gebhart/patrepeval huggingface dataset:
How to Improve Dietary Practices of 19–30yo Egyptian Women Living in Urban Areas? An Optifood Analysis (OR25-04-19) (2019)

The double burden of malnutrition is rising in several Arab countries due to rapid changes in dietary patterns and lifestyle. Egyptian women have one of the highest BMI worldwide, and nearly one quarter of them suffer from anemia. The objective was to identify changes needed in dietary practices and product offer, which could help to rebalance nutrient intakes for women living in urban Egypt. Food intakes were obtained from a 4-days dietary record in 127 women (19–30 yo) and food prices were collected in modern and in traditional trades. Modeling analyses (Optifood software) were used to identify problem nutrients and design affordable food-based recommendations (FBRs): we assessed whether locally and consumed foods could theoretically be combined to ensure nutrient adequacy, at a fixed cost, without exceeding recommendations in energy and SFAs, total sugars and sodium. Fortified foods were included in additional modeling analyses to test their potential to improve intakes of the most problematic micronutrient to cover. Preliminary results from modeling analyses indicated that iron is the most problematic recommendation to cover from a combination of local and consumed foods. Daily consumption of fruits, vegetables, grains, milk or yoghurt, and tahini associated with smart food choices in the meat-fish-eggs category would result in a low percentage of women at risk for 11 out of 12 micronutrients modeled. Among the fortified foods tested, iron fortified bread, rice, milk and yoghurt would be promising vectors to improve iron intakes. Local foods can ensure nutrient adequacy of most nutrients. However, strategies are needed to promote acceptable FBRs to rebalance the diet of Egyptian women. Iron fortified products could help to improve iron intakes for this population at risk of anemia. Danone Research.
QRS detection using a fuzzy neural network (2002)

We developed a QRS detection algorithm which uses a fuzzy neural network (FNN) to process lead II recordings of the ECG. We trained and tested our algorithm using the MIT/BIH arrhythmia database, and compared our results to existing algorithms. For tapes 100, 105 and 108, our FNN reduced the total number of combined false-positive and false-negative detections from 174 to 44.
Spectral broadening of femtosecond laser pulses in fibers with a photonic-crystal cladding (2000)

Changes in the spectra of femtosecond laser pulses propagating through fibers with a cladding having the structure of a two-dimensional photonic crystal are experimentally investigated. It is demonstrated that the waveguide properties of defect modes of photonic-crystal fibers provide an opportunity to considerably increase the efficiency of spectral broadening of short laser pulses as compared with conventional fibers.
Design and Fabrication of a 3D Scaffold for Tissue Engineering Bone (2000)

Autogenous cell transplantation is one of the most promising new techniques being developed for bone generation as it eliminates problems of donor site scarcity, immune rejection and pathogen transfer. Osteoblasts obtained from an individual patient can be grown in culture and seeded onto a three-dimensional scaffold that will slowly degrade and resorb as the bone or cartilage structures grow and assimilate in vivo. The three-dimensional (3D) scaffold provides the necessary support for cells to maintain their differentiated state and defines the overall shape of the new bone and cartilage. The necessity of using a scaffold structure as the basic template of engineering tissues has encouraged the study the application of advanced manufacturing technologies in this field. For example, rapid prototyping (RP) technologies such as fused deposition modeling (FDM) can be used to fabricate complex 3D structures based on two- dimensional (2D) cross-sectional data obtained by slicing a computer-aided design (CAD) models. FDM is currently being applied in our laboratory to fabricate bioresorbable 3D scaffolds of various porosities and micro-architecture for tissue engineering bone.
Increased Clearance and Degradation of [3H]Insulin in Streptozotocin Diabetic Rats (1981)

