gebhart/patrepeval huggingface dataset:
High-level expression of the Neisseria meningitidis lgtA gene in Escherichia coli and characterization of the encoded N-acetylglucosaminyltransferase as a useful catalyst in the synthesis of GlcNAc 1->3Gal and GalNAc 1->3Gal linkages (1999)

We have expressed the Neisseria meningitidis lgtA gene at a high level in Escherichia coli. The encoded beta-N-acetylglucosaminyltransferase, referred to as LgtA, which in the bacterium is involved in the synthesis of the lacto-N-neo-tetraose structural element of the bacterial lipooligosaccharide, was obtained in an enzymatically highly active form. This glycosyltransferase appeared to be unusual in that it displays a broad acceptor specificity toward both alpha- and beta-galactosides, whether structurally related to N- or O-protein-, or lipid-linked oligosaccharides. Product analysis by one- and two-dimensional 400 MHz 1H- and 13C-NMR spectroscopy reveals that LgtA catalyzes the introduction of GlcNAc from UDP-GlcNAc in a beta 1-->3-linkage to accepting Gal residues. The enzyme can thus be characterized as a UDP-GlcNAc:Gal alpha/beta-R beta 3-N-acetylglucosaminyltransferase. Although lactose is a highly preferred acceptor substrate the recombinant enzyme also acts efficiently on monomeric and dimeric N-acetyllactosamine revealing its potential value in the synthesis of polylactosaminoglycan structures in enzyme assisted procedures. Furthermore, LgtA shows a high donor promiscuity toward UDP-GalNAc, but not toward other UDP-sugars, and can catalyze the introduction of GalNAc in beta 1-->3-linkage to alpha- or beta-Gal in the acceptor structures at moderate rates. LgtA therefore shows promise to be a useful catalyst in the preparative synthesis of both GlcNAc beta 1-->3Gal and GalNAc beta 1-->3Gal linkages.
The state of the art of dynamic coatings (2001)

The present review highlights the mechanisms of action and efficiency of three major classes of dynamic coatings so far adopted in capillary electrophoresis: (i) amines to oligo-amines, (ii) neutral synthetic and natural polymers, and (iii) neutral and zwitter-ionic surfactants. Their merits and efficacy have been explored in depth via a novel quantitation technique consisting of eluting, by frontal analysis, any adsorbed proteinaceous material, which can then be correctly quantified as a peak as it moves in front of the detector window. This is achieved by loading sodium dodecyl sulfate (SDS) micelles onto the cathodic side and migrating them electrophoretically into the capillary lumen, where they efficiently sweep any adsorbed polypeptide material. It is found that a common trend, for all quenchers, is linked to a hydrophobicity scale: the more hydrophobic the inhibitor, the better it minimizes potential interactions of macromolecules with the wall. This seems to be true for all the classes of dynamic modifiers tested. Finally, we describe a novel, dynamic to static quencher: it is a quaternary piperazine, bearing a reactive iodine atom at the end of a butyl tail (N(methyl-N-omega-iodo-butyl),N'-methyl piperazine). This molecule first binds to the wall, at alkaline pH values, via ionic and hydrogen bonds. Once docked onto the wall, the reactive tail forms a covalent link with the silica surface, to which it then remains permanently affixed.
Preparation of Ru(CO)(diene)<sub>2</sub> Complexes by Electron‐Beam Evaporation of Ruthenium. Preliminary Communication (1984)

Abstract Ru‐atoms (0.5–1.5 g) have been generated by electron bombardment and, in separate experiments, were co‐condensed at 7 K with excess of 2,3‐dimethylbutadiene or 1,3‐ or 1,4‐cyclohexadiene. The complexes Ru(CO)(η 4 ‐C 6 H 10 ) 2 ( 1 ) and Ru(CO)(η 4 ‐C 6 H 8 ) 2 ( 2 ), respectively, have been isolated in 25–30% yields on warming the condensate under CO.
Stereoselectivity in the Hydroboration of C4-C-Methylene Groups (1987)

