Miracle-dz/UniFAR-FTUs huggingface dataset:
Introduction to the special focus issue on the impact of diet on gut microbiota composition and function and future opportunities for nutritional modulation of the gut microbiome to improve human health

ABSTRACT Over the past decade, application of culture-independent, next generation DNA sequencing has dramatically enhanced our understanding of the composition of the gut microbiome and its association with human states of health and disease. Host genetics, age, and environmental factors such as where and who you live with, use of pre-, pro- and antibiotics, exercise and diet influence the short- and long-term composition of the microbiome. Dietary intake is a key determinant of microbiome composition and diversity and studies to date have linked long-term dietary patterns as well as short-term dietary interventions to the composition and diversity of the gut microbiome. The goal of this special focus issue was to review the role of diet in regulating the composition and function of the gut microbiota across the lifespan, from pregnancy to old age. Overall dietary patterns, as well as perturbations such as undernutrition and obesity, as well as the effects of dietary fiber/prebiotics and fat composition are explored.
Displacement Ductility Capacity Of Fixed-Head Piles

This study performs a parametric study on the displacement ductility capacity of a fixed-head pile. The Winkler-beam model is employed, in which both the soil nonlinearity and pile nonlinearity are adequately considered. In this parametric study, the pile is regarded as a limited ductility structure which conditionally allows the pile deformation to enter the plastic range during loadings. The analysis variables include the axial force, the pile diameter, the longitudinal reinforcement ratio, and the soil stiffness. The relationships of the displacement ductility capacity of the pile to the curvature ductility capacity and to the over-strength ratio of the pile section are examined through a large number of pushover analyses. Results show that the axial force level, the pile diameter, and the steel ratio remarkably influence the displacement ductility capacity of a fixed-head pile. Their influence can be represented mainly by the over-strength ratio of the pile section. Besides, the influence of the soil stiffness is insignificant: the displacement ductility capacity slightly decreases with the soil stiffness.
A referenceless Nyquist ghost correction workflow for echo planar imaging of hyperpolarized [1‐13C]pyruvate and [1‐13C]lactate

Single‐shot echo planar imaging (EPI), which allows an image to be acquired using a single excitation pulse, is used widely for imaging the metabolism of hyperpolarized 13C‐labelled metabolites in vivo as the technique is rapid and minimizes the depletion of the hyperpolarized signal. However, EPI suffers from Nyquist ghosting, which normally is corrected for by acquiring a reference scan. In a dynamic acquisition of a series of images, this results in the sacrifice of a time point if the reference scan involves a full readout train with no phase encoding. This time penalty is negligible if an integrated navigator echo is used, but at the cost of a lower signal‐to‐noise ratio (SNR) as a result of prolonged T2* decay. We describe here a workflow for hyperpolarized 13C EPI that requires no reference scan. This involves the selection of a ghost‐containing background from a 13C image of a single metabolite at a single time point, the identification of phase correction coefficients that minimize signal in the selected area, and the application of these coefficients to images acquired at all time points and from all metabolites. The workflow was compared in phantom experiments with phase correction using a 13C reference scan, and yielded similar results in situations with a regular field of view (FOV), a restricted FOV and where there were multiple signal sources. When compared with alternative phase correction methods, the workflow showed an SNR benefit relative to integrated 13C reference echoes (>15%) or better ghost removal relative to a 1H reference scan. The residual ghosting in a slightly de‐shimmed B0 field was 1.6% using the proposed workflow and 3.8% using a 1H reference scan. The workflow was implemented with a series of dynamically acquired hyperpolarized [1‐13C]pyruvate and [1‐13C]lactate images in vivo, resulting in images with no observable ghosting and which were quantitatively similar to images corrected using a 13C reference scan.
How small could a pup sound? The physical bases of signaling body size in harbor seals

