Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Mitogenome Analysis Reveals Mitochondrial Genome Differentiation in Ectomycorrhizal and Asymbiotic Amanita Species

In this present study, we assembled and analyzed the mitogenomes of two asymbiotic and six ectomycorrhizal Amanita species based on next-generation sequencing data. The size of the eight Amanita mitogenomes ranged from 37,341 to 137,428 bp, and we considered introns to be one of the main factors contributing to the size variation of Amanita. The introns of the cox1 gene experienced frequent gain/loss events in Amanita; and the intron position class cox1P386 was lost in the six ectomycorrhizal Amanita species. In addition, ectomycorrhizal Amanita species had more repetitive sequences and fewer intergenic sequences than asymbiotic Amanita species in their mitogenomes. Large-scale gene rearrangements were detected in the Amanita species we tested, including gene displacements and inversions. On the basis of the combined mitochondrial gene set, we reconstructed the phylogenetic relationships of 66 Basidiomycetes. The six ectomycorrhizal Amanita species were of single origin, and the two saprophytic Amanita species formed two distinct clades. This study is the first to elucidate the functions of the mitogenome in the evolution and ecological adaptation of Amanita species.
Differential Response of the American Lobster Homarus americanus to the Invasive Asian Shore Crab Hemigrapsus sanguineus and Green Crab Carcinus maenas

ABSTRACT The American lobster Homarus americanas shares rocky shore habitats and resources with two common invasive crab species in the northwest Atlantic: the green crab Carcinus maenas and the Asian shore crab Hemigrapsus sanguineus. Juvenile or early benthic phase (EBP) lobsters live under the same boulders as these crabs and are potentially vulnerable to crab predation and competition. Time-lapse photography was used to quantify aggressive interactions between EBP lobsters and invasive crabs in the laboratory. Lobsters behaved far more aggressively toward Asian shore crabs (initiating 11.8 attacks/h) than green crabs (4.9 attacks/h). Crab behavior varied widely as well, as green crabs were five times more likely to attack EBP lobsters than were Asian shore crabs. Thus, lobsters initiated 75.5% of aggressive interactions with Asian shore crabs, compared with only 22.3% with green crabs. Invasion history was a possible reason for this disparity, as green crabs have shared geographic range with American lobsters for more than 100 y. compared with only more than 10 y for Asian shore crabs. Differences in lobster responses to the two crab species suggest that aggressive behavior is the default for EBP lobsters and that they attacked the novel species (H. sanguineus) because they had not developed avoidance behavior to the potential crab threat. Green crabs posed more of a predation threat than Asian shore crabs, consuming over 80% of lobsters in 24-h trials. These results suggest that invasion history and predator—prey adaptation may shape the behavior and ecological interactions of native and invasive species.
Frontal aslant tracts as correlates of lexical retrieval in MS

ABSTRACT Introduction Previous studies reveal that a newly described white matter pathway, the frontal aslant tract (FAT), connecting inferior and superior frontal gyri has a role in speech and language functions. We explored the role of this tract in a phonemic and semantic fluency tasks in a cohort of multiple sclerosis patients diagnosed with cognitive impairment. Methods Thirty-five MS patients with varying degrees of cognitive impairment underwent diffusion tensor imaging and the Controlled Associated Word Test. Fractional anisotropy (FA) of FAT and arcuate fasciculus (AF) were obtained through a supervised, atlas-based tissue segmentation and parcellation method. Phonemic and semantic fluency scores were obtained from COWAT. We ran a multivariate regression model, and partial correlation analyses adjusted for age, education, and lesion load, and corrected for multiple comparisons. False discovery rate (FDR) was used for the correction of multiple comparisons. Results Bilateral FAT FA showed significant association with phonemic verbal fluency task (Left; r = 0.46, p = 0.0058 and right; r = 0.46, p = 0.0059) but not semantic fluency task and this relation remained significant after FDR correction (p = 0.02 bilaterally). Although left AF showed some significant association with phonemic fluency task, this relation was insignificant after FDR correction. Conclusion We show that bilateral FAT are correlates of phonemic verbal fluency task but not semantic in an MS cohort with cognitive impairment. This finding suggests that FAT is more specialized in lexical retrieval function as semantic fluency test encompasses all the functions except the lexical retrieval.
Invertebrate life-history trade-offs and dispersal across a pond-permanence gradient

