gebhart/patrepeval huggingface dataset:
The algicidal mechanism of prodigiosin from Hahella sp. KA22 against Microcystis aeruginosa (2017)

In recent years, Microcystis aeruginosa blooms have occurred throughout the world, causing huge economic losses and destroying aquatic ecosystems. It is necessary to develop effective and ecofriendly methods to control M. aeruginosa blooms. Here, we report a high algicidal activity of prodigiosin (PG) against M. aeruginosa as well as the algicidal mechanism. PG showed high algicidal activity against M. aeruginosa, with a 50% lethal dose (LD<sub>50</sub>) of 5.87 μg/mL in 72 h. A combination of methods, including propidium iodide and Annexin V-fluorescein staining assays and light and electron microscopy indicated the existence of two modes of cell death with features similar to those in eukaryotic programmed cell death: necrotic-like and apoptotic-like. Biochemical and physiological analyses showed that PG generates reactive oxygen species (ROS), which induce lipid peroxidation, damage the membrane system and destroy the function of the photosystem. A proteomics analysis revealed that many proteins were differentially expressed in response to PG stress and that most of these proteins were involved in important metabolic processes, which may trigger necrotic-like or apoptotic-like cell death. The present study sheds light on the multiple toxicity mechanisms of PG on M. aeruginosa and its potential for controlling the occurrence of M. aeruginosa blooms in lakes.
Xanthone additives for blood storage that maintain its potential for oxygen delivery (1988)

Two xanthones, 2-hydroxyethoxy-6-(5-tetrazoyl) (BW A440C) and 2-ethoxy-6-(5-tetraozyl) (BW A827C), are members of a chemical series tested in vitro as potential additives to citrate-phosphate-dextrose-adenine (CPDA-1) medium for blood storage. P50 was maintained in the presence of these compounds during 42 days' storage by a partial maintenance of 2,3 diphosphoglycerate (2,3 DPG) and by a direct effect on hemoglobin previously reported for BW A827C. Red cell 2,3 DPG levels for BW A440C (n = 5), BW A827C (n = 5), and control (n = 6), respectively, were 3.38 +/- 0.47, 3.44 +/- 0.25, and 1.20 +/- 0.10 mM +/- SEM on day 7; 1.16 +/- 0.13, 1.52 +/- 0.37, and 0.16 +/- 0.02 mM on day 21; and 0.67 +/- 0.09, 0.61 +/- 0.08, and 0.06 +/- 0.006 mM on day 42. Red cell adenine triphosphate levels at the same time intervals were 1.84 +/- 0.09, 1.46 +/- 0.18, and 2.11 +/- 0.04 mM; 2.10 +/- 0.05, 2.07 +/- 0.17, and 2.13 +/- 0.05 mM; and 1.42 +/- 0.13, 1.37 +/- 0.13, and 1.38 +/- 0.06 mM, respectively. The degree of hemolysis was less with the addition of the compounds, and the methemoglobin formation, plasma Na+ and K+, and lactate production were unaffected by the compounds.
ChemInform Abstract: SYNTHESIS OF FERULIC ACID DERIVATIVES PART 3, AMIDES AND MANNICH BASES FROM VANILLALACETONE (1975)

Abstract Durch Umsetzung mit Thionylchlorid und den Aminen (II) wird Acetylferulasäure (I) in die Amide (III) übergeführt, aus denen durch Hydrolyse mit verdünnter Natronlauge oder mit konzentrierter Salzsäure und Methanol die Ferulasäureamide (IV) er = halten werden.
The Zinc Finger Gene <i>ZIC2</i> Has Features of an Oncogene and Its Overexpression Correlates Strongly with the Clinical Course of Epithelial Ovarian Cancer (2012)

ZIC2, a transcription factor related to the sonic hedgehog pathway, is a strong discriminant between MAL and LMP tumors: it may be a major determinant of outcome of EOTs.
A Cell-Free Translation–Translocation System Reconstituted with Subcellular Fractions from the Wall-less Variantfz;sg;os-1VofNeurospora crassa (1998)

A translation-translocation system reconstituted with subcellular fractions from the wall-less variant fz;sg;os-1V of Neurospora crassa reproduces in vitro translocation and processing of a secretory protein. The translation extract was isolated from the wall-less variant by gently lysing cells by a freeze-thaw procedure. This method yielded more extract then the method developed previously (R. Addison, J. Biol. Chem. 262: 17031, 1987) as well as reducing microsomal contamination. The microsomal fraction was isolated from lysed cells using a series of discontinuous sucrose gradients. The resultant microsomes were less inhibitory to translation of various transcripts and consisted of a more homogenous mixture of vesicles then microsomes prepared previously. Polyclonal antibodies directed against a polypeptide of approximately 75 kDa from the microsomes were used in indirect-immunofluorescence microscopy. The resultant fluorescent pattern shows a network of tubulo-reticular structures in a juxtanuclear region, which is the pattern expected of the rough endoplasmic reticulum.
Isolation and characterization of novel plasmid-encoded umuC mutants (1994)

