gebhart/patrepeval huggingface dataset:
Highly Enantioselective Alkynylation of Trifluoropyruvate with Alkynylsilanes Catalyzed by the BINAP−Pd Complex: Access to α-Trifluoromethyl-Substituted Tertiary Alcohols (2010)

A highly enantioselective alkynylation catalyzed by the dicationic (S)-BINAP−Pd complex with a variety of alkynylsilanes and trifluoropyruvate is described. The catalytic reaction is applicable to highly enantioselective addition of polyyne to trifluoropyruvate to construct α-trifluoromethyl-substituted tertiary alcohols as enantiomerically enriched forms. The alkynyl products can be converted into a chiral allene bearing a trifluoromethyl group.
The Coenzyme A Biosynthetic Enzyme Phosphopantetheine Adenylyltransferase Plays a Crucial Role in Plant Growth, Salt/Osmotic Stress Resistance, and Seed Lipid Storage (2008)

Coenzyme A (CoA) is an essential cofactor in the metabolism of both prokaryotic and eukaryotic organisms and a universal five-step pathway is utilized to synthesize CoA from pantothenate. Null mutations in two of the five steps of this pathway led to embryo lethality and therefore viable reduction-of-function mutations are required to further study its role in plant biology. In this article, we have characterized a viable Arabidopsis (Arabidopsis thaliana) T-DNA mutant affected in the penultimate step of the CoA biosynthesis pathway, which is catalyzed by the enzyme phosphopantetheine adenylyltransferase (PPAT). This ppat-1 knockdown mutation showed an approximately 90% reduction in PPAT transcript levels and was severely impaired in plant growth and seed production. The sum of CoA and acetyl-CoA levels was severely reduced (60%-80%) in ppat-1 seedlings compared to wild type, and catabolism of storage lipids during seedling establishment was delayed. Conversely, PPAT overexpressing lines showed, on average, approximately 1.6-fold higher levels of CoA + acetyl-CoA levels, as well as enhanced vegetative and reproductive growth and salt/osmotic stress resistance. Interestingly, dry seeds of overexpressing lines contained between 35% to 50% more fatty acids than wild type, which suggests that CoA biosynthesis plays a crucial role in storage oil accumulation. Finally, biochemical analysis of the recombinant PPAT enzyme revealed an inhibitory effect of CoA on PPAT activity. Taken together, these results suggest that the reaction catalyzed by PPAT is a regulatory step in the CoA biosynthetic pathway that plays a key role for plant growth, stress resistance, and seed lipid storage.
Direct measurement and matched-field inversion approaches to array shape estimation (1996)

Accurate knowledge of array shape is essential for carrying out full wavefield (matched-field) processing. Direct approaches to array element localization (AEL) include both nonacoustic (tilt-heading sensors) and acoustic (high-frequency, transponder-based navigation) methods. The low-frequency signature emitted from a distant source also can be used in an inversion approach to determine array shape. The focus of this paper is on a comparison of the array shape results from these three different methods using data from a 120-m aperture vertical array deployed during SWellEx-3 (Shallow Water evaluation cell Experiment 3). Located 2 m above the shallowest array element was a self-recording package equipped with depth, tilt, and direction-of-tilt sensors, thereby permitting AEL to be performed non-acoustically. Direct AEL also was performed acoustically by making use of transponder pings (in the vicinity of 12 kHz) received by high-frequency hydrophones spaced every 7.5 m along the vertical array. In addition to these direct approaches, AEL was carried out using an inversion technique where matched-field processing was performed on a multitone (50-200 Hz), acoustic source at various ranges and azimuths from the array. As shown, the time-evolving array shape estimates generated by all three AEL methods provide a consistent picture of array motion throughout the 6-h period analyzed.
A Small-Angle Neutron Scattering Study of Water in Carbon Dioxide Microemulsions (1997)

