gebhart/patrepeval huggingface dataset:
An Efficient Method for Generating Poxvirus Recombinants in the Absence of Selection (2011)

The use of selectable markers (ecogpt) and selection pressures to aid in detection of poxvirus (Vaccinia, VV) recombinants has been implicated in the unintended introduction of second site mutations. We have reinvestigated the use of the helper virus system described by Scheiflinger et al. and adapted by Yao and Evans which produces recombinants at a high frequency in the absence of any selection, at a rate of 6–100%. Our system uses fowlpox virus (FPV) as the infectious helper virus which in infected cells provides the enzymatic apparatus for transcription and replication of a purified, transfected VV genome and for recombination with a second transfected PCR generated DNA fragment. To optimize the system, a PCR DNA fragment was generated that contained poxvirus promoter driven gfp and lacZ genes inserted within the coding sequences of the viral thymidine kinase gene. This PCR fragment was co-transfected together with VV genomic DNA. Recombinant VV was identified by plaquing the mixture on cells non-permissive for FPV and selection of green fluorescent or LacZ positive recombinant vaccinia plaques. The system was optimized using FPV permissive cells (CEF) and non-permissive cells (A549, CV-1) for both the initial infection/transfection and the subsequent selection. Up to 70% of the progeny vaccinia virus contained the gfp/LacZ insertion. In order to test for the presence of FPV/VV intertypic recombinants or other unintended mutations, recombinant wtVV (RwtVV) was regenerated from the gfp/LacZ viruses and evaluated by RFLP analysis and pathogenesis in animals. While all RwtVVs were viable in cell culture, in many of the RwtVV isolates, RFLP differences were noted and while some recombinant viruses exhibited wild type behavior in mice, a wide range of virulence indicative of unintended changes suggests that mutants created by “rescue” systems require careful analysis particularly before use for in vivo studies employing animal models.
Concave Tetrathiafulvalene‐Type Donors as Supramolecular Partners for Fullerenes (2007)

The cap fits! A new class of concave π-extended tetrathiafulvalene (TTF) derivatives, truxene-TTFs, were prepared and characterized, and their self-assembly with fullerenes was investigated (see picture). Truxene-TTFs represent the first example of TTF-related electron donors that serve, without chemical modification, as monotopic receptors for fullerenes in solution. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2007/z604327_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Changes in the Lung Lipids of Rabbits and Guinea-pigs Exposed to the Inhalation of Silica Dust (1960)

Eight rabbits and 24 guinea-pigs were exposed to a silica dust cloud of about 40,000 pp./ml. (0·3-3·0 μ) and killed at four-weekly intervals up to 30 weeks. The guinea-pigs showed an increase of lung lipid and phospholipid; the latter showed a parallel with the rising collagen level estimated chemically. In the rabbits there was no increase of either lipid or phospholipid. The likely explanation is that the silica did not reach the lungs in sufficient quantity.
<i>In Vivo</i> Bactofection: <i>Listeria</i> Can Function as a DNA-Cancer Vaccine (2006)

The development of an effective therapeutic vaccine to induce cancer-specific immunity remains an unsolved yet pressing priority requiring novel vaccine strategies. Here we have generated a series of vaccines in which bacteria deliver a plasmid encoding a tumor antigen under the control of a mammalian promoter in an attempt to induce an antitumor immune response. Utilizing a plasmid release mechanism involving the suicide of the carrier bacteria, we were able to engineer Listeria monocytogenes to induce antitumor immunity to a physiologically relevant tumor antigen, the cervical cancer oncoprotein E7. In a mouse model of cervical cancer, we were able to slow tumor growth and induce an effector CD8(+) T-cell response against the immunodominant epitope for E7. The CD8(+) T cells generated could both home to and penetrate the tumor. This is the first demonstration of in vivo efficacy of bactofection vectors in treating solid tumors. However, although this delivery system was more effective than administering plasmid alone, it was not as effective as L. monocytogenes engineered to deliver the E7 protein in impacting on established tumor growth.
On the Tractable Counting of Theory Models and its Application to Truth Maintenance and Belief Revision (2001)

