gebhart/patrepeval huggingface dataset:
Onconase cytotoxicity relies on the distribution of its positive charge (2009)

Onconase (ONC) is a member of the ribonuclease A superfamily that is toxic to cancer cells in vitro and in vivo. ONC is now in Phase IIIb clinical trials for the treatment of malignant mesothelioma. Internalization of ONC to the cytosol of cancer cells is essential for its cytotoxic activity, despite the apparent absence of a cell-surface receptor protein. Endocytosis and cytotoxicity do, however, appear to correlate with the net positive charge of ribonucleases. To dissect the contribution made by the endogenous arginine and lysine residues of ONC to its cytotoxicity, 22 variants were created in which cationic residues were replaced with alanine. Variants with the same net charge (+2 to +5) as well as equivalent catalytic activity and conformational stability were found to exhibit large (> 10-fold) differences in toxicity for the cells of a human leukemia line. In addition, a more cationic ONC variant could be either much more or much less cytotoxic than a less cationic variant, again depending on the distribution of its cationic residues. The endocytosis of variants with widely divergent cytotoxic activity was quantified by flow cytometry using a small-molecule fluorogenic label, and was found to vary by twofold or less. This small difference in endocytosis did not account for the large difference in cytotoxicity, implicating the distribution of cationic residues as being critical for lipid-bilayer translocation subsequent to endocytosis. This finding has fundamental implications for understanding the interaction of ribonucleases and other proteins with mammalian cells.
Results from a phase III trial (GRID) evaluating regorafenib (REG) in metastatic gastrointestinal stromal tumour (GIST): Subgroup analysis of outcomes based on pretreatment characteristics. (2013)

10551 Background: REG, an oral receptor kinase inhibitor with activity against KIT, PDGFR, VEGFR, FGFRs, and other oncologic targets, demonstrated significant improvement in progression-free survival (PFS) over placebo (PL) in a phase III study (GRID) of patients (pts) with advanced GIST following failure of at least imatinib (IM) and sunitinib (SU). To understand the impact of pts’ baseline characteristics on outcome, we performed an exploratory analysis of REG effects across pt subgroups based on sex, age, and mitotic index of primary GIST tissue, as well as duration and number of lines of previous therapies. Methods: Adult pts with metastatic GIST (n=199) progressing after at least IM and SU were randomized 2:1 to receive oral REG 160 mg or PL once daily for the first 3 weeks of each 4-week cycle. Subgroup analysis of centrally assessed PFS was performed, based on sex, age (&lt;65, ≥65 years), mitotic index of primary GIST (&lt;5, ≥5 to &lt;10, ≥10 mits/50 hpf), duration of IM and SU treatment (&lt;6, ≥6 to &lt;18, ≥18 months), and number of prior anticancer treatment lines (2 or ≥3). Mitotic index data on primaries were available for 119 patients. Results: REG demonstrated improvement in PFS vs PL in all subgroups, as summarized in the Table. Conclusions: REG had substantial efficacy in all patient subgroups included in this analysis. Clinical trial information: NCT01271712. [Table: see text]
Measurement of ϒ(1S) Elliptic Flow at Forward Rapidity in Pb-Pb Collisions at sNN=5.02  TeV (2019)

The first measurement of the ϒ(1S) elliptic flow coefficient (v_{2}) is performed at forward rapidity (2.5<y<4) in Pb-Pb collisions at sqrt[s_{NN}]=5.02 TeV with the ALICE detector at the LHC. The results are obtained with the scalar product method and are reported as a function of transverse momentum (p_{T}) up to 15 GeV/c in the 5%-60% centrality interval. The measured ϒ(1S)v_{2} is consistent with 0 and with the small positive values predicted by transport models within uncertainties. The v_{2} coefficient in 2<p_{T}<15 GeV/c is lower than that of inclusive J/ψ mesons in the same p_{T} interval by 2.6 standard deviations. These results, combined with earlier suppression measurements, are in agreement with a scenario in which the ϒ(1S) production in Pb-Pb collisions at LHC energies is dominated by dissociation limited to the early stage of the collision, whereas in the J/ψ case there is substantial experimental evidence of an additional regeneration component.
Fiber optic magnetic field sensor based on domain wall motion in garnet film waveguides (1991)

