bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete lung agenesis caused by complex genomic rearrangements with neo-TAD formation at the SHH locus
Authors: Melo Uirá Souto , Piard Juliette , Fischer-Zirnsak Björn , Klever Marius-Konstantin , Schöpflin Robert , Mensah Martin Atta , Holtgrewe Manuel , Arbez-Gindre Francine , Martin Alain , Guigue Virginie , Gaillard Dominique , Landais Emilie , Roze Virginie , Kremer Valerie , Ramanah Rajeev , Cabrol Christelle , Harms Frederike L. , Kornak Uwe , Spielmann Malte , Mundlos Stefan , Van Maldergem Lionel 
Published: August 2021

AbstractDuring human organogenesis, lung development is a timely and tightly regulated developmental process under the control of a large number of signaling molecules. Understanding how genetic variants can disturb normal lung development causing different lung malformations is a major goal for dissecting molecular mechanisms during embryogenesis. Here, through exome sequencing (ES), array CGH, genome sequencing (GS) and Hi-C, we aimed at elucidating the molecular basis of bilateral isolated lung agenesis in three fetuses born to a non-consanguineous family. We detected a complex genomic rearrangement containing duplicated, triplicated and deleted fragments involving the SHH locus in fetuses presenting complete agenesis of both lungs and near-complete agenesis of the trachea, diagnosed by ultrasound screening and confirmed at autopsy following termination. The rearrangement did not include SHH itself, but several regulatory elements for lung development, such as MACS1, a major SHH lung enhancer, and the neighboring genes MNX1 and NOM1. The rearrangement incorporated parts of two topologically associating domains (TADs) including their boundaries. Hi-C of cells from one of the affected fetuses showed the formation of two novel TADs each containing SHH enhancers and the MNX1 and NOM1 genes. Hi-C together with GS indicate that the new 3D conformation is likely causative for this condition by an inappropriate activation of MNX1 included in the neo-TADs by MACS1 enhancer, further highlighting the importance of the 3D chromatin conformation in human disease.
Impaction of regurgitation jet on anterior mitral leaflet is associated with diastolic dysfunction in patients with bicuspid aortic valve and mild insufficiency: a cardiovascular magnetic resonance study
Authors: Galea Nicola , Pambianchi Giacomo , Cundari Giulia , Sturla Francesco , Marchitelli Livia , Putotto Carolina , Versacci Paolo , De Paulis Ruggero , Francone Marco , Catalano Carlo 
Published: August 2021

AbstractTo assess the impact of regurgitant jet direction on left ventricular function and intraventricular hemodynamics in asymptomatic patients with bicuspid aortic valve (BAV) and mild aortic valve regurgitation (AR), using cardiac magnetic resonance (CMR) feature tracking and 4D flow imaging. Fifty BAV individuals were retrospectively selected: 15 with mild AR and posterior regurgitation jet (Group-PJ), 15 with regurgitant jet in other directions (Group-nPJ) and 20 with no regurgitation (Controls). CMR protocol included cine steady state free precession (SSFP) sequences and 4D Flow imaging covering the entire left ventricle (LV) cavity and the aortic root. Cine-SSFP images were analyzed to assess LV volumes, longitudinal and circumferential myocardial strain. Circumferential and longitudinal peak diastolic strain rate (PDSR) and peak diastolic velocity (PDV) were reduced in group PJ if compared to group nPJ and control group (PDSR = 1.10 ± 0.2 1/s vs. 1.34 ± 0.5 1/s vs. 1.53 ± 0.3 1/s, p:0.001 and 0.68 ± 0.2 1/s vs. 1.17 ± 0.2 1/s vs. 1.05 ± 0.4 1/s ; p < 0.001, PDV = − 101.6 ± 28.1 deg/s vs. − 201.4 ± 85.9 deg/s vs. − 221.6 ± 67.1 deg/s; p < 0.001 and − 28.1 ± 8 mm/s vs. − 38.9 ± 11.1 mm/s vs. − 43.6 ± 14.3 mm/s, p < 0.001, respectively), whereas no differences have been found in systolic strain values. 4D Flow images (available only in 9 patients) showed deformation of diastolic transmitral streamlines direction in group PJ compared to other groups. In BAV patients with mild AR, the posterior direction of the regurgitant jet may hamper the complete mitral valve opening, disturbing transmitral flow and slowing the LV diastolic filling.
Extreme longevity variants at the FOXO3 locus may moderate FOXO3 isoform levels
Authors: Frankum Ryan , Jameson Tom S. O. , Knight Bridget A. , Stephens Francis B. , Wall Benjamin T. , Donlon Timothy A. , Torigoe Trevor , Willcox Bradley J. , Willcox D. Craig , Allsopp Richard C. , Harries Lorna W. 
Published: August 2021

