gebhart/patrepeval huggingface dataset:
Alternative reactions at the interface of glycolysis and citric acid cycle inSaccharomyces cerevisiae (2016)

Pyruvate and acetyl-coenzyme A, located at the interface between glycolysis and TCA cycle, are important intermediates in yeast metabolism and key precursors for industrially relevant products. Rational engineering of their supply requires knowledge of compensatory reactions that replace predominant pathways when these are inactivated. This study investigates effects of individual and combined mutations that inactivate the mitochondrial pyruvate-dehydrogenase (PDH) complex, extramitochondrial citrate synthase (Cit2) and mitochondrial CoA-transferase (Ach1) in Saccharomyces cerevisiae. Additionally, strains with a constitutively expressed carnitine shuttle were constructed and analyzed. A predominant role of the PDH complex in linking glycolysis and TCA cycle in glucose-grown batch cultures could be functionally replaced by the combined activity of the cytosolic PDH bypass and Cit2. Strongly impaired growth and a high incidence of respiratory deficiency in pda1Δ ach1Δ strains showed that synthesis of intramitochondrial acetyl-CoA as a metabolic precursor requires activity of either the PDH complex or Ach1. Constitutive overexpression of AGP2, HNM1, YAT2, YAT1, CRC1 and CAT2 enabled the carnitine shuttle to efficiently link glycolysis and TCA cycle in l-carnitine-supplemented, glucose-grown batch cultures. Strains in which all known reactions at the glycolysis-TCA cycle interface were inactivated still grew slowly on glucose, indicating additional flexibility at this key metabolic junction.
Cu-Catalyzed Asymmetric Allylic Alkylations of Aromatic and Aliphatic Phosphates with Alkylzinc Reagents. An Effective Method for Enantioselective Synthesis of Tertiary and Quaternary Carbons (2004)

Efficient enantioselective Cu-catalyzed allylic alkylations of aromatic and aliphatic allylic phosphates bearing di- and trisubstituted olefins are disclosed. Enantioselective C-C bond forming reactions are promoted in the presence of 10 mol % readily available chiral amino acid-based ligand (5 steps, 40% overall yield synthesis) and 5 mol % (CuOTf)2 x C6H6. Reactions deliver tertiary and quaternary stereogenic carbon centers regioselectively and in 78-96% ee. Data regarding the effect of variations in ligand structure on the efficiency and enantioselectivity of the alkylation process, as well as a mechanistic working model, are presented. The suggested model involves a dual role for the chiral Cu complex: association of the Cu(I) center to the olefin is facilitated by a two-point binding between the carbonyl of the ligand's amide terminus and the P=O of the substrate.
Design and modeling of a micromechanical surface bonding system (2002)

Optimization of the design of a micromechanical surface fastening system is discussed based on a simple cantilevered beam model. Theoretical estimates indicate that the bonding strength of these microstructures can be as high as 11-17 MPa, or 1500-2000 psi. The equivalent surface energy corresponding to the stored strain energy during separation of two interlocked sample pairs is 14.6 mu J/cm/sup 2/. The authors also report preliminary experimental results; a bonding strength of 1.1 MPa or 160 psi per unit interlocked area has been achieved, which is in agreement with the theoretical approximation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A multilevel non-uniform grid algorithm for acceleration of volumetric integral equation based solvers for analysis of arbitrarily shaped dielectric radomes (2011)

A fast algorithm combined with the volume integral equation (VIE) is proposed for analyzing antenna radiation properties in the presence of an arbitrary shaped dielectric radome. The discrete form of the VIE is obtained using the method of moments (MOM). Evaluation of electromagnetic fields is accelerated using the multilevel volumetric non-uniform grid algorithm (MLVNG). The algorithm is based on phase and amplitude compensation of fields which are produced by a bounded volume of source distribution. The compensated field is band-limited function of its coordinates, which allows sampling it on a sparse non-uniform spherical grid at rates proportional to the source volume. Tight sampling rules are suggested in order to reduce the computational complexity of the field evaluation. The computational complexity of the MLVNG algorithm is demonstrated on representative example.
ChemInform Abstract: Photochemical Cleavage of Carbonate in Cp*Rh(CO3)·2 H2O. (1989)

