dataesr/scientific-paragraphs-categorization huggingface dataset:
GBD model life table system and the database of empirical life tables To produce a complete set of age-specific mortality rates (an abridged life table) for each location, we used the GBD model life table system, which identifies a reference life table for each location, year, and sex, on the basis of the nearest matches found in our empirical life table database. 14 As we have revised the population denominators used to create the empirical life tables in GBD 2017, we have substantially updated and revised the database of empirical life tables as well. In previous GBD iterations, we excluded life tables based on implausible patterns of variation in death rates in the age groups older than 40 years. As with previous GBD cycles, we have two sets of life tables that meet inclusion criteria: a universal set that is used for all locations to identify matches and a location-specific set that is used for each location along with the universal set.
We have formalised the inclusion criteria for life tables for both the location-specific and the universal set, and those are listed in section 2. We have also set the number of matches searched for in the databases to be 100 for all locations; to ensure that locations with high-quality data primarily rely on their own age patterns of mortality, we have modified the space-time weighting scheme through a 25-fold increase in the country-specific weights compared with GBD 2016, with an additional 15-fold increase in 0-year and 1-year lag country-specific weights and a three-fold increase in the 2-year, 3-year, and 4-year lag country-specific weights. We also generated a new geographical strata of life table weights for subnational locations that are within the same country, which were assigned the same value as the original GBD 2016 country-specific weights.
For both all-cause mortality and cause-specific mortality analyses in GBD, we amassed a comprehensive database on human mortality from full VR systems and sample VR systems such as the Sample Registration System (SRS) from India and the Disease Surveillance Point system from China. These data sources provided a total of 42 138 empirical life tables, which also include subnational locations. After applying inclusion criteria, we use 35 177 life tables, of which 10 885 are universal and 24 292 location-specific. The GBD model life tables varied in quality in accordance with the coverage of a location's VR: for locations where VR coverage was high, the standard was overwhelmingly derived from observed mortality patterns, whereas in locations where VR coverage was low, the standard was based on locations with similar under-5 and adult mortality rates, with more weight given to life tables that were closer geographically and temporally.
Regional, cause-specific UIs were used to estimate uncertainty for events where only point-estimate mortality data were available. For GBD 2017, we have recoded the locations of all events using a new suite of software developed in-house to match differently coded locations in the fatal discontinuities database to GBD locations, taking advantage of detailed location information that was presented in nonstandardised ways-eg, sources that included the name of a city or village instead of latitude and longitude. We first overlaid the portions of the database with latitude-longitude coordinates to the most detailed GBD location. When coordinates were not available, we used three web-based geocoding services-the Google Maps, OpenStreetMap, and Geonames geocoding application programming interfaces-to get a set of possible latitude and longitude coordinates from the location, overlaid those coordinates on to GBD locations, and then used the most common result from the three services to assign a GBD location.
Since discontinuities for recent years are not well tracked in the available databases, we have supplemented these data bases with online searches. For GBD 2017, we syste matised the identification of events missing from our database by mining Twitter accounts of major news providers for common terms associated with such events, like "earthquake" and "casualties. " This provided 62 events. Once events were identified, news reports of death totals, location, and date were used. The age pattern of deaths is rarely identified in databases of fatal discontinuities. In order to estimate an age and sex distribution, events were first assigned to a GBD cause. Events were then split based on both the global age and sex distribution of that cause of death and the age and sex distribution of the population in the GBD location of the event, following the GBD causes of death age-sex-splitting algorithm.
HIV/AIDS in countries with large epidemics and incomplete VR We produced estimates of adult HIV/AIDS incidence and prevalence using the estimation and projection package (EPP), a Bayesian model developed by UNAIDS. 45 Our implementation of EPP made use of GBD-estimated demographic parameters, mortality rates for people on and off antiretroviral therapy, and CD4 progression rates to fit a model to HIV/AIDS prevalence data from surveillance sites and representative surveys. EPP-generated inci dence and prevalence time series were used as inputs into Spectrum, a compartmental  HIV/AIDS progression model originally developed by UNAIDS. Spectrum generated a full set of age-sexspecific HIV/AIDS mortality rates using detailed demographic parameters that align with those used for EPP. In countries with VR data, we adjusted age-specific and sex-specific incidence rates to produce mortality estimates that better fit observed deaths.
