gebhart/patrepeval huggingface dataset:
Genomic profiling of stage II and III colon cancers reveals APC mutations to be associated with survival in stage III colon cancer patients (2016)

Tumor profiling of DNA alterations, i.e. gene point mutations, somatic copy number aberrations (CNAs) and structural variants (SVs), improves insight into the molecular pathology of cancer and clinical outcome. Here, associations between genomic aberrations and disease recurrence in stage II and III colon cancers were investigated. A series of 114 stage II and III microsatellite stable colon cancer samples were analyzed by high-resolution array-comparative genomic hybridization (array-CGH) to detect CNAs and CNA-associated chromosomal breakpoints (SVs). For 60 of these samples mutation status of APC, TP53, KRAS, PIK3CA, FBXW7, SMAD4, BRAF and NRAS was determined using targeted massive parallel sequencing. Loss of chromosome 18q12.1-18q12.2 occurred more frequently in tumors that relapsed than in relapse-free tumors (p < 0.001; FDR = 0.13). In total, 267 genes were recurrently affected by SVs (FDR < 0.1). CNAs and SVs were not associated with disease-free survival (DFS). Mutations in APC and TP53 were associated with increased CNAs. APC mutations were associated with poor prognosis in (5-fluorouracil treated) stage III colon cancers (p = 0.005; HR = 4.1), an effect that was further enhanced by mutations in MAPK pathway (KRAS, NRAS, BRAF) genes. We conclude that among multiple genomic alterations in CRC, strongest associations with clinical outcome were observed for common mutations in APC.
Protein tyrosine phosphatase N2 regulates TNFα-induced signalling and cytokine secretion in human intestinal epithelial cells (2010)

TNFα induces PTPN2 expression in IECs. Loss of PTPN2 promotes TNFα-induced mitogen-activated protein kinase signalling and the induction of inflammatory mediators. These data indicate that PTPN2 activity could play a crucial role in the establishment of chronic inflammatory conditions in the intestine, such as CD.
Vascular anatomy of the pig kidney glomerulus: a qualitative study of corrosion casts. (1992)

Pig kidney glomerular vascular anatomy was studied by scanning electron microscopy of vascular corrosion casts. A generalized vascular architecture is presented to describe the pig kidney glomerulus based upon the observation of 3,800 vascular cast glomeruli. The relative simplicity of the pig glomerular vascular architecture has allowed the characterization of different vascular segments more completely than has been possible in other mammals. Based upon relationships to the afferent arteriole, a nomenclature and definition of primary, secondary, tertiary and anastomotic vessels is proposed for the distributing vessels comprising the glomerular tuft. The existence and formation of a large central hemispheric vessel deep within the confines of a glomerular hemisphere is micrographically documented. Micrographic evidence is presented supporting the formation of the single efferent arteriole by the merging of two central hemispheric vessels within the confines of the glomerular tuft. Failure of the merging of these two vessels may result in multiple efferent arterioles.
A Vertical Handover Algorithm Based on Velocity Pre-decision and Fuzzy Logic for Heterogeneous Private Network (2020)

With the arrival of fifth-generation (5G) cellular networks, various industries have increasingly higher requirements for mobile Internet. The police mobile communication network is also seeking the interconnection between Police Digital Trunking (PDT) narrowband network and Broadband Trunking Communication (B-TrunC) network in China. In the future, the private mobile communication network will inevitably evolve towards the direction of large bandwidth and high rate to support more abundant mobile private network applications. Vertical handover technology is an essential key technology in hybrid networks composed of wide and narrow band networks. This paper proposes a vertical handover algorithm based on velocity pre-decision and fuzzy logic (VPD-FL). Firstly the velocity predecision algorithm can reduce the calculation of handover decisions, and then the fuzzy logic method is used to evaluate network performance indicators. Simulation and numerical results show that the VPD-FL algorithm has better network performance than the traditional vertical handover algorithm.
Generic Penetration of the SSRI Market. (2008)

