Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of soybean seed vigor and size on seedling growth.

Soybean [Glycine max (L.) Merrill] seed vigor can affect yield either indirectly by influencing plant populations or more directly by affecting plant growth. Greenhouse experiments were conducted to evaluate the relationship between seed vigor and seedling growth. Seed lots of six cultivars with acceptable standard germination (>82%) and highl and low-vigor levels based on the speed of germination and accelerated aging germination tests were selected. In a first set of experiments, large and small size classes were selected from each seed lot of two cultivars (DeSoto and Pershing) using round hole screens. Seeds were planted in the greenhouse and seedling dry weight (excluding the cotyledons) and leaf area were measured at 5,10, 15, and 20 d after emergence (DAE) on seedlings that exhibited no cotyledon injuries and emerged on the same day. Within a vigor level, seedlings from large seeds were heavier at the first and final harvests than seedlings from small seeds by an average of 55 and 57%, respectively. Seed size had no effect on specific growth rate (SGR) (mg mg"1 day"1) or net assimilation rate (NAR) (g m"2 d"1). Seed vigor had no effect on SGR, NAR, or seedling weight at 20 DAE. In a second set of experiments, individual seed conductivity of seeds from highand low-vigor seed lots of four cultivars ('SS443', 'Harper', 'BE-29' and 'Williams 82') was measured and related to seedling dry weight accumulation. There was no significant relationship between conductivity and seedling dry weight at 20 DAE for seedlings with no cotyledon injury. However, an average of 49% of the seedlings from low vigor seedlots showed cotyledon injury at emergence vs. 20% for high-vigor seedlots. Seedlings with cotyledon injury emerged slower and had less dry weight at 20 DAE. The data indicate that seed vigor has no effect on the ability of the seedling to accumulate dry weight if there is no injury to the cotyledons. Additional index words: Glycine max (L.) Merrill, Growth analysis, Germination, Physical injury, Conductivity.
Systema Naturae or the outline of living world classification

Summary Here we present the short outline of the classification of living things (to the level of classes), given with two main goals: to provide a compact, synthetic overview of the biological diversity; and to supply users with up-todate information of latest taxonomic achievements. The latter is especially important in the recent epoch of “molecular revolution” in the taxonomy.
Prediabetes Is Independently Associated with Subclinical Carotid Atherosclerosis: An Observational Study in a Non-Urban Mediterranean Population

This was a prospective, observational study to compare the burden of subclinical atherosclerosis as measured by carotid ultrasonography in a cohort of subjects with prediabetes vs. subjects with normal glucose tolerance (NGT) from a non-urban Mediterranean population. Atherosclerosis was assessed through carotid intima-media thickness (c-IMT), the presence/absence of carotid plaques, and plaque number. Among 550 subjects included, 224 (40.7%) had prediabetes. The mean c-IMT and the prevalence of carotid plaque were significantly higher in the prediabetes group compared to the NGT group (0.72 vs. 0.67 mm, p < 0.001; and 37.9% vs. 19.6%; p < 0.001, respectively). Older age, male gender, and increased systolic blood pressure were positively correlated with c-IMT and were independent predictors of the presence of plaques. In contrast, prediabetes and low-density lipoprotein (LDL)-c were predictors of the presence of plaque (odds ratio [OR] = 1.64; 95% confidence interval [CI] = 1.05–2.57; p = 0.03 and OR = 1.01; 95% CI = 1.00–1.02; p = 0.006, respectively) together with tobacco exposure and the leukocyte count (OR = 1.77; 95% CI = 1.08–2.89; p = 0.023 and OR = 1.20; 95% CI = 1.05–1.38; p = 0.008, respectively). In a non-urban Mediterranean population, prediabetes was associated with established subclinical carotid atherosclerosis. These findings could have implications for the prevention and treatment of CV risk in these subjects before the first symptoms of cardiovascular disease appear.
The genus Hydroptila Dalman (Trichoptera, Hydroptilidae) in Japan

The Japanese species of Hydroptila Dalman (Trichoptera, Hydroptilidae) are reviewed, confirming 10 described species, and introducing 2 new species. For clear comparisons and to include new details, males and females of all species, including the 2 new species, H. ogasawaraensis Ito and H. nanseiensis Ito, are redescribed or described anew. Hydroptila itoi Kobayashi is synonymized with H. dampfi Ulmer and H. thuna Olah and H. botosaneanui Kumanski are recorded for the Japanese fauna for the first time. Hydroptila usuguronis Matsumura is reassigned to the genus Psychomyia Latreille (Psychomyiidae).
The Glycocalyx core protein Glypican 1 protects vessel wall endothelial cells from stiffness-mediated dysfunction and disease.

