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Fission program at n_TOF
(2019)
Since its start in 2001 the n_TOF collaboration developed a measurement program on fission, in view of advanced fuels in new generation reactors. A special effort was made on measurement of cross sections of actinides, exploiting the peculiarity of the n_TOF neutron beam which spans a huge energy domain, from the thermal region up to GeV. Moreover fission fragment angular distributions have also been measured. An overview of the cross section results achieved with different detectors is presented, including a discussion of the 237Np case where discrepancies showed up between different detector systems. The results on the anisotropy of the fission fragments and its implication on the mechanism of neutron absorption, and in applications, are also shown.
We describe 70 cases of monocled cobra (Naja kaouthia) bite admitted to Chittagong Medical College Hospital, Bangladesh. The biting snakes were identified by examining the dead snake and/or detecting N. kaouthia venom antigens in patients' serum. Bites were most common in the early morning and evening during the monsoon (May-July). Ligatures were routinely applied to the bitten limb before admission. Thirty-seven patients consulted traditional healers, most of whom made incisions around the bite site. Fifty-eight patients experienced severe neurotoxicity and most suffered swelling and pain of the bitten limb. The use of an Indian polyvalent antivenom in patients exhibiting severe neurotoxicity resulted in clinical improvement but most patients experienced moderate-to-severe adverse reactions. Antivenom did not influence local blistering and necrosis appearing in 19 patients; 12 required debridement. Edrophonium significantly improved the ability of patients to open the eyes, endurance of upward gaze, and peak expiratory flow rate suggesting that a longer-acting anticholinesterase drug (neostigmine) could be recommended for first aid. The study suggested that regionally appropriate antivenom should be raised against the venoms of the major envenoming species of Bangladesh and highlighted the need to improve the training of staff of local medical centers and to invest in the basic health infrastructure in rural communities.
Biallelic mutations in TMEM126B cause severe complex i deficiency with a variable clinical phenotype
(2016)
Complex I deficiency is the most common biochemical phenotype observed in individuals with mitochondrial disease. With 44 structural subunits and over 10 assembly factors, it is unsurprising that complex I deficiency is associated with clinical and genetic heterogeneity. Massively parallel sequencing (MPS) technologies including custom, targeted gene panels or unbiased whole-exome sequencing (WES) are hugely powerful in identifying the underlying genetic defect in a clinical diagnostic setting, yet many individuals remain without a genetic diagnosis. These individuals might harbor mutations in poorly understood or uncharacterized genes, and their diagnosis relies upon characterization of these orphan genes. Complexome profiling recently identified TMEM126B as a component of the mitochondrial complex I assembly complex alongside proteins ACAD9, ECSIT, NDUFAF1, and TIMMDC1. Here, we describe the clinical, biochemical, and molecular findings in six cases of mitochondrial disease from four unrelated families affected by biallelic (c.635G>T [p.Gly212Val] and/or c.401delA [p.Asn134Ilefs∗2]) TMEM126B variants. We provide functional evidence to support the pathogenicity of these TMEM126B variants, including evidence of founder effects for both variants, and establish defects within this gene as a cause of complex I deficiency in association with either pure myopathy in adulthood or, in one individual, a severe multisystem presentation (chronic renal failure and cardiomyopathy) in infancy. Functional experimentation including viral rescue and complexome profiling of subject cell lines has confirmed TMEM126B as the tenth complex I assembly factor associated with human disease and validates the importance of both genome-wide sequencing and proteomic approaches in characterizing disease-associated genes whose physiological roles have been previously undetermined.
Climate change research is increasingly focusing on the dynamics among species, ecosystems and climates. Better data about the historical behaviours of these dynamics are urgently needed. Such data are already available from ecology, archaeology, palaeontology and geology, but their integration into climate change research is hampered by differences in their temporal and geographical scales. One productive way to unite data across scales is the study of functional morphological traits, which can form a common denominator for studying interactions between species and climate across taxa, across ecosystems, across space and through time—an approach we call ‘ecometrics’. The sampling methods that have become established in palaeontology to standardize over different scales can be synthesized with tools from community ecology and climate change biology to improve our understanding of the dynamics among species, ecosystems, climates and earth systems over time. Developing these approaches into an integrative climate change biology will help enrich our understanding of the changes our modern world is undergoing.