In this article, we investigate the penetration of generic selective serotonin reuptake inhibitors (SSRIs) in the US market and the implications for patient out-of-pocket expense. The data suggest that generic penetration into the SSRI market has grown from approximately nine percent in 2000, the year that the patent for Prozac((R)) expired, to 72 percent in 2007. For December, 2007, the difference in patient out-of-pocket expense for branded vs. generic agents was, on average, $55.42 for patients paying by cash (i.e., they had no prescription drug insurance) and $22.39 for patients with insurance coverage.
Defects Inducing Ferromagnetism in Carbon-Doped ZnO Films (2010)

Carbon-doped ZnO films were prepared on c-cut sapphire substrates by conventional PLD method. All films exhibit RT ferromagnetism. However, the samples deposited at low temperature and low pressure with low C concentration show large <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">M</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">s</sub> . The substitution of carbon for O in ZnO causes the electron transfer of 3d orbital of Zn ion, which results in the generation of a net spin with one half in the d-orbit of Zn, and accordingly makes ferromagnetism possible. XPS and Auger results indicate the formation of donor defects such as V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">O</sub> or/and Zn <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i</sub> in the film, which makes the net spin align, accordingly induces magnetic ordering of the films. Both a certain number of donor defects and the net spin of Zn ions caused by the substitution of O by C are two key factors in inducing magnetic ordering in C-doped ZnO films. Therefore, defect-induced ferromagnetism is reasonable to explain the observed magnetism in our experiment.
A “fussock” (1878)

Journal Article A “fussock” Get access Thomas Bird Thomas Bird 1Bomford Search for other works by this author on: Oxford Academic Google Scholar Notes and Queries, Volume s5-X, Issue 261, 28 December 1878, Page 521, https://doi.org/10.1093/nq/s5-X.261.521d Published: 28 December 1878
Mutational analysis of the role of charged residues in target-cell binding, potency and specificity of the pediocin-like bacteriocin sakacin P (2002)

The significance of charged residues for the target-cell binding, potency and specificity of pediocin-like bacteriocins has been studied by site-directed mutagenesis of sakacin P. Most of the charged residues are located in the N-terminal half, which is thought to mediate the initial binding of these bacteriocins to target cells through electrostatic interaction. All the mutated peptides in which the net positive charge was reduced by one (by replacing a charged residue with threonine) exhibited reduced binding to target cells and a 2-15-fold reduction in potency. The least deleterious of these mutations was the removal of the positive charge in position 8 (H8T). This mutation was, in fact, less deleterious than the conservative His to Lys mutation, indicating that the positive charge in position 8 per se is not of major importance. Somewhat more deleterious was the removal of positive charges at the N- and C-terminal ends (K1T, K43T). Most deleterious was the elimination of the positive charge at positions 11 and (but to a lesser extent) 12, demonstrating the importance of the cationic patch in the middle of the N-terminal half of pediocin-like bacteriocins. Mutated peptides in which the net positive charge was increased by one were also constructed. Some of these exhibited increased cell binding and a potency that was the same as (44K, i.e. an extra positive charge at the C-terminus), or somewhat greater (T20K) than, that of sakacin P, whereas others (0K, i.e. an extra positive charge at the N-terminus) had reduced potency. Sakacin P contains only one negatively charged residue (Asp17). This negative charge and its orientation in space were crucial for activity, since the Asp to Asn mutation and (especially) the conservative Asp to Glu mutation were deleterious. Mutations that made the peptide less cationic had, overall, less effect on the potency toward the Carnobacterium piscicola strain than on the potency toward the three other strains tested, whereas the opposite was the case for mutations that made the peptide more cationic. Thus, charged residues in the N-terminal half may - apparently via the initial electrostatic binding of the bacteriocin to target cells - influence the target-cell specificity.
Accuracy of image fusion of normal upper abdominal organs visualized with In111 Octreotide SPECT/CT using a 16 slice CT/SPECT scanner (2007)

