dataesr/scientific-paragraphs-categorization huggingface dataset:
5 km. The Nyquist wavelength, that is, the smallest wavelength that can sampled, is thus 5 km. It is shown in Figure  2f  and intersects the range of estimated mode-19 wavelengths. Mode 19 hence becomes the highest observable mode regarding the horizontal resolution criterion. We estimated the vertical wavelength of mode n, m n , through the relation 𝑘𝑘𝑛𝑛 𝑚𝑚𝑛𝑛 = ( 𝜔𝜔 2 -𝑓𝑓 2 𝑁𝑁 2 -𝜔𝜔 2 ) 1∕2. ( 2 ) As it intrinsically depends on the local stratification, we estimated m n at different depths between 125 and 1,725 m with a depth interval of 125 m (Figure  2g ). Mode 19 features the shortest wavelength in the pycnocline below 500 m : m 19 ≈ 150 m. This is much larger than the Nyquist wavelength, which is 48 m, given the bin width of the SADCP data (24 m, see Section 2. 2). Resolving the horizontal wavelength is thus more limiting than resolving the vertical wavelength for observing the highest modes.
Finescale Parameterization of Turbulent Kinetic Energy Dissipation Dissipation rates of turbulent kinetic energy along the sections were estimated from a finescale parameterization based on the internal wavefield content measured with the SADCP. We used the  Gregg et al. (2003)  parameterization, which needs a knowledge of the shear-to-strain ratio R ω of the internal wavefield. In the absence of concurrent CTD data during SADCP sections to compute an instantaneous R ω , we used an averaged vertical profile of R ω computed from the 22 CTD profiles (see Section 2. 3) combined with the simultaneous lowered-ADCP profiles obtained from two 300-kHz ADCPs mounted on the rosette frame. Following  Gregg (1989) , the variance of the vertical shear of the horizontal velocities was obtained from finite differences, here calculated over a length scale of 96 m (two consecutive bins) after having vertically smoothed the velocity with a three-point Hanning filter.
Data Availability Statement SADCP data are freely available online  (Sarradin & Matabos, 2022). LADCP and CTD data are freely available online  (Ferron et al. , 2022). TPXO9-atlas barotropic tide currents were made available by Dr. Svetlana Erofeeva who was contacted through https://www. tpxo. net/tpxo-products-and-registration. Geostrophic surface currents from absolute dynamic topography were downloaded from the Copernicus Marine Environment Monitoring Service (near-real time L4 product, Copernicus Marine Service, 2022).
This is especially so because, although many different tests are available that link variation in taxon abundances to (1) trait variation, (2) taxon turnover between habitats or environments and (3) the distance decay of similarities between samples, none quantify the importance of these relative to each other. The MEF as applied here, however, is capable of and designed to do exactly this by decomposing variation to separate information explained by each of these aspects in a four-step model (Fig. 1  and Box S2). Its application to an unprecedented large tree inventory database on genus level taxonomy consisting of > 2,000 1-ha plots distributed over Amazonia  4  and a genus trait database of 13 key functional traits representing global axes of plant strategies  5  allows us to advance the study of Amazonian tree community dynamics from a new cross-disciplinary perspective.
Predictive power of the four-step model. Using a uniform prior and CWM values (Community Weighted Means) as constraints accounted for 23% on average of total deviance between observed and predicted relative abundances (measured by R  2  KL values, see Box S2 Eq. 5). Filtered by forest type this was 34% for podzol forests, várzea 25%, igapó 23%, swamp forests 34%, 21% and 24% for Guyana Shield and Pebas terra firme respectively and 20% for Brazilian Shield terra firme forests (see Table  S1  for detailed decomposition). Using observed metacommunity relative abundances as prior regardless of functional traits accounted for on average 56% for the combined dataset with for all forest types between 51 and 55%, except for the Guyana Shield terra firme with 62%. The hybrid model (including both traits as constraints and the metacommunity prior) performed slightly better for the combined dataset (average 60%) with a minimum of 57% for swamp and várzea forests and a maximum of 66% for Guyana Shield terra firme forests.
To compensate for spurious relationships between regional abundances and local trait constraints, regardless of selection, explanatory power was regarded relative to model bias yielding the pure trait and metacommunity effects (Box S3, Fig. 2  and Table  S1 ). This lowered the proportion of information accounted for and yielded average pure metacommunity effects of 40% for the overall dataset ranging between 26 and 45% for each forest type separately with pure trait effects explaining only 5% of information for the combined dataset on average with for each forest type between 3 and 9%. Although the latter was lowered substantially, the explanatory power did appear to be strongly dependent on forest type. The online supplementary material provides additional results relating to the predictive power of each model as well as the spatial gradient of the pure trait and metacommunity effects (Figs.
