bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chromatin accessibility and regulatory vocabulary across indicine cattle tissues
Authors: Alexandre Pâmela A. , Naval-Sánchez Marina , Menzies Moira , Nguyen Loan T. , Porto-Neto Laercio R. , Fortes Marina R. S. , Reverter Antonio 
Published: September 2021

AbstractBackgroundSpatiotemporal changes in the chromatin accessibility landscape are essential to cell differentiation, development, health, and disease. The quest of identifying regulatory elements in open chromatin regions across different tissues and developmental stages is led by large international collaborative efforts mostly focusing on model organisms, such as ENCODE. Recently, the Functional Annotation of Animal Genomes (FAANG) has been established to unravel the regulatory elements in non-model organisms, including cattle. Now, we can transition from prediction to validation by experimentally identifying the regulatory elements in tropical indicine cattle. The identification of regulatory elements, their annotation and comparison with the taurine counterpart, holds high promise to link regulatory regions to adaptability traits and improve animal productivity and welfare.ResultsWe generate open chromatin profiles for liver, muscle, and hypothalamus of indicine cattle through ATAC-seq. Using robust methods for motif discovery, motif enrichment and transcription factor binding sites, we identify potential master regulators of the epigenomic profile in these three tissues, namely HNF4, MEF2, and SOX factors, respectively. Integration with transcriptomic data allows us to confirm some of their target genes. Finally, by comparing our results with Bos taurus data we identify potential indicine-specific open chromatin regions and overlaps with indicine selective sweeps.ConclusionsOur findings provide insights into the identification and analysis of regulatory elements in non-model organisms, the evolution of regulatory elements within two cattle subspecies as well as having an immediate impact on the animal genetics community in particular for a relevant productive species such as tropical cattle.
Response and oil degradation activities of a northeast Atlantic bacterial community to biogenic and synthetic surfactants
Authors: Nikolova Christina N. , Ijaz Umer Zeeshan , Magill Clayton , Kleindienst Sara , Joye Samantha B. , Gutierrez Tony 
Published: September 2021

Abstract
Background
Biosurfactants are naturally derived products that play a similar role to synthetic dispersants in oil spill response but are easily biodegradable and less toxic. Using a combination of analytical chemistry, 16S rRNA amplicon sequencing and simulation-based approaches, this study investigated the microbial community dynamics, ecological drivers, functional diversity and robustness, and oil biodegradation potential of a northeast Atlantic marine microbial community to crude oil when exposed to rhamnolipid or synthetic dispersant Finasol OSR52.

Results
Psychrophilic Colwellia and Oleispira dominated the community in both the rhamnolipid and Finasol OSR52 treatments initially but later community structure across treatments diverged significantly: Rhodobacteraceae and Vibrio dominated the Finasol-amended treatment, whereas Colwellia, Oleispira, and later Cycloclasticus and Alcanivorax, dominated the rhamnolipid-amended treatment. Key aromatic hydrocarbon-degrading bacteria, like Cycloclasticus, was not observed in the Finasol treatment but it was abundant in the oil-only and rhamnolipid-amended treatments. Overall, Finasol had a significant negative impact on the community diversity, weakened the taxa-functional robustness of the community, and caused a stronger environmental filtering, more so than oil-only and rhamnolipid-amended oil treatments. Rhamnolipid-amended and oil-only treatments had the highest functional diversity, however, the overall oil biodegradation was greater in the Finasol treatment, but aromatic biodegradation was highest in the rhamnolipid treatment.

