gebhart/patrepeval huggingface dataset:
Fragile X Mental Retardation Protein Regulates the Levels of Scaffold Proteins and Glutamate Receptors in Postsynaptic Densities (2009)

Functional absence of fragile X mental retardation protein (FMRP) causes the fragile X syndrome, a hereditary form of mental retardation characterized by a change in dendritic spine morphology. The RNA-binding protein FMRP has been implicated in regulating postsynaptic protein synthesis. Here we have analyzed whether the abundance of scaffold proteins and neurotransmitter receptor subunits in postsynaptic densities (PSDs) is altered in the neocortex and hippocampus of FMRP-deficient mice. Whereas the levels of several PSD components are unchanged, concentrations of Shank1 and SAPAP scaffold proteins and various glutamate receptor subunits are altered in both adult and juvenile knock-out mice. With the exception of slightly increased hippocampal SAPAP2 mRNA levels in adult animals, altered postsynaptic protein concentrations do not correlate with similar changes in total and synaptic levels of corresponding mRNAs. Thus, loss of FMRP in neurons appears to mainly affect the translation and not the abundance of particular brain transcripts. Semi-quantitative analysis of RNA levels in FMRP immunoprecipitates showed that in the mouse brain mRNAs encoding PSD components, such as Shank1, SAPAP1-3, PSD-95, and the glutamate receptor subunits NR1 and NR2B, are associated with FMRP. Luciferase reporter assays performed in primary cortical neurons from knock-out and wild-type mice indicate that FMRP silences translation of Shank1 mRNAs via their 3'-untranslated region. Activation of metabotropic glutamate receptors relieves translational suppression. As Shank1 controls dendritic spine morphology, our data suggest that dysregulation of Shank1 synthesis may significantly contribute to the abnormal spine development and function observed in brains of fragile X syndrome patients.
Preparation, Reactivity, and Structural Peculiarities of Hydroxyalkyl-Functionalized “Second-Generation” Ruthenium Carbene Complexes (2003)

The preparation, immobilization, and structure of “second-generation” ruthenium benzylidene metathesis catalysts bearing hydroxyalkyl chains on their N-heterocyclic carbene ligands are described. Complexes of this type are prone to rearrange their ligand sphere such that the neutral ligands get cis- rather than trans-disposed. Moreover, treatment of complex 7d with pyridine results in an unprecedented ionization by loss of one of its chloride ligands. The resulting cationic species 13, though devoid of catalytic activity, is the first member of a new type of ruthenium carbene complexes characterized by an octahedral coordination geometry and a donor/acceptor interaction between the metal center and the tethered hydroxyl group. The trans-configured hydroxyalkyl-functionalized complexes 8a and 8b, the cis-configured compound 10, and the ion pair 13 have been structurally characterized by X-ray crystallography.
Wyner–Ziv Coding of Video: An Error-Resilient Compression Framework (2004)

This paper addresses the problem of video coding in a joint source-channel setting. In particular, we propose a video encoding algorithm that prevents the indefinite propagation of errors in predictively encoded video-a problem that has received considerable attention over the last decade. This is accomplished by periodically transmitting a small amount of additional information, termed coset information, to the decoder, as opposed to the popular approach of periodic insertion of intra-coded frames. Perhaps surprisingly, the coset information is capable of correcting for errors, without the encoder having a precise knowledge of the lost packets that resulted in the errors. In the context of real-time transmission, the proposed approach entails a minimal loss in performance over conventional encoding in the absence of channel losses, while simultaneously allowing error recovery in the event of channel losses. We demonstrate the efficacy of the proposed approach through experimental evaluation. In particular, the performance of the proposed framework is 3-4 dB superior to the conventional approach of periodic insertion of intra-coded frames, and 1.5-2 dB away from an ideal system, with infinite decoding delay, operating at Shannon capacity.
Pro-Oxidant and Antioxidant Effects of Estrogens (2003)

