dataesr/scientific-paragraphs-categorization huggingface dataset:
truncatula and L. japonicus genomic databases. For instance, AGO3 and AGO9 are absent both in Lotus and M. truncatula genomic databases  (Capitão et al. , 2011; Young et al. , 2011). However, according to its strong similarity with the soybean AGO9, we propose to rename MtAGO11a  (Capitão et al. , 2011)  in MtAGO9. In addition, as AGO2 and AGO3 belong to the same clade, it is possible that the absence of AGO3 in the two model legumes is compensated by the presence of an additional AGO2 homolog (two AGO2 homogs instead of AGO2 and AGO3). In Arabidopsis, several evidences from Atago2 mutants pointed out that AGO2 but not AGO3 plays fundamental roles in defense against particular virus infections  (Harvey et al. , 2011; Wang et al. , 2011) , suggesting that they may have specialized functions.
On the other hand, expression analysis suggest that AGO2 and AGO3 are more expressed in seeds than other tissues and accumulation of smRNA species is similar in ago2 and ago3 mutants  (Takeda et al. , 2008). These latter experiments support that there is functional redundancy of AGO2 and AGO3 in Arabidopsis, notably in seeds. Because of their fundamental roles in miRNA function, absence of clear homologs of AGO1 and AGO10 genes in M. truncatula databases was much more striking. In Arabidopsis, functional analyses suggested that AGO1 mainly acts through slicing and controls miRNA function. On the other hand, AGO10 acts through translational repression of the miRNA targets and belongs to the same clade (for references see  Manavella et al. , 2011). As Atago10 mutants are affected neither in gene silencing nor in smRNA accumulation  (Takeda et al.
0, March 2011), this TC was split into two contigs (TC188472 and TC194233), which in fact correspond to the so-called MtAGO12a/b genes. Although these AGO12 isoforms fall into the AGO1/AGO10 clade, they are more closely related to AGO10 (Figure  5 ). Thus, the absence of AGO1, but also of AGO5, in M. truncatula databases remains intriguing and may be due to the lack of completion of the M. truncatula genome. Vaucheret (2008)  and  Kapoor et al. (2008)  reported that new AGO genes arise from gene duplication events. This type of gene diversification clearly appears in the phylogenetic tree which shows that, for many AtAGOs, more than one homolog was found in nearly all plant species we compared. Looking at the phylogenetic relationships inside the AGO4/6/8/9 clade, AGO4 diversification was important in all species with 2-4 homologs.
, 2009; Parker, 2010) ; The PIWI domain is responsible of the catalytic activity of AGO proteins  (Baumberger and Baulcombe, 2005) ; the PAZ domain is necessary to recognize the 3 end of the smRNA for loading into the RISC and determines the AGO specificity. Among the identified domains in legume AGOs (Data Sheet 4), only some appeared unusual. For instance, GmAGO10c and MtAGO4a lacked PAZ and DUF1785 domains, suggesting that they are pseudogenes. On the other hand, MtAGO12c (Medtr2g059590,  Capitão et al. , 2011)  had no PIWI domain. For that, we assume that this protein, even if it also belongs to the AGO1/AGO10 clade, may certainly not play similar functions than AGO1. Again, more precise analyses of the corresponding genomic regions and completion of the genome sequencing are required to support the absence of these sequences as errors in gene annotation due to the presence of very long introns for instance may explain some of the difficulties to detect gene homologs in legumes.
Phylogenetic trees were constructed thanks to T-Coffee software. The phylogenetic tree was generated with MEGA4. 0 software using the Neighbor joining tree  (Capitão et al. , 2011). The four AGO clades are indicated in the right part of the figure. and AGO3 may be replaced by Asp (DDD) without affecting their endonuclease activity  (Baumberger and Baulcombe, 2005; Montgomery et al. , 2008)  and the same happened for 9 AGO proteins in rice  (Kapoor et al. , 2008). As shown in Data Sheet 1, all legume AGOs with a PIWI domain present either a DDH or a DDD motif, like in Arabidopsis. In addition,  Baumberger and Baulcombe (2005)  reported that a conserved Histidine residue at position +800 in the PIWI domain of AGO1 was required for its endonuclease activity, at least in-vitro. As expected, according to their role in RNA-dependent DNA methylation rather than RNA cleavage, AtAGO4/6/8/9 proteins contain another aminoacid residue, an alanine (A), a serine (S) or a proline (P), at this conserved position.