Abstract Conditions for the hydroxylation of an exocyclic methylene group at C4 of a pyranoside ring via hydroboration have been examined with a view to determining the optimum procedure for obtaining the axially-oriented C4-CH2OH group. The regio- and stereochemical outcome of the reactions rely not only on the hydroborating reagent used, but, to a surprising degree, on the nature of the protecting group at the “remote” C6-OH. Silyl ethers are preferred because the only by-product formed is the tertiary alcohol, which can be recycled through dehydration to the starting alkene by treatment with thionyl chloride.
Substrate Selection for Fundamental Studies of Electrocatalysts and Photoelectrodes: Inert Potential Windows in Acidic, Neutral, and Basic Electrolyte (2014)

The selection of an appropriate substrate is an important initial step for many studies of electrochemically active materials. In order to help researchers with the substrate selection process, we employ a consistent experimental methodology to evaluate the electrochemical reactivity and stability of seven potential substrate materials for electrocatalyst and photoelectrode evaluation. Using cyclic voltammetry with a progressively increased scan range, we characterize three transparent conducting oxides (indium tin oxide, fluorine-doped tin oxide, and aluminum-doped zinc oxide) and four opaque conductors (gold, stainless steel 304, glassy carbon, and highly oriented pyrolytic graphite) in three different electrolytes (sulfuric acid, sodium acetate, and sodium hydroxide). We determine the inert potential window for each substrate/electrolyte combination and make recommendations about which materials may be most suitable for application under different experimental conditions. Furthermore, the testing methodology provides a framework for other researchers to evaluate and report the baseline activity of other substrates of interest to the broader community.
Copper Chelation Chemistry and its Role in Copper Radiopharmaceuticals (2006)

Molecular imaging is an important scientific discipline that plays a major role in clinical medicine and pharmaceutical development. While several imaging modalities including X-ray computed tomography (CT) and magnetic resonance imaging (MRI) generate high-resolution anatomical images, positron emission tomography (PET) and single photon emission computed tomography (SPECT) offer insight into the physiological processes that occur within a living organism. Of these two nuclear medicine imaging techniques, PET has advantages with respect to sensitivity and resolution, and this has led to the production and development of many positron emitting radionuclides that include non-traditional radionuclides of the transition metals. Copper-64 (t(1/2) = 12.7 h, beta(+): 17.4%, E(beta+max) = 656 keV; beta(-): 39%, E(beta-max) = 573 keV) has emerged as an important positron emitting radionuclide that has the potential for use in diagnostic imaging and radiotherapy. However, (64)Cu must be delivered to the living system as a stable complex that is attached to a biological targeting molecule for effective imaging and therapy. Therefore, significant research has been devoted to the development of ligands that can stably chelate (64)Cu. This review discusses the necessary characteristics of an effective (64)Cu chelator, while highlighting the development and evaluation of (64)Cu-complexes attached to biologically-targeted ligands.
In Situ hybridization and its diagnostic applications in pathology (1997)

In situ hybridization (ISH) is a technique by which specific nucleotide sequences are identified in cells or tissue sections. These may be endogenous, bacterial or viral, DNA or RNA. On the basis of research applications, the technique is now being translated into diagnostic practice, mainly in the areas of gene expression, infection and interphase cytogenetics. Diagnostic applications are most often based on short nucleotide sequences (oligomers) labelled with non-isotopic reporter molecules, and sites of binding may be localized by histochemical or immunohistochemical methods. The technique can be applied to routinely fixed and processed tissues; with some targets, it is even possible to obtain hybridization in autopsy material. ISH has been used to detect messenger RNA (mRNA) as a marker of gene expression, where levels of protein storage are low; for example, to confirm an endocrine tumour as the source of excess hormone production. Its application in infectious diseases has to date been mainly in viral infections, such as the typing of human papillomavirus (HPV) or the detection of Epstein-Barr virus by the presence of small nuclear RNAs (EBERs). The expression of mRNAs for histone proteins has been used to detect cells in S phase, and related methods may be applied to detect apoptotic cells. Using probes to chromosome-specific sequences, it is possible to detect aneuploidy, and to document changes in specific chromosomes, which may have prognostic significance in some tumours, such as B-cell chronic lymphatic leukaemia. Using sequence-specific probes, translocations can be identified, such as the t(11;12) of Ewing's sarcoma. This review presents an outline of the technique of in situ hybridization and discusses areas of current and potential diagnostic application.
Insulin-like growth factor-1 protects human dopaminergic SH-SY5Y cells from Salsolinol-induced toxicity (2003)

