dartR v2: An accessible genetic analysis platform for conservation, ecology and agriculture

Innumerable approaches to analyse genetic data are now available to guide conservation, ecological and agricultural projects. However, streamlined and accessible tools are needed to bring these approaches within the reach of a broader user base. dartR was released in 2018 to lessen the intrinsic complexity of analysing single nucleotide polymorphisms (SNPs) and dominant markers (presence/absence of amplified sequence tags) by providing user-friendly data quality control and marker selection functions. dartR users have grown steadily since its release and provided valuable feedback on their interaction with the package allowing us to enhance dartR capabilities. Here, we present Version 2 of dartR. In this version, we substantially increased the number of available functions from 45 to 144. In addition to improved functionality, we focused on enhancing the user experience by extending plot customisation, function standardisation, increasing user support and function speed. dartR provides functions for various stages in analysing genetic data, from data manipulation to reporting. dartR provides many functions for importing, exporting and linking to other packages, to provide an easy-to-navigate conduit between data generation and analysis options already available via other packages. We also implemented simulation functions whose results can be analysed seamlessly with several other dartR functions. As more methods and approaches mature to inform conservation, we envision that accessible platforms to analyse genetic data will play a crucial role in translating science into practice

Quantitative Nanomechanical Properties of Multilayer Films Made of Polysaccharides through Spray Assisted Layer-by-Layer Assembly.

Nanomechanical properties of alginate/chitosan (Alg/Chi) multilayer films, obtained through spray assisted layer-by-layer assembly, were studied by means of PeakForce quantitative nanomechanical mapping atomic force microscopy (PF-QNM AFM). Prepared at two different alginate concentrations (1.0 and 2.5 mg/mL) and a fixed chitosan concentration (1.0 mg/mL), Alg/Chi films have an exponential growth in thickness with a transition to a linear growth toward a plateau by increasing the number of deposited bilayers. Height, elastic modulus, deformation, and adhesion maps were simultaneously recorded depending on the number of deposited bilayers. The elastic modulus of Alg/Chi films was found to be related to the mechanism of growth in contrast to the adhesion and deformation. A comparison of the nanomechanical properties obtained for non-cross-linked and thermally cross-linked Alg/Chi films revealed an increase of the elastic modulus after cross-linking regardless alginate concentration. The incorporation of iron oxide nanoparticles (NPs), during the spray preparation of the films, gave rise to nanocomposite Alg/Chi films with increased elastic moduli with the number of incorporated NPs layers. Deformation maps of the films strongly suggested the presence of empty spaces associated with the method of preparation. Finally, adhesion measurements point out to a significant role of NPs on the increase of the adhesion values found for nanocomposite films.journal article2017 01 092016 12 15importe

APROVECHAMIENTO ALIMENTARIO DE INFLORESCENCIAS EN LA REGIÓN SIERRA DEL ESTADO DE TABASCO

This paper presents results from the research project named “Identification of theTraditional Alimentary Culture in the Stateof Tabasco”, SIGOLFO 97-06-007-T. Basedon questionnaires distributed in communities about 100 and 500 inhabitants, at leastone of them in each community being anindigenous speaker, it was found that theirinhabitants, for ancestral and cultural customs, are devoted to gathering plant species for supplying supplementary sustenance. The most important alternative vegetable source being gathered is inflorescences of species like Erythrinaamericana Mill., Calathea macrosepala(Aubl.) Lindl., Spathiphyllum phryniifolium Schott, Astrocaryum mexicanumLiebm., Chamaedora sp. aff. pinnatifronsLiebm. ex Mart. y Chamaedora cataractarum (Mart.). It was found that the consumption of inflorescences prevails in these communities as a nutrition base during periodsof food shortage or special celebrationssuch as Holy Week when Catholics do noteat meat.La presente información es parte de los resultados encontrados en el proyecto de investigación “Identificación de la CulturaAlimentaria Tradicional en el Estado deTabasco”, SIGOLFO 97-06-007-T. Con baseen la aplicación de cuestionarios en comunidades comprendidas entre 100 y 500 habitantes con al menos uno de ellos conhabla indígena, se encontró que por costumbres ancestrales y culturales se dedican a la recolección de especies vegetalespara suplementar su fuente de alimentación, con especies vegetales alternativas,siendo de gran importancia la recolecciónde inflorescencias de especies como:Erythrina americana Mill, Calatheamacrosepala (Aulb.) Lindl., Spathiphyllum phryniifolium Schoot,Astrocaryum mexicanum Liebmann,Chamaedora sp. aff. pinnatifrons Liebm.ex Mart y Chamaedora cataractarum(Mart). Se pudo constatar que prevaleceen las comunidades un gran arraigo delconsumo de especies con inflorescenciacomo una base de la alimentación durantelos periodos de escasez de alimentos o durante festividades como la Semana Santa,época en la cual de manera tradicional no se consume carne de ninguna especie yrara vez pescado o pollo