3 Chapter One: General Introduction . 5 Chapter Two: Constraints on the flexibility of growth and development control generalist invertebrate distributions across an unpredictable disturbance gradient. 19 Chapter Three: Flexible and inflexible generalist life-history strategies when exposed to contrasting predator and drying stresses. 53 Chapter Four: Dispersal sustains generalist metapopulations across a pond-permanence gradient: population genetic patterns of a damselfly (Odonata: Coenagrionidae: Xanthocnemis zealandica). 82 Chapter Five: Unpredictable disturbances ameliorate life-history trade-offs, increase nichewidth, influence speciation and affect responses to climate warming . 130 Acknowledgements . 149 References . 153
GENETIC MONITORING OF SCANDINAVIAN BROWN BEAR EFFECTIVE POPULATION SIZE AND IMMIGRATION

Abstract We used microsatellite marker data taken from Scandinavian brown bear (Ursus arctos) tissue samples collected by hunters and biologists to estimate population genetic parameters important for bear management. Specifically, we show evidence of a small effective population size (N̂e = 44.8; 95% CI: 30.9 to 73.2) and low rates of immigration (m̂ = 0.01; 95% CI: 0.00 to 0.05) into the brown bear population along the southern edge of their range in Scandinavia. The ratio of genetic effective size to population size is approximately 0.06–0.14, which falls within the range of values found in previous studies of brown bears. The large confidence intervals around the immigration estimate reflect considerable uncertainty. Nonetheless, these values deserve attention because they are near thresholds of short-term management concern and worthy of long-term monitoring. If the genetic effective size remains this small and immigration remains low, then this population could be subject to the loss of fitness as a consequence of inbreeding effects.
The diet of Great Tit Parus major nestlings in a Mediterranean Iberian forest: the important role of spiders

Pagani-Nunez, E. , Ruiz, I, Quesada, J., Negro, J. J. & Senar, J. C. , 2011. The diet of Great Tit Parus major nestlings in a Mediterranean Iberian forest: the important role of spiders. Animal Biodiversity and Conservation, 34.2: 355-361. Abstract The diet of Great Tit Parus major nestlings in a Mediterranean Iberian forest: the important role of spiders. — The diet of the Great Tit Parus major when rearing chicks has been described in many studies. However, data from the Mediterranean area is scarce. Here we describe the diet of nestlings in a population of Great Tits in a Medi- terranean forest in Barcelona (north-east Spain) during two breeding seasons using two methods: neck-collars and video recording. The main prey were caterpillars (44% from neck-collar data and 62% from video-recorded data), but in our latitudes spiders also seemed to be an important food resource (24% from neck-collar data and 42% from video-recorded data). We did not find any significant differences in the quantity of spiders collected by parents in relation to stage of chick development, main vegetation surrounding nest boxes, size of the brood, or year. Our results stress the importance of spiders as a food source in Mediterranean habitats.
HD‐ZIP IV gene Roc8 regulates the size of bulliform cells and lignin content in rice

Abstract The morphology of bulliform cells located on the upper epidermis of leaves is one of the most important cell structures affecting leaf shape. Although many mechanisms regulating the development of bulliform cells have been reported, the fine regulatory mechanisms governing this process have rarely been described. To identify novel components regulating rice leaf morphology, a mutant showing a constitutively rolling phenotype from the seedling stage to flowering, known as crm1‐D, was selected for further analysis. Anatomical analyses in crm1‐D were attributable to the size reduction of bulliform cells. The crm1‐D was controlled by a single dominant nuclear gene. Map‐based cloning revealed that Roc8, an HD zipper class IV family member, was responsible for the crm1‐D phenotype. Notably, the 50‐bp sequence in the 3′‐untranslated region (3′‐UTR) of the Roc8 gene represses Roc8 at the translational level. Moreover, the roc8 knockdown lines notably increased the size of bulliform cells. A series of assays revealed that Roc8 negatively regulates the size of bulliform cells. Unexpectedly, Roc8 was also observed to positively mediate lignin biosynthesis without incurring a production penalty. The above results show that Roc8 may have a practical application in cultivating materials with high photosynthetic efficiency and low lignin content.
Little divergence in ribosomal DNA internal transcribed spacer ‐1 and ‐2 sequences among non‐digitate species of Laminaria (Phaeophyceae) from Hokkaido, Japan

