gebhart/patrepeval huggingface dataset:
Probing Variable Axial Ligation in Nickel Superoxide Dismutase Utilizing Metallopeptide-Based Models:  Insight into the Superoxide Disproportionation Mechanism (2007)

Nickel superoxide dismutase (NiSOD) is a bacterial metalloenzyme that possesses a mononuclear Ni-center and catalyzes the disproportionation of O2*- by cycling between NiII and NiIII oxidation states. Herein we present evidence from several SOD active metallopeptide maquettes ([Ni(SODM2H(1)X)]; SODM2H(1)X = H2N-XCDLPCG-COOH; X = H, D, or A) that the Ni-center of NiSOD most likely remains five-coordinate during SOD catalysis using thin-film voltammetry. N3- and CN- titration studies suggest that O2*- disproportionation by [Ni(SODM2H(1)X)] proceeds via an outersphere mechanism. Computationally derived values for the nuclear reorganization energy of the [NiII(SODM2)]/[NiIII(SODM2)] self-exchange reaction combined with the experimentally determined value for ko ( approximately 450 s-1) suggest that axial ligation enhances the O2*- disproportionation reaction in [Ni(SODM2)] (and NiSOD by analogy) by optimizing the NiII/NiIII redox couple such that it is close to the midpoint of the O2*- reduction and oxidation couples.
Transporting information and energy simultaneously (2008)

The fundamental tradeoff between the rates at which energy and reliable information can be transmitted over a single noisy line is studied. Engineering inspiration for this problem is provided by powerline communication, RFID systems, and covert packet timing systems as well as communication systems that scavenge received energy. A capacity-energy function is defined and a coding theorem is given. The capacity-energy function is a non-increasing concave cap function. Capacity-energy functions for several channels are computed.
Hydrogen Transport in a Model 9979 Shipping Package with Inner Convenience Cans (2020)

Radiolytic hydrogen production and accumulation inside containment packages is a concern at any facility responsible for their packaging, storage, transportation, and/or disposal. When hydrogen gas accumulates to concentrations above the Lower Flammability Limit (LFL) which is 4% or 40,000 ppm in air, the possibility of a deflagration or explosion increases. This concern persists over the course of the package lifetime which is unlimited when disposed of by burial or in permanent repositories. Here, we report on a numerical model used to predict the concentration of hydrogen within each layer of a Model 9979 package containing a convenience can assembly. Simulations show the hydrogen concentration to always be highest in the inner convenience can containing the radioactive source. When the radioactive source is within the Los Alamos National Laboratory (LANL) Packaging Limits, the hydrogen concentration is shown to remain well below the LFL at all times including packaging, storage, transportation, and disposal. A hydrogen transport model is presented for a Model 9979 package system containing a nested arrangement of convenience cans, which are tin oxide coated steel cans of various sizes with a slip-lid assembly. The inner convenience can contains the radioactive source material along with an unknown quantity of incidental water acquired from humid air or processing. While visible organic materials such as paper and plastics were purposely excluded from the inner can, it is not possible to claim the wastes are entirely organic free. The inner convenience can is tape sealed and placed into a plastic bag which is horsetail closed (i.e., twisted and taped). The bagged can is placed into an outer convenience can that is also tape sealed. The can assembly is then placed into the 30 gallon drum and subsequently placed inside the 55 gallon drum in the 9979 package. Here we assume hydrogen gas is produced in the inner convenience can from alpha radiolysis of water at a rate dependent on the quantity of uranium isotopes and water present. The hydrogen transport model was used to calculate hydrogen accumulations within the package’s five layers at different times and conditions. These simulations serve two purposes; (i) to build confidence in the model by comparing predicted values to measured values, and (ii) to check the steady state hydrogen concentrations that are approached at long times in the package’s lifetime. Model simulations were compared to gas samples taken from the 30 gallon drum after storage at LANL’s Chemistry and Metallurgy Research (CMR) building for around 500 days. Hydrogen concentration calculations over much longer periods (i.e., more than 270 years) included extreme storage durations, transportation at extreme cold temperatures, and disposal of packages assuming different average temperatures.
Clioquinol promotes the degradation of metal-dependent amyloid-β (Aβ) oligomers to restore endocytosis and ameliorate Aβ toxicity (2014)

