bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features
Authors: Ray John P. , de Boer Carl G. , Fulco Charles P. , Lareau Caleb A. , Kanai Masahiro , Ulirsch Jacob C. , Tewhey Ryan , Ludwig Leif S. , Reilly Steven K. , Bergman Drew T. , Engreitz Jesse M. , Issner Robbyn , Finucane Hilary K. , Lander Eric S. , Regev Aviv , Hacohen Nir 
Published: March 2020

AbstractGenome-wide association studies have associated thousands of genetic variants with complex traits and diseases, but pinpointing the causal variant(s) among those in tight linkage disequilibrium with each associated variant remains a major challenge. Here, we use seven experimental assays to characterize all common variants at the multiple disease-associated TNFAIP3 locus in five disease-relevant immune cell lines, based on a set of features related to regulatory potential. Trait/disease-associated variants are enriched among SNPs prioritized based on either: (1) residing within CRISPRi-sensitive regulatory regions, or (2) localizing in a chromatin accessible region while displaying allele-specific reporter activity. Of the 15 trait/disease-associated haplotypes at TNFAIP3, 9 have at least one variant meeting one or both of these criteria, 5 of which are further supported by genetic fine-mapping. Our work provides a comprehensive strategy to characterize genetic variation at important disease-associated loci, and aids in the effort to identify trait causal genetic variants.
Transforming solid-state precipitates via excess vacancies
Authors: Bourgeois Laure , Zhang Yong , Zhang Zezhong , Chen Yiqiang , Medhekar Nikhil V. 
Published: March 2020

AbstractMany phase transformations associated with solid-state precipitation look structurally simple, yet, inexplicably, take place with great difficulty. A classic case of difficult phase transformations is the nucleation of strengthening precipitates in high-strength lightweight aluminium alloys. Here, using a combination of atomic-scale imaging, simulations and classical nucleation theory calculations, we investigate the nucleation of the strengthening phase θ′ onto a template structure in the aluminium-copper alloy system. We show that this transformation can be promoted in samples exhibiting at least one nanoscale dimension, with extremely high nucleation rates for the strengthening phase as well as for an unexpected phase. This template-directed solid-state nucleation pathway is enabled by the large influx of surface vacancies that results from heating a nanoscale solid. Template-directed nucleation is replicated in a bulk alloy as well as under electron irradiation, implying that this difficult transformation can be facilitated under the general condition of sustained excess vacancy concentrations.
Major antigenic site B of human influenza H3N2 viruses has an evolving local fitness landscape
Authors: Wu Nicholas C. , Otwinowski Jakub , Thompson Andrew J. , Nycholat Corwin M. , Nourmohammad Armita , Wilson Ian A. 
Published: March 2020

AbstractAntigenic drift of influenza virus hemagglutinin (HA) is enabled by facile evolvability. However, HA antigenic site B, which has become immunodominant in recent human H3N2 influenza viruses, is also evolutionarily constrained by its involvement in receptor binding. Here, we employ deep mutational scanning to probe the local fitness landscape of HA antigenic site B in six different human H3N2 strains spanning from 1968 to 2016. We observe that the fitness landscape of HA antigenic site B can be very different between strains. Sequence variants that exhibit high fitness in one strain can be deleterious in another, indicating that the evolutionary constraints of antigenic site B have changed over time. Structural analysis suggests that the local fitness landscape of antigenic site B can be reshaped by natural mutations via modulation of the receptor-binding mode. Overall, these findings elucidate how influenza virus continues to explore new antigenic space despite strong functional constraints.
Global lake thermal regions shift under climate change
Authors: Maberly Stephen C. , O’Donnell Ruth A. , Woolway R. Iestyn , Cutler Mark E. J. , Gong Mengyi , Jones Ian D. , Merchant Christopher J. , Miller Claire A. , Politi Eirini , Scott E. Marian , Thackeray Stephen J. , Tyler Andrew N. 
Published: March 2020

