bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards a mechanistic understanding of microalgae–bacteria interactions: integration of metabolomic analysis and computational models
Authors: Daly Giulia , Ghini Veronica , Adessi Alessandra , Fondi Marco , Buchan Alison , Viti Carlo 
Published: May 2022

Abstract
Interactions amongst marine microalgae and heterotrophic bacteria drive processes underlying major biogeochemical cycles and are important for many artificial systems. These dynamic and complex interactions span the range from cooperative to competitive, and it is the diverse and intricate networks of metabolites and chemical mediators that are predicted to principally dictate the nature of the relationship at any point in time. Recent advances in technologies to identify, analyze, and quantify metabolites have allowed for a comprehensive view of the molecules available for exchange and/or reflective of organismal interactions, setting the stage for development of mechanistic understanding of these systems. Here, we (i) review the current knowledge landscape of microalgal–bacterial interactions by focusing on metabolomic studies of selected, simplified model systems; (ii) describe the state of the field of metabolomics, with specific focus on techniques and approaches developed for microalga–bacterial interaction studies; and (iii) outline the main approaches for development of mathematical models of these interacting systems, which collectively have the power to enhance interpretation of experimental data and generate novel testable hypotheses. We share the viewpoint that a comprehensive and integrated series of -omics approaches that include theoretical formulations are necessary to develop predictive and mechanistic understanding of these biological entities.
Associations Between Use of Paid Help and Care Experiences Among Medicare–Medicaid Enrolled Older Adults With and Without Dementia
Authors: Fabius Chanee D , Okoye Safiyyah M , Mulcahy John , Burgdorf Julia G , Wolff Jennifer L 
Published: May 2022

Abstract

Objectives
Community-living older Medicare and Medicaid enrollees (“dual-enrollees”) have high care needs and commonly receive paid and unpaid long-term services and supports (LTSS) to help with routine activities. Little is known about whether receiving paid help or individuals’ state and neighborhood environmental context (“LTSS environment”) relates to dual-enrollees’ care experiences.

Methods
We examine a sample of n = 979 community-dwelling dual-enrollees with disabilities from 2011 to 2015 National Health and Aging Trends Study, linked to measures of neighborhood disadvantage and state Medicaid home and community-based services (HCBS) generosity. Logistic regression models stratified by dementia status assess associations between paid help and: (a) adverse consequences due to unmet care needs, and (b) participation restrictions in valued activities, among dual-enrollees with and without dementia, adjusting for individual and LTSS environmental characteristics.

Results
Use of paid help was greater for those with (versus without) dementia (46.9% vs. 37.8%). Neighborhood disadvantage was associated with greater use of paid help among dual-enrollees living with dementia. High state Medicaid HCBS generosity was associated with the use of paid help, regardless of dementia status. Dual-enrollees with dementia receiving paid help had higher odds of experiencing adverse consequences due to unmet need (adjusted odds ratio = 2.05; 95% confidence interval 1.16–3.61; p = .02)―no significant associations were observed for participation restrictions. Use of paid help and LTSS environment were not significantly associated with care experiences for dual-enrollees without dementia.

Discussion
Findings highlight the complexities of caring for dual-enrollees, particularly those with dementia, and emphasize the need to strengthen the delivery of paid care with considerations for the LTSS environment.
Multimethod palaeointensity results from a rapidly emitted upper Miocene lava flow sequence in São Vicente (Cape Verde): new data for the African record
Authors: Calvo Rathert M , Carrancho Á , Morales J , Pérez-Rodríguez N , Lebedev V A , Caccavari A , Vegas N , Goguitchaichvili A 
Published: May 2022

