Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapeseed‐to‐Wheat Yield Ratio in Different Production Environments and Effects on Subsequent Summer Crops Yields

Winter crop production in eastern Argentina and western Uruguay has been limited to wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.), forming a double annual cropping system with soybean [Glycine max (L.) Merr. ] and maize (Zea mays L.) during summer seasons. Currently, double annual cropping system covers less than 30% of the area. Past studies suggests that the rapeseed (Brassica napus L.)/wheat yield ratio ranges from 40 to 60%, and the inclusion of rapeseed in the system could improve grain yield of the following crops. The objectives of this study were to: (i) quantify the rapeseed/wheat yield ratio under different cropping systems; (ii) quantify the differential yield of summer crops compared with wheat and rapeseed while keeping a similar harvest date for winter crops and planting date for summer crops, respectively; and (iii) assess the economic result of the evaluated cropping systems. Rapeseed and wheat crops were sown in a long-term rotation trial where different cropping systems were evaluated. Experiments were conducted for two seasons (2014 and 2015) and in each summer season after the winter crop harvest, soybean (2014–2015) and maize (2015–2016) were sown. No yield differences were detected for wheat and rapeseed as a result of the previous cropping systems, and the rapeseed/wheat yield ratio was about 55%. Higher summer crop yields were obtained after rapeseed compared with wheat (11 and 17% for soybean and maize, respectively). Producers may be able to enhance both production levels and profitability by adopting a more diverse cropping sequence.
Incidence and Severity of Common Bean (Phaseolus vulgaris L.) Pests in Agro-Ecological Zones and Farming Systems of Western Kenya

ABSTRACT Infestation by insect pests is a serious problem in legume up scaling activities and a threat to future production in Kenya. The survey aimed at determining incidence and severity of insect pests of common beans in different districts and agro-ecological zones of western Kenya. Foliage beetle incidence was highest in the hot and drier LM3 (72.6%) and LM4 (92.1%) zones during the long and short rains, respectively. Leaf hopper incidence was highest in LM4 (26.8%) and (59.3%) whereas bean fly incidence was highest in UM3 (12.4%) and LH1 (2.9%). Whitefly incidence was highest in LM3 (13.0%) and LM2 (17.9%) and aphid incidence was highest in LM1 (16.5%) and UM1 (40.8%). Plant bug incidence was highest in LM1 (16.5%) and LM2 (5.8%). Flower thrips incidence was highest in LM2 (20.7%) and (34.2%) in both seasons. Bean flies (7.2%) and Spodoptera (2.9%) incidences were higher during the long rains. Foliage beetle incidence (52.7%), aphids (22.6%), leaf hopper (27.9%) and flower thrips (17.8%) were higher during the short rains. Whitefly (7.9%), thrip (9.7%) incidences and foliage beetle severity (2.1) were lower on improved cultivars in LM2 areas in Homa Bay. Intercropping reduced aphid incidence (18.3%) and severity (1.3) in UM1 areas in Vihiga district. Inorganic fertiliser reduced bean fly (3.8%) and thrips (11.8%) incidences in UM1 areas in Vihiga and in LM2 areas in Siaya districts, respectively, compared with fields without fertiliser. The result is important in the development of strategies in bean insect pest management and control.
Designing a Rule-based Wizard for Visualizing Statistical Data on Thematic Maps

Thematic maps are used in a wide range of scientific fields to illustrate specific geographic phenomena. For their correct construction, the mapmaker has to select the appropriate data, and then consider different parameters and constraints in order to visualize them effectively. In this paper, these parameters were analyzed, so that a consistent and standardized workflow for producing thematic maps could be set up. This workflow served as the basis for designing and implementing a step-by-step wizard-based application. Its goal is to guide mapmakers—experts or laypersons—to create cartographically sound thematic maps based on statistical data, in a user-friendly way. To standardize the procedure, we analyzed the relationships between different mapping techniques and the types of data with which they are used to illustrate a geographic phenomenon. Based on this analysis, we created a new taxonomy of mapping techniques and used it to automate the selection procedure within the wizard. This analysis could also be of general use for researchers producing thematic maps in different mapping applications.
Endocrine Disruptors: Very Low Doses with Genuinely High Impacts on Male Reproduction

