Miracle-dz/UniFAR-FTUs huggingface dataset:
The pMELTS: A revision of MELTS for improved calculation of phase relations and major element partitioning related to partial melting of the mantle to 3 GPa

We describe a newly calibrated model for the thermodynamic properties of magmatic silicate liquid. The new model, pMELTS, is based on MELTS [ Ghiorso and Sack, 1995 ] but has a number of improvements aimed at increasing the accuracy of calculations of partial melting of spinel peridotite. The pMELTS algorithm uses models of the thermodynamic properties of minerals and the phase equilibrium algorithms of MELTS, but the model for silicate liquid differs from MELTS in the following ways: (1) The new algorithm is calibrated from an expanded set of mineral‐liquid equilibrium constraints from 2439 experiments, 54% more than MELTS. (2) The new calibration includes mineral components not considered during calibration of MELTS and results in 11,394 individual mineral‐liquid calibration constraints (110% more than MELTS). Of these, 4924 statements of equilibrium are from experiments conducted at elevated pressure (200% more than MELTS). (3) The pMELTS model employs an improved liquid equation of state based on a third‐order Birch‐Murnaghan equation, calibrated from high‐pressure sink‐float and shockwave experiments to 10 GPa. (4) The new model employs a revised set of end‐member liquid components. The revised components were chosen to better span liquid composition‐space. Thermodynamic properties of these components are optimized as part of the mineral‐liquid calibration. Comparison of pMELTS to partial melting relations of spinel peridotite from experiments near 1 GPa indicates significant improvements relative to MELTS, but important outstanding problems remain. The pMELTS model accurately predicts oxide concentrations, including SiO2, for liquids from partial melting of MM3 peridotite at 1 GPa from near the solidus up to ∼25% melting. Compared to experiments, the greatest discrepancy is for MgO, for which the calculations are between 1 and 4% high. Temperatures required to achieve a given melt fraction match those of the experiments near the solidus but are ∼60°C high over much of the spinel lherzolite melting interval at this pressure. Much of this discrepancy can probably be attributed to overstabilization of clinopyroxene in pMELTS under these conditions. Comparison of pMELTS calculations to the crystallization and partial melting experiments of Falloon et al. [1999] shows excellent agreement but also suffers from exaggerated calculated stability of clinopyroxene. Finally, comparison of pMELTS calculations to the garnet peridotite experiments of Walter [1998] at 3–7 GPa reveals disparities between calculations and experiments that increase with pressure. The most prominent of these disparities is manifest as overprediction of the stability of garnet and underprediction of that of olivine. Part of this problem may be attributed to inadequacies in the Birch‐Murnaghan equation of state in reproducing the behavior of highly compressible liquids at high pressures and temperatures.
Matrine induces Akt/mTOR signalling inhibition‐mediated autophagy and apoptosis in acute myeloid leukaemia cells

Pharmacological modulation of autophagy has been referred to as a promising therapeutic strategy for cancer. Matrine, a main alkaloid extracted from Sophora flavescens Ait, has antitumour activity against acute myelocytic leukaemia (AML). Whether autophagy is involved in antileukaemia activity of matrine remains unobvious. In this study, we demonstrated that matrine inhibited cell viability and colony formation via inducing apoptosis and autophagy in AML cell lines HL‐60, THP‐1 and C1498 as well as primary AML cells. Matrine promoted caspase‐3 and PARP cleavage dose‐dependently. Matrine up‐regulated the level of LC3‐II and down‐regulated the level of SQSTM1/p62 in a dose‐dependent way, indicating that autophagy should be implicated in anti‐AML effect of matrine. Furthermore, the autophagy inhibitor bafilomycin A1 relieved the cytotoxicity of matrine by blocking the autophagic flux, while the autophagy promoter rapamycin enhanced the cytotoxicity of matrine. Additionally, matrine inhibited the phosphorylation of Akt, mTOR and their downstream substrates p70S6K and 4EBP1, which led to the occurrence of autophagy. In vivo study demonstrated that autophagy was involved in antileukaemia effect of matrine in C57BL/6 mice bearing murine AML cell line C1498, and the survival curves showed that mice did benefit from treatment with matrine. Collectively, our findings indicate that matrine exerts antitumour effect through apoptosis and autophagy, and the latter one might be a potential therapeutic strategy for AML.
Sleep patterns predictive of daytime challenging behavior in individuals with low‐functioning autism

