Miracle-dz/UniFAR-FTUs huggingface dataset:
Decomposition of Leaf Litter in Semideciduous Submontane Forest, in The Southern State of Espírito Santo

The objective of this work was to understand the relationship between decomposition of leaf litter and climatic elements and determine the mineralization of nutrients in the decomposition process in a fragment of Semideciduous Submontane Forest, located in southern state of of Espírito Santo. Overall, 84 litterbags were deposited in 12 permanent plots, collecting one litterbag per plot for 30, 60, 90, 150, 210, 270 and 360 days after the beginning of the experiment. The leaf material remaining in the litterbag was oven-dried and weighed, with later analysis of nutritional compounds. The leaf litter decomposition rate was 1.42, 75.95% of decomposing litter at the end of the evaluation period. Mineralization occurred in the following order: K, Corg. , Mg, S, P, N and Ca. There was a positive correlation of average and minimum air temperature, as well as accumulated precipitation and leaf litter decomposition .
Improving and Maintaining Winter Hardiness and Frost Tolerance in Bread Wheat by Genomic Selection

Winter hardiness is a major constraint for autumn sown crops in temperate regions, and thus an important breeding goal in the development of new winter wheat varieties. Winter hardiness is though influenced by many environmental factors rendering phenotypic selection under field conditions a difficult task due to irregular occurrence or absence of winter damage in field trials. Controlled frost tolerance tests in growth chamber experiments are, on the other hand, even with few genotypes, often costly and laborious, which makes a genomic breeding strategy for early generation selection an attractive alternative. The aims of this study were thus to compare the merit of marker-assisted selection using the major frost tolerance QTL Fr-A2 with genomic prediction for winter hardiness and frost tolerance, and to assess the potential of combining both measures with a genomic selection index using a high density marker map or a reduced set of pre-selected markers. Cross-validation within two training populations phenotyped for frost tolerance and winter hardiness underpinned the importance of Fr-A2 for frost tolerance especially when upweighting its effect in genomic prediction models, while a combined genomic selection index increased the prediction accuracy for an independent validation population in comparison to training with winter hardiness data alone. The prediction accuracy could moreover be maintained with pre-selected marker sets, which is highly relevant when employing cost reducing fingerprinting techniques such as targeted genotyping-by-sequencing. Genomic selection showed thus large potential to improve or maintain the performance of winter wheat for these difficult, costly, and laborious to phenotype traits.
Complete mitochondrial genome of the Greenland wolf, Canis lupus orion

Abstract The Greenland wolf, Canis lupus orion as s subspecies of the gray wolf, is native to Greenland. Here, we assembled a complete 16,650 bp genome for the C. l. orion mitochondrion by employing Illumina HiSeq platform. The complete mitochondrial genome contained 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and one control region. Overall DNA sequence of the C. l. orion mitochondrion was identical to that of gray wolf C. l. lupus, although slight difference was observed in their control regions. The genomic structure of C. l. orion mitochondrion was conserved with the gene arrangements of mitogenomes published in Canidae, and phylogenetic analysis confirmed the sister relationship among Canis sp. This information will provide essential molecular reference to elucidate biogeography, phylogenetic distance, and evolutionary history in gray wolves.
Sustainable Production of Robusta Coffee under a Changing Climate: A 10-Year Monitoring of Fertilizer Management in Coffee Farms in Vietnam and Indonesia

Assessing and prescribing fertilizer use is critical to profitable and sustainable coffee production, and this is becoming a priority concern for the Robusta coffee industry. In this study, annual survey data of 798 farms across selected Robusta coffee-producing provinces in Vietnam and Indonesia between 2008 and 2017 were used to comparatively assess the fertilizer management strategies in these countries. Specifically, we aimed to characterize fertilizer use patterns in the key coffee-growing provinces and discuss the potential for improving nutrient management practices. Four types of chemical (NPK, super phosphate, potassium chloride and urea) and two of natural (compost and lime) fertilizers were routinely used in Vietnam. In Indonesia, NPK and urea were supplemented only with compost. Farmers in Vietnam applied unbalanced quantities of chemical fertilizers (i.e., higher rates than recommended) and at a constant rate between years whereas Indonesian farmers applied well below the recommended rates because of poor accessibility and financial support. The overuse of chemical fertilizers in Vietnam threatens the sustainability of Robusta coffee farming. Nevertheless, there is a potential for improvement in both countries in terms of nutrient management and sustainability of Robusta coffee production by adopting the best local fertilizer management practices.
Direct measurements of carbon exchange at forest disturbance sites: a review of results with the eddy covariance method

