gebhart/patrepeval huggingface dataset:
Carrier Frequency Offset Estimation for Uplink OFDMA Using Partial FFT Demodulation (2010)

Fast and accurate Carrier Frequency Offset (CFO) estimation is a problem of significance in many multi-carrier modulation based systems, especially in uplink Orthogonal Frequency Division Multiple Access (OFDMA) where the presence of multiple users exacerbates the inter-carrier interference (ICI) and results in multi-user interference (MUI). In this paper, a new technique called partial FFT demodulation is proposed. Estimators for the CFO are derived by considering an approximated matched filter for each user, implemented efficiently using several FFTs operating on sub-intervals of an OFDM block. Through simulations, the feasibility and performance of the proposed estimators are demonstrated. Associated trade-offs are discussed.
Biological evaluation and molecular docking study of metabolites from Salvadora Persica L. Growing in Egypt (2019)

Pharmacognosy Magazine ,2019,15,61,232-237.DOI:10.4103/pm.pm_361_18Published:March 2019Type:Original Article Authors:Mohammed M Ghoneim, Wael M Afifi, Mohamed Ibrahim, Mohamed Elagawany, Maan T Khayat, Mohamed H Aboutaleb, and Ahmed M Metwaly Author(s) affiliations:Mohammed M Ghoneim1, Wael M Afifi2, Mohamed Ibrahim3, Mohamed Elagawany4, Maan T Khayat5, Mohamed H Aboutaleb6, Ahmed M Metwaly2 1Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt; Department of Natural Products, School of Pharmacy, Almaarefa Colleges for Science and Technology, Riyadh, Saudia Arabia 2Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt 3Department of Organic Chemistry, College of Pharmacy, Misr University for Science and Technology, Al-Motamayez District, Damnhour, Egypt 4Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Damnhour University, Damnhour, Egypt 5Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudia Arabia 6Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Horus University, New Damietta 34517, Egypt Abstract:Background: Methicillin-resistant Staphylococcus aureus (MRSA) is a resistant staph bacterium to several antibiotics causing several lives-threating diseases such as pneumonia and sepsis. Meswak, Salvadora persica, exhibited promising antimicrobial properties before. Objective: Exploring the anti-MRSA activity of S. persica L. metabolites and its mechanism of action on a molecular level. Materials and Methods: Structure elucidation of the isolated metabolites was carried out by spectroscopic data (one-dimensional and two-dimensional nuclear magnetic resonance). The biological activities of the isolated metabolites against MRSA were evaluated and the molecular mode of action against the dehydrosqualene synthase enzyme have been done. Results: Four compounds have been isolated and identifies to be; apigenin (1), luteolin (2), astragalin (3), and kaempferol-3-O-rhamnoside (4). Compounds 1–4 showed good anti-MRSA activities with IC50 values of 10.3, 11.5, 3.5, and 4.5 μg/mL, respectively. In consistent, astragalin and kaempferol-3 rhamnoside showed close high docking scores. Herein, we are reporting the molecular determinates of activity of these new scaffolds as anti-MRSA, which would be of great importance to developing new anti-MRSA candidates. Keywords:Anti-methicillin-resistant Staphylococcus aureus, antimicrobial activities, dehydrosqualene synthase enzyme, docking molecular study, Salvadora persicaView:PDF (1.91 MB)
Effect of Serum and Insulin Modulation on the Organization and Morphology of Matrix Synthesized by Bovine Corneal Stromal Cells (2009)

The in vitro production of highly organized collagen fibrils by corneal keratocytes in a three-dimensional scaffold-free culture system presents a unique opportunity for the direct observation of organized matrix formation. The objective of this investigation was to develop such a culture system in a glass substrate (for optical accessibility) and to directly examine the effect of reducing serum and/or increasing insulin on the stratification and secretion of aligned matrix by fourth- to fifth-passage bovine corneal stromal keratocytes. Medium concentrations of 0%, 1%, or 10% fetal bovine serum and 0% or 1% insulin-transferrin-selenium were investigated. High-resolution differential interference contrast microscopy, quick-freeze/deep-etch, and conventional transmission electron microscopy were used to monitor the evolution, morphology, and ultrastructure of the cell-matrix constructs. In a medium containing 1% each of serum and insulin-transferrin-selenium, stromal cells stratified and secreted abundant and locally aligned matrix, generating the thickest cell-matrix constructs (allowing handling with forceps). The results of this study have the potential to significantly advance the field of developmental functional engineering of load-bearing tissues by (i) elucidating cues that modulate in vitro cell secretion of organized matrix and (ii) establishing an optically accessible cell culture system for investigating the mechanism of cell secretion of aligned collagen fibrils.
Role of Ornibactin Biosynthesis in the Virulence of Burkholderia cepacia : Characterization of pvdA , the Gene Encoding l -Ornithine N 5 -Oxygenase (1999)

