bluuebunny/crossref_metadata_2025_split huggingface dataset:
GeMI: interactive interface for transformer-based Genomic Metadata Integration
Authors: Serna Garcia Giuseppe , Leone Michele , Bernasconi Anna , Carman Mark J 
Published: April 2022

Abstract
The Gene Expression Omnibus (GEO) is a public archive containing &gt;4 million digital samples from functional genomics experiments collected over almost two decades. The accompanying metadata describing the experiments suffer from redundancy, inconsistency and incompleteness due to the prevalence of free text and the lack of well-defined data formats and their validation. To remedy this situation, we created Genomic Metadata Integration (GeMI; http://gmql.eu/gemi/), a web application that learns to automatically extract structured metadata (in the form of key-value pairs) from the plain text descriptions of GEO experiments. The extracted information can then be indexed for structured search and used for various downstream data mining activities. GeMI works in continuous interaction with its users. The natural language processing transformer-based model at the core of our system is a fine-tuned version of the Generative Pre-trained Transformer 2 (GPT2) model that is able to learn continuously from the feedback of the users thanks to an active learning framework designed for the purpose. As a part of such a framework, a machine learning interpretation mechanism (that exploits saliency maps) allows the users to understand easily and quickly whether the predictions of the model are correct and improves the overall usability. GeMI’s ability to extract attributes not explicitly mentioned (such as sex, tissue type, cell type, ethnicity and disease) allows researchers to perform specific queries and classification of experiments, which was previously possible only after spending time and resources with tedious manual annotation. The usefulness of GeMI is demonstrated on practical research use cases.
Database URL
http://gmql.eu/gemi/
Calculation of normal and leaky modes for horizontal stratified models based on a semi-analytical spectral element method
Authors: Shi Caiwang , Ren Hengxin , Li Zhengbo , Chen Xiaofei 
Published: April 2022

SUMMARY
The dispersion curves of surface waves controlled by normal modes have been widely used for the retrieval of subsurface structures. However, only the S-wave velocity structures can be retrieved in most cases because normal modes are primarily sensitive to S-wave velocities. Compared with normal modes, leaky modes, which depend on subsurface structures as well and are more sensitive to P-wave velocities, are rarely applied for subsurface imaging. Besides the difficulties of extracting leaky modes from field data, the calculation of leaky modes also prevents the practical application because traditional methods need to search the leaky-mode roots in the complex frequency-wavenumber domain and thus suffer from root skipping. Recently, some new observation methods support the extraction of multi-order leaky mode dispersion, an effective method for calculating leaky modes is consequently required for further investigation. In this paper, a semi-analytical spectral element method (SASEM) is proposed to solve for the normal and leaky modes of elastic waves propagating in a stratified model with a half-space substrate. The transparent boundary condition and semi-infinite element method are used to model the elastic wavefields in the half-space substrate. Then, a linear eigenvalue problem is derived for the modal calculation. Through simple eigenvalue decomposition, we can obtain the solutions of both normal and leaky modes stably and efficiently without any prior estimations, which makes SASEM very friendly to forward modelling and inversion. Several numerical tests were performed to verify the effectiveness of SASEM, as well as to demonstrate its features of high accuracy and no root skipping. Besides the models composed of several homogeneous layers, SASEM was applied to a vertically inhomogeneous offshore model to demonstrate its wide applicability. Analyses on the oscillations of the solved modes show that the leaky modes differ from the normal modes because of the increasing wavefields in the half-space. Moreover, modal analyses confirm that a part of the leaky modes (guided-P modes) is more dependent on the P waves, whereas the other modes are primarily determined by the S waves. Consequently, the effective calculation of leaky modes makes it possible to constrain the P-wave velocity using leaky-mode dispersion curves.
Explicit Isogenies of Prime Degree Over Quadratic Fields
Authors: Banwait Barinder S 
Published: April 2022

