bluuebunny/crossref_metadata_2025_split huggingface dataset:
NOAA/NCEI and University of Colorado candidate models for IGRF-13
Authors: Alken P. , Chulliat A. , Nair M. 
Published: February 2021

AbstractThe International Geomagnetic Reference Field (IGRF) is a set of parameters representing the large-scale internal part of Earth’s magnetic field. The 13th generation IGRF requested candidate models for a definitive main field for 2015.0, a provisional main field for 2020.0, and a predictive secular variation covering the period 2020.0–2025.0. The University of Colorado (CU) and the National Centers for Environmental Information (NCEI), part of the National Oceanic and Atmospheric Administration (NOAA), have produced these three candidate models for consideration in IGRF-13. In this paper, we present the methodology used to derive our candidate models. Our candidates were built primarily from Swarm satellite data, and also relied on geomagnetic indices derived from the ground observatory network. The ground observatories played a crucial role as independent data in validating our candidates. This paper also provides a retrospective assessment of the CU/NCEI candidate model to the previous IGRF (IGRF-12) and discusses the impact of differences between candidate and final IGRF models on global model errors.
Geomagnetic secular variation forecast using the NASA GEMS ensemble Kalman filter: A candidate SV model for IGRF-13
Authors: Tangborn Andrew , Kuang Weijia , Sabaka Terence J. , Yi Ce 
Published: February 2021

Abstract
We have produced a 5-year mean secular variation (SV) of the geomagnetic field for the period 2020–2025. We use the NASA Geomagnetic Ensemble Modeling System (GEMS), which consists of the NASA Goddard geodynamo model and ensemble Kalman filter (EnKF) with 400 ensemble members. Geomagnetic field models are used as observations for the assimilation, including gufm1 (1590–1960), CM4 (1961–2000) and CM6 (2001–2019). The forecast involves a bias correction scheme that assumes that the model bias changes on timescales much longer than the forecast period, so that they can be removed by successive forecast series. The algorithm was validated on the time period 2010-2015 by comparing with CM6 before being applied to the 2020–2025 time period. This forecast has been submitted as a candidate predictive model of IGRF-13 for the period 2020–2025.

Graphical abstract
Innovative seismic imaging of volcanogenic massive sulfide deposits, Neves-Corvo, Portugal — Part 2: Surface array
Authors: Donoso George A. , Malehmir Alireza , Brodic Bojan , Pacheco Nelson , Carvalho João , Araujo Vitor 
Published: February 2021

Seismic methods are an affordable and effective way of studying the subsurface for mineral exploration. With the goal of testing new technologies for mineral exploration in highly challenging mining areas, in early 2019, an innovative seismic survey was conducted at the Neves-Corvo mine, south Portugal. We have focused on the data and results from the surface array data, whereas other work deals with the underground seismic data. The surface seismic survey consisted of two perpendicular 2D profiles positioned above the known world-class tier-1 Lombador deposit. Simultaneously, a survey inside the active underground mine took place, being unique because it included the testing of a prototype system that enabled accurate GPS-time (microsecond accuracy) synchronization inside the mine tunnels, approximately 650 m below the surface profiles. Due to the active mining operations, the surface data are noisy. To handle this, a carefully tailored processing algorithm was developed and applied to enhance reflections in the data, interpreted to originate from lithologic contacts and the Lombador deposit. The results and interpretations from 2D processing were validated taking advantage of the known deposit geometry using 3D exploding reflector modeling and pseudo-3D cross-dip analysis. These analyses suggest that there is an out-of-plane signature of the Lombador deposit on the surface data. Additionally, source points activated in the exploration tunnels and simultaneously recorded on the surface profiles allowed for the creation of a 2D velocity model that was used for migration and time-to-depth conversion, providing a reliable 2D seismic section of the subsurface under the surface profiles. We determine that limited surface coverage 2D surveys and a velocity model derived from the tunnel-to-surface seismic recordings allow for imaging of key subsurface geologic structures and delineating mineral deposits of economic interest.
Identification of regulatory elements required for Stra8 expression in fetal ovarian germ cells of the mouse
Authors: Feng Chun-Wei , Burnet Guillaume , Spiller Cassy M. , Cheung Fiona Ka Man , Chawengsaksophak Kallayanee , Koopman Peter , Bowles Josephine 
Published: February 2021

