gebhart/patrepeval huggingface dataset:
The conserved apicomplexan Aurora kinase TgArk3 is involved in endodyogeny, duplication rate and parasite virulence (2016)

Aurora kinases are eukaryotic serine/threonine protein kinases that regulate key events associated with chromatin condensation, centrosome and spindle function and cytokinesis. Elucidating the roles of Aurora kinases in apicomplexan parasites is crucial to understand the cell cycle control during Plasmodium schizogony or Toxoplasma endodyogeny. Here, we report on the localization of two previously uncharacterized Toxoplasma Aurora-related kinases (Ark2 and Ark3) in tachyzoites and of the uncharacterized Ark3 orthologue in Plasmodium falciparum erythrocytic stages. In Toxoplasma gondii, we show that TgArk2 and TgArk3 concentrate at specific sub-cellular structures linked to parasite division: the mitotic spindle and intranuclear mitotic structures (TgArk2), and the outer core of the centrosome and the budding daughter cells cytoskeleton (TgArk3). By tagging the endogenous PfArk3 gene with the green fluorescent protein in live parasites, we show that PfArk3 protein expression peaks late in schizogony and localizes at the periphery of budding schizonts. Disruption of the TgArk2 gene reveals no essential function for tachyzoite propagation in vitro, which is surprising giving that the P. falciparum and P. berghei orthologues are essential for erythrocyte schizogony. In contrast, knock-down of TgArk3 protein results in pronounced defects in parasite division and a major growth deficiency. TgArk3-depleted parasites display several defects, such as reduced parasite growth rate, delayed egress and parasite duplication, defect in rosette formation, reduced parasite size and invasion efficiency and lack of virulence in mice. Our study provides new insights into cell cycle control in Toxoplasma and malaria parasites and highlights Aurora kinase 3 as potential drug target.
The interplay between metabolic alterations, diastolic strain rate and exercise capacity in mild heart failure with preserved ejection fraction: a cardiovascular magnetic resonance study (2018)

Myocardial steatosis is pronounced in mild HFpEF, and is independently associated with impaired diastolic strain rate which is itself related to exercise capacity. Steatosis may adversely affect exercise capacity by indirect effect occurring via impairment in diastolic function. As such, myocardial triglyceride may become a potential therapeutic target to treat the increasing number of patients with HFpEF.
Chemical Screen for Vancomycin Antagonism Uncovers Probes of the Gram-Negative Outer Membrane (2021)

The outer membrane of Gram-negative bacteria is a formidable permeability barrier which allows only a small subset of chemical matter to penetrate. This outer membrane barrier can hinder the study of cellular processes and compound mechanism of action, as many compounds including antibiotics are precluded from entry despite having intracellular targets. Consequently, outer membrane permeabilizing compounds are invaluable tools in such studies. Many existing compounds known to perturb the outer membrane also impact inner membrane integrity, such as polymyxins and their derivatives, making these probes nonspecific. We performed a screen of ∼140 000 diverse synthetic compounds, for those that antagonized the growth inhibitory activity of vancomycin at 15 °C in <i>Escherichia coli</i>, to enrich for chemicals capable of perturbing the outer membrane. This led to the discovery that liproxstatin-1, an inhibitor of ferroptosis in human cells, and MAC-0568743, a novel cationic amphiphile, could potentiate the activity of large-scaffold antibiotics with low permeation into Gram-negative bacteria at 37 °C. Liproxstatin-1 and MAC-0568743 were found to physically disrupt the integrity of the outer membrane through interactions with lipopolysaccharide in the outer leaflet of the outer membrane. We showed that these compounds selectively disrupt the outer membrane while minimally impacting inner membrane integrity, particularly at the concentrations needed to potentiate Gram-positive-targeting antibiotics. Further exploration of these molecules and their structural analogues is a promising avenue for the development of outer membrane specific probes.
Kinetic Analysis of Escherichia coli 2-C-Methyl-d-erythritol-4-phosphate Cytidyltransferase, Wild Type and Mutants, Reveals Roles of Active Site Amino Acids (2004)

