Miracle-dz/UniFAR-FTUs huggingface dataset:
Amazon River influence on nitrogen fixation and export production in the western tropical North Atlantic

As part of the ANACONDAS program, we investigated the role of the Amazon plume in stimulating offshore nitrogen fixation and export production during the river's high‐discharge period (May–June 2010). Using the shipboard underway system, we performed high‐resolution sampling of over 450,000 km2 of surface waters, characterizing the distribution of nutrients, phytoplankton, particulate organic matter (POM), and stable carbon and nitrogen isotopes of POM in the offshore plume. We found distinct regional variations in diazotroph communities, with the Diatom‐Diazotroph Associations (DDA) Hemiaulus hauckii – Richelia intracellularis dominating the low N : P mesohaline waters to the northwest of the plume axis and Trichodesmium spp. primarily occupying oceanic waters to the east. Nutrient availability broadly shaped diazotroph distributions along the salinity gradient, but habitat longevity may also play a role in the finer‐scale distributions of communities, particularly of DDAs. H. hauckii and Trichodesmium spp. affected the nitrogen and carbon budgets in fundamentally different ways within the plume‐influenced regions, with H. hauckii making much greater contributions to the particulate nitrogen pool and to CO2 drawdown than Trichodesmium spp. , leading to much higher export fluxes. Our findings provide an important constraint on the role of the Amazon plume in creating distinct niches and roles for diazotrophs in the nutrient and carbon budgets of the western tropical North Atlantic.
Effect of Organic Manures, Biofertilizers and Micronutrients on Growth, Yield and Quality of Onion ( Allium cepa L.)

A field experiment was conducted during the Rabi season to find out the effect of organic manures, biofertilizers and micronutrients on growth, yield and quality of onion cv. NHRDF Red - 2. There were 13 treatments viz. , T 0 (Recommended dose of fertilizers), T 1 Poultry manure, T 2 vermicompost, T 3 Azotobacter , T 4 VAM, T 5 Azotobacter +RDF (50%)+zinc, T 6 Azotobacter +RDF(75%)+zinc, T 7 VAM+RDF(50%)+boron, T 8 VAM+RDF (75%)+boron, T 9 RDF (25%)+VAM+poultry manure (50%)+ Azotobacter +boron, T 10 (RDF (25%)+VAM+vermicompost (50%)+ Azotobacter +boron, T 11 RDF (25%)+VAM+poultry manure (50%) Azotobacter +zinc, T 12 RDF (25%)+VAM+vermicompost 50% Azotobacter +zinc and the experiment was laid out under RBD with three replications. The study clearly revealed that there were significant effects of various treatments on the growth, yield and quality attributes of onion. The number of leaves per plant (12.15), plant height (73.02cm), neck thickness (22.00mm), bulb length (6.46 cm), bulb diameter (7.20cm), yield (398.36 kg/ha -1 ) were recorded maximum in treatment T 12 whereas T.S. S (14 °B), vitamin C (12.11mg/100g), total sugars (10.52%), reducing sugar (6.23%) and non-reducing sugar (4.28%) were found maximum in T 10 treatment as compared to other treatment. However, T 12 was good for higher yield improvement and T 10 was the best for quality improvement among the all treatments under study, the application of T 12 (RDF (25%)+VAM+Vermicompost 50% Azotobacter +Zinc) may be suggested for successful cultivation of onion in Lucknow.
BIOTIC AND ABIOTIC INFLUENCES ON THE EVOLUTION OF ELEVATIONAL RANGE LIMTS AND LIFE-HISTORY STRATEGIES OF TROPICAL BIRDS