Abstract Vocal communication is a crucial aspect of animal behavior. The mechanism which most mammals use to vocalize relies on three anatomical components. First, air overpressure is generated inside the lower vocal tract. Second, as the airstream goes through the glottis, sound is produced via vocal fold vibration. Third, this sound is further filtered by the geometry and length of the upper vocal tract. Evidence from mammalian anatomy and bioacoustics suggests that some of these three components may covary with an animal’s body size. The framework provided by acoustic allometry suggests that, because vocal tract length (VTL) is more strongly constrained by the growth of the body than vocal fold length (VFL), VTL generates more reliable acoustic cues to an animal’s size. This hypothesis is often tested acoustically but rarely anatomically, especially in pinnipeds. Here, we test the anatomical bases of the acoustic allometry hypothesis in harbor seal pups Phoca vitulina. We dissected and measured vocal tract, vocal folds, and other anatomical features of 15 harbor seals post-mortem. We found that, while VTL correlates with body size, VFL does not. This suggests that, while body growth puts anatomical constraints on how vocalizations are filtered by harbor seals’ vocal tract, no such constraints appear to exist on vocal folds, at least during puppyhood. It is particularly interesting to find anatomical constraints on harbor seals’ vocal tracts, the same anatomical region partially enabling pups to produce individually distinctive vocalizations.
Seasoning ingredients in a medium–fat diet regulate lipid metabolism in peripheral tissues via the hypothalamic–pituitary axis in growing rats

Abstract We fed rats noodle (N) -diet containing 30 wt. % instant noodle with a 26% fat-to-energy ratio for 30 days (N-group). Compared with rats that were fed the same amount of nutrients (C-group), the N-group showed lower liver triacylglycerol levels and higher fecal cholesterol levels. We then analyzed transcriptome of the hypothalamic–pituitary (HP), the liver and the white adipose tissue (WAT). Thyroid stimulating hormone (Tshb), and its partner, glycoprotein hormone genes were up-regulated in the HP of N-group. Sterol regulatory element binding transcription factors were activated in the liver of N-group, while an up-regulation of the angiogenic signal occurred in the WAT of N-group. N-group showed higher urine noradrenaline (NA) level suggesting that these tissue signals are regulated by NA and Tshb. The N-diet contains 0.326 wt. % glutamate, 0.00236 wt. % 6-shogaol and Maillard reaction products. Our results suggest that these ingredients may affect lipid homeostasis via the HP axis. Summary of physiological pathway accelerated by seasoning ingredients in instant noodle.
Center of Pressure and Perceived Stability in Basketball Shoes With Soft and Hard Midsoles.

This study aimed to investigate the effects of varying midsole hardness on center of pressure (COP) and perceived stability during basketball-specific tasks, as well as the correlation between COP and perception measurements. A total of 20 male basketball players performed 45° cutting and layup while wearing basketball shoes with soft and hard midsoles. COP trajectories were obtained from the Pedar insole system. Stability perceptions at the forefoot and rearfoot were assessed using 150-mm visual analogue scales. Results indicated greater COP mediolateral deviations in soft midsole compared with hard midsole during layup (soft: 16.6 [4.7] mm, hard: 15.8 [4.6] mm, P = .03) but not 45° cutting (soft: 15.7 [5.9] mm, hard: 15.8 [5.6] mm, P = .60). While 16 out of 20 participants preferred soft midsole, no significant difference in visual analogue scale ratings was found between shoes for both tested movements. There was no significant correlation between COP and perceived stability during layup or 45° cutting. In conclusion, midsole hardness of basketball shoes did not consistently affect mediolateral stability of the foot during 45° cutting and layup. Subjective perception alone cannot be used to indicate mediolateral deviation of the foot when executing basketball-specific maneuvers.
Stable Specification Searches in Structural Equation Modeling Using a Multi-objective Evolutionary Algorithm

