dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements This work was supported by  ANR  ( Agence Nationale de la Recherche)  and  CGI  ( Commissariat à l'Investissement d' Avenir) through Labex SEAM (Science and Engineering for Advanced Materials and devices ;  ANR 11 LABX 086 ,  ANR 11 IDEX 05 02 ), by the  CNRS (Defi Nano)  and  DIM C'Nano Ile de France. We are grateful to the personnel of the  Paris Cardiovascular Research Center (PARCC)  for animal facility, especially to L. Pidial, to  F. Gendron  and  Y. Klein  for magnetic experiments and to  B. Caron  and  D. Elgrabli  for ICP-MS measurements performed at ISTeP, UMR 7193  CNRS/Université Pierre et Marie Curie. This work has also benefited from the.
This project and PB have received funding from the  7th Framework program  of the  EU ,  SP3-People , support for training and career development for researchers ( Marie Curie), Network for Initial Training (ITN ),  FP7-PEOPLE-2011-ITN , under the  Marie Skłodowska-Curie  grant agreement  N˚289903. This work has been supported in part by grants from the  IHU prometteur OPERA  and the 'Cluster 1 region  Rhone-Alpes. 'PM is a senior member of and supported by the  'Institut Universitaire de France. ' The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
In the Recommendations section, each technology has been assessed according to its suitability for application to EED and this assessment includes an evaluation of the cost, invasiveness and appropriateness for developing countries of each device and/or technique. This assessment was performed in a qualitative manner based on currently available information (for example, the present cost and size of the devices) and the opinions of the authors as to feasible future develop ment. Technique suitability for use in developing countries was determined in a qualitative manner after consideration of the need for advanced infrastructure and high levels of training for either system use or data analysis. Probable deployment time scales have also been assigned to each technique based on the current states of development and the degree of valid ation work that will be required before application to EED.
Modern systems use Fourier domain techniques to achieve A-scans at hundreds of kHz or even MHz (REF. 67)  rates by acquiring data from all depths simultaneously. OCT is inherently fibre compatible and a wide range of endoscopic systems have been developed. The main challenge is the fabrication of a high speed lateral scanning mechanism at the distal tip. A number of forward viewing probes have been reported (for example REF. 68) using similar approaches to distal scanning endomicroscopes, and although these have been used in the gastrointestinal tract (for example REF. 69), side viewing devices are more suited to imaging large areas of lumina. Side viewing probes are readily fabricated by incorporating a right angled prism and one or more micro-lenses at the distal tip of a fibre. Proximally driven rotation of the fibre probe, or rotation of the prism using a micro-motor, generates circular cross-sectional images, while pull-back of the probe enables collection of volu metric datasets  70  over large regions of tissue.
Recommendations Although each of the techniques described above has potential applications in EED, they differ not only in terms of their format, the information they provide, and the type and scale of study they will be most appropriate for, but also in their technological maturity. The TRLs of each technology are listed in TABLE  1 , along with additional information including the expected development timescales. The TRL scale (adapted from a scale originally developed by NASA) ranges from 1 to 9, with '1' indicating an initial concept and '9' representing a mature, commercialized device  102. Other factors rele vant to the adoption of these techniques for EED are also listed, including cost, invasiveness and suitability for developing world use. These additional factors are particu larly important for large scale studies (given issues that can be expected at scale, such as the need for widespread deployment and the analysis of large datasets), although less-so for early aetiological investigations in small groups of patients.
Fingerclip-style spectrometers could be used to monitor the leakage of orally administered contrast agents from the gut to the blood stream, prov iding functional information pertinent to EED. This approach will require validation, either using some of the high-TRL imaging instruments discussed earlier or L:M tests. Once this validation is complete, fluorescence spectroscopy will be applicable to large-scale studies in remote locations due to its practically noninvasive methodology, low cost, simplicity of data analysis and ease of deployment. Interestingly, there might be scope to extend this approach for use with multiple molecu lar probes to evaluate further aspects of intestinal pathophysiology. Finally, PAI could in the future also offer a noninvasive experimental protocol for the assessment of gut permeability (similar to that described for fluorescence spectroscopy), with an external PAI probe used to image the small intestine from outside of the body.