The role of the insulin-receptor compartment in the pharmacokinetics of intravenously injected insulin in rats was studied. Since streptozotocin-diabetes in rats results in increased insulin binding to tissues in vitro, insulin pharmacokinetics in streptozotocin-diabetic rats were compared to controls, using semisynthetic [(3)H]insulin as the tracer. The initial distribution volume for [(3)H]insulin was elevated by 60% in diabetic rats. By contrast, no difference in initial distribution volume for [(14)C]inulin was observed, and the absolute values were lower than those found for [(3)H]insulin. The metabolic clearance rate of [(3)H]insulin was elevated by 44% in diabetic rats. That these differences were the result of increased binding of insulin to a specific receptor compartment in diabetic rats was shown by three additional experiments. The first involved receptor saturation by injection of 10 U native insulin 2 min before the tracer injection, resulting in identical [(3)H]insulin disappearance rates in the two groups of rats. The second consisted of displacing [(3)H]insulin from receptors by injecting 10 U unlabeled insulin 6 min after the tracer injection. Displacement of intact [(3)H]insulin from receptors and subsequent reappearance in the circulation occurred in both control and diabetic animals; however, such displacement was 25% greater in the diabetic rats. Finally, treatment of diabetic rats with insulin for 8 d normalized [(3)H]insulin clearance even though the tracer was injected at a time when the animals were again hyperglycemic and hypoinsulinemic. This suggests that down-regulation of insulin receptors had occurred during insulin therapy. These results confirm that a specific compartment for insulin exists (the insulin-receptor compartment) and that this compartment plays an important role in insulin clearance.
Protein C Inhibitor (Serpin A5) in ePFT Collected Pancreas fluid: A Potential Biomarker of Chronic Pancreatitis (CP) (2011)

Purpose: To characterize differential protein expression profiles using proteomic analysis of pancreas fluid (PF) from patients with severe CP and controls. Methods: PF was collected from two cohorts (CP and controls) using the ePFT method and subjected to comprehensive proteomic analysis (GeLC-MS/MS) and protein identification as follows: PF was collected from the duodenum after secretin stimulation (ChiRhoStim); centrifuged to remove particulate matter; proteins precipitated, subjected to SDS-PAGE fractionation; followed by In-gel tryptic digestion and proteomic analysis. Bioinformatic analysis was performed to determine protein identification and molecular function. Statistical analysis was performed with QSPEC statistical software comparing spectral counts of proteins using Bayesian statistical methods. Protein filtering strategy: A Bayes factor greater than 10 and a greater than 2-fold difference in protein expression between cohorts was statistically significant (p< 0.05). Fisher exact test for measure of association. Results: A total of 18 subjects (9 CP and 9 controls) underwent secretin stimulated, ePFT PF collection and proteomic analysis (GeLC-MS/MS) based on our previously published sample handling and methods protocols. All CP patients had severe CP (Cambridge Class IV imaging, EUS score 6-9). All controls had chronic dyspepsia with no evidence of CP (Cambridge Class 0 imaging, EUS score 0-3). The mean peak [HC03] for CP and controls was 37.7 ± 13.3 versus 93.4 ± 13.6 mEq/L. (p < 0.05). GeLC-MS/MS analysis revealed the largest dataset of non-redundant proteins (n = 1392) from human PF to date. Protein filtering strategy revealed several statistically significant (Bayes factor >10; fold change >2) up-regulated proteins [serpin A5, neprilysin, mucin 13, annexin A5 and defensin 5] and down-regulated proteins [trypsin, chymotrypsin, lipase and aminopeptidase]. Biological function analysis revealed that the highest percentage of down-regulated proteins were protease enzymes. The highest percentage of up-regulated proteins were protein binding. Protein C Inhibitor [Serpin A5, table]; a serine protease inhibitor / “binder” was the top-hit protein in 8/9 CP and 0/9 control PF samples (p = 0.00041): Sensitivity (89%), Specificity (100%), PPV (100%), NPV (90%) and diagnostic accuracy of 94.4% [74.2, 99.0]. Conclusion: 1) Protein C Inhibitor (Serpin A5) is up-regulated and proteases are down-regulated in pancreas fluid of patients with severe chronic pancreatitis compared to controls. 2) Protein C Inhibitor expression in PF may serve as a diagnostic biomarker for chronic pancreatitis. Clinical Implication: Further investigation of Serpin A5 in milder forms of chronic pancreatitis is warranted.
Substitution scanning identifies a novel, catalytically active ibrutinib-resistant BTK cysteine 481 to threonine (C481T) variant (2016)

