gebhart/patrepeval huggingface dataset:
Herbivorous fish microbiome adaptations to sulfated dietary polysaccharides (2022)

Abstract Background. Gut microbiota of kyphosid herbivorous fish, known for feeding almost exclusively on red and brown macroalgae rich in sulfated polysaccharides, contain highly compartmentalized, herbivore-specific taxonomic compositions. The current study explores protein functional activities of microbial taxa comprising this system in digestive compartment-specific metagenomes, identifying specific enzyme associations contributing to macroalgal decomposition. Results. Assembled metagenomes from proximal gut samples were enriched in taxa most closely related to environmental marine species, especially Vibrio -related Gammaproteobacteria, which progressively decline in hindgut compartments in favor of host-specific groups often found in terrestrial vertebrate microbiomes, including Alistipes -related Bacteroidota, Clostridia-related Bacillota, uncharacterized Verrucomicrobiota, and Desulfovibrio-related Deltaproteobacteria. Predicted degradative capacity for sulfated macroalgal polysaccharides is highly enriched in fish hindgut samples, concomitant with expansion of Bacteroidota, Bacillota, and Verrucomicrobiota clades. Extracellularly exported arylsulfatase (SulfAtlas) and carbohydrate active enzyme (CAZy) classes associated with red and brown macroalgal digestion are greatly expanded in kyphosid fish gut versus terrestrial ruminant metagenomes. Genomic mapping of these fish gut-enriched gene functions reveals quantitative signatures suggesting polysaccharide utilization loci associations and coordinated networks of extracellularly exported enzymes targeting specific macroalgal polysaccharides. Co-localization frequencies provide insight into potential gene duplication events and suggest preferred substrates for previously uncharacterized arylsulfatase classes. Conclusions. Metagenomic networks of co-localized polysaccharide hydrolysis and sulfatase gene functions have been used to demonstrate distinct patterns of fish gut compartment-specific microbial enzymes targeting complex sulfated polysaccharides. These patterns reveal previously undescribed potential for cooperative exported enzyme activities and highlight prospective contributions of multiple bacterial taxa to overall digestive capabilities.
Registration of ‘Tatanka’ Hard Red Winter Wheat (2017)

‘Tatanka’ (Reg. No. CV‐1133, PI 681595) hard red winter wheat ( Triticum aestivum L.) was developed at the Agricultural Research Center‐Hays, Kansas State University, and released by the Kansas Agricultural Experiment Station in 2016. Tatanka was selected from a single cross of KS07HW81/‘T151’ made in 2006 at Hays, KS. The objective of this cross was to develop a hard red or hard white winter wheat cultivar with adaptation to dryland production in western Kansas. Tatanka was developed using a modified bulk breeding method. Tatanka is an F 7 –derived line with experimental number KS12H56‐6‐4 and was tested in yield trials across Kansas. Tatanka has medium maturity, medium height, above average grain volume weight, and below average protein concentration. In general, it has good milling and baking quality. Tatanka was released because of its high grain yield potential in western Kansas and its resistance to stripe rust and Soil‐borne wheat mosaic virus .
A DNA virus infecting the marine brown alga Pilayella littoralis (Ectocarpales, Phaeophyceae) in culture (1998)

A new large DNA virus (PlitV-1) infects the marine filamentous brown alga Pilayella littoralis. It was collected in Alaska and infects other P. littoralis isolates of different geographic origin. The virus has an icosahedral capsid of c. 161 nm in diameter, enclosing an electron-dense core. The genome consists of double-stranded DNA and is approximately 280 000 base pairs in size. The virus is latent in somatic cells of the host and is propagated only upon induction of the host's reproductive organs. It causes deformed sporangia, resulting in infertility, and is structurally similar to other brown algal viruses. PCR amplification of a genomic sequence coding for part of a structural glycoprotein of the Ectocarpus siliculosus virus EsV-1 produced a fragment of similar size to that obtained with EsV-1.
Metabolomics and modelling approaches for systems metabolic engineering (2022)