Phase behavior and small angle neutron scattering (SANS) experiments were performed on mixtures of D2O/CO2/ammonium carboxylate perfluoropolyether (PFPE) surfactant as a function of pressure (192−287 bar) and D2O composition (0.8−2.0 wt %) at 35 °C. SANS measurements provided direct evidence of water-swollen inverted micelles in CO2. At a constant PFPE concentration of 2.1 wt % in CO2, the microemulsion core radius increased from 20 to 36 Å as the D2O concentration increased from 0.8 to 2.0 wt %. For a constant water concentration, parameters extracted from model fits of the SANS spectra indicated that as the phase boundary was approached on reducing pressure, micellar structure remained essentially unchanged, while critical fluctuations increased.
A family of transcripts encoding water channel proteins: tissue-specific expression in the common ice plant. (1995)

Seawater-strength salt stress of the ice plant (Mesembryanthemum crystallinum) initially results in wilting, but full turgor is restored within approximately 2 days. We are interested in a mechanistic explanation for this behavior and, as a requisite for in-depth biochemical studies, have begun to analyze gene expression changes in roots coincident with the onset of stress. cDNAs that suggested changes in mRNA amount under stress were found; their deduced amino acid sequences share homologies with proteins of the Mip (major intrinsic protein) gene family and potentially encode aquaporins. One transcript, MipB, was found only in root RNA, whereas two other transcripts, MipA and MipC, were detected in roots and leaves. Transcript levels of MipB were of low abundance. All transcripts declined initially during salt stress but later recovered to at least prestress level. The most drastic decline was in MipA and MipC transcripts. MipA mRNA distribution in roots detected by in situ hybridization indicated that the transcript was present in all cells in the root tip. In the expansion zone of the root where vascular bundles differentiate, MipA transcript amounts were most abundant in the endodermis. In older roots, which had undergone secondary growth, MipA was highly expressed in cell layers surrounding individual xylem strands. MipA was also localized in leaf vascular tissue and, in lower amounts, in mesophyll cells. Transcripts for MipB seemed to be present exclusively in the tip of the root, in a zone before and possibly coincident with the development of a vascular system. MipA- and MipB-encoded proteins expressed in Xenopus oocytes led to increased water permeability. mRNA fluctuations of the most highly expressed MipA and MipC coincided with turgor changes in leaves under stress. As the leaves regained turgor, transcript levels of these water channel proteins increased.
DNA Nanostructures as Programmable Biomolecular Scaffolds (2015)

This Review focuses on how to use DNA nanostructures as scaffolds to organize biological molecules. First, we introduce the use of structural DNA nanotechnology to engineer rationally designed nanostructures. Second, we survey approaches used to generate protein-DNA conjugates. Third, we discuss studies exploring DNA scaffolds to create DNA nanodevices to analyze protein structures, to engineer enzyme pathways, to create artificial light-harvesting systems, and to generate nanomachines in vitro and in vivo. Future challenges and perspectives of using DNA nanostructures as programmable biomolecular scaffolds are addressed at the end.
Adjuvant Activity of a Nontoxic Mutant ofEscherichia coliHeat-Labile Enterotoxin on Systemic and Mucosal Immune Responses Elicited against a Heterologous Antigen Carried by a LiveSalmonella entericaSerovar Typhimurium Vaccine Strain (2000)

ABSTRACT Systemic and mucosal antibody responses against both the major subunit of colonization factor antigen I (CFA/I) of enterotoxigenic Escherichia coli (ETEC) and the somatic lipopolysaccharide expressed by recombinant bivalent Salmonella vaccine strains were significantly enhanced by coadministration of a detoxified derivative with preserved adjuvant effects of the ETEC heat-labile toxin, LT (R192G) . The results further support the adjuvant effects of LT (R192G) and represent a simple alternative to improve responses against passenger antigens expressed by orally delivered Salmonella vaccine strains.
IκB: a Specific Inhibitor of the NF-κB Transcription Factor (1988)

In cells that do not express immunoglobulin kappa light chain genes, the kappa enhancer binding protein NF-kappa B is found in cytosolic fractions and exhibits DNA binding activity only in the presence of a dissociating agent such as sodium deoxycholate. The dependence on deoxycholate is shown to result from association of NF-kappa B with a 60- to 70-kilodalton inhibitory protein (I kappa B). The fractionated inhibitor can inactivate NF-kappa B from various sources--including the nuclei of phorbol ester-treated cells--in a specific, saturable, and reversible manner. The cytoplasmic localization of the complex of NF-kappa B and I kappa B was supported by enucleation experiments. An active phorbol ester must therefore, presumably by activation of protein kinase C, cause dissociation of a cytoplasmic complex of NF-kappa B and I kappa B by modifying I kappa B. this releases active NF-kappa B which can translocate into the nucleus to activate target enhancers. The data show the existence of a phorbol ester-responsive regulatory protein that acts by controlling the DNA binding activity and subcellular localization of a transcription factor.
Performing "Competency to Be Executed" Evaluations: A Psycholegal Analysis for Preventing the Execution of the Insane (1988)