Conclusions EED is a widespread condition in developing countries, in some cases affecting almost entire regional populations, and has severe negative impacts on the physical and cognitive development of children. Given that EED remains poorly understood, it is vital that new technologies and approaches are investigated and implemented to improve understanding of the disease and to help guide the development of new therapies. We have identified and assessed optical biopsy techniques with potential to assist in this area. Although many optical methodologies could potentially be applied, we have highlighted endoscopy (including HD, NBI and capsule endoscopy), fluorescence endomicroscopy, OCT, fluorescence spectroscopy and PAI as the most promising. These will provide data not only on structural changes in the intestine, but also on the degree of intestinal permeability.
In addition, the correction of iron overload by phlebotomy is not always sufficient to normalize pituitary function  [29]. These data emphasize that the age at diagnosis and the stage of the disease -especially liver complicationsare determining factors for the success of phlebotomy, perhaps because of other indirect effects of Idiopathic Hereditary Hemochromatosis (IHH) (e. g. diabetes and cirrhosis). It is crucial to establish the diagnosis and to start treatment at an early stage of the disease. Thus, patients diagnosed for hereditary hemochromatosis and suffering from infertility or other reproductive disorders should have a brain Magnetic Resonance Imaging (MRI) and a Gonadotropin Releasing Hormone (GnRH) test in order to detect pituitary iron deposits. They could thus be treated by a combined therapy of hCG and phlebotomy.
Acknowledgements Collaborators in ESICM Working Group on Gastrointestinal Function:  Claudia Spies ,  Klinik für Anästhesiologie mit Schwerpunkt operative Intensivmedizin der Charité-Universitätsmedizin Berlin, Campus Virchow Klinikum, Berlin ;  Pietro Vecchiarelli ,  Intensive Care Unit ,  Ospedale Belcolle ,  Strada Sammartinese ,  Belcolle Hospital , Viterbo, Italy;  Anne Berit Guttormsen ,  Department of Anesthesia and Intensive Care, Haukeland University Hospital, Bergen, Norway. The costs covering the open access publication of this article were covered by the  International Fluid Academy (IFA). The IFA is integrated within the not-for-profit charitable organization iMERiT ( International Medical Education and Research Initiative)  under  Belgian Law , and IFA website (http://www. fluidacademy.
In 2017, chloroplast genomes of four other Chinese Juglans species were investigated (J. sigillata, J. cathayensis, J. hopeiensis, and J. mandshurica) by a combination of de novo and reference-guided  (Hu et al. 2016 -NCBI Accession number KT963008) assembly of whole chloroplast genomes  (Hu et al. 2017). Chloroplast genome lengths ranged between 159,714 (J. hopeiensis) and 160,367 (J. regia) bp with 36. 1% GC content and contained 129 genes each, 88 protein-coding genes, 40 tRNA genes, and eight rRNA genes. Seventy-nine genes were chosen for analysis of selective pressure, and five genes were found to be under positive selection. Another recent study indicates some putative mis-annotated and unannotated genes from chloroplast genome sequence of J. regia  (Chakraborty 2016). Recently, the phylogenetic position of J.
Progress on transcriptomics Transcriptomics is the study of the complete set of RNAs encoded by the genome at specific times and under specific conditions. ESTs generate millions of short single-pass nucleotide sequence reads for transcriptome exploration (Nagaraj. 2006 ). Availability of this information in walnut has increased the development of markers like SSRs which are derived from cDNA libraries. These are more evolutionarily conserved and therefore have higher transferability to related species than non-coding sequences. The first construction of walnut ESTs was accomplished in J. regia (Table  5 ). Five thousand twenty-five ESTs from seed coat tissues covering 16. 41 Mb  (Muir et al. 2004 ) have been submitted to NCBI database (https://www. ncbi. nlm. nih. gov). Three years later, an additional 13,559 ESTs were developed (2715 from leaves and 10,844 from roots) from J.
Moreover, a diet with increased PUFA from walnuts is also linked to longterm beneficial effects on type II diabetes  (Tapsell et al. 2009). Dietary walnut fingerprinting using HPLC-q-ToF-MS analysis characterized some urinary biomarkers, such as fatty acids metabolites,  (Garcia-Aloy et al. 2014 ) and positive effects of walnut consumption on inflammatory processes, vascular reactivity, glycemic control (Ros 2010), and oxidative stress  (Zhao et al. 2014)  were described. However, walnuts also can be responsible for food-induced allergies, an emergent public health problem, and techniques to detect and characterize J. regia and J. nigra allergens have been developed  (Costa et al. 2014). Since August 2017, 115 bioactivity screening studies of J. mandshurica and J. regia have become available on NCBI database (https://www.
