gebhart/patrepeval huggingface dataset:
Loss of mitochondrial membrane potential is associated with increase in mitochondrial volume: Physiological role in neurones (2005)

Mitochondrial volume homeostasis is a housekeeping cellular function, thought to help regulate oxidative capacity, apoptosis, and mechanical signaling. The volume is mainly regulated by potassium flux into and out of the matrix and controlled by the electrochemical potential. Mitochondrial depolarization will therefore affect this flux but studies showing how have not been consistent, and it is unclear what mitochondrial volume changes also occur. The aim of the present study was to investigate mitochondrial volume changes in permeabilized neurons under various bioenergetic conditions using deconvolution confocal microscopy. Under control conditions, mitochondria in situ appeared rod-shaped with mean length, surface area, and volume values of 2.29+/-0.10 microm, 1.41+/-0.10 microm2, and 0.062+/-0.006 microm3, respectively (n=42). Valinomycin, a K+-selective ionophore, increased mitochondrial volume by 63+/-22%, although surface area was almost unchanged because mitochondrial shape became more spherical. Pinacidil, an opener of mitochondrial ATP-dependent channels, produced similar effects, although some mitochondria were insensitive to its action. Mitochondrial depolarization with the protonophore FCCP, or with respiratory chain inhibitors antimycin and sodium azide was associated with a considerable increase in mitochondrial volume (by 75%-140%). Effects of mitochondrial modulators were also studied in intact neurones. Tracking of single mitochondria showed that during 65+/-2% of their time, mitochondria were motile with an average velocity of 0.19+/-0.01 microm/s. Antimycin, azide, and FCCP induced mitochondrial swelling and significantly decreased mitochondrial motility. In the presence of pinacidil, swollen mitochondria had reduced their motility, although mitochondria with normal volume stayed motile. These data show that mitochondrial depolarization was followed by significant swelling, which, in turn, impaired mitochondrial trafficking.
Hydrogen peroxide, organic hydroperoxide, and formaldehyde as primary pollutants from biomass burning (1997)

Hydrogen peroxide, organic hydroperoxide species, and formaldehyde were found to be enhanced within biomass burning plumes during the Transport and Atmospheric Chemistry near the Equator ‐ Atlantic (TRACE A) experiment. This enhancement could have resulted from direct emission by the fires or by secondary photochemical production. In this study, direct production of hydroperoxide and formaldehyde from biomass burning is proposed and examined through comparisons of hydroperoxide and formaldehyde measurements, obtained from three fire flights in TRACE A, with model estimates, with other measurement data, and with results from fire experiments at the University of Rhode Island (URI). For highest concentrations of hydroperoxide and formaldehyde, model predictions fall short of those observed, and an additional source is required. H 2 O 2 and CH 3 OOH were noted to increase with CO and were significantly correlated with other measured species known to be produced from biomass burning. The enhancements of H 2 O 2 and CH 3 OOH relative to CO were different between flights in which the relative enhancements of CO to CO 2 were also different. The enhancement ratio of H 2 O 2 and CH 3 OOH relative to CO was 1–5×10 −2 and 2–4×10 −3 , respectively. CH 2 O was correlated with CO. The enhancement ratios of CH 2 O were determined in relation to both CO and CO 2 for three flights and were 7–19×10 −3 and 3–5×10 −4 , respectively. The correlations of CH 2 O with other measured combustion species were more significant than those of H 2 O 2 and CH 3 OOH. To determine whether hydroperoxide and formaldehyde can be directly produced from biomass burning, simple biomass fire experiments were performed at URI. These species were observed to be clearly elevated in test biomass fires. These experiments present unequivocal evidence for the direct production of hydrogen peroxide and formaldehyde from biomass burning. The results from both TRACE A and our fire experiments also fit possible mechanisms of direct formation of hydroperoxide and formaldehyde in combustion processes. The atmospheric implication of the direct production of these species from biomass burning is their contribution to odd‐hydrogen radical production, thereby affecting the oxidizing capacity of the atmosphere before O 3 would be photochemically developed. In TRACE A, odd‐hydrogen radical production from the direct source of these species is estimated to be near 30% of the total radical production.
Phase diagram of the interacting Majorana chain model (2015)