The nuclear ribosomal DNA internal transcribed spacer (ITS‐1 and ITS‐2) sequences were determined for 10 of 12 Japanese non‐digitate Laminaria species, Kjell‐maniella gyrata (Kjellman) Miyabe, Costaria costata (Turner) Saunders, Alaria praelonga Kjellman and Chorda filum (L.) Stackhouse collected at Hokkaido. Phyloge‐netic analyses (maximum parsimony and distance matrix) of these sequences, including published data for L. sac‐charina (L.) Lamouroux from Canada, showed strong nucleotide conservation among these species of Laminaria, but two phylogenetically distinct species groups were recognized. A L. japonica group encompassing L. yapon/ca Areschoug, L. religiosa Miyabe, L. ochotensis Miyabe, L. diabolica Miyabe, L. longipedalis Okamura, L. angustata Kjellman and L. longissima Miyabe; and a L. saccharina group including L. coriacea Miyabe, L. sac‐charina, L. cichorioides Miyabe and L. yendoana Miyabe. As to other laminarialean genera, Kjellmaniella gyrata was most closely related to the genus Laminaria, being related to the second Laminaria species group based on both parsimony and distant tree values.
Mapping developmental trajectories and subtype diversity of normal and glaucomatous human retinal ganglion cells by single‐cell transcriptome analysis

Glaucoma is characterized by a progressive degeneration of retinal ganglion cells (RGCs), leading to irreversible vision loss. Currently, there is no effective treatment for RGC degeneration. We used a disease‐in‐a‐dish stem cell model to examine the developmental susceptibility of RGCs to glaucomatous degeneration, which may inform on the formulation of therapeutic approaches. Here, we used single‐cell transcriptome analysis of SIX6 risk allele (SIX6risk allele) primary open angle glaucoma patient‐specific and control hRGCs to compare developmental trajectories in terms of lineage‐ and stage‐specific transcriptional signature to identify dysregulated stages/genes, and subtype composition to estimate the relative vulnerability of RGCs to degeneration because their ability to regenerate axons are subtype‐specific. The developmental trajectories, beginning from neural stem cells to RGCs, were similar between SIX6risk allele and control RGCs. However, the differentiation of SIX6risk allele RGCs was relatively stalled at the retinal progenitor cell stage, compromising the acquisition of mature phenotype and subtype composition, compared with controls, which was likely due to dysregulated mTOR and Notch signaling pathways. Furthermore, SIX6risk allele RGCs, as compared with controls, expressed fewer genes corresponding to RGC subtypes that are preferentially resistant to degeneration. The immature phenotype of SIX6risk allele RGCs with underrepresented degeneration‐resistant subtypes may make them vulnerable to glaucomatous degeneration.
Safety of Rapid Infliximab Infusions in Children: A Systematic Review.

OBJECTIVES To assess whether the in incidence of Infusion Reactions (IR) increases after rapid (≤1 hour) Infliximab (IFX) infusions, compared to standard (2-3 hour) infusions in children. METHODS Systematic review including studies describing the number of IR after rapid IFX infusion in children aged 0-18 years. RESULTS Four records were included (three retrospective, n = 498, 347 standard infusions, 3703 rapid infusions). Reported incidences of IR ranged from 0-2% of infusions in standard groups (reported 95% CI's ranged from 0-7%) and from 0-2% of infusions in rapid groups (reported 95% CI's ranged from 0-12%). None of the studies included reported a significant difference in incidence of IR between the two groups. CONCLUSIONS There is insufficient evidence to conclude whether the rate of IR after rapid IFX increases. The consistent finding of no increase in IR in all studies and the low rate of observed IR suggests there is no significant difference in rate of IR.
Carbon allocation in calcareous grassland under elevated CO2: a combined 13C pulse‐labelling/soil physical fractionation study