AIMS Arterial stiffness is an underlying risk factor and a hallmark of cardiovascular diseases. The endothelial cell (EC) glycocalyx is a glycan rich surface layer that plays a key role in protecting against EC dysfunction and vascular disease. However, the mechanisms by which arterial stiffness promotes endothelial cell dysfunction and vascular disease are not fully understood, and whether the mechanism involves the protective endothelial glycocalyx is yet to be determined. We hypothesized that endothelial glycocalyx protects the endothelial cells lining the vascular wall from dysfunction and disease in response to arterial stiffness. METHODS AND RESULTS Cells cultured on polyacrylamide (PA) gels of substrate stiffness 10 kPa (mimicking the subendothelial stiffness of aged, unhealthy arteries) showed a significant inhibition of glycocalyx expression compared to cells cultured on softer PA gels (2.5 kPa, mimicking the subendothelial stiffness of young, healthy arteries). Specifically, gene and protein analyses revealed that a glycocalyx core protein Glypican 1 was inhibited in cells cultured on stiff PA gels. These cells had enhanced endothelial cell dysfunction as determined by enhanced cell inflammation (enhanced inflammatory gene expression, monocyte adhesion and inhibited nitric oxide expression), proliferation and EndMT. Removal of Glypican 1 using gene-specific silencing with siRNA or gene overexpression using a plasmid revealed that Glypican 1 is required to protect against stiffness-mediated endothelial cell dysfunction. Consistent with this, using a model of age-mediated stiffness, older mice exhibited a reduced expression of Glypican 1 and enhanced endothelial cell dysfunction compared to young mice. Glypican1 gene deletion in knockout mice (GPC1 -/-) exacerbated endothelial dysfunction in young mice, which normally had high endothelial expression, but not in old mice that normally expressed low levels.Endothelial cell dysfunction was exacerbated in young, but not aged, Glypican 1 knockout mice (GPC1 -/-). CONCLUSIONS Arterial stiffness promotes EC dysfunction and vascular disease at least partly through the suppression of the glycocalyx protein Glypican 1. Glypican 1 contributes to the protection against endothelial cell dysfunction and vascular disease in endothelial cells. TRANSLATIONAL PERSPECTIVE This work reveals for the first time the effect of arterial stiffness on the glycocalyx protein Glypican 1 in endothelial cell function. Stiffness promotes endothelial cell dysfunction and subsequently vascular disease at least partly through the suppression of Glypican 1. Thus, Glypican 1 could be a novel therapeutic candidate for the treatment/reversal of arterial stiffness-mediated vascular disease.
Analysis of Motor Intervention Program on the Development of Gross Motor Skills in Preschoolers

This study aimed to investigate the influence of a structured movement activity program on the motor development of children aged three to five years attending preschool. Participants were 136 preschool students with normative development at three to four years old who lived in the Region of Murcia (Spain). The McCarthy Children’s Psychomotricity and Aptitude Scales (MSCA) battery of psychomotor tests was used to evaluate the motor development profiles of preschoolers before and after the intervention. The sample was divided into two groups: an intervention group (28 students) and a comparison group (108 students). A structured 24 week physical education program was used in the intervention group. An experiential program based on free play was used in the comparison group during the same period. Preschoolers in both groups got a significant improvement in the contrast of pre-intervention with post-intervention in limb coordination. Statistically significant differences in the post-intervention measurements between the comparison group and the intervention group on arm and leg coordination were observed, whereby the intervention group presented higher arm coordination values (F1,134 = 14,389, p = 0.000, η2 = 0.097) and higher leg coordination values (F1,134 = 19,281, p = 0.000, η2 = 0.126) than the comparison group. It was pointed out that structured physical activity education is better educational methodology than free play to achieve adequate motor development in preschool children.
Deep-learning-based model observer for a lung nodule detection task in computed tomography