Methods Empirical data. The ATDN  4, 13, 14  consists of over 2000 tree inventory plots distributed over the Amazon basin and the Guiana Shield, collectively referred to as Amazonia (a map of all current plots can be found at https:// atdn. myspe cies. info/). Only those plots with trees ≥ 10 cm diameter at breast height were used, leaving 2011 plots with a mean of 558 individuals per plot identified to at least genus level. Most plots used are 1 ha in size (1414) with 492 being smaller (minimum size of 0. 1 ha) and 105 larger (maximum size of 80 ha). Genera have been standardized to the W3 Tropicos database 15 using the Taxonomic Name Resolution Service (TNRS, see  16  ). After filtering based on above criteria and solving nomenclature issues, 1,121,935 individuals belonging to over 828 genera remained.
Plots were distributed over seven abiotically different forest types: Podzol forests (PZ), Igapó (IG, black water flood forests), Várzea (VA white water flood forests), Swamp (SW) and Terra firme forests (TF) with subregions BS (Brazilian Shield), GS (Guyana Shield) and PB (Pebas) (see also  17  for details regarding these forest types). Trait data were extracted from several sources. Wood density was mostly derived from  18. Traits related to leaf characteristics mostly came from four large datasets  [19] [20] [21] [22] [23] [24]  , including additional data from other sources  [25] [26] [27]  as well as unpublished data (J. Lloyd, A. A. de Oliveira, L. Poorter, M. van de Sande & Mazzei, M. van de Sande & L. Poorter). Data on seed mass came from  [28] [29] [30]  as well as different flora's and tree guides.
As for many traits it has been shown earlier that the interspecific variability was larger than the intraspecific variability, this allowed the use of data from different sources to at least calculate a mean species trait value. Genus trait values were subsequently computed as genus-level means of species values if known within the genus and considered constant for each genus. Genus level of taxonomy was used as the available trait database had the most information on this taxonomic level (see Table  1 ). Unknown values for traits were estimated by Multiple Imputation with Chained Equations (MICE, see  15  ) by delta adjustment, subtracting a fixed amount (delta), with sensitivity of this adjustment to the imputations of the observed versus imputed data analysed using density plots (Fig. S8 ) and a linear regression model.
This procedure was done using the mice package  38  , available on the R repository, under predictive mean matching (pmm setting, 50 iterations). Results showed imputations were stable and showed near identical patterns with each imputation scenario (see Figs. S5-S6 and Table  S2 ). After imputation, all trait values were transformed to Community Weighted Means (CWM) of each trait (J) for each plot (K) ( T JK ) as T JK = S i=1 t ij ra ik with ra the relative abundance of the ith genus in the kth plot following earlier uses  37. MEF procedure predictions and ecological inference. Figure  1  provides a schematic procedure overview, box S1 provides an overview of important terms and Boxes S2-S3 further mathematical details. Initially, a maximally uninformative prior is specified, where q i (Box S1 Eq.
In contrast with standard linear regression models having squared goodness-of-fits measurements, the R  2  KL is much more related to the concept of relative entropy, quantifying the information lost when one distribution is compared to another by means of quantifying the statistical distance between two distributions  40. Pure trait, pure metacommunity, joint metacommunity-trait and unexplained effects are calculated as proportions of total biologically relevant information (Box S1 and Box S2). Data was rarefied to smallest sample size (swamp forests; 28) and calculations bootstrapped 25 times. Results indicated no significant change compared to using all data, hence the total dataset was used for all analyses. Strength and direction of selection. Predictions of genus relative abundances are computed as a function of traits reflected in the CWM values and a series of constants (λ jk : the Lagrange Multipliers).
Acknowledgements This paper is the result of the work of hundreds of different scientists and research institutions in the Amazon over the past 80 years. Without their hard work this analysis would have been impossible. The 25-ha  Long-Term Ecological Research Project of Amacayacu  is a collaborative project of the  Instituto Amazónico de Investigaciones Científicas Sinchi  and the  Universidad Nacional de Colombia Sede Medellín , in partnership with the  Unidad de Manejo Especial de Parques Naturales Nacionales  and the  Center for Tropical Forest Science of the Smithsonian Tropical Research Institute (CTFS). The Amacayacu Forest Dynamics Plot is part of the  Center for Tropical Forest Science , a global network of large-scale demographic tree plots. We acknowledge the Director and staff of the  Amacayacu National Park  for supporting and maintaining the project in this National Park.