1764 Objectives: Although SPECT/CT (HRCT) scanners have the potential for precise fused registration of anatomic structures, physiological motion during the acquisition of both studies may alter the appearance of organ shape, size or location. The aim of this study was to assess the consistency in location and measured size of upper abdominal organs with In111 Octreotide SPECT and CT using a combined SPECT high resolution CT system. Methods: We evaluated ten consecutive patients who underwent clinical SPECT/CT scans for suspected/follow-up of somatostatin avid tumors using a 16 slice CT/SPECT system (Philips, Precedence). Both SPECT and CT images were acquired with patients in tidal breathing. CT scans were performed without iv. contrast. We separately determined the location of the cranial and caudal margins for liver, spleen, and bilateral kidneys, on SPECT and CT. Differences between the two modalities in terms of location and measured organ size were investigated. Results: The results of the analysis are presented in the attached table. The upper pole of the left kidney could not be reliably identified on the SPECT images due to proximity of spleen. Due to the mild uptake of radiotracer in the liver, and the narrow, elongated shape of the inferior liver tip, the full inferior extent of liver radiotracer activity was also not reliably assessed. Conclusions: The upper abdominal normal organs appear slightly larger on SPECT compared with CT with the windows selected for clinical interpretation. Intraperitoneal organs (spleen) had a larger cranio-caudal displacement between SPECT and CT than the retroperitoneal organs (kidneys). Overall, registration quality with the high quality CT/SPECT system was excellent.
Texture descriptor based on local approximations (2014)

This paper proposes a novel texture descriptor based indices of degrees of local approximating polynomials. An input image is divided into non-overlapping patches which are reshaped into a one-dimensional source vectors. These vectors are approximated using local polynomial functions of various degrees. For each element of the source vector, these approximations are ranked according to the difference between the original and approximated values. A set of indices of polynomial degrees form a local feature. This procedure is repeated for every pixel. Finally, a proposed texture descriptor is obtained from the frequency histogram of all obtained local features. A nearest neighbor classifier utilizing distance metric is used to evaluate a performance of the introduced descriptor on the following datasets: Brodatz, KTH-TIPS, KTH-TIPS2b, UCLA and Columbia-Utrecht (CUReT) with respect to different methods of texture analysis and classification. A proper parameter setup of the proposed texture descriptor is discussed. The results of this comparison demonstrate that the proposed method is competitive with the recent statistical approaches such as local binary patterns (LBP), local ternary patterns, completed LBP, Weber’s local descriptor, and VZ algorithms (VZ-MR8 and VZ-Joint). At the same time, on KTH-TIPS2-b and KTH-TIPS datasets, the proposed method is slightly inferior to some of the state-of-the-art methods.
Probing the heme-thiolate oxygenase domain of inducible nitric oxide synthase withRu(II) andRe(I) electron tunneling wires (2008)

Nitric oxide synthase (NOS) catalyzes the production of nitric oxide from L-arginine and dioxygen at a thiolate-ligated heme active site. Although many of the reaction intermediates are as yet unidentified, it is well established that the catalytic cycle begins with substrate binding and rate-limiting electron transfer to the heme. Here we show that Ru(II)-diimine and Re(I)-diimine electron tunneling wires trigger nanosecond photoreduction of the active-site heme in the enzyme. Very rapid generation of a reduced thiolate-ligated heme opens the way for direct observation of short-lived intermediates in the NOS reaction cycle.
SPAAN: a software program for prediction of adhesins and adhesin-like proteins using neural networks (2004)

ramu@igib.res.in.
The Effects of Different Levels of Ambient Oxygen in an Oxygen-Enriched Surgical Environment and Production of Surgical Fires (2018)

Surgical fires require an oxygen-enriched environment, a flammable substrate, and an ignition source. We hypothesized ambient oxygen concentration is proportional to the latency time to combustion and the incidence of surgical fires that are detected. We examined latency time and number of events, utilizing the VanCleave et al model of intraoral fire ignition under 60, 80, and 100% oxygen concentration and flow rates of 4 and 10 L/min. Results demonstrated that ambient oxygen concentration and flow rate correlated positively to the initiation of combustion. The number of combustion events with 60% oxygen was significantly lower than with both 80% ( p = .0168) and 100% ( p = .002). Likewise, the number of events with 80% oxygen was significantly lower than with 100% oxygen ( p = .0019). Flow rate has a significant effect on the time to the first event ( p = .0002), time to first audible pop ( p = .0039), and time to first flash or fire ( p < .0001). No combustion occurred at oxygen concentrations less than 60% or flows less than 4 L/min. We conclude that latency time to combustion is directly proportional to ambient oxygen concentration and flow rate. Minimum oxygen concentration and flow rate were identified in our model. Further research is indicated to determine the minimal clinical oxygen concentration and flow rate needed to support combustion of an intraoral fire in a patient.
A time-resolved immunoassay to measure serum antibodies to the rotavirus VP6 capsid protein (2012)