Increased severity of problematic daytime behavior has been associated with poorer sleep quality in individuals with autism spectrum disorder. In this work, we investigate whether this relationship holds in a real‐time setting, such that an individual's prior sleep can be used to predict their subsequent daytime behavior. We analyzed an extensive real‐world dataset containing over 20,000 nightly sleep observations matched to subsequent challenging daytime behaviors (aggression, self‐injury, tantrums, property destruction and a challenging behavior index) across 67 individuals with low‐functioning autism living in two U.S. residential facilities. Using support vector machine classifiers, a statistically significant predictive relationship was found in 81% of individuals studied (P < 0.05). For all five behaviors examined, prediction accuracy increased up to approximately eight nights of prior sleep used to make the prediction, indicating that the behavioral effects of sleep may manifest on extended timescales. Accurate prediction was most strongly driven by sleep variability measures, highlighting the importance of regular sleep patterns. Our findings constitute an initial step towards the development of a real‐time monitoring tool to pre‐empt behavioral episodes and guide prophylactic treatment for individuals with autism. Autism Res 2018, 11: 391–403. © 2017 International Society for Autism Research, Wiley Periodicals, Inc.
Different contributions of nonmuscle myosin IIA and IIB to the organization of stress fiber subtypes in fibroblasts

We demonstrated that myosin IIA and IIB are essential for the formation of transverse arcs and ventral stress fibers, respectively. Furthermore, we illustrated the roles of both isoforms in lamellar flattening and also raised the possibility that actin filaments in ventral stress fibers are in a stretched conformation.
Neurocognitive and Educational Outcomes in Children and Adolescents with CKD: A Systematic Review and Meta-Analysis.

BACKGROUND AND OBJECTIVES Poor cognition can affect educational attainment, but the extent of neurocognitive impairment in children with CKD is not well understood. This systematic review assessed global and domain-specific cognition and academic skills in children with CKD and whether these outcomes varied with CKD stage. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS Electronic databases were searched for observational studies of children with CKD ages 21 years old or younger that assessed neurocognitive or educational outcomes. Risk of bias was assessed using a modified Newcastle-Ottawa scale. We used random effects models and expressed the estimates as mean differences with 95% confidence intervals stratified by CKD stage. RESULTS Thirty-four studies (25 cross-sectional, n=2095; nine cohort, n=991) were included. The overall risk of bias was high because of selection and measurement biases. The global cognition (full-scale intelligence quotient) of children with CKD was classified as low average. Compared with the general population, the mean differences (95% confidence intervals) in full-scale intelligence quotient were -10.5 (95% confidence interval, -13.2 to -7.72; all CKD stages, n=758), -9.39 (95% confidence interval, -12.6 to -6.18; mild to moderate stage CKD, n=582), -16.2 (95% confidence interval, -33.2 to 0.86; dialysis, n=23), and -11.2 (95% confidence interval, -17.8 to -4.50; transplant, n=153). Direct comparisons showed that children with mild to moderate stage CKD and kidney transplants scored 11.2 (95% confidence interval, 2.98 to 19.4) and 10.1 (95% confidence interval, -1.81 to 22.0) full-scale intelligence quotient points higher than children on dialysis. Children with CKD also had lower scores than the general population in executive function and memory (verbal and visual) domains. Compared with children without CKD, the mean differences in academic skills (n=518) ranged from -15.7 to -1.22 for mathematics, from -9.04 to -0.17 for reading, and from -14.2 to 2.53 for spelling. CONCLUSIONS Children with CKD may have low-average cognition compared with the general population, with mild deficits observed across academic skills, executive function, and visual and verbal memory. Limited evidence suggests that children on dialysis may be at greatest risk compared with children with mild to moderate stage CKD and transplant recipients.
Inferring Preferences from Choices Under Uncertainty

