Miracle-dz/UniFAR-FTUs huggingface dataset:
Discordance and concordance between morphological and taxonomic diversity

Morphological and taxonomic diversity each provide insight into the expansion and contraction of major biological groups, while the nature of the relationship between these two aspects of diversity also has important implications for evolutionary mechanisms. In this paper, I compare morphological and taxonomic diversity within the classes Blastoidea and Trilobita, and within the trilobite clades Libristoma, Asaphina, Proetida, Phacopida, and Scutelluina. Blastoid morphology is quantified with homologous landmarks on the theca, and trilobite form is measured with a Fourier description of the cranidium. Morphological diversity is measured as the total variance among forms in morphological space (proportional to the mean squared distance among forms). Blastoid taxonomic diversity is based on published compilation of stratigraphic ranges of genera. The Zoological Record was used to determine the number of new species of trilobites described since the publication of the Treatise; temporal patterns in species richness are similar to those for generic richness based on the Treatise, suggesting a common underlying signal. Morphological variety and taxonomic richness often increase together during the initial diversification of a clade. This pattern is consistent with diffusion through morphospace, although some form of adaptive radiation cannot be ruled out. Morphological diversity varies little throughout much of the history of Proetida, a pattern that may suggest major constraints on the magnitude and direction of evolution, and that agrees with the perception of Proetida as a morphologically conservative group. Two major patterns are seen during the decline of clades. In Blastoidea, Trilobita, Libristoma, and Asaphina, morphological diversity is maintained at substantial levels, and in fact continues to increase, even in the face of striking reductions in taxonomic richness. This pattern suggests continued diffusion through morphospace and taxonomic attrition that is effectively non-selective with respect to morphology. In Phacopida, Scutelluina, and to some extent in Proetida, morphological diversity decreases along with taxonomic diversity. This pattern suggests heterogeneities such as elevated extinction and/or reduced origination in certain regions of morphospace. As found previously for the echinoderm subphylum Blastozoa, all studied clades of trilobites except Proetida show maximal morphological diversity in the Mid–Late Ordovician and maximal taxonomic diversity sometime during the Ordovician, suggesting some degree of common control on diversification patterns in these groups.
Comparison of Multiple Breath Washout and Spirometry in Children with Primary Ciliary Dyskinesia and Cystic Fibrosis and Healthy Controls.

RATIONALE In cystic fibrosis (CF), the lung clearance index (LCI) derived from multiple breath washout (MBW) is more sensitive in detecting early lung disease than FEV1; MBW has been less thoroughly evaluated in young patients with PCD. OBJECTIVES To evaluate (1) sensitivity of MBW and spirometry for detection of mild lung disease in young children with PCD and CF compared to healthy controls (HC), and (2) compare patterns of airway obstruction between disease populations. METHODS Multicenter, single visit, observational study in children with PCD and CF with an FEV1 >60% predicted and HC, ages 3-12 years. Nitrogen MBW and spirometry were performed and over-read for acceptability. Chi-square and Kruskall-Wallis tests compared demographic and lung function measures between groups, linear regression evaluated the effect of disease state and Spearman's rank correlation coefficient was used to compare LCI and spirometric measurements. RESULTS 25 children with PCD, 49 with CF, and 80 HC were enrolled, among whom 17 PCD (68%), 36 CF (73%), and 53 (66%) HC performed both acceptable spirometry and MBW and comprised the analytic cohort. Median age was 9.0 years (IQR 6.8-11.1). LCI was abnormal (>7.8) in 10/17 (59%) PCD patients and 21/36 (58%) CF patients, whereas FEV1 was abnormal in 3/17 (18%) PCD patients and 6/36 (17%) CF patients. LCI was significantly elevated in PCD and CF compared to HC (ratio of geometric mean vs. HC: PCD 1.27 (95% CI: 1.15-1.39) and CF 1.24 (95% CI: 1.15-1.33)). Children with PCD had lower FEF25-75 percent predicted compared to children with CF (62% (IQR: 50-78%) versus 85% (IQR: 68-99%), p=0.05). LCI did not correlate with FEV1. CONCLUSIONS LCI is more sensitive than FEV1 in detecting lung disease in young PCD patients, similar to CF. LCI holds promise as a sensitive endpoint for assessment of early PCD lung disease.
Muscle Cell Morphogenesis, Structure, Development and Differentiation Processes Are Significantly Regulated during Human Ovarian Granulosa Cells In Vitro Cultivation

