gebhart/patrepeval huggingface dataset:
Tuning the Optical and Electrochemical Properties of M(CO)4(phenanthroline) Compounds via Substituents on the Phenanthroline Ligand: An Upper-Division Inorganic Laboratory (2010)

This experiment involves the preparation and characterization of M(CO)4(L∧L) compounds, where L∧L is 1,10-phenanthroline or a related derivative and M is Cr or Mo. The purpose of the experiment is to study the effects of electron-withdrawing or electron-donating phenanthroline substituents on the resulting properties of the metal compound, analogous to current research being done on materials for dye-sensitized solar cells. The degree of electron donation is controlled via 3,4,7,8-tetramethyl (electron donating) or 5-chloro (electron withdrawing) substitution of phenanthroline. The compounds are studied using IR, UV−vis, and cyclic voltammetry. Trends are observed in these data as a function of the relative electron-donating character of the ligand. The effects of changing the central metal atom are also examined. This experiment follows a research-based model, which can be completed in a single six-hour session.
Functional and Structural Changes in a Canine Model of Hereditary Primary Angle-Closure Glaucoma (2010)

Canine hereditary angle-closure glaucoma is characterized by a progressive increase in intraocular pressure, loss of optic nerve function, and retinal ganglion cell loss.
The helium line lambda 10830 angstrom units in late-type stars. (1968)

He 10830 angstrom Fraunhofer line in late type stars determined from spectroscopic stellar observations indicating hot chromospheres existence
Low-energy MOS depletion modulators in silicon-on-insulator micro-donut resonators coupled to bus waveguides (2011)

Electrical, optical and electro-optical simulations are presented for a waveguided, resonant, bus-coupled, p-doped Si micro-donut MOS depletion modulator operating at the 1.55 μm wavelength. To minimize the switching voltage and energy, a high-K dielectric film of HfO₂ or ZrO₂ is chosen as the gate dielectric, while a narrow ring-shaped layer of p-doped poly-silicon is selected for the gate electrode, rather than metal, to minimize plasmonic loss loading of the fundamental TE mode. In a 6-μm-diam high-Q resonator, an infrared intensity extinction ratio of 6 dB is predicted for a modulation voltage of 2 V and a switching energy of 4 fJ/bit. A speed-of-response around 1 ps is anticipated. For a modulator scaled to operate at 1.3 μm, the estimated switching energy is 2.5 fJ/bit.
Effect of tissue transglutaminase on the solubility of proteins containing expanded polyglutamine repeats (2004)

The expansion of a polyglutamine (polyQ) domain in neuronal proteins is the molecular genetic cause of at least eight neurodegenerative diseases. Proteins with a polyQ domain that is greater than 40 Q (Q40) residues form insoluble intranuclear and cytoplasmic inclusions. Expanded polyQ proteins self-associate by non-covalent interactions and become insoluble. They can also be covalently cross-linked by tissue transglutaminase (TTG), a calcium-dependent enzyme present in cells throughout the nervous system. However, it remains unclear whether TTG cross-linking directly contributes to the insolubility of the expanded polyQ proteins. Using an in vitro solubility assay, we found TTG cross-linked Q62 monomers into high molecular weight soluble complexes in a calcium-dependent reaction. Inhibition of TTG cross-linking by primary amine substrates including putrescine and biotinylated pentylamine antagonized TTG's ability to form soluble complexes. In contrast, primary amines (histamine and lysine) that were less effective inhibitors of TTG cross-linking did not inhibit Q62 from becoming insoluble. In summary, TTG can increase the solubility of expanded polyQ proteins by catalyzing intermolecular cross-links. This demonstrates directly that TTG will reduce the ability of expanded polyQ proteins from becoming insoluble. Furthermore, the effectiveness of a primary amine substrate at inhibiting formation of insoluble inclusions may be related to their ability to inhibit intermolecular cross-linking by TTG.
Mechanistic Insights Revealed by the Crystal Structure of a Histidine Kinase with Signal Transducer and Sensor Domains (2013)