Escherichia coli 2-C-methyl-D-erythritol-4-phosphate cytidyltransferase (YgbP or IspD) catalyzes the conversion of 2-C-methyl-D-erythritol 4-phosphate (MEP) and cytidine triphosphate (CTP) to 4-diphosphocytidyl-2-C-methylerythritol (CDPME). Pulse chase experiments established that the reaction involves an ordered sequential mechanism with mandatory initial binding of CTP. On the basis of analysis of the previously reported crystal structures of apo-YgbP as well as YgbP complexed with both CTP.Mg(2+) and CDPME.Mg(2+) [Richard, S. B., Bowman, M. E., Kwiatkowski, W., Kang, I., Chow, C., Lillo, A. M., Cane, D. E., and Noel, J. P. (2001) Nat. Struct. Biol. 8, 641-648], a group of active site residues were selected for site-directed mutagenesis and steady-state kinetic analysis. Both Lys27 and Lys213 were shown to be essential to catalytic activity, consistent with their proposed role in stabilization of a pentacoordinate phosphate transition state resulting from in-line attack of the MEP phosphate on the alpha-phosphate of CTP. In addition, Thr140, Arg109, Asp106, and Thr165 were all shown to play critical roles in the binding and proper orientation of the MEP substrate.
Application of Combinatorial Procedures in the Search for Serine-Protease-Like Activity with Focus on the Acyl Transfer Step (2000)

Recursive deconvolution of a 729-membered peptide library has identified three active sequences, in which both Ser and His are present in one of the two tripeptidic chains generated on a steroidal scaffold (see structural formula), for the cleavage of an activated p-nitrophenyl ester. This combinatorial approach aims at searching for serine-protease-like activity.
EndophilinA-dependent coupling between activity-dependent calcium influx and synaptic autophagy is disrupted by a Parkinson-risk mutation (2022)

Abstract Neuronal activity and neurotransmitter release cause use-dependent decline in protein function. However, it is unclear how this is coupled to local protein turnover and quality control mechanisms. Here we show that the endocytic protein Endophilin-A (EndoA/ENDOA1) couples activity-induced calcium influx to synaptic autophagy and neuronal survival. We identify single mutations in the EndoA flexible region that either increases EndoA diffusion and promotes autophagosome formation in the absence of calcium, or immobilizes EndoA and blocks autophagy, even in the presence of calcium. Hence, the EndoA flexible region is a switch that responds to calcium, regulating EndoA nanoscale synaptic organization and association with autophagosomes driving their formation. Interestingly, a pathogenic variant in the human ENDOA1 variable region that confers risk to Parkinson’s disease (PD), also confines ENDOA1 to the synaptic plasma membrane and equally blocks autophagy in flies in vivo and in induced human neurons. Thus, our work reveals a mechanism neurons use to connect neuronal activity to local protein turnover by autophagy, which is critical for neuronal survival.
New twist on the helical nanofilament phase of bent-core liquid crystals (2014)

Recent cryo-TEM studies in the helical nanofilament (HNF) phase of several bent-core liquid crystal materials having blue structural color showed that in subsequent layers the nanofilaments twist with respect to each other by about 37º angle, leading to a secondary helical structure that can explain their opal appearance. In this paper, after summarizing these observations, we show additional features that help understanding why the same bent-core homologs P-n-O-PIMB with n ≥ 9 do not show structural color.
Supplementary Table 3 from A Targeted RNAi Screen of the Breast Cancer Genome Identifies <i>KIF14</i> and <i>TLN1</i> as Genes That Modulate Docetaxel Chemosensitivity in Triple-Negative Breast Cancer (2023)

&lt;p&gt;PDF File - 86K, List of cell lines (from Neve et al. 2006, see text) with clinical annotations for analysis of KIF14 and TLN1 expression within each clinical subtype of breast cancer.&lt;/p&gt;
ELLIPSOID ZONE MAPPING AND OUTER RETINAL CHARACTERIZATION AFTER INTRAVITREAL OCRIPLASMIN (2016)

Mapping of EZ is feasible to assess EZ-RPE volume and overall EZ integrity with en face thickness mapping. Alterations in EZ occur in a significant proportion of eyes after ocriplasmin therapy. The EZ-RPE volume and the EZ-RPE central foveal area typically recover to baseline by 3 months. This effect appears to be panretinal and associated with subjective symptoms.
Structure of aldolase fromThermus thermophilusHB8 showing the contribution of oligomeric state to thermostability (2004)

