gebhart/patrepeval huggingface dataset:
Microbial Conversion of Glycerol to 1,3-Propanediol: Physiological Comparison of a Natural Producer, Clostridium butyricum VPI 3266, and an Engineered Strain, Clostridium acetobutylicum DG1(pSPD5) (2006)

Clostridium acetobutylicum is not able to grow on glycerol as the sole carbon source since it cannot reoxidize the excess of NADH generated by glycerol catabolism. Nevertheless, when the pSPD5 plasmid, carrying the NADH-consuming 1,3-propanediol pathway from C. butyricum VPI 3266, was introduced into C. acetobutylicum DG1, growth on glycerol was achieved, and 1,3-propanediol was produced. In order to compare the physiological behavior of the recombinant C. acetobutylicum DG1(pSPD5) strain with that of the natural 1,3-propanediol producer C. butyricum VPI 3266, both strains were grown in chemostat cultures with glycerol as the sole carbon source. The same "global behavior" was observed for both strains: 1,3-propanediol was the main fermentation product, and the qH2 flux was very low. However, when looking at key intracellular enzyme levels, significant differences were observed. Firstly, the pathway for glycerol oxidation was different: C. butyricum uses a glycerol dehydrogenase and a dihydroxyacetone kinase, while C. acetobutylicum uses a glycerol kinase and a glycerol-3-phosphate dehydrogenase. Secondly, the electron flow is differentially regulated: (i) in C. butyricum VPI 3266, the in vitro hydrogenase activity is 10-fold lower than that in C. acetobutylicum DG1(pSPD5), and (ii) while the ferredoxin-NAD+ reductase activity is high and the NADH-ferredoxin reductase activity is low in C. acetobutylicum DG1(pSPD5), the reverse is observed for C. butyricum VPI 3266. Thirdly, lactate dehydrogenase activity is only detected in the C. acetobutylicum DG1(pSPD5) culture, explaining why this microorganism produces lactate.
l -Arginine-dependent suppression of apoptosis in Trypanosoma cruzi : Contribution of the nitric oxide and polyamine pathways (2001)

Until recently, a capacity for apoptosis and synthesis of nitric oxide *NO) were viewed as exclusive to multicellular organisms. The existence of these processes in unicellular parasites was recently described, with their biological significance remaining to be elucidated. We have evaluated L-arginine metabolism in Trypanosoma cruzi in the context of human serum-induced apoptotic death. Apoptosis was evidenced by the induction of DNA fragmentation and the inhibition of [3H]thymidine incorporation, which were inhibited by the caspase inhibitor Ac-Asp-Glu-Val-aspartic acid aldehyde (DEVD-CHO). In T. cruzi exposed to death stimuli, supplementation with L-arginine inhibited DNA fragmentation, restored [3H]thymidine incorporation, and augmented parasite *NO production. These effects were inhibited by the *NO synthase inhibitor N(omega)-nitroarginine methyl ester (L-NAME). Exogenous *NO limited DNA fragmentation but did not restore proliferation rates. Because L-arginine is also a substrate for arginine decarboxylase (ADC), and its product agmatine is a precursor for polyamine synthesis, we evaluated the contribution of polyamines to limiting apoptosis. Addition of agmatine, putrescine, and the polyamines spermine and spermidine to T. cruzi sustained parasite proliferation and inhibited DNA fragmentation. Also, the ADC inhibitor difluoromethylarginine inhibited L-arginine-dependent restoration of parasite replication rates, while the protection from DNA fragmentation persisted. In aggregate, these results indicate that T. cruzi epimastigotes can undergo programmed cell death that can be inhibited by L-arginine by means of (i) a *NO synthase-dependent *NO production that suppresses apoptosis and (ii) an ADC-dependent production of polyamines that support parasite proliferation.
Hypoxic Stress Induces Cardiac Myocyte–Derived Interleukin-6 (1995)

