gebhart/patrepeval huggingface dataset:
1-Benzenesulfinyl Piperidine/Trifluoromethanesulfonic Anhydride:  A Potent Combination of Shelf-Stable Reagents for the Low-Temperature Conversion of Thioglycosides to Glycosyl Triflates and for the Formation of Diverse Glycosidic Linkages (2001)

The combination of 1-benzenesulfinyl piperidine (BSP) and trifluoromethanesulfonic anhydride (Tf(2)O) forms a new, powerful, metal-free thiophile that can readily activate both armed and disarmed thioglycosides, via glycosyl triflates, in a matter of minutes at -60 degrees C in dichloromethane, in the presence of 2,4,6-tri-tert-butylpyrimidine (TTBP). The glycosyl triflates are rapidly and cleanly converted to glycosides, upon treatment with alcohols, in good yield and selectivity.
Structurally Complex and Highly Active RNA Ligases Derived from Random RNA Sequences (1995)

Seven families of RNA ligases, previously isolated from random RNA sequences, fall into three classes on the basis of secondary structure and regiospecificity of ligation. Two of the three classes of ribozymes have been engineered to act as true enzymes, catalyzing the multiple-turnover transformation of substrates into products. The most complex of these ribozymes has a minimal catalytic domain of 93 nucleotides. An optimized version of this ribozyme has a kcat exceeding one per second, a value far greater than that of most natural RNA catalysts and approaching that of comparable protein enzymes. The fact that such a large and complex ligase emerged from a very limited sampling of sequence space implies the existence of a large number of distinct RNA structures of equivalent complexity and activity.
Bacterial Secretion Chaperones (2011)

Many Gram-negative bacteria are able to invade hosts by translocation of effectors directly into target cells in processes usually mediated by two very complex secretion systems (SSs), named type III (T3) and type IV (T4) SSs. These syringe-needle injection devices work with intervention of specialized secretion chaperones that, unlike traditional molecular chaperones, do not assist in protein folding and are not energized by ATP. Controversy still surrounds secretion chaperones primary role, but we can say that these chaperones act as: (i) bodyguards to prevent premature aggregation, or as (ii) pilots to direct substrate secretion through the correct secretion system. This family of chaperones does not share primary structure similarity but amazingly equal 3D folds. This mini review has the intent to present updated structural and functional data for several important secretion chaperones, either alone or in complex with their cognate substrates, as well to report on the common features and roles of T3, T4 and flagellar chaperones.
Experimental Murine Candidiasis: Pathological and Immune Responses in T-Lymphocyte-Depleted Mice (1978)

Mice depleted of T-lymphocytes by thymectomy and irradiation (TXB) and immunologically competent mice were compared for gross and histological pathology as well as immune responses after cutaneous and/or intravenous challenge with Candida albicans. In response to a first cutaneous inoculation with viable Candida, TXB, sham-operated (SXB), and unmanipulated (normal) mice, all developed lesions of comparable size, duration, and histopathology. When challenged a second time cutaneously, normal and SXB mice developed lesions which were greatly increased in size when compared with those produced by a first cutaneous infection, whereas TXB mice developed lesions comparable in size to those initiated by the first infection. Histologically, the first and second lesions in all animals were acute abscesses predominantly comprised of polymorphonuclear leukocytes. The larger second lesions in SXB and normal mice were accompanied by detectable circulating antibody and by delayed hypersensitivity. Neither circulating antibody nor delayed hypersensitivity were stimulated in the TXB mice. When challenged intravenously, all previously uninfected mice, regardless of T-cell status, were equally susceptible to C. albicans. Contrary to SXB or normal mice, however, TXB mice which had been infected cutaneously were not more resistant to a subsequent intravenous challenge as judged by 6-week survival. The results suggest that T-cells do not play a significant role in innate resistance of mice to systemic candidiasis, but that such cells are important in the development of acquired resistance.
The essential yeast RNA binding protein Npl3p is methylated (1996)

