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opencc-zeroDec 2015View details →

Data from: Consistency of VDJ rearrangement and substitution parameters enables accurate B cell receptor sequence annotation

VDJ rearrangement and somatic hypermutation work together to produce antibody-coding B cell receptor (BCR) sequences for a remarkable diversity of antigens. It is now possible to sequence these BCRs in high throughput; analysis of these sequences is bringing new insight into how antibodies develop, in particular for broadly-neutralizing antibodies against HIV and influenza. A fundamental step in such sequence analysis is to annotate each base as coming from a specific one of the V, D, or J genes, or from an N-addition (a.k.a. non-templated insertion). Previous work has used simple parametric distributions to model transitions from state to state in a hidden Markov model (HMM) of VDJ recombination, and assumed that mutations occur via the same process across sites. However, codon frame and other effects have been observed to violate these parametric assumptions for such coding sequences, suggesting that a non-parametric approach to modeling the recombination process could be useful. In our paper, we find that indeed large modern data sets suggest a model using parameter-rich per-allele categorical distributions for HMM transition probabilities and per-allele-per-position mutation probabilities, and that using such a model for inference leads to significantly improved results. We present an accurate and efficient BCR sequence annotation software package using a novel HMM "factorization" strategy. This package, called partis (https://github.com/psathyrella/partis/), is built on a new general-purpose HMM compiler that can perform efficient inference given a simple text description of an HMM.

opencc-zeroDec 2015View details →

Data from: Timing of head movements is consistent with energy minimization in walking ungulates

Many ungulates show a conspicuous nodding motion of the head when walking. Until now, the functional significance of this behaviour remained unclear. Combining in vivo kinematics of quadrupedal mammals with a computer model, we show that the timing of vertical displacements of the head and neck is consistent with minimizing energy expenditure for carrying these body parts in an inverted pendulum walking gait. Varying the timing of head movements in the model resulted in increased metabolic cost estimate for carrying the head and neck of up to 63%. Oscillations of the head–neck unit result in weight force oscillations transmitted to the forelimbs. Advantageous timing increases the load in single support phases, in which redirecting the trajectory of the centre of mass (COM) is thought to be energetically inexpensive. During double support, in which—according to collision mechanics—directional changes of the impulse of the COM are expensive, the observed timing decreases the load. Because the head and neck comprise approximately 10% of body mass, the effect shown here should also affect the animals' overall energy expenditure. This mechanism, working analogously in high-tech backpacks for energy-saving load carriage, is widespread in ungulates, and provides insight into how animals economize locomotion.

opencc-zeroNov 2021View details →

Data for: Plasmids do not consistently stabilize cooperation across bacteria, but may promote broad pathogen host-range

Horizontal gene transfer via plasmids could favour cooperation in bacteria, because transfer of a cooperative gene turns non-cooperative cheats into cooperators. This hypothesis has received support from theoretical, genomic and experimental analyses. In contrast, we show here, with a comparative analysis across 51 diverse species, that genes for extracellular proteins, which are likely to act as cooperative 'public goods', were not more likely to be carried on either: (i) plasmids compared to chromosomes; or (ii) plasmids that transfer at higher rates. Our results were supported by theoretical modelling which showed that while horizontal gene transfer can help cooperative genes initially invade a population, it has less influence on the longer-term maintenance of cooperation. Instead, we found that genes for extracellular proteins were more likely to be on plasmids when they coded for pathogenic virulence traits, in pathogenic bacteria with a broad host-range.

opencc-by-sa-4.0Jul 2024View details →

Code and data for "Personality matters – The interplay between consistent individual differences and mouse welfare in female C57BL6/J mice"

R code and data used for the manuscript "Personality matters – The interplay between consistent individual differences and mouse welfare in female C57BL6/J mice"

FIGURE 17 in Can a rainbow consist of a single colour? A new comprehensive generic arrangement of the 'Iris sensu latissimo' clade (Iridaceae), congruent with morphology and molecular data

FIGURE 17. Approximate distribution area of Limniris sect. Laevigatae (incl. ser. Tripetalae).