Parkinson's disease (PD) is characterized by an extensive loss of dopaminergic neurons in the substantia nigra pars compacta. Salsolinol (SAL), a dopamine-derived tetrahydroisoquinoline, has been suspected to be involved in the etiology of PD. In the present study, the neuroprotective effect of insulin-like growth factor-1 (IGF-1) was studied against SAL-induced toxicity in human dopaminergic SH-SY5Y cells. SAL (100 microM) decreased cell viability in SH-SY5Y cells significantly after 24 h exposure. Both exogenous IGF-1 and IGF-1 gene transfer significantly prevented the SAL-induced cell death and increased cell viability. Wortmannin, a specific phosphatidylinositol-3-kinase (PI-3 kinase) inhibitor, completely blunted the IGF-1-induced neuroprotection, suggesting that PI-3 kinase pathway is critical in mediating the neuroprotective effects of IGF-1. These results suggest that IGF-1 may be a useful growth factor in the treatment of PD.
Suppressing the coffee stain effect: how to control colloidal self-assembly in evaporating drops using electrowetting (2011)

We study the influence of electrowetting on the formation of undesired solute residues, so-called coffee stains, during the evaporation of a drop containing non-volatile solvents. Electrowetting is found to suppress coffee stains of both colloidal particles of various sizes and DNA solutions at alternating (AC) frequencies ranging from a few Hertz to a few tens of kHz. Two main effects are shown to contribute to the suppression: (i) the time-dependent electrostatic force prevents pinning of the three phase contact line and (ii) internal flow fields generated by AC electrowetting counteract the evaporation driven flux and thereby prevent the accumulation of solutes along the contact line.
A Review: The Role of Remote Sensing in Precision Agriculture (2010)

Precision agriculture is an emerging farm management strategy that is changing the way people farm. At present, there is an increasing commitment to reduce reliance on excessive chemical inputs in agriculture. Numerous technologies have been applied to make agricultural products safer and to lower their adverse impacts on the environment, a goal that is consistent with sustainable agriculture. Precision agriculture has emerged as a valuable component of the framework to achieve this goal. This review highlights on remote sensing technology and describes how it can be used as an effective tool in precision agriculture.
Crystal Structure of the D94S/G98E Variant of Rat α-Parvalbumin. An Explanation for the Reduced Divalent Ion Affinity (2005)

Simultaneous replacement of Asp-94 with serine and Gly-98 with glutamate in rat alpha-parvalbumin creates a CD-site ligand array in the context of the EF-site binding loop. Previous work has shown that, relative to the wild-type CD site, this engineered site has markedly reduced Ca(2+) affinity. Seeking an explanation for this phenomenon, we have obtained the crystal structure of the alpha D94S/G98E variant. The Ca(2+) coordination within the engineered EF site of the 94/98E variant is nearly identical to that within the CD site, suggesting that the attenuated affinity of the EF site in 94/98E is not a consequence of suboptimal coordination geometry. We have also examined the divalent ion binding properties of the alpha 94/98E variant in both Na(+)- and K(+)-containing buffers. Although the Ca(2+) and Mg(2+) affinities are higher in K(+) solution, the increases are comparable to those observed for wild-type alpha. Consistent with that finding, the apparent Na(+) stoichiometry, estimated from stability studies conducted as a function of Na(+) concentration, is 1.0 +/- 0.1, identical to that of wild-type alpha. Thus, the reduced affinity for divalent ions is evidently not the result of heightened monovalent ion competition. The thermodynamic analysis indicates that the less favorable Gibbs free energy of binding reflects a substantial enthalpic penalty. Significantly, the crystal structure reveals a steric clash between Phe-57 and the C(gamma) atom of Glu-98. The consequent displacement of Phe-57 also produces a close contact with Ser-55. Thus, steric interference may be the source of the enthalpic penalty.
A phase I trial evaluating the safety and immunogenicity of a candidate tuberculosis vaccination regimen, ChAdOx1 85A prime – MVA85A boost in healthy UK adults (2019)

