University of Algarve

Abstract Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Availability: Biopython is freely available, with documentation and source code at www.biopython.org under the Biopython license. Contact: All queries should be directed to the Biopython mailing lists, see www.biopython.org/wiki/_Mailing_listspeter.cock@scri.ac.uk.

An important issue in multiobjective optimization is the quantitative comparison of the performance of different algorithms. In the case of multiobjective evolutionary algorithms, the outcome is usually an approximation of the Pareto-optimal set, which is denoted as an approximation set, and therefore the question arises of how to evaluate the quality of approximation sets. Most popular are methods that assign each approximation set a vector of real numbers that reflect different aspects of the quality. Sometimes, pairs of approximation sets are also considered. In this study, we provide a rigorous analysis of the limitations underlying this type of quality assessment. To this end, a mathematical framework is developed which allows one to classify and discuss existing techniques.

Generic Mapping Tools (GMT) is an open‐source software package for the analysis and display of geoscience data, helping scientists to analyze, interpolate, filter, manipulate, project, and plot time series and gridded data sets. The GMT toolbox includes about 80 core and 40 supplemental program modules sharing a common set of command options, file structures, and documentation. Its power to process data and produce publication‐quality graphic presentations has made it vital to a large scientific community that now includes more than 25,000 individual users. GMT's website ( http://gmt.soest.hawaii.edu/ ) exceeds 20,000 visits per month, and server logs show roughly 2000 monthly downloads.

Abstract The Generic Mapping Tools (GMT) software is ubiquitous in the Earth and ocean sciences. As a cross‐platform tool producing high‐quality maps and figures, it is used by tens of thousands of scientists around the world. The basic syntax of GMT scripts has evolved very slowly since the 1990s, despite the fact that GMT is generally perceived to have a steep learning curve with many pitfalls for beginners and experienced users alike. Reducing these pitfalls means changing the interface, which would break compatibility with thousands of existing scripts. With the latest GMT version 6, we solve this conundrum by introducing a new “modern mode” to complement the interface used in previous versions, which GMT 6 now calls “classic mode.” GMT 6 defaults to classic mode and thus is a recommended upgrade for all GMT 5 users. Nonetheless, new users should take advantage of modern mode to make shorter scripts, quickly access commonly used global data sets, and take full advantage of the new tools to draw subplots, place insets, and create animations.

autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

All plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa. These microorganisms showing endophytic lifestyles play crucial roles in plant development, growth, fitness, and diversification. The increasing awareness of and information on endophytes provide insight into the complexity of the plant microbiome. The nature of plant-endophyte interactions ranges from mutualism to pathogenicity. This depends on a set of abiotic and biotic factors, including the genotypes of plants and microbes, environmental conditions, and the dynamic network of interactions within the plant biome. In this review, we address the concept of endophytism, considering the latest insights into evolution, plant ecosystem functioning, and multipartite interactions.

