gebhart/patrepeval huggingface dataset:
CRISPR/Cas9: a molecular Swiss army knife for simultaneous introduction of multiple genetic modifications in Saccharomyces cerevisiae (2015)

A variety of techniques for strain engineering in Saccharomyces cerevisiae have recently been developed. However, especially when multiple genetic manipulations are required, strain construction is still a time-consuming process. This study describes new CRISPR/Cas9-based approaches for easy, fast strain construction in yeast and explores their potential for simultaneous introduction of multiple genetic modifications. An open-source tool (http://yeastriction.tnw.tudelft.nl) is presented for identification of suitable Cas9 target sites in S. cerevisiae strains. A transformation strategy, using in vivo assembly of a guideRNA plasmid and subsequent genetic modification, was successfully implemented with high accuracies. An alternative strategy, using in vitro assembled plasmids containing two gRNAs, was used to simultaneously introduce up to six genetic modifications in a single transformation step with high efficiencies. Where previous studies mainly focused on the use of CRISPR/Cas9 for gene inactivation, we demonstrate the versatility of CRISPR/Cas9-based engineering of yeast by achieving simultaneous integration of a multigene construct combined with gene deletion and the simultaneous introduction of two single-nucleotide mutations at different loci. Sets of standardized plasmids, as well as the web-based Yeastriction target-sequence identifier and primer-design tool, are made available to the yeast research community to facilitate fast, standardized and efficient application of the CRISPR/Cas9 system.
Building Blocks for n‐Type Organic Electronics: Regiochemically Modulated Inversion of Majority Carrier Sign in Perfluoroarene‐Modified Polythiophene Semiconductors (2003)

A new family of perfluoroarene-modified thiophene semiconductors 1–3 has been synthesized to assess the influence of perfluoroarene introduction and regiochemistry on molecular and thin-film transistor properties. Compound 1 is an n-type semiconductor with a mobility approaching 0.1 cm2 V−1 s−1 whereas 2 and 3 exhibit p-type behavior. These results show that the origin of n-type carrier mobility is not solely a consequence of solution/film LUMO and HOMO energies. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2003/z51253_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.
Preparation and Properties of Antibodies to GD3 and GM1 Gangliosides (1980)

Gangliosides GD3 and GM1 were coupled to proteins by their carboxyl groups and antisera were raised against the complexes. Anti-ganglioside antibodies were isolated by affinity chromatography on ganglioside-aminopropyl silica gel columns, and the specificity of the antibodies was determined by a quantitative microcomplement fixation assay. Antibodies to GD3 were highly specific and did not crossreact with GM3, lactosyl ceramide, or other glycolipids. Purified antibodies to GM1, in contrast, crossreacted with asialo-GM1, GD1b, and, to a lesser extent, GM2 and asialo-GM2. A derivative of GM1, containing a C-7 sialic acid residue produced by periodate oxidation, reacted with the ani-GM1 antibodies almost as readily as with GM1. The specificities of anti-GM1 antibodies elicited by the covalent ganglioside-protein complexes were similar to those produced by immunization with noncovalent complexes of GM1 and methylated bovine serum albumin. The ganglioside-protein complexes described here should be useful for preparing antibodies to polysialogangliosides that contain neuraminidase-sensitive linkages.
Label Distribution Protocol (LDP) 'Typed Wildcard' Forward Equivalence Class (FEC) (2010)

The Label Distribution Protocol (LDP) specification for the Wildcard Forward Equivalence Class (FEC) element has several limitations.This document addresses those limitations by defining a Typed Wildcard FEC Element and associated procedures.In addition, it defines a new LDP capability to address backward compatibility.
Seeing Citrulline: Development of a Phenylglyoxal-Based Probe To Visualize Protein Citrullination (2012)