A novel fiber optic magnetometer based on the Faraday effect in a magnetic garnet thin-film ridged waveguide is described. The single-mode film has planar magnetization aligned parallel and antiparallel to the light propagation direction by a gradient bias field, and a single domain wall crosses the light path. The motion of this wall in response to an applied field changes the Faraday rotation in the film. Operation of this field or current sensor in both the transmission mode and the single fiber reflection mode has been demonstrated. Optical output varying linearly with ac or dc fields up to 15 Oe, with a minimum detectable field of 0.05 Oe, has been observed. This domain wall motion scheme in a zero birefringence waveguide can also be used in a polarization controller.
Is the failing heart out of fuel or a worn engine running rich? A study of mitochondria in old spontaneously hypertensive rats (2008)

Hypertension now affects about 600 million people worldwide and is a leading cause of death in the Western world. The spontaneously hypertensive rat (SHR), provides a useful model to investigate hypertensive heart failure (HF). The SHR model replicates the clinical progression of hypertension in humans, wherein early development of hypertension is followed by a long stable period of compensated cardiac hypertrophy that slowly progresses to HF. Although the hypertensive failing heart generally shows increased substrate preference towards glucose and impaired mitochondrial function, the cause-and-effect relationship between these characteristics is incompletely understood. To explore these pathogenic processes, we compared cardiac mitochondrial proteomes of 20-month-old SHR and Wistar-Kyoto controls by iTRAQ-labelling combined with multidimensional LC/MS/MS. Of 137 high-scoring proteins identified, 79 differed between groups. Changes were apparent in several metabolic pathways, chaperone and antioxidant systems, and multiple subunits of the oxidative phosphorylation complexes were increased (complexes I, III and IV) or decreased (complexes II and V) in SHR heart mitochondria. Respiration assays on skinned fibres and isolated mitochondria showed markedly lower respiratory capacity on succinate. Enzyme activity assays often also showed mismatches between increased protein expression and activities suggesting elevated protein expression may be compensatory in the face of pathological stress.
Detecting Exercise Induced Stress using the Photoplethysmogram (2006)

The effect of exercise on the cardiovascular system has been studied extensively using a wide range of physiological sensors. Athletes now commonly use EKG-based monitors to ascertain heart rate, but these devices cannot directly monitor the level of physical stress. We hypothesize that the low frequency spindle waves seen in the photoplethysmographs (PPG) of exercising individuals may be useful for noninvasively detecting hemodynamic stressors to the human vascular system. In a clinical trial with nine healthy subjects performing the Bruce Protocol treadmill test these low frequency spindle waves were observed in the forehead and ear PPG in all subjects before the onset of volitional fatigue. As volitional fatigue approached, the spindle waves become more pronounced, decreased in period and then within several seconds of the cessation of the protocol they disappeared. Using a software-based detector, these distinct spindle waves can be reliably detected. This technique holds promise for the automatic detection and characterization of exercise induced physical stress.
Reply to “Comment on ‘Thermal phase noise in Fabry-Pérot resonators and fiber Bragg gratings’ ” (2015)

The previous Comment clarifies a few key points that were unclear in an earlier paper by its authors, in particular their definitions of phase and of phase noise. We now agree that this earlier paper was modeling the resonance-frequency fluctuations of a Fabry-Perot resonator, whereas our article [Phys. Rev. A 89, 033818 (2014)] was modeling the noise in the phase of the resonator's output field. In light of the Comment, the two pictures are indeed consistent. The resonance-frequency fluctuations are independent of group index, whereas the phase noise in the output field is proportional to group index. This important dependence was pointed out in our paper [Phys. Rev. A 89, 033818 (2014)]. From a more physical standpoint, we argue that phase noise can be described without resorting to the concept of signal-to-noise ratio and that, although the phase noise is of course in part a property of the fiber itself, its group-index dependence is introduced solely by the resonator.
Measurement Of Low Angle Scatter (1985)