The Hubbard and spinless fermion chains are paradigms of strongly correlated systems, very well understood using the Bethe ansatz, density matrix renormalization group (DMRG), and field theory/renormalization group (RG) methods. They have been applied to one-dimensional materials and have provided important insights for understanding higher-dimensional cases. Recently, an interacting fermion model has been introduced, with possible applications to topological materials. It has a single Majorana fermion operator on each lattice site and interactions with the shortest possible range that involve four sites. We present a thorough analysis of the phase diagram of this model in one dimension using field-theory/RG and DMRG methods. It includes a gapped supersymmetric region and a gapless phase with coexisting Luttinger liquid and Ising degrees of freedom. In addition to a first-order transition, three critical points occur: tricritical Ising, Lifshitz, and a generalization of the commensurate-incommensurate transition. We also survey various gapped phases of the system that arise when the translation symmetry is broken by dimerization and find both trivial and topological phases with 0, 1, and 2 Majorana zero modes bound to the edges of the chain with open boundary conditions.
Proteome-wide characterization of signalling interactions in the hippocampal CA4/DG subfield of patients with Alzheimer’s disease (2015)

Alzheimer's disease (AD) is the most common form of dementia; however, mechanisms and biomarkers remain unclear. Here, we examined hippocampal CA4 and dentate gyrus subfields, which are less studied in the context of AD pathology, in post-mortem AD and control tissue to identify possible biomarkers. We performed mass spectrometry-based proteomic analysis combined with label-free quantification for identification of differentially expressed proteins. We identified 4,328 proteins, of which 113 showed more than 2-fold higher or lower expression in AD hippocampi than in control tissues. Five proteins were identified as putative AD biomarkers (MDH2, PCLO, TRRAP, YWHAZ, and MUC19 isoform 5) and were cross-validated by immunoblotting, selected reaction monitoring, and MALDI imaging. We also used a bioinformatics approach to examine upstream signalling interactions of the 113 regulated proteins. Five upstream signalling (IGF1, BDNF, ZAP70, MYC, and cyclosporin A) factors showed novel interactions in AD hippocampi. Taken together, these results demonstrate a novel platform that may provide new strategies for the early detection of AD and thus its diagnosis.
Sterols from Centaurea pumilio L. with cell proliferative activity: In vitro and in silico studies (2023)

Abstract Numerous studies highlighted the impact of natural products, particularly phytosterols, in wound healing while providing less expensive alternatives to chemically synthesized drugs, with less side effects. Centaurea pumilio L. (family Asteraceae) is a rare and endangered species of genus Centaurea with few reports concerning its chemistry. Our phytochemical investigation for the non-polar fraction of its aerial parts led to the isolation and identification of the new compound ( 6 ) identified as stigmast-1,5-dien-3- O -β- d -glucopyranoside along with five known sterols and triterpenes ( 1–5 ) identified as taraxasterol, β-sitosterol, stigmasterol, β-sitosterol glucoside, and stigmasterol-3- O -β- d -glucopyranoside. Structures of the isolated compounds have been characterized using 1D, 2D NMR, and mass spectral analyses. The cell viability and proliferative activity of the isolated compounds were evaluated using an MTT assay on cultured human primary umbilical vein endothelial cells (HUVEC). None of the compounds exhibited any sign of cytotoxicity. Nonetheless, compounds 5 and 6 moderately enhanced the HUVEC cell growth by 14 and 16%, respectively, at the maximal tested dose (50 µg/mL). As inhibition of glycogen synthase kinase 3-β (GSK3-β) enzyme is important to enhance the wound healing process; therefore, molecular docking was performed to understand the possible interactions between bioactive compounds 5 and 6 and GSK-3β binding pocket active amino acid residues. Both compounds were able to bind to the substrate‑binding site of GSK-3β and potentially interact with the key active site residues, forming strong π and hydrogen interactions with the catalytic site residues, revealing lower binding energy (−7.185 and −6.303 kcal/mol, respectively) than that of indirubin-3-monooxime (−5.303 kcal/mol); thereby representing strong natural replacements candidates for GSK-3β inhibitors.
Hydrothermal Fabrication of Ag-Decorated MoSe₂/Reduced Graphene Oxide Ternary Hybrid for H₂S Gas Sensing (2020)