The Supreme Court's decision in Ford v. Wainwright held that the eighth amendment prohibits execution of the insane. As a result, prisoners awaiting execution now have a constitutional right not to be executed if they are found incompetent. By constitutionalizing what had been largely a common law or statutory right, the Court also instructed states to establish procedures to insure that execution of the insane did not in fact occur. Historically, those procedures that governed the determination of competency to suffer execution centered around "competency to be executed examinations" performed by mental health professionals. Many of these procedures failed to take into account ethical and practical dilemmas inherent in the performance of such examinations. Today most states, including Nebraska, have yet to reform their laws to comply with the Court's holding in Ford. The purpose of this Comment is to present a psycholegal analysis examining how psychology may best be considered when constructing constitutional statutes. Part II of this comment outlines the contours of the legal context which govern "competency to be executed" evaluations. Primarily, this is accomplished by noting the recent Supreme Court decision that both establishes a substantive right for prisoners and suggests procedures a state may adopt to safeguard this right. Part III explores the nature of the specific assessment of competency by examining both legal and psychological tests. Specifically reviewed are the ethical and practical considerations facing an evaluator called upon to perform a ''competency to be executed" evaluation. In Part IV, Nebraska's current statutory procedure for determining competency to suffer executions is analyzed and shown to be constitutionally defective. Finally, recommendations are made to both remedy Nebraska's statute and facilitate the interaction of law with psychology in conducting assessments of competency to suffer execution.
Limitation on image resolution imposed by a random medium (1978)

In underwater photography, it was reported that clear photographs were obtained through water with large (10-15) optical distances even though the MTF rolls off at a few cycles per mrad. This paper presents an explanation of this apparent contradiction by showing that at a large optical distance where the total coherent intensity is negligibly small compared with the total incoherent intensity, it is still possible to form the Airy disk due to the coherent intensity. We present the condition under which this can take place and applied the results to an imaging system in still water and in water with particulate matter.
Hormonal and Local Factors Control the Immunohistochemical Distribution of Immunocytes in the Rat Uterus before Conceptus Implantation: Effects of Ovariectomy, Fallopian Tube Section, and Injection (1991)

The distribution of immunocytes in the rat uterus undergoes profound changes during early pregnancy. This study was designed to evaluate the respective contributions of hormonal and local factors to regulation of the distribution and number of MCA341+ monocyte-macrophage antigen-bearing cells and T-lymphocyte-polymorphonuclear leukocyte (PMN) antigen-bearing cells before and during implantation of the fertilized ovum. Immunohistological data in normal rat pregnancy were compared to those found in cycling rats, ovariectomized rats, pseudopregnant rats (the oviducts of which had been sectioned on Day 0.5 of pregnancy), and pregnant rats injected with the antiprogesterone RU-486 on Day 0.5 of pregnancy. Four major events were observed: (1) transient accumulation of T-lymphocyte-PMN antigen-bearing cells in the endometrium close to the lumen and occurring only in the pregnant state 12 h after mating; (2) accumulation of an MCA341+ antigen-bearing monocyte-macrophage subset in the uterus, especially the luminal endometrium, 12 h after ovulation in pregnant as well as cycling rats; (3) progressive disappearance of these labeled cells starting 1 day after ovulation in the pregnant and nonpregnant states and influenced by RU-486 injection; (4) relative persistence of labeled cells in the deep endometrium before the implantation of the conceptus--which requires the presence of fertilized ovum in the genital tract. In conclusion, a complex multifactorial and sequential control of the distribution and number of cells bearing MCA341+ monocyte-macrophage or T-lymphocyte antigens appears to be at work before and during implantation of the rat conceptus, and may involve hormonal factors as well as local factors produced by the embryo or trophoblastic cells.
Failure mechanisms of polyester fiber anterior cruciate ligament implants: A human retrieval and laboratory study (1999)