Abstract. Purpose: Task-based image quality assessment using model observers (MOs) is an effective approach to radiation dose and scanning protocol optimization in computed tomography (CT) imaging, once the correlation between MOs and radiologists can be established in well-defined clinically relevant tasks. Conventional MO studies were typically simplified to detection, classification, or localization tasks using tissue-mimicking phantoms, as traditional MOs cannot be readily used in complex anatomical background. However, anatomical variability can affect human diagnostic performance. Approach: To address this challenge, we developed a deep-learning-based MO (DL-MO) for localization tasks and validated in a lung nodule detection task, using previously validated projection-based lesion-/noise-insertion techniques. The DL-MO performance was compared with 4 radiologist readers over 12 experimental conditions, involving varying radiation dose levels, nodule sizes, nodule types, and reconstruction types. Each condition consisted of 100 trials (i.e., 30 images per trial) generated from a patient cohort of 50 cases. DL-MO was trained using small image volume-of-interests extracted across the entire volume of training cases. For each testing trial, the nodule searching of DL-MO was confined to a 3-mm thick volume to improve computational efficiency, and radiologist readers were tasked to review the entire volume. Results: A strong correlation between DL-MO and human readers was observed (Pearson’s correlation coefficient: 0.980 with a 95% confidence interval of [0.924, 0.994]). The averaged performance bias between DL-MO and human readers was 0.57%. Conclusion: The experimental results indicated the potential of using the proposed DL-MO for diagnostic image quality assessment in realistic chest CT tasks.
Effect of pelleted vs. ground starter with or without hay on preweaned dairy calves

The objective of this study was to evaluate the effect of the physical form of starter and inclusion of hay in the diet of preweaning dairy calves on performance, digestibility, ruminal development, and mRNA expression of genes involved in ruminal metabolism. Holstein × Gyr crossbred male calves (n = 38 1day old) were assigned to 3 treatments for 9 weeks: Control (n = 13; pellet starter with 4 mm diameter and 18 mm length and 4% steam-flaked corn), Ground (n = 12; same starter of the control but ground pass through a 4.0 mm sieve), or Ground plus 5% chopped Tifton hay GH (n = 13). All calves were fed 4 L/d of whole milk up to 63 d of age and were abruptly weaned at 64 d of age. Water and diets were offered ad libitum. Samples of ruminal contents were obtained from all animals at 30, 45, and 60 d of age to evaluate pH, ammonia nitrogen, and volatile fatty acids (VFA). At 55 d of age, an apparent digestibility assay was performed using 18 animals (n = 6/ treatment). At 65 d of age, the 18 animals were euthanized to evaluate the development of the digestive tract. The physical form of starter and the dietary inclusion of hay did not influence starter intake (Control 326 g/d, Ground 314 g/d and GH 365 g/d), daily weight gain (Control 541g/d, Ground 531g/d and GH 606g/d), feed efficiency, apparent nutrient digestibility, energy partitioning, nitrogen balance, ruminal pH, ammonia nitrogen concentration, VFA, the development of the digestive tract and the mRNA expression of genes involved in AGV metabolism.
PHOTOREVERSIBLE CONTROL OF HETEROPHYLLY IN HIPPURIS VULGARIS L.

