Miracle-dz/UniFAR-FTUs huggingface dataset:
Extreme Multiple Reticulate Origins of the Pteris cadieri Complex (Pteridaceae)

The Pteris cadieri complex displays extensive morphological variation and seems to have originated through hybridization. However, the members of this complex reproduce by apogamy, which usually limits genetic variation. To evaluate the hypotheses of hybrid origins, the pattern of evolution in this species complex is reconstructed. Multiple methodologies were used. Diploids, triploids, and tetraploids were identified by chromosome counts and flow cytometry. Nuclear DNA markers (cytosolic phosphoglucose isomerase gene, PgiC) were used, together with chloroplast DNA markers (atpB-rbcL spacer and rbcL gene) to infer the biparental and maternal lineages of the Pteris cadieri complex. The three cpDNA haplotype groups and five PgiC alleles found in this study indicate that the evolution of the Pteris cadieri complex has been extremely reticulate. Up to 11 taxa belonging to eight morphs were identified. By comparing genetic variation in the Pteris cadieri in two independent areas, Hainan and Taiwan, we inferred that hybridization has occurred independently in different areas. Furthermore, we found evidence for phenological divergence (evergreen and deciduous) within Taiwan. We propose that the Pteris cadieri complex originated from different genetic lineages through multiple hybridizations in different geographical areas, leading to its present morphological diversity.
Activation Function-1 of Estrogen Receptor Cells through Differential Requirement for Inflammatory and Steady-State Dendritic Estradiol Promotes Functional Responses in

17 b -Estradiol (E2) has been shown to regulate GM-CSF– or Flt3 ligand–driven dendritic cell (DC) development through estrogen receptor (ER) a signaling in myeloid progenitors. ER a regulates transcription of target genes through two distinct activation functions (AFs), AF-1 and AF-2, whose respective involvement varies in a cell type– or tissue-speciﬁc manner. In this study, we investigated the role of ER a AFs in the development and effector functions of inﬂammatory DCs, steady-state conventional DCs, and plasmacytoid DCs (pDC), using mouse lacking either AF-1 or AF-2. In agreement with previous works, we showed that E2 fostered the differentiation and effector functions of inﬂammatory DCs through ER a -dependent upregulation of IFN regulatory factor (IRF)-4 in GM-CSF–stimulated myeloid progenitors. Interestingly, whereas AF-1 was required for early IRF-4 upregulation in DC precursors, it was dispensable to enhance IRF-4 expression in differentiated DCs to a level compatible with the development of the more functional Ly6C 2 CD11b + DC subset. Presence of E2 had no effect on progenitors from either knock-in mice with 7-aa deletion in helix 12 of ER a , lacking AF-2, or ER a 2 / 2 mice. By contrast, in Flt3 ligand–driven DC differentiation, activation of AF-1 domain was required to promote the development of more functionally competent conventional a of our study demonstrates that ER a uses AF-1 differently in steady-state and inﬂammatory DC lineages to regulate their innate functions, suggesting that selective ER modulators could be used to target speciﬁc DC subsets. The Journal of Immunology , 2013, 190: 5459–5470.
Infection routes of Aeromonas salmonicida in rainbow trout monitored in vivo by real-time bioluminescence imaging.

Recent development of imaging tools has facilitated studies of pathogen infections in vivo in real time. This trend can be exemplified by advances in bioluminescence imaging (BLI), an approach that helps to visualize dissemination of pathogens within the same animal over several time points. Here, we employ bacterial BLI for examining routes of entry and spread of Aeromonas salmonicida susbp. salmonicida in rainbow trout. A virulent Danish A. salmonicida strain was tagged with pAKgfplux1, a dual-labelled plasmid vector containing the mutated gfpmut3a gene from Aequorea victoria and the luxCDABE genes from the bacterium Photorhabdus luminescens. The resulting A. salmonicida transformant exhibited growth properties and virulence identical to the wild-type A. salmonicida, which made it suitable for an experimental infection, mimicking natural conditions. Fish were infected with pAKgfplux1 tagged A. salmonicida via immersion bath. Colonization and subsequent tissue dissemination was followed over a 24-h period using the IVIS spectrum imaging workstation. Results suggest the pathogen's colonization sites are the dorsal and pectoral fin and the gills, followed by a progression through the internal organs and an ensuing exit via the anal opening. This study provides a tool for visualizing colonization of A. salmonicida and other bacterial pathogens in fish.
Gradual increase in the risk of match injury in Norwegian male professional football: A 6‐year prospective study