Cardiac myocytes respond to hypoxic stress to augment the production of IL-6, and the IL-6 derived from cardiac myocytes may play an important role in the progression of myocardial dysfunction observed in cardiac ischemia-reperfusion injury.
Efficient photoinduced generation of radical cations in solvents of medium and low polarity (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEfficient photoinduced generation of radical cations in solvents of medium and low polarityWilliam P. Todd, Joseph P. Dinnocenzo, Samir Farid, Joshua L. Goodman, and Ian R. GouldCite this: J. Am. Chem. Soc. 1991, 113, 9, 3601–3602Publication Date (Print):April 1, 1991Publication History Published online1 May 2002Published inissue 1 April 1991https://pubs.acs.org/doi/10.1021/ja00009a062https://doi.org/10.1021/ja00009a062research-articleACS PublicationsRequest reuse permissionsArticle Views523Altmetric-Citations76LEARN 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
Cloning and functional expression of a cDNA encoding the catalytic subunit of bovine enterokinase. (1993)

Enterokinase (enteropeptidase) is a heterodimeric serine protease that is responsible for the physiological activation of trypsinogen by highly specific cleavage of the trypsinogen activation peptide following the sequence (Asp)4-Lys. In this paper, we report the cloning and functional expression of a cDNA encoding the catalytic domain (light chain) of bovine enterokinase. The nucleotide sequence of this cloned cDNA predicts a 235-amino acid polypeptide that shares a high degree of homology with a variety of mammalian serine proteases involved in digestion, coagulation, and fibrinolysis. We have developed a novel expression method for the enzyme which utilizes the secretory leader and propeptide of the mammalian serine protease PACE fused to the enterokinase light chain amino terminus. Efficient cleavage of the paired dibasic amino acid cleaving enzyme (PACE) propeptide was achieved by coexpression with human PACE or yeast KEX2. The mature product migrates at 43,000 Da on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, comparable to light chain derived from bovine duodena, and exhibited high levels of activity in cleaving the enterokinase-specific fluorogenic substrate Gly-(Asp)4-Lys-beta-naphthylamide. The recombinant single-chain form of enterokinase was also capable of activating trypsinogen, indicating that the specificity of the enzyme for its natural substrate is retained even in the absence of the noncatalytic enterokinase heavy chain.
Genetic Determinants of Immunity and Integration of Temperate Myxococcus xanthus Phage Mx8 (1998)

An 8.1-kb fragment of the temperate Myxococcus xanthus phage Mx8 genome, when cloned into a plasmid vector, permits site-specific integration of the plasmid and confers superinfection immunity. Sequence analysis of a 9.5-kb region of Mx8 DNA containing this fragment reveals 19 densely packed open reading frames, four of which have predicted products with known or suspected activities. The Mx8 imm gene, required for superinfection immunity, has a sequence similar to that of Arabidopsis thaliana G-box-binding factor 1. Mx8 makes a DNA adenine methylase, Mox, and integrase, Int, related to other methylases and integrases. The int gene has two alternate translation initiation codons within the extensively overlapping uoi (upstream of int) gene. Comparison of the predicted product of the uoi gene with Salmonella phage P22 and Streptomyces plasmid Xis proteins shows that temperate phage excisionases may use variations of a helix-turn-helix motif to recognize specific DNA sequences.
Somatic mutation of vascular endothelial growth factor receptors in juvenile hemangioma (2001)

