Miracle-dz/UniFAR-FTUs huggingface dataset:
The Simons Genome Diversity Project: A Global Analysis of Mobile Element Diversity

Abstract Ongoing retrotransposition of Alu, LINE-1, and SINE–VNTR–Alu elements generates diversity and variation among human populations. Previous analyses investigating the population genetics of mobile element insertions (MEIs) have been limited by population ascertainment bias or by relatively small numbers of populations and low sequencing coverage. Here, we use 296 individuals representing 142 global populations from the Simons Genome Diversity Project (SGDP) to discover and characterize MEI diversity from deeply sequenced whole-genome data. We report 5,742 MEIs not originally reported by the 1000 Genomes Project and show that high sampling diversity leads to a 4- to 7-fold increase in MEI discovery rates over the original 1000 Genomes Project data. As a result of negative selection, nonreference polymorphic MEIs are underrepresented within genes, and MEIs within genes are often found in the transcriptional orientation opposite that of the gene. Globally, 80% of Alu subfamilies predate the expansion of modern humans from Africa. Polymorphic MEIs show heterozygosity gradients that decrease from Africa to Eurasia to the Americas, and the number of MEIs found uniquely in a single individual are also distributed in this general pattern. The maximum fraction of MEI diversity partitioned among the seven major SGDP population groups (FST) is 7.4%, similar to, but slightly lower than, previous estimates and likely attributable to the diverse sampling strategy of the SGDP. Finally, we utilize these MEIs to extrapolate the primary Native American shared ancestry component to back to Asia and provide new evidence from genome-wide identical-by-descent genetic markers that add additional support for a southeastern Siberian origin for most Native Americans.
Use of a human embryonic stem cell model to discover GABRP, WFDC2, VTCN1 and ACTC1 as markers of early first trimester human trophoblast.

Human placental development during early pregnancy is poorly understood. Many conceptuses are lost at this stage. It is thought that preeclampsia, intrauterine growth restriction, and other placental syndromes that manifest later in pregnancy may originate early in placentation. Thus, there is a need for models of early human placental development. Treating human embryonic stem cells (hESC) with BMP4 (bone morphogenic protein 4) plus A83-01 (ACTIVIN/NODAL signaling inhibitor) and PD173074 (fibroblast growth factor 2 or FGF2 signaling inhibitor) (BAP conditions) induces differentiation to the trophoblast lineage (hESCBAP), but it is not clear which stage of trophoblast differentiation these cells resemble. Here, comparison of the hESCBAP transcriptome to those of trophoblasts from human blastocysts, trophoblast stem cells, and placentas collected in the first - third trimester of pregnancy by Principal Component Analysis (PCA) suggests that hESC after 8 days BAP treatment most resemble first trimester syncytiotrophoblasts. To further test this hypothesis, transcripts were identified that are expressed in hESCBAP but not in cultures of trophoblasts isolated from term placentas. Proteins encoded by four genes, GABRP (Gamma-Aminobutyric Acid Type A Receptor Subunit Pi), WFDC2 (WAP Four-Disulfide Core Domain 2), VTCN1 (V-Set Domain Containing T Cell Activation Inhibitor 1), and ACTC1 (Actin Alpha Cardiac Muscle 1), immunolocalized to placentas at four to nine weeks gestation, and their expression declined with gestational age (R2 = .61-.83). None are present at term. Expression was largely localized to syncytiotrophoblast of both hESCBAP cells and placental material from early pregnancy. WFDC2, VTCN1 and ACTC1 have not previously been described in placenta. These results support the hypothesis that hESCBAP represent human trophoblast analogous to that of early first trimester and are a tool for discovery of factors important to this stage of placentation.
Causes of death in patients diagnosed with gastric adenocarcinoma in Sweden, 1970‐2014: A population‐based study

