gebhart/patrepeval huggingface dataset:
Endoplasmic Reticulum Stress Proteins Block Oxidant-induced Ca2+ Increases and Cell Death (1998)

Oxidants are important human toxicants. Increased intracellular free Ca2+ may be critical for oxidant toxicity, but this mechanism remains controversial. Furthermore, oxidants damage the endoplasmic reticulum (ER) and release ER Ca2+, but the role of the ER in oxidant toxicity and Ca2+ regulation during toxicity is also unclear. tert-Butylhydroperoxide (TBHP), a prototypical organic oxidant, causes oxidative stress and an increase in intracellular free Ca2+. Therefore, we addressed the mechanism of oxidant-induced cell death and investigated the role of ER stress proteins in Ca2+ regulation and cytoprotection after treating renal epithelial cells with TBHP. Prior ER stress induces expression of the ER stress proteins Grp78, Grp94, and calreticulin and rendered cells resistant to cell death caused by a subsequent TBHP challenge. Expressing antisense RNA targeted to grp78 prevents grp78 induction sensitized cells to TBHP and disrupted their ability to develop cellular tolerance. In addition, overexpressing calreticulin, another ER chaperone and Ca2+-binding protein, also protected cells against TBHP. Interestingly, neither prior ER stress nor calreticulin expression prevented lipid peroxidation, but both blocked the rise in intracellular free Ca2+ after TBHP treatment. Loading cells with EGTA, even after peroxidation had already occurred, also prevented TBHP-induced cell death, indicating that buffering intracellular Ca2+ prevents cell killing. Thus, Ca2+ plays an important role in TBHP-induced cell death in these cells, and the ER is an important regulator of cellular Ca2+ homeostasis during oxidative stress. Given the importance of oxidants in human disease, it would appear that the role of ER stress proteins in protection from oxidant damage warrants further consideration.
Cytotoxic effects of Mn(III)N-alkylpyridylporphyrins in the presence of cellular reductant, ascorbate (2011)

Due to the ability to easily accept and donate electrons Mn(III)N-alkylpyridylporphyrins (MnPs) can dismute O(2)(·-), reduce peroxynitrite, but also generate reactive species and behave as pro-oxidants if conditions favour such action. Herein two ortho isomers, MnTE-2-PyP(5+), MnTnHex-2-PyP(5+), and a meta isomer MnTnHex-3-PyP(5+), which differ greatly with regard to their metal-centered reduction potential, E(1/2) (Mn(III)P/Mn(II)P) and lipophilicity, were explored. Employing Mn(III)P/Mn(II)P redox system for coupling with ascorbate, these MnPs catalyze ascorbate oxidation and thus peroxide production. Consequently, cancer oxidative burden may be enhanced, which in turn would suppress its growth. Cytotoxic effects on Caco-2, Hela, 4T1, HCT116 and SUM149 were studied. When combined with ascorbate, MnPs killed cancer cells via peroxide produced outside of the cell. MnTE-2-PyP(5+) was the most efficacious catalyst for peroxide production, while MnTnHex-3-PyP(5+) is most prone to oxidative degradation with H(2) , and thus the least efficacious. A 4T1 breast cancer mouse study of limited scope and success was conducted. The tumour oxidative stress was enhanced and its microvessel density reduced when mice were treated either with ascorbate or MnP/ascorbate; the trend towards tumour growth suppression was detected.
Effects of Substitution of Proposed Zn(II) Ligand His81 or His64 in Phage T4 Gene 32 Protein: Spectroscopic Evidence for a Novel Zinc Coordination Complex (1994)