The treatment strategy for ulcerative colitis [UC] is mainly based on the severity, distribution [proctitis, left-sided, extensive]1 and pattern of disease. The latter includes relapse frequency, disease course, response to previous medications, side effects of medication, and extra-intestinal manifestations. Age at onset, and disease duration are also important factors. It is important to distinguish patients with severe UC necessitating hospital admission from those with mild or moderately active disease who can be managed as outpatients. The best validated and most widely used index for identifying severe UC remains that of Truelove and Witts.2 Patients with bloody stool frequency ≥ 6/day and a tachycardia [> 90 min−1], or temperature > 37.8°C, or anaemia [haemoglobin < 10.5 g/dl], or an elevated erythrocyte sedimentation rate [ESR] [> 30 mm/h] have severe UC. Only one additional criterion in addition to the bloody stool frequency ≥ 6/day is needed to define a severe attack.3,4 In practice, a C-reactive protein [CRP] of 30 mg/l can be substituted for the ESR. A mesalamine 1-g suppository once daily is the preferred initial treatment for mild or moderately active proctitis [EL1]. Mesalamine foam or enemas are an alternative [EL1], but suppositories deliver the drug more effectively to the rectum and are better tolerated [EL3]. Topical mesalamine is more effective than topical steroids [EL1]. Combining topical mesalamine with oral mesalamine or topical steroids is more effective [EL2] Refractory proctitis may require treatment with systemic steroids, immunosuppressants, and/or biologics [EL4] Topical mesalamine [5-aminosalicylic acid or 5-ASA] is the first-line therapy for proctitis. A Cochrane systematic review of 38 clinical trials of treatment of proctitis and left-sided colitis confirmed its superiority over placebo for inducing symptomatic, endoscopic, histological response and remission.5 The pooled odds ratio [OR] was: 8.3 for symptomatic remission (8 trials, 95% confidence interval [CI] 4.28–16.12; p < 0.00001); 5.3 for endoscopic remission [7 trials, 95% CI 3.15–8.92; p < 0.00001]; and 6.3 for histological remission [5 trials, 95% CI 2.74–14.40; p < 0.0001]. Suppositories are more appropriate than enemas in proctitis as they better target the site of inflammation and are more acceptable for patients.6 There is no dose response for topical therapy above a dose of 1 g 5-ASA daily.5,7 Once-daily topical therapy is as effective as divided doses.8,9 A meta-analysis found no difference between oral and topical 5-ASA for induction of remission (risk ratio [RR] for no remission with topical 5-ASA: 0.82, 95% CI 0.52–1.28) or time to remission [24.8 vs 25.5 days, respectively], but the trials included in this meta-analysis enrolled patients with UC of any extent, not specifically proctitis.10 In the single trial that included only patients with proctitis, rectal 5-ASA was more effective than oral 5-ASA alone.11 However, if oral 5-ASA is used alone, 3.6 g of a pH-dependent release preparation appears to be more effective than lower doses or placebo.12 Moreover in patients with proctosigmoiditis, 5-ASA granules rather than tablets are more likely to obtain clinical [78% vs 55%, p < 0.001] and endoscopic [67% vs 43%, p < 0.001] remission.13 The combination of oral and topical 5-ASA is more effective than either alone in patients with disease extending < 50 cm from the anal verge,14 although there is no trial of combination therapy for proctitis alone. Combining topical 5-ASA and topical steroids also helps: beclomethasone dipropionate [3 mg] and 5-ASA [2 g] enemas produced significantly better clinical, endoscopic, and histological improvement than either agent alone.15 Two meta-analyses have shown that topical 5-ASA is more effective than topical steroids, whether assessing symptomatic, endoscopic, or histological remission.16 Consequently topical steroids be to patients who have an or who are to topical A trial shown that g rectal foam alone is more than placebo in inducing remission at in patients with mild to vs p < drug not with topical and endoscopic be confirmed in those with to with oral topical 5-ASA and/or topical Refractory proctitis may require treatment with systemic steroids, or The of proctitis is in to moderately active left-sided ulcerative colitis be with an ≥ 1 with oral mesalamine ≥ [EL1], is more effective than oral or topical or topical steroids alone [EL1]. Topical mesalamine is more effective than topical steroids [EL1]. Once-daily with mesalamine is as effective as divided doses are appropriate in patients with to severe and in those with mild who not to mesalamine [EL1]. beclomethasone dipropionate and as oral in patients with mild to moderately active ulcerative colitis can be in patients with mild to disease who are or to left-sided colitis is an for hospital admission oral and topical 5-ASA is the first-line therapy for mild to moderately active left-sided with an of to remission of CI and time to remission vs 25.5 p as with oral 5-ASA However, either oral or topical 5-ASA alone is more effective than Topical therapy rectal 5-ASA than oral found between foam and enemas induction of or endoscopic either are appropriate for left-sided UC. enemas are not to enemas and may be better meta-analyses have confirmed the superiority of rectal 5-ASA over rectal a meta-analysis of trials that rectal beclomethasone is to rectal that g rectal foam alone is to remission at for mild to left-sided trials with oral and/or rectal 5-ASA and g foam or enemas are 5-ASA is no more effective than oral for to remission 95% CI but is better tolerated for an 95% CI There is no difference in or between and divided doses of between the 5-ASA It was that is likely to the clinical trial ≥ oral 5-ASA remission more effectively than lower doses for to remission at of 95% CI Patients with disease may from the dose of The for the of oral steroids in patients with mild to left-sided UC the response to and of and the In the the time to of rectal was in patients g and in those was for although of therapy remission was if a rectal days, or from not of appropriate 5-ASA additional therapy with oral systemic steroids be However, that a of patients who have not to oral 5-ASA may clinical remission a of g of the initial beclomethasone dipropionate is but not better than not to be in the treatment of Two trials and have oral with placebo in patients with mild to left-sided and UC. The clinical and endoscopic remission vs and endoscopic vs for and In the was also with oral at a dose of and no difference was In the was also with and no difference was the was not to of trials that the of is to left-sided disease and not A trial oral with placebo in patients with mild to moderately active UC with oral clinical, endoscopic, and histological remission at more than for an alternative therapy to to However, there no trial between and to moderately active ulcerative colitis be with an 1 with oral mesalamine ≥ [EL1]. Once-daily with mesalamine is as effective as divided doses [EL1]. are appropriate in patients with to severe and in those with mild who not to mesalamine [EL1]. colitis is an for hospital admission for treatment the of clinical trials in mild to UC patients with and left-sided of the for this is in 5-ASA is more effective than placebo for the induction of remission of mild to The of oral and rectal 5-ASA was shown in a trial of patients to oral 5-ASA with a 1-g 5-ASA vs oral 5-ASA with a placebo of the clinical remission at with with oral 5-ASA alone In as in left-sided oral 5-ASA to oral with a better Once-daily 5-ASA is as effective as divided of the 5-ASA and with no difference There may be a for over daily oral 5-ASA is more effective than lower doses for inducing remission for to remission at of 95% CI an initial dose of for moderately active UC may be of to to 5-ASA is an to oral systemic if a 5-ASA ≥ or as therapy a treatment with steroids can be are to 5-ASA dose based on > 50 in patients in clinical for the superiority of oral over 5-ASA from in active included patients with appropriate for moderately active disease is for 1 the daily dose in an are with relapse and doses of are for active with a release and systemic are an alternative to beclomethasone dipropionate [5 daily for for a is with a to daily for in a A of patients with active left-sided or UC that oral beclomethasone dipropionate an to that of g The of release for active UC was the of a previous Cochrane systematic review of was likely to clinical remission than oral 5-ASA 95% CI with no over placebo 95% CI review