ABSTRACT
In mice, the entry of germ cells into meiosis crucially depends on the expression of stimulated by retinoic acid gene 8 (Stra8). Stra8 is expressed specifically in pre-meiotic germ cells of females and males, at fetal and postnatal stages, respectively, but the mechanistic details of its spatiotemporal regulation are yet to be defined. In particular, there has been considerable debate regarding whether retinoic acid is required, in vivo, to initiate Stra8 expression in the mouse fetal ovary. We show that the distinctive anterior-to-posterior pattern of Stra8 initiation, characteristic of germ cells in the fetal ovary, is faithfully recapitulated when 2.9 kb of the Stra8 promoter is used to drive eGFP expression. Using in vitro transfection assays of cutdown and mutant constructs, we identified two functional retinoic acid responsive elements (RAREs) within this 2.9 kb regulatory element. We also show that the transcription factor DMRT1 enhances Stra8 expression, but only in the presence of RA and the most proximal RARE. Finally, we used CRISPR/Cas9-mediated targeted mutation studies to demonstrate that both RAREs are required for optimal Stra8 expression levels in vivo.
Long-term Outcomes After Surgical Resection of Pancreatic Metastases from Renal Clear-Cell Carcinoma
Authors: Malleo Giuseppe , Salvia Roberto , Maggino Laura , Marchegiani Giovanni , D’Angelica Michael , DeMatteo Ronald , Kingham Peter , Pulvirenti Alessandra , Sereni Elisabetta , Jarnagin William R. , Bassi Claudio , Allen Peter J. , Butturini Giovanni 
Published: February 2021

Abstract
Background
Pancreatic metastases (PM) from renal cell carcinoma (RCC) are uncommon. We herein describe the long-term outcomes associated with pancreatectomy at two academic institutions, with a specific focus on 10-year survival.

Methods
This investigation was limited to patients undergoing pancreatectomy for PM between 2000 and 2008 at the University of Verona and Memorial Sloan Kettering Cancer Center, allowing a potential for 10 years of surveillance. The probabilities of further RCC recurrence and RCC-related death were estimated using a competing risk analysis (method of Fine and Gray) to account for patients who died of other causes during follow-up.

Results
The study population consisted of 69 patients, mostly with isolated metachronous PM (77%). The median interval from nephrectomy to pancreatic metastasectomy was 109 months, whereas the median post-pancreatectomy follow-up was 141 months. The 10-year cumulative incidence of new RCC recurrence was 62.7%. In the adjusted analysis, the relative risk of repeated recurrence was significantly higher in PM synchronous to the primary RCC (sHR = 1.27) and in patients receiving extended pancreatectomy (sHR = 3.05). The 10-year cumulative incidence of disease-specific death was 25.5%. The only variable with an influence on disease-specific death was the recurrence-free interval following metastasectomy (sHR = 0.98). In patients with repeated recurrence, the 10-year cumulative incidence of RCC-related death was 35.4%.

Conclusion
In a selected group of patients followed for a median of 141 months and mostly with isolated metachronous PM, resection was associated with a high possibility of long-term disease control in surgically fit patients with metastases confined to the pancreas.
The clinical effectiveness of reconstructing 18F-sodium fluoride PET/CT bone using Bayesian penalized likelihood algorithm for evaluation of metastatic bone disease in obese patients
Authors: Usmani Sharjeel , Ahmed Najeeb , Gnanasegaran Gopinath , Rasheed Rashid , Marafi Fahad , Alnaaimi Mashari , Omar Mohammad , Musbah Ahmed , al Kandari Fareeda , De Schepper Stijn , Van den Wyngaert Tim 
Published: February 2021

Objective:
A new Bayesian penalized likelihood reconstruction algorithm for positron emission tomography (PET) (Q.Clear) is now in clinical use for fludeoxyglucose (FDG) PET/CT. However, experience with non-FDG tracers and in special patient populations is limited. This pilot study aims to compare Q.Clear to standard PET reconstructions for 18F sodium fluoride (18F-NaF) PET in obese patients.

Methods:
30 whole body 18F-NaF PET/CT scans (10 patients with BMI 30–40 Kg/m2 and 20 patients with BMI &gt;40 Kg/m2) and a NEMA image quality phantom scans were analyzed using ordered subset expectation maximization (OSEM) and Q.Clear reconstructions methods with B400, 600, 800 and 1000. The images were assessed for overall image quality (IQ), noise level, background soft tissue, and lesion detectability, contrast recovery (CR), background variability (BV) and contrast-to-noise ratio (CNR) for both algorithms.

