gebhart/patrepeval huggingface dataset:
Insights into the molecular basis of thermal stability from the analysis of ion‐pair networks in the Glutamate Dehydrogenase family (1998)

The recent structure determination of glutamate dehydrogenase from the hyperthermophile Pyrococcus furiosus and the comparison of this structure with its counterparts from the mesophiles Clostridium symbiosum and Escherichia coli has highlighted the formation of extended networks of ion-pairs as a possible explanation for the superior thermal stability of the hyperthermostable enzyme. In the light of this, we have carried out a homology-based modelling study using sequences of a range of glutamate dehydrogenases drawn from species which span a wide spectrum of optimal growth temperatures. We have attempted to analyse the extent of the formation of ion-pair networks in these different enzymes and tried to correlate this with the observed thermal stability. The results of this analysis indicate that the ion-pair networks become more fragmented as the temperature stability of the enzyme decreases and are consistent with a role for the involvement of such networks in the adaptation of enzymes to extreme temperatures.
Heuristics for the Whitehead Minimization Problem (2005)

In this paper we discuss several heuristic strategies which allow one to solve the Whitehead minimization problem much faster (on most inputs) than the classical Whitehead algorithm. The mere fact that these strategies work in practice leads to several interesting mathematical conjectures. In particular, we conjecture that the length of most nonminimal elements in a free group can be reduced by a Nielsen automorphism which can be identified by inspecting the structure of the corresponding Whitehead graph.
MACHINABLE Dy-CONTAINING &beta;-Ca<SUB>3</SUB>(PO<SUB>4</SUB>)<SUB>2</SUB> CERAMICS PREPARED BY HEATING THE MIXTURES OF HYDROXY-APATITE AND DyPO<SUB>4</SUB> (2001)

The Dy-containing β-Ca3(PO4)2 ceramics obtained by heating the mixtures of hydroxy-apatite (Ca10(PO4)6(OH)2) and tetragonal DyPO4 with mixing mole ratio ((Ca+Dy)/P)=1.52-1.49 at 1300°C, and with mole ratio=1.57-1.49 at 1350-1400°C for 3h in air, were found to be machinable; they can be drilled and cut easily using a conventional inexpensive metallic Fe-Co-W (mostly Fe) drills or gravers. The relative density was larger than 95% at 1350-1400°C for the (Ca+Dy)/P mole ratio=1.57-1.49. The bending strength, Vickers' hardness and thermal expansion coefficient of the machinable Dy-containing β-TCP ((Ca+Dy)/P ratio=1.57-1.49) ceramics sintered at 1350°C for 3h were in the range 20-50 MPa, 2.8-3.9 GPa and 11~12x10-6/°C (~1000°C), respectively.
Dispersion management optimization for 160Gb/s transmission systems using RZ or CS-RZ modulation formats (2002)

Through numerical simulations, a full dispersion management optimisation of 160Gbit/s transmissions over 3×100km of standard fibre is caried out using RZ or CS-RZ modulation formats. While dispersion management has been optimised, a performance comparison of these formats is also computed.
A 2-Micron Power Oscillator for High Pulse Energy Doppler Lidar Transmitter (1995)

Two micrometer solid state lasers(1-5) have received considerable attention for detection of wind velocities as well as for remote sensing of carbon dioxide and water vapor in the atmosphere. High-power Q-switched holmium lasers are also useful for generating tunable mid-infrared radiation for optical remote sensing and/or infrared counter measure systems.
New amorphous-silicon electrically programmable nonvolatile switching device (1982)

The paper reports preliminary data on the characteristics of a new electronic switching device based on amorphous silicon structures. The device is polar, and is switched from OFF to ON (WRITE) or ON to OFF (ERASE) by voltages opposite signs; the threshold voltage for the WRITE operation is 4 –8 V, depending on the device, and for ERASE it is ̃ 1 V. The OFF and ON resistances are typically l MΩ, and in the range 50–300Ω, respectively. Experimental devices have been switched through 105 WRITE and ERASE cycles, and the prospects are that this could be considerably increased. Particularly notable features of the new memory device are its extremely fast transition times (100 ns or less for both the WRITE or ERASE operations) and the very low energy involved in the switching transition (&lt;10−6 J). Present results indicate that the threshold voltages are only slightly dependent on temperature.
Click Chemistry in Crystals (2012)