Burkholderia cepacia is a frequent cause of respiratory infections in cystic fibrosis patients. B. cepacia has been shown to produce at least four siderophores which may play a role in the virulence of this organism. To characterize genes involved in the synthesis of siderophores, Tn5-OT182 mutants were isolated in strain K56-2, which produces two siderophores, salicylic acid (SA) and ornibactins. Two mutants were characterized that did not produce zones on Chrome Azurol S agar in a commonly used assay to detect siderophore activity. These mutants were determined to produce sevenfold more SA than K56-2 yet did not produce detectable amounts of ornibactins. These mutants, designated I117 and T10, had a transposon insertion in genes with significant homology to pyoverdine biosynthesis genes of Pseudomonas aeruginosa. I117 contained an insertion in a pvdA homolog, the gene for the enzyme L-ornithine N(5)-oxygenase, which catalyzes the hydroxylation of L-ornithine. Ornibactin synthesis in this mutant was partially restored when the precursor L-N(5)-OH-Orn was added to the culture medium. T10 contained an insertion in a pvdD homolog, which is a peptide synthetase involved in pyoverdine synthesis. beta-Galactosidase activity was iron regulated in both I117 and T10, suggesting that the transposon was inserted downstream of an iron-regulated promoter. Tn5-OT182 contains a lacZ gene that is expressed when inserted downstream of an active promoter. Both I117 and T10 were deficient in uptake of iron complexed to either ornibactins or SA, suggesting that transposon insertions in ornibactin biosynthesis genes also affected other components of the iron transport mechanism. The B. cepacia pvdA homolog was approximately 47% identical and 59% similar to L-ornithine N(5)-oxygenase from P. aeruginosa. Three clones were identified from a K56-2 cosmid library that partially restored ornibactin production, SA production, and SA uptake to parental levels but did not affect the rate of (59)Fe-ornibactin uptake in I117. A chromosomal pvdA deletion mutant was constructed that had a phenotype similar to that of I117 except that it did not hyperproduce SA. The pvdA mutants were less virulent than the parent strain in chronic and acute models of respiratory infection. A functional pvdA gene appears to be required for effective colonization and persistence in B. cepacia lung infections.
Phosphodiesterase inhibition and lipolytic action of the stereoisomers of trimetoquinol. (1976)

The isomers and racemate of trimetoquinol [TMQ; 6-7-dihydroxy-1-(3',4',5'-trimethoxybenzyl)-1,2,3,4-tetrahydroisoquinoline] as well as N-(3',4',5'-trimethoxyphenethyl)dopamine were all shown to be effective at promoting glycerol release from rat epididymal fat tissue. The rank order of potency observed for these compounds was (-)-TMQ greater than or equal to (+/-)-TMQ greater than greater than (+)-TMQ = N-(3',4',5-trimethoxyphenethyl)dopamine. (+/-)-TMQ and (-)-TMQ were the only agents capable of producing a maximal lipolytic response. None of the compounds tested were able to exhibit significant c-AMP phosphodiesterase inhibition. This study is the first report which shows that the beta-adrenoceptor activity of the isomers of TMQ does not correlate with an inhibition of c-AMP phosphodiesterase. An alternate mechanism of action for these compounds is proposed.
Biocompatible, pH-sensitive AB2 miktoarm polymer-based polymersomes: preparation, characterization, and acidic pH-activated nanostructural transformation (2012)