Juvenile hemangiomas are the most common tumors of infancy, occurring in as many as 10% of all births. These benign vascular lesions enlarge rapidly during the first year of life by hyperplasia of endothelial cells and attendant pericytes and then spontaneously involute over a period of years, leaving loose fibrofatty tissue. Several hypotheses have been put forth concerning hemangiogenesis, including the possibility that the tumor is the result of somatic mutation in one or more components of critical vascular growth-regulatory pathways. To test this hypothesis, we obtained 15 proliferative-phase hemangiomas after surgical resection and dissected them to enrich for the lesional (endothelial and pericytic) components of each specimen. To determine whether hemangiomas represent a clonal expansion from a single progenitor cell, we assayed X-inactivation patterns for each lesion by using the polymorphic X-linked human androgen receptor gene. Twelve of 14 informative hemangiomas showed a significant degree of allelic loss after methylation-based and transcription-based polymerase chain reaction clonality assays, suggesting a nonrandom X-inactivation pattern and, thus, a monoclonal origin. We then sequenced genes encoding the receptors of the vascular endothelial growth factors (VEGFs) as candidates for potential somatic mutation. Mutations were found in two of the 15 hemangioma specimens: a missense mutation (P1147S) in the kinase domain of the VEGFR2 (FLK1/KDR) gene in one specimen and a missense mutation (P954S) in the kinase insert of the VEGFR3 (FLT4) gene in another specimen. In each case, the mutation was detected in tumor tissue but not in adjacent normal tissue. These results suggest that one potential mechanism involved in hemangioma formation is the alteration of the VEGF signaling pathway in endothelial and/or pericytic cells.
Inhibition of eukaryotic translation by nucleoside 5'-monophosphate analogs of mRNA 5'-cap: changes in N7 substituent affect analog activity (1989)

Nucleotide cap analogues of 7-methylguanosine 5'-monophosphate (m7GMP) were synthesized in which the 7-methyl moiety was replaced with 7-ethyl (e7), 7-propyl (p7), 7-isopropyl (ip7), 7-butyl (b7), 7-isobutyl (ib7), 7-cyclopentyl (cp7), 7-(carboxymethyl) (cm7), 7-benzyl (bn7), 7-(2-phenylethyl) [7-(2-PhEt)], and 7-(1-phenylethyl) [7-(1-PhEt)]. These derivatives were assayed as competitive inhibitors of capped mRNA translation in reticulocyte lysate. We observed that N7 alkyl and alicyclic substituents larger than ethyl significantly decreased the inhibitory activity of these cap analogues presumably by decreasing their affinity for cap binding proteins, which participate in the initiation of translation. This result defined a maximum size for this class of N7 substituents in the nucleotide binding domain of cap binding proteins. Like m7GMP, the N7-substituted GMP derivatives synthesized in this study were found to be predominantly in the anti conformation as determined by proton NMR analyses. However, bn7GMP and 7-(2-PhEt)GMP, which have aromatic N7 substituents, were more effective than m7GMP as competitive inhibitors of translation. The increased affinity of bn7GMP for cap binding proteins was further examined by synthesis of beta-globin mRNA containing 5'-bn7G, 5'-m7G, or 5'-e7G cap structures. These modified mRNAs were tested as translation templates. Messenger RNA capped with bn7G was observed to increase the translation activity of the template 1.8-fold relative to that of its m7G-capped mRNA counterpart. By contrast, e7G-capped mRNA was 25% less active than m7G-capped mRNA.2+V photo-cross-linking of m7G-capped mRNA to cap binding proteins
Scientific problems in the regulation of red blood cell products (2012)

Attempts to expand the useful regulatory requirements for RBC storage system licensure are limited by poor understanding of the storage lesion and its effect of RBC performance. Measures of (51) Cr 24-hour in vivo recovery remain critical and resources for this measure are limiting. The interaction between limited testing resources and large donor variability remains a major limit on RBC storage system development. It is important that new required tests contribute meaningful information and not make development and licensure of better products more difficult.
Bioaerosol Science, Technology, and Engineering: Past, Present, and Future (2011)