Structural equation modelling (SEM) is a statistical technique for testing and estimating causal relations using a combination of statistical data and qualitative causal assumptions [1]– [3]. SEM allows for both confirmatory and exploratory modeling. In exploratory modeling one starts with the specification of a hypothesis, which is tested against measurements by measuring how well the model fits the data. In exploratory modeling one searches the model space without stating a prior hypothesis. Exploratory modeling has the benefit that no prior background knowledge is needed, but has the drawback that the model search space grows super-exponentially since for n variables the number of SEM models is n4n. In the present paper we use an evolutionary algorithm approach to deal with the large search space in order to obtain good solutions within a reasonable amount of computation time. In addition, instead of dealing with one objective, we deal with multiple objectives to obtain more robust specifications. For this we employ the multi-objective evolutionary algorithm (MOEA) approach by using the Non- Dominated Sorting Genetic Algorithm-II (NSGA-II). At the end, to confirm the stability of a specification, we employ a stability selection approach. We validate our approach on a data set which is generated from an artificial model. Experimental results show that our procedure allows for stable inference of a causal model.
Wide-Field Lensing Mass Maps from DES Science Verification Data: Methodology and Detailed Analysis

Weak gravitational lensing allows one to reconstruct the spatial distribution of the projected mass density across the sky. These "mass maps" provide a powerful tool for studying cosmology as they probe both luminous and dark matter. In this paper, we present a weak lensing mass map reconstructed from shear measurements in a 139 sq. deg area from the Dark Energy Survey (DES) Science Verification (SV) data. We compare the distribution of mass with that of the foreground distribution of galaxies and clusters. The overdensities in the reconstructed map correlate well with the distribution of optically detected clusters. We demonstrate that candidate superclusters and voids along the line of sight can be identified, exploiting the tight scatter of the cluster photometric redshifts. We cross-correlate the mass map with a foreground magnitude-limited galaxy sample from the same data. Our measurement gives results consistent with mock catalogs from N-body simulations that include the primary sources of statistical uncertainties in the galaxy, lensing, and photo-z catalogs. The statistical significance of the cross-correlation is at the 6.8-sigma level with 20 arcminute smoothing. A major goal of this study is to investigate systematic effects arising from a variety of sources, including PSF and photo-z uncertainties. We make maps derived from twenty variables that may characterize systematics and find the principal components. We find that the contribution of systematics to the lensing mass maps is generally within measurement uncertainties. In this work, we analyze less than 3% of the final area that will be mapped by the DES; the tools and analysis techniques developed in this paper can be applied to forthcoming larger datasets from the survey.
A method for calculating equivalent diameter of fiber in self-compacting fiber reinforced concrete

This paper presents a method for calculating the equivalent diameter of fiber in self-compacting fiber reinforced concrete (SCFRC). The key idea is to utilize a small amount of particles with a narrow particle size distribution to replace the fibers by the same volume, without causing any obvious changes of the properties of concrete in both fresh and hardened states. Some test methods, such as slump-flow, V-funnel, air content and compressive strength, were employed to evaluate the properties change of the concrete. The results show that the equivalent diameter of the fiber (L_f/d_f=13 mm/0.2 mm, L_f and d_f means the length and diameter of fiber respectively) is 2.2 mm, which means the fiber can be treated as a type of spherical aggregate with the diameter of 2.2 mm in the application of particle packing-based concrete design models.
Chronic Disease and Health Risk Behaviors Among Rural Agricultural Workforce in Queensland

ABSTRACT Introduction: Little is known of the lifestyle behaviors and prevalence of chronic disease in the Australian agricultural workforce. This study aimed to assess behavioral risk factors and the prevalence of chronic disease among attendees of agricultural events in rural Queensland. Methods: Data on lifestyle risk factors and prevalence of diabetes and cardiovascular diseases were collected from participants in four separate cross-sectional studies in rural southern Queensland. Anthropometric measures, blood pressure, serum cholesterol, and glucose levels of consenting participants were assessed by trained medical students under the supervision of rural clinicians. Data were analyzed using SPSS 22 statistical software package and t-tests and chi-square tests were used to compare differences between groups. Results: A total of 702 attendees participated; the majority were agricultural workers (n = 393). Greater psychological distress was reported among participants from these rural communities (42%) than in the Australian population (31%); however, levels of psychological distress was similar between agricultural workers and others in the sample. Fewer people in these agricultural communities reported smoking (10%), and they reported being more active (86%) than the average Australian, but a greater proportion reported high-risk alcohol consumption (53%) and were found to be hypertensive (31%). These findings were accentuated among agricultural workers. Conclusion: This method of investigation both raises awareness in the community and identifies health risks for further management in a group that has otherwise been poorly defined. Resident agricultural workers have different health risks and behaviors, though psychological distress appears to be borne across these communities.
Short-Term Sustained Hypoxia Elevates Basal and Hypoxia-Induced Ventilation but Not the Carotid Body Chemoreceptor Activity in Rats

