gebhart/patrepeval huggingface dataset:
Characterization of sugar metabolism in the stem of Tachisuzuka, a whole-crop silage rice cultivar with high sugar content in the stem (2018)

Tachisuzuka, a rice cultivar for whole-crop silage, is characterized by a small panicle and high sugar content in the stem. Our previous study suggests that the high sugar content in the stem of Tachisuzuka is due to a factor other than the small panicle. To characterize sugar metabolism in the stem of Tachisuzuka, here we compared carbohydrate content, enzyme activity, and the expression of genes involved in sugar metabolism in the stem between Tachisuzuka and its parental variety, Kusanohoshi. Thinning the panicles of Kusanohoshi increased the starch content in the leaf sheath and internode but did not increase the sucrose content in the leaf sheath to the same level as that of Tachisuzuka. This suggests that Tachisuzuka has high potential to accumulate sucrose in its leaf sheath. Comparison of enzyme activity showed that the hexokinase activities in the leaf sheath tended to be higher in Tachisuzuka than Kusanohoshi or panicle-thinned Kusanohoshi, suggesting that glucokinase or fructokinase affects sugar accumulation in the stem of Tachisuzuka. Comparative transcriptome analysis revealed the differences in expression levels of carbohydrate-related genes between Tachisuzuka and Kusanohoshi. In particular, the expression levels of ISA2, which encodes starch-debranching enzyme, and TMT2, which encodes tonoplast monosaccharide transporter – both of which maybe involved in sugar accumulation in grass stems – were higher in Tachisuzuka than Kusanohoshi. Thus, these enzymes and transporters may contribute to the high sugar content in the stem of Tachisuzuka.
Ecological factors rather than barriers to dispersal shape genetic structure of algal symbionts in horizontally-transmitting corals (2016)

Abstract Many reef-building corals acquire their algal symbionts ( Symbiodinium sp.) from the local environment upon recruitment. This horizontal transmission strategy where hosts pair with locally available symbionts could serve to increase coral fitness across diverse environments, as long as hosts maintain high promiscuity and symbionts adapt locally. Here, we tested this hypothesis in two coral species by comparing host and symbiont genetic structures across different spatial scales in Micronesia. Each host species associated with two genetically distinct Symbiodinium lineages, confirming high promiscuity in broadly dispersing hosts. However, contrary to our initial expectation, symbiont genetic structure was independent of physical barriers to dispersal between islands, unlike genetic structure of their hosts that was nearly perfectly explained by ocean currents. Instead, Symbiodinium consistently demonstrated genetic divergence among local reefs and between the two host species at each island, although not necessarily between distant islands. These observations indicate that Symbiodinium lineages disperse much more broadly than previously thought and continuously adapt to specific hosts and reef environments across their range, following the classical Baas Becking’s hypothesis: “Everything is everywhere, but the environment selects”. Overall, our findings confirm that horizontal transmission could be a mechanism for broadly dispersing coral species to enhance their local fitness by associating with locally adapted symbionts. Dramatic differences in factors driving the genetic structures of horizontally-transmitting corals and their Symbiodinium imply that viewing their combined genomes as a single entity (‘hologenome’) would not be useful in the context of their evolution and adaptation.
An Anomalous Case of Diastereoselectivity in Diels-Alder Reactions Using Chiral Dienes: Is π Stacking Involved? (1990)

Two new chiral dienes, compounds 1 and 2, we synthesized and reacted with maleic anhydride at room temperature. When R is a phenyl group the diastereofacial selectivity is 10:1. Curiously when R is a cyclohexyl group this ratio decreases to 2:1.
Direct targeting of FOXP3 in Tregs with AZD8701, a novel antisense oligonucleotide to relieve immunosuppression in cancer (2022)

Antisense inhibitors of FOXP3 offer a promising novel cancer immunotherapy approach. AZD8701 is being developed clinically as a first-in-class FOXP3 inhibitor for the treatment of cancer currently in Ph1a/b clinical trial (NCT04504669).
Oxidative Reactions of the MoIV Dialkyl Complex [{(3‐CF3C6H4NCH2CH2)2NMe}Mo(CH2SiMe3)2] (2007)