SUMMARY
We present new radiometric ages and full-vector palaeomagnetic data from São Vicente Island, Cape Verde. Samples were obtained from a sequence of 11 flows. A K-Ar age determination was performed on the lowermost flow of the sequence, yielding an upper Miocene age of 6.07 ± 0.16 (2σ) Ma. Considering the normal polarity observed in all flows, the age of the sequence could be narrowed down to an interval between 6.03 and 6.23 Ma.
The mean palaeomagnetic direction of the studied sequence was compared with the expected direction, calculated from the African Apparent Polar Wander Path (5 Ma). While inclinations approximately agree, the palaeodeclination appears westwardly deviated by 26.5° ± 2.9°. Moreover, nearly no scatter of virtual geomagnetic poles around their mean value is observed and its comparison with the scatter observed in palaeomagnetic directions obtained from geomagnetic field model SHA.DIF.14k suggests that the sequence was very rapidly emplaced in only a few centuries. Thus, the obtained anomalous palaeomagnetic direction seems to reflect the effect of non-averaged secular variation, although a local vertical-axis counter-clockwise rotation of the sequence, cannot be entirely ruled out.
Thellier–Coe palaeointensity experiments on 66 specimens yielded 22 successful determinations and multispecimen (MS) palaeointensity experiments on 11 samples yielded 8 successful determinations. In the upper part of the sequence, Thellier–Coe determinations fail due to the presence of multidomain (MD) grains, but the MS method yields successful results in several of these flows, demonstrating that this method can provide reliable palaeointensity determinations on samples with a higher MD grain fraction. A mean palaeointensity BSV = (18.5 ± 1.9) µT is obtained from the joint analysis of the results from both methods. This value lies clearly below the present-day value BP = 33.1 μT. The virtual axial dipole moment (VADM = 4.3 × 1022 Am2), however, cannot be considered anomalous if compared to available upper Miocene–Pliocene data and represents a new high-reliability contribution to the very limited African palaeointensity database.
Calibration of the near-surface seismic structure in the SCEC community velocity model version 4
Authors: Hu Zhifeng , Olsen Kim B , Day Steven M 
Published: May 2022

SUMMARYThe near-surface seismic structure (to a depth of about 1000 m), particularly the shear wave velocity (VS), can strongly affect the propagation of seismic waves and, therefore, must be accurately calibrated for ground motion simulations and seismic hazard assessment. The VS of the top (&lt;300 m) crust is often well characterized from borehole studies, geotechnical measurements, and water and oil wells, while the velocities of the material deeper than about 1000 m are typically determined by tomography studies. However, in depth ranges lacking information on shallow lithological stratification, typically rock sites outside the sedimentary basins, the material parameters between these two regions are typically poorly characterized due to resolution limits of seismic tomography. When the alluded geological constraints are not available, models, such as the Southern California Earthquake Center (SCEC) Community Velocity Models (CVMs), default to regional tomographic estimates that do not resolve the uppermost VS values, and therefore deliver unrealistically high shallow VS estimates. The SCEC Unified Community Velocity Model (UCVM) software includes a method to incorporate the near-surface earth structure by applying a generic overlay based on measurements of time-averaged VS in top 30 m (VS30) to taper the upper part of the model to merge with tomography at a depth of 350 m, which can be applied to any of the velocity models accessible through UCVM. However, our 3-D simulations of the 2014 Mw 5.1 La Habra earthquake in the Los Angeles area using the CVM-S4.26.M01 model significantly underpredict low-frequency (&lt;1 Hz) ground motions at sites where the material properties in the top 350 m are significantly modified by the generic overlay (‘taper’). On the other hand, extending the VS30-based taper of the shallow velocities down to a depth of about 1000 m improves the fit between our synthetics and seismic data at those sites, without compromising the fit at well-constrained sites. We explore various tapering depths, demonstrating increasing amplification as the tapering depth increases, and the model with 1000 m tapering depth yields overall favourable results. Effects of varying anelastic attenuation are small compared to effects of velocity tapering and do not significantly bias the estimated tapering depth. Although a uniform tapering depth is adopted in the models, we observe some spatial variabilities that may further improve our method.
Using convolutional neural networks to develop starting models for near-surface 2-D full waveform inversion
Authors: Vantassel Joseph P , Kumar Krishna , Cox Brady R 
Published: May 2022

