Miracle-dz/UniFAR-FTUs huggingface dataset:
Don't Fall for Tuning Parameters: Tuning-Free Variable Selection in High Dimensions With the TREX

Lasso is a popular method for high-dimensional variable selection, but it hinges on a tuning parameter that is difficult to calibrate in practice. In this study, we introduce TREX, an alternative to Lasso with an inherent calibration to all aspects of the model. This adaptation to the entire model renders TREX an estimator that does not require any calibration of tuning parameters. We show that TREX can outperform cross-validated Lasso in terms of variable selection and computational efficiency. We also introduce a bootstrapped version of TREX that can further improve variable selection. We illustrate the promising performance of TREX both on synthetic data and on two biological data sets from the fields of genomics and proteomics.
Bio-based edible coatings for the preservation of fishery products: A Review

ABSTRACT The popularity of preprocessed fresh fishery products such as fillets and peeled shrimps is growing in today s market due to their convenience for subsequent processing and cooking. However, fishery products are highly perishable because of the combined actions of biochemical reactions and microbial metabolism. Various methods have been proposed to address this problem. Among these methods, bio-based edible coating has been highlighted as a promising solution. This review updates and summarizes the recent literature on the application of coatings for the preservation of fishery products including the aspects of coating carriers, composite natural preservatives and coating methods, and a discussion of the protective effects based on microbial, physicochemical and sensorial evaluations. Moreover, some challenges and future research directions regarding optimization of formulas and exploration of mechanisms of coating are also discussed. Given consumer demand for fresh fishery products with long shelf life, edible coatings that are environmentally friendly and effective alternative will be used to extend the shelf life of fishery products.
Analysis of Microarray-Identified Genes and MicroRNAs Associated with Idiopathic Pulmonary Fibrosis

The aim of this study was to identify potential microRNAs and genes associated with idiopathic pulmonary fibrosis (IPF) through web-available microarrays. The microRNA microarray dataset GSE32538 and the mRNA datasets GSE32537, GSE53845, and GSE10667 were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed miRNAs (DE-miRNAs)/genes (DEGs) were screened with GEO2R, and their associations with IPF were analyzed by comprehensive bioinformatic analyses. A total of 45 DE-microRNAs were identified between IPF and control tissues, whereas 67 common DEGs were determined to exhibit the same expression trends in all three microarrays. Furthermore, functional analysis indicated that microRNAs in cancer and ECM-receptor interaction were the most significant pathways and were enriched by the 45 DE-miRNAs and 67 common DEGs. Finally, we predicted potential microRNA-target interactions between 17 DE-miRNAs and 17 DEGs by using at least three online programs. A microRNA-mediated regulatory network among the DE-miRNAs and DEGs was constructed that might shed new light on potential biomarkers for the prediction of IPF progression.
Hormonal control of thermogenesis in perfused muscle of Muscovy ducklings.

Endocrine stimulation of muscle nonshivering thermogenesis (NST) in ducklings was investigated in vitro using a perfused hindlimb preparation maintained at 25°C. Effects of flow rate, norepinephrine (NE), epinephrine, and glucagon on perfused muscle oxygen consumption (M˙o 2) and perfusion pressure were studied. Control ducklings ( Cairina moschata, 5 wk old) reared at thermoneutrality (25°C, TN) were compared with two age-matched groups exhibiting muscle NST in vivo: cold-acclimated ducklings (4°C, 4 wk, CA) and glucagon-treated ducklings (103 nmol/kg twice daily, intraperitoneally, GT). BasalM˙o 2was higher in CA than in TN or GT ducklings and increased in all groups with elevated flow rates. Catecholamines increased bothM˙o 2and perfusion pressure. The maximal effect onM˙o 2was higher in CA (+36%) and GT ducklings (+43%) than in controls (+31%), but was associated with reduced vasoconstriction. Flow rate did not consistently potentiate the NE response. At high doses, catecholamines became inhibitory onM˙o 2while a monotonous increase of pressure was still observed. Glucagon, by contrast, slightly decreased bothM˙o 2and pressure. This vasodilatory effect was greater in CA ducklings than controls in preconstricted preparations. In vivo, low-dose epinephrine induced a modest thermogenic effect (+10%) in CA ducklings. These findings showed that duckling muscle thermogenesis is directly stimulated in vitro by catecholamines but not by glucagon. Higher in vitro thermogenic effects of NE in ducklings that were expected to exhibit muscle NST in vivo suggests catecholamine involvement in muscle NST in vivo. Potential vascular control of avian muscle NST is discussed.
Measurement of Gross Photosynthesis, Respiration in the Light, and Mesophyll Conductance Using H218O Labeling1[OPEN]