AbstractWater temperature is critical for the ecology of lakes. However, the ability to predict its spatial and seasonal variation is constrained by the lack of a thermal classification system. Here we define lake thermal regions using objective analysis of seasonal surface temperature dynamics from satellite observations. Nine lake thermal regions are identified that mapped robustly and largely contiguously globally, even for small lakes. The regions differed from other global patterns, and so provide unique information. Using a lake model forced by 21st century climate projections, we found that 12%, 27% and 66% of lakes will change to a lower latitude thermal region by 2080–2099 for low, medium and high greenhouse gas concentration trajectories (Representative Concentration Pathways 2.6, 6.0 and 8.5) respectively. Under the worst-case scenario, a 79% reduction in the number of lakes in the northernmost thermal region is projected. This thermal region framework can facilitate the global scaling of lake-research.
Organotypic human skin culture models constructed with senescent fibroblasts show hallmarks of skin aging
Authors: Weinmüllner Regina , Zbiral Barbara , Becirovic Adnan , Stelzer Elena Maria , Nagelreiter Fabian , Schosserer Markus , Lämmermann Ingo , Liendl Lisa , Lang Magdalena , Terlecki-Zaniewicz Lucia , Andriotis Orestis , Mildner Michael , Golabi Bahar , Waidhofer-Söllner Petra , Schedle Karl , Emsenhuber Gerhard , Thurner Philipp J. , Tschachler Erwin , Gruber Florian , Grillari Johannes 
Published: March 2020

AbstractSkin aging is driven by intrinsic and extrinsic factors impacting on skin functionality with progressive age. One factor of this multifaceted process is cellular senescence, as it has recently been identified to contribute to a declining tissue functionality in old age. In the skin, senescent cells have been found to markedly accumulate with age, and thus might impact directly on skin characteristics. Especially the switch from young, extracellular matrix-building fibroblasts to a senescence-associated secretory phenotype (SASP) could alter the microenvironment in the skin drastically and therefore promote skin aging. In order to study the influence of senescence in human skin, 3D organotypic cultures are a well-suited model system. However, only few “aged” skin- equivalent (SE) models are available, requiring complex and long-term experimental setups. Here, we adapted a previously published full-thickness SE model by seeding increasing ratios of stress-induced premature senescent versus normal fibroblasts into the collagen matrix, terming these SE “senoskin”. Immunohistochemistry stainings revealed a shift in the balance between proliferation (Ki67) and differentiation (Keratin 10 and Filaggrin) of keratinocytes within our senoskin equivalents, as well as partial impairment of skin barrier function and changed surface properties. Monitoring of cytokine levels of known SASP factors confirmedly showed an upregulation in 2D cultures of senescent cells and at the time of seeding into the skin equivalent. Surprisingly, we find a blunted response of cytokines in the senoskin equivalent over time during 3D differentiation.
Melting of charge order in the low-temperature state of an electronic ferroelectric-like system
Authors: Hassan Nora M. , Thirunavukkuarasu Komalavalli , Lu Zhengguang , Smirnov Dmitry , Zhilyaeva Elena I. , Torunova Svetlana , Lyubovskaya Rimma N. , Drichko Natalia 
Published: March 2020

AbstractStrong electronic interactions can drive a system into a state with a symmetry breaking. Lattice frustration or competing interactions tend to prevent symmetry breaking, leading to quantum disordered phases. In spin systems frustration can produce a spin liquid state. Frustration of a charge degree of freedom also can result in various exotic states, however, experimental data on these effects is scarce. In this work we demonstrate how in a Mott insulator on a weakly anisotropic triangular lattice a charge ordered state melts on cooling down to low temperatures. Raman scattering spectroscopy finds that $$\kappa$$
κ
-(BEDT-TTF)$${}_{2}$$

2

Hg(SCN)$${}_{2}$$

2

Cl enters an insulating “dipole solid” state at $$T=30\,{\mathrm{K}}$$

T
=
30

K

, but below $$T=15\,{\mathrm{K}}$$

T
=
15

K

the order melts, while preserving the insulating energy gap. Based on these observations, we suggest a phase diagram relevant to other quantum paraelectric materials.
Manipulating long-lived topological surface photovoltage in bulk-insulating topological insulators Bi2Se3 and Bi2Te3
Authors: Ciocys Samuel , Morimoto Takahiro , Mori Ryo , Gotlieb Kenneth , Hussain Zahid , Analytis James G. , Moore Joel E. , Lanzara Alessandra 
Published: March 2020

