dataesr/scientific-paragraphs-categorization huggingface dataset:
Objective: To (i) systematically review the literature to determine the factors influencing diet and dietary behaviour in women living in urban Africa; (ii) present these in a visual map; and (iii) utilize this to identify potentially important areas for future research. Design: Systematic mapping review. The review protocol was registered at PROSPERO (http://www. crd. york. ac. uk/PROSPERO/; registration number CRD42015017749). Six databases were systematically searched, followed by reference and citation searching. Eligibility criteria included women aged 18-70 years living in urban Africa, any design/methodology, exploring any driver, using any measure of dietary behaviour. Quality appraisal occurred parallel with data extraction. Twelve predominantly cross-sectional quantitative studies were included; reported in seventeen publications.
Language was limited to English and French. No publication type limit was applied to yield an adequate representation of the relevant available literature. Following scoping searches, the date was limited to 1971 onwards as studies concerning health behaviour in the context of the epidemiological transition began at that time  (23). The search strategy (see Supplemental Table  2 ) was then used on six online databases in April 2015: EMBASE, MEDLINE, PsychINFO, CINAHL, ASSIA and African Index Medicus. The WHO International Clinical Trials Registry (ICTRP) was searched for ongoing trials and the University of Sheffield Library Catalogue (STARPlus) for relevant theses. The reference lists of included literature and records citing them were also searched alongside data extraction and quality assessment.
All checklist items had a defined 'yes', 'no', 'partial' or 'N/A' grading  (24). Data were extracted from included studies initially by a single reviewer with a standardized form which was initially piloted and modified appropriately. Extracted data comprised that presented in Tables  1  and 2 , with the addition of a column for 'effect of determinant(s) on dietary behaviour' and how each determinant and dietary behaviour was measured (the latter being reported in the online supplementary material, Supplemental Tables  3 4 5 6 ). Income level was categorized according to the World Bank  (25)  , and the level of each determinant was guided by the ecological framework  (17). Extracted data were then checked by another reviewer as double data extraction is more valid  (26). Extracted data informed the iterative synthesis of a visual 'map' of drivers of dietary behaviour to gain a sense of the nature of research available within the topic area.
Acknowledgements Financial support: This research received no specific grant from any funding agency in the public, commercial or not-for-profit sectors. E. C. is supported by the  South African DST/NRF Centre of Excellence in Human Development. Conflicts of interest: None. Authorship: S. C. G. designed the research question with the help of M. H. , R. P. and H. A. O. -K. S. C. G. conducted the research and analysed the data with oversight and guidance from M. H. , H. A. O. -K. , R. P. and E. C. H. A. O. -K. checked 10 % of excluded records at title/abstract and full-text screening stages. M. H. , R. P. and E. C. checked data extraction and quality assessment. S. C. G. led the writing of the manuscript with the help of M. H. , R. P. , E. C. and  H. A. O. -K. All  authors took responsibility for the final editing, reviewing and approval of the manuscript.
), indicating that the overall quality of the studies was fairly high. Strengths comprised sufficient description of the study question/objective, sample selection/ characteristics, data analysis and appropriate design/sample Records identified via database searching (n 6054): MEDLINE, n 1475 EMBASE, n 2240 CINAHL, n 314 Additional records identified via other sources (n 11): STARPlus, n 11 WHO ICTRP, n 0 PsychINFO, n 1968 ASSIA, n 52 African Index Medicus, n 5 Records after duplicates removed (n 4722) Records screened Records excluded (n 4722) (n 4601) Public Health Nutrition assessed for eligibility (n 121) Records identified during data extraction (n 4) Full-text articles Full-text articles excluded, with reasons (n 108): Included in qualitative synthesis (n studies 12) (n records 17) • Setting not Africa, n 77 • Phenomenon of interest not determinants, n 11 • Evaluation does not distinguish between men and women, n 10 • Evaluation focused on children, n 1 • Evaluation does not distinguish between diet and exercise, n 1 • Evaluation not diet or dietary behaviour, n 2 • Unable to obtain full text, n 5 • Review containing no includable studies, n 1.