Metabolic engineering involves the manipulation of microbes to produce desirable compounds through genetic engineering or synthetic biology approaches. Metabolomics involves the quantitation of intracellular and extracellular metabolites, where mass spectrometry and nuclear magnetic resonance based analytical instrumentation are often used. Here, the experimental designs, sample preparations, metabolite quenching and extraction are essential to the quantitative metabolomics workflow. The resultant metabolomics data can then be used with computational modelling approaches, such as kinetic and constraint-based modelling, to better understand underlying mechanisms and bottlenecks in the synthesis of desired compounds, thereby accelerating research through systems metabolic engineering. Constraint-based models, such as genome scale models, have been used successfully to enhance the yield of desired compounds from engineered microbes, however, unlike kinetic or dynamic models, constraint-based models do not incorporate regulatory effects. Nevertheless, the lack of time-series metabolomic data generation has hindered the usefulness of dynamic models till today. In this review, we show that improvements in automation, dynamic real-time analysis and high throughput workflows can drive the generation of more quality data for dynamic models through time-series metabolomics data generation. Spatial metabolomics also has the potential to be used as a complementary approach to conventional metabolomics, as it provides information on the localization of metabolites. However, more effort must be undertaken to identify metabolites from spatial metabolomics data derived through imaging mass spectrometry, where machine learning approaches could prove useful. On the other hand, single-cell metabolomics has also seen rapid growth, where understanding cell-cell heterogeneity can provide more insights into efficient metabolic engineering of microbes. Moving forward, with potential improvements in automation, dynamic real-time analysis, high throughput workflows, and spatial metabolomics, more data can be produced and studied using machine learning algorithms, in conjunction with dynamic models, to generate qualitative and quantitative predictions to advance metabolic engineering efforts.
Bias effects on RF passive structures in HR Si substrates (2006)

This work addresses the issue of parasitic conduction at the substrate surface in high resistivity (HR) SOI and oxidized bulk wafers. Surface conduction is related to the presence of free carriers at the SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> /Si interface and is known to cause severe substrate resistivity degradation. Its impacts on RF losses of coplanar waveguides, substrate crosstalk properties and on the quality factor of spiral inductors are presented and discussed
Identification of 4-(1H-Imidazol-4(5)-ylmethyl)pyridine (Immethridine) as a Novel, Potent, and Highly Selective Histamine H3Receptor Agonist (2004)

In this study, the piperidine ring of immepip and its analogues was replaced by a rigid heterocyclic pyridine ring. Many compounds in the series exhibit high affinity and agonist activity at the human histamine H(3) receptor. Particularly, the 4-pyridinyl analogue of immepip (1c, immethridine) is identified as a novel potent and highly selective histamine H(3) receptor agonist (pK(i) = 9.07, pEC(50) = 9.74) with a 300-fold selectivity over the closely related H(4) receptor.
Optimization and Mechanistic Characterization of Pyridopyrimidine Inhibitors of Bacterial Biotin Carboxylase (2019)

A major challenge for new antibiotic discovery is predicting the physicochemical properties that enable small molecules to permeate Gram-negative bacterial membranes. We have applied physicochemical lessons from previous work to redesign and improve the antibacterial potency of pyridopyrimidine inhibitors of biotin carboxylase (BC) by up to 64-fold and 16-fold against <i>Escherichia coli</i> and <i>Pseudomonas aeruginosa</i>, respectively. Antibacterial and enzyme potency assessments in the presence of an outer membrane-permeabilizing agent or in efflux-compromised strains indicate that penetration and efflux properties of many redesigned BC inhibitors could be improved to various extents. Spontaneous resistance to the improved pyridopyrimidine inhibitors in <i>P. aeruginosa</i> occurs at very low frequencies between 10<sup>-8</sup> and 10<sup>-9</sup>. However, resistant isolates had alarmingly high minimum inhibitory concentration shifts (16- to >128-fold) compared to the parent strain. Whole-genome sequencing of resistant isolates revealed that either BC target mutations or efflux pump overexpression can lead to the development of high-level resistance.
Multiscale partition-based Kolmogorov-Sinai Entropy: a preliminary HRV study on Heart Failure vs. Atrial Fibrillation (2022)