Abstract Irradiation of the title complex (I) at 351 nm leads to photochemical cleavage of the carbonate ligand to form CO 2 and a metal‐oxo intermediate which reacts with the starting material to produce the dimer complex (II).
Embryonic development in allis shad Alosa alosa : A baseline for stress studies (2022)

From experimentations in optimal conditions, we identified the main features of embryogenesis of allis shad Alosa alosa. We propose to use this outcome as endpoints to evaluate the impact of stressors on A. alosa embryogenesis in future studies. Eggs are spherical in shape, transparent and non-adhesive. Mass hatching occurs between 120 and 144 hpf at an incubation temperature of 20°C. Abnormalities of larvae were minor (1.10% of hatched individuals).
Molecular Screening of Wine Lactic Acid Bacteria Degrading Hydroxycinnamic Acids (2008)

The potential to produce volatile phenols from hydroxycinnamic acids was investigated for lactic acid bacteria (LAB) isolated from Spanish grape must and wine. A PCR assay was developed for the detection of LAB that potentially produce volatile phenols. Synthetic degenerate oligonucleotides for the specific detection of the pdc gene encoding a phenolic acid decarboxylase were designed. The pdc PCR assay amplifies a 321 bp DNA fragment from phenolic acid decarboxylase. The pdc PCR method was applied to 85 strains belonging to the 6 main wine LAB species. Lactobacillus plantarum, Lactobacillus brevis, and Pediococcus pentosaceus strains produce a positive response in the pdc PCR assay, whereas Oenococcus oeni, Lactobacillus hilgardii, and Leuconostoc mesenteroides strains did not produce the expected PCR product. The production of vinyl and ethyl derivatives from hydroxycinnamic acids in culture media was determined by high-performance liquid chromatography. A relationship was found between pdc PCR amplification and volatile phenol production, so that the LAB strains that gave a positive pdc PCR response produce volatile phenols, whereas strains that did not produce a PCR amplicon did not produce volatile phenols. The proposed method could be useful for a preliminary identification of LAB strains able to produce volatile phenols in wine.
Co‐Catalyzed Reductive Cyclization of Azido and Cyano Substituted α,β‐Unsaturated Esters with NaBH4: Enantioselective Synthesis of (R)‐Baclofen and (R)‐Rolipram. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Measurement of the Z boson differential production cross section using its invisible decay mode (Z → $$ \nu \overline{\nu} $$) in proton-proton collisions at $$ \sqrt{s} $$ = 13 TeV (2021)

A bstract Measurements of the total and differential fiducial cross sections for the Z boson decaying into two neutrinos are presented at the LHC in proton-proton collisions at a center-of-mass energy of 13 TeV. The data were collected by the CMS detector in 2016 and correspond to an integrated luminosity of 35.9 fb − 1 . In these measurements, events are selected containing an imbalance in transverse momentum and one or more energetic jets. The fiducial differential cross section is measured as a function of the Z boson transverse momentum. The results are combined with a previous measurement of charged-lepton decays of the Z boson. The measured total fiducial cross section for events with Z boson transverse momentum greater than 200 GeV is $$ {3000}_{-170}^{+180} $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msubsup> <mml:mn>3000</mml:mn> <mml:mrow> <mml:mo>−</mml:mo> <mml:mn>170</mml:mn> </mml:mrow> <mml:mrow> <mml:mo>+</mml:mo> <mml:mn>180</mml:mn> </mml:mrow> </mml:msubsup> </mml:math> fb.
The COVID-19 Pandemic—A Potential Role for Antivirals in Mitigating Pandemics (2023)

The COVID-19 pandemic has served as a stark reminder that outbreaks of novel pathogens (i.e., those not previously encountered by humans) have always plagued mankind and will continue to do so. The COVID-19 pandemic has also taught us that a single exposure to a novel pathogen is typically not sufficient to build robust population immunity that exists against common respiratory viruses. Robust population-level immunity can be achieved through repeated natural infection (typically at the cost of high mortality and overwhelmed public health resources) and/or repeated vaccination (which may be limited by vaccine availability, a country's economic resources, and/or vaccine hesitancy). Here, we suggest that the broader use of antivirals could be a mitigation strategy to limit severe disease and the burden on healthcare systems during widespread virus circulation while allowing the buildup of population immunity.
Indications for Pacemakers, ICDs and CRT (2008)

