gebhart/patrepeval huggingface dataset:
Tuning the reactivity of semiconductor surfaces by functionalization with amines of different basicity (2010)

Surface functionalization of semiconductors has been the backbone of the newest developments in microelectronics, energy conversion, sensing device design, and many other fields of science and technology. Over a decade ago, the notion of viewing the surface itself as a chemical reagent in surface reactions was introduced, and adding a variety of new functionalities to the semiconductor surface has become a target of research for many groups. The electronic effects on the substrate have been considered as an important consequence of chemical modification. In this work, we shift the focus to the electronic properties of the functional groups attached to the surface and their role on subsequent reactivity. We investigate surface functionalization of clean Si(100)-2 × 1 and Ge(100)-2 × 1 surfaces with amines as a way to modify their reactivity and to fine tune this reactivity by considering the basicity of the attached functionality. The reactivity of silicon and germanium surfaces modified with ethylamine (CH(3)CH(2)NH(2)) and aniline (C(6)H(5)NH(2)) is predicted using density functional theory calculations of proton attachment to the nitrogen of the adsorbed amine to differ with respect to a nucleophilic attack of the surface species. These predictions are then tested using a model metalorganic reagent, tetrakis(dimethylamido)titanium (((CH(3))(2)N)(4)Ti, TDMAT), which undergoes a transamination reaction with sufficiently nucleophilic amines, and the reactivity tests confirm trends consistent with predicted basicities. The identity of the underlying semiconductor surface has a profound effect on the outcome of this reaction, and results comparing silicon and germanium are discussed.
Extending Universal Nodal Excitations Optimizes Superconductivity in Bi 2 Sr 2 CaCu 2 O 8+δ (2009)

Understanding the mechanism by which d wave superconductivity in the cuprates emerges and is optimized by doping the Mott insulator is one of the major outstanding problems in condensed-matter physics. Our high-resolution scanning tunneling microscopy measurements of the high-transition temperature (Tc) superconductor Bi2Sr2CaCu2O8+delta show that samples with different Tc values in the low doping regime follow a remarkably universal d wave low-energy excitation spectrum, indicating a doping-independent nodal gap. We demonstrate that Tc instead correlates with the fraction of the Fermi surface over which the samples exhibit the universal spectrum. Optimal Tc is achieved when all parts of the Fermi surface follow this universal behavior. Increasing the temperature above Tc turns the universal spectrum into an arc of gapless excitations, whereas overdoping breaks down the universal nodal behavior.
Persistence of Rare Salmonella Typhi Genotypes Susceptible to First-Line Antibiotics in the Remote Islands of Samoa (2022)

For decades, the remote island nation of Samoa (population ~200,000) has faced endemic typhoid fever despite improvements in water quality, sanitation, and economic development. We recently described the epidemiology of typhoid fever in Samoa from 2008 to 2019 by person, place, and time; however, the local Salmonella enterica serovar Typhi (S. Typhi) population structure, evolutionary origins, and genomic features remained unknown. Herein, we report whole genome sequence analyses of 306 S. Typhi isolates from Samoa collected between 1983 and 2020. Phylogenetics revealed a dominant population of rare genotypes 3.5.4 and 3.5.3, together comprising 292/306 (95.4%) of Samoan versus 2/4934 (0.04%) global S. Typhi isolates. Three distinct 3.5.4 genomic sublineages were identified, and their defining polymorphisms were determined. These dominant Samoan genotypes, which likely emerged in the 1970s, share ancestry with other 3.5 clade isolates from South America, Southeast Asia, and Oceania. Additionally, a 106-kb pHCM2 phenotypically cryptic plasmid, detected in a 1992 Samoan S. Typhi isolate, was identified in 106/306 (34.6%) of Samoan isolates; this is more than double the observed proportion of pHCM2-containing isolates in the global collection. In stark contrast with global S. Typhi trends, resistance-conferring polymorphisms were detected in only 15/306 (4.9%) of Samoan S. Typhi, indicating overwhelming susceptibility to antibiotics that are no longer effective in most of South and Southeast Asia. This country-level genomic framework can help local health authorities in their ongoing typhoid surveillance and control efforts, as well as fill a critical knowledge gap in S. Typhi genomic data from Oceania. <b>IMPORTANCE</b> In this study, we used whole genome sequencing and comparative genomics analyses to characterize the population structure, evolutionary origins, and genomic features of S. Typhi associated with decades of endemic typhoid fever in Samoa. Our analyses of Samoan isolates from 1983 to 2020 identified a rare S. Typhi population in Samoa that likely emerged around the early 1970s and evolved into sublineages that are presently dominant. The dominance of these endemic genotypes in Samoa is not readily explained by genomic content or widespread acquisition of antimicrobial resistance. These data establish the necessary framework for future genomic surveillance of S. Typhi in Samoa for public health benefit.
A Review of U.S. Navy Atmospheric Model Products in the Arabian Gulf - An Examination of NORAPS and COAMPS (2001)

