dataesr/scientific-paragraphs-categorization huggingface dataset:
Historical and spatial distribution of Laminaria rodriguezii Data on the historical and current distribution of L. rodriguezii in the Adriatic were obtained from published and unpublished records. Unpublished data included specimens Page 3 of 12 69 of L. rodriguezii housed in the main European and all Croatian herbaria, data collected during biological field surveys coordinated by the Institute of Oceanography and Fisheries in Split (IOF), and data obtained from fishermen since 2011. ROV surveys were conducted by IOF in May 2010 on eight transects in the areas with historical records of L. rodriguezii (Fig. 1b, c ). ROVs were equipped with robot arms, enabling in situ collections of specimens. To evaluate the extinction risk of L. rodriguezii in the Adriatic Sea as one of the subregions of the Mediterranean Sea, we used the IUCN Red List criteria and guidelines for regional level  (IUCN 2012).
Polymerase chain reactions (PCR) were performed using specific primers for nuclear ribosomal DNA (SSU, ITS), the plastid-encoded rbcL and Rubisco spacer, and the mitochondrion-encoded genes cox1, cox3, and nad6. Primers and PCR conditions used are provided in the appendix. The new sequences were compared with published sequences using BLAST  (Altschul et al. 1997) ; ITS, Rubisco spacer and 5′-COI sequences were manually aligned in Se-Al™ v2. 0a11 (Sequencing Alignment Editor Version 2. 0 alpha 11; http://tree. bio. ed. ac. uk/software/seal/) with published sequences. Neighbour-joining distance analyses using Kimura-2-parameter distances, maximum parsimony and maximum likelihood analyses were performed in PAUP  (Swofford 2002).
2012 ). In the sensitive, variable markers ITS and Rubisco spacer, L. rodriguezii showed most similarity with a cluster formed by L. ochroleuca, L. pallida and L. abyssalis (henceforth OPA clade), followed by L. digitata (Hudson) Lamouroux and L. hyperborea (Gunnerus) Foslie (Table  S3 ). In the mitochondrial marker (5′-COI), genetic distances within the OPA cluster were ≤ 1. 6 %, and L. rodriguezii was as divergent from the OPA clade (3. 3-4. 4 %) as from L. digitata (0. 44 %) and L. hyperborea (0. 39 %). Analyses of the combined dataset of ITS, Rubisco spacer and COI consistently placed L. rodriguezii in a highly supported clade together with the OPA clade (Fig. 2 ). In the more conservative rbcL and SSU, many species from the Laminariales showed highly similar sequences but phylogenetic analyses were not performed because sequences of the OPA clade were unavailable.
Two species of Saccharina served as outgroup  (Lane et al. 2006). Parsimony and maximum likelihood analyses of the same dataset, as well as analyses of data of the single markers, gave similar results, in most cases placing L. rodriguezii in a highly supported clade together with L. ochroleuca, L. pallida and L. abyssalis. Numbers at nodes indicate bootstrap support from 1000 resamplings for distance, parsimony and likelihood analyses, respectively. Accessions of sequences are provided in Table  4  bottom currents with E-SSE directions (Fig. S6 ) could not transport fragments from Palagruža Island to locations where L. rodiguezi was collected during MEDITS campaigns (Fig. 1b ; 10-30 km in N-NE direction). Anyway, depths reported by earlier studies based on bottom trawling surveys must be considered with a certain caution.
Without direct observation by ROV, exact data on light intensity on the bottom and ideally supporting, ecophysiological experiments, we cannot be sure that L. rodriguezii can develop at such extreme depth. The lower depth limits for kelp is assumed to be at 1 % of surface irradiance  (Lüning and Dring 1979) ; however, this may not apply for L. rodriguezii. Secchi values measured in the last 15 years were around 20 m, with a maximum of 30 m. Such surface values of transparency only might be indicative and indeed reveal no information about the light intensity reaching the bottom. Giaccone  (Giaccone 1967 ) noted how Secchi disks were visible up to 35 m near the island of Ustica (Italy) where L. rodriguezii populations occurred between 45 and 85 m depth. At 85 m, the seabed at Ustica was too steep and formed an environment with low luminosity that did not allow life of photosynthetic organisms.