The causes of death in patients with gastric adenocarcinoma have not been well characterized. This nationwide population‐based cohort study included 56 240 patients diagnosed with gastric adenocarcinoma in 1970‐2014 in Sweden. We used competing‐risks regression to compare cause‐specific risks of death in patients with different characteristics and a multiple‐cause approach to assess proportions of deaths attributable to each cause. Among 53 049 deaths, gastric cancer was the main (77.7% of all deaths) underlying cause. Other major underlying causes were nongastric malignancies (8.0%), ischemic heart disease or cerebrovascular disease (6.5%), and respiratory diseases (1.4%). Risk of death from gastric cancer steadily decreased in patients with cardia adenocarcinoma over the study period, but remained relatively stable in patients with noncardia adenocarcinoma since the 1980s. Risk of death from other malignancies increased during later calendar periods (subhazard ratio [SHR] = 2.16, 95% confidence interval [CI] 1.97‐2.38, comparing 2001‐2014 with 1970‐1980). Compared with men, the risk of death in women with cardia adenocarcinoma was higher from gastric cancer (SHR = 1.18, 95% CI 1.10‐1.27), but lower from other malignancies (SHR = 0.80, 95% CI 0.71‐0.91). In multiple‐cause models, 60.4%‐71.2% of all deaths were attributable to gastric cancer and 9.5%‐12.1% to other malignancies. The temporal trends of cause‐specific risks from multiple‐cause models were similar to those of underlying causes. Our findings suggest that although most deaths in patients with gastric adenocarcinoma are due to gastric cancer, other causes of death are common. Patients with cardia adenocarcinoma face considerable increasing risk of death from other causes over time, particularly from other malignancies.
Nucleation processes in a mediterranean bird-dispersed plant

1. The spatial distribution of Pistacia lentiscus, a Mediterranean bird-dispersed plant, in abandoned orchards was found to be strongly linked to the presence of trees or shrubs that act as perches. 2. These perches not only attract seed-disperser birds but also produce favourable microenvironmental conditions for seed germination and seedling establishment. 3. Soil moisture content after a rainfall was always greater beneath perches than not beneath perches. Favourable water potentials for seed germination were maintained for a longer time beneath a perch than elsewhere. 4. After a rainfall, soil was compacted faster where not beneath perches. Seedling radicle penetration into soil was strongly associated with soil compactation.
Developmental delay and mortality of Bemisia tabaci (Hemiptera: Aleyrodidae) parasitized by two aphelinids, Encarsia bimaculata and Eretmocerus sp. nr. furuhashii (Hymenoptera: Aphelinidae)

Nymphal developmental periods and mortality of Bemisia tabaci when exposed to two parasitoids Encarsia bimaculata and Eretmocerus sp. nr. furuhashii at different nymphal stages were studied in the laboratory. Developmental periods of various nymphal instars were significantly delayed among instars when parasitized by E. bimaculata and Eretmocerus sp. nr. furuhashii. Developmental periods of 1st–4th nymphal instars when originally parasitized by E. bimaculata were 20.13, 19.19, 18.65 and 17.93 days, respectively. Developmental periods were protracted when instars were parasitized by Er. sp. nr. furushashii with values of 23.16, 21.37, 20.76 and 20.31 days. However, averaged developmental periods of B. tabaci immatures without parasitism were 14.10 days. Mortalities of B. tabaci immatures were significantly different among instars when parasitized by E. bimaculata or Er. sp. nr. furuhashii. Mortality was highest at the 3rd instar and lowest at the 1st instar when parasitized by E. bimaculata, whereas when parasitized by Er. sp. nr. furuhashii, the highest mortality was found at the 3rd instar and the lowest was at the 4th instar. Mortality of B. tabaci caused by parasitoids host feeding was higher on 1st and the 4th nymphal stages than on 2nd and the 3rd stages, regardless of the species of wasps. These results indicated that deleterious effects of parasitism on whitefly development occurred on the instar that followed the instar at which parasitism has occurred; parasitism and host feeding by the aphelinid wasps are important factors that significantly influence whitefly mortality.
Rearing of Non-Descendant Offspring in an Allodapine Bee, Exoneura bicolor Smith (Hymenoptera: Apidae: Xylocopinae): A Preferred Strategy or Queen Coercion?