Results:
CNR for clinical cases was higher for Q.Clear than OSEM (p &lt; 0.05). Mean CNR for OSEM was (21.62 ± 8.9), and for Q.Clear B400 (31.82 ± 14.6), B600 (35.54 ± 14.9), B800 (39.81 ± 16.1), and B1000 (40.9 ± 17.8). As the β value increased the CNR increased in all clinical cases. B600 was the preferred β value for reconstruction in obese patients. The phantom study showed Q.Clear reconstructions gave lower CR and lower BV than OSEM. The CNR for all spheres was significantly higher for Q.Clear (independent of β) than OSEM (p &lt; 0.05), suggesting superiority of Q.Clear.

Conclusion:
This pilot clinical study shows that Q.Clear reconstruction algorithm improves overall IQ of 18F-NaF PET in obese patients. Our clinical and phantom measurement results demonstrate improved CNR and reduced BV when using Q.Clear. A β value of 600 is preferred for reconstructing 18F-NaF PET/CT with Q.Clear in obese patients.

Advances in knowledge:
18F-NaF PET/CT is less susceptible to artifacts induced by body habitus. Bayesian penalized likelihood reconstruction with18F-NaF PET improves overall IQ in obese patients.
ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework
Authors: Mehta Subina , Crane Marie , Leith Emma , Batut Bérénice , Hiltemann Saskia , Arntzen Magnus Ø , Kunath Benoit J. , Delogu Francesco , Sajulga Ray , Kumar Praveen , Johnson James E. , Griffin Timothy J. , Jagtap Pratik D. 
Published: February 2021

The Human Microbiome Project (HMP) aided in understanding the role of microbial communities and the influence of collective genetic material (the ‘microbiome’) in human health and disease. With the evolution of new sequencing technologies, researchers can now investigate the microbiome and map its influence on human health. Advances in bioinformatics methods for next-generation sequencing (NGS) data analysis have helped researchers to gain an in-depth knowledge about the taxonomic and genetic composition of microbial communities. Metagenomic-based methods have been the most commonly used approaches for microbiome analysis; however, it primarily extracts information about taxonomic composition and genetic potential of the microbiome under study, lacking quantification of the gene products (RNA and proteins). Conversely, metatranscriptomics, the study of a microbial community’s RNA expression, can reveal the dynamic gene expression of individual microbial populations and the community as a whole, ultimately providing information about the active pathways in the microbiome. In order to address the analysis of NGS data, the ASaiM analysis framework was previously developed and made available via the Galaxy platform. Although developed for both metagenomics and metatranscriptomics, the original publication demonstrated the use of ASaiM only for metagenomics, while thorough testing for metatranscriptomics data was lacking. In the current study, we have focused on validating and optimizing the tools within ASaiM for metatranscriptomics data. As a result, we deliver a robust workflow that will enable researchers to understand dynamic functional response of the microbiome in a wide variety of metatranscriptomics studies. This improved and optimized ASaiM-metatranscriptomics (ASaiM-MT) workflow is publicly available via the ASaiM framework, documented and supported with training material so that users can interrogate and characterize metatranscriptomic data, as part of larger meta-omic studies of microbiomes.
Exact Facetial Odd-Cycle Separation for Maximum Cut and Binary Quadratic Optimization
Authors: Jünger Michael , Mallach Sven 
Published: February 2021

The exact solution of the NP-hard (nondeterministic polynomial-time hard) maximum cut problem is important in many applications across, for example, physics, chemistry, neuroscience, and circuit layout—which is also due to its equivalence to the unconstrained binary quadratic optimization problem. Leading solution methods are based on linear or semidefinite programming and require the separation of the so-called odd-cycle inequalities. In their groundbreaking research, F. Barahona and A. R. Mahjoub have given an informal description of a polynomial-time algorithm for this problem. As pointed out recently, however, additional effort is necessary to guarantee that the inequalities obtained correspond to facets of the cut polytope. In this paper, we shed more light on a so enhanced separation procedure and investigate experimentally how it performs in comparison with an ideal setting where one could even employ the sparsest, most violated, or geometrically most promising facet-defining odd-cycle inequalities. Summary of Contribution: This paper aims at a better capability to solve binary quadratic optimization or maximum cut problems and their various applications using integer programming techniques. To this end, the paper describes enhancements to a well-known algorithm for the central separation problem arising in this context; it is demonstrated experimentally that these enhancements are worthwhile from a computational point of view. The linear relaxations of the aforementioned problems are typically solved using fewer iterations and cutting planes than with a nonenhanced approach. It is also shown that the enhanced procedure is only slightly inferior to an ideal, enumerative, and, in practice, intractable global cutting-plane selection.
Diffraction-limited broadband optical meta-power-limiter
Authors: Hsu Liyi , Ndao Abdoulaye 
Published: February 2021