H218O labeling and IRMS can be used to measure gross photosynthesis, mesophyll conductance, and respiratory uptake in the light in leaflets exposed to 21% and 2% O2. A fundamental challenge in plant physiology is independently determining the rates of gross O2 production by photosynthesis and O2 consumption by respiration, photorespiration, and other processes. Previous studies on isolated chloroplasts or leaves have separately constrained net and gross O2 production (NOP and GOP, respectively) by labeling ambient O2 with 18O while leaf water was unlabeled. Here, we describe a method to accurately measure GOP and NOP of whole detached leaves in a cuvette as a routine gas-exchange measurement. The petiole is immersed in water enriched to a δ18O of ∼9,000‰, and leaf water is labeled through the transpiration stream. Photosynthesis transfers 18O from H2O to O2. GOP is calculated from the increase in δ18O of O2 as air passes through the cuvette. NOP is determined from the increase in O2/N2. Both terms are measured by isotope ratio mass spectrometry. CO2 assimilation and other standard gas-exchange parameters also were measured. Reproducible measurements are made on a single leaf for more than 15 h. We used this method to measure the light response curve of NOP and GOP in French bean (Phaseolus vulgaris) at 21% and 2% O2. We then used these data to examine the O2/CO2 ratio of net photosynthesis, the light response curve of mesophyll conductance, and the apparent inhibition of respiration in the light (Kok effect) at both oxygen levels. The results are discussed in the context of evaluating the technique as a tool to study and understand leaf physiological traits.
Mortality risk of chronic kidney disease: A comparison between the adult populations in urban China and the United States

Background Chronic kidney disease (CKD) is a risk factor for all-cause mortality in the United States, but the evidence from China is limited. We investigate whether prognosis of CKD (mortality) differs between the two countries. In particular, we sought to compare the strength of association between CKD stage and all-cause mortality, by country. Methods Mortality-linked data from China National Survey of Chronic Kidney Disease (urban population, n = 25,269) and US NHANES (2005–2010, n = 15,209) for adults >20 years old were analyzed. The Chinese cohort was followed until Dec 31, 2013, while the NHANES cohort until Dec 31, 2011. CKD was defined by eGFR <60ml/min/1.73m2 or albuminuria (defined as ACR ≥30mg/g). Weighted Cox models were used to evaluate the association between the two CKD indicators and mortality. Both stratified and combined models (with country interactions) were explored. Results The Chinese sample had a lower proportion of eGFR<60 ml/min/1.73m2 (3.7% vs. 6.9%) and albuminuria (7.6% vs. 9.0%), compared to the US. Higher rates of mortality were observed with higher stages of CKD in both countries. HRs for mortality in the more advanced CKD categories reached 2.18 (1.14–4.15) in China and 1.66 (1.18–2.32) in the US in the absence of albuminuria, and 2.30 (1.13–4.68) and 3.04 (2.33–3.96) in the presence of albuminuria. No significant interactions were detected between country and these categories. Conclusion The association between albuminuria and reduced eGFR and all-cause mortality was similar in both countries, with albuminuria being associated with the larger effect size compared to lower eGFR.
Perceptions of Depression and Access to Mental Health Care Among Latino Immigrants

Compared with non-Latino Whites, Latino immigrants have a lower prevalence of depression. However, they are also less likely to seek professional mental health services. Our objective was to compare and contrast perceptions of depression and access to mental health care among four of the largest Latino immigrant subgroups in Florida (Puerto Rican, Cuban, Mexican, and Colombian). We conducted a total of 120 interviews (30 men and women from each subgroup). Thematic analysis of qualitative data revealed that participants across the four groups were aware of the signs and symptoms of depression and had similar perceptions of depression. However, notable differences by subgroup emerged with regard to perceptions of access to mental health care. We suggest that the variation stems from differences in life experiences and the immigration context. Understanding the variances and nuances of Latino immigrants’ cultural construction of depression and immigration experience will enable practitioners to better serve this community.
Contact length in grinding: Part 2: Evaluation of contact length models