AbstractThe appearance of topologically protected spin-momentum locked surface states in topological insulators gives rise to robust room temperature spin currents making them ideal candidates for the realization of spintronic devices. New methods are needed to access and manipulate such currents with timescales that are compatible with modern electronics. Here we reveal that an optically induced long-lived (~10 ns), spin-polarized surface state excitation in topological insulators can be easily tuned in both magnitude and duration. Time-resolved angle-resolved photoemission spectroscopy, together with a quantitative model, reveals the ideal conditions for a surface photovoltage in two different topological insulators. Our model predicts that the reported effects are an intrinsic property of topological insulators, as long as the chemical potential falls within the band gap. This work demonstrates that persistent excited topological surface states are photon-accessible and easily tuned in both magnitude and duration, merging photonics- and spintronics-based devices in the same material.
Impact of cardiac interoception cues and confidence on voluntary decisions to make or withhold action in an intentional inhibition task
Authors: Rae Charlotte L. , Ahmad Aysha , Larsson Dennis E. O. , Silva Marta , Praag Cassandra D. Gould van , Garfinkel Sarah N. , Critchley Hugo D. 
Published: March 2020

AbstractInteroceptive signals concerning the internal physiological state of the body influence motivational feelings and action decisions. Cardiovascular arousal may facilitate inhibition to mitigate risks of impulsive actions. Baroreceptor discharge at ventricular systole underpins afferent signalling of cardiovascular arousal. In a modified Go/NoGo task, decisions to make or withhold actions on ‘Choose’ trials were not influenced by cardiac phase, nor individual differences in heart rate variability. However, cardiac interoceptive awareness and insight predicted how frequently participants chose to act, and their speed of action: Participants with better awareness and insight tended to withhold actions and respond slower, while those with poorer awareness and insight tended to execute actions and respond faster. Moreover, self-reported trait urgency correlated negatively with intentional inhibition rates. These findings suggest that lower insight into bodily signals is linked to urges to move the body, putatively by engendering noisier sensory input into motor decision processes eliciting reactive behaviour.
Vitamin A supplement after neonatal Streptococcus pneumoniae pneumonia inhibits the progression of experimental asthma by altering CD4+T cell subsets
Authors: Tian Yonglu , Tian Qinqin , Wu Yi , Peng Xin , Chen Yunxiu , Li Qinyuan , Zhang Guangli , Tian Xiaoyin , Ren Luo , Luo Zhengxiu 
Published: March 2020

AbstractStudies demonstrated that pneumonia can decrease vitamin A productions and vitamin A reduction/deficiency may promote asthma development. Our previous study showed that neonatal Streptococcus pneumoniae (S. pneumoniae) infection promoted asthma development. Whether neonatal S. pneumoniae pneumonia induced asthma was associated with vitamin A levels remains unclear. The aim of this study was to investigate the effects of neonatal S. pneumoniae pneumonia on vitamin A expressions, to explore the effects of vitamin A supplement after neonatal S. pneumoniae pneumonia on adulthood asthma development. Non-lethal S. pneumoniae pneumonia was established by intranasal inoculation of neonatal (1-week-old) female BALB/c mice with D39. S. pneumoniae pneumonia mice were supplemented with or without all-trans retinoic acid 24 hours after infection. Vitamin A concentrations in lung, serum and liver were measured post pneumonia until early adulthood. Four weeks after pneumonia, mice were sensitized and challenged with OVA to induce allergic airway disease (AAD). Twenty-four hours after the final challenge, the lungs and bronchoalveolar lavage fluid (BALF) were collected to assess AAD. We stated that serum vitamin A levels in neonatal S. pneumoniae pneumonia mice were lower than 0.7µmol/L from day 2–7 post infection, while pulmonary vitamin A productions were significantly lower than those in the control mice from day 7–28 post infection. Vitamin A supplement after neonatal S. pneumoniae pneumonia significantly promoted Foxp3+Treg and Th1 productions, decreased Th2 and Th17 cells expressions, alleviated airway hyperresponsiveness (AHR) and inflammatory cells infiltration during AAD. Our data suggest that neonatal S. pneumoniae pneumonia induce serum vitamin A deficiency and long-time lung vitamin A reduction, vitamin A supplement after neonatal S. pneumoniae pneumonia inhibit the progression of asthma by altering CD4+T cell subsets.
Anthropogenic electromagnetic fields (EMF) influence the behaviour of bottom-dwelling marine species
Authors: Hutchison Zoë L. , Gill Andrew B. , Sigray Peter , He Haibo , King John W. 
Published: March 2020