We address in this paper the problem of counting the models of a propositional theory under incremental changes to its literals. Specifcally, we show that if a propositional theory Δ is in a special form that we call smooth, deterministic, decomposable negation normal form (sd-DNNF), then for any consistent set of literals S, we can simultaneously count (in time linear in the size of Δ) the models of Δ ∪ S and the models of every theory Δ ∪ T where T results from adding, removing or flipping a literal in S. We present two results relating to the time and space complexity of compiling propositional theories into sd-DNNF. First, we show that if a conjunctive normal form (CNF) has a bounded treewidth, then it can be compiled into an sd-DNNF in time and space which are linear in its size. Second, we show that sd-DNNF is a strictly more space efficient representation than Free Binary Decision Diagrams (FBDDs). Finally, we discuss some applications of the counting results to truth maintenance systems, belief revision, and model-based diagnosis.
<title>Phase-strain-temperature model for structurally embedded interferometric optical fiber strain sensors with applications</title> (1991)

The fundamental theory which relates optical phase changes to applied strain and temperature fields in structurally embedded interferometric optical fiber sensors of all types is described. The theory is developed in a unified manner through a careful discussion of basic assumptions and definitions. This theory is then applied to Mach-Zehnder, Michelson, intrinsic and extrinsic Fabry-Perot, polarimetric, and modal-domain sensors. Theoretical investigation of the phase-strain-temperature theory applied to all of these sensors embedded in transversely isotropic specimens under five different load conditions is used to investigate the importance of transverse strain terms.
Bacillus thuringiensis and Bacillus weihenstephanensis Inhibit the Growth of Phytopathogenic Verticillium Species (2017)

<i>Verticillium</i> wilt causes severe yield losses in a broad range of economically important crops worldwide. As many soil fumigants have a severe environmental impact, new biocontrol strategies are needed. Members of the genus <i>Bacillus</i> are known as plant growth-promoting bacteria (PGPB) as well as biocontrol agents of pests and diseases. In this study, we isolated 267 <i>Bacillus</i> strains from root-associated soil of field-grown tomato plants. We evaluated the antifungal potential of 20 phenotypically diverse strains according to their antagonistic activity against the two phytopathogenic fungi <i>Verticillium dahliae</i> and <i>Verticillium longisporum</i>. In addition, the 20 strains were sequenced and phylogenetically characterized by multi-locus sequence typing (MLST) resulting in 7 different <i>Bacillus thuringiensis</i> and 13 <i>Bacillus weihenstephanensis</i> strains. All <i>B. thuringiensis</i> isolates inhibited <i>in vitro</i> the tomato pathogen <i>V. dahliae</i> JR2, but had only low efficacy against the tomato-foreign pathogen <i>V. longisporum</i> 43. All <i>B. weihenstephanensis</i> isolates exhibited no fungicidal activity whereas three <i>B. weihenstephanensis</i> isolates showed antagonistic effects on both phytopathogens. These strains had a rhizoid colony morphology, which has not been described for <i>B. weihenstephanensis</i> strains previously. Genome analysis of all isolates revealed putative genes encoding fungicidal substances and resulted in identification of 304 secondary metabolite gene clusters including 101 non-ribosomal polypeptide synthetases and 203 ribosomal-synthesized and post-translationally modified peptides. All genomes encoded genes for the synthesis of the antifungal siderophore bacillibactin. In the genome of one <i>B. thuringiensis</i> strain, a gene cluster for zwittermicin A was detected. Isolates which either exhibited an inhibitory or an interfering effect on the growth of the phytopathogens carried one or two genes encoding putative mycolitic chitinases, which might contribute to antifungal activities. This indicates that chitinases contribute to antifungal activities. The present study identified <i>B. thuringiensis</i> isolates from tomato roots which exhibited <i>in vitro</i> antifungal activity against <i>Verticillium</i> species.
MurJ is the flippase of lipid-linked precursors for peptidoglycan biogenesis (2014)