CONCLUDING REMARKS Since five years, the rapid progress of genomic technologies has allowed the construction and high-throughput sequencing of a very large set of smRNA libraries in model legumes, in particular from M. truncatula and G. max. Compilation of data from miRBase and smRNA deep sequencings revealed the largest set of novel miRNA families ever observed in a plant family. Few conserved and legume-specific miRNAs have been functionally studied. Further analysis of the legume miRNAs as well as phased siRNAs and their putative targets will be essential to better understand the role of smRNAs in the control of key processes during nodule development, nitrogen fixation and defense against pathogens. On the other hand, DCL and AGO proteins are key players in smRNA biogenesis and functions, which are highly conserved processes in plants.
Phylogenetic tree of AGO proteins in M. truncatula, L. japonicus, G. max, A. thaliana, P. trichocarpa, and O. sativa. Full length sequences of the predicted AGO proteins from A. thaliana, P. trichocarpa and O. sativa were retrieved from Genbank (NCBI). DCL from M. truncatula, soybean (G. max) and L. japonicus were searched by tBLASTX in genomic sequence databases: legumes Lotus japonicus (Miyakogusa. jp 2. 5, Sato et al. , 2008), Medicago truncatula (Mt 3. 5. 1, Young et al. , 2011),.
ACKNOWLEDGMENTS Pilar Bustos-Sanmamed  was the recipient of a  Marie Curie Postdoctoral IE Fellowship  (European Commision, MEDEPIMIR, N •  PIEF-GA-2010-273743 ). Jérémie Bazinwork  was supported by a post-doctoral contract from  University Paris Diderot Paris 7, France. This work was supported by the program Saclay Plant Sciences ( SPS ,  ANR-10-LABX-40 ).
5| Phylogenetic tree of AGO proteins in M. truncatula, L. japonicus, G. max, A. thaliana, P. trichocarpa, and O. sativa. Full length sequences of the predicted AGO proteins from A. thaliana, P. trichocarpa and O. sativa were retrieved from Genbank (NCBI). DCL from M. truncatula, soybean (G. max) and L. japonicus were searched by tBLASTX in genomic sequence databases: legumes Lotus japonicus (Miyakogusa. jp 2. 5, Sato et al. , 2008), Medicago truncatula (Mt 3. 5. 1, Young et al. , 2011),.
Multi-site observational study Data to support the short form adaptation was collected in a US-based, non-randomized, multi-center, standalone observational study in male and female patients who have MS with and without NDO. MS patients were recruited through neurology practices to complete patient reported outcome assessments (PRO) (the ABSST and the Overactive Bladder Questionnaire -Short Form (OAB-q-SF)) as well as a demographic and health information form. Written informed consent was needed before the subject could participate in any part of the study. All research involving patient interviews and patient completion of questions were in compliance of the Helsinki Declaration and had full Institutional Review Board (IRB) approval from Copernicus Group (an independent institutional review board organized and operating in compliance with regulations governing institutional review boards set forth in 21 CFR and ICH guidelines, as well as 45 CFR when applicable.
Acknowledgements The authors would like to acknowledge the following for their help in the development of this manuscript:  Vasudha Mukherjee Bal  and  Marcy Fitzrandolph  for managing and overseeing the qualitative design and development of the ABSST. Benjamin Banderas  for managing the quantitative phase of the study. Beth Anderson  and  Jeanne Cloppse of Lawrence and Company  for their assistance in site-identification, publication strategy and manuscript development through-out study. No medical writer was used in the development of this manuscript.
Acknowledgements. We thank  JC Thiers ,  C Foure ,  A Matassa-Ohm  for excellent technical help and  Dr. V Gallet  ( SNCF Laboratory, Toulouse, France ) for providing human serum. We are grateful to  Dr. F Lezoualc 'h for critical reading of the manuscript. These studies were supported by grants from  INSERM and Toulouse 3 University  to INSERM U1048 team 10.
Real data experiments: p»n We propose to test the performance of our method on ARCENE dataset which is one of the five NIPS 2003 feature selection challenge data sets. The data set is obtained from UCI Machine Learning Repository [http://archive. ics. uci. edu/ml]. For this two-class classification problem with continuous input variables, the aim is to distinguish cancer versus normal patterns from mass-spectrometric data. The samples include patients with cancer (ovarian or prostate cancer), and healthy or control patients. ARCENE was obtained by merging three mass-spectrometry data sets to obtain enough training and test data for a benchmark. The original features indicate the abundance of proteins in human sera having a given mass value. Based on those features one must separate cancer patients from healthy patients.
