Miracle-dz/UniFAR-FTUs huggingface dataset:
Individual Variation in Metabolism and Reproduction of Mus: Are Energetics and Life History Linked?

The possibility of functional relationships between energetics and life-history characteristics has been of considerable interest to evolutionary ecologists. Among species of mammals, life-history variables generally are not correlated with mass-independent basal metabolic rate, with the possible exceptions of maximal intrinsic rate of increase, litter size and reproductive effort during lactation. Whether this is generally true at the level of variation among individuals within a population (individual variation) is unclear. Therefore, we tested whether basal or maximal metabolic rates of random-bred female mice (Mus domesticus) were correlated with the size of their litters, litter mass, or mean offspring mass. The effects of variation in maternal mass, maternal age, experimental block and duration of fasting (for basal metabolic rate) were removed by calculating residuals from multiple regression equations. Basal and maximal metabolic rate were not significantly correlated with any of the life-history variables we studied. Thus, our results are generally consistent with those from interspecific comparisons of mammals: little evidence suggests necessary associations between metabolic rates and life history.
Clinical and molecular sub-classification of hepatocellular carcinoma relative to alpha-fetoprotein level in an Asia-Pacific island cohort

Aim Increased serum alpha-fetoprotein (AFP) levels are associated with specific molecular sub-classes of hepatocellular carcinoma (HCC), supporting AFP as a predictive or therapeutic biomarker for precision treatment of this disease. Considering recent efforts to validate HCC molecular classification systems across different populations, we applied existing signature-based classification templates to Hawaii cohorts and examined whether associations between HCC molecular sub-class, AFP levels, and clinical features found elsewhere can also be found in Hawaii, a region with a unique demographic and risk factor profile for HCC. Methods Whole-genome expression profiling was performed on HCC tumors collected from 40 patients following partial hepatectomy. Tumors underwent transcriptome-based categorization into 3 molecular sub-classes (S1, S2, and S3). Patient groups based on molecular sub-class and AFP level were then compared with regards to clinical features and survival. Differences associated with AFP level and other clinical parameters were also examined at the gene signature level by gene set enrichment analysis. Results Statistically confident (false discovery rate < 0.05) sub-classifications were made in 98% (39/40) of tumors. Patient sub-groups differed significantly with regards to serum AFP level, with significantly lower levels in the S3 sub-group as compared to S1 (P = 0.048) and S2 (P = 0.010). Serum AFP > 400 ng/mL predicted significant tumor enrichment for genes corresponding to MYC target activation, high cell proliferation, poor clinical prognosis, and the S2 sub-class. AFP > 400 ng/mL and non-S3 tumor classification were found to be significant predictors of overall survival. Conclusion Distinct sub-classes of HCC associated with different molecular features and survival outcomes can be detected with statistical confidence in a Pacific Island cohort. Molecular classification signatures and other predictive markers for HCC that are valid for all patient populations are needed to support multi-center efforts to develop targeted therapies for HCC.
Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

Summary: pybedtools is a flexible Python software library for manipulating and exploring genomic datasets in many common formats. It provides an intuitive Python interface that extends upon the popular BEDTools genome arithmetic tools. The library is well documented and efficient, and allows researchers to quickly develop simple, yet powerful scripts that enable complex genomic analyses. Availability: pybedtools is maintained under the GPL license. Stable versions of pybedtools as well as documentation are available on the Python Package Index at http://pypi.python. org/pypi/pybedtools. Contact: dalerr@niddk.nih. gov; arq5x@virginia.edu Supplementary Information: Supplementary data are available at Bioinformatics online.
Visual Speech Recognition for a Person with Severe Hearing Loss Using Deep Canonical Correlation Analysis

Recently, we proposed an audio-visual speech recognition system based on a neural network for a person with an articulation disorder resulting from severe hearing loss. In the case of a person with this type of articulation disorder, the speech style is quite different from that of people without hearing loss, making a speaker-independent acoustic model for unimpaired persons more or less useless for recognizing it. Our proposed system has shown high performance; however, some problems remain. Although the feature extraction networks are trained using the phone labels as the target class, it is difficult to obtain the correct alignment for their speech. Also, it is necessary to consider a gap between audio and visual feature spaces to treat the different modalities. In this paper, we propose a feature extraction method using deep canonical correlation analysis to tackle these weaknesses. The effectiveness of this approach was confirmed through word-recognition experiments in noisy environments, where our feature extraction method outperformed the conventional methods.
Mathematical ratios lead to spurious conclusions regarding age- and sex-related differences in resting metabolic rate.

