bluuebunny/crossref_metadata_2025_split huggingface dataset:
Morphological characterization of trichomes shows enormous variation in shape, density and dimensions across the leaves of 14 Solanum species
Authors: Watts Sakshi , Kariyat Rupesh 
Published: October 2021

Abstract
Trichomes are the epidermal appendages commonly observed on plant surfaces including leaves, stem and fruits. Plant trichomes have been well studied as a structural plant defence designed to protect plants against abiotic and biotic stressors such as UV rays, temperature extremities and herbivores. Trichomes are primarily classified into glandular and non-glandular trichomes, based on the presence or absence of a glandular head. The plant genus Solanum is the largest genus of family Solanaceae that houses ~3500 species of ecological and economic importance have a diverse set of trichomes that vary in density and morphology. However, due to the incomplete and contradictory classification system, trichomes have subjective names and have been largely limited to be grouped into glandular or non-glandular types. Through this study, we did a complete workup to classify and characterize trichomes on both adaxial and abaxial leaf surface of 14 wild and domesticated species of the genus Solanum. Using electron microscopy, statistical analyses and artistic rendition, we examined finer details of trichomes and measured their density and dimensions to compile a detailed data set which can be of use for estimating the variation in trichome types, and their density, with consequences for understanding their functional roles. Our study is the first of its kind that provides us with a better and well-defined classification, density and dimension analysis to complete the morphological classification of trichomes on both leaf surfaces of a diverse range of members in Solanum genus.
Population-scale detection of non-reference sequence variants using colored de Bruijn graphs
Authors: Krannich Thomas , White W Timothy J , Niehus Sebastian , Holley Guillaume , Halldórsson Bjarni V , Kehr Birte 
Published: October 2021

AbstractMotivationWith the increasing throughput of sequencing technologies, structural variant (SV) detection has become possible across tens of thousands of genomes. Non-reference sequence (NRS) variants have drawn less attention compared with other types of SVs due to the computational complexity of detecting them. When using short-read data, the detection of NRS variants inevitably involves a de novo assembly which requires high-quality sequence data at high coverage. Previous studies have demonstrated how sequence data of multiple genomes can be combined for the reliable detection of NRS variants. However, the algorithms proposed in these studies have limited scalability to larger sets of genomes.ResultsWe introduce PopIns2, a tool to discover and characterize NRS variants in many genomes, which scales to considerably larger numbers of genomes than its predecessor PopIns. In this article, we briefly outline the PopIns2 workflow and highlight our novel algorithmic contributions. We developed an entirely new approach for merging contig assemblies of unaligned reads from many genomes into a single set of NRS using a colored de Bruijn graph. Our tests on simulated data indicate that the new merging algorithm ranks among the best approaches in terms of quality and reliability and that PopIns2 shows the best precision for a growing number of genomes processed. Results on the Polaris Diversity Cohort and a set of 1000 Icelandic human genomes demonstrate unmatched scalability for the application on population-scale datasets.Availability and implementationThe source code of PopIns2 is available from https://github.com/kehrlab/PopIns2.Supplementary informationSupplementary data are available at Bioinformatics online.
The PERCEIVE quantitative study: PrEdiction of Risk and Communication of outcome following major lower-limb amputation: protocol for a collaboratiVE study
Authors: Gwilym Brenig L , Waldron Cherry-Ann , Thomas-Jones Emma , Preece Ryan , Milosevic Sarah , Brookes-Howell Lucy , Pallmann Philip , Harris Debbie , Massey Ian , Burton Jo , Stewart Philippa , Samuel Katie , Jones Sian , Cox David , Edwards Adrian , Twine Chris , Bosanquet David C ,   Vascular and Endovascular Research Network, Ambler G K , Benson R , Dattani N , Dovell G , Forsythe R , Hitchman L , Nandhra S , Onida S , Saratzis A , Shalhoub J 
Published: October 2021

Abstract

Background
Accurate prediction of outcomes following surgery with high morbidity and mortality rates is essential for informed shared decision-making between patients and clinicians. It is unknown how accurately healthcare professionals predict outcomes following major lower-limb amputation (MLLA). Several MLLA outcome-prediction tools have been developed. These could be valuable in clinical practice, but most require validation in independent cohorts before routine clinical use can be recommended. The primary aim of this study is to evaluate the accuracy of healthcare professionals’ predictions of outcomes in adult patients undergoing MLLA for complications of chronic limb-threatening ischaemia (CLTI) or diabetes. Secondary aims include the validation of existing outcome-prediction tools.

