bluuebunny/crossref_metadata_2025_split huggingface dataset:
Leveraging the Historical Landsat Catalog for a Remote Sensing Model of Wetland Accretion in Coastal Louisiana
Authors: Jensen D. J. , Cavanaugh K. C. , Thompson D. R. , Fagherazzi S. , Cortese L. , Simard M. 
Published: June 2022

AbstractA wetland's ability to vertically accrete—capturing sediment and biological matter for soil accumulation—is key for maintaining elevation to counter soil subsidence and sea level rise. Wetland soil accretion is comprised of organic and inorganic components largely governed by net primary productivity and sedimentation. Sea level, land elevation, primary productivity, and sediment accretion are all changing across Louisiana's coastline, destabilizing much of its wetland ecosystems. In coastal Louisiana, analysis from 1984 to 2020 shows an estimated 1940.858 km2 of total loss at an average rate of 53.913 km2/year. Here we hypothesize that remote sensing timeseries data can provide suitable proxies for organic and inorganic accretionary components to estimate local accretion rates. The Landsat catalog offers decades of imagery applicable to tracking land extent changes across coastal Louisiana. This dataset's expansiveness allows it to be combined with the Coastwide Reference Monitoring System's point‐based accretion data. We exported normalized difference vegetation index (NDVI) and red‐band surface reflectance data for every available Landsat 4–8 scene across the coast using Google Earth Engine. Water pixels from the red‐band were transformed into estimates of total suspended solids to represent sediment deposition—the inorganic accretionary component. NDVI values over land pixels were used to estimate bioproductivity—representing accretion's organic component. We then developed a Random Forest regression model that predicts wetland accretion rates (R2 = 0.586, MAE = 0.333 cm/year). This model can inform wetland vulnerability assessments and loss predictions, and is to our knowledge the first remote sensing‐based model that directly estimates accretion rates in coastal wetlands.
Genetics of Alzheimer’s disease: an East Asian perspective
Authors: Miyashita Akinori , Kikuchi Masataka , Hara Norikazu , Ikeuchi Takeshi 
Published: June 2022

AbstractAlzheimer’s disease (AD) is an age-related multifactorial neurodegenerative disorder. Advances in genome technology, including next generation sequencing have uncovered complex genetic effects in AD by analyzing both common and rare functional variants. Multiple lines of evidence suggest that the pathogenesis of AD is influenced by multiple genetic components rather than single genetic factor. Previous genetic studies on AD have predominantly included European ancestry cohorts; hence, the non-European population may be underrepresented, potentially leading to reduced diversity in AD genetic research. Additionally, ethnic diversity may result in dissimilar effects of genetic determinants in AD.APOEgenotypes are a well-established genetic risk factor in AD, with the East Asian population having a higher risk of AD associated with theAPOEε4 allele. To date, seven genome-wide association studies (GWAS) have been conducted in East Asians, which report a total of 26 AD-associated loci. Several rare variants, including the p.H157Y variant inTREM2, and the p.G186R and p.R274W variants inSHARPINare associated with risk of AD in East Asians. Extending genetic studies to diverse populations, including East Asians is necessary, which could yield more comprehensive insights into AD, and here we review the recent findings regarding the genetic determinants of AD from an East Asian perspective.
Context-dependent amygdala–prefrontal connectivity during the dot-probe task varies by irritability and attention bias to angry faces
Authors: Naim Reut , Haller Simone P. , Linke Julia O. , Jaffe Allison , Stoddard Joel , Jones Matt , Harrewijn Anita , Kircanski Katharina , Bar-Haim Yair , Brotman Melissa A. 
Published: June 2022

AbstractIrritability, defined as proneness to anger, is among the most common reasons youth are seen for psychiatric care. Youth with irritability demonstrate aberrant processing of anger-related stimuli; however, the neural mechanisms remain unknown. We applied a drift-diffusion model (DDM), a computational tool, to derive a latent behavioral metric of attentional bias to angry faces in youth with varying levels of irritability during functional magnetic resonance imaging (fMRI). We examined associations among irritability, task behavior using a DDM-based index for preferential allocation of attention to angry faces (i.e., extra-decisional time bias; Δt0), and amygdala context-dependent connectivity during the dot-probe task. Our transdiagnostic sample, enriched for irritability, included 351 youth (ages 8–18; M = 12.92 years, 51% male, with primary diagnoses of either attention deficit/hyperactivity disorder [ADHD], disruptive mood dysregulation disorder [DMDD], an anxiety disorder, or healthy controls). Models accounted for age, sex, in-scanner motion, and co-occurring symptoms of anxiety. Youth and parents rated youth’s irritability using the Affective Reactivity Index. An fMRI dot-probe task was used to assess attention orienting to angry faces. In the angry-incongruent vs. angry-congruent contrast, amygdala connectivity with the bilateral inferior frontal gyrus (IFG), insula, caudate, and thalamus/pulvinar was modulated by irritability level and attention bias to angry faces, Δt0, all ts350 > 4.46, ps < 0.001. In youth with high irritability, elevated Δt0 was associated with a weaker amygdala connectivity. In contrast, in youth with low irritability, elevated Δt0 was associated with stronger connectivity in those regions. No main effect emerged for irritability. As irritability is associated with reactive aggression, these results suggest a potential neural regulatory deficit in irritable youth who have elevated attention bias to angry cues.
Epigenome-wide DNA methylation in obsessive-compulsive disorder
Authors: Schiele Miriam A. , Lipovsek Jan , Schlosser Pascal , Soutschek Michael , Schratt Gerhard , Zaudig Michael , Berberich Götz , Köttgen Anna , Domschke Katharina 
Published: June 2022