Irreversible Bruton tyrosine kinase (BTK) inhibitors, ibrutinib and acalabrutinib have demonstrated remarkable clinical responses in multiple B-cell malignancies. Acquired resistance has been identified in a sub-population of patients in which mutations affecting BTK predominantly substitute cysteine 481 in the kinase domain for catalytically active serine, thereby ablating covalent binding of inhibitors. Activating substitutions in the BTK substrate phospholipase Cγ2 (PLCγ2) instead confers resistance independent of BTK. Herein, we generated all six possible amino acid substitutions due to single nucleotide alterations for the cysteine 481 codon, in addition to threonine, requiring two nucleotide substitutions, and performed functional analysis. Replacement by arginine, phenylalanine, tryptophan or tyrosine completely inactivated the catalytic activity, whereas substitution with glycine caused severe impairment. BTK with threonine replacement was catalytically active, similar to substitution with serine. We identify three potential ibrutinib resistance scenarios for cysteine 481 replacement: (1) Serine, being catalytically active and therefore predominating among patients. (2) Threonine, also being catalytically active, but predicted to be scarce, because two nucleotide changes are needed. (3) As BTK variants replaced with other residues are catalytically inactive, they presumably need compensatory mutations, therefore being very scarce. Glycine and tryptophan variants were not yet reported but likely also provide resistance.
A porous PdO microrod-based electrochemical sensor for nanomolar-level Cu2+ released from cells (2014)

Highly porous PdO microrods (PoPdOMRs) with a well-defined morphology, large surface area and active sites were synthesized via a facile wet chemical method for the first time. A sensitive and selective electrochemical sensor was thus developed by using the PoPdOMRs as a sensing platform. The PoPdOMR modified sensor exhibited a response time of less than 8 s, a linear range between 1.0 × 10<sup>-9</sup> and 8.0 × 10<sup>-5</sup> mM, and a sensitivity up to 112 μA μM<sup>-1</sup> cm<sup>-2</sup> for the determination of Cu<sup>2+</sup>. A sound sensing selectivity towards Cu<sup>2+</sup> in the presence of interfering ions was also observed. On the basis of this sensor, the trace amount of Cu<sup>2+</sup> released from Raw 264.7 cells was successfully recorded, which makes the PoPdOMR electrocatalyst promising for the development of effective electrochemical sensors for a wide range of potential applications in bioanalysis and environmental chemistry.
The war against polypharmacy: a new cost-effective geriatric-palliative approach for improving drug therapy in disabled elderly people. (2007)

Application of the geriatric-palliative methodology in the disabled elderly enables simultaneous discontinuation of several medications and yields a number of benefits: reduction in mortality rates and referrals to acute care facilities, lower costs, and improved quality of living.
Making practical use of IPv6 anycasting: mobile IPv6 based approach (2006)

Anycast is a new IPv6 function in which an anycast address can be assigned to multiple nodes that provide the same service. The anycast packet is transmitted to one appropriate node selected out of all the nodes assigned to the same anycast address. Although it is expected that anycast will be used in various ways, the use of anycast is quite limited today. This is because anycast functionalities are still unclear, and it is difficult to realize a global anycast that requires existing routing protocols to be radically changed. In this paper, we clarify and classify some essential anycast issues and propose a new and practical communication architecture, based on mobile IPv6 architecture, that overcomes the anycast difficulties.
Kinetic studies of the intracellular transport of procollagen and fibronectin in human fibroblasts. Effects of the monovalent ionophore, monensin. (1980)

The monovalent ionophore, monensin, has been found to inhibit the secretion of both procollagen and fibronectin from human fibroblasts in cell culture. The kinetics of inhibition, as well as those for the release of inhibition, suggested that both proteins may be cotransported in the cell. In the present study, we have examined the intracellular translocation and release into the culture medium of procollagen and fibronectin, in the presence or absence of monensin. Pulse-chase studies were combined with subcellular fractionation of the fibroblasts to determine the rates of intracellular movement. We found that monensin did not significantly affect either the subcellular fractionation, or the distribution of organelle marker enzymes along the gradient, and that procollagen moved from a region of high buoyant density (primarily endoplasmic reticulum), through a mid-density region (primarily Golgi elements), to a region of low buoyant density before exiting from the cell. Monensin markedly decreased the rate of transit from one region to the other; kinetic analysis of the data showed a greater than 3-fold decrease in the rate constants for intracellular movement into the low buoyant density components and thence to the culture medium. The density gradient distribution of fibronectin was affected by monensin in similar fashion, indicating that it and procollagen probably follow the same intracellular route. Since monensin causes both proteins to accumulate in highest abundance in regions of the density gradient corresponding to Golgi and endoplasmic reticulum, the site of ionophore blockade appears to be within the Golgi apparatus. Thus, procollagen and fibronectin share a common intracellular route prior to entering the Golgi region of the cell.
ChemInform Abstract: GLYCOSIDES OF GLOBULARIACEAE. PART 5. IRIDOID AND ARYL GLUCOSIDES FROM GLOBULARIA NUDICAULIS AND GLOBULARIA NANA (1982)

