dataesr/scientific-paragraphs-categorization huggingface dataset:
DWV load decreases when the temperature increases We next investigated the effect of rearing temperatures on DWV loads in bees reared in cages (Fig. 5A  and B , N = 289 pools of 5 bees). For the dataset corresponding to the temperature treatments ranging from 28 °C to 43 °C the best model considered colony as a random effect variable, and IVL and the interaction between time and treatment as fixed effect variables (Tables  S1-S3 , Model 2). The model explained 40% of the viral load variance, with fixed effect variables explaining 39%. IVL influenced D2 and D7 viral loads: higher initial viral loads were associated with higher viral loads over time (D2 or D7) (see Fig. S7 ). Viral loads after two days of treatment (D2) were higher for T28 than T37, T40 and T43 (Table  S4 ). Viral load after 7 days (D7) differed.
88 × 10 13 and 1. 99 × 10 13 , respectively, p = 0. 0115), but a significant decrease for T43 (median value = 3. 13 × 10 12 and 2. 28 × 10 12 , respectively, p = 0. 0083, Table  S4 ). No difference in viral load between D2 and D7 was observed for the other temperatures. For the dataset comparing T15 and T34 DWV loads (experiment 3), the best model considered colony as a random effect variable, and the three following interactions as fixed effect variables: IVL and treatment, IVL and date, and date and temperature (Tables  S1-S3 , Model 3). The model explained 92% of the viral load variance, with fixed effect variables explaining 84%. The three interactions complicated the interpretation of Model 3 results (Table  S5 ), and significant differences have to be considered with caution, given the low number of colony replicates (n = 3).
Acknowledgements. References. Bios. Acknowledgements This work was financially supported by  National Natural Science Foundation of China  (Nos. 81673172 ,  21475144 ,  21275152  and  91227116  to A. L. , Nos. 21706273, 21878324 to Z. Z. ) ,  Major Program  of  Shandong Province Natural Science Foundation  ( ZR2018ZC0125 ) to A. L. , the  CAS Pioneer Hundred Talent Program  (Type C, reference #  2016-081 ) to Z. Z. ,  Platform Chimie NanoBio ICMG FR 2607 (PCN-ICMG)  to S. C. , and  ANR  ( ENZYMOR-ANR-16-CE05-0024 ) to E. L. X. X. acknowledges a  Government of Ireland Postgraduate Scholarship  ( GOIPG/2014/659 ) and a H. C. Ørsted COFUND  fellowship.
Background: According to the 2015 report of the Joint United Nations Program on Human Immunodeficiency Virus (HIV) and Acquired Immune Deficiency Syndrome (AIDS), the prevalence rates of HIV infection among men who have sex with men (MSM) varied from 6 to 37% depending on the country, far exceeding the national prevalence rates. The present study on HIV infection among men who have sex with men in sub-Saharan Africa was conducted to describe the different sampling methods used to identify this target population and compare the prevalence rates of HIV infection among MSM to that of men in the general population. Methods: The selection of studies to be included was carried out in the principal electronic databases. The 2009 Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) directives were used throughout the entire process.
Data source and search strategy The search was carried out using the following electronic databases: PubMed, EMBASE, Cochrane, Web of Science, Scopus and Google Scholar. The PICOS (Population Intervention Comparison Outcomes Study design) approach was used in this search strategy (Additional file 1). The following keywords were employed in this search: "HIV," "prevalence," "men," "men who have sex with men," and "sub-Saharan Africa. " The published studies included did not deal with both the MSM and general male population simultaneously (Additionnel file 2). They provided the HIV infection prevalence among MSM. In an approach similar to that of Baral et al. [6] , we consulted the Macro International database for Demographic and Health Surveys in each country in sub-Saharan Africa (http://dhsprogram.
Data collection Data collection was carried out using a previously designed tool (Additional file 3). It was used to collect the following information: the identification of studies, target population, method used, software employed for data analysis, and results. This extraction was carried out independently by two (2) reviewers. Disagreements between the two were usually resolved through discussion based on the information to be retrieved as found in the data collection guide. The assessment of the risks of bias was performed using the Mixed Methods Appraisal Tool (MMAT)  [8].
Results The study selection process began on November 15, 2016. Five hundred thirty-six documents were found: 532 studies in electronic databases and 4 in UNAIDS reports. After eliminating the duplicates, 299 documents were retained. After reading their titles and abstracts and checking whether they met inclusion criteria, some studies were excluded (195). Thus, 104 articles were selected to be read in full. The reasons for exclusion were related to non-compliance with the target population, geographic area, exposure, type of estimate and frequency measurements calculated in the study. At the end of this process, 17 articles completely met the inclusion criteria and were selected (Fig. 1 ). The characteristics of the studies included in this literature review are summarized in Table  1. The average prevalence rate of HIV was 17.