Summary 1 To test whether plant–soil C fluxes in natural grassland increase under elevated atmospheric CO2 concentration, intact calcareous grassland monoliths exposed to ambient or elevated CO2 were pulse-labelled and the dynamics of the 13C label followed throughout the rest of the growing season. 2 The experiment revealed no increased fluxes of C to soils at elevated CO2. The only changes found were relatively small shifts towards increased C allocation to roots by the end of the growing season. This effect was probably because wetter soil under elevated CO2 prolonged the growing period. At elevated CO2, plant C pools increased below ground (+28%) at the end of the season, resulting in slightly increased root : shoot ratios. Plant 13C pools increased significantly below ground. There were no effects of CO2 enrichment on 13C in soil microbes, fine roots or earthworms. 3 Elevated CO2 caused a shift in soil particle size distribution towards smaller aggregate sizes, but had no effect on the total C and 13C content of low- and high-density soil fractions. 4 The absence of effects of CO2 on the labelling of soil microbial biomass, and of C and 13C accumulation in low-density macro-organic fractions, suggest that there is no significant effect of elevated CO2 on root exudation or turnover, agreeing with published labelling studies, but conflicting with CO2-exchange budgets.
Effect of sea buckthorn leaves on growth performance and calcium metabolism in Arbor Acres broilers.

The objective of this study was to investigate the effects of sea buckthorn leaves as feed additives on growth performance and calcium metabolism of Arbor Acres broilers.A total of 240 1-day-old healthy male Arbor Acre broilers were randomly used for 4 groups,each group with six replicates,and each replicate with ten AA broilers.The four groups were basal diet,basal diet supplemented with 0.25%,0.5% and 1% sea buckthorn leaves,respectively.The experiment was conducted for 49 d.The results showed that ADFI was significantly increased by 0.5% sea buckthorn leaves(P0.05) and F/G was significantly decreased by 15.17% compared to control(P0.05). The concentration of BGP,ALP and 1,25-(OH)2D3 in serum was increased significantly by 1% sea buckthorn leaves compared to control (P0.05). The digestibility of calcium was not significantly affected by sea buckthorn leaves at any dose (P0.05). But AA broilers fed supplemental 1% sea buckthorn leaves had significantly increased the digestibility of phosphorous by 64% (P0.05). Tibia calcium,tibia phosphorus,bone ash and bone density were not significantly affected by sea buckthorn leaves (P0.05). However,tibia phosphorus and bone density showed increasing trend with the increase of the sea buckthorn leave dose(P=0.0345;P=0.0123). In total,0.5% sea buckthorn leaves was beneficial to the growth performance in AA broilers.1% sea buckthorn leaves improved absorption of the calcium and phosphorous and deposition of calcium.Therefore,sea buckthorn leaves is one of potent phyto-additives to prevent AA broiler thigh disease.
Residential burglary victimization

The current study employed the International Crime Victimization Survey for 142,665 subjects in 35 countries to compare residential burglary patterns across countries by their developmental levels. The mixed-level modeling shows that households in less developed countries were more likely to experience residential burglary than those in highly developed countries. In addition, married status and low income levels were positively, while living in a detached house was negatively, related to burglary victimization. These findings are consistent with routine activity theory.
DAX1 a sex determining gene in fish

