gebhart/patrepeval huggingface dataset:
Aspartyl‐phosphate phosphatases deactivate the response regulator components of the sporulation signal transduction system in Bacillus subtilis (1996)

Bacteria use two-component signal transduction systems to sense and respond to their environment. A sensor kinase and a response-regulator transcription factor work in concert by phosphorylation/dephosphorylation through kinase and phosphatase activities to maintain a level of phosphorylated response regulator commensurate with the level of signal input. Signal input can be accommodated through stimulation of the kinase activity or the phosphatase activity of the two-component system. With some notable exceptions, the sensor kinases recognize a single stimulatory ligand. A new dimension in the regulation of two-component signal transduction systems was discovered in the Rap phosphatases which dephosphorylate the SpoOF response-regulator of Bacillus subtilis independent of the sensor kinases. This family of phosphatases is encoded by at least six chromosomal genes. Although not all of the phosphatases of the family have activity on phosphorylated SpoOF, the two best-characterized members, RapA and RapB, prevent sporulation by dephosphorylating this response regulator component of the phosphorelay. Phosphatase activity of RapA is regulated by a gene, phrA, in the same transcriptional unit, that encodes a peptide secreted from the cell which may serve as a quorum sensor. Most of the Rap phosphatase operons have a gene coding for a protein with some similarity to PhrA in their transcription units, but it is uncertain whether all of these play a role in regulation. The Rap phosphatases are postulated to be a mechanism for allowing signals other than those that affect the sensor kinases to regulate the signal transduction pathway. They may have been recruited to help regulate sporulation because the multiple signals regulating this process may outstrip the recognition capacity of the kinases.
Recurrent Laryngeal Nerve Identification and Assessment during Thyroid Surgery: Laryngeal Palpation (2004)

Abstract Electrical identification and monitoring of the recurrent laryngeal nerve (RLN) has been proposed as an adjunct to standard visual identification of the nerve during thyroid and parathyroid surgery. This study was undertaken to assess laryngeal palpation as an intraoperative technique for identifying and assessing the RLN during surgery and to investigate the relation between laryngeal palpation and associated laryngeal electromyographic (EMG) activity. The postcricoid region of the larynx during surgery was palpated through the posterior hypopharyngeal wall to sense posterior cricoarytenoid muscle contraction in response to ipsilateral RLN stimulation (i.e., the “laryngeal twitch response.”) Laryngeal palpation was performed in a series of 449 consecutive thyroid and parathyroid surgeries with 586 RLNs at risk. All patients underwent preoperative and postoperative laryngoscopy to assess vocal cord mobility. In a subset of patients, laryngeal palpation and simultaneous laryngeal EMG recordings were compared during intraoperative RLN stimulation. In this series, there was no permanent RLN paralysis. There was one case of temporary RLN paralysis secondary to neural stretch that resolved 6 weeks postoperatively (temporary paralysis rate: 0.2% of patients, 0.2% of nerves at risk). Intraoperative laryngeal palpation of the laryngeal twitch response reliably correlated with normal postoperative vocal cord function. Loss of the laryngeal twitch response occurred in the single case of temporary paralysis in the setting of an anatomically intact nerve. Laryngeal palpation correlated well with simultaneous laryngeal EMG activity. There were no palpation‐induced laryngeal injuries or laryngeal edema. There were also no RLN injuries due to repetitive neural stimulation. Intraoperative laryngeal palpation during RLN stimulation is a safe, reliable method for neural monitoring that can assist in RLN identification and assessment during thyroid and parathyroid surgery. Most importantly, it provides important prognostic information regarding ipsilateral vocal cord function at the completion of the initial side of the thyroid or parathyroid surgery. Intraoperative laryngeal palpation allows the surgeon to stage contralateral surgery if RLN damage is diagnosed, thereby avoiding the potential for bilateral vocal cord paralysis. We believe that laryngeal palpation is useful as an adjunct to formal EMG monitoring during thyroid and parathyroid surgery.
Differentiation of embryonic stem cells through controlled release of growth factors from microspheres (2009)