Destruction of the cosmic γ-ray emitter 26Al in massive stars: study of the key 26Al(n,p) reaction
(2021)
The 26Al(n,p)26Mg reaction is the key reaction impacting on the abundances of the cosmic γ-ray emitter 26Al produced in massive stars and impacts on the potential pollution of the early solar system with 26Al by asymptotic giant branch stars. We performed a measurement of the 26Al(n,p)26Mg cross section at the high-flux beam line EAR-2 at the n_TOF facility (CERN). We report resonance strengths for eleven resonances, nine being measured for the first time, while there is only one previous measurement for the other two. Our resonance strengths are significantly lower than the only previous values available. Our cross-section data range to 150 keV neutron energy, which is sufficient for a reliable determination of astrophysical reactivities up to 0.5 GK stellar temperature.
A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters, pathways and metabolites is currently dispersed throughout the literature, making it difficult to exploit. To facilitate consistent and systematic deposition and retrieval of data on biosynthetic gene clusters, we propose the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard.
The slow neutron capture process (s-process) is responsible for producing about half of the elemental abundances heavier than iron in the universe. Neutron capture cross sections on stable isotopes are a key nuclear physics input for s-process studies. The 72Ge(n, γ) cross section has an important influence on production of isotopes between Ge and Zr during s-process in massive stars and therefore experimental data are urgently required. 72Ge(n, γ) was measured at the neutron time-of-flight facility n_TOF (CERN) for the first time at stellar energies. The measurement was performed using an enriched 72GeO2 sample at a flight path of 185m with a set of liquid scintillation detectors (C6D6). The motivation, experiment and current status of the data analysis are reported.
Sedimentary charcoal records are widely used to reconstruct regional changes in fire regimes through time in the geological past. Existing global compilations are not geographically comprehensive and do not provide consistent metadata for all sites. Furthermore, the age models provided for these records are not harmonised and many are based on older calibrations of the radiocarbon ages. These issues limit the use of existing compilations for research into past fire regimes. Here, we present an expanded database of charcoal records, accompanied by new age models based on recalibration of radiocarbon ages using IntCal20 and Bayesian age-modelling software. We document the structure and contents of the database, the construction of the age models, and the quality control measures applied. We also record the expansion of geographical coverage relative to previous charcoal compilations and the expansion of metadata that can be used to inform analyses. This first version of the Reading Palaeofire Database contains 1676 records (entities) from 1480 sites worldwide. The database (RPDv1b – Harrison et al., 2021) is available at https://doi.org/10.17864/1947.000345.
The Siwalik formations of northern Pakistan consist of deposits of ancient rivers that existed throughout the early Miocene through the late Pliocene. The formations are highly fossiliferous with a diverse array of terrestrial and freshwater vertebrates, which in combination with exceptional lateral exposure and good chronostratigraphic control allows a more detailed and temporally resolved study of the sediments and faunas than is typical in terrestrial deposits. Consequently the Siwaliks provide an opportunity to document temporal differences in species richness, turnover, and ecological structure in a terrestrial setting, and to investigate how such differences are related to changes in the fluvial system, vegetation, and climate. Here we focus on the interval between 10.7 and 5.7 Ma, a time of significant local tectonic and global climatic change. It is also the interval with the best temporal calibration of Siwalik faunas and most comprehensive data on species occurrences. A methodological focus of this paper is on controlling sampling biases that confound biological and ecological signals. Such biases include uneven sampling through time, differential preservation of larger animals and more durable skeletal elements, errors in age-dating imposed by uncertainties in correlation and paleomagnetic timescale calibrations, and uneven taxonomic treatment across groups. We attempt to control for them primarily by using a relative-abundance model to estimate limits for the first and last appearances from the occurrence data. This model also incorporates uncertainties in age estimates. Because of sampling limitations inherent in the terrestrial fossil record, our 100-Kyr temporal resolution may approach the finest possible level of resolution for studies of vertebrate faunal changes over periods of millions of years. Approximately 40,000 specimens from surface and screenwash collections made at 555 