A low angle scatter instrument (LASI) has been designed and built at Montana State University under contract to the Los Alamos National Labora-tory. The instrument is capable of measuring scatter at 0.1 ° from the specular beam on most samples and at 0.01 on high scatter samples. Samples may be either reflective or transmissive components. LASI consists of a small aperture detector (100 Am nominal) that is scanned through a focused beam under computer control. The system measures light intensity over approximately nine orders of magnitude. Because the instrument produces some scatter, scans are made with and without the sample present. Following a normalization process, the two data sets are compared to determine the scatter due to the sample alone. Extensive software is used to control the data-taking process, analyze the data, and present the results in graphical form. In this paper a review of the instrument is presented, rather than an extensive survey of scattering data. The basic design problems involved in making these types of instruments are discussed, and procedures for taking measurements are given. We conclude that the major constraint on this type of measurement is scatter from the instrument itself. The difficulties involved in obtaining optics with small amounts of low angle scatter emphasize the need for this type of instrumentation.
On Detecting Pollution Attacks in Inter-Session Network Coding (2011)

Dealing with pollution attacks in inter-session network coding is challenging due to the fact that sources, in addition to intermediate nodes, can be malicious. In this work, we precisely define corrupted packets in inter-session pollution based on the commitment of the source packets. We then propose three detection schemes: one hash-based and two MAC-based schemes: InterMacCPK and SpaceMacPM. InterMacCPK is the first multi-source homomorphic MAC scheme that supports multiple keys. Both MAC schemes can replace traditional MACs, e.g., HMAC, in networks that employ inter-session coding. All three schemes provide in-network detection, are collusion-resistant, and have very low online bandwidth and computation overhead.
Influence of Particle Size and Material Properties on Mucociliary Clearance from the Airways (2010)

Mucociliary clearance (MC), designed by evolution to eliminate inhaled and possibly noxious material from the airways, considerably limits the benefit of inhalation therapy. Although the principles of MC seem to be understood, there are still many open questions on mucociliary particle clearance. In this study a trachea-based in vitro model was used to investigate the effect of particle size, zeta-potential, and mucoadhesive particle properties on mucociliary particle clearance. As different sized particles (50-6000 nm) were tested at equal mass concentrations, size related factors, namely particle number and particle surface area, varied by several orders of magnitude between the experiments. Surprisingly, particle clearance for 50 nm up to 6000 nm-sized polystyrene particles did not differ significantly (p < 0.05): 50 nm (2.9 +/- 0.6 mm/min); 100 nm (3.8 +/- 0.9 mm/min); 1000 nm (3.8 +/- 0.8 mm/min); 6000 nm (3.2 +/- 0.6 mm/min). In clear contrast, particles prepared from different PLGA-based copolymers (polylactic-co-glycolic acid) showed a significant effect on particle transport. PEG-PLGA particles (polyethylene glycol) showed the fastest and normal transport rates (5.9 +/- 1.7 mm/min) compared to the ICRP's (International Commission of Radiological Protection) standard value for average tracheal transport rates (5.5 mm/min). Mucoadhesive chitosan-PLGA particles were transported at the slowest rate (0.7 +/- 0.3 mm/min) of all particles tested. Overall, particle size and zeta-potential seem to be relatively uncritical, whereas material properties and the related particle surface chemistry significantly influence mucociliary particle clearance. Considering these findings in future drug formulation seems to be a promising strategy to improve inhalation therapy by prolonged particle/drug residence time within the airways.
Design and fabrication of 3μm silicon-on-insulator waveguide integrated Ge electro-absorption modulator (2011)

We present the design and fabrication of a waveguide-based Ge electro-absorption (EA) modulator integrated with a 3 µm silicon-on-isolator (SOI) waveguide. The proposed Ge EA modulator employs a butt-coupled horizontally-oriented p-i-n structure. The optical design achieves a low-loss transition from Ge to Si waveguides. The interaction between the optical mode of the waveguide and the bias induced electric field in the p-i-n structure was maximized to achieve high modulation efficiency. By balancing the trade-offs between the extinction ratio and the insertion loss of the device, an optimal working regime was identified. The measurement results from a fabricated device were used to verify the design. Under a -4Vpp reverse bias, the device demonstrates a total insertion loss (including the transition loss) of 2.7-5.2 dB and an extinction ratio of 4.9-8.2 dB over the wavelength range of 1610-1640 nm. Subtracting the contribution of the transition loss, the Δα/α value for the fabricated device was estimated to be between 2.2 and 3.2 with an electric field around 55 kV/cm.
Human epidermal melanocyte and keratinocyte melanotropin receptors: visualization by melanotropic peptide conjugated macrospheres (polyamide beads) (1997)