3  Assessment of the prevalence ratio HIV infection among MSM compared to men in the general population and the prevalence of HIV infection among MSM compared to men in the general population of countries in sub Saharan Africa authors used the RDS method for sampling subjects, only half of them produced weighted data that considered the overall contribution of each referral chain  [44, 56, 57]. This situation may affect the representativeness of the MSM in the studies. Otherwise, MSM are included in men of the general population. This could have increased estimates of HIV infection prevalence in the general population of men. Selection bias is also possible because our research did not extend to unpublished articles and conference abstracts, which could affect the results of our systematic review.
This could be partly responsible for the degree of associations observed in our study. To minimize this bias, DHS data and annual progress reports were sought to complement and refine the information provided by conventional databases. The extent to which MSM are included, excluded or unidentified in these national estimates affects both their validity and the ability of our study to compare the prevalence of HIV among MSM with that among men in the general population. This may result in a classification bias or even an underestimation of the final result. However, the sensitivity analysis carried out for this purpose showed similar results in both groups.
Acknowledgements The authors are sincerely grateful to  Frédéric Bergeron , information specialist for his advice and guidance in the documentary research strategy at the  University of Laval in Quebec, Canada. (CNRRPEC-CNHU/Bénin ), Cotonou, Benin. 2  Institut Régional de Santé Publique (IRSP), Université d'Abomey-Calavi (UAC), Ouidah, Bénin. 3 Centre de Recherche sur les Soins et Services de Première Ligne de l'Université Laval (CERSSPL-UL) ,  Université Laval, Québec ,  Canada. 4Axe Santé des populations et pratiques optimales en santé  Centre de Recherche du CHU de Québec, Université Laval, Hôpital du Saint-Sacrement, Quebec City, Canada. 5Centre  Inter-facultaire de Formation et de Recherche en Environnement pour le Développement (CIFRED) ,  Université d'Abomey-Calavi (UAC), Calavi, Benin.
Ø endings in Dutch dialects In this section, we review the main instances of zero morpheme discussed in the literature on Dutch varieties, which generally builds on data collected in the Syntactic Atlas of Dutch Dialects (SAND,  Barbiers et al. 2005; 2008)  and to a lesser extent the Goeman-Taeldeman-Van Reenen Project Database (GTRP;  Goeman & Taeldeman 1996). SAND and GTRP also represent the main source of the data discussed in the present paper. When necessary, though, data have been included that are collected in publications concerning specific Dutch varieties (indicated in the relevant sections). The case studies discussed below focus on verbal inflection (section 2. 2) and adjectival concord (section 2. 3). After introducing the relevant data and the main analyses that have been proposed, we suggest a refinement of the latter in terms of Turbidity Theory, which is illustrated in the next section.
The same holds for the prs. 2pl form, which is leven in B&M, but leef in the database. To sum up, even though they are mostly similar to our data, the data of B&M a) contain only single forms, whereas in some cases we found multiple alternatives, b) they sometimes contain different forms than in our data, and c) they sometimes contain forms where we found none. In order to harmonize the two data sets we would have to remove some competing forms, change others and add forms where no data is present, but is unclear how this should be done. See Kim  Sang (2016)  for a full report on the reproduction of B&M data. Some generalizations that seem to hold for the whole set of dialects have been proposed by B&M, according to whom a) all the 4-affixes systems display a -st prs. 2sg verbal ending 1 2 and a du/dich 2sg pronoun 13 and b) the prs.
3sg verbal ending is spelled out by -t. Interestingly, though, there are dialects with a 4-suffixes system that seem to violate a). The variety spoken in Bree, for instance, displays a prs. 2sg -s ending, rather than the 12 Some variation can be found by comparing SAND and GTRP data. For instance, the GTRP database gives  As shown by  Goeman (1999) , many Dutch dialects show an optional process of word final t-deletion, which is particularly productive in the Betuwe region. 14 This process is conditioned by the morphological category of the relevant form, as -t deletes more frequently along the following scale: (regular) sup < n < pst. ptcp < prs. 3sg < prs. 2sg < pst. 15 Together with the presence of the du/dich 2sg pronoun, which otherwise occurs only in varieties displaying the -st prs.
