Miracle-dz/UniFAR-FTUs huggingface dataset:
Great Basin mammal diversity in relation to landscape history

Abstract The alternating mountain ranges and desert basins of the Great Basin in the western United States support higher species diversity of mammals than any other region of comparable area in temperate North America. Topographically complex regions have strong environmental gradients and heterogeneous habitats that result in fragmented geographic ranges over long periods and may promote speciation. In order to evaluate the influence of topography and climate on mammal diversification, we traced the history of mammal diversity during the formation of basin-and-range topography. We compiled species-occurrence data from the NeoMap database of fossil mammals and calculated standing diversity, origination rate, extinction rate, diversification rate (originations − extinctions), and turnover rate (originations + extinctions) for million-year intervals. We evaluated changes in faunal composition (species in mammalian orders and species in rodent families) over time and assessed whether significant changes in diversity and faunal composition tracked major changes in landscape history. Neogene geologic evolution generated by tectonic activity and changing climate created the topographic complexity and habitat heterogeneity of the Great Basin. Over the last 30 million years, extensional tectonic processes caused an older high plateau to collapse and stretch from east to west, resulting in longitudinal expansion by ~235 km to form the Great Basin. Average elevation decreased by 1–3 km. Global warming and associated increases in regional precipitation from 17 to 14 million years ago (mya; the Miocene Climatic Optimum [MCO]) interrupted the long-term trend of Cenozoic cooling and aridification. From 30 to 2 mya, Great Basin mammal diversity peaked during the MCO, then declined over the later Miocene and Pliocene. The major changes in diversity over time were robust to sampling effects. Faunal composition changed episodically, with increasing proportions of rodents, lagomorphs, and carnivores and decreasing proportions of ungulates and proboscideans. The highest diversification rate occurred during the MCO with smaller but significant diversification rates later in the Neogene. The highest turnover rates occurred during and immediately following the MCO. Comparison of rodent faunas of the Great Basin and the Great Plains showed substantial differences in the timing and magnitude of diversification and changes in taxonomic composition. These patterns support the hypothesis that climate change over complex topography stimulated diversification in the Great Basin.
Digestible Lysine Requirements of Hen Turkeys from 6 to 12 Weeks of Age

Two floor pen trials were conducted to determine the digestible lysine requirement of hen turkeys from 46 to 57 days and 71 to 85 days of age, or what is more commonly referred to as the 6 to 12 week period. 2000 Nicholas White female poults were obtained and fed an NRC-type corn-soybean meal diet until the trials began. For the first experiment, 240 46-day-old birds were banded, weighed, computer sorted, and assigned a treatment with 8 birds per pen. In the second experiment, 240 71-day-old birds were weighed, banded, computer sorted, and assigned a treatment with 5 birds per pen. Birds in both trials were fed experimental diets with digestible lysine levels ranging from 0.85 to 1.21% in the 46 to 57 day period and 0.70 to 1.05% in the 71 to 85 day period. Two low protein diets were used and the levels of digestible lysine were obtained by titrating L-lysine HCl into the low protein diets. In order to obtain sufficient amino acid levels and nitrogen levels to support growth equal to the high protein positive control diet, synthetic amino acids were added back into the low-protein diet. Both experiments were of a complete randomized block design. For the first experiment, there were 7 treatments with 4 replicates per treatment. For the second experiment, there were 8 treatments with 6 replicates per treatment. In each experiment, the highest level of lysine was reduced to half of the replicates in order to provide space for the positive control groups which were fed a standard corn and soybean meal diet based on NRC (1994) recommendations. Experimental data were analyzed by analysis of variance and segmented analysis. Segmented analysis indicated that the digestible lysine requirements for the 46 to 57 day period to be 1.04% for body weight gain and 1.07% for feed conversion. In the second trial, the analysis indicated that the digestible lysine requirements for body weight gain and feed conversion to be 0.86% and 0.82%, respectively.
Optimization Modeling of Ethanol Production from Shorgum bicolor grain: Comparison between Separate Hydrolysis Fermentation and Simultaneous Saccharification Fermentation

