gebhart/patrepeval huggingface dataset:
Characterization of a second lysine decarboxylase isolated from Escherichia coli (1997)

We report here on the existence of a new gene for lysine decarboxylase in Escherichia coli K-12. The hybridization experiments with a cadA probe at low stringency showed that the homologous region of cadA was located in lambda Kohara phage clone 6F5 at 4.7 min on the E. coli chromosome. We cloned the 5.0-kb HindIII fragment of this phage clone and sequenced the homologous region of cadA. This region contained a 2,139-nucleotide open reading frame encoding a 713-amino-acid protein with a calculated molecular weight of 80,589. Overexpression of the protein and determination of its N-terminal amino acid sequence defined the translational start site of this gene. The deduced amino acid sequence showed 69.4% identity to that of lysine decarboxylase encoded by cadA at 93.7 min on the E. coli chromosome. In addition, the level of lysine decarboxylase activity increased in strains carrying multiple copies of the gene. Therefore, the gene encoding this lysine decarboxylase was designated Idc. Analysis of the lysine decarboxylase activity of strains containing cadA, ldc, or cadA ldc mutations indicated that ldc was weakly expressed under various conditions but is a functional gene in E. coli.
The distribution of functional impairment across the lateral border of acutely ischemic myocardium. (1986)

To evaluate the degree and lateral extent of dysfunction in nonischemic myocardium adjacent to ischemic muscle, we measured systolic wall thickening with sonomicrometers during circumflex coronary occlusion in 12 anesthetized, open-chest dogs. The locations of the wall thickness measurements relative to the perfusion boundary were determined with myocardial blood flow (microspheres) maps constructed from multiple, small tissue samples. Five minutes after circumflex occlusion, systolic wall thickening in the central ischemic zone decreased from 3.00 +/- 0.61 (mean +/- SD) mm to -0.61 +/- 0.36 mm (P less than 0.01). In nonischemic myocardium greater than 10 mm from the perfusion boundary, systolic wall thickening increased from 2.56 +/- 0.57 to 3.24 +/- 0.72 mm (P less than 0.01). In nonischemic myocardium within 10 mm of the perfusion boundary, systolic wall thickening was slightly but significantly reduced compared with control (2.72 +/- 0.80 to 2.44 +/- 0.79 mm, P less than 0.05), supporting the concept of regional dysfunction in nonischemic myocardium at the lateral borders of an ischemic area. Sigmoid curves were fitted to the data to model changes in wall thickening as a continuous function of distance from the perfusion boundary. This allowed estimation of the extent of dysfunction into nonischemic myocardium which averaged less than 8 mm (approximately 30 degrees of endocardial circumference) at one border. The level of functional impairment in this zone was relatively modest, and systolic wall thickening in the immediate border area was reduced more than 50% from control only in tissue characterized by a blood supply of mixed ischemic and nonischemic origin. We conclude that a functional border zone exists lateral to an acutely ischemic area, but measurement of regional function produces relatively small exaggeration of the size of the acutely ischemic zone if severe reduction in mechanical performance is used to define the extent of the ischemic area.
The Way Things Move: Looking Under the Hood of Molecular Motor Proteins (2000)

The microtubule-based kinesin motors and actin-based myosin motors generate motions associated with intracellular trafficking, cell division, and muscle contraction. Early studies suggested that these molecular motors work by very different mechanisms. Recently, however, it has become clear that kinesin and myosin share a common core structure and convert energy from adenosine triphosphate into protein motion using a similar conformational change strategy. Many different types of mechanical amplifiers have evolved that operate in conjunction with the conserved core. This modular design has given rise to a remarkable diversity of kinesin and myosin motors whose motile properties are optimized for performing distinct biological functions.
Arabidopsis AtGPAT1, a Member of the Membrane-Bound Glycerol-3-Phosphate Acyltransferase Gene Family, Is Essential for Tapetum Differentiation and Male Fertility (2003)

Membrane-bound glycerol-3-phosphate acyltransferase (GPAT; EC 2.3.1.15) mediates the initial step of glycerolipid biosynthesis in the extraplastidic compartments of plant cells. Here, we report the molecular characterization of a novel GPAT gene family from Arabidopsis, designated AtGPAT. The corresponding polypeptides possess transmembrane domains and GPAT activity when expressed heterologously in a yeast lipid mutant. The functional significance of one isoform, AtGPAT1, is the focus of the present study. Disruption of the AtGPAT1 gene causes a massive pollen development arrest, and subsequent introduction of the gene into the mutant plant rescues the phenotype, illustrating a pivotal role for AtGPAT1 in pollen development. Microscopic examinations revealed that the gene lesion results in a perturbed degeneration of the tapetum, which is associated with altered endoplasmic reticulum profiles and reduced secretion. In addition to the sporophytic effect, AtGPAT1 also exerts a gametophytic effect on pollen performance, as the competitive ability of a pollen grain to pollinate is dependent on the presence of an AtGPAT1 gene. Deficiency in AtGPAT1 correlates with several fatty acid composition changes in flower tissues and seeds. Unexpectedly, however, a loss of AtGPAT1 causes no significant change in seed oil content.
ExpandedC9ORF72Hexanucleotide Repeat in Depressive Pseudodementia (2014)

