bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigating Sexual Dimorphism of Human White Matter in a Harmonized, Multisite Diffusion Magnetic Resonance Imaging Study
Authors: Seitz Johanna , Cetin-Karayumak Suheyla , Lyall Amanda , Pasternak Ofer , Baxi Madhura , Vangel Mark , Pearlson Godfrey , Tamminga Carol , Sweeney John , Clementz Brett , Schretlen David , Viher Petra Verena , Stegmayer Katharina , Walther Sebastian , Lee Jungsun , Crow Tim , James Anthony , Voineskos Aristotle , Buchanan Robert W , Szeszko Philip R , Malhotra Anil , Keshavan Matcheri , Koerte Inga K , Shenton Martha E , Rathi Yogesh , Kubicki Marek 
Published: July 2020

Abstract
Axonal myelination and repair, critical processes for brain development, maturation, and aging, remain controlled by sexual hormones. Whether this influence is reflected in structural brain differences between sexes, and whether it can be quantified by neuroimaging, remains controversial. Diffusion-weighted magnetic resonance imaging (dMRI) is an in vivo method that can track myelination changes throughout the lifespan. We utilize a large, multisite sample of harmonized dMRI data (n = 551, age = 9–65 years, 46% females/54% males) to investigate the influence of sex on white matter (WM) structure. We model lifespan trajectories of WM using the most common dMRI measure fractional anisotropy (FA). Next, we examine the influence of both age and sex on FA variability. We estimate the overlap between male and female FA and test whether it is possible to label individual brains as male or female. Our results demonstrate regionally and spatially specific effects of sex. Sex differences are limited to limbic structures and young ages. Additionally, not only do sex differences diminish with age, but tracts within each subject become more similar to one another. Last, we show the high overlap in FA between sexes, which implies that determining sex based on WM remains open.
Resting-State Fluctuations Underlie Free and Creative Verbal Behaviors in the Human Brain
Authors: Broday-Dvir Rotem , Malach Rafael 
Published: July 2020

Abstract
Resting-state fluctuations are ubiquitous and widely studied phenomena of the human brain, yet we are largely in the dark regarding their function in human cognition. Here we examined the hypothesis that resting-state fluctuations underlie the generation of free and creative human behaviors. In our experiment, participants were asked to perform three voluntary verbal tasks: a verbal fluency task, a verbal creativity task, and a divergent thinking task, during functional magnetic resonance imaging scanning. Blood oxygenation level dependent (BOLD)-activity during these tasks was contrasted with a control- deterministic verbal task, in which the behavior was fully determined by external stimuli. Our results reveal that all voluntary verbal-generation responses displayed a gradual anticipatory buildup that preceded the deterministic control-related responses. Critically, the time–frequency dynamics of these anticipatory buildups were significantly correlated with resting-state fluctuations’ dynamics. These correlations were not a general BOLD-related or verbal-response related result, as they were not found during the externally determined verbal control condition. Furthermore, they were located in brain regions known to be involved in language production, specifically the left inferior frontal gyrus. These results suggest a common function of resting-state fluctuations as the neural mechanism underlying the generation of free and creative behaviors in the human cortex.
SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission
Authors: Harilal Divinlal , Ramaswamy Sathishkumar , Loney Tom , Suwaidi Hanan Al , Khansaheb Hamda , Alkhaja Abdulmajeed , Varghese Rupa , Deesi Zulfa , Nowotny Norbert , Alsheikh-Ali Alawi , Abou Tayoun Ahmad 
Published: July 2020

Abstract

Background
With the gradual reopening of economies and resumption of social life, robust surveillance mechanisms should be implemented to control the ongoing COVID-19 pandemic. Unlike RT-qPCR, SARS-CoV-2 whole genome sequencing (cWGS) has the added advantage of identifying cryptic origins of the virus, and the extent of community-based transmissions versus new viral introductions, which can in turn influence public health policy decisions. However, the practical and cost considerations of cWGS should be addressed before it is widely implemented.

Methods
We performed shotgun transcriptome sequencing using RNA extracted from nasopharyngeal swabs of patients with COVID-19, and compared it to targeted SARS-CoV-2 genome amplification and sequencing with respect to virus detection, scalability, and cost-effectiveness. To track virus origin, we used open-source multiple sequence alignment and phylogenetic tools to compare the assembled SARS-CoV-2 genomes to publicly available sequences.