Resting metabolic rate (RMR) data have been normalized by dividing RMR by fat-free mass (FFM) (ie, ratio method), or by using a regression-based approach. We compared both data-normalization procedures on age- and sex-related differences in RMR. The ratio method showed no differences in adjusted RMR between older men (0.084 +/- 0.004 kJ.FFM-1.min-1) and younger men (0.082 +/- 0.003 kJ.FFM-1.min-1), whereas analysis of covariance showed a lower (P < 0.01) adjusted RMR in older men (4.81 +/- 0.04 kJ/min) than in younger men (5.14 +/- 0.04 kJ/min). In another example, the ratio method showed that women had a higher (P < 0.05) adjusted RMR (0.10 +/- 0.004 kJ/min) than did men (0.08 +/- 0.003 kJ/min), whereas analysis of covariance showed a lower (P < 0.01) adjusted RMR in women (4.45 +/- 0.03 kJ/min) than in men (4.62 +/- 0.03 kJ/min). The ratio method provides misleading conclusions regarding sex- and age-related differences in RMR when compared with a regression-based approach.
EvoFIT: A holistic, evolutionary facial imaging technique for creating composites

EvoFIT, a computerized facial composite system is being developed as an alternative to current systems. EvoFIT faces are initially presented to a witness with random characteristics, but through a process of selection and breeding, a composite is "evolved. " Comparing composites constructed with E-FIT, a current system, a naming rate of 10% was found for EvoFIT and 17% for E-FIT. Analysis revealed that target age was limiting factor for EvoFIT and a second study with age-appropriate targets visible during composite construction produced a naming rate similar to E-FIT. Two more-realistic studies were conducted that involved young target faces and two current systems (E-FIT and PROfit). Composites from both of these experiments were poorly named but a significant benefit emerged for EvoFIT.
Endogenous synthesis of arginine plays an important role in maintaining arginine homeostasis in postweaning growing pigs.

This study was conducted to determine whether endogenous synthesis of arginine plays a role in regulating arginine homeostasis in postweaning pigs. Pigs were fed a sorghum-based diet containing 0. 98% arginine and were used for studies at 75 d of age (28.4 kg body weight). Mitochondria were prepared from the jejunum and other major tissues for measuring the activities of Delta1-pyrroline-5-carboxylate (P5C) synthase and proline oxidase (enzymes catalyzing P5C synthesis from glutamate and proline, respectively) and of ornithine aminotransferase (OAT) (the enzyme catalyzing the interconversion of P5C into ornithine). For metabolic studies, jejunal enterocytes were incubated at 37 degrees C for 30 min in Krebs-Henseleit bicarbonate buffer containing 2 mmol/L L-glutamine, 2 mmol/L L-[U-14C]proline, and 0-200 micromol/L gabaculine (an inhibitor of OAT). The activities of P5C synthase, proline oxidase and OAT were greatest in enterocytes among all of the tissues studied. Incubation of enterocytes with gabaculine resulted in decreases (P < 0.05) in the synthesis of ornithine and citrulline from glutamine and proline. When gabaculine was orally administered to pigs (0.83 mg/kg body weight) to inhibit intestinal synthesis of citrulline from glutamine and proline, plasma concentrations of citrulline (-26%) and arginine (-22%) decreased (P < 0.05), whereas those of alanine (+21%), ornithine (+17%), proline (+107%), taurine (+56%) and branched-chain amino acids (+21-40%) increased (P < 0.05). On the basis of dietary arginine intake and estimated arginine utilization, the endogenous synthesis of arginine in the 28-kg pig provided >/=50.2% of total daily arginine requirement. Taken together, our results suggest an important role for endogenous synthesis of arginine in regulating arginine homeostasis in postweaning growing pigs, as previously shown in neonatal pigs.
Postexercise macronutrient oxidation: a factor dependent on postexercise macronutrient intake.