This report increases the range of clinicopathologic presentations of C9ORF72 expanded hexanucleotide repeat to include psychiatric disorders such as depressive pseudodementia.
CasOT: a genome-wide Cas9/gRNA off-target searching tool (2014)

http://eendb.zfgenetics.org/casot/ CONTACT: zfgenetics@gmail.com or bzhang@pku.edu.cn Supplementary Information: Supplementary data are available at Bioinformatics online.
Nanowire Sensors for Medicine and The Life Sciences (2006)

The interface between nanosystems and biosystems is emerging as one of the broadest and most dynamic areas of science and technology, bringing together biology, chemistry, physics and many areas of engineering, biotechnology and medicine. The combination of these diverse areas of research promises to yield revolutionary advances in healthcare, medicine and the life sciences through, for example, the creation of new and powerful tools that enable direct, sensitive and rapid analysis of biological and chemical species, ranging from the diagnosis and treatment of disease to the discovery and screening of new drug molecules. Devices based on nanowires are emerging as a powerful and general platform for ultrasensitive, direct electrical detection of biological and chemical species. Here, representative examples where these new sensors have been used for detection of a wide-range of biological and chemical species, from proteins and DNA to drug molecules and viruses, down to the ultimate level of a single molecule, are discussed. Moreover, how advances in the integration of nanoelectronic devices enable multiplexed detection and thereby provide a clear pathway for nanotechnology, enabling diverse and exciting applications in medicine and life sciences, are highlighted.
Proteolytic 18O‐labeling strategies for quantitative proteomics (2006)

A number of proteomic techniques have been developed to quantify proteins in biological systems. This review focuses on the quantitative proteomic technique known as "proteolytic 18O-labeling." This technique utilizes a protease and H(2)18O to produce labeled peptides, with subsequent chromatographic and mass spectrometric analysis to identify and quantify (relative) the proteins from which the peptides originated. The technique determines the ratio of individual protein's expression level between two samples relative to each other, and can be used to quantitatively examine protein expression (comparative proteomics) and post-translational modifications, and to study protein-protein interactions. The present review discusses various aspects of the 18O-labeling technique, including: its history, the advantages and disadvantages of the proteolytic 18O-labeling technique compared to other techniques, enzymatic considerations, the problem of variable incorporation of 18O atoms into peptides with a discussion on recent advancements of the technique to overcome it, computational tools to interpret the data, and a review of the biological applications.
Identification of the Minimal Phosphoacceptor Site Required for in Vivo Activation of Interferon Regulatory Factor 3 in Response to Virus and Double-stranded RNA (2003)

The ubiquitously expressed latent interferon regulatory factor (IRF) 3 transcription factor is activated in response to virus infection by phosphorylation events that target a cluster of Ser/Thr residues, (382)GGASSLENTVDLHISNSHPLSLTSDQY(408) at the C-terminal end of the protein. To delineate the minimal phosphoacceptor sites required for IRF-3 activation, several point mutations were generated and tested for transactivation potential and cAMP-response element-binding protein-binding protein/p300 coactivator association. Expression of the IRF-3 S396D mutant alone was sufficient to induce type I IFN beta, IFNalpha1, RANTES, and the interferon-stimulated gene 561 promoters. Using SDS-PAGE and immunoblotting with a novel phosphospecific antibody, we show for the first time that, in vivo, IRF-3 is phosphorylated on Ser(396) following Sendai virus infection, expression of viral nucleocapsid, and double-stranded RNA treatment. These results demonstrate that Ser(396) within the C-terminal Ser/Thr cluster is targeted in vivo for phosphorylation following virus infection and plays an essential role in IRF-3 activation. The inability of the phosphospecific antibody to detect Ser(396) phosphorylation in lipopolysaccharide-treated cells suggests that other major pathways may be involved in IRF-3 activation following Toll-like receptor 4 stimulation.
Predicting user activity level in social networks (2013)