The structure of [(CF3N2NMe)Mo(CH2SiMe3)2] (in which (CF3N2NMe)2- is [(3-CF3C6H4NCH2CH2)2NMe]2-) is approximately trigonal bipyramidal with one axial and one equatorial alkyl ligand. Heating of solutions of [(CF3N2NMe)Mo(CH2SiMe3)2] in [D6]benzene in the presence of five equivalents of 2-butyne led to diamagnetic [(CF3N2NMe)Mo(CHSiMe3)(eta(2)-MeC[triple bond]CMe)], whose structure is approximately square pyramidal with the alkyne occupying the axial site. Addition of one equivalent of cyclohexene sulfide to [(CF3N2NMe)Mo(CH2SiMe3)2] at room temperature produced the diamagnetic, dimeric molybdenum(IV) sulfido complex, [{(CF3N2NMe)MoS}2]. This complex is composed of two approximately trigonal bipyramidal centers, each containing one axial and one equatorial sulfur atom. Oxidation of [(CF3N2NMe)Mo(CH2SiMe3)2] with hexachloroethane resulted in formation of tetramethylsilane, HCl, and the sparingly soluble, red alkylidyne complex, [{(CF3N2NMe)Mo(CSiMe3)Cl}2]. This complex forms a dimer through bridging chlorides. The oxidation reactions of [(CF3N2NMe)Mo(CH2SiMe3)2] with 2-butyne, cyclohexene sulfide, or C2Cl6 are all proposed to proceed by alpha-hydrogen abstraction in the Mo(VI) species to yield (initially) the Mo=CHSiMe3 species and tetramethylsilane.
Statistical Aspects of Near-Infrared Spectroscopy for the Characterization of Errors and Model Building (2017)

Due to the complex nature of near-infrared (NIR) spectra, it is usually very difficult to provide quantitative interpretations of spectral data. As a consequence, careful building and validation of calibration models are of fundamental importance prior to development of useful applications of NIR technologies. For this reason, this work presents a statistical study about the NIR spectroscopy, analyzing the NIR behavior when the experimental conditions are changed. Near-infrared spectra were measured at different temperatures and stirring velocities for systems containing a pure solvent and a suspension of polymer powder in order to perform the error analysis. Then, mixtures of xylene and toluene were analyzed through NIR at different temperatures and stirring velocities and the obtained data were used to build calibration models with multivariate techniques. The results showed that the precision of the NIR measurements depends on the analytical conditions and that unavoidable fluctuations of spectral data (or spectral data variability) are strongly correlated, leading to full covariance matrices of spectral fluctuations, which has been surprisingly neglected during quantitative analyses. In particular, modeling of the xylene/toluene NIR data performed with different multivariate techniques revealed that the principal directions are not preserved when the real covariance matrix of measurement errors is taken into account.
d‐Arg[Hyp3‐Thi5‐d‐Tic7‐Tic8]‐bradykinin, a potent antagonist of smooth muscle BK2 receptors and BK3 receptors (1991)

D-Arg[Hyp3-Thi5-D-Tic7-Tic8]-bradykinin (NPC 16731) inhibited bradykinin (BK) binding and BK-induced contraction in guinea-pig ileum, being markedly more potent than D-Phe7-BK analogues as a BK2 receptor antagonist. In isolated trachea NPC 16731, unlike other BK2 antagonists, inhibited BK binding and BK-induced contraction, and 45Ca2+ efflux in tracheal smooth muscle cells. That NPC 16731 potently inhibits BK effects in trachea provides further evidence for the existence of the airway BK3 receptor.
Chord-length distribution function for two-phase random media (1993)

A statistical correlation function of basic importance in the study of two-phase random media (such as suspensions, porous media, and composites) is the chord-length distribution function p(z). We show that p(z) is related to another fundamentally important morphological descriptor studied by us previously, namely, the lineal-path function L(z), which gives the probability of finding a line segment of length z wholly in one of the phases when randomly thrown into the sample. We derive exact series representations of the chord-length distribution function for media comprised of spheres with a polydispersivity in size for arbitrary space dimension D. For the special case of spatially uncorrelated spheres (i.e., fully penetrable spheres), we determine exactly p(z) and the mean chord length ${\mathit{l}}_{\mathit{C}}$, the first moment of p(z). We also obtain corresponding formulas for the case of impenetrable (i.e., spatially correlated) polydispersed spheres.
Expression of RXFP1 Is Decreased in Idiopathic Pulmonary Fibrosis: Implications for Relaxin-based Therapies (2016)