In heathland populations of the Australian allodapine bee Exoneura bicolor, the presence of overlapping broods in some colonies creates opportunities for eusocial-like sib rearing. By artificially orphaning colonies in observation nests, we investigated whether sib-rearing by some older daughters occurs in the absence of any potential for coercion by parental females. We found strong evidence for sib-rearing in the absence of parental females in 40% of our nests and weaker evidence in another 40%. of those colonies with strong evidence of sib-rearing, 65% of such rearing occurred in nests where there was also no opportunity for coercion by adult siblings. These results indicate that sib-rearing in E. bicolor does not require coercion by adult nestmates. A variety of factors that may make sib-rearing a preferred strategy in the absence of coercion are discussed.
huij, Ilse; (2014) A RE-AIM evaluation of evidence-based multi-level interventions to improve obesity-related behaviours in adults: a systematic review

Background: This systematic literature review describes the potential public health impact of evidence-based multi-level interventions to improve obesity-related behaviours in adults, using the Reach, Efficacy, Adoption, Implementation and Maintenance (RE-AIM) framework. Methods: Electronic databases (PubMed, Embase, and The Cochrane Library) were searched to identify intervention studies published between January 2000 and October 2013. The following inclusion criteria were used: (1) the study included at least one outcome measure assessing obesity-related behaviours (i.e. diet, physical activity or sedentary behaviour), (2) the study collected data over at least one year and (3) the study’s intervention targeted adults, was conducted in a specified geographical area or worksite, and was multi-level (i.e. targeting both individual and environmental level). Evidence of RE-AIM of the selected interventions was assessed. Potential public health impact of an intervention was evaluated if information was provided on at least four of the five RE-AIM dimensions. Results: Thirty-five multi-level interventions met the inclusion criteria. RE-AIM evaluation revealed that the included interventions generally had the potential to: reach a large number of people (on average 58% of the target population was aware of the intervention); achieve the assumed goals (89% found positive outcomes); be broadly adopted (the proportion of intervention deliverers varied from 9% to 92%) and be sustained (sixteen interventions were maintained). The highest potential public health impact was found in multi-level interventions that: 1) focused on all levels at the beginning of the planning process, 2) guided the implementation process using diffusion theory, and 3) used a website to disseminate the intervention. Conclusions: Although most studies underreported results within the RE-AIM dimensions, the reported Reach, Effectiveness, Adoption, Implementation and Maintenance were positively evaluated. However, more information on external validity and sustainability is needed in order to take informed decisions on the choice of interventions that should be implemented in real-world settings to accomplish long-term changes in obesity-related behaviours.
Geographic variation in skulls of the harbor porpoise, Phocoena phocoena

Les auteurs ont mesure les crânes de 108 marsouins. La comparaison des variations observees entre les individus de l'est et de l'ouest de l'Atlantique nord, de l'est et de l'ouest du Pacifique nord par des analyses de co-variance et en composantes principales, fait apparaitre des differences entre chacun de ces groupes. Ces resultats montrent une bonne differenciation des populations eloignees et un flux genique faible entre elles. Ce type de variation geographique implique des variations phylogenetiques entre les marsouins des quatre regions
Structural equation modelling the ‘control of gut overgrowth’ in the prevention of ICU acquired Gram-negative infection.

Background: Conceptually, the ‘control of gut overgrowth’ (COGO) is key in mediating prevention against infection with Gram-negative bacilli by topical antibiotic prophylaxis, a common constituent of Selective Digestive Decontamination (SDD) regimens. However, the relative importance of the other SDD components; enteral and protocolized parenteral antibiotic prophylaxis, versus other methods of infection prevention and versus other contextual exposures cannot be resolved within individual studies. Methods: Seven candidate generalized structural equation models founded on COGO concepts were confronted with Pseudomonas and Acinetobacter bacteremia as well as ventilator associated pneumonia data derived from >200 infection prevention studies. The following group level exposures were included in the models; use and mode of antibiotic prophylaxis, antiseptic and non-decontamination methods of infection prevention; proportion receiving mechanical ventilation; trauma ICU; mean length of ICU stay and concurrency versus non-concurrency of topical antibiotic prophylaxis study control groups. Results: In modelling Pseudomonas and Acinetobacter gut overgrowth as latent variables, anti-septic interventions had the strongest negative effect against Pseudomonas gut overgrowth but no intervention was significantly negative against Acinetobacter gut overgrowth. Strikingly, protocolized parenteral antibiotic prophylaxis and concurrency each have positive effects in the model, enteral antibiotic prophylaxis is neutral and Acinetobacter bacteremia incidences are high within topical antibiotic prophylaxis studies, moreso with protocolized parenteral antibiotic prophylaxis exposure. Paradoxically, topical antibiotic prophylaxis (moreso with protocolized parenteral antibiotic prophylaxis) appears to provide the strongest summary prevention effects against overall bacteremia and overall VAP. Conclusions: Structural equation modelling of published Gram-negative bacilli infection data enables a test of the COGO concept. Paradoxically, Acinetobacter and Pseudomonas bacteremia incidences are unusually high among studies of topical antibiotic prophylaxis.
Enzyme electrophoresis, 18S rRNA sequences, and levels of phylogenetic resolution among several species of freshwater planarians (Platyhelminthes, Tricladida, Paludicola)

