Miracle-dz/UniFAR-FTUs huggingface dataset:
CONSUMPTION, SURVIVAL AND GROWTH IN THE INVASIVE FRESHWATER SNAIL POMACEA CANALICULATA: DOES FOOD FRESHNESS MATTER?

Understanding factors that determine the fitness of invasive species may help us predict their spread and impact. Previous studies of the survival, growth and reproduction of Pomacea canaliculata, a freshwater apple snail native to South America now widely spread in Asia, North America and Hawaii, have emphasized the use of fresh leaves as food. We compared the consumption and growth of P. canaliculata reared on fresh and decaying leaves of three species of macrophytes with contrasting content of phenolics (general plant defence chemicals) and nutrients. We conducted 1-day consumption assays using adult snails and a 1-month survival and growth experiment using snails of various sizes. Our results showed that the consumption, survival and growth of P. canaliculata were determined by plant nutrients and phenolics, rather than plant freshness. For Murdannia nudiflora, a species with low phenolic content, fresh leaves with high nitrogen content were more palatable and valuable for growth than decaying leaves with low nitrogen content. Survival was high and not different between the fresh and decaying leaf treatments. For Myriophyllum aquaticum, decaying leaves with moderate nitrogen and low phenolic contents were more palatable and valuable for snail survival and growth than fresh leaves with high nitrogen and high phenolic contents. For Polygonum barbatum, a species with low nitrogen and medium phenolic contents, both fresh and decaying leaves were unpalatable, resulted in low snail survivorship, and did not support snail growth. The results thus indicate that P. canaliculata can utilize both fresh and decaying leaves of adequate levels of nutrients and low levels of phenolics. This dietary flexibility may have contributed to its successful colonization of many types of freshwater wetlands in regions where high-quality fresh leaves are not available throughout the year.
On casting importance weighted autoencoder to an EM algorithm to learn deep generative models

We propose a new and general approach to learn deep generative models. Our approach is based on a new observation that the importance weighted autoencoders (IWAE, Burda et al. [2015]) can be understood as a procedure of estimating the MLE with an EM algorithm. Utilizing this interpretation, we develop a new learning algorithm called importance weighted EM algorithm (IWEM). IWEM is an EM al-gorithm with self-normalized importance sampling (snIS) where the proposal distribution is carefully selected to reduce the variance due to snIS. In addition, we devise an annealing strategy to stabilize the learning algorithm. For missing data problems, we propose a modiﬁed IWEM algorithm called miss-IWEM. Using multiple benchmark datasets, we demonstrate empirically that our proposed methods out-perform IWAE with signiﬁcant margins for both fully-observed and missing data cases.
Air Movement in Laboratory Infections [and Discussion]

Microbiological safety cabinets are designed to contain aerosols generated during work with pathological material. The three currently available types are described, and the use of an operator protection factor to characterize containment by open-fronted class I and II types is discussed. Methods for measuring operator protection are outlined and current cabinet containment performance is reviewed. Illustrations are given of the extension of safety-cabinet test methods to special facilities for handling carcinogenic or radio-pharmaceutical material and to the evaluation of complete rooms housing specific containment facilities. The safety-cabinet operator protection factor is proposed as a suitable index for assessing containment by laboratory fume cupboards.
N‐poor ecosystems may respond more to elevated [CO2] than N‐rich ones in the long term. A model analysis of grassland.