Two-component systems (TCSs) are important for the adaptation and survival of bacteria and fungi under stress conditions. A TCS is often composed of a membrane-bound sensor histidine kinase (SK) and a response regulator (RR), which are relayed through sequential phosphorylation steps. However, the mechanism for how an SK is switched on in response to environmental stimuli remains obscure. Here, we report the crystal structure of a complete cytoplasmic portion of an SK, VicK from Streptococcus mutans. The overall structure of VicK is a long-rod dimer that anchors four connected domains: HAMP, Per-ARNT-SIM (PAS), DHp, and catalytic and ATP binding domain (CA). The HAMP, a signal transducer, and the PAS domain, major sensor, adopt canonical folds with dyad symmetry. In contrast, the dimer of the DHp and CA domains is asymmetric because of different helical bends in the DHp domain and spatial positions of the CA domains. Moreover, a conserved proline, which is adjacent to the phosphoryl acceptor histidine, contributes to helical bending, which is essential for the autokinase and phosphatase activities. Together, the elegant architecture of VicK with a signal transducer and sensor domain suggests a model where DHp helical bending and a CA swing movement are likely coordinated for autokinase activation.
Triple-Band Metamaterial Inspired Antenna for Future Terahertz (THz) Applications (2022)

For future healthcare in the terahertz (THz) band, a triple-band microstrip planar antenna integrated with metamaterial (MTM) based on a polyimide substrate is presented. The frequencies of operation are 500, 600, and 880 GHz. The triple-band capability is accomplished by etching metamaterial on the patch without affecting the overall antenna size. Instead of a partial ground plane, a full ground plane is used as a buffer to shield the body from back radiation emitted by the antenna. The overall dimension of the proposed antenna is 484 × 484 μm2. The antenna's performance is investigated based on different crucial factors, and excellent results are demonstrated. The gain for the frequencies 500, 600, 880 GHz is 6.41, 6.77, 10.1 dB, respectively while the efficiency for the same frequencies is 90%, 95%, 96%, respectively. Further research has been conducted by mounting the presented antenna on a single phantom layer with varying dielectric constants. The results show that the design works equally well with and without the phantom model, in contrast to a partially ground antenna, whose performance is influenced by the presence of the phantom model. As a result, the presented antenna could be helpful for future healthcare applications in the THz band.
A simple, reproducible and cost-effective procedure to analyse gut phageome: from phage isolation to bioinformatic approach (2019)

The microbiota of the human gut is a complex and rich community where bacteria and their viruses, the bacteriophages, are dominant. There are few studies on the phage community and no clear standard for isolating them, sequencing and analysing their genomes. Since this makes comparisons between studies difficult, we aimed at defining an easy, low-cost, and reproducible methodology. We analysed five different techniques to isolate phages from human adult faeces and developed an approach to analyse their genomes in order to quantify contamination and classify phage contigs in terms of taxonomy and lifestyle. We chose the polyethylene glycol concentration method to isolate phages because of its simplicity, low cost, reproducibility, and of the high number and diversity of phage sequences that we obtained. We also tested the reproducibility of this method with multiple displacement amplification (MDA) and showed that MDA severely decreases the phage genetic diversity of the samples and the reproducibility of the method. Lastly, we studied the influence of sequencing depth on the analysis of phage diversity and observed the beginning of a plateau for phage contigs at 20,000,000 reads. This work contributes to the development of methods for the isolation of phages in faeces and for their comparative analysis.
Verification of Relational Data-Centric Dynamic Systems with External\n Services (2012)