Key words topochemical reaction - 1,3-dipolar cycloaddition - green chemistry
ChemInform Abstract: Ritter Reaction of Terpenoids. Part 4. Remarkable Tendency to Produce 3‐Aza‐bicyclo(3.3.1)non‐2‐ene Systems from Mono and Sesquiterpenes. (1996)

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 Learning Progression for Geometric Transformations (2019)

In this paper, a learning progression for geometric transformations is developed based on research that demonstrates the importance of viewing transformations as functions of the plane. The 5 levels of the progression reflect a student's evolving understanding of transformations as functions and their evolving understanding of the domain of these transformation as functions. The learning progression developed here is designed to be in alignment with the Common Core State Standards in Mathematics (CCSSM), in that a student who is placed at a particular level in the learning progression would have mastered the Common Core standards at the corresponding grade level. The description of the learning progression also includes sample tasks at each level that are intended to target that level of the progression.
A prior image model with mixed continuity constraints for Bayesian PET image reconstruction (2003)

Describes a novel image prior model with mixed continuity constraints for Bayesian PET image reconstruction. If an image can be partitioned into partial-volume and various pure regions, the author models the image as a piece-wise smooth function through a Gibbs prior. Within each pure or partial-volume region, the image intensity is governed by a thin-plate energy function. Both first- and second-order edge detection techniques are applied to estimate region boundaries. Instead of using the binary processes representing region boundaries, a controlled-continuity approach is adopted to influence boundary formation. The rationale is that while the first-order edge detection captures the jumps between two pure regions, the second-order one locates the crease connecting a pure region to partial-volume region. This model is referred as a modified weak-plate model with controlled continuity. Results indicate that a superior improvement of image quality using this approach can be obtained.
The Generation of Narrative Interpretations in Laboratory Medicine (2001)

The logistical details for organizing effective interpretive rounds in a laboratory medicine subspecialty must be carefully established so that expert opinions are provided in a timely fashion in a patient-specific report, rather than as a collection of fixed comments associated with a particular laboratory result generated by a computer This report describes the test batteries for interpretations, the billing for interpretations, clinical examples of interpretations, and interpretations for which billing is not typically performed in several clinical or laboratory areas in our institution. These include coagulation disorders, hemoglobin and anemia evaluations, autoimmune disorders, serum protein analysis, toxicology, molecular diagnostics, and transfusion medicine. The information in this report should provide sufficient detail to allow development of interpretive services with successful billing for the areas in laboratory medicine described.
A Low Cost Flexible Digital Twin Platform for Spacecraft Lithium-ion Battery Pack Degradation Assessment (2019)

Lithium-ion battery is widely utilized in space applications with its significant performance advantages. The safety and reliability of lithium-ion battery are critical for spacecraft. It is essential to assess the performance degradation and estimate the state of lithium-ion battery. Meanwhile, as a brand new terminology of Cyber-physical Systems (CPS), the Digital Twin is used in the smart manufacturing and industry due to its advantages on real-time, stability and reliability. Thus, the Digital Twin can be used in lithium-ion battery pack to ensure the real-time, stability and reliability. So far, the Digital Twin has not been used for lithium-ion battery application about management and assessment. As a result, a digital twin platform, which is developed based on low-cost modules and software, is built to assess spacecraft lithium-ion battery pack degradation for the first time in this paper. It is also flexible because it can load different degradation algorithms and be suitable for different types of batteries. Firstly, the overview of the digital twin is introduced. The Visual Software and the Assessment Unit are described in detail. Secondly, the platform test and evaluation is achieved. We test and verify the basic function and core function of the digital twin platform using the real test data of spacecraft lithium-ion battery pack. Testing results prove that the Digital Twin platform can realize the basic function of digital and the degradation assessment for spacecraft lithium-ion battery pack.
Electronic Structure and Chemical Nature of Oxygen Dopant States in Carbon Nanotubes (2014)

