Photometric redshifts for the Kilo-Degree Survey. Machine-learning analysis with artificial neural networks

We present a machine-learning photometric redshift analysis of the Kilo-Degree Survey Data Release 3, using two neural-network based techniques: ANNz2 and MLPQNA. Despite limited coverage of spectroscopic training sets, these ML codes provide photo-zs of quality comparable to, if not better than, those from the BPZ code, at least up to zphot<0.9 and r<23.5. At the bright end of r<20, where very complete spectroscopic data overlapping with KiDS are available, the performance of the ML photo-zs clearly surpasses that of BPZ, currently the primary photo-z method for KiDS. Using the Galaxy And Mass Assembly (GAMA) spectroscopic survey as calibration, we furthermore study how photo-zs improve for bright sources when photometric parameters additional to magnitudes are included in the photo-z derivation, as well as when VIKING and WISE infrared bands are added. While the fiducial four-band ugri setup gives a photo-z bias $\delta z=-2e-4$ and scatter $\sigma_z<0.022$ at mean z = 0.23, combining magnitudes, colours, and galaxy sizes reduces the scatter by ~7% and the bias by an order of magnitude. Once the ugri and IR magnitudes are joined into 12-band photometry spanning up to 12 $\mu$, the scatter decreases by more than 10% over the fiducial case. Finally, using the 12 bands together with optical colours and linear sizes gives $\delta z<4e-5$ and $\sigma_z<0.019$. This paper also serves as a reference for two public photo-z catalogues accompanying KiDS DR3, both obtained using the ANNz2 code. The first one, of general purpose, includes all the 39 million KiDS sources with four-band ugri measurements in DR3. The second dataset, optimized for low-redshift studies such as galaxy-galaxy lensing, is limited to r<20, and provides photo-zs of much better quality than in the full-depth case thanks to incorporating optical magnitudes, colours, and sizes in the GAMA-calibrated photo-z derivation.Comment: A&A, in press. Data available from the KiDS website http://kids.strw.leidenuniv.nl/DR3/ml-photoz.php#annz

Bright galaxy sample in the Kilo-Degree Survey Data Release 4::selection, photometric redshifts, and physical properties

We present a bright galaxy sample with accurate and precise photometric redshifts (photo-zs), selected using $ugriZYJHK_\mathrm{s}$ photometry from the Kilo-Degree Survey (KiDS) Data Release 4 (DR4). The highly pure and complete dataset is flux-limited at $r<20$ mag, covers $\sim1000$ deg$^2$, and contains about 1 million galaxies after artifact masking. We exploit the overlap with Galaxy And Mass Assembly (GAMA) spectroscopy as calibration to determine photo-zs with the supervised machine learning neural network algorithm implemented in the ANNz2 software. The photo-zs have mean error of $|\langle \delta z \rangle| \sim 5 \times 10^{-4}$ and low scatter (scaled mean absolute deviation of $\sim 0.018(1+z)$), both practically independent of the $r$-band magnitude and photo-z at $0.05 < z_\mathrm{phot} < 0.5$. Combined with the 9-band photometry, these allow us to estimate robust absolute magnitudes and stellar masses for the full sample. As a demonstration of the usefulness of these data we split the dataset into red and blue galaxies, use them as lenses and measure the weak gravitational lensing signal around them for five stellar mass bins. We fit a halo model to these high-precision measurements to constrain the stellar-mass--halo-mass relations for blue and red galaxies. We find that for high stellar mass ($M_\star>5\times 10^{11} M_\odot$), the red galaxies occupy dark matter halos that are much more massive than those occupied by blue galaxies with the same stellar mass. The data presented here are publicly released via the KiDS webpage at http://kids.strw.leidenuniv.nl/DR4/brightsample.php.Comment: Matches the published version. Data available at http://kids.strw.leidenuniv.nl/DR4/brightsample.ph

Paternal origins and migratory episodes of domestic sheep.