Endocrine disruptors (EDs) are chemical substances that affect physiological processes in the body via hormonal regulation. They are often detected in food, plastic water bottles, cosmetics, and many other daily need items. Thereafter, EDs are detected in many bodily fluids, pointing out the real exposure to even very low doses. Permanent and long-term utilization of EDs has harmful effects on male reproductive health mainly due to interference with sex hormone synthesis and mechanism of action. However, with decreasing dosage of EDs, the possibilities of unpredictable modes of action arise. In addition to various molecular actions of individual EDs, the interference of individual ones represents another dimension of the ED issue. This review provides an overview of the EDs and their possible impact on reproductive health in males, with focus on sperm quality with the mighty potential of epigenetic transmission to further generations. The “posttranslational” effect of EDs in really low doses in real exposure routes is stigmatized in this review, being strongly considered as creeping molecular action of individual EDs as well as amplifications of their copresence in the environment.
Phenotypic Characterization of Uda Sheep in Maiduguri, Northern Nigeria

The study used a total of 255 (122 males and 133 females) Uda sheep were randomly sampled from the population. The parameters considered were body weight (BW), body length (BL), height at wither (HW), chest circumference (CC), head length (HL), head wide (HW), ear length (EL), horn length (HRL), horn circumference (HRC), tail length (TL),Â rump wide (RW), rump length (RL), height at rump (HR), foreleg (FLG), hind leg (HLD) and neck length (NL). The weight (Kg) was measured by using glasfiberband with model number WJ515 and the height measurement (cm) was done using a graduated measuring rule. The data obtained were analyzed using General Linear Model Procedure of SAS and Means differences were compared using Duncan Multiple Range Test. The result showed that age have significant (P 0.005) different, although they are statistically the same but showed slight increase with increase in age. The effect of sex on phenotypic traits of uda sheep showed HRL, HRC and HDW are significant (P<0.005) different. The phenotypic correlation showed both positive and negative correlation between phenotypic traits. The study concluded that this research will initiate a selection and breeding programme for the improvement of Nigerian uda sheep.
An isoform-specific allele of the sax-7 locus

An isoform-specific allele of the sax-7 locus Dylan Rahe, Ines Carrera , Filip Cosmanescu and Oliver Hobert 1. Department of Biological Sciences, Columbia University, New York, NY, USA, Howard Hughes Medical Institute 2. Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY, USA 3. Current Address: School of Chemistry, University of the Republic, Montevideo, Uruguay
Individual variation in early‐life telomere length and survival in a wild mammal

Individual variation in survival probability due to differential responses to early‐life environmental conditions is important in the evolution of life histories and senescence. A biomarker allowing quantification of such individual variation, and which links early‐life environmental conditions with survival by providing a measure of conditions experienced, is telomere length. Here, we examined telomere dynamics among 24 cohorts of European badgers (Meles meles). We found a complex cross‐sectional relationship between telomere length and age, with no apparent loss over the first 29 months, but with both decreases and increases in telomere length at older ages. Overall, we found low within‐individual consistency in telomere length across individual lifetimes. Importantly, we also observed increases in telomere length within individuals, which could not be explained by measurement error alone. We found no significant sex differences in telomere length, and provide evidence that early‐life telomere length predicts lifespan. However, while early‐life telomere length predicted survival to adulthood (≥1 year old), early‐life telomere length did not predict adult survival probability. Furthermore, adult telomere length did not predict survival to the subsequent year. These results show that the relationship between early‐life telomere length and lifespan was driven by conditions in early‐life, where early‐life telomere length varied strongly among cohorts. Our data provide evidence for associations between early‐life telomere length and individual life history, and highlight the dynamics of telomere length across individual lifetimes due to individuals experiencing different early‐life environments.
Growth of Acacia mearnsii De Wild and Eucalyptus globulus Labill in monoculture and mixed-plantations with simple lines and double lines of planting.