Motivated by the limitations of liposomal drug delivery systems, we designed a novel histidine-based AB(2)-miktoarm polymer (mPEG-b-(polyHis)(2)) equipped with a phospholipid-mimic structure, low cytotoxicity, and pH-sensitivity. Using "core-first" click chemistry and ring-opening polymerization, mPEG(2kDa)-b-(polyHis(29kDa))(2) was successfully synthesized with a narrow molecular weight distribution (1.14). In borate buffer (pH 9), the miktoarm polymer self-assembled to form a nano-sized polymersome with a hydrodynamic radius of 70.2 nm and a very narrow size polydispersity (0.05). At 4.2 µmol/mg polymer, mPEG(2kDa)-b-(polyHis(29kDa))(2) strongly buffered against acidification in the endolysosomal pH range and exhibited low cytotoxicity on a 5 d exposure. Below pH 7.4 the polymersome transitioned to cylindrical micelles, spherical micelles, and finally unimers as the pH was decreased. The pH-induced structural transition of mPEG(2kDa)-b-(polyHis(29kDa))(2) nanostructures may be caused by the increasing hydrophilic weight fraction of mPEG(2kDa)-b-(polyHis(29kDa))(2) and can help to disrupt the endosomal membrane through proton buffering and membrane fusion of mPEG(2kDa)-b-(polyHis(29kDa))(2). In addition, a hydrophilic model dye, 5(6)-carboxyfluorescein encapsulated into the aqueous lumen of the polymersome showed a slow, sustained release at pH 7.4 but greatly accelerated release below pH 6.8, indicating a desirable pH sensitivity of the system in the range of endosomal pH. Therefore, this polymersome that is based on a biocompatible histidine-based miktoarm polymer and undergoes acid-induced transformations could serve as a drug delivery vehicle for chemical and biological drugs.
Application of plug–plug technique to ACE experiments for discovery of peptides binding to a larger target protein: A model study of calmodulin‐binding fragments selected from a digested mixture of reduced BSA (2013)

To discover peptide ligands that bind to a target protein with a higher molecular mass, a concise screening methodology has been established, by applying a "plug-plug" technique to ACE experiments. Exploratory experiments using three mixed peptides, mastoparan-X, β-endorphin, and oxytocin, as candidates for calmodulin-binding ligands, revealed that the technique not only reduces the consumption of the protein sample, but also increases the flexibility of the experimental conditions, by allowing the use of MS detection in the ACE experiments. With the plug-plug technique, the ACE-MS screening methodology successfully selected calmodulin-binding peptides from a random library with diverse constituents, such as protease digests of BSA. Three peptides with Kd values between 8-147 μM for calmodulin were obtained from a Glu-C endoprotease digest of reduced BSA, although the digest showed more than 70 peaks in its ACE-MS electropherogram. The method established here will be quite useful for the screening of peptide ligands, which have only low affinities due to their flexible chain structures but could potentially provide primary information for designing inhibitors against the target protein.
Impaired neurogenesis, learning and memory and low seizure threshold associated with loss of neural precursor cell survivin (2010)

The findings highlight the critical role that survivin plays during neural development, deficiencies of which dramatically impact on postnatal neural function.
Dupilumab in patients with prurigo nodularis: two randomized, double-blind, placebo-controlled phase 3 trials (2023)

Prurigo nodularis (PN) is a chronic inflammatory skin disease with intensely pruritic nodules. The LIBERTY-PN PRIME and PRIME2 phase 3 trials enrolled adults with PN with ≥20 nodules and severe itch uncontrolled with topical therapies. Dupilumab, a fully human monoclonal antibody, blocks the shared receptor component for interleukin (IL)-4 and IL-13. Patients were randomized 1:1 to 300 mg dupilumab or placebo subcutaneously every 2 weeks for 24 weeks. The primary endpoint was pruritus improvement, measured by proportion of patients with a ≥4-point reduction in Worst Itch Numeric Rating Scale (WI-NRS) from baseline at week 24 (PRIME) or week 12 (PRIME2). Key secondary endpoints included nodule number reduction to ≤5 at week 24. PRIME and PRIME2 enrolled 151 and 160 patients, respectively. Both trials met all the pre-specified primary and key secondary endpoints. A ≥4-point WI-NRS reduction at week 24 in the dupilumab and placebo arms was achieved by 60.0% and 18.4% of patients, respectively, in PRIME (95% confidence interval (CI), 27.8-57.7 for the difference, P < 0.001) and at week 12 by 37.2% and 22.0% of patients, respectively, in PRIME2 (95% CI, 2.3-31.2; P = 0.022). Dupilumab demonstrated clinically meaningful and statistically significant improvements in itch and skin lesions versus placebo in PN. Safety was consistent with the known dupilumab safety profile.ClinicalTrials.gov identifiers: NCT04183335 and NCT04202679 .
A man with retrograde ejaculation (2015)