Enzyme polymorphism and 18S rRNA sequences have been used to measure genetic distances between several species of Platyhelminthes belonging to different taxa including freshwater and parasitic forms. We have used these data to address unresolved phylogenetic and taxonomic problems with this group at several different levels ranging from phylum to subgenus. The main conclusions supported by the data seem to be the following: (i) 18S rRNA data strongly suggest that the Platyhelminthes are monophyletic, being a sister-group to the other Eubilateria; a similar conclusion applies to the Paludicola as to the rest of Platyhelminthes studied; (ii) 18S rRNA and enzyme data indicate that the family Dugesiidae of the Paludicola is monophyletic with respect to the other two families, Planariidae and Dendrocoelidae; and (iii) the subgenus Schmidtea of the genus Dugesia is monophyletic with respect to the other two subgenera of Dugesia, Dugesia and Girardia. Other aspects of the relationships of subgenera and families .
Habilidade competitiva de cultivares de trigo com plantas daninhas

Competitive ability is an important tool for integrated weed management. The objective of this work was to evaluate the potential of wheat cultivars in competing with the weeds Italian ryegrass and wild radish, at different periods of coexistence. The experiment was arranged in a randomized block design, in a factorial scheme 4 x 2 x 3, with three replicates. The following wheat cultivars were allocated in Factor A: BRS Guamirin - short cycle and short plant height; Fundacep Cristalino - short cycle and medium plant height; Fundacep Raizes - medium cycle and medium plant height; and BRS 296 - short cycle and tall plant height. In Factor B, absence or presence of weed control, and in Factor C, weed management time (throughout the crop cycle or until pre-harvest, up to 15 days after seeding and 30 days after seeding - DAS). The Fundacep Cristalino cultivar - short cycle and medium plant height- showed more competitive ability than the Italian ryegrass and wild radish, compared to the other cultivars, in all the periods evaluated. Weed control in wheat must be performed early, especially for cultivars with lower competitive ability.
Systematic relationships of the Guianan brush-tailed rat (Isothrix sinnamariensis ) and its first occurrence in Guyana / Systématique du rat à queue en brosse de Guyane ( Isothrix sinnamariensis ) et première découverte en Guyane

Abstract Isothrix sinnamariensis was originally described and known only from French Guiana. We document the first occurence of this species from Guyana. A single sub-adult male was collected in lowland tropical rainforest near the headwaters of the Essequibo River. Although smaller in external and cranial size than the two adult females of the type description, our third known specimen represents the basal lineage to the type-series clade, with an average sequence difference of 1.72% based on cytochrome b mitochondrial DNA sequences. However, the degree of morphological and genetic divergence (2.67%) between I. sinnamariensis and its sister taxon I. pagurus is substantially less than the chromosomal differences originally used to distinguish them as two separate species. In contrast, distinctive karyotypes, morphological differences, and higher levels of mtDNA divergence (13.48%) between the other two species recognized, I. negrensis that was recently separated from I. bistriata , suggest an earlier and deeper diversification for these taxa.
Male size and survival: the effects of male combat and bird predation in Dawson’s burrowing bees, Amegilladawsoni

1. Males of Dawson’s burrowing bee, Amegilla dawsoni, occur in two size classes, large majors and small minors. Major males compete aggressively for emerging females in completely exposed emergence areas, whereas minors often employ an alternative mating tactic, which involves rapid patrolling in the vegetated periphery of emergence areas.
Junctional adhesion molecule-A-induced endothelial cell migration on vitronectin is integrin αvβ3 specific