Understanding how biotic interactions and abiotic constraints influence community assembly and composition is a fundamental issue in community ecology. Addressing this issue is particularly tractable in the context of tropical mountains which have large variation in community diversity, high rates of species turnover and strong gradients in abiotic conditions. Here, we examined elevational patterns of avian community structure in tropical Malaysia to assess changes in the relative strength of biotic interactions and abiotic constraints. We used metrics based on phylogenetic relatedness and functional traits associated with resource acquisition and tolerance of abiotic challenges to identify patterns and causes of elevational differences in community structure. High elevation communities were composed of more phylogenetically and functionally similar species than would be expected by chance (clustered), while middle and low elevation communities showed little structure, with few communities composed of more dissimilar species (overdispersed) than expected by chance. Traits associated with resource acquisition were clustered at high elevations, suggesting low resource and habitat diversity were the primary drivers of clustering in those communities. Traits typically associated with tolerance of cold temperatures and low atmospheric pressure showed no elevational patterns. All traits were neutral or overdispersed at low elevations suggesting an absence of strong abiotic filters or an increased influence of interspecific competition. However, relative bill size, which is important for thermoregulation, was larger in low elevation communities, suggesting abiotic factors were also influential there. Regardless of metric, clustered and neutral communities were far more frequent than overdispersed communities, implying that interspecific competition among close relatives may not be a pervasive driver of elevational distributions
Murine model of neonatal cytomegalovirus infection

Congenital HCMV infection of developing CNS is a major cause of long-term neuronal morbidity. Prevention of neurological damage due to CNS infection is considered as the primary goal of vaccine strategies and passively administered biologics. Due to species specificity of CMVs animal models have been developed in order to paradigmatically analyze the course of CMV infections. While different animal models provide good tools for studies of HCMV infections in the immunocompromised host, no single animal model completely recapitulates the pathogenesis of congenital HCMV infection. The murine model of perinatal MCMV infection in newborn mice has been proven as powerful tool to analyze the pathogenesis of congenital HCMV infection and mechanisms of the immune response which control CNS infection in the developing brain. This chapter describes a model of MCMV infection in neonatal mice that represents various aspects of HCMV infection in neonates, and thus, could be highly predictive for possible antiviral interventions in humans.
Yellow Rail (Coturnicops noveboracensis) Occupancy in the Context of Fire in Mississippi and Alabama, USA

Abstract. The Yellow Rail (Coturnicops noveboracensis) is a migratory bird with many aspects of its ecology poorly understood. The objective of this study was to examine effects of fire, vegetation structure, and landscape variables on site occupancy and detection probabilities for Yellow Rails overwintering in coastal pine savannas of Mississippi and Alabama. Between December and April, 2012–2013, dragline surveys for Yellow Rail were conducted at three conservation areas: two in Jackson County, Mississippi, and one in Mobile County, Alabama, USA. Site occupancy for Yellow Rail was 0.81 ± 0.06 (SD) with detection probabilities of 0.79 ± 0.09 (SD). Yellow Rail occupancy related negatively with time since fire, indicating fire provides conditions attractive to Yellow Rail overwintering throughout the study area. Yellow Rail use of wetland and fire-maintained habitats within coastal Mississippi during winter, coupled with continued loss of open grasslands and inadequate management of fire-dependent pine savanna habitats throughout the southeastern USA highlights the continued need to prioritize the conservation and effective management of herbaceous-dominated ecosystems.
Evaluation of two potential Cucumis spp. resources for grafting melons

Cultivation of Cucumis melo is hampered by soil stresses. Grafting is used to overcome these limitations. Different cucurbits belonging to several genera have been used as rootstocks for melons: Cucurbita, Lagenaria, Luffa, etc. However, negative effects on fruit quality appear in some rootstock-scion combinations. The selection of new resistant rootstocks that do not cause this negative impact in quality is necessary to improve melon cultivation. In this work, we evaluated two rootstocks, closer genetically to melon scions than those usually employed: a) an F1 hybrid between a commercial melon (C. melo subspecies melo var. inodorus market class Piel de Sapo) and one exotic accession (C. melo subspecies agrestis var. chinensis) with resistance to Monosporacus cannonballus, the causal agent of melon vine decline, and with a certain level of tolerance to Fusarium oxysporum f. sp. melonis race 1.2, that causes Fusarium wilt, and b) an accession of Cucumis metuliferus, highly resistant to M. cannonballus, F. oxysporum 1.2 and evaluated and classified as highly resistant to Meloidogyne spp. in this work. Grafting compatibility of these two selected genotypes with commercial melons was good. All grafted plants displayed higher vigour and earlier flowering than ungrafted plants. Fruits from plants grafted onto C. metuliferus showed similar quality than those from ungrafted/selfgrafted plants. However, fruits from plants grafted onto the F1 (inodorus × chinensis) had in this experiment lower brix degree than the ungrafted controls. The resistance to soil borne pathogens found in C. metuliferus and the good performance regarding plant development and fruit quality of the scions indicate that this species is a promising rootstock for melons.
Maternal programming of offspring antipredator behavior in a seabird

