gebhart/patrepeval huggingface dataset:
<i>Shigella flexneri</i>O-antigens revisited: final elucidation of the O-acetylation profiles and a survey of the O-antigen structure diversity (2012)

Shigella flexneri is an important human pathogen causing shigellosis. Strains of S. flexneri are serologically heterogeneous and, based on O-antigens, are currently classified into 14 types. Structures of the O-antigens (O-polysaccharides) of S. flexneri have been under study since 1960s but some gaps still remained. In this work, using one- and two-dimensional (1) H- and (13) C-NMR spectroscopy, the O-polysaccharides of several S. flexneri types were reinvestigated, and their structures were either confirmed (types 2b, 3b, 3c, 5b, X) or amended in respect to the O-acetylation pattern (types 3a, Y, 6, 6a). As a result, the O-acetylation sites were defined in all O-polysaccharides that had not been studied in detail earlier, and the long story of S. flexneri type strain O-antigen structure elucidation is thus completed. New and published data on the S. flexneri O-antigen structures are summarized and discussed in view of serological and genetic relationships of the O-antigens within the Shigella group and between S. flexneri and Escherichia coli.
Novel Paramagnetic Contrast Agents for Molecular Imaging and Targeted Drug Delivery (2004)

Molecular biology and genomic sciences are revealing the early biological signatures for many diseases. In response, the Molecular Imaging community is rapidly developing contrast agents to visualize the nascent pathological changes and to concomitantly deliver treatment directly to the site of disease. The evaluation, development and use of these new agents require a complementary understanding of contrast chemistry and imaging techniques. The fundamental issues surrounding magnetic contrast agent development, rational drug delivery, MR molecular imaging, and their interdependence are elucidated.
Characterization of Gel-separated Glycoproteins Using Two-step Proteolytic Digestion Combined with Sequential Microcolumns and Mass Spectrometry (2004)

Protein glycosylation can be vital for changing the function or physiochemical properties of a protein. Abnormal glycosylation can lead to protein malfunction, resulting in severe diseases. Therefore, it is important to develop techniques for characterization of such modifications in proteins at a sensitivity level comparable with state-of-the-art proteomics. Whereas techniques exist for characterization of high abundance glycoproteins, no single method is presently capable of providing information on both site occupancy and glycan structure on a single band excised from an electrophoretic gel. We present a new technique that allows characterization of low amounts of glycoproteins separated by gel electrophoresis. The method takes advantage of sequential specific and nonspecific enzymatic treatment followed by selective purification and characterization of the glycopeptides using graphite powder microcolumns in combination with mass spectrometry. The method is faster and more sensitive than previous approaches and is compatible with proteomic studies.
Improved transport properties for ZnO films on Al<sub>2</sub>O<sub>3</sub>(11$\bar2$0) by MOCVD (2014)

Abstract ZnO films on Al 2 O 3 (112 $\bar2$ 0) with excellent transport properties were grown using metalorganic chemical vapor deposition (MOCVD) with a high speed rotating disk and a separated showerhead. Diisopropylzinc and tert ‐butanol were used as Zn and O precursors, respectively. Hall‐effect measurements revealed that the ZnO films in this work showed a high mobility of 140 cm 2 /Vs and a low carrier concentration of 1.5×1017 cm –3 , both of which are comparable to those grown by molecular beam epitaxy or pulsed laser deposition. This report should open a way to the mass production of single crystalline ZnO films which should be usable for optoelectronic devices. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The human blastocyst: morphology and human chorionic gonadotrophin secretion in vitro (1991)