Most inducible mutagenesis in Escherichia coli is dependent upon the activity of the UmuDC proteins. The role of UmuC in this process is poorly understood, possibly because of the limited number of genetically characterized umuC mutants. To better understand the function of the UmuC protein in mutagenic DNA repair, we have isolated several novel plasmid-encoded umuC mutants. A multicopy plasmid that expressed UmuC at physiological levels was constructed and randomly mutagenized in vitro by exposure to hydroxylamine. Mutated plasmids were introduced into the umu tester strain RW126, and 16 plasmids that were unable to promote umuC-dependent spontaneous mutator activity were identified by a colorimetric papillation assay. Interestingly, these plasmid mutants fell into two classes: (i) 5 were expression mutants that produced either too little or too much wild-type UmuC protein, and (ii) 11 were plasmids with structural changes in the UmuC protein. Although hydroxylamine mutagenesis was random, most of the structural mutants identified in the screen were localized to two regions of the UmuC protein; four mutations were found in a stretch of 30 amino acids (residues 133 to 162) in the middle of the protein, while four other mutations (three of which resulted in a truncated UmuC protein) were localized in the last 50 carboxyl-terminal amino acid residues. These new plasmid umuC mutants, together with the previously identified chromosomal umuC25, umuC36, and umuC104 mutations that we have also cloned, should prove extremely useful in dissecting the genetic and biochemical activities of UmuC in mutagenic DNA repair.
Catalytic Features of the Botulinum Neurotoxin A Light Chain Revealed by High Resolution Structure of an Inhibitory Peptide Complex (2008)

The Clostridium botulinum neurotoxin serotype A light chain (BoNT/A-LC) is a Zn(II)-dependent metalloprotease that blocks the release of acetylcholine at the neuromuscular junction by cleaving SNAP-25, one of the SNARE proteins required for exocytosis. Because of the potential for use of the toxin in bioterrorism and the increasingly widespread application of the toxin in the medical field, there is significant interest in the development of small-molecule inhibitors of the metalloprotease. Efforts to design such inhibitors have not benefited from knowledge of how peptides bind to the active site since the enzyme-peptide structures available previously either were not occupied in the vicinity of the catalytic Zn(II) ion or did not represent the product of SNAP-25 substrate cleavage. Herein we report the 1.4 A-resolution X-ray crystal structure of a complex between the BoNT/A-LC and the inhibitory peptide N-Ac-CRATKML, the first structure of the light chain with an inhibitory peptide bound at the catalytic Zn(II) ion. The peptide is bound with the Cys S gamma atom coordinating the metal ion. Surprisingly, the cysteine sulfur is oxidized to the sulfenic acid form. Given the unstable nature of this species in solution, is it likely that oxidation occurs on the enzyme. In addition to the peptide-bound structure, we report two structures of the unliganded light chain with and without the Zn(II) cofactor bound at 1.25 and 1.20 A resolution, respectively. The two structures are nearly identical, confirming that the Zn(II) ion plays a purely catalytic role. Additionally, the structure of the Zn(II)-bound uncomplexed enzyme allows identification of the catalytic water molecule and a second water molecule that occupies the same position as the peptidic oxygen in the tetrahedral intermediate. This observation suggests that the enzyme active site is prearranged to stabilize the tetrahedral intermediate of the protease reaction.
Raman spectra and athermal laser annealing of<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi mathvariant="normal">Ge</mml:mi><mml:mrow><mml:msub><mml:mrow><mml:mo>(</mml:mo><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">S</mml:mi></mml:mrow><mml:mrow><mml:mi>x</mml:mi></mml:mrow></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">Se</mml:mi></mml:mrow><mml:mrow><mml:mn>1</mml:mn><mml:mo>−</mml:mo><mml:mi>x</mml:mi></mml:mrow></mml:msub></mml:mrow><mml:mo>)</mml:mo></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math>glasses (1983)