2-Deoxyribose-5-phosphate aldolase catalyzes a reversible aldol condensation of two aldehydes via formation of a covalent Schiff-base intermediate at the active lysine residue. The crystal structure of 2-deoxyribose-5-phosphate aldolase from Thermus thermophilus HB8 has been determined with and without the substrate at atomic resolution. This enzyme, which has a unique homotetramer structure, has been compared with the previously reported crystal structures of two orthologues from Escherichia coli and Aeropyrum pernix. In contrast to the similar alpha/beta-barrel fold of the monomers, substantial quaternary structural differences are observed between these three enzymes. Further comparison of the subunit-subunit interface areas of these aldolases showed a clear positive correlation between the interface area and the living temperature of the source organism. From these results, it is concluded that the oligomeric state of 2-deoxyribose-5-phosphate aldolase is important for the thermostability and not for the catalytic function.
Les resurfaçages minces adhérents en béton renforcé de fibres comme méthode de réhabilitation des chaussées de béton (1990)

The progressive and rapid deterioration of cement concrete road systems makes frequent rehabilitation necessary if an acceptable level of service is to be maintained. When a road's structural capacity is still satisfactory, simple resurfacing to correct surface faults is an acceptable option. Several different types of resurfacing are possible, depending on adhesion developed at the interface. Dimensioning and selection of application techniques are still today purely empirical matters. However, major discoveries have been made about the behaviour of overlays, especially regarding cracking. For example, reflection in the overlay of the cracks of the old pavement is inevitable with a bonded interface. The old cracks must, therefore, be repaired first. However, with steel fibre reinforced concrete, the knitting effect of the fibres will stabilize the cracks. Road-work performed along autoroute 40 in the suburbs of Montreal provided an opportunity to monitor the behaviour of a thin bonded overlay of fibre-reinforced concrete. Examination of the road more than 2 years after it was recommissioned clearly indicated that the fibres had a positive effect on the condition of the road. Key words: rehabilitation, resurfacing, roads, concrete, steel fibre, cracking, bonding. [Journal translation]
ChemInform Abstract: Postsynthetic Modification of Metal—Organic Frameworks — A Progress Report (2011)

Abstract Review: 73 refs.
Abstract 2525: Modulation of src and STAT3 pathways with dasatinib in patients with metastatic pancreatic cancer (2010)

Abstract BACKGROUND: Cancer of the pancreas is the fourth leading cause of cancer-related death in the United States with less than 5% living for more than 5 years. These dismal statistics reflect the early metastasis of cancer cells. Overexpression or activation of Src and STAT3 are commonly detected in pancreas cancer leading to increased cell proliferation and migration. Dasatinib is a broad spectrum ATP competitive inhibitor of protein tyrosine kinases including the SRC family of kinases. We conducted a pilot trial of single agent dasatinib in patients with metastatic pancreas cancer. METHODS: Patients with metastatic pancreatic cancer were enrolled and treated with dasatinib 70 mg twice per day. Due to the difficulty of obtaining serial biopsies on pancreas cancer patients correlative studies were performed on peripheral blood mononuclear cells as a surrogate. Peripheral blood mononuclear cells were collected at baseline, 6 hours after the first dose and at the beginning of the next cycle. Western blots were performed to evaluate Src and STAT3 protein levels. RESULTS: Seven patients were enrolled in the trial with two patients completing two cycles of chemotherapy. Two patients withdrew for toxicity with one patient having grade 4 diarrhea and grade 3 vomiting. The second patient withdraw for grade 3 fatigue and grade 2 diarrhea. Two patients completed 2 cycles and had minor grade 1-2 toxicities attributable to dasatinib but had progressive disease upon restaging. Three patients did not want to continue on study and were removed in the first cycle. Western blots performed on peripheral blood mononuclear cells showed a rapid decrease of phosphorylated STAT3 (p-STAT3) six hours after treatment in three patients but only one patient had a corresponding decrease in phosphorylated Src (p-Src). For two patients the p-STAT3 levels remained low after completion of the first cycle. These patients had an overall survival of 50 weeks and 61 weeks. The overall survival for the other patients ranged from 8-12 weeks. CONCLUSION: Because pancreatic cancer remains resistant to current therapies despite recent advances in the development of molecular targeted therapies, there is an urgency to understand these pathways. Our patient with a rapid decrease in p-STAT3 and p-Src six hours after treatment had an overall survival of 61 weeks which reflects the biology of the tumor but also suggests the importance of simultaneously inhibiting these pathways. Since STAT is a target of Janus kinase, additional studies evaluating JAK activity are being done. Future clinical trials combining molecular targeted therapies in addition to traditional cytotoxics are warranted as we strive to improve the survival of our patients with this deadly disease. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2525.
Comparative study of native oxide impacts on low energy doping processes (2010)