Mothers can transmit information to offspring via eggs or via placenta to prepare them for the environment they will experience, but evidence on maternal anticipatory effects is still mixed. Using an experimental approach, we found that gull mothers exposed to predators prior to egg laying had chicks with stronger antipredator responses than chicks of control mothers. Our results suggest that mothers may program offspring behavior via eggs.
Identification of potential key genes affecting soybean growth under salt stress via transcriptome study

Soybean is one of the most important economic crops in the world. However, the salinization of soil results in the decrease of soybean yield as it is only a moderately salt-tolerant crop. We treated three soybean cultivars with low and high concentrations of NaCl. The differentially expressed genes between the control group and the salt treatment group were identified by mRNA sequencing and analyzed by gene ontology and Kyoto encyclopedia of genes and genomes annotations. We performed weighted gene co-expression network analysis on all samples and found genes most related to the phenotype. After verifying the results of differentially expressed genes by quantitative PCR, we finally identified Glyma06G01990, Glyma08G22730, Glyma019G05140, and Glyma06G20160 as key genes affecting the soybean growth under salt stress. Additional key words: differentially expressed genes, Glycine max, RNA-seq, WGCNA. Submitted 11 February 2020, last revision 24 June 2020, accepted 25 June 2020. Abbreviations: DEGs differentially expressed genes; GO gene ontology; KEGG Kyoto encyclopedia of genes and genomes; WGCNA weighted gene co-expression network analysis. Acknowledgements: This study was funded by the Agriculture Scientific and Technological Innovation Project of Shandong Academy of Agricultural Sciences (grant No. CXGC2016A02), Agricultural Variety Improvement Project of Shandong Province (grant Nos. 2019LZGC017, 2019LZGC004), and Shandong Province Modern Agricultural Technology System Coarse Cereals Innovation Team. The first two authors equally participate in this work. * Corresponding author; e-mail: dinghanfengsd@outlook.com This is an open access article distributed under the terms of the Creative Commons BY-NC-ND Licence
Occluding junctions regulate germline differentiation and stem cell niche homeostasis in the Drosophila melanogaster testis

ii Preface . iii Table of contents . iv List of figures . vii List of abbreviations . ix Acknowledgments . xi Dedication . xii CHAPTER ONE: Introduction . 1 1.1 The germline and sexual reproduction . 1 1.2 Spermatogenesis . 2 1.3 Soma-germline interactions during spermatogenesis . 3 1.4 Drosophila melanogaster: A model for spermatogenesis . 5 1.5 Formation of the stem cell niche . 8 1.6 Stem cell maintenance . 10 1.6. 1 Germline stem cell maintenance . 10 1.6. 2 Cyst stem cell maintenance . 12 1.6. 3 Stem cells form part of the niche . 13 1.7 Stem cell differentiation . 15 1.7. 1 Bag of marbles and germline differentiation . 15 1.7. 2 Encapsulation by differentiating cyst cells . 17 1.7. 3 Signalling in the spermatocyst . 18 1.8 Other models of spermatogenesis . 19 1.8. 1 Mammalian spermatogenesis . 20 1.8. 2 The blood-testis-barrier . 23 1.8. 3 Other soma-germline barriers . 25 1.9 Aims and scope of thesis . 27
Influence of freezing, lyophilisation and air‐drying on the total monomeric anthocyanins, vitamin C and antioxidant capacity of selected berries

Fresh berries are a rich source of antioxidants. The choice of a method for preserving these fruits determines, among other things, keeping their antioxidant capacity. The aim of this study was to estimate the contents of monomeric anthocyanins and vitamin C and to assess the antioxidant capacity of the fruit of black chokeberry, black elder, common bilberry, thornless blackberry and raspberry depending on the method of preservation in the process of freezing, lyophilisation and air-drying. In fruits frozen at 18 °C as compared with the fresh fruits, losses of anthocyanins and vitamin C of 10% and 14%, respectively, were found. During lyophilisation and air-drying, losses of anthocyanins as compared with fresh fruits accounted for 82% and 94%, respectively, of vitamin C 84% and 89%. Regardless of the preservation method, chokeberry was characterised by the richest resource of anthocyanins and the highest antioxidant capacity, followed by black elder.
not-so-BigGAN: Generating High-Fidelity Images on Small Compute with Wavelet-based Super-Resolution