The aim of this study was to monitor injury incidence and pattern in Norwegian male professional football over six consecutive seasons and compare the risk of injury between the preseason and competitive season. All time loss injuries were recorded by the medical staff of each club. In total, 2365 injuries were recorded. The incidence of acute injuries was 15.9/1000 match hours [95% confidence interval (CI): 14.9–16.8], 1.9/1000 training hours (95% CI: 1.7–2.0), and 1.4 (95% CI: 1.3–1.5) overuse injuries/1000 h. A linear regression model found an annual increase of 1.06 acute match injuries/1000 h (95% CI: 0.40–1.73), corresponding to a total increase of 49% during the 6‐year study period. When accounting for interteam variation and clustering effects using a general estimating equation model, the increase in injury incidence was 0.92 (95% CI: −0.11–1.95, P = 0.083). No difference in the risk of acute match injuries (rate ratio (RR): 0.86, 95% CI: 0.73–1.01), acute training injuries (RR: 1.16, 95% CI: 0.99–1.36), or overuse injuries (RR: 1.04, 95% CI: 0.89–1.21) was observed between the preseason and competitive season. In conclusion, the overall risk of acute match injuries in Norwegian male professional football increased by 49% during the study period, although this increase was not fully consistent across teams. We detected no change in the risk of training and overuse injuries or any difference between the preseason and competitive season.
Transferable anticancer innate immunity in spontaneous regression/complete resistance mice

Spontaneous regression/complete resistance (SR/CR) mice resist very high doses of cancer cells that are lethal to WT mice even at low doses. In this study, we show that this resistance is mediated by rapid infiltration of leukocytes, mostly of innate immunity, in both primary and repeated challenges. Formation of rosettes with infiltrating natural killer cells, neutrophils, and macrophages was required for the subsequent destruction of cancer cells through rapid cytolysis. Highly purified natural killer cells, macrophages, and neutrophils from the SR/CR mice independently killed cancer cells in vitro. The independent killing activity by each subset of effector cells is consistent with the observation that the resistance was abolished by depleting total infiltrating leukocytes but not by depleting only one or two subsets of leukocytes. The resistance was completely transferable to WT recipient mice through SR/CR splenocytes, bone marrow cells, or enriched peritoneal macrophages, either for prevention against subsequent cancer challenges or eradication of established malignancy at distant sites.
Cardiovascular repair with bone marrow-derived cells

While bone marrow (BM)-derived cells have been comprehensively studied for their propitious pre-clinical results, clinical trials have shown controversial outcomes. Unlike previously acknowledged, more recent studies have now confirmed that humoral and paracrine effects are the key mechanisms for tissue regeneration and functional recovery, instead of transdifferentiation of BM-derived cells into cardiovascular tissues. The progression of the understanding of BM-derived cells has further led to exploring efficient methods to isolate and obtain, without mobilization, sufficient number of cell populations that would eventually have a higher therapeutic potential. As such, hematopoietic CD31+ cells, prevalent in both bone marrow and peripheral blood, have been discovered, in recent studies, to have angiogenic and vasculogenic activities and to show strong potential for therapeutic neovascularization in ischemic tissues. This article will discuss recent advancement on BM-derived cell therapy and the implication of newly discovered CD31+ cells.
Case Series of Monoamniotic and Pseudomonoamniotic Twin Gestations

We retrospectively evaluated a series of 18 monoamniotic and 7 pseudomonoamniotic (secondary to rupture in the membrane dividing monochorionic diamniotic twins) twin gestations managed after 20 weeks' gestation. There were no significant differences in the incidence of neonatal death or umbilical cord entanglement between the monoamniotic and pseudomonoamniotic twin gestations (33 versus 21%, P = 0.94 and 72 versus 43%, P = 0.36). Therefore, the same serious management may be needed for pseudomonoamniotic twin gestations as for monoamniotic twin gestations.
Lef1-dependent hypothalamic neurogenesis inhibits anxiety