A ChAdOx1 85A prime - MVA85A boost is well tolerated and immunogenic in healthy UK adults.
Automated procedure for candidate compound selection in GC-MS metabolomics based on prediction of Kovats retention index (2009)

Supplementary data are available at Bioinformatics online.
Yeast Mannans inhibit binding and phagocytosis of zymosan by mouse peritoneal macrophages (1983)

We have examined the effects of various mannans, glycoproteins, oligosaccharides, monosaccharides, and sugar phosphates on the binding and phagocytosis of yeast cell walls (zymosan) by mouse peritoneal macrophages. A phosphonomannan (PO(4):mannose ratio = 1:8:6) from kloeckera brevis was the most potent inhibitor tested; it inhibited binding and phagocytosis by 50 percent at concentrations of approximately 3-5 mug/ml and 10 mug/ml, respectively. Removal of the phosphate from this mannan by mild acid and alkaline phosphatase treatment did not appreciably reduce its capacity to inhibit zymosan phagocytosis. The mannan from saccharomyces cerevisiae mutant LB301 inhibits phagocytosis by 50 percent at 0.3 mg/ml, and a neutral exocellular glucomannan from pichia pinus inhibited phagocytosis by 50 percent at 1 mg/ml. Cell wall mannans from wild type S. cervisiae X2180, its mnn2 mutant which contains mannan with predominantly 1(arrow)6- linked mannose residues, yeast exocellular mannans and O-phosphonomannans were less efficient inhibitors requiring concentrations of 1-5 mg/ml to achieve 50 percent reduction in phagocytosis. Horseradish peroxidase, which contains high-mannose type oligosaccharides, was also inhibitory. Mannan is a specific inhibitor of zymosan binding and phagocytosis. The binding and ingestion of zymosan but not of IgG- or complement-coated erythrocytes can be obliterated by plating macrophages on substrates coated with poly-L-lysin (PLL)-mannan. Zymosan uptake was completely abolished by trypsin treatment of the macrophages and reduced by 50-60 percent in the presence of 10 mM EGTA. Pretreatment of the macrophages with chloroquine inhibited zymosan binding and ingestion. These results support the proposal that the macrophage mannose/N-acetylglucosamine receptor (P. Stahl, J.S. Rodman, M.J. Miller, and P.H. Schlesinger, 1978, Proc. Natl. Acad. Sci. U.S.A. 75:1399-1403, mediates the phagocytosis of zymosan particles.
Correction of Pectus Excavatum and Pectus Carinatum Assisted by the Endoscope (1997)

Six patients with pectus excavatum and two patients with pectus carinatum had their conditions corrected by a partial costal cartilage resection with a sternal osteotomy through a 2.5-cm to 4-cm skin incision located just above the xyphoid process assisted by an endoscope. In addition to the incision, stab wounds of less than 3 mm in diameter were also made, in some cases, for insertion of the surgical instruments to facilitate the operation. The ribs and rib cartilages were exposed beyond the affected area through a prexyphoid incision under endoscopic control. The mobility of the skin incision site was thus enhanced, and it was possible to perform most of the subperichondrial partial costal cartilage resection under direct visualization. The pleura was freed from the sternum under endoscopic visualization. The advantages of this technique include minimal operative scars and the ability to free the pleura from the sternum under endoscopically magnified visualization, which prevents rupturing of the pleura in the retrosternal area.
Acinetobacter Infection Is Associated with Acquired Glucose Intolerance in Burn Patients (2005)

Infection with antibiotic-resistant Acinetobacter spp. is an increasing problem in critical care environments worldwide. Acinetobacter spp. are known to produce an insulin-cleaving protease. We hypothesized that infection with Acinetobacter spp. was associated with the acquisition of glucose intolerance in burn patients. Data were collected prospectively on all 473 patients admitted to the Burns Centre between January 2002 and March 2003. A total of 3.4% of patients acquired glucose intolerance during admission. Patients with Acinetobacter spp. infection were 9.8 times more likely to develop glucose intolerance than those without the infection (P < .0001). The association persisted after controlling for TBSA (P < .001). In patients with deep Acinetobacter spp. infection, 47% had glucose intolerance, compared with 12% in those with infection of the burn only (P = .03). In patients with pre-existing diabetes mellitus, 27% developed Acinetobacter spp. infection compared with only 8.5% of patients without diabetes (P = .04). This study demonstrates a clear association between Acinetobacter spp. infection and glucose intolerance in burns patients.
Construction and Characterization of a<i>Pseudomonas aeruginosa</i>Mucoid Exopolysaccharide-Alginate Conjugate Vaccine (2003)

