gebhart/patrepeval huggingface dataset:
Design of a photoreactive analogue of the Escherichia coli heat-stable enterotoxin STIb: Use in identifying its receptor on rat brush border membranes (photoaffinity labeling/synthetic peptide) (2016)

The Escherichia coli heat-stable enterotoxin, STIb was prepared by solid-phase peptide synthesis and purified to homogeneity by high-pressure liquid chromatogra- phy. This analogue was lodinated and shown to bind specifi- cally to rat intestinal membranes. The radiolabeled peptide was derivatized at the amino terminus with the photoreactive heterobifunctional crosslinking agent N-hydroxysuccinimidyl p-benzoylbenzoate. This photoreactive probe also exhibited binding specificity. It was mixed with rat intestinal brush border membranes and photolyzed in the presence or absence of excess unlabeled STIb. Polyacrylamide gel electrophoresis performed in the presence of sodium dodecyl sulfate and 2-mercaptoethanol indicated that the peptide probe was cross- linked specifically to two molecular species of 57 and 75 kDa. One or both of these molecules appear to constitute the enterotoxin receptor or to be In close proximity to It.
Reaktionen cyclischer Oxalylverbindungen, 35. Untersuchung von Reaktionsmechanismen durch Isotopenmarkierung, 11. Zur Umsetzung von 4‐Benzoyl‐5‐phenylfuran‐2,3‐dion mit S‐Heterocumulenen — Präparative und mechanistische Aspekte (1993)

Reactions of Cyclic Oxalyl Compounds, 35 [1] . — Mechanistic Investigation Aided by Isotopic Labeling, 11 [2] . — On the Reaction of 4‐Benzoyl‐5‐phenylfuran‐2,3‐dione with S‐Heterocumulenes — Preparative and Mechanistic Aspects [3] The furan‐2,3‐dione 1 combines with N ‐sulfinylamines or sulfur diimides to afford the pyrrole‐2,3‐diones 2 , while with N ‐tosylsulfinylamine the (α‐iminobenzyl)furandione 3 is obtained. (α‐Iminobenzyl)pyrrolediones 4 are formed in the reaction of 2c with N ‐tosylsulfinylamine or from 3 with N ‐tosylsulfur diimides. Diisopropylcarbodiimide and the pyrroledione 2c or the (iminobenzyl)furandione 3a undergo [4 + 2] cycloaddition reactions accompanied by novel and surprising rearrangements to furnish the bicyclic compounds 5 and 6 , respectively. The molecular skeleton of 6 was confirmed by an X‐ray diffraction analysis. With the aid of 17 O‐labeling experiments and 17 O‐NMR spectroscopy mechanistic pathways including novel rearrangements were made evident.
Electrodeless Reverse Electrodialysis Patches as an Ionic Power Source for Active Transdermal Drug Delivery (2018)

Abstract Reverse electrodialysis (RED) is one of the promising sustainable technologies generating electric power from the mixing energy of two different salt solutions. Most of the reports on the RED systems are focused on scale‐up development and the improvement of maximum power density. However, regarding biocompatible and eco‐friendly natures, the RED system also has a great potential use where low electrical power is necessary, in particular for skin‐wearable biomedical devices. In this work, electronics‐free RED patches are devised as an ionic power source for active transdermal drug delivery. The electrodeless RED patches generate reliable voltages, which are proportional to the number of ion‐exchange membranes and salinity ratios, and successfully facilitate in vitro delivery of ionic drugs through mouse skin without involving any electronic component for the first time; 9, 20, and 36‐fold increases with lidocaine, ketorolac, and risedronate, respectively. Indeed, by using an osteoporosis‐induced mouse model, the RED patch delivery demonstrates powerful in vivo therapeutic effects against the diffusion‐based topical administration. The new ionic power source can allow transport of various types of drugs in the transdermal route and, more importantly, can be used for the operation of other portable biomedical devices.
Special Section Guest Editorial: Pioneers in Biomedical Optics: Special Section Honoring Professor Tayyaba Hasan (2010)

The <i>Journal of Biomedical Optics</i> (JBO) is a Gold Open Access journal that publishes peer-reviewed papers on the use of novel optical systems and techniques for improved health care and biomedical research.
Correction: Hypomethylating agents synergize with irinotecan to improve response to chemotherapy in colorectal cancer cells (2020)

