dataesr/scientific-paragraphs-categorization huggingface dataset:
All 10,209 sequences in the canine-related cluster were extracted and used for the remainder of the study. Canis familiaris and genus Vulpes (i. e. , foxes) were the most common sources of canine-clustering sequences, accounting for 51. 9% and 8. 4%, respectively. Other families, including the Bovidae, Hominidae, Mustelidae, Felidae, Mephitidae, and Herpestidae, contributed the remaining sequences. The location of the sampling impacted the predominant source of sequences, with most European sequences coming from the genus Vulpes and those in Asia and Africa primarily coming from household dogs. In Asia, the Hominidae and Mustelidae families, particularly the Chinese ferret badger, were major sources of sequences (Fig. 1b, d ). Since the 1970s nearly all continents have experienced an exponential increase in RABV sequence submissions to the NCBI Virus database.
Years of canine-maintained RABV spread To investigate the geographic transmission of canine RABV, we inferred the ancestral locations at the country level on the full and subsampled trees with PastML (https://github. com/amholtz/ GlobalRabies/tree/main/data/ACR_Results)  33. We created a consensus tree with 6,096 sequences by taking the union of all sequences in subsampled trees and reducing the full-canine tree through pruning. The clade ancestral estimates that were consistent between the aggregated subsamples and the full tree are shown in Fig. 3. For the first time, we estimated the country origin of 34 out of the 44 identified canine-mediated clades in the consensus tree, with ancestral estimates as well for their internal nodes, revealing historical transmission between and across the clades (Supplementary Table  4  and Fig.
We investigate the opposite approach and shows its advantage in terms of inference power. Our analysis is based on more than 10,000 RABV partial and whole-genome sequences available in the NCBI Virus database  5. Our pipeline employs a concatenated alignment of the five RABV gene fragments, with gaps for the regions absent in partial sequences (Supplementary Fig. 2 ). The phylogenetic analyses were performed with time-efficient inference methods suited for large data sets: an approximate maximum-likelihood phylogenetic analysis using Fas-tTree, time-scaling with the least-square dating method of LSD2, and ancestral geographic character inference using a maximum-likelihood method implemented in PastML. We validated our pipeline by comparing its results to those from previous studies, to phylogenetic analyses using subsampled data sets and to those utilizing more complex evolutionary models accounting for potential evolutionary rate changes between genes and for potential selection pressure:  26, 29, 39, 40  Using a larger data set, we obtained a compatible tree topology and compatible (between different trees and evolutionary models) but more precise dating (Fig.
Data set compilation A total of 25,787 sequences of rabies virus (RABV) were obtained from the NCBI Virus database 5 in September 2021. A quality check was conducted to remove sequences that were (1) missing date and country information, (2) older than 1972 (for sequencing quality), (3) identified as vaccine or laboratory strains, (4) or shorter than 200 nucleotides in length. As a result, 14,752 sequences were retained for this study. Sequence filtering is demonstrated in Supplementary Fig. 1 , and a complete list of sequences with criteria for exclusion can be found in Supplementary Table 1 ('exclusion' column).
Sequence alignment An initial global alignment using a custom script (https://github. com/ amholtz/GlobalRabies/blob/main/R/clean_RABV. R)  33  was used to define the sequences based on which gene their nucleotides correspond to. Sequences with more than 200 nucleotides in a gene-coding region, were sorted into gene-specific fasta files. For example, WGS were included in the N, P, M, G, and L files. All sequences in these independent files were then cut at the start codons (according to the reference genome) of the corresponding gene (top, Supplementary Fig. 2 ). Each newly cut gene-specific fasta file (void of non-coding regions) was then aligned against the (also cut) corresponding reference sequence, using MAFFT (v7. 505) with the FFT-NS-1 strategy, addfragments, and keep-length method  53.