Análisis bibliométrico de la literatura publicada sobre SIDA en el Sur de África

The purpose of this work is to present the results of a bibliometric research conducted on AIDS in Africa, Southern. The literature production and communication patterns were analysed in an attempt to obtain indicators so as to support the decision making processes related to the prevention and control of AIDS. An Internet MEDLINE bibliographic search was conducted on AIDS and Africa, Southern for the period 1980-2001. The research was limited to studies conducted on humans; and indicators related to productivity, geographic distribution by country, language and subject content were identified.A total of 1.820 postings were retrieved and analysed. Main production was distributed among South Africa (42.36%), Zimbabwe (20.44%) and Zambia (19.90%). Most of the documents corresponded to articles published in scientific journals (55.33%). English was the main language used (97.75%); and the production in collaboration of two or more authors was significant (55.61%). The subject content of the research was related mainly to Health Education, Infant, and Sex Behaviour. A high production at the national level —mainly local universities— and the influence of USA and United Kingdom academic institutions was also found. A comparison with other geographic regions as well as the lines for further research actions are described.El propósito de este trabajo es el de presentar los resultados de un proyecto de investigación bibliométrica realizado sobre SIDA en la región del Sur de África. El estudio pretende identificar los mecanismos de producción y comunicación de la literatura existentes, en un esfuerzo por apoyar a los procesos de toma de decisiones relacionados con la prevención y el control del SIDA. Se realizó una investigación bibliográfica en MEDLINE sobre SIDA (AIDS) y el Sur de África (Africa Southern), para el período 1980-2001. La investigación se limitó a estudios realizados en seres humanos; y se buscaron indicadores relacionados con el tipo de producción, periodicidad anual, distribución geográfica por país, cobertura de idioma y temática.Se encontró un total de 1.820 registros. La producción mayor se registró para South Africa (42,36%), Zimbabwe (20,44%) y Zambia (19,90%). En su mayoría, la producción correspondió a artículos publicados en revistas científicas (55,33%); en idioma inglés (97,75%) y derivada de la colaboración de dos o más autores (55,61%). La cobertura temática se orientó a estudios sobre educación para la salud, investigaciones sobre infantes, y la conducta sexual. Se encontró un alto índice de producción nacional, principalmente de universidades locales; además de la influencia en la región de instituciones académicas de los Estados Unidos de Norteamérica y el Reino Unido. Se presentan comparaciones con los resultados obtenidos de otras regiones geográficas y se describen algunas líneas de investigación necesarias para continuar este tipo de análisis

Nitrogen hydrides in interstellar gas II. Analysis of Herschel/HIFI observations towards W49N and G10.6-0.4 (W31C)

We have used the Herschel-HIFI instrument to observe interstellar nitrogen hydrides along the sight-lines towards W49N and G10.6-0.4 in order to elucidate the production pathways leading to nitrogen-bearing species in diffuse gas. All detections show absorption by foreground material over a wide range of velocities, as well as absorption associated directly with the hot-core source itself. As in the previously published observations towards G10.6-0.4, the NH, NH2 and NH3 spectra towards W49N show strikingly similar and non-saturated absorption features. We decompose the absorption of the foreground material towards W49N into different velocity components in order to investigate whether the relative abundances vary among the velocity components, and, in addition, we re-analyse the absorption lines towards G10.6-0.4 in the same manner. Abundances, with respect to molecular hydrogen, in each velocity component are estimated using CH. The analysis points to a co-existence of the nitrogen hydrides in diffuse or translucent interstellar gas with a high molecular fraction. Towards both sources, we find that NH is always at least as abundant as both o-NH2 and o-NH3, in sharp contrast to previous results for dark clouds. We find relatively constant N(NH)/N(o-NH3) and N(o-NH2)/N(o-NH3) ratios with mean values of 3.2 and 1.9 towards W49N, and 5.4 and 2.2 towards G10.6-0.4, respectively. The mean abundance of o-NH3 is ~2x10^-9 towards both sources. The nitrogen hydrides also show linear correlations with CN and HNC towards both sources, and looser correlations with CH. The upper limits on the NH+ abundance indicate column densities < 2 - 14 % of N(NH). Surprisingly low values of the ammonia ortho-to-para ratio are found in both sources, ~0.5 - 0.7 +- 0.1. This result cannot be explained by current models as we had expected to find a value of unity or higher.Comment: 35 pages, 74 figure

Scale-dependent plant diversity in Palaearctic grasslands: a comparative overview