Conclusion
Overall, the natural marine microbial community in the northeast Atlantic responded differently to crude oil dispersed with either synthetic or biogenic surfactants over time, but oil degradation was more enhanced by the synthetic dispersant. Collectively, our results advance the understanding of how rhamnolipid biosurfactants and synthetic dispersant Finasol affect the natural marine microbial community in the FSC, supporting their potential application in oil spills.
A nonparametric probabilistic method to enhance PGD solutions with data-driven approach, application to the automated tape placement process
Authors: Ghnatios Chady , Barasinski Anais 
Published: September 2021

AbstractA nonparametric method assessing the error and variability margins in solutions depicted in a separated form using experimental results is illustrated in this work. The method assess the total variability of the solution including the modeling error and the truncation error when experimental results are available. The illustrated method is based on the use of the PGD separated form solutions, enriched by transforming a part of the PGD basis vectors into probabilistic one. The constructed probabilistic vectors are restricted to the physical solution’s Stiefel manifold. The result is a real-time parametric PGD solution enhanced with the solution variability and the confidence intervals.
Behavioural and energetic consequences of competition among three overwintering swan (Cygnus spp.) species
Authors: Wood Kevin A. , Newth Julia L. , Hilton Geoff M. , Rees Eileen C. 
Published: September 2021

AbstractBackgroundWinter numbers of the northwest European population of Bewick’s Swans (Cygnus columbianus bewickii) declined recently by c. 40%. During the same period, numbers of two sympatric and ecologically-similar congeners, the Mute Swan (Cygnus olor) and Whooper Swan (Cygnus cygnus) showed increases or stability. It has been suggested that these opposing population trends could have a causal relationship, as Mute and Whooper Swans are larger and competitively dominant to Bewick’s Swans in foraging situations. If so, effects of competition of Mute and Whooper Swans on Bewick’s Swans should be detectable as measurable impacts on behaviour and energetics.MethodsHere, we studied the diurnal behaviour and energetics of 1083 focal adults and first-winter juveniles (“cygnets”) of the three swan species on their winter grounds in eastern England. We analysed video recordings to derive time-activity budgets and these, together with estimates of energy gain and expenditure, were analysed to determine whether individual Bewick’s Swans altered the time spent on key behaviours when sharing feeding habitat with other swan species, and any consequences for their energy expenditure and net energy gain.ResultsAll three swan species spent a small proportion of their total time (0.011) on aggressive interactions, and these were predominantly intraspecific (≥ 0.714). Mixed-effects models indicated that sharing feeding habitat with higher densities of Mute and Whooper Swans increased the likelihood of engaging in aggression for cygnet Bewick’s Swans, but not for adults. Higher levels of interspecific competition decreased the time spent by Bewick’s Swan cygnets on foraging, whilst adults showed the opposite pattern. When among low densities of conspecifics (< c. 200 individuals/km2), individual Bewick’s Swans spent more time on vigilance in the presence of higher densities of Mute and Whooper Swans, whilst individuals within higher density Bewick’s Swan flocks showed the opposite pattern. Crucially, we found no evidence that greater numbers of interspecific competitors affected the net energy gain of either adult or cygnet Bewick’s Swans.ConclusionsWe found no evidence that Bewick’s Swan net energy gain was affected by sharing agricultural feeding habitat with larger congeners during winter. This was despite some impacts on the aggression, foraging and vigilance behaviours of Bewick’s Swans, especially among cygnets. It is unlikely therefore that competition between Bewick’s Swans and either Mute or Whooper Swans at arable sites in winter has contributed to the observed decline in Bewick’s Swan numbers. Further research is needed, however, to test for competition in other parts of the flyway, including migratory stopover sites and breeding areas.
The migration ban policy cycle: a comparative analysis of restrictions on the emigration of women domestic workers
Authors: Shivakoti Richa , Henderson Sophie , Withers Matt 
Published: September 2021