ABSTRACT Boreal and temperate forests cover a large part of the Earth. Forest ecosystems are a key focus for research because of their role in the carbon (C) balance and cycle. Increasing atmospheric temperatures, different disturbances (fire, storm and insects) and forest management (clear-cutting) will change considerably the C status of forest ecosystems. Using the eddy covariance (EC) method, we can define interactions among environmental factors that influence the C-balance and whether a forest ecosystem is functioning as a C-sink or C-source or possibly is C-neutral. In our review of published studies of different disturbances, we found that most of the post-disturbance studies based on EC method focused on the effects of forest fire and clear-cutting, only a few studies studies focused on the effects of storms and insects. Generally a forest is a C-source until several years after disturbance and then a forest is able to absorb C and become a C-sink. Recovery to C-sink status required up to 20 years in clear-cut areas. Recovery following wildfire disturbance was much longer, possibly more than 50 years. Recovery to C-sink status required approximately 5 years after storm and insect outbreak, however we can not predict overall recovery period because of the missing data.
Effect of selected dietary regimens on recovery from moderate acute malnutrition in young Malian children

Moderate acute malnutrition (MAM) remains a major public health concern and research is needed on optimal dietary treatment regimens. We randomly assigned 12 rural health centers in Dioila Health District, Mali to provide 1 of 4 dietary regimens approximating WHO recommended nutrient profiles: 1) lipid‐based, ready‐to‐use supplementary food (Plumpy'Sup, PS); 2) special corn soy blend for MAM (CSB++); 3) locally processed, fortified food (Misola); or 4) locally milled flours and micronutrient powder. 1284 non‐edematous children aged 6–35 mo with initial arm circumference (MUAC) <12.5 and ≥11.0 cm or weight‐for‐length Z‐score (WLZ) <‐2.0 WHO standard and ≥70 % NCHS reference median were offered ~500 kcal/d of assigned diet in addition to home food intake for 12 wks. Among 1121 children (87.3%) who completed the study, the mean±SD change in weight from baseline was greater with PS than all 3 other regimens, which did not differ from each other (1.15±0.57 kg, 0.96±0.55 kg, 0.96±0.53 kg, 0.91±0.54 kg for respective study groups, p<0.001 ANOVA). MUAC changes followed a similar pattern, but length did not differ significantly among groups. Recovery from MAM (WLZ>‐2.0, MUAC>12.5cm) was highest with PS compared with the 3 other regimens (71%, 56%, 59%, 53% for respective groups, p<0.001 Scheffe). PS is more effective than the other dietary regimens, but benefits must be considered in relation to product costs and availability. This study was supported by UNICEF and WFP.
Intra-genus metabolic diversity facilitates co-occurrence of multiple Ferrovum species at an acid mine drainage site

Background Ferrovum spp. are abundant in acid mine drainage sites globally where they play an important role in biogeochemical cycling. All known taxa in this genus are Fe(II) oxidizers. Thus, co-occurring members of the genus could be competitors within the same environment. However, we found multiple, co-occurring Ferrovum spp. in Cabin Branch, an acid mine drainage site in the Daniel Boone National Forest, KY. Results Here we describe the distribution of Ferrovum spp. within the Cabin Branch communities and metagenome assembled genomes (MAGs) of two new Ferrovum spp. In contrast to previous studies, we recovered multiple 16S rRNA gene sequence variants suggesting the commonly used 97% cutoff may not be appropriate to differentiate Ferrovum spp. We also retrieved two nearly-complete Ferrovum spp. genomes from metagenomic data. The genomes of these taxa differ in several key ways relating to nutrient cycling, motility, and chemotaxis. Conclusions Previously reported Ferrovum genomes are also diverse with respect to these categories suggesting that the genus Ferrovum contains substantial metabolic diversity. This diversity likely explains how the members of this genus successfully co-occur in Cabin Branch and why Ferrovum spp. are abundant across geochemical gradients.
Salt‐enhanced cultivation as a morphology engineering tool for filamentous actinomycetes: Increased production of labyrinthopeptin A1 in Actinomadura namibiensis

