Miracle-dz/UniFAR-FTUs huggingface dataset:
Sparse Hilbert-Schmidt Independence Criterion Regression

Feature selection is a fundamental problem for machine learning and statistics, and it has been widely studied over the past decades. However, the majority of feature selection algorithms are based on linear models, and the nonlinear feature selection problem has not been well studied compared to linear models, in particular for the high-dimensional case. In this paper, we propose the sparse Hilbert– Schmidt Independence Criterion (SpHSIC) regression, which is a versatile nonlinear feature selection algorithm based on the HSIC and is a continuous optimization variant of the well-known minimum redundancy maximum relevance (mRMR) feature selection al-gorithm. More speciﬁcally, the SpHSIC consists of two parts: the convex HSIC loss function on the one hand and the regularization term on the other hand, where we consider the Lasso, Bridge, MCP, and SCAD penalties. We prove that the sparsity based HSIC regression estimator satisﬁes the oracle property; that is, the sparsity-based estimator re-covers the true underlying sparse model and is asymptotically normally distributed. On the basis of synthetic and real-world experiments, we illustrate this theoretical property and highlight the fact that the proposed algo-rithm performs well in the high-dimensional setting.
SCALING FROM TREES TO FORESTS: TRACTABLE MACROSCOPIC EQUATIONS FOR FOREST DYNAMICS

Individual-based forest simulators, such as TASS and SORTIE, are spatial stochastic processes that predict properties of populations and communities by simulating the fate of every plant throughout its life cycle. Although they are used for forest management and are able to predict dynamics of real forests, they are also analytically intractable, which limits their usefulness to basic scientists. We have developed a new spatial individual-based forest model that includes a perfect plasticity formulation for crown shape. Its structure allows us to derive an accurate approximation for the individual-based model that predicts mean densities and size structures using the same parameter values and functional forms, and also it is analytically tractable. The approximation is represented by a system of von Foerster partial differential equations coupled with an integral equation that we call the perfect plasticity approximation (PPA). We have derived a series of analytical results including equilibrium abundances for trees of different crown shapes, stability conditions, transient behaviors, such as the constant yield law and self-thinning exponents, and two species coexistence conditions.
Rapid extraction of bacterial genomic DNA with guanidium thiocyanate

A method is described for the rapid isolation and purification of bacterial genomic DNA. A total of 215 bacterial strains representing species of Campylobacter, Corynebacterium, Escherichia, Legionella, Neisseria, Staphylococcus and Streptococcus, were lysed with guanidium thiocyanate. DNA was prepared using just three other reagents and one high‐speed centrifugation step. The method, which was applicable to both Gram‐positive and Gram‐negative bacteria, eliminated endogenous nuclease activity and avoided the need for phenol, RNase and protease treatments. The DNA was of high purity, high molecular mass and double‐stranded.
Ecology of a New England salt marsh

Measurements of the abundance of major populations, their metabolism, and the seasonal patterns of total system metabolism throughout a year were used to develop energy-flow diagrams for a New England salt-marsh embayment. The annual ecological energy budget for the embayment indicates that consumption exceeds production, so that the system must depend on inputs of organic detritus from marsh grasses. Gross production ranged from almost zero in winter to about 5 g 02 m-2 day-' in summer. Respiration values were similar, but slightly higher, with the maximum difference observed in fall. Populations of shrimp and fish were largest in fall, with a much smaller peak in spring. Few animals were present in the embayment from May to July, but fall populations of shrimp ranged from 250 to 800 m-2 and fish averaged over 10 m-2. Birds were most abundant in winter and spring. In spite of high numbers, no evidence was found that the marsh embayment exported large amounts of shrimp or fish to the estuary. Production of aboveground emergent grasses on the marsh equaled 840 g m-2 for tall Spartina alterniflora, 432 g m-2 for short S. alterniflora, and 430 g mr2 for S. patens. These values are similar to those for New York marshes, but substantially lower than the southern marsh types. The efficiency of production of marsh grasses in the New England marsh was lower than reported for southern areas. A simulation model based on the laboratory and field metabolism and biomass measurements of parts of the embayment system was developed to predict diurnal patterns of dissolved oxygen in the marsh. The model was verified with field measurements of diurnal oxygen curves. The model indicated the importance of the timing of high tides in determining oxygen levels and was used to explore simulated additions of sewage BOD and increases in temperature.
Linking teratogenesis, growth, and DNA photodamage to artificial ultraviolet b radiation in Xenopus laevis larvae

