Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Transcriptome Analysis of the Pacific Oyster Crassostrea gigas Characterized by Shell Colors: Identification of Genetic Bases Potentially Involved in Pigmentation

Background Shell color polymorphisms of Mollusca have contributed to development of evolutionary biology and population genetics, while the genetic bases and molecular mechanisms underlying shell pigmentation are poorly understood. The Pacific oyster (Crassostrea gigas) is one of the most important farmed oysters worldwide. Through successive family selection, four shell color variants (white, golden, black and partially pigmented) of C. gigas have been developed. To elucidate the genetic mechanisms of shell coloration in C. gigas and facilitate the selection of elite oyster lines with desired coloration patterns, differentially expressed genes (DEGs) were identified among the four shell color variants by RNA-seq. Results Digital gene expression generated over fifteen million reads per sample, producing expression data for 28,027 genes. A total number of 2,645 DEGs were identified from pair-wise comparisons, of which 432, 91, 43 and 39 genes specially were up-regulated in white, black, golden and partially pigmented shell of C. gigas, respectively. Three genes of Abca1, Abca3 and Abcb1 which belong to the ATP-binding cassette (ABC) transporters super-families were significantly associated with white shell formation. A tyrosinase transcript (CGI_10008737) represented consistent up-regulated pattern with golden coloration. We proposed that white shell variant of C. gigas could employ “endocytosis” to down-regulate notch level and to prevent shell pigmentation. Conclusion This study discovered some potential shell coloration genes and related molecular mechanisms by the RNA-seq, which would provide foundational information to further study on shell coloration and assist in selective breeding in C. gigas.
Concentration, spin and shape of dark matter haloes as a function of the cosmological model: WMAP1, WMAP3 and WMAP5 results

We investigate the effects of changes in the cosmological parameters between the Wilkinson Microwave Anisotropy Probe (WMAP) 1st, 3rd and 5th year results on the structure of dark matter haloes. We use a set of simulations that cover five decades in halo mass ranging from the scales of dwarf galaxies (V c ≈ 30 km s -1 ) to clusters of galaxies (V c ≈ 1000 km s -1 ). We find that the concentration mass relation is a power law in all three cosmologies. However, the slope is shallower and the zero-point is lower moving from WMAP1 to WMAP5 to WMAP3. For haloes of mass log M 200 /[h -1 M ⊙ ] = 10, 12 and 14 the differences in the concentration parameter between WMAP1 and WMAP3 are a factor of 1.55,1.41 and 1.29, respectively. As we show, this brings the central densities of dark matter haloes in good agreement with the central densities of dwarf and low surface brightness galaxies inferred from their rotation curves, for both the WMAP3 and WMAP5 cosmologies. We also show that none of the existing toy models for the concentration-mass relation can reproduce our simulation results over the entire range of masses probed. In particular, the model of Bullock et al. fails at the higher mass end (M ≥ 10 13 h-1 M ⊙ ), while the NFW model of Navarro, Frenk and White fails dramatically at the low-mass end (M ≤ 10 12 h -1 M ⊙ ). We present a new model, based on a simple modification of that of Bullock et al., which reproduces the concentration-mass relations in our simulations over the entire range of masses probed (10 10 ≤ M ≤ 10 15 h -1 M ⊙ ). Haloes in the WMAP3 cosmology (at a fixed mass) are more flatted compared to the WMAP1 cosmology, with a medium to long axis ration reduced by ≈ 0 per cent. Finally, we show that the distribution of halo spin parameters is the same for all three cosmologies.
Phylogeography of Ramalina menziesii, a widely distributed lichen‐forming fungus in western North America