Abstract
Let $K$ be a quadratic field which is not an imaginary quadratic field of class number one. We describe an algorithm to compute the primes $p$ for which there exists an elliptic curve over $K$ admitting a $K$-rational $p$-isogeny. This builds on work of David, Larson-Vaintrob, and Momose. Combining this algorithm with work of Bruin–Najman, Özman–Siksek, and most recently Box, we determine the above set of primes for the three quadratic fields, ${\mathbb {Q}}(\sqrt {-10})$, ${\mathbb {Q}}(\sqrt {5})$, and ${\mathbb {Q}}(\sqrt {7})$, providing the first such examples after Mazur’s 1978 determination for $K = {\mathbb {Q}}$. The termination of the algorithm relies on the Generalised Riemann Hypothesis.
Spatial distribution and multilevel analysis of factors associated with child marriage in Nigeria
Authors: Bolarinwa Obasanjo Afolabi , Seidu Abdul-Aziz , Tessema Zemenu Tadesse , Adu Collins , Oyeleye Olaoye James , Ahinkorah Bright Opoku 
Published: April 2022

AbstractBackgroundChild marriage among women has become a major threat to the rights of women, especially in low- and middle-income countries. The marriage of girls below age 18 y is a major public and global health challenge. Therefore, this study examined the spatial pattern and factors associated with child marriage in Nigeria.MethodsThe data were sourced from the 2018 Nigeria Demographic and Health Survey. The study included a total of 4283 young women aged 20–24 y. The findings were provided in the form of spatial maps and adjusted ORs (aORs) with 95% confidence interval (CI).ResultsHotspot areas for child marriage in Nigeria were located in Sokoto, Kebbi, Katsina, Kano, Jigawa, Yobe, Bauchi, Niger, Borno, Gombe, and Adamawa. The prevalence of child marriage in Nigeria was 41.50%. The likelihood of child marriage in Nigeria was high among those currently working (aOR=1.31; 95% CI 1.11 to 1.55) compared with young women who were not working. On the other hand, young women whose partners had secondary education and above (aOR=0.57; 95% CI 0.45 to 0.73) were less likely to report child marriage in Nigeria compared with those whose partners had no education.ConclusionsThe findings of the study indicate that there are several hotspots in Nigeria that need to be targeted when implementing interventions aimed at eliminating child marriage in the country.
Consumer perceptions of telehealth for mental health or substance abuse: a Twitter-based topic modeling analysis
Authors: Baird Aaron , Xia Yusen , Cheng Yichen 
Published: April 2022

Abstract

Objective
The objective of this study is to understand the primary topics of consumer discussion on Twitter associated with telehealth for mental health or substance abuse for prepandemic versus during-pandemic time-periods, using a state-of-the-art machine learning (ML) natural language processing (NLP) method.

Materials and Methods
The primary methodological phases of this project were: (1) collecting, cleaning, and filtering data (tweets) from January 2014 to June 2021, (2) describing the final corpus, (3) running and optimizing Bidirectional Encoder Representations from Transformers (BERT; using BERTopic in Python) models, and (4) human refinement of topic model results and thematic classification of topics.

Results
The number of tweets in this context increased by 4 times during the pandemic (2017 tweets prepandemic vs 8672 tweets during the pandemic). During the pandemic topics were more frequently mental health related than substance abuse related. Top during-pandemic topics were therapy, suicide, pain (associated with burnout and drinking), and mental health diagnoses such as ADHD and autism. Anxiety was a key topic of discussion both pre- and during the pandemic.

Discussion
Telehealth for mental health and substance abuse is being discussed more frequently online, which implies growing demand. Given the topics extracted as proxies for demand, the most demand is currently for telehealth for mental health primarily, especially for children, parents, and therapy for those with anxiety or depression, and substance abuse secondarily.