The frog embryo teratogenesis assay—Xenopus (FETAX) was used to illustrate sublethal endpoints indicative of ultraviolet B (UV‐B) radiation exposure in Xenopus laevis larvae. Xenopus laevis embryos were covered with plastic cutoff filters to manipulate UV dose, and irradiated under a light carriage consisting of two UV‐B and three UV‐A bulbs. At the end of day 2, 20% of the tadpoles from all treatments were removed, and DNA was extracted. Frequency of pyrimidine dimers was estimated by quantifying single‐strand breaks after incubating DNA with an endonuclease specific for cyclobutane pyrimidine dimers. Remaining tadpoles were sacrificed on day 5, and mortality, malformations, and growth data were recorded. Teratogenesis and growth inhibition were positively correlated with increasing UV‐B dose in all tests. Photodamage to DNA in experiment 1 increased with higher UV‐B doses. Teratogenesis positively correlated with the frequency of pyrimidine dimers. In experiment 2, significant variation with DNA photodamage in egg clutches was observed and no treatment effect was found. Usage of these sublethal endpoints in the field or laboratory would be helpful in discerning adaptational responses of developing amphibians to UV‐B radiation, and interactive effects between UV and photosensitive chemicals.
Assessment of Toll-like Receptors in the Ileum of Weanling Pigs- Responses to Feed Antibiotic Chlortetracycline and Gnotobiotic Conditions

It has been suggested that changes in diet at weaning in pigs induce intestinal inflammation which may be mediated through toll-like receptors (TLRs). We hypothesized that the use of antibiotics as growth promoters and subsequent changes in intestinal microbiota may mediate changes in the expression of TLRs in the intestine. Thus, this study was performed to assess the changes in intestinal TLRs in weanling pigs in response to the use of chlortetracycline as a growth promotant, and under gnotobiotic conditions. Eighteen cesarean-derived half-sib piglets were divided into three groups; antibiotic-fed, control (normal-fed) and gnotobiotic groups.TLR-2, -4, -5 and -9 gene expression and abundance of TLR-2 and -9 proteins in the ileum of pigs was assessed at 5 wk of age. No significant differences (p ? 0.5) in TLR-2, -4, -5 and -9transcript levels and abundanceof TLR-2 and -9 proteins among three groups of pigswere observed.
Genetic diversity and mitochondrial introgression in Scytosiphon lomentaria (Ectocarpales, Phaeophyceae) in the north-eastern Atlantic Ocean

Abstract: The common brown alga Scytosiphon lomentaria (Scytosiphonaceae) has generally been regarded as a species complex. In the Pacific, molecular data have shown that it includes more than one species; the diversity in other oceans, however, has not been examined. In the present study, the genetic diversity of S. lomentaria was investigated in 57 samples from the north-east Atlantic (mainly from Ireland) and two from the Mediterranean, which were compared with seven samples from Japan. Phylogenetic analyses based on the mitochondrial cytochrome oxidase subunit 3 gene (cox3) and nuclear ribosomal internal transcribed spacers (ITS1 and 2) revealed four separate monophyletic groups. Clades A1 and A2 consisted of the samples from the north-east Atlantic; the Mediterranean samples also belonged to A1. The affiliation of four samples was incongruent between cox3 and ITS trees, suggesting directional mitochondrial introgression from A2 to A1. Clades P1 and P2 contained nine samples from the north-east Atlantic, i.e. three Irish, all Norwegian and Icelandic samples, as well as all Pacific samples; in these clades, the cox3 and ITS data were congruent. This is the first documented record of Pacific lineages of Scytosiphon in the north-east Atlantic. Our results indicate that at least four species are passing under the name S. lomentaria in the north-east Atlantic and the Mediterranean.
Cellular interactions in the hormonal induction of α2u-globulin in rat liver