AbstractMany marine animals have evolved sensory abilities to use electric and magnetic cues in essential aspects of life history, such as to detect prey, predators and mates as well as to orientate and migrate. Potential disruption of vital cues by human activities must be understood in order to mitigate potential negative influences. Cable deployments in coastal waters are increasing worldwide, in capacity and number, owing to growing demands for electrical power and telecommunications. Increasingly, the local electromagnetic environment used by electro- and magneto-sensitive species will be altered. We quantified biologically relevant behavioural responses of the presumed, magneto-receptive American lobster and the electro-sensitive Little skate to electromagnetic field (EMF) emissions of a subsea high voltage direct current (HVDC) transmission cable for domestic electricity supply. We demonstrate a striking increase in exploratory/foraging behaviour in skates in response to EMF and a more subtle exploratory response in lobsters. In addition, by directly measuring both the magnetic and electric field components of the EMF emitted by HVDC cables we found that there were DC and unexpectedly AC components. Modelling, restricted to the DC component, showed good agreement with measured results. Our cross-disciplinary study highlights the need to integrate an understanding of the natural and anthropogenic EMF environment together with the responses of sensitive animals when planning future cable deployments and predicting their environmental effects.
Randomized Clinical Trial investigating Self-Assembling Peptide P11-4 for Treatment of Early Occlusal Caries
Authors: Doberdoli Dafina , Bommer Claudine , Begzati Agim , Haliti Fehim , Heinzel-Gutenbrunner Monika , Juric Hrvoje 
Published: March 2020

AbstractNon-invasive caries treatment is a major focus in modern dentistry. The present study was designed to evaluate the effectiveness of monomeric self-assembling peptide P11-4 (SAP P11-4) in combination with fluoride varnish or polymeric self-assembling peptide matrix (SAPM) in treatment of non-cavitated occlusal caries. Ninety children and adolescents were included in this randomized, gold-standard-controlled clinical trial. Test Group 1 received SAP P11-4 and twice fluoride varnish at baseline and Day 180, Test Group 2 received SAP P11-4 on baseline and twice weekly SAPM (home-application), and Control Group received fluoride varnish on baseline and Day 180. Caries progression was measured by laser fluorescence, Nyvad Caries Activity, ICDAS-II-codes, and investigator assessments. Laser fluorescence changes demonstrated superior results for Test Group 1 and 2, as values decreased compared to an increase for the Control Group (p < 0.0005). ICDAS-II codes at Day 360 showed partial regression for Test Group 1 (6.7%) and Test Group 2 (20.0%) and partial progression for Control Group (23.3%) (p < 0.01). Nyvad Caries Activity yielded superior caries inactivation for Test Groups, compared to Control Group (p = 0.002). This trial showed that SAP P11-4, applied either in combination with fluoride varnish or twice weekly SAPM, was a superior treatment for early caries compared to fluoride varnish alone.
Diatoms synthesize sterols by inclusion of animal and fungal genes in the plant pathway
Authors: Gallo Carmela , Landi Simone , d’Ippolito Giuliana , Nuzzo Genoveffa , Manzo Emiliano , Sardo Angela , Fontana Angelo 
Published: March 2020

AbstractDiatoms are ubiquitous microalgae that have developed remarkable metabolic plasticity and gene diversification. Here we report the first elucidation of the complete biosynthesis of sterols in the lineage. The study has been carried out on the bloom-forming speciesSkeletonema marinoiandCyclotella crypticathat synthesise an ensemble of sterols with chemotypes of animals (cholesterol and desmosterol), plants (dihydrobrassicasterol and 24-methylene cholesterol), algae (fucosterol) and marine invertebrates (clionasterol). In both species, sterols derive from mevalonate through cyclization of squalene to cycloartenol by cycloartenol synthase. The pathway anticipates synthesis of cholesterol by enzymes of the phytosterol route in plants, as recently reported in Solanaceae. Major divergences stem from reduction of Δ24(28) and Δ24(25) double bonds which, in diatoms, are apparently dependent on sterol reductases of fungi, algae and animals. Phylogenetic comparison revealed a good level of similarity between the sterol biosynthetic genes ofS. marinoiandC. crypticawith those in the genomes of the other diatoms sequenced so far.
Bisphenol A induces coronary endothelial cell necroptosis by activating RIP3/CamKII dependent pathway
Authors: Reventun P. , Sanchez-Esteban S. , Cook A. , Cuadrado I. , Roza C. , Moreno-Gomez-Toledano R. , Muñoz C. , Zaragoza C. , Bosch R. J. , Saura M. 
Published: March 2020