Junctional adhesion molecule-A (JAM-A) is a member of the immunoglobulin superfamily, and is mainly expressed in the tight junctions of both epithelial and endothelial cells. We have recently shown that JAM-A is involved in basic fibroblast growth factor (bFGF)-induced angiogenesis. Here, we show that, when ectopically expressed in human umbilical vein endothelial cells (HUVECs), JAM-A induced enhanced cell migration on vitronectin, but had no effect on fibronectin. Use of antibodies that block integrin function indicated that the migration on vitronectin is specific to integrin αvβ3 and not to integrin αvβ5. JAM-A-induced migration was inhibited by anti-JAM-A antibody. Additionally, overexpression of a JAM-A cytoplasmic domain deletion mutant failed to induce HUVEC migration. Addition of phosphoinositide 3-kinase and protein kinase C inhibitors blocked JAM-A-induced migration, suggesting that these kinases act downstream of JAM-A. Immunoprecipitation analysis showed that JAM-A interacts with integrin αvβ3, and this association was increased by engagement of the ligand-binding site of the integrin by Arg-Gly-Asp-Ser (RGDS) peptide. Furthermore, activation of both focal adhesion kinase (FAK) and mitogen-activated protein kinase (MAPK) on vitronectin was enhanced by JAM-A overexpression but not by its cytoplasmic domain deletion mutant. Taken together, these results suggest that signaling through JAM-A is necessary for αvβ3-dependent HUVEC migration and implicate JAM-A in the regulation of vascular function.
APPLICATION OF LATTICE-BOLTZMANN METHOD TO ROTORCRAFT AERODYNAMICS AND AEROACOUSTICS

The aim of this work is to evaluate the accuracy and the computational performances of the CFD/CAA solver PowerFLOW R ©, developed and distributed by Exa Corporation, to predict the unsteady aerodynamic loads, the rotor wake development and the noise radiation of helicopters in Blade-Vortex Interaction conditions. The employed benchmark configuration is the 40% geometrically and aeroelastically scaled model of a BO-105 4-bladed main rotor tested in the open-jet anechoic test section of the German-Dutch wind tunnel in the framework of the HART-II project. In the present study, only the baseline operating condition of the test matrix, without higher harmonic control, is considered. All simulations are performed by assuming a rigid blade motion, but a computational strategy is employed to take into account the effective elastic deformation motion of the blade measured during the experiments. As expected, modeling the elastic blade motion leads to more accurate predictions of both unsteady air-loads and noise footprint. The effects of the mesh resolution on the aerodynamic and aeroacoustic prediction is investigated. As a conclusive effort, the effects of fuselage scattering on the noise footprint are evaluated by using the same computational model to simulate two additional configurations: the isolated rotor of the HART-II configuration and the same rotor installed on a different helicopter fuselage. Significant far-field noise scattering effects are observed.
Capture efficiency of insect natural enemies from tall and short vegetation using vacuum sampling

SUMMARY Experiments were conducted in lucerne to determine the efficiency of vacuum sampling of insects and whether this was affected by the height of vegetation sampled. Three insects of significance as predators of pests in Australian lucerne were studied: transverse ladybird beetle (Coccinella transversalis Fabricius), pollen beetle (Dicranolaius bellulus (Guerin-Meneville)), and spined predatory shield bug (Oechalia schellembergii (Guerin-Meneville)). In a preliminary experiment comparing a commercially harvested area of lucerne with an unharvested area within the same crop, the proportions of released insects recaptured from unharvested lucerne were significantly lower than recoveries from the shorter, harvested lucerne. Resampling the tall lucerne after it was cut by hand gave cumulative recapture proportions which did not differ from those observed for the harvested lucerne. A second experiment with a randomised replicated design re-tested the hypotheses of the preliminary experiment for two insect species. Very similar results were obtained. This verification showed that recapture efficiencies from tall lucerne ranged between 0.60 and 0.74 but that resampling after hand cutting gave cumulative recapture proportions in excess of 0.86 which did not differ from recapture proportions from short lucerne.