If a decision maker, in a world of uncertainty a la Anscombe and Aumann (1963), can choose acts according to some objective probability distribution (by throwing dice for instance) from any given set of acts, then there is no set of acts that allows an experimenter to test more than the Axiom of EUOL (that the DM evaluates objective lotteries with an expected utility function). In fact there is no (common) experimental design that allows an experimenter to test more than EUOL. For any decision problem (or set of decision problems), for any preference relation that satisfies the Axiom EUOL, and for any optimal choice (or collection of choices) given this preference relation, there is another preference relation that satisfies EUOL plus the Savage axioms, for which this choice is also optimal.
Directed Functional Networks in Alzheimer's Disease: Disruption of Global and Local Connectivity Measures

Techniques available in graph theory can be applied to signals recorded from human brain. In network analysis of EEG signals, the individual nodes are EEG sensor locations and the edges correspond to functional relations between them that are extracted from EEG time series. In this paper, we study EEG-based directed functional networks in Alzheimer's disease (AD). To this end, directed connectivity matrices of 25 AD patients and 26 healthy subjects are processed and a number of meaningful graph theory metrics are studied. Our data show that functional networks of AD brains have significantly reduced global connectivity in alpha and beta bands (P < 0.05). The AD brains have significantly higher local connectivity than healthy controls in alpha and beta bands. This decreased profile in global connectivity can be linked to compensatory increased local connectivity as a result of wide-spread decline in the long-range connections. We also study resiliency of brain networks against targeted attack to hub nodes and find that AD networks are less resilient than healthy brains in alpha and beta bands.
Miscibility, UV resistance, thermal degradation, and mechanical properties of PMMA/SAN blends and their composites with MWCNTs

Poly(methyl methacrylate)/poly(styrene-co-acrylonitrile) (PMMA/SAN) blends, with varying concentrations, were prepared by melt-mixing technique. The miscibility is ensured by fixing the acrylonitrile (AN) content of styrene acrylonitrile (SAN) as 25% by weight. The blends were transparent as well. The Fourier transform infrared spectroscopic (FTIR) studies did not reveal any specific interactions, supporting the well accepted ‘copolymer repulsion effect’ as the driving mechanism for miscibility. Addition of SAN increased the stability of PMMA towards ultraviolet (UV) radiations and thermal degradation. Incorporation of even 0.05% by weight of multi-walled carbon nanotubes (MWCNTs) significantly improved the UV absorbance and thermal stability. Moreover, the composites exhibited good strength and modulus. However, at higher concentrations of MWCNTs (0.5 and 1% by weight) the thermo-mechanical properties experienced deterioration, mainly due to the agglomeration of MWCNTs. It was observed that composites with 0.05% by weight of finely dispersed and well distributed MWCNTs provided excellent protection in most extreme climatic conditions. Thus, PMMA/SAN/MWCNTs composites can act as excellent light screens and may be useful, as cost-effective UV absorbers, in the outdoor applications. © 2016 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2016, 133, 43628.
Subclonal diversity arises early even in small colorectal tumours and contributes to differential growth fates

Objective and design The goal of the study was to determine whether the mutational profile of early colorectal polyps correlated with growth behaviour. The growth of small polyps (6–9 mm) that were first identified during routine screening of patients was monitored over time by interval imaging with CT colonography. Mutations in these lesions with known growth rates were identified by targeted next-generation sequencing. The timing of mutational events was estimated using computer modelling and statistical inference considering several parameters including allele frequency and fitness. Results The mutational landscape of small polyps is varied both within individual polyps and among the group as a whole but no single alteration was correlated with growth behaviour. Polyps carried 0–3 pathogenic mutations with the most frequent being in APC, KRAS/NRAS, BRAF, FBXW7 and TP53. In polyps with two or more pathogenic mutations, allele frequencies were often variable, indicating the presence of multiple populations within a single tumour. Based on computer modelling, detectable mutations occurred at a mean polyp size of 30±35 crypts, well before the tumour is of a clinically detectable size. Conclusions These data indicate that small colon polyps can have multiple pathogenic mutations in crucial driver genes that arise early in the existence of a tumour. Understanding the molecular pathway of tumourigenesis and clonal evolution in polyps that are at risk for progressing to invasive cancers will allow us to begin to better predict which polyps are more likely to progress into adenocarcinomas and which patients are at greater risk of developing advanced disease.
Structure and function of the archaeal response regulator CheY