localities form the basis of our study. Sixty percent of the localities have maximum and minimum age estimates differing by 100 Kyr or less, 82% by 200 Kyr or less. The fossils represent 115 mammalian species or lineages of ten orders: Insectivora, Scandentia, Primates, Tubulidentata, Proboscidea, Pholidota, Lagomorpha, Perissodactyla, Artiodactyla, and Rodentia. Important taxa omitted from this study include Carnivora, Elephantoidea, and Rhinocerotidae. Because different collecting methods were used for large and small species, they are treated separately in analyses. Small species include insectivores, tree shrews, rodents, lagomorphs, and small primates. They generally weigh less than 5 kg. The sediments of the study interval were deposited by coexisting fluvial systems, with the larger emergent Nagri system being displaced between 10.1 and 9.0 Ma by an interfan Dhok Pathan system. In comparison to Nagri floodplains, Dhok Pathan floodplains were less well drained, with smaller rivers having more seasonally variable flow and more frequent avulsions. Paleosol sequences indicate reorganization of topography and drainage accompanying a transition to a more seasonal climate. A few paleosols may have formed under waterlogged, grassy woodlands, but most formed under drier conditions and more closed vegetation. The oxygen isotopic record also indicates significant change in the patterns of precipitation beginning at 9.2 Ma, in what may have been a shift to a drier and more seasonal climate. The carbon isotope record demonstrates that after 8.1 Ma significant amounts of C4 grasses began to appear and that by 6.8 Ma floodplain habitats included extensive C4 grasslands. Plant communities with predominantly C3 plants were greatly diminished after 7.0 Ma, and those with predominantly C4 plants, which would have been open woodlands or grassy woodlands, appeared as early as 7.4 Ma. Inferred first and last appearances show a constant, low level of faunal turnover throughout the interval 10.7–5.7-Ma, with three short periods of elevated turnover at 10.3, 7.8, and 7.3–7.0 Ma. The three pulses account for nearly 44% of all turnover. Throughout the late Miocene, species richness declined steadily, and diversity and richness indices together with data on body size imply that community ecological structure changed abruptly just after 10 Ma, and then again at 7.8 Ma. Between 10 and 7.8 Ma the large-mammal assemblages were strongly dominated by equids, with more balanced faunas before and after. The pattern of appearance and disappearance is selective with respect to inferred habits of the animals. Species appearing after 9.0 Ma are grazers or typical of more open habitats, whereas many species that disappear can be linked to more closed vegetation. We presume exceptions to this pattern were animals of the mixed C3/C4 communities or the wetter parts of the floodplain that did not persist into the latest Miocene. The pace of extinction accelerates once there is C4 vegetation on the floodplain. The 10.3 Ma event primarily comprises disappearance of taxa that were both common and of long duration. The event does not correlate to any obvious local environmental or climatic event, and the pattern of species disappearance and appearance suggests that biotic interactions may have been more important than environmental change. The 7.8 Ma event is characterized solely by appearances, and that at 7.3 Ma by a combination of appearances and disappearances. These two latest Miocene events include more taxa that were shorter ranging and less common, a difference of mode that developed between approximately 9.0 and 8.5 Ma when many short-ranging and rare species began to make appearances. Both events also show a close temporal correlation to changes in floodplain deposition and vegetation. The 7.8 Ma event follows the widespread appearance of C4 vegetation and is coincident with the shift from equid-dominated to more evenly balanced large-mammal assemblages. The 7.3 to 7.0 Ma event starts with the first occurrence of C4-dominated floras and ends with the last occurrence of C3-dominated vegetation. Absence of a consistent relationship between depositional facies and the composition of faunal assemblages leads us to reject fluvial system dynamics as a major cause of faunal change. The close correlation of latest Miocene species turnover and ecological change to expansion of C4 plants on the floodplain, in association with oxygen isotopic and sedimentological evidence for increasingly drier and more seasonal climates, causes us to favor explanations based on climatic change for both latest Miocene pulses. The Siwalik record supports neither “coordinated stasis” nor “turnover pulse” evolutionary models. The brief, irregularly spaced pulses of high turnover are characteristic of both the stasis and pulse models, but the high level of background turnover that eliminates 65–70% of the initial species shows there is no stasis in the Siwalik record. In addition, the steadily declining species richness and abrupt, uncoordinated changes in diversity do not fit either model.