Many compounds of great structural diversity possess varying degrees of estrogenic activity (Fig. 1). Estrogenic substances may contain a steroidal ring system as do, for instance, the ovarian hormones estradiol3 (E2), estrone (El), or the synthetic estrogens 17α-ethinylestradiol or mestranol. Nonsteroidal phenols with estrogenic activity include the potent synthetic estrogen diethylstilbestrol (DES) and environmental substances produced by plants (equol, coumestrol), or microbes (enterolactone). Some industrial chemicals have estrogenic activity, such as bisphenol A and nonylphenol. In addition to hormonal activity, both natural and synthetic estrogenic compounds containing a phenolic structure possess pro-oxidant and/or antioxidant activities.
Electrokinetic Trapping and Concentration Enrichment of DNA in a Microfluidic Channel (2003)

We report a simple and efficient method for enriching the concentration of charged analytes within microfluidic channels. The method relies on exerting spatial control over the electrokinetic velocity of an analyte. Specifically, the electroosmotic (eo) velocity of the buffer solution in one region of the microfluidic system opposes the electrophoretic (ep) velocity of the analyte in the other region. This results in ep transport of DNA to the location where the ep and eo velocities are equal and opposite. Accumulation of the analyte occurs at this location. This enrichment method is conceptually distinct from field-amplification stacking, isotachophoresis, micelle sweeping, size exclusion, and other methods that have been previously reported. The method requires no complex microfabricated structures, no special manipulation of the solvent, and the enriched analyte remains in solution rather than being captured on a solid support. A concentration enrichment factor of 800 can be achieved for 20mer DNA in a fluidic channel having dimensions of 100 mum x 25 mum x 5 mm. The time required to achieve this level of enrichment is 300 s, and the enriched zone has a minimum width of 100 mum.
Novel Urea‐Functionalized Quinacridone Derivatives: Ultrasound and Thermo Effects on Supramolecular Organogels (2010)

In investigations into the effects of environmental factors on organogels, two urea-functionalized quinacridone derivatives 1a and 1b have been designed and synthesized. These two compounds can respond to ultrasound and thermal stimuli in the organic test solvents, and exhibit pronounced aggregation properties. The field-effect (FE)-SEM images of xerogels show the characteristic gelation morphologies of 3D fibrous network structures. The concentration- and temperature-dependent (1)H NMR spectra suggest that the intermolecular π-π and hydrogen-bonding interactions of gelators are the main driving forces for the supramolecular assembly process. X-ray diffraction (XRD), UV/Vis absorption, and photoluminescent spectroscopy studies have been carried out and provide more information to define the molecular packing model in gelation states.
A Novel 4-Methylideneimidazole-5-one-Containing Tyrosine Aminomutase in Enediyne Antitumor Antibiotic C-1027 Biosynthesis (2003)

The C-1027 enediyne antibiotic contains an unusual 3-chloro-4,5-dihydroxy-beta-phenylalanine moiety that is thought to be derived from tyrosine by an aminomutase reaction. However, none of the genes identified within the C-1027 gene cluster encode proteins with strong homology to known aminomutases. The sgcC4 gene encodes a protein with strong homology to dehydroalanine-dependent histidine/phenylalanine ammonia lyases. The sgcC4 gene was expressed in E. coli, and overproduced SgcC4 was purified as a His6-tagged fusion protein. Biochemical characterization of the purified SgcC4 establishes that SgcC4 is an aminomutase that catalyzes the conversion of l-tyrosine to (S)-beta-tyrosine and employs 4-methylideneimidazole-5-one (MIO) at its active site. The latter was supported by borohydride and cyanide inhibition studies and confirmed by site-directed mutagenesis. The S153A mutant exhibited a 340-fold decrease in kcat/KM. SgcC4 represents a novel type of aminomutase, extending the known MIO chemistry from ammonia lyases into aminomutases.
Polymer chemistry and hydrogel systems (2004)

Hydrogels are an interesting class of materials that can be prepared by a variety of methods. The properties of these materials depend on their building blocks and the preparation procedures and can be largely varied.
Targeting of marrow-derived astrocytes to the ischemic brain (1999)

Bone marrow progenitor cells have been shown to contribute to a small proportion of cells in nonhematopoietic tissues including the brain. In the acute unilateral middle cerebral artery occlusion model in spontaneously hypertensive rats following male-to-female bone marrow transplantation, we present data suggesting that 55% more marrow-derived cells, in general, and 161% more GFAP-positive astrocytes, in particular, migrate preferentially to the ischemic cortex than to the contralateral non-ischemic hemisphere. In addition to their biological significance, our findings could have therapeutic implications. Marrow-derived progenitor cells could potentially be used as vehicles for ex vivo gene transfer to the brain.
Ultrastructural study of the neovagina following the utilization of human amniotic membrane for treatment of congenital absence of the vagina (1997)