The role of hepatocellular interaction in the androgen-dependent synthesis of rat alpha 2u-globulin was examined by immunochemical analysis of liver sections. Both after androgen administration to the ovariectomized female and during puberty in the male, only a subpopulation of hepatocytes became competent to synthesize alpha 2u-globulin. These competent hepatocytes first appeared as discontinuous patches along the wall of the central vein. After the formation of a confluent layer around the central vein, cellular competency was seen to propagate toward the periportal direction through the cords of hepatic cells. Although the periportal progression of cellular competency for the synthesis of alpha 2u-globulin appeared to be an all-or-none phenomenon, it did not require cell division. From these results we conclude that certain components of the central vein are necessary for the hormonal induction of alpha 2u-globulin in the rat liver. We also propose that a primary endocrine influence on the hepatic vein results in the production of a secondary paracrine mediator which can trigger the synthesis of alpha 2u-globulin in adjacent hepatocytes. Perivenous to periportal flow of this putative secondary mediator can explain cell recruitment for the synthesis of alpha 2u-globulin along the hepatic cords.
Influence of Agrobacterium rhizogenes on induction of hairy roots for enhanced production of artemisinin in Artemisia annua L. plants

Artemisinin production from plant tissue cultures and induction of hairy roots in vitro have been considered to be a promising alternative, which offer a high degree of genetic stability, grow rapidly and produce the higher spectrum of secondary metabolites than wild type plants. Hairy root cultures developed from infection of different explants of in vitro germinated Artemisia annua L. plant with Agrobacterium rhizogenes LBA 9402 strain were selected on the basis of high artemisinin content and growth. Integration of the TL-DNA ( rol gene) region of the pRi plasmid was confirmed by polymerase chain reaction (PCR) analysis of the gene located in this region. The effect of different environmental factors like temperature, pH, cultivation media and carbon source on growth and artemisinin production were studied in shake flask cultures. Detailed batch growth and production kinetics with sugar consumption profile were also established. Maximum volumetric productivity of 390 μg L -1 day -1 was obtained in hairy root cultures. Keywords: Agrobacterium , Artemisia annua L. , artemisinin, hairy root cultures
Predicting threat of climate change to the Chinese grouse on the Qinghai—Tibet plateau

The Chinese grouse Tetrastes sewerzowi is restricted to small mountain areas on the southeastern edge of Qinghai—Tibet plateau. Recent evidence indicates that the global climate has undergone rapid change. To assess the potential effects of climate change on Chinese grouse, we applied a maximum-entropy modeling (MaxEnt) method to predict the current and future distributions of this species for three time periods: 2020, 2050 and 2080 in two greenhouse-gas emissions scenarios (A2a and B2a), which assume a medium and a lower increase in CO2 emissions, respectively. Our modeling revealed that: 1) the size of suitable areas for grouse will decline over time, especially in emissions scenario A2a; 2) range shifts will happen at both latitudinal (northward shift) and elevational direction (upward). In addition, habitat expansion will be limited relative to loss, especially in the more distant future. Although the size of suitable area will not change greatly in the near future (e.g. 2020 and 2050), as predicted in the emissions scenario A2a in 2020, habitat will become more fragmented. Therefore, we suggest that the habitat fragmentation be considered with range shifts calculation while assessing the climate change threats. To cope with the ongoing climate change, either the protected area of the existing reserves should be expanded or new reserves should be established to accommodate range shifts. Reforestation and gouse population monitoring should also be conducted in the reserves to track response of grouse to climate change.
Preweaning mortality of Weddell seal pups

We examined mortality prior to weaning of Weddell seal pups (Leptonychotes weddellii), using resighting data collected from 1984 to 1993 on the annual ice of McMurdo Sound, Antarctica. Mortality rates were estimated using counts of dead pups found on the surface and mark–recapture techniques. The standard Jolly–Seber model for open populations fit the recapture data best and corresponded well to the known biology of these animals. Yearly mortality rates estimated by mark–recapture techniques ranged from 6 to 22%, with a mean across years of 13%. These values are twice as high as those previously reported for Weddell seals and those calculated from counts of dead pups in this study. This suggests that there is significant unseen mortality due either to undiscovered fatalities on the ice surface or to significant mortality occurring in the water.
The Chloroplast Envelope: Structure, Function, and Role in Leaf Metabolism