The Hurley Pasture Model was used to examine the short and long‐term responses of grazed grasslands in the British uplands to a step increase from 350 to 700 μmol mol–1 CO2 concentration ([CO2]) with inputs of 5 or 100 kg N ha–1 y–1. In N‐rich grassland, [CO2] doubling quickly increased net primary productivity (NPP), total carbon (Csys) and plant biomass by about 30%. By contrast, the N‐poor grassland underwent a prolonged ‘transient’, when there was little response, but eventually NPP, Csys and plant biomass more than doubled. The ‘transient’ was due to N immobilization and severe depletion of the soil mineral N pool. The large long‐term response was due to slow N accumulation, as a result of decreased leaching, decreased gaseous N losses and increased N2‐fixation, which amplified the CO2 response much more in the N‐poor than in the N‐rich grassland. It was concluded that (i) ecosystems use extra carbon fixed at high [CO2] to acquire and retain nutrients, supporting the contention of Gifford et al. (1996 ), (ii) in the long term, and perhaps on the real timescale of increasing [CO2], the response (in NPP, Csys and plant biomass) of nutrient‐poor ecosystems may be proportionately greater than that of nutrient‐rich ones, (iii) short‐term experiments on nutrient‐poor ecosystems may observe only the transient responses, (iv) the speed of ecosystem responses may be limited by the rate of nutrient accumulation rather than by internal rate constants, and (v) ecosystem models must represent processes affecting nutrient acquisition and retention to be able to simulate likely real‐world CO2 responses.
Revision of the brachycistidine genus Colocistis Krombein, 1942 (Hymenoptera, Tiphiidae)

Twelve species of the brachycistidine genus Colocistis Krombein, 1942 are reviewed and two new species, Colocistis chemsaki and C. oaxacana, are described from Baja California and Oaxaca, Mexico respectively. A key to the species and species distribution maps are provided.
Comparison of growth performance and genetic diversity of pearl oyster (Pinctada martensii) families in a breeding program

ranged from 2 to 4, with an average of 3.3. The average observed (Ho) and expected (He) heterozygosity of the four families varied from 0.476 to 0.573 and from 0.584 to 0.679, respectively. The results of the analysis of molecular variance (AMOVA) indicated that 88.4% of the total variations was attributed to the genetic variations within family, whereas only 11.6% variations among families. The results that there exists highly genetic diversity and genetic differentiation among the four families indicates desirable conditions for developing superior lines of the species by family mating.
Accelerating Gradient Boosting Machines

Gradient Boosting Machine (GBM) introduced by Friedman (2001) is a widely popular ensembling technique and is routinely used in competitions such as Kaggle and the KDD-Cup (Chen and Guestrin, 2016). In this work, we propose an Accelerated Gradient Boosting Machine (AGBM) by incorporating Nes-terov’s acceleration techniques into the design of GBM. The diﬃculty in accelerating GBM lies in the fact that weak (inexact) learners are commonly used, and therefore, with naive application, the errors can accumulate in the momentum term. To overcome it, we design a “corrected pseudo residual” that serves as a new target for ﬁtting a weak learner, in order to perform the z-update. Thus, we are able to derive novel computational guarantees for AGBM. This is the ﬁrst GBM type of algo-rithm with a theoretically-justiﬁed accelerated convergence rate.
FOREST BIOMASS OF CHINA: AN ESTIMATE BASED ON THE BIOMASS–VOLUME RELATIONSHIP

In this study, a method was developed to estimate the forest biomass of China based on the relationship between stand biomass and volume. Biomass-volume relationships were quantified for all the main forest types in China using 758 sets of data obtained from direct field measurements. These relationships were used to convert volume measurements into total biomass values (above- and belowground dry masses) based on 1984-1988 forest inventory data for China. The latter had been compiled from more than 250000 permanent and temporary field plots across the country. This data contained information on forest area and timber volume for each ape class and site class for all forest types at the provincial level. As a result, the total forest biomass of China was estimated as 9103 Tg (1 Tg 10(12) g), with 8592, 326, and 185 Tg from forests, special product plantations, and bamboo Forests, respectively. The area-weighted mean biomass density was 84 Mg/ha (1 Mg = 10(6) g). For comparison, two additional estimates, one based on the mean biomass density method and another based on the mean ratio of biomass to stem volume, were also derived. Compared to the biomass-volume relationship method, the mean biomass density method considerably overestimated the forest biomass of China (by 59.6%), while the mean ratio of biomass to stem volume method slightly underestimated it (by 12.1%). Despite the small forest biomass value due to a low forest cover, the area-weighted mean biomass density was comparable to those of other regions in the middle and high latitudes except in the United States. We believe that our study provided not only an appropriate estimate of forest biomass for China, but also an improved methodology for estimating forest biomass at the regional, national, and global level.
20 Years of Lipid Nanoparticles (SLN & NLC): Present State of Development & Industrial Applications