Women visiting sectional, questionnaire primary-care centres Savy et al. (2008) (39) and Becquey et al. (2010) (40) via interview Quantitative, cross-sectional, questionnaire Ouagadougou, Burkina Faso Low Women, 29-50 years 481 Random, from a database containing an exhaustive list of inhabitants Sodjinou et al. (2009, 2008) (41,42) Quantitative, cross-sectional, survey/ Cotonou, Benin Low Men and women, 25-60 years 200 Multistage cluster. Neighbourhoods, questionnaire households, then individuals Van Zyl et al. (2010) (43) Quantitative, cross- Johannesburg, South Upper middle Men and women, 341 randomly selected Convenience. Residents of Waswa (2011) (44) sectional, questionnaire Quantitative, cross- Africa Eldoret, Kenya Lower middle 19-30 years Women, 20-25 years 260 Johannesburg visiting a mall Stratified random according to sectional, questionnaire university department size including each year *QAS, quality assessment score.
02), respectively. Microbiota analysis performed in 16 cases and 78 controls showed an association between Clostridium neonatale and Staphylococcus aureus with NEC (P = 0. 001 and P = 0. 002). Conclusions: A slow rate of progression of enteral feeding and a less favorable direct-breastfeeding policy are associated with an increased risk of developing NEC. For a given level of risk assessed by propensity score, colonization by C. neonatale and/or S. aureus is significantly associated with NEC. This trial (EPIFLORE study) was registered at clinicaltrials. gov as NCT01127698.
Cohort EPIPAGE2 and ancillary EPIFLORE studies EPIPAGE 2 is an ongoing birth cohort study performed in 68 NICUs in France  (24). Eligible children were those born at 24-31 wk of gestation, admitted to the NICUs recruiting. 10 infants (to be able to characterize the nutritional strategies of the NICU), and alive at day 7, including transferred infants. EPIFLORE (Etude Epidemiliogique de la flore) (NCT01127698) is an ancillary study of EPIPAGE 2 consisting of the establishment of a collection of stools carried out in a subset of 20 NICUs.
Supported by the  French Institute of Public Health Research/Institute of Public Health  and its partners the  French Health Ministry , the  NIH and Medical Research , the  National Institute of Cancer , and the  National Solidarity Fund for Autonomy ; grant  ANR-11-EQPX-0038  from the  National Research Agency  through the  French Equipex Program of Investments  in the  Future ; grant  ANR-12-SV  and  ANR-12-BSV3-0025001/EPIFLORE  from the  National Research Agency  and the  PremUp Foundation. Stool collection was supported by a grant from  Nestec Research Center (Vers-chez-les-Blanc, Switzerland). No funder/sponsor had any role in the design and conduct of the study; collection, management, analysis, and interpretation of the data; the preparation, review, or approval of the manuscript; or the decision to submit the manuscript for publication.
Results and Discussion The cnt operon of P. aeruginosa is regulated by zinc level through the zinc-responsive regulator Zur. In silico analysis of the cnt gene cluster of P. aeruginosa PA14 strain indicated two overlapping open reading frames between cntL and cntM and between cntM and cntI, classically observed in operonic structures (Fig. 1 ). Further screening of the upstream cnt sequence for promoter regions using Bprom software  23  , revealed a σ70 promoter in the 200 base-pairs upstream from the annotated cntO ATG codon (Fig. 1 ). As already reported by Pederick and collaborators, a putative Zur binding box "GTTATagtATAtC" overlaps the -10 box of the predicted σ70 promoter  22, 24. This in silico analysis supports an operonic organization of the four cnt genes and strongly suggests a transcriptional activation of this operon under zinc depletion through the Zur repressor  25, 26.
Indeed, once in the extracellular medium, secreted metallophores are a common good, and a privileged access presumably gives a selective advantage. Pseudopaline is involved in nickel and zinc uptake, depending on the chelating properties of the media. In order to address the involvement of pseudopaline in metal uptake in vivo, we compared the intracellular concentration of various metals in PA14 WT, ΔcntL and ΔcntL::cntL strains. Cells were grown in pseudopaline-synthesis conditions determined above (MS medium) and the intracellular metal concentration was measured by ICP-MS. Under these growth conditions we observed a significant 90% reduction of intracellular nickel concentration in the ΔcntL mutant strain (Fig. 5a ), which was mostly recovered in the complemented strain. The levels of all the other metals were not changed in the ΔcntL mutant strain compared to the WT strain (data not shown).
Electrophoresis was performed using 12% SDS-polyacrylamide gel at room temperature and 25 mA/gel. Immunoblotting was performed as previously described  36  , with rabbit primary and peroxidase-conjugated secondary antibodies respectively directed against V5 epitope (Bethyl/interchim) (dilution 1:5,000) and rabbit IgG (Sigma) (dilution 1:25000). The peroxidase reaction was developed by chemiluminescence (Pierce), scanned and analyzed with ImageQuant LAS 4000 camera and TL analysis software (GE Healthcare Life sciences).