Two different process configurations, simultaneous saccharification and fermentation (SSF), and separate hydrolysis and fermentation (SHF), were compared for ethanol production from Shorgum bicolor grain. Optimization modeling for glucoamylase and Zymomonas mobilis concentration in both of SSF and SHF were carried out to obtain optimal concentration of ethanol production. The optimum condition was achieved using 0.021 % (v/v) of glucoamylase, and 30.19% (v/v) of Z. mobilis for SHF. In contrast, the optimum condition for SSF was 0.021 % (v/v) of glucoamylase and 17.51% (v/v) of Z. mobilis . The model predicted SHF processing to be superior. The superiority of SHF over SSF was confirmed experimentally, the result showed ethanol yield of SHF was 134.80 g L -1 and ethanol yield of SSF was 115.66 g L -1 after 72 h incubation time. A high similarity was observed between the predicted and experimental results, demonstrating the accuracy of the model.
Daphnia can protect diatoms from fungal parasitism

Many phytoplankton species are susceptible to chytrid fungal parasitism. Much attention has been paid to abiotic factors that determine whether fungal infections become epidemic. It is still unknown, however, how biotic factors, such as interactions with zooplankton, affect the fungal infection process. Because the size of fungal zoospores is well within the preferred range of food particle size for Daphnia, we hypothesize that Daphnia will affect the fungal infection process by reducing the abundance of fungal zoospores. To examine the effects of zooplankton on the fungal parasitism of phytoplankton, we performed grazing experiments. These experiments revealed that Daphnia significantly decreased fungal parasitism by grazing on the fungal zoospores. Daphnia also had a small positive effect on fungal infection, probably by increasing the encounter rate between fungi and host phytoplankton cells. These results suggest that Daphnia can affect the seasonal succession of chytrids and their host phytoplankton species. In addition, these results imply that zoospore‐producing fungi may play an ecological role as food sources for Daphnia in aquatic food webs.
Temperature‐induced stress leads to bleaching in larger benthic foraminifera hosting endosymbiotic diatoms

Physiological mechanisms of bleaching were studied on larger benthic foraminifera (LBF) hosting endosymbiotic diatoms. Amphistegina radiata, Heterostegina depressa, and Calcarina hispida were exposed to increasing temperatures in static temperature experiments (23°C to 33°C, 6 d). Photosynthetic activity (Fv : Fm, measured with a pulse‐amplitude modulated fluorometer), chlorophyll a (a proxy for symbiont biomass), and motility (a proxy for overall fitness of the foraminifera) were reduced in specimens at 32°C to 33°C, and cytoplasm color changes associated with bleaching were observed. A 30‐d flow‐through experiment at three temperatures (26°C to 31°C) and three levels of inorganic nitrate concentration (0.5 to 1.4 µmol L−1) confirmed negative effects of temperature at 31°C for A. radiata (including growth) and H. depressa. Another Calcarina species, Calcarina mayorii, was not affected. This suggests that temperature effects are species‐specific. However, elevated nutrient concentrations did not affect any of the parameters measured. Temperatures > 30°C stress the foram–diatom endosymbiosis in some LBF species, which may lead to subsequent bleaching of the host. Given that a 2–3°C increase led to rapid bleaching of most species, we propose that, similar to corals, these species are threatened by sea‐surface temperature increase predicted for tropical reef waters in the near future.
Ferrier Lecture - Growth and plasticity in the nervous system