the of in left-sided and as treatment to with are needed to in active UC. Two induction trials of the preparation also to a over placebo in mild to as to in left-sided There is for a of to therapy to However, meta-analyses between the and trials meta-analyses to this have on in active UC. patients remission with than with in one In there was no difference between and that from more and more to those of A trial as an A of patients placebo enemas or from a for patients clinical and endoscopic remission at with with placebo trials confirmed are and the of for to remission in active UC. are in to define the best of preferred frequency and duration of to and There is to on and of therapy in is a of the Patients with UC have and a A trial the and of a that at of trial included patients with UC of left-sided or one placebo and doses of the in remission and endoscopic between placebo and pooled not and respectively], the for histological remission and is a with and and in patients with mild to active UC clinical response and endoscopic at in patients who of as with placebo and p the of in patients with active UC. The remission at was in and of patients to the and placebo However, the of patients who symptomatic remission and and histological as as remission at significantly in patients who the of the and of of and inflammation in of UC. the and of a in UC and response not significantly between and placebo However, remission and response in patients to in It is to the of or in clinical clinical trials are Patients with bloody ≥ 6/day and any of systemic > 90 temperature > 37.8°C, < erythrocyte sedimentation rate [ESR] > 30 or C-reactive protein [CRP] > 30 have severe colitis and be to hospital for treatment Patients with or > have a of patients with severe UC require appropriate to the and the of It is to that for the of disease or are or of and that the is not Patients on therapy a with is to at an patients likely to require and to to The are not and clinical A of severe UC shown that therapy with or is not with a In the was significantly in than and in those with treatment for severe active ulcerative colitis is steroids [EL1]. with [EL2] is an alternative in of to patients of and for and anaemia be if needed Patients are best for a and a are or doses are no more but lower doses are is as effective as be for a as extending therapy to no additional A systematic review of trials of therapy for severe patients from an response to steroids or of CI of the 95% CI to was 95% CI and of between and p of was not to between and to A that was as effective as for severe of patients in with also the for Consequently with based on is a in those patients with severe UC who steroids, as those to patients with or those with that are appropriate in addition to steroids and to and and of at is or can and to the and is with a disease and appropriate stool and for is more in patients with severe UC and is with and oral be and therapy be if although this may not be to the of is in patients with disease a disease and is not to if the is is most appropriate and with than in colitis vs not of and may topical therapy or 5-ASA] if tolerated and although there have no systematic in severe only if is as in a of admission to or to an is or to trials of oral or or in UC have shown no in addition to to a above an between and The response to steroids be best the in treatment [EL1], [EL1], or be is if there is no improvement of therapy [EL4] the clinical trials of for patients with severe UC to steroids have However, is important that not with the to with or of as this the and with the important that be and with the the one who to to that appropriate therapy can be in a the or there of patients in one strategy is preferred over the response to therapy be and if a to to one therapy a therapy be are needed to that in severe colitis can be divided clinical, and in clinical a combination of clinical and a and a if this not have to disease and be used for is are as A stool frequency > on of was with a rate of a frequency > or between and with a > mg/l on in that as the index is more widely used than the that may not be in only of those with the > or a temperature > on admission was with a to in the for in a of In this of response to steroids was < in stool frequency patients to an of the of rather than the of > cm or on a with in A that the of an or more of was with in of The of patients with that with the for but this is not widely used in clinical have shown that endoscopic at admission may also the for In a from patients with severe UC and an ulcerative colitis endoscopic index of of or needed therapy with or or the most severe endoscopic are in the of the and can be a is not and an of in patients with severe UC. clinical, and A of 30 patients who to that patients with on and Truelove and a rate of of in to of a stool frequency over days, or of and 30 on was with the for in to Two have confirmed the of in the treatment of severe The only included patients who of patients steroids on on placebo to 95% CI In a patients to either or of with dose based on at in and respectively], with to in the and in the not patients at a dose of the dose used in clinical from and clinical trials, between and of patients to and in the patients on at in the and in in and a time to response of days, in However, the index of and its side of that in the only of patients with severe UC A Cochrane that in trials that there was for more effective than treatment alone for severe UC. In of and of who to over A review of the of patients with for severe colitis that to an oral was a in 95% CI p < to therapy and at have confirmed as that the of in this Patients who have UC to therapy may be for is a that a to of shown over placebo in patients with included patients with severe remission in any A response was of patients on to of patients on to and of patients on placebo was to a difference in patients with severe In a in oral of was significantly more effective than placebo to remission and endoscopic in patients with A systematic review and meta-analysis the of trials and those of that clinical response at was significantly with than with placebo 95% CI p at and and The in patients with UC with to be at although this included a as a single dose [5 is an effective therapy in patients with severe UC to A included patients and who with at significantly lower in patients with placebo vs p 95% CI Patients with active disease who of steroids more than patients with more severe disease at and a review of for severe colitis to steroids have shown of patients in the a rate at of patients and placebo although of therapy was not and between A of patients therapy of and and from therapy patients on in the in and to for have of response to in patients with severe and/or disease. and severe endoscopic are with or to clinical endoscopic and above at and at with A found that is in of patients with UC and that of in the therapy is with at are lower in severe with moderately severe although is not whether induction is with better The also appears to the response to A of patients that patients a single are more likely to require at than those who or more with p A that a induction is the treatment of for in severe A that an induction strategy of was with a in the for in 50 patients with severe was from in a of UC patients with The trial patients with severe colitis > of steroids, to for oral or at and at oral and steroids from The trial was to treatment with than between and of response at relapse between and as of remission at or treatment patients in to treatment at was in patients in the with patients in the difference 95% CI p The rate in the vs the was vs not significantly between and on vs on The trial found no difference of or the of in patients with severe UC with or A meta-analysis of also found remission in patients with severe UC or of hospital and have but treatment the of as therapy with the between for therapy be be in patients with a or in of the of side effects in this a severe colitis treatment with an at an appropriate dose and is important to whether remission are that may the of is an important for that not the of In there is as to whether the of although one of patients found no between therapy and In only a single at therapy with a or be for therapy a systematic review that included and response and remission and at and at in of in and in may that the of therapy in UC is However, the is for the of therapy can be on the of the therapy can be in in between the and therapy in an based 30 UC with and for to be effective in an in patients with severe