Sex determination is an essential process for the survival and evolution of vertebrate species. Although most vertebrates rely on a classical system of male heterogamety (males are XY whereas females are XX) or variations thereof, different fish species do not rely exclusively on these classical chromosomal systems, and instead, display a diverse array of sex determining mechanisms that include different forms of hermaphroditism and environmental sex determination. Thus, no simple genetic sex determining system can be generalized for fish. However, different studies have shown that most of the genes that are involved within the genetic sex determining cascade in vertebrate species that use chromosomal systems are also found in fish species that appear not to have heterogametic sex chromosomes, suggesting that they may have conserved functions despite the sex determining system in use. One of the genes that have been shown to be determinant for mammalian sex determination is the DAX1 gene. Indeed, mutations in human DAX1 and DAX1 mouse knockout models have resulted in genetic male sex reversal. Interestingly, this gene has been isolated in two different fish species and, due to its high conservation, led us to hypothesize that it may also have retained similar functions in fish. In order to test this hypothesis, we have decided to work with the European sea bass, which is a fish species that lack heterogametic sex chromosomes, but posess a sex determining mechanism that is strongly influenced by temperature (TSD). Thus, we have proceeded to the isolation of the full length sequence and gene structure of DAX1 in the European sea bass (sbDAX1). In the process, we have also identified a duplicate DAX gene (named sbDAX2), and another member of the DAX1 nuclear receptor family called SHP (sbSHP). The three nuclear receptors presented a conserved gene structure and putative protein domains as found in mammalian homolog genes. The tissue distribution of the three nuclear receptor members revealed a dimorphic pattern of expression within the hypothalamus-pituitary-gonadal (HPG) axis of male and female fish, suggesting that they may be involved in reproduction. In addition, during the sex determining period, larvae grown at either feminizing (15oC) or masculinizing (21oC) temperatures also presented a dimorphic pattern of expression of all three receptors, since larvae grown at low temperature showed repressed gene expression, while at higher temperature they were significantly upregulated. In addition, mRNA expression of other candidate sex determining genes, SOX9.1, SOX9.2 and SF1, was also similar to that obtained for the DAX duplicate genes and SHP. Thus, we have presented data
The impact of minimal extrathyroidal extension in the recurrence of papillary thyroid cancer patients

ABSTRACT Objective We aimed to evaluate the impact of minimal extrathyroidal extension (mETE) alone on the risk of recurrence of papillary thyroid carcinoma (PTC). The impact of other factors, including multifocality, age, tumor size, and stimulated thyroglobulin (sTg) values was also assessed. Subjects and methods We retrospectively analyzed 1,108 PTC patients from a medical institution, who presented tumors ≤ 4 cm without any adverse characteristics other than mETE. Patients were classified according to their response to initial treatment 12 to 24 months after surgery as proposed by the 2015 American Thyroid Association (ATA) guideline. Statistical analysis was performed using multivariate logistic regression and receiver operating characteristic (ROC) curve. Results In the multivariate logistic regression analysis, mETE did not have an impact on the response to initial treatment (p = 0.44), similar to multifocality, age, and tumor size. Initial Tg value was the only variable associated with a poor response (p < 0.01, odds ratio = 1.303, 95% confidence interval 1.25-1.36). The ROC analysis revealed that Tg was significant (area under curve = 0.8750); the cutoff value of sTg as a predictor of poor response was 10 ng/mL (sensitivity = 72.2%, specificity = 98.5%). Conclusion For low-risk PTC presenting mETE as the only aggressive feature, the initial sTg value is essential to identify patients who may have a poor response after initial treatment and benefit from further treatment. Arch Endocrinol Metab. 2020;64(3):251-6
Overview of biological effects of Quercetin on ovary

Over the last few decades, using natural products has been increased to treat different diseases. Today, great attention has been pointed toward the usage of natural products such as flavonoids, especially Quercetin (QUR), in the treatment of diseases. QUR as a natural antioxidant has been traditionally used to prevent or treat a variety of diseases such as cancer, cardiovascular disease, polycystic ovary syndrome (PCOS), obesity, chronic inflammation, and reproductive system dysfunction. Several studies demonstrated that QUR acts as an anti‐inflammatory, anti‐apoptotic, antioxidant, and anticancer agent. With this in view, in this study, we intended to describe an overview of the biological effects of QUR on the ovary. QUR improves the quality of oocytes and embryos. It affects the proliferation and apoptosis and decreases the oxidative stress in granulosa cells (GCs). Furthermore, QUR can be used as a complementary and alternative therapy in ovarian cancer and it has beneficial effects in the treatment of PCOS patients. It seems that QUR as a supplementary factor has different activities for the treatment of different disorders and it also has bidirectional activities. However, further investigations are needed for understanding the efficacy of QUR in the treatment and improvement of gynecological patients.