2014). Four extractable protein fractions were obtained according to their solubility (glutenin 72. 06%, albumin 7. 54%, globulin 15. 67%, and prolamin 4. 73%). These could constitute a good source of essential amino acids for adults. SDS-PAGE analysis showed that molecular weights ranged from 14. 4 to 66. 2 kDa and two-dimensional gel electrophoresis (2DE) profiles showed that isoelectric points were between 4. 8 and 6. 8. Walnut allergen stability during roasting in J. regia was investigated by liquid chromatography-mass spectrometry  (Downs et al. 2016). Results showed an increase in mature 7S and 11S globulins, known allergens, after roasting for 20 min at 180 °C, probably due to an increase in protein digestibility. Since August 2017, 56,050 protein sequences from J. regia are now available on NCBI database (https:// www.
California breeding program In the USA, germplasm collections are maintained by the Walnut Improvement Program at the University of California in Davis, CA, and the USDA National Clonal Germplasm Repository in Winters, CA. The UC Walnut Improvement Program objectives include breeding to improve scion cultivars and rootstocks for the California walnut industry, development of better knowledge and methods in order to make breeding more efficient, acquisition, development, and maintenance of diverse germplasm with traits useful for future breeding, and application of new molecular and genomic methods for walnut improvement. Detailed information about the Walnut Improvement Program is available from the Walnut Research Reports Database at the University of California, Fruit and Nut Research Information Center website (http://ucanr.
Acknowledgments We gratefully thank  Joseph A. Grant  ( Cooperative Extension Farm Advisor, San Joaquin County, California ),  Patrick J. Brown , and  Charles A. Leslie  ( UC Davis, Department of Plant Sciences, California ) for helping us to draft the BCalifornia breeding program^part. We acknowledge  Philippe Jardel  (Walnut producer in Martel, France),  Eloïse Tranchand  ( Walnut Experimental Station of Creysse, France ), and  Guillaume Charrier  ( INRA Clermont-Ferrand, France ) for providing us information about perspectives in French walnut. We thank again  Charles A. Leslie  and  William Nicolas  ( CNRS Bordeaux, France ) for English language revision. Finally, this work could be achieved thanks to a fixed-term contract funded by the  INRA  and the Ctifl.
This study suggests that the dietary source of the SFAs might determine their implication in obesity. The main strength of our study is that it includes data from a country where the incidence of obesity has increased tremendously within a short period of time, escalating from 40% to more than 65% in 40 years (1), suggesting a lifestyle implication in this steady increase. The silhouettes available in our study showed that the majority of the participants were lean during childhood and adolescence and had developed obesity during life course, bringing upfront the implication of the environment and food consumption as promoter of the obesity in Mexico. However, our study is limited by its cross-sectional design. Blood samples and anthropometric measurements were collected together during recruitment, and therefore the association between obesity and FAs found should be interpreted in this specific context.
Angeles-Llerenas, M. J. Gunter, I. Romieu, and V. Chajès. Association between serum phospholipid fatty acid levels and adiposity in Mexican women. J. Lipid Res. 2017. 58: 1462-1470. Supplementary key words obesity • desaturation index • body mass index • waist-to-hip ratio. This work was partially funded by a postdoctoral fellowship from the International Agency for Research on Cancer. This work was undertaken during the tenure of the postdoctoral fellowship of E. K. A. , from the IARC, partially supported by the European Commission FP7 Marie Curie Actions-People-Cofounding of Regional, National and International Programmes (COFUND). The CAMA study was financially supported by National Council of Science and Technology, Mexico Grant 2002-C01-7462. The authors declare no conflicts of interest.