Alzheimer's disease (AD) is a common, progressive neurodegenerative disorder without effective disease-modifying therapies. The accumulation of amyloid-β peptide (Aβ) is associated with AD. However, identifying new compounds that antagonize the underlying cellular pathologies caused by Aβ has been hindered by a lack of cellular models amenable to high-throughput chemical screening. To address this gap, we use a robust and scalable yeast model of Aβ toxicity where the Aβ peptide transits through the secretory and endocytic compartments as it does in neurons. The pathogenic Aβ 1-42 peptide forms more oligomers and is more toxic than Aβ 1-40 and genome-wide genetic screens identified genes that are known risk factors for AD. Here, we report an unbiased screen of ∼140,000 compounds for rescue of Aβ toxicity. Of ∼30 hits, several were 8-hydroxyquinolines (8-OHQs). Clioquinol (CQ), an 8-OHQ previously reported to reduce Aβ burden, restore metal homeostasis, and improve cognition in mouse AD models, was also effective and rescued the toxicity of Aβ secreted from glutamatergic neurons in Caenorhabditis elegans. In yeast, CQ dramatically reduced Aβ peptide levels in a copper-dependent manner by increasing degradation, ultimately restoring endocytic function. This mirrored its effects on copper-dependent oligomer formation in vitro, which was also reversed by CQ. This unbiased screen indicates that copper-dependent Aβ oligomer formation contributes to Aβ toxicity within the secretory/endosomal pathways where it can be targeted with selective metal binding compounds. Establishing the ability of the Aβ yeast model to identify disease-relevant compounds supports its further exploitation as a validated early discovery platform.
Zinc In DNA Replication And Transcription (1987)

The objective of this review is to provide an overview of intermittent fasting regimens, summarize the evidence on the health benefits of intermittent fasting, and discuss physiological mechanisms by which intermittent fasting might lead to improved ...Read More
Evaluation of DNA extraction and handling procedures for PCR-based copepod feeding studies (2009)

Molecular methods are becoming increasingly common for taxonomic and ecological studies of marine and freshwater plankton. Recently, nucleic acids have been used as target molecules for identification and quantification of prey species in studies of trophic interactions. A critical step in the quantification of mesozooplankton feeding by molecular analysis is the isolation of microalgal DNA from predator guts and in the food environment. It is essential that total genomic DNA extraction provides maximum quantitative yield suitable for downstream analysis. In this study, we compared the efficacy and experimental variability of eight different protocols for total genomic DNA extraction from free-living microalgae and microalgae within the gut of copepods. We also developed and evaluated different sampling procedures for copepods prior to genomic extraction. The optimal protocol was evaluated using real time quantitative polymerase chain reaction (qPCR) and the integrity of the genomic DNA was determined by amplifying PCR targets of increasing size. Considerable variability was observed between purification protocols. Qiagen DNeasy® Blood & Tissue kit was the most efficient of the tested methods for genomic extraction from both free-living microalgae and microalgae inside copepod guts. Furthermore, the appropriate handling of predator copepods prior to genomic extraction was essential for quantitative gut content estimates.
Lithium‐Pretreated Hard Carbon as High‐Performance Sodium‐Ion Battery Anodes (2018)

Abstract Hard carbon (HC) is the state‐of‐the‐art anode material for sodium‐ion batteries (SIBs). However, its performance has been plagued by the limited initial Coulombic efficiency (ICE) and mediocre rate performance. Here, experimental and theoretical studies are combined to demonstrate the application of lithium‐pretreated HC (LPHC) as high‐performance anode materials for SIBs by manipulating the solid electrolyte interphase in tetraglyme (TEGDME)‐based electrolyte. The LPHC in TEGDME can 1) deliver &gt; 92% ICE and ≈220 mAh g −1 specific capacity, twice of the capacity (≈100 mAh g −1 ) in carbonate electrolyte; 2) achieve &gt; 85% capacity retention over 1000 cycles at 1000 mA g −1 current density (4 C rate, 1 C = 250 mA g −1 ) with a specific capacity of ≈150 mAh g −1 , ≈15 times of the capacity (10 mAh g −1 ) in carbonate. The full cell of Na 3 V 2 (PO 4 ) 3 ‐LPHC in TEGDME demonstrated close to theoretical specific capacity of ≈98 mAh g −1 based on Na 3 V 2 (PO 4 ) 3 cathode, ≈2.5 times of the value (≈40 mAh g −1 ) with nontreated HC. This work provides new perception on the anode development for SIBs.
Low-Temperature Sintering of In-Plane Self-Assembled ZnO Nanorods for Solution-Processed High-Performance Thin Film Transistors (2007)