AbstractThe rs2802292, rs2764264 and rs13217795 variants of FOXO3 have been associated with extreme longevity in multiple human populations, but the mechanisms underpinning this remain unclear. We aimed to characterise potential effects of longevity-associated variation on the expression and mRNA processing of the FOXO3 gene. We performed a comprehensive assessment of FOXO3 isoform usage across a wide variety of human tissues and carried out a bioinformatic analysis of the potential for longevity-associated variants to disrupt regulatory regions involved in isoform choice. We then related the expression of full length and 5′ truncated FOXO3 isoforms to rs13217795 genotype in peripheral blood and skeletal muscle from individuals of different rs13217795 genotypes. FOXO3 isoforms displayed considerable tissue specificity. We determined that rs13231195 and its tightly aligned proxy variant rs9400239 may lie in regulatory regions involved in isoform choice. The longevity allele at rs13217795 was associated with increased levels of full length FOXO3 isoforms in peripheral blood and a decrease in truncated FOXO3 isoforms in skeletal muscle RNA. We suggest that the longevity effect of FOXO3 SNPs may in part derive from a shift in isoform usage in skeletal muscle away from the production of 5′ truncated FOXO3 isoforms lacking a complete forkhead DNA binding domain, which may have compromised functionality.
Hunting colours: origin and reuse of glass tesserae from the Wierum terp
Authors: Crocco Rosa , Huisman Hans , Sablerolles Yvette , Henderson Julian , van Os Bertil , Nieuwhof Annet 
Published: August 2021

AbstractMosaic glass tesserae were imported to Dutch sites during the Early Medieval period, probably to address the demand for coloured glass needed in ornamental bead manufacture. Although challenging, because of the uncertainty of the material’s context, the Wierum Early Medieval collection represents an extraordinary opportunity, being the most significant find of glass tesserae in the Netherlands to date. The combined use of electron microprobe analysis (EMPA) and hand-held X-ray fluorescence spectrometry (HH XRF) allowed us to examine glass tesserae and other vitreous samples from the site. Low levels for magnesium and potassium oxides (<1.5 wt%) and the chemical components linked with the silica source, fluxes, opacifiers and chromophores are compatible with an older Roman soda-lime-silica glass production. Alumina and calcium oxide contents together with the adoption of antimony-based opacifiers are compatible with mosaic tesserae of a first to third century AD Roman tradition. We assume that these tesserae were collected during the spoliation of a lavish building and reused for glass objects produced locally. The hypothesis seems to be confirmed by the presence in the collection of tesserae still embedded in mortar, stone tesserae fragments and a rounded fragment of Egyptian blue.
Modelling and analysis of the stability of a harbour wharf’s embankment with regards to its failure
Authors: Dmochowski Grzegorz , Berkowski Piotr , Szołomicki Jerzy , Gronostajska Barbara , Krążelewski Jarosław 
Published: August 2021

Abstract
The article presents the process of creating a computational model for the stability analysis of a harbour wharf’s embankment with regards to its failure. The described elements that were taken into account at the stage of data preparation are: historical analysis of the structure (structural calculations, and the calculations of the stability of the embankment), results of the author’s own soil and material tests (concrete, steel), environmental conditions (atmospheric and water), the possible load systems that acted on the facility, and also the results from the 3D model of the wharf’s structure. On this basis, five computational schemes were prepared for computer simulations of the stability of the embankment in a plain state of deformations. Various stages and conditions of its operation were taken into account. In conclusion, a possible course of the process of destruction of the structure of the harbour wharf, and the river embankment that cooperates with it, was proposed.
Russia's return to Africa: a comparative study of Egypt, Algeria and Morocco
Authors: Němečková Tereza , Melnikovová Lea , Piskunova Natalia 
Published: August 2021