BACKGROUND It has been widely shown that exercise increases postexercise fat oxidation and energy expenditure. OBJECTIVE The aim of this study was to investigate the effect of exercise on postexercise substrate oxidation and energy expenditure when the exercise-induced expenditure of energy and macronutrients oxidized is compensated by an equivalent intake immediately after exercise. DESIGN Twenty-four-hour energy expenditure (24EE) and macronutrient oxidation of 8 young men were measured in a whole-body indirect calorimeter under the 2 following, randomly assigned conditions: 1) a control session of sedentary activities in the calorimeter for 61 h and 2) a similar session preceded by 60 min of exercise at 50% of maximal oxygen consumption. Immediately after exercising, subjects ingested a milk shake containing the same amount of energy (above resting metabolic rate) expended during exercise and with a food quotient corresponding to the mean exercise respiratory quotient. 24EE and substrate oxidation were compared between conditions on a day-to-day basis (days 1, 2, and 3) and for the 61-h observation period. RESULTS There was no difference in 24EE between the 2 conditions. Moreover, the composition of the postexercise fuel mix oxidized, as reflected by the respiratory quotient, was strictly the same under the 2 conditions. CONCLUSION Voluntary postexercise compensations in energy and macronutrient intakes play a major role in the ability of exercise to alter postexercise substrate utilization.
PERK-mediated Autophagy in Osteosarcoma Cells Resists ER Stress-induced Cell Apoptosis

Osteosarcoma is a bone cancer that develops commonly in children and adolescents. However, osteosarcoma treatments often fail by the development of chemoresistance to apoptosis, and the molecular mechanisms remain unclear. In this study, we propose that autophagy is responsible for osteosarcomatous resistance to apoptosis. We implicate PERK-mediated autophagy as a significant contributor to apoptosis resistance due to ER stress in osteosarcoma cells. By immunostainings and western blots, we identified that PERK activated osteosarcomatous autophagy via inhibiting mTORC1 pathway, thereby preventing cell apoptosis. While using RNAi, we knocked down PERK and found that autophagy was suppressed, result in osteosarcomatous apoptosis. Our results identify a novel role of PERK-mediated autophagy as a significant mechanism for osteosarcoma cell survival. These results will help to understand the mechanism of chemoresistance in osteosarcoma cells, and indicate a novel target for improving osteosarcoma therapy.
Does Working Memory Impact Functional Outcomes in Individuals With ADHD: A Qualitative and Comprehensive Literature Review

Objective: Working Memory (WM) is a domain of executive functioning often impaired in individuals with ADHD. Although assumed to cause difficulties across functioning, the scope of impairments from WM deficits in ADHD has not been investigated. The aim of this study was to examine outcomes associated with WM deficits in ADHD. Method: We conducted a search of the scientific literature on WM deficits, and Freedom From Distractibility (FFD), in ADHD using PubMed and PsycInfo databases. Results: The final sample included 11 controlled studies of WM/FFD deficits in ADHD with operationalized assessment of outcomes in academic, social, and emotional areas. WM assessment was divided into auditory-verbal memory (AVM) and spatial-visual memory (SWM). Seven studies examined WM deficits in academic functioning, eight studies assessed WM deficits in social functioning, and three assessed WM deficits in psychopathology. Conclusion: The majority of the literature suggests that WM deficits affect primarily academic functioning.
Sodium iron EDTA [NaFe(III)EDTA] as a food fortificant: erythrocyte incorporation of iron and apparent absorption of zinc, copper, calcium, and magnesium from a complementary food based on wheat and soy in healthy infants.