The impacts of the native oxides and the impurity loss mechanisms of low energy doping process for both p-type and n-type implants have been quantitatively studied using secondary ion mass spectrometry/angle-resolved x-ray photoelectron spectroscopy method. The low energy doping processes include conventional beamline implant and plasma immersion ion implantation (PIII). It has been found that the native oxides play very significant roles on the low energy implants, especially for PIII due to its unique impurity profiles. The results show very different behaviors on p-type and n-type implants because of the SiO2∕Si interface segregation mechanisms. p-type (boron-based) doping loses more impurities into the native oxide, but n-type (arsenic-based) doping does not lose impurities. These results can be used to optimize the semiconductor processes such as implant, strip, clean, and thermal-annealing process.
Elliptical orbit constellations-a new paradigm for higher efficiency in space systems? (2002)

Several systems are being developed for satellite cellular telephone use. Examples are Iridium, Globalstar, ICO, and ELLIPSO. Systems designers seem to prefer sub-synchronous multi-satellite arrays over geostationary satellites as they can more easily communicate with small low-power handheld cellular telephones, and they also have less signal latency (time delay). The flexibility of the elliptic orbit allows a biasing of earth coverage towards a given latitude. Increased coverage is obtained by placing apogees in a stable orbit over a preferred latitude. If the orbit is both elliptical and sun-synchronous, it can also be biased towards a given (local) time of day. With apogees appearing during daytime, greater capacity is ensured during the peak usage hours for telephone communications. Tailored elliptical-orbit constellations may well become the paradigm for many of these new telecommunications space systems. Lower cost elliptic-orbit constellations, with fewer satellites, may well prove more profitable than circular arrays for many other space applications, as well.
WE-C-217BCD-08: Rapid Monte Carlo Simulations of DQE(f) of Scintillator-Based Detectors (2012)

The number of launched particles and corresponding execution times for a DQE simulation can be dramatically reduced allowing for accurate computation with modest computer hardware. NIHRO1 CA138426. Several authors work for Varian Medical Systems.
Mie theory interpretations of light scattering from intact cells (2005)

We present a Mie theory-based analysis of angularly resolved light scattering from intact cells that involves the product of a particle size distribution rho and the scattering cross section sigma. The analysis shows that the ability to size intracellular organelles depends strongly upon the assumed functional form of the particle size distribution; however, the product sigma rho extracts the dominant light scatterers regardless of this choice. We examine goniometer measurements from our own and another laboratory and find that this analysis reconciles seemingly conflicting results and confirms that mitochondrial-sized organelles dominate scattering from intact cells in the angular range 50 degrees - 90 degrees.
Analysis of Carotenoid Composition in Petals of Calendula (Calendula officinalisL.) (2005)

Nineteen carotenoids were identified in extracts of petals of orange- and yellow-flowered cultivars of calendula (Calendula officinalis L.). Ten carotenoids were unique to orange-flowered cultivars. The UV-vis absorption maxima of these ten carotenoids were at longer wavelengths than that of flavoxanthin, the main carotenoid of calendula petals, and it is clear that these carotenoids are responsible for the orange color of the petals. Six carotenoids had a cis structure at C-5 (C-5'), and it is conceivable that these (5Z)-carotenoids are enzymatically isomerized at C-5 in a pathway that diverges from the main carotenoid biosynthesis pathway. Among them, (5Z,9Z)-lycopene (1), (5Z,9Z,5'Z,9'Z)-lycopene (3), (5'Z)-gamma-carotene (4), and (5'Z,9'Z)-rubixanthin (5) has never before been identified. Additionally, (5Z,9Z,5'Z)-lycopene (2) has been reported only as a synthesized compound.
Design and implementation of a Ka-band corrugated feed horn for reflector antennas (2013)