It has been hypothesized that ACL implant failure is often caused by bone impingement in knee extension following malplacement of the tibial tunnel. This study examined polyethylene terephtalate fiber ACL implants retrieved from a clinical study, and, to confirm the hypothesis, also set up a laboratory study intended to duplicate the failure mechanism. SEM and TEM examination of 25 ruptured implants gave details of fiber failure morphology, with shearing into longitudinal fibrils, followed by rupture, when the fibrils burst apart. Cadaver joints were run in a knee simulator, with deliberately impinging ACL implants. SEM examination of implants abraded in the knee in vitro showed identical fiber damage patterns, thus confirming the impingement hypothesis.
HDL and ApoA Prevent Cell Death of Endothelial Cells Induced by Oxidized LDL (1997)

We have previously demonstrated that toxic doses of mildly oxidized LDL evokes in cultured cells a delayed and sustained rise of cytosolic [Ca2+], eliciting in turn irreversible cell damage and leading finally to cell death. HDL and delipidated apolipoprotein (apo). A prevented effectively the toxic effect of oxidized LDL to bovine aortic endothelial cells, in a time- and dose-dependent manner. The major part of the protective effect was mimicked by purified apoA-I, whereas purified apoA-II exhibited only very low protective activity. The protective effect was independent of the paraoxonase-linked HDL activity. The protective effect of HDL is independent of the contact of HDL with oxidized LDL, as shown by preincubation of oxidized LDL with HDL or apoA. In contrast, the protective effect was dependent on the integrity of apoA and on the contact of HDL with cells, thus suggesting that HDL acts directly on cells by enhancing their resistance against oxidized LDL. Preincubation experiments show that the protective effect is dependent on the duration of the contact of cells with HDL (maximal effect observed after 12 to 16 hours' preincubation), is also dependent on protein synthesis, and is persistent for at least 48 hours after the end of the contact of HDL with cells. Finally, effective concentrations of HDL inhibit the Ca2+ peak, which is directly involved in the cytotoxic effect of oxidized LDL, as shown by the inhibitory effect of Ca2+ chelators. All together, these results suggest that HDL, mainly apoA-I, increases the resistance of endothelial cells against oxidized LDL and prevents its toxic (apoptotic) effect by blocking the pathogenic intracellular signaling (culminating in sustained Ca2+ rise) involved in cell death.
Parasitophorous vacuoles of Leishmania mexicana acquire macromolecules from the host cell cytosol via two independent routes (1999)

The intracellular parasite Leishmania survives and proliferates in host macrophages. In this study we show that parasitophorous vacuoles of L. mexicana gain access to cytosolic material via two different routes. (1) Small anionic molecules such as Lucifer Yellow are rapidly transported into the vacuoles by an active transport mechanism that is sensitive to inhibitors of the host cell's organic anion transporter. (2) Larger molecules such as fluorescent dextrans introduced into the host cell cytosol are also delivered to parasitophorous vacuoles. This transport is slower and sensitive to modulators of autophagy. Infected macrophages were examined by two novel assays to visualize and quantify this process. Immunoelectron microscopy of cells loaded with digoxigenin-dextran revealed label in multivesicular endosomes, which appeared to fuse with parasitophorous vacuoles. The inner membranes of the multivesicular vesicles label strongly with antibodies against lysobisphosphatidic acid, suggesting that they represent a point of confluence between the endosomal and autophagosomal pathways. Although the rate of autophagous transfer was comparable in infected and uninfected cells, infected cells retained hydrolyzed cysteine proteinase substrate to a greater degree. These data suggest that L. mexicana-containing vacuoles have access to potential nutrients in the host cell cytosol via at least two independent mechanisms.
Cerium Phosphate Nanotubes: Synthesis, Valence State, and Optical Properties (2004)

A strong blue emission is observed for hybrid Ce3+/Ce4+ cerium phosphate nanotubes, whereas Ce3+ phosphate nanowires exhibit a characteristic double-peak UV luminescence (see picture). These cerium phosphate systems were obtained by annealing novel cerium(IV) phosphate nanotubes at different temperatures.
Condensation of oligonucleotides assembled into nicked and gapped duplexes: potential structures for oligonucleotide delivery (2005)