ZnO is an attractive active semiconducting material for thin-film transistor (TFT) applications due to its high band gap, high mobility, ease of forming Ohmic contacts, and low toxicity. Here we present a process for solution fabrication of ZnO TFTs based on a simple, double-layer spin-coating process during which a dense layer of in-plane zinc oxide nanorods is deposited first, followed by coating of a chemical precursor solution and low-temperature annealing. First, a lower ZnO nanorod concentration can lead to the self-assembly of nanorods along the in-plane direction to form a relatively dense semiconductor layer. Then the chemical precursor solution sinters the nanorods and improves the contact between them. The n-channel TFTs exhibit high ON/OFF ratio of 105−106, mobilities of ∼1.2 cm2 V-1 s-1 and low threshold voltages of about −4 V with low hysteresis. We show that the quality of the semiconductor film and the minimum annealing temperature depends sensitively on the thickness and composition of the two layers.
A nine‐level T‐type inverter (9L‐TTI) with voltage boost capability (2023)

Abstract This paper introduces a 9L T‐type boost inverter (9L‐TTI) based multilevel topology, which generates a nine‐level output voltage in the boost mode. This topology uses 12 switching elements alongside less voltage stress and one switched capacitor unit. This is the significant advantage of the mentioned topology. Following the discussion of the advantages of the provided design, a comparative study is conducted. This results in a reduction in device counts, cost‐effectiveness, and voltage stress on the devices. For switching scheme, fundamental switching frequency‐based modulation is incorporated by having nearest level control (NLC) technique. For proper validation of this work, it is also demonstrated through test results. Here the results are demonstrated at different load conditions, which include resistive and inductive loads. Further, it is demonstrated at different modulation indices and total harmonic distortion (THD) of converter voltage and current for RL‐load, is validated from the power quality improvement point.
Single-camera polarization-sensitive spectral-domain OCT by spatial frequency encoding (2010)

We present a polarization-sensitive spectral-domain optical-coherence-tomography system that is capable of retrieving, with a single camera, both retardation and optical axis orientation. The method is based on a differentiation between orthogonal polarization channels through spatial modulation introduced by an electro-optic modulator. Proof-of-principle measurements using a wave plate as a sample are provided, and results of the method for in vivo imaging of the birefringent structures within the human nail fold are presented. Furthermore, we demonstrate the capability of such systems to perform ultra-high-speed polarization-sensitive imaging at 100.000 A-scans/s.
The Signaling Pathways Project: an integrated ‘omics knowledgebase for mammalian cellular signaling pathways (2018)

Abstract Integrated mining of public transcriptomic and ChIP-Seq datasets has the potential to illuminate facets of mammalian cellular signaling pathways not yet explored in the research literature. Here, we designed a web knowledgebase, the Signaling Pathways Project (SPP), which incorporates stable community classifications of the four major categories of signaling pathway node (receptors, enzymes, transcription factors and co-nodes) and their cognate bioactive small molecules (BSMs). We then mapped over 10,000 public transcriptomic or cistromic experiments to their relevant signaling pathway node, BSM or biosample of study. To provide for prediction of pathway node-target transcriptional regulatory relationships, we generated consensus ‘omics signatures, or consensomes, based on measures of significant differential expression of genomic targets across all underlying transcriptomic experiments. To expose the SPP knowledgebase to researchers, a web browser interface accommodates a variety of routine data mining strategies. Consensomes were validated using alignment with literature-based knowledge, gene target-level integration of transcriptomic and ChIP-Seq data points, and in bench experiments that confirmed previously uncharacterized node-gene target regulatory relationships. SPP is freely accessible at https://beta.signalingpathways.org .
G1000806 Anti-Vibration Measuers by Operational Transfer Path Analysis Method (2015)