Several approaches for estimating complexity in physiological time series at various time scales have recently been developed, with a special focus on heart rate variability (HRV) series. While numerous multiscale complexity quantifiers have been investigated, a multiscale Kolmogorov-Sinai (K-S) entropy for the characterization of cardiovascular dynamics still has to be properly assessed. In this pilot study, we investigate the Algorithmic Information Content, which is calculated using an effective compression algorithm, to quantify multiscale partition- based K-S entropy on experimental HRV series. Data were gathered from publicly available datasets comprising long-term, unstructured recordings from 10 healthy subjects, as well as 10 patients with congestive heart failure (CHF) and 10 patients with atrial fibrillation. Results show that multiple time scales and domain partitions statistically discern healthy vs. pathological cardiovascular dynamics. We conclude that the proposed multiscale partition-based K-S entropy may constitute a viable tool for the complexity assessment of cardiovascular variability series.
Synthesis, Binding Affinity at Glutamic Acid Receptors, Neuroprotective Effects, and Molecular Modeling Investigation of Novel Dihydroisoxazole Amino Acids (2005)

The four stereoisomers of 5-(2-amino-2-carboxyethyl)-4,5-dihydroisoxazole-3-carboxylic acid(+)-4, (-)-4, (+)-5, and (-)-5 were prepared by stereoselective synthesis of two pairs of enantiomers, which were subsequently resolved by enzymatic procedures. These four stereoisomers and the four stereoisomers of the bicyclic analogue 5-amino-4,5,6,6a-tetrahydro-3aH-cyclopenta[d]isoxazole-3,5-dicarboxylic acid (+)-2, (-)-2, (+)-3, and (-)-3 were tested at ionotropic and metabotropic glutamate receptor subtypes. The most potent NMDA receptor antagonists [(+)-2, (-)-4, and (+)-5] showed a significant neuroprotective effect when tested in an oxygen glucose deprivation (OGD) cell culture test. The same compounds were preliminarily assayed using Xenopus oocytes expressing cloned rat NMDA receptors containing the NR1 subunit in combination with either NR2A, NR2B, NR2C, or NR2D subunit. In this assay, all three derivatives showed high antagonist potency with preference for the NR2A and NR2B subtypes, with derivative (-)-4 behaving as the most potent antagonist. The biological data are discussed on the basis of homology models reported in the literature for NMDA receptors and mGluRs.
Dose-Dependent Effects of IL-17 on IL-13–Induced Airway Inflammatory Responses and Airway Hyperresponsiveness (2013)

The Th2 cytokine IL-13 regulates several aspects of the asthmatic phenotype, including airway inflammation, airway hyperresponsiveness, and mucus production. The Th17 cytokine IL-17A is also implicated in asthma and has been shown to both positively and negatively regulate Th2-dependent responses in murine models of allergic airways disease. Our objective in this study was to better understand the role of IL-17 in airway inflammation by examining how IL-17 modifies IL-13-induced airway inflammatory responses. We treated BALB/c mice intranasally with IL-13 or IL-17 alone or in combination for 8 consecutive days, after which airway hyperresponsiveness, inflammatory cell influx into the lung, and lung chemokine/cytokine expression were assessed. As expected, IL-13 increased airway inflammation and airway hyperresponsiveness. IL-13 also increased numbers of IL-17-producing CD4(+) and γδ T cells. Treating mice with a combination of IL-13 and IL-17 reduced infiltration of IL-17(+) γδ T cells, but increased the number of infiltrating eosinophils. In contrast, coadministration of IL-13 with a higher dose of IL-17 decreased all IL-13-induced inflammatory responses, including infiltration of both IL-17(+)CD4(+) and γδ T cells. To examine the inhibitory activity of IL-17-expressing γδ T cells in this model, these cells were adoptively transferred into naive recipients. Consistent with an inhibitory role for γδ T cells, IL-13-induced infiltration of eosinophils, lymphocytes, and IL-17(+)CD4(+) T cells was diminished in recipients of the γδ T cells. Collectively, our data indicate that allergic airway inflammatory responses induced by IL-13 are modulated by both the quantity and the cellular source of IL-17.
The Endothelial Glycocalyx: A Possible Therapeutic Target in Cardiovascular Disorders (2022)