Here we present an extensive overview of plant diversity values in Palaearctic grasslands for seven standard grain sizes from 0.0001 to 100 m². The data originate from 20 studies, including the Field Workshops of the Eurasian Dry Grassland Group (EDGG), ranging geographically from Spain in the west to Siberia in the east, from Sicily in the south to Estonia in the north and from the sea coast up to 3100 m a.s.l. The majority of data is from dry grasslands (Festuco-Brometea, Koelerio-Corynephoretea, Cleistogenetea squarrosae), but there are also some mesic, wet, saline, acidic, alpine and Mediterranean grasslands included. Among others, we compiled data from 1795 1-m², 1109 10-m² and 338 100-m² plots. In all cases we present mean, minimum and maximum richness for the seven grain sizes, plus, in cases where also terricolous bryophytes and lichens had been recorded, the same values for total “plant” species richness, non-vascular plant species richness and fraction of non-vascular plants. The maximum richness values were 82, 101 and 134 for all “plants”, and 79, 98 and 127 vascular plants at grain sizes of 1 m², 10 m² and 100 m², respectively (all in Transylvania, Romania). Our overview comprises new, hitherto unpublished world records of vascular plant species richness at the scales of 0.0001 m² (9) and 0.001 m² (19, both shoot presence), from meso-xeric, basiphilous grasslands in Navarre, Spain, which is much higher than the previously known maxima. The highest values of non-vascular plant richness at 1 m², 10 m² and 100 m², respectively, were 49, 64 and 64, respectively (all in Sedo-Scleranthenea communities of Öland, Sweden, and Saaremaa, Estonia). In general, the dry, alpine and Mediterranean grasslands were much richer than the studied mesic, wet or saline grasslands at any spatial scale. The presented set of mean, minimum and maximum values and their metadata is publically available and will be continuously updated. These data can serve as a reference of “normal” richness, both in fundamental and applied research. To facilitate the application, we provide an easy formula based on the power-law species-area relationship that allows the estimation of richness values at intermediate grain sizes not included in our dataset. In conclusion, our data emphasise the role of Palaearctic grasslands as global hotspot of small-scale vascular plant diversity, while at the same time highlighting that in some grassland types also the bryophyte and lichen diversity can be extraordinarily high

Utilization of mechanical power and associations with clinical outcomes in brain injured patients. a secondary analysis of the extubation strategies in neuro-intensive care unit patients and associations with outcome (ENIO) trial

BackgroundThere is insufficient evidence to guide ventilatory targets in acute brain injury (ABI). Recent studies have shown associations between mechanical power (MP) and mortality in critical care populations. We aimed to describe MP in ventilated patients with ABI, and evaluate associations between MP and clinical outcomes.MethodsIn this preplanned, secondary analysis of a prospective, multi-center, observational cohort study (ENIO, NCT03400904), we included adult patients with ABI (Glasgow Coma Scale &lt;= 12 before intubation) who required mechanical ventilation (MV) &gt;= 24 h. Using multivariable log binomial regressions, we separately assessed associations between MP on hospital day (HD)1, HD3, HD7 and clinical outcomes: hospital mortality, need for reintubation, tracheostomy placement, and development of acute respiratory distress syndrome (ARDS).ResultsWe included 1217 patients (mean age 51.2 years [SD 18.1], 66% male, mean body mass index [BMI] 26.3 [SD 5.18]) hospitalized at 62 intensive care units in 18 countries. Hospital mortality was 11% (n = 139), 44% (n = 536) were extubated by HD7 of which 20% (107/536) required reintubation, 28% (n = 340) underwent tracheostomy placement, and 9% (n = 114) developed ARDS. The median MP on HD1, HD3, and HD7 was 11.9 J/min [IQR 9.2-15.1], 13 J/min [IQR 10-17], and 14 J/min [IQR 11-20], respectively. MP was overall higher in patients with ARDS, especially those with higher ARDS severity. After controlling for same-day pressure of arterial oxygen/fraction of inspired oxygen (P/F ratio), BMI, and neurological severity, MP at HD1, HD3, and HD7 was independently associated with hospital mortality, reintubation and tracheostomy placement. The adjusted relative risk (aRR) was greater at higher MP, and strongest for: mortality on HD1 (compared to the HD1 median MP 11.9 J/min, aRR at 17 J/min was 1.22, 95% CI 1.14-1.30) and HD3 (1.38, 95% CI 1.23-1.53), reintubation on HD1 (1.64; 95% CI 1.57-1.72), and tracheostomy on HD7 (1.53; 95%CI 1.18-1.99). MP was associated with the development of moderate-severe ARDS on HD1 (2.07; 95% CI 1.56-2.78) and HD3 (1.76; 95% CI 1.41-2.22).ConclusionsExposure to high MP during the first week of MV is associated with poor clinical outcomes in ABI, independent of P/F ratio and neurological severity. Potential benefits of optimizing ventilator settings to limit MP warrant further investigation