Granulosa cells (GCs) have many functions and are fundamental for both folliculogenesis and oogenesis, releasing hormones and communicating directly with the oocyte. Long-term in vitro cultures of GCs show significant stem-like characteristics. In the current study, RNA of human ovarian granulosa cells was collected at 1, 7, 15 and 30 days of long-term in vitro culture. Understanding the process of differentiation of GCs towards different cell lineages, as well as the molecular pathways underlying these mechanisms, is fundamental to revealing other possible stemness markers of this type of cell. Identifying new markers of GC plasticity may help to understand the aetiology and recurrence of a wide variety of diseases and health conditions and reveal possible clinical applications of the ovarian tissue cells, affecting not only the reproductive ability but also sex hormone production. Granulosa cells were the subject of this study, as they are readily available as remnant material leftover after in vitro fertilisation procedures and exhibit significant stem-like characteristics in culture. The change in gene expression was investigated through a range of molecular and bioinformatic analyses. Expression microarrays were used, allowing the identification of groups of genes typical of specific cellular pathways. This candidate gene study focused on ontological groups associated with muscle cell morphogenesis, structure, development and differentiation, namely, “muscle cell development”, “muscle cell differentiation”, “muscle contraction”, “muscle organ development”, “muscle organ morphogenesis”, “muscle structure development”, “muscle system process” and “muscle tissue development”. The results showed that the 10 most upregulated genes were keratin 19, oxytocin receptor, connective tissue growth factor, nexilin, myosin light chain kinase, cysteine and glycine-rich protein 3, caveolin 1, actin, activating transcription factor 3 and tropomyosin, while the 10 most downregulated consisted of epiregulin, prostaglandin-endoperoxide synthase 2, transforming growth factor, interleukin, collagen, 5-hydroxytryptmine, interleukin 4, phosphodiesterase, wingless-type MMTV integration site family and SRY-box 9. Moreover, ultrastructural observations showing heterogeneity of granulosa cell population are presented in the study. At least two morphologically different subpopulations were identified: large, light coloured and small, darker cells. The expression of genes belonging to the mentioned ontological groups suggest the potential ability of GCs to differentiate and proliferate toward muscle lineage, showing possible application in muscle regeneration and the treatment of different diseases.
Perceived Discrimination, Psychological Distress and Cardiovascular Risk in Migrants in Spain

The aim of the present study is to determine the effect of discrimination and psychological distress on the cardiovascular health of immigrants, as well as to analyse potential differences based on age, gender, length of residence in host country and geographic origin. The sample was formed by 1714 immigrants from Africa, Eastern Europe and Latin America. Of the sample, 48.7% were men and 51.3% were women. Most relevant results show that discrimination (t = 4.27; p = 0.000) and psychological distress (t = 4.35; p = 0.000) experienced by immigrants predict their cardiovascular risk. Furthermore, psychological distress mediates the relation between discrimination and risk (t = 4.03; p = 0.000). Significant differences between men and women were found, as well as differences based on ethnicity, although to a lesser extent. Age affects the relation between discrimination, psychological distress and arterial hypertension and hypercholesterolemia. Results are notably relevant for the design of preventive health programmes for immigrants and intervention strategies in order to prevent diseases that may imply cardiovascular risks and seriously affect immigrants’ health.
RADIO-TAGGED PACIFIC GOLDEN-PLOVERS: THE HAWAII–ALASKA LINK, SPRING DESTINATIONS, AND BREEDING SEASON SURVIVAL