Conclusions
Scarce telehealth resources can be allocated more efficiently if topics of consumer discussion are included in resource allocation decision- and policy-making processes.
Lex petrolea in international arbitration—a very English dissent
Authors: Betin Batuhan 
Published: April 2022

Abstract
This article begins by supplementing the existing criticism which rejects the recognition of lex petrolea as an autonomous system of law. It then proceeds to discuss the practical application of lex petrolea as ‘substantive law’ in international arbitration disputes. This is inspected through the lens of international and comparative law, although sections of the article focus specifically on English law. The author presents three practical conclusions. First, although parties to an arbitration may elect the rules of lex mercatoria and (by analogy) lex petrolea to govern the merits of their dispute under the lex arbitri of most Civil Law European jurisdictions, this is not possible in England under the Arbitration Act 1996. Secondly, an arbitrator may not disapply the parties’ choice of substantive law and instead resolve the dispute through the application of lex petrolea. Such a decision will likely result in the annulment of the award. Thirdly, awards relating to petroleum disputes are incapable of creating binding precedent and therefore do not create indissoluble rules of private international law. Moreover, proponents of lex petrolea such as Bishop and Childs have failed to identify any novel rules of customary international law through their doctrinal study of petroleum related arbitral awards.
Determining Intraosseous Needle Placement Using Point-of-Care Ultrasound in a Swine (Sus scrofa) Model
Authors: Kyle Adrianna I , Auten Jonathan D , Zarow Gregory J , Natarajan Ramesh , Bianchi William D , Speicher Matthew V , Palma James , Gaspary Micah J 
Published: April 2022

ABSTRACT

Objective
Intraosseous (IO) access is critical in resuscitation, providing rapid access when peripheral vascular attempts fail. Unfortunately, misplacement commonly occurs, leading to possible fluid extravasation and tissue necrosis. Current research exploring the utility of bedside ultrasound in confirming IO line placement is limited by small sample sizes of skeletally immature subjects or geriatric cadaveric models. The objective of this study was to investigate the potential value of ultrasound confirming IO needle placement in a live tissue model with bone densities approximated to the young adult medical or trauma patient.

Materials and Methods
In this randomized, blinded prospective study, IO devices were placed into the bilateral humeri of 36 sedated adult swine (N = 72) with bone densities approximating that of a 20-39-year-old adult. Of the 72 lines, 53 were randomized to the IO space (“correct”) and 19 into the subcutaneous tissue (“incorrect”). Four emergency physicians with variable ultrasound experience and blinded to needle location independently assessed correct or incorrect needle placements based on the presence of an intramedullary “flare” on color power Doppler (CPD) during a saline flush. Participants adjusted the ultrasound beam trajectory and recorded assessments up to three times, totaling 204 separate observations.

Results
Overall, sensitivity for placement confirmation was 72% (95% CI: 64%-79%). Specificity was 79% (95% CI: 66%-89%). First assessment and final assessment results were similar. More experienced sonographers demonstrated greater success in identifying inaccurate placements with a specificity of 86% (95% CI: 63%-96%).

Conclusion
Within the context of this study, point-of-care ultrasound with CPD did not reliably confirm IO line placement. However, more accurate assessments of functional and malpositioned catheters were noted in sonographers with greater than 4 years of experience. Future study into experienced sonographers’ use of CPD to confirm IO catheter placement is needed.
Joining the Navy to Become a Physician: The Typical Experience
Authors: Goodrich Eric 
Published: April 2022

ABSTRACT

Introduction
The decision to enter the Navy as a physician is a major career choice. However, there are no published studies that address the typical Navy physician’s experience in the Health Professions Scholarship Program (HPSP) and Uniformed Services University of the Health Sciences (USUHS) programs. The purpose of this qualitative study is to describe the typical Navy physician’s experience in the HPSP and USUHS programs.

Materials and Methods
An anonymous online survey containing 47 questions was distributed to 63 Navy HPSP and USUHS physicians who started internships from 2008 to 2015. Participants were chosen by using purposeful, criterion, and snowball sampling methods with whom the author had a professional relationship during his military experience. The survey data were plotted in Excel spreadsheets and graphs according to six sub-research questions. Mean, SD, Likert scale 1-5, and grouping of free text responses were recorded.

Results
A total of 54 out of 63 Navy physicians (85.7%) responded to the survey. Navy physicians got their first-choice residency selection of 67.3% of the time, 34.6% went straight through residency without interruptions, 44.2% answered definitely or probably that military match changed their residency selection compared to them applying for civilian residency, and 46.2% answered definitely or probably that it was more difficult to get into military versus civilian residency. Participants answered definitely or probably that military experience puts them ahead of civilians in terms of leadership (82.7%), prior medical experience (46.2%), and applying for civilian residency (76.2%). Common positive themes of free-text answers included having financial stability, unique life experiences, and serving their country. Common negative themes included lack of career control, lack of knowledge regarding HPSP/USUHS programs, and delay in residency and career.

