gebhart/patrepeval huggingface dataset:
Probing isomeric differences of phosphorylated carbohydrates through the use of ion/molecule reactions and FT-ICR MS (2003)

Through the use of ion/molecule reactions and tandem mass spectrometry, phosphate position is assigned in both phosphorylated monosaccharides and oligosaccharides. In previous work phosphate moieties of monosaccharides were stabilized under collisional activation, by first derivatizing the deprotonated monosaccharide with trimethyl borate through an ion/molecule reaction, and the phosphate position determined through marker ions generated in tandem mass spectra. In this work, the methodology is extended to larger phosphorylated oligomers employing chlorotrimethylsilane (TMSCl) as the ion/molecule reagent. Phosphorylated monosaccharides were first investigated to determine diagnostic ions for phosphate linkage in monomeric standards. It was observed that the diagnostic ions showed both linkage and some monosaccharide stereochemical information. Furthermore, it was observed that TMS addition stabilized the phosphate moiety under collisionally activated conditions. Upon identification of the diagnostic ions, the methodology was applied to lactose-1-phosphate. It was found that TMSCl, stabilized the phosphate moiety upon collisional activation, and furthermore, the phosphate linkage could be determined through tandem mass spectrometric analysis. As a further extrapolation to biologically relevant problems, the methodology was applied to a lipophosphoglycan analog from the protozoan parasite Leishmania. This sample contains bridging phosphates which were converted to terminal phosphates through collision induced dissociation. The sample was then analyzed in the same manner as lactose-1-phosphate, yielding phosphate linkage information and stereochemical information. This study showed that, using the developed methodology, phosphate linkage can be determined from both monosaccharides and larger oligosaccharides; furthermore it is applicable to samples in which the phosphates are either terminating or bridging.
Fast Measurement of Radiation Efficiency of Antennas using Parallel Modulated Probe Array (2006)

A measurement method using the modulated scattering technique (MST) has been proposed to measure the electromagnetic field rapidly. A simultaneous measurement method using parallel modulated probe (PMP) array has been developed. In this method, each modulated probe element is modulated by a low-frequency modulation signal with different frequency and the modulated signal is combined and received by a broadband microwave receiver. In this report, the simultaneous measurement method using the PMP array is applied to the measurement of the radiation efficiency of antennas to investigate the accuracy of the measurement method.
A multi-chain polymer slip-spring model with fluctuating number of entanglements: Density fluctuations, confinement, and phase separation (2017)

Coarse grained simulation approaches provide powerful tools for the prediction of the equilibrium properties of polymeric systems. Recent efforts have sought to develop coarse-graining strategies capable of predicting the non-equilibrium behavior of entangled polymeric materials. Slip-link and slip-spring models, in particular, have been shown to be capable of reproducing several key aspects of the linear response and rheology of polymer melts. In this work, we extend a previously proposed multi-chain slip-spring model in a way that correctly incorporates the effects of the fluctuating environment in which polymer segments are immersed. The model is used to obtain the equation of state associated with the slip-springs, and the results are compared to those of related numerical approaches and an approximate analytical expression. The model is also used to examine a polymer melt confined into a thin film, where an inhomogeneous distribution of polymer segments is observed, and the corresponding inhomogeneities associated with density fluctuations are reflected on the spatial slip-spring distribution.
Still stable after 11 years: A Catharanthus roseus Hairy root line maintains inducible expression of anthranilate synthase (2016)

Hairy root cultures generated using Agrobacterium rhizogenes are an extensively investigated system for the overproduction of various secondary metabolite based pharmaceuticals and chemicals. This study demonstrated a transgenic Catharanthus roseus hairy root line carrying a feedback-insensitive anthranilate synthase (AS) maintained chemical and genetic stability for 11 years. The AS gene was originally inserted in the hairy root genome under the control of a glucocorticoid inducible promoter. After 11 years continuous maintenance of this hairy root line, genomic PCR of the ASA gene showed the presence of ASA gene in the genome. The mRNA level of AS was induced to 52-fold after feeding the inducer as compared to the uninduced control. The AS enzyme activity was 18.4 nmol/(min*mg) in the induced roots as compared to 2.1 nmol/(min*mg) in the control. In addition, the changes in terpenoid indole alkaloid concentrations after overexpressing AS were tracked over 11 years. The major alkaloid levels in induced and control roots at 11 years are comparable with the metabolite levels at 5 years. This study demonstrates the long term genetic and biochemical stability of hairy root lines, which has important implications for industrial scale applications. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:66-69, 2017.
Pathophysiology of Type 2 Diabetes in Koreans (2018)

