dataesr/scientific-paragraphs-categorization huggingface dataset:
| Relationship between ecosystem photosynthetic capacity and leaf nitrogen concentration This study evaluates the relevance of synchronizing measurements of plant functional traits and EFPs in space and time for joint analyses. We analyzed the relationship between the best estimates for ecosystem photosynthetic capacity selected as described above, and CWM of plant traits, for example, N%. N% is chosen here, as the relationship between N% and photosynthetic processes is well established (e. g. ,  Field & Mooney, 1986; Reich, Walters, & Ellsworth, 1997)  at the leaf scale and to a lesser extent at ecosystem scale (e. g. ,  Kergoat et al. , 2008; Ollinger et al. , 2008). The relationship with other traits is included in the supporting information (Fig. S2 ). Three different combinations of synchronizing ecosystem photosynthetic capacity and N% were tested: (1) Ecosystem photosynthetic capacity derived from the La Thuile database and species N% derived from TRY (no synchronization in For each combination of ecosystem photosynthetic capacity and N%, the slope and R 2 of the linear regression were determined.
| Relationship between ecosystem photosynthetic capacity and plant functional traits Using a linear relationship, the N% based on data from the TRY database explained 27% of the variance of site averaged GPP sat (20% of GPP sat. structure ) (Figure  4a , Table  2 ). N% derived from TRY and in situ were strongly correlated (Fig. S5 ), and the R 2 of the relationship between N% and GPP sat , and GPP sat. structure improved from 0. 27 to 0. 39 and from 0. 20 to 0. 32, respectively, when in situ N% was used (Figure  4b , Table  2 ). In addition, site averaged estimates of GPP sat and GPP sat. structure were replaced by GPP sat and GPP sat. structure from the years of in situ sampling R 2 increased to 0. 50 and 0. 37, respectively (Figure  4c , Table  2 ). The fit is even better when a nonlinear fit was used for Figure  4a ,b (distance correlation increased from 0.
| Essential plant traits for ecosystem photosynthesis capacity The variable selection analysis conducted with the stepwise regression using time-space synchronized data of ecosystem photosynthetic capacity estimates and in situ measured plant traits and LAI showed that the variability of GPP sat and GPP sat. structure between sites is best explained by leaf C/N ratio and P area 2 (considering AIC as the selection criteria). However, only C/N was a significant predictor for both of the ecosystem photosynthetic capacity estimates. The selected model explained 61% and 54% of the variance of GPP sat and GPP sat. structure , respectively (Table  4 ).
| Robustness of ecosystem photosynthetic capacity-plant trait relationship to relaxed time-space synchrony of measurements Here, we show that the general pattern of the relationship between ecosystem photosynthetic capacity and plant traits (slopes of the linear regression, Figure  4 ) is apparently independent using locally measured traits (in situ) or species mean values from the TRY database. In addition, the relationships are independent of whether all data corresponded to the same year or the ecosystem photosynthetic capacity represented the multiyear averages of ecosystem photosynthetic capacity we used (most cases, Fig. S2 ). However, we observed a strong degradation of the explained variance when the synchronization in time and space was relaxed. The predictive power of plant functional traits for ecosystem photosynthetic capacity substantially improved when variation of species abundance, intraspecific variability of plant traits, and interannual variability of ecosystem photosynthetic capacity were accounted for.
In particular, the N/P ratio is related to photosynthetic capacity via the connection between the allocation of P into P-rich ribosomal RNA and of N to protein synthesis  (Hessen, Jensen, Kyle, & Elser, 2007). As P is also used in carbon fixation as N, it influences the nitrogenphotosynthesis relationship by constraining the response of photosynthesis to N when P is low  (Reich et al. , 2009; Walker et al. , 2014). However, more data are needed to build robust models that predict ecosystem photosynthetic capacity directly from plant functional traits and stoichiometry. Currently, no consensus exists on which traits are most important to be measured at the sites in order to monitor the effect of plants on ecosystem functioning in response to their environment. Trait-ecosystem functioning studies with more data are needed to allow for robust conclusion on a suit of traits in this regard.
In conclusion, to quantitatively evaluate the link between ecosystem photosynthetic capacity and plant traits to improve predictions of ecosystem carbon uptake, continuous observations of species composition and plant traits at FLUXNET sites can be the key. We showed that currently the evaluation is limited by the scarcity of observations of both species composition and traits. We therefore suggest systematic sampling of plant traits, species abundance, and auxiliary data for upscaling traits at FLUXNET sites in parallel to flux measurements. In addition, remote sensing can be a solution in the future to acquire canopy level traits, circumventing upscaling issues of in situ measurements and may contribute to better detection of temporal and spatial variation of ecosystem level plant traits in synchrony with ecosystem photosynthetic capacity.
