bluuebunny/crossref_metadata_2025_split huggingface dataset:
Melismas in the Speculum musicae
Authors: Kelly Thomas Forrest 
Published: November 2021

Abstract
Eight melodies, one for each of the ecclesiastical modes, are given as optional additions to responsories and other chants in the 14th-century Speculum musicae of Jacobus of Liège. The melodies have paired phrases resembling those of contemporaneous dance music. The paucity of surviving melodies of this sort, and their almost exclusive association with secular music, make this series particularly fascinating.
A shift in women’s health? Older workers’ self-reported health and employment settings during the COVID-19 pandemic
Authors: Wels Jacques , Hamarat Natasia 
Published: November 2021

AbstractBackgroundThe first wave of COVID-19 has had a massive impact on work arrangements settings in many European countries with potential effects on health that are likely to vary across gender.MethodsFocusing on the workforce aged 50 and over in 27 European countries using data from SHARE wave 8 (N = 11,221), the study applies a generalized logit mixed-effects model to assess the relationship between negative and positive change in self-reported health since the start of the pandemic and change in employment settings using an interaction effect between gender and employment arrangements to distinguish their specific association by gender after controlling for socio-economic covariates and multicollinearity.ResultsFemale respondents have higher probabilities to declare a positive health when working fully or partially from home or when temporarily and permanently unemployed. However, introducing the main effect of gender exacerbates discrepancies and such benefits fade away. Differences across countries do not significantly change the estimates.ConclusionThe benefits of work arrangements to improve women’s health during the first wave of COVID-19 have not compensated the negative effect of gender discrepancies exacerbated by the pandemic to the extent that employment arrangements have no role, or just a negative impact, in modulating them.
A data library of Candida albicans functional genomic screens
Authors: Gervais Nicholas C , Halder Viola , Shapiro Rebecca S 
Published: November 2021

ABSTRACT
Functional genomic screening of genetic mutant libraries enables the characterization of gene function in diverse organisms. For the fungal pathogen Candida albicans, several genetic mutant libraries have been generated and screened for diverse phenotypes, including tolerance to environmental stressors and antifungal drugs, and pathogenic traits such as cellular morphogenesis, biofilm formation and host–pathogen interactions. Here, we compile and organize C. albicans functional genomic screening data from ∼400 screens, to generate a data library of genetic mutant strains analyzed under diverse conditions. For quantitative screening data, we normalized these results to enable quantitative and comparative analysis of different genes across different phenotypes. Together, this provides a unique C. albicans genetic database, summarizing abundant phenotypic data from functional genomic screens in this critical fungal pathogen.
Genetic Data and the Right to Privacy: Towards a Relational Theory of Privacy?
Authors: Costello Róisín Á 
Published: November 2021

Abstract
This article examines the lacunae in contemporary understandings of the right to privacy which genetic data exposes. In particular, the article argues that the nature of genetic data challenges modern, individualistic conceptions of privacy which have come to dominate human rights law in the twenty-first century. The article suggests that the seeds of a new understanding of privacy which integrates existing individualistic understanding with the need to acknowledge the relational nature of modern privacy can be located in the jurisprudence of the European Court of Human Rights and Court of Justice of the European Union. The article offers some initial thoughts on how a relational theory of privacy based on this jurisprudence would function, and argues that further engagement with how to reconcile the collective impacts of genetic data processing and individualistic understandings of privacy is needed.
Intra- and inter-annual variability in the fat content of Atlantic herring (Clupea harengus) as revealed by routine industry monitoring
Authors: Kenyon Susan , Pastoors Martin , Mackinson Steven , Cornulier Thomas , Marshall C Tara 
Published: November 2021