Salt‐enhanced cultivation as a morphology engineering tool for the filamentous actinomycete Actinomadura namibiensis was evaluated in 500‐mL shaking flasks (working volume 100 mL) with the aim of increasing the concentration of the pharmaceutically interesting peptide labyrinthopeptin A1. Among the inorganic salts added to a complex production medium, the addition of (NH4)2SO4 led to the highest amount of labyrinthopeptin A1 production. By using 50 mM (NH4)2SO4, the labyrinthopeptin A1 concentration increased up to sevenfold compared to the non‐supplemented control, resulting in 325 mg L−1 labyrinthopeptin A1 after 10 days of cultivation. The performance of other ammonium‐ and sulfate‐containing salts (e.g., NH4Cl, K2SO4) was much lower than the performance of (NH4)2SO4. A positive correlation between the uptake of glycerol as one of the main carbon sources and nongrowth‐associated labyrinthopeptin productivity was found. The change in the cell morphology of A. namibiensis in conjunction with increased osmolality by the addition of 50 mM (NH4)2SO4, was quantified by image analysis. A. namibiensis always developed a heterogeneous morphology with pellets and loose mycelia present simultaneously. In contrast to the non‐supplemented control, the morphology of (NH4)2SO4‐supplemented cultures was characterized by smaller and circular pellets that were more stable against disintegration in the stationary production phase.
Higher order interactions and coexistence theory

Higher order interactions (HOIs) have been suggested to stabilize diverse ecological communities. However, their role in maintaining species coexistence from the perspective of modern coexistence theory is unknown. Here, using a three-species Lotka-Volterra model, we derive a general rule for species coexistence modulated by HOIs. We show that negative HOIs that intensify pairwise competition, can promote coexistence across a wide range of fitness differences, provided that HOIs strengthen intraspecific competition more than interspecific competition. In contrast, positive HOIs that alleviate pairwise competition can also stabilize coexistence across a wide range of fitness differences, irrespective of differences in strength of inter- and intraspecific competition. Furthermore, we extend our three-species analytical result to multispecies competitive community and show, using simulations, that feasible multispecies coexistence is possible provided that strength of negative intraspecific HOIs is higher than interspecific HOIs. In addition, multispecies communities, however, become unstable with positive HOIs as such higher-order interactions could lead to disproportionately infeasible growth rates. This work provides crucial insights on the underlying mechanisms that could maintain species diversity and links HOIs with modern coexistence theory.
Assessment of Frozen Seafood Good Storage Practices in the 21st Supply Deposit of the Brazilian Army

The 21st Supply Deposit of the Brazilian Army (21st DSup), located in the city of São Paulo provides food raw materials for 16000 meals daily, and frozen fish is among the foodstuffs distributed. The objective of this study was to evaluate the good practices of seafood storage in the 21st DSup, identify issues of non-compliance that compromise food quality, and propose solutions. The system was evaluated, applying a checklist (RDC 275/2002) to evaluate the percentage of requirements in compliance with good practices. The 21st DSup was classified in Group 3, with 41% of items in conformance (< 50%), and we found that there is no hygienic-sanitary self-control program for storing cold seafood and other food supplies. The cold stores’ temperatures are not able to maintain products within the required standards of conservation. The seafood cold storage protocol of the 21st DSup does not guarantee temperature conformity. It is necessary to implement a hygienic-sanitary self-control program for food supply storage, which should begin with the development of a food safety culture.
Floodplains provide important amphibian habitat despite multiple ecological threats