Protein arginine deiminases (PADs) catalyze the hydrolysis of peptidyl arginine to form peptidyl citrulline. Abnormally high PAD activity is observed in a host of human diseases, but the exact role of protein citrullination in these diseases and the identities of specific citrullinated disease biomarkers remain unknown, largely because of the lack of readily available chemical probes to detect protein citrullination. For this reason, we developed a citrulline-specific chemical probe, rhodamine-phenylglyoxal (Rh-PG), which we show can be used to investigate protein citrullination. This methodology is superior to existing techniques because it possesses higher throughput and excellent sensitivity. Additionally, we demonstrate that this probe can be used to determine the kinetic parameters for a number of protein substrates, monitor drug efficacy, and identify disease biomarkers in an animal model of ulcerative colitis that displays aberrantly increased PAD activity.
Potentiation by sulfide of hydrogen peroxide-induced killing of Escherichia coli (1985)

L-Cysteine potentiates 100-fold the hydrogen peroxide-induced killing of a growing culture of Escherichia coli K-12 (Berglin et al., J. Bacteriol. 152:81-88). In the present study it is shown that hydrogen sulfide is formed from L-cysteine and that sodium sulfide could substitute for L-cysteine in the potentiation of hydrogen peroxide-induced killing of E. coli K-12. Addition of an amino acid, L-leucine, L-valine, or L-alanine, to an L-cysteine-containing medium with a growing culture of E. coli K-12 inhibited hydrogen sulfide formation and the potentiation of hydrogen peroxide-induced killing. These amino acids did not inhibit hydrogen sulfide formation from L-cysteine by a cell extract, and they did not inhibit the potentiation by sulfide of hydrogen peroxide-induced killing. This indicated that the amino acids protected the culture from L-cysteine-potentiated, hydrogen peroxide-induced killing by inhibiting the transport of L-cysteine into the cell. The potentiation by sodium sulfide of hydrogen peroxide-induced killing was abolished by the metal ion chelator 2,2'-bipyridyl. This indicated that metal ions, in addition to sulfide, were involved in the killing. Toxic effects of hydrogen peroxide are often presumed to be mediated by hydroxyl radicals formed in iron-catalyzed reactions. It was demonstrated that iron sulfide was more efficient than ferrous iron in catalyzing the formation of hydroxyl radicals from hydrogen peroxide. It was suggested that hydrogen sulfide formed in polymicrobial infections may play an important role in the host defense by potentiating the antimicrobial effect of hydrogen peroxide produced by phagocytic cells.
Water‐soluble polymers in agriculture: xanthan gum as eco‐friendly alternative to synthetics (2021)

Water-soluble polymers (WSPs) are a versatile group of chemicals used across industries for different purposes such as thickening, stabilizing, adhesion and gelation. Synthetic polymers have tailored characteristics and are chemically homogeneous, whereas plant-derived biopolymers vary more widely in their specifications and are chemically heterogeneous. Between both sources, microbial polysaccharides are an advantageous compromise. They combine naturalness with defined material properties, precisely controlled by optimizing strain selection, fermentation operational parameters and downstream processes. The relevance of such bio-based and biodegradable materials is rising due to increasing environmental awareness of consumers and a tightening regulatory framework, causing both solid and water-soluble synthetic polymers, also termed 'microplastics', to have come under scrutiny. Xanthan gum is the most important microbial polysaccharide in terms of production volume and diversity of applications, and available as different grades with specific properties. In this review, we will focus on the applicability of xanthan gum in agriculture (drift control, encapsulation and soil improvement), considering its potential to replace traditionally used synthetic WSPs. As a spray adjuvant, xanthan gum prevents the formation of driftable fine droplets and shows particular resistance to mechanical shear. Xanthan gum as a component in encapsulated formulations modifies release properties or provides additional protection to encapsulated agents. In geotechnical engineering, soil amended with xanthan gum has proven to increase water retention, reduce water evaporation, percolation and soil erosion - topics of high relevance in the agriculture of the 21st century. Finally, hands-on formulation tips are provided to facilitate exploiting the full potential of xanthan gum in diverse agricultural applications and thus providing sustainable solutions.
Coronary CT Angiography: Variability of CT Scanners and Readers in Measurement of Plaque Volume (2016)