Acknowledgments -We wish to thank  S. Blatt ,  S. Gopalakrishnan ,  A. C. Hewson ,  M. Koehl ,  Y. Oreg ,  M. Punk ,  S. Will ,  A. Tsvelik ,  G. Zarand ,  F. Zhou , and  M. Zwierlein  for helpful discussions. We would like to thank  Martin Zwierlein  for pointing out to us the possibility of using Feshbach bound states on impurity atoms to realize the Kondo effect in cold atomic systems and for a collaboration on related projects [48]. JB acknowledges financial support from the  DFG  through grant number  BA 4371/1-1. We also acknowledge support from  Harvard-MIT CUA, DARPA OLE program ,  AFOSR Quantum Simulation MURI, AFOSR MURI on Ultracold Molecules , the  ARO-MURI on Atomtronics, ARO MURI Quism program  and the  EU ERC Ferlodim.
However, reports suggest that many patients with NMIBC are not optimally managed as per current clinical practice guidelines  [9] [10] [11]. The present individual patient data survey (IPDS) was designed to investigate clinical practice patterns in the management of intermediate-and high-risk NMIBC. In particular, the use of BCG in each of these risk categories was examined and compared with the 2008 (the year preceding the start of treating patients included in this IPDS) EAU and 2007 AUA guidelines for NMIBC management.
ACKNOWLEDGMENTS. ABSTRACT. EXECUTIVE SUMMARY. 1. BACKGROUND. 2. TERMS OF REFERENCE. 3. SCIENTIFIC RATIONALE. 3. 1. Introduction. 3. 2. Scope of opinion, definition of active substances considered. 3. 2. 1. Definitions. 3. 2. 1. 1. Official definitions. 3. 2. 1. 2. Other definitions. 3. 2. 2. Active substances. 3. 3. Production, use and fate of biocides. 3. 3. 1. Biocides in health care. 3. 3. 1. 1. Biocides (disinfectants) on medical devices and surfaces. 3. 3. 1. 2. Biocides (disinfectants and antiseptics) used on skin and mucosa 21 3. 3. 2. Biocides in consumer products. 3. 3. 2. 1. General aspects. 3. 3. 2. 2. Cosmetics and personal care products. 3. 3. 2. 3. Household products. 3. 3. 2. 4. Triclosan in consumer products and textiles. 3. 3. 3. Biocides in food production. 3. 3. 3. 1. Biocides as disinfectants.
Earth system processes exhibit complex patterns across time, as do the models that seek to replicate these processes. Model output may or may not be significantly related to observations at different times and on different frequencies. Conventional model diagnostics provide an aggregate view of model-data agreement, but usually do not identify the time and frequency patterns of model-data disagreement, leaving unclear the steps required to improve model response to environmental drivers that vary on characteristic frequencies. Wavelet coherence can quantify the times and timescales at which two time series, for example time series of models and measurements, are significantly different. We applied wavelet coherence to interpret the predictions of 20 ecosystem models from the North American Carbon Program (NACP) Site-Level Interim Synthesis when confronted with eddy-covariance-measured net ecosystem exchange (NEE) from 10 ecosystems with multiple years of available data.
e. , multiple databases) to arrive at a synthesis  (Friedlingstein et al. , 2006; Schwalm et al. , 2010). In other words, such studies adopt a data-intensive approach to scientific inference  (Gray, 2009) , and techniques from nonlinear time-series analysis and knowledge discovery in databases (i. e. , "data mining") may provide important insights into the aggregate or divergent behavior of these model and observational databases. In this study, we quantify significant relationships among 20 ecosystem models and 10 multi-year time series of NEE measurements from the North American Carbon Program (NACP) Site-Level Interim Synthesis  (Schwalm et al. , 2010)  using a technique called wavelet coherence  (Grinsted et al. , 2004; Torrence and Webster, 1999). Wavelet coherence is conceptually similar to a measure of correlation between data series across time and timescale (related to frequency).