Funding HtS and RS were supported by grant  407232/2013-3 -PVE -MEC/MCTI/CAPES/CNPq/ FAPs; CB was supported by grant  FAPESP 95/3058-0 -CRS 068/96   WWF Brasil -The Body Shop ; DS, JFM, JE, PP and JC benefited from an " Investissement d' Avenir " grant managed by the  Agence Nationale de la Recherche  ( CEBA :  ANR-10-LABX- 25-01 ); HLQ/MAP/JLLM received financial supported by  MCT/CNPq/CT-INFRA/GEOMA #550373/2010-1  and #  457515/2012-0 , and JLLM were supported by grant  CAPES/PDSE # 88881. 135761/2016-01and   CAPES/Fapespa  # 1530801 ; The  Brazilian National Research Council (CNPq)  provided a productivity grant to EMV (Grant  308040/2017-1 ); Floristic identification in plots in the RAINFOR forest monitoring network have been supported by the  Natural Environment Research Council  (grants  NE/B503384/1 ,  NE/ D01025X/1 ,  NE/I02982X/1 ,  NE/F005806/1 ,  NE/D005590/1  and  NE/I028122/1 ) and the  Gordon and Betty Moore Foundation ; B.
Two general BMC-H assembly behaviors To complete published data compiled in Table  S1 , we investigated the assembly of CcmK from Syn6803 and Syn7942 inside E. coli by TEM (Fig  S2 ). Only CcmK1 6803 and CcmK3 6803 images differed from those obtained for the control strain (empty vector). Although unclear, stripped motifs might occur with CcmK1 6803. With CcmK3 6803 , homogenous spherical patches suggestive of IB were often present at cellular poles. The lack of noticeable observations for CcmK proteins contrasts with nanotubes, filaments and spherical structures reported for many other BMC-H (Table  S1 ). Assembly potential was also assessed by AFM and TEM taking purified proteins conditioned at comparable concentrations in the presence of a phosphate buffer. 2D flat-organizations were recurrently imaged by AFM with all CcmK proteins (see Fig.
Different 2D-assembly modes identified in BMC-H crystals Our intention was to investigate BMC-H assembly behavior by MD simulations taking advantage of crystallographic data. By the time of the realization of this study, there existed about 60 BMC-H structures deposited in the Protein Databank (plus 8 entries from reconstructed shells published in the course of this work, see Table  S2 ). Thirty-four structures were from wild-type (WT) proteins. Within this group, we focused our work on the 18 crystal structures that displayed hexamers organized as piled 2D layers (see below). These structures could be categorized in four groups according to the BMC-H disposition, which differed by lateral displacements and distances between interacting hexamers (Fig. 1  and Table  S2 ). The first assembly type (hereafter called Ass-A) is characterized by a short distance between the two key Lys residues from interacting hexamers.
Variable curving trends supported by all-atom molecular dynamics The last hypothesis was challenged by means of all-atom MD. We followed the approach described in a previous study  21  , in which MD runs were launched on ensembles of three interacting hexamers, extracted from crystal structures showing tiled BMC-H (PDB codes indicated in Table  S3 ). Tri-hexameric ensembles were selected as best compromise to describe the situation in BMC shells while keeping reasonable computational costs. After energy minimization, MD were run (AMBER forcefield) with proteins embedded in explicit hydration boxes under quasi-physiological conditions (see M&M). All different assembly types mentioned in the previous section were covered. Hexamer tilting and bending angles were monitored for intermediate structures extracted in the course of each trajectory (250 ps snapshots), as well as interhexamer distances calculated from the hexamers center of mass in the MD average structure.
ochraceum BMC shell structure (5V74). Worth-mentioning, the results were reproduced using CHARMM as forcefield in similar independent simulations launched on PduA Sent (average bending of -23°) and CsoS1A Hneap (-16°). Assembly fate was more uncertain for non-Ass-A organizations. Bending and tilting were variable (Fig. 3 ), the reproducibility between runs being considerably poorer than with Ass-A, as illustrate strong data dispersion (Table  S3 ). With some cases, the tri-hexamer remained close to flat independently of the run [e. g. CcmK1 6803 (3BN4) or CcmK4 7942 ]. But for most other cases, behavior was instable, even conducting to inversions of bending orientation (e. g. EutM Ecol or BMC-H Hoch ). As possible exception, CcmK2 6803 (3DNC) evolved from its Ass-C dispositions in the two runs much like Ass-A assemblies.