Micromanipulation of human oocytes and embryos has provided new opportunities for both the treatment of infertility and the preimplantation diagnosis of genetic disease. It is important to determine whether manipulated embryos develop normally in vitro, as an indication of their suitability for transfer. However, at present there is little information on the development of non-manipulated embryos in vitro for comparison. We have therefore monitored morphological changes and human chorionic gonadotrophin (HCG) secretion in 36 non-manipulated human embryos, including 26 blastocysts and 10 cavitating morulae, daily from day 3 to day 14 of culture. Hatching was observed in 10 (38.5%) blastocysts and five of these adhered to the culture dish and appeared viable until day 14. The secretion of HCG was first detected on day 8, peaked at day 10 (51.11 +/- 8.7 mIU/ml) and then declined but was still detectable in four blastocysts on day 14. There was no overall difference in HCG secretion by hatched blastocysts and those which remained within the zona. However, those hatched blastocysts which showed adherence had significantly increased (P less than 0.05) HCG secretion. For individual blastocysts, the pattern of HCG secretion correlated well with the assessment of morphology. These data provide the basis for comparative studies of morphological changes and HCG secretion in manipulated embryos.
Vaccine against<i>Helicobacter pylori</i>: Inevitable approach (2016)

Over three decades have passed since the discovery of Helicobacter pylori (H. pylori), and yet many questions about its treatment remain unanswered. For example, there is no certainty regarding continued use of current antibiotic therapy against H. pylori. The bad news is that even combined regimens are also unable to eradicate bacterial colonization. The worst problem with H. pylori chemotherapy is that even if we identify the most successful regimen, it cannot eliminate the risk of re-infection. This problem is further complicated by the fact that clinicians have no information as to whether probiotics are useful or not. Moreover, to date, we have no large scale produced vaccine effective against H. pylori. Due to the relatively rapid and abundant dissemination of guidelines globally reported concerning management of gastric cancer prevention and therapeutic regimens, clinicians may choose a vaccine as better effective weapon against H. pylori. Therefore, a radical shift in adopted strategies is needed to guide ultimate decisions regarding H. pylori management. In light of failures in vaccine projects, we should identify better vaccine design targeting conserved/essential genes. The unique character and persistence of H. pylori pose obstacles to making an effective vaccine. Preferably, in developing countries, the best reasonable and logical approach is to recommend prophylactic H. pylori vaccine among children as an obligatory national program to limit primary colonization. Trying to produce a therapeutic vaccine would be postponed until later. In reality, we should not forget to prescribe narrow spectrum antibiotics. In the current review, I draw a route to define the best adopted strategy against this rogue bacterium.
Silencing of HIF-1α by RNA Interference in Human Glioma Cells In Vitro and In Vivo (2008)

Higher-grade gliomas are distinguished by increased vascular endothelial cell proliferation and peritumoral edema. These are thought to be instigated by vascular endothelial growth factor, which in turn is regulated by cellular oxygen tension. Hypoxia inducible factor-1alpha (HIF-1alpha) is a main responder to intracellular hypoxia and is overexpressed in many human cancers, including gliomas. Here we present methods for investigating the role of HIF-1alpha in glioma growth in vivo and in vitro using RNA interference in U251, U87, and U373 glioma cells.
Graphene-clad microfibre saturable absorber for ultrafast fibre lasers (2016)

Graphene, whose absorbance is approximately independent of wavelength, allows broadband light-matter interactions with ultrafast responses. The interband optical absorption of graphene can be saturated readily under strong excitation, thereby enabling scientists to exploit the photonic properties of graphene to realize ultrafast lasers. The evanescent field interaction scheme of the propagating light with graphene covered on a D-shaped fibre or microfibre has been employed extensively because of the nonblocking configuration. Obviously, most of the fibre surface is unused in these techniques. Here, we exploit a graphene-clad microfibre (GCM) saturable absorber in a mode-locked fibre laser for the generation of ultrafast pulses. The proposed all-surface technique can guarantee a higher efficiency of light-graphene interactions than the aforementioned techniques. Our GCM-based saturable absorber can generate ultrafast optical pulses within 1.5 μm. This saturable absorber is compatible with current fibre lasers and has many merits such as low saturation intensities, ultrafast recovery times, and wide wavelength ranges. The proposed saturable absorber will pave the way for graphene-based wideband photonics.
Application of an ex ovo chicken chorioallantoic membrane model for two-photon excitation photodynamic therapy of age-related macular degeneration (2003)