The development of microspheres for the sustained delivery of protein and small drug delivery has been utilised in tissue engineering and drug delivery applications. However problems exist in obtaining a controlled and predictable release pattern of the encapsulated molecules from these materials. In this study, microspheres with a zero order release kinetic profile and no lag phase were developed from a novel PLGA based polymer blend. \n\nThe novel PLGA based polymer blend was made from blending PLGA with varying compositions of the triblock co-polymer PLGA-PEG-PLGA. These blends were subsequently used in the fabrication of lysozyme and dexamethasone loaded microspheres. \n\nBlending of the triblock copolymer with PLGA resulted in a reduction of the glass transition temperature (36.1ºC against 59.7ºC) and an increased mechanical strength (25.25 ± 1.26MPa against 0.26 ± 0.05MPa) for PLGA and 30% triblock w/w microspheres respectively. An incremental increase in the triblock composition within the Triblock/PLGA blends resulted in a corresponding reduction in glass transition temperature of the microspheres. \n\nVarying the triblock composition within the microspheres showed no significant effect on entrapment efficiency (EE) of lysozyme (protein) and dexamethasone (drug) within fabricated microspheres (EE ~ 60% for and 75% for loading weight 5% w/w for lysozyme and dexamethasone microspheres respectively). Controlled release experiments showed incorporation of the triblock increased the burst release of the protein and drug molecules from the microspheres and improved their release kinetics, with zero-order release profile (post burst phase) observed at a triblock composition of 30% w/w. A positive correlation between the amount of triblock within the triblock / PLGA blend and the rate of protein and drug release was also observed. \n\nThe induction of osteogenesis and chondrogenesis within stem cells seeded on dexamethasone and ascorbate phosphate, and TGF-β3 loaded scaffolds was successfully demonstrated. Zonal release of TGF-β3 and BMP4 proteins from a bilayered scaffold was also demonstrated. However experiments conducted to demonstrate the tissue zonation within a bone cartilage bilayered construct developed from embryonic stem cell seeded TGF-β3 and BMP4 loaded bilayered scaffolds yielded inconclusive data. \n\nThese results suggests that protein and drug loaded injectable microspheres for tissue engineering applications can be formed from triblock/PLGA blends, and that by varying the triblock composition, the temperature at which the microspheres form scaffolds, the release kinetics and the mechanical strength of the resulting scaffolds can be controlled.
A Family of Highly Ordered Mesoporous Polymer Resin and Carbon Structures from Organic−Organic Self-Assembly (2006)

The syntheses of a family of highly ordered mesoporous polymers and carbon frameworks from organic−organic assembly of triblock copolymers with soluble, low-molecular-weight phenolic resin precursors (resols) by an evaporation induced self-assembly strategy have been reported in detail. The family members include two-dimensional hexagonal (space group, p6m), three-dimensional bicontinuous (Ia3̄d), body-centered cubic (Im3̄m), and lamellar mesostructures, which are controlled by simply adjusting the ratio of phenol/template or poly(ethylene oxide)/poly(propylene oxide) in the templates. A five-step mechanism from organic−organic assembly has been demonstrated. Cubic FDU-14 with a gyroidal mesostructure of polymer resin or carbon has been synthesized for the first time by using the copolymer Pluronic P123 as a template in a relatively narrow range. Upon calcination at 350 °C, the templates should be removed to obtain mesoporous polymers, and further heating at above a critical temperature of 600 °C transforms the mesoporous polymers to the homologous carbon frameworks. The mesoporous polymer resin and carbon product materials exhibit ordered structures, high surface areas, (670−1490 m2/g), large pore volumes (0.65−0.85 cm3/g), and uniform, large pore sizes (7.0−3.9 nm), as well as very thick pore walls (6−8 nm). The carbon open frameworks with covalently bonded constructions and thick pore walls exhibit high thermal stability (>1400 °C). Our results show that the feed gas used during the calcination has a great influence on the porosity of the products. The presence of a small amount of oxygen facilitates the large pore sizes and high surface areas of mesoporous materials with different mesostructures. An extraction method employing sulfuric acid can also decompose the template from hexagonal mesostructured polymers with little framework shrinkage. Preliminary studies of the mechanical and electrochemical properties of mesoporous carbon molecular sieves are also presented.
Differential Counteraction of Ethylene Effects by Gibberellin A3 and N6-Benzyladenine in Senescing Citrus Peel (1977)