T4 gene 32 protein (gp32), the prototype helix-destabilizing or single-stranded (ss) DNA binding protein, contains one tightly coordinated Zn2+ ion bound tetrahedrally by three cysteines (residues 77, 87, and 90) and a fourth non-thiol donor. In previous work, it was shown that the proposed non-thiol ligand His81 could be readily substituted with nonliganding glutamine and alanine residues without deleterious effects on gp32 structure and simple assays of ssDNA binding. In this paper we show that exchange broadening of bulk 35Cl- anion by protein-bound Zn(II) is not observed in the His81-->Ala (H81A) mutant, unless the coordination site is disrupted with an organomercurial, p-mercuriphenylsulfonate. This suggests that, in the mutant protein, anions, and by implication solvent molecules, do not gain access to a newly formed inner shell Zn(II) coordination site as a result of mutagenesis. H81A gp32 is characterized by nearly wild-type helix-destabilizing activity on poly(d[A-T]) and highly cooperative binding to the polynucleotide poly(A) at pH 7.7 over the temperature range from 20 to 42 degrees C at 0.35 M NaCl, exhibiting only a approximately 2.5-4-fold decrease in poly(A) affinity. Limited proteolysis experiments show that an additional tryptic cleavage site maps to the Arg111-Lys112 bond within the protease-resistant core domain of the H81A gp32 following long incubation times and results in the accumulation of a 16-kDa subcore fragment. This new cleavage site is within the internal LAST motif, which has been proposed to be directly involved in cooperative ssDNA binding [Casas-Finet, J. R., & Karpel, R. L. (1993) Biochemistry 32, 9735-9744]. Thus substitution of His81 with Ala subtly alters the conformation or dynamics of the backbone around the LAST motif, which may be manifest as a moderately lower cooperative binding affinity of H81A gp32 for polynucleotides. H81A gp32, however, is fully functional in stimulating in vitro homologous pairing catalyzed by the T4 recombinase uvsX protein. Since substitution of His81 with a nonliganding Ala is nearly silent, we propose an alternative mode of Zn(II) coordination in T4 gene 32 protein, involving His64 rather than His81 as the fourth non-thiol ligand. That replacement of His64, and not His81, with Cys results in marked changes in the first coordination sphere of ligands as evidenced by the optical spectrum of Co(II)-substituted H64C gp32 is consistent with the noninvolvement of His81 and implicates a novel His64-X12-Cys77-X9-Cys87-X2-Cys90 coordination motif, unique among zinc-containing nucleic acid binding proteins.
Respiratory Nitrate Ammonification byShewanella oneidensisMR-1 (2006)

Anaerobic cultures of Shewanella oneidensis MR-1 grown with nitrate as the sole electron acceptor exhibited sequential reduction of nitrate to nitrite and then to ammonium. Little dinitrogen and nitrous oxide were detected, and no growth occurred on nitrous oxide. A mutant with the napA gene encoding periplasmic nitrate reductase deleted could not respire or assimilate nitrate and did not express nitrate reductase activity, confirming that the NapA enzyme is the sole nitrate reductase. Hence, S. oneidensis MR-1 conducts respiratory nitrate ammonification, also termed dissimilatory nitrate reduction to ammonium, but not respiratory denitrification.
A Monolithically Integrated Pressure/Oxygen/Temperature Sensing SoC for Multimodality Intracranial Neuromonitoring (2014)

A fully integrated SoC for multimodality intracranial neuromonitoring is presented in this paper. Three sensors including a capacitive MEMS pressure sensor, an electrochemical oxygen sensor and a solid-state temperature sensor are integrated together in a single chip with their respective interface circuits. Chopper stabilization and dynamic element matching techniques are applied in sensor interface circuits to reduce circuit noise and offset. On-chip calibration is implemented for each sensor to compensate process variations. Measured sensitivity of the pressure, oxygen, and temperature sensors are 18.6 aF/mmHg, 194 pA/mmHg, and 2 mV/°C, respectively. Implemented in 0.18 m CMOS, the SoC occupies an area of 1.4 mm × 4 mm and consumes 166 μW DC power. A prototype catheter for intracranial pressure (ICP) monitoring has been implemented and the performance has been verified with ex vivo experiment.
Surface structure and properties of plant seed oil bodies (1992)