Acknowledgments Thanks are due to Klaus Lüning for a gametophyte culture of L. abyssalis, and to Britta Schaffelke for a herbarium specimen of L. rodriguezii from the western Mediterranean. We are grateful to the Total Foundation (Paris) for funding this study within the framework of the project "Brown algal ecology and biodiversity in the eastern Mediterranean Sea", and to the MASTS pooling initiative (Marine Alliance for Science and Technology for Scotland, funded by the Scottish Funding Council and contributing institutions; grant reference HR09011), as well as Croatian Ministry of Science, Education and Sports for supporting project "Benthic communities in the Adriatic Sea (Project ID: 0001005)".
Locality and Sampling This study covers the eastern part of the Fram Strait, where Atlantic water (AW) is transported northward by the West Spitsbergen Current (WSC). Data were collected during five cruises in 2014: January (06. 01-15. 01), March (05. 03-10. 03), May (15. 05-02. 06), August (07. Transects were made across the core of AW inflow at 79 and 79. 4 • N during May, August and November. Further north (80. 5 to 82. 6 • N) we investigated the WSC southern branch into the Arctic Ocean in January, March and August (Figure  1 ). The choice of sampling area and stations was largely determined by the extension of the sea ice (Figure  3 ). Vertical profiles of temperature, salinity and fluorescence were recorded on each sampling occasion using a SBE 911plus system. Water masses were defined based on the criteria presented in Table  1.
The incubation experiments ran for 5 to 10 days but we show data only from the initial 5 days of incubation in order to better represent dynamics of the initial communities. Incubation water was sampled daily for enumeration of microorganisms and every second day for nutrients. Prior to setup, all bottles, carboys and silicon tubs were acid washed and then rinsed with Milli-Q R water. During the summer cruises (May and August) the experimental bottles were incubated on deck in plexiglass tanks with seawater flow-through (continuously pumped from 7 m depth), keeping the temperature close to in situ (May: 1. 7 ± 1. 6 • C and August: 1 ± 0. 8 • C). A nylon net was wrapped around each bottle to reduce the PAR to about 30% of the surface irradiation. In the winter months (January, March, November), incubations were kept in a cooling room at a constant temperature of 2 • C and in darkness, except in March were an in situ light cycle was set (16 h darkness and 8 h at 5 µmol photons m -2 s -1 ).
DNA Extraction, PCR Cloning and Phylogenetic Analysis Environmental samples for molecular analysis were collected by filtering water onto 0. 22 µm pore size Millipore R Sterivex filters. The filters were immediately flash frozen in liquid nitrogen and stored at -80 The 229 MicroPolar sequences include 174 unique fulllength sequences. Together with 721 petB sequences from a non-redundant reference database (representing most of the genetic diversity so far identified within Prochlorococcus and Synechococcus genera;  Farrant et al. , 2016) , the MicroPolar sequences were used to define operational taxonomical units (OTUs) at 97% identity using Mothur v1. 34. 4 (Table  S2 ). Since all MicroPolar sequences clustered with clades I and IV reference sequences, a subset of the petB database, comprising only the 117 reference sequences of these clades, as well as the 174 unique MicroPolar petB sequences was used for a subsequent analysis.
Phylogenetic reconstructions were based on multiple alignments of petB nucleotide sequences generated using MAFFT v7. 164b with default parameters  (Katoh and Standley, 2014). A maximum likelihood tree was inferred using PHYML v3. 0,  (Guindon and Gascuel, 2003)  with the HKY + G substitution model, as determined using jModeltest v2. 1. 4 (Darriba et al. , 2012)  and estimation of the gamma distribution parameter of the substitution rates among sites and of the proportion of invariable sites. The tree was drawn using iTOL  (Letunic and Bork, 2007). The 229 sequences retrieved from MicroPolar were recruited using BLASTN (v2. 2. 28+) against the full petB database: reads with more than 90% of their sequence aligned and with more than 80% sequence identity to their BLASTN best-hit were taxonomically assigned to their best-hit and subsequently used to build per-sequence read counts tables.
Synechococcus Diversity The gene petB, which has proved to display a high taxonomic resolution for picocyanobacteria  (Mazard et al. , 2012) , was used as phylogenetic marker for Synechococcus genetic diversity. Only petB sequences related to clade I and IV were retrieved from our dataset (MicroPolar). Based on a petB reference database (including 117 sequences from clade I and IV, described in  Farrant et al. , 2016) , enriched with the 174 unique petB sequences retrieved from MicroPolar samples, 41 OTUs were defined at 97% ID within clade I and IV (Figure  7 ). The petB sequences obtained in the present study correspond more specifically to sub-clades Ib and IVb, with a clear dominance of subclade Ib. Although none of these 41 OTUs form a new subclade, 17 OTUs were composed of only MicroPolar sequences and were not represented in the previous reference database (colored branches, Figure  7 ).