colitis no from and is as or of the ≥ with systemic and the of of severe more and have the and of UC. In addition to treatment with oral be stool is confirmed for from an is on the of There is a of for treatment to be is the most of severe colitis and can be with or It a of to and There is that clinical remission the index hospital admission and the for Patients for severe who are to therapy and to are likely to require of whether or is used as patients with clinical, or endoscopic of more severe disease at are more likely to require It is important to the of disease. is that the disease is to However, alternative to of an of the active drug to the as or disease the initial is to review treatment and to be of the stool and The is to that therapy and used on the of topical therapy and whether was used in with an dose of oral can be to in patients with may drug there is a be Patients with active colitis or proctitis, who oral with oral and rectal 5-ASA have disease. admission for to remission in a of there is from the of as oral or rectal oral or rectal or disease is likely to be the have a of acid although with and trials have from alternative topical as and have that may patients with to of patients who have a for UC only have The of and for UC is Patients with disease be with a with at for or In of treatment therapy with an alternative or be is significantly more effective than 5-ASA at clinical and endoscopic remission in UC. In an patients to or oral 5-ASA in addition to of patients clinical and endoscopic remission with with 5-ASA 95% CI In an in patients remission with at and of 55%, and that are in patients who steroids are remission was a of the trials of in UC. the and trials included patients with confirmed active colitis treatment with and/or or with and/or and/or 5-ASA and to placebo or of patients the on steroids, who the of ≥ those who at of those remission with of those placebo but not have on the of in In the of in patients with to severe patients with confirmed active colitis treatment with and/or to at at and from A of of the and of a of previous In of who at with to placebo < of in the who at in remission with in the placebo The of in patients with confirmed active UC to steroids and/or 5-ASA and/or was in the In of induction and with a of induction trials In the patients of response to induction therapy at to treatment with either placebo or of patients on on ≥ for those patients of those with and who placebo remission are more effective than placebo in and remission in those at important is the of combination therapy with and The trial that a combination of is more effective than was a trial in patients with to severe who to remission at was of patients with of alone and of alone therapy not for or or in patients important is the of a the of a In the of clinical remission at was not in the The of clinical remission at was in this on vs on p although the difference from placebo for as as was in the than in the The of remission at in those patients steroids at was not in the A meta-analysis the clinical rate of a the of a in patients to UC of to The response rate from to the remission between and However, to in was not to the a remission was also a of the trial of in confirmed active to the trials included an induction trial of with to or placebo a induction for the from a who induction to steroids and/or and/or A of of patients in the 1 trial at and previous In those who at and who to induction therapy and to remission at with to placebo < treatment with previous treatment with the of in the induction or that patients with disease or previous have a A that of UC and patients in clinical remission on the of of are not in a trial patients with The remission at as a with no > 1 and of was in patients to and patients who placebo The rate of clinical remission at as a with no > was for and for placebo trial to that is for induction of remission in UC. However, clinical remission steroids at more than and was with better of disease to oral steroids be either with steroids [EL4] or with at for or therapy with a [EL4] or [EL2] may be an also be In patients with active of as or be steroids are an in patients with active patients with moderately active UC are not in steroids have to be more in a of disease to oral However, of the patients in this therapy and have shown of in patients with of remission in patients steroids at the trials included disease as a criterion and of therapy a of However, although of at and dose doses used may have and is not to or patients and trial for in In the UC patients to oral at or or placebo Two the clinical response and in the and and in the placebo that included patients with to severe oral with at a to the was with clinical response of in the and in the placebo at have A systematic review and meta-analysis that clinical response at was significantly with than with placebo 95% CI p at and and of patients with to severe UC and with and Two trials have the of oral as induction therapy in patients with to severe patients or of patients at was in and in the vs and in the placebo of and with It not for in trial of the 1 and that of patients who 1 and of patients who clinical remission at are needed to the and of in to severe UC. Patients with colitis to be with [EL1], with at for or In of treatment a [EL4] or [EL2] be and if therapy not a clinical disease is best and to the and active UC that is to of or disease. A strategy to and remission be with the In the of therapy be and have for in UC to also shown to be effective in this The 1 and trials included patients with active disease at either dose [5 or clinical remission in a significantly of patients at than although the response for the of patients was not A Cochrane systematic of trials of for patients with to severe UC to and/or that at and was more effective than placebo at inducing clinical remission at 95% CI review not the in the to In the trial superiority of over placebo for the induction of remission of UC and of the patients at In patients clinical remission at in with patients placebo for those with remission for with for In the of patients on A for patients was not clinical remission at in patients with patients placebo A of patients either or for moderately active UC clinical response in patients with no difference in the response between patients or to although only patients with and patients with therapy at The trial of included of patients with to active treatment with not A is whether to an therapy in patients with The only included patients with and patients to be either in or to > the a from may not be to to therapy in The for the of and in patients is based on that and/or of and of of clinical trials of to a for or The 1 trial included of patients and of patients and for response to induction therapy not the of previous but only those with previous with no of in a for with placebo was but not vs p in the this of previous a of a significantly remission rate at 1 for those induction who to therapy for those with vs for those < vs for those on treatment with not the of in on therapy with a of an initial are included of patients with a of previous in not significantly in this of that patients with a of may have a to The 1 and trials of included patients who may be an in patients with to severe UC to once the There is to the of but no clinical trial included this with the patients is as to the and of therapy with may be a more appropriate for The have to that of the and the have and and and Two trials have shown that the and have and in and that are in trials are on and clinical the the to be in and The on The of therapy in ulcerative colitis is to and [EL2] The that most to patients is clinical an in stool frequency and of rectal and confirmed is not the only to the of and trials have In trial have to induction and in the this clinical response to induction therapy as a with the of therapy as a or as a or as an for in those who have to and at the of induction the of remission to between treatment is for patients [EL1]. therapy is acceptable patients with proctitis of remission of treatment with or therapy remission A for remission endoscopic is to duration of an endoscopic of as to a of the 1 and trials, that patients with at a of remission at 30 of with clinical not that treatment specifically as an are with clinical and is that patients in a with disease. of treatment is disease [EL1], disease and of and of previous treatment of the most treatment used for inducing remission the most of treatment [EL1], and [EL2] have for relapse in patients with In one of a