Results
We found considerable improvement in whole genome sequencing data quality and viral detection using amplicon-based target enrichment of SARS-CoV-2. With enrichment, more than 99% of the sequencing reads mapped to the viral genome, compared to an average of 0.63% without enrichment. Consequently, an increase in genome coverage was obtained using substantially less sequencing data, enabling higher scalability and sizable cost reductions. We also demonstrated how SARS-CoV-2 genome sequences can be used to determine their possible origin through phylogenetic analysis including other viral strains.

Conclusions
SARS-CoV-2 whole genome sequencing is a practical, cost-effective, and powerful approach for population-based surveillance and control of viral transmission in the next phase of the COVID-19 pandemic.
Endothelial dysfunction in COVID-19: a position paper of the ESC Working Group for Atherosclerosis and Vascular Biology, and the ESC Council of Basic Cardiovascular Science
Authors: Evans Paul C , Rainger G Ed , Mason Justin C , Guzik Tomasz J , Osto Elena , Stamataki Zania , Neil Desley , Hoefer Imo E , Fragiadaki Maria , Waltenberger Johannes , Weber Christian , Bochaton-Piallat Marie-Luce , Bäck Magnus 
Published: July 2020

Abstract
The COVID-19 pandemic is an unprecedented healthcare emergency causing mortality and illness across the world. Although primarily affecting the lungs, the SARS-CoV-2 virus also affects the cardiovascular system. In addition to cardiac effects, e.g. myocarditis, arrhythmias, and myocardial damage, the vasculature is affected in COVID-19, both directly by the SARS-CoV-2 virus, and indirectly as a result of a systemic inflammatory cytokine storm. This includes the role of the vascular endothelium in the recruitment of inflammatory leucocytes where they contribute to tissue damage and cytokine release, which are key drivers of acute respiratory distress syndrome (ARDS), in disseminated intravascular coagulation, and cardiovascular complications in COVID-19. There is also evidence linking endothelial cells (ECs) to SARS-CoV-2 infection including: (i) the expression and function of its receptor angiotensin-converting enzyme 2 (ACE2) in the vasculature; (ii) the prevalence of a Kawasaki disease-like syndrome (vasculitis) in COVID-19; and (iii) evidence of EC infection with SARS-CoV-2 in patients with fatal COVID-19. Here, the Working Group on Atherosclerosis and Vascular Biology together with the Council of Basic Cardiovascular Science of the European Society of Cardiology provide a Position Statement on the importance of the endothelium in the underlying pathophysiology behind the clinical presentation in COVID-19 and identify key questions for future research to address. We propose that endothelial biomarkers and tests of function (e.g. flow-mediated dilatation) should be evaluated for their usefulness in the risk stratification of COVID-19 patients. A better understanding of the effects of SARS-CoV-2 on endothelial biology in both the micro- and macrovasculature is required, and endothelial function testing should be considered in the follow-up of convalescent COVID-19 patients for early detection of long-term cardiovascular complications.
Genome sequencing of four culinary herbs reveals terpenoid genes underlying chemodiversity in the Nepetoideae
Authors: Bornowski Nolan , Hamilton John P , Liao Pan , Wood Joshua C , Dudareva Natalia , Buell C Robin 
Published: July 2020

Abstract
Species within the mint family, Lamiaceae, are widely used for their culinary, cultural, and medicinal properties due to production of a wide variety of specialized metabolites, especially terpenoids. To further our understanding of genome diversity in the Lamiaceae and to provide a resource for mining biochemical pathways, we generated high-quality genome assemblies of four economically important culinary herbs, namely, sweet basil (Ocimum basilicum L.), sweet marjoram (Origanum majorana L.), oregano (Origanum vulgare L.), and rosemary (Rosmarinus officinalis L.), and characterized their terpenoid diversity through metabolite profiling and genomic analyses. A total 25 monoterpenes and 11 sesquiterpenes were identified in leaf tissue from the 4 species. Genes encoding enzymes responsible for the biosynthesis of precursors for mono- and sesqui-terpene synthases were identified in all four species. Across all 4 species, a total of 235 terpene synthases were identified, ranging from 27 in O. majorana to 137 in the tetraploid O. basilicum. This study provides valuable resources for further investigation of the genetic basis of chemodiversity in these important culinary herbs.
Inflammatory Bowel Disease Management During the COVID-19 Outbreak: The Ten Do’s and Don’ts from the ECCO-COVID Taskforce
Authors: Magro F , Rahier J-F , Abreu C , MacMahon E , Hart A , van der Woude C J , Gordon H , Adamina M , Viget N , Vavricka S , Kucharzik T , Leone S , Siegmund B , Danese S , Peyrin-Biroulet L 
Published: July 2020