BACKGROUND Phytic acid is a strong inhibitor of iron absorption from fortified foods. In adults, this inhibitory effect can be overcome by adding ascorbic acid with the iron fortificant or by using a "protected" iron compound such as NaFeEDTA. In addition, the use of NaFeEDTA as an iron fortificant has been reported to increase zinc absorption in adult women. No information is available on iron bioavailability from NaFeEDTA or the influence of NaFeEDTA on minerals and trace elements in infants. OBJECTIVE We aimed to compare iron bioavailability from a complementary food based on wheat and soy fortified with either NaFeEDTA or ferrous sulfate plus ascorbic acid. The apparent absorption of zinc, copper, calcium, and magnesium was evaluated in parallel. DESIGN Stable-isotope techniques were used in a crossover design to evaluate erythrocyte incorporation of iron 14 d after administration of labeled test meals and the apparent absorption of zinc, copper, calcium, and magnesium on the basis of fecal monitoring in 11 infants. RESULTS Geometric mean erythrocyte incorporation of iron was 3.7% (NaFeEDTA) and 4.9% (ferrous sulfate plus ascorbic acid) (P = 0.08). No significant differences in the apparent absorption of zinc, copper, calcium, or magnesium were observed between test meals (n = 10). CONCLUSIONS Iron bioavailability from a high-phytate, cereal-based complementary food fortified with either NaFeEDTA or ferrous sulfate plus ascorbic acid was not significantly different. NaFeEDTA did not influence the apparent absorption of zinc, copper, calcium, or magnesium. NaFeEDTA does not provide any nutritional benefit compared with the combination of a highly bioavailable iron compound and ascorbic acid.
Variations in cross‐cultural perception of riverscapes in relation to in‐channel wood

Human perception of riverscapes with and without large wood (LW) has been investigated with a photo-questionnaire submitted to 2250 students in ten countries, capturing reactions to 20 pictures in terms of naturalness, danger, aesthetics and need for improvement. Principal component analysis performed on average scores per country per item showed that the primary discriminating factors are human modification, turbulence and extent of water shown in the scenes. Wood discriminated the perception of student groups, but other factors are also critical. Features associated with human activity (channel deepening and straightening, rip-rapping) were perceived to be less aesthetically pleasing than wood. Perception of the most dangerous riverscapes is not specifically affected by wood, but by turbulent flows and wide rivers. The presence of wood clearly discriminated the need for human intervention. Perceptions differed among countries, reflecting different cultural contexts. Students from Germany, Sweden and Oregon perceived LW more positively as a natural and wild component of watercourses. These perceptions are linked to positive attitudes towards natural riverscapes. Other students, such as those from China, Russia or India, perceived rivers with wood as needing regulation and maintenance. Whatever the socio-cultural context, large wood elicits an emotional influence on how one perceives riverscapes.
All Ink-jet Printing Strategy for Extensive Exploration of One Chemical Action with Three Interactive Variations

A simple method was created and implemented through the technology of ink-jet printing to study the effects of three chemical factors (chemical reagents) to the ninhydrin reaction. The effects of each single reagent and their interactions on the reaction were studied in one experiment. The three reagents all have effects on ninhydrin reaction, and the effects under the different combinations of reagents were presented on a chip. This work was completed efficiently with a smaller experimental workload compared with the traditional method.
Understanding changes and deformations on multi-temporal rock face point clouds

The paper outlines an approach to compare two digital surfaces of a rock face in order to extract geometric changes and deformations. The method requires the preliminary registration of each point cloud by using techniques typical of TLS. Then, point clouds are segmented in several regions, each of them referred to a plane; this task allows to interpolate all data to obtain a set of grid DEMs per epoch. Then each pair of corresponding DEMs are subtracted point-wise to obtain the ∆DEM of the differences along elevation. This is then processed along a three-step procedure. First possible systematic errors or low-frequency deformations are extracted by looking for a linear component. Secondly, the remaining ∆DEM is check against major changes, i.e. loss of material or vegetation growth. Finally, deformations of the cliff are enhanced by analyzing the mean displacement through the convolution with a square window applied to the ∆DEM filtered out from holes and bushes. This technique improves the original precision of each measured point, because deformation is evaluated as mean of a sample on the ∆DEM. The method has been tested so far on both synthetically generated and simple real data sets.
Extraction and Performance Characterization of the Carexmeyeriana Fiber