Peptidoglycan (PG) is a polysaccharide matrix that protects bacteria from osmotic lysis. Inhibition of its biogenesis is a proven strategy for killing bacteria with antibiotics. The assembly of PG requires disaccharide-pentapeptide building blocks attached to a polyisoprene lipid carrier called lipid II. Although the stages of lipid II synthesis are known, the identity of the essential flippase that translocates it across the cytoplasmic membrane for PG polymerization is unclear. We developed an assay for lipid II flippase activity and used a chemical genetic strategy to rapidly and specifically block flippase function. We combined these approaches to demonstrate that MurJ is the lipid II flippase in Escherichia coli.
A History of Classical Poetry: Sanskrit - Pali - Prakrit. Siegfried Lienhard. (1987)

A History of Classical Poetry: Sanskrit - Pali - Prakrit. Siegfried Lienhard. (A History of Indian Literature, Vol. III, Fasc. 1) Otto Harrassowitz, Wiesbaden 1984. viii + 307 pp. DM 128.
Characterization of porous low-k films using variable angle spectroscopic ellipsometry (2006)

Variable angle spectroscopic ellipsometry (VASE™) is used as a tool to characterize properties such as optical constant, thickness, refractive index depth profile, and pore volume fraction of single and bilayer porous low-k films. The porous films were prepared using sacrificial pore generator (porogen) approach. Two sets of porous films with open- and closed-pore geometries were measured. Three models were used for data analysis: Cauchy, Bruggeman effective medium approximation (BEMA), and graded layer. Cauchy, a well-known model for transparent films, was used to obtain thickness and optical constant, whereas BEMA was utilized to calculate the pore volume fraction from the ellipsometric data. The Cauchy or BEMA models were then modified as graded layers, resulting in a better fit and a better understanding of the porous film. The depth profile of the porous film implied a more porous layer at the substrate-film interface. We found 3%–4% more porosity at the interface compared with the bulk for both films. This work shows that VASE™, a nondestructive measurement tool, can be used to characterize single- and multigraded layer porous films quickly and effectively.
Chemical Imaging of Poplar Wood Cell Walls by Confocal Raman Microscopy (2006)

Confocal Raman microscopy was used to illustrate changes of molecular composition in secondary plant cell wall tissues of poplar (Populus nigra x Populus deltoids) wood. Two-dimensional spectral maps were acquired and chemical images calculated by integrating the intensity of characteristic spectral bands. This enabled direct visualization of the spatial variation of the lignin content without any chemical treatment or staining of the cell wall. A small (0.5 microm) lignified border toward the lumen was observed in the gelatinous layer of poplar tension wood. The variable orientation of the cellulose was also characterized, leading to visualization of the S1 layer with dimensions smaller than 0.5 mum. Scanning Raman microscopy was thus shown to be a powerful, nondestructive tool for imaging changes in molecular cell wall organization with high spatial resolution.
One‐Photon Annihilation of Thermal Positrons in the Interstellar Medium (1998)

In the interstellar medium, one-photon annihilation of thermal positrons with bound atomic electrons is investigated. The total annihilation rate of thermal positrons with an interstellar element is calculated considering the K- and higher shell (L, M, and N) contributions from abundant many-electron atoms. The results show that the main contributions to one-photon annihilation are H, He, and C atoms in hot medium (≡ kT/Ry)=1, H, Mg, and He atoms in warm medium =0.1, Mg, H, and Fe atoms in cold medium =0.01, respectively. In a hot medium, positrons are mostly annihilated with the K-shell electrons; for example, the K-shell electrons of H and He atoms. However, in a cold medium positrons are annihilated with higher shell electrons; for example, the M-shell electrons of Mg atom and the N-shell electrons for Fe atom give main contributions.
Glycyrrhizin combined with acitretin improve clinical symptom of psoriasis via reducing Th17 cell differentiation and related serum cytokine concentrations. (2015)

Compound glycyrrhizin in combination with acitretin can improve the clinical efficacy significantly when compared with of the solely acitretin medication for psoriasis treatments via down regulating Th17 cell differentiation.
Devastated Crops: Multifunctional Efficacy for the Production of Nanoparticles (2013)

Integration of green chemistry principles to nanotechnology is one of the key issues in nanoscience research. Biological methods were used to synthesize metal and metal oxide nanoparticles of specific shape and size since they enhance the properties of nanoparticles in greener route. Plant‐mediated methods devoid the use of toxic chemicals in the synthetic protocols which has adverse effects on the environment. Owing to the rich biodiversity of plants and their potential secondary constituents, plants and plant parts have gained attention in recent years as medium for nanoparticles′ synthesis. In this review, we present the current status of nanoparticles synthesis using devastated crops.
A critical introduction to mathematical modelling of the aerobic deterioration of silage (1993)

Abstract The last 3 years have seen the publication of a number of papers featuring mathematical models of the aerobic deterioration silage. Here, we provide an overview of this work. A brief summary is given of the reasons why quantitative understanding of the mechanisms behind aerobic deterioration is of interest. We discuss the use of modelling as an investigative tool, considering the modelling approaches which have been used and the limitations of these approaches. The previous publications in this field are considered chronologically. We describe each in depth, highlighting the assumptions they embody and their relation to each other. A highly‐simplified model is used to demonstrate shortcomings common to all the models described previously. The paper concludes by discussing the most interesting questions yet to be answered in this field and suggests some possible strategies for tackling them.
PHASIC MUSCULAR ACTIVITY AND MUSCULAR TONUS IN REM SLEEP (1973)

The phasic EMG which is recorded from the submental muscle during REM sleep is quantitatively evaluated and expressed as the % phasic EMG. As for normal subjects, the % phasic EMG is distributed from 2 to 5%. In the patients with idiopathic Parkinsonism who showed muscle rigidity in the upper limbs, the % phasic EMG was considerably higher than in normal subjects. However, there was no relation between finger tremor and the % phasic EMG. In Huntington's chorea, the % phasic EMG was zero.From these observations, it is supposed that the abnormal state of the muscle tonus of the whole body has relation to the % phasic EMG obtained during REM sleep. However, this relation was not found in three schizophreniacs who showed a slight increase of muscle tonus.Finally, some consideration was given as to the physiological and biochemical mechanisms which participate in muscle rigidity and in the appearance of the phasic EMG during REM sleep.
Accuracy of MSCT coronary angiography with 64-slice technology: first experience (2005)

Sixty-four-slice CT provides a high diagnostic accuracy in assessing coronary artery stenoses.
The Esterification of Acylated α-Amino Acids (1948)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Esterification of Acylated α-Amino AcidsHeinrich Rinderknecht and Carl NiemannCite this: J. Am. Chem. Soc. 1948, 70, 7, 2605–2606Publication Date (Print):July 1, 1948Publication History Published online1 May 2002Published inissue 1 July 1948https://doi.org/10.1021/ja01187a515RIGHTS & PERMISSIONSArticle Views291Altmetric-Citations9LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (284 KB) Get e-Alerts Get e-Alerts
Age of illicit drug initiation (2001)

Information is provided on the question of age of drug use initiation and relevant policy implications by examining four recent drug use studies. Data is taken from the 1998 National Drug Strategy Household Survey, the 1999 Illicit Drug Reporting System, the 1999 Drug Use Monitoring in Australia project and the 1998 Illicit Drugs and Property Crime Survey. The findings show that those who use drugs and commit crime are likely to have started using drugs earlier than drug users who do not have criminal careers.
Metabolism of chlorinated methanes, ethanes, and ethylenes by a mixed bacterial culture growing on methane (1989)