Poor air hygiene as a result of bioaerosol contamination has caused diverse forms of adverse health effects and diseases. In addition, global biosecurity is threatened by purposeful use of biowarfare agents and the vulnerability of people to the infectious agents. Accordingly, developments in high-volume biosampling, including aerosol-to-hydrosol techniques with low cut-off size, real-time bioaerosol detection, adequate biological quantification, and exposure control, as well as the investigation of the link between disease outcome and bioaerosol exposure, are current areas of bioaerosol research. Although milestone progress has been achieved both in bioaerosol sampling and analysis techniques since late 1800s, compared to atmospheric chemistry the bioaerosol field is still understudied. This is partially because of the lack of both bioaerosol scientists and multidisciplinary collaboration. It is becoming necessary to develop a pool of scientists with different expertise, e.g., bioaerosol scientists, environmental engineers, biomedical engineers, epidemiologists, microbiologists, chemists, physicists, as well as researchers in other engineering fields, in mitigating bioaerosol-related adverse health effects, eliminating diseases, and preventing and controlling epidemic outbreaks. This work is conducted to broadly review current state-of-the-art sciences and technologies in the bioaerosol field. In tackling the challenges ahead, the review also provides perspectives for bioaerosol research needs, and further reminds bioaerosol scientists of those existing technologies in other fields that can be leveraged. In view of the past, forward-looking hypotheses and revolutional perspectives are needed to be formed in order to allow the bioaerosol research have major impacts in the academic community in this new millennium.
Neural computation by concentrating information in time. (1987)

An analog model neural network that can solve a general problem of recognizing patterns in a time-dependent signal is presented. The networks use a patterned set of delays to collectively focus stimulus sequence information to a neural state at a future time. The computational capabilities of the circuit are demonstrated on tasks somewhat similar to those necessary for the recognition of words in a continuous stream of speech. The network architecture can be understood from consideration of an energy function that is being minimized as the circuit computes. Neurobiological mechanisms are known for the generation of appropriate delays.
Altered Pathogenesis of a Mutant of the Murine Coronavirus MHV-A59 Is Associated with a Q159L Amino Acid Substitution in the Spike Protein (1997)

C12, an attenuated, fusion delayed, very weakly hepatotropic mutant of mouse hepatitis virus strain A59 (MHV-A59( has been further characterized. We have previously shown that C12 has two amino acid substitutions relative to wild type virus in the spike protein, Q159L (within a region of S1 shown to bind to viral receptor in an in vitro assay) and H716D (in the proteolytic cleavage recognition site). We have sequenced the rest of the 31-kb genome of C-12 and compared it to wild type virus. Only three additional amino acids substitutions were found, all encoded within the replicase gene. Analysis of C12 in vivo in C57Bl/6 mice has shown that despite the fact that this virus replicates in the brain to titers at least as high as wild type and causes acute encephalitis similar to wild-type, this virus causes a minimal level of demyelination and only at very high levels of virus inoculation. Thus acute encephalitis is not sufficient for the induction of demyelination by MHV-A59. Analysis of mutants isolated at earlier times from the same persistently infected glial cell culture as C12, as well as mutants isolated from a second independent culture of persistently infected glial cells, suggests that both the weakly demyelinating and the weakly hepatotropic phenotypes of C12 are associated with the Q159L amino acid substitution.
Purification and Properties of an exo-α-Amylase fromPseudomonas stutzeri (1982)

A maltotetraose-forming amylase from Pseudomonas stutzeri was highly purified by adsorption on starch granules and by chromatographies on Sephadex G-100 and DEAE-cellulose. The purified enzyme showed a single band in polyacrylamide gel electrophoreses with or without sodium dodecylsulfate. The optimum pH for enzyme action on starch was 6.0-6.5, and the optimum temperature was 45°C. The purified enzyme attacked starch from the non-reducing end to produce α-anomer oligosaccharides. This indicated that the enzyme was an exo-α-amylase which had not hitherto been found. The enzyme activity was markedly inhibited by the addition of Cu2+, Hg2+, N-bromosuccinimide and 2,3-butanedione. The molecular weight of the enzyme determined by the method of Weber and Osborn was about 5.7 × 104. The isoelectric point of the enzyme was estimated to be 5.3 by polyacrylamide gel electrofocusing. The Km and k0 values of this enzyme for starch, glycogen, short chain amylose and some maltooligosaccharides were calculated from Lineweaver-Burk plots.
The “ART” of Linkage: Pre-Treatment Loss to Care after HIV Diagnosis at Two PEPFAR Sites in Durban, South Africa (2010)