We performed low temperature photoluminescence (PL) studies on individual oxygen-doped single-walled carbon nanotubes (SWCNTs) and correlated our observations to electronic structure simulations. Our experiment reveals multiple sharp asymmetric emission peaks at energies 50-300 meV red-shifted from that of the E11 bright exciton peak. Our simulation suggests an association of these peaks with deep trap states tied to different specific chemical adducts. In addition, oxygen doping is also observed to split the E11 exciton into two or more states with an energy splitting <40 meV. We attribute these states to dark states that are brightened through defect-induced symmetry breaking. While the wave functions of these brightened states are delocalized, those of the deep-trap states are strongly localized and pinned to the dopants. These findings are consistent with our experimental observation of asymmetric broadening of the deep trap emission peaks, which can result from interaction between pinned excitons and one-dimensional phonons. Exciton pinning also increases the sensitivity of the deep traps to the local dielectric environment, leading to a large inhomogeneous broadening. Observations of multiple spectral features on single nanotubes indicate the possibility of different chemical adducts coexisting on a given nanotube.
A NOVEL DE-INTERLACE BASED ON SPATIO-TEMPORAL WEIGHT ADAPTIVE AND EDGE-DIRECTED INTERPOLATION (2006)

De-interlace is an image format conversion from interlaced image to progressive one. In this paper, a de-interlacing algorithm based on spatio-temporal weight and edge direction is presented. It consists of motion detection, low-angle edge detection, spatio-temporal weight calculation, and adaptive interpolation. Same-parity fields motion estimation is adopted to improve the accuracy of motion estimation. And edge direction adaptive interpolation is proposed to sharpen edges and remove the saw-tooth artifacts in which the minimum 6deg edge can be detected. Experimental results show that the proposed method achieves high image quality and low hardware complexity
Solid–Liquid Phase Boundaries in the System: Glycine–NaOH–NaHCO3–H2O (2022)

In this work, the solid–liquid equilibrium (SLE) of the systems glycine (Gly)–H2O, Gly–NaOH–H2O, Gly–NaHCO3–H2O, and Gly–NaOH–NaHCO3–H2O was determined using a freezing point depression (FPD) setup. A total of 131 new data points are listed in the concentration range 0 < b (sodium glycinate (SG)) < 25 mol SG/kg water. The system Gly–NaOH–H2O with five different mole ratios (nNaOH:nGly) 1:1, 1:2, 1:5, 2:1, and 5:1 and the CO2-loaded system Gly–NaOH–NaHCO3–H2O were analyzed in a loading range of 0.1–1 mol CO2 per mol SG. Eutectic points and hydrate formations were identified in the systems Gly–H2O, Gly–NaOH–H2O, and Gly–NaOH–NaHCO3–H2O. The solubility of SG increased linearly with higher concentrations for systems with an excess of NaOH. The solubility of SG decreased significantly with an excess addition of NaOH and glycine. The same trend was observed in the CO2-loaded system. The new data create a better understanding of phase equilibria in this system. This understanding is useful for the thermodynamic modeling of the system, which can potentially be used for CO2 capture. The data give a clear representation of the degree of safe operation in terms of managing a plant without solid formation.
Flux 2 Editorial (2016)

DOAJ is a unique and extensive index of diverse open access journals from around the world, driven by a growing community, committed to ensuring quality content is freely available online for everyone.
MYB30 Orchestrates Systemic Reactive Oxygen Signaling and Plant Acclimation (2020)

Systemic acquired acclimation (SAA) is a key biological process essential for plant survival under conditions of abiotic stress. SAA was recently shown to be controlled by a rapid systemic signaling mechanism termed the reactive oxygen species (ROS) wave in Arabidopsis (<i>Arabidopsis thaliana</i>). MYB30 is a key transcriptional regulator mediating many different biological processes. MYB30 was found to act downstream of the ROS wave in systemic tissues of Arabidopsis in response to local high light (HL) stress treatment. However, the function of MYB30 in systemic signaling and SAA is unknown. To determine the relationship among MYB30, the ROS wave, and systemic acclimation in Arabidopsis, the SAA response to HL stress of <i>myb30</i> mutants and wild-type plants was determined. Although <i>myb30</i> plants were found to display enhanced rates of ROS wave propagation and their local tissues acclimated to the HL stress, they were deficient in SAA to HL stress. Compared to wild type, the systemic transcriptomic response of <i>myb30</i> plants was also deficient, lacking in the expression of over 3,500 transcripts. A putative set of 150 core transcripts directly associated with MYB30 function during HL stress was determined. Our study identifies MYB30 as a key regulator that links systemic ROS signaling with systemic transcriptomic responses, SAA, and plant acclimation to HL stress. In addition, it demonstrates that plant acclimation and systemic ROS signaling are interlinked and that the lack of systemic acclimation drives systemic ROS signaling to occur at faster rates, suggesting a feedback mechanism (potentially involving MYB30) between these two processes.
High Quality Bio-Oil Obtained from Catalyzed Pyrolysis of Olive Mill Solid Wastes in a Bi-Functional Reactor (2021)