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Soft X-ray characterization of perpendicular recording media (2002)

Various spectroscopy, imaging, and scattering techniques exploit core-level resonances accessible in the soft X-ray energies to obtain magnetic information in thin films with elemental specificity. In this paper, we describe the emerging technique of resonant soft X-ray small-angle scattering (SAS) as a probe of magnetic and chemical variations in recording media on the nanometer scale. In particular, we characterize the grain size of a CoB-Pd multilayer media and magnetic and chemical grain sizes in perpendicular CoPtCr media.
On the spectral coexistence of GSO and NGSO FSS systems: power control mechanisms and a methodology for inter‐site distance determination (2016)

Summary The coexistence of geostationary satellite orbit (GSO) and non‐GSO (NGSO) fixed satellite service systems within the same spectrum to enhance the spectrum efficiency in Ka band has attracted many interests lately. However, the coexistence of GSO‐NGSO satellite systems with limited shared spectrum can cause in‐line interference from a satellite to other satellite's earth terminals. In this context, this contribution investigates three possible power control approaches to mitigate the in‐line interference caused by an NGSO satellite to the GSO earth terminal, while the NGSO satellite is crossing the GSO satellite's illumination zone. Moreover, three types of interference mitigation techniques, namely, range‐based, traffic‐aware, and cognitive power control techniques are investigated. Furthermore, to increase the spectrum efficiency of the GSO‐NGSO fixed satellite service terrestrial network, we formulate and solve an optimization problem with the objective of minimizing the inter‐site distance between earth user‐terminals. More specifically, we find the minimum distance from a GSO earth terminal, where an NGSO earth terminal can be implemented subject to minimizing received interference level at the victim system. Finally, our comparative results show that the cognitive power control technique performs the best in protecting the victim receiver from the in‐line interference. Copyright © 2016 John Wiley &amp; Sons, Ltd.
Progress towards a medical image through CFD analysis toolkit for respiratory function assessment on a clinical time scale (2009)

A semi-automated end-to-end medical image through computational fluid dynamics (CFD) analysis toolkit has been developed, with the ultimate goal of providing clinical-time-scale (hours) diagnostic information for respiratory disease and injury assessment. A software system is in place that proceeds from a standard clinical image format, through lobe and upper bronchi segmentation, upper airway ldquothinningrdquo, airway generation partitioning, and truncation, lower bronchiole lobe volume filling, octree-based unstructured mesh generation for the upper airways, quasi-one-dimensional geometric modeling for the lower airways, and CFD analysis of respiration. Each of these components is presented.
Nanocellulose, a Versatile Green Platform: From Biosources to Materials and Their Applications (2018)

With increasing environmental and ecological concerns due to the use of petroleum-based chemicals and products, the synthesis of fine chemicals and functional materials from natural resources is of great public value. Nanocellulose may prove to be one of the most promising green materials of modern times due to its intrinsic properties, renewability, and abundance. In this review, we present nanocellulose-based materials from sourcing, synthesis, and surface modification of nanocellulose, to materials formation and applications. Nanocellulose can be sourced from biomass, plants, or bacteria, relying on fairly simple, scalable, and efficient isolation techniques. Mechanical, chemical, and enzymatic treatments, or a combination of these, can be used to extract nanocellulose from natural sources. The properties of nanocellulose are dependent on the source, the isolation technique, and potential subsequent surface transformations. Nanocellulose surface modification techniques are typically used to introduce either charged or hydrophobic moieties, and include amidation, esterification, etherification, silylation, polymerization, urethanization, sulfonation, and phosphorylation. Nanocellulose has excellent strength, high Young's modulus, biocompatibility, and tunable self-assembly, thixotropic, and photonic properties, which are essential for the applications of this material. Nanocellulose participates in the fabrication of a large range of nanomaterials and nanocomposites, including those based on polymers, metals, metal oxides, and carbon. In particular, nanocellulose complements organic-based materials, where it imparts its mechanical properties to the composite. Nanocellulose is a promising material whenever material strength, flexibility, and/or specific nanostructuration are required. Applications include functional paper, optoelectronics, and antibacterial coatings, packaging, mechanically reinforced polymer composites, tissue scaffolds, drug delivery, biosensors, energy storage, catalysis, environmental remediation, and electrochemically controlled separation. Phosphorylated nanocellulose is a particularly interesting material, spanning a surprising set of applications in various dimensions including bone scaffolds, adsorbents, and flame retardants and as a support for the heterogenization of homogeneous catalysts.
WormBase single-cell tools (2022)

