Miracle-dz/UniFAR-FTUs huggingface dataset:
A Maximum Likelihood Method for Linking of Particle-in-Cell and Monte Carlo Simulations

To support the design and analysis of x-ray radiographic facilities and experiments at Los Alamos, we have developed an integrated chain model, which is a set of linked physics simulation codes to generate self-consistent synthetic radiographs of experiments [1]. The expectation-maximization (EM) algorithm [2] has recently been used to great advantage to link particle- in-cell (PIC) methods, which model electron propagation to a converter target, and Monte Carlo transport methods, which model bremsstrahlung photon generation and transport through the radiographic object onto a detector. The EM algorithm is a maximum- likelihood technique to estimate the probability density function (PDF) of a set of measurements. A high performance implementation of the EM algorithm to characterize multidimensional data sets using a PDF parameterized as a Gaussian mixture has been developed (GMIX). The resulting PDFs compare favorably to histograms / tallies---no binning artifacts and less noisy (especially in the tails). GMIX is being used extensively in the radiographic chain model to quantify bremsstrahlung x-ray emission from rod-pinch diodes and other devices. In particular, the PIC simulation code MERLIN is used to model the dynamics of the rod-pinch diode in the Los Alamos radiographic machine Cygnus for the linked calculations. The rod-pinch diode used in Cygnus consists of a 9- mm diameter aperture cathode and a 0.75- mm diameter needle anode. A TEM pulse launched at one simulation boundary sets up the voltage required for the electron emission. The electron trajectories are followed self-consistently in the electromagnetic fields as the electron beam pinches at the anode tip with energies up to 2.25 MeV. The Monte Carlo transport code MCNP is used to track the bremsstrahlung photons generated by electrons incident on the anode tip. GMIX is used to “upsample” the PIC electrons to provide a suitably large population for the Monte Carlo calculation (10 7 or greater) that would have been computationally expensive to generate directly. The motivation, the mathematical properties, and the implementation details, and applications of GMIX to plasma and Monte Carlo simulations will be discussed, including: improved coupling of PIC to Monte Carlo simulations, adaptive PIC simulations, and characterization of the Cygnus radiographic parameters such as energy and angular spectra, spot size, and dose.
The effects of bluephase LED light on fibroblasts

Objective: The aim of this study was to evaluate the effect of Bluephase light emitting diode (LED) light on cell viability, colony-forming ability and proliferation in V79 cell culture and to determine how much the temperature of the nutrient medium rose. Methods: The investigation included a low (L), soft start (S) and high (H) illumination mode for 20, 40 and 80 seconds. The viability was determined by the trypan blue exclusion test, colony-forming ability by counting colonies 7 days after exposure and cell proliferation by the cell counts on 5 post-exposure days. The temperature change during illumination was recorded (0.1°C sensitivity). Results: In each experimental condition, 90–95% of the cells were viable, which was in the same range as the controls. Colony-forming ability was not found to be significantly lower (P<.05). A significant decrease in proliferation was recorded on the 4th post-exposure day with S and H irrespective of time, on the 3rd day with S for 80 s and H for 40 and 80 s, and with S and H for 80 s on the 2nd day (P<.05). The temperature rise was significant with S (P<.05) and H (P<.05), irrespective of exposure duration. Conclusion: Dependent on total energy density, LED blue light affects the mitotic activity of cells in its path to a certain extent. Altered mitotic activity was not noted with illumination at the low power mode (intensity of 421.7 ±1.1 mW/cm2). The greatest temperature rise was 8.3 °C and occurred at the highest intensity and exposure duration.
Investigation of EFM capabilities for probing interphases in nanodielectric materials: A numerical study

Interphases are usually considered to be responsible for the physical properties of nanocomposites unexplainable by general mixture laws. The prediction of the effective dielectric permittivity of nanodielectrics needs to consider the intrinsic dielectric permittivity of the interphase and its volume. However, no reliable experimental method has been yet developed in order to characterize the interphase at the nanoscale. This work aims at verifying via numerical simulations, the electrostatic force microscope (EFM) signal behavior, capabilities and limits, in order to detect and characterize nanoparticles and interphases present in nanodielectric materials. We showed at first the form of the EFM signal to be expected in front of a nanodielectric material. Then, we simulated the effect of the dimensions and the dielectric permittivities of the nanodielectric filler, interphase and matrix on the EFM signal. Consequences on the detectability and physical determination of the interphase using EFM were discussed.
Convergent Evolution in the Genetic Basis of Müllerian Mimicry in Heliconius Butterflies