We present an ultrastructural study of the utilization of human amniotic membrane in the treatment of congenital absence of the vagina in 10 patients. All patients were surgically treated with application of an amniotic membrane graft using the modified McIndoe and Bannister technique. Sixty days after surgery, samples of the vaginal neoepithelium were collected for transmission electron microscopy analysis. The ultrastructural findings consisted of a lining of mature squamous epithelium indicating the occurrence of metaplasia of the amniotic epithelium into the vaginal epithelium. The cells were arranged in layers as in the normal vaginal epithelium, i.e., superficial, intermediate and deep layers. There were desmosomes and cytoplasmic intermediate cytokeratin filaments, as well as some remnant features of the previous amniotic epithelium. These findings suggest that human amniotic membrane is able to complete metaplasia into squamous cells but the mechanism of this cellular transformation is unknown.
New targets in the acute treatment of headache (2005)

The prospect of a non-vasoconstrictor acute migraine therapy offers a real opportunity to patients, and perhaps more importantly, provides a therapeutic rationale to plant migraine and cluster headache firmly in the brain as neurological problems.
Studies on Natural ST2 Gene Products in the Human Leukemic Cell Line UT-7 Using Monoclonal Antihuman ST2 Antibodies (1995)

Eight species of murine monoclonal antibodies against human ST2 protein, which is highly similar in protein sequence to the interleukin 1 receptor, were produced. The fusion was carried out between the murine myeloma cell line PAI and murine lymph node or spleen cells from mice immunized with the recombinant ST2 protein produced in Escherichia coli. Characterization of these monoclonal antibodies by immunoblot analysis revealed that they all reacted with recombinant, N-glycosylated ST2 protein that was secreted from COS7 cells transiently transfected with a mammalian expression vector carrying ST2 cDNA. The recombinant N-glycosylated ST2 protein could be immunoprecipitated by 5 out of 6 species of the IgG class monoclonal antibodies. Furthermore, these antibodies were also able to detect, by immunofluorescence, the membrane-bound chimeric molecule possessing an extracellular portion of human ST2 and a transmembrane and cytoplasmic portion of murine receptor type ST2L expressed on COS7 cells, indicating that these monoclonal antibodies were useful for detecting the natural membrane-bound ST2 in human cells. Combining immunoprecipitation and immunofluorescence with the aid of these monoclonal antibodies, together with the reverse transcriptase-polymerase chain reaction method, the human leukemic cell line UT-7 was demonstrated to express human ST2 mRNA and protein. The identification of the ST2 gene product in UT-7 cells may help investigators elucidate the function of the human ST2 gene.
Ocular safety of cationic emulsion of cyclosporine in an in vitro corneal wound-healing model and an acute in vivo rabbit model. (2012)

The combination of these in vitro and in vivo models evaluated the tolerance/cytotoxicity and the dynamic wound healing potential of CsA in different formulations. While CsA-AEm, CsA-CEm, and CsA-Oil are generally well tolerated, only CsA-CEm appeared to maintain the HCE cells' normal healing rate in vitro and low levels of inflammation in vivo.
Suppression of androgen receptor expression by dibenzoylmethane as a therapeutic objective in advanced prostate cancer. (2007)

These data provide new insights into how DBM regulates AR function and cell growth, as well as providing promising evidence to support DBM as a chemotherapeutic agent for prostate cancer through suppression of the function of the androgen receptor.
An underwater acoustic telemetry modem for eco-sensing (2005)

An underwater acoustic telemetry modem is presented for ecological research (eco-sensing) applications. The modem is intended for the physical layer (PHY) in an <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ad hoc</i> network of "AquaNodes". Each AquaNode will incorporate an acoustic modem, router and host processor with standardized interfaces to oceanographic sensors. The transmitted waveforms use a composite Walsh/m-sequence format in which each bit in an 8-bit long Walsh function is spread by a 7-chip m-sequence. The resulting waveform has a 5 kHz bandwidth for robustness to multipath and achieves a 133 bps data rate. An 11 msec, time-guard band for channel clearing eliminates the need for equalization. The receiver employs a generalized multiple hypothesis test with a matching pursuits (GMHT-MP) inner loop for symbol-by-symbol channel estimation. Symbol-error rate (SER) results demonstrate that the GMHT-MP is superior to the noncoherent RAKE receiver at usable SERs (<10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> ) and can accommodate up to 10 msec, multipath spreads with Doppler spreads on the order of 1 Hz
The melon fruit fly, Bactrocera cucurbitae: A review of its biology and management (2005)