The objective of this study was to evaluated the development in height (m), DBH (cm) and wood production (m3/ha) of Acacia mearnsii De Wild and Eucalyptus globulus Labill species in monocultures and mixed-plantatios with simple and double lines of planting in the state of Rio Grande do Sul – RS. The experiment was installed in 2005, on two farms in municipality of Piratini – RS, where was planted the species Eucalyptus globulus Labill (E) and Acacia mearnsii De Wild (A), in monoculture and mixed in simple lines (50%E:50%A – LS) and double lines (50%E:50%A – LD). To evaluate the effects of mixed-plantings in the development of the species, the growth was analysed annually in october between 2006 and 2013; and in 2014 was realized the volume evaluation by the Smalian method. The black wattle had their height growth benefited for the mixed-plantations, 13,96 m at 50%E:50%A – LS and 13,56 m at 50%E:50%A – LD, while in monoculture it showed a height of 13.23 m. for eucalyptus was not observed advantages in height growth, because the mixed-plantations were equal to the monoculture; The DBH was influenced by the mixed-plantings for both species, positively to the black wattle, being up to 15% higher than monoculture, and negatively for eucalyptus, reaching 17% less than monoculture differences that are explained by variations in spacing provided to keep the conventional spacing of planting the species in the intercropping treatments. The productivity of black wattle in the mixed-plantings (97,97 m3/ha at 50%E:50%A – LS and 90,93 m3/ha at 50%E:50%A – LD) was higher than 50% of monoculture, which did not occur for eucalyptus. The total productivity of mixed-plantings were statistically equal the monocultures.
Host-endosymbiont co-evolution shaped chloroplast translational regulation

ABSTRACT The interaction between organisms and their environment generates evolutionary forces able to modify a living species. The process of gene expression, from the transcription of information encoded in a gene to the synthesis of a functional polypeptide, largely relies on evolution, which plays a significant role in determining the factors that control and regulate gene expression. Nowadays, chloroplasts are the result of a complex evolutionary history, elicited by the intracellular cohabitation of an ancient photosynthetic cyanobacterium inside a mitochondriate eukaryotic cell. In this paper, we try to describe the recent investigations on mechanisms that regulate chloroplast translation, both in Chlamydomonas reinhardtii and in land plants. After a general description of plastid translational machinery, ribosome structure with related proteins and nuclear-encoded proteins regulating plastid translation in these organisms, we focus on specific examples of chloroplast translation regulation in the green lineage. In the end, we provide a comparison between plastid translation regulation in green algae and land plants, showing that in both cases chloroplast gene expression is prevalently regulated at post-transcriptional and translational level, although with different strategies.
Identification of Lysine Carboxylation Sites in Proteins by Integrating Statistical Moments and Position Relative Features via General PseAAC

Carboxylation is one of the most biologically important post-translational modifications and occurs on lysine, arginine, and glutamine residues of a protein. Among all these three, the covalent attachment of the carboxyl group with the lysine side chain is the most frequent and biologically important type of carboxylation. For studying such biological functions, it is essential to correctly determine the lysine sites sensitive to carboxylation. Herein, we present a computational model for the prediction of the carboxylysine site which is based on machine learning. Various position and composition relative features have been incorporated into the Pse- AAC for construction of feature vectors and a neural network is employed as a classifier. The model is validated by jackknife, cross-validation, self-consistency, and independent testing. The results of the self-consistency test elaborated that model has 99.76% Acc, 99.76% Sp, 99.76% Sp, and 0.99 MCC. Using the jackknife method, prediction model validation gave 97.07% Acc, while for 10-fold cross-validation, prediction model validation gave 95.16% Acc. The results of independent dataset testing were 94.3% which illustrated that the proposed model has better performance as compared to the existing model PreLysCar; however, the accuracy can be improved further, in the future, due to the increasing number of carboxylysine sites in proteins.
A revolutionary protocol to describe understudied hyperdiverse taxa and overcome the taxonomic impediment