Abstract
Fat content indicates individual condition and fuels annual reproductive cycles in many fish species. These cycles, coupled with ecosystem changes, can result in large intra- and inter-annual fluctuations in fat content. However, quantifying this variability is challenging when scientific sampling does not cover the full reproductive cycle. Scottish and Dutch fish processors routinely measure muscle fat content of North Sea autumn-spawning herring (Clupea harengus) throughout fishing seasons. We validated these high temporal resolution data by estimating a strong intra-annual signal in fat content, which matched herring reproductive status. Fat content increased from 4.5% 95% CI [0.03, 0.06] to 16.1% 95% CI [0.15, 0.17] during May and June before plateauing and decreasing to 9.1% 95% CI [0.08, 0.10] in September, which coincided with the onset of spawning. We also examined inter-annual variability in the seasonal pattern and the timing and magnitude of peak fat content from 2006 to 2020. Inter-annually, fat content differed from the mean pattern during the feeding or spawning periods in years 2013, 2015–2017, 2019, and 2020. There was no difference in the timing and magnitude of peak fat content between years. Our study validates the scientific use of routinely collected fat content data from pelagic fish processors.
Enhancing PCORnet Clinical Research Network data completeness by integrating multistate insurance claims with electronic health records in a cloud environment aligned with CMS security and privacy requirements
Authors: Waitman Lemuel R , Song Xing , Walpitage Dammika Lakmal , Connolly Daniel C , Patel Lav P , Liu Mei , Schroeder Mary C , VanWormer Jeffrey J , Mosa Abu Saleh , Anye Ernest T , Davis Ann M 
Published: November 2021

Abstract

Objective
The Greater Plains Collaborative (GPC) and other PCORnet Clinical Data Research Networks capture healthcare utilization within their health systems. Here, we describe a reusable environment (GPC Reusable Observable Unified Study Environment [GROUSE]) that integrates hospital and electronic health records (EHRs) data with state-wide Medicare and Medicaid claims and assess how claims and clinical data complement each other to identify obesity and related comorbidities in a patient sample.

Materials and Methods
EHR, billing, and tumor registry data from 7 healthcare systems were integrated with Center for Medicare (2011–2016) and Medicaid (2011–2012) services insurance claims to create deidentified databases in Informatics for Integrating Biology & the Bedside and PCORnet Common Data Model formats. We describe technical details of how this federally compliant, cloud-based data environment was built. As a use case, trends in obesity rates for different age groups are reported, along with the relative contribution of claims and EHR data-to-data completeness and detecting common comorbidities.

Results
GROUSE contained 73 billion observations from 24 million unique patients (12.9 million Medicare; 13.9 million Medicaid; 6.6 million GPC patients) with 1 674 134 patients crosswalked and 983 450 patients with body mass index (BMI) linked to claims. Diagnosis codes from EHR and claims sources underreport obesity by 2.56 times compared with body mass index measures. However, common comorbidities such as diabetes and sleep apnea diagnoses were more often available from claims diagnoses codes (1.6 and 1.4 times, respectively).

Conclusion
GROUSE provides a unified EHR-claims environment to address health system and federal privacy concerns, which enables investigators to generalize analyses across health systems integrated with multistate insurance claims.
Adsorption of Therapeutic and Recreational Drugs During Prolonged Storage of Plasma Samples in Gel Separator Tubes
Authors: Shepard Cara L , Bliumkin Liora 
Published: November 2021