FIGURE 24 in Can a rainbow consist of a single colour? A new comprehensive generic arrangement of the 'Iris sensu latissimo' clade (Iridaceae), congruent with morphology and molecular data

FIGURE 24. Approximate distribution areas: A) Chamaeiris (red); B) Dielsiris (yellow).

FIGURE 14 in Can a rainbow consist of a single colour? A new comprehensive generic arrangement of the 'Iris sensu latissimo' clade (Iridaceae), congruent with morphology and molecular data

FIGURE 14. Approximate distribution areas: A) Evansia (yellow); B) Tectiris (red).

FIGURE 11 in Can a rainbow consist of a single colour? A new comprehensive generic arrangement of the 'Iris sensu latissimo' clade (Iridaceae), congruent with morphology and molecular data

FIGURE 11. Approximate distribution area of Iris sect. Iris.

FIGURE 8 in Can a rainbow consist of a single colour? A new comprehensive generic arrangement of the 'Iris sensu latissimo' clade (Iridaceae), congruent with morphology and molecular data

FIGURE 8. Approximate distribution areas: A) Siphonostylis (yellow); B) Gattenhofia (red).

FIGURE 26 in Can a rainbow consist of a single colour? A new comprehensive generic arrangement of the 'Iris sensu latissimo' clade (Iridaceae), congruent with morphology and molecular data

FIGURE 26. Approximate distribution areas: A) Rodionenkoa (red); B) Lophiris (yellow).

opencc-zeroDec 2012View details →

Data from: Social status and personality: stability in social state can promote consistency of behavioural responses

Stability of 'state' has been suggested as an underlying factor explaining behavioural stability and animal personality (i.e. variation among, and consistency within individuals in behavioural responses), but the possibility that stable social relationships represent such states remains unexplored. Here, we investigated the influence of social status on the expression and consistency of behaviours by experimentally changing social status between repeated personality assays. We used male domestic fowl (Gallus gallus domesticus), a social species that forms relatively stable dominance hierarchies, and showed that behavioural responses were strongly affected by social status, but also by individual characteristics. The level of vigilance, activity and exploration changed with social status, whereas boldness appeared as a stable individual property, independent of status. Furthermore, variation in vocalization predicted future social status, indicating that individual behaviours can both be a predictor and a consequence of social status, depending on the aspect in focus. Our results illustrate that social states contribute to both variation and stability in behavioural responses, and should therefore be taken into account when investigating and interpreting variation in personality.

opencc-by-4.0Jul 2021View details →

Full year of consistent Direct Normal Irradiance data at 1-min, 10-min and 1-hour time steps.

Full year of consistent Direct Normal Irradiance data at 1-min, 10-min and 1-hour time steps. The consistency is obtained by building the 10-min and 1-hour time step years from the 1-min year. The measurements correspond to the year 2016 and were taken by the meteorological station of the Group of Thermodynamics and Renewable Energy (GTER) of the University ofSeville. The geographical coordinates of the measurement station are: Latitude: 37º24’42’’ North, Longitude:  -6º 00’21’’ East. This measurement station measures solar DNI with a sampling and logging frequency of 0.2 Hz and an ISO first class EppleyNIP pyrheliometer mounted on a sun tracker Kipp and Zonen 2AP.

opencc-by-4.0Aug 2022View details →

Data Set "A simple and consistent quantum-chemical fragmentation scheme for proteins that includes two-body contributions"

Data set accompanying the publication "A simple and consistent quantum-chemical fragmentation scheme for proteins that includes two-body contributions" This dataset contains: - PDB files of all structures used as test cases - PyADF scripts for running MFCC-MBE(2) calculations - Jupyter notebook for generating plots including raw numerical data - Total energies (in a.u.) for the different test cases

opencc-by-4.0Apr 2023View details →

Data and code associated with "How consistently do species leaf out or flower in the same order? Understanding the factors that shape this characteristic of plant communities."

R script and data used in analyses for the manuscript, "How consistently do species leaf out or flower in the same order? Understanding the factors that shape this characteristic of plant communities." by C. Beiter & T. Crimmins, published in the International Journal of Biometeorology.