Arginine methylation is a prevalent modification found in many RNA binding proteins, yet little is known about its functional consequences. Using a monoclonal antibody, 1E4, we have shown that the yeast NPL3 gene product Np13p, an essential RNA binding protein with repeated RGG motifs, is arginine-methylated in vivo. The 1E4 epitope can be generated by incubating recombinant Np13p with partially purified bovine arginine methyltransferase block this reaction. Np13p methylation requires S-adenosyl-L-methionine and also occurs in yeast extracts. An Np13p deletion mutant lacking the RGG domain is not a substrate for methylation, suggesting that the methylation sites lie within the RGG motifs. The discovery of arginine methylation in a genetically tractable organism provides a powerful entrée to understanding the function of this modification, particularly in view of the many roles postulated for Np13p in RNA processing and transport. The recent discovery of phosphorylated serine residues within the RGG domain suggests a hypothesis in which a molecular switch governed by methylation and phosphorylation regulates the biochemical properties of the Np13p RGG domain.
Synthesis of Trifluoromethanesulfinamidines and -sulfanylamides (2008)

Fluorinated moieties constitute important substituents used in many applications to modify the properties of molecules. The action of DAST onto Ruppert's reagent yields to a not isolable intermediate that can then react with various primary amines to give trifluoromethanesulfinamidines and trifluoromethanesulfanylamides. Such compounds were unknown until now and constitute interesting new families of fluorinated molecules.
Black Hat Python: Python Programming for Hackers and Pentesters (2014)

Python is the language of choice for hackers and security analysts for creating powerful and effective tools. Ever wonder how they do it?A follow-up to the perennial best-seller Gray Hat Python, Justin Seitz's Black Hat Python explores the darker side of Python's capabilitieswriting network sniffers, manipulating packets, infecting virtual machines, creating stealthy trojans, extending the popular web hacking tool Burp Suite, and more. You'll learn how to:Create a trojan command-and-control using Github Detect sandboxing and automate common malware tasks, like keylogging and screenshotting Escalate Windows privileges with creative process control Use offensive memory forensics tricks to retrieve password hashes and inject shellcode into a virtual machine Abuse Windows COM automation to perform a man-in-the-browser attack Exfiltrate data from a network most sneakily Insider techniques and creative challenges show you how to extend the hacks, and are sure to make Black Hat Python irresistible to anyone interested in offensive security.
Profile hidden Markov models. (1998)

The recent literature on profile hidden Markov model (profile HMM) methods and software is reviewed. Profile HMMs turn a multiple sequence alignment into a position-specific scoring system suitable for searching databases for remotely homologous sequences. Profile HMM analyses complement standard pairwise comparison methods for large-scale sequence analysis. Several software implementations and two large libraries of profile HMMs of common protein domains are available. HMM methods performed comparably to threading methods in the CASP2 structure prediction exercise.
A Role for Macrophage Inflammatory Protein-3α/CC Chemokine Ligand 20 in Immune Priming During T Cell-Mediated Inflammation of the Central Nervous System (2003)

Chemokines are a family of cytokines that exhibit selective chemoattractant properties for target leukocytes and play a significant role in leukocyte migration. In this study, we have investigated the role of the C-C chemokine, macrophage inflammatory protein (MIP)-3alpha/CC chemokine ligand 20, in the pathogenesis of experimental autoimmune encephalomyelitis (EAE), a model of T cell-dependent inflammation. Expression in the CNS of MIP-3alpha, as determined by RT-PCR, increased in a time-dependent manner such that peak expression correlated with peak clinical disease. Similarly, levels of immunoreactive MIP-3alpha in the draining lymph nodes increased up to 10-fold 9 days postimmunization and remained elevated for up to 21 days postimmunization. The increased production of MIP-3alpha coincided with onset of clinical disease. Treatment of mice with specific neutralizing anti-MIP-3alpha Abs significantly reduced the severity of both clinical EAE and neuroinflammation by inhibiting the sensitization of lymphocytes to the specific Ag and release of lymphocytes from the draining lymph nodes. In contrast, adoptive transfer experiments indicated that MIP-3alpha was not essential for the effector phase of EAE. Together, these data demonstrate that MIP-3alpha plays a critical role in the sensitization phase of EAE.
LIF is more potent than BDNF in promoting neurite outgrowth of mammalian auditory neurons in vitro (2001)