AbstractThe article analyses Russia's recent return to Africa. It attempts to answer the question to what extent Russia has abandoned its traditional tools of cooperation such as nuclear energy and military cooperation and engaged in new ‘smart’ ones as indicated by former Foreign Minister Ivanov in 2011. The paper builds on three case studies of African countries having the largest trade volume with Russia in 2018, i.e. Egypt, Algeria and Morocco, and analyses their changing relationship with Russia over the last decade. The results show that Russia has not abandoned its traditional tools but has intensified the use of new ones. The North African region as such has regained significance in Russia's foreign policy. Bilateral relations with all three North African countries have increased at both political and economic levels recently.
A mixed-integer least-squares formulation of the GNSS snapshot positioning problem
Authors: Waserman Eyal , Toledo Sivan 
Published: August 2021

AbstractThis paper presents a formulation of snapshot positioning as a mixed-integer least-squares problem. In snapshot positioning, one estimates a position from code-phase (and possibly Doppler-shift) observations of global navigation satellite system (GNSS) signals without knowing the time of departure (timestamp) of the codes. Solving the problem allows a receiver to determine a fix from short radio-frequency snapshots missing the timestamp information embedded in the GNSS data stream. This is used to reduce the time to first fix in some receivers, and it is used in certain wildlife trackers. This paper presents two new formulations of the problem and an algorithm that solves the resulting mixed-integer least-squares problems. We also show that the new formulations can produce fixes even with huge initial errors, much larger than permitted in Van Diggelen's widely-cited coarse-time navigation method.
Detection of Major and Mild Neurocognitive Disorder with the Verbal Naming Test
Authors: Spalding-Wilson Kelsey , Harris Grant , Windham Victoria A. , Strutt Adriana M. , Yochim Brian P. 
Published: August 2021

AbstractObjective:The Verbal Naming Test (VNT) is an auditory-based measure of naming or word finding. The current multisite study sought to evaluate the reliability and validity of the VNT in the detection of major and mild neurocognitive disorder (NCD).Method:This study analyzed clinical data from two outpatient neuropsychology clinics (N = 188 and N = 77) and a geriatric primary care clinic (N = 104). Cronbach’s alpha and Spearman correlations with other measures were calculated. ROC analyses were used to calculate sensitivity, specificity, positive predictive power, and negative predictive power for the detection of major and mild NCD per DSM-5 (Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition) criteria.Results:The VNT was found to have strong reliability (Cronbach’s alpha = .90) and high convergent validity with a commonly used picture-naming task (NAB Naming, Spearman’s rho = .65, p < .001). The VNT showed good sensitivity and specificity for the detection of NCDs, particularly major NCD, with an area under the curve of .85, sensitivity of .80, and specificity of .75. A possible discontinue rule is also suggested for clinicians to use.Conclusions:These findings provide compelling evidence for the use of the VNT to detect neurocognitive impairment in a clinical setting. The VNT provides a reliable alternative to picture-naming tasks, which may be advantageous when working with visually impaired patients or conducting evaluations over telehealth.
Avatar-Based Self-Influence in a Traditional CMC Environment
Authors: Beyea David , Van der Heide Brandon , Ewoldsen David , Eden Allison , Meng Jingbo 
Published: August 2021

Abstract. Dubbed the Proteus effect, research has shown that avatars influence user behavior in virtual reality and video game environments ( Yee & Bailenson, 2007 , 2009 ); however, does this same effect occur in the less dynamic but more prevalent traditional computer-mediated communication (CMC)? As CMC evolves to allow user avatars, the question of its influence increases in importance. This study examines the Proteus effect in traditional CMC, which tends to be dominated by text-based communication. Embodiment is presented as a moderator for the Proteus effect. Two methods for inducing embodiment (via choice and via familiarizing tasks) were tested along with a proposed model for the Proteus effect in social media environments. A 2 (avatar) × 2 (embodiment by choice) × 2 (embodiment by familiarizing tasks) between-subject design with 406 participants showed a significant main effect of familiarizing tasks on embodiment, an interaction effect of avatar embodiment and avatar condition on aggressive behavior, and an unpredicted main effect of embodiment on aggressive attitude.
End‐Member Venusian Core Scenarios: Does Venus Have an Inner Core?
Authors: O'Neill Craig 
Published: August 2021