The pathophysiology of type 2 diabetes is characterized by variable degrees of insulin resistance and impaired insulin secretion. Both genetic and environmental factors serve as etiologic factors. Recent genetic studies have identified at least 83 variants associated with diabetes. A significant number of these loci are thought to be involved in insulin secretion, either through β-cell development or β-cell dysfunction. Environmental factors have changed rapidly during the past half century, and the increased prevalence of obesity and diabetes can be attributed to these changes. Environmental factors may affect epigenetic changes and alter susceptibility to diabetes. A recent epidemiologic study revealed that Korean patients with type 2 diabetes already had impaired insulin secretion and insulin resistance 10 years before the onset of diabetes. Those who developed diabetes showed impaired β-cell compensation with an abrupt decrease in insulin secretion during the last 2 years before diabetes developed. The retrograde trajectory of the disposition index differed according to the baseline subgroups of insulin secretion and insulin sensitivity. We hope that obtaining a more detailed understanding of the perturbations in the major pathophysiologic process of diabetes on the individual level will eventually lead to the implementation of precision medicine and improved patient outcomes.
Characterization and comparative analyses of transcriptomes for <i>in vivo</i> and <i>in vitro</i> produced peri-implantation conceptuses and endometria from sheep (2016)

An increasing number of reports indicate that in vitro fertilization (IVF) is highly associated with long‑term side effects on embryonic and postnatal development, and can sometimes result in embryonic implant failure. While high‑throughput gene expression analysis has been used to explore the mechanisms underlying IVF-induced side effects on embryonic development, little is known about the effects of IVF on conceptus-endometrial interactions during the peri-implantation period. Using sheep as a model, we performed a comparative transcriptome analysis between in vivo (IVO; in vivo fertilized followed by further development in the uterus) and in vitro produced (IVP; IVF with further culture in the incubator) conceptuses, and the caruncular and intercaruncular areas of the ovine endometrium. We identified several genes that were differentially expressed between the IVO and IVP groups on day 17, when adhesion between the trophoblast and the uterine luminal epithelium begins in sheep. By performing Gene Ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, we found that, in the conceptus, differentially expressed genes (DEGs) were associated mainly with functions relating to cell binding and the cell cycle. In the endometrial caruncular area, DEGs were involved in cell adhesion/migration and apoptosis, and in the intercaruncular area, they were significantly enriched in pathways of signal transduction and transport. Thus, these DEGs are potential candidates for further exploring the mechanism underlying IVF/IVP-induced embryonic implant failure that occurs due to a loss of interaction between the conceptus and endometrium during the peri-implantation period.
Cross-reactivities of cyclosporin G (NVa2 cyclosporin) and metabolites in cyclosporin A immunoassays (1993)

Immunoassays of cyclosporin A (CsA) have been routinely used to measure CsG. We investigated the cross-reactivities of CsG and its metabolites, as well as the proportion CsG constitutes in relation to total drug measured, for six CsG metabolites (GM1, GM9, GM4N, GM1c, GM1c9, GM19) in the following CsA assays: Sandimmune selective RIA (SS), Sandimmune nonselective RIA (NS), Cyclotrac SP-RIA (CT), fluorescence polarization immunoassay (FPIA), and enzyme immunoassay (EMIT). The cross-reactivity of CsG in these assays was as follows: SS, FPIA, CT, approximately 100%; NS, approximately 40%; EMIT, < 2%. The cross-reactivities of CsG metabolites were investigated in all assays except EMIT and varied among metabolites and assays. The most significant variance was found with the NS assay, where most of the metabolites exhibited cross-reactivities of > 40%. In contrast, in the SS, FPIA, and CT assays, cross-reactivities of < 5% were observed for most of the metabolites. The ranking of cross-reactivities of CsG metabolites in the assays is SS = CT < FPIA < NS. The degree of cross-reactivity did not change significantly when the SS, CT, and FPIA assays were calibrated with CsG instead of CsA--whether parent CsG was present or not. The data suggest that the SS, CT, and FPIA methods would be suitable for the routine monitoring of CsG.
Multilayer Actuator Composed of PZN–PZT and PZN–PZT/Ag Fabricated by Co‐Extrusion Process (2005)