MIC currents are recorded after dialyzing intracellular media by an intrapipette solution containing EGTA to chelate intracellular Mg 2+. MIC currents develop during the cytosol dialysis and reach a steady state in ~15 minutes (Figure  2A , averaged trace of nine cells). These currents have a typical shape of TRPM7-like currents with a small inward component (-2. 6±0. 9 pA. pF -1 at -100 mV), a reversal potential close to 0 mV, and a strong outward rectification (19. 5±3. 6 pA. pF -1 at +100 mV; Figure  2B , averaged trace of nine cells). Intracellular Mg 2+ inhibits MIC currents in a concentration-dependent manner. The free Mg 2+ concentration in the patch clamp pipette is calculated using the WEBMAX software. MIC currents are inhibited by free [Mg 2+ ] i of 210 μM, 400 μM, and 680 μM (Figure  2C ).
RT-PCR and Quantitative RT-PCR RNA extraction was performed using the standard Trizol-phenol-chloroform protocol. Total RNA (1 μg) was reverse-transcribed into cDNA with random hexamers and Multi-Scribe Reverse Transcriptase (Applied Biosystems). PCRs were carried out using an iCycler thermal cycler (Biorad) and Taq DNA polymerase (Invitrogen) with, respectively, 30 and 40 cycles for β-actin and TRPM7 primers. PCR products were visualized on agarose gels and quantified using Quantity One Software (Biorad). Results were expressed as TRPM7 expression normalized to β-actin expression for semiquantitative RT-PCR experiments. Quantitative RT-PCR was performed on a LightCycler system (Roche) using a mix containing SYBR green (Applied Biosystem). TRPM7 mRNA quantities were normalized to β-actin as a housekeeping gene.
2 with CsOH). Free [Mg 2+ ] i was estimated using the program WEBMAXC STANDARD (http://www. stanford. edu/~cpatton/webmaxcS. htm). Signals were filtered at 1 kHz and digitized at 5 kHz using an Axopatch 200B patch clamp amplifier (Molecular Devices Inc. ) combined with a 1322A Digidata (Molecular Devices Inc. ). The MIC current was recorded after the dialysis of intracellular media by 0 Mg intrapipette solution. The MIC current was calculated as the difference between the steady-state current activated by the depletion of [Mg 2+ ] i and the basal current recorded few minutes after patch rupture. MIC currents were expressed as current densities (in pA. pF -1 ) by dividing the current intensity (in pA) by the cell capacitance (in pF). Electrophysiological protocols and analyses were made using pClamp 10, Clampfit (both by Molecular Devices), and Origin 6.
Statistical Analysis Data are presented as mean±SEM, n refers to the number of separate experiments or to the number of cells, and N refers to the number of cell line passages. Statistical analyses were made using Student's t tests or Mann-Whitney rank sum test depending on sample normality or paired Wilcoxon signed rank test using Sigma-Stat 3. 0 (Systat Software, Inc. ). When more than two conditions were compared, a Kruskal-Wallis one-way analysis of variance was used followed by Dunn's method post hoc tests using SigmaStat 3. 0 (Systat Software, Inc. ).
Bioinformatics analysis Blastp searches were performed against predicted B. cellulosolvens proteins, using deduced amino acid sequences of the known cohesin and dockerin modules as queries  [16, 17, 33]. Hits above an E-value of 10 -4 were examined individually, by searching for characteristic sequence features. For example, for dockerin modules, we searched for two Ca 2+ -binding repeats, putative helices and linker regions. Multiple sequence alignments were created using the Clustal Omega server [http:// www. ebi. ac. uk/Tools/msa/clustalo/]. Phylogenetic trees were generated by iTOL version 3 [http://itol. embl. de/] according to the "One Click" Phylogeny analysis tool [http://www. phylogeny. fr/simple_phylogeny. cgi]. Signal peptide sequences were predicted using the SignalP server [http://www.