However, since it lacks the pronunciation relation, /ə/ does not make it to the phonetic modules and is thus inaudible. If the attributive 'dead' agrees with a f/pl noun, though, /ə/ enjoys both a projection and a pronunciation relation. As a consequence, it triggers intervocalic weakening and is audible. 21  A similar approach also holds for the Limburg dialects data shown below. In these dialects, feminine, plural and neuter attributive adjectives all lack the schwa ending. Nevertheless, feminine and plural adjectives contrast with neuter adjectives  (Van Oostendorp 2005; Hermans 2009 ). Given the absence of any ending, the contrast needs to be expressed in another way: the tonal profile. As shown in (  21 ), whereas neuter adjectives display Accent 1, feminine, schwa-less adjectives display Accent 2, namely the same tonal profile of masculine adjectives, which crucially end in schwa 22 : (21) Accent 2 Accent 1 wíís wíìs-Ø wíìz-ə wise.
A total of 2040 projection images were recorded during the scan with a rotation step of 0. 10°. The reconstruction of the 3-D image was done using the Feldkamp algorithm  (Feldkamp et al. 1984)  implemented in a commercial software (SkyScan NRecon). Suitable alignment, beam hardening, and ring artefact corrections were used. In order to analyze the mineral distributions of the samples, the tomographic images were denoised, the various material phases were segmented from each other and the distributions of each mineral phase were analyzed separately. First a non-linear variance-based noise-reduction filter  (Gonzalez and Woods 2002)  was used to denoise the 3-D X-μCT images. Before further processing, the LTDE-SD-GRD1 sample was segmented into two sub-samples: the first one contained the alteration rim and the second one contained the less altered rock matrix.
Scanning electron microscopy In order to have structural information on micrometer scale, to identify the minerals and their alteration products (e. g. clays) in the samples, the samples were analyzed using a field emission scanning electron microscope (FE-SEM) Hitachi S-4800 model with Oxford instruments X-sight X-ray diffractometer (EDS). The FE-SEM-EDS was used in high vacuum mode with COMPO back scattered signal, 20 kV accelerating voltage and 1 nA probe current. The FE-SEM-EDS system was operated by Oxford Instruments INCA and AZtec softwares and the semiquantitative analytical data obtained for elemental composition was normalized to 100 %.
When taking into account the beta correction factor (Siitari-Kauppi 2002), the activities can be converted to a spatial porosity distribution using equation 𝜖 𝑛 = 𝜌 𝑟 𝜌 0 ⁄ 1 + (𝜌 𝑟 𝜌 0 ⁄ -1) 𝐴 𝑛 𝐴 0 ⁄ 𝐴 𝑛 𝐴 0 (1) where εn is porosity of a pixel n, ρr local density of the rock, ρ0 density of C-14-PMMA, An the activity of pixel n and A0 the activity of C-14-PMMA. Now the total connected porosity (εp) of the sample can be determined by equation 𝜖 𝑝 = ∑ 𝜖 𝑛 𝑁 𝑛=1 𝑁 (2) where N is the total number of pixels. The spatial porosity distributions and total porosities were determined using Eqs. (  1 ) and (  2 ) and an in-house built MATLAB-script (MathWorks Inc. , Natick, Massachusetts, USA) that applies the MATLAB Image Processing Toolbox. Fractures were detected from autoradiographs using the algorithm depicted by  Mazurier et al.
For example, when analyzing the impact of increasing access to physical activity spaces, we did not simply assume that a community started from a baseline access level of zero, but instead we used publicly available information about each community's policies and environment to estimate the baseline level for each lever. Baseline lever settings were determined by reviewing data and literature on the existing environment for physical activity, nutrition, tobacco, and clinical services policies, such as city, county, and state information from the literature, and secondary data sources, such as the US Census Bureau and the National Health and Nutrition Examination Survey.
Translating CTG activities into PRISM inputs Building on previous work  (11) , we used the RE-AIM (reach, effectiveness, adoption, implementation, maintenance) framework to translate CTG activities into PRISM lever inputs for simulation modeling  (25) (26) (27). The evaluation focused on reach and effectiveness. To assess reach, we used awardee-submitted estimates of the number of people reached by their activities. CDC provided awardees with written guidance on estimating reach, including metrics, definitions, and potential data sources. Awardees were also encouraged to obtain technical assistance from CDC project officers when estimating intervention reach. Reach was operationalized as the estimated number of people in the target population who had increased access to (eg, those living within 1 mile of a park), are protected by (eg, a workplace smoke-free policy), or affected by (eg, patients covered by a community health worker program) an intervention  (6).