The study of users' social behaviors has gained much research attention since the advent of various social media such as Facebook, Renren and Twitter. A major kind of applications is to predict a user's future activities based on his/her historical social behaviors. In this paper, we focus on a fundamental task: to predict a user's future activity levels in a social network, e.g. weekly activeness, active or inactive. This problem is closely related to Social Customer Relationship Management (Social CRM). Compared to traditional CRM, the three properties: user diversity, social influence, and dynamic nature of social networks, raise new challenges and opportunities to Social CRM. Firstly, the user diversity property implies that a global predictive model may not be precise for all users. On the other hand, historical data of individual users are too sparse to build precisely personalized models. Secondly, the social influence property suggests that relationships between users can be embedded to further boost prediction results on individual users. Finally, the dynamical nature of social networks means that users' behaviors may keep changing over time. To address these challenges, we develop a personalized and social regularized time-decay model for user activity level prediction. Experiments on the social media Renren validate the effectiveness of our proposed model compared with some baselines including traditional supervised learning methods and node classification methods in social networks.
Dual Roles of the Cardin-Weintraub Motif in Multimeric Sonic Hedgehog (2011)

The fly morphogen Hedgehog (Hh) and its mammalian orthologs, Sonic, Indian, and Desert hedgehog, are secreted signaling molecules that mediate tissue patterning during embryogenesis and function in tissue homeostasis and regeneration in the adult. The function of all Hh family members is regulated at the levels of morphogen multimerization on the surface of producing cells, multimer release, multimer diffusion to target cells, and signal reception. These mechanisms are all known to depend on interactions of positively charged Hh amino acids (the Cardin-Weintraub (CW) motif) with negatively charged heparan sulfate (HS) glycosaminoglycan chains. However, a precise mechanistic understanding of these interactions is still lacking. In this work, we characterized ionic HS interactions of multimeric Sonic hedgehog (called ShhNp) as well as mutant forms lacking one or more CW residues. We found that deletion of all five CW residues as well as site-directed mutagenesis of CW residues Lys(33), Arg(35), and Lys(39) (mouse nomenclature) abolished HS binding. In contrast, CW residues Arg(34) and Lys(38) did not contribute to HS binding. Analysis and validation of Shh crystal lattice contacts provided an explanation for this finding. We demonstrate that CW residues Arg(34) and Lys(38) make contact with an acidic groove on the adjacent molecule in the multimer, suggesting a new function of these residues in ShhNp multimerization rather than HS binding. Therefore, the recombinant monomeric morphogen (called ShhN) differs in CW-dependent HS binding and biological activity from physiologically relevant ShhNp multimers, providing new explanations for functional differences observed between ShhN and ShhNp.
A Sorptive Behavior of Monolayer-Protected Gold Nanoparticle Films Containing Alkanethiols and Alkanedithiols (2003)

ADVERTISEMENT RETURN TO ISSUEPREVCommentA Sorptive Behavior of Monolayer-Protected Gold Nanoparticle Films Containing Alkanethiols and AlkanedithiolsJay W. GrateView Author Information Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352Cite this: Anal. Chem. 2003, 75, 23, 6759Publication Date (Web):October 23, 2003Publication History Published online23 October 2003Published inissue 1 December 2003https://pubs.acs.org/doi/10.1021/ac030280bhttps://doi.org/10.1021/ac030280barticle-commentaryACS PublicationsCopyright © 2003 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views356Altmetric-Citations14LEARN 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 InRedditEmail PDF (16 KB) Get e-AlertscloseSUBJECTS:Aromatic compounds,Hydrocarbons,Metal nanoparticles,Nanomaterials,Nanoparticles Get e-Alerts
Real-Time Nucleic Acid Sequence-Based Amplification in Nanoliter Volumes (2003)

Real-time nucleic acid sequence-based amplification (NASBA) is an isothermal method specifically designed for amplification of RNA. Fluorescent molecular beacon probes enable real-time monitoring of the amplification process. Successful identification, utilizing the real-time NASBA technology, was performed on a microchip with oligonucleotides at a concentration of 1.0 and 0.1 microM, in 10- and 50-nL reaction chambers, respectively. The microchip was developed in a silicon-glass structure. An instrument providing thermal control and an optical detection system was built for amplification readout. Experimental results demonstrate distinct amplification processes. Miniaturized real-time NASBA in microchips makes high-throughput diagnostics of bacteria, viruses, and cancer markers possible, at reduced cost and without contamination.
Revealing Zion's Daughters: Women in Puritan Jurisprudence (2007)