To visualize differences in rates of evolution according to each gene, phylogenetic trees using FastTree (v2. 1. 11)  55  were estimated using the previously reported settings, according to five gene-specific multiple sequence alignments. Gene-specific evolutionary rates were then determined using LSD2  59  following outlier removal (Supplementary Fig. 5 ). Subsampling. The full-canine tree was subsampled to reduce geographic bias towards countries with a disproportionally high number of sequences by employing a custom script (https://github. com/ amholtz/GlobalRabies/blob/main/python/py_subsampling. py)  33  which removes sequences from oversampled countries by phylogenetic diversity  60  given an input tree. At each step of the algorithm, the tip with the shortest branch among those sequences corresponding to over-represented countries is removed.
Purifying selection model To quantify the effect of purifying and diversifying selection on the time calibration, we used the software package HyPhy 67 on the smaller data set of 236 whole-genome sequence subset from Troupin et al. 26  to lighten the computational load  26. This subset is made of only WGS and its dating has been previously analyzed, such that it is useful to assess model variations. Site-specific rates of the numbers of nonsynonymous and synonymous (dN and dS) substitutions per set were inferred in each codon using the Mixed Effects Model of Evolution (MEME)  68  , Fixed Effects Likelihood (FEL)  69  and the adaptive Branch-Site Random Effects model (aBSREL)  70  in HyPhy. The dN/dS ratio was then used by each model to optimize and re-estimate branch lengths of the tree with a fixed topology (Supplementary Methods 1).
Phylogeographic reconstruction and subsampling consensus Ancestral geographic characters of canine RABV transmission were investigated using the fast likelihood method available in PastML version 1. 9. 34  71  to reconstruct the historical spread of canine RABV. Marginal probabilities of locations of ancestral nodes were estimated given the geographic location of sampled sequences in a rooted timecalibrated tree. To assess the confidence in state estimates of internal nodes with respect to potential geographic sampling bias, we repeated PastML on each of the five independent and uniquely subsampled reconstructed and time-calibrated trees and compared the ancestral state estimates. Only ancestral state estimates with marginal posterior probabilities of 50% or greater were considered. A custom script (https://github.
Regional and colonization history ancestral character reconstruction ACR using PastML version 1. 9. 34  71  was repeated on the 6096-sequence aggregated tree for two geographic characters. The first defined the character using a World Bank regional grouping variable using R package countrycode  34  (Fig. 4 ) which reflects cultural and geographic similarities. This resulted in the grouping of 120 countries in the original data set into 18 regions. The second defined the character according to the colonial history of the sequence country of isolation (Fig. 5 ). Colonial powers were considered from 1600 to 1950, resulting in five states: British, Spanish, French, Portuguese, and Russian Empires (not including USSR satellite states). Countries with more than one colonial history were considered a member of the empire that maintained the longest and largest control (for example, India is grouped by the British Empire, even though a small part was also a French colony for several hundred years).
Introduction event exploration To visualize human-mediated transmissions of RABV, long geographic distances over short time intervals were located on the phylogeny using a custom script (https://github. com/amholtz/GlobalRabies/blob/main/ R/introduction_events_FullTree. R)  33. The package cepiigeodist  72  was used to calculate geographic distances between each most-populated city in the country. Character states from the phylogeographic analysis were considered only if there was a consensus between the aggregated subsamples and the full-canine tree. A branch of length Y with a resolved consistent parent node state A and a resolved consistent child node state B was considered as a transmission from country A to country B over Y years. Transmissions within countries and between neighboring countries were discarded, resulting in 232 long-range transmissions.
Acknowledgements The authors thank  S. L. Kosakovsky Pond  for his help running HyPhy and interpreting the results. We would also like to thank  Edward Holmes ,  Jake Faber  and  Joël Brehin  for their helpful reading and critical comments in the review of the manuscript. G. B. acknowledges support from the  Research Foundation -Flanders (Fonds voor Wetenschappelijk Onderzoek -Vlaanderen, FWO, Belgium ; grant  n°G098321N ,  G0E1420N ) and from the  Internal Funds KU Leuven  (Grant No. C14/18/ 094 ). A. H. acknowledges École doctorale  Frontières de l'Innovation en Recherche et Education-Programme Bettencourt. A. H is funded by the  INCEPTION programme (Investissements d'Avenir  grant  ANR-16-CONV-0005 ). This work was funded by  Institut Pasteur.