Significance Motility is a key feature for the success of microorganisms, as it allows the movement to optimal growth environments. Bacteria and archaea possess filamentous motility structures capable of rotation. However, both molecular machines consist of fundamentally different proteins and lack structural similarity. Intriguingly, some archaea possess the chemotaxis system. This system allows bacteria to travel along chemical gradients and is dependent on interaction of the response regulator CheY with the motor of the motility structure. In this study, we map the changes of the CheY protein structure required for its interaction with components of the archaeal motility machinery. Motility is a central feature of many microorganisms and provides an efficient strategy to respond to environmental changes. Bacteria and archaea have developed fundamentally different rotary motors enabling their motility, termed flagellum and archaellum, respectively. Bacterial motility along chemical gradients, called chemotaxis, critically relies on the response regulator CheY, which, when phosphorylated, inverses the rotational direction of the flagellum via a switch complex at the base of the motor. The structural difference between archaellum and flagellum and the presence of functional CheY in archaea raises the question of how the CheY protein changed to allow communication with the archaeal motility machinery. Here we show that archaeal CheY shares the overall structure and mechanism of magnesium-dependent phosphorylation with its bacterial counterpart. However, bacterial and archaeal CheY differ in the electrostatic potential of the helix α4. The helix α4 is important in bacteria for interaction with the flagellar switch complex, a structure that is absent in archaea. We demonstrated that phosphorylation-dependent activation, and conserved residues in the archaeal CheY helix α4, are important for interaction with the archaeal-specific adaptor protein CheF. This forms a bridge between the chemotaxis system and the archaeal motility machinery. Conclusively, archaeal CheY proteins conserved the central mechanistic features between bacteria and archaea, but differ in the helix α4 to allow binding to an archaellum-specific interaction partner.
Discrepancies between modified Medical Research Council dyspnea score and COPD assessment test score in patients with COPD

Background and objective According to the Global Initiative for Chronic Obstructive Lung Disease (GOLD) guidelines, either a modified Medical Research Council (mMRC) dyspnea score of ≥2 or a chronic obstructive pulmonary disease (COPD) assessment test (CAT) score of ≥10 is considered to represent COPD patients who are more symptomatic. We aimed to identify the ideal CAT score that exhibits minimal discrepancy with the mMRC score. Methods A receiver operating characteristic curve of the CAT score was generated for an mMRC scores of 1 and 2. A concordance analysis was applied to quantify the association between the frequencies of patients categorized into GOLD groups A–D using symptom cutoff points. A κ-coefficient was calculated. Results For an mMRC score of 2, a CAT score of 15 showed the maximum value of Youden’s index with a sensitivity and specificity of 0.70 and 0.66, respectively (area under the receiver operating characteristic curve [AUC] 0.74; 95% confidence interval [CI], 0.70–0.77). For an mMRC score of 1, a CAT score of 10 showed the maximum value of Youden’s index with a sensitivity and specificity of 0.77 and 0.65, respectively (AUC 0.77; 95% CI, 0.72–0.83). The κ value for concordance was highest between an mMRC score of 1 and a CAT score of 10 (0.66), followed by an mMRC score of 2 and a CAT score of 15 (0.56), an mMRC score of 2 and a CAT score of 10 (0.47), and an mMRC score of 1 and a CAT score of 15 (0.43). Conclusion A CAT score of 10 was most concordant with an mMRC score of 1 when classifying patients with COPD into GOLD groups A–D. However, a discrepancy remains between the CAT and mMRC scoring systems.
Where Are the M Dwarf Disks Older Than 10 Million Years?