Protein detection by dot blot. A nitrocellulose membrane was incubated 5 min with transfer buffer and dried at room temperature for 3 min. A 5 µL drop of SDS-PAGE protein sample (equivalent to 0. 5 OD 600 units was loaded onto nitrocellulose membranes. After drying, the proteins were transferred on the nitrocellulose for 5 min at 80 V and 0. 1 A using a Fast Blotter System (Pierce). Immunoblotting was perform with SNAP i. d. ® 2. 0 Protein Detection System. The membrane was blocked 5 min in TBS (1X) Tween 20 (0. 1%) skim milk (0. 5%), washed 4 times with TBS-Tween, incubated 10 min in TBS-Tween-milk with primary rabbit antibody directed against the V5 epitope (dilution 1:5,000), washed 4 times with TBS-Tween, incubated 10 min in TBS-Tween-milk with anti-rabbit peroxidase-conjugated antibody and the peroxidase reaction was developed by chemioluminescence, scanned with ImageQuant LAS 4000 camera and analyzed by the ImageQuant TL analysis software.
Acknowledgements This work was supported by the  ANR-14-CE09-0007-03  grant allocated to PA, RV, RL and EBD and the grant from " Vaincre la Mucoviscidose " (RFI20160501495) allocated to RV and PA. We thank  B. Douzi  for fruitful discussions,  B. Ize  for RNA preparation and  C. Soscia  for technical support as well as  O. Uderso ,  I. Bringer  and  A. Brun  for material and media preparations. We also thank  C. Laffont ,  C. Price  and  U. K. Trinler  for reading this manuscript.
CAZymes have been grouped into sequence-based families in the continuously updated CAZy database  (9). The protein-fold, catalytic apparatus, and mechanism are generally conserved in each family  (9) , although substrate specificity can vary  (10). Arabinogalactan proteins (AGPs) are a structurally diverse but poorly characterized group of plant glycans. These molecules are highly glycosylated members of the hydroxyprolinerich glycoprotein superfamily of plant cell wall proteins, with 90% of their total mass being glycans. The core structure of the glycan component of AGPs comprises a backbone of ␤1,3-galactan that is substituted at O-6 with ␤1,6-galactooligosaccharides. These side chains can then be further decorated with arabinose, rhamnose, (methyl) D-glucuronic acid (GlcA), and less frequently, with fucose or xylose moieties  (11) (12) (13).
The protein comprises 470 amino acids and has no sequence simi-larity with any known CAZyme or members of the CAZy database. The capacity of BT0263 to act on AGPs from larchwood, wheat, and GA was investigated. BT0263 only released Rha from GA indicating that the protein is an exo-acting enzyme (Fig. 1A , Table  1 ). BT0263 had a pH optimum of ϳ5 (Fig. 1B ) and experiments performed with BACCELL_00875 demonstrated the new family is likely not to be metal dependent (Table  2 ).
Briefly, this mechanism operates by a general base abstracting a proton from C5 of UA sugars, as this hydrogen is particularly acidic due to the presence of the carboxylic acid group also on C5. This results in an enolate transition state that collapses resulting in the formation of a conjugated double bond between the C4 and C5 and elimination of the glycosidic oxygen from C4, which is concomitantly protonated  (24, 25). This results in the formation of unsaturated UA (⌬4,5-UA) products, which have the characteristic UV signal at A 235 nm observed here  (26). To further confirm the activity of BT0263 as a new PL, we recombinantly expressed BT3687, encoded by AGP-PUL2, as the enzyme is a member of family GH105 in the CAZy database  (9). All members of GH105 characterized to date act exclusively on ⌬4,5-UA-O-R (R is generally a sugar) generated by PLs that act on rhamnogalacturonan-I and ulvan.
Briefly, this family operates through a mechanism where a general acid/base protonates the double bond, resulting in a hemiketal intermediate, which proceeds through either a glycosyl-enzyme, or an epoxide, intermediate causing glycosidic bond cleavage and loss of the C4 -C5 double bond  (27, 28). The activity of these enzymes can therefore be monitored by loss of the UV signal at 235 nm. When the products of oligosaccharides generated by BT0265 and then the lyase BT0263 were incubated with BT3687 the UV signal was lost (Fig. 1D ). Furthermore, the reduction in mass of the BT0263-treated oligosaccharide after incubation with BT3687 was 158, which is entirely consistent with the loss of ⌬4,5-UA with bond cleavage occurring between C1 and O4 of the scissile linkage (Fig. 2, B  and C ). These data confirm that BT0263 is a new PL cleaving the O4 -C4 bond between Rha-␣1,4-GlcA generating a Rha and ⌬4,5-UA linked to an oligosaccharide.