The rotavirus (RV) inner capsid protein VP6 is widely used to evaluate immune response during natural infection and in vaccine studies. Recombinant VP6 from the most prevalent circulating rotavirus strains in each subgroup (SG) identified in a birth cohort of children in southern India [SGII (G1P[8]) and SGI (G10P[11])] were produced. The purified proteins were used to measure VP6-specific antibodies in a Dissociation-Enhanced Lanthanide Fluorometric Immunoassay (DELFIA). The ability of the assay to detect a ≥2 fold rise in IgG level in a panel of serum samples from a longitudinal study was compared to a gold standard virus-capture ELISA. A strong association was observed between the assays (p<0.001; chi-squared test) with assay performances remaining similar when the samples were subdivided as having a fold change increase in VP6 antibody levels (a) within 90 days of RV RNA detection in stool or (b) if no RV RNA was detected within that time period. This study demonstrates the suitability of using recombinant proteins to measure anti-RV immune responses and serves as a "proof of principle" to examine the antibody responses generated to other recombinant RV proteins and thereby possibly identify a correlate of protection.
Emittance Measurements for High Charge State Ion Beams Extracted from the AECR-U Ion Source (2001)

In order to investigate the ion-optical parameters of the AECR-U injection line into the 88-Inch Cyclotron, an electrostatic-deflection-type emittance scanner has been designed and constructed. It allows fast on-line measurements, while tuning the ion beam through the cyclotron. Emittance measurements have been performed for various high charge state ions. First results indicate a strong mass dependence of the normalized beam emittance. For example the normalized rms emittance for protons (0.24 π · mm · mrad) is four times higher than for O6+ (0.06 π · mm · mrad) and about 8 times higher than Kr19+ (0.03 π · mm · mrad). Furthermore it was found, that the emittance values are approximately independent of the current at the medium ion beam intensities. The predominant factor on the beam emittance is shown to be the plasma stability. The emittance measurements and the results are discussed in the paper.
Electromagnetic modeling and simulation of a directly-modulated L-band microstrip patch antenna (2007)

An electromagnetic simulation model of an L-band microstrip patch antenna with integrated PIN diodes is constructed using Ansoft High Frequency Structure Simulator (HFSS) and is analyzed to explore how the antenna's input impedance, center frequency and carrier wave radiation pattern are impacted by biasing the PIN diodes with a baseband modulation signal. By exploring the radiation characteristics of this specific example of direct antenna modulation, as applied to a patch antenna structure, the first steps are taken towards a general model of the direct antenna modulation technique.
Protein abundances and interactions coevolve to promote functional complexes while suppressing non-specific binding (2010)

How do living cells achieve sufficient abundances of functional protein complexes while minimizing promiscuous non-functional interactions? Here we study this problem using a first-principle model of the cell whose phenotypic traits are directly determined from its genome through biophysical properties of protein structures and binding interactions in crowded cellular environment. The model cell includes three independent prototypical pathways, whose topologies of Protein-Protein Interaction (PPI) sub-networks are different, but whose contributions to the cell fitness are equal. Model cells evolve through genotypic mutations and phenotypic protein copy number variations. We found a strong relationship between evolved physical-chemical properties of protein interactions and their abundances due to a "frustration" effect: strengthening of functional interactions brings about hydrophobic interfaces, which make proteins prone to promiscuous binding. The balancing act is achieved by lowering concentrations of hub proteins while raising solubilities and abundances of functional monomers. Based on these principles we generated and analyzed a possible realization of the proteome-wide PPI network in yeast. In this simulation we found that high-throughput affinity capture - mass spectroscopy experiments can detect functional interactions with high fidelity only for high abundance proteins while missing most interactions for low abundance proteins.
Association of lower nighttime diastolic blood pressure and hypoxia with silent myocardial injury: The Japan Morning Surge‐Home Blood Pressure study (2020)