We present 11.7 μm observations of nine late-type dwarfs obtained at the Keck I 10 m telescope in 2002 December and 2003 April. Our targets were selected for their youth or apparent IRAS 12 μm excess. For all nine sources, excess infrared emission is not detected. We find that stellar wind drag can dominate the circumstellar grain removal and plausibly explain the dearth of M dwarf systems older than 10 Myr with currently detected infrared excesses. We predict that M dwarfs possess fractional infrared excesses on the order of LIR/L* ~ 10-6 and that this may be detectable with future efforts.
Repetitive DNAs and shrink genomes: A chromosomal analysis in nine Columbidae species (Aves, Columbiformes)

Abstract An extensive karyotype variation is found among species belonging to the Columbidae family of birds (Columbiformes), both in diploid number and chromosomal morphology. Although clusters of repetitive DNA sequences play an important role in chromosomal instability, and therefore in chromosomal rearrangements, little is known about their distribution and amount in avian genomes. The aim of this study was to analyze the distribution of 11 distinct microsatellite sequences, as well as clusters of 18S rDNA, in nine different Columbidae species, correlating their distribution with the occurrence of chromosomal rearrangements. We found 2n values ranging from 76 to 86 and nine out of 11 microsatellite sequences showed distinct hybridization signals among the analyzed species. The accumulation of microsatellite repeats was found preferentially in the centromeric region of macro and microchromosomes, and in the W chromosome. Additionally, pair 2 showed the accumulation of several microsatellites in different combinations and locations in the distinct species, suggesting the occurrence of intrachromosomal rearrangements, as well as a possible fission of this pair in Geotrygon species. Therefore, although birds have a smaller amount of repetitive sequences when compared to other Tetrapoda, these seem to play an important role in the karyotype evolution of these species.
Muscle morphology of the vastus lateralis is strongly related to ergometer performance, sprint capacity and endurance capacity in Olympic rowers

ABSTRACT Rowers need to combine high sprint and endurance capacities. Muscle morphology largely explains muscle power generating capacity, however, little is known on how muscle morphology relates to rowing performance measures. The aim was to determine how muscle morphology of the vastus lateralis relates to rowing ergometer performance, sprint and endurance capacity of Olympic rowers. Eighteen rowers (12♂, 6♀, who competed at 2016 Olympics) performed an incremental rowing test to obtain maximal oxygen consumption, reflecting endurance capacity. Sprint capacity was assessed by Wingate cycling peak power. M. vastus lateralis morphology (volume, physiological cross-sectional area, fascicle length and pennation angle) was derived from 3-dimensional ultrasound imaging. Thirteen rowers (7♂, 6♀) completed a 2000-m rowing ergometer time trial. Muscle volume largely explained variance in 2000-m rowing performance (R2 = 0.85), maximal oxygen consumption (R2 = 0.65), and Wingate peak power (R2 = 0.82). When normalized for differences in body size, maximal oxygen consumption and Wingate peak power were negatively related in males (r = −0.94). Fascicle length, not physiological cross-sectional area, attributed to normalized peak power. In conclusion, vastus lateralis volume largely explains variance in rowing ergometer performance, sprint and endurance capacity. For a high normalized sprint capacity, athletes may benefit from long fascicles rather than a large physiological cross-sectional area.
Rates of preterm birth following antenatal maternal exposure to severe life events: a population-based cohort study.

BACKGROUND Preterm birth and other pregnancy complications have been linked to maternal stress during pregnancy. We investigated the association between maternal exposure to severe life events and risk of preterm birth. METHODS Mothers of all singleton live births (n = 1.35 million births) in Denmark between 1 January 1979 and 31 December 2002 were linked to data on their children, parents, siblings and partners. We defined exposure as death or serious illness in close relatives in the first or second trimesters or in the 6 months before conception. Log-linear binomial regression was used to estimate the effect of exposure on preterm birth, very preterm birth and extremely preterm birth. RESULTS There were 58 626 (4.34%) preterm births (<37 weeks), 11 732 (0.87%) very preterm births and 3288 (0.24%) extremely preterm births in the study cohort. Severe life events in close relatives in the 6 months before conception increased the risk of preterm birth by 16% (relative risk, RR = 1.16, [95% CI: 1.08-1.23]). Severe life events in older children in the 6 months before conception increased the risk of preterm birth by 23% (RR = 1.23, [95% CI: 1.02-1.49]) and the risk of very preterm birth by 59% (RR = 1.59, [95% CI: 1.08-2.35]). CONCLUSIONS Our population-based cohort study suggests that maternal exposure to severe life events, particularly in the 6 months before pregnancy, may increase the risk of preterm and very preterm birth.