Method
This study is an international, multicentre prospective observational study including adult patients undergoing a primary MLLA for CLTI or diabetes. Healthcare professionals’ accuracy in predicting outcomes at 30-days (death, morbidity and MLLA revision) and 1-year (death, MLLA revision and ambulation) will be evaluated. Sixteen existing outcome-prediction tools specific to MLLA will be examined for validity. Data collection began on 1 October 2020; the end of follow-up will be 1 May 2022. The C-statistic, Hosmer–Lemeshow test, reclassification tables and Brier score will be used to evaluate the predictive performance of healthcare professionals and prediction tools, respectively.

Study registration and dissemination
This study will be registered locally at each centre in accordance with local policies before commencing data collection, overseen by local clinician leads. Results will be disseminated to all centres, and any subsequent presentation(s) and/or publication(s) will follow a collaborative co-authorship model.
One Market to Rule Them All: How Financial Integration Influenced Inequality in the European Union
Authors: Burghof Hans-Peter , Gehrung Marcel 
Published: October 2021

Abstract
Financial integration is seen as a major driver of economic growth and wealth. Its effects on income inequality have been analyzed for the bank branch deregulation in the USA and foreign bank entry in India. Another prominent example of financial integration and liberalization, so far, has been ignored: the introduction and progression of the European Single Market. By using a difference-in-difference design, we investigate the effects of the Single Banking License introduced in 1993 on economic growth and several inequality measures. This directive abolished any cross-country restrictions on banks in EU Member States and allowed them to freely branch into other Member States. This constitutes a fundamental change in the competitive environment of financial markets. We show that the European Single Financial Market positively influenced economic growth across a variety of subsamples of EU Member States. The effects on income inequality indicate that inequality across states was reduced. Additional regressions with the unemployment rate and top and bottom 20% income shares support this finding and show a reduction of unemployment in previously less developed countries accompanied by an increase in the bottom income shares across all Member States. (JEL codes: D63, E44, G21 and O11).
Coronavirus Disease 2019 Vaccine-Breakthrough Infections Requiring Hospitalization in Mayo Clinic Florida Through August 2021
Authors: Bosch Wendelyn , Cowart Jennifer B , Bhakta Shivang , Carter Rickey E , Wadei Hani M , Shah Sadia Z , Sanghavi Devang K , Pollock Benjamin D , Neville Matthew R , Oman Sven P , Speicher Leigh , Scindia Ameya D , Matson Mark W , Moreno Franco Pablo 
Published: October 2021

Abstract
We characterized coronavirus disease 2019 (COVID-19) breakthrough cases admitted to a single center in Florida. With the emergence of delta variant, an increased number of hospitalizations was seen due to breakthrough infections. These patients were older and more likely to have comorbidities. Preventive measures should be maintained even after vaccination.
Patient-reported vs. physician-estimated symptoms before and after transcatheter aortic valve replacement
Authors: Arnold Suzanne V , Manandhar Pratik , Vemulapalli Sreekanth , Vekstein Andrew M , Kosinski Andrzej S , Spertus John A , Cohen David J 
Published: October 2021

AbstractAimsIn contrast to patient-reported health status measures (such as the Kansas City Cardiomyopathy Questionnaire), the New York Heart Association class is based on a physician's assessment of heart failure symptoms and functional limitations on behalf of the patient. We sought to determine the concordance and predictors of physician under- and overestimation of symptoms prior to and after transcatheter aortic valve replacement (TAVR).Methods and resultsThe analytic cohort included 172 667 patients within the Society of Thoracic Surgeons/American College of Cardiology Transcatheter Valve Therapy Registry who underwent transfemoral TAVR. At baseline, physicians underestimated patients’ symptoms in 47.4%, correctly assessed symptoms in 26.6%, and overestimated symptoms in 26.0%. At 30 days after TAVR, these proportions were 22.8%, 50.3%, and 26.9%, respectively. Using nominal logistic regression with random intercepts to account for within-hospital clustering, we found that physicians were more likely to incorrectly estimate patients’ symptoms when patients were older, women, had a prior stroke, had severe lung disease, had atrial fibrillation, or were more obese. There was marked variability in the rates of underestimation, correct estimation, and overestimation across the 641 sites.ConclusionAmong patients undergoing treatment for severe aortic stenosis, physicians estimate patients’ symptoms and functional status poorly both prior to and after TAVR, with different patterns. These findings emphasize the need to collect patient-reported health status to more reliably assess the benefits of TAVR in routine clinical practice.
Outcomes in very low birthweight infants with severe congenital heart defect following cardiac surgery within the first year of life
Authors: Boos Vinzenz , Berger Felix , Cho Mi-Young , Photiadis Joachim , Bührer Christoph , Pfitzer Constanze 
Published: October 2021