The complex topography and climate history of western North America offer a setting where lineage formation, accumulation and migration have led to elevated inter‐ and intraspecific biodiversity in many taxa. Here, we study Ramalina menziesii, an epiphytic lichenized fungus with a range encompassing major ecosystems from Baja California to Alaska to explore the predictions of two hypotheses: (i) that the widespread distribution of R. menziesii is due to a single migration episode from a single lineage and (ii) that the widespread distribution is due to the formation and persistence of multiple lineages structured throughout the species' range. To obtain evidence for these predictions, we first construct a phylogenetic tree and identify multiple lineages structured throughout the species' range – some ancient ones that are localized and other more recent lineages that are widely distributed. Second, we use an isolation with migration model to show that sets of ecoregion populations diverged from each other at different times, demonstrating the importance of historical and current barriers to gene flow. Third, we estimated migration rates among ecoregions and find that Baja California populations are relatively isolated, that inland California ecoregion populations do not send out emigrants and that migration out of California coastal and Pacific Northwest populations into inland California ecoregions is high. Such intraspecific geographical patterns of population persistence and dispersal both contribute to the wide range of this genetically diverse lichen fungus and provide insight into the evolutionary processes that enhance species diversity of the California Floristic Province.
Large Scale Parallel Computing and Scalability Study for Surface Combatant Static Maneuver and Straight Ahead Conditions Using CFDShip-Iowa

Scalability studies are performed for CFDShip-Iowa URANS/DES curvilinear and Cartesian grid solvers and calculations are performed using largest grids to date. Verification and validation study is performed for V4-DES solution for DTMB 5415 with bilge keels at 20 static drift using up to 250M grid. The instantaneous and mean flow field is analyzed to identify flow separation patterns, vortical structures and associated instabilities. V6 RANS solution of 5415 bare hull at straight ahead condition on 276M grid is compared with benchmark V4-blended k-ω/k-, V4-wallfunction, V4-DES results and EFD data to identify limitations of wall-layer modeling using WF for immersed boundary method.
Therapeutic Failures with Miconazole

A retrospective review of therapeutic failures of miconazole in three patients is presented. Miconazole, a new imidazole derivative, is a broad-spectrum antifungal agent purportedly effective topically, orally, and parenterally against a number of species of fungi. Three patients with the following culturally proven deep fungal infections were treated with miconazole: (i) destructive arthritis (Sporothrix schenckii), (ii) meningoencephalitis (Cryptococcus neoformans), and (iii) disseminated aspergillosis (Aspergillus fumigatus). All the organisms were susceptible in vitro to 1.56 μg or less of miconazole per ml using a broth dilution technique. In each patient, miconazole administered intravenously in dosages of 30 mg/kg per day failed to control or eradicate infection. Miconazole serum levels ranged from <0.5 to 4.35 μg/ml as determined by radial diffusion bioassay. Cerebrospinal fluid levels were virtually undetectable. In one patient (C. neoformans), miconazole was given intraventricularly in doses of 15 mg without response. Therapeutic failures were attributed to suboptimal body fluid levels of miconazole. The reason(s) for such low levels of activity was not clear, but may have been poor penetrance into tissues, in vitro inactivation, and/or unusually rapid excretion. Untoward reactions from miconazole included fever, chills, nausea, vomiting, and phlebitis.
Efficient Simulation of Solution Curves and Bifurcation Loci in Injection-Locked Oscillators

A new method is presented for the two-level harmonic-balance analysis of multivalued synchronized solution curves in injection-locked oscillators. The method is based on the extraction of a nonlinear admittance function, which describes the circuit response from the input source terminals. It does not require any optimization or parameter switching procedures, this constituting a significant advantage compared with previous analysis techniques. With additional mathematical conditions, it enables a straightforward determination of the turning point and Hopf bifurcation loci that delimit the stable injection-locked operation bands. The codimension two bifurcation point at which the turning point and Hopf bifurcation loci merge is analyzed in detail, as well as the saddle-connection locus. As it is shown, a second intersection of the saddle-connection locus with the turning point locus acts as a boundary between synchronization points and points associated with jumps and hysteresis. The likely observation of chaotic solutions in the neighborhood of the saddle-connection locus is discussed too. The techniques have been validated by application to several injection-locked oscillators, obtaining good agreement with the experimental results.
Crack diagnostics in beams using wavelets, kurtosis and skewness