The objectives of this research were to determine whether melanotropin receptors are characteristic membrane markers of human epidermal melanocytes. Methodologies were developed to visualize these receptors by light microscopy. Multiple copies (up to a thousand) of [Nle4,D-Phe7] alpha-MSH, a superpotent analog of alpha-melanocyte stimulating hormone (alpha-MSH), were conjugated to a macromolecular carrier, large polyamide beads (macrospheres). Incubation in the presence of the I conjugated macrospheres resulted in binding of human epidermal melanocytes to the macrospheres. Specificity of the binding of melanocytes to the melanotropin-conjugated macrospheres was demonstrated by several studies: (i) Binding of melanocytes to the conjugate was specific since it could be blocked by prior incubation of the cells in the presence of the unconjugated hormone analog; (ii) The macrospheres after removal of the bound ligand did not bind to the melanocytes; (iii) Another peptide hormone ligand (e.g., a substance-P analog) attached to the macrospheres failed to bind to the melanocytes; (iv) B16/F10 mouse melanoma cells known to express melanotropin receptors bound to the macrospheres; (v) Cells of nonmelanocyte origin (e.g., mammary cancer cells, lung cancer cells, fibroblasts) did not bind to the macrospheres. One exception was that human epidermal keratinocytes also expressed melanotropin receptors as determined by all the criteria established for epidermal melanocytes. Thus, cell specific melanotropin receptors appear to be characteristic cell surface markers of epidermal melanocytes and keratinocytes.
Error floor of unequalized wireless personal communications systems with MSK modulation and training-sequence-based adaptive sampling (1997)

We analyze the error floor of unequalized personal communications systems using minimum-shift keying (MSK) with training-sequence-based adaptive sampling in a two-delay fading channel. We include Gaussian filtering of the input, finite accuracy in determining the optimum sampling time, and filtering at the receiver. We prove that for pure MSK and low time dispersion, training-sequence-based adaptive sampling can completely avoid errors caused by intersymbol interference. The actual errors are caused by "secondary" effects (filtering and finite-resolution sampling) in conjunction with the channel time dispersion. Errors occur if the normalized phasor of the channel impulse response falls into certain error regions; the computation of these regions gives physical insights into the error mechanism and allows a highly efficient computation of the average bit-error rate (BER). The average BER varies as K/spl middot/(S/T)/sup 2/, where S is the RMS delay spread and T is the bit length. The proportionality constant K depends on the Gaussian filtering in the transmitter, the receiver filtering, and the amount of oversampling. The BER can be orders of magnitude lower than for the (quasi-) fixed sampling case, in which timing is derived solely based on the channel delay power profile. For two-branch diversity reception, we show that the BER is proportional to (S/T)/sup 4/.
Data center transport mechanisms: Congestion control theory and IEEE standardization (2008)

Data Center Networks present a novel, unique and rich environment for algorithm development and deployment. Projects are underway in the IEEE 802.1 standards body, especially in the Data Center Bridging Task Group, to define new switched Ethernet functions for data center use. One such project is IEEE 802.1Qau, the Congestion Notification project, whose aim is to develop an Ethernet congestion control algorithm for hardware implementation. A major contribution of this paper is the description and analysis of the congestion control algorithm - QCN, for Quantized Congestion Notification- which has been developed for this purpose. A second contribution of the paper is an articulation of the Averaging Principle: a simple method for making congestion control loops stable in the face of increasing lags. This contrasts with two well-known methods of stabilizing control loops as lags increase; namely, (i) increasing the order of the system by sensing and feeding back higher-order derivatives of the state, and (ii) determining the lag and then choosing appropriate loop gains. Both methods have been applied in the congestion control literature to obtain stable algorithms for high bandwidth-delay product paths in the Internet. However, these methods are either undesirable or infeasible in the Ethernet context. The Averaging Principle provides a simple alternative, one which we are able to theoretically characterize.
Correction: dehydratase mediated 1-propanol production in metabolically engineered Escherichia coli (2012)