1.1 Introduction 1.1.1 Aim of project .To compare the abundance of invertebrate and weed seed food resources available to birds on orzanic and conventional farmland. The objective of the studv was to assess accurately the likely benefit of these farming systems to birds feeding on farrn'land, by sampling invertebrates and weed seeds. 1.1.2 Factors implicit to achieving the project aims Variation between farms within one system could influence' invertebrate or weed seed abundance and bias results, To minimise such effects and provide results 'representative of the farming systems as a whole, sampling was based on an extensive approach; farms were sampled in groups. The inference that either of the farming systems is beneficial to feeding birds is dependent on: (i) prior knowledge of the relevance of a particular invertebrate or seed as a food-source: evidence (ii) that this foodsource is present in sufficient abundance and (iii) that the food-source is readily accessible, The methodology described below was refined to address these criteria. 1.1.3 Methodology Sampling concentrated on cereal crops, with an additional comparison of organic grass ley fields at a limited number of sites. Sampling initially consisted of sucking invertebrates from the crop using a vacuum insect net and extraction from soil cores. To aid the interpretation of results from this sampling, it was decided that more information was required on the diet of birds. This was achieved by analysing faecal sacs for undigested fragments of invertebrates that therefore represented a dietary component. Skylark chick faecal sacs were chosen for analysis as this was the key species for the intensive ornithological studies and samples could be taken during routine fieldwork. As a result of this study, the main invertebrate sampling technique was changed to pitfall traps, since this was a superior method for assessing those invertebrates found to be important food-sources. It was also anticipated that pitfall trapping would provide more accurate estimates of invertebrate availability, with greater numbers per sample, than the previous two techniques. Studies of weed seed food resources consisted of field surveys using a quadrat to assess the presence and abundance of species, and the use of a small hand held suction machine to suck seeds from post-harvest stubble. The interpretation of the results emphasised the aspects of the ecology of species known to be food-sources that might influence their availability to birds. 1.2 Soil core and vacuum samples 1.2.1 Significantly more dipteran immature stages and Coleoptera were found in soil cores on organic grass ley fields and significantly more earthworms on organic cereal fields than conventional cereal fields. Earthworms and dipteran larvae such as tipulids are known to be important food-sources for birds that specialize in soil invertebrates. 1.2.2 Total numbers of invertebrates trapped by both methods did not differ significantly between the two farming systems. Significantly more invertebrates were trapped, however, by both methods on organic grass ley fields than either conventional or organic cereals. 1.2.3 Significantly more Staphylinidae tCol.), especially the species Tachyporus hypnorum, were found on conventional fields, The relevance of this species as a food-source is, however, doubtful. 1.2.4 The weevil Sitona lineatus and the carabid Demetrias atricapillus were found in significantly greater numbers on organic fields. The former may constitute a food-source for skylarks, which have been shown to feed on this insect under laboratory conditions. 1.3 Faecal sac analysis 1.3.1 Carabid beetles were an important component of skylark chick diet, forming 47 % of identifications. In some cases it was possible to identify the species present. 1.3.2 Coleoptera, other than carabids, from the families Elateridae, Curculionidae, Chrysomelidae and Staphylinidae were identified as food-sources. 1.3.3 Spiders and tipul ids were also important components. 1.3.4 Reservations are expressed that the technique may under-represent soft-bodied invertebrates, which are susceptible to complete digestion by skylark chicks. 1.4 Pitfall trap samples 1.4.1 Twelve key species of carabid beetles were analysed. of which five cornmon species were trapped in significantly greater numbers on organic farms. These were Pterostichus melanarius (the dominant species captured), Pterostichus madidus, Harpalus affinis, Harpalus rufipes and Nebria brevi collis. The other species analysed showed no significant variance between farming systems. 1.4.2 Williams' Index of Diversity was significantly greater for conventional fields, although caution is expressed over the reliability of this result due to the small sample size of species. 1.5 Botanical studies 1.5.1 The abundance of weed plants in quadrats was significantly greater on organic fields. 