[This corrects the article DOI: 10.1371/journal.pone.0176139.].
Antagonism of androgen and estrogen effects in guinea pig seminal vesicle epithelium and fibromuscular stroma by keoxifene (LY156758) (1989)

Using separated epithelium (SVE) and fibromuscular stroma (SVM) of guinea pig seminal vesicle, the antihormonal effects of daily subcutaneous administration (14 and 28 days) of the benzothiophene keoxifene (LY156758; [6-hydroxy-2-(4-hydroxyphenyl)benzo(b) thien-3-yl] [4-(2-1-piperidinyl) ethoxyl] phenyl) methanone hydrochloride) in intact, castrate, and androgen/estrogen-maintained castrate animals was evaluated. The compound was devoid of agonist activity in castrated males, in that the compound had no stimulatory effect on SVM wet weight or DNA content. In vitro cytosolic binding of [3H]estradiol (E2) in the SVM was decreased in a concentration-dependent manner by keoxifene, but the compound did not perturb the binding of [3H]dihydrotestosterone (DHT) in the SVM or SVE. Likewise, keoxifene administration to castrated males treated with exogenous steroids antagonized the estrogen-induced hyperplastic response of the SVM, whereas no interference with androgen-induced growth of the SVM or SVE was observed. Keoxifene treatment of intact male guinea pigs produced regression of the androgen-sensitive SVE as well as the androgen/estrogen-sensitive SVM. Keoxifene-induced decreases in guinea pig serum testosterone levels were associated with this activity. Histological analysis of the seminal vesicle under these conditions suggests androgen deprivation. These findings indicate that keoxifene is a physiological antagonist of androgen action in the intact male guinea pig. The pure estrogen antagonist properties of keoxifene and its ability to decrease accessory sex organ epithelium and fibromuscular stroma in vivo suggest potential applications of the benzothiophenes in the medical management of prostatic neoplasia.
Optically induced quasi-phase matching in strontium barium niobate (1995)

We observe dynamic ferroelectric domain gratings in strontium barium niobate (SBN) induced by photorefractive space charge fields. The optically induced modulation of the spontaneous polarization attains a maximum of 1%. Quasi-phase matched second harmonic enhancements are observed above the ferroelectric-paraelectric phase transition due to the glassy ferroelectric nature of SBN. We find that the second harmonic power is significantly enhanced by recording gratings in optically fatigued rather than electrically poled crystals.
The Selective Packaging and Annealing of Primer tRNALys3 in HIV-1 (2004)

In HIV-1, tRNA(Lys3) serves as the primer for reverse transcriptase, and during viral assembly, the tRNA(Lys) isoacceptors, tRNA(Lys1,2) and tRNA(Lys3), are selectively packaged into the virion. In this review, we shall first discuss the evidence for the formation of a tRNA(Lys) packaging complex, whose components include Gag, GagPol, genomic RNA, lysyl-tRNA synthetase (LysRS), and tRNA(Lys). Evidence suggests that the formation of this complex involves a Gag/GagPol/viral genomic RNA complex interacting with a tRNA(Lys)/ LysRS complex, with Gag interacting with both GagPol and LysRS, and GagPol interacting with the tRNA(Lys). The interaction of Gag with LysRS is quite specific, does not require the presence of tRNA(Lys), and LysRS is believed to be the target that allows the specific packaging of tRNA(Lys) into the virion. The parameters influencing these interactions, and the molecular sites of interaction, will be discussed. The selective packaging of tRNA(Lys3) into HIV-1 facilitates annealing of tRNA(Lys) to the 5' region of viral RNA genome. This region contains a series of stem loops, and there exists several regions in both the viral RNA and the tRNA(Lys) that are believed to be important for tRNA(Lys) annealing. The annealing is facilitated by viral proteins such as unprocessed Gag, nucleocapsid, and reverse transcriptase.
Formation of Enamines via Catalytic Dehydrogenation by Pincer-Iridium Complexes (2019)

