gebhart/patrepeval huggingface dataset:
Genetic modification in cellulose‐synthase reduces crystallinity and improves biochemical conversion to fermentable sugar (2009)

Abstract The cellulose synthase (CESA) membrane complex synthesizes microfibrils of cellulose that surround all plant cells. Cellulose is made of sugar ( β ,1‐4 glucan) and accessing the sugar in cellulose for biofuels is of critical importance to stem the use of fossil fuels and avoid competition with food crops and pristine lands associated with starch‐based biofuel production. The recalcitrance of cellulose to enzymatic conversion to a fermentable form of sugar is related to the degree of hydrogen bonding or crystallization of the glucan chain. Herein, we isolate the first viable low biomass‐crystallinity mutant by screening for altered cell wall structure using X‐ray scattering as well as screening for enzymatic conversion efficiency on a range of cell wall mutants in the model plant Arabidopsis thaliana (L.) Heynh. Through detailed analysis of the kinetics of bioconversion we identified a mutant that met both selection criteria. This mutant is ixr1‐2 , which contains a mutation in a highly conserved consensus sequence among the C‐terminal transmembrane regions within CESA3 . A 34% lower biomass crystallization index and 151% improvement in the efficiency of conversion from raw biomass to fermentable sugars was measured relative to that of wild type (Col‐0). Recognizing the inherent ambiguities with an insoluble complex substrate like cellulose and how little is still understood regarding the regulation of CESA we propose a general model for how to manipulate CESA enzymes to improve the recalcitrance of cellulose to enzymatic hydrolysis. This study also raises intriguing possibilities as to the functional importance of transmembrane anchoring in CESA complex and microfibril formation.
GaAs(111)<i>A</i>-(2×2) reconstruction studied by scanning tunneling microscopy (1990)

Atomic-resolution scanning tunneling microscope (STM) images have been obtained from the GaAs(111)A (gallium-terminated) surface. The STM images conclusively show that the (2\ifmmode\times\else\texttimes\fi{}2) periodicity arises from a regular array of gallium vacancies in agreement with a previously proposed model. It is shown that this reconstruction is explained by the reduction in energy that is achieved by the complete transfer of electrons from gallium dangling bonds into arsenic dangling bonds, which are then exactly filled.
Response of Canola Cultivars to <i>Sclerotinia sclerotiorum</i> in Controlled and Field Environments (2006)

Sclerotinia stem rot (SSR), caused by Sclerotinia sclerotiorum, can be a devastating disease of canola (Brassica napus) in the northern United States. No canola cultivars are marketed as having resistance to SSR. Field trials were established in Red Lake Falls, MN (2001, 2003, and 2004) and Carrington, ND (2001, 2002, 2003, and 2004) to evaluate canola cultivars for resistance to SSR. These cultivars also were evaluated for resistance to SSR under controlled conditions using the following methods: petiole inoculation technique (PIT), detached leaf assay (DLA), and oxalic acid assay (OAA). Significant (P ≤ 0.05) differences were detected among cultivars for SSR and yield in the field trials, with SSR levels varying from low to high among years and locations. Cultivars with consistent high levels and low levels of SSR in the field trials were identified. Significant (P ≤ 0.05) differences were detected among cultivars for SSR using the PIT and OAA methods, but not the DLA method. No significant (P ≤ 0.05) correlations between SSR levels in the controlled studies with SSR levels in the field trials were detected; however, significant negative correlations were detected between SSR area under the disease process curve values from the PIT method and yield from Carrington, ND in 2001 and 2002. Although the PIT and OAA methods differentiated cultivars, neither method was able to predict the reaction of cultivars to SSR in the field, indicating that field screening for SSR resistance is still critical for the development of resistant cultivars.
Cancer stem cells and hepatocellular carcinoma (2009)