The term Blue Carbon (BC) was first coined a decade ago to describe the disproportionately large contribution of coastal vegetated ecosystems to global carbon sequestration. The role of BC in climate change mitigation and adaptation has now reached international prominence. To help prioritise future research, we assembled leading experts in the field to agree upon the top-ten pending questions in BC science. Understanding how climate change affects carbon accumulation in mature BC ecosystems and during their restoration was a high priority. Controversial questions included the role of carbonate and macroalgae in BC cycling, and the degree to which greenhouse gases are released following disturbance of BC ecosystems. Scientists seek improved precision of the extent of BC ecosystems; techniques to determine BC provenance; understanding of the factors that influence sequestration in BC ecosystems, with the corresponding value of BC; and the management actions that are effective in enhancing this value. Overall this overview provides a comprehensive road map for the coming decades on future research in BC science.

Abstract Motivation The availability of user‐friendly, high‐resolution global environmental datasets is crucial for bioclimatic modelling. For terrestrial environments, WorldClim has served this purpose since 2005, but equivalent marine data only became available in 2012, with pioneer initiatives like Bio‐ORACLE providing data layers for several ecologically relevant variables. Currently, the available marine data packages have not yet been updated to the most recent Intergovernmental Panel on Climate Change (IPCC) predictions nor to present times, and are mostly restricted to the top surface layer of the oceans, precluding the modelling of a large fraction of the benthic diversity that inhabits deeper habitats. To address this gap, we present a significant update of Bio‐ORACLE for new future climate scenarios, present‐day conditions and benthic layers (near sea bottom). The reliability of data layers was assessed using a cross‐validation framework against in situ quality‐controlled data. This test showed a generally good agreement between our data layers and the global climatic patterns. We also provide a package of functions in the R software environment ( sdmpredictors ) to facilitate listing, extraction and management of data layers and allow easy integration with the available pipelines for bioclimatic modelling. Main types of variable contained Surface and benthic layers for water temperature, salinity, nutrients, chlorophyll, sea ice, current velocity, phytoplankton, primary productivity, iron and light at bottom. Spatial location and grain Global at 5 arcmin ( c . 0.08° or 9.2 km at the equator). Time period and grain Present (2000–2014) and future (2040–2050 and 2090–2100) environmental conditions based on monthly averages. Major taxa and level of measurement Marine biodiversity associated with sea surface and epibenthic habitats. Software format ASCII and TIFF grid formats for geographical information systems and a package of functions developed for R software.