Deterioration of lung function in patients with cystic fibrosis (CF) is closely associated with chronic pulmonary infection with mucoid Pseudomonas aeruginosa. The mucoid exopolysaccharide (MEP) from P. aeruginosa has been shown to induce opsonic antibodies in mice that are protective against this chronic infection. MEP-specific opsonic antibodies are also commonly found in the sera of older CF patients lacking detectable P. aeruginosa infection. When used in a human vaccine trial, however, MEP only minimally induced opsonic antibodies. To evaluate whether conjugation of MEP to a carrier protein could improve its immunogenicity, we bound thiolated MEP to keyhole limpet hemocyanin (KLH) by using succinimidyl-4-(N-maleimidomethyl)cyclohexane-1-carboxylate (SMCC) as a linker. In contrast to the native MEP polymer, the MEP-KLH conjugate vaccine induced high titers of MEP-specific immunoglobulin G (IgG) in C3H-HeN mice and in a rabbit. Sera from mice immunized with MEP-KLH conjugate, but not from animals immunized with comparable doses of native MEP, demonstrated opsonic killing activity. Vaccination with MEP-KLH conjugate induced opsonic antibodies broadly cross-reactive to heterologous mucoid strains of P. aeruginosa. Preexisting nonopsonic antibodies to MEP are found in normal human sera, including young CF patients, and their presence impedes the induction of opsonic antibodies. Induction of nonopsonic antibodies by either intraperitoneal injection of MEP or injection or feeding of the cross-reactive antigen, seaweed alginate, reduced the level of overall IgG elicited by follow-up immunization with the MEP-KLH conjugate. However, the opsonic activity was lower only in the sera of MEP-KLH conjugate-immunized mice with preexisting antibodies induced by MEP but not with antibodies induced by seaweed alginate. Immunization with MEP-KLH elicited a significant proportion of antibodies specific to epitopes involving O-acetate residues, and this subpopulation of antibodies mediated opsonic killing of mucoid P. aeruginosa in vitro. These results indicate that conjugation of MEP to KLH significantly enhances its immunogenicity and the elicitation of opsonic antibodies in mice and rabbits, that the conjugate induces opsonic antibodies in the presence of preexisting nonopsonic antibodies, and that opsonic antibodies to MEP are directed at epitopes that include acetate residues on the uronic acid polymer.
Non-supervised determination of allograph sub-classes for on-line omni-scriptor handwriting recognition (1999)

We present a novel clustering algorithm dedicated to the determination of character allographs. The "problem of the allographs" specific of the dynamic handwriting in omni-scriptor context renders the implementation of "classical" clustering algorithms particularly delicate because it introduces the notion of heterogeneous classes characterized by strongly variable example densities. We propose an hybrid clustering algorithm that combines a prototype placement stage and an adaptation stage. The first realizes an under-optimal determination of kernels in the different clusters composing the classes. It is followed by a kernel adaptation stage driving to an optimization of their position. The process drastically reduces the number of references to examine during a k-nn classification while preserving to the classifier a high level of performances. The experience has been driven on an extensive alphabet comprising 80 classes (upper- and lower-case letters, digits and mathematical symbols). Recognition rate, evaluated on near 35000 examples from the UNIPEN database show the sturdiness of the modelization.
A Visit to Nepal, 1990 (1990)

Kathmandu was the first point of contact we had with this nation of diverse peoples and religions - a city said to have as many gods as people and located in a lush valley at 1341 metres on the ancient trade routes linking Nepal, Tibet, China and India. For half the year snow blocks the Himalayan passes to the north and to the south are the low lying Terai jungles, deadly with malaria in summer. Thus the early traders often spent months in Kathmandu waiting for the seasons to change. 'And the wildest dreams of Kew are the facts of Kathmandu' claims the line from Rudyard Kipling. Even today one can walk past a Russian trained architect programming his computer in one street to another lane where the stallholder trades dried animal dung.