Purpose To determine reader and computed tomography (CT) scan variability for measurement of coronary plaque volume. Materials and Methods This HIPAA-compliant study followed Standards for Reporting of Diagnostic Accuracy guidelines. Baseline coronary CT angiography was performed in 40 prospectively enrolled subjects (mean age, 67 years ± 6 [standard deviation]) with asymptomatic hyperlipidemia by using a 320-detector row scanner (Aquilion One Vision; Toshiba, Otawara, Japan). Twenty of these subjects underwent coronary CT angiography repeated on a separate day with the same CT scanner (Toshiba, group 1); 20 subjects underwent repeat CT performed with a different CT scanner (Somatom Force; Siemens, Forchheim, Germany [group 2]). Intraclass correlation coefficients (ICCs) and Bland-Altman analysis were used to assess interreader, intrareader, and interstudy reproducibility. Results Baseline and repeat coronary CT angiography scans were acquired within 19 days ± 6. Interreader and intrareader agreement rates were high for total, calcified, and noncalcified plaques for both CT scanners (all ICCs ≥ 0.96) without bias. Scanner variability was ±18.4% (coefficient of variation) with same-vendor follow-up. However, scanner variability increased to ±29.9% with different-vendor follow-up. The sample size to detect a 5% change in noncalcified plaque volume with 90% power and an α error of .05 was 286 subjects for same-CT scanner follow-up and 753 subjects with different-vendor follow-up. Conclusion State-of-the-art coronary CT angiography with same-vendor follow-up has good scan-rescan reproducibility, suggesting a role of coronary CT angiography in monitoring coronary artery plaque response to therapy. Differences between coronary CT angiography vendors resulted in lower scan-rescan reproducibility. <sup>©</sup> RSNA, 2016 Online supplemental material is available for this article.
In-situ evolution of a reconfigurable antenna (2002)

Evolvable hardware research has traditionally focused on evolvable circuits for applications such as computation, control, and signal processing. However, antennas have the potential to be evolvable as well. They are a crucial part of space vehicles, and, like electronic circuits, must eventually become evolvable to ensure survivability and maximum usefulness. The evolvable antenna system in this paper shows that an evolutionary algorithm and a reconfigurable antenna can be used to optimize signal reception in "real" surroundings, rather than in simulation or on a carefully controlled antenna range.
A galE via (Vi antigen-negative) mutant of Salmonella typhi Ty2 retains virulence in humans (1988)

We have recently described the construction of a galE derivative of Salmonella typhi Ty2 (Ty2H1) which had a 0.4-kilobase deletion in the galE gene and was sensitive to galactose-induced lysis when cultured with greater than or equal to 0.06 mM galactose (D. M. Hone, R. Morona, S. Attridge, and J. Hackett, J. Infect. Dis. 156:167-174, 1987). We now report the selection of a rifampin-resistant, via derivative of Ty2H1, EX462. Compared with the Ty2 parent strain, EX462 was serum sensitive and highly attenuated in the mouse mucin virulence assay. When four human volunteers ingested 7 X 10(8) viable EX462, two became ill and developed a typhoidlike disease with fever and bacteremia. Blood isolates from these individuals were indistinguishable from the vaccine strain by a variety of criteria. We concluded that, even in a via background, the galE mutation was not attenuating for S. typhi in humans.
The Atrial Natriuretic Factor Promoter Is a Downstream Target for Nkx-2.5 in the Myocardium (1996)

The recently described NK2 family of homeodomain proteins are key developmental regulators. In Drosophila melanogaster, two members of this family, bagpipe and tinman, are required for visceral and cardiac mesoderm formation, respectively. In vertebrates, tinman appears to represent a family of closely related NK2 genes, including Nkx-2.5, that are expressed at an early stage in precardiac cells. Consistent with a role for Nkx-2.5 in heart development, inactivation of the Nkx-2.5 gene in mice causes severe cardiac malformations and embryonic lethality. However, little is known about the molecular action of Nkx-2.5 and its targets in cardiac muscle. In this paper, we report the identification and characterization of a functional and highly conserved Nkx-2.5 response element, termed the NKE, in the proximal region of the cardiac atrial natriuretic factor (ANF) promoter. The NKE is composed of two near-consensus NK2 binding sites that are each able to bind purified Nkx-2.5. The NKE is sufficient to confer cardiac cell-specific activity to a minimal TATA-containing promoter and is required for Nkx-2.5 activation of the ANF promoter in heterologous cells. Interestingly, in primary cardiocyte cultures, the NKE contributes to ANF promoter activity in a chamber- and developmental stage-specific manner, suggesting that Nkx-2.5 and/or other related cardiac proteins may play a role in chamber specification. This work provides the identification of a direct target for NK2 homeoproteins in the heart and lays the foundation for further molecular analyses of the role of Nkx-2.5 and other NK2 proteins in cardiac development.
In vivo activity of CRISPR‐mediated virus defence in a hyperthermophilic archaeon (2011)

Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas systems are found widespread in bacterial and archaeal genomes and exhibit considerable diversity. However, closer insights into the action of most of the CRISPR modules have remained elusive in particular in Archaea as a result of the lack of suitable in vivo test systems. Here we demonstrate CRISPR/Cas-based immune defence in the hyperthermophilic archaeon Sulfolobus solfataricus. Recombinant variants of the SSV1 virus containing a gene of the conjugative plasmid pNOB8 that represents a target for a corresponding CRISPR spacer in the chromosome were tested in transfection experiments. Almost 100% immunity against the recombinant virus was observed when the chromosomal CRISPR spacer matched perfectly to the protospacer. Different from bacterial systems immunity was still detected, albeit at decreased levels, when mutations distinguished target and spacer. CRISPR/Cas targeting was independent of the transcription of the target gene. Furthermore, a mini-CRISPR locus introduced on the viral DNA with spacers targeting the (non-essential) chromosomal beta-galactosidase gene was unstable in host cells and triggered recombination with the indigenous CRISPR locus. Our experiments demonstrate in vivo activity of CRISPR/Cas in archaea for the first time and suggest that - unlike the recently demonstrated in vitro cleavage of RNA in Pyrococcus- DNA is targeted in this archaeon.
Tailoring Enzyme Systems for Food Processing (1989)

Three illustrations are used to review the various approaches taken by the enzyme industry in tailoring enzyme preparations to meet the production and product quality needs of the food industry. Tailored enzyme preparations have been able to convert the corn syrup industry from an acid-based industry to an enzymebased industry, to overcome the problems created in the baking industry as grain technology improved and automation was introduced, and to rescue the cheese industry as the supply of bovine rennet decreased and the demand for cheese and cheese flavor increased.
Cloning and sequencing of complementary DNAs encoding the alpha-subunit of translational initiation factor eIF-2. Characterization of the protein and its messenger RNA. (1987)

A clone encoding the alpha-subunit of eukaryotic initiation factor 2 (eIF-2 alpha) was isolated from a lambda gt11 expression library of rat brain cDNAs. The fusion protein expressed by the recombinant phage reacts with eIF-2 alpha antiserum except when the serum is preadsorbed with pure eIF-2. The translation of hybrid-selected HeLa cell mRNA produces two proteins which are indistinguishable from authentic HeLa eIF-2 alpha and its phosphorylated form when analyzed by electrophoresis in two-dimensional isoelectrofocusing/sodium dodecyl sulfate-polyacrylamide gels and by partial protease digestion. HeLa cell eIF-2 alpha mRNA migrates as a single band of about 1600 nucleotides. The rat cDNA insert was sequenced, and the region coding for eIF-2 alpha was identified. A human cDNA clone was obtained by hybridization screening with the rat cDNA, and its sequence was determined also. Both rat and human eIF-2 alpha proteins comprise 315 amino acids (36.1 kDa) and differ by only three amino acids. The eIF-2 alpha mRNA is found exclusively in polysomes containing 10 or more ribosomes in exponentially growing HeLa cells. In serum-depleted cells which synthesize eIF-2 and bulk protein more slowly than exponential cells, the level of eIF-2 alpha mRNA is not changed, the average polysome size is reduced to 7, and little or no eIF-2 alpha mRNA is detected in the ribonucleoprotein fraction. These results are consistent with the view that eIF-2 alpha mRNA translation is very efficient compared to other mRNAs in the cell.
A simple and practical algorithm for differentially private data release (2010)