A multilayer ceramic actuator composed of piezoelectrically active Pb(Zn 1/3 Nb 2/3 ) 0.2 –Pb(Zr 0.5 Ti 0.5 )O 0.8 (PZN–PZT) layers and electrically conducting PZN–PZT/Ag layers was fabricated by the co‐extrusion process. For the piezoelectric layers, PZN–PZT, which is sinterable at a low temperature (900°C), was used. For the conducting layers, a PZN–PZT/Ag composite, made by mixing silver particles with the PZN–PZT matrix, was employed. For the co‐extrusion process, piezoelectric and conducting feedrods were made by mixing the PZN–PZT and PZN–PZT/Ag, respectively, with a thermoplastic polymer. The initial feedrods, which were composed of five 3 mm‐thick PZN–PZT layers, two 1.5 mm‐thick PZN–PZT layers, and six 1 mm‐thick PZN–PZT/Ag layers, were co‐extruded through a 24 mm × 2 mm reduction die at 105°C to produce continuous multilayered green sheets. The sheets were stacked, warm pressed, and sintered at 900°C for 4 h after binder burnout. The sintered multilayer actuator showed distinct layers without any reaction products or cracks at the interface. The thicknesses of the piezoelectric and conducting layers were about 200 and 70 μm, respectively. The displacement of the multilayer actuator, composed of 40 piezoelectric layers (with a total height of 10.8 mm), was about 10 μm at an applied voltage of 500 V.
Generalised two‐box cascaded Hammerstein‐like digital predistorter for wide‐band RF power amplifiers (2016)

A generalised two‐box cascaded Hammerstein‐like (GTBC‐H) digital predistorter is proposed for linearising wide‐band RF power amplifiers (PAs). The GTBC‐H predistorter is composed of a static nonlinearity block for countervailing the strong static nonlinearities and a dynamic nonlinearity block for compensating the memory effects of RF PAs. The proposed predistorter adds extended cross‐terms of the leading terms and some lagging envelope terms in the dynamic nonlinearity block to compensate the memory effects of wide‐band RF PAs more effectively. A 460 MHz and a 1.94 GHz Doherty RF PA are utilised to validate the performance of the proposed predistorter when a three‐carrier wide‐band CDMA and a single‐carrier long‐term evaluation signal are applied separately. The validation results illustrate that the proposed GTBC‐H predistorter can further suppress the residual out‐of‐band emission over the augmented Hammerstein, the enhanced Hammerstein and the parallel‐LUT‐MP‐EMP predistorter.
Activation of the Alternative Complement Pathway by Fungal Melanins (2002)

Melanins are complex biological pigments formed by the oxidative polymerization of phenolic and/or indolic compounds. These pigments have been implicated in the pathogenesis of some microbial infections, malignancies, degenerative disorders, and autoimmune diseases. Recent studies have demonstrated that melanins have antigenic and anti-inflammatory properties. These findings led us to further explore the interaction of melanins with the immune system. Melanin particles ("ghosts") were isolated from in vitro-melanized Cryptococcus neoformans cells and Aspergillus niger conidia and then incubated in normal human serum containing (125)I-labeled complement C3. The results demonstrated deposition of C3 fragments onto the melanin ghosts as early as 1 min after incubation, with maximum deposition occurring after 12 min for C. neoformans-derived melanin ghosts and after 25 min for A. niger-derived melanin ghosts. The blocking of classical pathway activation did not affect the kinetics or total deposition of C3 onto the melanin ghosts, indicating that melanins activate complement through the alternative pathway. Immunofluorescence analysis of lungs from BALB/c mice injected intratracheally with C. neoformans-derived melanin ghosts demonstrated deposition of C3 fragments onto the ghosts. Small granulomas were also observed surrounding the ghosts. However, melanization of the C. neoformans cell wall did not alter the kinetics or total deposition of C3 fragments onto the fungal cells. The finding that melanin surfaces can activate the complement system suggests a potential mechanism for the pathogenesis of some degenerative and/or autoimmune processes that involve melanized cells as well as another potential role for melanin in the virulence of melanin-producing microorganisms.
Functional expression of M1, M3 and M5 muscarinic acetylcholine receptors in yeast (2001)