Efficient pincer-ligated iridium catalysts are reported for the dehydrogenation of simple tertiary amines to give enamines, and for the dehydrogenation of β-functionalized amines to give the corresponding 1,2-difunctionalized olefins. Experimentally determined kinetic isotope effects in conjunction with DFT-based analysis support a dehydrogenation mechanism involving initial pre-equilibrium oxidative addition of the amine α C-H bond followed by rate-determining elimination of the β-C-H bond.
A Chronological Edge-Driven Approach to Temporal Subgraph Isomorphism (2018)

A useful technique for adversary activity graph analytics is to perform subgraph isomorphism; searching for a specific graph pattern within a larger graph. Many of the networks that may be useful for adversary activity analysis are temporal networks, in which the chronological ordering of the edges has importance to the meaning of the data. Performing temporal subgraph matching requires the edges in the subgraphs to match the order of the temporal graph motif we are searching for. Previous methods for solving this rely on the use of static subgraph matching to find potential matches first, before filtering them based on edge order to find the true temporal matches. We present a new algorithm for temporal subgraph isomorphism that performs the subgraph matching directly on the chronologically sorted edges. By restricting our search to only the subgraphs with chronologically correct edges, we can improve the performance of the algorithm significantly in many cases. We present experimental timing results to show significant performance improvements on publicly available datasets for a number of different temporal query graph motifs with four or more nodes. We also demonstrate a practical example of how temporal subgraph isomorphism can produce more meaningful results than traditional static subgraph searches.
Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2 (2008)

The precise regulation of many alternative splicing (AS) events by specific splicing factors is essential to determine tissue types and developmental stages. However, the molecular basis of tissue-specific AS regulation and the properties of splicing regulatory networks (SRNs) are poorly understood. Here we comprehensively predict the targets of the brain- and muscle-specific splicing factor Fox-1 (A2BP1) and its paralog Fox-2 (RBM9) and systematically define the corresponding SRNs genome-wide. Fox-1/2 are conserved from worm to human, and specifically recognize the RNA element UGCAUG. We integrate Fox-1/2-binding specificity with phylogenetic conservation, splicing microarray data, and additional computational and experimental characterization. We predict thousands of Fox-1/2 targets with conserved binding sites, at a false discovery rate (FDR) of approximately 24%, including many validated experimentally, suggesting a surprisingly extensive SRN. The preferred position of the binding sites differs according to AS pattern, and determines either activation or repression of exon recognition by Fox-1/2. Many predicted targets are important for neuromuscular functions, and have been implicated in several genetic diseases. We also identified instances of binding site creation or loss in different vertebrate lineages and human populations, which likely reflect fine-tuning of gene expression regulation during evolution.
MRI of Tibialis Anterior Skeletal Muscle in Myotonic Dystrophy Type 1 (2011)

Muscle MRI is helpful to depict muscle abnormalities but does not seem to be a reliable indicator of skeletal muscle involvement in DM1 since the decrease in TAmuscle force is not correlated with MRI abnormalities in some patients.
Learning to Optimize Quasi-Newton Methods (2022)

Fast gradient-based optimization algorithms have become increasingly essential for the computationally efficient training of machine learning models. One technique is to multiply the gradient by a preconditioner matrix to produce a step, but it is unclear what the best preconditioner matrix is. This paper introduces a novel machine learning optimizer called LODO, which tries to online meta-learn the best preconditioner during optimization. Specifically, our optimizer merges Learning to Optimize (L2O) techniques with quasi-Newton methods to learn preconditioners parameterized as neural networks; they are more flexible than preconditioners in other quasi-Newton methods. Unlike other L2O methods, LODO does not require any meta-training on a training task distribution, and instead learns to optimize on the fly while optimizing on the test task, adapting to the local characteristics of the loss landscape while traversing it. Theoretically, we show that our optimizer approximates the inverse Hessian in noisy loss landscapes and is capable of representing a wide range of inverse Hessians. We experimentally verify that our algorithm can optimize in noisy settings, and show that simpler alternatives for representing the inverse Hessians worsen performance. Lastly, we use our optimizer to train a semi-realistic deep neural network with 95k parameters at speeds comparable to those of standard neural network optimizers.
Normalization Techniques for Statistical Inference from Magnetic Resonance Imaging (2013)