Treatment of mature citrus fruit (Citrus sinensis) with ethylene induced rapid chlorophyll destruction, a rise in respiration, a release of free amino acids, an accumulation of reducing sugars, and an appearance of phenylalanine ammonia lyase activity. Gibberellin A(3) (GA(3)) and N(6)-benzyladenine (BA) opposed the effects of ethylene on chlorophyll, amino acids, and to a lesser extent, reducing sugar levels. The ethylene-induced respiratory rise was only slightly modified by GA(3) and BA. Phenylalanine ammonia lyase activity was not affected by GA(3).The antagonism between ethylene and the senescence-delaying regulators GA(3) and BA seems to operate mainly within the chloroplast, but might not be confined to this compartment. The accumulation of reducing sugars exhibits the antagonism although it is not apparently related to the chloroplast.
DISC1-binding proteins in neural development, signalling and schizophrenia (2011)

In the decade since Disrupted in Schizophrenia 1 (DISC1) was first identified it has become one of the most convincing risk genes for major mental illness. As a multi-functional scaffold protein, DISC1 has multiple identified protein interaction partners that highlight pathologically relevant molecular pathways with potential for pharmaceutical intervention. Amongst these are proteins involved in neuronal migration (e.g. APP, Dixdc1, LIS1, NDE1, NDEL1), neural progenitor proliferation (GSK3β), neurosignalling (Girdin, GSK3β, PDE4) and synaptic function (Kal7, TNIK). Furthermore, emerging evidence of genetic association (NDEL1, PCM1, PDE4B) and copy number variation (NDE1) implicate several DISC1-binding partners as risk factors for schizophrenia in their own right. Thus, a picture begins to emerge of DISC1 as a key hub for multiple critical developmental pathways within the brain, disruption of which can lead to a variety of psychiatric illness phenotypes.
Characterization of JC human polyomavirus infection in a Portuguese population (2010)

JC virus (JCV) is ubiquitous in the human population, infecting children asymptomatically. After primary infection, JCV persists in the host throughout life and is often excreted in the urine. Two hundred thirty-four urine samples and 78 serum samples, collected from 171 healthy individuals and 63 patients infected with HIV, were used to characterize JCV infection in a Portuguese population. Using PCR, JCV DNA was detected in 38% of the urine samples. A significant difference in the excretion rate was observed between patients infected with HIV (51%) and healthy individuals (33%). The frequency of JCV viruria increased with age in healthy individuals, but not in patients infected with HIV. JCV urinary load was determined by real-time quantitative PCR and was independent of gender, age, HIV infection, and CD4+ cell count. Overall, the JCV genotype detected most commonly was 1B, followed by genotypes 2B and 4. The detection and quantitation of JCV-specific antibodies were performed in serum samples by an established enzyme immunoassay (EIA). Antibodies to JCV were observed in 91% of the patients tested, irrespective of HIV infection. A positive correlation between JCV urinary load and antibody titers was demonstrated. The present study provides the first characterization of seroprevalence and urinary excretion of JCV in a Portuguese population and revealed similar results to those observed in other European countries. A comparison between healthy individuals and patients infected with HIV, despite identical values of seroprevalence, showed some differences in the pattern of urinary excretion. J. Med. Virol. 82:494-504, 2010. (c) 2010 Wiley-Liss, Inc.
A GPU based real-time video compression method for video conferencing (2013)