Abstract : Recent U.S. Navy operational atmospheric products, the Navy Operational Regional Atmospheric Prediction System (NORAPS) and the Coupled Ocean/Atmosphere Mesoscale Prediction System (COAMPS), are reviewed relative to the Arabian Gulf waters. Only the most recent complete calendar years of each product are considered. The structure and description of five products (air temperature, heat flux, surface pressure. wind speed, and wind stress) relevant to the Naval Research Laboratory's coastal modeling efforts for the Arabian Gulf are explained. A detailed discussion of the dynamics and variability observed in the annual and seasonal mean fields is presented. Within this context, the NORAPS and COAMPS products are contrasted. Observations for each of the five atmospheric quantities have been identified in the literature. RMS errors and correlations are computed from comparisons between the Navy atmospheric basin-wide mean products and the observed data. These comparisons provide an avenue to assess the quality of the atmospheric data products with respect to the observed environment. Good agreement between the atmospheric data products and the open literature is found for scalar quantities such as air temperature and surface pressure. Wind speeds and wind stresses tend to be underpredicted with respect to the Winter Shamal though no definitive conclusions can be reached about overall quality due to the high degree of variability in the observed wind sources. On the contrary, heat flux products are determined to be quite poor, at least over Arabian Gulf waters when compared to available observations. Lastly, the preprocessing of the atmospheric products prior to implementation in an oceanic modeling context is included as an appendix.
Meloidogyne luci n. sp. (Nematoda: Meloidogynidae), a root-knot nematode parasitising different crops in Brazil, Chile and Iran (2014)

A new root-knot nematode parasitising vegetables, flowers and fruits in Brazil, Iran and Chile, is described as Meloidogyne luci n. sp. The female has an oval to squarish perineal pattern with a low to moderately high dorsal arc and without shoulders, similar to M. ethiopica . The female stylet is robust and 15-16 μm long; the distance from the dorsal pharyngeal gland orifice to the stylet base (DGO) is 3-4 μm. Males have a high, rounded head cap continuous with the body contour. The labial disc is fused with the medial lips to form an elongated lip structure. The head region is not marked by incomplete annulations. Male stylet robust, 20.8-23.0 μm long with rounded knobs; the DGO is 2.5-4.5 μm. The stylet of second-stage juveniles (J2) is 12.0-13.5 μm long and the DGO to the stylet base is 2.3-3.3 μm. The J2 tail is conoid with finely rounded terminus and is 40.0-48.5 μm long. Biochemically, the esterase phenotype L3 (: 1.05, 1.10, 1.25) is unique and is the most useful character to differentiate M. luci n. sp. from all other Meloidogyne species. Reproduction is by mitotic parthenogenesis (2 n = 42-46 chromosomes). In a differential host test, the population from Lavandula spica , Caxias do Sul, RS State, Brazil, reproduced on tomato cv. Rutgers, tobacco cv. NC95 and pepper cv. California Wonder. No reproduction occurred on watermelon cv. Charleston Gray, cotton cv. Deltapine 61 or peanut cv. Florunner. In Neighbour-Joining analyses of ITS and D2-D3 rRNA sequences, populations of M. luci n. sp. from Brazil, Chile and Iran clustered together and were clearly separated from other Meloidogyne spp., thus confirming that all three populations are very similar and conspecific.
Agility of Spin Hall Nano-Oscillators (2021)