State-of-the-art models for high-resolution image generation, such as BigGAN and VQVAE-2, require an incredible amount of compute resources and/or time (512 TPU-v3 cores) to train, putting them out of reach for the larger research community. On the other hand, GAN-based image super-resolution models, such as ESRGAN, can not only upscale images to high dimensions, but also are efficient to train. In this paper, we present not-so-big-GAN (nsb-GAN), a simple yet cost-effective two-step training framework for deep generative models (DGMs) of high-dimensional natural images. First, we generate images in low-frequency bands by training a sampler in the wavelet domain. Then, we super-resolve these images from the wavelet domain back to the pixel-space with our novel wavelet super-resolution decoder network. Wavelet-based down-sampling method preserves more structural information than pixel-based methods, leading to significantly better generative quality of the low-resolution sampler (e.g., 64x64). Since the sampler and decoder can be trained in parallel and operate on much lower dimensional spaces than end-to-end models, the training cost is substantially reduced. On ImageNet 512x512, our model achieves a Frechet Inception Distance (FID) of 10.59 -- beating the baseline BigGAN model -- at half the compute (256 TPU-v3 cores).
Nonadiabatic noncyclic geometric quantum computation in Rydberg atoms

Nonadiabatic geometric quantum computation (NGQC) has been developed to realize fast and robust geometric gate. However, the conventional NGQC is that all of the gates are performed with exactly the sameamount of time, whether the geometric rotation angle is large or small, due to the limitation of cyclic condition. Here, we propose an unconventional scheme, called nonadiabatic noncyclic geometric quantum computation(NNGQC), that arbitrary single- and two-qubit geometric gate can be constructed via noncyclic non-Abeliangeometric phase. Consequently, this scheme makes it possible to accelerate the implemented geometric gatesagainst the effects from the environmental decoherence. Furthermore, this extensible scheme can be applied invarious quantum platforms, such as superconducting qubit and Rydberg atoms. Specifically, for single-qubit gate,we make simulations with practical parameters in neutral atom system to show the robustness of NNGQC and also compare with NGQC using the recent experimental parameters to show that the NNGQC can significantly suppress the decoherence error. In addition, we also demonstrate that nontrivial two-qubit geometric gate can berealized via unconventional Rydberg blockade regime within current experimental technologies. Therefore, ourscheme provides a promising way for fast and robust neutral-atom-based quantum computation.
Quantum Time–Space Tradeoff for Finding Multiple Collision Pairs

We study the problem of finding K collision pairs in a random function f : [N] → [N] by using a quantum computer. We prove that the number of queries to the function in the quantum random oracle model must increase significantly when the size of the available memory is limited. Namely, we demonstrate that any algorithm using S qubits of memory must perform a number T of queries that satisfies the tradeoff T3 S ≥ Ω (K3 N). Classically, the same question has only been settled recently by Dinur [22], who showed that the Parallel Collision Search algorithm of van Oorschot and Wiener [36] achieves the optimal time–space tradeoff of T2 S = Θ (K2 N). Our result limits the extent to which quantum computing may decrease this tradeoff. Our method is based on a novel application of Zhandry’s recording query technique [42] for proving lower bounds in the exponentially small success probability regime. As a second application, we give a simpler proof of the time–space tradeoff T2 S ≥ Ω (N3) for sorting N numbers on a quantum computer, which was first obtained by Klauck, Špalek, and de Wolf [30].
Establishing synthetic pathways in Escherichia coli for biosynthesis of C3 and C4 high value commodity chemicals