Abstract Aus Globularia nudicaulis wurden die Iridoide Asperulosid (I), Aucubin (IIa) und Melampyrosid (IIb) sowie die Glucoside (IV) isoliert und aus Globularia nana das neue Iridoid Lytanthosalin (IIc) und die Iridoide (I), (IIa), Catalpol (IIIa) und Globularin (IIIb).
Image Thresholding for Optical Character Recognition and Other Applications Requiring Character Image Extraction (1983)

Two new, cost-effective thresholding algorithms for use in extracting binary images of characters from machine- or hand-printed documents are described. The creation of a binary representation from an analog image requires such algorithms to determine whether a point is converted into a binary one because it falls within a character stroke or a binary zero because it does not. This thresholding is a critical step in Optical Character Recognition (OCR). It is also essential for other Character Image Extraction (CIE) applications, such as the processing of machine-printed or handwritten characters from carbon copy forms or bank checks, where smudges and scenic backgrounds, for example, may have to be suppressed. The first algorithm, a nonlinear, adaptive procedure, is implemented with a minimum of hardware and is intended for many CIE applications. The second is a more aggressive approach directed toward specialized, high-volume applications which justify extra complexity.
In vivo assessment of thermal damage in the liver using optical spectroscopy (2004)

Resection is not a viable treatment option for the majority of liver cancer patients. Alternatives to resection include thermotherapies such as radio-frequency ablation; however, these therapies lack adequate intraoperative feedback regarding the degree and margins of tissue thermal damage. In this proof of principle study, we test the ability of fluorescence and diffuse reflectance spectroscopy to assess local thermal damage in vivo. Spectra were acquired in vivo from healthy canine liver tissue undergoing radio-frequency ablation using a portable fiber-optic-based spectroscopic system. The major observed spectral alterations on thermal coagulation were a red shift in the fluorescence emission peak at 480 nm, a decrease in the overall fluorescence intensity, and an increase in the diffuse reflectance from 450 to 750 nm. Spectral changes were quantified and correlated to tissue histology. We found a good correlation between the proposed spectral correlates of thermal damage and histology. The results of this study suggest that fluorescence and diffuse reflectance spectroscopy show strong potential as tools to monitor liver tissue thermal damage intraoperatively.
Active Sites in Complement Component C3 Mapped by Mutations at Indels (1998)

Engineered mutants of human complement component C3 were used to test the idea that sites of length polymorphisms in protein families (indels) can guide a search for protein:protein interaction sites. Sequence changes were introduced at each of the 27 indels in the C3/4/5 protein family, and mutants at 26 indels were expressed by transiently transfected COS cells. Expressed proteins were assayed 1) for concentration, by ELISA and by autoradiography of radiolabeled protein; 2) for classical pathway hemolytic activity; 3) for susceptibility to proteolytic activation by the alternative pathway and cobra venom factor C3 convertases; and 4) for susceptibility to complement factor I in the presence of factor H. Most of the mutations did not appreciably alter expression or activity relative to wild-type C3, consistent with the idea that most indels occur at the protein surface. Mutations at four indels severely damaged C3 functional activity, but did not affect the stability or structure of the protein, as assessed by their effects on expression by COS cells and on susceptibility to cleavage by C3 convertases and factor I. These indels are therefore near functionally important amino acid residues; they represent good candidates for sites of protein:protein interactions. Mutation of the sequence at a fifth indel altered the equilibrium between the latent and reacted C3 conformations, and mutations at 4 other indels substantially decreased both protein activity and expression. The mutants provided an overview of the structural and functional roles played by different parts of C3.
Evaluation of potential ferromagnetic coupling units: the bis(TMM) [bis(trimethylenemethane)] approach to high-spin organic molecules (1993)