After publication of this work [1], we have noticed accidental errors that were introduced during our revision process. In our revision process, to address review comments we reduced the number of significant digits for the results of our enzyme assay experiments. As we reduced the number of significant digits to two in Tables In order to maintain consistency between the text and the tables, we would like to correct Tables These changes will in no manner affect the outcome/interpretation of the experiments as described in the original publication and will not affect the merit of this work. In addition, we would like to modify the "Competing Interests" as below.
Software-based evaluation of aortic annulus dimensions in dual-source CT angiography prior to Transcatheter Aortic Valve Replacement (TAVR): comparison to manual analysis (2013)

Purpose: Cardiac CT permits 3-dimensional visualization of the aortic annulus and is therefore a potentially valuable diagnostic tool to plan Transcatheter Aortic Valve Replacement (TAVR). Automated software programmes might be helpful to reliably determining aortic annulus dimensions and might facilitate the evaluation process. Methods: CT data sets (DSCT, high-pitch spiral data acquisition mode, 40-60 mL contrast, 4 mL/s) of 50 patients scheduled for TAVR were evaluated by both an automated software prototype and two experienced CT investigators in a consensus reading. The following Aortic Annulus parameters (AA) were determined: Max, min and mean diameter of the Aortic Annulus (AA); distances of coronary ostia to the AA level. Subsequently, the results obtained by the automated software were compared with the manually determined dimensions using correlation measurements as well as Bland-Altman analysis. Results: The automated software and the two investigators assessed the following AA parameters (mean±SD; mean difference; correlation): Max Diameter (D) of the aortic annulus (AA) 29.1±2.2 vs. 27.9±2.1mm (1.2±1.4mm; r=0.77). Min D 22.1±2.1 vs. 22.5±2.0mm (-0.3±1.2mm; r=0.84). Mean D (Dmean) 25.6±1.9 vs. 25.2±1.8mm (0.4±0.9mm; r=0.88). Effective D according to AA area (Deff/A) 25.4±1.9 vs. 25.4±1.8mm (0.01±1.0mm; r=0.87). Effective D according to AA perimeter (Deff/P) 26.1±1.9 vs. 27.4±2.1mm (-1.3±1.2mm; r=0.82). Distance of LCA to AA 16.0±2.1 vs. 13.6±2.6mm (2.4±2.0mm; r=0.65). Distance of RCA to AA 18.5±2.6 vs. 14.8±2.8mm (3.7±2.1mm; r=0.71). Bland-Altman analysis showed significant differences between software and investigators concerning Dmean (p<0.01) and Deff/P (p<0.001), but not for Deff/A (p=0.92). Diameter differences ≥3mm between software and manual interpretation occurred in 2 patients for assessing Deff/P, but in none using Dmean and Deff/A for aortic annulus sizing. There were substantial differences in assessing distances of the coronary ostia to the AA plane (p<0.001). Conclusions: Software-guided evaluation of aortic annulus dimensions by CT angiography might be useful for initial analyses. Especially in assessing the "effective" diameter of the aortic annulus according to its area, the software showed reliable results with minimal differences compared to manual interpretation. Substantial differences exist concerning the distances of the coronary ostia to the aortic annulus plane.
Gear Fault Location Detection for Split Torque Gearbox Using AE Sensors (2012)

In comparison with a traditional planetary gearbox, the split torque gearbox (STG) potentially offers lower weight, increased reliability, and improved efficiency. These benefits have driven helicopter object exchange models (OEMs) to develop products using STG. However, the unique structure of the STG creates a problem on how to locate the gear faults in an STG. As of today, only limited research on STG fault detection using vibration and acoustic emission (AE) sensors has been conducted. In this paper, an effective gear fault location detection methodology using AE sensors for STG is presented. The methodology uses wavelet transform to process AE sensor signals at different locations to determine the arrival time of the AE bursts. By analyzing the arrival time of the AE bursts, the gear fault location can be determined. The parameters of the wavelets are optimized by using an ant colony optimization algorithm. Real seeded gear fault experimental tests on a notional STG are conducted. AE signals at different locations of the gearbox with both healthy and damaged output driving gears are collected simultaneously to determine the location of the damaged gear. Experimental results have shown the effectiveness of the presented methodology.