INTRODUCTION 140 ISOLATION OF ENVELOPES . 141 COMPOSITION AND STRUCTURE OF THE ENVELOPE . 142 ENZYME ACTIVITIES OF THE ENVELOPE. 145 PERMEABILITY OF THE INNER ENVELOPE MEMBRANE . 146 Gases 146 Neutral Compounds 146 Ions and Acids 147 SPECIFIC METABOLITE TRANSPORT . 149 Phosphate and Phosphate Ester Transport 149 Dicarboxylate Transport 1 5 1 ATP and ADP Transport 1 5 1 Glucose Transport 1 5 1 Amino Acid Transport 152 Transport of Pyruvate 152 THE pH GRADIENT ACROSS THE CHLOROPLAST ENVELOPE 152 PROTON TRANSFER BETWEEN THE STROMA AND THE EXTERNAL SPACE . 1 54 GRADIENT COUPLING . 1 56 METABOLIC SIGNIFICANCE OF THE PHOSPHATE AND DICARBOXYLATE TRANSLOCATORS 1 59 CONCLUDING REMARKS . 162
Mechanisms of action of particular endocrine-disrupting chemicals

Abstract In vertebrates, nuclear receptors are important for the growth, differentiation and development of many organs. A large number of chemicals including pesticides, plastic components, heavy metals, hydrocarbons or pharmaceutical, present in food and in the environment are able to interfere with these receptors producing adverse effects during vertebrate development or reproductive cycle. In this review, we summarise the molecular mechanisms of action of nuclear receptors. We discuss how these receptors may be activated in vivo by different exogenous chemicals and discuss reporter assays and cell experimental models that provided useful mechanistic information about several classes of environmental contaminants.
Effects of Different Calcium Concentrations Supplemented on the Diet of Partula gibba on their Morphometric Growth Parameters, Weight and Reproduction Success

ABSTRACT Partula gibba, commonly known as the Fat Guam Partula, is endemic to Guam and Northern Mariana Islands, and it is listed as endangered in the IUCN Red List of Threatened Species. The effects of calcium concentration on its growth and reproductive success were studied. The snails were divided into six groups, fed ad libitum on a diet based on the one formulated by Frame and Clarke at the Nottingham University approximately 25 years ago or variants in which cuttlebone was substituted by various concentrations of calcium carbonate. Shell height, thickness and width, aperture/lip height and width where recorded every month for a whole year, and all were found to be significantly positively correlated with the percentage of added calcium carbonate in the diet (range 0–40% dry wt:wt). Morphometric growth parameters of snails fed 20% added calcium carbonate did not differ significantly from the diet with added cuttlebone (20%), with the exception of their reproductive success, which was lower with the cuttlebone treatment. Reproduction success (expressed by the number of newborns per adult per month) was also significantly and positively correlated over the range of added calcium carbonate to the diet.
Insular arctic ground squirrels (Spermophilus parryii) of the North Pacific: indigenous or exotic?

Abstract We lack critical information for oceanic archipelagos worldwide related to the origin and status of insular faunas. In southwestern Alaska, in particular, a need exists to tease apart whether specific insular populations are naturally occurring or are the result of exotic introductions by humans. We analyzed variation in mitochondrial sequences of the cytochrome-b gene and 8 nuclear microsatellite loci across 215 individuals representing 17 populations (12 insular) to refine our understanding of the history of the previously identified Southwest clade of arctic ground squirrels (Spermophilus parryii). We found significant geographic structure that suggests long-term isolation and diversification (Ushugat Island and Cold Bay), but we also documented closely related populations that are likely the result of human-mediated introductions. The latter instances (Kavalga and Unalaska islands) corroborate reports from early Alaska explorers.
Untargeted metabolic profiling of winery‐derived biomass waste degradation by Aspergillus niger