For cell lysate-based ELISA, the 96-well ELISA plates were coated with cellobiose-grown B. cellulosolvens cell lysate, and graded concentrations of the desired Xyn-Docs were used to examine cohesin-dockerin interactions. Absorbance was plotted as a function of Xyn-Doc fusion proteins concentration. For comparative purposes, the reference concentration of a Xyn-Doc standard that generates a maximum response was used in order to normalize the data as a relative binding of maximum response, as described earlier  [35]. The results were presented as a heatmap (iTOL version 3, http://itol. embl. de/), whereby each node is associated with multiple numerical values, which are displayed as a set of colored boxes. Dataset values are mapped to a color gradient corresponding to the binding strength.
cellulosolvens will be of type II and vice versa  [16]. Remarkably, we observe this pattern in all B. cellulosolvens cellulosomal proteins that have orthologues in other cellulosome-producing bacteria. The cohesin modules within the scaffoldins exhibit a variety of intriguing sequence features. This bacterium also has some unique cohesin sequences which are somewhat different from the canonical type I or type II classification, according to the majority of known cellulosomal systems  [21, 53]. Multiple sequence alignment of the cohesins can be found in Additional file 3: Figure  S2  (the file includes scaffoldin accession numbers). Of the various B. cellulosolvens cohesins, 75 are classified into the two main types: type I (33 modules) and type II (42 modules). In addition to the canonical cohesin types I and II (and type III of the ruminococci), three B.
Funding This research was supported by Grant No. 1349  from the  Israel Science Foundation  (ISF) and by the  United States-Israel Binational Science Foundation (BSF) , Jerusalem, Israel. In addition, a  joint Research Grant  (No. 2566/16 ) from the  Israel Science Foundation (ISF)-National Natural Science Foundation of China (NSFC)  entitled "Decoding the Pseudobacteroides cellulosolvens biomasssensing mega-regulon" is gratefully acknowledged. The authors appreciate the support of the  European Union ,  Area NMP. 2013. 1. 1-2:Self-assembly of naturally occurring nanosystems: CellulosomePlus Project number:  604530  and  European Union Horizon 2020  contract: Sustainable production of next generation biofuels from waste streams:  Waste2Fuels. This research was funded in part by the  Bioenergy Science Center (BESC) , which is a  U.
Secondly, in the 'Other solid foods' category, foods exceeding 400 kcal/100 g allocated to Class 1 were systematically downgraded to Class 2, or from Class 2 to Class 3, and foods with an ED > 500 kcal/100 g and a sodium (Na) content >200 mg/100 g allocated to Class 3 were downgraded to Class 4. Only three foods of the CIQUAL database were affected by the second exception. In fact, in the majority of cases, expressing SAIN SENS per 100 kcal was sufficient to penalise foods with a high energy density, because of their automatically low SAIN SENS. However, rare cases remained where, despite a high energy density, some foods could access favourable SENS classes thanks to their relatively low LIM SENS (e. g. potato crisps with low amounts of sugar, SFA and limited amount of sodium). The second exception was therefore introduced to fully take into account global recommendation to reduce the intake of energy-dense foods to prevent excessive weight and obesity  [24, 25].
Application of the SENS algorithm to the French database and statistical analysis After removing duplicates, a final sample of 1065 foods and beverages (alcoholic beverages excluded) from the CIQ-UAL 2013 database distributed across 26 food groups (listed in Table  3 ) was included for analysis. The amount of fibres (/100 g of foods) available in the CIQUAL 2013 database was estimated using the AOAC method. Some of the information required to estimate SENS class was missing from the CIQUAL food composition tables, which was completed with data on free sugars following the methodology published elsewhere  [26]. For this study, standard recipes were provided by the French Agency for Food, Environmental and Occupational Health & Safety (limited access database), and were used to estimate the percentages of FV, cheese, other dairy products, cereals, fish and eggs.
In contrast, the original FSA-Ofcom was shown to be highly correlated to the energy density of foods yet only loosely correlated to nutrient density scores  [32]. There are limitations to address. The food database used for this study was too generic to fully demonstrate the precise discriminative capacity of the SENS algorithm within a narrow range of food products. However, during the iterative development process, the classification was cotested on both the CIQUAL database of generic food products and on a database of real food products (n = 1737), and it was the resulting classifications at each step of the process that helped forge the final SENS algorithm  [16]. For instance, while generic cheeses mainly scored in Class 3, 'real' cheese products were well scattered from Class 2 to Class 4 (data not shown).
Acknowledgements Several food companies and sectors have financially contributed, as stakeholders to this project:  Atla ,  Auchan Retail ,  Boissons rafraîchissantes de France, Carrefour, Casino, Findus, Fleury Michon, Marie Sablé, Monoprix, Système U, Unijus. This contribution reflects their involvement for the improvement of the provision of food information to consumers and should not be considered as a support to the system described in this publication.