We have measured and interpreted the Raman spectra of bulk $\mathrm{Ge}{({\mathrm{S}}_{x}{\mathrm{Se}}_{1\ensuremath{-}x})}_{2}$ glasses for compositions in the range $0\ensuremath{\le}x\ensuremath{\le}0.25$, both at low power levels and at sufficiently high power levels to induce thermally reversible (at $T\ensuremath{\lesssim}\frac{{T}_{g}}{2}$) athermal microcrystallization. Substitution of Se by S in ${\mathrm{G}\mathrm{e}({\mathrm{Se}}_{1/2})}_{4}$ tetrahedra produced narrow satellites to the narrow ${A}_{1}$ symmetric breathing mode which are easily resolved. The splittings of these satellites are compared to those of the corresponding molecular lines of $\mathrm{Ge}{\mathrm{Cl}}_{n}{\mathrm{Br}}_{4\ensuremath{-}n}$ and are the basis for the molecular models discussed in the accompanying paper of Aronovitz et al. Athermal microcrystallization is achieved near liquid-nitrogen temperature. Addition of S up to $x=0.25$ is found to inhibit but not prevent thermal revitrification at room temperature ${T}_{r}\ensuremath{\sim}\frac{{T}_{g}}{2}$ on a time scale of hours.
Oblique reconstructions in tomosynthesis. I. Linear systems theory (2013)

This work justifies the feasibility of oblique reconstructions in tomosynthesis. It is demonstrated that pitched test objects are most easily visualized with oblique reconstructions instead of conventional reconstructions. In order to achieve high image quality over a broad range of pitches, the object must be thin. By analyzing the effect of reconstruction pitch and object thickness on image quality, this paper generalizes the previous LS model for tomosynthesis.
Repair After Next Turn: The Last Structurally Provided Defense of Intersubjectivity in Conversation (1992)

Organizational features of ordinary conversation and other talk-in-interaction provide for the routine display of participants' understanding of one anothers' conduct and of the field of action, thereby building in a routine grounding for intersubjectivity. This same organization provides interactants the resources for recognizing breakdowns of intersubjectivity and for repairing them. This article sets the concern with intersubjectivity in theoretical context, sketches the organization by which it is grounded and defended in ordinary interaction, describes the practices by which trouble in understanding is dealt with, and illustrates what happens when this organization fails to function. Some consequences for contemporary theory and inquiry are suggested.
Application of Biotin, Digoxigenin or Fluorescein Conjugated Deoxynucleotides to Label DNA Strand Breaks for Analysis of Cell Proliferation and Apoptosis Using Flow Cytometry (1995)

A flow cytometric method has recently been developed using biotinylated dUTP (b-dUTP) in a reaction catalyzed by terminal deoxynucleotidyl transferase (TdT) to identify the endonuclease-induced DNA strand breaks occurring during apoptosis. Counterstaining of DNA makes it possible to relate apoptosis to cell cycle position or DNA index. In the present study, we compared this method with one using digoxigenin-conjugated dUTP (d-dUTP) to label apoptotic cells. The discrimination of apoptotic from nonapoptotic cells was similar when incorporation of d-dUTP was compared with b-dUTP. Both techniques resulted in a 20-30 fold increase in staining of apoptotic over nonapoptotic cells although somewhat less background fluorescence was observed with the d-dUTP. Direct labeling with fluoresceinated dUTP (f-dUTP) was less sensitive in detecting DNA strand breaks, but had the advantage of simplicity. The principle of labeling DNA strand breaks using TdT was also employed to identify DNA replicating cells. To this end, the cells were incubated in the presence of BrdUrd, then exposed to UV light to selectively photolyse DNA containing the incorporated BrdUrd. DNA strand breaks resulting from the photolysis were then labeled with b-dUTP or d-dUTP. This approach is an alternative to immunocytochemical detection of BrdUrd incorporation, but unlike the latter does not require prior DNA denaturation, thus can be applied when the denaturation step must be avoided. The method was sensitive enough to recognize DNA synthesizing cells that were incubated with BrdUrd for only 5 min, the equivalent of replication of less than 1% of the cell's genome. The discrimination between apoptotic vs. BrdUrd incorporating-cells is based on different extractability of DNA following cell fixation. This method can be applied to analyze both cell proliferation (DNA replication) and death (by apoptosis) in a single measurement.
Bone Regeneration <i>via</i> a Mineral Substrate and Induced Angiogenesis (2004)