Acknowledgements. First and foremost, we wish to thank all of the researchers involved in eddy covariance data collection and curation, and in model development and testing. P. C. Stoy thanks  Matteo Detto  and  Aslak Grinsted  for helpful discussions and code examples regarding wavelet coherence and the  National Science Foundation  (Scaling ecosystem function: Novel Approaches from MaxEnt and Multiresolution, DBI # 1021095 ). We would like to thank the  North American Carbon Program Site-Level Interim Synthesis team , the Modeling and Synthesis Thematic Data Center, and the  Oak Ridge National Laboratory Distributed Active Archive Center , and  Larry Flanagan  for collecting, organizing, and distributing the model output and flux observations required for this analysis. We also thank  Robert Bemis  for creating the MATLAB code that followed the suggestions of Light and Bartlein (2004) for improved use of color in images.
On the one hand, Feferman and Vaught proved  [11, Theorem 8. 2]  that WMSO(N, EqCard) (without <) is decidable, by reduction to Presburger Arithmetic; the interested reader can find applications of this result to constraint databases  [22]  and verification  [16]. On the other hand it is easy to show that + and × are definable in WMSO(N, <, EqCard), from which we get undecidability of the theory (see Proposition 3. 1). Klaedtke and Ruess  [15]  extend the undecidability result to the case where EqCard is replaced by any predicate R(X 1 ,. , X r , Y 1 ,. , Y s ) which holds iff |X 1 | + • • • + |X r | < |Y 1 | + • • • + |Y s |. They also introduce the notion of Parikh automaton, which allows them to obtain decidability results for some syntactical fragment of the logic. The above results suggest that one cannot add very expressive cardinality relations to WMSO(N, <) while keeping decidability of the theory.
Acknowledgements. We wish to thank  • Bruno Courcelle  for raising questions which led to this work, and for his help during the preparation of the paper;  • Arthur Milchior  for his careful reading of a preliminary version of the paper; • the organizers of the 30th Days of  Weak Arithmetics  held in 2011 at Paris 7 University, where we learned about Bruno Courcelle's question; • the anonymous referee who suggested to use the formula (3. 2) in the proof of Theorem 3. 4 and Proposition 4. 6, which led to a great simplification of the initial proofs.
This article quantifies the relationship between sea ice cover (SIC) on the Southern Ocean and precipitation and river discharges over southeastern and eastern South America. The period of analysis covers from 1981 to 2008 and includes monthly mean data of SIC over the Ross, Amundsen-Bellingshausen and Weddell Seas, as well as atmospheric variables and discharges of selected rivers in eastern South America. To isolate the effect of known modes of climate variability on SIC, the signals of El Niño-Southern Oscillation and the Southern Annual Mode are removed from all time series through regression analysis. Composites of precipitation differences over South America reveal a pattern of enhanced rainfall activity over the South Atlantic Convergence Zone (SACZ) in summer (JFM) when SIC is above average particularly over the Weddell Sea area, while winter (ASO) SIC anomalies show negative and significant correlations with rainfall over much of South America.
However, until now the potential relationships (if any) existing between SIC around Antarctica and South American climate are not clear. The scope of this article is to analyse the covariability between SIC and precipitation anomalies over South America. Three distinct regions around Antarctica are selected and analysed individually: Ross Sea, Amundsen-Bellingshausen Sea and Weddell Sea and their relationships with patterns of rainfall anomalies are assessed. An analysis of long-term trends in SIC and their possible links to precipitation variability over South America is also performed. The article is organized as follows: Section 2 includes the description of SIC, precipitation, streamflow and circulation variables datasets along with the methodologies. Section 3 includes the analysis on SIC and precipitation variability and covariability.
Data and methodology SIC data was taken from the HadISST dataset  (Rayner et al. , 2003 and updates)  for the whole SH and precipitation data was obtained from CMAP  (Xie and Arkin, 1997)  covering the South American region. The atmospheric circulation related to the SICprecipitation anomalies was analysed using data from the NCEP/NCAR Reanalysis  (Kalnay et al. , 1996)  and includes monthly mean 850 and 700 hPa geopotential height (Z850 and Z700, respectively), specific humidity (q) and temperature (T) from 1000 to 700 hPa, precipitable water and zonal and meridional wind components (u and v, respectively) from 1000 to 250 hPa. As all datasets considered in this article have at least partially been derived using remote sensing data, the period of analysis was selected so as to be included in the satellite era and runs from January 1981 to July 2008.