Metal To evaluate this possibility the biochemical properties of two PL27 full-length proteins, BACCELL_00875 and BACFIN_ 07013 derived from Bacteroides cellulosilyticus and Bacteroides finegoldii, respectively, were determined. Both proteins displayed the same activity as BT0263 (Table  1 ), showing that rhamno-glucurono lyase activity is a common feature of PL27. These data also indicate that the catalytic domain in PL27 enzymes comprises the 400-residue C-terminal domain. The potential role of the N-terminal domain is discussed below.
These mutants were E537Q, R593A, D596A, D596N, W599A, H612A, and Y613F. The effect of all of these mutations was significant with E537Q, R593A, D596A, D596N, and H612A substitutions causing a ϳ4,000to ϳ10,000-fold reduction in k cat /K m , whereas the loss of Trp 613 at the top of the pocket resulted in a more dramatic 50,000-fold reduction (Table  3 ). The only mutation that completely inactivated the enzyme was Y613F, suggesting that this residue, sitting deep in the pocket (Fig. 3, B  and C ), is likely a significant component of the catalytic apparatus. A Dalilite search  (31)  was performed to find relatives to BACCELL_00875 that display a similar fold. This search returned a N-acyl-D-glucosamine 2-epimerase, 7% identity (PDB ID 1FP3), a cellobiose 2-epimerase, 10% identity (PDB ID 3WKF), and an ␣-1,6-D-mannanase, 10% identity, belonging to the GH76 family (PDB ID 4V1R).
These homologs, however, had high root mean square deviations (r. m. s. deviations) Ͼ3. 2 and Z-scores Ͻ26. The location of the active site in these enzymes, however, is similar to the position of the proposed catalytic center active of BACCELL_00875 but the catalytic residues do not overlay with Tyr 613 , and the ligands for these enzymes could not be satisfactorily accommodated in the deep pocket of the PL27 family. The closest characterized lyase homolog, a member of family PL15, displays 5% identity (PDB ID 3AFL (  29 )) and has r. m. s. deviations Ͼ4. 0 and Z-score Ͻ11. Again, the location of the active site of the PL15 lyases and the deep pocket (the proposed catalytic center) of BACCELL_00875 are conserved. However, the catalytic residues of the PL15 enzyme, a histidine and tyrosine acting as the general base and acid, respectively, do not overlay with Tyr 613 in BACCELL_00875.
Crystal structure of BT3687 The unsaturated glucuronidase BT3687 was also crystallized and its structure solved by molecular placement using PDB code 4CE7 as the search model  (32). The enzyme also has an (␣/␣) 6 -barrel-fold, as has been shown previously for other members of the GH105 family  (33). The active site location within GH105 enzymes is conserved and allows identification of the putative catalytic residues of BT3687 as Asp 116 and Asp 160 (Fig. 4A ), which overlay well with catalytic apparatus of other structurally characterized members (YteR, YteR2, and Nu_GH105 (28, 32)) of family GH105 (Fig. 4B ). Mutation of Asp 116 and Asp 160 to Ala in BT3687 completely ablated catalytic activity in the B. thetaiotaomicron enzyme (Table  3 ). The Ϫ1 active site pocket of BT3687 is lined with the hydrophobic amino acids Trp 56 , Trp 158 , Met 164 , Trp 225 , and Trp 231 , and appears to be a general feature of GH105 enzymes with YteR, YteR2, and Nu_GH105 all containing the equivalent residues (Fig.
Phylogeny of the new PL family The spread of the new PL family PL27 was investigated through iterative BLASTP and HMM searches. The limited sequence diversity, even between prokaryote and eukaryote sequences, and the absence of any distantly related family in the CAZy database, facilitated the delineation of this family and the construction of a phylogenetic tree (Fig. 5 ). Members are present in several bacterial phyla, particularly the Bacteroidetes (ϳ50 sequences) where ϳ80% are in the Bacteroides genus. Interestingly, within a single species that contains the lyase, this family is not widely distributed in the different strains, a feature that is not shared with other CAZy families. Also noteworthy is the split of the homologs into two distinct proteins in B. thetaiotaomicron. In ϳ50% of the strains in this species the lyase lacks the N-terminal 200 residues comprising the ␤-sandwich domains (these lyases are labeled as FUSED in Fig.