Abstract A non-linear curve fit method was used to identify model parameters for the prediction of contact length in grinding. The evaluation shows that the model based on a surface roughness factor demonstrates a high degree of correlation with experimental trends and behaviour. It was found that the roughness parameter R r is insensitive to depth of cut, speed ratio and material hardness, but is sensitive to the wheel-workpiece material combinations and whether grinding is conducted with or without coolant.
Retinoic Acid Increases Fatty Acid Oxidation and Irisin Expression in Skeletal Muscle Cells and Impacts Irisin In Vivo

Background/Aims: All-trans retinoic acid (ATRA) has protective effects against obesity and metabolic syndrome. We here aimed to gain further insight into the interaction of ATRA with skeletal muscle metabolism and secretory activity as important players in metabolic health. Methods: Cultured murine C2C12 myocytes were used to study direct effects of ATRA on cellular fatty acid oxidation (FAO) rate (using radioactively-labelled palmitate), glucose uptake (using radioactively-labelled 2-deoxy-D-glucose), triacylglycerol levels (by an enzymatic method), and the expression of genes related to FAO and glucose utilization (by RT-real time PCR). We also studied selected myokine production (using ELISA and immunohistochemistry) in ATRA-treated myocytes and intact mice. Results: Exposure of C2C12 myocytes to ATRA led to increased fatty acid consumption and decreased cellular triacylglycerol levels without affecting glucose uptake, and induced the expression of the myokine irisin at the mRNA and secreted protein level in a dose-response manner. ATRA stimulatory effects on FAO-related genes and the Fndc5 gene (encoding irisin) were reproduced by agonists of peroxisome proliferator-activated receptor β/δ and retinoid X receptors, but not of retinoic acid receptors, and were partially blocked by an AMP-dependent protein kinase inhibitor. Circulating irisin levels were increased by 5-fold in ATRA-treated mice, linked to increased Fndc5 transcription in liver and adipose tissues, rather than skeletal muscle. Immunohistochemistry analysis of FNDC5 suggested that ATRA treatment enhances the release of FNDC5/irisin from skeletal muscle and the liver and its accumulation in interscapular brown and inguinal white adipose depots. Conclusion: These results provide new mechanistic insights on how ATRA globally stimulates FAO and enhances irisin secretion, thereby contributing to leaning effects and improved metabolic status.
Electronic and Magnetic Properties of Double Perovskites and Oxide Interfaces

Transition metal oxides exhibit a wide range of fascinating phenomena ranging from high Tc superconductivity to colossal magnetoresistance. In this thesis, we examine the novel electronic and magnetic properties of double perovskites and oxide interfaces. First we focus on Sr2FeMoO6 which has a half-metallic ground state and a ferrimagnetic Tc=420 K, well above the room temperature. There are very few half-metals in nature and along with its high Tc, Sr2FeMoO6 has enormous potential in spintronics applications. We develop a minimal model that couples the conduction electrons on Mo (4d1) to the core spins of Fe (3d5). Delocalization of conduction electrons and maximizing the kinetic energy drives the long-range magnetic order. “Integrating out” the conduction electrons, we derive a new effective Hamiltonian, Heff , only for the localized spins. Heff is unique to double perovskites, and with its peculiar double square root form, it is different from standard Heisenberg or Anderson-Hasegawa Hamiltonians. Using Heff , we perform the first 3D, finite temperature calculations of double perovskites, going well beyond previous mean field or small cluster calculations. Next we consider Sr2CrOsO6 which has the highest Tc among all perovskites with a net moment. Its insulating behavior is puzzling given that Cr and Os are in the 3d3 and 5d3 configurations, half filled in t2g orbitals. The net moment at low temperature is M(0)=0.75 μB and non-monotonic magnetization as a function of temperature are quite unusual. To address these questions, we organize the problem through the hierarchy of its energy scales. To deal with the highest energy scale, the charge sector, we develop a multi-band Hubbard model that has different on-site Coulomb correlations on the Cr and Os sites. We solve this model using slave-rotor mean field theory which captures the essentials of the metal-Mott
Concrete filled steel tubular structures from theory to practice