AbstractHospital samples collected in gel separator tubes are often submitted to forensic toxicology laboratories for analysis in impaired driving and death investigations. Drug adsorption to the gel separator material may lead to underestimation of the drug concentration present at the time of sample collection, potentially affecting the interpretation of analytical results. Using liquid chromatography--tandem mass spectrometry (LC--MS-MS), decreases in plasma concentration of 53 drugs and metabolites relevant to forensic toxicology casework were investigated in samples stored in BD Vacutainer® PSTTM tubes for up to 3 months. After storage for only 1 day, approximately 50% of the drugs and metabolites had significantly lower concentrations in plasma separation tubes (PSTs) compared to non-gel tubes (up to 27% lower). After storage for 3 months, approximately 75% of the drugs and metabolites had significantly lower concentrations in PSTs compared to non-gel tubes (up to 69% lower). Fentanyl, carfentanil, ketamine, diphenhydramine and several antidepressants were among the drugs most susceptible to adsorption. Central nervous system stimulants (e.g., methamphetamine and amphetamine) as well as naturally-occurring and semi-synthetic opioids (e.g., morphine, hydromorphone and oxycodone) were among the drugs least susceptible to adsorption and displayed only minimal relative decreases in concentration (if any) over the 3-month sample storage period. The potential for decreases in drug concentration due to adsorption of drugs to the gel material should be considered for toxicological interpretation based on the analysis of a sample collected in a gel separator tube.
The impacts of marking on bats: mark-recapture models for assessing injury rates and tag loss
Authors: Mellado Breno , Carneiro Lucas de Oliveira , Nogueira Marcelo Rodrigues , Monteiro Leandro Rabello 
Published: November 2021

AbstractThe individual identification of animals is essential for long-term population ecology studies. Injuries and tag loss can negatively impact animal welfare and parameter estimates. We used time-to-failure curves and multistate mark-recapture models to estimate injury rates, body condition decline, tag loss and survival probabilities associated with two tags commonly used in bats: metallic arm bands and steel ball chain collars. We monitored two colonies of Carollia perspicillata at União Biological Reserve, southeastern Brazil, from 2013 to 2019. Every other month, we marked individuals with arm bands, collars or both. Collars did not cause noticeable injuries, but were lost at a higher rate than arm bands (1.5–2.5 times). The arm band-related injury probability between captures was ~ 0.2, and after 17 months half the marked animals developed injuries. Animals marked as juveniles were less likely to get injured than adults. Injuries were associated with a lower body condition in females. Body condition was positively associated with apparent survival; however, a direct effect of arm band injuries on survival estimates was not observed. The tag loss rates caused a negative bias in survival estimates. Mark-recapture studies should evaluate the efficacy of the marking technique, accounting for potential animal injury, tag loss, and bias in parameter estimation. Marking individuals should be limited to studies that monitor species with high recapture probability, using the least harmful tags possible, and balancing the burden to the animals with the potential to generate knowledge.
In-utero gastric perforation from combined duodenal and esophageal atresia without consistent polyhydramnios
Authors: Lyttle Bailey D , Liechty Kenneth , Corkum Kristine , Galan Henry , Behrendt Nicholas , Zaretsky Michael , Bruny Jennifer , Derderian S Christopher 
Published: November 2021

Abstract
We present a case in which prenatal imaging at 21-weeks’ gestation suggested duodenal atresia with a double-bubble sign and enlarged stomach. Fetal magnetic resonance imaging findings demonstrated dilation of the stomach and proximal duodenum favoring duodenal atresia but no indications of esophageal atresia. Subsequent prenatal imaging demonstrated interval spontaneous decompression of the stomach without the development of polyhydramnios, obscuring the diagnosis. Postnatally, initial abdominal radiography showed a gasless abdomen, and an oral gastric tube could not pass the mid-esophagus, raising concern for pure esophageal atresia. Intraoperative findings were consistent with duodenal atresia, pure esophageal atresia and a gastric perforation due to a closed obstruction. In this case report, we review the prenatal diagnostic challenges and the limited literature pertaining to this unique pathology.
Correlation between optical flux and polarization variations in flat-spectrum radio quasars on diverse time-scales
Authors: Pandey Ashwani , Rajput Bhoomika , Stalin C S 
Published: November 2021