Clues as to the possible nature of the processes of learning and form discrimination are provided by certain similarities between the nervous system of cephalopods and mammals. These are the presence of (1) large numbers of small neurons, (2) self-re-exciting chains of neurons, (3) arrangements for interaction of the effects proceeding from each point of a stimuated sensory surface. The optic and tactile receiving centres of Octopus both contain elaborate interlaced arrangements of fibres that would allow for diffusion of effects of a local stimulus and interaction of effects from different loci. There is also provision for interaction between tactile and optic information after it has been synthesized in this way. The uppermost lobe of the brain (lobus verticalis) receives the final product of this interaction and appears to have the function of conserving the information. After its removal an octopus is able to retain a learned inhibition for only a few minutes, as against many hours in the normal animal. The course of these learning processes in Octopus strongly suggests that self-regenerating circuit systems are involved, but these can hardly be the only basis for the stable learning of higher animals. The study of the factors controlling the growth of regenerating nerve fibres shows that the nature of peripheral contacts made determines the size of the fibres. Evidence is also given that the size reached by nerve cells and their dendrites depends upon the amount of afferent influence that falls upon them. Every part of the nervous system is thus doubly dependent on influences it receives and on the cells that it can influence. The continual renewal of the finer branches of the fibres may well be controlled by these influences. Slight changes as a result of the combinations set up during functioning would be sufficient to alter the probable course of excitation within the nervous networks and thus to provide a stable basis for learned reactions.
Microbial Bioremediation in Omics era: Opportunities and Challenges

Bioremediation is a sustainable solution to clean up the organic pollutants from the contaminated sites. Both plants and microbes play leading roles in bioremediation processes. Compared to phytoremediation, microbial bioremediation is paid more attention and has wide applications since microorganisms are ubiquitous in the environment and they are able to function under various conditions, especially at really extreme environmental conditions where plants cannot survive.
A new Parametopella species (Crustacea: Amphipoda: Stenothoidae) from Antholoba achates (Anthozoa: Actiniaria) from Coquimbo, Chile (with remarks on Parametopa alaskensis (Holmes))

This paper describes a new species in the genus Parametopella (Amphipoda: Stenothoidae), P. antholobae sp. nov., collected among the tentacles of the sea anemone Antholoba achates, found in shallow water near Coquimbo, Chile. A key to all Parametopella species is provided. The type specimen of the superficially similar species Parametopa alaskensis (Holmes) was studied; that species remains in Parametopa.
Robust Semisupervised Generative Adversarial Networks for Speech Emotion Recognition via Distribution Smoothness

Despite the recent great achievements in speech emotion recognition (SER) with the development of deep learning, the performance of SER systems depends strongly on the amount of labeled data available for training. Obtaining sufficient annotated data, however, is often extremely time consuming and costly and sometimes even prohibitive because of privacy and ethical concerns. To address this issue, this article proposes the semisupervised generative adversarial network (SSGAN) for SER to capture underlying knowledge from both labeled and unlabeled data. The SSGAN is derived from a GAN, but the discriminator of the SSGAN can not only classify its input samples as real or fake but also distinguish their emotional class if they are real. Thus, the distribution of realistic inputs can be learned to encourage label information sharing between labeled and unlabeled data. This article proposes two advanced methods, i.e., the smoothed SSGAN (SSSGAN) and the virtual smoothed SSGAN (VSSSGAN), which, respectively, smooth the data distribution of the SSGAN via adversarial training (AT) and virtual adversarial training (VAT). The SSSGAN smooths the conditional label distribution given inputs using labeled examples, while the VSSSGAN smooths the conditional label distribution without label information (“virtual” labels). To evaluate the effectiveness of the proposed methods, four publicly available and frequently used corpora are selected to conduct experiments in intradomain and interdomain situations. The results illustrate that the proposed methods are superior to the state-of-the-art methods. Specifically, in experimental settings with mismatched and semimismatched unlabeled training sets, the SSSGAN and VSSSGAN are more robust than the SSGAN because of the distributional smoothness.
Drought Tolerance Responses of Purple Lovegrass and 'Adagio' Maiden Grass

Nonnative Miscanthus sinensis Anderss 'Adagio' and native Eragrostis specta- bilis (Pursh) Steud. were evaluated for drought tolerance in a rain-excluded landscape setting in sandy soil in response to irrigation application volumes of 0 L, 0.25 L, 0.5 L, or 0.75 L. As irrigation rates increased, plant mass, canopy size, and shoot-to-root ratios increased for both species, being greatest at the 0.75-L rate. Shoot dry weight, root dry weight, total biomass, and shoot-to-root ratios were greater for E. spectabilis than M. sinensis. Cumulative water stress integral was also greater for E. spectabilis. Greater growth in conjunction with higher cumulative water stress indicates the native E. spectabilis is anisohydric and more drought-tolerant than the isohydric nonnative M. sinensis.
Thyroid function and egg characteristics of laying hens in response to dietary methionine levels