6a ). The RMSD between TM287 and TM288 decreases from 2. 55 Å to 1. 98 Å as the transporter is converted from the IF to the OF conformation, indicating that OF TM287/288 is more symmetric (Supplementary Fig. 6b ). Whereas a similar degree of symmetry was observed between the half-transporters of OF ABCB1 (PDB: 6C0V, RMSD of 2. 07 Å), the equivalent superimpositions exhibit substantial asymmetries in the OF structure of MRP1 (PDB: 6BHU, RMSD of 4. 54 Å), mostly owing to asymmetries in the TMDs (Supplementary Fig. 6b ). Extracellular gate opening is less pronounced in MRP1 and even less so in ABCB1, and the gate remains almost completely closed in the outward-occluded structure of McjD 4 (Supplementary Fig. 6b ). Hence, structures of OF and Occ ABC exporters show their largest structural variation in the extracellular gates.
To probe the atomic details of the conformational dynamics underlying the IF-OF transition, we performed MD simulations of TM287/288 in a POPC lipid bilayer starting from the IF crystal structure (PDB: 4Q4A), after docking a second ATP-Mg molecule into the consensus site  11  and introducing the 2xDtoA mutations in the extracellular gate. As in our previous MD simulations of wild-type TM287/288  11  , we observed spontaneous large-scale conformational transitions from the IF conformation via an Occ state to an OF conformation; this complete transition was observed in 3 out of 20 independent 500 ns simulations (Supplementary Fig. 10 ). Despite the limited statistics, the transition appears to be slightly more frequent than for the wild-type (6 out of 100 simulations  11  ), in agreement with our experimental results and the notion that the polar contacts of the two aspartate residues increase the energy barrier of extracellular gate opening.
NBD opening is further slowed down if the 2xDtoA mutations are combined with the EtoA mutation for both ATP-Mg and ATP-EDTA. From this dataset one can draw two major conclusions. First, ATP hydrolysis weakens the NBD dimer and is required to reset the transporter to the IF state under physiological conditions where ATP and Mg 2+ are always present. And second, strong contacts at the extracellular gate are mandatory to exert a mechanical force onto the NBDs to facilitate fast NBD opening in order to reset the transport back to its IF state.
Diffraction data were collected with a wavelength of 1. 0 Å at 100 K at the beamlines X06DA and X06SA at the Swiss Light Source (SLS, Villigen, Switzerland). Diffraction data were processed with the program XDS  39  and truncated using the Diffraction Anisotropy Server with default settings  40  due to strong or severe anisotropy, what lead to improved electron density maps (Supplementary Table  1 , Supplementary Fig. 13 ). The TM287/288(EtoA) -Sb_TM#35 -ATPγS-Mg complex structure was solved by molecular replacement in Phaser 41 using a modified homology model based on Sav1866 (PDB: 2HYD). The crystals belong to the space group P2 1 containing two TM287/288 heterodimers and two sybodies per asymmetric unit. After a few cycles of model building in Coot  42  and refinement in Buster (www. globalphasing.
com), a poly-alanine model of a nanobody (PDB: 1ZVH) was manually placed into additional electron density. Multiple iterations of model building in Coot and TLS refinement in Buster resulted in a final model with good geometry (Ramachandran favored/outliers: 96. 54%/0. 08%) (Supplementary Table  1 ). Chains A (TM287), B (TM288) and E (Sb_TM#35) were used for structural analysis and figures. In order to determine the TM287/288(2xDtoA/EtoA) -Sb_TM#35 -ATP-Mg complex structure, the final TM287/288(EtoA) -Sb_TM#35 -ATPγS-Mg complex structure was used for refinement against the TM287/288(2xDtoA/EtoA) -Sb_TM#35 -ATP-Mg data. The 2xDtoA mutations were introduced and the ATPγS replaced by ATP in Coot. TLS refinement in Buster resulted in a final model with good geometry (Ramachandran favored/outliers: 96.
58%/0. 24%) (Supplementary Table  1 ). Chains A (TM287) and B (TM288) were used for structural comparison with the TM287/288(EtoA) -Sb_TM#35 -ATPγS-Mg complex structure. The TM287/288(2xDtoA/EtoA) -Nb_TM#1 -ATPγS-Mg complex structure was solved by molecular replacement in Phaser using the TM287/288(EtoA) -Sb_TM#35 structure without the sybody. The crystals belong to the space group P2 1 containing two TM287/288 heterodimers and two nanobodies per asymmetric unit. After some cycles of model building in Coot and refinement in Buster, Phaser was used to place the missing nanobody using a homology model based on PDB entry 5OCL. Multiple iterations of model building in Coot and TLS refinement in Buster resulted in a final model with good geometry (Ramachandran favored/ outliers: 94. 68%/0. 24%) (Supplementary Table  1 ).