The condensation of nucleic acids into well-defined particles is an integral part of several approaches to artificial cellular delivery. Improvements in the efficiency of nucleic acid delivery in vivo are important for the development of DNA- and RNA-based therapeutics. Presently, most efforts to improve the condensation and delivery of nucleic acids have focused on the synthesis of novel condensing agents. However, short oligonucleotides are not as easy to condense into well-defined particles as gene-length DNA polymers and present particular challenges for discrete particle formation. We describe a novel strategy for improving the condensation and packaging of oligonucleotides that is based on the self-organization of half-sliding complementary oligonucleotides into long duplexes (ca. 2 kb). These non-covalent assemblies possess single-stranded nicks or single-stranded gaps at regular intervals along the duplex backbones. The condensation behavior of nicked- and gapped-DNA duplexes was investigated using several cationic condensing agents. Transmission electron microscopy and light-scattering studies reveal that these DNA duplexes condense much more readily than short duplex oligonucleotides (i.e. 21 bp), and more easily than a 3 kb plasmid DNA. The polymeric condensing agents, poly-l-lysine and polyethylenimine, form condensates with nicked- and gapped-DNA that are significantly smaller than condensates formed by the 3 kb plasmid DNA. These results demonstrate the ability for DNA structure and topology to alter nucleic acid condensation and suggest the potential for the use of this form of DNA in the design of vectors for oligonucleotide and gene delivery. The results presented here also provide new insights into the role of DNA flexibility in condensate formation.
Alpha-melanocyte-stimulating hormone is a mammotrophic factor released by neurointermediate lobe cells after estrogen treatment (1992)

When neurointermediate lobe (NIL) cells from ovariectomized rats are exposed to 17 beta-estradiol (E2) in vitro, they release a substance that rapidly induces the recruitment of additional PRL cells into the secretory pool. In the present study we tested the hypothesis that this mammotrophic factor is alpha MSH. Cocultures of anterior pituitary and NIL cells were incubated for 18 h, exposed to various treatments for 3 h, and then subjected to a reverse hemolytic plaque assay to quantify the percentage of all pituitary cells that released PRL. Combined exposure to E2 and NIL cells caused a significant increase in the fraction of anterior pituitary cells that released PRL, and the presence of TRH during the reverse hemolytic plaque assay did not affect the magnitude of the response. Treatment with dopamine (which inhibits alpha MSH release) reversed the recruitment of PRL secretors induced by E2 stimulation of NIL cells. Likewise, immunoneutralization with an antiserum directed against alpha MSH abolished the response. Furthermore, alpha MSH alone could substitute for E2 and NIL cells in evoking the recruitment response, whereas none of several other POMC-derived peptides had any consistent effect. Taken together, these results demonstrate that alpha MSH is a mammotrophic factor released by NIL cells in response to E2.
Color Transfer Using Probabilistic Moving Least Squares (2014)

This paper introduces a new color transfer method which is a process of transferring color of an image to match the color of another image of the same scene. The color of a scene may vary from image to image because the photographs are taken at different times, with different cameras, and under different camera settings. To solve for a full nonlinear and nonparametric color mapping in the 3D RGB color space, we propose a scattered point interpolation scheme using moving least squares and strengthen it with a probabilistic modeling of the color transfer in the 3D color space to deal with mis-alignments and noise. Experiments show the effectiveness of our method over previous color transfer methods both quantitatively and qualitatively. In addition, our framework can be applied for various instances of color transfer such as transferring color between different camera models, camera settings, and illumination conditions, as well as for video color transfers.
EXPRESSION OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR, UROKINASE-TYPE PLASMINOGEN ACTIVATOR RECEPTOR AND PLASMINOGEN ACTIVATOR INHIBITORS IN PATIENTS WITH RENAL CELL CARCINOMA: CORRELATION WITH TUMOR ASSOCIATED MACROPHAGE AND PROGNOSIS (2005)

Our results suggest that PAI-1 is an important regulator of tumor progression and survival, and PAI-1 may modulate them via TAM. On the other hand, PAI-2 has a minimum role in survival. Our results may help discussions of treatment strategy in patients with RCC.