IPF is characterized by the loss of RXFP1 expression. RXFP1 expression is directly associated with pulmonary function in patients with IPF. The relaxin-like effects of CGEN25009 in vitro are dependent on expression of RXFP1. Our data suggest that patients with IPF with the highest RXFP1 expression would be predicted to be most sensitive to relaxin-based therapies.
Azimuthal Current-Neutralization of a Rotational Light Ion Beam by a Plasma (1983)

The rotational motion of a light ion beam and a plasma immersed in a uniform magnetic field is investigated within the framework of the macroscopic fluid equations including force terms due to radial pressure variations. Drift motion caused by the radial electric and magnetic forces rotates the beam fluid element and the plasma electron fluid element in the same azimuthal direction. The motion leads to the over-neutralization of the azimuthal beam current by the plasma electron current. It is found that the ion beam is compact and never hollowed out in over-neutralized states. The radial density profiles of the beam are obtained and the condition for radially confined equilibria in those over-neutralized states is examined.
GEANT4 - a new and robust tool for biophotonics Monte Carlo simulations (2014)

Recently, a validated tissue optics plug-in based on the Geometry and Tracking 4 (GEANT4) Monte Carlo framework was developed for radiation-induced light transport in biological media. However, the novelty of the work extends beyond the simulation of light generated by ionizing radiation (i.e., the Cherenkov effect and scintillation), as users may take advantage of the many inherent features associated with GEANT4 (i.e., complex heterogeneous geometries, multiple sources and detectors, comprehensive data recording options, and advanced software visualization). Furthermore, with the recently updated plug-in users may utilize such features as user-defined input source spectra for broadband optical sources and detection, custom user-defined scattering phase functions, and simulations in voxelized geometries generated from imported DICOM stacks to name a few. The plug-in, user guide, and a number of example files are available online at http://www.dartmouth.edu/optmed/research-projects/monte-carlo-software/.
LaeA-dependent production of small molecules of Aspergillus niger that compete with specific antibodies that bind to human immune receptors (2022)

Abstract Microorganisms secrete a variety of compounds into their environment such as proteins, carbohydrates, and secondary metabolites. These molecules play diverse roles in the interaction of microbes with their abiotic and biotic environment. Little is known about secreted fungal molecules mediating immune evasion. Here we screened culture media of three Aspergilli to assess whether these fungi secrete molecules that can compete with specific antibodies that bind to human immune receptors. Culture media of Aspergillus fumigatus Af293, Aspergillus tubingensis CBS 133792 and the non-acidifying mutant strain Aspergillus niger D15#26 contained components that showed competition for binding to a total of 13 receptors, of which PSGL-1, CXCR1, and CXCR2, were shared between the three species. Filtration experiments showed that most, if not all, interacting components were ≤ 3 kDa. Production of the components that competed with antibodies to bind to CD88 and CXCR2 was shown to be regulated by LaeA. The component(s) that competed for binding to CXCR1 was not only produced in the non-acidifying strain Aspergillus niger D15#26 but also in the non-acidifying oahA deletion strain of Aspergillus niger . Together, these data show that Aspergillus species might produce small molecules that interact with human immune receptors.
Hybrid data and model driven algorithms for angular power spectrum estimation (2020)

We propose two algorithms that use both models and datasets to estimate angular power spectra from channel covariance matrices in massive MIMO systems. The first algorithm is an iterative fixed-point method that solves a hierarchical problem. It uses model knowledge to narrow down candidate angular power spectra to a set that is consistent with a measured covariance matrix. Then, from this set, the algorithm selects the angular power spectrum with minimum distance to its expected value with respect to a Hilbertian metric learned from data. The second algorithm solves an alternative optimization problem with a single application of a solver for nonnegative least squares programs. By fusing information obtained from datasets and models, both algorithms can outperform existing approaches based on models, and they are also robust against environmental changes and small datasets.
Sub-channel allocation in green powered heterogeneous cognitive radio networks (2016)