Supplementary data are available at <i>Bioinformatics Advances</i> online.
OC077: Acceleration/ejection time ratio in the fetal pulmonary artery as a predictor of fetal lung maturity (2008)

Fetal lung maturity is an important consideration when an obstetrician decides to deliver a fetus before full term. Biochemical standards of fetal lung maturity (FLM) include the lecithin/sphingomyelin ratio (L/S) and the presence of phosphatidylglycerol (PG) in amniotic fluid. Sonographic markers have been described previously but have not been accurate to predict FLM. Fetal pulmonary artery flow velocity waveforms (FEPAF) changes are noticed with the advance of gestational age. The relationship between FEPAF and biochemical standard measurements of FLM has not been tested to date. We evaluated the correlation of the changes in FEPAF with FLM. We obtained FEPAF with color Doppler-guided spectral Doppler ultrasound in 25 fetuses at a median of 36 weeks' gestation (range 34–39 weeks) prior to clinically indicated FLM amniocentesis. Acceleration/ejection time ratio (A/Et), systolic/diastolic (S/D) ratio, resistance index (RI) and pulsatility index (PI) were measured. Results were compared to GA, EFW, L/S measured by thin layer chromatography and PG by latex agglutination. Data was collected and analyzed using SPSS to calculate Spearman's rho (rs) and Multivariate regression. Three cases were excluded due to meconium or blood contamination of the samples. We found a significant correlation of A/Et and PI with increasing levels of L/S (rs = −0.766, P<0.001 and rs = −0.5221, P<0.005 respectively) however FEPAF also showed a significant correlation between PI with EFW and GA (rs = −0.537, P<0.005 and rs = −0.518, P<0.005 respectively). The significant correlation between A/Et and L/S levels remained after correcting for GA and EFW. Only four cases were negative for PG and in all A/Et index was high. Low A/Et is significantly correlated with high levels of L/S and presence of PG with no correlation to GA or EFW. This is a rapid and non-invasive procedure that could potentially be a helpful tool to determine FLM.
Detection of Highly Enriched Uranium Using a Pulsed D-D Fusion Source (2007)

This paper overviews the work that has been done to date towards the development of a compact, reliable means to detect Highly Enriched Uranium (HEU) and other fissile materials utilizing a pulsed Inertial Electrostatic Confinement (IEC) D-D fusion device. To date, the UW IEC device has achieved 115 kV pulses in excess of 2 ampere, with pulsed neutron rates of 1.8x109 n/s during a 0.5 ms pulse at 10 Hz. MCNP modeling indicates that detection of samples of U-235 as small as 10 grams is achievable at current neutron production rates, and initial pulsed and steady-state HEU detection experiments have verified these results.
Linear and Nonlinear Finite Element Analysis of an Exhaust Manifold With Included Bellows (2007)

The aim of this paper is to examine the utility of nonlinear analysis for structural response to thermal and mechanical loads, for a structure containing alternating regions of high and low stiffness as a result of inclusion of bellow sections. Utility is measured by comparison of results of linear and nonlinear analyses. The specific example used is that of an exhaust manifold for a large diesel engine. The paper discusses modeling of geometric and material nonlinearity, and makes recommendations in regard to which nonlinear effects are thought to be significant, based on the linear/nonlinear comparisons. The paper also contains general comments on the finite element modeling of structures containing bellows.
Serial Procalcitonin Predicts Mortality in Severe Sepsis Patients: Results From the Multicenter Procalcitonin MOnitoring SEpsis (MOSES) Study (2017)

Results of this large, prospective multicenter U.S. study indicate that inability to decrease procalcitonin by more than 80% is a significant independent predictor of mortality and may aid in sepsis care.
Review article: the pathophysiology of thrombocytopenia in hepatitis C virus infection and chronic liver disease (2007)

The development of thrombocytopenisa in patients with chronic liver disease is complex and multifactorial.
Fiber-coupled monocentric lens imaging (2013)

Monocentric lenses have proven exceptionally capable of high numerical aperture wide-field imaging - provided the overall system can accommodate a spherically curved image surface. We will present a summary of recent work on the design optimization and experimental demonstrations of monocentric wide-field imaging, including systems based on waveguide coupling of the image to conventional focal plane sensor(s).