Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

ASYMPTOTIC METHODS IN ASYMMETRIC ROTOR THEORY∗THEORY^{*}

$^{*}$Supported by the Geophysics Research Directorate, Air Force Cambridge Research Laboratories. $^{1}$E. K. Gora, International Symposium on Molecular Structure and Spectroscopy, Tokyo, 1962. Paper C, 208-1. $^{2}$S. Golden, J. Chem. Phys. 16, 78 (1948). $^{3}$R. B. Dingle and H. W. Mueller, Journal fuer Mathematik, 211, 11 (1962).Author Institution: Physics Department, Providence College“Asymptotic methods for the treatment of asymmetric rotor problems in the domain of high J and low $K^{1}$ have been generalized in two ways: (1) A non-linear differential equation with periodic coefficients takes the place of the linear Mathieu type equation, which has first been used by $Golden^{2}$ to calculate approximately asymmetric rotor eigenvalues, and which has served as starting point to derive asymptotic formulas in reference 1. The characteristic matrix of this non-linear equation is infinite, but its elements are exactly identical with the elements of a reduced form of the asymmetric rotor matrix within their domain of definition. (2) A procedure permitting extension of asymptotic expansions for eigenvalues and eigenfunctions of the Mathieu equation into the domain of noticeable symmetry type splitting has recently been developed by Dingle and $Mueller.^{3}$ This procedure is now adapted to the derivation of the corresponding asymptotic formulas in asymmetric rotor theory for energy levels and transitions for which symmetry-type splittings are noticeable but still small. The inclusion of such symmetry type corrections extends appreciably the domain of applicability of the asymptotic methods.

AN ASYMPTOTIC METHOD IN ASYMMETRIC ROTOR THEORY: EXTENSION TO ANGULAR MOMENTUM OPERATORS OF HIGHER ORDER.

Supported by the Air Force Cambridge Research Laboratories, Office of Aerospace Research. $^{1}$ Edwin K. Gora, J. Mol, Spectry. 16, 378 (1965).Author Institution: Physics Department, Providence College Providence,An asymptotic $method^{1}$ previously used to derive explicit formulas for asymmetric rotor eigenvalues in the domain of high J and low K has been extended to the derivation of the corresponding formulas for various angular momentum operators of higher order. Such formulas should be useful in the theory of higher order centrifugal distortion effects in asymmetric rotor molecules, but might also be of interest in applications to some other problems. The method is based on the possibility of approximating matrices of the type encountered in the quantum mechanics of angular momentum by matrices generated by Mathieu-type differential equations. Asymptotic methods available in the theory of such differential equations are then used to derive asymptotic expansion formulas for the eigenvalues of the equations. These formulas approximate the desired matrix eigenvalues

AN INVESTIGATION OF THE ALGEBRAIC STRUCTURE OF VIBRATIONAL-ROTATIONAL INTERACTION TERMS OF HIGH ORDER IN POLYATOMIC MOLECULES.

This research was supported by the Air Force Cambridge Research Laboratories, Office of Aerospace Research.Author Institution: Physics Department, Providence College, ProvidenceIn recent years, the theory of vibrational-rotational (v-r) interactions in polyatomic molecules has reached a formidable degree of complexity, in particular, in its applications to the derivation of terms of sixth power in the angular momentum. In an attempt to simplify these derivations, and to extend some of them to terms of eighth to twelfth power in the angular momentum, we have developed an algebraic procedure which follows closely the conventional treatment of v-r interactions in diatomic molecules. The minimum of an energy function consisting of the rotational kinetic energy of a non-rigid asymmetric rotor and of the potential energy of a more-dimensional anharmonic oscillator is chosen as the origin of a new coordinate system. A ``Minimization Theorem'' simplifies substantially the algebraic procedures. The derivation of general results is straightforward but the structure of the terms of high order thus obtained is rather involved. Only a systematic analysis of these structures, and the development of methods suitable for the evaluation of these terms makes the application of our results to particular molecular models feasible

CONTACT TRANSFORMATIONS IN CLOSED FROM COMBINED WITH MINIMIZATION IN THE THEORY OF VIBRATIONAL-ROTATIONAL INTERACTIONS

This research was supported in part by N.A.S.A. $^{1}$Report AFCRL--69--0247.Author Institution: Physics Department, Providence CollegeWe reported $previously^{1}$ that an algebraic minimization procedure could be used to simplify the derivation of centrifugal distortion constants of high order, but the relation between this procedure and the conventional use of successive contact transformations had not been clearly understood at that time. As we see it now, the minimization procedure is equivalent to a contact transformation in closed from where the transformation function S($p_{i}$,$q_{i}$) is linear in the conjugate variables $p_{i}$, $q_{i}$, and is used to eliminate linear terms in these variables in the Hamiltonian. Such a transformation represents a translation in more-dimensional phase-space. It appears not to have been noticed previously that exact formulas can also be derived when the transformation function is of second order in $p_{i}$, $q_{i}$. The transformations thus generated can be interpreted as rotations in phase-space, and can be combined with the translations. The transformations themselves can be easily performed in closed form, but the exact determination of the parameters needed in the transformation functions presents a more difficult though solvable problem