AbstractOur knowledge of COVID-19 is changing and evolving rapidly, with novel insights and recommendations, almost on a daily basis. It behooves the medical community to provide updated information on a regular basis, on best practice to facilitate optimal care of infected patients and on appropriate advice for the general population. This is particularly important in the case of patients with chronic conditions, such as inflammatory bowel disease [IBD]. In this review, we have compiled existing evidence on the impact of COVID-19 in IBD patients and provide guidance on the most appropriate care to adopt during the pandemic. Our review highlights that IBD, per se, is not a risk factor for COVID-19. However, all IBD patients with symptoms should be tested for SARS-CoV-2 and the procedures for disease management should be carefully adapted: [i] in SARS-CoV-2-positive IBD patients, medical treatments should be re-evaluated [with a particular focus on corticosteroids] always with the purpose of treating active disease and maintaining remission; [ii] non-urgent surgeries and endoscopic procedures should be postponed for all patients; [iii] online consultancy should be implemented; and [iv] hospitalization and surgery should be limited to life-threatening situations.
Spontaneous pneumothorax and subpleural bullae in a patient with COVID-19: a 92-day observation
Authors: Fan Qianqian , Pan Feng , Yang Lian 
Published: July 2020

Abstract
This report describes a patient with COVID-19 who developed spontaneous pneumothorax and subpleural bullae during the course of the infection. Consecutive chest computed tomography images indicated that COVID-19-associated pneumonia had damaged the subpleural alveoli and distal bronchus. Coughing might have induced a sudden increase in intra-alveolar pressure, leading to the rupture of the subpleural alveoli and distal bronchus and resulting in spontaneous pneumothorax and subpleural bullae. At the 92-day follow-up, the pneumothorax and subpleural bullae had completely resolved, which indicated that these complications had self-limiting features.
Perioperative outcomes of segmentectomies versus lobectomies in high-risk patients: an ESTS database analysis
Authors: Brunelli Alessandro , Decaluwe Herbert , Gossot Dominique , Guerrera Francesco , Szanto Zalan , Falcoz Pierre Emmanuel 
Published: July 2020

Abstract

OBJECTIVES
We queried the European Society of Thoracic Surgeons (ESTS) database with the aim to assess cardiopulmonary morbidity and 30-day mortality of segmentectomies and lobectomies in patients with a Eurolung-predicted mortality above the upper interquartile and classified as high risk.

METHODS
A total of 61 492 patients registered in the ESTS database (2007–2018) and submitted to lobectomy (55 353) or segmentectomy (6139) were divided into high risk or low risk according to a Eurolung-predicted mortality cut-off of 2.5% (corresponding in our population to the upper interquartile). Predicted versus observed mortalities were compared within each type of operation by using binomial test of proportion. Observed morbidity and mortality rates were compared between the 2 procedures using the χ2 test.

RESULTS
A total of 14 007 lobectomies and 1251 segmentectomies were classified as high risk. In the high-risk group, the cardiopulmonary morbidity and 30-day mortality rates observed in segmentectomies were lower than in lobectomies (morbidity: 12% vs 17%, P &lt; 0.0001; mortality: 2.4% vs 3.7%, P = 0.018). In segmentectomy patients, the observed mortality rate was lower than the Eurolung-predicted one (2.4% vs 3.8%, P = 0.009), while in the lobectomy patients, there was no difference between observed and predicted mortality (3.7% vs 3.8%, P = 0.9). In the low-risk group, the cardiopulmonary morbidity and 30-day mortality rates observed in segmentectomies were lower than in lobectomies (morbidity: 4.5% vs 7.8%, P &lt; 0.0001; mortality: 0.6% vs 1.0%, P = 0.01). In segmentectomy patients, the observed mortality rate was lower than the Eurolung-predicted one (0.6% vs 1.0%, P = 0.0003), while in the lobectomy patients, there was no difference between observed and predicted mortality (1.0% vs 1.1%, P = 0.06).