While innate behaviors are conserved throughout the animal kingdom, it is unknown whether common signaling pathways regulate the development of neuronal populations mediating these behaviors in diverse organisms. Here, we demonstrate that the Wnt/ß-catenin effector Lef1 is required for the differentiation of anxiolytic hypothalamic neurons in zebrafish and mice, although the identity of Lef1-dependent genes and neurons differ between these 2 species. We further show that zebrafish and Drosophila have common Lef1-dependent gene expression in their respective neuroendocrine organs, consistent with a conserved pathway that has diverged in the mouse. Finally, orthologs of Lef1-dependent genes from both zebrafish and mouse show highly correlated hypothalamic expression in marmosets and humans, suggesting co-regulation of 2 parallel anxiolytic pathways in primates. These findings demonstrate that during evolution, a transcription factor can act through multiple mechanisms to generate a common behavioral output, and that Lef1 regulates circuit development that is fundamentally important for mediating anxiety in a wide variety of animal species.
Splicing promotes rapid and efficient mRNA export in mammalian cells

The numerous steps in protein gene expression are extensively coupled to one another through complex networks of physical and functional interactions. Indeed, >25 coupled reactions, often reciprocal, have been documented among such steps as transcription, capping, splicing, and polyadenylation. Coupling is usually not essential for gene expression, but instead enhances the rate and/or efficiency of reactions and, physiologically, may serve to increase the fidelity of gene expression. Despite numerous examples of coupling in gene expression, whether splicing enhances mRNA export still remains controversial. Although splicing was originally reported to promote export in both mammalian cells and Xenopus oocytes, it was subsequently concluded that this was not the case. These newer conclusions were surprising in light of the observations that the mRNA export machinery colocalizes with splicing factors in the nucleus and that splicing promotes recruitment of the export machinery to mRNA. We therefore reexamined the relationship between splicing and mRNA export in mammalian cells by using FISH, in combination with either transfection or nuclear microinjection of plasmid DNA. Together, these analyses indicate that both the kinetics and efficiency of mRNA export are enhanced 6- to 10-fold (depending on the construct) for spliced mRNAs relative to their cDNA counterparts. We conclude that splicing promotes mRNA export in mammalian cells and that the functional coupling between splicing and mRNA export is a conserved and general feature of gene expression in higher eukaryotes.
Comparative anatomy of zebrafish paired and median fin muscles: basis for functional, developmental, and macroevolutionary studies

In the last decades, Danio rerio became one of the most used model organisms in various evo‐devo studies devoted to the fin skeletal anatomy and fin‐limb transition. Surprisingly, there is not even a single paper about the detailed anatomy of the adult muscles of the five fin types of this species. To facilitate more integrative developmental, functional, genetic, and evolutionary studies of the appendicular musculoskeletal system of the zebrafish and to provide a basis for further comparisons with other fishes and tetrapods, we describe here the identity, overall configuration, and attachments of appendicular muscles in a way that can be easily understood and implemented by non‐anatomist researchers. We show that the muscle pattern of the caudal fin is very different from patterns seen in other fins but is very consistent within teleosts. Our observations support the idea of the developmental and evolutionary distinction of the caudal fin and point out that the musculature of the adult zebrafish pectoral and pelvic fins is in general very similar. Both paired fins have superficial and deep layers of abductors and adductors going to all/most rays plus the dorsal and ventral arrectors going only to the first ray. Nevertheless, we noted three major differences between the pelvic and pectoral fins of adult zebrafishes: (i) the pectoral girdle lacks a retractor muscle, which is present in the pelvic girdle – the retractor ischii; (ii) the protractor of the pelvic girdle is an appendicular/trunk muscle, while that of the pectoral girdle is a branchiomeric muscle; (iii) the first ray of the pectoral fin is moved by an additional arrector‐3. The anal and dorsal fins consist of serially repeated units, each of which comprises one half‐ray and three appendicular muscles (one erector, depressor, and inclinator) on each side of the body. The outermost rays are attachment points for the longitudinal protractor and retractor. Based on our results, we discuss whether the pectoral appendage might evolutionarily be closer to the head than to the pelvic appendage and whether the pelvic appendage might have been derived from the trunk/median fins. We discuss a hypothesis of paired fin origin that is a hybrid of the fin‐fold and Gegenbaur's theories. Lastly, our data indicate that D. rerio is indeed an appropriate model organism for the appendicular musculature of teleosts in particular and, at least in the case of the paired fins, also of actinopterygians as a whole.
Experimental approaches to identify small RNAs and their diverse roles in bacteria – what we have learnt in one decade of MicA research