Data availability Data were downloaded via NCBI Virus Database: https://www. ncbi. nlm. nih. gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ ss=Lyssavirus%20rabies,%20taxid:11292. Information on geography, country codes, colonization was incorporated via R packages: cepiigeogist, countrycode. All data used in this analysis are available on https://github. com/amholtz/GlobalRabies (https://doi. org/10. 5281/ zenodo. 8047854)  33.
The developments of the open-source Open-Molcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report offers an overview of the chemical phenomena and processes OpenMolcas can address, while showing that OpenMolcas is an attractive platform for state-of-the-art atomistic computer simulations.
INTRODUCTION The MOLCAS package has its origin in 1989 as a departmental development project in the Theoretical Chemistry group at Lund University, Sweden. The group around Prof. B. O. Roos developed the project, with a few invited scientists, keeping the project as a closed-source programming effort. 2] [3] [4] [5] [6] [7]  Starting with the 2018 release of the open-source program package Open-Molcas, under the Lesser General Public License (LGPL),  8  further development has been a community effort. These efforts have already been the subject of additional publications. 9, 10 ere, a compilation of the continuing development efforts of the growing OpenMolcas community is put forward, as it progressed from early 2020 until late 2022. In this presentation, original developments and modifications to existing codes will be presented.
Selected-CI computations, in the form of the semistochastic heat-bath configuration interaction  26  selfconsistent field (S)HCI-SCF approach, are accessible via the recent interface to Dice. 25, 26 An interesting alternative to electronic structure characterizations, arising from the interface with GronOR, is offered by the nonorthogonal configuration interaction (NOCI) strategy. The QCMaquis module in latest OpenMolcas implements new DMRG-based methods for explicitly correlated and excited-state electronic structure calculations. Moreover, it integrates a new Python-based version of AutoCAS, which enables automating and streamlining CAS-based calculations. Multireference configuration interaction (MRCI) methods represent a robust approach toward dynamic correlation effects, relying on a multiconfigurational, often but not limited to the CAS-type reference wave function.
MRCI-based calculations in the latest OpenMolcas environment are made possible by a number of interfaces. Fully uncontracted MRCI calculations are now possible through the RelaxSE interface, with a specific focus on the accurate determination of magnetic excitations. Uncontracted MRCI techniques provide substantial support in accurately capturing screening effects (dynamical correlation), arising from the interaction of the magnetic centers with the bridging ligands. The OpenMolcas-RelaxSE interface complements the established OpenMolcas-COLUMBUS interface in performing MRCI computations. Additionally, the latest OpenMolcas-COLUMBUS interface provides the means for computing full nonadiabatic coupling vectors and spin-orbit interactions at the MRCI level of theory. Driven by the advances in OpenMolcas, the COLUMBUS package has also been released as an open-source project, and its interoperability with OpenMolcas has been enhanced.
The Stochastic-GASSCF  52  that emerges from the Open-Molcas-NECI interface also allows stochastic-MRCI-like calculations, using SD bases, and with the possibility to spinpurify the targetted wave functions. Multiconfigurational second-order perturbation theory (PT2) approaches, such as CASPT2 and RASPT2, represent another tool in OpenMolcas to tackle correlation effects involving electrons and orbitals outside the active space, i. e. , external correlation. PT2 techniques have contributed greatly to the popularity of the OpenMolcas package over the years. In the latest OpenMolcas environment, new and robust quasidegenerate variants of CASPT2 have been implemented; these combine the best features of MS-CASPT2 and XMS-CASPT2 in a single approach. These can be used for both calculating accurate relative energies and properly describing near-degenerate regions of the potential energy surface.
D available within the MOLCAS 7 and the OpenMolcas 9 chemistry software packages, only supports the cumulative GAS constraints. 17 Another similar approach is the occupation restricted multiple active spaces self-consistent field (ORMAS-SCF) method, that only supports local constraints. 106 The recent Stochastic-GAS algorithm allows both local and cumulative constraints, while allowing much larger active space sizes. Special GASSCF wave functions, optimized by conventional techniques (Davidson) were combined with the post-MCSCF MC-PDFT approach and proved their utility for modeling transition metal chemistry; they are the separated pair  108  and the extended separated pair  109  approximations. One-and two-body RDMs can be stochastically sampled as for stochastic FCI or CAS wave functions.