Hepatocellular carcinoma (HCC) is the fifth most common cancer worldwide, with a median survival of 6-16 m. Factors responsible for the poor prognosis include late onset diagnosis, underlying cirrhosis and resistance to chemotherapy; 40% of HCCs are clonal and therefore potentially arise from progenitor/stem cells. New insights are provided from several signaling pathways, such as STAT3, NOTCH, hedgehog and transforming growth factor-beta (TGFbeta), which are involved in stem cell renewal, differentiation, survival, and are commonly deregulated in HCC. Control of stem cell proliferation by the TGFbeta, Notch, Wnt and Hedgehog pathways to suppress hepatocellular cancer and to form the endoderm suggest a dual role for this pathway in tumor suppression as well as progression of differentiation from a stem or progenitor stage. This review provides a rationale for detecting and analyzing tumor stem cells as one of the most effective ways to treat cancers such as hepatocellular cancer.
Serological response to Japanese encephalitis vaccine in a group of school children in South Arcot district of Tamil Nadu. (1993)

A trial with Biken Japanese encephalitis (JE) vaccine made in Japan was carried out in South Arcot district of Tamil Nadu state, India. A total of 113 school children were included in the trial. The efficacy (as determined by serological response) and safety of the vaccine were evaluated. Side effects, though minor, were noted in 54.9 per cent of the children after each dose. The serum antibody titres were determined by mouse neutralization test, plaque reduction neutralization test and haemagglutination inhibition test. An antibody response to two-dose primary vaccination schedule was observed in 72.7 per cent, whereas 87.8 per cent of the vaccines responded positively after the booster dose administered one year after. Only about 20 per cent of the children had persisting antibodies one year after the primary vaccination. The results indicated a probable need of the third dose in the primary vaccination schedule.
Reflection compensation mediated by electric and magnetic resonances of all-dielectric metasurfaces [Invited] (2017)

All-dielectric nanostructures have recently emerged as a promising alternative to plasmonic devices, as they also possess pronounced electric and magnetic resonances and allow effective light manipulation. In this work, we study optical properties of a composite structure that consists of a silicon nanoparticle array (metasurface) and high-index substrate aiming at clarifying the role of substrate on reflective properties of the nanoparticles. We develop a simple semi-analytical model that describes interference of separate contributions from the nanoparticle array and the bare substrate to the total reflection. Applying this model, we show that matching the magnitudes and setting the π-phase difference of the electric and magnetic dipole moments induced in nanoparticles, one can obtain a suppression of reflection from the substrate coated with metasurface. We perform numerical simulations of sphere and disk nanoparticle arrays for different permittivities of the substrate. We find full agreement with the semi-analytical results, which means that the uncoupled-element model adequately describes nanostructure reflective properties, despite the effects of induced bi-anisotropy. The model explains the features of the reflectance spectrum, such as a number of dips and their spectral positions, and shows why it may not coincide with the spectral positions of Mie resonances of the single nanoparticles forming the system. We also address practical aspects of the antireflective device engineering: we show that the uncoupled-element model is applicable to the structures on top of silicon substrates, including lithographically defined nanopillars. The reflectance suppression from the nanoparticle array on top of the silicon substrate can be achieved in a broad spectral range with a disordered nanoparticle array and for a wide range of incidence angles.
Explicit Solution for Magnetometer Calibration (2014)

A definitive solution is provided in this paper for solving the magnetometer calibration problem by means of ellipsoid fitting. This is achieved by providing an explicit solution for the ensuing constrained least squares problem, which requires a careful exploitation of the design matrices and a detailed analysis of symbolically calculated eigenvalues and eigenvectors. The end result is a direct solution for the magnetometer calibration problem without any recursive loop whatsoever. This is the most favorable solution one can expect for the magnetometer calibration problem, since now the computation time is exclusively determined by the number of data points. Hence, this solution is numerically reliable, fast, and particularly relevant for sliding window adaptive calibration. Simulation results show that the proposed solution is more accurate and faster than the best one available so far.
<i>Nitrospira</i> -Like Bacteria Associated with Nitrite Oxidation in Freshwater Aquaria (1998)