Olive Mill Solid Wastes (OMSW) released in nature without any treatment is a major environmental problem in the Mediterranean region. In this work, the catalyzed pyrolysis of OMSW has been investigated. A catalyst based on SBA-15 mesoporous silica doped with chromium ferrite nanoparticles was prepared by the double solvent technique (DS). The prepared catalyst was characterized by scanning electron microscopy (SEM), Wide and Small Angle X-ray Scattering (WAXS, SAXS), Energy Dispersive X-ray (EDX) and FT-IR spectroscopies. Reverse spinel chromium ferrite nanoparticles were located inside the SBA-15 pores as confirmed by SEM images. The obtained catalyst was tested for pyrolysis reactions of OMSW. Several parameters were studied to optimize the conditions of the pyrolysis reaction in order to increase the bio-oil conversion yield. The GC-MS results demonstrated that the quality of the obtained bio-oil was improved by decreasing the quantity of phenolic and oxygenated components as well as the size of the obtained molecules. The produced bio-oil from pyrolysis of OMSW is identical to that obtained from the pyrolysis of commercial cellulose under the same conditions. A 37% conversion yield of bio-oil was obtained for the best conditions.
Effect of respiration on cardiac filling at rest and during exercise in Fontan patients: A clinical and computational modeling study (2015)

Due to the absence of a sub-pulmonary ventricle, the Fontan circulation is sensitive to respiration-induced changes in intrathoracic pressure. However, the importance of a ‘respiratory pump’ in creating forward flow remains controversial. We aimed at evaluating the effect of respiration on ventricular filling during exercise using clinical data and computational modeling predictions. Ten Fontan patients (6 male, 20 ± 4 years) underwent ungated cardiac magnetic resonance (CMR) imaging at rest and during supine bicycle exercise to evaluate systemic ventricular volumes (end-diastolic volume index (EDVi), end-systolic volume index (ESVi) and stroke volume index (SVi)) during normal respiration and a Valsalva maneuver. Respiratory-dependent SV was calculated. Clinical results were compared to predictions made by a closed-loop lumped-parameter (LPN) computational model of Fontan circulation. Inspiration resulted in increased EDVi (98 ± 16 to 103 ± 15 mL; P = 0.001), SVi (55 ± 9 to 59 ± 9 mL; P = 0.001) and cardiac index (3.9 ± 0.7 to 4.2 ± 0.8 L/min; P = 0.002), whereas ESVi (P = 0.096) remained unchanged. The effect of inspiration on EDVi (mean effect + 6 ± 1 mL; P < 0.0001) and SVi (+ 4 ± 1 mL; P < 0.0001) was maintained during exercise. Respiratory-dependent SVi tended to increase during exercise (3 ± 2% to 5 ± 3%; P = 0.084). Valsalva resulted in decreased EDVi (P = 0.001), ESVi (P = 0.003) and SVi (P = 0.005). Computational modeling indicated higher EDV and SV at end-inspiration and expiration, showing a phased time delay between peak caval vein flow and peak SV. In Fontan patients, inspiration resulted in increased ventricular filling at rest and during exercise. Results were confirmed using a computational model indicating a phased time delay between peak SV and peak caval vein flow.
Through-focus EUV multilayer defect repair with nanomachining (2013)