1.5.2 The abundance of weed seeds was not significantly different between farming systems. However, the relative proportions of monocotyledonous and dicotyledonous seeds in samples differed between farming systems. A larger proportion of the seeds from organic fields were dicotyledonous and from conventional fields were monocotyledonous. 1.5.3 Preliminary examination of the size of plants and the number of seeds produced suggested that those on organic fields may have been nitrogen deficient. 1.5.4 Weed species were significantly more diverse on organic fields. although diversity has less relevance to bird feeding than abundance. 1.6 Proposals for future work 1.6.1 Replication of the pitfall trapping exercise in subsequent years would substantiate the trends established from the data of one season. It would also be beneficial 10 extend the range (If habitats sampled to take into account set-aside and other crops besides cereals. 1.6.2 More comprehensive information. on the diet of farmland birds in general. could he achieved by analysing the faecal sacs of a wider variety of species. 1.6.3 Greater integration of field studies on birds with invertebrate sampling would enhance the effectiveness of the latter as an indicator of diet. Areas of farmland frequently selected as feeding sites by birds could be sampled intensively for invertebrates and compared to other areas, selected at random. This would provide useful information on the invertebrates likely to be important as food-sources and the habitats that favour them. 1.6.4 Extending the range of farms sampled would provide more accurate results. 1.6.5 More work is required to-investigate the possible link between nitrogen deficiency in plams and organic systems, and its implications for the provision of bird food-sources, particularly for weed abundance and phytophagous insects.
Twenty-nine species of caddisflies in the genus Agapetus Curtis in eastern and central North America are reviewed. Twelve are described as new species: Agapetus aphallus (known only from females); Agapetus baueri, Agapetus flinti, Agapetus harrisi, Agapetus hesperus, Agapetus ibis, Agapetus kirchneri, Agapetus meridionalis, Agapetus pegram, Agapetus ruiteri, Agapetus stylifer, and Agapetus tricornutus. Agapetus rossi Denning 1941 is recognized as a junior subjective synonym of Agapetus walkeri (Betten and Mosely 1940), new synonym. A key to males is provided, and species’ distributions are mapped.
The editorial board of Aging reviews research papers published in 2009,which they believe have or will have a significant impact on aging research.Among many others, the topics include genes that accelerate aging or incontrast promote longevity in model organisms, DNA damage responsesand telomeres, molecular mechanisms of life span extension by calorierestriction and pharmacologic interventions into aging. The emergingmessage in 2009 is that aging is not random but determined by agenetically-regulated longevity network and can be decelerated bothgenetically and pharmacologically.
Diagnosing and treating acute severe and recurrent antivenom-related anaphylaxis (ARA) is challenging and reported experience is limited. Herein, we describe our experience of severe ARA in patients with neurotoxic snakebite envenoming in Nepal. Patients were enrolled in a randomised, double-blind trial of high vs. low dose antivenom, given by intravenous (IV) push, followed by infusion. Training in ARA management emphasised stopping antivenom and giving intramuscular (IM) adrenaline, IV hydrocortisone, and IV chlorphenamine at the first sign/s of ARA. Later, IV adrenaline infusion (IVAI) was introduced for patients with antecedent ARA requiring additional antivenom infusions. Preantivenom subcutaneous adrenaline (SCAd) was introduced in the second study year (2012). Of 155 envenomed patients who received ≥ 1 antivenom dose, 13 (8.4%), three children (aged 5−11 years) and 10 adults (18−52 years), developed clinical features consistent with severe ARA, including six with overlapping signs of severe envenoming. Four and nine patients received low and high dose antivenom, respectively, and six had received SCAd. Principal signs of severe ARA were dyspnoea alone (n=5 patients), dyspnoea with wheezing (n=3), hypotension (n=3), shock (n=3), restlessness (n=3), respiratory/cardiorespiratory arrest (n=7), and early (n=1) and late laryngeal oedema (n=1); rash was associated with severe ARA in 10 patients. Four patients were given IVAI. Of the 8 (5.1%) deaths, three occurred in transit to hospital. Severe ARA was common and recurrent and had overlapping signs with severe neurotoxic envenoming. Optimising the management of ARA at different healthy system levels needs more research. This trial is registered with NCT01284855.