While computed tomography and other imaging techniques are measured in absolute units with physical meaning, magnetic resonance images are expressed in arbitrary units that are difficult to interpret and differ between study visits and subjects. Much work in the image processing literature on intensity normalization has focused on histogram matching and other histogram mapping techniques, with little emphasis on normalizing images to have biologically interpretable units. Furthermore, there are no formalized principles or goals for the crucial comparability of image intensities within and across subjects. To address this, we propose a set of criteria necessary for the normalization of images. We further propose simple and robust biologically motivated normalization techniques for multisequence brain imaging that have the same interpretation across acquisitions and satisfy the proposed criteria. We compare the performance of different normalization methods in thousands of images of patients with Alzheimer's Disease, hundreds of patients with multiple sclerosis, and hundreds of healthy subjects obtained in several different studies at dozens of imaging centers.
Evaluation of Functional Erythropoietin Receptor Status in Skeletal Muscle In Vivo: Acute and Prolonged Studies in Healthy Human Subjects (2012)

Acute exposure to recombinant human erythropoietin is not associated by detectable activation of the Epo-R or downstream signalling targets in human skeletal muscle in the resting situation, whereas more prolonged exposure induces significant changes in the skeletal muscle proteome. The absence of functional Epo receptor activity in human skeletal muscle indicates that the long-term effects are indirect and probably related to an increased oxidative capacity in this tissue.
A New Technique for Inferior Hypogastric Plexus Block: A Coccygeal Transverse Approach -A Case Report- (2012)

Chronic pelvic pain is a common problem with variable etiology. The sympathetic nervous system plays an important role in the transmission of visceral pain regardless of its etiology. Sympathetic nerve block is effective and safe for treatment of pelvic visceral pain. One of them, the inferior hypogastric plexus, is not easily assessable to blockade by local anesthetics and neurolytic agents. Inferior hypogastric plexus block is not commonly used in chronic pelvic pain patients due to pre-sacral location. Therefore, inferior hypogastric plexus is not readily blocked using paravertebral or transdiscal approaches. There is only one report of inferior hypogastric plexus block via transsacral approach. This approach has several disadvantages. In this case a favorable outcome was obtained by using coccygeal transverse approach of inferior hypogastric plexus. Thus, we report a patient who was successfully given inferior hypogastric plexus block via coccygeal transverse approach to treat chronic pelvic pain conditions involving the lower pelvic viscera.
Ubiquitin Specific Protease 13 Regulates Tau Accumulation and Clearance in Models of Alzheimer’s Disease1 (2019)

Ubiquitin Specific Protease-13 (USP13) is a de-ubiquinating enzyme that regulates protein ubiquitination and clearance. The role of USP13 is largely unknown in neurodegeneration. In this study we aim to demonstrate whether tau accumulation and/or clearance depends on ubiquitination/de-ubiquitination via USP-13. We used transgenic animal models of human amyloid precursor protein (APP) or P301L tau mutations and genetically knocked-down USP13 expression via shRNA to determine USP13 effects on tau ubiquitination and levels. We found a two-fold increase of USP13 levels in postmortem Alzheimer's disease (AD) brains. USP13 knockdown significantly increased the activity of the 20S proteasome and reduced the levels of hyper-phosphorylated tau (p-tau) in primary cortical neurons. USP13 knockdown also reduced the levels of amyloid and increased p-tau ubiquitination and clearance in transgenic animal models that overexpress murine tau as a result of the expression of familial APP mutations (TgAPP) and the human mutant P301L tau (rTg4510), respectively. Clearance of p-tau appears to be mediated by autophagy in these animal models. Taken together, these data suggest that USP13 knockdown reduces p-tau accumulation via regulation of ubiquitination/de-ubiquitination and mediates its clearance via autophagy and/or the proteasome. These results suggest that USP13 inhibition may be a therapeutic strategy to reduce accumulation of plaques and toxic p-tau in AD and human tauopathies.
Pathogen-Associated Molecular Pattern-Triggered Immunity: Veni, Vidi…? (2010)