Two-photon excitation photodynamic therapy (TPE-PDT) is being investigated as a clinical treatment for age-related macular degeneration (AMD). TPE-PDT has the potential to provide a more specific and therefore advantageous therapy regime than traditional one-photon excitation PDT. The highly vascularized 8 to 9-day-old chicken chorioallantoic membrane (CAM) is used to model the rapid growth of blood vessels in the wet form of AMD. Using an ex ovo model system for the CAM, ablation studies were successful in mimicking the leaky vessels found in AMD. In addition, the distribution and localization of liposomal Verteporfin were investigated in order to characterize the photosensitizing drug in vivo. Localization of the photosensitizer appears to be greatest on the upper vessel wall, which indicates a potentially strong treatment locale for TPE-PDT.
The Development of Fracture Mechanics for Elastomers (1994)

Abstract The energy balance, or fracture mechanics, approach has proved successful in treating a number of fracture phenomena and unifying them in terms of what is believed to be a basic characteristic, the crack growth behavior when expressed in terms of the energy release rate T . It has also enabled some of the underlying physical factors to be identified and incorporated into appropriate theories. There are, however, some important limitations and outstanding problems which remain. For example, we do not at present have any quantitative understanding of what determines the precise form of the crack growth characteristic under repeated stressing. During the development of the approach, numerous checks were made of its validity by comparative experiments on different test piece geometries. This is important, as it is not certain that such comparisons will invariably give equivalent results and that the T vs. rate of tear relation is a true material characteristic. For example, if a test piece, such as the “split” test piece in Figure 2(d), is subjected to large pre-extensions in the direction of tearing, the tear resistance in some cases may apparently be much reduced from its unprestrained value. (Anisotropy is produced which is believed to be important in knotty tear development). Gent and Kim found a similar effect with laterally pre-strained pure shear test pieces. Also, if tear measurements are made with an edge crack test piece of natural rubber and the strains become great enough to produce crystallization in the main bulk of the test piece, the stick-slip behavior is suppressed and the tear strength appears to be increased. Thus it appears that in some cases the assumption that the strains just around the tip at the instant of tearing are independent of the bulk deformation is not true. Fortunately these cases seem to be the exception rather than the rule, but their occurrence demands continuing caution. Some peel tests of rubber-to-metal bonds for example show apparently anomalous force dependencies on peel angle. The current interest in the understanding and prediction of strength and durability of elastomer articles stems from the increasing importance attached to avoiding premature failure in service. The growing availability of finite element programs capable of dealing with large strains has already meant that force-deflection behavior can be at least approximately designed for; but a corresponding failure design procedure based on fracture mechanics is still in the stage of development.
Fundamental basis for distance relaying with symmetrical components (1977)

The paper derives the performance equation of a high speed distance relay which is based upon the theory of symmetrical components. A single equation is shown to be adequate for handling all types of faults which are likely to occur on a three-phase power system. Errors created by system loading and fault-path resistance are considered. A numerical example illustrates the principle of operation of the relay. The relay is especially suited to a digital computer based protection system.
Rapid Determination of Rifampin Resistance in Clinical Isolates of <i>Mycobacterium tuberculosis</i> by Real-Time PCR (2005)

Real-time PCR was used to determine rifampin resistance in clinical isolates of Mycobacterium tuberculosis. Ninety-six rifampin-resistant isolates and 23 rifampin-susceptible isolates were included in the study. A 305-bp region covering the 81-bp "rifampin resistance-determining region" of rpoB was amplified. Two hybridization probe pairs that covered the most frequent mutation sites in rpoB, codon regions 526 to 531 and 513 to 516, were used. The results obtained by real-time PCR were compared to those obtained by the proportion method. For detection of rifampin resistance, the real-time PCR assay yielded a sensitivity of 92.7% and a specificity of 100%. Real-time PCR is a very rapid method, and it can be especially helpful for the reporting of resistant clinical isolates in a very short period of time.
Practical authentication for distributed computing (1990)