This approach has not been used for the analysis of adult mortality largely because there are fewer overlapping data sources in these age groups. In future work, we will explore whether such an approach should be used for settings with VR and sibling history data. Following standard demographic approaches, we use death distribution methods to assess the completeness of VR data. We use variants of the three standard death distribution methods, synthetic extinct generations, generalised growth balance, and the hybrid of the two, that were developed and validated using simulation data and data in settings where registration is known to be complete. 33 Although we use optimised versions of these methods, the results of these methods are accompanied by large uncertainty intervals, as shown in studies using simulated data.
Given the importance of these methods for using incomplete VR in demographic analyses, more research on the death distribution methods is warranted. The development of GBD population estimates 31 also led to a complete overhaul of the empirical life table database used for the GBD model life table system. This database is used to identify the reference standard for the pro bability of death at each age. For this cycle, we defined objective criteria to assign life tables based on observed deaths (corrected for under-reporting as required) and estimated populations into three groups: high-quality life tables used in the universal database, lower-quality life tables used for only the locations from which that life table was measured, and life tables that were rejected as too low quality. To deal with small number issues, we also considered life tables computed on 3-year, 5-year, and 7-year moving averages of observed death rates.
Of 42 138 life tables evaluated, 25•8% were in the high-quality category, 57•5% were in the lower-quality category, and 16•7% were rejected. Because of the large number of candidate life tables, we developed objective criteria that could be applied in an automated fashion based on the variance of the slope of the log death rate versus age curve, mortality declines over the age of 65 years, crossovers in the probability of death between 1 and 5 years (4q1) and between 0 and 1 year (1q0), and large swings in death rates in adjacent age groups. In future work, these criteria could be enhanced by the addition of other screening criteria, particularly at older ages where death rates approach very high levels above the age of 85 years. This more formalised approach to the life table database is necessary because, with each iteration of estimation, the population denominators can change, and thus the shape of the life tables can change.
Application of this approach means that we have a much richer database of high-quality life tables than is reflected in the older demographic model life table systems; Ansley Coale and Paul Demeny (1966) used only 192 life tables, whereas the UN Model Life Table System (1955) used only 158 life tables. 51, 52 Our larger database of life tables captures many more nuanced patterns that relate to the preponderance of different causes of death in different locations such as infectious diseases, injuries, and some non-communicable causes. We estimate uncertainty in death rates, and this uncertainty currently reflects sampling error, nonsampling error, and estimation error for the under-5 death rate, the probability of death between 15 and 60 years, and the model life table system, along with uncertainty due to HIV in countries with epidemics with a peak prevalence greater than 0•5%.
In locations with VR data, this creates a circularity where population distribution within the terminal age group depends on death rates in those age groups that depend on population denominators. We deal with this circu larity by looping through the entire population estima tion process several times to reach a stable estimate of population and death rates. Nevertheless, this inter dependence means that estimates of death rates with partial or complete VR in locations with substantial age misreporting might be biased. Fourth, our estimates of death rates at ages 5-9 and 10-14 years in settings without VR data depend on the selection of a model life table reference using the under-5 death rates, the adult mortality rate, and the database of empirical mortality patterns in the life table database.
Acknowledgments Research reported in this publication was supported by the  Bill & Melinda Gates Foundation , the  University of Melbourne, Public Health England , the  Norwegian Institute of Public Health, St. Jude Children's Research Hospital , the  National Institute on Aging of the National Institutes of Health  (award  P30AG047845 ), and the  National Institute of Mental Health of the National Institutes of Health  (award  R01MH110163 ). The content is solely the responsibility of the authors and does not necessarily represent the official views of the funders. Data for this research was provided by  MEASURE Evaluation , funded by the  United States Agency for International Development (USAID). Views expressed do not necessarily reflect those of  USAID , the  US Government , or MEASURE Evaluation.