CONCLUSIONS
Segmentectomy was found associated with a 0.65 relative risk of mortality rate compared to lobectomy in patients deemed at higher surgical risk.
Characterization of the β-glucuronidase Pn3Pase as the founding member of glycoside hydrolase family GH169
Authors: Wantuch Paeton L , Jella Satya , Duke Jeremy A , Mousa Jarrod J , Henrissat Bernard , Glushka John , Avci Fikri Y 
Published: July 2020

AbstractPaenibacillus sp. 32352 is a soil-dwelling bacterium capable of producing an enzyme, Pn3Pase that degrades the capsular polysaccharide of Streptococcus pneumoniae serotype 3 (Pn3P). Recent reports on Pn3Pase have demonstrated its initial characterization and potential for protection against highly virulent S. pneumoniae serotype 3 infections. Initial experiments revealed this enzyme functions as an exo-β1,4-glucuronidase cleaving the β(1,4) linkage between glucuronic acid and glucose. However, the catalytic mechanism of this enzyme is still unknown. Here, we report the detailed biochemical analysis of Pn3Pase. Pn3Pase shows no significant sequence similarity to known glycoside hydrolase (GH) families, thus this novel enzyme establishes a new carbohydrate-active enzyme (CAZy) GH family. Site-directed mutagenesis studies revealed two catalytic residues along with truncation mutants defining essential domains for function. Pn3Pase and its mutants were screened for activity, substrate binding and kinetics. Additionally, nuclear magnetic resonance spectroscopy analysis revealed that Pn3Pase acts through a retaining mechanism. This study exhibits Pn3Pase activity at the structural and mechanistic level to establish the new CAZy GH family GH169 belonging to the large GH-A clan. This study will also serve toward generating Pn3Pase derivatives with optimal activity and pharmacokinetics aiding in the use of Pn3Pase as a novel therapeutic approach against type 3 S. pneumoniae infections.
Disruption of foxc1 genes in zebrafish results in dosage-dependent phenotypes overlapping Axenfeld-Rieger syndrome
Authors: Ferre-Fernández Jesús-José , Sorokina Elena A , Thompson Samuel , Collery Ross F , Nordquist Emily , Lincoln Joy , Semina Elena V 
Published: July 2020

Abstract
The Forkhead Box C1 (FOXC1) gene encodes a forkhead/winged helix transcription factor involved in embryonic development. Mutations in this gene cause dysgenesis of the anterior segment of the eye, most commonly Axenfeld-Rieger syndrome (ARS), often with other systemic features. The developmental mechanisms and pathways regulated by FOXC1 remain largely unknown. There are two conserved orthologs of FOXC1 in zebrafish, foxc1a and foxc1b. To further examine the role of FOXC1 in vertebrates, we generated foxc1a and foxc1b single knockout zebrafish lines and bred them to obtain various allelic combinations. Three genotypes demonstrated visible phenotypes: foxc1a−/− single homozygous and foxc1−/− double knockout homozygous embryos presented with similar characteristics comprised of severe global vascular defects and early lethality, as well as microphthalmia, periocular edema and absence of the anterior chamber of the eye; additionally, fish with heterozygous loss of foxc1a combined with homozygosity for foxc1b (foxc1a+/−;foxc1b−/−) demonstrated craniofacial defects, heart anomalies and scoliosis. All other single and combined genotypes appeared normal. Analysis of foxc1 expression detected a significant increase in foxc1a levels in homozygous and heterozygous mutant eyes, suggesting a mechanism for foxc1a upregulation when its function is compromised; interestingly, the expression of another ARS-associated gene, pitx2, was responsive to the estimated level of wild-type Foxc1a, indicating a possible role for this protein in the regulation of pitx2 expression. Altogether, our results support a conserved role for foxc1 in the formation of many organs, consistent with the features observed in human patients, and highlight the importance of correct FOXC1/foxc1 dosage for vertebrate development.
The Human Right to Land, for Peasants and for All: Tracing the Social Function of Property to 1948
Authors: Heri Corina 
Published: July 2020

ABSTRACT
In 1948, Article 17 of the Universal Declaration of Human Rights (UDHR) pioneered a right to (individual and collective) ownership of property. Today, the right to property—specifically the social function of property, which was a mainstay of the discussions—can be linked to the idea of a human right to land, which has been particularly prevalent in the discourse concerning the creation of human rights protections specific to peasants. The peasant rights process highlights a number of normative and implementation gaps in international human rights law, including relating to land use and tenure. The present contribution will argue that the claims made in this context are neither new nor niche but relate to universal human rights entitlements and have existed at least since the drafting of the UDHR. They are not only an iteration of an age-old class struggle but are at the forefront of a contemporary critique of the existing international legal system as a whole. While existing human rights, including the right to property, can be part of a response to these critiques, however, neither peasant rights nor the activists who promote them can be expected to resolve them alone.
Error-based output tracking for a one-dimensional wave equation with harmonic type disturbance
Authors: Tian Ziqing , Wu Xiao-Hui 
Published: July 2020