In recent years, the need for a high-power laser has been of great interest for different applications, including direct-laser processing, light detection, medicine, and lighting. However, high-power lasers with high intensities give rise to fundamental problems for optical detectors and imaging systems with low threshold damage, which still need reliable solutions. Here we report and numerically demonstrate a hybrid system that synergistically combines a broadband OPL with a transmittance difference between on-state (70°C) and off-state (25°C) about 62.5%, and a diffraction-limited broadband metalens from 1534 to 1664 nm. Such a metalens power limiter could be used in any system requiring an intermediate focal plane in the optical path to the detector from damage by exposure to high-intensity lasers.
Association between physicians’ and patients’ perspectives of shared decision making in primary care settings in Japan: The impact of environmental factors
Authors: Goto Yuko , Miura Hisayuki , Son Daisuke , Scholl Isabelle , Kriston Levente , Härter Martin , Sato Kotaro , Kusaba Tesshu , Arai Hidenori 
Published: February 2021

PurposeShared decision-making (SDM) has only lately begun attaining recognition from the Japanese medical community. The purpose of this study was to create a Japanese version of the SDM-Q-Doc, which is a scale that measures SDM from the perspective of physicians, and to clarify its psychometric characteristics and identify the issues and factors that affect SDM.MethodsThe participants were 23 physicians and 130 patients who visited primary care clinics in Japan for the first time. Immediately following physician–patient interviews, the Japanese version of SDM-Q-9 and SDM-Q-Doc were administered to patients and physicians, respectively. For convergent validity, physician confidence in the medical interview (PCMI) was used. After the determination of internal consistency and validity of the SDM-Q-Doc, the relations among each item of SDM-Q-Doc, SDM-Q-9, physicians’ sociodemographic attributes, and a presence or absence of nurse’s attendance during outpatient consultation were assessed by a multiple regression analysis and structural equation modeling (SEM).ResultsA factor analysis confirmed that the Japanese version of the SDM-Q-Doc displays a one-factor structure with a high internal consistency (Cronbach’s α = 0.87, ω = 0.88). The correlation between the PCMI and SDM-Q-Doc confirmed an appropriate convergent validity (r = 0.406; p < 0.001).Multiple regression analyses showed that the attendance of a nurse during consultation significantly affected one item of the SDM-Q-Doc, which in turn affected one item of the SDM-Q-9. SEM showed a good fit of model for these three items.ConclusionThe Japanese version of the SDM-Q-Doc’s internal consistency and validity in the outpatient medical consultations in Japan were confirmed. Further, this study suggests the role of a nurse’s attendance during a physician–patient consultation on facilitating the SDM. Further, using the Japanese version of the SDM-Q-Doc will promote communication skills training for medical professionals by checking the quality of SDM.
Usefulness of staging chest-CT in patients with operable breast cancer
Authors: Hong Jung Hee , Goo Jin Mo , Moon Hyeong-Gon , Chang Jung Min , Lee Jong Hyuk , Park Chang Min 
Published: February 2021

Objective
The aim of this study was to investigate the usefulness of staging chest-CT in terms of diagnostic yield and false-referral rate in patients with operable breast cancer.

Materials and methods
This study was approved by the institutional review border. In this retrospective study, we reviewed patients who underwent staging chest-CT between January 2014 and June 2016. Reference standard was defined as a combination of pathology and radiologic tumor changes in accordance with primary tumor or metastatic lesions and stability during the 12-month follow-up period. We calculated diagnostic yield and false-referral rates stratified by pathologic stage. The important ancillary findings of staging chest-CT were also recorded.