In 1990, the lipid nanoparticles were invented in the laboratories, the first patent filings took place in 1991. The lipid nanoparticles were developed as alternative to traditional carriers such as polymeric nanoparticles and liposomes. After 20 years of lipid nanoparticles, the present state of development is reviewed - academic progress but also the development state of pharmaceutical products for the benefit of patients. Meanwhile many research groups are active worldwide, their results are reviewed which cover many different administration routes: dermal and mucosal, oral, intravenous/ parenteral, pulmonary but also ocular. The lipid nanoparticles are also used for peptide/protein delivery, in gene therapy and various miscellaneous applications (e.g. vaccines). The questions of large scale production ability, accepted regulatory status of excipients, and - important for the public perception - lack of nanotoxicity are discussed, important pre-requisites for the use of each nanocarrier in products. Identical to the liposomes, the lipid nanoparticles entered first the cosmetic market, product examples are presented. Presently the pharmaceutical product development focuses on products for unmet needs and on niche products with lower development costs (e.g. ocular delivery), which can be realized also by smaller companies. A pharmaceutical perspective for the future is given, but also outlined the opportunities for non-pharmaceutical use, e.g. in nutraceuticals.
Phenology, litterfall, growth, and root biomass in a tidal floodplain forest in the Amazon estuary

A dinâmica de floresta sujeita a inundacao parece ser fortemente influenciada pela frequencia e intensidade de disturbios naturais como a inundacao. Em uma antiga floresta sucessional de varzea proxima ao porto de Belem, Brasil, testou-se esta hipotese pela medicao sazonal dos padroes de fenologia, incluindo queda de serrapilheira, em relacao a duas variaveis chaves: chuva e nivel da mare. Em adicao, estimamos o crescimento anual da comunidade florestal pela medicao do incremento do diâmetro de troncos ao longo do tempo e desenvolvimento radicular. Encontrou-se alta correlacao entre florescimento e frutificacao com chuva e nivel da mare, porem as correlacoes entre a queda da serrapilheira e estas variaveis foram geralmente fracas. Ao contrario de nossa hipotese, biomassa de raizes ate 1 m de profundidade nao variou significativamente ao longo do gradiente topografico, e esta foi menor a intermediaria em todos os niveis topograficos do que em outras florestas neotropicais. A queda de serrapilheira e o incremento de troncos foram superiores do que em outras florestas tropicais, indicando uma alta produtividade neste ecossistema.
The prediction of fatty acid structure from selected ions in electron impact mass spectra of fatty acid methyl esters

The possibility of fatty acid identification from ions in the mass region of 50–110 amu in electron impact mass spectra has been studied by application of various multivariate techniques. The focus has mainly been on the prediction of the number of double bonds in methylene-interrupted polyunsaturated fatty acids isolated from marine lipids. The number of double bonds in these fatty acids could be predicted with high accuracy, both by partial least squares regression on all ions in this region, and by multiple linear regressions on selected subsets of 5–6 ions. The subsets with optimal predictive power have been found, and the ability to distinguish between methylene interrupted polyunsaturated fatty acids and other fatty acids have also been evaluated.
Stochastic Variance-Reduced Algorithms for PCA with Arbitrary Mini-Batch Sizes

We present two stochastic variance-reduced PCA algorithms and their convergence analyses. By deriving explicit forms of step size, epoch length and batch size to ensure the optimal runtime, we show that the proposed algorithms can attain the optimal runtime with any batch sizes. Also, we establish global convergence of the algorithms based on a novel approach, which studies the optimality gap as a ratio of two expectation terms. The framework in our analysis is general and can be used to analyze other stochastic variance-reduced PCA algorithms and improve their analyses. Moreover, we introduce practical implementations of the algorithms which do not require hyper-parameters. The experimental results show that the proposed methodsd outperform other stochastic variance-reduced PCA algorithms regardless of the batch size.
Characterization of Acetate-Utilizing Bacteria in Soil Sequences From Major Ecological Subregions of California