This experiment was conducted to evaluate the effects of dietary methionine (met) levels on thyroid function, egg characteristics and protein and energy efficiency of laying hens. A total number of 216 commercial laying hens at 23 weeks of age were randomly allocated to six treatments (four replicates with nine birds in each), and fed 6 dietary have deficiency in met supplement (0.24, 0.29, 0.34, 0.39, 0.44 and 0.49% met). With increasing dietary met level from 0.24 to 0.49%, plasma triiodothyronine (T3) showed an inverted U relationship. Plasma thyroxin (T4) was similar between all treatments. Protein and energy efficiency were increased by increasing dietary Met levels. Egg shape index was significantly higher and lower with 0.29 and 0.39% met levels in diet, respectively. Egg surface area and unit surface shell weight increased by increasing dietary met level from 0.24 to 0.49%, and shell ratio decreased linearly. Shell weight increased significantly by increased met level of diet to 0.34%. Albumin index and Haugh unit were significantly lower in hens which fed the three higher levels of met (0.39 to 0.49%). It is concluded that met deficiency alters normal thyroid hormone metabolism, but the effect was dependent on the degree of deficiency. Furthermore, optimal supplementation of met in diets deficient in met, could improve egg quality of laying hens. Key words: Metionine, egg characteristics, triiodothyronine, thyroxine, laying hens.
CORRELATION BETWEEN PARASITE PREVALENCE AND ADULT SIZE IN A TREMATODE-MOLLUSC SYSTEM: EVIDENCE FOR EVOLUTIONARY GIGANTISM IN THE FRESHWATER SNAIL GALBA TRUNCATULA?

The snail-trematode host-parasite system has been widely studied, as trematodes are known to greatly influence the fitness of their hosts. Indeed, during their development, the trematodes castrate the snail and one possible consequence of infection is gigantism of the snail. Snail gigantism is usually investigated experimentally by comparing the size of healthy and artificially infected snails. Here, I focused on naturally infected populations in order to investigate if snails submitted to trematode pressure have evolved specific life-history traits to respond to the parasite prevalence in their natural population. To this end, I estimated the correlations between measures of size (obtained from healthy laboratory individuals originating from populations) and the parasite prevalence at the population level. I found that the adult size of populations was positively correlated with population prevalence, an indication that gigantism might be operating. Moreover, I found a positive relation between growth and fecundity in healthy populations, while no such trade off was found in highly parasitized populations, suggesting that there may be a cost in fecundity to this gigantism.
Phenotypic characterization of indigenous rice (Oryza sativa L.) germplasm collected from the state of Nagaland, India

Nagaland is one of the eight states in the north-eastern region of India, where a considerable diversity exists in cultivated rice. Recent exploration in this tribal-dominated state has resulted in a collection of 130 rice accessions growing under diverse agroecological conditions. The agromorphological characterization data of 124 rice landraces revealed a significant variability in plant architecture and grain morphological and quality traits. Multivariate analyses including principal component analysis (PCA) and cluster analysis were performed to assess the patterns of morphological variation. The PCA extracted 12 components, which explained 75.4% of the total variation for 38 quantitative and qualitative traits. The cluster analysis grouped 124 rice landraces into five clusters, and the number of landraces in each cluster ranged from 1 to 59. The correlations among the traits are discussed, which will be useful in considering traits for genetic improvement in grain yield and quality. The landraces have been conserved in the national genebank for further utilization.
TOLERANCE VALUES OF STREAM CADDISFLIES (TRICHOPTERA) IN THE LOWER COLORADO RIVER BASIN, USA