4A ). Despite comparable to calculations on CcmK2 6803 27 , CcmK1 6803 binding energy was very weak, about 2 to 4 times smaller than for CcmK4 or PduA, respectively. When the PMF was screened along the reaction coordinate that leads from Ass-A to Ass-B (further extended on both sides), while hexamers were constrained flat, the highest stability was attained around crystal dispositions, supporting a preference of PduA Sent for Ass-A, or of CcmK4 7942 for Ass-B/C arrangements (Fig. 4B ). Although CcmK1 6803 did not manifest a clear preference, globally these data supported that arrangements occurring in 2D-tiling crystals represent energy minima. Besides, shallow profiles fitted with the high plasticity of BMC-H interfaces, indicating that transitions between different assemblies, separated by small energetic barriers (few kBT), should be feasible.
A notable discovery was that BMC-H experimental assembly behavior appears to be related to the type of organization found in crystals that exhibit internal 2D-layered organizations. Bending cases like PduA Sent , PduJ Sent or CsoS1A Hneap exhibited Ass-A dispositions, whilst other arrangements are noticed in structures of CcmK, EutM Ecol , EutM Cdif or BMC-H Hoch. Most often, assembly units were laterally displaced by approximately 8-10 Å (Ass-B), when compared to Ass-A. If such relationship was correct, crystal data would indicate that proteins like CsoS1C Hneap , CsoS1 Pmar and BMC-H Ahyd should form rounded structures, temptingly also BMC-H that attained Ass-A states even when mutated: CmcB Ecol (7MN4, K25A-E55G mutant), CmcC Ecol (7MPX, K25A-E35G) or CutR Sint (6XPI, K66A). However, this rule is not obeyed by all BMC-H, since EutM is prone to form rounded structures but adopts Ass-B configurations in crystals.
Indeed, PMF profiles estimated here supported that highest stabilization is attained in different flat dispositions of PduA Sent and CcmK4 7942 hexamers. Although CcmK1 6803 profile was unexpectedly shallow, that CcmK never reached an Ass-A disposition in crystals (10 PDB entries) solidly points to global minima different from Ass-A. Yet, the structures of all reconstituted BMC shells prove that Ass-A is the mode of organization that conducts to closed assemblies (Table  S2 ), also for shells composed of CcmK proteins  16. All-atom MDs robustly demonstrated the experimental curving capabilities of Ass-A-organized BMC-H. Not only PduA Sent , but also all other Ass-A BMC-H rapidly and robustly bent. The known bending orientation was reproduced, i. e. the convex face lying towards the inner side of the compartment.
In fact, structures averaged over the MD were strikingly similar to those found in minimalist shells, which all appear to derive from Ass-A arrangements. Comparison with data published for PduA Sent bi-hexamers  14  indicate that assembly might be better simulated on tri-hexamer ensembles, although in our hands a preference for curved dispositions was even demonstrated on bi-hexamers extracted from minimalist BMC-H Hoch and CcmK 7418 shells. BMC-H with Ass-B, Ass-C or Ass-D organizations behaved less clear-cut, bending and even tilting values being much dispersed over the MD trajectories. Globally, however, Ass-B or Ass-C trihexamers seem to fluctuate around flat dispositions. This was seen for individual MD runs [e. g. CcmK4 7942 (4OX6)], or was concluded from independent MDs [e. g. CcmK2 6803 behavior in assemblies prepared from crystals 2A1B and 3CIM].
Cryoelectron microscopy (Cryo-EM) 3. 5µL sample drops were deposited on parafilm for 20 min. Glow-discharged lacey carbon grids were then placed onto the drops and incubated for 1min. Grids were transferred to the thermostatic chamber of a Leica EM-GP automatic plunge freezer, set at 20°C and 95% humidity. Excess solution was removed by blotting with Whatman n°1 filter paper for 0. 2-0. 6 seconds, and the grids were immediately flash frozen in liquid ethane at -185°C. Frozen specimens were placed in a Gatan 626 cryo-holder, and cryo EM was carried out on a Jeol 2100 microscope, equipped with a LaB6 cathode and operating at 200 kV, under low dose conditions. Images were acquired with SerialEM software, with defocus of 1. 5-2. 5 μm, on a Gatan US4000 CCD camera. This device was placed at the end of a GIF Quantum energy filter (Gatan, Inc.