This paper aims at maximizing the sum rate of secondary users (SUs) in Orthogonal Frequency Division Multiplexing (OFDM)-based Heterogeneous Cognitive Radio (CR) Networks by considering some practical limitations such as various traffic demands of SUs, interference constraint and imperfect spectrum sensing. The CR system operates in a slotted mode, in which the SUs have no power supplies and harvest energy from ambient radio signal. Assuming SUs operate in a time switching fashion, the time slot is partitioned into three non-overlapping parts devoted for energy harvesting, spectrum sensing and data transmission. Then, the general problem of sum rate maximization is formulated as a mixed integer programming task. Since this problem is intractable, we propose a sub-channel allocation scheme based on a factor called Energy Figure of Merit to approximately satisfy SUs' rate requirements. Then, the integer constraints of the optimization problem are removed and the problem can be reduced to a convex optimization task. Considering the trade-off between fractions of the time slot, we focus on finding the optimal structures of SUs that maximize the total throughput while guaranteeing the rate requirements of both real-time (RT) and non-real-time (NRT) SUs. The numerical results validate the effectiveness and efficiency of our sub-channel allocation method as well as performance gain of the optimal structure.
ChemInform Abstract: Synthesis and Antitumor Activity of 4‐Aminomethylthioxanthenone and 5‐Aminomethylbenzothiopyranoindazole Derivatives. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A Porous POSiSil Suited for Pressure‐Driven Reversible Confinement of Solutions: PSS‐2 (2019)

Polyoligosiloxysilicone (POSiSil; designated PSS-2) is a copolymer of double four-ring (D4R) cyclosilicate and dimethylsiloxane. It is synthesized by linking D4R units in tetrabutylammonium cyclosilicate crystals with dimethyldichlorosilane. The structure of PSS-2 was revealed using solid state NMR spectroscopy. In this 3D copolymer D4R units are connected systematically by short siloxane chains most likely composed of 2 to 3 dimethylsiloxane monomers. Controlling the conversion of the parent material allows for tuning the porosity of PSS-2. Residual parent material is embedded inside PSS-2 polymer and can be eliminated by calcination. This leaves nanovoids inside PSS-2, which is moderately hydrophobic. Pressure-driven intrusion-extrusion cycles of aqueous solution exhibit hysteresis, thus, PSS-2 can be used as reversible confinement for liquids with a capacity of around 1000 mm<sup>3</sup> g<sup>-1</sup> in porosity.
Impact of deep levels on the electrical conductivity and luminescence of gallium nitride codoped with carbon and silicon (2005)

The impact of C incorporation on the deep level spectrum of n-type and semi-insulating GaN:C:Si films grown by rf plasma-assisted molecular-beam epitaxy (MBE) was investigated by the combination of deep level transient spectroscopy, steady-state photocapacitance, and transient deep level optical spectroscopy. The deep level spectra of the GaN:C:Si samples exhibited several band-gap states. A monotonic relation between systematic doping with C and quantitative trap concentration revealed C-related deep levels. A deep acceptor at Ec−2.05eV and a deep donor at Ec−0.11eV are newly reported states, and the latter is the first directly observed deep level attributed to the CGa defect. A configuration-coordinate model involving localized lattice distortion revealed strong evidence that C-related deep levels at Ec−3.0eV and Eν+0.9eV are likely identical and associated with the yellow luminescence in C-doped GaN films. Of the deep levels whose trap concentration increase with C doping, the band-gap states at Ec−3.0 and 3.28eV had the largest concentration, implying that free-carrier compensation by these deep levels is responsible for the semi-insulating behavior of GaN:C:Si films grown by MBE. The differing manner by which C incorporation in GaN may impact electrical conductivity in films grown by MBE and metal-organic chemical-vapor deposition is discussed.
Compact Physical Models for Power Supply Noise and Chip/Package Co-Design of Gigascale Integration (2007)

Compact physical models are derived for predicting power supply noise of chips in the gigascale integration (GSI) era. These models consider both IR-drop and simultaneous switching noise (SSN) and give a quick full waveform description of the first droop power supply noise as well as its peak value. The derivation of these models proceeds by considering a frequency domain representation of power grids and later obtaining time domain equivalents. The derived models enable chip/package co-design in current and future technology nodes by allowing a designer to make tradeoffs in various chip and package parameters such as on-chip wire area, number and sizes of power/ground I/O pads and amount of decoupling capacitance. SPICE simulations show that the worst case peak noise model has less than 4% error.
Inhibition of pinocytosis by hygrolidin family antibiotics: Possible correlation with their selective effects on oncogene-expressed cells. (1991)