Neurotrophic factors are known to play a crucial role in the elongation and guidance of auditory nerve fibres to their targets within the organ of Corti. Maintenance of these neural connections following deafness would clearly influence the efficacy of therapies for hearing recovery. The growth factors leukaemia inhibitory factor (LIF), brain-derived neurotrophic factor (BDNF) and transforming growth factor-beta 5 (TGF-beta5) were tested for their efficacy in promoting neurite outgrowth from dissociated cultures of early postnatal rat auditory neurons. Our results indicate that while BDNF enhances neurite outgrowth in a strong fashion, LIF is more potent; moreover, the combined administration of both factors has even greater neuritogenic capacities. TGF-beta5, although neurotrophic, has no neuritogenic activity on cultured auditory neurons. LIF and BDNF may therefore be potential candidates when developing pharmacological therapies for hearing recovery.
Using black-box persistent state manifest for dependency management in patching and upgrading J2EE based applications (2005)

This paper describes a new approach to J2EE based software upgrade and patch management using black-box persistent state manifests which helps in self-managing the upgrade and patching process of Java based applications. We created a tool called object version checker which uses black-box based persistent state manifests to aid in software upgrades and patches to check the versions of installed components and identify components that are not installed correctly and cause potential problems to the whole enterprise. We provide a theoretical insight of the requirements, usage and usefulness of the tool.
Detoxification of Bacterial Lipopolysaccharides (Endotoxins) by a Human Neutrophil Enzyme (1986)

Lipopolysaccharides in the cell walls of Gram-negative bacteria elicit toxic as well as potentially beneficial inflammatory responses in animals. It is now reported that tissue toxicity caused by lipopolysaccharides is preferentially reduced by an enzymatic activity in human neutrophils. Acyloxyacyl hydrolysis removes fatty acyl chains that are linked to the hydroxyl groups of 3-hydroxytetradecanoyl residues in the bioactive lipid A moiety of the lipopolysaccharides. Maximal acyloxyacyl hydrolysis reduced lipopolysaccharide tissue toxicity, as measured in the dermal Shwartzman reaction, by a factor of 100 or more. In contrast, the ability of the deacylated lipopolysaccharides to stimulate B lymphocytes to divide was decreased only by a factor of 12. It is suggested that during tissue invasion by Gram-negative bacteria acyloxyacyl hydrolysis may be a defense mechanism that reduces the toxicity of lipopolysaccharides while preserving some of their potentially beneficial inflammatory and immune stimuli.
Heparin-binding protein: Another neutrophil granule protein ... another new biomarker?* (2011)

University of Kansas School of Medicine–Wichita, Wichita, KS The author has not disclosed any potential conflicts of interest.
3.4 W monolithic erbium-doped all-fiber laser at 3.55 μm (2017)

Summary form only given. Mid-infrared fiber lasers operating around 3.5 μm find applications in various fields such as remote sensing, polymer processing and spectroscopy. Recent demonstrations based on the <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> F <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">9/2</sub> → <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">9/2</sub> transition in Er <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3+</sup> :ZrF <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> fibers have shown effective laser emission up to 1.52 W [1] by relying on a dual-wavelength pumping (DWP) scheme. This novel approach mitigates the low Stokes efficiency associated with single-wavelength pumping and reduces ion bottlenecking in lower lying energy states. Here, we report the first monolithic DWP erbium doped all-fiber laser bounded by two fiber Bragg gratings (FBGs) emitting ~ 3.4 W at 3.55 μm with a total optical efficiency of 22 %. To the best of our knowledge, these results represent the highest output power and efficiency ever achieved at this wavelength in a rare-earth doped fiber laser.
Photoencapsulation of chondrocytes in poly(ethylene oxide)-based semi-interpenetrating networks (2000)

A photopolymerizing hydrogel system provides an efficient method to encapsulate cells. The present work describes the in vitro analysis of bovine and ovine chondrocytes encapsulated in a poly(ethylene oxide)-dimethacrylate and poly(ethylene glycol) semi-interpenetrating network using a photopolymerization process. One day after encapsulation, (3-[4,5-dimethylthiazol-2-y1]-2, 5-diphenyl-2H-tetrazolium bromide) (MTT) and light microscopy showed chondrocyte survival and a dispersed cell population composed of ovoid and elongated cells. Biochemical analysis demonstrated proteoglycan and collagen contents that increased over 2 weeks of static incubation. Cell content of the gels initially decreased and stabilized. Biomechanical analysis demonstrated the presence of a functional extracellular matrix with equilibrium moduli, dynamic stiffness, and streaming potentials that increased with time. These findings suggest the feasibility of photoencapsulation for tissue engineering and drug delivery purposes.
Architectural support for translation table management in large address space machines (1993)