The neotropical butterflies Heliconius melpomene and H. erato are Müllerian mimics that display the same warningly colored wing patterns in local populations, yet pattern diversity between geographic regions. Linkage mapping has previously shown convergent red wing phenotypes in these species are controlled by loci on homologous chromosomes. Here, AFLP bulk segregant analysis using H. melpomene crosses identified genetic markers tightly linked to two red wing-patterning loci. These markers were used to screen a H. melpomene BAC library and a tile path was assembled spanning one locus completely and part of the second. Concurrently, a similar strategy was used to identify a BAC clone tightly linked to the locus controlling the mimetic red wing phenotypes in H. erato. A methionine rich storage protein (MRSP) gene was identified within this BAC clone, and comparative genetic mapping shows red wing color loci are in homologous regions of the genome of H. erato and H. melpomene. Subtle differences in these convergent phenotypes imply they evolved independently using somewhat different developmental routes, but are nonetheless regulated by the same switch locus. Genetic mapping of MRSP in a third related species, the “tiger” patterned H. numata, has no association with wing patterning and shows no evidence for genomic translocation of wing-patterning loci.
New multi-rod linear actuator for direct-drive, wide mechanical band pass applications

In this article, a new multi-rod linear actuator is presented. This actuator has been developed for high thrust density and wide mechanical band pass applications. The multi-airgap concept is first illustrated and explained. Its advantages are highlighted thanks to finite element method optimizations. Next, the multi-rod prototype technology is discussed. Lastly, experimental measurements for prototype forces are provided.
ISPs as nodes or sets of links?

We consider the contract-switching paradigm for studying the inter-domain traffic engineering problem. In the contract-switching paradigm, each ISP in the Internet is abstracted as a set of edge-to-edge contract links. We formulate the optimal routing problem for the contract-switching paradigm by considering three objectives, namely: 1) maximizing throughput, 2) minimizing delay, and 3) minimizing bandwidth usage. We solve the optimization problems on realistic network topologies and show that the routing solutions developed using the contract-switching paradigm provides significant improvement in performance compare to the BGP routing framework with respect to the three objectives. Moreover, our simulation study also reveals that the contract-switching paradigm performs close to the best performance that can be achieved in the Internet in the absence of any abstractions.
Bioavailability of Heme Iron in Biscuit Filling Using Piglets as an Animal Model for Humans

The objective of this work was to evaluate the bioavailability of heme iron added to biscuit filling. It comprised two stages: first, the development of the heme iron enriched biscuit filling; second, the evaluation of the bioavailability of the mineral in fattening piglets. Two groups were selected randomly and fed: a) Low iron feed and biscuits with heme iron supplemented filling; b) Normal feed (with ferrous sulphate). Weight and blood parameters were measured every fifteen days. Averages were compared after duplicate analyses. The filling had a creamy appearance, chocolate taste and smell, appropriate spreadability, heme iron content of 2.6 mg per gram and a shelf-life of a month. The heme iron supplemented pigs registered a greater (P<0.05) weight gain (27.8% more than the control group). Mortality in the heme iron group was 10%, compared to 50% in the control group. The amount of iron measured in the different compartment was greater in the heme group (3315 mg) than in the control group (2792 mg). However, the amount of iron consumed in the latter was greater. We show that an acceptable product with high heme iron content can be formulated, suitable for use as biscuit filling. The heme iron supplement produced better weight increase and lesser mortality in fattening pigs. The bioavailability of heme iron was 23% greater (P<0.05) compared to ferrous sulphate.
Malaria in pregnancy in rural Mozambique: the role of parity, submicroscopic and multiple Plasmodium falciparum infections