Whether marked nocturnal blood pressure (BP) reduction is associated with cardiovascular disease (CVD) is still controversial. In addition, no report has yet discussed the relationship between lower nocturnal BP and CVD, involving modification by nighttime hypoxia. We evaluated 840 patients who had one or more cardiovascular risk factors by measuring their high-sensitivity cardiac troponin T (Hs-cTnT), N-terminal pro-B-type natriuretic peptide (NT-pro BNP), and nighttime saturation levels and performing ambulatory BP monitoring. The lowest tertile in nighttime diastolic BP (DBP) (≤66 mmHg) had increased likelihood of the presence of ≥0.014 ng/ml of Hs-cTnT compared with the second tertile (odds ratio [OR] 1.91, 95% confidence interval [CI] 1.01-3.63), and the lowest tertile of minimum blood oxygen saturation (≤81%) had increased likelihood of the presence of ≥0.014 ng/ml of Hs-cTnT compared with the third tertile (OR 2.15, 95% CI 1.13-4.10). Additionally, the patients with both lowest tertile of nighttime DBP and minimum SpO2 showed increased likelihood of the presence of ≥0.014 ng/ml of Hs-cTnT compared with those without this combination (OR 2.93, 95% CI 1.40-6.16). On the other hand, these associations were not found in the presence of ≥125 pg/ml of NT-pro BNP. In the clinical population, each of lower nocturnal DBP and nighttime hypoxia was associated with asymptomatic myocardial injury, which was represented as higher Hs-cTnT, and coexisting lower nocturnal DBP and nighttime hypoxia had an additive effect on the risk of myocardial injury.
Metamaterials face-off [Speaker's Corner] (2009)

In 1967, a Soviet physicist named Veselago published an article that explored the technical ramifi cations if a material with negative permittivity or permeability was discovered. However, it was nearly 30 years later that the British physicist Pendry first described how traditional materials could be periodically loaded with electrically small and closely spaced split-ring resonators or parallel wires to produce an aggregate material that he claimed exhibited either macroscopic negative permeability or permittivity. Soon after, David Smith et al. reported the results of a work that combined such periodic loading to produce material that was also claimed to exhibit both negative permeability and permittivity. About a year later, Caloz and Itoh, Eleftheriades et al., and Oliner independently described how these properties could be realized by periodically loading traditional trans mission media with electrically small and closely spaced series capacitance and shunt inductance. Since these seminal publications appeared, hundreds of papers and articles and several books have been written about this class of materials and their applications.
Development of a cold engine simulator to carry out acoustic and fluid-dynamic experiments with exhaust systems (2002)

status: Published
Manual Stimulation of the Suprahyoid-Sublingual Region Diminishes Polynnervation of the Motor Endplates and Improves Recovery of Function After Hypoglossal Nerve Injury in Rats (2008)

The data show that manual stimulation of denervated muscles improves functional outcome following peripheral nerve injury. This suggests immediate potential for enhancing clinical rehabilitation strategies.
Exploiting the p53 Pathway for Therapy (2017)

The excitement around the entry into the clinic of the first generation of p53-specific drugs has become muted as the hoped-for dramatic clinical responses have not yet been seen. However, these pioneer molecules have become exceptionally powerful tools in the analysis of the p53 pathway and, as a result, a whole spectrum of new interventions are being explored. These include entirely novel and innovative approaches to drug discovery, such as the use of exon-skipping antisense oligonucleotides and T-cell-receptor-based molecules. The extraordinary resources available to the p53 community in terms of reagents, models, and collaborative networks are generating breakthrough approaches to medicines for oncology and also for other diseases in which aberrant p53 signaling plays a role.