Abstract One hundred and four caddisfly species within 42 genera and 17 families were collected from 93 stream sites in the xeric landscape of the lower Colorado River Basin, USA. Species richness showed a significant negative correlation with channel embeddedness. Forestland had higher species richness than grassland, desert, or urban caddisfly assemblages, and fewer caddisfly species occurred in the salt-cedar (Tamarix) than in willow-alder (Salix-Alnus) and cottonwood-sycamore (Populus-Plantanus) riparian communities. Hydroptilidae comprised nearly 35% of the average relative abundance of caddisflies and were generally tolerant of impaired stream environments. Hydroptila arctia composed the greatest relative proportion of species. Adjusted specific conductance and channel embeddedness metrics showed close agreement with published tolerance values for caddisfly species listed by the U.S. Environmental Protection Agency; genera were in less agreement. Amphicosmoecus canax, Brachycentrus americanus, Culoptila moselyi, Glossosoma ventrale, Ochrotrichia ildria, Psychoglypha schuhi, and Ylodes reuteri were most commonly associated with streams with low salinities and low embeddedness, whereas Cheumatopsyche enonis, Hydropsyche auricolor, Hydroptila ajax, Hydroptila arctia, Neotrichia okopa, Smicridea signata, and Smicridea fasciatella reached highest numeric importance in streams with high salinities and embeddedness.
Oxidation of atmospheric methane in Northern European soils, comparison with other ecosystems, and uncertainties in the global terrestrial sink

This paper reports the range and statistical distribution of oxidation rates of atmospheric CH4 in soils found in Northern Europe in an international study, and compares them with published data for various other ecosystems. It reassesses the size, and the uncertainty in, the global terrestrial CH4 sink, and examines the effect of land‐use change and other factors on the oxidation rate.
Role of the gM/gN glycoprotein complex in the final assembly and egress of human cytomegalovirus (HCMV)

HCMV consists of a dsDNA genome enclosed by, an icosahedral capsid surrounded by a layer of tegument proteins; the virion structure is enclosed in a lipid envelope rich in virus expressed glycoproteins. The HCMV envelope contains an incompletely defined number of glycoproteins. The glycoprotein M (gM) and glycoprotein N (gN) form a gM/gN protein complex which is the most abundant protein component of the HCMV envelope. Recent studies have indicated that deletion of the viral gene encoding either gM or gN is lethal for HCMV. The gM C-terminal cytoplasmic tail (gM-CT) revealed an acidic cluster and a tyrosine-based trafficking motifs. Mutant viruses that lacked the entire cytoplasmic tail of gM or both trafficking motifs were not viable. These results suggested that the trafficking motifs in the gM-CT are indispensable for virus replication. Mutant viruses with acidic cluster deletion or alanine substitutions in the tyrosine-based motif were viable but exhibited a delayed growth phenotype resulting in reduced infectious virus production. These results suggested that gM-CT possibly interacts with cellular proteins that regulate the rate of gM/gN intracellular trafficking. We found that the gM-CT interacts with FIP4 effector of the Rab11. Depletion of FIP4 expression or inhibition of Rab11 function during HCMV infection resulted in lower infectious virus production. It has been previously shown that simultaneous interactions of FIP4 with Arf6/Arf5 and Rab11 were important for vesicular transport of proteins into the endosomal recycling
Modeling Thermal Behavior in Multi-layered GaN HEMT-like Structures

Thermal behavior in multi-layered semiconductor structures like the one present in a Gallium Nitride high electron mobility transistor (GaN-HEMT) is investigated for the heat-flow towards the substrate. A compact analytical model is formulated to predict the peak as well as depth dependent temperature in the structure. Modeling results are verified against detailed three-dimensional TCAD thermal simulations of GaN-on-Si structures with GaN layer thickness of $\mathbf{3}\mu\mathbf{m}$ and Si substrate thickness of $\mathbf{100}\mu\mathbf{m}$. Excellent modeling accuracy is observed for different heat source geometries and power dissipation. In addition, the proposed model is extended to estimate the static thermal coupling factor in multifinger transistors with high level of accuracy.