ACKNOWLEDGMENTS We thank all the people who made this study possible by participating in leaf sampling and sharing flux and plant trait data. We appreciate all the good discussions at the  Max Planck Institute of Biogeochemistry. We thank  Ulrich Weber  for preparing part of the flux and remote sensing data. We thank  Jurgen van Hal  and  Richard van Logtesteijn  at the  VU University in Amsterdam  for measuring the plant traits and  Katrin Fleischer  for helping for leaf sampling at NL-Loo site. We also thank  Martina Mund  for sending us litter fall data from species of  DE-Hai  from which we estimated the abundances. We thank the anonymous reviewers and the associate editor for their constructive comments that improved both the readability and the robustness of the manuscript. The authors affiliated with the MPI BGC acknowledge funding by the  European Union 's  Horizon 2020 project BACI  under grant agreement No.
We acknowledge the financial support to the eddy covariance data harmonization provided by  CarboEuropeIP ,  FAO-GTOS-TCO, iLEAPS ,  Max Planck Institute for Biogeochemistry, National Science Foundation ,  University of Tuscia, Université Laval, Environment Canada  and  US Department of Energy  and the database development and technical support from  Berkeley Water Center ,  Lawrence Berkeley National Laboratory, Microsoft Research eScience ,  Oak Ridge National Laboratory, University of California-Berkeley  and the  University of Virginia , and the  IceMe of NUIST. The authors would | 7363 MUSAVI et Al. like to thank all the PIs of eddy covariance sites, technicians, postdoctoral fellows, research associates, and site collaborators involved in FLUXNET who are not included as coauthors of this article, but without whose work this analysis would not have been possible.
The experimental strategy employed bypassed the effects of synonymous variants on DNA-binding factors or on splicing. Moreover, there are no significant differences in the receptor expression at mRNA and protein levels  [11]. Using RNAsnp software  [26, 27]  to determine local RNA secondary structure changes induced by single nucleotide polymorphism (SNP), no significant differences were estimated between ERWT and ERαA87 mRNAs (not shown). Differences in miRNA and other non-coding hybridization sites as well as transcription factor-binding sites were assessed using RegRNA 2. 0 software  [28]  and no differences were found either (data not shown).
Codons and tRNAs Involved in Decoding Alanine 87 Interestingly, Ala87 is the central alanine of a group of three consecutive alanines. Figure  1  shows the three consecutive alanine codons within the coding sequence. In ERWT, the three codons are GCT GCG GCG; in ERAla87, they become GCT GCC GCG. According to the human codon usage reported in the Genomic tRNA Database  [29] , these three codons are used as follows: GCT: 1. 84%, GCG: 0. 74% and GCC: 2. 77%. This implies that in ERWT a local repetition of the less-used codons occurs (Ala87 and Ala88), whereas in ERAla87, one of the less-used codons is substituted by the most frequently used, also eliminating the codon repetition. (Number of genes and codon usage for alanine codons in human cells is shown in Table  1a ). Table  1. (a) Number of genes and codon usage for alanine codons in human cells.
a. Alanine tRNA Genes in Human Genome According to the Genomic tRNA Database [29] Anticodon (5 -without modifications recognizes: wt * tRNA-UGC: -without modifications recognizes: wt, Ala87 Ó -with modifications recognizes: wt tRNA-UGC: -without modifications recognizes: Ala87 Looking at the tRNAs involved in decoding alanine codons (see Table  1b ,c)  [30, 34, 35] , it is interesting to note the differences in their ability to recognize the GCG codon present in ERWT or the GCC codon present in ERAla87. In fact, tRNA Ala -AGC, without posttranscriptional modifications in its anticodon, is able to recognize both codons; meanwhile, when adenine in the anticodon is converted to inosine, tRNA Ala -IGC is only capable of recognizing the GCC codon. Therefore, there will be at least the same or even more tRNA molecules capable of decoding the GCC than the GCG codon from the tRNA Ala -I/AGC population that is available for translation.