The article reviews distribution records of Deroceras invadens (previously called D. panormitanum and D. caruanae), adding significant unpublished records from the authors’ own collecting, museum samples, and interceptions on goods arriving in the U.S.A. By 1940 D. invadens had already arrived in Britain, Denmark, California, Australia and probably New Zealand; it has turned up in many further places since, including remote oceanic islands, but scarcely around the eastern Mediterranean (Egypt and Crete are the exceptions), nor in Asia. Throughout much of the Americas its presence seems to have been previously overlooked, probably often being mistaken for D. laeve. New national records include Mexico, Costa Rica, and Ecuador, with evidence from interceptions of its presence in Panama, Peru, and Kenya. The range appears limited by cold winters and dry summers; this would explain why its intrusion into eastern Europe and southern Spain has been rather slow and incomplete. At a finer geographic scale, the occurrence of the congener D. reticulatum provides a convenient comparison to control for sampling effort; D. invadens is often about half as frequently encountered and sometimes predominates. Deroceras invadens is most commonly found in synanthropic habitats, particularly gardens and under rubbish, but also in greenhouses, and sometimes arable land and pasture. It may spread into natural habitats, as in Britain, South Africa,
Australia and Tenerife. Many identifications have been checked in the light of recent taxonomic revision, revealing that the sibling species D. panormitanum s.s. has spread much less extensively. A number of published or online records, especially in Australia, have turned out to be misidentifications of D. laeve.
We provide new state and county records of biting midges in the genus Culicoides Latreille (Diptera: Ceratopogonidae) from the southeastern United States collected with CDC miniature light traps during 2007–2012 in Florida, Georgia, Alabama, Mississippi, Louisiana, Arkansas, and Texas. The primary goals of the surveys were to identify the presence of exotic Culicoides, and determine the ranges of known and possible vectors of bluetongue virus (BTV) and epizootic hemorrhagic disease virus (EHDV). Included are the fi rst records of: Culicoides (Amossovia) beckae Wirth and Blanton from Louisiana and Mississippi, C. (A.) oklahomensis Khalaf from Alabama and Arkansas, C. (Avaritia) alachua Jamnback and Wirth from Alabama, C. (Culicoides) neopulicaris Wirth from Alabama, C. (Drymodesmyia) butleri Wirth and Hubert from Texas, C. (Hoffmania) insignis Lutz from Mississippi, C. (Oecacta) barbosai Wirth and Blanton from Georgia, C. (Silvaticulicoides) loisae Jamnback from Alabama, and C. kirbyi Glick and Mullen from Mississippi. We also provide new Florida county records for C. alachua, C. barbosai, C. (Beltranmyia) hollensis (Melander and Brues), C. insignis, and C. (Monoculicoides) sonorensis Wirth and Jones; a new Georgia county record for C. alachua; and new Alabama county records for C. insignis, and C. sonorensis.
Background: Currently, there is inadequate evidence on which to base clinical management of neurotoxic snakebite envenoming, especially in the choice of initial antivenom dosage. This randomised controlled trial compared the effectiveness and safety of high versus low initial antivenom dosage in victims of neurotoxic envenoming.
Methodology/ Principal findings: This was a balanced, randomised, double-blind trial that was conducted in three health care centers located in the Terai plains of Nepal. Participants received either low (two vials) or high (10 vials) initial dosage of Indian polyvalent antivenom. The primary composite outcome consisted of death, the need for assisted ventilation and worsening/recurrence of neurotoxicity. Hourly evaluations followed antivenom treatment. Between April 2011 and October 2012, 157 snakebite victims were enrolled, of which 154 were analysed (76 in the low and 78 in the high initial dose group). Sixty-seven (43·5%) participants met the primary outcome definition. The proportions were similar in the low (37 or 48.7%) vs. high (30 or 38.5%) initial dose group (difference = 10·2%, 95%CI [-6·7 to 27·1], p = 0·264). The mean number of vials used was similar between treatment groups. Overall, patients bitten by kraits did worse than those bitten by cobras. The occurrence of treatment-related adverse events did not differ among treatment groups. A total of 19 serious adverse events occurred, including seven attributed to antivenom.
