the results, it was found that there was a strong correlation between the photovoltaic effect of CuInSe 2 thin films and the existence of the photoluminescence peak at 1420 nm. The origin of this peak and its behavior were investigated through the dependence of the photoluminescence spectra on the temperature and excitation intensity and the effect of air annealing.
The so-called cis–trans isomerism of the compound Fepy4(NCS)2 (1966)

The properties of the yellow compound Fepy4(NCS)2 and of its so-called “black isomer” have been examined by a variety of physical methods. We conclude that the yellow form has a trans configuration, but that the “black” modification is really the yellow form containing a small, and probably variable, amount of some iron(III) derivative. Some properties of the complex Fepy3(NCS)3 are reported.
Circularly Polarized Folded Reflectarray Antenna (2023)

This paper presents the analysis and design of an integrated low-profile circularly-polarized folded reflectarray antenna (FRA) for wireless communication applications in the ku band. The proposed FRA consists of a main reflectarray (MR), a tilted linearly polarized (LP) planar dipole antenna and a transmitarray. The main reflectarray consists of 713 pentagonal patch elements on a grounded dielectric substrate. The reflecting elements are adjusted to produce a 90° phase shift between the reflection coefficients in the two principal planes. On the other hand, the transmitarray consists of conducting circular patches printed on a dielectric slab. The combination of the reflectarray and transmitarray are designed to convert the linearly polarized radiation of the feeding planar dipole antenna to circular polarization. In this work a small focal to diameter ratio (F/ D) is chosen to be 0. 4 to reduce the overall antenna size. This design operates in the band from 11.5 to 12.5 GHz and the results show that the maximum antenna gain 22 dBi and the AR is 1.17 dB at 12 GHz.
Transcriptomic Responses of the Softwood-Degrading White-Rot Fungus Phanerochaete carnosa during Growth on Coniferous and Deciduous Wood (2011)

To identify enzymes that could be developed to reduce the recalcitrance of softwood resources, the transcriptomes of the softwood-degrading white-rot fungus Phanerochaete carnosa were evaluated after growth on lodgepole pine, white spruce, balsam fir, and sugar maple and compared to the transcriptome of P. carnosa after growth on liquid nutrient medium. One hundred fifty-two million paired-end reads were obtained, and 63% of these reads were mapped to 10,257 gene models from P. carnosa. Five-hundred thirty-three of these genes had transcripts that were at least four times more abundant during growth on at least one wood medium than on nutrient medium. The 30 transcripts that were on average over 100 times more abundant during growth on wood than on nutrient medium included 6 manganese peroxidases, 5 cellulases, 2 hemicellulases, a lignin peroxidase, glyoxal oxidase, and a P450 monooxygenase. Notably, among the genes encoding putative cellulases, one encoding a glycosyl hydrolase family 61 protein had the highest relative transcript abundance during growth on wood. Overall, transcripts predicted to encode lignin-degrading activities were more abundant than those predicted to encode carbohydrate-active enzymes. Transcripts predicted to encode three MnPs represented the most highly abundant transcripts in wood-grown cultivations compared to nutrient medium cultivations. Gene set enrichment analyses did not distinguish transcriptomes resulting from softwood and hardwood cultivations, suggesting that similar sets of enzyme activities are elicited by P. carnosa grown on different wood substrates, albeit to different expression levels.
Tailor‐Made Modification of a Gold Surface for the Chemical Binding of a High‐Activity [FeFe] Hydrogenase (2011)

Abstract Hydrogenases are iron–sulfur proteins that catalyze hydrogen turnover in a wide range of microorganisms. Three different classes have been described, and among these [FeFe] hydrogenases are the most active in H 2 evolution. Hydrogenases are redox enzymes that have been shown to exchange electrons with graphite and modified noble metal electrodes. Making use of the latter, diffusible electron carriers are required to enable redox catalysis, as proteins do not specifically bind to the electrode surface. Diffusion‐limited electron transfer can be replaced by electron injection into immobilized hydrogenase by binding the redox mediator to the electrode surface. Here, we present the synthesis and spectroelectrochemical characterization of 1‐(10‐mercaptodecyl)‐1′‐benzyl‐4,4′‐bipyridinium dibromide (MBBP), which is used as redox‐active linker. Cr HydA1, the high‐activity [FeFe] hydrogenase from Chlamydomonas reinhardtii , is immobilized on the linker‐modified gold electrode. Each surface modification step is controlled in situ by surface‐enhanced infrared absorption spectroscopy (SEIRAS). Functionality of the electrode–protein hybrid is demonstrated by recording the linker‐supported current. The specificcatalytic rate of hydrogen evolution by Cr HydA1 (2.9 μmol H 2 min –1 mg –1 hydrogenase) promises a valuable approach for further optimization of this novel bioelectrical interface.
A phone-assistive device based on Bluetooth technology for cochlear implant users (2003)