The physiological, anti-inflammatory, and anti-coagulant properties of endothelial cells (ECs) rely on a complex carbohydrate-rich layer covering the luminal surface of ECs, called the glycocalyx. In a range of cardiovascular disorders, glycocalyx shedding causes endothelial dysfunction and inflammation, underscoring the importance of glycocalyx preservation to avoid disease initiation and progression. In this review we discuss the physiological functions of the glycocalyx with particular focus on how loss of endothelial glycocalyx integrity is linked to cardiovascular risk factors, like hypertension, aging, diabetes and obesity, and contributes to the development of thrombo-inflammatory conditions. Finally, we consider the role of glycocalyx components in regulating inflammatory responses and discuss possible therapeutic interventions aiming at preserving or restoring the endothelial glycocalyx and therefore protecting against cardiovascular disease.
Selective Area Growth: A Promising Way for Recessed Gate GaN MOSFET With High Quality MOS Interface (2016)

Based on the selective area growth (SAG) technique, an enhancement mode GaN recessed gate MOSFET was fabricated successfully with negligible gate trapping effect, presenting an extremely small threshold voltage (Vth) hysteresis of 50 mV at a gate bias swing up to 10 V. Compared with the larger Vth hysteresis of a recessed gate GaN MOSFET fabricated by dry-etching, the correlation between the Vth hysteresis and the lattice damage related traps caused by plasma dry etching process has been confirmed. Furthermore, the SAG recessed MOSFET shows a lower turn-ON resistance due to the higher MOS channel mobility. We believe that all of these superior performance of SAG MOSFET are attributed to the damage free high quality GaN surface at the Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> /GaN MOS interface, which indicates that the SAG is a promising alternative technique toward stable GaN MOSFET for the power switching applications.
Non¿binary error correcting codes with noiseless feedback, localized errors, or both (2006)

The two models described in this paper having as ingredients feedback resp. localized errors give possibilities for code constructions not available in the standard model of error correction and also for probabilistic channel models. For the feedback model we present here a coding scheme, which we call the rubber method, because it is based on erasing letters. It is the first scheme achieving the capacity curve for q ges 3. It could be discovered only in the g-ary case for q ges 3, because the letter zero is not used as an information symbol, but solely for error correction. However an extension of the method from using single zeros to blocks of zeros also gives Berlekamp's result - by a different scheme. In the model with feedback and localized errors the help of feedback is addressed. We give an optimal construction for one-error correcting codes with feedback and localized errors
Search for the double-βdecay ofGe76 (1986)

A systematic study of the radioactive background in materials used in Ge-detector fabrication was conducted prior to the construction of an ultralow-background, 135 ${\mathrm{cm}}^{3}$ prototype detector. The background from primordial radioactivities in the new system was lower by factors of between 1.5\ifmmode\times\else\texttimes\fi{}${10}^{3}$ and 2.5\ifmmode\times\else\texttimes\fi{}${10}^{4}$ when compared to commercial low-background detectors. Data were collected for 8089 h with the detector located 1438 m underground, resulting in improved lower limits for the half-lives for both two-neutrino and neutrinoless \ensuremath{\beta}\ensuremath{\beta} decay of $^{76}\mathrm{Ge}$ to the ground state of $^{76}\mathrm{Se}$ and for the neutrinoless \ensuremath{\beta}\ensuremath{\beta} decay to the first excited state of $^{76}\mathrm{Se}$. The results of four recent theoretical calculations are compared in detail and used to extract limits on 〈${m}_{\ensuremath{\nu}}$〉, the Majorana mass of ${\ensuremath{\nu}}_{e}$, and on the amplitudes of the couplings of right-handed Majorana neutrinos. The best combination of the lowest background data from recent experiments results in a new limit ${T}_{1/2}^{0\ensuremath{\nu}}$\ensuremath{\gtrsim}3\ifmmode\times\else\texttimes\fi{}${10}^{23}$ yr, corresponding to 〈${m}_{\ensuremath{\nu}}$〉2.4 eV neglecting right-handed couplings or 2.8 eV including both right-handed neutrino couplings.
Crystal growth and scintillation properties of NdF<inf>3</inf> single crystal (2009)

NdF <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> single crystal was efficiently grown from the melt by the micro-pulling-down (¿-PD) method. The grown crystal had a single phase confirmed by XRD. Then Optical properties and ¿-ray excited scintillation properties in Vacuum Ultraviolet (VUV) wavelength region were investigated. It showed 60-80% transmittance down to 170 nm, and broad luminescence centered at 175 nm. The light yield and decay time of it were also evaluated under 5.5 MeV ¿-ray excitation ( <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">241</sup> Am). The light yield was evaluated to be 60 ± 6 [Ph / 5.5 MeV-¿], and the decay time was also evaluated to be 6.9 ns under 5.5 MeV a-ray excitation.
RamLink: a high-bandwidth point-to-point memory architecture (2003)

The authors describe RamLink, a memory interface architecture that allows RAM chips to be connected with point-to-point links in a ring topology. Low-voltage differential driver technology allows for very high throughput: 500 Mbytes/s on an 8-b-parallel data path. A RamLink memory subsystem consists of a memory controller and one or more (maximum 64) RamLink memory chips. A few RamLink chips, built from a conventional DRAM (dynamic RAM) process, provide a simple high-bandwidth memory subsystem. Preliminary simulations verify that the RamLink architecture has a very high system bandwidth with latency comparable to that of conventional memory systems. RamLink is inspired by the IEEE Scalable Coherent Interface specification (P1596) and has been authorized as an IEEE working group (P1596.4).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A quick PCB thermal calculator to aid system design of exposed pad packages (2011)

Thermal design of PCBs (Printed Circuit Boards) is important for electronic packages which are intended to be primarily cooled by heat flow into the PCB. Designing the required PCB coverage area through detailed numerical simulations can be computationally expensive. This article presents a quick approach to predict Junction-to-Air thermal resistance of exposed pad packages based on pre-generated detailed thermal simulations and interpolation methodology. The modeling methodology is derived from validated measurements on Quad and Inline packages with different PCB copper coverage areas. Thermal data is pre-generated through parametric simulations conducted with varying package sizes, pad sizes, and PCB copper coverage areas. The interpolation methodology quickly provides a thermal resistance versus copper coverage area curve. The interpolation approach is validated through detailed simulations on cases not included in the pre-generated thermal data. Such a quick prediction capability of temperature rise of exposed pad packages for different PCB copper coverage areas can be a valuable tool for thermal design of PCB layout.
Rapid detemplation of nanozeolite β: microwave-assisted Fenton-like oxidation (2012)

An in situ microwave-assisted Fenton-like oxidation has been developed for detemplation of the nanozeolite β without any pretreatment. The influencing factors on the removal of structure-directing agents (SDAs) in the nanozeolite β, such as the composition of Fenton-like reagents (pH, H2O2/TEA+, Fe3+/H2O2) and microwave operation conditions, are investigated, to find that the SDAs in the micropores and solution of the as-prepared nanozeolites could be completely eliminated within 15 min. In comparison with those obtained by the traditional high-temperature calcination, the Fenton-treated nanozeolite particles not only preserve their monodispersity and large external surface area, but also avoid the formation of extra-framework aluminum, which renders an enhanced catalytic performance in fructose dehydration.