Nowadays the identification of small RNAs (sRNAs) and characterization of their role within regulatory networks takes a prominent place in deciphering complex bacterial phenotypes. Compared to the study of other components of bacterial cells, this is a relatively new but fast‐growing research field. Although reports on new sRNAs appear regularly, some sRNAs are already subject of research for a longer time. One of such sRNAs is MicA, a sRNA best described for its role in outer membrane remodeling, but probably having a much broader function than anticipated. An overview of what we have learnt from MicA led to the conclusion that even for this well‐described sRNA, we still do not have the overall picture. More general, the story of MicA might become an experimental lead for unraveling the many sRNAs with unknown functions. In this review, three important topics in the sRNA field are covered, exemplified from the perspective of MicA: (i) identification of new sRNAs, (ii) target identification and unraveling the biological function, (iii) structural analysis. The complex mechanisms of action of MicA deliver some original insights in the sRNA field which includes the existence of dimer formation or simultaneous cis and trans regulation, and might further inspire the understanding of the function of other sRNAs.
Urinary PAH Metabolites Influenced by Genetic Polymorphisms of GSTM1 in Male Hospital Incinerator Workers

Urinary PAH Metabolites Influenced by Genetic Polymorphisms of GSTM1 in male Hospital Incinerator Workers: Kyoung Ho Lee, et al. Department of Preventive Medicine, Seoul National University College of Medicine, Institute for Environmental Medicine, SNURC Korea—Hospital waste incinerator workers are exposed to various pyrolysis products including polycyclic aromatic hydrocarbons (PAHs). We evaluated their exposure by assessing urinary 1‐hydroxypyrene glucuronide (1‐OHPG), as an internal dose of PAH exposure. The potential effect of genetic polymorphisms of GSTM1/ T1 involved in PAH metabolisms was also investigated. Pre‐ and post‐shift samples were collected from 28 hospital incinerator workers. Urinary 1‐OHPG was assayed by synchronous fluorescence spectroscopy (SFS) after immunoaffinity purification with the monoclonal antibody 8E11. Genotypes of GSTM1/T1 were assessed by PCR‐based methods. Information on smoking habits and use of personal protective equipment were collected by means of a self‐administered questionnaire. The Mann‐Whitney test was used to compare group means of these biomarkers. Urinary 1‐OHPG levels were similar in pre‐ and post‐shift urine samples. The arithmetic mean concentrations of urinary 1‐OHPG were 0.16 ± 0.04 µmol/mol creatinine pre‐shift and 0.19 ± 0.09 µmol/mol creatinine post‐shift, but urinary 1‐OHPG levels were significantly higher in individuals with the GSTM1 null genotype than with the GSTM1 present genotype (p=0.05, by Mann‐Whitney test). Our results suggest that the urinary 1‐OHPG levels in hospital waste incinerator workers may be modified by the GSTM1 genotype, but these findings remain to be confirmed in future studies involving larger sample sizes.
Knowledge, attitudes and practices (KAP) relating to brucellosis in smallholder dairy farmers in two provinces in Pakistan