The domestication and subsequent global dispersal of livestock are crucial events in human history, but the migratory episodes during the history of livestock remain poorly documented [1-3]. Here, we first developed a set of 493 novel ovine SNPs of the male-specific region of Y chromosome (MSY) by genome mapping. We then conducted a comprehensive genomic analysis of Y chromosome, mitochondrial DNA, and whole-genome sequence variations in a large number of 595 rams representing 118 domestic populations across the world. We detected four different paternal lineages of domestic sheep and resolved, at the global level, their paternal origins and differentiation. In Northern European breeds, several of which have retained primitive traits (e.g., a small body size and short or thin tails), and fat-tailed sheep, we found an overrepresentation of MSY lineages y-HC and y-HB, respectively. Using an approximate Bayesian computation approach, we reconstruct the demographic expansions associated with the segregation of primitive and fat-tailed phenotypes. These results together with archaeological evidence and historical data suggested the first expansion of early domestic hair sheep and the later expansion of fat-tailed sheep occurred ∼11,800-9,000 years BP and ∼5,300-1,700 years BP, respectively. These findings provide important insights into the history of migration and pastoralism of sheep across the Old World, which was associated with different breeding goals during the Neolithic agricultural revolution

Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment

We present the results for CAPRI Round 50, the fourth joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of twelve targets, including six dimers, three trimers, and three higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly related templates were found for the individual subunits. Twenty-five CAPRI groups including eight automatic servers submitted ~1250 models per target. Twenty groups including six servers participated in the CAPRI scoring challenge submitted ~190 models per target. The accuracy of the predicted models was evaluated using the classical CAPRI criteria. The prediction performance was measured by a weighted scoring scheme that takes into account the number of models of acceptable quality or higher submitted by each group as part of their five top-ranking models. Compared to the previous CASP-CAPRI challenge, top performing groups submitted such models for a larger fraction (70–75%) of the targets in this Round, but fewer of these models were of high accuracy. Scorer groups achieved stronger performance with more groups submitting correct models for 70–80% of the targets or achieving high accuracy predictions. Servers performed less well in general, except for the MDOCKPP and LZERD servers, who performed on par with human groups. In addition to these results, major advances in methodology are discussed, providing an informative overview of where the prediction of protein assemblies currently stands.Cancer Research UK, Grant/Award Number: FC001003; Changzhou Science and Technology Bureau, Grant/Award Number: CE20200503; Department of Energy and Climate Change, Grant/Award Numbers: DE-AR001213, DE-SC0020400, DE-SC0021303; H2020 European Institute of Innovation and Technology, Grant/Award Numbers: 675728, 777536, 823830; Institut national de recherche en informatique et en automatique (INRIA), Grant/Award Number: Cordi-S; Lietuvos Mokslo Taryba, Grant/Award Numbers: S-MIP-17-60, S-MIP-21-35; Medical Research Council, Grant/Award Number: FC001003; Japan Society for the Promotion of Science KAKENHI, Grant/Award Number: JP19J00950; Ministerio de Ciencia e Innovación, Grant/Award Number: PID2019-110167RB-I00; Narodowe Centrum Nauki, Grant/Award Numbers: UMO-2017/25/B/ST4/01026, UMO-2017/26/M/ST4/00044, UMO-2017/27/B/ST4/00926; National Institute of General Medical Sciences, Grant/Award Numbers: R21GM127952, R35GM118078, RM1135136, T32GM132024; National Institutes of Health, Grant/Award Numbers: R01GM074255, R01GM078221, R01GM093123, R01GM109980, R01GM133840, R01GN123055, R01HL142301, R35GM124952, R35GM136409; National Natural Science Foundation of China, Grant/Award Number: 81603152; National Science Foundation, Grant/Award Numbers: AF1645512, CCF1943008, CMMI1825941, DBI1759277, DBI1759934, DBI1917263, DBI20036350, IIS1763246, MCB1925643; NWO, Grant/Award Number: TOP-PUNT 718.015.001; Wellcome Trust, Grant/Award Number: FC00100