Abstract

OBJECTIVES
Very low birthweight (&lt;1500 g, VLBW) infants with severe congenital heart defect (CHD) are at increased risk for perinatal and operative mortality. This study aims to describe morbidity, long-term mortality and neuro-developmental outcome in early childhood in VLBW infants who received cardiac surgery for severe CHD within 1 year after birth.

METHODS
Monocentric observational study on VLBW infants with severe CHD born between 2008 and 2017. Neurodevelopmental impairment at 2 years corrected age was defined as cognitive deficit, cerebral palsy or major neurosensory deficit.

RESULTS
A total of 24 patients were included. Twenty-one (87.5%) infants underwent cardiac surgery with hypothermia during cardiopulmonary bypass (median temperature 30.3°C, interquartile range 27.0–32.0°C) at a median age of 96 (40–188) days. Seven (29.2%, 95% confidence interval 14.9–49.2%) patients died within the first year after cardiac surgery. Survival rates decreased with increasing STAT mortality category of the surgical procedure. Neurodevelopmental impairment at 2 years of corrected age was found in 9 out of 17 (52.9%) surviving infants, with 8 infants (47.1%) presenting with a cognitive deficit or delay and 4 infants (23.5%) being diagnosed with cerebral palsy. Survival without neuro-developmental impairment was 29.2% (n = 7, 95% confidence interval 14.9–49.2%) in the entire study cohort. Eighty percent of the newborns with dextro-transposition of the great arteries, but no patient with univentricular anatomy, survived without neuro-developmental impairment.

CONCLUSIONS
Individual VLBW infants with severe CHD may develop well despite the high combined risk for adverse outcomes. The type of cardiac malformation may affect early- and long-term outcomes.
Out-of-Pocket Health Expenditures and Health Care Services Use Among Older Americans With Cognitive Impairment: Results From the 2008–2016 Health and Retirement Study
Authors: Jenkins Derek , Stickel Ariana , González Hector M , Tarraf Wassim 
Published: October 2021

Abstract

Background and Objectives
The evidence base on health services use and cost burdens associated with transition to severe cognitive impairment (SCI) and dementia is underdeveloped. We examine how the change in cognitive impairment status influences nursing home use, hospitalizations, and out-of-pocket (OOP) expenditures.

Research Design and Methods
We use prospective data from the Health and Retirement Study (2007/2008–2015/2016) on adults 70 years and older meeting research criteria for cognitive impairment not dementia (CIND) at baseline (unweighted n = 1,692) to fit 2-part models testing how reversion to normal cognition, stability (CIND maintenance), and transition into SCI/dementia influence change in yearly nursing home use, hospitalizations, and OOP expenditures.

Results
Over 8 years, 5.9% reverted, 15.9% remained CIND, 14.9% transitioned to SCI/dementia, and 63.3% died. We observed substantial increases in the propensity of any nursing home use which were particularly pronounced among those who transitioned or died during follow-up and similar but less pronounced differences in patterns of inpatient hospitalizations. Average baseline OOP spending was similar among reverters ($1156 [95% confidence interval = 832–1,479]), maintainers ($1,145 [993–1,296]), and transitioners ($1,385 [1,041–1,730]). Individuals who died during follow-up spent $2,529 (2,101–2,957). By the eighth year of follow-up, spending among reverters increased to $1,402 (869–1,934) and $2,188 (1,402–2,974) and $8,988 (5,820–12,157) for maintainers and transitioners, respectively. Average spending at the wave preceding death was $7,719 (4,345–11,094). Estimates were only partly attenuated through adjustment to covariables.