We present new theoretical results on differentially private data release useful with respect to any target class of counting queries, coupled with experimental results on a variety of real world data sets. Specifically, we study a simple combination of the multiplicative weights approach of [Hardt and Rothblum, 2010] with the exponential mechanism of [McSherry and Talwar, 2007]. The multiplicative weights framework allows us to maintain and improve a distribution approximating a given data set with respect to a set of counting queries. We use the exponential mechanism to select those queries most incorrectly tracked by the current distribution. Combing the two, we quickly approach a distribution that agrees with the data set on the given set of queries up to small error. The resulting algorithm and its analysis is simple, but nevertheless improves upon previous work in terms of both error and running time. We also empirically demonstrate the practicality of our approach on several data sets commonly used in the statistical community for contingency table release.
Atomic Layer Deposition of Iridium Thin Films (2004)

Thin films of metallic iridium were grown by atomic layer deposition (ALD) in a wide temperature range of 225-375°C from tris(2,4-pentanedionato)iridium and oxygen. The films had low resistivity and low impurity contents and good adhesion to the substrate. The film growth rate saturated to a constant value as the precursor pulse times were increased, thus verifying the self-limiting growth mechanism. In addition, the film thickness depended linearly on the number of deposition cycles. The development of the surface morphology with increasing film thickness was studied by atomic force microscopy (AFM). AFM and X-ray reflectivity analysis showed that the films had smooth surfaces. The films showed a preferred (111) orientation as studied by X-ray diffraction. The results show that high-quality iridium films can be grown by ALD. © 2004 The Electrochemical Society. All rights reserved.
Inactivation of Tumor Suppressor p53 by Mot-2, a hsp70 Family Member (1998)

The mortalin genes, mot-1 and mot-2, are hsp70 family members that were originally cloned from normal and immortal murine cells, respectively. Their proteins differ by only two amino acid residues but exhibit different subcellular localizations, arise from two distinct genes, and have contrasting biological activities. We report here that the two proteins also differ in their interactions with the tumor suppressor protein p53. The pancytosolic mot-1 protein in normal cells did not show colocalization with p53; in contrast, nonpancytosolic mot-2 and p53 overlapped significantly in immortal cells. Transfection of mot-2 but not mot-1 resulted in the repression of p53-mediated transactivation in p53-responsive reporter assays. Inactivation of p53 by mot-2 was supported by the down-regulation of p53-responsive genes p21(WAF-1) and mdm-2 in mot-2-transfected cells only. Furthermore, NIH 3T3 cells transfected with expression plasmid encoding green fluorescent protein-tagged mot-2 but not mot-1 showed an abrogation of nuclear translocation of wild-type p53. These results demonstrate a novel mechanism of p53 inactivation by mot-2 protein.
Structural Basis for Autoinhibition and Mutational Activation of Eukaryotic Initiation Factor 2α Protein Kinase GCN2*[boxs] (2005)

The GCN2 protein kinase coordinates protein synthesis with levels of amino acid stores by phosphorylating eukaryotic translation initiation factor 2. The autoinhibited form of GCN2 is activated in cells starved of amino acids by binding of uncharged tRNA to a histidyl-tRNA synthetase-like domain. Replacement of Arg-794 with Gly in the PK domain (R794G) activates GCN2 independently of tRNA binding. Crystal structures of the GCN2 protein kinase domain have been determined for wild-type and R794G mutant forms in the apo state and bound to ATP/AMPPNP. These structures reveal that GCN2 autoinhibition results from stabilization of a closed conformation that restricts ATP binding. The R794G mutant shows increased flexibility in the hinge region connecting the N- and C-lobes, resulting from loss of multiple interactions involving Arg794. This conformational change is associated with intradomain movement that enhances ATP binding and hydrolysis. We propose that intramolecular interactions following tRNA binding remodel the hinge region in a manner similar to the mechanism of enzyme activation elicited by the R794G mutation.