Oxidation of nitrite to nitrate in aquaria is typically attributed to bacteria belonging to the genus Nitrobacter which are members of the alpha subdivision of the class Proteobacteria. In order to identify bacteria responsible for nitrite oxidation in aquaria, clone libraries of rRNA genes were developed from biofilms of several freshwater aquaria. Analysis of the rDNA libraries, along with results from denaturing gradient gel electrophoresis (DGGE) on frequently sampled biofilms, indicated the presence of putative nitrite-oxidizing bacteria closely related to other members of the genus Nitrospira. Nucleic acid hybridization experiments with rRNA from biofilms of freshwater aquaria demonstrated that Nitrospira-like rRNA comprised nearly 5% of the rRNA extracted from the biofilms during the establishment of nitrification. Nitrite-oxidizing bacteria belonging to the alpha subdivision of the class Proteobacteria (e.g., Nitrobacter spp.) were not detected in these samples. Aquaria which received a commercial preparation containing Nitrobacter species did not show evidence of Nitrobacter growth and development but did develop substantial populations of Nitrospira-like species. Time series analysis of rDNA phylotypes on aquaria biofilms by DGGE, combined with nitrite and nitrate analysis, showed a correspondence between the appearance of Nitrospira-like bacterial ribosomal DNA and the initiation of nitrite oxidation. In total, the data suggest that Nitrobacter winogradskyi and close relatives were not the dominant nitrite-oxidizing bacteria in freshwater aquaria. Instead, nitrite oxidation in freshwater aquaria appeared to be mediated by bacteria closely related to Nitrospira moscoviensis and Nitrospira marina.
Role of the Mitochondrial Permeability Transition in Apoptotic and Necrotic Death After Ischemia / Reperfusion Injury to Hepatocytes (2003)

Reperfusion of ATP-depleted tissues after warm or cold ischemia causes pH-dependent necrotic and apoptotic cell death. In hepatocytes and other cell types as well, the mechanism underlying this reperfusion-induced cell death involves onset of the mitochondrial permeability transition (MPT). Opening of permeability transition (PT) pores in the mitochondrial inner membrane initiates the MPT, an event blocked by cyclosporin A (CsA) and pH less than 7.4. Thus, both acidotic pH and CsA prevent MPT-dependent reperfusion injury. Glycine also blocks reperfusion-induced necrosis but acts downstream of PT pore opening by stabilizing the plasma membrane. After the MPT, ATP availability from glycolysis or other source determines whether cell injury after reperfusion progresses to ATP depletion-dependent necrosis or ATP-requiring apoptosis. Thus, apoptosis and necrosis after reperfusion share a common pathway, the MPT. Cell injury progressing to either necrosis or apoptosis by shared pathways can be more aptly termed necrapoptosis.
The 2009 pandemic H1N1 neuraminidase N1 lacks the 150-cavity in its active site (2010)

Chinese Academy of Sciences [KSCX2-YW-R-158, 2009Y2BS2]; Ministry of Science and Technology of China [2010CB534004, 2011CB504703
Spontaneous and deflected drift-trajectories in orthogonal acceleration time-of-flight mass spectrometry (1994)

Orthogonal acceleration is a method for gating ions from an ion beam into a time-of-flight (TOF) mass spectrometer. The technique involves a pulsed electric field to apply acceleration directed orthogonally to an ion beam. This approach is useful for coupling continuous ion sources to TOF mass analyzers. Most instruments of this type, which have been described in the literature, use steering electrodes after the orthogonal acceleration step. Those velocity components of ions originating from the ion beam velocity are minimized so that the deflected drift-trajectory is parallel to a transverse flight tube. In an alternative geometry the ion beam velocity is conserved and the drift-trajectory after the orthogonal acceleration step is spontaneous. The differences between the space-time focusing ability with spontaneous and deflected drift-trajectories are discussed and investigated. Trajectory calculations indicate that deflection fields placed after the orthogonal acceleration step distort the ion packet because, in this geometry, the flight-time to the detector is dependent on the position that the ions enter the steering optics. Increasing the duty-cycle efficiency by sampling longer sections of the continuous ion beam leads to a degradation of resolving power. Employing a spontaneous drift-trajectory after orthogonal acceleration provides the advantage that the arrival time spread for isobaric ions is, in principle, independent of the length of the ion beam sampled. The major implication of these findings is that simultaneously optimized sensitivity and resolving power may not be achievable with the deflected drift-trajectory instruments. The calculations are in agreement with results from the published data of a number of groups who have built instruments based on the orthogonal acceleration principle.
Dual wavelength optical metrology using ptychography (2013)