Here we elucidate and justify a DNA barcode approach to insect species description that can be applied to name tens of thousands of species of Ichneumonoidea and many other species-rich taxa. Each description consists of a lateral habitus image of the specimen, a COI barcode diagnosis, and the holotype specimen information required by the International Code of Zoological Nomenclature. We believe this approach, or a slight modification of it, will be useful for many other underdescribed hyperdiverse taxa, especially in the tropics. Due to the extreme species-richness of the Ichneumonoidea, the very low percentage of described species, and the lack of detailed biological information for most described species, the standard taxonomic approach is inefficient and overwhelmingly time consuming. A DNA barcode-based approach to initial description will provide a solid foundation of species hypotheses from which more comprehensive descriptions can be developed as other data, time, and budgets permit. Here we elucidate this view and detailed methodology that can generally be applied to species-rich underdescribed taxa. A real example is given by describing species in two genera, Hemichoma and Zelomorpha, reared from the Área de Conservación Guanacaste in northwestern Costa Rica. The generic type species Zelomorphaarizonensis is given a DNA barcode diagnosis and the following new species are described: Zelomorphaangelsolisi, Zelomorphabobandersoni, Zelomorphadanjohnsoni, Zelomorphadonwindsori, Zelomorphaeffugia, Zelomorphajohnchemsaki, Zelomorphakellyanneae, Zelomorphalarrykirkendalli, Zelomorphamariyavladmirovnae, Zelomorphamikeiviei, Zelomorphamyricagaleae, Zelomorphanoahjaneae, Zelomorphapaulgoldsteini, Zelomorphaterryerwini, Zelomorphawillsflowersi, Hemichomadonwhiteheadi, Hemichomafrankhovorei, and Hemichomajohnkingsolveri.
Relationship Between Steroid Hormones and Metabolic Profile in Women With Polycystic Ovary Syndrome

Polycystic ovary syndrome (PCOS) is commonly associated with a higher cardiometabolic risk. The relationship between steroid hormones and cardiometabolic profile in PCOS has been evaluated, but no single hormonal predictor of this association has been identified to determine. To determine the relationship between steroid hormones and cardiometabolic risk factors in PCOS women. Study included 64 women diagnosed with PCOS. Fasting blood samples were analyzed for biochemical, metabolic parameters and sex steroid hormones. PCOS women with BMI≥27 had significantly higher serum free testosterone (FT), free androgen index (FAI), estrone (E1) (p=0.014, p=0.02, p=0.01) than those with normal weight. In all subjects E1 positively correlated with BMI (p=0.0067), serum insulin (p=0.0046), HOMA-IR (p=0.0125) and negatively with HDL-cholesterol (p=0.009). FAI positively correlated with serum cholesterol (p=0.0457), triacylglycerols (TAG) (p=0.0001), HOMA-IR (p=0.037), and glycemia (p=0.0001), negatively with HDL-cholesterol (p=0.029). In multiple linear regression model E1 most significantly predicted HOMA-IR, whereas FT/FAI predicted HDL-cholesterol and BMI. We conclude that PCOS women with marked overweight or obesity have higher FT, FAI and E1 as compared with nonobese PCOS subjects. E1 and FT may predict worse cardiometabolic profile in PCOS.
Contaje de mitosis en imágenes histológicas mediante redes neuronales convolucionales