Abstract To learn more about mid-Pacific migration, we radio-tagged 40 Pacific Golden-Plovers (Pluvialis fulva) in spring 1999 on their wintering territories in Hawaii. The birds departed in late April, and with aerial monitoring we relocated 10 of them in Alaska. Seven individuals were in or near the Nushagak River lowlands in southwestern Alaska. Nesting Pacific Golden-Plovers were discovered there in 1994 disjunct from the previously known breeding range. The remaining three radio-tagged birds were found north of Bethel on the Yukon–Kuskokwim Delta. Our results suggest that breeding is continuous from the Nushagak region west through the uplands north of Bristol Bay to the Yukon–Kuskokwim Delta. Thus, plovers wintering in Hawaii apparently nest across a wide area of Alaska. We present a revised Alaska breeding distribution map for the species which differs significantly from AOU Checklist boundaries. The temporary attachment of transmitters (they are shed during summer molting) had no apparent effect on survival within our sample population. Birds that had carried transmitters returned to their winter territories in Hawaii at a rate nearly identical to banded plovers not radio-tagged.
Cell-Fate Determination from Embryo to Cancer Development: Genomic Mechanism Elucidated

Elucidation of the genomic mechanism that guides the cell-fate change is one of the fundamental issues of biology. We previously demonstrated that whole genome expression is coordinated by the emergence of a critical point at both the cell-population and single-cell levels through the physical principle of self-organized criticality. In this paper, we further examine the genomic mechanism that determines the cell-fate changes from embryo to cancer development. The state of the critical point, acting as the organizing center of the cell fate, determines whether the genome resides in a super- or sub-critical state. In the super-critical state, a specific stochastic perturbation can spread over the entire system through the “genome engine”, an autonomous critical-control genomic system, whereas in the sub-critical state, the perturbation remains at a local level. The cell-fate changes when the genome becomes super-critical. We provide a consistent framework to develop a time-evolutional transition theory for the biological regulation of the cell-fate change.
The Human TAZ Gene Complements Mitochondrial Dysfunction in the Yeast taz1Δ Mutant

Barth syndrome is a genetic disorder that is caused by different mutations in the TAZ gene G4.5. The yeast gene TAZ1 is highly homologous to human TAZ, and the taz1Δ mutant has phospholipid defects similar to those observed in Barth syndrome cells, including aberrant cardiolipin species and decreased cardiolipin levels. Subcellular fractionation studies revealed that Taz1p is localized exclusively in mitochondria, which supports the theory that tafazzins are involved in cardiolipin remodeling. Because cardiolipin plays an important role in respiratory function, we measured the energy transformation and osmotic properties of isolated mitochondria from the taz1Δ mutant. Energy coupling in taz1Δ mitochondria was dependent on the rate of oxidative phosphorylation, as coupling was diminished when NADH was used as a respiratory substrate but was unaffected when ethanol was the substrate. Membrane stability was compromised in taz1Δ mitochondria exposed to increased temperature and hypotonic conditions. Mitochondria from taz1Δ also displayed decreased swelling in response to ATP, which induces the yeast mitochondrial unspecific channel, and to alamethicin, a membrane-disrupting agent. Coupling was measured in taz1Δ cells containing different splice variants of the human TAZ gene. Only the variant that restores wild type cardiolipin synthesis (lacking exon 5) restored coupling in hypotonic conditions and at elevated temperature. These findings may shed light on the mitochondrial deficiencies observed in Barth syndrome.
Randomised controlled trial of 1% and 5% 5-fluorouracil creams compared with 90% trichloroacetic acid solution for anogenital wart treatment

To evaluate the efficacy and safety of 1% and 5% 5-fluorouracil (5-FU) creams compared with 90% trichloroacetic acid (TCA) for the treatment of anogenital warts. we conducted a randomised controlled study in 72 subjects allocated to three groups: 1% 5-FU, 90% TCA and 5% 5-FU; 90% TCA was administered once a week, whereas 5-FU cream was applied three times a week. Response to therapy and side-effects were evaluated weekly for seven weeks. Evaluation at week 7 demonstrated that there was no significant difference in the efficacy between 1% 5-FU cream and 90% TCA (p = 0.763) or between 5% 5-FU cream and 90% TCA (p = 0.274). Subjective side-effects with 1% 5-FU were significantly milder than 90% TCA; however, significantly milder objective side-effects were observed only at weeks 2, 6 and 7. The subjective side-effects with 5% 5-FU were also significantly milder than 90% TCA; however, significantly milder objective side-effects were observed only at week 2. 5-FU may become an alternative topical therapy as it offers the benefit of self-application; furthermore, a concentration of 1% 5-FU cream is recommended due to milder side-effects.
Characterizing pain flares in adolescent inflammatory and non‐inflammatory musculoskeletal disorders: A qualitative study using an interpretative phenomenological approach

Adolescents with musculoskeletal disorders experience acute exacerbations in pain, colloquially called “pain flares” in adult literature. This study aimed to explore adolescents' lived experience of pain flares, including what pain flares are, why they occur, how they are managed and what lasting effects they have on adolescents.
Light regulation of root and leaf NO3 - uptake and reduction in the floating macrophyte Lemna minor.