The present study aimed to assess the extent of knowledge and understanding of brucellosis in smallholder dairy farmers and identify practices at the farm and household level that might pose a risk for humans contracting brucellosis. Between February and June 2015 a cross-sectional study was conducted among smallholder farms (n = 420) in five districts of Punjab and two districts of Sindh province. Farmers were interviewed using a questionnaire to obtain information on farmers’ knowledge about brucellosis and the potential risks for contracting the disease that are present for dairy farmers and their families. Logistic regression and ordinal logistic models were used to investigate potential predictors for risky behaviours. The results show almost all farmers (97%) were not aware of the modes of transmission of brucellosis. Relating to risk, the majority (66%) of the farmers’ families were reported to consume raw milk and its products, live in shared housing with animals (49%) and not cover hand cuts during contact with animals (74%). All farmers performed at least one risky practice on a regular basis for brucellosis transmission from animal to human. A multivariable analysis highlighted that the respondents with no formal education and those who had not heard of the disease displayed greater risky behaviour. Poor understanding of the disease, presence of multiple risky practices on farm and at the household, and incorrect perception supports the need for an educational awareness program in order to ensure uptake of improved practices.
A 17–35 GHz Broadband, High Efficiency PHEMT Power Amplifier Using Synthesized Transformer Matching Technique

This paper presents a 17 GHz to 35 GHz broadband power amplifier (PA) using 0.15-μm GaAs pHEMT technology. The synthesized transformer using microstrip line matching technique is proposed in this PA design to enhance the broadband frequency response and minimize the chip size. The design procedures are also presented. A high efficiency broadband PA in commercial 0.15 μm GaAs pHEMT process with the best P1dB of 22 dBm, Psat of 23.5 dBm, and PAE of 40% are demonstrated to verify the design concepts. This PA has the highest PAE, smallest chip size, and wide fractional bandwidth among the broadband GaAs HEMT PAs from K to Ka band.
Potential Reporting Bias in fMRI Studies of the Brain

Background Functional magnetic resonance imaging (fMRI) studies have reported multiple activation foci associated with a variety of conditions, stimuli or tasks. However, most of these studies used fewer than 40 participants. Methodology After extracting data (number of subjects, condition studied, number of foci identified and threshold) from 94 brain fMRI meta-analyses (k = 1,788 unique datasets) published through December of 2011, we analyzed the correlation between individual study sample sizes and number of significant foci reported. We also performed an analysis where we evaluated each meta-analysis to test whether there was a correlation between the sample size of the meta-analysis and the number of foci that it had identified. Correlation coefficients were then combined across all meta-analyses to obtain a summary correlation coefficient with a fixed effects model and we combine correlation coefficients, using a Fisher’s z transformation. Principal Findings There was no correlation between sample size and the number of foci reported in single studies (r = 0.0050) but there was a strong correlation between sample size and number of foci in meta-analyses (r = 0.62, p<0.001). Only studies with sample sizes <45 identified larger (>40) numbers of foci and claimed as many discovered foci as studies with sample sizes ≥45, whereas meta-analyses yielded a limited number of foci relative to the yield that would be anticipated from smaller single studies. Conclusions These results are consistent with possible reporting biases affecting small fMRI studies and suggest the need to promote standardized large-scale evidence in this field. It may also be that small studies may be analyzed and reported in ways that may generate a larger number of claimed foci or that small fMRI studies with inconclusive, null, or not very promising results may not be published at all.
Granular flows : fluidization and anisotropy

This work discusses the flow of granular materials (e.g. sand). Even though a single particle is a simple object, the collective behavior of billions of particles can be very complex. In a surprisingly large amount of cases, it is not exactly known how a granular material behaves, and this while these kinds of materials are omnipresent in everyday life, industry, and nature Similar to materials such as water, which can occur as ice, liquid water and vapor, sand can also exist in different phases of matter. If you for instance walk on the beach, sand behaves like a solid, but if you pour it out of your shoes afterwards, it flows like a liquid. This thesis is dedicated to experiments where we investigate what happens when you try to “liquefy” sand by weakly vibrating it. We use an experimental setup which enables us to study how much stress is required to make sand flow, depending on the desired flow rate and the amount of vibrations. These experiments reveal several physical principles that turn out to be important towards understanding the unique behavior of these kinds of materials