The melon fruit fly, Bactrocera cucurbitae (Coquillett) (Diptera: Tephritidae) is distributed widely in temperate, tropical, and sub-tropical regions of the world. It has been reported to damage 81 host plants and is a major pest of cucurbitaceous vegetables, particularly the bitter gourd (Momordica charantia), muskmelon (Cucumis melo), snap melon (C. melo var. momordica), and snake gourd (Trichosanthes anguina). The extent of losses vary between 30 to 100%, depending on the cucurbit species and the season. Its abundance increases when the temperatures fall below 32 degrees C, and the relative humidity ranges between 60 to 70%. It prefers to infest young, green, soft-skinned fruits. It inserts the eggs 2 to 4 mm deep in the fruit tissues, and the maggots feed inside the fruit. Pupation occurs in the soil at 0.5 to 15 cm below the soil surface. Keeping in view the importance of the pest and crop, melon fruit fly management could be done using local area management and wide area management. The melon fruit fly can successfully be managed over a local area by bagging fruits, field sanitation, protein baits, cue-lure traps, growing fruit fly-resistant genotypes, augmentation of biocontrol agents, and soft insecticides. The wide area management program involves the coordination of different characteristics of an insect eradication program (including local area options) over an entire area within a defensible perimeter, and subsequently protected against reinvasion by quarantine controls. Although, the sterile insect technique has been successfully used in wide area approaches, this approach needs to use more sophisticated and powerful technologies in eradication programs such as insect transgenesis and geographical information systems, which could be deployed over a wide area. Various other options for the management of fruit fly are also discussed in relation to their bio-efficacy and economics for effective management of this pest.
The Helicase-Like Domain of Plant Potexvirus Replicase Participates in Formation of RNA 5′ Cap Structure by Exhibiting RNA 5′-Triphosphatase Activity (2001)

Open reading frame 1 (ORF1) of potexviruses encodes a viral replicase comprising three functional domains: a capping enzyme at the N terminus, a putative helicase in the middle, and a polymerase at the C terminus. To verify the enzymatic activities associated with the putative helicase domain, the corresponding cDNA fragment from bamboo mosaic virus (BaMV) was cloned into vector pET32 and the protein was expressed in Escherichia coli and purified by metal affinity chromatography. An activity assay confirmed that the putative helicase domain has nucleoside triphosphatase activity. We found that it also possesses an RNA 5'-triphosphatase activity that specifically removes the gamma phosphate from the 5' end of RNA. Both enzymatic activities were abolished by the mutation of the nucleoside triphosphate-binding motif (GKS), suggesting that they have a common catalytic site. A typical m(7)GpppG cap structure was formed at the 5' end of the RNA substrate when the substrate was treated sequentially with the putative helicase domain and the N-terminal capping enzyme, indicating that the putative helicase domain is truly involved in the process of cap formation by exhibiting its RNA 5'-triphosphatase activity.
Polarization of the human motor cortex through the scalp (1998)

Direct currents (DC) applied directly to central nervous system structures produce substantial and long-lasting effects in animal experiments. We tested the functional effects of very weak scalp DC (< 0.5 mA, 7 s) on the human motor cortex by assessing the changes in motor potentials evoked by transcranial magnetic brain stimulation. We performed four different experiments in 15 healthy volunteers. Our findings led to the conclusion that such weak (< 0.5 mA) anodal scalp DC, alternated with a cathodal DC, significantly depresses the excitability of the human motor cortex, providing evidence that a small electric field crosses the skull and influences the brain. A possible mechanism of action of scalp DC is the hyperpolarization of the superficial excitatory interneurones in the human motor cortex.
Virulence of Newcastle disease virus is determined by the cleavage site of the fusion protein and by both the stem region and globular head of the haemagglutinin–neuraminidase protein (2005)