El diagnóstico último del cáncer se realiza por los patólogos mediante el análisis de imágenes histológicas. Uno de los marcadores más importantes en el pronóstico y detección temprana del mismo es el denominado grado de proliferación, que se estima mediante el contaje de figuras mitóticas en imágenes histológicas tintadas con hematoxilina y eosina. Los patólogos realizan este contaje de mitosis de manera manual. Este proceso es costoso y subjetivo, existiendo discrepancias entre los expertos. En los últimos años, el aumento de microscopios escáneres ha permitido la digitalización de las muestras histológicas y su posterior procesamiento. En este trabajo se presenta un método para el contaje automático de mitosis en imágenes histológicas. Este método comprende dos fases: 1) selección de regiones candidatas a mitosis basada en técnicas convencionales de procesamiento de imagen; 2) clasificación mediante Redes Neuronales Convolucionales y técnicas de Deep Learning. El método ha sido validado sobre una base de datos con 656 casos, y se ha obtenido una sensibilidad de 0.617 y un valor de F1 de 0.541 en consonancia con el estado del arte.
Chloroplast phylogenomics of liverworts: a reappraisal of the backbone phylogeny of liverworts with emphasis on Ptilidiales

As one of the four main lineages diverging from the early diversification of land plants, the phylogeny of liverworts holds the information about nearly 500 Myr of independent adaptation to changing environments. Thus, resolving the phylogenetic history of liverworts will provide unique insights into the successful diversification of early land plants in terrestrial ecosystems. However, the deep diverging events of this group remain incompletely resolved, such as the definite position of Ptilidiales. Here, we aimed to reconstruct the backbone relationships of liverworts using 84 protein‐coding chloroplast genes, a dataset comprising 35 representatives from all major lineages of liverworts, and three phylogenetic analyses, namely maximum parsimony, maximum likelihood and Bayesian inference. To test the impact of composition biases, the phylogenetic analyses were carried out using three alignments representing the same dataset either as: (i) nucleotides, (ii) amino acids, or (iii) recoded nucleotides applying ambiguity base code. Chloroplast genome data consistently supported the monophyletic origin of three major lineages in liverworts, as well as the majority of backbone relationships. Ptilidiales were found to be sister to Jungermanniales. The rapid accumulation of G/C tracks as a consequence of increased GC content is an important cause for the long branches inferred in this group. Our study not only provides empirical evidence to support the significance of plastid genome sequencing to reconstruct the phylogeny of this important plant lineage, but also suggests that the GC content has played a critical role in the evolutionary dynamics of plastid genomes in land plants.
Macroecology in the age of Big Data – Where to go from here?

Recent years have seen an exponential increase in the amount of data available in all sciences and application domains. Macroecology is part of this “Big Data” trend, with a strong rise in the volume of data that we are using for our research. Here, we summarize the most recent developments in macroecology in the age of Big Data that were presented at the 2018 annual meeting of the Specialist Group Macroecology of the Ecological Society of Germany, Austria and Switzerland (GfÖ). Supported by computational advances, macroecology has been a rapidly developing field over recent years. Our meeting highlighted important avenues for further progress in terms of standardized data collection, data integration, method development and process integration. In particular, we focus on (a) important data gaps and new initiatives to close them, for example through space‐ and airborne sensors, (b) how various data sources and types can be integrated, (c) how uncertainty can be assessed in data‐driven analyses and (d) how Big Data and machine learning approaches have opened new ways of investigating processes rather than simply describing patterns. We discuss how Big Data opens up new opportunities, but also poses new challenges to macroecological research. In the future, it will be essential to carefully assess data quality, the reproducibility of data compilation and analytical methods, and the communication of uncertainties. Major progress in the field will depend on the definition of data standards and workflows for macroecology, such that scientific quality and integrity are guaranteed, and collaboration in research projects is made easier.
Mountain building, climate cooling and the richness of cold‐adapted plants in the Northern Hemisphere

The summits of mountain ranges at mid‐latitude in the Northern Hemisphere share many ecological properties with the Arctic, including comparable climates and similar flora. We hypothesize that the orogeny during the Oligocene‐Miocene combined with global cooling led to the origin and early diversification of cold‐adapted plant lineages in these regions. Before the establishment of the Arctic cryosphere, adaptation and speciation in high elevation areas of these mountain ranges may have led to higher species richness compared to the Arctic. Subsequent colonization from mid‐latitude mountain ranges to the Arctic may explain similar but poorer flora.