AbstractPolicies banning women domestic workers from migrating overseas have long been imposed by labour-sending states in the Indo-Pacific region. This article presents the complexities surrounding such bans by developing an overarching model of a migration ban policy cycle, which provides a theoretical framework for understanding the circumstances under which migration bans arise and play out. It examines the history of migration bans for four prominent labour-sending states – Indonesia, Nepal, the Philippines and Sri Lanka - to assess the causes, outcomes and extent of regional convergence of these policies. In doing so, we uncover two prominent policy narratives. The first involves labour diplomacy, where countries employ bans to negotiate superior working conditions and rights for migrant workers. The second concerns paternalist states as ‘protector’, where states are primarily motivated to reaffirm traditional gender norms. We conclude that migration bans have been most effective, both in curbing departures and achieving desired outcomes, when they are primarily motivated by labour issues and not gender politics. Nevertheless, even when used as a form of diplomatic negotiation, migration bans heighten the vulnerability of domestic workers to exploitation by pushing them into irregular pathways fraught with risk.
Concentrations and pharmacokinetic parameters of MRI and SPECT hepatobiliary agents in rat liver compartments
Authors: Pastor Catherine M. , Joly Florian , Vilgrain Valérie , Millet Philippe 
Published: September 2021

Abstract
Background
In hepatobiliary imaging, systems detect the total amount of agents originating from extracellular space, bile canaliculi, and hepatocytes. They add in situ concentration of each compartment corrected by its respective volume ratio to provide liver concentrations. In vivo contribution of each compartment to liver concentration is inaccessible. Our aim was to quantify the compartmental distribution of two hepatobiliary agents in an ex vivo model and determine how their liver extraction ratios and cholestasis (livers lacking canalicular transporters) might modify it.

Methods
We perfused labelled gadobenate dimeglumine (Bopta, 200 μM, 7% liver extraction ratio) and mebrofenin (Meb, 64 μM, 94% liver extraction ratio) in normal (n = 18) and cholestatic (n = 6) rat livers. We quantified liver concentrations with a gamma counter placed over livers. Concentrations in hepatocytes and bile canaliculi were calculated. Mann-Whitney and Kruskal-Wallis tests were used.

Results
Hepatocyte concentrations were 2,043 ± 333 μM (Meb) versus 360 ± 69 μM (Bopta, p < 0.001). Meb extracellular concentrations did not contribute to liver concentrations (1.3 ± 0.3%). The contribution of Bopta extracellular concentration was 12.4 ± 1.9% (p < 0.001 versus Meb). Contribution of canaliculi was similar for both agents (16%). Cholestatic livers had no Bopta in canaliculi but their hepatocyte concentrations increased in comparison to normal livers.

Conclusion
Hepatocyte concentrations are correlated to liver extraction ratios of hepatobiliary agents. When Bopta is not present in canaliculi of cholestatic livers, hepatocyte concentrations increase in comparison to normal livers. This new understanding extends the interpretation of clinical liver images.
Evaluating health disparities in access to genomic testing for metastatic non-small cell lung cancer patients.
Authors: Yoon Brian , Weeraratne Dilhan , Arriaga Yull Edwin , Huang Hu , Osterman Travis John 
Published: September 2021

113 Background: Over the past decade, genomic testing has become standard of care for metastatic non-small cell lung cancer (NSCLC). These tests qualify patients for additional anti-cancer therapies and should be performed in all patients. Small scale studies at the institutional level have revealed that there may be disparities in genomic testing in NSCLC and not all patients may have similar access to care. In this study, we use the IBM Explorys Electronic Health Record (EHR) database to conduct a nationwide retrospective, observational study to understand how gender, race, insurance type, and spoken language impacts the rate of genomic testing in metastatic NSCLC patients. Methods: From Jan 1st, 2015 to Dec 31st, 2020, the IBM Explorys EHR database comprised 128,119 lung cancer patients using the SNOMED-CT concept of Primary Malignant Neoplasm of the Lung (CID 93880001). As structured staging information was not available, metastatic NSCLC patients were imputed by removing patients who received thoracic surgeries (presumably stage I or II) and those who received radiation therapy (presumably stage III). Following imputation, 120,470 patients with metastatic NSCLC were queried for testing for EGFR, ALK, ROS1, and/or RET. Odds ratios and chi-squared tests were computed for gender, race, insurance type, and spoken language comparing patients that received genomics testing to those who did not. Results: Genomic testing was taken significantly more by male patients (OR: 1.35, p<0.0001), and by Caucasian patients (OR: 1.39, p<0.0001). Compared to the public insurance plans, the genomic testing was significantly more in patients with private insurance plans (OR: 2.48, p<0.0001) and self-pay patients (OR: 2.84, p<0.0001). Patients speaking English as their first language significantly less likely took genomic testing (OR: 0.81, p<0.05). Conclusions: This study aims to identify gaps in health disparities in gender, race/ethnicity, and insurance type for genomic testing that should be standard practice. Future investigation and attention to this issue appears necessary to begin moving from documenting disparities, to understanding them, and ultimately to reducing them.[Table: see text]
Patient- and provider-level predictors of mortality among patients with metastatic renal cell carcinoma receiving oral anticancer agents.
Authors: Spees Lisa , Dinan Michaela Ann , Jackson Bradford E. , Baggett Christopher , Wilson Lauren E. , Greiner Melissa A. , Kaye Deborah , Zhang Tian , George Daniel J. , Scales Charles D. , Pritchard Jessica , Leapman Michael S. , Gross Cary Philip , Wheeler Stephanie B. 
Published: September 2021