Recent years have seen a great increase in the everyday use of real-time video communication over the internet through video conferencing applications. Limitations on computational resources and network bandwidth require video encoding algorithms that provide acceptable quality on low bitrates and can support various resolutions inside the same stream. In this work, the authors present a scalable video coding algorithm based on the contourlet transform that incorporates both lossy and lossless methods, as well as variable bitrate encoding schemes in order to achieve compression. Furthermore, due to the transform utilized, it does not suffer from blocking artifacts that occur with many widely adopted compression algorithms. The proposed algorithm is designed to achieve real-time performance by utilizing the vast computational capabilities of modern GPUs, providing satisfactory encoding and decoding times at relatively low cost. These characteristics make this method suitable for applications like video conferencing that demand real-time performance. The performance and quality evaluation of the algorithm shows that the proposed algorithm achieves satisfactory quality and compression ratio.
The Biological Effects of Retinoids on Cell Differentiation and Proliferation (1988)

The retinoids are the natural and synthetic analogues of retinol or vitamin A. These molecules are able to modulate differentiation and proliferation processes in several cell types. The presence of retinoids is essential for inducing or maintaining the differentiation of epithelial cells. On the other hand, when excess retinol is added to the culture medium, the differentiation of some mesenchymal cells is impaired. Retinoids also promote the differentiation of carcinoma cells of various origins: embryonal carcinoma, leukaemic and melanoma cells. While their effect on the proliferation of normal cells appears variable, these molecules inhibit the growth of cells treated with a tumoural promoter, or spontaneously transformed cells, and they prevent tumour promotion. Various mechanisms of action might be involved: retinoids could act at the level of the genome with or without the participation of their binding proteins. They might also influence glycoconjugate biosynthesis and interact, through certain glycosylation reactions, with growth factor receptors. The role of vitamin A and its structural analogues in cell differentiation and growth is of great therapeutic interest.
Phenacyl esters of fatty acids via crown ether catalysts for enhanced ultraviolet detection in liquid chromatography (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhenacyl esters of fatty acids via crown ether catalysts for enhanced ultraviolet detection in liquid chromatographyH. D. Durst, M. Milano, E. J. Kikta, S. A. Connelly, and Eli. GrushkaCite this: Anal. Chem. 1975, 47, 11, 1797–1801Publication Date (Print):September 1, 1975Publication History Published online1 May 2002Published inissue 1 September 1975https://doi.org/10.1021/ac60361a025RIGHTS & PERMISSIONSArticle Views1110Altmetric-Citations343LEARN 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 InReddit PDF (583 KB) Get e-Alerts Get e-Alerts
Structural Biology of Antimicrobial Peptides by NMR Spectroscopy (2006)

Antimicrobial peptides are key components of innate immunity of all life forms. Understanding the structureactivity relationship of these peptides is essential for developing them into novel therapeutics that substitutes traditional antibiotics. NMR spectroscopy can provide insights into membrane-targeting antimicrobial peptides from a variety of angles. First, three-dimensional structures of antimicrobial peptides can be determined by solution NMR using short-chain phosphatidylglycerol micelles as a novel bacterial membrane-mimetic model. Natural abundance 15N and 13C chemical shifts of short peptides offer a practical approach for the refinement of distance-based structures. Isotope labeling will allow structures of antimicrobial peptides with longer or difficult sequences to be determined in lipid micelles or bicelles and further refined by residual dipolar couplings. The in-plane or transmembrane orientation of antimicrobial peptides in lipid bilayers can be determined by solid-state NMR. Second, the impact of antimicrobial peptides on the structure and dynamics of lipid bilayers can be probed by 31P and 2H NMR spectroscopy. Third, intermolecular nuclear Overhauser effects (NOE) provide direct evidence for the location of the peptides in the membranes and are key restraints for establishing the structure of peptide-lipid complexes. Peptide-lipid NOE patterns also reflect the penetration depth of peptides in membranes. A deeper penetration is required for a basic peptide to exert its membrane perturbation potential on acidic membranes. The combination of solution and solid-state NMR depicts a more complete picture how antimicrobial peptides perturb bacterial membranes. The membrane-bound structures of antimicrobial peptides can be harnessed to guide peptide engineering to improve the therapeutic index.
Where's the Tube? Evaluation of Hand-held Ultrasound in Confirming Endotracheal Tube Placement (2004)