Agreeing to bind: the case of Russian

This contribution offers an analysis of the structural constraints on the interpretation of the Russian anaphoric expressions sebja and svoj. It accounts for a number of intricate binding patterns, such as the ‘animacy effect’ in the case of non-local binding and apparent irregularities in subject orientation and complementarity in local and long-distance binding. We show that these patterns can be accounted for in a unified manner by Multiple Agree-based dependencies established separately for person and number features, assuming the presence of a ϕ-incomplete number-only probe low in the structure. As a result of the valuation procedure the reflexives end up only partially valued and thus remain distinct from pronominals

The total cost of rearing a heifer on Dutch dairy farms: calculated versus perceived cost

BACKGROUND: As farmers do not often keep a record of the expenditures for rearing, an economic tool that provides insight into the cost of rearing is useful. In the Netherlands, an economic tool (Jonkos) has been developed that can be used by farmers to obtain insight into the cost of rearing on their farm. The first objective of this study is to calculate the total cost of rearing young stock in Dutch dairy herds using Jonkos. The second objective is to compare the calculated total cost of rearing with the farmers' own estimation of the cost of rearing (the perceived cost). FINDINGS: Information was available for 75 herds that reared their own young stock and who had used the Jonkos tool. The perceived cost of rearing young stock was only available for 36 herds. In the 75 herds, the average herd size was 100 dairy cows. The average calculated total cost of rearing a heifer was €1,790. The average perceived total cost of rearing a heifer (including labour and housing costs) was €1,030. CONCLUSION: Most Dutch farmers in the study underestimated the total cost of rearing. The Jonkos economic tool has the advantage that herd-specific information can be entered as input values. The output of the tool can improve the awareness of farmers about the total costs of rearing. This awareness can lead to a higher priority of young stock rearing and consequently to an improved quality of young stock rearing

Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment

We present the results for CAPRI Round 50, the fourth joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of twelve targets, including six dimers, three trimers, and three higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly related templates were found for the individual subunits. Twenty-five CAPRI groups including eight automatic servers submitted ~1250 models per target. Twenty groups including six servers participated in the CAPRI scoring challenge submitted ~190 models per target. The accuracy of the predicted models was evaluated using the classical CAPRI criteria. The prediction performance was measured by a weighted scoring scheme that takes into account the number of models of acceptable quality or higher submitted by each group as part of their five top-ranking models. Compared to the previous CASP-CAPRI challenge, top performing groups submitted such models for a larger fraction (70–75%) of the targets in this Round, but fewer of these models were of high accuracy. Scorer groups achieved stronger performance with more groups submitting correct models for 70–80% of the targets or achieving high accuracy predictions. Servers performed less well in general, except for the MDOCKPP and LZERD servers, who performed on par with human groups. In addition to these results, major advances in methodology are discussed, providing an informative overview of where the prediction of protein assemblies currently stands

Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment

We present the results for CAPRI Round 50, the fourth joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of twelve targets, including six dimers, three trimers, and three higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly related templates were found for the individual subunits. Twenty-five CAPRI groups including eight automatic servers submitted ~1250 models per target. Twenty groups including six servers participated in the CAPRI scoring challenge submitted ~190 models per target. The accuracy of the predicted models was evaluated using the classical CAPRI criteria. The prediction performance was measured by a weighted scoring scheme that takes into account the number of models of acceptable quality or higher submitted by each group as part of their five top-ranking models. Compared to the previous CASP-CAPRI challenge, top performing groups submitted such models for a larger fraction (70–75%) of the targets in this Round, but fewer of these models were of high accuracy. Scorer groups achieved stronger performance with more groups submitting correct models for 70–80% of the targets or achieving high accuracy predictions. Servers performed less well in general, except for the MDOCKPP and LZERD servers, who performed on par with human groups. In addition to these results, major advances in methodology are discussed, providing an informative overview of where the prediction of protein assemblies currently stands