Angiogenesis and biomineral substrates play major roles in bone development and regeneration. We hypothesized that macroporous scaffolds of biomineralized 85:15 poly(lactide-co-glycolide), which locally release vascular endothelial growth factor-165 (VEGF), would direct simultaneous regeneration of bone and vascular tissue. The presence of a bone-like biomineral substrate significantly increased regeneration of osteoid matrix (32 +/- 7% of total tissue area; mean +/- SD; p < 0.05) and mineralized tissue (14 +/- 2%; P < 0.05) within a rat cranium critical defect compared with a non-mineralized polymer scaffold (19 +/- 8% osteoid and 10 +/- 2% mineralized tissue). Further, the addition of VEGF to a mineralized substrate significantly increased the generation of mineralized tissue (19 +/- 4%; P < 0.05) compared with mineralized substrate alone. This appeared to be due to a significant increase in vascularization throughout VEGF-releasing scaffolds (52 +/- 9 vessels/mm(2); P < 0.05) compared with mineralized scaffolds without VEGF (34 +/- 4 vessels/mm(2)). Surprisingly, there was no significant difference in total osteoid between the two samples, suggesting that increased vascularization enhances mineralized tissue generation, but not necessarily osteoid formation. These results indicate that induced angiogenesis can enhance tissue regeneration, supporting the concept of therapeutic angiogenesis in tissue-engineering strategies.
Design and networking considerations for FACE (2004)

As we step into the twenty first century, we are surrounded by technology wearing its way into our day-to-day life. making every aspect of it more convenient and organized. Yet, in every household there is one front, i.e. the process of cooking, which has not been sufficiently automated. Even in a commercial environment (restaurant kitchens), the process of cooking remains largely manual. We investigate the potential for a fully automated cooking environment (FACE). We start by describing the architecture of FACE and present an overview of its components and their functionality. Then, we explore communication considerations between various FACE components and discuss existing solutions for addressing the basic networking needs. We also provide a detailed example to describe the workflow in FACE and help illustrate the communication requirements between FACE components. Ultimately, our aim is to provide the vision for a flexible, highly integrated and fully coordinated cooking environment.
Over-the-counter Analgesics: A Toxicologic Perspective (2002)

The decision to use any analgesic is a balance of benefit and risk. In the case of analgesics, it is important to balance the therapeutic benefit against both the risk in therapeutic use and the risk (and ease of treatment) in overdose. Paracetamol in therapeutic dose carries little risk of adverse events. Less than 0.1% of the estimated 30 million paracetamol users in the United Kingdom attend hospital with a paracetamol overdose each year, and approximately 200 people die, most of whom presented late or did not receive antidote, N-acetylcysteine, within 12 hours. Nonsteriodal anti-inflammatory drugs (NSAIDs) have greater adverse effects in therapeutic use than paracetamol but also have a lower incidence of severe features or death in overdose. There is no antidote available for NSAID poisoning. Aspirin carries both significant adverse effects in therapeutic dose and a substantial risk in overdose, for which there is no antidote. Its risk-benefit profile is probably the poorest of all analgesics currently available over-the-counter (OTC); this is reflected in current trends both in analgesic use and overdose figures. Although a number of options to reduce deaths from poisoning by OTC analgesics have been considered, few are practical, and all must take account of the public health benefits provided by these drugs. A perspective should be retained that the vast majority of the population in Australia, the United States, the United Kingdom, and Denmark derive therapeutic benefit from OTC analgesics and do not take them in overdose. The majority of those who do take overdoses come to little or no harm. Management of serious poisoning by paracetamol, aspirin, or NSAIDs remains a medical challenge.
Phenyl-substituted fluorene-dimer cored anthracene derivatives: highly fluorescent and stable materials for high performance organic blue- and white-light-emitting diodes (2010)

A new series of highly fluorescent blue-emitting materials based on fluorene and anthracene hybrids are designed and synthesized for organic light-emitting diodes (OLEDs). These materials feature a phenyl-substituted fluorene dimer as a bulky and rigid core and anthracene as a functional active group. The novel use of a phenyl-substituted fluorene dimer as building skeleton to design functional molecules is reported for the first time. The thermal, photophysical, electrochemical, and electroluminescent (EL) properties are presented, as well as combined density functional study of their geometry and electronic structure. These compounds show excellent thermal resistance with high glass transition temperature (Tg) in the range 159–257 °C, thermal decomposition temperature (Td) 441–495 °C, and high fluorescent quantum yield (ΦF = 0.61–0.96, relative to 9,10-diphenylanthracene) as well as good film-forming and morphological stability. Remarkably, high-performance blue OLEDs are also fabricated in a simple three-layer device architecture using these compounds as emissive layer with luminance efficiency of 2.2–5.1 cd A−1 as a non-doped blue emitter and even higher efficiency of up to 13.6 cd A−1 and maximum external quantum efficiency 4.8% is obtained when doped a blue fluorescent dye, 4,4′-(1E,1′E)-2,2′(biphenyl-4,4′diyl)bis(ethane-2,1-diyl)bis(N,N-dip-tolyaniline) (DPAVBi). Furthermore, we fabricate highly efficient fluorescent white OLEDs employing an interesting emission in the longer wavelength of one of our compound combined with DPAVBi emission to achieve stable white light emission in a binary blend single emissive layer with high efficiency of 14.8 cd A−1 (5.3 lm W−1) and maximum brightness of 50248 cd m−2.
Bidirectional pumping of Er-doped fibers using detuned 980-nm lasers (2002)