Summary Our goals for this project focus on characterization of organisms that consume acetate, an organic acid central to carbon transformations in anaerobic soils. To assess the acetate-utilizing bacterial community in a large breadth of California soil types, we have focused on several wellstudied soil sequences from around the state. The selected soil sequences represent eight of the major California ecological subregions as designated by the USDA Natural Resources Conservation Service and are among the best-studied soils in the state. To characterize the acetate-utilizing bacterial community in these soils, we used stable isotope probing, which allows the linkage of a metabolic activity and the identity of the microorganism carrying out that activity. Using the empirically determined acetate-utilizing rate and substrate utilization efficiency for each soil under aerobic and anaerobic conditions, we incubated the soil samples with [1, 2] 13 C-acetate for the optimal time and temperature. Following separation of labeled DNA from unlabeled DNA by CsCl gradient ultracentrifugation, amplified portions of the 16S rRNA gene and separated them by denaturing gradient gel electrophoresis. DGGE and cluster analysis of soil samples indicated low diversity of acetate utilizing organisms with no clear correlation between location and microbial community composition. Analysis of DNA sequence of clones correlated directly to DGGE bands of anaerobically incubated samples revealed a predominance of Betaproteobacteria of the orders Burkholdariaceae and Oxalobacteraceae and Firmicutes of the genera Bacillus or Clostridia. The Firmicutes were found in nearly all of the samples, whereas, the distribution of the Betaproteobacteria was more limited. Unsurprisingly, most of the closest relatives were from soils, and many were from anoxic rice paddy soils. Several closest relatives of these groups are facultative denitrifying bacteria, consistent with the incubation conditions.
ARE BIOENERGETIC PROPERTIES LINKED WITH SHELL FLUCTUATING ASYMMETRY AND HETEROZYGOSITY IN ICELAND SCALLOP, CHLAMYS ISLANDICA?

Abstract We investigated the relationship between physiological properties, swimming performance, shell fluctuating asymmetry, and heterozygosity at allozyme loci in the Iceland scallop, Chlamys islandica, in an attempt to describe potential physiological mechanisms for the negative relationship between shell fluctuating asymmetry and survival of this species in pearl nets (Fréchette & Daigle 2002). No clear relationship was observed between shell fluctuating asymmetry and the different physiological and genetic parameters, although the maximum number of contractions in a series during escape tests and the specific activity of arginine kinase in the adductor muscle were linked with shell asymmetry before the application of corrections for multiple comparisons. Pyruvate kinase activity in soft tissues was higher in animals that were heterozygous at 2 loci compared with those that were heterozygous at 4 loci. Although our exploratory study suggests that shell asymmetry may reflect bioenergetic difficulties, further study is required to confirm such links.
Metaknowledge

The growth of electronic publication and informatics archives makes it possible to harvest vast quantities of knowledge about knowledge, or “metaknowledge. ” We review the expanding scope of metaknowledge research, which uncovers regularities in scientific claims and infers the beliefs, preferences, research tools, and strategies behind those regularities. Metaknowledge research also investigates the effect of knowledge context on content. Teams and collaboration networks, institutional prestige, and new technologies all shape the substance and direction of research. We argue that as metaknowledge grows in breadth and quality, it will enable researchers to reshape science—to identify areas in need of reexamination, reweight former certainties, and point out new paths that cut across revealed assumptions, heuristics, and disciplinary boundaries.
Commemorating 100 years since Hjort's 1914 treatise on fluctuations in the great fisheries of northern Europe: where we have been, where we are, and where we are going

Theyear 2014marks the 100th anniversary of JohanHjort’s seminal treatise, Fluctuations in the great fisheries of northern Europe, viewed in the light of biological research. This special issue of the ICES Journal ofMarine Science commemorates this anniversary. The thirty-two articles that appear herein demonstrate the deep influence that Johan Hjort’s work has had, and continues to have, on fisheries and marine science.
Copper uptake in Typha latifolia as affected by iron and manganese plaque on the root surface