Data-centric dynamic systems are systems where both the process controlling\nthe dynamics and the manipulation of data are equally central. In this paper we\nstudy verification of (first-order) mu-calculus variants over relational\ndata-centric dynamic systems, where data are represented by a full-fledged\nrelational database, and the process is described in terms of atomic actions\nthat evolve the database. The execution of such actions may involve calls to\nexternal services, providing fresh data inserted into the system. As a result\nsuch systems are typically infinite-state. We show that verification is\nundecidable in general, and we isolate notable cases, where decidability is\nachieved. Specifically we start by considering service calls that return values\ndeterministically (depending only on passed parameters). We show that in a\nmu-calculus variant that preserves knowledge of objects appeared along a run we\nget decidability under the assumption that the fresh data introduced along a\nrun are bounded, though they might not be bounded in the overall system. In\nfact we tie such a result to a notion related to weak acyclicity studied in\ndata exchange. Then, we move to nondeterministic services where the assumption\nof data bounded run would result in a bound on the service calls that can be\ninvoked during the execution and hence would be too restrictive. So we\ninvestigate decidability under the assumption that knowledge of objects is\npreserved only if they are continuously present. We show that if infinitely\nmany values occur in a run but do not accumulate in the same state, then we get\nagain decidability. We give syntactic conditions to avoid this accumulation\nthrough the novel notion of "generate-recall acyclicity", which takes into\nconsideration that every service call activation generates new values that\ncannot be accumulated indefinitely.\n
Isolated atrial myocytes: adenosine and acetylcholine increase potassium conductance (1983)

Adenosine (Ado), like acetylcholine (ACh), hyperpolarizes and shortens the atrial action potential (AP). To elucidate the underlying mechanism of Ado and ACh actions, intracellular APs and membrane currents were measured in calcium-tolerant single myocytes isolated from guinea pig atria. Both Ado and ACh hyperpolarize the resting membrane to the potassium equilibrium potential (Ek) and cause a marked abbreviation of the AP. Analysis of membrane currents reveal that Ado and ACh increase the steady-state currents. The Ado- and ACh-induced current reverses polarity at -92 mV, a value that corresponds well with a calculated EK of -90 mV. Thus the Ado- and the ACh-sensitive current can be interpreted as a potassium current. It is suggested that Ado, like ACh, increases the potassium conductance via a common mechanism.
Role of Cathode in Single Chamber Sofc (2008)

The role of the catalytic activity of the cathode materials on the open circuit voltage (OCV) of single clamber solid oxide fuel cell (SC-SOFC) was investigated. Ni-cermet has been proven to be as a very efficient catalyst for fuel and used as anode. On the other hand, typical cathode materials (perovskite oxides) are also known as catalytically active for fuel oxidation and therefore affect the OCV of the cell. Cells with a mixture of doped ceria and (La, Sr)(Co; Fe)O 3 (LSCF) as cathode, and Ag as reference electrode on doped ceria electrolyte (SDC) were prepared and tasted in single chamber configuration. The OCV increased as SDC content decreased and reached values as high as 0.1V for pure LSCF. A pomer density of∼140 mW/cm 2 was obtained at 600°C using Ni-cermed anode and LSCF-10% SDC cathode.
Transforming Self-Rated Health and the SF-36 Scales to Include Death and Improve Interpretability (2001)

These easily interpretable transformed variables permit keeping persons who die in the analyses. Using the transformed variables for longitudinal analyses of health when deaths occur, either for secondary or primary analysis, is recommended. This approach can be applied to other measures of health.
Refractive-index matching enhanced polarization sensitive optical coherence tomography quantification in human brain tissue (2021)

Abstract The importance of polarization-sensitive optical coherence tomography (PS-OCT) has been increasingly recognized in human brain imaging. Despite the recent progress of PS-OCT in revealing white matter architecture and orientation, quantification of fine-scale fiber tracts in the human brain cortex has been a challenging problem, due to a low birefringence in the gray matter. In this study, we investigated the effect of refractive index matching by 2,2’-thiodiethanol (TDE) immersion on the improvement of PS-OCT measurements in ex vivo human brain tissue. We obtain the cortical fiber orientation maps in the gray matter, which reveals the radial fibers in the gyrus, the U-fibers along the sulcus, as well as distinct layers of fiber axes exhibiting laminar organization. Further analysis shows that index matching reduces the noise in axis orientation measurements by 56% and 39%, in white and gray matter, respectively. Index matching also enables precise measurements of apparent birefringence, which was underestimated in the white matter by 82% but overestimated in the gray matter by 16% prior to TDE immersion. Mathematical simulations show that the improvements are primarily attributed to the reduction in the tissue scattering coefficient, leading to an enhanced signal-to-noise ratio in deeper tissue regions, which could not be achieved by conventional noise reduction methods.
Shift and scale-invariant correlator using a radially stretched phase-only filter (1995)