This paper demonstrates a H2 S gas sensor based on Ag-MoSe2/reduced graphene oxide (rGO) ternary composite material via hydrothermal method was studied. The microstructures, morphologies and compositional characteristics of the Ag-MoSe2/rGO nanocomposite were completely tested by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), transmission electron microscope (TEM) and energy dispersive spectrometer (EDS). By exposing it to various concentrations of H2 S gas from 0.1 ppm to 30 ppm at room temperature, the gas sensing properties of the Ag-MoSe2/rGO sensor were examined. The experimental data indicated that the H2 S gas sensor has a high response, quite response-recovery performances, excellent selectivity and reproducibility toward H2 S gas. Moreover, the work also investigates the effect of Ag loading in the compound on the H2 S gas sensing. The sensing mechanism of the Ag-MoSe2/rGO film sensor can be attributed to the modulation of potential barrier with electron transfer and the synergistic effect of the ternary compound nanostructures. This paper shows that in diverse applications, the prepared Ag-MoSe2/rGO composite is a potential candidate for detecting H2 S gas at room temperature.
Eribulin penetrates brain tumor tissue and prolongs survival of mice harboring intracerebral glioblastoma xenografts (2019)

Glioblastoma is one of the most devastating human malignancies for which a novel efficient treatment is urgently required. This pre-clinical study shows that eribulin, a specific inhibitor of telomerase reverse transcriptase (TERT)-RNA-dependent RNA polymerase, is an effective anticancer agent against glioblastoma. Eribulin inhibited the growth of 4 TERT promoter mutation-harboring glioblastoma cell lines in vitro at subnanomolar concentrations. In addition, it suppressed the growth of glioblastoma cells transplanted subcutaneously or intracerebrally into mice, and significantly prolonged the survival of mice harboring brain tumors at a clinically equivalent dose. A pharmacokinetics study showed that eribulin quickly penetrated brain tumors and remained at a high concentration even when it was washed away from plasma, kidney or liver 24 hours after intravenous injection. Moreover, a matrix-assisted laser desorption/ionization mass spectrometry imaging analysis revealed that intraperitoneally injected eribulin penetrated the brain tumor and was distributed evenly within the tumor mass at 1 hour after the injection whereas only very low levels of eribulin were detected in surrounding normal brain. Eribulin is an FDA-approved drug for refractory breast cancer and can be safely repositioned for treatment of glioblastoma patients. Thus, our results suggest that eribulin may serve as a novel therapeutic option for glioblastoma. Based on these data, an investigator-initiated registration-directed clinical trial to evaluate the safety and efficacy of eribulin in patients with recurrent GBM (UMIN000030359) has been initiated.
6-Amino-1-benzyl-4-(4-chlorophenyl)-3-(4-pyridyl)-1,4-dihydropyrano[2,3-c]pyrazole-5-carbonitrile (2008)

The crystal structure of the title compound, C(25)H(18)ClN(5)O, was determined in the course of our studies on the synthesis of 1,4-dihydro-pyrano[2,3-c]pyrazole as an inhibitor of the p38 mitogen-activated protein kinase (MAPK). The compound was prepared via a base-catalysed synthesis from 1-benzyl-3-(4-pyrid-yl)-1H-pyrazol-5(4H)-one with p-chloro-aldehyde and malononitrile. The crystal data obtained were used to generate a three-dimensional pharmacophore model for in silico database screening. The phenyl ring is disordered over two positions, with site occupancy factors of 0.55 and 0.45. The dihedral angles between the 1,4-dihydropyrano[2,3-c]pyrazole unit and the chloro-phenyl and pyridine rings are 83.7 (1) and 16.0 (1)°, respectively. The chloro-phenyl and pyridine rings make a dihedral angle of 86.8 (2)°.
CHAPTER 7. The Potential of Modified Diatom Frustules for Solar Energy Conversion (2017)

Research on sustainable energy production is of growing interest in light of the limited fossil fuel stocks and increasing energy demands. An ideal solar harvesting device should potentially include low-cost, non-toxic and three-dimensional inorganic materials. Diatom biosilica or frustules exemplify the above features and are a perfect host material. Diatoms are natural three-dimensional nanoarchitectures with convoluted, tailorable chemistries, formed as a result of a biomineralisation process. They are made up of silicon dioxides and silicates, which are natural insulators of both electrical conduction and light absorption. To overcome their natural insulating properties and allow frustules to be used as an electrode/photoelectrode material, one can modify their structure by metal/material glazing or by converting them into silicon or titanium dioxide. This allows the frustules to obtain conductive or semi-conductive properties, while retaining their original morphology. Additionally, three-dimensional nanostructures of certain polymers/metals can be fabricated using diatom frustules as a template. The resulting three-dimensional polymers/metals can be used as a scaffold for designing electrode/photoelectrode materials. In this chapter, the literature on the modification and application of diatom frustules as a natural platform for dye-sensitised solar cells and photoelectrochemical hydrogen production is reviewed.
Dissociation of Voluntary and Emotional Innervation after Stroke (2010)