The goal of this study was to functionally express the three G(q)-coupled muscarinic receptor subtypes, M(1), M(3) and M(5), in yeast (Saccharomyces cerevisiae). Transformation of yeast with expression constructs coding for the full-length receptors resulted in very low numbers of detectable muscarinic binding sites (B(max) < 5 fmol/mg). Strikingly, deletion of the central portion of the third intracellular loops of the M(1), M(3) and M(5) muscarinic receptors resulted in dramatic increases in B(max) values (53-214 fmol/mg). To monitor productive receptor/G-protein coupling, we used specifically engineered yeast strains that required agonist-stimulated receptor/G-protein coupling for cell growth. These studies showed that the shortened versions of the M(1), M(3) and M(5) receptors were unable to productively interact with the endogenous yeast G protein alpha-subunit, Gpa1p, or a Gpa1 mutant subunit that contained C-terminal mammalian Galpha(s) sequence. In contrast, all three receptors gained the ability to efficiently couple to a Gpa1/Galpha(q) hybrid subunit containing C-terminal mammalian Galpha(q) sequence, indicating that the M(1), M(3) and M(5) muscarinic receptors retained proper G-protein coupling selectivity in yeast. This is the first study to report the expression of muscarinic receptors in a coupling-competent form in yeast. The strategy described here, which involves structural modification of both receptors and co-expressed G proteins, should facilitate the functional expression of other classes of G protein-coupled receptors in yeast.
Benign-by-design preparation of iron oxides/humins catalytic nanocomposites (2017)

The current acid-catalyzed conversion of biomass feedstocks yields substantial quantities of undesired by-products called humins, for which applications are yet to be found. This work aims to provide a starting point for valorisation of humins via preparation of humin-based iron oxide catalytic nanocomposites from humins and thermally treated humins (foams) via solvent-free methodologies including ball milling and thermal degradation. The prepared materials were found to be active in the microwave-assisted selective oxidation of isoeugenol (conversions &gt;87%) to vanillin, proving the feasibility to use humin by-products as template/composite materials.
Cell biological responses of osteoblasts on anodized nanotubular surface of a titanium‐zirconium alloy (2013)

Anodization of titanium and its alloys, under controlled conditions, generates a nanotubular architecture on the material surface. The biological consequences of such changes are poorly understood, and therefore, we have analyzed the cellular and molecular responses of osteoblasts that were plated on nanotubular anodized surface of a titanium-zirconium (TiZr) alloy. Upon comparing these results with those obtained on acid etched and polished surfaces of the same alloy, we observed a significant increase in adhesion and proliferation of cells on anodized surfaces as compared to acid etched or polished surface. The expression of genes related to cell adhesion was high only on anodized TiZr, but that of genes related to osteoblast differentiation and osteocalcin protein and extracellular matrix secretion were higher on both anodized and acid etched surfaces. Examination of surface morphology, topography, roughness, surface area and wettability using scanning electron microscopy, atomic force microscopy, and contact angle goniometry, showed that higher surface area, hydrophilicity, and nanoscale roughness of nanotubular TiZr surfaces, which were generated specifically by the anodization process, could strongly enhance the adhesion and proliferation of osteoblasts. We propose that biological properties of known bioactive titanium alloys can be further enhanced by generating nanotubular surfaces using anodization.
Fair and adaptive online set-based cache partitioning (2011)