In order to assess whether the genetic populations sampled in MicroPolar cruises could be related to other cold-water populations, we also recruited Illumina reads from 62 surface water metagenomes collected during the Tara Oceans cross-ocean ecosystem study using the same petB database  (Karsenti et al. , 2011; Farrant et al. , 2016)  (https://doi. pangaea. de/10. 1594/PANGAEA. 840718, note that the Tara Oceans samples analyzed here do not include recent Arctic samples from the latest Tara Ocean cruise as they are not yet published). These data showed that the two most abundant MicroPolar OTUs in subclade Ib (Arctic732-2b_1b_1A and Arctic732-35b_1b_1A) had a low relative abundance in Tara Oceans stations. Other OTUs identified in MicroPolar samples were also poorly represented in the Tara Oceans dataset, with the notable exception of two subclade Ib OTUs, "MP_may_P1_1m_E08_Ib_I" and "MP_may_P1_1m_D10_Ib_IA" (formed only of MicroPolar sequences), that were dominant in Tara Oceans coldest stations (<14 • C), and of the subclade IVb OTU "Ellet21_IVb_IVC" present in the Tara Oceans dataset at all temperatures and especially at cold (<14 • C) and intermediate (18-22 • C) temperatures.
Similarly, by combining our observations with data from the Tara Ocean we confirmed the latitudinal shift previously described within the Synechococcus genus between the warm-adapted clades II and III and the coldadapted clades I and IV  (Zwirglmaier et al. , 2008; Mazard et al. , 2012; Farrant et al. , 2016). Interestingly, clade IV was clearly dominating in Atlantic waters from the Tara Oceans dataset and its relative contribution seemed to increase with temperature in August and November in MicroPolar samples, while clade I appeared to dominate in colder Arctic waters. Thus, although this would need to be confirmed by physiological characterization of representative strains, it suggests that clade I could be adapted to colder waters than clade IV. Overall, it seems that temperature is the main driver of Synechococcus abundance and diversity in this area.
Furthermore, sequences obtained from August and November are mainly found in two OTUs within subclade Ib, gathering reference sequences retrieved only at high latitude from the Barents Sea (72 • N) and the North Atlantic Ocean (57 • N), but hardly detected in the Tara Oceans dataset. Altogether, these results point toward the existence of Synechococcus populations endemic to these Arctic or subarctic areas. The peak-values of Synechococcus were clearly associated with the Atlantic inflow (salinity > 34. 9) and abundances decreased exponentially with decreasing temperature and were most often low in ice-associated water. This, along with the tendency of decreasing concentrations with decreasing salinity, is in accordance with the suggestion of Synechococcus being an indicator of saline Atlantic water transported into the Arctic  (Murphy and Haugen, 1985; Gradinger and Lenz, 1995)  as well as the low tolerance to wide salinity ranges of obligate marine Synechococcus  (Waterbury et al.
ACKNOWLEDGMENTS We thank the helpful crew of RV  Helmer Hanssen  and  RV Lance  and to the MicroPolar and CarbonBridge teams for always being helpful during sample collection. A special thank you to  Jean-Éric Tremblay  for providing ammonium measurements and to  Sophie Radeke  for steadfast assistance at the flow cytometer and to  Hilde M. K. Stabell  for making the clone library. We also thank  Daniel Vaulot  for fruitful discussions.
Association with MTX is required by the French and European marketing authorisation for abatacept (ABA). Very few data are available regarding the use of ABA in intravenous monotherapy apart from the very recently published AVERT trial  [10]. In the present study, we analysed data from the Orencia and Rheumatoid Arthritis (ORA) registry to compare ABA monotherapy with an ABA + csDMARD combined strategy, using the retention rate as the principal outcome. This study provides the first evaluation of the efficacy and safety of the ABA monotherapy strategy in ORA patients.
The ORA registry The ORA registry is an ongoing, nationwide, prospective French cohort study that investigates the long-term safety and efficacy of ABA in the treatment of RA. It was established in June 2008 by the French Society of Rheumatology upon the drug's approval for use in France  [11]. The last patient in that study was included in the ORA registry in 2010. The ORA registry received approval from the French authorities and patients were included after written informed consent was obtained. Data at baseline, month 3 (M3) and month 6 (M6) were collected by trained clinical nurses or technicians in each centre.
Statistical analysis Statistical analysis was performed using the STATA/SE software, version 13. 1 (College Station, TX, USA: StataCorp LP). Appropriate testing was performed according to the results of normality tests. Student's t test and the Mann-Whitney test (or Wilcoxon's test for paired values) were used to analyse quantitative data, and the chi-square or Fisher's exact test was used to analyse qualitative data. A p value <0. 05 was considered statistically significant.
Baseline demographics and characteristics of the population Of the 1032 patients included in the ORA registry, 829 (80. 3 %) had been followed for at least 6 months at the time of analysis. Of these 829 patients, 276  (33. 3 %)  received ABA as a monotherapy at M0. A flow chart of the patient exclusion strategy is shown in Fig. 2. Exclusions were primarily due to missing data. The median age and disease duration were 60 (range: 20-89) and 14 (range: 2-51) years, respectively. The patients with fully available data for analysis were 90 % positive for anticitrullinated protein antibodies (for a 70. 9 % in the whole registry)  [12]. ABA was administered as the first biological treatment in 12 % of the patients. One anti-TNF agent was used prior to ABA in 24 % of the patients, two agents in 40 % of the patients, and three agents in approximately 24 % of the patients.
Corticosteroids Corticosteroids were frequently co-administered with ABA in RA in general and in the ORA registry in particular. Increases in corticosteroid dosage could reflect the poor effectiveness of DMARDs, whereas corticosteroid tapering or withdrawal might attest to DMARD efficacy. Data regarding the corticosteroid doses at M0 and M6 were available for 323 patients. The frequency of patients who required an increase in corticosteroid dose was equivalent between the StartMONO and.
A galvanic corrosion reaction, due to the electropotential difference between the metals, is induced when copper is in contact with the more noble gold  [17]. In this bimetallic system copper (which has the lower electrode potential) acts as a sacrificial anode, hence promoting faster copper corrosion. In our experiments, samples modeling this Cu/Au system resided within a portable cell for one week while in situ data were collected. Samples were made with three differing surface area ratios of Cu/Au in order to study the effect of increased Cu/Au contact on corrosion in utero. The corrosion potential (E corr ) was recorded continuously to monitor the electrochemical behavior of one sample.
The hardware is easily adapted for use on different beam lines. The portable cell functions as a three-electrode electrochemical cell and uses custom made working and Ag/AgCl reference electrodes as previously described  [20]. A 1 mm diameter platinum counter electrode stretches along one of the long sides of the cell, adjacent to the working electrodes. The electrode is attached to the outside of the cell through a small Pt connection block and a length of 1 mm diameter wire (part 5, Fig. 1 ). Further design specifications for the portable cell can be found in the Supplementary Information. The corrosion potential (E corr ) is monitored using a modified voltage data logger (Matchtech Volt 101A, USA). The working electrode output and reference electrode are attached to the voltage logger. This device was chosen for its portability and voltage detection range (±3 V).
However, the input impedance of the device had to be buffered to account for the high output impedance of the portable cell. The output impedance of the cell's electrode system was measured using aqueous electrolyte and found to be 375 kΩ. The voltage logger was buffered to 300 MΩ with a purpose built high input impedance amplifier to ensure that it did not shunt the cell. E corr data was collected every 1 s from Sample 1 by the data logger for the duration of the experiment. For shorter measurements and not during transportation, a Palmsens handheld potentiometer (Palmsens BV, The Netherlands) can alternatively be used. This device can conduct a wider range of electrochemical measurements, such as cyclic voltammetry and chronopotentiometry at the working electrodes to collect other electrochemical data  [21].
Monitoring the corrosion of copper in situ Fig. 2  shows the internal temperature of the cell as a function of time. Readings were taken manually whenever there was access to the hutch and the temperature controller. The temperature dropped below 36 °C only during the setting up of the experiment when the cell was initially removed from its insulated transportation box. However once electrolyte pumping was restarted body temperature was reinstated over the course of 2 h and remained within range for the rest of the experiment. Fig. 2  also shows E corr of Sample 1 during the entire experiment. The E corr has been recorded at -0. 2 V for similar experiments with copper in this electrolyte  [25] , which shows the multiple cell setup is not adversely affecting the detection of electrochemical data from individual samples.