Storage triacylglycerols (TAG) in plant seeds are present in small discrete intracellular organelles called oil bodies. An oil body has a matrix of TAG, which is surrounded by phospholipids (PL) and alkaline proteins, termed oleosins. Oil bodies isolated from mature maize (Zea mays) embryos maintained their discreteness, but coalesced after treatment with trypsin but not with phospholipase A2 or C. Phospholipase A2 or C exerted its activity on oil bodies only after the exposed portion of oleosins had been removed by trypsin. Attempts were made to reconstitute oil bodies from their constituents. TAG, either extracted from oil bodies or of a 1:2 molar mixture of triolein and trilinolein, in a dilute buffer were sonicated to produce droplets of sizes similar to those of oil bodies; these droplets were unstable and coalesced rapidly. Addition of oil body PL or dioleoyl phosphatidylcholine, with or without charged stearylamine/stearic acid, or oleosins, to the medium before sonication provided limited stabilization effects to the TAG droplets. High stability was achieved only when the TAG were sonicated with both oil body PL (or dioleoyl phosphatidylcholine) and oleosins of proportions similar to or higher than those in the native oil bodies. These stabilized droplets were similar to the isolated oil bodies in chemical properties, and can be considered as reconstituted oil bodies. Reconstituted oil bodies were also produced from TAG of a 1:2 molar mixture of triolein and trilinolein, dioleoyl phosphatidylcholine, and oleosins from rice (Oryza sativa), wheat (Triticum aestivum), rapeseed (Brassica napus), soybean (Glycine max), or jojoba (Simmondsia chinensis). It is concluded that both oleosins and PL are required to stabilize the oil bodies and that oleosins prevent oil bodies from coalescing by providing steric hindrance. A structural model of an oil body is presented. The current findings on seed oil bodies could be extended to the intracellular storage lipid particles present in diverse organisms.
Short‐term evaluation of autologous transplantation of bone marrow–derived mesenchymal stem cells in patients with cirrhosis: Egyptian study (2013)

This study suggested the safety, feasibility, and efficacy of the intrasplenic injection of autologous BM stromal cells in improving liver function in Egyptian patients with cirrhosis.
Heterogeneous photocatalyst materials for water splitting (2008)

This critical review shows the basis of photocatalytic water splitting and experimental points, and surveys heterogeneous photocatalyst materials for water splitting into H2 and O2, and H2 or O2 evolution from an aqueous solution containing a sacrificial reagent. Many oxides consisting of metal cations with d0 and d10 configurations, metal (oxy)sulfide and metal (oxy)nitride photocatalysts have been reported, especially during the latest decade. The fruitful photocatalyst library gives important information on factors affecting photocatalytic performances and design of new materials. Photocatalytic water splitting and H2 evolution using abundant compounds as electron donors are expected to contribute to construction of a clean and simple system for solar hydrogen production, and a solution of global energy and environmental issues in the future (361 references).
Irreversible Electroporation of the Pancreas Using Parallel Plate Electrodes in a Porcine Model: A Feasibility Study (2017)

Pancreatic tissue can be successfully ablated using two parallel paddles around the tissue. A serial application of 4x50J was most effective in creating a homogeneous necrotic lesion.
Dielectrophoresis: Using Inhomogeneous AC Electrical Fields to Separate and Manipulate Cells (1996)

AbstractDielectrophoresis is the motion of particles caused by electrical polarization effects in inhomogeneous (nonuniform) electric fields. Unlike electrophoresis, the particles do not require a net electrical charge for motion to occur and AC rather than DC fields are employed to exploit the dielectric properties of the particles. Factors controlling the effective dielectric properties of cells and microorganisms include electrical double layers associated with surface charges, the conductivity and permittivity of their membranes and any cell walls, and their morphologies and structural architectures. In recent years, several laboratories have developed separation and manipulation techniques for cells and microorganisms based on dielectrophoresis, using both static and traveling AC fields. In this article, the basic physical factors influencing the dielectrophoretic behavior of particles are outlined, and ways in which these can be employed to achieve selective separation of cells and microorganisms are described.Key Words: bacteriabioparticlescell fractionationdielectric polarizabilitymicroelectrodesselective separation
Vertical-injection top-emitting quantum-well lasers using transparent conductive metal-oxide contacts (1991)

Due to the vertical cavity property of the vertical-cavity surface-emitting Lasers (VCSELs), the optical path is parallel with the current path. This makes the designs of contacts and mirrors more complicated than with horizontal-cavity lasers. Several schemes have been used to solve this difficulty. One is a top-emitting laser with a tunneled current passing through the ion damaged region.1 Another scheme is a bottom-emitting laser with etched substrate.2 In this work, a vertical-injection top-emitting scheme is employed.3,4 Optically transparent and electrically conductive cadmium tin oxide is used for the first time as contacts right on top of the laser emitting windows. The current is vertically injected into the active region. Using this new vertical-injection configuration, the current does not have to go through the ion damaged region, which has higher resistance, and the resistance induced heating is minimized. At the same time, top-emission is maintained to simplify the structure.
Novel Poly(amido‐amine)‐Based Hydrogels as Scaffolds for Tissue Engineering (2005)