summary The freshwater macrophyte Hippuris vulgaris exhibits heterophylly. During July and August aerial-type leaves occur even on immersed shoots down to a depth of 15 m in two clear-water limestone lochs in Scotland. Complementary field and laboratory data indicate that a high intensity photoperiod and temperatures above 10°C are prerequisites for aerial-type leaf production on submerged shoots. In these conditions, regular injections of additional sucrose, the natural photosynthate, at 05 mol kg−1 fresh weight will not induce the aerial-type leaf. There is relatively little attenuation of blue light with depth in these lakes and additional blue light just after the photoperiod does not induce the aerial-type leaf. There is no evidence for an ontogenetic or circadian photoperiodic requirement for the production of aerial-type leaves, or that heterophylly is mediated by ethylene. However, a low ratio of red (R 660 run) to far red (FR 730 run) light throughout, or very dimly for a brief period just after, the photoperiod treatment regularly induces aerial leaf formation on submerged shoots of any length. A similar low R/FR ratio is found naturally in these lakes in summer at depths where submerged aerial leaves occur. Selective attenuation of far red by lakewaters raises the R/FR ratio steeply with increasing depth. At R/FR ratios above a critical range, which is similar in field and laboratory, aerial leaf formation is inhibited and only submerged-type leaves are formed. Simply by changing the R/FR ratio, either during or briefly after the photoperiod, transitions between submerged and aerial-type leaves are repeatedly reversible, implying direct phytochrome control.
GENE TREES, SPECIES TREES, AND SYSTEMATICS: A Cladistic Perspective

▪ Abstract The proliferation of molecular data in systematics has opened a Pandora's box of alternate approaches to inferring hierarchical patterns of relationship among taxa. In this review, we examine practical and theoretical reasons for employing some methods and avoiding others. We offer a philosophical overview of the relationship between systematics patterns and evolutionary processes, and we discuss the differential emphasis given to each of these areas by opposing methodological camps. We review the sources and types of incongruence between data partitions from different sources and recommend a specific procedure for contending with incongruence. We then focus on inference of relationships among closely related taxa, with particular emphasis on mtDNA as a source of characters, its advantages and potential pitfalls. We conclude with a review of several widely cited empirical studies and suggest that the gene tree–species tree problem may be less severe than its prevalence in the literature would s.
Deep Prototypical Networks With Hybrid Residual Attention for Hyperspectral Image Classification

Recently, convolutional neural networks (CNNs) have attracted enormous attention in pattern recognition and demonstrated excellent performance in hyperspectral image (HSI) classification. However, high-dimensional HSI dataset versus limited training samples is easy to cause the overfitting phenomenon in deep neural networks. Additionally, the intraclass distance of the embedding features extracted through the softmax-based CNNs may be greater than that of the interclass, which makes it difficult to further improve the classification accuracy. To address these issues, this article proposes a deep prototypical network with hybrid residual attention, which can effectively investigate the spectral–spatial information in the HSI. Specifically, in order to improve the generalization capability of the model, feature extraction with a hybrid residual attention module is presented to enhance the critical spectral–spatial features and suppress the useless ones in the classification task. Furthermore, a novel discriminant distance-based cross-entropy loss is proposed to increase the intraclass compactness, to obtain more superior results. Extensive experiments on three benchmark datasets are carried out to convincingly evaluate the proposed framework. With the generation of optimal prototypes representing each class and more discriminative embedding features, encouraging classification results are achieved compared with state-of-the-art methods.
DIFFERENCES IN RATE OF CYTOCHROME-b EVOLUTION AMONG SPECIES OF RODENTS

Abstract Although molecular evolution often appears to proceed in a clocklike fashion, examples to the contrary are increasing in number. Our study compares rate of cytochrome-b evolution in 21 rodent species, each of which belongs to a different genus. In these comparisons, substitutions at synonymous sites appear to be saturated, precluding inferences about rate of synonymous substitution. Rate of nonsynonymous substitution differs significantly among many of the rodents studied. However, the cause or causes of these differences in substitution rate remains in question. Differences in generation time, body size, or metabolic rate do not seem to be associated with rate of nonsynonymous substitution in these rodents. Effective population size remains a viable explanation of the observed rate heterogeneity. However, we suggest that a search for simple causes of differences in rate of molecular evolution may be difficult in light of numerous aspects of an organism's biology that may together influence evolutionary rates over space and time.
Minimum viable metapopulation size of a beetle, Osmoderma eremita, living in tree hollows