ABSTRACT
Study of the polarization behaviour in blazars is a powerful tool to discern the role of the magnetic field in the variable emission process in their relativistic jets. We present here the results of our systematic investigation on the correlation between optical flux and polarization variations for eight flat-spectrum radio quasars on various time-scales using data from the Steward Observatory that covers a period of ∼10 years. On long time-scales (∼several months), from a total of 79 observing cycles, we found a significant positive correlation between optical flux and optical polarization degree (PD) in 34 observing cycles, a negative correlation in three cycles, and no correlation in 42 cycles. On short time-scales (∼few days), in 47 out of a total of 55 epochs we found a positive correlation between optical flux and PD, while for the remaining eight epochs an anticorrelation was detected between the two quantities. Moreover, we noticed a significant positive correlation between optical and γ-ray fluxes in 14 epochs, and a negative correlation between the two in one epoch. While the observed optical flux changes fit the shock-in-jet model well, the observed changes in PD are not explainable by changes in the power-law spectral index of the relativistic electrons in the jet. Instead, the observed varied correlations between optical flux and PD could be due to multizone emission regions or the enhanced flux coinciding with the emergence of a new emission knot with its magnetic field either aligned or misaligned with the large-scale magnetic field.
Physical modelling of viscous disc evolution around magnetized neutron star. Aql X-1 2013 outburst decay
Authors: Lipunova Galina , Malanchev Konstantin , Tsygankov Sergey , Shakura Nikolai , Tavleev Andrei , Kolesnikov Dmitry 
Published: November 2021

ABSTRACT
We present a model of a viscously evolving accretion disc around a magnetized neutron star. The model features the varying outer radius of the hot ionized part of the disc due to cooling and the varying inner radius of the disc due to interaction with the magnetosphere. It also includes hindering of accretion on the neutron star because of the centrifugal barrier and irradiation of the outer disc and companion star by X-rays from the neutron star and disc. When setting inner boundary conditions, we take into account that processes at the inner disc occur on a time-scale much less than the viscous time-scale of the whole disc. We consider three types of outflow from the disc inner edge: zero outflow, one based on MHD calculations, and a very efficient propeller mechanism. The light curves of an X-ray transient after the outburst peak can be calculated by a corresponding, publicly available code. We compare observed light curves of the 2013 burst of Aql X-1 in X-ray and optical bands with modelled ones. We find that the fast drop of the 0.3–10 keV flux can be solely explained by a radial shrinking of the hot disc. At the same time, models with the neutron star magnetic field &gt;108 G have better fits because the accretion efficiency behaviour emphasizes the ‘knee’ on the light curve. We also find that a plato emission can be produced by a `disc-reservoir' with stalled accretion.
J01020100−7122208: an accreted evolved blue straggler that was not ejected from a supermassive black hole
Authors: De Brito Silva Danielle , Jofré Paula , Bourbert Douglas , Koposov Sergey E , Prieto Jose L , Hawkins Keith 
Published: November 2021

ABSTRACT
J01020100−7122208 is a star whose origin and nature still challenges us. It was first believed to be a yellow supergiant ejected from the Small Magellanic Cloud, but it was more recently claimed to be a red giant accelerated by the Milky Way’s central black hole. In order to unveil its nature, we analysed photometric, astrometric, and high-resolution spectroscopic observations to estimate the orbit, age, and 16 elemental abundances. Our results show that this star has a retrograde and highly-eccentric orbit, $e=0.914_{-0.020}^{+0.016}$. Correspondingly, it likely crossed the Galactic disc at 550 pc from the Galactic Centre. We obtained a spectroscopic mass and age of $1.09\pm 0.10\, {\rm M}_\odot$ and 4.51 ± 1.44 Gyr, respectively. Its chemical composition is similar to the abundance of other retrograde halo stars. We found that the star is enriched in europium, having [Eu/Fe] = 0.93 ± 0.24, and is more metal-poor than reported in the literature, with [Fe/H] = −1.30 ± 0.10. This information was used to conclude that J01020100−7122208 is likely not a star ejected from the central black of the Milky Way or from the Small Magellanic Cloud. Instead, we propose that it is simply a halo star that was likely accreted by the Milky Way in the distant past, but its mass and age suggest it is probably an evolved blue straggler.
Velocity monitoring of γ Cas stars reveals their binarity status
Authors: Nazé Yaël , Rauw Gregor , Czesla Stefan , Smith Myron A , Robrade Jan 
Published: November 2021