Virulence of Newcastle disease virus (NDV) is mainly determined by the amino acid sequence surrounding the fusion (F) protein cleavage site, since host proteases that cleave the F protein of virulent strains are present in more tissues than those that cleave the F protein of non-virulent strains. Nevertheless, comparison of NDV strains that carry exactly the same F protein cleavage site shows that significant differences in virulence still exist. For instance, virulent field strain Herts/33 with the F cleavage site 112RRQRRF117 had an intracerebral pathogenicity index of 1.88 compared with 1.28 for strain NDFLtag, which has the same cleavage site. This implies that additional factors contribute to virulence. After generating an infectious clone of Herts/33 (FL-Herts), we were able to map the location of additional virulence factors by exchanging sequences between FL-Herts and NDFLtag. The results showed that, in addition to the F protein cleavage site, the haemagglutinin-neuraminidase (HN) protein also contributed to virulence. The effect of the HN protein on virulence was most prominent after intravenous inoculation. Interestingly, both the stem region and the globular head of the HN protein seem to be involved in determining virulence.
The NLRP3 Inflammasome Promotes Renal Inflammation and Contributes to CKD (2010)

Inflammation significantly contributes to the progression of chronic kidney disease (CKD). Inflammasome-dependent cytokines, such as IL-1β and IL-18, play a role in CKD, but their regulation during renal injury is unknown. Here, we analyzed the processing of caspase-1, IL-1β, and IL-18 after unilateral ureteral obstruction (UUO) in mice, which suggested activation of the Nlrp3 inflammasome during renal injury. Compared with wild-type mice, Nlrp3(-/-) mice had less tubular injury, inflammation, and fibrosis after UUO, associated with a reduction in caspase-1 activation and maturation of IL-1β and IL-18; these data confirm that the Nlrp3 inflammasome upregulates these cytokines in the kidney during injury. Bone marrow chimeras revealed that Nlrp3 mediates the injurious/inflammatory processes in both hematopoietic and nonhematopoietic cellular compartments. In tissue from human renal biopsies, a wide variety of nondiabetic kidney diseases exhibited increased expression of NLRP3 mRNA, which correlated with renal function. Taken together, these results strongly support a role for NLRP3 in renal injury and identify the inflammasome as a possible therapeutic target in the treatment of patients with progressive CKD.
Design of New Plant Products: Engineering of Fatty Acid Metabolism (1994)

PLANTS AS CHEMICAL FACTORIES Manipulation of biosynthetic pathways in transgenic plants offers a number of exciting opportunities for plant biochemists and molecular biologists to redesign plant metabolism toward production of specific higher-value products. Here I review several recent examples that have demonstrated that plant fatty acid metabolism can be manipulated in useful ways to produce new and potentially more valuable vegetable oils. A number of factors have converged to make metabolic engineering of fatty acid metabolism particularly attractive. Although for centuries plant breeders have manipulated plant metabolism, the primary goal has been to produce better yields of crops for human and animal consumption, and in the past 100 years, efforts to increase yields of the basic food crops have had dramatic success. Through a number of technological advances, yields per hectare have risen manyfold, resulting in substantial surplus capacity worldwide. These surpluses are a reflection of the high yields that can be obtained when optimum agronomic practices are applied to highly developed crop varieties. As a result, the United States spends $20 to $30 billion annually on a variety of programs designed to deal with farm overproduction capacity.
Alanine-scanning Mutagenesis of a C-terminal Ligand Binding Domain of the Insulin Receptor α Subunit (1996)

A recent affinity labeling study has suggested that amino acids 704-717 of the C terminus of the insulin receptor represent a contact site for insulin. To determine whether these amino acids are part of a ligand binding site, we have performed alanine-scanning mutagenesis of this region. Mutant cDNAs encoding recombinant secreted receptors were transiently expressed in 293 EBNA cells, and their insulin binding properties were evaluated. Of the 14 residues in this region only 4 amino acids, Asp-707, Val-712, Pro-716, and Arg-717, could be mutated to alanine without compromising insulin binding. The reduction in affinity resulting from the individual mutation of the remaining amino acids varied from an increase in Kd to 3.69 x 10(-9) M (Asn-711) to greater than 10(-6) M (Thr-704, Phe-705, Glu-706, and His-710); the Kd of native secreted recombinant receptor is 0.56 x 10(-9) M.