BACKGROUND Falciparum malaria affects pregnant women, especially primigravidae, but before malaria control programmes targeted to them can be designed, a description of the frequency and parity pattern of the infection is needed. There is little information on the frequency and effect of submicroscopic malaria infection, as well as on multiplicity of Plasmodium falciparum genotypes in pregnancy. This study aimed to describe the prevalence of malaria parasitaemia and anaemia and their relation to parity and age in pregnant women, during two malaria transmission seasons in a rural area of southern Mozambique. It also tried to assess the frequency and effect on anaemia of submicroscopic and multiple falciparum infections.
Reducing Pyrrolysine tRNA Copy Number Improves the Performance of Genetic Code Expansion in Live Cell Imaging of Bioorthogonally Labeled Proteins

Genetic code expansion technology enables the incorporation of non-canonical amino acids (NCAAs) into proteins expressed in live cells. The NCAA is commonly encoded by an in-frame amber stop codon (TAG) and the methodology relies on the use of an orthogonal aminoacyl tRNA synthetase and its cognate amber suppressor tRNA; e.g., the pyrrolysine synthetase / tRNA CUA (PylT) pair. It is widely accepted that in cultured mammalian cells, intracellular concentration of amber suppressor pyrrolysine tRNA is a limiting factor in amber-suppression efficiency. Therefore, multiple copies of pylT are usually encoded in current expression systems in order to improve NCAA 1 . CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi. org/10.1101/161984 doi: bioRxiv preprint first posted online Jul. 11, 2017;
Phase II trial of sorafenib in patients with recurrent or metastatic squamous cell carcinoma of the head and neck or nasopharyngeal carcinoma.

PURPOSE To determine the efficacy and safety of single-agent sorafenib in patients with recurrent and/or metastatic squamous cell carcinoma of the head and neck (SCCHN) and nasopharyngeal carcinoma (NPC). PATIENTS AND METHODS In this single-arm phase II trial, oral continuous sorafenib was administered in 28-day cycles. Patients had <or= one line of chemotherapy for recurrent and/or metastatic disease, Eastern Cooperative Oncology Group performance status of <or= 2, and adequate organ function. At the end of stage 1, efficacy criteria for further accrual were not met, but the study was amended to enroll an additional five patients for paired tumor biopsies. RESULTS Twenty-seven and 26 patients were eligible for toxicity and efficacy evaluations, respectively. One patient (3.7%; 95% CI, 0.1% to 19.0%) achieved a partial response. Disease stabilization was maintained in 10 patients (37.0%; 95% CI, 22.4% to 61.2%). The median time to progression was 1.8 months (95% CI, 1.6 to 3.4 months), and median overall survival time was 4.2 months (95% CI, 3.6 to 8.7 months). Sorafenib was well tolerated with few grade 3 and no grade 4 toxicities. Biomarker analysis of paired tumor samples before and after treatment with sorafenib revealed a decrease of pERK in all five patients, with a decrease in Ki67 in four patients, consistent with a disruption of ERK signaling. The antiapoptotic protein Mcl-1 was downregulated in four patients, and there was also evidence of antiangiogenic activity. CONCLUSION Sorafenib was well tolerated and had modest anticancer activity comparable to monotherapy with other targeted agents in this group of patients. Further development in combination with radiation or other agents may be warranted.
Prevalence of overweight and obesity among Portuguese youth: a study in a representative sample of 10-18-year-old children and adolescents.

PURPOSE The aim of this research was to report the prevalence of overweight and obesity in a representative sample of Portuguese youth. METHODS This was a school-based study performed in Portugal. A total of 22 048 children and adolescents aged 10-18 years were included in the study. The World Health Organization (WHO) and the International Obesity Task Force (IOTF) cut-offs were used to categorise overweight and obese participants. RESULTS Using IOTF cut-offs the prevalence of overweight and obesity was 17.0 and 4.6% in girls, and 17.7 and 5.8% in boys, respectively (p < 0.001 for overweight and p > 0.05 for obesity), whereas WHO cut-offs resulted in overweight and obesity prevalence scores of 23.1 and 9.6% in girls, and 20.4 and 10.3% in boys, respectively (p < 0.001 for overweight and p >0.05 for obesity). With IOTF cut-offs, a lower prevalence of obesity and overweight was observed at higher ages, in both genders. With the WHO cut-offs, a lower prevalence of obesity and overweight was observed at higher ages, in boys. In girls, the prevalence of overweight and obesity increases from 10 to 12 years of age and decreases from the age of 13 to 18 years. CONCLUSION The prevalence for overweight/obesity among Portuguese children and adolescents vary according to the cut-off points used and are also of concern requiring strategies to promote healthy weight gain among children and adolescents.
Relationship Between Serum Total Testosterone Concentration and Augmentation Index at Radial Artery in Japanese Postmenopausal Patients