SUMMARY
Non-invasive subsurface imaging using full waveform inversion (FWI) has the potential to fundamentally change near-surface (&lt;30 m) site characterization by enabling the recovery of high-resolution (metre-scale) 2-D/3-D maps of subsurface elastic material properties. Yet, FWI results are quite sensitive to their starting model due to their dependence on local-search optimization techniques and inversion non-uniqueness. Starting model dependence is particularly problematic for near-surface FWI due to the complexity of the recorded seismic wavefield (e.g. dominant surface waves intermixed with body waves) and the potential for significant spatial variability over short distances. In response, convolutional neural networks (CNNs) are investigated as a potential tool for developing starting models for near-surface 2-D elastic FWI. Specifically, 100 000 subsurface models were generated to be representative of a classic near-surface geophysics problem; namely, imaging a two-layer, undulating, soil-over-bedrock interface. A CNN has been developed from these synthetic models that is capable of transforming an experimental wavefield acquired using a seismic source located at the centre of a linear array of 24 closely spaced surface sensors directly into a robust starting model for FWI. The CNN approach was able to produce 2-D starting models with seismic image misfits that were significantly less than the misfits from other common starting model approaches, and in many cases even less than the misfits obtained by FWI with inferior starting models. The ability of the CNN to generalize outside its two-layered training set was assessed using a more complex, three-layered, soil-over-bedrock formation. While the predictive ability of the CNN was slightly reduced for this more complex case, it was still able to achieve seismic image and waveform misfits that were comparable to other commonly used starting models, despite not being trained on any three-layered models. As such, CNNs show great potential as tools for rapidly developing robust, site-specific starting models for near-surface elastic FWI.
An anisotropic equation of state for high-pressure, high-temperature applications
Authors: Myhill R 
Published: May 2022

SUMMARY
This paper presents a strategy for extending scalar (P–V–T) equations of state to self-consistently model anisotropic materials over a wide range of pressures and temperatures under nearly hydrostatic conditions. The method involves defining a conventional scalar equation of state (V(P, T) or P(V, T)) and a fourth-rank tensor state variable $\boldsymbol {\Psi }(V,T)$ whose derivatives can be used to determine the anisotropic properties of materials of arbitrary symmetry. This paper proposes two functional forms for $\boldsymbol {\Psi }(V,T)$ and provides expressions describing the relationship between $\boldsymbol {\Psi }$ and physical properties including the deformation gradient tensor, the lattice parameters, the isothermal elastic compliance tensor and thermal expansivity tensor. The isothermal and isentropic stiffness tensors, the Grüneisen tensor and anisotropic seismic velocities can be derived from these properties. To illustrate the use of the formulations, anisotropic models are parametrized using numerical simulations of cubic periclase and experimental data on orthorhombic San Carlos olivine.
Green’s Function of a Subgraph of a Complete Graph
Authors: Lin Yong , Ngai Sze-Man , Yau Shing-Tung 
Published: May 2022

Abstract
By using heat kernel expansions for the Laplacian on a subgraph of a complete graph, we obtain formal expansions for the Green function of the Laplacian on a subgraph of a complete graph. We study this formal series for both the cases that the subgraph is complete and not complete, and in both cases, we obtain precise information about the convergence of the series.
On the Numerical Dimension of Calabi–Yau 3-Folds of Picard Number 2
Authors: Hoff Michael , Stenger Isabel 
Published: May 2022

Abstract
We show that for any smooth Calabi–Yau threefold $X$ of Picard number $2$ with infinite birational automorphism group, the numerical dimension $\kappa _\sigma $ of the extremal rays of the movable cone of $X$ is $\frac {3}{2}$. Furthermore, we provide new examples of Calabi–Yau threefolds of Picard number $2$ with infinite birational automorphism group.
PrankWeb 3: accelerated ligand-binding site predictions for experimental and modelled protein structures
Authors: Jakubec David , Skoda Petr , Krivak Radoslav , Novotny Marian , Hoksza David 
Published: May 2022

Abstract
Knowledge of protein–ligand binding sites (LBSs) enables research ranging from protein function annotation to structure-based drug design. To this end, we have previously developed a stand-alone tool, P2Rank, and the web server PrankWeb (https://prankweb.cz/) for fast and accurate LBS prediction. Here, we present significant enhancements to PrankWeb. First, a new, more accurate evolutionary conservation estimation pipeline based on the UniRef50 sequence database and the HMMER3 package is introduced. Second, PrankWeb now allows users to enter UniProt ID to carry out LBS predictions in situations where no experimental structure is available by utilizing the AlphaFold model database. Additionally, a range of minor improvements has been implemented. These include the ability to deploy PrankWeb and P2Rank as Docker containers, support for the mmCIF file format, improved public REST API access, or the ability to batch download the LBS predictions for the whole PDB archive and parts of the AlphaFold database.
United States: highlights of legal and tax differences of statutory foundations and private foundations
Authors: Georgiev Lyubomir , Walsh Gregory , Hunter Chelsea , Lasky Rebecca , Sanders Olga 
Published: May 2022