Essential oils are complex mixtures isolated from aromatic plants which may possess antioxidant and anti-inflammatory activities of interest in thye food and cosmetic industries as well as in the human health field. In this work, a review was done on the most recent publications concerning their antioxidant and anti-inflammatory activities. At the same time a survey of the methods generally used for the evaluation of antioxidant activity and some of the mechanisms involved in the anti-inflammatory activities of essential oils are also reported.

Forecasting has always been at the forefront of decision making and planning. The uncertainty that surrounds the future is both exciting and challenging, with individuals and organisations seeking to minimise risks and maximise utilities. The large number of forecasting applications calls for a diverse set of forecasting methods to tackle real-life challenges. This article provides a non-systematic review of the theory and the practice of forecasting. We provide an overview of a wide range of theoretical, state-of-the-art models, methods, principles, and approaches to prepare, produce, organise, and evaluate forecasts. We then demonstrate how such theoretical concepts are applied in a variety of real-life contexts. We do not claim that this review is an exhaustive list of methods and applications. However, we wish that our encyclopedic presentation will offer a point of reference for the rich work that has been undertaken over the last decades, with some key insights for the future of forecasting theory and practice. Given its encyclopedic nature, the intended mode of reading is non-linear. We offer cross-references to allow the readers to navigate through the various topics. We complement the theoretical concepts and applications covered by large lists of free or open-source software implementations and publicly-available databases. © 2021 The Author(s)

Abstract genclone 1.0 is designed for studying clonality and its spatial components using genotype data with molecular markers from haploid or diploid organisms. genclone 1.0 performs the following tasks. (i) discriminates distinct multilocus genotypes (MLGs), and uses permutation and resampling approaches to test for the reliability of sets of loci and sampling units for estimating genotypic and genetic diversity (a procedure also useful for nonclonal organisms); (ii) computes statistics to test for clonal propagation or clonal identity of replicates; (iii) computes various indices describing genotypic diversity; and (iv) summarizes the spatial organization of MLGs with adapted spatial autocorrelation methods and clonal subrange estimates.

Subfossil pollen and plant macrofossil data derived from 14C-dated sediment profiles can provide quantitative information on glacial and interglacial climates. The data allow climate variables related to growing-season warmth, winter cold, and plant-available moisture to be reconstructed. Continental-scale reconstructions have been made for the mid-Holocene (MH, around 6 ka) and Last Glacial Maximum (LGM, around 21 ka), allowing comparison with palaeoclimate simulations currently being carried out as part of the fifth Assessment Report (AR5) of the Intergovernmental Panel on Climate Change. The synthesis of the available MH and LGM climate reconstructions and their uncertainties, obtained using modern-analogue, regression and model-inversion techniques, is presented for four temperature variables and two moisture variables. Reconstructions of the same variables based on surface-pollen assemblages are shown to be accurate and unbiased. Reconstructed LGM and MH climate anomaly patterns are coherent, consistent between variables, and robust with respect to the choice of technique. They support a conceptual model of the controls of Late Quaternary climate change whereby the first-order effects of orbital variations and greenhouse forcing on the seasonal cycle of temperature are predictably modified by responses of the atmospheric circulation and surface energy balance.