Virtual memory page translation tables provide mappings from virtual to physical addresses. When the hardware controlled Translation Lookaside Buffers (TLBs) do not contain a translation, these tables provide the translation. Approaches to the structure and management of these tables vary from full hardware implementations to complete software based algorithms.
Germ-line tumor formation caused by activation of glp-1, a Caenorhabditis elegans member of the Notch family of receptors (1997)

Caenorhabditis elegans germ-line proliferation is controlled by an inductive interaction between the somatic distal tip cell and the germ line. GLP-1, a member of the Notch family of transmembrane receptors, is required continuously in the germ line to transduce the proliferative signal. In the absence of GLP-1, all proliferative germ cells exit the mitotic cell cycle and enter meiotic prophase. We have characterized an activating mutation in glp-1, oz112gf, that has the opposite phenotype. Homozygous glp-1(oz112gf) hermaphrodites and males have a completely tumorous germ line in which germ cells never leave the mitotic cycle. In glp-1(oz112gf) heterozygotes, germ-line polarity is established correctly, but as adults age, the distal proliferative population expands leading to a late-onset tumorous phenotype. The mutant receptor is constitutively active, promoting proliferation in the absence of ligand. The normal distal-proximal spatial restriction of GLP-1 expression is lost in tumorous and late-onset tumorous animals; ectopically proliferating germ cells contain membrane-associated GLP-1. The correlation between proliferation and expression, both in wild-type where glp-1 signalling is limited by localized ligand and in glp-1(oz112gf) where signalling is ligand-independent, suggests that glp-1 signalling positively regulates GLP-1 expression. In addition to germ-line defects, glp-1(oz112gf) causes inappropriate vulval cell fate specification. A missense mutation in a conserved extracellular residue, Ser642, adjacent to the transmembrane domain, is sufficient to confer the glp-1(oz112gf) mutant phenotypes. Two mammalian Notch family members, TAN-1 and int-3, are proto-oncogenes. Thus, activating mutations in both invertebrate and vertebrate Notch family members can lead to tumor formation.
Impact of Mammalian Target of Rapamycin Inhibition on Lymphoid Homing and Tolerogenic Function of Nanoparticle-Labeled Dendritic Cells following Allogeneic Hematopoietic Cell Transplantation (2008)

Dendritic cells (DC) play a major role in the pathogenesis of graft-vs-host disease (GvHD). Directed modification of surface molecules on DC that provide instructive signals for T cells may create a tolerogenic DC phenotype that affects GvHD severity. To investigate the impact of the mammalian target of rapamycin (mTOR) inhibitor rapamycin (RAPA) on in vivo migratory capacities, tolerogenic function, and B7 superfamily surface expression on DC following allogeneic hematopoietic cell transplantation (aHCT), we generated a platform for magnetic resonance imaging and bioluminescence imaging based cell trafficking studies. Luciferase transgenic DC were labeled with superparamagnetic iron oxide nanoparticles bound to a murine IgG Ab that allowed for Fc-gammaR-mediated endocytosis. Locally injected luc(+) DC could be tracked within their anatomical context by bioluminescence imaging and magnetic resonance imaging after aHCT, based on stable intracellular localization of superparamagnetic iron oxide-IgG complexes. RAPA preconditioned DC (DC-R) displayed reduced expression of MHC class II, B7-1 (CD80), and B7-2 (CD86) but not B7-H4 whose ligation of T cells has a profound inhibitory effect on their proliferation and cytokine secretion. DC-R of recipient genotype reduced GvHD severity that is compatible with their tolerogenic phenotype. CCR5, CCR7, and CD62L expression was not affected by mTOR inhibition, which allowed for DC-R in vivo trafficking to secondary lymphoid compartments where immunregulation is required. This study is the first to delineate the impact of RAPA on DC migration and tolerogenic function after aHCT. Modification of the DC phenotype by mTOR inhibition may have therapeutic potential in an attempt to reduce GvHD following aHCT.
MxA protein in capillary blood of children with viral infections (1999)