Spin Hall nano-oscillators can generate radio-frequency output from direct-current input, and being planar structures with well defined geometry leaves them suitable for integration into microwave technologies. Control over output amplitude and frequency can be achieved by tuning magnetic field and direct current, but little is known about how these oscillators respond to input that changes rapidly, on the nanosecond time scale. This study shows that input current pulses just a few ns in duration are sufficient to generate rf output. Also, pulsing current and external rf inputs further improves the frequency and amplitude stability of the magnetization oscillations.
Failure modes of spinal cord stimulation hardware (2006)

The results of this analysis of SCS hardware failures may be used as a basis for refining surgical technique and designing the next generation of SCS hardware.
Polycaprolactone–starch blends with corn-based coupling agent: physical properties and in vitro analysis (2012)

In an attempt to improve properties of polycaprolcatone-starch blend, this study uses zein as coupling agent in preparing the blend through a single-step process. Zein, which has affinity to both polar and non-polar groups, is expected to improve miscibility between the blends' constituents and its overall biocompatibility. Mechanical properties of the blend were tested and further characterizations (Fourier transform infrared spectroscopy, thermal properties) were performed to analyze the effect of zein as an addition to the blend's physical properties. The blend's biocompatibility was examined by indirect methods (contact angle and weight gain after immersion in simulated body fluid) and in vitro analysis. No significant effect on the blend's strength and stiffness was caused by adding zein. Hydrophilicity and cell affinity were improved when zein was added. Zein did not perform as a coupling agent that improved miscibility between polycaprolactone and starch, but its addition improved the blend's biocompatibility.
miRNome profiling of LSC-enriched CD34+CD38−CD26+ fraction in Ph+ CML-CP samples from Argentinean patients: a potential new pharmacogenomic tool (2021)

Chronic myeloid leukemia (CML) is a myeloid stem cell neoplasm characterized by an expansion of myeloid progenitor cells and the presence of BCR-ABL1 oncoprotein. Since the introduction of specific BCR-ABL1 tyrosine kinase inhibitors (TKI), overall survival has improved significantly. However, under long-term therapy patients may have residual disease that originates from TKI-resistant leukemic stem cells (LSC). In this work, we analyzed the miRNome of LSC-enriched CD34<sup>+</sup>CD38<sup>-</sup>CD26<sup>+</sup> and normal hematopoietic stem cells (HSC) fractions obtained from the same chronic phase (CP) CML patients, and stem and progenitor cells obtained from healthy donors (HD) by next-generation sequencing. We detected a global decrease of microRNA levels in LSC-enriched CD34<sup>+</sup>CD38<sup>-</sup>CD26<sup>+</sup> and HSC fractions from CML-CP patients, and decreased levels of microRNAs and snoRNAs from a genomic cluster in chromosome 14, suggesting a mechanism of silencing of multiple non-coding RNAs. Surprisingly, HSC from CML-CP patients, despite the absence of <i>BCR-ABL1</i> expression, showed an altered miRNome. We confirmed by RT-qPCR that the levels of miR-196a-5p were increased more than nine-fold in CD26<sup>+</sup> (<i>BCR-ABL1</i> <sup><i>+</i></sup> ) vs. CD26<sup>-</sup> (<i>BCR-ABL1</i> <sup>-</sup>) CD34<sup>+</sup>CD38<sup>-</sup> fractions from CML-CP patients at diagnosis, and <i>in silico</i> analysis revealed a significant association to lipid metabolism and hematopoiesis functions. In the light of recent descriptions of increased oxidative metabolism in CML LSC-enriched fractions, these results serve as a guide for future functional studies that evaluate the role of microRNAs in this process. Metabolic vulnerabilities in LSCs open the road for new therapeutic strategies. This is the first report of the miRNome of CML-CP CD34<sup>+</sup>CD38<sup>-</sup> fractions that distinguishes between CD26<sup>+</sup> (<i>BCR-ABL1</i> <sup><i>+</i></sup> ) and their CD26<sup>-</sup> (<i>BCR-ABL1</i> <sup><i>-</i></sup> ) counterparts, providing valuable data for future studies.
Application of Viral Gene Transfer in Studies of Neurogenic Hypertension (2005)

