dataesr/scientific-paragraphs-categorization huggingface dataset:
Back-mapping of sequencing reads on the viral scaffolds revealed an average coverage of 9x, with a 15. 1 kb-long scaffold showing a coverage of 17x, likely representing the inverted repeat regions characteristic of malacoherpesvirus genomes. With the total length of 174. 3 kb, the genome of MalacoHV1 encodes 107 predicted proteins, with 42 showing the highest similarity to HaHV-1 and 2 to OsHV-1 homologs. One protein showed the highest similarity (E-value = 5. 76e -35 , amino acidic identity = 33%) to a protein of the sea slug gastropod Elysia chlorotica (RUS69626. 1, Supplementary Table  3 ). The geographical origin and the sample type of the dataset, the number of contigs composing the genome, the total length, the encoded ORFs, the average coverage, the proposed name and the relative sequence ID are reported for the novel malacoherpes-like viruses.
Since BIN153 and BIN155 were originated from the meta-assemblies, the average coverage was calculated based on the sample with the highest coverage. Overall, these results suggest that the newly identified virus is not closely related to either of the two currently known malacoherpesviruses and is likely to represent a new species in the family. The MCP sequence of MalacoHV1 was used to create a more sensitive MCP profile hidden Markov model (HMM), which was then used to scan the global Tara Oceans database, resulting in the detection of 4 additional MCP homologs. Binning of the datasets including the MCP homologs yielded 4 metagenome-assembled genomes (MAGs), varying in length from 145 to 200 kb and including a total of 129 contigs (Table  1 ). The first MCP homolog was encoded on a 76. 7 kb-long contig (contig_012) carrying 40 predicted genes, with 13 proteins showing significant similarity (Evalue <0.
3 ). By contrast, in BIN76 and BIN142, the identified MCP homologs were encoded on contigs of a few kilobases, with maximum of 3 ORFs similar to those of known malacoherpesviruses and no other contigs in these bins encoded putative viral proteins. Thus, BIN76 and BIN142 were not considered further. Finally, to identify additional malacoherpesvirus relatives, we performed tblastn searches queried with the malacoherpesvirus proteomes against the NCBI nucleotide database, which yielded positive hits in 5 scaffolds of the blue mussel Mytilus edulis genome (MEDU_EUS, from an animal collected in Normandy, France; Table  1 ). These sequences collectively amounted to 135. 5 kb of a putative novel malacoherpesvirus genome, called MalacoHV3/Nor/ 2022, encoding 100 proteins, 61% of which showed moderate similarity (max: 65%, min: 23%, median: 37% amino acidic identity) to OsHV-1 proteins, whereas one was most similar (although with low sequence identity of 25%) to ORF89 of HaHV-1 (Figure  2 , Supplementary Table  3 ).
Discussion The small number of described malacoherpesviruses raised a question of whether these viruses are rare in marine ecosystems or whether they have been systematically overlooked in previous analyses  (Iranzo et al. , 2016; Mushegian et al. , 2018). Somewhat unexpectedly, extensive searches of malacoherpesvirus-like MCPs in global sequencing datasets, including marine metagenomic datasets, performed in this study did not uncover the suspected hidden malacoherpesvirus diversity in marine ecosystems. Two nonmutually exclusive possibilities could explain the scarcity of these viruses. First, malacoherpesviruses could be genuinely rare, present in low titres in marine environments. Second, the analyzed datasets are biased toward sequences from the plankton fraction, i. e. , unicellular organisms and extracellular virus particles; hence, viruses of multicellular eukaryotes could be underrepresented, highlighting the need to expand the exploration of the ocean viromes to animals and other multicellular eukaryotes.
Similarly, based on the fact that contigs representing the MalacoHV3 genome originate from the blue mussel M. edulis sequencing dataset, MalacoHV3 likely infects a bivalve host. Consistently, MalacoHV3 genome has low GC% content, possibly revealing a host adaptation. Indeed, bivalve genomes have lower GC% content compared to gastropods  (Adachi et al. , 2021). The presence of malacoherpesvirus core proteins in several mollusc species further pointed to possible host associations, but additional genomic data is needed to substantiate these findings. Notably, the membrane fusion protein that we found in several metazoan genomes is homologous to  For 6 malacoherpesvirus orthologs, the presence among the described viruses and among 54 selected metazoan species is reported as number of identified genes, together with the total number of identified genes.
Study design and patients This post hoc analysis included patients with active PsA who participated in five phase III clinical trials: FUTURE 2 (N=397), FUTURE 3 (N=414), FUTURE 4 (N=341), FUTURE 5 (N=996) and MAXIMISE (n=498). The design, eligibility criteria, methodology and statistical analysis of these individual studies have been published previously. [25] [26] [27] [28] [29]  As the FUTURE 1 study did not include week 52 data from the secukinumab 300 mg group, and used intravenous loading rather than subcutaneous, it was not used as part of this analysis. 30  While the FUTURE 2-5 studies included patients with active PsA, the MAXIMISE study specifically assessed axial manifestations in patients with PsA. All analyses were based on the pooled full analysis set (FAS) population of 2504 patients.
In the main analysis, patients were stratified into two groups based on baseline SUA level. Patients with hyperuricaemia were defined as having baseline SUA ≥360 µmol/L, whereas patients with normouricaemia were selected based on baseline SUA <360 µmol/L and without history of gout and/or UA-lowering therapies (ULTs). Different sensitivity analyses were performed by level of UA threshold in serum of 300 µmol/L and 420 µmol/L and in patients with or without history of gout and/or ULT. Patients with gout were defined as patients with either a history of gout and/or concomitant ULT or adverse events of gout. Information on the presence or absence of gout and on the use of ULTs was obtained from the data reported by investigators on patient medical history and previous or concomitant medications in the case report forms at patient screening, enrolment and follow-up visits.
Efficacy, structural outcomes and patient-reported outcomes The efficacy of secukinumab in patients with hyperuricaemia or gout was assessed in the pooled dataset of the FUTURE 2-5 studies and the MAXIMISE study across key manifestations of PsA, such as peripheral arthritis, enthesitis, dactylitis, spinal pain and discomfort, nail disease and psoriasis severity. Secukinumab efficacy was assessed across patient improvement in peripheral arthritis using the percentage of participants meeting American College of Rheumatology (ACR) response criteria. This represents a percentage improvement of ≥20% (ACR20), ≥50% (ACR50) and ≥70% (ACR70), at all scheduled postbaseline visits up to week 52. Treatment efficacy was further assessed by examining the percentage of patients with resolution of enthesitis using the Leeds Enthesitis Index (LEI) score or in the case of the MAXIMISE study, the Spondyloarthritis Research Consortium of Canada (SPARCC) score.
The percentage of patients with resolution of dactylitis, at all scheduled postbaseline visits up to week 52, was examined using the Leeds Dactylitis Index (LDI) score. The LEI score is based on the presence or absence of pain or tenderness at enthesitis sites, while the LDI score is based on finger circumference across all dactylitic digits. The efficacy of secukinumab in patients with hyperuricaemia or gout was further assessed by the mean change from baseline using Bath Ankylosing Spondylitis Disease Activity Index (BASDAI) response, using data from the MAXIMISE study only. The mean change in severity of nail disease was determined using the modified Nail Psoriasis Severity Index (mNAPSI) score. Finally, the percentage of patients observed to have experienced a 90% psoriasis resolution, or more, using PASI score, following treatment with secukinumab, was also examined.
2  Patients with PsA with hyperuricaemia from the pooled FUTURE 2-5  [25] [26] [27] [28]  studies and the MAXIMISE  29  study dataset were more frequently associated with hypertension and diabetes mellitus, when compared with patients with PsA with normouricaemia. This is reflective of current literature, as different studies have shown that PsA with hyperuricaemia, and PsA with gout, share comorbidities. 6 7 24.
In addition, the mean swollen joints count at baseline in our analysis was 11, which may also account for the lack of difference found in our study. The frequency and severity of skin psoriasis in this PsA dataset support different literature reports in psoriasis, where the number of psoriatic lesions has been shown to be significantly increased in patients with higher SUA levels compared with those with normal SUA levels. An association between both extent and change in PASI score and serum urate level has also been shown. 42  Furthermore, a recent meta-analysis found that in European, American and Southeast Asian countries, patients with moderate to severe psoriasis or those with metabolic syndrome and obesity were more likely to have higher UA levels. 14  In contrast with the literature reporting a higher rate of erosive and destructive disease,  24 43  we could not identify any relevant differences in the baseline radiographic characteristics between patients with normouricaemia and patients with hyperuricaemia, except for patients with hyperuricaemic level ≥420 µmol/L who had a more severe baseline vdH-mTSS.
32  Here, we examined whether there was any relevant difference in terms of efficacy of secukinumab in patients with hyperuricaemia compared with patients with normouricaemia with active PsA in our dataset from the FUTURE 2-5  [25] [26] [27] [28]  studies and the MAXIMISE  29  study. An early and sustained efficacy of secukinumab was shown up to week 52 across all key manifestations of PsA. Secukinumab was also associated with an improvement in health-related quality of life in both patients with hyperuricaemia, irrespective of the threshold of hyperuricaemia, and patients with normouricaemia. We acknowledge that the findings from this current dataset have several limitations owing to: the post hoc nature of these analyses; the inclusion criteria of the FUTURE 2-5 studies which were primarily designed as PsA trials and excluded patients with uncontrolled comorbidities; no assessment of axial manifestations was performed, except in the MAXIMISE study; the lack of placebo group in the studies beyond week 16 (FUTURE 2-5) and week 12 (MAXIMISE).
Acknowledgements The authors thank the patients who participated in the studies and the study investigators. Manuscript writing support was provided by  M. D Zuber Birajdar ,  Dhanya Mukundan  and  Rajeeb Ghosh ,  Novartis Healthcare Pvt Ltd, Hyderabad, India  and  Kate Killick ,  Novartis Ireland Ltd. The authors thank  Andrew Franklin  ( Novartis Pharma AG, Basel, Switzerland ) who provided editorial support and guidance during manuscript development.
org) and the SPFRMO (sprfmo. int) websites. The goal of the desk review was double, namely, reconstructing CALA-MASUR's history and activities as well as identifying the key areas of improvement that CALAMASUR has emphasized in its statements, with the aim of attracting the attention of the RFMO member states. To achieve the latter, the desk review was carried out in two steps: a) identifying key improvement areas prioritized by CALAMASUR and b) extracting key words per area. This first exercise resulted in the identification of one key concept (squid and its variants in Spanish -jibia, pota and calamar), 5 major concepts that refer to improvement areas and 121 related keywords. The resulting database identified the dates that each keyword was used in each of the documents. In the second phase, we quantified the number of appearances of the variants of the word squid in all the SPRFMO documents since its inception.
This included 1399 documents published in pdf format at the SPRFMO website. This search included all documents publicly available between 2006 and 2022. Data from the year 2022 is incomplete due to the timing when this analysis was carried out  (Apr, 2022). The range of documents used included SPRFMO reports of Scientific Committee, Compliance and Technical Committee, SPRMFO Commission, Annual reports, and National reports, as well as their various annexes available at the SPRFMO website. In the third phase, we quantified the direct impact of CALAMASUR on the SPRFMO agenda by analyzing the appearance of the 121 related keywords within the SPRMFO documents that contained the key concept (squid) and its variants in Spanish (jibia, pota and calamar). It should be noted that further to the papers presented at the RFMO, CALAMASUR did regular interventions (media releases, interviews) in national, regional and international media.
None of those media appearances were considered for the analysis of keywords. Yet, the CALAMASUR agenda in the media did not divert from their positions at the RFMO. It should be noted that during the research period, squid fisheries and particularly distant water fleets have been subject of increased scrutiny by media, non-governmental organizations (NGOs) (e. g. , Yi Chiao Lee et al. , 2018), and academia (e. g. ,  Sala et al. , 2018) , mainly due to reports of IUU fishing and violations of human rights at sea. It is not possible to discern the effects of this increased public attention per se with our methodology, mostly considering that CALAMASUR made use of these evidences in their papers and interventions at the RFMO. By merging the all-documents key word count database with an additional database containing the dates (month and year) when CAL-AMASUR presented documents using the identified keywords, we were able to evaluate the connection between the interventions of CALA-MASUR and the evolution of the frequency with which the set of key words and the major topics they represented were discussed in the global set of SPRMFO documents.
We used R package pdftools  (Ooms 2021 ) in R version 4. 1. 3 (R Core Team, 2022) for text extraction from SPRMFO documents. We created a table with the number of key word occurrences (see all key words in Fig. 3 ) in each of the documents and then aggregated these counts by year of publication with a script written in R 4. 1. 3. Computer codes and materials for reproduction of our results are available upon requests to the corresponding author.
The latter included encouraging the regular operation of the Squid Working Group -which at that time had only met in 2017, as a way to ensure the operation of a data collection and monitoring program, as well as the development of a regional stock assessment model  (CALAMASUR 2018). This first position statement was made public through media releases; yet, it was not included as a SPRFMO observer paper due to the short time between its development and the 6th SPRFMO Commission Meeting. From 2018 onwards, CALAMASUR was formalized and achieved observer status at the SPRFMO. By 2019, CALAMASUR started to be active at the RFMO and has, since then, presented position statements and discussion papers at most SPRFMO meetings. During the Jan 2019 7th SPRFMO Commission Meeting, CALAMA-SUR requested SPRFMO to work on an independent stock assessment, ensure there is enough data from the different operating fleets, implement monthly reports for catch and effort similar to the existing ones for jack mackerel and implement a VMS system that enables SPRFMO staff to monitor the operation of distant waters fleets (CALAMASUR 2019a).
The numbers in each bubble represent the quantity of related key words associated to each concept. The tree only shows a selection of keywords per improvement area. The 121 keywords extracted from CALAMASUR papers are available at the plots in Fig. 3. and Xu 2021), the new model -built upon a recent review of cephalopods stock assessments that recommended the use of depletion models running at rapid time steps  (Arkhipkin et al. , 2021) , was successfully tested by the Ecuadorian Institute for Aquaculture and Fisheries Research (IPIAP), whose national delegation presented a paper at the same SC using national data  (Roa-Ureta et al. , 2021). The 2021 SC officially recommended for the first time (see SPRFMO 2017; SPRFMO 2019b; SPRFMO 2020c for previous discussions), the collection of a joint dataset in 2021 in order to inform the development of the stock assessment based on the model proposed  (SPRFMO 2021d).
Presence of keywords in RFMO documents The evolution of 121 keywords belonging to five major issues across 508 SPRFMO documents that contained mentions of the word squid and its variants is shown in Fig. 3. Note that the data from the last year (  2022 ) is incomplete due to the timing of this review (April 2022). All key words from the five major issues have increased in frequency in SPRFMO documents and most of the general upward trend has happened after 2015 (Fig. 3 ). Moreover, consistent rises in keyword mentions occurred after CALAMASUR documents were presented in late 2019 and early 2020, both with respect to the 2006-2020 mean and the more recent 2015-2020 mean number of mentions (Fig. 3 ). The largest impacts from CALAMASUR documents presented between 2019 and 2020 happened in enforcement and compliance, followed by science for management and regulations and management, although effort limitation and on-board observers have also been impacted substantially.
Bringing co-management at the RFMO level Co-management literature has clearly showed the benefits of participation of resource users in fisheries decision making, even in the absence of data rich science  (Roa-Ureta et al. , 2020). The FAO Small-Scale Fisheries Guidelines (FAO 2015) demands ensuring active, free, effective, meaningful and informed participation of small-scale fishing communities in decision-making processes related to fishery resources and areas where they operate. Yet, authors have commonly circumscribed co-management to management actions happening at the local and even community level (see e. g. , the classic works of  Berkes et al. , 2001; Pomeroy and Rivera-Guieb 2006) , without fully considering the need for cross-scale linkages of community-based initiatives with higher levels of governance (see  Cudney-Bueno and Basurto 2009).
Damage thresholds were calculated by using maximum likelihood to fit relationships between PLRC or PLCF (y) as functions of water stress (x = RWC d ). We pooled all leaves for each species, and, since the shape of these relationships can vary across species  (Trueba et al. , 2019) , fitted each species with linear y ¼ a þ bx ð Þ , exponential y ¼ ae Àbx À Á , and sigmoidal y ¼ a= 1 þ e À xÀc ð Þ=b ð Þ À Á À Á functions using the LIKELIHOOD package in R (v. 4. 1. 0; Murphy, 2015; Table  S2 ; Figs S1, S2). We selected the best-fit model for each species, as either the model with the lowest AICc value (Akaike Information Criterion corrected for small sample sizes), if that value was ≥ 2 units below the other models, or the most parsimonious model with an AICc value within 2 units of the lowest AICc  (Burnham & Anderson, 2010).
β s represents the effect of dry season intensity on growth in the following wet season for each species s. A more negative β s indicates a species' growth rate is more strongly reduced after an intense dry season, and thus, less resilient to drought. We tested whether larger safety margins were associated with a less negative β s. The model was fitted with an adaptive form of the Hamiltonian Monte Carlo sampling  (Carpenter et al. , 2017)  using the RSTAN package (Stan Development Team, 2018) and weakly informative priors (Methods S1).
04-0. 1, P > 0. 05, n = 8). Table  6  r 2 values for the correlations between the percent recovery in sap flow after, compared with before, the 2018 dry season (Δ sapflow ), dry season midday leaf water potentials (Ψ MD ), and the safety margins between Ψ MD and the thresholds for persistent damage and hydraulic damage during dehydration (e. g. Ψ MD -Ψ@PLRC 35 ). Table  S1  Dataset used to calculate PLRC, PLCF, and the thresholds for persistent damage to rehydration capacity and chlorophyll fluorescence. Table  S2  Best-fit models relating the relative water content of the dehydrated leaves (RWC d ) to PLRC and PLCF. Table  S3  Trait dataset for the eight focal species. Table  S4  Uncertainty estimates for the RWC thresholds for persistent damage. Table  S5  Safety margins for incipient (12%) embolism for the trees measured for sapflow resilience to drought.
Acknowledgements This work has benefited from support of a grant from  Investissement d'Avenir grants  of the  ANR  ( CEBA : ANR-10-LABX-25-01 ). MKB was also supported by the  UC Davis Viticulture and Enology Department and College of Agriculture and Natural Resources. We thank  Valentine Alt ,  Jocelyn Cazal , and  Ariane Mirabel  for their assistance with tree climbing and sampling. We would like to thank  Benoit Burban  for the setting up of the sapflow sensors and his technical assistance. Part of this work was carried out at the  Jet Propulsion Laboratory, California Institute of Technology , under a contract with the  National Aeronautics and Space Administration (NASA).
| E. multilocularis presence data Presence data for Em were compiled from georeferenced records from across Europe. Of these, 212 were downloaded from the freely accessible EmsB Website for Echinococcus Typing-EWET Project (https://ewet-db. univ-fcomte. fr/) developed by  Knapp et al. (2017) , a database of the microsatellite profiles of E. multilocularis covering 12 European countries. In addition, an exhaustive literature search performed on 6 February 2020 in the SCOPUS and Google Scholar databases provided the remainder of the occurrence records. The search was performed using the keywords "Echinococcus multilocularis" AND "Europe", resulting in a set of publications from which we selected those that: (i) reported the presence of the parasite in the most common definitive host, V. vulpes, and; (ii) indicated the precise coordinates, or at least the municipality where infected foxes were collected.
If only municipality was available, we used Google Maps to calculate the coordinates of the centre of the municipality for a particular record. Since the red fox is the most highly cited definitive host for Em  (Romig et al. , 2017) , and studies of intermediate and other hosts are scarce, to guarantee the coherence of the dataset, we excluded studies involving hosts other than red fox (e. g. humans, companion animals, intermediate hosts or rare definitive hosts). To remove spatial sampling bias from the occurrence records, which could have resulted in an over-representation of the associated environmental parameters and, consequently, a biased prediction of Em distribution, the area of Europe between 24° W to 44° E longitude and 30° N to 80° N latitude was divided into 57,120 raster cells (0.
g. mean annual temperature, annual precipitation), seasonality (e. g. annual range in temperature and precipitation) and extreme or limiting environmental factors (e. g. temperature of the coldest and warmest month, precipitation of the wet and dry quarters). We downloaded current climatic indices (computed over the period  from the WorldClim 2 dataset  (Fick & Hijmans, 2017). The bioclimatic data for the 2041-2060 period were based on three Representative Concentration Pathways (RCPs;  Moss et al. , 2008; Weynat et al. , 2009) , or climate scenarios: RCP2. 6 (optimistic scenario), RCP4. 5 (moderate scenario) and RCP8. 5 (pessimistic scenario). To represent the components of uncertainty in future projections, we used three General Circulation Models retrieved from the WorldClim Coupled Model Intercomparison Project-Phase 5 dataset  (Taylor et al.