Estimating uncertainties of property values derived from a charge-density model is not straightforward. A methodology, based on calculation of sample standard deviations (SSD) of properties using randomly deviating chargedensity models, is proposed with the MoPro software. The parameter shifts applied in the deviating models are generated in order to respect the variancecovariance matrix issued from the least-squares refinement. This 'SSD methodology' procedure can be applied to estimate uncertainties of any property related to a charge-density model obtained by least-squares fitting. This includes topological properties such as critical point coordinates, electron density, Laplacian and ellipticity at critical points and charges integrated over atomic basins. Errors on electrostatic potentials and interaction energies are also available now through this procedure.
Introduction Errors on electron-density-derived properties, such as topological characteristics or electrostatic potential, are generally poorly addressed in the relevant literature. To the best of our knowledge, no available computer software designed for charge-density analysis on the basis of multipolar modelling computes properly analytical standard deviations on electrondensity-derived properties. For instance, in the XD2006 program  (Volkov et al. , 2006) , there is a feature that allows one to compute estimated uncertainties of the electron density (r), of the Laplacian r 2 and of dipole moment values using the variance-covariance matrix, but it only accounts for the contributions of some of the parameters used in the  Hansen & Coppens (1978)  model, i. e. monopole and multipole populations.
, 1987)  framework. For instance, they obtained, this way, average experimental errors 0 rep;exp () = 0. 07 e A ˚À3 and 0 rep;exp (r 2 ) = 3. 3 e A ˚À5 associated, respectively, with electron density and with Laplacian values at the bond critical points. The most comprehensive and statistically sound reproducibility study on a wide range of electron-density-derived parameters was undertaken by  Kamin ´ski et al. (2014). They used 13 independently collected high-resolution X-ray diffraction data sets of -oxalic acid dihydrate. From these data, obtained using similar experimental setups, they derived 13 oxalic acid charge-density models which were refined following identical strategies. This approach allowed them to analyse the normality of the error distribution in experimental data and in residual electron densities using the Shapiro-Wilk statistical test and, more importantly, to obtain very informative results in terms of dispersion of structural/chargedensity model parameters and of charge-density-derived property values.
Data collection A single-crystal high-resolution and highly redundant X-ray data collection of the BOH2 compound was performed on a Rigaku MicroMax-HF rotating-anode diffractometer equipped with a Pilatus 200K hybrid pixel detector using Mo K radiation ( = 0. 71073 A ˚). The crystal was mounted on a Kapton micromount. The data collection was carried out at 90 (1) K under a stream of nitrogen using the Oxford 700 Plus Cryosystems gas-flow apparatus. The diffraction data were collected using ! scans of 0. 5 intervals with the CrystalClear-SM Expert 2. 1b29 software  (Rigaku, 2013)  up to a resolution of 0. 41 A ˚(sin/ < 1. 22 A ˚À1 ). The exposure times were 5 and 40 s per frame for low-and high-resolution data, respectively. Data reduction and absorption correction were performed using the Crys-AlisPro 1.
Structure solution and refinement The structure of the BOH2 compound has already been determined  (Gelbrich et al. , 2000). In our study, the structure of BOH2 was solved using the SIR2014 software  (Burla et al. , 2015). In particular all the H atoms were located in the difference Fourier map. An initial independent atom model (IAM) refinement was undertaken using the SHELXL2014 software  (Sheldrick, 2015).