Alphabetic orthographies differ in the transparency of their letter-sound mappings, with English orthography being less transparent than other alphabetic scripts. The outlier status of English has led scientists to question the generality of findings based on English-language studies. We investigated the role of phonological awareness, memory, vocabulary, rapid naming, and nonverbal intelligence in reading performance across five languages lying at differing positions along a transparency continuum (Finnish, Hungarian, Dutch, Portuguese, and French). Results from a sample of 1,265 children in Grade 2 showed that phonological awareness was the main factor associated with reading performance in each language. However, its impact was modulated by the transparency of the orthography, being stronger in less transparent orthographies. The influence of rapid naming was rather weak and limited to reading and decoding speed. Most predictors of reading performance were relatively universal across these alphabetic languages, although their precise weight varied systematically as a function of script transparency.

Sponges (phylum Porifera) are early-diverging metazoa renowned for establishing complex microbial symbioses. Here we present a global Porifera microbiome survey, set out to establish the ecological and evolutionary drivers of these host-microbe interactions. We show that sponges are a reservoir of exceptional microbial diversity and major contributors to the total microbial diversity of the world's oceans. Little commonality in species composition or structure is evident across the phylum, although symbiont communities are characterized by specialists and generalists rather than opportunists. Core sponge microbiomes are stable and characterized by generalist symbionts exhibiting amensal and/or commensal interactions. Symbionts that are phylogenetically unique to sponges do not disproportionally contribute to the core microbiome, and host phylogeny impacts complexity rather than composition of the symbiont community. Our findings support a model of independent assembly and evolution in symbiont communities across the entire host phylum, with convergent forces resulting in analogous community organization and interactions.

Accurate text classification and placement remain challenges in U.S. higher education, with traditional automated systems like Accuplacer functioning as "black-box" models with limited assessment transparency. This study evaluates Large Language Models (LLMs) as complementary placement tools by comparing their classification performance against a human-rated gold standard and Accuplacer. A 450-essay corpus was classified using Claude, Gemini, GPT-3.5-turbo, and GPT-4o across four prompting strategies: Zero-shot, Few-shot, Enhanced, and Enhanced+ (definitions with examples). Two classification approaches were tested: (i) a 1-step, 3 class classification task, distinguishing DevEd Level 1, DevEd Level 2, and College-level texts in one single run; and (ii) a 2-step classification task, first separating College vs. Non-College texts before further classifying Non-College texts into DevEd sublevels. The results show that structured prompt refinement improves the precision of LLMs' classification, with Claude Enhanced + achieving 62.22% precision (1 step) and Gemini Enhanced + reaching 69.33% (2 step), both surpassing Accuplacer (58.22%). Gemini and Claude also demonstrated strong correlation with human ratings, with Claude achieving the highest Pearson scores (ρ = 0.75; 1-step, ρ = 0.73; 2-step) vs. Accuplacer (ρ = 0.67). While LLMs show promise for DevEd placement, their precision remains a work in progress, highlighting the need for further refinement and safeguards to ensure ethical and equitable placement.

Aging constitutes the key risk factor for age-related diseases such as cancer and cardiovascular and neurodegenerative disorders. Human longevity and healthy aging are complex phenotypes influenced by both environmental and genetic factors. The fact that genetic contribution to lifespan strongly increases with greater age provides basis for research on which "protective genes" are carried by long-lived individuals. Studies have consistently revealed FOXO (Forkhead box O) transcription factors as important determinants in aging and longevity. FOXO proteins represent a subfamily of transcription factors conserved from Caenorhabditis elegans to mammals that act as key regulators of longevity downstream of insulin and insulin-like growth factor signaling. Invertebrate genomes have one FOXO gene, while mammals have four FOXO genes: FOXO1, FOXO3, FOXO4, and FOXO6. In mammals, this subfamily is involved in a wide range of crucial cellular processes regulating stress resistance, metabolism, cell cycle arrest, and apoptosis. Their role in longevity determination is complex and remains to be fully elucidated. Throughout this review, the mechanisms by which FOXO factors contribute to longevity will be discussed in diverse animal models, from Hydra to mammals. Moreover, compelling evidence of FOXOs as contributors for extreme longevity and health span in humans will be addressed.