This chapter reviews the use of viral gene transfer to disentangle the complexities of neurogenic hypertension. Viral gene manipulation allows lasting and controllable genetic manipulation in selected areas of the brain in different species and strains, including experiments in the spontaneously hypertensive rat, an established model of hypertension. Recent evidence indicates that, in contrast to pharmacological tools that may act on any cellular target within a given area of the brain, viral vectors deliver transgene in a nonuniform manner, and its concentration in different types of cells may vary greatly. This occurs as a result of both transductional tropism of a viral vector system and the transciptional activity of the promoter in different cellular types which are present in any brain nucleus. Properties of adenoviral and lentiviral vectors are compared and contrasted. Application of viral vectors for overexpression of biologically active molecules, expression of dominant negative proteins, pathway tracking, and other experiments to study central mechanisms of cardiovascular control are discussed. In summary, virally mediated gene delivery to the brain is a powerful research tool that can be used to address a wide range of questions related to mechanisms of human essential hypertension.
In Vivo Hydrating Calcium Aluminate Coatings for Anchoring of Metal Implants in Bone (2005)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Nanosecond electro-optics of a nematic liquid crystal with negative dielectric anisotropy (2014)

We study a nanosecond electro-optic response of a nematic liquid crystal in a geometry where an applied electric field E modifies the tensor order parameter but does not change the orientation of the optic axis (director N ̂). We use a nematic with negative dielectric anisotropy with the electric field applied perpendicularly to N ̂. The field changes the dielectric tensor at optical frequencies (optic tensor) due to the following mechanisms: (a) nanosecond creation of the biaxial orientational order, (b) uniaxial modification of the orientational order that occurs over time scales of tens of nanoseconds, and (c) the quenching of director fluctuations with a wide range of characteristic times up to milliseconds. We develop a model to describe the dynamics of all three mechanisms. We design the experimental conditions to selectively suppress the contributions from the quenching of director fluctuations (c) and from the biaxial order effect (a) and thus, separate the contributions of the three mechanisms in the electro-optic response. As a result, the experimental data can be well fitted with the model parameters. The analysis provides a rather detailed physical picture of how the liquid crystal responds to a strong electric field on a time scale of nanoseconds. The paper provides a useful guidance in the current search for the biaxial nematic phase. Namely, the temperature dependence of the biaxial susceptibility allows one to estimate the temperature of the potential uniaxial-to-biaxial phase transition. An analysis of the quenching of director fluctuations indicates that on a time scale of nanoseconds, the classic model with constant viscoelastic material parameters might reach its limit of validity. The effect of nanosecond electric modification of the order parameter can be used in applications in which one needs to achieve ultrafast (nanosecond) changes in optical characteristics, such as birefringence.
Crystal Structure of Botulinum Neurotoxin Type G Light Chain:  Serotype Divergence in Substrate Recognition, (2005)

The seven serotypes (A-G) of botulinum neurotoxins (BoNTs) block neurotransmitter release through their specific proteolysis of one of the three proteins of the soluble N-ethylmaleimide-sensitive-factor attachment protein receptor (SNARE) complex. BoNTs have stringent substrate specificities that are unique for metalloprotease in that they require exceptionally long substrates (1). To understand the molecular reasons for the unique specificities of the BoNTs, we determined the crystal structure of the catalytic light chain (LC) of Clostridium botulinum neurotoxin type G (BoNT/G-LC) at 2.35 A resolution. The structure of BoNT/G-LC reveals a C-terminal beta-sheet that is critical for LC oligomerization and is unlike that seen in the other LC structures. Its structural comparison with thermolysin and the available pool of LC structures reveals important serotype differences that are likely to be involved in substrate recognition of the P1' residue. In addition, structural and sequence analyses have identified a potential exosite of BoNT/G-LC that recognizes a SNARE recognition motif of VAMP.
A non‐JA producing oxophytodienoate reductase functions in salicylic acid‐mediated antagonism with jasmonic acid during pathogen attack (2023)