• The regulation of NO3 - uptake kinetics and reduction in relation to long- and short-term changes in irradiance was explored in roots and photosynthetic tissues of Lemna minor. • The NO3 - uptake kinetics, nitrate reductase activity, plant morphology, chlorophyll and tissue NO3 - , organic-N, starch and sugars were measured on roots and fronds of L. minor grown at four combinations of irradiance- and NO3 - availability. • Long-term acclimatizations paralleled those of terrestrial plants. Short-term changes in irradiance, however, changed frond NO3 - uptake proportionally with frond chlorophyll and N content, indicating a relationship between responsiveness and the metabolic potential of the plants. Root uptake changed to balance the change in frond uptake keeping whole plant uptake varying by < 40%. Nitrate reductase activity was primarily located in the roots and was correlated with frond uptake, indicating a transport of NO3 - from shoot to root before reduction. • This study shows that irradiance can affect the contribution of root and leaf uptake by aquatic plants and that roots play a major role in NO3 - reduction despite large foliar uptake.
Effect of essential orange (Citrus sinensis L.) oil on rumen microbial fermentation using in vitro gas production technique.

The aim of the current study was to evaluate the effect of increasing doses of essentialorange oilin vitrogas production, volatile fatty acid (VFA), methane, ammonia production, metabolisable energy (ME), organic matter digestibility (OMD), true dry matter digestibility (TDMD) and neutral detergent fiber digestibility (NDFD). Gas productions of soybean meal weremeasuredat 0, 3, 6, 12, 24, 48, 72 and 96 h incubation times in the presence (100, 200, 400, 800 and 1200 mg/L) and in the absence of essentialorange oil. The gas production kinetics were estimated using the non-linear exponentialequation y = A (1 -exp -ct ). The supplementation of essential orange oil significantly (P<0.001) decreased fermentation parameters and estimated parameters such as the potential gas production (A), ME, TDMD, OMD, NDFD, total VFA, mand ammonia production s.The mean reductions in A, ME, TDMD, NDFD, OMD, total VFA, methane and ammonia production swere0.022,0.033, 0.00209, 0.0197, 0.0213, 0.0414, 0.0207, 0.0093 units per mg essential orange oil supplementation respectively. The current study revealed that essential orange oil hadsignificant anti-microbial activity causing an inhib ition of the overall fermentation process . Therefore, before large scale implementation, further investigations are required to determine the effect of essential orange oil on voluntary food intake, animal performance and the profitability of the supplemen tationin vivo.
Crocin Improves the Quality of Cryopreserved Goat Semen in Different Breeds