AbstractVenus's lack of a magnetic field suggests it may not have an inner core; however, evidence of Venus's internal density structure has historically been limited by its slow rotation. New moment of inertia (MoI) estimates allow us to constrain its internal density and thermal structure. Here, we use a mineral‐physics solver, and incorporate equations of state for silicate mantle minerals and core phases, to calculate radial density profiles for variable core and mantle compositions, and estimate the MoI and planetary mass, and optimal outer and inner core radii. For Earth‐like core compositions, our best fit radius for Venus's core is 3,147.1 ± 16.8 km, with no inner core—implying the liquid core has not cooled sufficiently to start crystallizing. However, for enriched light‐element concentrations in the core (>∼11 wt%), solutions fit large, light cores (∼4,000 km), and large inner cores (>∼2,000 km), underpinning the need for tighter cosmochemical/geophysical constraints on these endmembers.
Prefrontal cortex interactions with the amygdala in primates
Authors: Murray Elisabeth A. , Fellows Lesley K. 
Published: August 2021

AbstractThis review addresses functional interactions between the primate prefrontal cortex (PFC) and the amygdala, with emphasis on their contributions to behavior and cognition. The interplay between these two telencephalic structures contributes to adaptive behavior and to the evolutionary success of all primate species. In our species, dysfunction in this circuitry creates vulnerabilities to psychopathologies. Here, we describe amygdala–PFC contributions to behaviors that have direct relevance to Darwinian fitness: learned approach and avoidance, foraging, predator defense, and social signaling, which have in common the need for flexibility and sensitivity to specific and rapidly changing contexts. Examples include the prediction of positive outcomes, such as food availability, food desirability, and various social rewards, or of negative outcomes, such as threats of harm from predators or conspecifics. To promote fitness optimally, these stimulus–outcome associations need to be rapidly updated when an associative contingency changes or when the value of a predicted outcome changes. We review evidence from nonhuman primates implicating the PFC, the amygdala, and their functional interactions in these processes, with links to experimental work and clinical findings in humans where possible.
Prefrontal-hippocampal interactions supporting the extinction of emotional memories: the retrieval stopping model
Authors: Anderson Michael C. , Floresco Stan B. 
Published: August 2021

AbstractNeuroimaging has revealed robust interactions between the prefrontal cortex and the hippocampus when people stop memory retrieval. Efforts to stop retrieval can arise when people encounter reminders to unpleasant thoughts they prefer not to think about. Retrieval stopping suppresses hippocampal and amygdala activity, especially when cues elicit aversive memory intrusions, via a broad inhibitory control capacity enabling prepotent response suppression. Repeated retrieval stopping reduces intrusions of unpleasant memories and diminishes their affective tone, outcomes resembling those achieved by the extinction of conditioned emotional responses. Despite this resemblance, the role of inhibitory fronto-hippocampal interactions and retrieval stopping broadly in extinction has received little attention. Here we integrate human and animal research on extinction and retrieval stopping. We argue that reconceptualising extinction to integrate mnemonic inhibitory control with learning would yield a greater understanding of extinction’s relevance to mental health. We hypothesize that fear extinction spontaneously engages retrieval stopping across species, and that controlled suppression of hippocampal and amygdala activity by the prefrontal cortex reduces fearful thoughts. Moreover, we argue that retrieval stopping recruits extinction circuitry to achieve affect regulation, linking extinction to how humans cope with intrusive thoughts. We discuss novel hypotheses derived from this theoretical synthesis.
The microbiome extends host evolutionary potential
Authors: Henry Lucas P. , Bruijning Marjolein , Forsberg Simon K. G. , Ayroles Julien F. 
Published: August 2021