Exposure to chronic sustained hypoxia (SH), as experienced in high altitudes, elicits an increase in ventilation, named ventilatory acclimatization to hypoxia (VAH). We previously showed that rats exposed to short-term (24 h) SH exhibit enhanced abdominal expiratory motor activity at rest, accompanied by augmented baseline sympathetic vasoconstrictor activity. In the present study, we investigated whether the respiratory and sympathetic changes elicited by short-term SH are accompanied by carotid body chemoreceptor sensitization. Juvenile male Holtzman rats (60–80 g) were exposed to SH (10% O2 for 24 h) or normoxia (control) to examine basal and hypoxic-induced ventilatory parameters in unanesthetized conditions, as well as the sensory response of carotid body chemoreceptors in artificially perfused in situ preparations. Under resting conditions (normoxia/normocapnia), SH rats (n = 12) exhibited higher baseline respiratory frequency, tidal volume, and minute ventilation compared to controls (n = 11, P < 0.05). SH group also showed greater hypoxia ventilatory response than control group (P < 0.05). The in situ preparations of SH rats (n = 8) exhibited augmented baseline expiratory and sympathetic activities under normocapnia, with additional bursts in abdominal and thoracic sympathetic nerves during late expiratory phase that were not seen in controls (n = 8, P < 0.05). Interestingly, basal and potassium cyanide-induced afferent activity of carotid sinus nerve (CSN) was similar between SH and control rats. Our findings indicate that the maintenance of elevated resting ventilation, baseline sympathetic overactivity, and enhanced ventilatory responses to hypoxia in rats exposed to 24 h of SH are not dependent on increased basal and sensorial activity of carotid body chemoreceptors.
Graphene–organic composites for electronics: optical and electronic interactions in vacuum, liquids and thin solid films

Graphene exhibits exceptional mechanical, optical and electrical properties that are unfortunately accompanied by poor processability and tunability of its properties. The controlled interaction of graphene with tailor-made organic semiconductors (OSs) can offer a solution to solve these two problems simultaneously. The use of well-chosen organic semiconducting molecules interacting with graphene enables optimal control over the molecular self-assembly process forming low-dimensional graphene–organic architectures. Moreover, OSs allow modulation of numerous physical and chemical properties of graphene, including controlled electrical doping, ultimately making it possible to boost the performance of conventional organic electronic devices. Significantly, the interaction of organic molecules with graphene is strong not only at short distances but it is relevant also at longer distances, up to 30 nm. This feature article reviews some of the most enlightening results in the field, giving an overview of the interaction between graphene and organic molecules, starting from the simplest systems at the molecular scale, single molecules on single layer graphene in UHV, up to mesoscopic, more complex systems i.e., thick interpenetrated layers of graphene–organic composites embedded in working electronic or photovoltaic devices.
Human epidermal growth factor receptor 4 (HER4) is a favorable prognostic marker of breast cancer: a systematic review and meta-analysis