Four new hydrocarbon tetraradicals, 1-4, each composed of two triplet trimethylenemethane (TMM) subunits linked&#13;\nby a potential ferromagnetic coupling unit (FC), were synthesized and characterized by variable-temperature electron paramagnetic resonance (EPR) spectroscopy. Simulation of the EPR powder spectra and a priori calculation of the zero-field splitting parameters&#13;\naided spectral assignment. The Heisenberg Hamiltonian appears to quantitatively model relative spin-state energies in 1-4. In three cases ferromagnetic coupling was achieved, as evidenced by quintet ground states in the resulting tetraradicals. In one case, strong evidence for antiferromagnetic coupling was obtained.
The Metal Loading Ability of β-Amyloid N-Terminus: A Combined Potentiometric and Spectroscopic Study of Copper(II) Complexes with β-Amyloid(1−16), Its Short or Mutated Peptide Fragments, and Its Polyethylene Glycol (PEG)-ylated Analogue (2008)

Alzheimer's disease (AD) is becoming a rapidly growing health problem, as it is one of the main causes of dementia in the elderly. Interestingly, copper(II) (together with zinc and iron) ions are accumulated in amyloid deposits, suggesting that metal binding to Abeta could be involved in AD pathogenesis. In Abeta, the metal binding is believed to occur within the N-terminal region encompassing the amino acid residues 1-16. In this work, potentiometric, spectroscopic (UV-vis, circular dichroism, and electron paramagnetic resonance), and electrospray ionization mass spectrometry (ESI-MS) approaches were used to investigate the copper(II) coordination features of a new polyethylene glycol (PEG)-conjugated Abeta peptide fragment encompassing the 1-16 amino acid residues of the N-terminal region (Abeta(1-16)PEG). The high water solubility of the resulting metal complexes allowed us to obtain a complete complex speciation at different metal-to-ligand ratios ranging from 1:1 to 4:1. Potentiometric and ESI-MS data indicate that Abeta(1-16)PEG is able to bind up to four copper(II) ions. Furthermore, in order to establish the coordination environment at each metal binding site, a series of shorter peptide fragments of Abeta, namely, Abeta(1-4), Abeta(1-6), AcAbeta(1-6), and AcAbeta(8-16)Y10A, were synthesized, each encompassing a potential copper(II) binding site. The complexation properties of these shorter peptides were also comparatively investigated by using the same experimental approach.
A comparative study of the anisotropic dynamic and static elastic moduli of unconventional reservoir shales: Implication for geomechanical investigations (2016)

ABSTRACT We obtained the complete set of dynamic elastic stiffnesses for a suite of “shales” representative of unconventional reservoirs from simultaneously measured P- and S-wave speeds on single prisms specially machined from cores. Static linear compressibilities were concurrently obtained using strain gauges attached to the prism. Regardless of being from static or dynamic measurements, the pressure sensitivity varies strongly with the direction of measurement. Furthermore, the static and dynamic linear compressibilities measured parallel to the bedding are nearly the same whereas those perpendicular to the bedding can differ by as much as 100%. Compliant cracklike porosity, seen in scanning electron microscope images, controls the elastic properties measured perpendicular to the rock’s bedding plane and results in highly nonlinear pressure sensitivity. In contrast, those properties measured parallel to the bedding are nearly insensitive to stress. This anisotropy to the pressure dependency of the strains and moduli further complicates the study of the overall anisotropy of such rocks. This horizontal stress insensitivity has implications for the use of advanced sonic logging techniques for stress direction indication. Finally, we tested the validity of the practice of estimating the fracture pressure gradient (i.e., horizontal stress) using our observed elastic engineering moduli and found that ignoring anisotropy would lead to underestimates of the minimum stress by as much as 90%. Although one could ostensibly obtain better values or the minimum stress if the rock anisotropy is included, we would hope that these results will instead discourage this method of estimating horizontal stress in favor of more reliable techniques.