AbstractEpidemiological studies link long term exposure to xenoestrogen Bisphenol-A to adverse cardiovascular effects. Our previous results show that BPA induces hypertension by a mechanism involving CamKII activation and increased redox stress caused by eNOS uncoupling. Recently, CamKII sustained activation has been recognized as a central mediator of programmed cell death in cardiovascular diseases, including necroptosis. However, the role of necroptosis in cardiac response to BPA had not yet been explored. Mice exposed to BPA for 16 weeks showed altered heart function, electrical conduction, and increased blood pressure. Besides, a stress test showed ST-segment depression, indicative of cardiac ischemia. The hearts exhibited cardiac hypertrophy and reduced vascularization, interstitial edema, and large hemorrhagic foci accompanied by fibrinogen deposits. BPA initiated a cardiac inflammatory response, up-regulation of M1 macrophage polarization, and increased oxidative stress, coinciding with the increased expression of CamKII and the necroptotic effector RIP3. In addition, cell death was especially evident in coronary endothelial cells within hemorrhagic areas, and Evans blue extravasation indicated a vascular leak in response to Bisphenol-A. Consistent with the in vivo findings, BPA increased the necroptosis/apoptosis ratio, the expression of RIP3, and CamKII activation in endothelial cells. Necrostatin-1, an inhibitor of necroptosis, alleviated BPA induced cardiac dysfunction and prevented the inflammatory and hemorrhagic response in mice. Mechanistically, silencing of RIP3 reversed BPA-induced necroptosis and CamKII activation in endothelial cells, while inhibition of CamKII activation by KN-93 had no effect on RIP3 expression but decreased necroptotic cell death suggesting that BPA induced necroptosis is mediated by a RIP 3/CamKII dependent pathway. Our results reveal a novel pathogenic role of BPA on the coronary circulation. BPA induces endothelial cell necroptosis, promotes the weakening of coronary vascular wall, which caused internal ventricular hemorrhages, delaying the reparative process and ultimately leading to cardiac dysfunction.
The association between breastmilk oligosaccharides and faecal microbiota in healthy breastfed infants at two, six, and twelve weeks of age
Authors: Borewicz Klaudyna , Gu Fangjie , Saccenti Edoardo , Hechler Christine , Beijers Roseriet , de Weerth Carolina , van Leeuwen Sander S. , Schols Henk A. , Smidt Hauke 
Published: March 2020

AbstractSeveral factors affect gut microbiota development in early life, among which breastfeeding plays a key role. We followed 24 mother-infant pairs to investigate the associations between concentrations of selected human milk oligosaccharides (HMOs) in breastmilk, infant faeces, and the faecal microbiota composition in healthy, breastfed infants at two, six and 12 weeks of age. Lactation duration had a significant effect on breastmilk HMO content, which decreased with time, except for 3-fucosyllactose (3FL) and Lacto-N-fucopentaose III (LNFP III). We confirmed that microbiota composition was strongly influenced by infant age and was associated with mode of delivery and breastmilk LNFP III concentration at two weeks, with infant sex, delivery mode, and concentrations of 3′sialyllactose (3′SL) in milk at six weeks, and infant sex and Lacto-N-hexaose (LNH) in milk at 12 weeks of age. Correlations between levels of individual breastmilk HMOs and relative abundance of OTUs found in infant faeces, including the most predominant Bifidobacterium OTUs, were weak and varied with age. The faecal concentration of HMOs decreased with age and were strongly and negatively correlated with relative abundance of OTUs within genera Bifidobacterium, Parabacteroides, Escherichia-Shigella, Bacteroides, Actinomyces, Veillonella, Lachnospiraceae Incertae Sedis, and Erysipelotrichaceae Incertae Sedis, indicating the likely importance of these taxa for HMO metabolism in vivo.