Chain A (TM287), B (TM288) and E (Nb_TM#1) were used for figures. The TM287/288(2xDtoA/EtoA) -Nb_TM#2 -ATPγS-Mg complex structure was solved by molecular replacement in Phaser using the TM287/288(EtoA) -Sb_TM#35 structure without the sybody. The crystals belong to the space group P1 containing two TM287/288 heterodimers and two nanobodies per asymmetric unit. After several cycles of model building in Coot and refinement in Buster, Phaser was used to place the missing nanobody using a poly-alanine homology model based on PDB entry 4LAJ. Multiple iterations of model building in Coot and TLS refinement in Buster resulted in a final model at 4. 2 Å resolution (Ramachandran favored/ outliers: 93. 34%/0. 83%) (Supplementary Table  1 ). Chain A (TM287), B (TM288) and E (Nb_TM#2) were used for figures.
Interspin distance simulations were performed with the software MMM2015 using the MTSL ambient temperature library  46, 47. Transport assay. L. lactis NZ9000 ΔlmrAΔlmrCD cells harboring the plasmids of wild-type or mutant EfrEF were grown in M17 medium supplemented with 0. 5% glucose and 5 µg/ml chloramphenicol to an OD 600 of 0. 4-0. 6 at 30 °C and the expression was induced by adding a nisin-containing culture supernatant of L. lactis NZ9700 for 2 h (1:1000 [v/v]). Cells were washed and resuspended using fluorescence buffer (50 mM KP i pH 7. 0 and 5 mM MgSO 4 ). Cells were diluted to an OD 600 of 0. 5 and energized by adding 0. 5% glucose. The accumulation of 5 µM ethidium was monitored at 30 °C using a Fluorescence Spectrometer LS-55 (Perkin Elmer, Schwerzenbach, Switzerland). Excitation and emission wavelengths (and slit widths) were set at 520 nm (10 nm) and 595 nm (15 nm)  16, 17.
Every measurement was done once and the data fitted with a 1:1 interaction model using the BioRad Proteon Analysis Software. In order to determine the half-lives of the OF ATP-bound state of the different TM287/288 variants, all five biotinylated variants were immobilized on a ProteOn™ NLC Sensor Chips at a density of 3000 RU. The experiment was conducted in 20 mM Tris-HCl pH 7. 5, 150 mM NaCl, 0. 015% (w/ v) β-DDM, and 1 mM MgCl 2 or 2. 5 mM EDTA at 25 °C at a flow-rate of 30 µl/min. In order to charge the transporter variants with ATP-Mg or ATP-EDTA, buffer containing 1 mM ATP together with either 1 mM MgCl 2 or 2. 5 mM EDTA was injected at the beginning of the experiment. Nanodisc preparation. Membrane scaffold protein MSP1E3D1 was subcloned from pINITIAL (provided by Prof. Raimund Dutzler) into pBXNH3 (addgene: Plasmid #47067) by FX cloning  36.
In brief, all-atom MD simulations of TM287/288 embedded in an explicitly solvated POPC bilayer were carried out with GROMACS  48. It should be noted that the source organism of TM287/288, the hyperthermophilic bacterium Thermotoga maritima, has a unique lipid composition  49  , which is difficult to implement for MD simulations. For the simulations initiated from the IF structure (PDB: 4Q4A), ATP-Mg was docked into the consensus site and D41 TM287 and D65 TM288 were replaced by alanines. We conducted 20 individual simulations of 500 ns each (i. e. , 10 μs in total) at 375 K. In addition, the OF state was simulated starting from the crystal structure (PDB: 6QUZ) shown in Fig. 1a  after removing the sybody and replacing ATPγS by ATP. Furthermore, the same set of simulations was carried out for the ATP-bound OF structure in which the 2xDtoA mutations were introduced in silico (another 8 μs in total).
Acknowledgements We thank all members of the  Seeger lab  for stimulating discussions. We acknowledge  Beat Blattmann  and  Céline Stutz-Ducommun  of the  Protein Crystallization Center UZH  for performing the crystallization screening, and the staff of the  SLS  beamlines  X06SA  and  X06DA  for their support during data collection. E. B. would like to thank  G. Jeschke  ( ETH Zurich ) for providing the Q-band resonator. The  Steinbuch Centre for Computing (SCC) in Karlsruhe/Germany  provided computational resources. The  Institute of Medical Microbiology  and the  University of Zurich  are acknowledged for financial support. M. K. thanks  Natural Sciences and Engineering Research Council of Canada (NSERC)  and the  Canada Research Chairs Program  for financial support. This work was funded by a  SNF Professorship of the Swiss National Science Foundation  ( PP00P3_144823 , to.