The rapid consumption of oil for fuel and chemicals is leading to carbon dioxide emission at vast quantities each year. At this hour the need is to gradually reduce the reliance on oil for large scale manufacture of fuels and chemicals. The development of renewable/ alternative energy technologies and the production of “green chemicals” provide a means to address these concerns. The biological manufacture of C3-C6 commodity chemicals has gained much attention over the past decade due to their large annual market and wide industrial applications. Metabolic engineering has enabled the biological manufacture of these chemicals via construction of novel metabolic pathways or enhancement of existing ones. In this work, we engineer Escherichia coli for the production high value bulk chemicals – 1,2propanediol, 1-propanol and 1,4-butanediol. We systematically engineer E. coli to enhance the production of 1,2-propanediol to maximize yield from glucose. Building on this work, we identify an optimal diol dehydratase and expand the 1,2-propanediol pathway to establish a novel platform for 1-propanol production from glucose. Deriving inspiration from rational design approaches we then engineer the diol dehydratase to enhance activity toward a non-native substrate. We demonstrate an alliance of protein engineering strategies and metabolic engineering strategies to achieve the production of 1,4-butanediol from xylose via a novel
A Peculiar Phenomenon of Cold-shocked Bacteria Recovered on Sano- Gam Media

This study was conducted in order to display the peculiar appearance of bacteria which were recovered on Sano-Gam Media. The studied bacteria were Escherichia coli , Salmonella spp. , Staphylococcus aureus , Proteus vulgaris and Klebsiella pneumoniae . Some of the tested bacteria recovered on SANO-GAM media reflected peculiar growth appearance which had been noticed as high carbon dioxide production by Salmonella spp. , in Glucose medium. A huge mist growth of P . vulgaris , spider network and crystal manifestation of E. coli colonies , strange accumulation of K. pneumoniae on Cu Sano-Gam medium were observed as button-like colonies of Salmonella spp. , and ferrum stained colonies of E. coli were seen. From the positive point of view the new invented Sano-Gam media were being able to recover all tested bacteria nicely irrespectively whether they have expressed their growth peculiarly or not.
First record of the steppic relict Astragalus exscapus L. subsp. exscapus in the Apennines (Abruzzo, Italy), and biogeographic implications

Abstract Astragalus exscapus L. subsp. exscapus (Fabaceae) is a rare and declining perennial herb with a very fragmented distribution range. It is interpreted as a relict of the glacial steppe flora. In Italy, it was known until now only from the Alpine “dry valleys”, namely from Val d’Aosta and Val Venosta/Vinschgau. We report on the discovery of a population on the slopes of the Fucino basin in the Central Apennines (Abruzzo, Italy). The finding significantly expands the known species range (the site is >600 km away from the nearest known populations), suggesting that during Pleistocene steppic phases it had a wide distribution across Europe. A. exscapus adds to a number of other steppic relicts found in the Fucino basin, highlighting that some inner valleys of the Central Apennines, featuring a relatively continental climate, perform as “interglacial refugia” for the steppe flora. Further research is needed to ascertain the species’ local distribution and abundance, and to clarify its vicariance history; however, the finding underlines the need to re-evaluate priorities in landscape management, as in the Apennines dry grasslands are often given low values compared to forests and are frequently destroyed by afforestation practices with non-native conifers.
Environmentally and behaviourally mediated co-occurrence of functional traits in bird communities of tropical forest fragments.

Two major theories of community assembly - based on the assumption of limiting similarity' or 'habitat filtering', respectively - predict contrasting patterns in the spatial arrangement of functional traits. Previous analyses have made progress in testing these predictions and identifying underlying processes, but have also pointed to theoretical as well as methodological shortcomings. Here we applied a recently developed methodology for spatially explicit analysis of phylogenetic meta-community structure to study the pattern of co-occurrence of functional traits in Afrotropical and Neotropical bird species inhabiting forest fragments. Focusing separately on locomotory, dietary, and dispersal traits, we tested whether environmental filtering causes spatial clustering, or competition leads to spatial segregation as predicted by limiting similarity theory. We detected significant segregation of species co-occurrences in African fragments, but not in the Neotropical ones. Interspecific competition had a higher impact on trait co-occurrence than filter effects, yet no single functional trait was able to explain the observed degree of spatial segregation among species. Despite high regional variability spanning from spatial segregation to aggregation, we found a consistent tendency for a clustered spatial patterning of functional traits among communities in fragmented landscapes, particularly in non-territorial species. Overall, we show that behavioural effects, such as territoriality, and environmental effects, such as the area of forest remnants or properties of the landscape matrix in which they are embedded, can strongly affect the pattern of trait co-occurrence. Our findings suggest that trait-based analyses of community structure should include behavioural and environmental covariates, and we here provide an appropriate method for linking functional traits, species ecology and environmental conditions to clarify the drivers underlying spatial patterns of species co-occurrence.