Hearing-impaired people, and particularly hearing-aid and cochlear-implant users, often have difficulty communicating over the telephone. The intelligibility of telephone speech is considerably lower than the intelligibility of face-to-face speech. This is partly because of lack of visual cues, limited telephone bandwidth, and background noise. In addition, cellphones may cause interference with the hearing aid or cochlear implant. To address these problems that hearing-impaired people experience with telephones, this paper proposes a wireless phone adapter that can be used to route the audio signal directly to the hearing aid or cochlear implant processor. This adapter is based on Bluetooth technology. The favorable features of this new wireless technology make the adapter superior to traditional assistive listening devices. A hardware prototype was built and software programs were written to implement the headset profile in the Bluetooth specification. Three cochlear implant users were tested with the proposed phone-adapter and reported good speech quality.
Synthesis of Dioxa-1,7-naphthicorrole and Its Oxidized Porphyrinoid as a Potential Built-In Linker for Biomolecules (2022)

The first aromatic benzicorrole termed naphthicorrole was synthesized with a carbon donor containing more than six members. Its oxidized (enedione-embedded) porphyrinoid was also obtained using different meso-aryl substitutions under sequential oxidation conditions. The resulting enedione motif of the nonaromatic porphyrinoid was regioselective to the C2 position for S or N nucleophiles. Thus, the oxidized porphyrinoid was tested as a built-in linker for biomolecules. The progress of the reaction was visually monitored due to their different conjugation pathways.
Efficient Synthesis of a Complete Donor/Acceptor Bis(aryl)diyne Family. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Fodor's 95 Great Britain (1994)

Contains descriptions, region-by-region, of scenic walks and drives, aristocratic homes, literary and historic sites, sports and shopping, and reviews of over 700 hotels and 1200 restaurants to suit all budgets. It also contains essays on the Royal Family, art and architecture.
[Randomized phase II trial to compare S-1 and S-1/PSK for advanced or recurrent gastric cancer-lessons from the results]. (2011)

When considering PS 0 in 8 patients enrolled, an overall survival was comparable to that observed in S-1 group of other phase III trials. Standard chemotherapy for advanced gastric cancer was changed to S-1/CDDP by SPIRITS phase III trial which was presented just after this trial was initiated, which would be a major cause of slow accrual. When conducting phase III trial, we should carefully determine design and standard arm by considering on-going phase III trial.
In the name of the rose: a roadmap for rose research in the genome era (2019)

The recent completion of the rose genome sequence is not the end of a process, but rather a starting point that opens up a whole set of new and exciting activities. Next to a high-quality genome sequence other genomic tools have also become available for rose, including transcriptomics data, a high-density single-nucleotide polymorphism array and software to perform linkage and quantitative trait locus mapping in polyploids. Rose cultivars are highly heterogeneous and diverse. This vast diversity in cultivated roses can be explained through the genetic potential of the genus, introgressions from wild species into commercial tetraploid germplasm and the inimitable efforts of historical breeders. We can now investigate how this diversity can best be exploited and refined in future breeding work, given the rich molecular toolbox now available to the rose breeding community. This paper presents possible lines of research now that rose has entered the genomics era, and attempts to partially answer the question that arises after the completion of any draft genome sequence: 'Now that we have "the" genome, what's next?'. Having access to a genome sequence will allow both (fundamental) scientific and (applied) breeding-orientated questions to be addressed. We outline possible approaches for a number of these questions.
Supplementary Table from Outcomes in Patients with Poor-Risk Cytogenetics with or without <i>TP53</i> Mutations Treated with Venetoclax and Azacitidine (2023)

Supplementary Table from Outcomes in Patients with Poor-Risk Cytogenetics with or without &lt;i&gt;TP53&lt;/i&gt; Mutations Treated with Venetoclax and Azacitidine
Oxidizing Capacity of Periodate Activated with Iron-Based Bimetallic Nanoparticles (2014)

Nanosized zerovalent iron (nFe0) loaded with a secondary metal such as Ni or Cu on its surface was demonstrated to effectively activate periodate (IO4-) and degrade selected organic compounds at neutral pH. The degradation was accompanied by a stoichiometric conversion of IO4- to iodate (IO3-). nFe0 without bimetallic loading led to similar IO4- reduction but no organic degradation, suggesting the production of reactive iodine intermediate only when IO4- is activated by bimetallic nFe0 (e.g., nFe0-Ni and nFe0-Cu). The organic degradation kinetics in the nFe0-Ni(or Cu)/IO4- system was substrate dependent: 4-chlorophenol, phenol, and bisphenol A were effectively degraded, whereas little or no degradation was observed with benzoic acid, carbamazepine, and 2,4,6-trichlorophenol. The substrate specificity, further confirmed by little kinetic inhibition with background organic matter, implies the selective nature of oxidant in the nFe0-Ni(or Cu)/IO4- system. The comparison with the photoactivated IO4- system, in which iodyl radical (IO3•) is a predominant oxidant in the presence of methanol, suggests IO3• also as primary oxidant in the nFe0-Ni(or Cu)/IO4- system.