This chapter contains sections titled: Indications for permanent pacing Indications for the implantable cardioverter-defibrillator Contraindications to implantable cardioverter-defibrillator therapy Acknowledgement References
3-Amino-1-methylpyrazin-1-ium iodide (2023)

&lt;p&gt;In the cation of the title compound, C5H8N3+center dot I-, the C-N(H-2) bond distance [1.338 (8) angstrom] is at the lower end of the range for aryl amines. In the crystal structure, cations and anions are linked via N-H center dot center dot center dot I hydrogen bonds, forming centrosymmetric four-component clusters. &lt;/p&gt;
Replication kinetics of Chinese hamster chromosomes as revealed by bivariate flow karyotyping (1983)

Abstract In this paper we show that the replication kinetics of individual chromosomes can be estimated by bivariate flow cytometric analysis of chromosomes isolated from 5‐bromo‐2′‐deoxyuridine (BrdUrd) treated cells. To study the timing of replication of chromosomes, Chinese hamster M3–1 cells were grown for different times in BrdUrd containing medium. Colcemid was added during the last 90 minutes of each BrdUrd labeling period. Chromosomes were isolated from the Colcemid blocked mitotic cells and stained with Hoechst 33258 (HO) and chromomycin A3 (CA3). Bivariate HO‐CA3 flow karyotypes were measured in a dual beam flow cytometer. Labeling cells with BrdUrd for 2, 2 1/2, 3, 3 1/2, and 4 hours before chromosome isolation resulted in progressive quenching of the HO fluorescence of chromosomes Y and 10, 11, M2 while the HO fluorescence of all other chromosomes was either not quenched or was only slightly quenched. The CA3 fluorescence of all chromosomes was slightly enhanced by BrdUrd treatment. A quantitative evaluation of the quenching of HO fluorescence suggested that: a) greater than 50% of HO binding DNA of chromosomes 10, 11, M2 is synthesized in the last quarter of S phase; b) the Y chromosome synthesizes more than 50% of HO binding DNA in the last tenth of S phase making the Y chromosome the latest replicating M3‐1 chromosome. All other chromosomes have synthesized greater than 50% of their HO binding DNA before the last third of S phase.
Protective Effects of Isorhamnetin against Hydrogen Peroxide-Induced Apoptosis in C2C12 Murine Myoblasts (2015)

Objectives: It was investigated the cytoprotective efficacies of isorhamnetin, a flavonoid originally derived from Hippophae rhamnoides L., against oxidative stress-induced apoptosis in C2C12 myoblasts. Methods: The effects of isorhamnetin on cell growth, apoptosis and reactive oxygen species (ROS) generation were evaluated by trypan blue dye exclusion assay, 4',6-diamidino-2-phenylindole staining and flow cytometry. The levels of apoptosis-regulatory and nuclear factor erythroid 2-related factor 2 (Nrf2) signaling pathway-related proteins, and caspase activities (caspase-3 and -9) were determined by Western blot analysis and colorimetric assay, respectively. Results: Our results revealed that treatment with isorhamnetin prior to hydrogen peroxide (H2O2) exposure significantly increased the C2C12 cell viability and, indicating that the exposure of C2C12 cells to isorhamnetin conferred a protective effect against oxidative stress. Isorhamnetin also effectively attenuated H2O2-induced apoptosis and ROS generation, which was associated with the restoration of the upregulation of Bax and downregulation of Bcl-2 induced by H2O2. In addition, H2O2 enhanced the activation of caspase-9 and -3, and degradation of poly (ADPribose)-polymerase, a typical substrate protein of activated caspase-3; however, these events were almost totally reversed by pretreatment with isorhamnetin. Moreover, isorhamnetin increased the levels of heme oxygenase-1, a potent antioxidant enzyme, associated with the induction of Nrf2. Conclusions: Our data indicated that isorhamnetin may potentially serve as an agent for the treatment and prevention of muscle disorders caused by oxidative stress.
Correctness and security at odds (2015)