Multipolar refinement The charge-density model was refined against diffraction intensities using the program MoPro  (Guillot et al. , 2001; Jelsch et al. , 2005). The program is based on the multipolar scattering factor formalism of  Hansen & Coppens (1978)  and allows the definition of restraints on stereochemistry, thermal motion and charge-density parameters. Data resolution was truncated at 0. 45 A ˚as the very high resolution reflections showed decreasing values of hF o 2 i/hF c 2 i well below unity, as verified with the XDRK software  (Zhurov et al. , 2008). For the same reason, an I/ I > 0. 35 cutoff was applied. The evolution of hF o 2 i/hF c 2 i as a function of reciprocal resolution s is shown in the supporting information. The multipole expansion was done at the octupolar level for B, C and O atoms and the dipole level for H atoms.
The core and valence spherical scattering factors were calculated using the wavefunctions for isolated atoms from  Su & Coppens (1998)  and the anomalous dispersion coefficients were taken from  Kissel et al. (1995). The MoPro program has numerous functionalities with respect to constraints, restraints and similarity applying to the stereochemistry and charge density. For the H atoms, the values of anisotropic U ij parameters were fixed to those obtained from the SHADE3 server  (Madsen & Hoser, 2014). The H-X distances of H atoms were restrained to the values obtained from neutron diffraction studies  (Allen & Bruno, 2010)  with a restraint sigma rest of 0. 01 A ˚. Distance X-H similarity restraints were also applied to chemically equivalent groups ( rest = 0. 01 A ˚). The charge-density model was subsequently refined against diffraction intensities.
The electron-density maps, local topological properties and intermolecular electrostatic energies were computed using the VMoPro module of the MoPro suite  (Guillot et al. , 2001; Jelsch et al. , 2005)   (Domagała & Jelsch, 2008)  were applied to the electron-density parameters such as contraction/expansion and 0 , valence and multipole populations P val and P lm. The optimal weight opt of the restraints applying to the chargedensity parameters (atom equivalence and local symmetry) was set to 0. 2, as determined by minimizing the global R free factor  (Bru ¨nger, 1992; Zarychta et al. , 2011). The parameters and 0 of H atoms were restrained to be similar ( rest = 0. 02). The molecular parameters including scale factor, xyz, U ij , P val , P lm , and 0 were refined together with the block diagonal option and finally using the full normal matrix until convergence, yielding wR 2 (I) = 3.
6%. The crystallographic details of the refinement are given in Table  1. The topological charges were integrated on atomic basins using the program BADER  (Tang et al. , 2009). A parallelepiped embedding the BOH2 molecule extracted from the crystal lattice was defined with a margin of 3 A ˚around the atomic nuclei. For each deviating model, the total electron density of the molecule inside this parallelepiped was computed using the program VMoPro, with a grid step of 0. 05 A ˚along each direction and then saved as a Gaussian cube file. Then, the program BADER was used for atomic basin definition and charge integration. The sum of the integrated electron charges was smaller than the total number of electrons in the molecule with an average lack of 0. 47 e (SSD = 0. 0028 e) for a total number of 102 electrons.
Least-squares refinement and uncertainties The least-squares refinement is implemented in MoPro  (Guillot et al. , 2001; Jelsch et al. , 2005) , software dedicated to charge-density refinement. A multipolar charge-density model defined according to the formalism of  Hansen & Coppens (1978)  can be refined for crystal structures when ultra high resolution X-ray diffraction data have been measured. For macromolecular structures, the transferability principle can be used to define a multipolar electron-density model. When the refinement is performed against the reflection intensities, the minimized function E is defined as E ¼ P H W H ½I obs H À I calc H ðXÞ 2 ð1Þ where I calc H and I obs H are the calculated and observed reflection intensities, respectively, and X is the vector of the model parameters being considered in the corresponding refinement stage.
The software MoPro generates random Gaussian numbers using the 'ratio of uniform deviates' method introduced by  Kinderman & Monahan (1977)  and augmented with quadratic bounding curves by  Leva (1992). To avoid rare events which would lead to meaningless deviating charge-density models, the algorithm is modified to generate random numbers following a truncated Gaussian function. This modification consists of reducing the infinity support of the Gaussian probability density function to a [À4; 4] interval and of normalizing the resulting function in order to obtain a unitary variance. Following the Monte Carlo procedure described in this section, several deviating charge-density models are generated using equation (  12 ). The studied properties are computed on all these models and the SSDs are deduced from the sample values.