This paper presents the relationship between Gaussian beam and reflector antennas and deals with the most important conical corrugated feed horn design parameters for reflector antennas. Furthermore, a compact, easily to manufacture and easily to frequency-scale conical corrugated horn with more than 40% relative bandwidth is proposed. The hybrid-mode (HE <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">11</sub> ) conical corrugated feed horn operating from 26.5 to 40GHz has been designed, fabricated and measured.
1277: Evidence for the Involvement of Spinal Cyclooxygenase-2 in Detrusor Overactivity in the Rats (2006)

You have accessJournal of UrologyDiscussed Poster, Tuesday, May 23, 2006, 1:00 - 4:00 pm1 Apr 20061277: Evidence for the Involvement of Spinal Cyclooxygenase-2 in Detrusor Overactivity in the Rats Hitoshi Masuda, Michael B. Chancellor, Kazunori Kihara, William C. de Groat, and Naoki Yoshimura Hitoshi MasudaHitoshi Masuda More articles by this author , Michael B. ChancellorMichael B. Chancellor More articles by this author , Kazunori KiharaKazunori Kihara More articles by this author , William C. de GroatWilliam C. de Groat More articles by this author , and Naoki YoshimuraNaoki Yoshimura More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(18)33490-6AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "1277: Evidence for the Involvement of Spinal Cyclooxygenase-2 in Detrusor Overactivity in the Rats." The Journal of Urology, 175(4S), p. 411 © 2016 by American Urological AssociationFiguresReferencesRelatedDetails Volume 175Issue 4SApril 2006Page: 411 Advertisement Copyright & Permissions© 2016 by American Urological AssociationMetricsAuthor Information Hitoshi Masuda More articles by this author Michael B. Chancellor More articles by this author Kazunori Kihara More articles by this author William C. de Groat More articles by this author Naoki Yoshimura More articles by this author Expand All Advertisement PDF downloadLoading ...
Temperature dependence of bulk viscosity in water using acoustic spectroscopy (2011)

Despite its fundamental role in the dynamics of compressible fluids, bulk viscosity has received little experimental attention and there remains a paucity of measured data. Acoustic spectroscopy provides a robust and accurate approach to measuring this parameter. Working from the Navier-Stokes model of a compressible fluid one can show that the bulk viscosity makes a significant and measurable contribution to the frequency-squared acoustic attenuation. Here we employ this methodology to determine the bulk viscosity of Millipore water over a temperature range of 7 to 50 degrees Celsius. The measured attenuation spectra are consistent with the theoretical predictions, while the bulk viscosity of water is found to be approximately three times larger than its shear counterpart, reinforcing its significance in acoustic propagation. Moreover, our results demonstrate that this technique can be readily and generally applied to fluids to accurately determine their temperature dependent bulk viscosities.
Paroxysmal Cold Hemoglobinuria: Transmission and Scanning Electron Microscopy Features of Erythrocytes (1975)

Djaldetti, Meir, Elion, Dorith, Bessler, Hana, and Fishman, Pnina: Paroxysmal cold hemoglobinuria. Tranmission and scanning electron microscopy features of erythrocytes. Am J Clin Pathol 63. 804-810, 1975. The case history of a patint with paroxysmal cold hemoglobinuria of the chronic iduipathic type is reported. The patient showed a marked dependency on the external temperature, with severe hemolytic anemia and hemoglobinuria during the winter. Examination of the erythrocytes with the transmission electron microscope showed abnormal forms identified as ropalocytes, whereas examination with the scanning electron microscope revealed "holes" in the erythrocytes. (Key words: Paroxysmal cold hemoglobinuria' Ultrastructure of erythrocytes.
A Novel Wireless Photoplethysmography Blood-Flow Volume Sensor for Assessing Arteriovenous Fistula of Hemodialysis Patients (2017)

A novel blood-flow volume (BFV) sensor is presented for assessing quality of arteriovenous fistula in hemodialysis patients via noninvasive reflectance-type photoplethysmography (PPG). BFV is nowadays in clinic practices evaluated using an ultrasound Doppler monitor, which is expensive, bulky, and can only be operated by well-trained medical personnels. This study is devoted to develop a low-cost, small-sized, portable, and easy-to-use PPG sensor that is capable of continuous measurement of BFV. New designs of front-end analog circuits, signal processing, and an intelligent neural network calibration method are employed to finally achieve high correlation (R <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> = 0.7176), as opposed to the ultrasound Doppler monitor, with the root-mean-squared errors successfully controlled under 289 ml/min.