For many years, plant pathology was divided into two schools of thought. It was clear that purified molecules or crude extracts from microbes or plants (referred to as general elicitors) could induce activation of general defense responses ([Boller, 1995][1]). Geneticists instead were studying plant
First report on quantum dot coated CMOS CID arrays for the UV and VUV (2013)

A technique has been developed for coating commercial off the shelf (COTS) detector arrays with a thin, uniform layer of quantum dots. The quantum deposition is accomplished using an Optomec Aerosol Jet rapid prototyping system. When illuminated by UV andvacuumUV (VUV) the quantum dots will fluoresce and those emitted photons will be detected by the underlying detector array. The size of the quantum dots used determines the fluorescence wavelength and that would be matched to the peak sensitivity of the underlying detector array. The devices have been tested at the NIST synchrotron facility in Gaithersburg and have shown sensitivity down to 150nm. Performance at wavelengths below 150nm is limited by absorption by solvent residues from deposition process.
Binding of 4',6-diamidino-2-phenylindole (DAPI) to GC and mixed sequences in DNA: intercalation of a classical groove-binding molecule (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBinding of 4',6-diamidino-2-phenylindole (DAPI) to GC and mixed sequences in DNA: intercalation of a classical groove-binding moleculeW. David Wilson, Farial A. Tanious, Henryk J. Barton, Robert L. Jones, Lucjan Strekowski, and David W. BoykinCite this: J. Am. Chem. Soc. 1989, 111, 13, 5008–5010Publication Date (Print):June 1, 1989Publication History Published online1 May 2002Published inissue 1 June 1989https://pubs.acs.org/doi/10.1021/ja00195a080https://doi.org/10.1021/ja00195a080research-articleACS PublicationsRequest reuse permissionsArticle Views610Altmetric-Citations117LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
The Fundamental Reason the S&P DTI Generates Core Returns (2012)

The idea that an investment has fundamental source returns should give an investor confidence that its future performance will not be dependent on management skill nor past performance. Commodities derive their source returns differently than financial assets. Understanding this difference is the key to understanding why the Standard & Poor's Diversified Trends Indicator (S&P DTI) total return is so consistently profitable over 12-month periods. For equities, investors are offered future dividends as a core return, which allows businesses to obtain capital to grow; for debt, investors are offered interest as a core return on loans; and for commodities, investors are paid a risk transfer premium for their capital to hedge and ensure an edge to obtaining their profits. In the S&P DTI, this amounts to a simulated and real compounded price return.
Atmospheric impregnation of porous silicon at room temperature (1991)

Microporous and mesoporous Si layers contain a very large surface area that affects both their optical and electrical properties. Secondary ion mass spectroscopy (SIMS) analysis is used for the first time to simultaneously monitor all the major impurities on that surface. SIMS data on a microporous layer demonstrate that its chemical composition changes dramatically with time during ambient air exposure. Similar trends are observed for mesoporous layers. Extended storage in air at room temperature converts the hydride surface of freshly anodized layers to that of a contaminated native oxide. Characterization techniques need to take the metastability of the hydride surface into account since the structural, optical, and electrical properties of porous Si can consequently change with time upon exposure to ambient air. Low-temperature photoluminescence and spectroscopic ellipsometry data on freshly anodized and ‘‘aged’’ microporous and mesoporous layers are chosen to illustrate typical changes in optical properties and the timescales involved. Spreading resistance analysis is also shown for the first time to provide depth information on the resistivities of porous layers and their variation with extended exposure to air. Implications for other characterization techniques are briefly discussed.
Tunable Squeezing Using Coupled Ring Resonators on a Silicon Nitride Chip (2015)

We demonstrate continuous tuning of the degree of squeezing from 0.5 to 2 dB (0.9 to 4 dB inferred on chip) by externally controlling the coupling condition of a Si3N4 double ring OPO using integrated microheaters.
Extremely Low Astigmatism and Aspect Ratio in 650nm-Band Self-Pulsing AlGaInP Lasers with Strained-Quantum-Well Saturable-Absorbing Layer (1996)

1996 International Conference on Solid State Devices and Materials,Extremely Low Astigmatism and Aspect Ratio in 650nm-Band Self-Pulsing AlGaInP Lasers with Strained-Quantum-Well Saturable-Absorbing Layer