Peroxisome-localized oxo-phytodienoic acid (OPDA) reductases (OPR) are enzymes converting 12-OPDA into jasmonic acid (JA). However, the biochemical and physiological functions of the cytoplasmic non-JA producing OPRs remain largely unknown. Here, we generated Mutator-insertional mutants of the maize OPR2 gene and tested its role in resistance to pathogens with distinct lifestyles. Functional analyses showed that the opr2 mutants were more susceptible to the (hemi)biotrophic pathogens Colletotrichum graminicola and Ustilago maydis, but were more resistant to the necrotrophic fungus Cochliobolus heterostrophus. Hormone profiling revealed that increased susceptibility to C. graminicola was associated with decreased salicylic acid (SA) but increased JA levels. Mutation of the JA-producing lipoxygenase 10 (LOX10) reversed this phenotype in the opr2 mutant background, corroborating the notion that JA promotes susceptibility to this pathogen. Exogenous SA did not rescue normal resistance levels in opr2 mutants, suggesting that this SA-inducible gene is the key downstream component of the SA-mediated defences against C. graminicola. Disease assays of the single and double opr2 and lox10 mutants and the JA-deficient opr7opr8 mutants showed that OPR2 negatively regulates JA biosynthesis, and that JA is required for resistance against C. heterostrophus. Overall, this study uncovers a novel function of a non-JA producing OPR as a major negative regulator of JA biosynthesis during pathogen infection, a function that leads to its contrasting contribution to either resistance or susceptibility depending on pathogen lifestyle.
An investigation of volute cross-sectional shape on turbocharger turbine under pulsating conditions in internal combustion engine (2015)

Engine downsizing is a proven method for CO2 reduction in Internal Combustion Engine (ICE). A turbocharger, which reclaims the energy from the exhaust gas to boost the intake air, can effectively improve the power density of the engine thus is one of the key enablers to achieve the engine downsizing. Acknowledging its importance, many research efforts have gone into improving a turbocharger performance, which includes turbine volute. The cross-section design of a turbine volute in a turbocharger is usually a compromise between the engine level packaging and desired performance. Thus, it is beneficial to evaluate the effects of cross-sectional shape on a turbine performance. This paper presents experimental and computational investigation of the influence of volute cross-sectional shape on the performance of a radial turbocharger turbine under pulsating conditions. The cross-sectional shape of the baseline volute (denoted as Volute B) was optimized (Volute A) while the annulus distribution of area-to-radius ratio (A/R) for the two volute configurations are kept the same. Experimental results show that the turbine with the optimized volute A has better cycle averaged efficiency under pulsating flow conditions, for different loadings and frequencies. The advantage of performance is influenced by the operational conditions. After the experiment, a validated unsteady computational fluid dynamics (CFD) modeling was employed to investigate the mechanism by which performance differs between the baseline volute and the optimized version. Computational results show a stronger flow distortion in spanwise direction at the rotor inlet with the baseline volute. Furthermore, compared with the optimized volute, the flow distortion is more sensitive to the pulsating flow conditions in the baseline volute. This is due to the different secondary flow pattern in the cross-sections, hence demonstrating a direction for desired volute cross-sectional shape to be used in a turbocharger radial turbine for internal combustion engine.
Capillary filtration coefficient: the technique and its application to the small intestine (1979)

In this review, we discuss the physiological basis of the capillary filtration coefficient (Kf,c), and its measurement in the small intestine. First the various techniques by which Kf,ccan be measured are discussed and assessed; the second part of the review considers the volumetric method of determining Kf,c in more detail, in an attempt to identify the causes of variability in published values for intestinal Kf,c. Finally, we discuss changes in intestinal Kf,c due to sympathetic nerve stimulation and the administration of drugs and hormones. The majority of estimates of intestinal Kf,c are about 0.38 to 0.60 (innervated) to 0.60 to 0.75 (denervated) cm3·min−1·kPa−1·100g−1. These values are increased by most vasodilator drugs and hormones, and decreased by sympathetic nerve stimulation and by vasoconstrictor drugs.
ChemInform Abstract: Asymmetric Ring Opening Reaction of Oxabenzonorbornadienes with Amines Promoted by Iridium/NMDPP Complex. (2015)

Abstract A wide variety of primary and secondary amines are suitable nucleophiles for the title reaction to form ring opening products with good levels of enantioselectivity.