Conclusions
The principal findings in this study are that most Navy physicians favored paid medical school/financial support, working overseas and in unique operational climates, having unique life experiences, leadership skills, and prior military experience put them ahead of their civilian colleagues, thought the Navy experience was worth it, and would join again if given the opportunity. However, most Navy physicians had a lack of career control due to needs of the Navy, lack of knowledge regarding residency selection, operational billets, and active duty service obligation, had more difficulty getting into a military residency of their choice versus civilians, and had interrupted residency training/training delays. The Navy would possibly benefit from a nationwide HPSP/USUHS physician mentorship program and an educational seminar to increase medical student applicant knowledge, which may improve recruiting and retention.
forge: the f(R)-gravity cosmic emulator project – I. Introduction and matter power spectrum emulator
Authors: Arnold Christian , Li Baojiu , Giblin Benjamin , Harnois-Déraps Joachim , Cai Yan-Chuan 
Published: April 2022

ABSTRACT
We present a large suite of cosmological simulations, the forge (F-of-R Gravity Emulator) simulation suite, which is designed to build accurate emulators for cosmological observables in galaxy clustering, weak gravitational lensing, and galaxy clusters for the f(R)-gravity model. A total of 200 simulations explore the cosmological parameter space around a standard Planck cosmology with a Latin hypercube, for 50 combinations of $\bar{f}_{R0}$, Ωm, σ8, and h with all other parameters fixed. For each parameter combination, or node, we ran four independent simulations, one pair using 10243 particles in $500\, h^{-1}\, \mathrm{Mpc}$ simulation boxes to cover small scales, and another pair using 5123 simulation particles in $1.5\, h^{-1}\, \mathrm{Gpc}$ boxes for larger scales. Each pair of initial conditions is selected such that sample variance on large scales is minimized on average. In this work we present an accurate emulator for the matter power spectrum in f(R) gravity trained on forge. We have verified, using the cross-validation technique, that the emulator accuracy is better than $2.5{{\, \rm per\, cent}}$ for the majority of nodes, particularly around the centre of the explored parameter space, up to scales of $k = 10\, h \, \mathrm{Mpc}^{-1}$. We have also checked the power spectrum emulator against simulations that are not part of our training set and found excellent agreement. Due to its high accuracy on small scales, the forge matter power spectrum emulator is well suited for weak-lensing analysis and can play a key tool in constraining f(R) gravity using current and future observational data.
Constraints on the origins of hypervelocity stars: velocity distribution, mergers, and star formation history
Authors: Generozov Aleksey , Perets Hagai B 
Published: April 2022

ABSTRACT
In recent years surveys have identified several dozen B stars in the Milky Way halo moving faster than the local escape speed. The origin of most of these hypervelocity stars (HVSs) is still poorly constrained. Here we show that the velocity distribution, and in particular the deficiency in &gt;700 km s−1 HVSs is inconsistent with binary disruptions by the massive black hole (MBH) in the Galactic Centre. This conclusion holds in the full and empty loss-cone regime, and for secular instabilities in eccentric discs. Accounting for multiple close encounters between binaries and the MBH does not qualitatively change the results. Moreover, there is no observed counterpart population in the Galactic Centre that is consistent with the HVSs. The star formation history could be tuned explain the HVS velocity distribution, but this tuning would produce a mismatch with the observed HVS flight times. Frequent stellar collisions of the binary components due to interactions with the MBH do not significantly impact the velocity distribution in the Galactic halo. Such collisions, however, can leave observable remnants in the Galactic Centre, and potentially explain the origins of G2-like dust clouds.
Newcomers and suburbanites can drive the evolution of the size–stellar mass relation of early-type galaxies in galaxy clusters
Authors: Matteuzzi Massimiliano , Marinacci Federico , Nipoti Carlo , Andreon Stefano 
Published: April 2022