The state of the art of concrete-filled steel tubes is presented generally in this paper. The general response of concrete-filled steel tubular columns is discussed with an emphasis on the composite action between the steel tube and its concrete core. The engineering practices of concrete filled steel tubes in industrial works, structural frames and supports, loading bridges, compressive members of truss, subway columns, electricity transmitting poles, spacious construction, high-rise or super high-rise buildings and bridge structures are introduced. Finally, the need for further research, such as behavior of concrete filled steel tubular structures during construction, concrete quality control, steel residual stress effects, creep and fatigue is identified.
Convex Analysis on the Hermitian Matrices

There is growing interest in optimization problems with real symmetric matrices as variables. Generally the matrix functions involved are spectral: they depend only on the eigenvalues of the matrix. It is known that convex spectral functions can be characterized exactly as symmetric convex functions of the eigenvalues. A new approach to this characterization is given, via a simple Fenchel conjugacy formula. We then apply this formula to derive expressions for subdifferentials, and to study duality relationships for convex optimization problems with positive semidefinite matrices as variables. Analogous results hold for Hermitian matrices.
Neutrophil transfer of miR-223 to lung epithelial cells dampens acute lung injury in mice

Intercellular transfer of miR-223 from neutrophils to alveolar epithelial cells reduces lung inflammation in a mouse model of ventilator-induced lung injury or pulmonary bacterial infection. Starting an intercellular conversation In a new study, Neudecker et al. show that transfer of microRNA-223 (miR-223) from neutrophils to lung alveoli helps to dampen lung inflammation and promotes the resolution of ventilator-induced lung injury in mice. The authors suggest that neutrophils secrete microRNAs in microvesicles that are then taken up by alveolar epithelial cells. They show that miR-223–deficient mice are prone to lung injury, whereas overexpression of miR-223 is protective. Intercellular transfer of microRNAs can mediate communication between critical effector cells. We hypothesized that transfer of neutrophil-derived microRNAs to pulmonary epithelial cells could alter mucosal gene expression during acute lung injury. Pulmonary-epithelial microRNA profiling during coculture of alveolar epithelial cells with polymorphonuclear neutrophils (PMNs) revealed a selective increase in lung epithelial cell expression of microRNA-223 (miR-223). Analysis of PMN-derived supernatants showed activation-dependent release of miR-223 and subsequent transfer to alveolar epithelial cells during coculture in vitro or after ventilator-induced acute lung injury in mice. Genetic studies indicated that miR-223 deficiency was associated with severe lung inflammation, whereas pulmonary overexpression of miR-223 in mice resulted in protection during acute lung injury induced by mechanical ventilation or by infection with Staphylococcus aureus. Studies of putative miR-223 gene targets implicated repression of poly(adenosine diphosphate–ribose) polymerase–1 (PARP-1) in the miR-223–dependent attenuation of lung inflammation. Together, these findings suggest that intercellular transfer of miR-223 from neutrophils to pulmonary epithelial cells may dampen acute lung injury through repression of PARP-1.
Differences in birthweight curves between newborns of immigrant mothers vs. infants born in their corresponding native countries: systematic overview.