This paper presents a diagnostic technique using wavelets, kurtosis and skewness for detecting crack location and severity in beams. The first three mode shapes of a damaged beam are used for detecting crack locations in beams with varying boundary conditions. Damage due to an edge-crack is modelled by a conventional macroscopic torsional spring element. Multiple families of wavelets with varying scales and vanishing moments are used so as to distinguish between their ability to detect crack locations by using the mode shapes of the damaged beam. Crack detection is followed by determination of the crack size by using statistical measures of the mode shapes such as kurtosis and skewness. These two measures are highly sensitive to small changes in mode shapes resulting from crack initiation or crack propagation, and have been used in other fields of damage detection. Several simulations are presented to showcase the application of the proposed technique, and to highlight the differences between multiple wavelets and the parameters associated with the wavelets. The proposed diagnostic technique is also tested for robustness by adding noise to the mode shapes. The simulation results and preliminary experimental results indicate that the statistical measures of kurtosis and skewness can be used in conjunction with wavelets in order to provide a viable crack diagnostic technique for beam structures.
Dairy Product Consumption and Risk of Non-Hodgkin Lymphoma: A Meta-Analysis

Many epidemiologic studies have explored the association between dairy product consumption and the risk of non-Hodgkin lymphoma (NHL), but the results remain controversial. A literature search was performed in PubMed, Web of Science and Embase for relevant articles published up to October 2015. Pooled relative risks (RRs) with 95% confidence intervals (CIs) were calculated with a random-effects model. The dose-response relationship was assessed by restricted cubic spline. A total of 16 articles were eligible for this meta-analysis. The pooled RRs (95% CIs) of NHL for the highest vs. lowest category of the consumption of total dairy product, milk, butter, cheese, ice cream and yogurt were 1.20 (1.02, 1.42), 1.41 (1.08, 1.84), 1.31 (1.04, 1.65), 1.14 (0.96, 1.34), 1.57 (1.11, 2.20) and 0.78 (0.54, 1.12), respectively. In subgroup analyses, the positive association between total dairy product consumption and the risk of NHL was found among case-control studies (RR = 1.41, 95% CI: 1.17–1.70) but not among cohort studies (RR = 1.02, 95% CI: 0.88–1.17). The pooled RRs (95% CIs) of NHL were 1.21 (1.01, 1.46) for milk consumption in studies conducted in North America, and 1.24 (1.09, 1.40) for cheese consumption in studies that adopted validated food frequency questionnaires. In further analysis of NHL subtypes, we found statistically significant associations between the consumption of total dairy product (RR = 1.73, 95% CI: 1.22–2.45) and milk (RR = 1.49, 95% CI: 1.08–2.06) and the risk of diffuse large B-cell lymphoma. The dose-response analysis suggested that the risk of NHL increased by 5% (1.05 (1.00–1.10)) and 6% (1.06 (0.99–1.13)) for each 200 g/day increment of total dairy product and milk consumption, respectively. This meta-analysis suggested that dairy product consumption, but not yogurt, may increase the risk of NHL. More prospective cohort studies that investigate specific types of dairy product consumption are needed to confirm this conclusion.
The Validity of Phallometric Assessment With Rapists: Comments on Looman & Marshall (2005)

In a recent article Looman and Marshall (2005) questioned the validity of phallometric assessment of rapists based on the results of a study of incarcerated rapists and child molesters. In this commentary we offer (1) a critique of the methods used and conclusions reached by Looman and Marshall and (2) a discussion of important methodological issues relevant to phallometry. We conclude that the correct inference from Looman and Marshall's study is that rapists, as a group, show a pattern of sexual arousal to audiotaped scenarios of coercive and non-coercive sex that significantly differs from the pattern of groups of non-sex offenders, in agreement with the general literature on this question.
Cystatin-C is an independent prognostic factor for survival in multiple myeloma and is reduced by bortezomib administration