Abstract
The article approaches the analysis of foundations primarily from an entity classification and tax point of view. First, the authors address the various options how a foreign foundation can be classified under U.S. tax law. Subsequently, the authors take a closer look at U.S. statutory foundations, which now exist under the laws of New Hampshire and Wyoming. In a third section, they explain the concept of a private foundation, which under U.S. federal tax law refers to a tax-exempt charitable organization. These private foundations are compared with statutory foundations with regard to their legal and tax law differences. The authors come to the conclusion that the ability to tailor a statutory foundation to meet specific needs using an entity with legal personality is very likely its greatest attribute that founders find attractive.
Comparing the Liver Safety Profiles of 4 Next-Generation CGRP Receptor Antagonists to the Hepatotoxic CGRP Inhibitor Telcagepant Using Quantitative Systems Toxicology Modeling
Authors: Woodhead Jeffrey L , Siler Scott Q , Howell Brett A , Watkins Paul B , Conway Charles 
Published: May 2022

Abstract
Calcitonin gene-related peptide (CGRP) signaling inhibitors have shown efficacy in both the acute and preventive treatment of migraine. Telcagepant, a first-generation CGRP receptor antagonist, was effective but failed in clinical trials due to hepatotoxicity. Subsequently, although 4 next-generation CGRP receptor antagonists (rimegepant, zavegepant, atogepant, and ubrogepant) were being advanced into late-stage clinical trials, due to telcagepant’s failure, more confidence in the liver safety of these compounds was needed. DILIsym v6A, a quantitative systems toxicology (QST) model of drug-induced liver injury (DILI), was used to model all 5 compounds and thus to compare the 4 next-generation CGRP receptor antagonists to telcagepant. In vitro experiments were performed to measure the potential for each compound to inhibit bile acid transporters, produce oxidative stress, and cause mitochondrial dysfunction. Physiologically based pharmacokinetic models were produced for each compound in order to appropriately estimate liver exposure. DILIsym predicted clinical elevations of liver enzymes and bilirubin for telcagepant, correctly predicting the observed DILI liability of the first-generation compound. By contrast, DILIsym predicted that each of the 4 next-generation compounds would be significantly less likely to cause DILI than telcagepant. Subsequent clinical trials have validated these predictions for each of the 4 compounds, and all 3 of the compounds submitted to FDA to date (rimegepant, ubrogepant, and atogepant) have since been approved by the FDA with no warning for hepatotoxicity. This work demonstrates the potential for QST modeling to prospectively differentiate between hepatotoxic and nonhepatotoxic molecules within the same class.
Identifying US Plastic Surgery Training Programs that Effectively Establish Gender and Ethnically Diverse Faculty
Authors: Onyekaba Ginikanwa , Mauch Jaclyn T. , McAuliffe Phoebe B. , Diatta Fortunay , Mellia Joseph A. , Morris Martin P. , Murphy Alexander I. , Broach Robyn B. , Fischer John P. , Butler Paris D. 
Published: May 2022

Background:
Successful strategies to improve the representation of female and ethnically underrepresented in medicine (UIM) physicians among US plastic and reconstructive surgery (PRS) faculty have not been adequately explored. Accordingly, we aimed to identify programs that have had success, and in parallel gather PRS program directors’ and chiefs/chairs’ perspectives on diversity recruitment intentionality and strategies.

Methods:
We conducted a cross-sectional analysis of the demographic composition of female and UIM faculty of PRS residency training programs. Separate lists of programs in the top quartile for female and UIM faculty representation were collated. Additionally, a 14-question survey was administered to program directors and chiefs/chairs of all 99 Accreditation Council for Graduate Medical Education-accredited PRS residency programs. The questions comprised three domains: (1) demographic information; (2) perceptions about diversity; and (3) recruitment strategies utilized to diversify faculty.