Discussion and Implications
A better understanding of variations in health services use and cost burdens among individuals with mild cognitive impairment can help guide targeted care and financial planning.
Aneuploidy rates and morphokinetic parameters of embryos cultured in distinct culture media: a sibling oocyte study
Authors: Quinn Molly M , Marsh Philip , Ribeiro Salustiano , Simbulan Rhodel K , Hickman Cristina , Berntsen Jørgen , Rosen Mitchell P 
Published: October 2021

Abstract

STUDY QUESTION
Do embryos from sibling oocytes assigned to distinct single-step media culture systems demonstrate differences in early embryo development, morphokinectics or aneuploidy rates?

SUMMARY ANSWER
Embryo quality, morphokinetic parameters and aneuploidy rates from trophectoderm biopsy were similar between sibling embryos cultured in distinct media systems from the time of gamete isolation.

WHAT IS KNOWN ALREADY
Studies on the effect of commercially available embryo culture media systems have demonstrated inconsistent impact on human embryonic development, morphokinetics, aneuploidy rates and clinical outcomes. In addition, these studies have been primarily randomized at the level of the embryo or the patient to culture media.

STUDY DESIGN, SIZE, DURATION
Prospective sibling oocyte cohort derived from 200 subjects undergoing IVF at a tertiary academic medical center between February 2018 and November 2019.

PARTICIPANTS/MATERIALS, SETTING, METHODS
Sibling oocytes were allocated to Global® or SAGE® media system based upon laterality of ovary from which they were retrieved. All embryos were cultured in a time-lapse incubator. Blastocysts underwent trophectoderm biopsy for preimplantation genetic testing for aneuploidy using next-generation sequencing.

MAIN RESULTS AND THE ROLE OF CHANCE
One hundred twenty-seven subjects (n = 127) had paired blastocysts for biopsy in each culture media system. There was no difference in top quality blastocyst formation (47.1 ± 31.0 vs 48.1 ± 27.2%; P = 0.87) nor aneuploidy rate (62.3 ± 34.0 vs 56.1 ± 34.4%; P = 0.07) for sibling embryos cultured in Global versus SAGE media system. Embryo morphokinetic parameters including time to each cell division from two cells (t2) to eight cells (t8), time to morula stage (tM), time to blastocele formation (tSB), time to fully formed blastocyst (tB) and time to expansion of the blastocyst (tEB) were similar between paired blastocysts from each culture media system.

LIMITATIONS, REASONS FOR CAUTION
Pregnancy outcomes and offspring health data were not available for analysis.

WIDER IMPLICATIONS OF THE FINDINGS
Commercially available culture media may not have a differential impact on embryo development and blastocyst aneuploidy rate when patient and stimulation-related factors are held constant.

STUDY FUNDING/COMPETING INTEREST(s)
There was no external funding for this study. C.H. is owner of a consultancy company, IVF Professionals, Chief Scientific Officer at Apricity, Executive Director at TMRW and co-owner and shareholder of Aria Fertility. She has received speaker fees, consulting fees and travel support from Cooper Surgical and Vitrolife. J.B. is an employee and shareholder of vitrolife.

TRIAL REGISTRATION NUMBER
N/A.
The abortion jurisprudence in Brazil: An analysis of ADPF 54 from feminist equality-based perspectives
Authors: Penteado Taís 
Published: October 2021

Abstract
Building on the feminist legal theory-driven analysis of equality-based approaches to voluntary abortion, this article offers a critical reading of the Brazilian Supreme Court decision on ADPF 54, the constitutional lawsuit that challenged the constitutionality of the application of the legislation that prohibits abortion in cases of fetal anencephaly. The article first presents the arguments and then offers feminist equality-based counterpoints that bring some vulnerabilities of the decision to the forefront. The article argues that, from the perspectives adopted, the arguments presented by the justices in ADPF 54 do not disrupt the logic that underlies the abortion prohibition norm and end up legitimizing it. Second, the principles used can be viewed skeptically. By missing inequality issues that permeate reproduction, the principles obscure power relations and as such, become potential tools for furthering inequalities. We conclude the article by delineating how, despite being cited only timidly as a precedent, ADPF 54 still resonates in other minor cases put before the Brazilian Supreme Court, imbuing them with the same set of problems. Having in mind the vulnerabilities of the arguments, the article makes a tentative normative assessment on how the use of a substantive equality principle as an analytical tool and guide for interpretation could mitigate the problems and offer responses with emancipatory potential.
Incidence, follow-up and outcomes of incidental abdominal aortic aneurysms in computed tomography
Authors: Sevil Fehim Can , Tort Mehmet , Özer Gökaslan Çiğdem , Sevil Hülya , Becit Necip 
Published: October 2021

Abstract

OBJECTIVES
The goal of our study was to determine the prevalence of abdominal aortic aneurysms (AAAs) that were incidentally diagnosed by computed tomography applied for different reasons and to discuss the risk factors that may cause AAA.