Soil was taken from the top 10 cm of a soil column that removed halogenated aliphatic hydrocarbons in the presence of natural gas. This soil was used as an enrichment inoculum to determine that the removals seen in the soil column were in fact of a microbiological nature. Methane served as the source of carbon and energy and was consumed immediately by the enrichments. After several transfers of the enrichments, a stable consortium of at least three bacterial types was obtained. The predominant bacterium was a non-motile, gram-negative coccus. This stable consortium was able to remove chlorinated methanes, ethanes, and ethylenes when grown with methane and oxygen in the headspace. Methane was required for the removals to be observed. Acetylene inhibited the removals, which further suggests the involvement of methanotrophs. Benzene and toluene were removed by the mixed culture with or without methane in the headspace. Fatty acid analysis of the mixed culture resulted in a profile that indicated that the predominant organism was a type II methanotroph. This study provides further evidence that methanotrophic bacteria are capable of cometabolizing a wide range of chlorinated methanes, ethanes, and ethylenes.
Predicting detection limits of enzyme-linked immunosorbent assay (ELISA) and bioanalytical techniques in general (2013)

The detection limit is one of the most important performance parameters for bioanalytical techniques. Here we present a generic method to estimate the detection limit of biomolecular assays based on a step-by-step analysis of the assay procedure. Enzyme-linked immunosorbent assay (ELISA) is used here as an example; however, much of the information presented in this article may be applied to other types of biomolecular assays and analytical techniques. A clear understanding of what affects the detection limit can help researchers to evaluate different bio-analytical techniques properly, and to design better strategies to optimize and achieve the best analytical performance.
Sequences of conserved region in the A subunit of DNA gyrase from nine species of the genus Mycobacterium: phylogenetic analysis and implication for intrinsic susceptibility to quinolones (1995)

The sequences of a conserved region in the A subunit of DNA gyrase corresponding to the quinolone resistance-determining region were determined for nine mycobacterial species and were compared. Although the nucleotide sequences were highly conserved, they clearly differentiated one species from another. The results of the phylogenetic analysis based on the sequences of the quinolone resistance-determining regions were compared with those provided by the 16S rRNA sequences. Deduced amino acid sequences were identical within the nine species except for amino acid 83, which was frequently involved in acquired resistance to quinolones in many genera, including mycobacteria. The presence at position 83 of an alanine for seven mycobacterial species (M. tuberculosis, M. bovis BCG, M. leprae, M. avium, M. kansasii, M. chelonae, and M. smegmatis) and of a serine for the two remaining mycobacterial species (M. fortuitum and M. aurum) correlated well with the MICs of ofloxacin for both groups of species, suggesting the role of this residue in intrinsic susceptibility to quinolones in mycobacteria.
Remote haptic feedback from a dynamic running machine (2009)

In this paper we present our efforts to design a system for feeding back useful haptic information from a highly dynamic running robot to a remote operator using a haptic device. Without adding additional sensors, the legs of the robot are used as feelers to give the operator the capability to both explore and manipulate the robot's environment and to gather meaningful information about properties not captured by visual feedback like weight, movability and structure of an encountered object. We show the capabilities of the system in a user study with both trained and untrained operators.
Slice-timing effects and their correction in functional MRI (2011)

Exact timing is essential for functional MRI data analysis. Datasets are commonly measured using repeated 2D imaging methods, resulting in a temporal offset between slices. To compensate for this timing difference, slice-timing correction (i.e. temporal data interpolation) has been used as an fMRI pre-processing step for more than fifteen years. However, there has been an ongoing debate about the effectiveness and applicability of this method. This paper presents the first elaborated analysis of the impact of the slice-timing effect on simulated data for different fMRI paradigms and measurement parameters, taking into account data noise and smoothing effects. Here we show, depending on repetition time and paradigm design, slice-timing effects can significantly impair fMRI results and slice-timing correction methods can successfully compensate for these effects and therefore increase the robustness of the data analysis. In addition, our results from simulated data were supported by empirical in vivo datasets. Our findings suggest that slice-timing correction should be included in the fMRI pre-processing pipeline.