A 72-year-old man presented with a sudden onset of slurred speech. His medical history was unremarkable, and he was taking no medications and did not smoke. The physical examination revealed left-sided facial paralysis and dysarthrophonia. Diffusion-weighted magnetic resonance imaging showed a hyperintensity in the right precentral gyrus, reflecting acute cerebral ischemia (Panel A, arrow). Three days after the stroke, the patient showed impaired voluntary innervation. When he was asked to smile on command, he was unable to fully smile because of facial paralysis on the left side (Panel B). However, during emotional encounters, the patient was able to overcome . . .
Environmental Gamma Radiation Monitoring by Means of TLD and Ionisation Chamber (1992)

In addition to the national radon monitoring programme being carried out by the external dosimetry laboratory of the Health Physics and Safety Centre, a large-scale survey for the monitoring of gamma outdoor radiation is planned. In this context CaSO4:Dy, CaF2:Dy and LiF:Mg,P,Cu have been systematically investigated. CaSO4:Dy is shown to be the best compromise for use in the field experiment. In order to check the passive method based on TL detectors, an active method using a high pressure ionisation chamber (HPIC) type RS-111 has been used. The experimental work was conducted for 1 year in the region of Algiers. The average dose rate in air over the whole monitoring period was found to be 63.50±4.60 nGy.h-1 and 67.70±6.70nGy.h-1, respectively, for the TLDs and the HPIC. A comparison of these two methods showed that these results agree within 7%. The passive method based on the TL detectors can be considered satisfactory and very convenient for a large-scale survey.
Biomineralization as an Inspiration for Materials Chemistry (2012)

Living organisms are well known for building a wide range of specially designed organic-inorganic hybrid materials such as bone, teeth, and shells, which are highly sophisticated in terms of their adaptation to function. This has inspired physicists, chemists, and materials scientists to mimic such structures and their properties. In this Review we describe how strategies used by nature to build and tune the properties of biominerals have been applied to the synthesis of materials for biomedical, industrial, and technological purposes. Bio-inspired approaches such as molecular templating, supramolecular templating, organized surfaces, and phage display as well as methods to replicate the structure and function of biominerals are discussed. We also show that the application of in situ techniques to study and visualize the bio-inspired materials is of paramount importance to understand, control, and optimize their preparation. Biominerals are synthesized in aqueous media under ambient conditions, and these approaches can lead to materials with a reduced ecological footprint than can traditional methods.
Oncogenic events triggered by AID, the adverse effect of antibody diversification (2007)

The generation of an efficient immune response depends on highly refined mechanisms of antibody diversification. Two of these mechanisms, somatic hypermutation (SHM) and class switch recombination (CSR), are initiated by activation-induced cytidine deaminase (AID) upon antigen stimulation of mature B cells. AID deaminates cytosines on the DNA of Ig genes thereby generating a lesion that can be processed into a mutation (SHM) or a DNA double-strand break followed by a recombination reaction (CSR). A number of mechanisms are probably responsible for regulating AID function, such as transcriptional regulation, subcellular localization, post-transcriptional modifications and target specificity, but the issue remains of how unwanted DNA damage is fully prevented. Most lymphocyte neoplasias are originated from mature B cells and harbour hallmark chromosome translocations of lymphomagenic potential, such as the c-myc/IgH translocations found in Burkitt lymphomas. It has been recently shown that such translocations are initiated by AID and that ataxia-telangiectasia mutated, p53 and ARF provide surveillance mechanisms to prevent these aberrations. In addition, evidence is accumulating that AID expression can be induced in B cells independently of the germinal centre environment, such as in response to some viral infections, and occasionally in non-B cells, at least in certain inflammation-associated neoplasic situations. The most recent findings on AID expression and function and their relevance to the generation of oncogenic lesions will be discussed.
Trigonal paramagnetic interface defect in epitaxial Ge3N4/(111)Ge (2009)