We describe an experimental implementation of ptychography to optical metrology, in particular topography measurement, in combination with the dual wavelength method. This is the first published account of the application of the dual wavelength method to ptychography or any other phase retrieval method in order to obtain surface height information over a wide range of scales, from small fractions of a wavelength up to many tens of wavelengths, in reflection mode. Moreover, the work presented here is the first report on the application of lensless reflection mode ptychography. Advantages of the ptychographic dual wavelength method are compared with other optical topography measurement techniques, especially with respect to the experimental procedures and constraints and the analysis of the data. We show that dual wavelength ptychography can remove material-specific phase changes which adversely affect topography measurements using white light profilometry.
Transcriptomics of psoriasis (2015)

Psoriasis is a chronic inflammatory multigenic dermatosis of unclear etiology. Recently, more and more studies have been carried out to investigate into its physiopathologic mechanism at transcriptome level. The methods used in these studies mainly include expressed sequence tag(EST)analysis, GeneChip, second-generation sequencing technology, etc. Some non-coding RNAs, including miR-21, miR-203 and miR-31, have been found to be expressed abnormally in psoriatic lesions, and closely related to the differentiation and proliferation of keratinocytes. These findings provide important evidences for the pathogenesis of psoriasis.


Key words: 
Psoriasis; Microchip analytical procedures; Multilocus sequence typing
Effectiveness of statins in Medicare-eligible patients and patients < 65 years using clinical practice data* (2007)

Rosuvastatin is more effective in lowering LDL-C in Medicare-eligible patients and patients < 65 years of age when compared with other statins in usual clinical practice. Moreover, RSV patients had higher LDL-C goal attainment rates when compared with other statins in high- and moderate-risk patients. The study results have implications for clinicians in selecting the optimal statin to meet individual patient care needs.
Eribulin: A Novel Cytotoxic Chemotherapy Agent (2012)

Eribulin is a promising new cytotoxic chemotherapy agent due to its ability to treat cancers that are refractory or resistant to other drugs as well as its manageable toxicity profile.
In vivo neutralization of a C2 domain–specific human anti–Factor VIII inhibitor by an anti-idiotypic antibody (2003)

Factor VIII (FVIII) administration elicits specific inhibitory antibodies (Abs) in about 25% of patients with hemophilia A. The majority of such Abs reacts with FVIII C2 domain. mAbBO2C11 is a high-affinity human monoclonal antibody (mAb) directed toward the C2 domain, which is representative of a major class of human FVIII inhibitors. Anti-idiotypic Abs were raised to mAbBO2C11 to establish their neutralizing potential toward inhibitors. One mouse anti-idiotypic mAb, mAb14C12, specifically prevented mAbBO2C11 binding to FVIII C2 domain and fully neutralized mAbBO2C11 functional inhibitory properties. Modeling of the 3-D conformation of mAb14C12 VH and alignment with the 3-D structure of the C2 domain showed putative 31 surface-exposed amino acid residues either identical or homologous to the C2 domain. These included one C2 phospholipid-binding site, Leu2251-Leu2252, but not Met2199-Phe2200. Forty putative contact residues with mAbBO2C11 were identified. mAb14C12 dose-dependently neutralized mAbBO2C11 inhibitory activity in mice with hemophilia A reconstituted with human recombinant FVIII (rFVIII), allowing full expression of FVIII activity. It also neutralized in an immunoprecipitation assay approximately 50% of polyclonal anti-C2 Abs obtained from 3 of 6 unrelated patients. mAb14C12 is the first example of an anti-idiotypic Ab that fully restores FVIII activity in vivo in the presence of an anti-C2 inhibitor. The present results establish the in vitro and in vivo proof of concept for idiotype-mediated neutralization of a major class of FVIII inhibitors.
Beta(3)-adrenoceptor agonist-induced increases in lipolysis, metabolic rate, facial flushing, and reflex tachycardia in anesthetized rhesus monkeys. (2001)