We consider the conflicts between requirements from security and post-silicon validation in SoC designs. Post-silicon validation requires hardware instrumentations to provide observability and controllability during on-field execution; this in turn makes the system prone to security vulnerabilities, resulting in potentially subtle security exploits. Mitigating such threats while ensuring that the system is amenable to post-silicon validation is challenging, involving close collaboration among security, validation, testing, and computer architecture teams. We examine the state of the practice in this area, the trade-offs and compromises made, and their limitations. We also discuss an emerging approach that we are contemplating to address this problem.
A Fluorine Scan of Thrombin Inhibitors to Map the Fluorophilicity/Fluorophobicity of an Enzyme Active Site: Evidence for CF⋅⋅⋅CO Interactions (2003)

A highly fluorophilic environment comprising the HCαCO unit of Asn 98 in the active site of thrombin was identified by X-ray crystallography of a complex formed between the enzyme and a synthetic inhibitor (see partial X-ray structure, distances are in Angstroms). Short CF⋅⋅⋅HCα and CF⋅⋅⋅CO contacts involving HCαCO fragments were also frequently observed in small-molecule X-ray crystal structures.
Cross-resistance of an amsacrine-resistant human leukemia line to topoisomerase II reactive DNA intercalating agents. Evidence for two topoisomerase II directed drug actions (1991)

HL-60/AMSA is a human leukemia cell line that is 50-100-fold more resistant than its drug-sensitive HL-60 parent line to the cytotoxic actions of the DNA intercalator amsacrine (m-AMSA). HL-60/AMSA topoisomerase II is also resistant to the inhibitory actions of m-AMSA. HL-60/AMSA cells and topoisomerase II are cross-resistant to anthracycline and ellipticine intercalators but relatively sensitive to the nonintercalating topoisomerase II reactive epipodophyllotoxin etoposide. We now demonstrate that HL-60/AMSA and its topoisomerase II are cross-resistant to the DNA intercalators mitoxantrone and amonafide, thus strongly indicating that HL-60/AMSA and its topoisomerase II are resistant to topoisomerase II reactive intercalators but not to nonintercalators. At high concentrations, mitoxantrone and amonafide were also found to inhibit their own, m-AMSA's, and etoposide's abilities to stabilize topoisomerase II-DNA complexes. This appears to be due to the ability of these concentrations of mitoxantrone and amonafide to inhibit topoisomerase II mediated DNA strand passage at a point in the topoisomerization cycle prior to the acquisition of the enzyme-DNA configuration that yields DNA cleavage and topoisomerase II-DNA cross-links. In addition, amonafide can inhibit the cytotoxic actions of m-AMSA and etoposide. Taken together, these results suggest that the cytotoxicity of m-AMSA and etoposide is initiated primarily by the stabilization of the topoisomerase II-DNA complex. Other topoisomerase II reactive drugs may inhibit the enzyme at other steps in the topoisomerization cycle, particularly at elevated concentrations.(ABSTRACT TRUNCATED AT 250 WORDS)
3D Printing of Resilin in Water by Multiphoton Absorption Polymerization (2023)

Abstract Resilin is an elastic rubber‐like protein found in the cuticles of insects. It incorporates outstanding properties of high resilience and fatigue lifetime, where kinetic energy storage is needed for biological functions such as flight and jumps. Since resilin is rich in tyrosine groups, localized photopolymerization is enabled due to the ability to introduce di‐tyrosine bonds by a ruthenium‐based photoinitiator. Using Multiphoton Absorption Polymerization 3D printing process, objects containing 100% recombinant resilin protein are printed in water at a submicron length scale. Consequently, protein‐based hydrogels with complex structures are printed using space positioning voxel polymerization. The objects are characterized by dynamic mechanical analysis using nanoindentation. Printing parameters such as printing speed and laser power are found to enable tuning the mechanical properties of the printed objects. The printed objects are soft and resilient, similar to native resilin, while presenting the highest resolution of a structure made entirely of a protein and better mechanical properties of common hydrogels and poly(dimethylsiloxane). Moreover, topography and mechanical properties enable cell growth and alignment without cell adhesion primers, thus facilitating biological applications. The fabrication of 3D resilin‐based hydrogel will open the way for potential applications based on biomimicking and in creating new functional objects.
Peptides transducteurs (2005)