A two-directional configuration with two fiber Bragg grating stabilized 980-nm lasers pumping an erbium-doped fiber coil and delivering up to 23-dBm output power is presented. Operating conditions leading to stable operation are discussed in terms of pump detuning and power. Configuration with no pump wavelength detuning is also discussed.
SULFUR: NEW USES NEEDED (1972)

THIS ARTICLE DESCRIBES BRIEFLY THE WORK NOW IN PROGRESS TO DEVELOP NEW USES FOR THE STOCKPILES OF RECOVERED SULFUR FROM VARIOUS AIR-POLLUTION-ABATEMENT PROGRAMS. A GREAT DEAL OF TESTING AND DEVELOPMENT IS GOING FORWARD, ESPECIALLY FOR ROAD-SURFACE AND SUBSURFACE APPLICATIONS. ONE SOURCE OF WASTE AGGREGATE WOULD BE SULFATED LIMESTONE FROM FLUE-GAS SCRUBBING PLANTS. ELEMENTAL SULFUR MAY BE SUBSTITUTED FOR LIMESTONE AGGREGATE IN ASPHALT PAVING MATERIAL UP TO ABOUT 13% OF THE COMPOSITION. INVESTIGATIONS INTO FLYASH FORMULATIONS HAVE LED TO THE LIKELIHOOD OF USING WASTE SULFATE IN CONCRETE-LIKE MIXTURES. SULFUR FOAM, AS SUBSURFACE INSULATION, COULD BE USED IN EVEN HIGHER VOLUMES FOR HIGHWAYS. DEVELOPMENT OF A TRAFFIC PAINT, STARTED OVER TEN YEARS AGO, HAS NOT REACHED COMMERCIALIZATION.
Experimental investigation of the compressibility behaviour of cement-solidified/stabilised zinc-contaminated kaolin clay (2014)

Heavy metal contamination has become a major environmental pollution issue in China, especially under the process of rapid urbanisation. Zinc contaminants are reported to be especially harmful for local ecosystems and biodiversity. In this study, a cement-based solidification/stabilisation technique was adopted to remediate zinc-contaminated kaolin clay and a series of one-dimensional oedometer tests was performed to investigate the compressibility of cement-stabilised zinc-contaminated soils. Compression curves were analysed using a simulation of the logistic function, and the yield stress (σ′ vp ), swelling index (C s ) at the pre-yield state and compression index (C c ) at the post-yield state were derived on the basis of the mathematical simulation. The effects of zinc concentration on σ′ vp , C s and C c are discussed. It is found that relatively high zinc concentrations (i.e. >0·1%) significantly influence the compression parameters and hence deteriorate the resistance to compression of the stabilised soils. The reduction in resistance to compression at high zinc concentrations is intrinsically attributed to the destruction of cementation structure/bonding in the stabilised soils. Physicochemically, this is attributed to the retardation effect of zinc contaminants on cement hydration processes.
Hybrid quantum dot-tin disulfide field-effect transistors with improved\nphotocurrent and spectral responsivity (2016)

We report an improved photosensitivity in few-layer tin disulfide (SnS2) field-effect transistors (FETs) following doping with CdSe/ZnS core/shell quantum dots (QDs). The hybrid QD-SnS2 FET devices achieve more than 500% increase in the photocurrent response compared with the starting SnS2-only FET device and a spectral responsivity reaching over 650 A/W at 400 nm wavelength. The negligible electrical conductance in a control QD-only FET device suggests that the energy transfer between QDs and SnS2 is the main mechanism responsible for the sensitization effect, which is consistent with the strong spectral overlap between QD photoluminescence and SnS2 optical absorption as well as the large nominal donor-acceptor interspacing between QD core and SnS2. We also find enhanced charge carrier mobility in hybrid QD-SnS2 FETs which we attribute to a reduced contact Schottky barrier width due to an elevated background charge carrier density.