Results
A total of 1,342 patients were included in this study. Of these, four patients (0.3%; 4/1342) had true pulmonary metastasis. Diagnostic yields of stage I, II, III disease were 0.0% (0/521), 0.3% (2/693), and 1.6% (2/128), respectively. The overall false-referral rate was 4.6% (62/1342); false-referral rates of stage I, II, and III disease were 5.0% (26/521), 3.8% (26/693), and 7.8% (10/128), respectively. No occult thoracic metastasis occurred within 12 months of staging chest-CT. Nineteen patients showed significant ancillary findings besides lung metastasis, including primary lung cancer (n = 9). The overall diagnostic yield of ancillary findings was 1.7% (23 of 1342).

Conclusions
The incidence of pulmonary metastasis was near zero for pathologic stages I/II and slightly higher (although still low; 1.6%). for stage III. Considering its low diagnostic yield and substantial false-referral rates, staging chest-CT might not be useful in patients with operable breast cancer.
Multimorbidity and its associated factors among adults aged 50 and over: A cross-sectional study in 17 European countries
Authors: Bezerra de Souza Dyego Leandro , Oliveras-Fabregas Albert , Espelt Albert , Bosque-Prous Marina , de Camargo Cancela Marianna , Teixidó-Compañó Ester , Jerez-Roig Javier 
Published: February 2021

Aims
To estimate the prevalence of multimorbidity among European community-dwelling adults, as well as to analyse the association with gender, age, education, self-rated health, loneliness, quality of life, size of social network, Body Mass Index (BMI) and disability.

Methods
A cross-sectional study based on wave 6 (2015) of the Survey of Health, Ageing and Retirement in Europe (SHARE) was conducted, and community-dwelling participants aged 50+ (n = 63,844) from 17 European countries were selected. Multimorbidity was defined as presenting two or more health conditions. The independent variables were gender, age group, educational level, self-rated health, loneliness, size of network, quality of life, BMI and disability (1+ limitations of basic activities of daily living). Poisson regression models with robust variance were fit for bivariate and multivariate analysis.

Results
The prevalence of multimorbidity was 28.2% (confidence interval–CI 95%: 27.5.8–29.0) among men and 34.5% (CI95%: 34.1–35.4) among women. The most common health conditions were cardiometabolic and osteoarticular diseases in both genders, and emotional disorders in younger women. A large variability in the prevalence of multimorbidity in European countries was verified, even between countries of the same region.

Conclusions
Multimorbidity was associated with sociodemographic and physical characteristics, self-rated health, quality of life and loneliness.
Aflibercept for treatment-naïve diabetic macula oedema in a multi-ethnic population: Real-world outcomes from North West London
Authors: Dinah Christiana , Ghulakhszian Arevik , Sim Sing Yue , Minocha Amal , Nokhostin Soroush , Posner Esther , Cheong-Lee Richard , George Sheena 
Published: February 2021

Purpose
To evaluate the clinical outcomes of patients with treatment–naïve diabetic macula oedema (DMO) treated with Aflibercept in routine clinic settings in ethnically diverse North West London (NWL) and compare to outcomes reported in the VIVID and VISTA clinical trials

Methods
This was a retrospective multicentre interventional case series. Two hundred and seventy eyes of 221 treatment-naïve patients at three NWL hospitals initiated on Aflibercept and who had at least 12 months follow-up were included in the study. Visual acuity, central subfield thickness and macula volume were recorded at baseline, month 3, 6 and 12.

Results
There were significant differences between the NWL cohort and participants in the VIVID and VISTA trials at baseline including higher HbA1c and a higher proportion of eyes with proliferative diabetic retinopathy in the NWL cohort. The mean VA, mean CSFT and mean MV at baseline was 66.4 (± 14.6) letters, 417 (± 94) μm and 10.3 (± 1.9) mm3. The mean VA gain at 12 months was 4.0 (± 11.8) letters (p < 0.001); a total of 26% of eyes gained ≥ 10 letters, 15% of eyes gained ≥ 15 letters and 6% lost ≥15 letters. At 12-months, the mean reduction in CSFT was 108 (± 96) μm (p<0.001) and the mean reduction in MV was 1.05 (± 1.21) mm3 (p<0.001). An average of 6.2 (± 2.3) injections was given over 12 months. There was a significant association between functional and anatomical response category at 3 months and response category at 12 months (p<0.001).

Conclusion
The effectiveness of treatment with Aflibercept for patients in NWL was meaningfully lower than was reported in the VIVID and VISTA clinical trials. A high proportion of patients with good visual acuity at baseline, poorer glycaemic control, worse diabetic retinopathy and under-treatment likely contributed to lower functional and anatomical outcomes.