This report raises the possibility that thoracic sonography may be another tool that could be used to confirm proper ETT placement. This technique may have merit in extreme environments, such as in remote, pre-hospital settings or during aerospace medical transports, in which auscultation is impossible due to noise, or capnography is not available, and thus, requires further scientific evaluation.
The active site structure of Na+/K+-transporting ATPase: location of the 5'-(p-fluorosulfonyl)benzoyladenosine binding site and soluble peptides released by trypsin. (1986)

When the dog kidney Na+/K+-transporting ATPase (EC 3.6.1.37, formerly EC 3.6.1.3) was labeled with an ATP analogue, 5'-(p-fluorosulfonyl)benzoyladenosine (FSBA), there was a concomitant loss of ATPase activity. The presence of ATP protected the enzyme from both labeling and inactivation. The ATP-sensitive incorporation of FSBA is associated only with modification of the alpha subunit from which two labeled tryptic peptides were purified and sequenced. To establish any regions of the enzyme protruding from the membrane, the native Na+/K+-transporting ATPase from the electric ray, Torpedo californica, was treated with trypsin; and four peptides, which were released into the water phase, were purified and sequenced. A comparison of the peptide sequences with the deduced amino acid sequences of the DNA coding for the alpha subunit of T. californica and sheep kidney reveal the following. (i) FSBA-labeled peptides from the dog kidney enzyme are located in the central hydrophilic domain and show almost complete sequence homology with the same region in the alpha subunit from the electric ray and sheep kidney. Furthermore, the sequence homology of one of the two labeled peptides can be extended to the sarcoplasmic Ca2+-transporting ATPase and B subunit of Escherichia coli K+-transporting ATPase. (ii) Three trypsin-exposed peptides are found in the central hydrophilic domain, and one peptide is in the hydrophilic segment near the C terminus of the alpha subunit. (iii) The active center of Na+/K+-transporting ATPase is likely to be constructed from at least four different stretches in the primary sequence and, irrespective of the different specificity of cations, the various cation transport ATPases that form phosphorylated enzyme appear to have a common structure at the catalytic site for ATP hydrolysis.
Response of cluster headache to psilocybin and LSD (2006)

The authors interviewed 53 cluster headache patients who had used psilocybin or lysergic acid diethylamide (LSD) to treat their condition. Twenty-two of 26 psilocybin users reported that psilocybin aborted attacks; 25 of 48 psilocybin users and 7 of 8 LSD users reported cluster period termination; 18 of 19 psilocybin users and 4 of 5 LSD users reported remission period extension. Research on the effects of psilocybin and LSD on cluster headache may be warranted.
Development of the magnetic tunnel junction MRAM at IBM: From first junctions to a 16-Mb MRAM demonstrator chip (2006)

This paper reviews the remarkable developments of the magnetic tunnel junction over the last decade and in particular, work aimed at demonstrating its potential for a dense, fast, and nonvolatile random access memory. The initial focus is on the technological roots of the magnetic tunnel junction, and then on the recent progress made with engineered materials for this device. Following that, we discuss the development of the magnetic random access memory (MRAM) technology, in which the magnetic tunnel junction serves as both the storage device and the storage sensing device. The emphasis is on work at IBM, including demonstrations of basic capabilities of the technology and work on a 16-Mb “product demonstrator” design in 180-nm node technology, which was targeted to be a realistic test bed for the MRAM technology. Performance and cost are compared with those of competing technologies. The paper also serves as an introduction to more specialized papers in this issue on MRAM device physics, magnetic tunnel junction materials and device characterization, MRAM processing, and MRAM design.