25× TBE, were pre-run at 6V/cm for 15-20 min, at 4 • C or at 38 • C. Binding reactions were loaded into the gels and run in an electric field of 6V/cm for 1 h. Gels were fixed in a 10% Ethanol 10% Acetic-Acid solution for 10 min, dried, exposed with a phosphor-imager screen and revealed with a Typhoon phosphor-imager scanner. For 4 • C experiments, the binding reactions were established on ice, and the electrophoretic mobility shift assays (EMSAs) were carried out at 4 • C, with pre-cooled acrylamide gels and running buffer. For 38 • C experiments, the binding reactions were incubated at 38 • C and the electrophoresis was carried out in an incubator at 38 • C, with pre-heated acrylamide gels and running buffer. The intensity of the bands was measured with ImageJ. Saturation curves were analysed with GraphPad Prism version 6 (Graphpad software, La Jolla, CA, USA, www.
ACKNOWLEDGEMENTS We thank  Yasuyuki Fujita  of  University College (London, UK ) for kindly providing us MDCK cells stably expressing the repressor pcDNA6/TR. We are grateful to  Rémi Salomon  for helpful suggestions and for providing clinical data on CAKUT patients. We also thank  Moshe Yaniv ,  Fabiola Terzi  and the members of the  Pontoglio lab , for helpful discussions and critical reading of the manuscript. We are very grateful to the  platform of 'Imagerie Cellulaire' of the Cochin Institute.
FUNDING ' Fondation pour la Recherche Médicale ' [équipe FRM DEQ2012032376];  Fondation Bettencourt-Schueller  ( Prix Coup d'Elan) ;  European Community 's  Seventh Framework Programme   FP7/2009 [241955 , SYSCILIA]; Trancyst ITN; ' Agence Nationale pour la Recherche'  and the  'Who Am I?' Laboratory of Excellence ; ' Ecole Normale Supérieure de Cachan' Fellowship  (to J. L. ); ' Ligue contre le Cancer' Fellowship  (to J. L. ); ' Fondation pour la Recherche Médicale ' Fellowship (to A. B. ); ' Association pour la Recherche sur le Cancer' (ARC) Fellowship  (to M. P. M. ). Funding for open access charge: ' Fondation pour la Recherche Médicale '.
Data Analysis We quantified the ability of the subjects to detect the change in stimulus statistics using two measures, hit rate and d-prime (d'). We also found reaction times to depend on the difficulty. These measures were computed as a function of change size and change time. Since change times were distributed continuously but with an exponential distribution, the set of change times was binned with approximately exponentially increasing bin size (in order to achieve comparable numbers of trials in each bin). To control for inattentive subjects, we set a 35 % threshold for the total false alarm rate. Two subjects were discarded according to this criterion leaving a total of 10 subjects for the data analysis, with false alarm rates around 25 %.
d' was computed separately for different times and change sizes, yielding only a limited number of trials per condition. To avoid degenerate cases (i. e. d' would be infinite for perfect scores), the analysis was not performed separately by subject, but over the pooled data. Confidence bounds (95 %) were then estimated by grouping data from all subjects. The analysis was verified on surrogate data from a random responder (binomial with very low p at each point in time), providing d' very close to 0 on a comparable number of trials.
Methods: We analysed in this multicentre study all patients treated for early TNBC in 12 French cancer centres. We explored the correlation between clinicopathological data and ALNI, with a specific focus on the dichotomisation between macrometastases and occult metastases, which is defined as the presence of isolated tumour cells or micrometastases. The prognostic value of ALNI both in terms of disease-free survival (DFS) and overall survival (OS) was also explored. Results: We included 1237 TNBC patients. Five-year DFS and OS were 83. 7% and 88. 5%, respectively. The identified independent prognostic features for DFS were tumour size 420 mm (hazard ratio (HR) ¼ 1. 86; 95% CI: 1. 11-3. 10, P ¼ 0. 018), lymphovascular invasion (HR ¼ 1. 69; 95% CI: 1. 21-2. 34, P ¼ 0. 002) and ALNI both in case of macrometastases (HR ¼ 1.
MATERIALS AND METHODS In this retrospective, multicentre cohort study, we analysed data from women with primary TNBCs treated in 12 French centres between 1987 and 2011. This work was approved by our institutional ethics committee and SocieteFranc¸aise de Chirurgie Oncologique. Patients' inclusion criteria. Patients with first-line treatment for early-stage invasive BC without metastasis at diagnosis and with no expression of ER, PR (o10% of cancer cells expressing ER/PR, as defined in the French guidelines) or ERBB2 identified by IHC (score 0 or 1) were included. For cases with an IHC score of 2, we looked for HER2 amplification using in situ hybridisation technologies  (Penault-Llorca et al, 2014). Exclusion criteria were clinical T4, bilateral disease, neoadjuvant treatment and any personal history of cancer.