Transduction peptides that cross the plasma membrane of live cells are commonly used for the in vitro and in vivo targeting of hydrophilic drugs into the cell interior. Although this family of peptides has recently increased and will probably continue to do so, the two mainly used peptides are derived from transcription factors. Indeed, TAT is a 12 amino acid long arginine-rich peptide present in the HIV transcription factor, and penetratin - or its variants - corresponds to 16 amino acids that define the highly conserved third helix of the DNA-binding domain (homeodomain) of homeoprotein transcription factors. In this review, we shall recall the different steps that have led to the discovery of transduction peptides and present the most likely hypotheses concerning the mechanisms involved in their internalization. At the risk of being incomplete or, even, biased, we shall concentrate on penetratins and TAT. The reason is that these peptides have been studied for over ten years leading to the edification of robust knowledge regarding their properties. This attitude will not preclude comparisons with other peptides, if necessary. Our goal is to describe the mode of action of these transduction peptides, their range of activity in term of cell types that accept them and cargoes that they can transport, and, also, some of the limitations that one can encounter in their use. Finally, based on the idea that peptide transduction is the technological face of a physiological property of some transcription factors, we shall discuss the putative physiological function of homeoprotein transduction, and, as a consequence, the possibility to use these factors as therapeutic proteins.
Factors Controlling the Multiplication of Untransformed and Transformed BHK2I Cells Under Various Environmental Conditions (1971)

This chapter contains section titled: Requirements of Bhgi Cells at Further Stages of Transformation The Cell Surface As the Primary Site of Action of Macromolecular Effectors Summary References Discussion
Effect of temporal autocorrelation due to physiological noise and stimulus paradigm on voxel-level false-positive rates in fMRI (1998)

Statistical mapping within a binary hypothesis testing framework is the most widely used analytical method in functional MRI of the brain. A common assumption in this kind of analysis is that the fMRI time series are independent and identically distributed in time, yet we know that fMRI data can have significant temporal correlation due to low-frequency physiological fluctuation (Weisskoff et al. [1993]; Proc Soc Magn Reson Med 9:7; Biswal et al. [1995]: Mag Reson Med 34:537-541). Furthermore, since the signal-to-noise ratio will vary with imaging rate, we should expect that the degree of correlation will vary with imaging rate. In this paper, we investigate the effect of temporal correlation and experimental paradigm on false-positive rates (type I error rates), using data synthesized through a simple autoregressive plus white-noise model whose parameters were estimated from real data over a range of imaging rates. We demonstrate that actual false-positive rates can be biased far above or below the assumed significance level alpha when temporal autocorrelation is ignored in a way that depends on both the degree of correlation as well as the paradigm frequency. Furthermore, we present a simple method, based on the noise model described above, for correcting such distortions, and relate this method to the extended general linear model of Worsley and Friston ([1995]: Neuroimage 2:173-181).
Evaluation of Nobuto Filter Paper Strips for the Detection of Avian Influenza Virus Antibody in Waterfowl (2011)

The utility of using Nobuto paper strips for the detection of avian influenza antibodies was examined in mallards (Anas platyrhynchos) experimentally infected with low pathogenic avian influenza viruses. Blood was collected 2 wk after infection and was preserved either as serum or whole blood absorbed onto Nobuto strips. Analysis of samples using a commercially available blocking enzyme-linked immunosorbent assay revealed comparable results (> or = 96% sensitivity for all methods) between sera stored at -30 C and the Nobuto strip preservation method even when the Nobuto strips were stored up to 3 mo at room temperature (RT). Significant differences were detected in the ratio of sample absorbance to negative control absorbance for Nobuto strips stored at RT compared with sera stored at -30 C, although these differences did not affect the ability of the test to reliably detect positive and negative samples. Nobuto strips are a convenient and sensitive alternative to the collection of serum samples when maintaining appropriate storage temperatures is difficult.