Issues related to authentication in a distributed computing environment are discussed. Authentication approaches used in Digital Equipment Corporation's Distributed System Security Architecture (DSSA) are described. Node, user, and process granularity authentication concerns are considered. Authentication is based on a global hierarchic naming structure and public-key cryptography. Directory-resident certificates associating entities with long-term keys are used in conjunction with dynamically signed certificates which represent transient bindings between entities. Distributed system elements can be mutually suspicious. At the node level, special topics considered include the relationship between authentication and secure loading and the relationship between authentication and rule-based policy support. At the user level, architecture requirements are identified and authentication protocol options based on smart cards and on user-entered passwords are described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Optimization of xDSL transmission systems (2003)

xDSL (digital subscriber line) is a group of technologies for transmitting high-speed digital signals over existing metallic cables. xDSL was originally studied in the USA. These technologies have spread to other areas of the world, including Europe and Asia. In this process of introducing this technology to the different areas, several new local but critical problems have emerged, due to the local system and cable situations. In Japan, TCM (time compressed multiplex)-ISDN is widely used. This ISDN causes periodic crosstalk noise of far end cross-talk (FEXT) and near end cross-talk (NEXT) to xDSL. For the optimization of the transmission performance to this type of noise, it is efficient to use different bit assignments corresponding to the FEXT period and NEXT period. NEC has proposed a solution of the optimization for ADSL (asymmetric DSL) transmission under the TCM-ISDN crosstalk noise environment. We have compared the following transmission methods, the existing ANSI ADSL, dual bitmap (DBM)-ADSL, single bitmap (SBM)-ADSL and TCM-ADSL, with some simulation results. This shows that the performance of ANSI ADSL is greatly degraded by the ISDN crosstalk disturbance, and DBM-ADSL improves the performance significantly. SBM and TCM-ADSL also have better performances in a long reach with small modifications. The study results are explained.
Characterization of first trimester fetal erythroblasts for non-invasive prenatal diagnosis (2003)

Isolating fetal erythroblasts from first trimester maternal blood offers a promising non-invasive alternative for prenatal diagnosis. The aim of this study was to characterize the biological properties of first trimester primitive erythroblasts to facilitate their enrichment from first trimester maternal blood. Primitive erythroblasts were the predominant cell type until 12 weeks gestation, after which time their numbers declined steeply; 100% were epsilon-globin-positive versus <0.06% definitive erythroblasts. Buoyant densities of first trimester fetal erythroblasts ranged from 1.077 to 1.130 g/ml, and optimal recoveries were obtained with Percoll 1118. Although primitive erythroblasts carried a negative surface charge and were resistant to NH(4)Cl lysis, these properties had only a limited role in fetal cell enrichment. Immunophenotyping showed that primitive, like definitive, erythroblasts were GPA+, CD47+, CD45- and CD35-, whereas CD71 expression was weak/undetectable on primitive erythroblasts but strongly positive on 100% of definitive erythroblasts; primitive erythroblasts were also CD36- whereas definitive erythroblasts were CD36+. We therefore used CD45/GPA selection of Percoll 1118-separated cells to demonstrate successful enrichment of male epsilon-globin-positive fetal erythroblasts from model mixtures, and as proof of principle from some first trimester maternal blood samples. Fetal cell enrichment protocols based on first trimester epsilon-globin-positive primitive erythroblasts may allow reliable enrichment of fetal cells from maternal blood for early non-invasive prenatal diagnosis of genetic disorders.
Identification of Processes Associated with Different Iron Sites in the Prussian Blue Structure by in Situ Electrochemical, Gravimetric, and Spectroscopic Techniques in the dc and ac Regimes (2011)