Abstract Aim To understand why and when areas of endemism (provinces) of the tropical Atlantic Ocean were formed, how they relate to each other, and what processes have contributed to faunal enrichment. Location Atlantic Ocean. Methods The distributions of 2605 species of reef fishes were compiled for 25 areas of the Atlantic and southern Africa. Maximum‐parsimony and distance analyses were employed to investigate biogeographical relationships among those areas. A collection of 26 phylogenies of various Atlantic reef fish taxa was used to assess patterns of origin and diversification relative to evolutionary scenarios based on spatio‐temporal sequences of species splitting produced by geological and palaeoceanographic events. We present data on faunal (species and genera) richness, endemism patterns, diversity buildup (i.e. speciation processes), and evaluate the operation of the main biogeographical barriers and/or filters. Results Phylogenetic (proportion of sister species) and distributional (number of shared species) patterns are generally concordant with recognized biogeographical provinces in the Atlantic. The highly uneven distribution of species in certain genera appears to be related to their origin, with highest species richness in areas with the greatest phylogenetic depth. Diversity buildup in Atlantic reef fishes involved (1) diversification within each province, (2) isolation as a result of biogeographical barriers, and (3) stochastic accretion by means of dispersal between provinces. The timing of divergence events is not concordant among taxonomic groups. The three soft (non‐terrestrial) inter‐regional barriers (mid‐Atlantic, Amazon, and Benguela) clearly act as ‘filters’ by restricting dispersal but at the same time allowing occasional crossings that apparently lead to the establishment of new populations and species. Fluctuations in the effectiveness of the filters, combined with ecological differences among provinces, apparently provide a mechanism for much of the recent diversification of reef fishes in the Atlantic. Main conclusions Our data set indicates that both historical events (e.g. Tethys closure) and relatively recent dispersal (with or without further speciation) have had a strong influence on Atlantic tropical marine biodiversity and have contributed to the biogeographical patterns we observe today; however, examples of the latter process outnumber those of the former.

Although clonal species are dominant in many habitats, from unicellular organisms to plants and animals, ecological and particularly evolutionary studies on clonal species have been strongly limited by the difficulty in assessing the number, size and longevity of genetic individuals within a population. The development of molecular markers has allowed progress in this area, and although allozymes remain of limited use due to their typically low level of polymorphism, more polymorphic markers have been discovered during the last decades, supplying powerful tools to overcome the problem of clonality assessment. However, population genetics studies on clonal organisms lack a standardized framework to assess clonality, and to adapt conventional data analyses to account for the potential bias due to the possible replication of the same individuals in the sampling. Moreover, existing studies used a variety of indices to describe clonal diversity and structure such that comparison among studies is difficult at best. We emphasize the need for standardizing studies on clonal organisms, and particularly on clonal plants, in order to clarify the way clonality is taken into account in sampling designs and data analysis, and to allow further comparison of results reported in distinct studies. In order to provide a first step towards a standardized framework to address clonality in population studies, we review, on the basis of a thorough revision of the literature on population structure of clonal plants and of a complementary revision on other clonal organisms, the indices and statistics used so far to estimate genotypic or clonal diversity and to describe clonal structure in plants. We examine their advantages and weaknesses as well as various conceptual issues associated with statistical analyses of population genetics data on clonal organisms. We do so by testing them on results from simulations, as well as on two empirical data sets of microsatellites of the seagrasses Posidonia oceanica and Cymodocea nodosa. Finally, we also propose a selection of new indices and methods to estimate clonal diversity and describe clonal structure in a way that should facilitate comparison between future studies on clonal plants, most of which may be of interest for clonal organisms in general.

In this review, our current understanding of the species Escherichia coli and its persistence in the open environment is examined. E. coli consists of six different subgroups, which are separable by genomic analyses. Strains within each subgroup occupy various ecological niches, and can be broadly characterized by either commensalistic or different pathogenic behaviour. In relevant cases, genomic islands can be pinpointed that underpin the behaviour. Thus, genomic islands of, on the one hand, broad environmental significance, and, on the other hand, virulence, are highlighted in the context of E. coli survival in its niches. A focus is further placed on experimental studies on the survival of the different types of E. coli in soil, manure and water. Overall, the data suggest that E. coli can persist, for varying periods of time, in such terrestrial and aquatic habitats. In particular, the considerable persistence of the pathogenic E. coli O157:H7 is of importance, as its acid tolerance may be expected to confer a fitness asset in the more acidic environments. In this context, the extent to which E. coli interacts with its human/animal host and the organism's survivability in natural environments are compared. In addition, the effect of the diversity and community structure of the indigenous microbiota on the fate of invading E. coli populations in the open environment is discussed. Such a relationship is of importance to our knowledge of both public and environmental health.