Floodplain ponds and wetlands are productive and biodiverse ecosystems, yet they face multiple threats including altered hydrology, land use change, and non-native species. Protecting and restoring important floodplain ecosystems requires understanding how organisms use these habitats and respond to altered environmental conditions. We developed Bayesian models to evaluate occupancy of six amphibian species across 103 off-channel aquatic habitats in the Chehalis River floodplain, Washington State, USA. The basin has been altered by changes in land use, reduced river–wetland connections, and the establishment of non-native American bullfrogs (Rana catesbeiana = Lithobates catesbeianus) and centrarchid fishes, all of which we hypothesized could influence native amphibian occupancy. Despite potential threats, the floodplain habitats had relatively high rates of native amphibian occupancy, particularly when compared to studies from non-floodplain habitats within the species’ native ranges. The biggest challenge for native amphibians appears to be non-native centrarchid fishes, which strongly reduced occupancy of two native amphibians: the northern red-legged frog (Rana aurora) and the northwestern salamander (Ambystoma gracile). Emergent vegetative cover increased occupancy probability for all five native amphibian species, indicating that plant management may offer a strategy to counter the negative effect of centrarchids by providing refuge from predation. We found that temporary and permanent hydroperiod sites supported different species; hence, both should be conserved on the landscape. Lastly, human-created and natural ponds had similar amphibian occupancy patterns, suggesting that pond construction offers a viable strategy for adding habitats to the floodplain landscape. Overall, floodplain ponds and wetlands provide important amphibian habitat, and we offer management strategies that will bolster amphibian occupancy in an altered floodplain landscape.
Persistent trajectory-modulated hippocampal neurons support memory-guided navigation

Trajectory-dependent splitter neurons in the hippocampus encode information about a rodent’s prior trajectory during performance of a continuous alternation task. As such, they provide valuable information for supporting memory-guided behavior. Here, we employed single-photon calcium imaging in freely moving mice to investigate the emergence and fate of trajectory-dependent activity through learning and mastery of a continuous spatial alternation task. We found that the quality of trajectory-dependent information in hippocampal neurons correlated with task performance. We thus hypothesized that, due to their utility, splitter neurons would exhibit heightened stability. We found that splitter neurons were more likely to remain active and retained more consistent spatial information across multiple days than did place cells. Furthermore, we found that both splitter neurons and place cells emerged rapidly and maintained stable trajectory-dependent/spatial activity thereafter. Our results suggest that neurons with useful functional coding properties exhibit heightened stability to support memory guided behavior.
Effect of roasting on the nutritional value and antioxidant components of Maya nut (Brosimum alicastrum: Moraceae)

T he study of foods with antioxidant properties has increased considerably in recent years due to the interest in nutraceutical compounds and their contributions to health. However, there are some seeds with antioxidant components that remain underutilized or unused, such as the Maya nut, the seed of Brosimum alicastrum Swartz (family Moraceae), which was consumed by the ancient Maya and other Mesoamerican peoples. The Maya nut is known in the region today as capomo , nuez de maya , mojo or ram ó n . The objective of this research was to evaluate the contents of minerals, nutritional compounds and antioxidants in fresh Maya nuts and with two roasting treatments (medium and high roasting at 90 °C for 20 and 35 min, respectively). In general, roasting did not affect the nutritional quality of the seeds, although the concentration of lipids and flavonoids decreased significantly ( P ≤ 0.05). Roasting significantly increased ( P ≤ 0.05) the content of condensed tannins
Motif elucidation in ChIP-seq datasets with a knockout control

Chromatin immunoprecipitation-sequencing (ChIP-seq) is widely used to find transcription factor binding sites, but suffers from various sources of noise. Knocking out the target factor mitigates noise by acting as a negative control. Paired wild-type and knockout experiments can generate improved motifs but require optimal differential analysis. We introduce peaKO—a computational method to automatically optimize motif analyses with knockout controls, which we compare to two other methods. PeaKO often improves elucidation of the target factor and highlights the benefits of knockout controls, which far outperform input controls. It is freely available at https://peako.hoffmanlab. org.
Identification, Structural Analysis, and Expression Profile of Genes Related to Starch Metabolism in Cassava (Manihot esculenta Crantz)