METHODS
A total of 5396 abdominal computed tomography examinations were performed, and the 103 incidentally detected AAAs were included in the study. Patients with and without AAA were compared in terms of age, gender, thoracic and abdominal aortic diameters and comorbid diseases.

RESULTS
The prevalence of the AAAs was 1.9%. Old age and male gender were significantly different between the groups (P &lt; 0.001). The reason for applying computed tomography in 52 (50.5%) patients with AAA was associated with malignancy. In the evaluation of all patients in the study, the aortic diameter was determined to be larger in patients with malignancy than in patients without malignancy (18.07 ± 4.1 mm vs 17.7 ± 3.9 mm, respectively; P &lt; 0.001). The thoracic aortic diameter was wider in patients with AAA compared to that in patients without AAA (37.2 ± 3.9 mm vs 33.9 ± 5.2 mm, respectively; P &lt; 0.001). The presence of coronary artery disease, diabetes mellitus, hypertension and a history of smoking in patients with AAA was significantly different from that of patients without AAA (P &lt; 0.001). There was no significant difference between the groups in terms of hyperlipidaemia and chronic obstructive pulmonary disease (P = 0.52 and P = 0.15, respectively).

CONCLUSIONS
Screening of older men with diseases such as malignancy, hypertension, diabetes mellitus and coronary artery disease for AAA is important for the early diagnosis and treatment of this disease.
HIV-1-RNA and total HIV-1-DNA loads in the genital compartment in men receiving dolutegravir- versus darunavir-based combined ART (cART) regimens during primary HIV infection
Authors: Mariaggi Alice-Andrée , Bauer Rebecca , Charre Caroline , Gardiennet Elise , Meiffredy Vincent , Ajana Faiza , Lacombe Karine , Pialoux Gilles , Cua Eric , Rouzioux Christine , Meyer Laurence , Cheret Antoine , Avettand-Fenoel Véronique 
Published: October 2021

Abstract

Background
Dolutegravir is a widespread integrase strand-transfer inhibitor (INSTI) recommended for treatment of primary HIV infection (PHI). PHI is a high-risk stage for sexual transmission because of the high viral load in semen. Yet dolutegravir concentrations in semen are lower than in blood during chronic treatment.

Objectives
To compare the kinetics of HIV-RNA and total HIV-DNA in the genital compartment in subjects receiving either tenofovir/emtricitabine/dolutegravir or tenofovir/emtricitabine/darunavir/cobicistat as a first-line combined ART (cART) at the time of PHI.

Patients and methods
Eighteen subjects receiving tenofovir/emtricitabine/dolutegravir and 19 receiving tenofovir/emtricitabine/darunavir/cobicistat enrolled in the ANRS169 OPTIPRIM-2 trial participated in the genital substudy.

Results
Between week (W) 0 and W2 HIV-RNA in seminal plasma (SP) decreased by 1 log10 copies/mL. Undetectable SP HIV-RNA was achieved in similar proportions between the two regimens at each timepoint. Overall, eight patients still presented detectable HIV-RNA or HIV-DNA in semen at W48; 15.4% and 28.6% presented detectable HIV-RNA and 9.1% and 14.3% presented detectable HIV-DNA in dolutegravir- and darunavir-based cART groups, respectively, with no significant difference.

Conclusions
For the first time, to the best of our knowledge, we showed that a dolutegravir-based regimen initiated as soon as PHI reduces HIV-RNA and HIV-DNA with no difference compared with a control group receiving a darunavir-based regimen. Although the viral purge in semen seems longer after treatment in PHI than CHI, due to high viral loads, early dolutegravir-based treatment initiation permits a major decay of both viral particles and infected cells in semen, efficiently reducing the high risk of transmission during PHI.