Data collection. After obtaining approval from our institutional ethics committee, data were collected from individual medical files. Information gathered included demographic (age at diagnosis), clinical (cTNM), pathological (pathological subtype, tumour grade determined by the Scarff-Bloom-Richardson scoring system, pathological tumour size, presence of lymphovascular invasion (LVI) assessed by haematoxylin and eosin staining, axillary lymph node status (ITC, micrometastasis or macrometastasis)) and therapeutic data (type of surgery, adjuvant chemotherapy). Axillary lymph node involvement assessment was performed using either SLNB after radioisotope and/or blue dye injection, or axillary lymph node dissection (ALND). We defined five groups: no lymph node metastasis (pN0), ITC (o0. 2 mm; pN0(i þ )), micrometastases (o2 mm; pN1mic), isolated macrometastasis (Z2 mm, pN1) and multiple macrometastases.
Only factors with a P-value p0. 05 in univariate analysis were kept for multivariate analysis. We compared the use of adjuvant chemotherapy according to clinicopathological features including ALNI status. We developed a score to predict DFS, according to the hazard ratios (HRs) from the Cox model in a training set representing two-thirds of our cohort (n ¼ 825). We looked at the presence of 0-3 risk factors resulting in a score of 0-3 for each sample. We then validated this score using a validation set including the last third of our cohort (n ¼ 412). We chose to split our cohort because no external cohort with appropriate clinicopathological individual data was available. To define both the training and validation sets, we classified all the cases according to their age in an ascending order: the first two patients were included in the training set and the third in the validation set.
Survival analyses were performed separately in the training and validation sets. Data concerning patients without disease progression or death at last follow-up were censored. Survival curves were estimated using the Kaplan-Meier method, and compared with the log-rank test. The Pearson's w 2 test was used to compare descriptive items. All statistical tests were two sided at the 5% level of significance and analyses were performed using the SPSS 16. 0 software for Windows (SPSS Inc. , Chicago, IL, USA). This work was carried out according to the Strengthening the Reporting of Observational Studies in Epidemiology criteria  (Vandenbroucke et al, 2007).
RESULTS Patient's characteristics. We collected data from 1237 patients with a primary early-stage TNBC. The main patient characteristics are summarised in Table  1. The mean age of the patients at diagnosis was 55. 7 years old (95% CI: 55-56. 4; median ¼ 56) and the mean tumour size was 20. 8 mm (95% CI: 19. 9-21. 7; median ¼ 17). Axillary lymph node dissection was performed for 588 patients (47. 6%) and 889 (71. 9%) underwent initial SLNB including 244 with a secondary ALND. Less than a quarter (22. 8%) of our patients presented an ALNI including 35 patients (2. 8%) with pN0(i þ ), 55 (4. 5%) with pN1mic and 191 (15. 5%) with pN1. Out of pN1 cases, 39. 8% (68 out the 171 cases with data available) had only one ALNI and 60. 2% (103/171) had two or more ALNI. When an SLNB was performed, one or more non-sentinel metastatic lymph nodes were identified for 0.
ACKNOWLEDGEMENTS This work was supported by  SIRIC  ( INCa-DGOS-Inserm 6038 grant ),  Institut Paoli-Calmettes  and  SocieteFranc¸aise de Chirurgie Oncologique. This work is published under the standard license to publish agreement. After 12 months the work will become freely available and the license terms will switch to a Creative Commons Attribution-NonCommercial-Share Alike 4. 0 Unported License.
15 or 0. 3 mg/kg daily dosage according to their response evaluated by PMR-AS at week 12. In this study, PMR-AS decreased after the first TCZ infusion and all the patients benefited from the lower GC dosage (0. 15 mg/kg instead of the classical 0. 3 mg/kg/day), thus resulting in a significant GC sparing effect compared with a theoretical dose of GC. All parameters of PMR-AS were ameliorated and a level of PMR-AS <10 was achieved for all patients with or without inclusion of the CRP level. Quality of life and imaging (PET) parameters were also significantly ameliorated after TCZ infusions. Thus, despite the fact that PMR-AS is a composite index of disease activity that includes CRP, TCZ improved different dimensions of the disease including clinical and imaging parameters. Finally, an open-label phase 2a study evaluated the rate of patients able to achieve remission under TCZ (ClinicalTrials.