AbstractThe microbiome shapes many host traits, yet the biology of microbiomes challenges traditional evolutionary models. Here, we illustrate how integrating the microbiome into quantitative genetics can help untangle complexities of host-microbiome evolution. We describe two general ways in which the microbiome may affect host evolutionary potential: by shifting the mean host phenotype and by changing the variance in host phenotype in the population. We synthesize the literature across diverse taxa and discuss how these scenarios could shape the host response to selection. We conclude by outlining key avenues of research to improve our understanding of the complex interplay between hosts and microbiomes.
A TALE/HOX code unlocks WNT signalling response towards paraxial mesoderm
Authors: Mariani Luca , Guo Xiaogang , Menezes Niels Alvaro , Drozd Anna Maria , Çakal Selgin Deniz , Wang Qinhu , Ferretti Elisabetta 
Published: August 2021

AbstractOne fundamental yet unresolved question in biology remains how cells interpret the same signalling cues in a context-dependent manner resulting in lineage specification. A key step for decoding signalling cues is the establishment of a permissive chromatin environment at lineage-specific genes triggering transcriptional responses to inductive signals. For instance, bipotent neuromesodermal progenitors (NMPs) are equipped with a WNT-decoding module, which relies on TCFs/LEF activity to sustain both NMP expansion and paraxial mesoderm differentiation. However, how WNT signalling activates lineage specific genes in a temporal manner remains unclear. Here, we demonstrate that paraxial mesoderm induction relies on the TALE/HOX combinatorial activity that simultaneously represses NMP genes and activates the differentiation program. We identify the BRACHYURY-TALE/HOX code that destabilizes the nucleosomes at WNT-responsive regions and establishes the permissive chromatin landscape for de novo recruitment of the WNT-effector LEF1, unlocking the WNT-mediated transcriptional program that drives NMPs towards the paraxial mesodermal fate.
Vacancy control in acene blends links exothermic singlet fission to coherence
Authors: Zeiser Clemens , Cruz Chad , Reichman David R. , Seitz Michael , Hagenlocher Jan , Chronister Eric L. , Bardeen Christopher J. , Tempelaar Roel , Broch Katharina 
Published: August 2021

AbstractThe fission of singlet excitons into triplet pairs in organic materials holds great technological promise, but the rational application of this phenomenon is hampered by a lack of understanding of its complex photophysics. Here, we use the controlled introduction of vacancies by means of spacer molecules in tetracene and pentacene thin films as a tuning parameter complementing experimental observables to identify the operating principles of different singlet fission pathways. Time-resolved spectroscopic measurements in combination with microscopic modelling enables us to demonstrate distinct scenarios, resulting from different singlet-to-triplet pair energy alignments. For pentacene, where fission is exothermic, coherent mixing between the photoexcited singlet and triplet-pair states is promoted by vibronic resonances, which drives the fission process with little sensitivity to the vacancy concentration. Such vibronic resonances do not occur for endothermic materials such as tetracene, for which we find fission to be fully incoherent; a process that is shown to slow down with increasing vacancy concentration.
Autonomous DNA nanostructures instructed by hierarchically concatenated chemical reaction networks
Authors: Deng Jie , Walther Andreas 
Published: August 2021

AbstractConcatenation and communication between chemically distinct chemical reaction networks (CRNs) is an essential principle in biology for controlling dynamics of hierarchical structures. Here, to provide a model system for such biological systems, we demonstrate autonomous lifecycles of DNA nanotubes (DNTs) by two concatenated CRNs using different thermodynamic principles: (1) ATP-powered ligation/restriction of DNA components and (2) input strand-mediated DNA strand displacement (DSD) using energy gains provided in DNA toeholds. This allows to achieve hierarchical non-equilibrium systems by concurrent ATP-powered ligation-induced DSD for activating DNT self-assembly and restriction-induced backward DSD reactions for triggering DNT degradation. We introduce indirect and direct activation of DNT self-assemblies, and orthogonal molecular recognition allows ATP-fueled self-sorting of transient multicomponent DNTs. Coupling ATP dissipation to DNA nanostructures via programmable DSD is a generic concept which should be widely applicable to organize other DNA nanostructures, and enable the design of automatons and life-like systems of higher structural complexity.