Biodegradable and biocompatible amphoteric poly(amido-amine) (PAA)-based hydrogels, containing carboxyl groups along with amino groups in their repeating unit, were considered as scaffolds for tissue engineering applications. These hydrogels were obtained by co-polymerising 2,2-bisacrylamidoacetic acid with 2-methylpiperazine with or without the addition of different mono-acrylamides as modifiers, and in the presence of primary bis-amines as crosslinking agents. Hybrid PAA/albumin hydrogels were also prepared. The polymerisation reaction was a Michael-type polyaddition carried out in aqueous media. The PAA hydrogels were soft and swellable materials. Cytotoxicity tests were carried out by the direct contact method with fibroblast cell lines on the hydrogels both in their native state (that is, as free bases) and as salts with acids of different strength, namely hydrochloric, sulfuric, acetic and lactic acid. This was done in order to ascertain whether counterion-specific differences in cytotoxicity existed. It was found that all the amphoteric PAA hydrogels considered were cytobiocompatible both as free bases and salts. Selected hydrogels samples underwent degradation tests under controlled conditions simulating biological environments, i.e. Dulbecco medium at pH 7.4 and 37 degrees C. All samples degraded completely and dissolved within 10 d, with the exception of hybrid PAA/albumin hydrogels that did not dissolve even after eight months. The degradation products of all samples turned to be non-cytotoxic. All these results led us to conclude that PAA-based hydrogels have a definite potential as degradable matrices for biomedical applications.
Biphenyltetrols and Dibenzofuranones from Oxidative Coupling of Resorcinols with 4‐Alkylpyrocatechols: New Ciues to the Mechanism of Insect Cuticle Sclerotization (1991)

Abstract Oxidation of 4‐alkylpyrocatechols 2 by means of an insect diphenoloxidase (laccase) or K 3 [Fe(CN) 6 ] yields, in the presence of resorcinols 1 (R 2  H), complex mixtures of products from which biphenyltetrols 3 (R 3  H) and dibenzofuranones 5 and 6 were isolated. It is suggested that similar homo‐coupling products are formed from pyrocatechols 2b and 2c in insects during cuticle sclerotization.
Matchmaking for online games and other latency-sensitive P2P systems (2009)

The latency between machines on the Internet can dramatically affect users' experience for many distributed applications. Particularly, in multiplayer online games, players seek to cluster themselves so that those in the same session have low latency to each other. A system that predicts latencies between machine pairs allows such matchmaking to consider many more machine pairs than can be probed in a scalable fashion while users are waiting. Using a far-reaching trace of latencies between players on over 3.5 million game consoles, we designed Htrae, a latency prediction system for game matchmaking scenarios. One novel feature of Htrae is its synthesis of geolocation with a network coordinate system. It uses geolocation to select reasonable initial network coordinates for new machines joining the system, allowing it to converge more quickly than standard network coordinate systems and produce substantially lower prediction error than state-of-the-art latency prediction systems. For instance, it produces 90th percentile errors less than half those of iPlane and Pyxida. Our design is general enough to make it a good fit for other latency-sensitive peer-to-peer applications besides game matchmaking.
Stable Curved Theta-Pinch Plasma in a Series of Caulked Cusp Fields (1970)

Curved theta-pinch experiments show that a toroidal drift of plasma is suppressed by a series of caulked cusp fields, produced with the aid of metal rings located inside the discharge tube. The introduction of rings is effective in the suppression of toroidal drift of the initial high-beta plasma, as well as in the stabilization of low-beta plasma in the later stage.
The oncofetal domain of fibronectin defined by monoclonal antibody FDC-6: its presence in fibronectins from fetal and tumor tissues and its absence in those from normal adult tissues and plasma. (1985)