116 Background: It is important to understand how emerging new therapies, such as oral anti-cancer agents (OAAs), diffuse across and can improve outcomes within real-world populations, which include age groups and racial groups not well-represented in clinical trials, such as people older than age 65 and Black patients. Our objectives were to examine whether disparities in mortality persist among patients with metastatic renal cell carcinoma (mRCC) receiving OAAs and whether these disparities may be partially explained by patient’s clinical characteristics or provider-level factors. Methods: We used linked state cancer registry data and multi-payer claims data to identify patients with mRCC who were diagnosed in 2004 through 2015 and had initiated an OAA and survived ≥ 90 days after initiating. Provider data were obtained from North Carolina Health Professions Data System and the National Plan & Provider Enumeration System. A patient’s modal provider was the provider most frequently on claims with a diagnosis code of RCC or metastatic cancer between 2 months prior to and 3 months following the index date. We estimated hazard ratios (HR) and corresponding 95% confidence limits (CL) using Cox proportional hazard models to evaluate which patient demographics, patient clinical characteristics, and provider-level factors were associated with 2-year all-cause mortality. Results: The cohort included 207 patients with mRCC. In unadjusted analyses, public insurance (Medicaid or Medicare), de novo metastatic diagnosis, frailty, polypharmacy, and a visit to a skilled nursing facility were associated with increased all-cause mortality. In multivariable models, clinical variables such as frailty (HR: 1.36, 95% CL: 1.11-1.67) and de novo metastatic diagnosis (HR: 2.63, 95%CL: 1.67-4.16) were associated with higher all-cause mortality. Additionally, Medicare-insured patients continued to have higher all-cause mortality compared to privately insured patients (HR: 2.35, 95% CL: 1.32-4.18). None of the provider-level covariates (i.e., specialization, experience, volume, or practice location) investigated were associated with all-cause mortality. Conclusions: Even when adjusting for age, frailty, and comorbidities, Medicare-insured patient had lower overall survival than privately-insured patients. Patient survival did not differ based on modal provider’s characteristics.
Analysis of racial disparities in time to treatment initiation and survival among patients with advanced cancers.
Authors: Zyczynski Teresa Maria , Smith Cardinale B. , Zhang Ying , Hao Yi 
Published: September 2021