Results:
Female and UIM faculty representation ranged from 0% to 63% and 0% to 50%, respectively. Survey responses were received from program directors and chiefs/chairs of 55 institutions (55% response rate). Twenty-five (43%) respondents felt their program was diverse. Fifty-one (80%) respondents felt diversity was important to the composition of PRS faculty. Active recruitment of diverse faculty and the implementation of a diversity, equity, and inclusion committee were among the most frequently cited strategies to establish a culturally sensitive and inclusive environment.

Conclusions:
These findings reveal that female and UIM representation among US PRS faculty remains insufficient; however, some programs have had success through deliberate and intentional implementation of diversity, equity, and inclusion strategies.
Healthcare Professionals' Electroencephalography Competency: A Disconnect Between Self-Assessment and Objective Testing
Authors: Linnavuori Elina , Leino-Kilpi Helena , Stolt Minna 
Published: May 2022

ABSTRACT

BACKGROUND: The role of the healthcare professional (HCP) in performing high-quality electroencephalography (EEG) is critical to ensuring accurate results. This study analyzes HCPs' subjectively and objectively assessed EEG competence to provide information on their EEG competence and competence needs for the development of their education and training. METHODS: The study was a descriptive cross-sectional study. The target group of the study was HCPs working in the clinical neurophysiology departments of university hospitals in Finland. The research data were collected using the EEG Competence instrument created for this research. The instrument consisted of a self-assessment section and a knowledge test component. RESULTS: The participants (N = 65; response rate, 81%) consisted of 34 registered nurses and 31 laboratory technologists. In the self-assessment section, the highest mean score was in patient observation (mean, 4.6) and the lowest was in EEG theoretical knowledge (mean, 3.9). In the test section, most of the respondents (73.8%) answered all questions correctly (maximum, 6 points). There was a positive correlation between age, work experience, own satisfaction with EEG competence, and subjective self-assessment. Those familiar with EEG guidelines and who participated in training days assessed their competence as significantly better (P < .05). Respondents who read EEG-related literature on their own identified artifacts better (P = .005). CONCLUSIONS: Laboratory technologists' and registered nurses' subjectively and objectively assessed EEG competence was high. In the future, the EEG competence instrument should be developed further, and more research is needed to assess its psychometric properties to provide more information on HCPs' competence in the diagnostic process.
Transgender Mastectomy
Authors: Bruce Madeleine K. , Joseph Walter J. , Grunwaldt Lorelei , Nguyen Vu T. , De La Cruz Carolyn 
Published: May 2022

Background
Chest masculinization surgeries are one of the most common gender-affirming procedures performed. There is a need for better understanding of the risk of breast cancer and postsurgical screening in female to male (FtM) individuals. This study aimed to evaluate the incidence of high-risk pathologic findings in FtM transgender patients undergoing gender-affirming chest reconstructive surgery.

Methods
Medical records were reviewed from all FtM patients undergoing gender-affirming chest reconstructive surgery from January 2010 to February 2021 by 3 plastic surgeons at the University of Pittsburgh Medical Center. Relative risk of malignant progression was used to stratify pathologic data. Subsequent management of atypical, in situ, and invasive pathology were recorded.

Results
A total of 318 patients were included in this study; the average age at surgery was 24.6 ± 8.1 years. Eighty-six patients (27%) had a family history of breast and/or ovarian cancer. Overall, 21 patients (6.6%) had some increased risk of breast cancer: 17 (5.3%) had proliferative lesions, mean age 38.2 ± 12.4 years; 2 had atypical ductal hyperplasia, ages 33.4 and 38.3 years; and 2 had invasive ductal carcinoma, ages 35.4 and 40.6 years.

Conclusions
In this study, we found that 6.6% of FtM transgender patients undergoing top surgery had an elevated risk of breast cancer, with 1.2% of patients having a greater than 2 times risk of breast cancer. These results highlight the importance of appropriate preoperative screening as well as pathological analysis of surgical specimens to help guide clinical care. The authors advocate for a thorough breast cancer risk assessment before surgery for all patients, as well as using pathologic findings to guide postoperative cancer screening and follow-up.