Osmoderma eremita, an endangered beetle restricted to hollow trees, was surveyed in stands of different size, isolation and physical characteristics in an area in south‐eastern Sweden. To infer habitat occupancy the presence/absence of fragments of adult body parts was used. Mark–release–recapture of adults with pitfall traps set in tree hollows was carried out to estimate local population size. Habitat occupancy/tree was higher in larger stands than in smaller stands, but there was no correlation between occupancy/stand and isolation of stands. This suggests dispersal is important in the population processes within stands, but not between stands. Osmoderma eremita was found in most of the larger stands and this probably mirrors the fact that the density of old‐growth oaks has been much higher in the area than today. Habitat fragmentation over the last two centuries has disrupted the network of habitat patches, thus preventing dispersal into smaller, younger stands. A minimum number of suitable trees aggregated in stands seems to be necessary to provide long‐term viability of local O. eremita populations. To preserve viable O. eremita populations, it is therefore necessary to increase size and connectivity of stands with hollow trees.
Population Fluctuations, Losses to Grazing, and Reproductive Success of Dactylorhiza sambucina on Bornholm, Denmark

Populations of the orchid Dactylorhiza sambucina are declining in number and size on the island of Bornholm, Denmark. To study the reasons for this trend, we compiled previously unpublished estimates of population sizes from 1987–2010 and found complicated fluctuations, as population sizes generally increased in the early 1990s but declined after that. We could find no effect of vegetation management, neither were the fluctuations related to suggested climatic factors. High proportions of plants were lost to grazing in the study year; same could be deduced for previous years when more than one census was available. Grazing in spring and early summer may therefore contribute to the decline of D. sambucina, as suggested by others. Populations seemed not to be affected by lack of pollination or population inbreeding, as fruit set and reproductive size was as high as in large and interconnected D. sambucina populations on Öland, Sweden, and as reported in other studies.
Patterns of Landscape Transformation in Colombia, with Emphasis in the Andean Region

Abstract Since pre-Columbian times, Colombia has undergone transformation of large parts of its natural ecosystems, in particular in the Andean region. To date, little is known about the patterns and processes of this transformation and their relation with socioeconomic and biophysical aspects. Traditionally, the lack of integration of multidisciplinary data has hampered the possibility to understand complex phenomena like this. An integrated approach helps to bring into a relevant contextual analysis, data that are normally analyzed separately. This paper presents an approach to understanding ecosystem transformation by linking and integrating, spatially, data on ecosystem distribution and transformation, with demographic, land use, and settlement history data on a national scale. The transformation is analyzed and documented in order to explain the present situation and to make some general predictions about future tendencies. The results show that the demographic and transformation patterns follow clear historical trends that can be spatially differentiated, and are related to natural regions—plains and mountains, and altitude belts—and to general land uses. In particular, the patterns of the Andes and the lowlands show historically distinct tendencies. The Andean region has higher densities and transformation proportions than the lowlands. The older settlement areas show higher densities and more intensive land use, and tend to be strongly related to the Andean region.
Generation mean analysis: a case study of yield and yield components in ksc704 maize (Zea mays L.) generations.

The choice of selection and breeding procedures for genetic improvement of maize or any other crop largely depends on the type and relative amount of genetic components and presence of non-allelic interaction. In this study six generations (p1, p2, f1, f2, bc1 and bc2) from b73(p1) × mo17(p2) cross of corn were evaluated for several agronomic traits including yield and its components at thorough agricultural station of Khorasan-eRazavi agriculture and natural resources research center, Mashhad, Iran, in the 2010 growing season. The experiment was carried out as a randomized complete block design with three replications. The results showed significant differences among generations for all traits. Most of the additive, dominance, additive × additive, additive × dominance and dominance × dominance effects were significant indicating the importance of the additive, dominance and epistatic modes of gene action in controlling the agronomic characters in maize. However, dominance variance was more important than additive variance for most of the traits such as ear length, kernel number per row, kernel number per ear and grain yield, which justifies the production of hybrid varieties in maize. Broad sense heritability of traits was 0.42-0.87 for B73 × MO17 cross. The estimated number of genes for grain yield in the late maturing hybrid, ksc704 (B73 × MO17), was around 10.