Renal impairment is a common complication of multiple myeloma, and serum cystatin-C is considered an accurate marker of glomerular filtration rate. The findings of this study suggest that serum cystatin-C is not only a sensitive marker of renal impairment, but also reflects tumor burden and is of prognostic value in multiple myeloma. Background Renal impairment is a common complication of multiple myeloma. Cystatin-C is considered an accurate marker of glomerular filtration rate in several renal disorders. Microarray analysis has revealed that cystatin-C is one of the most highly up-regulated genes in multiple myeloma. The aim of this study was to evaluate the serum levels of cystatin-C in myeloma patients, explore possible correlations with clinical data, including survival, and assess the effect of bortezomib on cystatin-C in relapsed multiple myeloma. Design and Methods We measured serum cystatin-C in 157 newly diagnosed, previously untreated myeloma patients, in 28 patients with relapsed disease pre- and post-bortezomib therapy and in 52 healthy controls, using a latex particle-enhanced nephelometric immunoassay. Results In newly diagnosed patients, cystatin-C was elevated and showed strong correlations with advanced ISS stage, extensive bone disease, high β2-microglobulin, high serum creatinine, and low creatinine clearance. Multivariate analysis revealed that only cystatin-C and lactate dehydrogenase had an independent prognostic impact on patients’ survival. The combination of cystatin-C and lactate dehydrogenase revealed three prognostic groups of patients: a high-risk group (both elevated cystatin-C and lactate dehydrogenase) with a median survival of 24 months, an intermediate-risk group (elevated cystatin-C or elevated lactate dehydrogenase) with a median survival of 48 months and a low-risk group (both low cystatin-C and lactate dehydrogenase) in which median survival has not yet been reached (p<0.001). Cystatin-C could also identify a subset of ISS-II patients with worse outcome. Relapsed patients had higher cystatin-C levels even compared to newly diagnosed patients. Treatment with bortezomib produced a significant reduction of cystatin-C, mainly in responders. Conclusions Serum cystatin-C is not only a sensitive marker of renal impairment but also reflects tumor burden and is of prognostic value in myeloma. Its reduction after treatment with bortezomib reflects bortezomib’s anti-myeloma activity and possibly bortezomib’s direct effect on renal function.
Linguistic Innovations and Interactional Features of Casual Online Communication in Japanese

This study explores the linguistic and interactional properties of informal asynchronous computer-mediated communication (CMC) in Japanese. Using Bulletin Board Systems (BBS) messages as the primary source of data, the study identifies innovative uses of kanji, other scripts and punctuation, and examines the incorporation of such informal spoken features as final particles. Young Japanese BBS users are found to employ colloquial language online as if conversing offline, and interact appropriately with their fellow participants in their Internet community.
A new approach to the canonical s-process model

A new approach to the canonical s-process model is proposed. It is based on an optimized superposition of s-process events at different temperatures and neutron densities which aims at reproducing the solar system abundances as precisely as possible. An iterative procedure enables us to assign unambiguously to each event contributing to the solar s-abundance curve a statistical weight which in turn determines the distribution of neutron exposures, temperatures and neutron densities responsible for the production of the s-elements. It is shown that the abundance predictions of the multi-event model are in good agreement with those of the widely used exponential model, at least when a restricted range of thermodynamic conditions is considered.When enlarging the range of thermodynamic conditions in which the s-process is allowed to develop, a larger set of nuclei appear to be produced in solar quantity by the s-process. The impact of the astrophysical and nuclear physics uncertainties on the residual r-abundance distribution representative of the solar system is analyzed.
Prevention of Diabetes Self-Management Program (PREDIAS): Effects on Weight, Metabolic Risk Factors, and Behavioral Outcomes

OBJECTIVE To evaluate the efficacy of the group program PREDIAS for diabetes prevention. RESEARCH DESIGN AND METHODS PREDIAS consists of 12 lessons and aims at lifestyle modification. The control group received written information about diabetes prevention. In this study, a total of 182 persons with an elevated diabetes risk participated (aged 56.3 ± 10.1 years, 43% female, and BMI 31.5 ± 5.3 kg/m2). RESULTS After 12 months, weight loss was significantly higher (P = 0.001) in PREDIAS than in the control group (−3.8 ± 5.2 vs. −1.4 ± 4.09 kg). There were also significant effects (P = 0.001) on fasting glucose (control group 1.8 ± 13.1 mg/dl vs. PREDIAS −4.3 ± 11.3 mg/dl), duration of physical activity per week (control group 17.9 ± 63.8 min vs. PREDIAS 46.6 ± 95.5 min; P = 0.03), and eating behavior. CONCLUSIONS PREDIAS significantly modified lifestyle factors associated with an elevated diabetes risk.
Microdialysis of rat skeletal muscle and adipose tissue: dynamics of the interstitial glucose pool.