Capillary blood of febrile children was lysed by using a lysis buffer containing ascorbic acid. MxA quantitation was performed by an immunochemiluminescent assay. The MxA values were significantly higher in capillary blood of infants with viral infections due to adenovirus (n = 5), rotavirus (n = 15), or respiratory syncytial virus (n = 28), than in capillary whole blood from infants with bacterial infections (n = 6) and healthy control patients (n = 20). A strong correlation was found between the MxA values in capillary whole blood and peripheral whole blood (r′ = 0.86, P < 0.0001, n = 48). The MxA values found at these two sites were compared with the levels of IFN-α obtained by a dissociation enhanced lanthanide fluoroimmunoassay. A correlation between these two values was found. The results show that the combination of collection of blood by finger prick and specific immunochemiluminescent assay for MxA protein measurement may be of value for the diagnosis of viral infections in children. J. Med. Virol. 59:547–551, 1999. © 1999 Wiley-Liss, Inc.
Building Bayesian networks through ontologies (2002)

To support building and maintaining knowledge-based systems for real-life application domains, sophisticated knowledge-engineering methodologies are available. As more and more Bayesian networks are being developed for complex applications, their construction and maintenance calls for the use of tailor-made knowledge-engineering methodologies. We have designed such a methodology and have studied its use within the domain of oesophageal cancer. Based upon expert knowledge and a previously constructed Bayesian network, we have built an ontology for this domain, from which we have constructed, in a sequence of steps, a new network. The use of our methodology has allowed us to address, in a structured fashion, the various intricate modelling issues involved.
Effect of Dialysis Dose and Membrane Flux in Maintenance Hemodialysis (2002)

Patients undergoing hemodialysis thrice weekly appear to have no major benefit from a higher dialysis dose than that recommended by current U.S. guidelines or from the use of a high-flux membrane.
PROGRESS TOWARD A METABOLIC INTERPRETATION OF GENETIC RECOMBINATION OF ESCHERICHIA COLI AND BACTERIOPHAGE LAMBDA (1974)

is a metabolically active cellular component of bacteria. Transcrip-DNA tion and replication can proceed continuously throughout the growth
Mitogenic activity of chicken chorioallantoic fluid is temporally correlated to vascular growth in the chorioallantoic membrane and related to fibroblast growth factors (1991)

The chorioallantoic membrane (CAM) is one of the most vascularized tissues in the chicken embryo. Capillary growth proceeds until day 10 of development and thereafter abruptly regresses. As it is generally accepted that the formation of new blood vessel is regulated by growth factors, we have investigated the presence of angiogenic and mitogenic factors in the chicken chorioallantois. In the present study, we show that chorioallantoic fluid (CAF) contains angiogenic substances that are probably synthesized in the CAM or the embryonic kidney. When applied in the chorioallantoic membrane assay, CAF from 9 day chicken embryos elicits a strong angiogenic response. This angiogenic activity of CAF is associated with pronounced mitogenic effects in vitro. Comparison of different embryonic fluids reveals that mitogenic activity is particularly evident in the CAF but not detectable in embryonic serum and amnion fluid. Expression of mitogenic activity is found to be temporally correlated with vascular growth in the CAM. High activity is detected in CAF prior to day 10 and then sharply decreases, thus preceding termination of capillary growth by one day. Heparin-sepharose affinity chromatography suggests that the biological activities of CAF probably correspond to the presence of acidic and basic fibroblast growth factor (aFGF and bFGF). In Western blot analyses of CAF, an immunoreactive bFGF-like protein of about 17 x 10(3) Mr is recognized by a monospecific anti-bFGF antiserum. This protein elutes at 2.4 M NaCl from the heparin-sepharose. The mitogenic activity of the CAF can be specifically blocked by the anti-bFGF antibody indicating bFGF to be the active mitogenic principle of the CAF. These results strongly suggest that basic and probably acidic FGF play an important role in the regulation of chorioallantoic vascular growth.