Conclusions: This first robust trial investigating antivenom dosage for neurotoxic snakebite envenoming shows that the antivenom currently used in Nepal performs poorly. Although the high initial dose regimen is not more effective than the low initial dose, it offers the practical advantage of being a single dose, while not incurring higher consumption or enhanced risk of adverse reaction. The development of new and more effective antivenoms that better target the species responsible for bites in the region will help improve future patients’ outcomes.
Trial registration: The study was registered on clinicaltrials.gov (NCT01284855) (GJ 5/1)
ANGIOGENES : knowledge database for protein-coding and noncoding RNA genes in endothelial cells
(2016)
Increasing evidence indicates the presence of long noncoding RNAs (lncRNAs) is specific to various cell types. Although lncRNAs are speculated to be more numerous than protein-coding genes, the annotations of lncRNAs remain primitive due to the lack of well-structured schemes for their identification and description. Here, we introduce a new knowledge database “ANGIOGENES” (http://angiogenes.uni-frankfurt.de) to allow for in silico screening of protein-coding genes and lncRNAs expressed in various types of endothelial cells, which are present in all tissues. Using the latest annotations of protein-coding genes and lncRNAs, publicly-available RNA-seq data was analyzed to identify transcripts that are expressed in endothelial cells of human, mouse and zebrafish. The analyzed data were incorporated into ANGIOGENES to provide a one-stop-shop for transcriptomics data to facilitate further biological validation. ANGIOGENES is an intuitive and easy-to-use database to allow in silico screening of expressed, enriched and/or specific endothelial transcripts under various conditions. We anticipate that ANGIOGENES serves as a starting point for functional studies to elucidate the roles of protein-coding genes and lncRNAs in angiogenesis.
The Anthropocene Epoch is characterized by novel and increasingly complex dependencies between the environment and human civilization, with many challenges of biodiversity management emerging as wicked problems. Problems arising from the management of biological invasions can be either tame (with simple or obvious solutions) or wicked, where difficulty in appropriately defining the problem can make complete solutions impossible to find. We review four case studies that reflect the main goals in the management of biological invasions – prevention, eradication, and impact reduction – assessing the drivers and extent of wickedness in each. We find that a disconnect between the perception and reality of how wicked a problem is can profoundly influence the likelihood of successful management. For example, managing species introductions can be wicked, but shifting from species-focused to vector-focused risk management can greatly reduce the complexity, making it a tame problem. The scope and scale of the overall management goal will also dictate the wickedness of the problem and the achievability of management solutions (cf. eradication and ecosystem restoration). Finally, managing species that have both positive and negative impacts requires engagement with all stakeholders and scenario-based planning. Effective management of invasions requires either recognizing unavoidable wickedness, or circumventing it by seeking alternative management perspectives.
Many recent studies in invasion science have identified species traits that determine either invasiveness or impact. Such analyses underpin risk assessments and attempts to prioritise management actions. However, the factors that mediate the capacity of an introduced species to establish and spread (i.e. its invasiveness) can differ from those that affect the nature and severity of impacts. Here we compare those traits correlated with invasiveness with those correlated with impact for Cactaceae (“cacti”) in South Africa. To assess impact magnitude, we scored 70 cacti (35 invasive and 35 non-invasive species) using the Generic Impact Scoring System (GISS) and identified traits correlated with impact using a decision tree approach. We then compared the traits correlated with impact with those identified in a recent study as correlated with invasiveness (i.e. native range size and growth form). We found that there is a significant correlation between native range size and both invasiveness and impact. Cacti with larger native ranges were more likely to become invasive (p=0.001) and cause substantial impacts (p=0.01). These results are important for prioritising efforts on the management of cactus species. Understanding when and why impact and invasiveness are correlated (as they appear to be for Cactaceae) is likely to be an important area of future research in risk assessment.
In a recent Discussion Paper, Hoffmann and Courchamp (2016) posed the question: are biological invasions and natural colonisations that different? This apparently simple question resonates at the core of the biological study of human-induced global change, and we strongly believe that the answer is yes: biological invasions and natural colonisations differ in processes and mechanisms in ways that are crucial for science, management, and policy. Invasion biology has, over time, developed into the broader transdisciplinary field of invasion science. At the heart of invasion science is the realisation that biological invasions are not just a biological phenomenon: the human dimension of invasions is a fundamental component in the social-ecological systems in which invasions need to be understood and managed.