Microdialysis was evaluated as a method for studying glucose metabolism in skeletal muscle. Dialysis probes (0.5 x 10 mm) were perfused at 0.5 or 1.0 microliter min-1. Based upon perfusion with glucose, the muscle interstitial glucose concentration was estimated to be 6.9 +/- 0.3 mM (n = 14), which was not significantly different from the blood glucose level. With insulin infusion (1200 mU kg-1 body wt i.v.), the insulin-induced change in the glucose concentration of the interstitial space of muscle was of equal magnitude to that of blood and adipose tissue. In spite of this, when the perfusion medium was not supplemented with glucose, the glucose concentration decreased more in skeletal muscle dialysates (to 36.7 +/- 4.9% of the initial level) than in blood (to 29.7 +/- 5.0%) but less than in adipose tissue (to 17.7 +/- 4.9% of the initial level) (P < 0.05). The results indicate that these differences are due to tissue-specific differences in the dynamic balance between the supply to, and removal from, the interstitial glucose pool. This balance is revealed as a result of the constant glucose drainage by the microdialysis probe. The present results show that, in skeletal muscle, increases in glucose uptake occur with a concomitant increase in tissue blood flow as revealed by the microdialysis ethanol technique, whereas in adipose tissue the glucose uptake increases in the absence of a corresponding increase in blood flow.
Towards Evaluating the Robustness of Neural Networks

Neural networks provide state-of-the-art results for most machine learning tasks. Unfortunately, neural networks are vulnerable to adversarial examples: given an input x and any target classification t, it is possible to find a new input x' that is similar to x but classified as t. This makes it difficult to apply neural networks in security-critical areas. Defensive distillation is a recently proposed approach that can take an arbitrary neural network, and increase its robustness, reducing the success rate of current attacks' ability to find adversarial examples from 95% to 0.5%. In this paper, we demonstrate that defensive distillation does not significantly increase the robustness of neural networks by introducing three new attack algorithms that are successful on both distilled and undistilled neural networks with 100% probability. Our attacks are tailored to three distance metrics used previously in the literature, and when compared to previous adversarial example generation algorithms, our attacks are often much more effective (and never worse). Furthermore, we propose using high-confidence adversarial examples in a simple transferability test we show can also be used to break defensive distillation. We hope our attacks will be used as a benchmark in future defense attempts to create neural networks that resist adversarial examples.
Submillimeter CO Emission from Shock-heated Gas in the L1157 Outflow

We present the CO J = 6-5, 4-3, and 3-2 spectra from the blueshifted gas of the outflow driven by the low-mass class 0 protostar in the L1157 dark cloud. Strong submillimeter CO emission lines with Tmb > 30 K have been detected at 63'' (~0.13 pc) south from the protostar. It is remarkable that the blue wings in the submillimeter lines are stronger by a factor of 3-4 than that of the CO J = 1-0 emission line. The CO line ratios suggest that the blueshifted lobe of this outflow consists of moderately dense gas of n(H2) = (1-3) × 104 cm-3 heated to Tkin = 50-170 K. It is also suggested that the kinetic temperature of the outflowing gas increases from ~80 K near the protostar to ~170 K at the shocked region in the lobe center, toward which the largest velocity dispersion of the CO emission is observed. A remarkable correlation between the kinetic temperature and velocity dispersion of the CO emission along the lobe provides us with direct evidence that the molecular gas at the head of the jet-driven bow shock is indeed heated kinematically. The lower temperature of ~80 K measured at the other shocked region near the end of the lobe is explained if this shock is in a later evolutionary stage, in which the gas has been cooled mainly through radiation of the CO rotational lines.
Ultrahigh Brilliance Multi-MeV γ-Ray Beams from Nonlinear Relativistic Thomson Scattering.

We report on the generation of a narrow divergence (θ_{γ}<2.5 mrad), multi-MeV (E_{max}≈18 MeV) and ultrahigh peak brilliance (>1.8×10^{20} photons s^{-1} mm^{-2} mrad^{-2} 0.1% BW) γ-ray beam from the scattering of an ultrarelativistic laser-wakefield accelerated electron beam in the field of a relativistically intense laser (dimensionless amplitude a_{0}≈2). The spectrum of the generated γ-ray beam is measured, with MeV resolution, seamlessly from 6 to 18 MeV, giving clear evidence of the onset of nonlinear relativistic Thomson scattering. To the best of our knowledge, this photon source has the highest peak brilliance in the multi-MeV regime ever reported in the literature.