Simple Summary In goat breeding, artificial insemination has a strong economic impact: It provides genetic improvement in intensive production systems and guarantees breed preservation in extensive systems. Sperm freezability is affected by several factors, such as breed species and freezing procedures. In addition, in goats, the seminal plasma enzyme phospholipase A reacts with egg yolk (component of semen extender), compromising sperm viability. Thus, seminal plasma is removed before freezing. This removal causes a decreasing level of antioxidants that prevent formation of toxic lipid peroxides with deleterious effects on fertility. Crocin is a water-soluble carotenoid that acts as an antioxidant, protecting cells and tissues against oxidation. Therefore, the aim of the present study was to assess the effect of crocin in the semen extender before cryopreservation. Five different goat breeds (Garganica, Jonica, Maltese Mediterranean Red and Saanen) were chosen to evaluate sperm qualitative characteristics, such as post-thawing sperm motility, viability, morphology and membrane integrity, as well as DNA fragmentation and intracellular ROS levels. The results highlighted that crocin supplementation in the extender decreased oxidative stress and improved sperm motility and the DNA integrity of frozen-thawed sperm in different breeds. Abstract The effect of crocin in the semen extender before cryopreservation was evaluated on sperm parameters of 20 bucks of five different breeds: Garganica (GA), Jonica (JO), Maltese (MA), Mediterranean Red (MR) and Saanen (SA). Semen samples were centrifuged, to remove seminal plasma, divided in two aliquots and diluted with Tris-egg-yolk-based extender, containing 0 (control group) and 1 mM crocin. Crocin concentration was established after a preliminary dose trial. On fresh and frozen-thawed sperm, motility, viability, morphology, membrane integrity, DNA fragmentation and ROS levels were evaluated. The freezing process led to a decrease (p < 0.05) in all the sperm parameters recorded, confirming the deleterious effect of cryopreservation on goat semen. The most interesting result regarding the inclusion of crocin in the extender before cryopreservation was as follows: Crocin significantly improved (p < 0.05) sperm motility in all breeds, except for Mediterranean Red, compared to the control group. Furthermore, 1 mM crocin reduced percentage of spermatozoa with DNA fragmentation with a marked decrement (p < 0.05) in Garganica and Saanen, as compared to the control group. Finally, intracellular ROS decreased (p < 0.01) in the crocin-treated sperm of all breeds, as compared to the control. In conclusion, supplementation of 1 mM crocin in the extender decreased oxidative stress, improving sperm motility and the DNA integrity of frozen-thawed sperm in different breeds.
Promoter Methylation of Selected Genes in Non-Small-Cell Lung Cancer Patients and Cell Lines

Specific gene promoter DNA methylation is becoming a powerful epigenetic biomarker in cancer diagnostics. Five genes (CDH1, CDKN2Ap16, RASSF1A, TERT, and WT1) were selected based on their frequently published potential as epigenetic markers. Diagnostic promoter methylation assays were generated based on bisulfite-converted DNA pyrosequencing. The methylation patterns of 144 non-small-cell lung cancer (NSCLC) and 7 healthy control formalin-fixed paraffin-embedded (FFPE) samples were analyzed to evaluate the applicability of the putative diagnostic markers. Statistically significant changes in methylation levels are shown for TERT and WT1. Furthermore, 12 NSCLC and two benign lung cell lines were characterized for promoter methylation. The in vitro tests involved a comparison of promoter methylation in 2D and 3D cultures, as well as therapeutic tests investigating the impact of CDH1/CDKN2Ap16/RASSF1A/TERT/WT1 promoter methylation on sensitivity to tyrosine kinase inhibitor (TKI) and DNA methyl-transferase inhibitor (DNMTI) treatments. We conclude that the selected markers have potential and putative impacts as diagnostic or even predictive marker genes, although a closer examination of the resulting protein expression and pathway regulation is needed.
Coronavirus Disease Pandemic (COVID-19): Challenges and a Global Perspective

The technology-driven world of the 21st century is currently confronted with a major threat to humankind, represented by the coronavirus disease (COVID-19) pandemic, caused by the severe acute respiratory syndrome, coronavirus-2 (SARS-CoV-2). As of now, COVID-19 has affected more than 6 million confirmed cases and took 0.39 million human lives. SARS-CoV-2 spreads much faster than its two ancestors, SARS-CoV and Middle East respiratory syndrome-CoV (MERS-CoV), but has low fatality rates. Our analyses speculate that the efficient replication and transmission of SARS-CoV-2 might be due to the high-density basic amino acid residues, preferably positioned in close proximity at both the furin-like cleavage sites (S1/S2 and S2′) within the spike protein. Given the high genomic similarities of SARS-CoV-2 to bat SARS-like CoVs, it is likely that bats serve as a reservoir host for its progenitor. Women and children are less susceptible to SARS-CoV-2 infection, while the elderly and people with comorbidities are more prone to serious clinical outcomes, which may be associated with acute respiratory distress syndrome (ARDS) and cytokine storm. The cohesive approach amongst researchers across the globe has delivered high-end viral diagnostics. However, home-based point-of-care diagnostics are still under development, which may prove transformative in current COVID-19 pandemic containment. Similarly, vaccines and therapeutics against COVID-19 are currently in the pipeline for clinical trials. In this review, we discuss the noteworthy advancements, focusing on the etiological viral agent, comparative genomic analysis, population susceptibility, disease epidemiology and diagnosis, animal reservoirs, laboratory animal models, disease transmission, therapeutics, vaccine challenges, and disease mitigation measures.