From the start of the experiment until day 7, the E corr steadily decreased to approximately -0. 1 V from 0. 1 V showing steady corrosion of the working electrode surface. The increase in E corr after day 7 demonstrates passivation of the electrode surface. Complementary in situ surface analysis (described below) supports this result. The individual XRD patterns recorded across the copper-gold boundary were summed to produce a set of 5 average images for each sample. In this way, the main differences between the three samples with increasing Cu/Au surface area ratios (and therefore increasing amounts of Cu/Au contact) could be observed. Fig. 3  shows the data obtained over the course of the 5-day synchrotron experiment. Sample 1 had the intermediate Cu/Au ratio. Fig. 3  shows that it had started corroding measurably by day 3 of the experiment.
Over the following four days the main products observed were cuprite (Cu 2 O) and copper (I)/(II) sulfides. From day 6, crystalline sodium chloride was also detected, having crystallized out of the SUF electrolyte. Thick, flaky cuprite crusts have been observed previously  [3] [4] [5]  during ex situ analysis. The formation of copper sulfides has been tentatively suggested elsewhere  [26]  but this is the first time they have been observed in situ immersed in SUF. Sulfide salts were not added to the SUF, so it is presumed the source of sulfide ions is albumin which is known to contain disulfide bonds  [27]. The concentration of each species on the surface is unknown but from the E corr data we can infer that passivating cuprite becomes the dominant species during the experiment, after the initial corrosion of the surface.
Acknowledgments The  University of Warwick's Physics Department and Universiteit Gent (BOF  Grant Number  01SF0112 ) are thanked for the PhD scholarship of  RAG. Research Fund -Flanders (FWO)  is also acknowledged. XMaS is a mid-range facility supported by  EPSRC. MedNet GmbH, Germany  is thanked for the barbed adapter parts which were provided free of charge to this project. Davy De Pauw (UGent)  and  Verschuren Hugo  NV manufactured the cell parts. The esaProject software is developed by  EVA Surface Analysis UK. VF acknowledges a  Marie Curie IEF (Pb coatings ).
The 51 Mb SureSelect Human All Exon kit V5 (Agilent technologies) was used for exome capture, and sequencing of WES libraries was carried out on a HiSeq2500 sequencer (Illumina)  [15]. The mean coverage depth was 244. 51× ((98. 22 > 30×; 99. 74 > 15× and 99. 93 > 5×). After de-multiplexing, sequences were aligned to the reference human genome hg19 using the Burrows-Wheeler Aligner. Downstream processing was carried out with the Genome Analysis Toolkit (GATK), SAMtools, and Picard, following documented best practices (https://www. broadinstitute. org/gatk/guide/ bp_step. php). Variant calls were made with the GATK Unified Genotyper. The annotation process was based on the ensembl database (75), dbsnp (135) EVS (ESP6500SI-V2), 1000 genome (2011 05 21) and EXAC (0. 3). Variants were annotated and analysed using the Polyweb software interface designed by the Bioinformatics platform of University Paris Descartes and Imagine Institute  [16].
As shown in Fig. 5e , bacitracin inhibits Dol-P-[ 14 C]Man production even in the absence of NYT indicating Dol-PP production via the presence of endogenous substrates for OST. Dol-P-[ 14 C]Man generation in the presence of bacitracin reveals a pre-existing DolP pool that, in microsomes from the patient, appears to be reduced by ~67 % compared to the control. Finally, it can be seen that microsomes from the patient also demonstrate lower NYT-provoked Dol-P-[ 14 C]Man synthesis. The ensemble of these data demonstrates a deficit in the quantity of DolP available for synthesis of Dol-P-[ 14 C]Man in the patient's cells. In order to evaluate the consequences of the reduced DolP levels in the patient's cells, the glycosylation status of ICAM was examined. Hypoglycosylated ICAM is rapidly degraded and this has been shown to yield low steady state levels of this protein in type I CDG cells  [24].
After filtering out variants occurring at > 1 % in human population data banks (the c. 911 T > C (p. F304S) ALG6 variant was detected but filtered out because it occurs at a frequency of 20-30 %), and selecting those associated with glycosylation or dolichol metabolism pathways, two genes were found with two variants: DHDDS and TNKS1 (Tables  1  and 2 ). TNKS1 (Tankyrase, TRF1-Interacting Ankyrin-Related ADP-Ribose Polymerase) functions include NAD + -dependent ADPribosyltransferase activity. Poly-ADP-ribosyltransferases are involved in various processes such as Wnt signaling, telomere length maintenance and vesicle trafficking  [27]. In certain situations, the chromosomal location of the TNKS1 gene (8p23. 1) is linked to a form of monogenic diabetes  [28]. Despite being lean and in other respects normal, TNKS1-deficient mice display hyperphagia and altered fatty acid metabolism without liver steatosis  [28].