BACKGROUND: Ascomycetes are capable of considerable lignocellulose degradation. However, there is limited knowledge on the metabolic profile of their biomass degradation. Metabolomic studies are capable of providing important biochemical information to understand and characterise fungal biomass degradation mechanisms. RESULTS: Winery biomass waste of Vitis vinifera var. Shiraz was subjected to Aspergillus niger mediated solid state fermentation for 8 days in 2H2O supplemented medium. Samples were collected every 24h, freeze-dried and derivatized before GC-MS analysis. Covariance-inverse multivariate statistics were used to classify the most significant metabolites. Metabolite-flux profiling classified 37 unique metabolites in 18 different pathways leading to or from glycolysis-tricarboxylic acid pathways. The majority of the sugars were consumed during the first 4 days; this was in order to synthesize fatty acids, amino acids and secondary metabolites. Inhibition started at day 5, as indicated by the accumulation of sugars and the plateauing of N-acetyl glucosamine (a major fungal cell wall component). CONCLUSIONS: A 4-day continuous yeast or mixed fungal fermentation will not only prevent product inhibition, but it will also aid in generating bio-ethanol. Inducing 2-keto-acid decarboxylases followed alcohol dehydrogenases at the onset of inhibition is predicted to aid in the generation of butanol isomers, which are considered valuable sources of fuel.
A Tight and Unified Analysis of Gradient-Based Methods for a Whole Spectrum of Differentiable Games

We consider diﬀerentiable games where the goal is to ﬁnd a Nash equilibrium. The machine learning community has recently started using variants of the gradient method ( GD ). Prime examples are extragradient ( EG ), the optimistic gradient method ( OG ) and consensus optimization ( CO ), which enjoy linear convergence in cases like bilinear games, where the standard GD fails. The full bene-ﬁts of theses relatively new methods are not known as there is no uniﬁed analysis for both strongly monotone and bilinear games. We provide new analyses of the EG ’s local and global convergence properties and use is to get a tighter global convergence rate for OG and CO . Our analysis covers the whole range of settings between bilinear and strongly monotone games. It reveals that these methods converges via diﬀerent mechanisms at these extremes; in between, it exploits the most favorable mechanism for the given problem. We then prove that EG achieves the optimal rate for a wide class of algorithms with any number of extrapolations. Our tight analysis of EG ’s convergence rate in games shows that, unlike in convex minimization, EG may be much faster than GD .
Epiphytic macrolichen communities correspond to patterns of sulfur and nitrogen deposition in the northeastern United States

Abstract Atmospheric deposition of sulfur (S) and nitrogen (N) has decreased steadily in the northeastern U.S. since the federal 1970 Clean Air Act was passed, yet deposition remains elevated above natural background levels throughout the region. Epiphytic macrolichens are highly sensitive to air pollution and their status is a good indicator of ecological health. We used deposition modeling for 2000–2013 and multiple metrics of lichen status (i.e., species composition, species richness, thallus condition, lichen sensitivity indices, lichen elemental analysis) to assess air pollution effects at 24 plots in four federally-mandated Class I areas. The areas (Lye Brook Wilderness, VT; Great Gulf and the Presidential Range-Dry River Wildernesses, NH; and Acadia National Park, ME) encompass a range of high to low deposition sites. We developed thallus condition scores and sensitivity groups and indices for S and N based on species patterns using deposition estimates gleaned from a larger, independent data base. Non-metric multidimensional scaling ordinations differentiated forest structure effects on lichen community composition from more complex deposition and elevation effects. Annual mean and cumulative deposition of N correlated strongly with decreases in lichen species richness and N-sensitive species, and poorer thallus condition. Cumulative dry deposition of S yielded the best fit to decreases in thallus condition, poorer community-based S Index values, and absence of many S-sensitive species. Multiple metrics provided consistent evidence that higher depositional loading was associated with greater adverse effects. In general, stronger correlations between present day lichen metrics and cumulative deposition (post-2000), compared to current deposition, emphasize the long-term nature of emissions impacts and continued need to control S and N emissions to restore the ecological health of lichen communities and linked biota.