Mass spectra were acquired over the m/z range 250 -3,000 with ion suppression below 700. The laser power setting varied around 50% of maximum with each spectrum acquired using between 1,500 and 4,000 laser shots in total, using Bruker flexControl software. Mass spectra were externally calibrated against an adjacent spot containing six peptides (des-Arg 1 -Bradykinin, 904. 681; Angiotensin I, 1,296. 685; Glu 1 -Fibri-nopeptide B, 1,750. 677; adrenocorticotropic hormone fragment (ACTH) (1-17 clip), 2,093. 086; ACTH (18 -39 clip), 2,465. 198; ACTH (7-38 clip), 3,657. 929 (Sigma)). Bruker flexAna-lysis software (version 3. 3) was used to perform the spectral processing.
Diffraction data were collected using synchrotron radiation at the Diamond Light Source on beamlines I02 and I04. The data were integrated using XDS  (39)  or iMosflm  (40) ; scaled and merged with Aimless  (41). The phase problem for BACCELL_00875 was solved by SeMet-single-wavelength anomalous dispersion using Hkl2map  (42)  and the Shelx suite  (43). Native data of BACCELL_00875 was solved using Phaser (44) using the SeMet-solved structure as search model. BT3687 was solved by molecular replacement using MrBump  (45). The best solution from MrBump was with search model 4CE7 prepared with Chainsaw (46) and solved with Phaser  (44). Buccaneer  (47)  and/or Arp-warp  (48)  were used for automated model building where needed. Recursive cycles of manual model building in COOT  (47)  and automatic refinement in Refmac5 (49) were performed to produce the final model; 5% of the observations were randomly selected for the R free set.
Family delineation and phylogeny BT0263 was used as an initial query against all available genomes in GenBank TM. Proteins with Ͼ60% identity were aligned to identify domain boundaries based on sequence conservation, and then used to build an HMM with HMMER (55). This model capturing the position-specific signal of conserved/ unconstraint residues was used to detect remote family members and iteratively rebuilt until family convergence, which occurred immediately. The sequences of family members were then aligned with Multalin (51) and the resulting alignment was used to construct a neighbor joining tree using BLOSUM62 substitution parameters  (52)  and BIO-NJ (53) and the tree was visualized using Dendroscope  (54).
2 (39. 2) 8. 4 (8. 4) 8. 8 (3. 9) Anomalous completeness 100 (99. 8) Anomalous redundancy 22. 5 (19. 8) Refinement R work /R free 20. 0/25. 0 16. 0/18. 0 12. 1/14. 8 No. atoms Protein 10,688 10,920 2,914 Water 244 1,019 299 B-factors Protein 41. 5 20. 9 12. 0 Water 36. 8 32. 0 23. 5 R. m. s. deviations Bond lengths (Å) 0. 0110 0. 0107 0. 0127 Bond angles (°) 1. 48 1. 45 1. 52 PDB code 5NOK 5NO8 5NOA a Values in parentheses represent outer shell.
The enhanced surveillance zones were selected based on: a high incidence of cholera during the previous five years; a sufficient large population denominator to determine incidence; a history of reliably providing surveillance reports on suspected cholera cases to the National MOH-Surveillance System; reliable health care access for the local population and diagnostic facilities to allow case identification. In these areas we included all health centers that treated the local population for severe diarrhea and collected additional data through community investigations. Usually, specific cholera treatment centers (CTC) were open only during cholera outbreak periods when declared by health provincial authorities. According to the area, the delay to open CTCs varied. Outside outbreaks patients with severe diarrhea were treated at general health centers or hospitals.
Africhol was integrated into the routine cholera surveillance and provided additional support beyond that supported by the MOH. For example, Africhol provided funding for specific additional staff such as a country focal point, a coordinator and a surveillance officer for each zone who ensured the proper conduct of the study, data collection, data quality and supervision of data entry. Also, in the enhanced surveillance zones, whenever possible most suspected cases were culture-tested, while in the routine system, only a few suspected cases at the start, during and at the end of an epidemic were usually tested for cholera. Africhol provided.
Discussion Our analysis is in line with previous published data showing that cholera in Mozambique is marked by spatial heterogeneity and seasonality, with a high concentration of cases during the rainy period between January and March  [5]  and inter-epidemic periods largely free of confirmed cases. Each surveillance zone showed a different pattern of suspected cases distributed over time, although there were clear similarities in the seasonality of suspected cases between the surveillance and outbreaks zones. This heterogeneity may be explained by the hypothesis that in Mozambique outbreaks do not evolve locally, but rather follow cholera reintroduction from distant epidemic regions  [7]. Our study allowed for the measurement of cholera incidence prospectively. Incidence of suspected cases varied widely between sites and between years within the same site.