A radial stretching of the phase only filter depending on the energy angular distribution of the target spectrum is used to perform shift and scale invariant pattern recognition. The complex conjugate of a basic size target Fourier transform and the cumulative energy angular distribution are calculated. Then the radially stretched filter providing the same energy contribution to the correlation peak independent on the target size is prepared and used in a conventional correlator, with spherical-wave illumination. The maximum scale ratio of recognizable objects equals 1:1.5. Computer simulations and experimental results, showing the performance of the filter are presented.
Defining remote medical practice: a consensus (2008)

More than three-quarters of Australia is classified as geographically remote. Remote areas are characterised by geographic isolation, cultural diversity, socioeconomic inequality, resource inequity, Indigenous health inequality, and a full range of extreme climatic conditions. Although several descriptive definitions have been developed for "remote health" and "remote practice", definitions of "remote medical practice" or "remote medicine" have not been previously published. In 2007, a working group of doctors and academics with experience in remote medicine was formed to develop the first advanced specialised remote medicine curriculum for remote doctors undertaking training with the Australian College of Rural and Remote Medicine. The first step was to define remote medical practice. Remote medical practice has eight key features: employment rather than private practice, isolation, use of telehealth, increased clinical acumen, extended practice, cross-cultural setting, multidisciplinary practice, and an emphasis on public health and personal security. From these eight features, we developed the first working definition of remote medical practice in the Australian context. Our definition will assist policymakers, medical colleges, standard setters, and educators to develop programs and resources for the future remote medical workforce.
PPAR-δ agonist affects adipo-chondrogenic differentiation of human mesenchymal stem cells through the expression of PPAR-γ (2020)

PPAR-γ has a considerable anti-inflammatory effect and a strong pro-adipogenic effect, which inhibits the chondrogenic effect. PPAR-γ is related with PPAR-δ and shows a chondrogenic effect at lower concentrations. And clinical HA gels shows various efficacy of chondrogenesis. This study suggested that PPAR-γ and PPAR-δ are key regulatory factors of chondrogenesis.
Supplementary Table 2 from Tumor-Specific Isoform Switch of the Fibroblast Growth Factor Receptor 2 Underlies the Mesenchymal and Malignant Phenotypes of Clear Cell Renal Cell Carcinomas (2023)

&lt;p&gt;XLSX file - 75K, Computational prediction of FGFR2 IIIb/c isoforms in normal kidney and ccRCC&lt;/p&gt;
Gene transcriptional profiles in human lymphoblastoid cells with low and high doses of irradiation (2012)

Objective To compare the gene expression difference between 0.1 and 5 Gy X-ray irradiated cells,and to explore its possible mechanism.Methods A cDNA microarray corresponding to 45033 human genes was used to analyze the transcriptional profiles of normal human lymphoblastoid AHH-1 cells at 4 h after 0.1 or 5 Gy irradiation.The genes with a fold change ≥ 2.0 were identified as the differentially expressed genes.real-lime PCR and Western blot were used to confirm the expression of PERP.Results The microarray assay showed that there were 760 up-regulated genes and 1222 down-regulated genes in the cells at 0.1 Gy,while there were 744 genes down-regulated and 457 genes up-regulated in the cells at 5 Gy.In addition,55 genes were commonly up-regulated and 339 genes commonly down-regulated at 0.1 and 5 Gy.The predominant biological processes of the differential genes responding to low-dose radiation include cell-cell signaling transduction and DNA damage response,and the altered genes after 5 Gy irradiation were related to cell proliferation,differentiation,and apoptosis.Moreover,the expression of PERP gene was down regulated,which was consistent with the data of microarrey assay.Conclusions The quantitative and qualitative differences in the gene expressions may contribute to the diversed biological effects induced by low or high doses of ionizina radiation.