In a multi-processing environment extra misses are endured in the last level shared cache because each process is trying to utilize the whole cache space, resulting in high interference between their working sets, and thus a degraded performance. In this paper, we propose a new cache partitioning scheme, which opposed to prior partitioning schemes in the literature, offers both high performance and fair allocation even with increasing number of simultaneously running processes and decreased cache associativity. The proposed scheme takes advantage of the broad number of sets in the cache by partitioning it dynamically set-wise. The partitioning presented is adaptive to accommodate to the changing requirements of the mix of running processes without the need for any offline information and with an eye on fair allocation of cache resources. Performance is evaluated by experimentation on different cache sizes with different associativity and comparison with the Least Recently Used baseline cache and partitioning schemes. We experimented on mixes from the Splash Benchmark Suite. The results shows a performance speedup up to 44% with an average speedup of 15% over all mixes, and also fairness improvement up to 46% in terms of the weighted harmonic mean, with an average of 14% over all mixes.
Inexpensive, Versatile, and Robust USB-Driven Sensor Platform (2017)

An ultralow cost vapor sensor platform is developed, incorporating a chemiresistor-based sensor that enables targeted sensing through surface functionalization. Humidity, ammonia, and acetone sensing are demonstrated by PEDOTPSS, DPP-CN, and graphene surface modification, respectively. The integrated USB connector, use of a standard HMI interface, and microcontroller interface allows us installation-free data collection on any device with a USB port.
RETRACTED: The Repeatability and Reproducibility Problem in the CVD Synthesis of 2D Materials: Towards a More Efficient and Sustainable Synthetic Process (2023)

Though Chemical Vapor Deposition (CVD) is a versatile process that has been widely used for synthesizing graphene, hexagonal boron nitride (h BN) and other 2-D materials, the process is plagued by issues of repeatability and reproducibility, the two important pillars of the scientific method. The primary reason for this is that we do not know or can directly measure the reaction environment inside the reactor (flow and thermal fields and reactant concentrations) that controls the growth process and the final film characteristics. In turn, we are unsure about the external parameters that control this reaction environment and can be measured instead. Consequently, experimental details currently monitored and reported in the literature are insufficient to ensure reproducibility, with process details typically reported only partially, and details about the reactor not included at all, further compounding the problem. In this paper, using the example of a hot-wall tube reactor that is typically used in the laboratory and the Computational Fluid Dynamics toolbox OpenFOAM, we have simulated the reactor environment and identified measurable reactor and process parameters that control this environment and explored its sensitivity to these external parameters. Based on our findings, we have devised a straightforward protocol for experimentalists to use for monitoring and reporting CVD processes in literature so that they become repeatable and reproducible, and, aid in analyzing and studying processes and mechanisms, rapid testing of ideas, process scale-up and an overall faster and more sustainable progress of the field.
Coherent Compton Effect (1981)

Interference effects have been observed when coherently related x-ray beams are Compton scattered from an atomic system. We use dynamical diffraction methods to prepare the initial x-ray state and observe the coherent Compton effect in both crosssection and profile measurements.
Scintillation response of nonactivated and activated NaI to random and channeled ions: Influence of the luminescence mechanism (1977)

Previous experiments have shown that the scintillation response to random positive-ion bombardment of alkali iodides, both nonactivated and activated, have similar characteristics even though the luminescence mechanisms are very different. This paper reports experiments on nonactivated NaI and NaI(Tl). The relative pulse height as a function of energy for randomly incident protons (3-14 MeV) and $^{16}\mathrm{O}$ ions (5-50 MeV) for both crystals has been recorded. Also, pulse-height spectra due to energetic $^{16}\mathrm{O}$ ions (10-50 MeV) channeled along the {100} plane and $〈100〉$ axis of nonactivated NaI at 100\ifmmode^\circ\else\textdegree\fi{}K are presented and compared with those obtained previously for NaI(Tl). The following observations are made: (i) The ratio of the relative number of photons per unit energy for $^{16}\mathrm{O}$ ions to that for protons is very nearly the same for both crystals. (ii) The ratio of light outputs for totally channeled particles to random particles is nearly the same for both crystals. (iii) The detailed characteristics of pulse-height spectra from channeled ions are very similar for the two crystals. These results indicate that the scintillation response is quite insensitive to the particular luminescence mechanism.