An IgG1 monoclonal antibody, FDC-6, was established, which defines a unique fibronectin (FN) domain, located between the "Hep-2" and the "Fib-2" domains, in the COOH-terminal region of FNs isolated from hepatoma, sarcoma, and fetal fibroblasts. A systematic study with this antibody indicates the presence of two classes of human FNs. (i) FN from fetal connective tissue, placenta, amniotic fluid, hepatoma, and colon carcinoma as well as cell lines from fetal tissues (WI-38), hepatomas (HuH-6 and HuH-7), and sarcoma (VA13) was characterized by the presence of the FDC-6-defined domain and by a high molecular weight (subunit Mr, 310,000-335,000). (ii) In contrast, FN from normal adult tissues and plasma was characterized by a lower molecular weight (subunit Mr, 285,000-295,000) and lack of reactivity with FDC-6 and is therefore devoid of the FDC-6-defined domain. The FDC-6-defined domain is therefore called the "oncofetal" domain, and FN containing this domain is hereby called "oncofetal FN" (onf FN). The onf FN is similar to the previously known "cellular-form" FN. FN from normal adult tissues and plasma, lacking the oncofetal domain, is hereby called "normal FN" (nor FN). The nor FN is similar to the previously known "plasma-form" FN. Development of FN from fetal to adult form is associated with loss of the oncofetal domain defined by the FDC-6 antibody, and oncogenic transformation is associated with activation in synthesis of the oncofetal domain defined by the FDC-6 antibody.
<title>Shape measurement by temporal phase unwrapping and spatial light modulator-based fringe projector</title> (1997)

A fringe projector based on a low-cost spatial light modulator has been used to measure the shapes of discontinuous objects. By changing the fringe phase and the fringe pitch, a sequence of wrapped phase maps can be acquired at different sensitivities. This sequence can then be converted to surface profile by the recently-proposed method of temporal unwrapping rather than by a conventional spatial unwrapping approach. The main advantages are that the method is simple and robust, and that objects with surface discontinuities are profiled as easily and accurately as smooth ones. Modifications to the basic temporal unwrapping method are proposed which provide significant improvements in reliability, accuracy and computation time.
Humoral immunity to AAV vectors in gene therapy: challenges and potential solutions. (2013)

Gene transfer trials with adeno-associated virus (AAV) vectors have initiated to unveil the therapeutic potential of this approach, with some of the most exciting results coming from clinical studies of gene transfer for hemophilia B, congenital blindness, and the recent market approval of the first AAV-based gene therapy in Europe. With clinical development, however, some of the limitations of in vivo gene transfer have emerged; in particular the host immune system represents an important obstacle to be overcome in terms of both safety and efficacy of gene transfer in vivo with AAV vectors. Results in humans undergoing gene transfer indicate that capsid-specific T cell responses directed against transduced cells may limit the duration of transgene expression following AAV gene transfer, and similarly anti-AAV neutralizing antibodies can completely prevent transduction of a target tissue, resulting in lack of efficacy. Anti-AAV neutralizing antibodies are highly prevalent in humans, and the frequency of subjects with detectable titers can reach up to two thirds of the population. The approach to the problem of preexisting humoral immunity to AAV so far has been the exclusion of seropositive subjects, but this solution is far from being optimal. Several additional strategies have been proposed and tested in a variety of preclinical animal models. Future studies will help defining the optimal strategy, or combination of strategies, to successfully treat subjects with preexisting antibodies to AAV due to natural infection or to prior administration of AAV vectors. These advancements will likely have a significant impact on the field of gene transfer with AAV vectors.
Tunnel magnetoresistance of 604% at 300K by suppression of Ta diffusion in CoFeB∕MgO∕CoFeB pseudo-spin-valves annealed at high temperature (2008)

The authors observed tunnel magnetoresistance (TMR) ratio of 604% at 300K in Ta∕Co20Fe60B20∕MgO∕Co20Fe60B20∕Ta pseudo-spin-valve magnetic tunnel junction annealed at 525°C. To obtain high TMR ratio, it was found critical to anneal the structure at high temperature above 500°C, while suppressing the Ta diffusion into CoFeB electrodes and in particular to the CoFeB∕MgO interface. X-ray diffraction measurement of MgO on SiO2 or Co20Fe60B20 shows that an improvement of MgO barrier quality, in terms of the degree of the (001) orientation and stress relaxation, takes place at annealing temperatures above 450°C. The highest TMR ratio observed at 5K was 1144%.