The effects of two beta(3)-adrenergic receptor agonists, (R)-4-[4-(3-cyclopentylpropyl)-4,5-dihydro-5-oxo-1H-tetrazol-1-yl]-N-[4-[2-[[2-hydroxy-2-(3-pyridinyl)ethyl]amino]ethyl]phenyl]benzenesulfonamide and (R)-N-[4-[2-[[2-hydroxy-2-(3-pyridinyl)- ethyl]amino]ethyl]phenyl]-1-(4-octylthiazol-2-yl)-5-indolinesulfonamide, on indices of metabolic and cardiovascular function were studied in anesthetized rhesus monkeys. Both compounds are potent and specific agonists at human and rhesus beta(3)-adrenergic receptors. Intravenous administration of either compound produced dose-dependent lipolysis, increase in metabolic rate, peripheral vasodilatation, and tachycardia with no effects on mean arterial pressure. The increase in heart rate in response to either compound was biphasic with an initial rapid component coincident with the evoked peripheral vasodilatation and a second more slowly developing phase contemporaneous with the evoked increase in metabolic rate. Because both compounds exhibited weak binding to and activation of rhesus beta(1)-adrenergic receptors in vitro, it was hypothesized that the increase in heart rate may be reflexogenic in origin and proximally mediated via release of endogenous norepinephrine acting at cardiac beta(1)-adrenergic receptors. This hypothesis was confirmed by determining that beta(3)-adrenergic receptor agonist-evoked tachycardia was attenuated in the presence of propranolol and in ganglion-blocked animals, under which conditions there was no reduction in the evoked vasodilatation, lipolysis, or increase in metabolic rate. It is not certain whether the beta(3)-adrenergic receptor-evoked vasodilatation is a direct effect of compounds at beta(3)-adrenergic receptors in the peripheral vasculature or is secondary to the release or generation of an endogenous vasodilator. Peripheral vasodilatation in response to beta(3)-adrenergic receptor agonist administration was not attenuated in animals administered mepyramine, indomethacin, or calcitonin gene-related peptide(8-37). These findings are consistent with a direct vasodilator effect of beta(3)-adrenergic receptor agonists.
Microarray‐based genotyping for blood groups: comparison of gene array and 5′‐nuclease assay techniques with human platelet antigen as a model (2005)

The data presented here validate the use of microarray for large-scale SNP typing for clinically relevant blood group alloantigens.
Social Relationships and Trust (2010)

While social relationships play an important role for individuals to cope with missing market institutions, they also limit individuals' range of trading partners. This paper aims at understanding the determinants of trust at various social distances when information asymmetries are present. Among participants from an informal housing area in Cairo we find that the increase in trust following a reduction in social distance comes from the fact that trustors are much more inclined to follow their beliefs when interacting with their friend. When interacting with an ex-ante unknown agent instead, the decision to trust is mainly driven by social preferences. Nevertheless, trustors underestimate their friend's intrinsic motivation to cooperate, leading to a loss in social welfare. We relate this to the agents' inability to signal their trustworthiness in an environment characterized by strong social norms.
Non‐invasive prenatal testing for trisomies 21, 18 and 13: clinical experience from 146 958 pregnancies (2015)

Using a stringent protocol, the good performance of NIPT shown by early validation studies can be maintained in large clinical samples. This technique can provide equally high sensitivity and specificity in screening for trisomy 21 in a low-risk, as compared to high-risk, population.
A Convenient Synthesis of L-(<i>S</i>)-Glyceraldehyde Acetonide from L-Ascorbic Acid (1986)

L-S)-glyceraldehyde acetonide is easily obtained from L-ascorbic acid by three-step procedure. Since the aldehyde is rather unstable in pure form it is more convenient to use it as an aqueous solution. It was used to synthesize L-(R)-glycerol acetonide, monocyclic-ß-lactams, and olefins (by Wittig reaction).
Plasma spouted/fluidized bed for materials processing (2010)

Plasma when coupled with spout/fluidized bed reactor for gas-solid reaction brings in several advantages such as high rate of heat and mass transfer, generation of high bulk temperature using a thin jet of plasma itself as a heat source. The science and technology of plasma and fluidization or spouted bed are well established except of these two put together for high temperature application. Plasma heating of fluid/ spouted bed can bring down the size of the equipment and increase the productivity. However the theory and practice of the hybrid technology has not been tested in a variety of applications that involves high temperature synthesis of materials, TRISO particle coating for nuclear fuel particle, thermal decomposition of refractory type ore, halogenations of minerals, particulate processes and synthesis of advanced materials. This paper gives an account of the use and exploitation of plasma coupled with spouted/ fluidized bed especially for material processing and also addresses the issues for adapting the same in the era of developing advanced high temperature materials.