Starch metabolism is known to be an important pathway in the growth and development of plants. This study was conducted to investigate the genome-wide identification and structural analysis of genes encoding uridine diphosphate glucose pyrophosphorylase (UGPase), a key enzyme in starch synthesis in cassava, and to analyze the expression profiles of these genes based on publicly available RNA-seq data. A total of 11 members were found in the UGPase gene family (MeUGP) in cassava. Ten of the MeUGP genes were successfully mapped onto the chromosomes of the current cassava genome assembly. Based on their nucleotide sequences, the lengths of the genomic DNA sequences of the MeUGP genes ranged from 3,200 to 11,601bp, while the size of the coding sequence (CDS) varied from 831 to 3,654bp. According to the recent RNA-seq data, we found that a majority of the MeUGP genes were expressed in at least 1 tissue under normal conditions. Interestingly, MeUGP4 was greatly expressed in the shoot apical meristem, while MeUGP10 was more specific in the root apical meristem. The expression profiles of these MeUGP genes should be carried out in various conditions in further studies.
Infection with Opportunistic Bacteria Triggers Severe Pulmonary Inflammation in Lupus-Prone Mice

Infection is a common cause of hospitalization and mortality in patients with systemic lupus erythematosus (SLE). How the underlying immune dysfunctions affect the antimicrobial immunity remains largely unknown. In the present study, employing the pulmonary infection model, we determined the antimicrobial defence of lupus-prone mice. After infecting with opportunistic bacterium Haemophilus influenzae (Hi), lupus-prone mice (B6/lpr) exhibited inefficient bacterial elimination and recovered slowly. They generated severer inflammation at the early stage of infection, as excessive accumulation of neutrophils and enhanced production of proinflammatory cytokines were observed in the lung. In addition, a large number of apoptotic cells were detected in the lungs of B6/lpr mice. For adaptive immune responses, B6/lpr mice were capable to generate enough protective Hi-specific Th17 cells. They evoked stronger Hi-specific γδ T17 response in both lungs and spleens. Unexpectedly, both CD4 and γδ T cells from lupus-prone mice showed deficiency in IFN-γ production. For humoral immune responses, compared with those of WT mice, the concentrations of Hi-specific IgA, IgM, and IgG, especially IgG, were significantly higher in the B6/lpr mice. Our findings suggest that lupus mice are capable to generate antibacterial immune responses; however, the overwhelming inflammation and overactivated immune responses increase the severity of infection.
Evaluation of macroalgal detritus as food source for juvenile Manila clam,
 Ruditapes philippinarum
 : Effects on growth, amino acid content and fatty acid composition

Sufficient high‐quality microalgae are required for indoor nursery of juvenile Ruditapes philippinarum. However, culturing numerous microalgae to support clam feeding is a heavy burden on many hatcheries. The effects of detritus from the macroalgae Ulva pertusa, Chondrus ocellatus and Undaria pinnatifida on the growth, amino acid content and fatty acid profile of R. philippinarum were assessed as potential substitute diets. The green microalga Tetraselmis cordiformis served as comparative diet. Results revealed that the clams ingesting distinct diets presented no significant differences in growth of soft tissues, but the nutritional component of these clams differed dramatically. The clams fed with Undaria + Tetraselmis had the highest content of essential amino acids and proteins. In addition, the clams fed with single macroalgal diets and mixed macroalgal detritus and Tetraselmis showed significantly higher or statistically equal levels in n‐3/n‐6 ratio and docosahexaenoic acid (DHA)/eicosapentaenoic acid (EPA) ratio with respect to Tetraselmis diets. The relative percentages of EPA and DHA in clams fed with Undaria were 28% and 63% higher than those fed with Tetraselmis, and the arachidonic acid abundances in clams ingesting Undaria + Tetraselmis and Tetraselmis were significantly higher than those in clams ingesting other diets. Together, the diets containing single Undaria or mixed Undaria + Tetraselmis produced Manila clams with nutritional advantages in terms of essential amino acids and polyunsaturated fatty acids. Thus, the detritus of macroalgae, especially Undaria, is an appropriate substitute diet, at least partially, for culture of nutrition‐improved R. philippinarum.