We carried out operational transfer path analysis using addisional mass for a structure subjected to floor vibration to identify a transfer path from the floor to an evaluation point via a support. The contribution of transfer path between the evaluation point and three supports was respectively investigated and the support with largest contribution was identified. We could reduce peek amplitude of evaluation point by anti-vibrational measure where a spring constant of the identified support was made small. Effectiveness of the operational transfer path analysis using additional mass was demonstrated.
Aquatic Diatoms‐Inspired Universal Adhesive Coacervates Triggered by Water (2023)

Adhesives with strong underwater adhesion performance are urgently needed in diverse areas. However, designing adhesives with long-term stability to diverse materials underwater in a facile way is challenging. Here, inspired by aquatic diatoms, a series of novel biomimetic universal adhesives is reported that shows tunable performance with robust and long-lasting stable underwater adhesion to various substrates, including wet biological tissues. The versatile and robust wet-contact adhesives are pre-polymerized by N-[tris(hydroxymethyl)methyl]acrylamide, n-butyl acrylate, and methylacrylic acid in dimethyl sulfoxide and spontaneously coacervated in water triggered by solvent exchange. The synergistic interaction between hydrogen bonding and hydrophobic interaction allows the hydrogels with instant and strong adhesion to various substrate surfaces. The slowly formed covalent bonds enhance cohesion and adhesion strength in hours. The spatial and timescale-dependent adhesion mechanism endows the adhesives with strong and long-lasting stable underwater adhesion to be coupled with fault-tolerant convenient surgical operations.
Immunization with live attenuated simian immunodeficiency virus induces strong type 1 T helper responses and β-chemokine production (1999)

Immunization with live attenuated simian immunodeficiency virus (SIV) strains has proved to be one of the most effective strategies to induce protective immunity in the SIV/macaque model. To better understand the role that CD4(+) T helper responses may play in mediating protection in this model, we characterized SIV-specific proliferative and cytokine responses in macaques immunized with live attenuated SIV strains. Macaques chronically infected with live attenuated SIV had strong proliferative responses to SIV proteins, with stimulation indices of up to 74. The magnitude of the proliferative response to SIV Gag varied inversely with the degree of attenuation; Gag-specific but not envelope-specific responses were lower in animals infected with more highly attenuated SIV strains. SIV-specific stimulation of lymphocytes from vaccinated macaques resulted in secretion of interferon-gamma, IL-2, regulated-upon-activation, normal T cells expressed and secreted (RANTES), macrophage inflammatory protein (MIP)-1alpha, and MIP-1beta but not IL-4 or IL-10. Intracellular flow cytometric analysis documented that, in macaques vaccinated with SIVmac239Deltanef, up to 2% of all CD4(+)T cells were specific for SIV p55. The ability of live attenuated SIV to induce a strong, sustained type 1 T helper response may play a role in the success of this vaccination approach to generate protection against challenge with wild-type SIV.
Inhibitory Effects of Hypoxia on Metabolic Switch and Osteogenic Differentiation of Human Mesenchymal Stem Cells (2013)

We previously demonstrated that metabolic switch and mitochondrial activation are required for osteogenic differentiation of human mesenchymal stem cells (hMSCs). However, stem cells in niches or transplanted into injured tissues constantly encounter hypoxic stress that hinders aerobic metabolism. Therefore, we investigated the effects of oxygen tension (1% vs. 21%) on metabolism and osteogenic differentiation of hMSCs. We found that hypoxia impaired osteogenic differentiation as indicated by attenuation of alkaline phosphatase activity and expression of osteogenic markers core binding factor a-1 and osteopontin. In addition, differentiation-induced mitochondrial activation was compromised as shown by the decrease in the expression of respiratory enzymes and oxygen consumption rate. On the contrary, anaerobic metabolism was augmented as revealed by the upregulation of glycolytic enzymes and increase of lactate production, rendering the cells to rely more on anaerobic glycolysis for energy supply. Moreover, administration of 2-deoxyglucose (a glycolytic inhibitor) but not antimycin A (a respiratory inhibitor) significantly decreased intracellular ATP levels of hMSCs differentiating under hypoxia. Treatment with cobalt chloride, a hypoxia-inducible factor-1α (HIF-1α) stabilizer, recapitulated the inhibitory effects of hypoxia, suggesting that HIF-1α is involved in the compromise of hMSCs differentiation. These results suggest that hypoxia inhibits metabolic switch and mitochondrial function and therefore suppresses osteogenic differentiation of hMSCs.
The Syntheses of Hydrotalcite-Like Compounds and Their Structures and Physico-Chemical Properties—I: the Systems Mg2+-Al3+-NO3−, Mg2+-Al3+-Cl−, Mg2+-Al3+-ClO4−, Ni2+-Al3+-Cl− and Zn2+-Al3+-Cl− (1975)