Background The significance of testosterone as a risk factor for cardiovascular disease (CVD) in females is controversial. This cross-sectional study aimed to elucidate the relationship between serum total testosterone concentration (T-T) and augmentation index at the radial artery (r-AIx) as a marker of arterial function in Japanese postmenopausal patients. Methods A total of 447 postmenopausal patients with traditional cardiovascular risk factors and/or a history of CVD (age (mean ± standard deviation (SD)), 73 ± 10 years) were enrolled. r-AIx was measured using tonometry, and the association between r-AIx and various clinical parameters, including T-T, was determined. Results r-AIx significantly increased (CVD vs. non-CVD: 99±11% vs. 91±11%, P < 0.001) and T-T significantly decreased (CVD vs. non-CVD: 0.31 ± 0.13 ng/mL vs. 0.49 ± 0.23 ng/mL, P < 0.001) in patients with CVD than in those without CVD. A significant negative correlation (r = -0.48; P < 0.001) between r-AIx and T-T was observed. Furthermore, multiple regression analysis indicated that T-T (t value = -7.7; P < 0.001), height (t value = -5.3; P < 0.001), d-ROMs test as a marker of oxidative stress in vivo (t value = 3.2; P < 0.001), CVD (t value = 2.9; P < 0.01), and pulse rate (t value = -2.7; P < 0.01) were independent variables for r-AIx as a subordinate factor. Conclusion This study revealed that low T-T is an important determining factor for an increase in r-AIx in Japanese postmenopausal patients. A prospective multicenter study with a large sample size is required to confirm the results of this study.
High-content screening for the discovery of pharmacological compounds: advantages, challenges and potential benefits of recent technological developments

Importance of the field: Screening compounds with cell-based assays and microscopy image-based analysis is an approach currently favored for drug discovery. Because of its high information yield, the strategy is called high-content screening (HCS). Areas covered in this review: This review covers the application of HCS in drug discovery and also in basic research of potential new pathways that can be targeted for treatment of pathophysiological diseases. HCS faces several challenges, however, including the extraction of pertinent information from the massive amount of data generated from images. Several proposed approaches to HCS data acquisition and analysis are reviewed. What the reader will gain: Different solutions from the fields of mathematics, bioinformatics and biotechnology are presented. Potential applications and limits of these recent technical developments are also discussed. Take home message: HCS is a multidisciplinary and multistep approach for understanding the effects of compounds on biological processes at the cellular level. Reliable results depend on the quality of the overall process and require strong interdisciplinary collaborations.
Crustal Azimuthal Anisotropy Beneath the Central North China Craton Revealed by Receiver Functions

To characterize crustal anisotropy beneath the central North China Craton (CNCC), we apply a recently developed deconvolution approach to effectively remove near‐surface reverberations in the receiver functions recorded at 200 broadband seismic stations and subsequently determine the fast orientation and the magnitude of crustal azimuthal anisotropy by fitting the sinusoidal moveout of the P to S converted phases from the Moho and intracrustal discontinuities. The magnitude of crustal anisotropy is found to range from 0.06 s to 0.54 s, with an average of 0.25 ± 0.08 s. Fault‐parallel anisotropy in the seismically active Zhangjiakou‐Penglai Fault Zone is significant and could be related to fluid‐filled fractures. Historical strong earthquakes mainly occurred in the fault zone segments with significant crustal anisotropy, suggesting that the measured crustal anisotropy is closely related to the degree of crustal deformation. The observed spatial distribution of crustal anisotropy suggests that the northwestern terminus of the fault zone probably ends at about 114°E. Also observed is a sharp contrast in the fast orientations between the western and eastern Yanshan Uplifts separated by the North‐South Gravity Lineament. The NW‐SE trending anisotropy in the western Yanshan Uplift is attributable to “fossil” crustal anisotropy due to lithospheric extension of the CNCC, while extensional fluid‐saturated microcracks induced by regional compressive stress are responsible for the observed ENE‐WSW trending anisotropy in the eastern Yanshan Uplift. Comparison of crustal anisotropy measurements and previously determined upper mantle anisotropy implies that the degree of crust‐mantle coupling in the CNCC varies spatially.
Thioredoxin-1 attenuates indomethacin-induced gastric mucosal injury in mice