Geometry properties: distances and angles The good accordance between SSD and e. s. d. values has been verified for the parameters used to describe the structure and charge density. For example, Fig. S3  shows the agreement between e. s. d. 's issued from the least-square normal matrix inversion using equation (  6 ) and the SSD values obtained from 20 deviating structures for the atomic fractional coordinates. The SSD has been calculated for the bond distances and angles. For comparison, e. s. d. 's have also been retrieved from the error propagation method implemented in the MoPro software, and the relative differences between the SSD and e. s. d. , |SSD À e. s. d. |/e. s. d. , are calculated to check the reliability of the error propagation method. In the plots SSD versus e. s. d. for the interatomic distances and angles between non-H atoms (Fig.
Topology of intermolecular interactions Intermolecular interactions play a key role in crystal engineering which is an important field in chemical crystallography; therefore estimation of errors on their properties is extremely timely. In the BOH2 crystal packing, 17 unique interatomic contacts shorter than 3 A ˚were identified between the reference molecule and its environment, involving eight distinct neighbour molecules (Table  3 ). The intermolecular (3,À1) CP search has been done using the software VMoPro on the 20 deviating models. All the OÁ Á ÁH hydrogen bonds show non-ambiguous bond paths between the two atoms. Two of the intermolecular contact CPs have unstable bond paths, in the sense that they lead to different linked atoms within the deviating models (Table  3 ). The first non-stable bond path involves the phenyl H4 atom of the molecule (Àx + 5 2 , y À 1 2 , z) which is connected to the phenyl C atoms of the reference molecule, C1 in 13 deviating models and C6 in the seven others.
Electrostatic energy Eight unique dimers of molecules in contact have been identified in the crystal packing. Considering each dimer, the intermolecular electrostatic energy is computed for the 20 perturbed models using the EP/MM method  (Volkov et al. , 2004)  as implemented in the software VMoPro, and the SSD is calculated as the uncertainty estimator (Table  5 ). Absolute errors of intermolecular electrostatic interaction energies in dimers of BOH2 molecules appear consistently of a few kJ mol À1. Therefore the SSD relative error is as low as 7% for the largest value E elec = À62. 2 kJ mol À1 but for the weakest interactions the SSD is larger than E elec itself. Such large relative errors confirm clearly that weak electrostatic interaction energies of a few kJ mol À1 cannot be interpreted as either stabilizing or destabilizing.
The thermal gradient was as follows: 100-180˚C at 8˚C/min, 180-220˚C at 4˚C/min and a constant temperature of 220˚C for 20 min. Fatty acids were identified with reference to a known standard mixture (Sigma, St Louis, MO, USA) and peaks were integrated using Varian Star Chromatography Software (Star Software, version 5). Individual FAs were expressed as a percentage of total FAME identified. Amounts of EPA+DHA (g fish -1 ) were calculated taking into account, for each tank, mean body lipid content (g fish -1 ) and the percentages of EPA and DHA in body lipids. Values were expressed as mean per dietary treatment.
For each reaction, 600ng of Cy3-cRNA were fragmented and hybridized on a sub-array, following the LIQA kit (Agilent) instructions. The hybridization reactions were allowed to run for 17h in a rotating hybridization oven (65˚C) prior to washing according to the manufacturer's instructions. Samples were randomized, preventing those from the same dietary treatment from being overrepresented in a particular batch in order to avoid unintentional biases. Slides were scanned with an Agilent Scanner (Agilent DNA Microarray Scanner, Agilent technologies, Massy, France) using the standard parameters for an 8x60K gene expression oligoarray (3μm-20 bits). Data were then obtained with the Agilent Feature Extraction software (10. 7. 1. 1) according to an appropriate gene expression (GE) protocol (GE1_107_Sep09).