gov NCT01396317). The effects of TCZ in patients with GCA have been documented in greater detail, with a huge number of single cases or large retrospective series (table 2). 24 29-36 ll patients with GCA received TCZ for unacceptable side effects of GC, as a steroid-sparing agent or alternatively for severe disease. Most of the patients had received one or several lines of immunosuppressants previous to TCZ, and a small number of them had received a TNFα inhibitor. GC dosage before TCZ initiation ranged from 6 to 60 mg daily of prednisone. TCZ monotherapy was given at 8 mg/kg, and was reduced for some patients to 4 mg/kg due to safety concerns (especially for neutropaenia). 35 36 For all these patients, clinical efficacy was observed between 1 and 3 months after the first TCZ infusion. A limited number of patients with GCA did not improve with TCZ treatment, especially those with ocular involvement who had persistent visual impairment.
38 The objective is to demonstrate that TCZ is able to induce and maintain disease remission at week 52 in patients with GCA. Positive results were recently announced, showing that TCZ initially combined with a 6-month steroid regimen more effectively sustained remission through 1 year compared with a 6-month or 12-month steroid-only regimen in patients with newly diagnosed and relapsing GCA. 39 Finally, the HORTOCI study (ClinicalTrials. gov NCT0190038) is another clinical trial that aims to evaluate the immunological changes observed in patients with GCA while receiving TCZ, especially on the Th17 cell subset. This is an open-label study of 12 months duration with a 3-month TCZ treatment and a pre-established GC reduction dose. Results from retrospective and prospective studies demonstrate the efficacy of TCZ in GCA and PMR.
Backgrounds/Aims: The aim of this study was to describe clinical and biological changes in a group of patients who underwent pancreaticoduodenectomy (PD) without any complication during the postoperative period. These changes reflect the "natural history" of PD, and a deviation should be considered as a warning sign. Methods: Between January 2000 and December 2009, 131 patients underwent PD. We prospectively collected and retrospectively analyzed demographic data, pathological variables, associated pathological conditions, and preoperative, intraoperative, and postoperative variables. Postoperative variables were validated using an external prospective database of 158 patients.
Studied internal population All consecutive patients who were candidates for elective PD in our department between January 2000 and December 2009 were considered eligible for the present study. Data for these patients were prospectively recorded and retrospectively analyzed. Exclusion criteria were age of 17 years or younger, and an uneventful postoperative course over the first 30 days. Surgical technique and perioperative care PD was performed without pylorus preservation. In all patients, PD was performed with an antrectomy and reconstruction with a serosa to mucosa hand-sewn end-to-side pancreaticogastrostomy, with non-absorbable monofilament sutures, on the posterior wall of the gastric body. In case of small wirsung (＜3 mm) or/and soft pancreas, an external catheter with multiple side holes was inserted into the pancreatic duct.
Data collection and postoperative follow-up PF was defined, according to the international study group,  16  as an amylase-rich fluid (amylase concentration 3 times superior than serum concentration) collected via needle aspiration of an intra-abdominal collection or from the drainage placed intraoperatively from day 3. PF were graded according to the clinical impact on the patient's hospital course (grades A, B, C). Delayed gastric emptying (DGE) was defined as the inability to resume oral feeding after the first postoperative week or prolonged use of a nasogastric aspiration tube. 17 Hemorrhage was defined according to the time of onset, site of bleeding, severity, and clinical impact. 18 ternal controlled population  Blood changes were listed in Table  3. The maximal fall in hemoglobin level occurred on day 3 and began to increase after POD 5, in patients with or without transfusions (Fig.
Functional classifi cation of animals is necessary to enhance the predictive power of food web models. However, while there is a large database for functional classifi cation of benthic invertebrates (Functional Feeding Groups, FFG) in the temperate zone, the attribution of individual species of riverine invertebrates is still in its infancies in the Neotropical Region. Diff erent authors hypothesized that diet breadth was larger in the Tropics, however detailed analyses are scarce. In the present study we aimed at classifying dominant benthic taxa of the Middle Paraná River fl oodplain (Argentina) into trophic guilds by diet and niche overlap analysis. We sampled twelve taxa of benthic invertebrates from a fl oodplain lake during low water season and performed a gut content analysis as a baseline for FFG classifi cation.