Indomethacin is one of non-steroidal anti-inflammatory drugs that are commonly used clinically and often cause gastric mucosal injury as a side effect. Generation of reactive oxygen species (ROS) and activation of apoptotic signaling are involved in the pathogenesis of indomethacin-induced gastric mucosal injury. Thioredoxin-1 (Trx-1) is a small redox-active protein with anti-oxidative activity and redox-regulating functions. The aim of this study was to investigate the protective effect of Trx-1 against indomethacin-induced gastric mucosal injury. Trx-1 transgenic mice displayed less gastric mucosal damage than wild type (WT) C57BL/6 mice after intraperitoneal administration of indomethacin. Administration of recombinant human Trx-1 (rhTrx-1) or transfection of the Trx-1 gene reduced indomethacin-induced cytotoxicity in rat gastric epithelial RGM-1 cells. Pretreatment with rhTrx-1 suppressed indomethacininduced ROS production and downregulation of phosphorylated Akt in RGM-1 cells. Survivin, a member of inhibitors of apoptosis proteins family, was downregulated by indomethacin, which was suppressed in Trx-1 transgenic mice or by administration of rhTrx-1 in RGM-1 cells. Trx-1 inhibits indomethacin-induced apoptotic signaling and gastric ulcer formation, suggesting that it may have a preventive and therapeutic potential against indomethacin-induced gastric injury.
Kicking the Digital Dog: A Longitudinal Investigation of Young Adults' Victimization and Cyber-Displaced Aggression

Using the general strain theory as a theoretical framework, the present longitudinal study investigated both face-to-face and cyber victimization in relation to cyber-displaced aggression. Longitudinal data were collected from 130 (70 women) young adults who completed measures assessing their victimization (face-to-face and cyber), cyber aggression, and both face-to-face and cyber-displaced aggression. Findings indicated that victimization in both social contexts (face-to-face and cyber) contributed to cyber-displaced aggression 6 months later (Time 2), after controlling for gender, cyber aggression, face-to-face displaced aggression, and cyber-displaced aggression at Time 1. A significant two-way interaction revealed that Time 1 cyber victimization was more strongly related to Time 2 cyber-displaced aggression when young adults had higher levels of face-to-face victimization at Time 1. Implications of these findings are discussed as well as a call for more research investigating displaced aggression in the cyber context.
A low cost brushless DC motor drive

This paper presents a low cost drive technique that allows three phase brushless DC machines to be driven without a DC link capacitor. The proposed technique uses a unique switching sequence and operates the machine without the intermediate DC link capacitor. The paper details the derivation of the switching sequence and presents a model for the motor drive in Matlab/Simulink environment. The performance of the technique is evaluated using a model of 320 W BLDC machine, which is operated in both torque and speed control modes, and simulated results indicate that the performance of the machine is comparable to existing techniques. The proposed technique is to implement, low in cost without a DC link capacitor, and would be attractive for low cost application where torque ripple is not a concern.
Enzyme kinetics at high enzyme concentration

We re-visit previous analyses of the classical Michaelis-Menten substrate-enzyme reaction and, with the aid of the reverse quasi-steady-state assumption, we challenge the approximation d[C]/dt ≈ 0 for the basic enzyme reaction at high enzyme concentration. For the first time, an approximate solution for the concentrations of the reactants uniformly valid in time is reported. Numerical simulations are presented to verify this solution. We show that an analytical approximation can be found for the reactants for each initial condition using the appropriate quasi-steady-state assumption. An advantage of the present formalism is that it provides a new procedure for fitting experimental data to determine reaction constants. Finally, a new necessary criterion is found that ensures the validity of the reverse quasi-steady-state assumption. This is verified numerically.