ABSTRACTAt fixed stellar mass M*, the effective radius Re of massive satellite early-type galaxies (ETGs) in galaxy clusters is, on average, larger at lower redshift. We study theoretically this size evolution using the state-of-the-art cosmological simulation IllustrisTNG100: we sampled 75 simulated satellite ETGs at redshift z = 0 with M* ≥ 1010.4M⊙ belonging to the two most massive (≈1014.6M⊙) haloes of the simulation. We traced back in time the two clusters’ main progenitors and we selected their satellite ETGs at z &gt; 0 with the same criterion adopted at z = 0. The Re–M* relation of the simulated cluster satellite ETGs, which is robustly measured out to z = 0.85, evolves similarly to the observed relation over the redshift range 0 ≲ z ≲ 0.85. In the simulation the main drivers of this evolution are the acquisition of new galaxies (‘newcomers') by the clusters and the transformation of member galaxies located at large cluster-centric distance (‘suburbanites’) at z = 0.85, which end up being massive satellite ETGs at z = 0. Though several physical processes contribute to change the population of satellite ETGs in the considered redshift interval, the shape of the stellar mass function of the simulated cluster ETGs is not significantly different at z = 0.85 and at z = 0, consistent with observations.
The Fundamental Planes of black hole activity for radio-loud and radio-quiet quasars
Authors: Bariuan Luis Gabriel C , Snios Bradford , Sobolewska Małgosia , Siemiginowska Aneta , Schwartz Daniel A 
Published: April 2022

ABSTRACT
We examine the Fundamental Plane of black hole activity for correlations with redshift and radio loudness in both radio-loud and radio-quiet quasar populations. Sources are compiled from archival data of both radio-loud and radio-quiet quasars over redshifts 0.1 &lt; z &lt; 5.0 to produce a sample of 353 sources with known X-ray, radio, and black hole mass measurements. A Fundamental Plane of accretion activity is fit to a sample of radio-loud and radio-quiet quasars, and we find a dichotomy between radio-loud and radio-quiet sources. The set of best-fitting equations that best describe the two samples are log LR = (1.12 ± 0.06)log LX − (0.20 ± 0.07)log M − (5.64 ± 2.99) for our radio-loud sample and log LR = (0.48 ± 0.06)log LX + (0.50 ± 0.08)log M + (15.26 ± 2.66) for our radio-quiet sample. Our results suggest that the average radio-quiet quasar emission is consistent with advection-dominated accretion, while a combination of jet and disc emission dominates in radio-loud quasars. We additionally examine redshift trends amongst the radio-loud and radio-quiet samples, and we observe a redshift dependence for the Fundamental Plane of radio-loud quasars. Lastly, we utilize the Fundamental Plane as a black hole mass estimation method and determine it useful in studying systems where standard spectral modelling techniques are not viable.
An implementation of viscous pressure-force (‘soft-sphere’) model in REBOUND for local ring simulations
Authors: Mondino-Llermanos A E , Salo H 
Published: April 2022

ABSTRACT
Numerical simulations are an essential tool for studying dynamics of dense, self-gravitating planetary rings. Here, we present a new implementation of a soft-sphere collision model into the parallel gravitational N-body code REBOUND. Specifically, our module is designed for simulations done in the local shearing sheet approximation, and includes a simple viscoelastic model for the contact forces between colliding particles. The soft-sphere treatment is particularly important in regimes where collisions cannot be treated as independent binary impacts, as is done in the hard-sphere method already implemented in the code. The new module is fully parallelized with MPI and it can be used in conjunction with the available gravity octree method, also fully parallelized, to perform self-gravitating simulations. We check the validity of our soft-sphere model by successfully reproducing the main steady-state properties of non-gravitating and self-gravitating systems reported in earlier literature. Moreover, we show that it gives realistic results also in the high optical depth and strong self-gravity regimes, where the hard-sphere method fails due to particle overlaps. In addition, we test the CPU-scaling and efficiency of the MPI-parallelization. The algorithm proves to retain much of the original REBOUND speed without sacrificing the accuracy of the results. Our new tool can thus be applied with confidence to planetary ring studies, such as those aimed at understanding the onset and evolution of viscous overstability in dense self-gravitating rings.