I GronOR uses the one-and two-electron integrals from OpenMolcas and a list of CI coefficients plus orbital occupations of the multideterminantal wave functions that are used to construct the MEBFs of the NOCI matrix. GronOR works with Slater determinants and therefore makes use of the PRSD keyword of the RASSCF module to write out the wave function in terms of determinants instead of configuration state functions. The list of coefficients and orbital occupations is saved in a separate file that is directly read by GronOR. The transformation of one-and two-electron integrals to a common MO basis is performed by the MOTRA module, in which the automatic orthogonalization of the orbitals has to be deactivated using the NOORth keyword. If the Cholesky decomposition of the integrals is used, MOTRA transforms the Cholesky vectors, and the auxiliary program rdcho reconstructs the two-electron integrals in the common MO basis.
Subsequently, the TRAINT and TRAONE files are written in a format that can be read by GronOR with the auxiliary program rdtraint. Both auxiliary programs are part of the GronOR repository on GitLab. 162. 6. Multireference Configuration Interaction. The MRCI capabilities of OpenMolcas are expanded with interfaces to COLUMBUS and RelaxSE, allowing calculations of nonadiabatic and spin-orbit couplings, and the use of uncontracted variants specialized in the treatment of magnetic excitations. Spin-Orbit and Nonadiabatic Interactions at the MRCI Level. COLUMBUS is a collection of programs for high-level ab initio molecular electronic structure calculations. 163, 164 CO-LUMBUS is distinguished by its flexible and powerful uncontracted MRCI functionality. 165, 166 Using the parallel implementation, it is routinely possible to solve CI problems with more than a billion configurations.
2, 6. 3, and 6. 7, respectively. In association with these new developments, the Open-Molcas DFT infrastructure has been completely rewritten, via the integration of the Libxc library  271  as standard platform for the implementation of density functionals. Old DFT code in OpenMolcas has been deprecated, and hundreds of additional functionals are introduced and are now available for standard DFT calculations as well as MC-PDFT computations. Functionals that depend on the electron density Laplacian are also supported for KS-DFT calculations (not yet for MC-PDFT). Hybrid MC-PDFT. Hybrid MC-PDFT (HMC-PDFT) introduces nonlocal exchange and correlation from the underlying multireference wave function into the MC-PDFT energy and is now available in OpenMolcas. 255 The HMC-PDFT energy is given by = + + = + E E E E E E (1 ) (1 ) HMC PDFT MC,class MC,nonclass on top ref MC PDFT (15)   where E MC,nonclass and E ref are, respectively, the nonclassical energy and the total energy computed from the reference wave function.
The individual components in eq 15 are computed and reported in the course of a standard MC-PDFT calculation; thus, unlike hybrid Kohn-Sham functionals, the HMC-PDFT calculation does not cost more than the nonhybrid counterpart. 3] [274] [275] [276] [277]  Benchmark tests on a diverse set of excitation energies suggest that for the tPBE on-top functional, the optimal hybridization parameter is λ = 0. 25, the same as in the "PBE0" exchange-correlation functional  278, 279  of Kohn-Sham density functional theory; this hybrid on-top functional is referred to as "tPBE0". 255, 272 he LAMBDA keyword is used in the MC-PDFT program to control the hybridization. The recommended tPBE0 functional, for instance, can be specified by LAMBDA = 0. 25. Using the same keyword, LAMBDA, the user can also change the values of the diagonal elements of the model-space Hamiltonian in multistate PDFT calculations (discussed below); the hybrid energies on the diagonal become a linear combination of the PDFT and conventional wave function energies of the intermediate-state wave functions.