ABSTRACT
The binary status of γ Cas stars has been discussed while theoretically examining the origin of their peculiar X-ray emission. However, except in two cases, no systematic radial velocity monitoring of these stars had been undertaken yet to clarify their status. We now fill this gap using TIGRE, CARMENES, and UVES high-resolution spectroscopy. Velocities were determined for 16 stars, revealing shifts and/or changes in line profiles. The orbit of six new binaries could be determined: the long periods (80–120 d) and small velocity amplitudes (5–7 km s−1) suggest low mass companions (0.6–1 M⊙). The properties of the known γ Cas binaries appear similar to those of other Be systems, with no clear-cut separation between them. One of the new systems is a candidate for a rare case of quadruple system involving a Be star. Five additional γ Cas stars display velocity variations compatible with the presence of companions, but no orbital solution could yet be formally established for them hence they only receive the status of ‘binary candidate’.
Evolution under Spatially Heterogeneous Selection in Solid Tumors
Authors: Li Guanghao , Yang Zuyu , Wu Dafei , Liu Sixue , Li Xuening , Li Tao , Li Yawei , Liang Liji , Zou Weilong , Wu Chung-I , Wang Hurng-Yi , Lu Xuemei 
Published: November 2021

AbstractSpatial genetic and phenotypic diversity within solid tumors has been well documented. Nevertheless, how this heterogeneity affects temporal dynamics of tumorigenesis has not been rigorously examined because solid tumors do not evolve as the standard population genetic model due to the spatial constraint. We therefore, propose a neutral spatial (NS) model whereby the mutation accumulation increases toward the periphery; the genealogical relationship is spatially determined and the selection efficacy is blunted (due to kin competition). In this model, neutral mutations are accrued and spatially distributed in manners different from those of advantageous mutations. Importantly, the distinctions could be blurred in the conventional model. To test the NS model, we performed a three-dimensional multiple microsampling of two hepatocellular carcinomas. Whole-genome sequencing (WGS) revealed a 2-fold increase in mutations going from the center to the periphery. The operation of natural selection can then be tested by examining the spatially determined clonal relationships and the clonal sizes. Due to limited migration, only the expansion of highly advantageous clones can sweep through a large part of the tumor to reveal the selective advantages. Hence, even multiregional sampling can only reveal a fraction of fitness differences in solid tumors. Our results suggest that the NS patterns are crucial for testing the influence of natural selection during tumorigenesis, especially for small solid tumors.
Single-molecule mitochondrial DNA sequencing shows no evidence of CpG methylation in human cells and tissues
Authors: Bicci Iacopo , Calabrese Claudia , Golder Zoe J , Gomez-Duran Aurora , Chinnery Patrick F 
Published: November 2021

Abstract
Methylation on CpG residues is one of the most important epigenetic modifications of nuclear DNA, regulating gene expression. Methylation of mitochondrial DNA (mtDNA) has been studied using whole genome bisulfite sequencing (WGBS), but recent evidence has uncovered technical issues which introduce a potential bias during methylation quantification. Here, we validate the technical concerns of WGBS, and develop and assess the accuracy of a new protocol for mtDNA nucleotide variant-specific methylation using single-molecule Oxford Nanopore Sequencing (ONS). Our approach circumvents confounders by enriching for full-length molecules over nuclear DNA. Variant calling analysis against showed that 99.5% of homoplasmic mtDNA variants can be reliably identified providing there is adequate sequencing depth. We show that some of the mtDNA methylation signal detected by ONS is due to sequence-specific false positives introduced by the technique. The residual signal was observed across several human primary and cancer cell lines and multiple human tissues, but was always below the error threshold modelled using negative controls. We conclude that there is no evidence for CpG methylation in human mtDNA, thus resolving previous controversies. Additionally, we developed a reliable protocol to study epigenetic modifications of mtDNA at single-molecule and single-base resolution, with potential applications beyond CpG methylation.