All-atom Molecular Dynamics Simulations Assemblies composed of three hexamers were prepared from available crystallographic structures (PDB ID indicated in Table  S2 ) after applying translation and symmetry operations. Glycerol and other crystallographic ligands were removed (sulfate ions associated to CsoS1A were deleted, or not, without evident difference). Ensembles were embedded in cuboid cells with dimensions extending 20 nm around all protein atoms, which were filled with explicit solvent. Each system was neutralized with NaCl (0. 9 % final concentration). Periodic boundary conditions were applied and unless otherwise mentioned the YASARA AMBER14 force field was selected. The cut-off for the Lennard-Jones potential and the short range electrostatics was 8 Ǻ. Long-range electrostatics were calculated using the Particle Mesh Ewald (PME) method with a grid spacing <0.
Use of the FIGO Nutrition Checklist in India. Abbreviations: FOGSI, Federation of Obstetric and Gynaecological Societies of India; ARTIST, Asian Research and Training Institute for Skill Transfer. *Data unpublished F I G U R E 3 The FIGO Nutrition Checklist in South Africa. Full data available from Soepnel et al. 11518793479, 2023, S1, Downloaded from https://obgyn. onlinelibrary. wiley. com/doi/10. 1002/ijgo. 14539 by Uppsala University Karin Boye, Wiley Online Library on [22/03/2023]. See the Terms and Conditions (https://onlinelibrary. wiley. com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License 25-hydroxyvitamin D (25[OH]D) levels below 50 nmol/L, in 54% of pregnant women globally. Although poorly defined in many regions, the breakdown by WHO region varied from 87% in Southeast Asia, 83% in the Western Pacific, 64% in the Americas, 57% in Europe,.
F I G U R E 2 2 Use of the FIGO Nutrition Checklist in India. Abbreviations: FOGSI, Federation of Obstetric and Gynaecological Societies of India; ARTIST, Asian Research and Training Institute for Skill Transfer. *Data unpublished F I G U R E 3 The FIGO Nutrition Checklist in South Africa. Full data available from Soepnel et al. 11518793479, 2023, S1, Downloaded from https://obgyn. onlinelibrary. wiley. com/doi/10. 1002/ijgo. 14539 by Uppsala University Karin Boye, Wiley Online Library on [22/03/2023]. See the Terms and Conditions (https://onlinelibrary. wiley. com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License 25-hydroxyvitamin D (25[OH]D) levels below 50 nmol/L, in 54% of pregnant women globally. Although poorly defined in many regions, the breakdown by WHO region varied from 87% in Southeast Asia, 83% in the Western Pacific, 64% in the Americas, 57% in Europe,.
[23]  This method was established to characterize homopolymers and  blends for organic solar cell energy level characterization and also proved to give reliable data for conjugated polyelectrolytes. [22]  Here, we performed a spectral onset determination from the evolution of the absorption intensity of the neutral and first reduced state during reduction for all four polymers. (Figure  S3 , Table  S1 , Supporting Information) The corresponding characteristic absorption spectra are shown in Figure  2E-H  and Figure  S9  (Supporting Information). The spectra were recorded at the indicated reduction potentials during the forward scan of the first cycle. According to the previous investigation of P(NDI2OD-T2), it is well-known that reduction from the neutral state with absorption maxima at 389 and 674 nm leads to a first reduced state with a maximum at 489 nm and a second reduced state with characteristic bands at 395 and 718 nm.
To take into account relativistic effects, due to the presence of the heavy selenium atoms, the Zero-Order Regular Approximation (ZORA) and the SARC/J auxiliary basis were included. In the structural models considered the alkyl and glycol chains have been considered however to a reduced size in order to save computational time. Tight-binding semiempirical calculations were carried out by using the code xTB. DFT calculations were carried out by using the code ORCA v. 5. 0. 3. [38]  OECT Fabrication and Characterization: Cr/Au source/drain electrodes were fabricated on Si/SiO2 substrate using standard photolithography, evaporation, and lift-off process. An interdigitated source/drain design (L/W = 6 um/9750 um) was chosen to get a large drain current. Polymer films were spin coated as described above, and manually patterned with a toothpick to define the channel area.