A fermentation broth of Streptomyces sp. SIPI-A4-0044 inhibited in vitro growth of src or ras oncogene-expressed (onc+) cells more strongly than that of oncogene-unexpressed (onc-) counterparts. The active components were isolated and identified as hygrolidin family antibiotics (HGL). In mixed cultures consisting of onc+ and onc- cells, at an appropriate ratio, HGL showed selective toxicity to focus like structures of onc+ cells, leaving monolayer areas of onc- cells little damaged. HGL rapidly inhibited pinocytosis, or the influx of neutral red into the cells, at concentrations partially inhibitory to the cell growth. In contrast, HGL only slightly inhibited the influx of 2-deoxyglucose, nucleosides and leucine and the syntheses of DNA, RNA and protein even at high concentrations. Upon prolonged exposure to sublethal concentrations of HGL, onc- cells but not onc+ cells recovered pinocytotic activity and resumed growth.
Trap Inlaid Cationic Hybrid Composite Material for Efficient Segregation of Toxic Chemicals from Water (2022)

Metal-based oxoanions are potentially toxic pollutants that can cause serious water pollution. Therefore, the segregation of such species has recently received significant research attention. Even though several adsorbents have been employed for effective management of chemicals, their limited microporous nature along with non-monolithic applicability has thwarted their large-scale real-time application. Herein, we developed a unique anion exchangeable hybrid composite aerogel material (IPcomp-6), integrating a stable cationic metal-organic polyhedron with a hierarchically porous metal-organic gel. The composite scavenger demonstrated a highly selective and very fast segregation efficiency for various hazardous oxoanions such as, HAsO<sub>4</sub><sup>2-</sup> , SeO<sub>4</sub><sup>2-</sup> , ReO<sub>4</sub><sup>-</sup> , CrO<sub>4</sub><sup>2-</sup> , MnO<sub>4</sub><sup>-</sup> , in water, in the presence of 100-fold excess of other coexisting anions. The material was able to selectively eliminate trace HAsO<sub>4</sub><sup>2-</sup> even at low concentration to well below the As<sup>V</sup> limit in drinking water defined by WHO.
Interrogation of 2000 Draw Tower Gratings for Quasi Distributed Sensing with Coherent-Correlation-OTDR (2022)

Utilizing a Coherent-Correlation-OTDR, 2000 draw tower gratings in 100 meter fiber with a spatial resolution of 50 mm were successfully interrogated. Spooling of the fiber results in variations of the FBG reflection spectra.
The contribution of the visual scene to disambiguation of optic flow with vestibular signals (2007)

Optic flow is generated by observer motion relative to stationary objects, by movement of objects relative to a stationary observer, and by combinations of those situations. To determine the relative contributions of object and self motion to the observed optic flow, the nervous system can use vestibular signals. An object’s speed relative to earth is given by the difference between its speed relative to the head and the head’s speed relative to the earth. The variance of the difference is the sum of the component variances. In contrast, if observers estimate self-motion from optic flow and vestibular signals, and assume a stationary visual scene, visual and vestibular estimates may be combined in a weighted average to yield more precise selfmotion estimates. So depending on whether the subject reports object motion or self-motion, the two-modality variance is predicted to be respectively higher or lower than the component variances. To test these predictions and the influence of the visual scene upon them, we measured speed-discrimination thresholds for fore-aft translations. There were two single-modality conditions, Visual and Vestibular, and two multi-modality conditions, Self-motion and Object motion. In the Visual, Vestibular, and Self-motion conditions, observers indicated if the movement was faster or slower than a standard. In the Object-motion condition, observers indicated if the object appeared to move with or against the self-motion. The experiment was run for two visual scenes, random-dots and ground plane with columns. In both scenes, multi-modal object-motion thresholds were, as predicted, higher than single-modality thresholds, and multimodal self-motion thresholds were, as predicted, generally lower than single- modality thresholds. For the ground plane scene, the self-motion thresholds could be consistently predicted by the weighted average of the single modalities, which was not the case for the random-dots condition.