293, 294 In the current version of OpenMolcas, a keyword WJOB has been added in the MCPDFT module to facilitate this. This keyword allows one to write the required information into the JOBIPH file. For MC-PDFT, only the energy of each state is written into the JOBIPH file because an MC-PDFT calculation is based on a previous wave function; for XMS-PDFT and CMS-PDFT, both the energies and the CI coefficients of the eigenstates (obtained by diagonalizing the model-space Hamiltonian in MS-PDFT) are written into the JOBIPH file. Then the JOBIPH file is read in the RASSI module, where spin-orbit coupling matrix elements are calculated by the atomic-mean-field approximation  295  to the Breit-Pauli Hamiltonian. The spin-orbit-inclusive states are calculated by the restricted-active-space state-interaction spinorbit (RASSI-SO) formalism  295, 296  that allows the Hamiltonian to be diagonalized even though the wave functions of the spinfree states with different multiplicities were calculated with different orbital sets.
ELECTRONIC SPECTROSCOPY The availability of more sophisticated and efficient methods, like those described in section 2, enables the simulation of more complex processes with a higher accuracy. However, for performing and interpreting such simulations, new developments are often required. This section details some recent developments that allow the use of OpenMolcas for the simulation of different types of magnetic properties and electronic spectroscopy, in particular those where the approximation of a fixed molecular structure�i. e. , frozen nuclei�can be made. First an improvement beyond the socalled Lines approximation in the calculation of anisotropic exchange interaction in binuclear systems, achieved by modifications to the SINGLE_ANISO module, is described. Subsequently alternative tools are presented, molcas_suite and angmom_suite�both open-source packages in PyPI� for the same type of analysis.
The methodology is implemented in the function PREX, entering the current version of the SINGLE_ANISO module. As an example, the derivation of anisotropic exchange parameters for a recently studied Dy III Mn II complex  303  is presented. The calculations with the SINGLE_ANISO program show that the ground Kramers doublet at the Dy III site = S ( 1/2) A is highly axial (g z ≫ g x , g y ). The CASSCF/ CASPT2/RASSI-SO calculations for the Dy III fragment (in which Zn substitutes Mn) have been done with OpenMolcas in a standard fashion for Ln complexes. 302 Since the Mn II ion is a high-spin one (S B = 5/2), the corresponding g-tensor is a priori isotropic, with g factors close to 2. 0, which exempts us from the ab initio investigation of this single-ion fragment. Repeating then the CASSCF/CASPT2/RASSI-SO calculations for the whole DyMn binuclear complex and applying PREX function to its lowest + + = S S ( 2 1)(2 1) 12 A B multiplets, the anisotropic exchange parameters are derived.
Model Hamiltonian Projection. As an alternative to the methodologies available within OpenMolcas presented in section 3. 1, model Hamiltonians for one or two spin centers with arbitrary angular momenta can be projected directly from the output of a CAS/RASSCF/(CASPT2)/RASSI-SO calculation (via the rassi. h5 file) using the open-source molcas_suite and angmom_suite packages available on PyPI. This implementation is based on the projection of a given set of ab initio states onto an arbitrary set of angular momentum eigenstates and the subsequent determination of parameters of numerous spin Hamiltonian terms using irreducible tensor operator techniques. The transformation from the ab initio eigenstates into a basis of well-defined angular momenta is carried out in two steps: (1) the spin-free ab initio states are projected via the group theoretical orthogonal projector = | | P L M L M , , L M L L L onto a set of LS-terms which transform under the (2L + 1)-dimensional irreducible representations of SO(3) and span the selected model space; then (2) the obtained terms are (de)coupled via Clebsch-Gordan vector (decomposition or) addition to yield the transformation to the final model basis.
Relativistic Hyperfine Coupling. The electronnucleus hyperfine coupling (HFC) is known to be extremely sensitive to relativistic effects-even finite nuclear volume corrections may exceed 10% in magnitude for isotopes such as 199 Hg. 309, 310  Furthermore, the orbital angular momentum may generate large contributions to the HFC in open-shell metal complexes, either directly or via SO coupling. 311 A set of options to calculate HFC was implemented in the RASSI module for RASSI-SO calculations,  312  following a similar approach as developed previously for electron g-factors. 294, 313 The initial HFC implementation  312  had a major limitation, in that the hyperfine integrals were nonrelativistic, thus limiting applications to light atoms or cases where so-called contact terms hardly contribute.