ABSTRACT In this investigation, Carexmeyeriana fiber (CMF) was extracted by using the ultrasound alkali--oxygen technology in the research, and the performance characterization of CMF was revealed. Parameters such as ultrasonic and alkali--oxygen acting times, and the concentrations of NaOH and H2O2 were optimized by using the multi-target orthogonal method. The performance characteristics of CMF were investigated by means of scanning electron microscopy, ultraviolet, Fourier transform infrared spectroscopy (FTIR), X-ray diffraction and other basic testing methods. The result revealed that the optimal parameters in the extraction process were ultrasonic irradiating for 70 min, soaking in the alkali--oxygen bath for 100 min, and the concentrations of NaOH as 8 g/L and H2O2 as 12 g/L. After extraction, the characteristic absorb peaks for the non-cellulose of CMF in the FTIR spectra decreased significantly, and the crystallinity increased from 46.5 to 50.6%. Warmth retention and excellent antibacterial properties of the extracted CMF were observed. It was expected that CMF can be developed as a functional fiber in the future.
Pathways toward high-performance perovskite solar cells: review of recent advances in organo-metal halide perovskites for photovoltaic applications

Abstract. Organo-metal halide perovskite–based solar cells have been the focus of intense research over the past five years, and power conversion efficiencies have rapidly been improved from 3.8 to >21%. This article reviews major advances in perovskite solar cells that have contributed to the recent efficiency enhancements, including the evolution of device architecture, the development of material deposition processes, and the advanced device engineering techniques aiming to improve control over morphology, crystallinity, composition, and the interface properties of the perovskite thin films. The challenges and future directions for perovskite solar cell research and development are also discussed.
A Monte Carlo Simulation of Radiation Damage of SiC and Nb Using JA-IPU Code

MC (Monte Carlo) simulation code, JA-IPU is used to study radiation damage of SiC irradiated to spallation neutron and AmBe neutron spectra. The code is based on the major physical processes of radiation damage on incorporation of atomic collision cascade and limited to 10 MeV neutron energy. A phenomenological relation for radiation swelling is also derived. Based on the calculation of swelling, DPA (displacement per atom), defect production efficiency and effective threshold energy, Ed from the data of MC simulation, SiC is inferred to be a highly radiation resistant material when compared with Nb and Ni metals which are used in composition of several reactor steels. Experimental results of hill-hock density measured using AFM (atomic force microscopy), also confirm radiation resistant behavior of SiC.
Biochemical and Molecular Actions of Nutrients Vitamin B-12 Deficiency Induces Anomalies of Base Substitution and Methylation in the DNA of Rat Colonic Epithelium

Derangements of one-carbon metabolism can directly affect the integrity of the genome by producing inappropriate uracil insertion into DNA and by altering patterns of DNA methylation. Vitamin B-12, a one-carbon nutrient, serves as a cofactor in the synthesis of precursors of biological methylation and in nucleotide synthesis. We therefore examined whether vitamin B-12 deficiency can induce these molecular anomalies in the colonic mucosa of rats. Weanling male Sprague-Dawley rats (n 30) were divided into 2 groups and fed either a vitamin B-12–deficient diet or a similar diet containing adequate amounts of the vitamin. Rats from each group were killed at 6 and 10 wk. Uracil misincorporation into DNA was measured by GC/MS and genomic DNA methylation was measured by LC/MS. Plasma vitamin B-12 concentrations in deficient rats were below detectable limits at 6 and 10 wk; in control rats, concentrations were 0.46 0.07 and 0.42 0.10 nmol/L at those times. Although the colon total folate concentration did not differ between the groups, the proportion that was methylfolate was marginally greater in the deficient rats at 10 wk (P 0.05) compared with control, consistent with the “methylfolate trap” that develops during vitamin B-12 deficiency. After 10 wk, the colonic DNA of the deficient rats displayed a 35% decrease in genomic methylation and a 105% increase in uracil incorporation (P 0.05). This vitamin B-12– deficient diet, which was of insufficient severity to cause anemia or illness, created aberrations in both base substitution and methylation of colonic DNA, which might increase susceptibility to carcinogenesis. J. Nutr. 134: