dataesr/scientific-paragraphs-categorization huggingface dataset:
Six  for extracting the 2012-2013 winter accumulation in the Mont-Blanc area. For Mera Glacier , field work was also supported by the  French National Research Agency (ANR)  through  ANR-PAPRIKA  and  ANR-PRESHINE  and has been supported by a grant from  LabexOSUG@2020  (Investissements d'avenir - ANR10 LABX56 ). LTHE and LGGE are part of LabExO-SUG@2020. This study was carried out within the framework of the Ev-K2- CNR  project in collaboration with the  Nepal Academy of Science and Technology  as foreseen by the  Memorandum of Understanding between Nepal and Italy , with contributions from the  Italian National Research Council , the  Italian Ministry of Education, University and Research  and the  Italian Ministry of Foreign Affairs. This publication is contribution number  50  of the  Nordic Centre of Excellence SVALI, "Stability and Variations of Arctic Land Ice ", funded by the  Nordic top-level initiative (TRI).
In this study, we present evidence for ocean warming, a rapid shift in distribution and the hybridization of these two closely related coastal marine fish species in the northern Benguela. This work was initiated after our observations of a rapid decline in catch rate and average size of A. coronus, with no apparent declines in the other dominant fish species, in a tourist-based recreational fishery in southern Angola. To investigate these trends, we analysed changes in coastal sea surface temperature off southwestern Africa (and specifically the ABFZ region) using satellite data since 1982. We examined the size frequency and catch and effort data, and temperature sensitivity derived from these data, for the three dominant species in the southern Angolan recreational fishery from 2005 to 2010 to uncouple the effects of exploitation from distributional shifts.
Sea surface temperature (SST) There are limited in situ oceanographic data for the coastal zone of the ABFZ. Remote sensing  (Meeuwis & Lutjeharms, 1990; Cole, 1999; Cole & Villacastin, 2000; Veitch et al. , 2006)  has, however, provided a source of environmental data, despite being primarily focussed on the offshore zone. The advanced high resolution radiometer (AVHRR) has been dominant platform used in the region, providing data for over three decades. In the present work, we used the night time SST estimated each day by the Pathfinder v5. 2 reanalysis dataset with a spatial resolution of 4 km 2 between 1982 and 2009. A quality flag of 4, considered the lowest quality level for acceptable data  (Kilpatrick et al. , 2001) , was imposed. Recent studies  (Valente & Silva, 2009; Lee et al. , 2010; Blythe & Silva, 2011)  have identified the MODIS sensor on board both NASA's Aqua and Terra platforms as more suitable for the estimation of environmental parameters in the coastal zone.
Validation of such estimates with in situ measurements is considered critical, particularly in areas where the spatial variability of SST gradients is high, such as in upwelling zones  (Dufois et al. , 2012). We obtained SST estimates from thermal infrared spectrophotometer data from the MODIS Terra satellite that passes over the region daily (at approximately 10:30 am). The MODIS Terra data, available from 2000 to 2010, have been processed using SeaDAS (http://seadas. gsfc. nasa. gov) at a resolution of 2 km  (Dufois et al. , 2012). Through a comparison (exact match up days) between satellite-derived and in situ daily SST measurements between May 2005 and December 2010 off Flamingo Lodge (S15 34. 239, E23 01. 128), a standard correction factor for the MODIS SST data was calculated for the region.
Catch per unit effort analysis Recreational fishery catch rate (CPUE = no. of fish. angler À1 h À1 ), calculated as the total number of fish captured per sampling event divided by the effort expended, was calculated for the three fish species as all are caught using the same fishing gear in what can be considered to be a mixed-species fishery. It is therefore hypothesised that if there is a decrease in relative abundance, CPUE, of a species, for example A. coronus, compared to two other species, then this decrease is most probably independent of fishing effort. CPUE data were disaggregated by life history stage for A. coronus and L. amia. As few juveniles were captured, P. saltatrix CPUE included both juveniles and adults. Species-specific cumulative frequencies of positive (>0) catches as a function of SST were constructed.
This morphological method was validated using a molecular (allozyme) electrophoresis technique  (Van Der Bank & Kirchner, 1997 ) that genetically distinguishes individuals of the two species. As no permit was available to sacrifice fish in Namibia during period 2, a molecular Polymerase Chain Reaction-based Restriction Fragment Length Polymorphism (PCR-RFLP) DNA approach (which can be applied to nonlethal fin clips taken from catch & release fish) was used to identify to species the sample data collected instead of the destructive otolith morphology approach. Extraction of total genomic DNA was conducted using a standard phenol: chloroform protocol  (Sambrook et al. , 1989)  and PCR amplification of a 700 base pair (bp) region of the mitochondrial cytochrome oxidase I (COI) gene was obtained with the universal primer pair FishF1 and FishR1  (Ward et al.
To check for spatial genetic homogeneity within the species (for standardized frequencies for hybridization tests) pairwise genetic differentiation between sampling sites was estimated for both mtDNA and microsatellite datasets, with statistical significance assessed after 10 000 permutations, in ARLE-QUIN  (Excoffier et al. , 2005). Microsatellites may under some circumstances have less power to detect hybrids than allozymes (due to higher allele numbers and much higher potential homoplasy in the former), so allelic frequencies were estimated for each locus/species and a preliminary simulation study conducted to investigate the suitability of the microsatellite dataset to detect hybridization events. Five hybrid states were modeled using HybridLab  (Nielsen et al. , 2006) : pure species, F1, F2, backcross 9 pure A.
coronus (b1), and backcross 9 pure A. inodorus (b2). For each state 60 hybrids were simulated, using as a starting dataset 30 genotypes confirmed as pure species from each putative parental Argyrosomus species  (Henriques, 2012). Confirmed pure species genotypes and simulated hybrid genotypes were run in STRUCTURE  (Pritchard et al. , 2000)  to test the accuracy of the software in detecting different levels of hybridization. Five independent iterations were run for two groups (K = 2) under the admixture model, with independent allele frequencies, for 50 000 MCMC iterations after an initial burn-in period of equal length. Identification of putative hybrids was based on the posterior probability of assignment (q) of each individual analysed to one or other parental species. A threshold of q = 0.
1 was chosen to separate parental (pure species) individuals and F1s or hybrids resulting from backcrosses  (V€ ah€ a & Primmer, 2006). In all analyses thresholds were set to q ≥ 0. 9 for pure A. coronus and q ≤ 0. 1 for A. inodorus, while individuals with 0. 1 < q < 0. 9 were considered hybrids. The Bayesian approach implemented in NewHybrids  (Anderson & Thompson, 2002)  was used to corroborate the results obtained with STRUCTURE, with the threshold of posterior probability set to qi = 0. 5  (Aboim et al. , 2010). Analyses were conducted using the Jeffreys prior for mixing and allelic frequencies, and run for 50 000 MCMC iterations. As all analyses conducted using the simulated genotype dataset revealed that both STRUCTURE and NewHybrids could accurately detect F1, F2, b1 and b2 hybrids, assessment of hybridization events and determination of hybrid status were performed on the test samples of 180 A.
coronus and A. inodorus, with population genetic divergence estimated at F ST = 0. 99 (P < 0. 001) for mtDNA and F ST = 0. 16 (P < 0. 001) for microsatellites. The assessment of microsatellites identified pronounced allele frequency differences between the species, and a number of alleles private to both A. coronus and A. inodorus in all six loci. When tested with the simulated hybrid dataset, the STRUCTURE analysis accurately detected all F1 and F2 hybrids, but lost precision in the detection of backcrosses in 50% of cases. The number of incorrect assignments was reduced when the Bayesian approach implemented in NewHybrids was used, with only 13% of the backcrosses to A. coronus and 5% to A. inodorus not identified. This suggested that the microsatellite dataset was powerful enough for hybridization inference.
Analysis of the test (sampled) dataset in STRUCTURE (corroborated the results of NewHybrids), combined with morphological evidence and mtDNA haplotypes, identified admixed species origins for five of 180 A. coronus (plus one further identified by NewHybrids alone) and two of 40 A. inodorus individuals (Fig. 4  and Table  2 ). The two A. inodorus 'hybrid' individuals displayed A. inodorus phenotype and mtDNA haplotype but were assigned  as A. coronus on nuclear genotype, whereas the six A. coronus 'hybrids' all displayed A. coronus type mtDNA and were identified as backcrosses with A. coronus according to their nuclear genotypes (Table  2 ).
Discussion The short-term MODIS Terra dataset indicated extremely rapid recent warming over the study area. Although such results might be interpreted as a cyclical decadal signal, which has been reported for the northern Benguela  (Hutchings et al. , 2009) , the similar warming trend (0. 60 °C/decade) identified in the mediumterm (three decade) analysis (Fig. 2a ) and in the offshore zone  (Monteiro et al. , 2008; Hutchings et al. , 2009)  was far greater than the global mean (1960-2009) of 0. 07 °C/decade  (Burrows et al. , 2011) , and higher than other ocean warming 'hotspots' such as the Antipodean region that has been warming at a rate of 0. 2 °C per decade since 1944  (Ridgway, 2007). Our findings suggest that the coastal waters of the ABFZ is a key study area, both from an oceanographic perspective to understand its role in the regional ocean environment, and from a biological perspective where the response of animals such as fishes may provide an indication of changes that are likely to occur globally in areas that are warming at a slower rate.
Acknowledgements We thank  S. Kruger  and all who participated in the genetic sample collection supporting this study. We thank  Flamingo Lodge ,  southern Angola , and its staff for accommodating and assisting us during this study. We thank  Timothy Richardson ,  Bruce Ellender ,  Alexander Winkler ,  Bernard Swart ,  Hilda Swart  and  Roy Bealey  for the CPUE data collection. This work was supported by the  National Research Foundation's South African Biosystems Initiative  under grant number  74457  and by the  South Africa/Angola -Research Partnership Programme Bilateral Agreement 2011  under grant number  81711  and by a  Fundac ßão da Ciência e Tecnologia (FCT)  grant (ref. SFRH/BD/36176/ 2007 ). Russell Chalmers provided assistance with the figures.
Trabectedin: Phase III studies Based on the strong rationale sustaining the association trabectedin/PLD and the favorable results from preclinical and Phase I studies, this combination was chosen for the direct comparison with PLD in the Phase III trial OVA-301 (NCT00113607). This study, planned in 2005, aimed at comparing trabectedin 1. 1 mg/m 2 /PLD 30 mg/m 2 every 21 days versus PLD 50 mg/m 2 every 28 days in ovarian, peritoneal, and tubal cancer recurring/progressing after firstline chemotherapy,  61  with the exclusion of refractory cases; patients were stratified according to the Eastern Cooperative Oncology Group Performance Status (0-1 versus 2) and platinum sensitivity (PFI ,6 months versus PFI $6 months). Originally, the primary endpoint was OS, but it was later amended to PFS at the end of 2006.
On the other hand, it was shown that median OS from the administration of subsequent platinum-based chemotherapy was longer in partially platinum-sensitive patients allocated to the trabectedin/PLD arm compared to those allocated to the PLD arm (median OS 13. 3 months versus 9. 8 months, respectively, HR: 0. 63, P=0. 0357), suggesting that the enhanced OS benefit with trabectedin/PLD compared to single agent PLD might be related to the prolongation of PFI. 64 This hypothesis has fuelled the setup of Phase III randomized studies aiming at clarifying whether the artificial prolongation of PFI with a nonplatinum drug may improve the effectiveness of the overall treatment in patients with a PFI of 6-12 months after completion of primary chemotherapy. In particular, the MITO-8 study (NCT00657878) randomizes patients to the combination carboplatin/paclitaxel versus PLD or topotecan or gemcitabine) and implies a crossover for both arms at disease progression.
On the other hand, the Inovatyon (International Ovarian Cancer Patients Trial With Yondelis) study (NCT01379989) investigates the superiority of trabectedin/PLD versus carboplatin/PLD in partially platinum-sensitive disease. As far as toxicity issues are concerned, Grade 3/4 anemia, neutropenia, and thrombocytopenia were documented in 14%, 63%, and 18% of trabectedin/PLD cases, and were significantly more frequent compared to PLD alone. Among nonhematological toxicities, Grade 3/4 elevation of sGOT and sGPT was reported in 38% of cases, but it was described as of short duration, and of decreased magnitude with subsequent cycles. On the other hand, hand and foot syndrome was documented in only 4% of cases in the combination arm compared to 20% in the PLD alone arm. In spite of the increased hematological toxicity in the trabectedin/PLD group, there was no deterioration of QoL/patient-reported outcome, as well as in QLQ-C30, OV28, and EQ-5D questionnaires.
65 Moreover, a very recent cost-effectiveness analysis based on the final survival data of the OVA-301 study confirmed a significant improvement of OS, and an increased cost-effectiveness ratio per quality-adjusted lifeyear compared to the original evaluation. 66 Based on these results, trabectedin/PLD combination can be considered as the most effective nonplatinum-based combination in partially platinum-sensitive disease; this combination can be exploited not only to artificially prolong PFI with the aim to increase sensitivity to subsequent platinum treatment, but also to provide patients with an equivalent therapeutic alternative to platinum agents in case of residual neurotoxicity, history of platinum hypersensitivity, or repeated treatments with platinum regimens. While awaiting for the identification of biomarkers predictive of trabectedin sensitivity, 67 other specific ovarian cancer clinical settings more likely to benefit from trabectedin or trabectedin combinations are actively investigated; given the strong rationale sustaining the role of BRCA 1/2 mutation or BRCAness in conditioning responsiveness to trabectedin, the MITO-15 (Multicenter Italian Trials in Ovarian Cancer and Gynecology) study (NCT01772979) has been conducted to investigate the efficacy of single agent trabectedin in relapsed ovarian cancer with BRCA mutation or exhibiting the BRCAness phenotype.
The trial has recently closed patient accrual, and analysis of data is ongoing. Finally, considering the recent introduction of bevacizumab in the first-line treatment, and the upcoming approval in the salvage setting, there is increasing interest in exploiting the combination of trabectedin with the antiangiogenetic drug. In this context, a Phase II study (NCT01735071) has been recently launched aimed at assessing the efficacy and safety of the combination trabectedin and bevacizumab with or without carboplatin in partially platinum-sensitive recurrent ovarian cancer patients.
Quantification The numbers of APP C NORs, the nodal length was counted from more than 3 different sections each mouse. More than 3 mice were analyzed each group. The length of node in the IF and EM analysis was counted using Image J software. The diameters of axons and fibers in more than 10 pictures taken under 6000£ magnification from each mouse were counted using Image J software. At least 3 mice were analyzed in each group. The g ratios were calculated as axonal diameter/fiber diameter.
Acknowledgments This work was supported by grants from  The Talent Program of Yunnan Province, China , and The  Professorial Fellowship of Monash University, Australia , to ZC Xiao from the  National Basic Research Program of China  ( 973 program ) (2013CB945602), A Project Funded by the  Priority Academic Program Development of Jiangsu Higher Education Institutions, Suzhou Science and Technology Development Program  ( SZS201205 ), and the  National Natural Science Foundation of China  ( 31171313  and  81271424 ), to QH Ma from MERLION, a  Singapore-France joint scientific program , to both ZC Xiao and  D Bagnard ; and from the  National Medical Research Council of Singapore  ( NMRC/1059/2006 ) to both GS Dawe and ZC Xiao. We are grateful to  Prof Dennis Selkoe  ( Harvard University ) for generously providing APP antibodies and to  Dr Hasan Mohajeri  ( University of Zurich ) for preparing the samples of APP transgenic mice.
Microarray analysis Cells used for microarray analysis were grown in bactopeptone medium at 30uC and 250 rpm. Samples were collected 2 hours after entry into stationary phase (t2). Entry into stationary phase (t0) was determined as the breakpoint of the growth curve, i. e. the time point when the slope of the growth curve starts to decrease, which usually occurs in the 407 strain around OD 2. 5 in these culture conditions. RNA isolation and cDNA synthesis, labeling and purification were performed as described previously  [6]. Microarray slides were printed at the microarray core facility of the Norwegian University of Science and Technology (NTNU). Design, printing, prehybridization, hybridization and scanning of the slides and analysis of the data was as previously described  [6]. The microarray experiments were based on four slides, all being true biological replicates.
Hemolysis assays The various strains were grown in LB medium at 37uC until they reached an OD 600 of 1. The hemolytic activity of the strains was assayed by loading a 5 ml drop of each culture on sheep blood agar plates. The agar plates were incubated overnight at 30uC and then scanned: the area of hemolysis and the colony size were determined from the scans with ImageJ software  [41]. To minimize differences due to variations in growth rates, a hemolytic index was calculated using the following formula: Table  1. Primers used in this study.
Influence of soil DNA extraction procedure on bacterial richness and diversity Bacterial rRNA gene sequences were successfully amplified by PCR and sequenced from all soils using each of the three DNA extraction procedures (Table  2 ). After bioinformatic filters, 2322 high-quality reads per sample were kept, analyzed and taxonomically identified using a curated database derived from SILVA  (Quast et al. , 2013)  (Table  3 ). Rarefaction curves of bacterial richness demonstrated that our sequencing depth allowed accurate description of the bacterial community diversity in each soil sample studied (Supporting Information Fig. S1 ). No significant differences were found between the three DNA extraction methods for the number of bacterial genera detected, the number of bacterial OTUs or for the Shannon and Evenness indices in any of the soils (Table  2 ).
Bioinformatic analysis of 16S and 18S rRNA gene sequences Bioinformatic analyses were done using the GnS-PIPE initially developed by the Genosol platform (INRA, Dijon, France)  (Terrat et al. , 2012)  and recently optimized. The parameters chosen for each bioinformatic step can be found in Table  3. First, all the 16S and 18S raw reads were sorted according to the multiplex identifier sequences. The raw reads were then filtered and deleted based on (i) their length, (ii) their number of ambiguities (Ns) and (iii) their primer(s) sequence(s). A PERL program was then applied for rigorous dereplication (i. e. clustering of strictly identical sequences). The dereplicated reads were then aligned using INFERNAL alignment  (Cole et al. , 2009) , and clustered into OTU using a PERL program that groups rare reads to abundant ones, and does not count differences in homopolymer lengths.
A filtering step was then carried out to check all single singletons (reads detected only once and not clustered, which might be artefacts, such as PCR chimeras) based on the quality of their taxonomic assignments. Finally, in order to compare the data sets efficiently and avoid biased community comparisons, the reads retained were homogenized by random selection closed to the lowest dataset. The retained high-quality reads were used for (i) taxonomyindependent analyses, determining several diversity and richness indices using the defined OTU composition at the genus level and (ii) taxonomy-based analysis using similarity approaches against dedicated reference databases from SILVA  (Quast et al. , 2013)  (see Table  3 ). The raw data sets are available on the European Bioinformatics Institute database system under project accession number PRJEB4825.
Statistical analyses The effects of the DNA extraction procedure on bacterial and fungal diversities were tested by analysis of variance (multiple paired comparisons). The effects of the DNA extraction procedure on bacterial and fungal community compositions were assessed by Kruskal-Wallis tests. All statistical analyses were performed under XLSTAT software (Addinsoft ® ). The bacterial and fungal communities from all samples were also compared by using UNIFRAC  (Lozupone and Knight, 2005) , based on the 16S and 18S phylogenetic trees computed with FASTTREE  (Price et al. , 2010).
Acknowledgements Thanks to the  National Research Infrastructure 'Agroécosystèmes ,  Cycles Biogéochimique et Biodiversité  (SOERE-ACBB http://www. soere-acbb. com/fr/)for providing support during the sampling campaign and making available the physico-chemical soil properties data. The funders [ National Agency for Research (through 'Investments for the Future' program ),  Regional Council of Burgundy and European Commission ) had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Funding Information This work involving technical facilities at the  GenoSol platform of the infrastructure ANAEE-France  received a grant from the  French  state through the  National Agency for Research under the program  ' Investments for the Future'  (reference  ANR-11-INBS-0001 ), as well as grants from the  Regional Council of Burgundy. This work was also supported by the  European Commission  within  EcoFINDERS  project ( FP7-264465 ). bs_bs_banner.
The error bars for each correlation are measured from the scatter of simulated lens reconstructions correlated with each catalogue map, and are in generally good agreement (at the 20% level) with analytical expectations. These catalogues are discussed in more detail below. 1. NVSS Quasars: The NRAO VLA Sky Survey (NVSS;  Condon et al. 1998 ) is a catalogue of approximately two million sources north of δ = -40 • which is 50% complete at 2. 5 mJy. Most of the bright sources are AGN-powered radio galaxies and quasars. We process this catalogue following  Smith et al. (2007) , pixelizing the catalogue at HEALPix N side = 256 and projecting out the azimuthally-symmetric modes of the galaxy distribution in ecliptic coordinates to avoid systematic striping effects in the NVSS dataset. We model the expected cross-correlation for this catalogue using a constant b(z) = 1.