The physicochemical properties of Prussian blue films are strongly dependent on the ratio Fe3+/Fe2+ in the structure. This ratio can be modulated by electrochemical techniques such as cyclic voltammetry, and some information about physicochemical properties can be extracted from in situ auxiliary techniques. Prussian blue films have been studied by the use of in situ vis–NIR spectroscopy, quartz crystal microbalance, and electrochemical techniques (cyclic voltammetry and electrochemical impedance spectroscopy). By cyclic voltammetry + absorbance derivative curves + mass derivative curves, it has been possible to identify at least three different processes during the reduction of Prussian blue films to the Everitt’s salt form. By numerical methods, it has been possible to deconvolute these curves and, thus, to obtain information separately from the three identified processes. These processes can be attributed to different Fe3+ sites in the PB structure with the participation of different counterions. By in situ electrochemical impedance + mass impedance + color impedance at a wavelength near 1000 nm, there has been observed a double loop plot with the color impedance where mass and electrochemical impedance show only one loop plot. Color impedance spectra contributions can be separated and identified separately by means of a nonlinear least-squares fitting procedure, and, thus, this double loop may be assigned to at least two different overlapped electrochemical processes. One of these electrochemical processes is related to Fe3+ sites (Fe(NC)5OH−) near the ferrocyanide vacancies in the Prussian blue structure, which are strongly affected by the pH of the outer solution.
Bicarbonate Inhibits N-Nitrosation in Oxygenated Nitric Oxide Solutions (1996)

N-Nitrosation in oxygenated nitric oxide (NO middle dot) solutions was previously shown to be significantly inhibited by phosphate and chloride presumably by anion scavenging of the nitrosating agent nitrous anhydride, N2O3 (Lewis, R. S., Tannenbaum, S. R., and Deen, W. M. (1995) J. Am. Chem. Soc. 117, 3933-3939). Here, bicarbonate is shown to exhibit this same inhibitory effect. Rate constants for reaction of morpholine, phosphate, and bicarbonate with N2O3 relative to N2O3 hydrolysis at pH 8.9 were determined to be (3.7 +/- 0.2) x 10(4) M-1, (4.0 +/- 0.9) x 10(2) M-1, and (9.3 +/- 1.5) x 10(2) M-1, respectively. The morpholine and phosphate rate constants at pH 8.9 are similar to those reported at pH 7.4 assuring that these results are relevant to physiological conditions. The rate constant for this previously unrecognized reaction of bicarbonate with N2O3 suggests the strong scavenging ability of bicarbonate; accordingly, bicarbonate may contribute to reducing deleterious effects of N2O3. This is biologically important due to substantial bicarbonate concentrations in vivo, approximately 30 mM. Bicarbonate was previously shown to alter peroxynitrite reactivity; however, carbon dioxide is the probable reactive species. Bicarbonate is therefore potentially important in determining the fate of two reactive species generated from nitric oxide, N2O3 and ONOO-, and may thus act as a regulator of NO middle dot-induced toxicity.
Challenges and Opportunities for Next-Generation Intracortically Based Neural Prostheses (2011)

Neural prosthetic systems aim to help disabled patients by translating neural signals from the brain into control signals for guiding computer cursors, prosthetic arms, and other assistive devices. Intracortical electrode arrays measure action potentials and local field potentials from individual neurons, or small populations of neurons, in the motor cortices and can provide considerable information for controlling prostheses. Despite several compelling proof-of-concept laboratory animal experiments and an initial human clinical trial, at least three key challenges remain which, if left unaddressed, may hamper the translation of these systems into widespread clinical use. We review these challenges: achieving able-bodied levels of performance across tasks and across environments, achieving robustness across multiple decades, and restoring able-bodied quality proprioception and somatosensation. We also describe some emerging opportunities for meeting these challenges. If these challenges can be largely or fully met, intracortically based neural prostheses may achieve true clinical viability and help increasing numbers of disabled patients.
Low-Energy-Spread Ion Bunches from a Trapped Atomic Gas (2009)

We present time-of-flight measurements of the longitudinal energy spread of pulsed ultracold ion beams, produced by near-threshold ionization of rubidium atoms captured in a magneto-optical atom trap. Well-defined pulsed beams have been produced with energies of only 1 eV and a root-mean-square energy spread as low as 0.02 eV, 2 orders of magnitude lower than the state-of-the-art gallium liquid-metal ion source. The low energy spread is important for focused ion beam technology because it enables milling and ion-beam-induced deposition at sub-nm length scales with many ionic species, both light and heavy. In addition, we show that the slowly moving, low-energy-spread ion bunches are ideal for studying intricate space charge effects in pulsed beams. As an example, we present a detailed study of the transition from space charge dominated dynamics to ballistic motion.