Based on a large cohort of clinical studies involving a total of 8024 patients and reporting the effects of HER4 on breast cancer prognosis, we conducted the first meta-analysis and review of this type. We identified 26 studies published between 1985 and 2016 and assessed the prognostic value of HER4 in breast cancer by either real-time quantitative reverse transcription-polymerase chain reaction (RT-PCR, for mRNA levels) or immunohistochemistry (IHC, for protein levels). Elevated expression of HER4 was significantly associated with longer relapse-free survival (RFS) (HR = 0.63; CI: 0.48−0.83; P = 0.001, random effects). Further subgroup analysis showed that our results were stable irrespective of subtype [Luminal: HR = 0.40, CI: 0.30−0.53, P < 0.001, fixed effects; triple negative breast cancer (TNBC): HR = 0.49, CI: 0.26−0.90, P = 0.02, fixed effects; and HER2-positive: HR = 0.53, CI: 0.40−0.71, P < 0.001, fixed effects]. Cytoplasmic HER4 was more effective than nuclear HER4 (HR = 0.74, CI: 0.60−0.92, P = 0.007, fixed effects) for predicting RFS. HER4 was also found to be a favorable prognostic marker for overall survival (OS) among patients with non-TNBC in the subgroup analysis (Luminal: HR = 0.71, CI: 0.52−0.95, P = 0.023, fixed effects; HER2-positive: HR = 0.48, CI: 0.26−0.89, P = 0.020, fixed effects).
Molding Process Design for Asphalt Mixture Based on Response Surface Methodology

AbstractThe values of key parameters, asphalt aggregate ratio, mixing/compacting temperature, striking/compacting times, and fiber content are usually determined according to bulk properties or empirical values when molding asphalt mixture, which is inefficient and subjective. In this study, a modified response surface methodology (RSM) method was introduced to comprehensively optimize design of asphalt mixture molding process with the optimal value of pavement performance as a response variable. The single-factor tests were first conducted to find the specific ranges of key factors in the response surface models. Then the response surface models between effect factors and three different pavement performance parameters were established based on the Box-Behnken design (BBD) theory. Lastly, the analytic hierarchy process (AHP) was applied to determine weights distribution of the effect factors, and the optimal values of effect factors and pavement performances were obtained. Results indicate that fitting e.
The Marginal Utility of Income

In normative public economics it is crucial to know how fast the marginal utility of income declines as income increases. One needs this parameter for cost-benefit analysis, for optimal taxation and for the (Atkinson) measurement of inequality. We estimate this parameter using four large cross-sectional surveys of subjective happiness and two panel surveys. Altogether, the data cover over 50 countries and time periods between 1972 and 2005. In each of the six very different surveys, using a number of assumptions, we are able to estimate the elasticity of marginal utility with respect to income. We obtain very similar results from each survey. The highest (absolute) value is 1.34 and the lowest is 1.19, with a combined estimate of 1.26. The results are also very similar for subgroups in the population. We also examine whether these estimates (which are based directly on the scale of reported happiness) could be biased upwards if true utility is convex with respect to reported happiness. We find some evidence of such bias, but it is small—yielding a new estimated elasticity of 1.24 for the combined sample.
Optoactivation of Locus Ceruleus Neurons Evokes Bidirectional Changes in Thermal Nociception in Rats

Pontospinal noradrenergic neurons are thought to form part of a descending endogenous analgesic system that exerts inhibitory influences on spinal nociception. Using optogenetic targeting, we tested the hypothesis that excitation of the locus ceruleus (LC) is antinociceptive. We transduced rat LC neurons by direct injection of a lentiviral vector expressing channelrhodopsin2 under the control of the PRS promoter. Subsequent optoactivation of the LC evoked repeatable, robust, antinociceptive (+4.7°C ± 1.0, p < 0.0001) or pronociceptive (−4.4°C ± 0.7, p < 0.0001) changes in hindpaw thermal withdrawal thresholds. Post hoc anatomical characterization of the distribution of transduced somata referenced against the position of the optical fiber and subsequent further functional analysis showed that antinociceptive actions were evoked from a distinct, ventral subpopulation of LC neurons. Therefore, the LC is capable of exerting potent, discrete, bidirectional influences on thermal nociception that are produced by specific subpopulations of noradrenergic neurons. This reflects an underlying functional heterogeneity of the influence of the LC on the processing of nociceptive information.