Defects within the multilayer mirrors of EUV photomasks have been a leading challenge for EUV lithography for quite some time. By creating non-planar surfaces, they distort both the amplitude and phase of reflected light. Amplitude errors generally create a CD error on wafer, whereas phase errors tend to cause asymmetric printing through focus. Since defect-free mask blanks are not expected to be available for initial high volume EUV manufacturing, defect mitigation, compensation, and repair strategies are essential. This paper describes a technique to repair both the amplitude and phase effects of multilayer defects. For a bump defect, the phase effect (i.e. tilted Bossung curve behavior) is corrected by removing multilayer material in the vicinity of the defect. This creates a phase effect opposite to that of the defect and the two effects cancel. The amplitude error (i.e. CD error) caused by both the defect and by the phase repair is then corrected by modifying the surrounding absorber pattern. The repairs in this paper are performed by nanomachining with an AFM repair tool. The concept is validated by a combination of simulation and experimental studies with data from the Actinic Inspection Tool (AIT) at the Lawrence Berkeley National Laboratories, the EUV Alpha Demo Tool (ADT) in Albany, New York, and an AFM repair tool. The process for a complete multilayer repair is described using an example native defect repair. Encouraging results indicate that nanomachining is capable of creating the complex nano-scale three dimensional topographies required for the repair. Repair strategies for both bump and pit defects are addressed. Multiple simulation studies are used to understand the requirements for such a repair and what type of repairs may be possible.
Cell Death and Synaptic Reorganizations Produced by Seizures (2001)

The events that follow epilepsy seizures are not restricted to the immediate period. A series of long-term alterations occurs, including synaptic rearrangements, which have an impact on the brain circuit's mode of operation. With models of temporal lobe epilepsy, seizures have been shown to generate long-lasting changes in synaptic efficacy (epileptic long-term potentiation) because of removal of the magnesium block, activation of N-methyl-D-aspartate receptors, and an increase in intracellular calcium. This novel form of synaptic plasticity provides a link between memory effects and pathologic processes. Additionally, high-affinity kainate autoradiography, Timm stain, intraventricular injection of kainic acid, and 3D reconstruction experiments clearly indicate that even brief seizures produce changes in synaptic efficacy, followed 2-3 weeks later by aberrant neosynapse formation. Several key steps have been identified in the cascade leading from transient hyperactivity episodes to long-lasting, quasi-permanent modification of the neuronal circuit organization. These include the activation of immediate-early genes, activation of growth factor genes within hours, alterations in glutamate receptors, glial hypertrophy, and cytoskeletal protein changes. The cascade is activated by the increase in intracellular calcium and leads to axonal growth and neosynapse formation, which in turn participates in the etiology of the syndrome by reducing the threshold for further seizures. In summary, study data imply that the mature epileptic circuit has unique features in comparison with those present before a seizure episode, including new receptors, ionic channels, and other proteins. It is therefore essential to develop novel strategies based on the unique mode of operation of the mature epileptic circuit, rather than on acute models of epilepsy.
Pointwise a Posteriori Error Analysis for an Adaptive Penalty Finite Element Method for the Obstacle Problem (2001)

Abstract Finite element approximations based on a penalty formulation of the elliptic obstacle problem are analyzed in the maximum norm. A posteriori error estimates, which involve a residual of the approximation and a spatially variable penalty parameter, are derived in the cases of both smooth and rough obstacles. An adaptive algorithm is suggested and implemented in one dimension.
DAMP production by human islets under low oxygen and nutrients in the presence or absence of an immunoisolating-capsule and necrostatin-1 (2015)

In between the period of transplantation and revascularization, pancreatic islets are exposed to low-oxygen and low-nutrient conditions. In the present study we mimicked those conditions in vitro to study the involvement of different cell death processes, release of danger-associated molecular patterns (DAMP), and associated in vitro immune activation. Under low-oxygen and low-nutrient conditions, apoptosis, autophagy and necroptosis occur in human islets. Necroptosis is responsible for DAMP-release such as dsDNA, uric acid, and HMGB1. The sensors of the innate immune system able to recognize these DAMPs are mainly TLR, NOD receptors, and C-type lectins. By using cell-lines with a non-functional adaptor molecule MyD88, we were able to show that the islet-derived DAMPs signal mainly via TLR. Immunoisolation in immunoprotective membranes reduced DAMP release and immune activation via retention of the relative large DAMPs in the capsules. Another effective strategy was suppressing necroptosis using the inhibitor nec-1. Although the effect on cell-survival was minor, nec-1 was able to reduce the release of HMGB1 and its associated immune activation. Our data demonstrate that in the immediate post-transplant period islets release DAMPs that in vitro enhance responses of innate immune cells. DAMP release can be reduced in vitro by immunoisolation or intervention with nec-1.