Abstract
In this paper, we consider output tracking for a one-dimensional wave equation, where the boundary disturbances are either collocated or non-collocated with control. The regulated output and the control are supposed to be non-collocated with control, which represents a difficult case for output tracking of PDEs. We apply the trajectory planning approach to design an observer, in terms of tracking error only, to estimate both states of the system and the exosystem from which the disturbances are produced. An error-based feedback control is proposed by solving a standard regulator equation. It is shown that (a) the closed-loop system is uniformly bounded whenever the exosystem is bounded; (b) when the disturbance is zero, the closed-loop is asymptotically stable; and (c) the tracking error converges to zero asymptotically as time goes to infinity. Numerical simulations are performed to validate the effectiveness of the proposed control.
Broad Antibody and Cellular Immune Response From a Phase 2 Clinical Trial With a Novel Multivalent Poxvirus-Based Respiratory Syncytial Virus Vaccine
Authors: Jordan Elke , Lawrence Steven J , Meyer Thomas P H , Schmidt Darja , Schultz Stephanie , Mueller Jutta , Stroukova Daria , Koenen Brigitte , Gruenert Robert , Silbernagl Guenter , Vidojkovic Sanja , Chen Liddy M , Weidenthaler Heinz , Samy Nathaly , Chaplin Paul 
Published: July 2020

Abstract

Background
Respiratory syncytial virus (RSV) is a major cause of severe respiratory disease in young children and the elderly. Protective immunity is not generated after repeated infections, but vaccination may hopefully prove effective.

Methods
This phase 2 clinical study investigated a multivalent RSV vaccine (MVA-BN-RSV) designed to induce broad antibody and cellular immune responses by encoding RSV surface proteins F, G (for both A and B subtypes), and internal antigens (M2, N). This study evaluated the immune response in adults aged ≥55 years to identify the optimal MVA-BN-RSV dose and vaccination schedule.

Results
A single dose increased the levels of neutralizing (plaque reduction neutralization test to RSV A and B) and total (IgG and IgA ELISA) antibodies (1.6 to 3.4-fold increase from baseline) and induced a broad Th1-biased cellular immune response (interferon-γ ELISPOT) to all 5 vaccine inserts (5.4 to 9.7-fold increases). Antibody responses remained above baseline for 6 months. A 12-month booster dose elicited a booster effect in antibody and T-cell responses (up to 2.8-fold from preboost levels). No drug-related serious adverse events were reported.

Conclusions
MVA-BN-RSV induces a broad immune response that persists at least 6 months and can be boosted at 12 months, without significant safety findings.

Clinical Trials Registration
NCT02873286
Human Respiratory Syncytial Virus-Induced Immune Signature of Infection Revealed by Transcriptome Analysis of Clinical Pediatric Nasopharyngeal Swab Samples
Authors: Nicolas De Lamballerie Claire , Pizzorno Andrés , Dubois Julia , Padey Blandine , Julien Thomas , Traversier Aurélien , Carbonneau Julie , Orcel Elody , Lina Bruno , Hamelin Marie-Eve , Roche Magali , Textoris Julien , Boivin Guy , Legras-Lachuer Catherine , Terrier Olivier , Rosa-Calatrava Manuel 
Published: July 2020

Abstract
Human respiratory syncytial virus (HRSV) constitutes one the main causes of respiratory infection in neonates and infants worldwide. Transcriptome analysis of clinical samples using high-throughput technologies remains an important tool to better understand virus-host complex interactions in the real-life setting but also to identify new diagnosis/prognosis markers or therapeutics targets. A major challenge when exploiting clinical samples such as nasal swabs, washes, or bronchoalveolar lavages is the poor quantity and integrity of nucleic acids. In this study, we applied a tailored transcriptomics workflow to exploit nasal wash samples from children who tested positive for HRSV. Our analysis revealed a characteristic immune signature as a direct reflection of HRSV pathogenesis and highlighted putative biomarkers of interest such as IP-10, TMEM190, MCEMP1, and TIMM23.