Abstract The basic salts of this system were prepared and their structures and physico-chemical properties were studies by electron microscopy, chemical analysis, X-ray powder diffraction, thermal analysis, i.r. absorption spectra, BET absorption, and acidity-basicity measurements. The salts were found to be new compounds analogous to hydrotalcite. They can be expressed by the formula; where M 2+ and M 3+ denote di- and trivalent cations, A − and A 2− denote mono- and divalent anions, respectively, and y = z 1 + 2 z 2 ; z 1 ≫ z 2 . The structures consist of positively charged Cd(OH) 2 -like basic layers and intermediate layers formed from anions and water molecules with the solid solution of divalent cation (M 2+ ) and trivalent cation (M 3+ ) being formed in the range of 0.6 &lt; x /( x + y ) &lt; 0.9. The anions of Cl − , NO 3 − and ClO 4 − are easily substituted by CO 3 2− . A large part of the NO 3 − makes a monodentate-type bond and the ClO 4 − a bridge-type bond.
Some Implications of Interactive Graphic Computer Systems for Data Analysis and Statistics (1970)

“Current facilities for computing, display, and real time interaction have developed substantially beyond our understanding of how to use them effectively in data analysis. Current limitations in data analysis technology are mainly in explicating and organizing the science of data analysis and of defining and implementing the necessary associated computer software. “From the statistical side of the discipline must come: broader, more permissive, empirically oriented concepts and theories; more inclusive and realistic classifications of objectives; more effective and coherent classifications of useful techniques; research toward more empirically informative techniques that will provide both exposure and summarization; more understanding and research on techniques of reforming and re-expressing variables; deeper insight into the psychology of graphs, pictures and output formats in general, both for interaction and for communication; progress toward standardized data structures of great flexibility and comprehensiveness. “From the computing side of the discipline is required software to provide: convenience with flexibility, simple and effective bookkeeping and history keeping, adequate editing, effective means for treating output as input, more flexible and general graphical presentations, and a variety of means to facilitate real time interaction. “Though some progress is being made on many of these needs, the technology of data analysis is still in its infancy.” (Tukey and Wilk, 1966) John Tukey and Martin Wilk have described what, they feel are the future needs in data analysis and statistics in the following terms.
Synthesis of pyrazolo(3,4-d)pyridazines from 5-(1-methylhydrazino)pyridazines by means of the Vilsmeier-Haack reaction. (1985)

Reaction of 2-substituted 5-(1-methylhydrazino)-3 (2H)-pyridazinones (2a-d) with dimethyl-formamide-phosphorus oxychloride afforded 5-substituted 1, 5-dihydro-1-methyl-4H-pyrazolo [3, 4-d] pyridazin-4-ones (3a-d) in good yields. However, concurrent formation of 5-substituted 2, 5-dihydro-2-(2-substituted 1-chlorovinyl)-4H-pyrazolo [3, 4-d] pyridazin-4-ones (6a-c, 12, 13) (minor products) and the 1-methyl-4H-derivatives (3a-c) (major ones) was observed, when starting with the corresponding 2-substituted 5-(2-acetyl-1-methylhydrazino)-3 (2H)-pyridazinones (5a-c, 9, 10) under similar reaction conditions. A plausible mechanism for the reaction is proposed.