The effects of iron (Fe) and manganese (Mn) plaque on the accumulation of copper (Cu) in Typha latifolia L. were investigated under laboratory conditions in nutrient solution cultures. Seedlings with and without Fe plaque on their roots, induced with 15 or 60 µg·mL1 Fe, were exposed to 0.04, 0.12, or 0.36 µg·mL1 Cu solutions, and seedlings with and without Mn plaque, induced with 15 or 60 µg·mL1 Mn, were exposed to 0.12 or 0.36 µg·mL1 Cu solutions for 24 days, respectively. In all cases, the amount and proportion of Cu adsorbed on the root surface increased with a higher concentration of Cu in the solutions. In the presence of Fe or Mn, T. latifolia adsorbed more Cu and had a higher proportion of Cu on its roots, especially the roots with heavy Mn or Fe plaque. Although more Fe than Mn accumulated on the roots in the form of plaque, the Mn plaque adsorbed more Cu. The data suggest that root plaque can act as a Cu reservoir, depending on the amount of Fe or Mn on the roots and the amount of Cu in the e.
The Dynamic Effects of Perceptions of Dread Risk and Unknown Risk on SNS Sharing Behavior During Emerging Infectious Disease Events: Do Crisis Stages Matter?

In response to the increasing prevalence of emerging infectious disease (EID) threats, individuals are turning to social media platforms to share relevant information in ever greater numbers. In this study, we examine whether risk perceptions related to user-generated content have dynamic impacts on social networking site (SNS) sharing behavior in different crisis stages. To answer this question, we applied psychometric analysis to evaluate how dread risk and unknown risk can characterize EID threats. Drawing broadly on the literature of risk perceptions, self-perception theory, and crisis stages, we relied on microblogs collected from Sina Weibo, utilizing the vector autoregression model to analyze dynamic relationships. We found that perceptions of dread risk have a dominant and immediate impact on SNS sharing behavior in the buildup, breakout, and termination stages of EID events. Perceptions of unknown risk have a dominant and persistent impact on sharing behavior in the abatement stage. The joint effect of these two types of risk perception reveal an antagonism impact on SNS sharing behavior, and perceptions of dreadand unknown risk have interaction effects from the buildup to termination stages of EID events. To check robustness, we analyzed keywords related to perceptions of dreadand unknown risk. The results of this study support the empirical application of Slovic’s risk perception framework for understanding the characteristics of EID threats and provide a picture of how perceptions of dreadand unknown risk exert differential time-varying effects on SNS sharing behavior during EID events. We also discuss theoretical and practical implications for the crisis management of EID threats. This study is among the first that uses usergenerated content in social media to investigate dynamic risk perceptions and their relationship to SNS sharing behavior, which may help provide a basis for timely and efficient risk communication.
Energetics and protomer communication in the dynamical structure of S100A13 in free and protein-bound states

Abstract S100A13 is S100 family of EF-hand-containing calcium-binding protein involved in the secretion of some growth factors and pro-inflammatory cytokines lacking signal peptides. The involvement of S100A13 in cancer progression and inflammatory diseases has been reported. In this study, structures generated during atomistic molecular dynamics simulation were studied. Dynamical network analysis data revealed that native inter-protomer communication network driven principally by vdW interaction (~550 kj/mol) is altered (Receptor for advanced glycation end products (RAGE) C2- and Fibroblast growth factor (FGF)-1-bound S100A13) or completely abolished (interleukin-1 (IL1)-α- and C2A-p40Syt1-bound S100A13) in protein-bound S100A13 homodimer. Bulk water density (weighted atomic density) around exposed S100A13 homodimer surface explored tends to follow the dynamical network lead as S100A13 homodimer appeared densely solvated in C2A-p40Syt1- and IL1)-α-bound states but not in RAGE C2- and FGF-1-bound biosystems. Furthermore, projection of radius of gyration and root mean square deviation (from native structure) variables of the generated structures along the 3D-free energy surface showed anti-parallel β-sheet proximal to Ca2+-binding loops-I/II in most metastable complexes retrieved from energy minima state with strong indications for β-sheet network formation during protein binding. Interaction between S100A13 homodimer and ligand–proteins may be dictated by the strength of vdW and electrostatic interaction with possible involvement of bulk water desolvation in some complexes. All these results strongly suggest that disruption of multiprotein receptor complex can be achieved by designing specific compounds targeting a specific aspect of S100A13/protein interaction; such drugs may have clinical usefulness in blocking angiogenesis, reversing cell proliferation and attenuating inflammatory processes.