We report on the observation by electron spin resonance (ESR) of an anisotropic paramagnetic defect at the interface of epitaxially grown Ge3N4/(111)Ge entities with nanometer thin Ge3N4 layers. The defect exhibits trigonal C3v symmetry characterized by g∥≈2.0023 and g⊥≈2.0032, and is observed most prominently after 10 eV optical excitation, with maximum areal density ≈2×1011 cm−2. The defect is suggested to concern the Ge K-type center, its occurrence appearing inherent to the specific heteroepitaxial interface matching.
Evaluation of a CO2 Foam Field Trial: Rangely Weber Sand Unit (1990)

Abstract A CO2 foam field trial was conducted in the Rangely Weber Sand Unit, located in northwestern Colorado. Chevron began the CO2 flood on a 1:1 water-alternating-gas, WAG, injection scheme in October 1986. Currently the project injects 250 MMCFD CO2. Forty percent of this is recycled CO2. CO2 production is a major concern and is caused by thief zones between injectors and producers. The objective of the field trial was to investigate whether foam may block some of the thief zones and thereby improve sweep efficiency and CO2 utilization. A pattern exhibiting severe CO2 breakthrough was chosen for the field trial. The injector, Gray A 10, is in communication with several offset producers. One of these wells, A.C. McLaughlin 4, produced more than 2 MMCFD gas within 10 days of placing Gray A10 on a CO2 cycle with virtually no tertiary oil. Gray A 10 was hydraulically fractured twice while it was a producer in the 1950's, but the fracture is not believed to be the sole cause of breakthrough in the pattern. The foam project started in April 1989 at the end of a water cycle. The treatment consisted of a 12,000 BBL surfactant slug followed by 55,000 BBL of 79% quality foam. Average surfactant concentration was about 0.46%, and Chevron Chaser CD1040 was used. Foam was emplaced by simultaneously injecting CO2 and surfactant solution through a coarse mixing device in the tubing. Results are encouraging. Injectivity and pressure transient data indicated that foam was emplaced in the reservoir. CO2 production in McLaughlin 4 was much lower during the trial while oil production was slightly higher. In contrast, both CO2 and oil production in the other offset producers increased somewhat. This could be evidence of CO2 diversion and improved sweep efficiency. Finally, foam reduced CO2 injectivity for as long as two months in the subsequent C02 chase after foam.
ATPase Cycle and DNA Unwinding Kinetics of RecG Helicase (2012)

The superfamily 2 bacterial helicase, RecG, is a monomeric enzyme with a role in DNA repair by reversing stalled replication forks. The helicase must act specifically and rapidly to prevent replication fork collapse. We have shown that RecG binds tightly and rapidly to four-strand oligonucleotide junctions, which mimic a stalled replication fork. The helicase unwinds such DNA junctions with a step-size of approximately four bases per ATP hydrolyzed. To gain an insight into this mechanism, we used fluorescent stopped-flow and quenched-flow to measure individual steps within the ATPase cycle of RecG, when bound to a DNA junction. The fluorescent ATP analogue, mantATP, was used throughout to determine the rate limiting steps, effects due to DNA and the main states in the cycle. Measurements, when possible, were also performed with unlabeled ATP to confirm the mechanism. The data show that the chemical step of hydrolysis is the rate limiting step in the cycle and that this step is greatly accelerated by bound DNA. The ADP release rate is similar to the cleavage rate, so that bound ATP and ADP would be the main states during the ATP cycle. Evidence is provided that the main structural rearrangements, which bring about DNA unwinding, are linked to these states.
The pharmacokinetics of antibiotics in cystic fibrosis (2020)

For systemic antibiotics, absorption is comparable in CF patients and non-CF controls. The volume of distribution (Vd) of most antibiotics is similar between people with CF with normal body composition and healthy individuals. However, there are a few exceptions, like cefotiam and tobramycin. Many antibiotic class-dependent changes in drug metabolism and excretion are reported, with an increased total body clearance for ß-lactam antibiotics, aminoglycosides, fluoroquinolones, and trimethoprim. We, therefore, recommend following class-specific guidelines for CF, mostly resulting in higher dosages per kg bodyweight in CF compared to non-CF controls. Higher local antibiotic concentrations in the airways can be obtained by inhalation therapy, with which eradication of bacteria may be achieved while minimizing systemic exposure and risk of toxicity.