BACKGROUND Newborn weight may vary between ethnic groups, but it is not known if birthweight differences exist between term babies born to immigrant mothers compared with those born in their corresponding native countries. METHODS We completed a systematic review of all birthweight curves published between 1980 and 2012, based on at least 100 singleton deliveries. We compared the 10th, 50th and 90th percentile birthweight values at 40 weeks gestation for male and female infants born in their native country vs. those infants born to mothers who had emigrated from their native country to Ontario, Canada. For the 50th percentile values, we also calculated a standardised pooled weighted difference and 95% confidence interval [CI] for both sexes. We also assessed whether birthweight differed over time, or if the differences varied by the Human Development Index (HDI) value for the native country. RESULTS A total of 31 studies from 21 different countries met the inclusion criteria, comprising 13 317 578 males and 12 859 119 females born at 40 weeks gestation. There was a small non-significant rise in reported birthweight percentile values between 1983 and 2006. Nearly all infants born to women in their native country had lower birthweights than those born to mothers who had emigrated from the same country to Canada at the 10th, 50th and 90th percentiles. Overall, the 50th percentile weights differed by 115 g [95% CI 74, 156] for males and 122 g [95% CI 95, 150] for females. As HDI or median birthweight increased, birthweight differences were less pronounced, but not significantly so. CONCLUSIONS Term birthweight percentiles are typically higher among term infants born to mother who immigrate to Canada than those of infants born in their respective native country.
A New Technique to Estimate Precipitation at Fine Scale Using Multifrequency Satellite Observations Over Indian Land and Oceanic Regions

A new technique has been developed to estimate rainfall at very fine scale (hourly rain rate at 0.05° ×0.05° spatial resolution) over India and associated oceanic regions (20° S-40° N, 40° E-130° E). By using infrared (IR) and 6.7-μm water vapor (WV) channel observations from Meteosat-7, a new rain index (RI) is computed. The index computation is composed of two steps. First, the IR and WV brightness temperatures are divided by their respective nonrainy thresholds to get the IR and WV rain coefficients. The product of these coefficients is defined as the RI. These RIs are collocated against rainfall from the Precipitation Radar (PR) on board the Tropical Rainfall Measuring Mission to develop a relationship between the index and the rain rate. This relationship was utilized to monitor rainfall by applying it to numerous cases of monsoon and tropical cyclones over India and associated oceanic regions. Detailed validation with rain gauges and independent PR observations and comparisons with Global Satellite Mapping of Precipitation (GSMaP) and a regional rainfall algorithm based on IR observations are performed in this study. The present technique shows a correlation coefficient (CC) of 0.74, a bias of 0.086 mm, and a root-mean-square error (rmse) of 4.78 mm when compared with rain gauge. On the other hand, the regional rainfall technique and GSMaP show CCs of 0.72 and 0.59, bias values of 1.59 and 0.338 mm, and rmses of 5.49 and 7.20 mm, respectively, compared with rain gauge. It is observed that the present technique is able to monitor the rainfall with good accuracy at very fine scale over India.
ADP Platelet Hyperreactivity Predicts Cardiovascular Disease in the FHS (Framingham Heart Study)

Background Platelet function is associated with adverse events in patients with cardiovascular disease (CVD). Methods and Results We examined associations of baseline platelet function with incident CVD events in the community‐based FHS (Framingham Heart Study). Participants free of prevalent CVD and without recent aspirin treatment with available data in the Framingham Offspring cohort (1991–1995) and Omni cohort (1994–1998) were included. Platelet function was measured with light transmission aggregometry using collagen (1.9 μg/mL), ADP (0.05–15 μmol/L), and epinephrine (0.01–15 μmol/L). We used proportional hazards models to analyze incident outcomes (myocardial infarction/stroke, CVD, and CVD mortality) with respect to platelet measures. The study sample included 2831 participants (average age, 54.3 years; 57% women). During follow‐up (median, 20.4 years), we observed 191 composite incident myocardial infarction or stroke events, 432 incident CVD cases, and 117 CVD deaths. Hyperreactivity to ADP and platelet aggregation at ADP concentration of 1.0 μmol/L were significantly associated with incident myocardial infarction/stroke in a multivariable model (hazard ratio, 1.68 [95% confidence interval, 1.13–2.50] [P=0.011] for hyperreactivity across ADP doses; and hazard ratio, 1.16 [95% confidence interval, 1.02–1.33] [P=0.029] for highest quartile of ADP response at 1.0 μmol/L versus others). No association was observed for collagen lag time or any epinephrine measures with incident myocardial infarction or stroke. Conclusions Intrinsic hyperreactivity to low‐dose ADP in our community‐based sample, who were free of CVD and any antiplatelet therapy, is associated with future arterial thrombosis during a 20‐year follow‐up. These findings reinforce ADP activation inhibition as a critical treatment paradigm and encourage further study of ADP inhibitor‐refractive populations.