Key words: 
Ionizing radiation; Gene chip; Dosage; GO analysis
Data for: Incorporating whey protein particulates produced with heat and ultrasound treatment into rennet gels and model non-fat cheese systems (2020)

Data for paper entitled "Incorporating whey protein particulates produced with heat and ultrasound treatment into rennet gels and model non-fat cheese systems"
Designing Biological Circuits: Synthetic Biology Within the Operon Model and Beyond (2021)

In 1961, Jacob and Monod proposed the operon model of gene regulation. At the model's core was the modular assembly of regulators, operators, and structural genes. To illustrate the composability of these elements, Jacob and Monod linked phenotypic diversity to the architectures of regulatory circuits. In this review, we examine how the circuit blueprints imagined by Jacob and Monod laid the foundation for the first synthetic gene networks that launched the field of synthetic biology in 2000. We discuss the influences of the operon model and its broader theoretical framework on the first generation of synthetic biological circuits, which were predominantly transcriptional and posttranscriptional circuits. We also describe how recent advances in molecular biology beyond the operon model-namely, programmable DNA- and RNA-binding molecules as well as models of epigenetic and posttranslational regulation-are expanding the synthetic biology toolkit and enabling the design of more complex biological circuits.
Nonlinear Fourier-transform spectroscopy revealing wave-packet dynamics of D+2with multicolor harmonic field (2014)

We report on a series of studies concerning D2 molecules irradiated by high-harmonic pulses generated from intense femtosecond laser pulses. The kinetic energy (KE) spectrum of dissociated D+ ion fragments with a scanning delay between two replica harmonic pulses exhibits specific characteristics that are completely different from a conventional interferometric autocorrelation signal. We have successfully determined and separated three distinct ionization/dissociation processes by analyzing KE-resolved interferometric fringes by Fourier transform. We call this method for analyzing the KE spectrum of ion fragments "nonlinear Fourier-transform spectroscopy (NFTS)." NFTS provides us molecular information in stationary states because it is intrinsically a frequency domain analysis. Nevertheless, we have resolved the real-time evolution of the vibrational wavepacket of D+ ions with a period of 22 fs by shortening the pulse duration of the fundamental laser pulse to 12 fs and extending the scanning delay range of two harmonic pulses to 150 fs. The probing process of the wavepacket can be described as a model with one-photon absorption of a multicolor harmonic field. We discuss a possible method of reconstructing the phase and magnitude of the wavepacket from the measured delay-KE spectrogram.
Targeted Dehydration As a Route to Site-Selective Atomic Layer Deposition at TiO2 Defects (2022)

Crystallographic perfection in epitaxial thin film heterostructures can eliminate interface defects that dilute unique properties and reduce device performance. However, the requirement for epitaxial perfection greatly limits the selection of material candidates and deposition processes. Using selective interface reactions (SIRs), an atomic layer deposition (ALD)-based technique, we target transformation of undesirable defect sites at imperfect surfaces. Defects on the TiO 2 surface affect the electronic properties, interfaces, and performance of optoelectronic devices that leverage TiO 2 interfaces. We present first principles calculations to predict the difference in hydration/hydroxylation of pristine TiO 2 terraces and minority atomic configurations (i.e. “defects”) including step edges and oxygen vacancies. We investigate hydroxylation differences through temperature dependent scanning tunneling microscopy (STM), and ultimately exploit these differences to selectively react ALD precursors at surface defect sites.
Spectral Analysis of a Finite-Difference Frequency-Domain Solver Based on the Quasi-TEM Approximation (2019)

A finite-difference frequency-domain (FDFD) solver, based on the quasi-TEM approximation, is analyzed to determine the validity of the quasi-TEM approximation as a function of frequency. A full-wave finite-difference time-domain characteristics in a transmission line structure (stripline) at frequencies in the vicinity of the lowest waveguide mode cutoff frequency. Results show that the transverse fields in the stripline are near constant over a wide range of frequencies, even at frequencies above the dominant waveguide mode cutoff frequency.