As river discharges are mainly driven by precipitation and temperature, further analysis is performed to link anomalous sea ice patterns with selected river streamflow anomalies at the outlet of large basins. Streamflow data were obtained from the Subsecretar ía de Recursos H ídricos (Undersecretary of Water Resources) of Argentina and the Operador Nacional do Sistema Elétrico (National Electric System Operator) of Brazil and consist of monthly mean discharges of the Uruguay River at Paso de los Libres (  29.
As for the SIC and rainfall time series, SAM and ENSO effects were also removed from discharge data through a linear regression analysis. Considering the previous lagged SIC-rainfall analysis, Tables  4  and 5  include statistics of streamflow changes during the months of October and November, respectively, associated to SIC variability over the Weddell Sea region in the previous September. As streamflow data tend not to follow a Gaussian distribution, medians (and not means) are presented for October and November along with the differences in high and low SIC conditions in September. Overall, during October (Table  4 ) the Uruguay and Iguazú Rivers have their streamflow diminished when SIC in the Weddell is above the 80% percentile in September. For the gauging stations in the Paraná and Sao Francisco Rivers the patterns of streamflow anomalies are opposite to that of the Uruguay River, with positive (negative) anomalies related to positive (negative) September SIC anomalies.
, 1995). As a rule, the surface was very small in the normal cat (ϳ50 -100 cm 2 ) and greatly increased in the days following unilateral vestibular lesion. To quantify the support surface, cats were placed in a device with a graduated transparent floor that allowed them to be photographed from underneath. Five repeated measurements were done for each cat tested at each postoperative time, and an average was calculated for each experimental session. The support surface was measured as the surface delimited by the four legs by an image analysis system (Canvas 9, Deneba Software). Data recorded after vestibular lesion were compared with prelesion values by using individual references, permitting each animal to act as its own control. Equilibrium function recovery. Locomotor balance function was quantified using an adapted rotating beam experimental device  (Xerri and Lacour, 1980).
This maximal rotation speed determined the maximal locomotor balance performance (Max P). Preoperative training on the rotating beam necessitated 6 -10 periods depending on the cats. Training was stopped when the cats' Max P was reached and stabilized at its highest level, which was found to be remarkably similar from one cat to another in each group. Statistical analysis. Statistical analysis was performed using Statview II software (SAS Institute). A two-way ANOVA was used to test for changes in the spontaneous nystagmus, the support surface, and the maximal equilibrium performance at the different postlesion delays. Results were considered statistically significant at p Ͻ 0. 05 (Table  1 ).
We found that ϳ60% of BrdU ϩ cells survived in the UVN-gabazine group (42% in the MVN, 70% in the IVN, 65% in the LVN, and 55% in the SVN compared with the number of BrdU ϩ cells at D3) and ϳ50% survived in the UVN-NaCl group (59% in the MVN, 57% in the IVN, 58% in the LVN, and 44% in the SVN). The data between these two groups were significantly different except for the MVN (UVN-NaCl versus UVN-gabazine). Strikingly, no BrdU ϩ cells were found in the UVNmuscimol group 30 d after UVN (Fig. 2B ).
Fate of newly generated cells in deafferented vestibular nuclei The BrdU ϩ surviving cells differentiated and acquired a neurochemical phenotype ϳ20 d after birth; cell differentiation was investigated by doubleimmunohistochemical labeling using BrdU combined with the four specific cell type markers: GFAP, NeuN, IBA1, and GAD67. Double immunohistochemistry against BrdU and GFAP at D30 showed that the UVN-NaCl and UVN-gabazine groups displayed numerous cells with costaining, whereas no surviving BrdU ϩ cells were observed at this delay in the UVN-muscimol group, suggesting that newborn cells that had incorporated BrdU at the third post-UVN day did not survive until 30 d postinjection (data not shown). The double labeling has been quantified only at D30 in the UVN-NaCl and UVN-gabazine groups since colabeled cells were not observed at the early time point D3.
Gabazine accelerates vestibular function recovery but muscimol drastically delays it After UVN, depression of resting activity discharge of the ipsilateral second-order vestibular neurons is responsible for the appearance of vestibular symptoms. Interestingly, pharmacological Only values recorded on the lesioned side are illustrated and data from both sides of control cats were pooled for direct comparison with the subgroups of vestibular deafferented cats. Different letters indicate significant differences between groups of animals: a, significantly different from NaCl group; b, significantly different from gabazine group; c, significantly different from muscimol group; and d, significantly different from control group. Analyzes were assessed by ANOVA followed by Scheffetest for all the VN and the groups ( p Ͻ 0.