The legal status of American women has consistently been portrayed as a linear progression flowing from a colonial jurisprudential repression and exclusion to a modern-day legal equity and a female influence within every aspect of justice. In this narrative of sequentially gained status, seventeenth-century Puritan law has stood as the exemplar of America’s most repressive jurisprudential treatment of women. However, when its characteristics are triangulated and its subordination of women is juxtaposed with its inclusion of a female voice, a new conception of America’s first legal system is seen. The notion of a linear progression is thus replaced with an understanding that the modern day equity enjoyed by women is a product of extensive legal fluctuation. Puritan women were clearly characterized as the subordinate gender and their secondary status evidenced in the symbolic silencing of heretical females and in legal coverture. However, stemming from the Puritan concept of a “Godly-society” attained through equitable legal status, New England women enjoyed liberal divorce laws and a significant presence within the court room when compared with contemporary England and the nineteenth century jurisprudence, which relegated women to the non-public sphere. Thus, as Laurel Thatcher Ulrich emphasizes, we “need to move from static concepts like “patriarchal New England society” to more intricate questions about the interplay of values and practice over time. Zion’s daughters have for too long been hidden.”
Chronic lymphocytic leukemia B cells of more than 1% of patients express virtually identical immunoglobulins (2004)

We examined the immunoglobulin (Ig) heavy chain variable region genes (V(H) genes) used by leukemia cells of 1220 unrelated patients with chronic lymphocytic leukemia (CLL). We found 1188 (97%) expressed Ig encoded by a single Ig V(H) subgroup, the most common of which was V(H)3 (571 or 48.1%), followed by V(H)1 (319 or 26.8%) and V(H)4 (241 or 20.2%). Using allele-specific primers, we found 13.8% of all samples (n = 164) used one major V(H)1-69 allele, designated 51p1, 163 of which were not somatically mutated. For these cases, there was marked restriction in the structure of the Ig third complementarity determining regions (CDR3s), which were encoded by a small number of unmutated D and J(H) gene segments. Strikingly, 15 of the 163 cases had virtually identical CDR3s encoded by the second reading frame of D3-16 and J(H)3. Further analysis revealed that each of these 15 samples used the same unmutated Ig kappa light-chain gene, namely A27. These data reveal that approximately 1.3% (15/1220) of all patients had leukemia cells that expressed virtually identical Ig. This finding provides compelling evidence that the Ig expressed by CLL B cells are highly selected and not representative of the Ig expressed by naive B cells.
Further results on mapping functions (2005)

In a previous paper as presented by Tarable et al. (2004), the authors introduced the concept of mapping functions as a tool to cope with the problem of collision-free memory mappings in turbo and LDPC parallel decoder implementations. In this paper, we address some implementation issues of the original solution, define a dual problem, which can be of high interest for practical implementations, and give the generalization of mapping functions to N > 2 parallel decoders.
Color and Constitution. IV.1 The Absorption of Phenol Blue (1941)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTColor and Constitution. IV.1 The Absorption of Phenol BlueL. G. S. Brooker and R. H. SpragueCite this: J. Am. Chem. Soc. 1941, 63, 11, 3214–3215Publication Date (Print):November 1, 1941Publication History Published online1 May 2002Published inissue 1 November 1941https://pubs.acs.org/doi/10.1021/ja01856a088https://doi.org/10.1021/ja01856a088research-articleACS PublicationsRequest reuse permissionsArticle Views254Altmetric-Citations69LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Hemoperfusion with a New Anion Exchange Resin Corrects the Metabolic Alkalosis in Pyloric Stenosis: An Experimental Demonstration (1992)

An experimental model of hypertrophic pyloric stenosis was made by suture of the pyloric wall and gastrostomy in 10 rabbits under general anesthesia. Blood sampling indicated severe alkalosis and hypochloremia 3h 30 min after surgery. To correct the derangement, we tested an ion exchange resin (Dowex SAR), coated with a methacrylic hydrogel. A cartridge containing 18 g of this resin was inserted in an extracorporeal circuit. This chloride charged resin achieved uptake of HCO3- ions, and elution of Cl- ions. The electrolytic balance was fully restored after 10 min of treatment.
Cancer Chemopreventive and Antioxidant Activities of Pterostilbene, a Naturally Occurring Analogue of Resveratrol (2002)

Pterostilbene, a natural methoxylated analogue of resveratrol, was evaluated for antioxidative potential. The peroxyl-radical scavenging activity of pterostilbene was the same as that of resveratrol, having total reactive antioxidant potentials of 237 +/- 58 and 253 +/- 53 microM, respectively. Both compounds were found to be more effective than Trolox as free radical scavengers. Using a plant system, pterostilbene also was shown to be as effective as resveratrol in inhibiting electrolyte leakage caused by herbicide-induced oxidative damage, and both compounds had the same activity as alpha-tocopherol. Pterostilbene showed moderate inhibition (IC50 = 19.8 microM) of cyclooxygenase (COX)-1, and was weakly active (IC50 = 83.9 microM) against COX-2, whereas resveratrol strongly inhibited both isoforms of the enzyme with IC50 values of approximately 1 microM. Using a mouse mammary organ culture model, carcinogen-induced preneoplastic lesions were, similarly to resveratrol, significantly inhibited by pterostilbene (ED50 = 4.8 microM), suggesting antioxidant activity plays an important role in this process.