127 Background: Racial disparities in cancer care have received increased attention in recent years. One previously identified disparity is in the time to treatment initiation (TTI) – a factor closely associated with outcomes. While most research in the US to date has focused on the Medicaid and Medicare populations, this study examined disparities between different racial/ethnic groups in TTI and overall survival (OS) among patients with cancer managed in the community setting. Methods: Using the Flatiron Health electronic health record database, patients diagnosed with advanced non-small cell lung cancer (aNSCLC), metastatic colorectal cancer (mCRC), metastatic breast cancer (mBC), multiple myeloma (MM), advanced gastroesophageal cancer (aGastric), advanced urothelial cancer (aUL), metastatic renal cell carcinoma (mRCC) or advanced melanoma (aMel) and treated with first-line (1L) therapy, with ≥1 month of follow-up during 2014-2019, were included. Patient characteristics, TTI and outcomes were compared across race/ethnicity groups classified as White, Black, Asian and Hispanic/Latino/Other (Other). Results: A total of 81,543 patients were evaluated (37% aNSCLC, 19% mCRC, 15% mBC, 8% MM, 6% aGastric, 5.2% aUL, 5.0% mRCC and 4.1% aMel); 67% were White, 9% Black, 3% Asian and 11% Other. Overall, TTI was similar across race/ethnicity groups (median range 1.1–1.2 months), and 44% of all patients received treatment ≤30 days post-diagnosis. Overall Survival (months). Median OS varied by tumor and race/ethnicity groups (Table). However, multivariate Cox proportional hazards analysis showed that Asian patients had better OS than Black patients in many cancers (hazard ratio [HR] 0.8 aNSCLC, 0.75 mBC, 0.63 aGastric, 0.59 aUL, 0.81 mCRC, 0.68 mRCC), while White patients had better survival than Black patients in mBC (HR 0.8) and aGastric (HR 0.87). Conclusions: In this real-word analysis, TTI did not differ by race/ethnicity group for any of the cancers examined. However, some differences in OS emerged on multivariate analysis – this was longer in Asian than Black patients in aNSCLC, mBC, mCRC, aGastric, aUL and mRCC, and longer in White than Black patients in mBC and aGastric. Given the small sample size in some groups, further analyses are needed to determine the influence of race/ethnicity on cancer care and outcomes.[Table: see text]
The impact of COVID-19 on breast cancer care: Delays in screening.
Authors: Dhahri Amina , Tegene Teshome 
Published: September 2021

130 Background: Breast cancer (BC) screening is an integral part of cancer prevention. COVID-19 posed multiple obstacles on ensuring continuity of cancer care. The short and long-term outcomes of the pandemic on BC screening is unknown. The purpose of this study is to examine the challenges the pandemic has on mammogram completion using a granular measure of social economic deprivation: Area deprivation index (ADI). Methods: A Retrospective cohort study was conducted at an academic hospital system at the epicenter of COVID-19 pandemic comparing BC screening rates during the year of 2019 (pre-COVID19) and 2020 (COVID-19). For the year 2020, only charts between January-February and July-December were reviewed. March-June period was avoided as the USA declared a national emergency and the American Cancer Society recommended to temporarily pause cancer screening. The outcome variable was mammogram completion. The predictor variables were: COVID-19 period, race, insurance, age and ADI. ADI is a validated dataset that ranks census block groups based on socioeconomic deprivation (SED). Chi-square and Wilcoxon rank sum test were used to compare categorical and continuous variables by receipt of mammography. A multivariate logistic regression was used for associations between mammogram completion and the predictor variables. Results: A total of 694 patients were deemed eligible for BC screening in the year of 2019 (394) and 2020 (300). During the follow up period, only 106 and 30 patients from the pre-COVID-19 and COVID-19 cohorts underwent BC screening, respectively. During the pandemic, 30/30 patients who completed their screening were African Americans and had a high SED. In a multivariable analysis, COVID-19 period is associated with 79% lower odds of mammogram completion (OR 0.21; 95% CI 0.13, 0.35). ADI and race were not associated with higher screening rates. Medicaid status is associated with higher odds of mammogram completion (OR 1.97; 95% CI 1.12, 3.47). Conclusions: COVID-19 caused significant disruption in BC screening. In an area with high SED and high COVID-19 infection rates, private insurance holders and white patients had low rates mammogram completion. One potential explanation is that these patients sought care elsewhere. [Table: see text]