Nearly half of HIV-infected persons at two high prevalence sites in Durban, South Africa, failed to have CD4 counts following HIV diagnosis. These high rates of pre-treatment loss to care highlight the urgent need to improve rates of linkage to HIV care after an initial positive HIV test.
Malware: Fighting Malicious Code (2003)

Reveals how attackers install malicious code and how they evade detection Shows how you can defeat their schemes and keep your computers and network safe! Details viruses, worms, backdoors, Trojan horses, RootKits, and other threats Explains how to handle today's threats, with an eye on handling the threats to comeKeep control of your systems out of the hands of unknown attackersIgnoring the threat of malware is one of the most reckless things you can do in today's increasingly hostile computing environment. Malware is malicious code planted on your computer, and it can give the attacker a truly alarming degree of control over your system, network, and data-all without your knowledge! Written for computer pros and savvy home users by computer security expert Edward Skoudis, Malware: Fighting Malicious Code covers everything you need to know about malware, and how to defeat it!This book devotes a full chapter to each type of malware-viruses, worms, malicious code delivered through Web browsers and e-mail clients, backdoors, Trojan horses, user-level RootKits, and kernel-level manipulation. You'll learn about the characteristics and methods of attack, evolutionary trends, and how to defend against each type of attack. Real-world examples of malware attacks help you translate thought into action, and a special defender's toolbox chapter shows how to build your own inexpensive code analysis lab to investigate new malware specimens on your own. Throughout, Skoudis' clear, engaging style makes the material approachable and enjoyable to learn. This book includes: Solutions and examples that cover both UNIX® and Windows® Practical, time-tested, real-world actions you can take to secure your systems Instructions for building your own inexpensive malware code analysis lab so you can get familiar with attack and defensive tools harmlessly!Malware: Fighting Malicious Code is intended for system administrators, network personnel, security personnel, savvy home computer users, and anyone else interested in keeping their systems safe from attackers.
Self-Assembled Monolayers and Multilayers of Conjugated Thiols, .alpha.,.omega.-Dithiols, and Thioacetyl-Containing Adsorbates. Understanding Attachments between Potential Molecular Wires and Gold Surfaces (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSelf-Assembled Monolayers and Multilayers of Conjugated Thiols, .alpha.,.omega.-Dithiols, and Thioacetyl-Containing Adsorbates. Understanding Attachments between Potential Molecular Wires and Gold SurfacesJames M. Tour, LeRoy Jones II, Darren L. Pearson, Jaydeep J. S. Lamba, Timothy P. Burgin, George M. Whitesides, David L. Allara, Atul N. Parikh, and Sundar AtreCite this: J. Am. Chem. Soc. 1995, 117, 37, 9529–9534Publication Date (Print):September 1, 1995Publication History Published online1 May 2002Published inissue 1 September 1995https://pubs.acs.org/doi/10.1021/ja00142a021https://doi.org/10.1021/ja00142a021research-articleACS PublicationsRequest reuse permissionsArticle Views4623Altmetric-Citations693LEARN 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
Optimization Techniques for the Synchronization of Concurrent Fluidic Operations in Pin-Constrained Digital Microfluidic Biochips (2011)

The implementation of bioassays in pin-constrained digital microfluidic biochips may involve pin-actuation conflicts if the concurrently-implemented fluidic operations are not carefully synchronized. We propose a two-phase optimization method to identify and synchronize the fluidic operations that can be executed in parallel. The goal is to implement these fluidic operations without pin-actuation conflict, and minimize the duration of implementing the outcome sequence after synchronization. We also extend the synchronization method with the addition of a small number of control pins, in order to further minimize the completion time while avoiding pin-actuation conflicts. The effectiveness of the proposed synchronization method is demonstrated for a representative 3-plex assay performed on a commercial pin-constrained biochip and for multiplexed in-vitro diagnostics performed on an experimental pin-constrained biochip.