AbstractIn adult patients with obsessive-compulsive disorder (OCD), altered DNA methylation has been discerned in several candidate genes, while DNA methylation on an epigenome-wide level has been investigated in only one Chinese study so far. Here, an epigenome-wide association study (EWAS) was performed in a sample of 76 OCD patients of European ancestry (37 women, age ± SD: 33.51 ± 10.92 years) and 76 sex- and age-matched healthy controls for the first time using the Illumina MethylationEPIC BeadChip. After quality control, nine epigenome-wide significant quantitative trait methylation sites (QTMs) and 21 suggestive hits were discerned in the final sample of 68 patients and 68 controls. The top hit (cg24159721) and four other significant QTMs (cg11894324, cg01070250, cg11330075, cg15174812) map to the region of the microRNA 12136 gene (MIR12136). Two additional significant CpG sites (cg05740793, cg20450977) are located in the flanking region of the MT-RNR2 (humanin) like 8 gene (MT-RNRL8), while two further QTMs (cg16267121, cg15890734) map to the regions of the MT-RNR2 (humanin) like 3 (MT-RNRL3) and MT-RNR2 (humanin) like 2 (MT-RNRL2) genes. Provided replication of the present findings in larger samples, the identified QTMs might provide more biological insight into the pathogenesis of OCD and thereby could in the future serve as peripheral epigenetic markers of OCD risk with the potential to inform targeted preventive and therapeutic efforts.
The Scottish RD survey 10 years on: the increasing incidence of retinal detachments
Authors: El-Abiary Mariam , Shams Fatemah , Goudie Colin , Yorston David 
Published: June 2022

Abstract
Background
The Scottish RD Survey reported an incidence of 12.05/100,000/yr in 2009. Data published from Denmark recently confirmed a 50% increase in RD presentations over the last 16 years. We set out to repeat the Scottish RD survey to determine if a similar trend has been observed in Scotland.

Methods
All 16 Scottish VR surgeons, who make up the collaboration of Scottish VR Surgeons (SCVRs) were asked to prospectively record all primary RDs presenting from 12th August 2019 to 11th August 2020. For consistency, the case definitions were the same as for the 2009 Scottish RD Survey. Basic demographic and clinical features were recorded. Age specific incidence was calculated from mid-year population estimates for 2019 obtained from the National Records of Scotland.

Results
There were 875 RRDs recorded, which gives an updated incidence of 16.02/100,000/year in Scotland. 62.8% occurred in males and the greatest increases were seen in males aged 50–59 (p = 0.0094), 60–69 (p = 0.0395) and females aged 40–49 (p = 0.0312) and 50–59 (p = 0.0024). The proportion of pseudophakic RRDs in this study is 29.4% (253/860). Compared to the 21.6% in the 2010 study, this represents a 28% increase (χ2 = 11.03, p = 0.0009). The proportion of macula-off RRDs remained generally stable at 58%.

Conclusion
Our study confirms that RRD is becoming more common in the UK, reflecting almost identical findings from Denmark. This trend is in part due to increasing myopia, increasing pseudophakia, and possibly other factors. This should be considered when planning VR services and allocating resources in the future.
Characterisation of a nucleo-adhesome
Authors: Byron Adam , Griffith Billie G. C. , Herrero Ana , Loftus Alexander E. P. , Koeleman Emma S. , Kogerman Linda , Dawson John C. , McGivern Niamh , Culley Jayne , Grimes Graeme R. , Serrels Bryan , von Kriegsheim Alex , Brunton Valerie G. , Frame Margaret C. 
Published: June 2022

AbstractIn addition to central functions in cell adhesion signalling, integrin-associated proteins have wider roles at sites distal to adhesion receptors. In experimentally defined adhesomes, we noticed that there is clear enrichment of proteins that localise to the nucleus, and conversely, we now report that nuclear proteomes contain a class of adhesome components that localise to the nucleus. We here define a nucleo-adhesome, providing experimental evidence for a remarkable scale of nuclear localisation of adhesion proteins, establishing a framework for interrogating nuclear adhesion protein functions. Adding to nuclear FAK’s known roles in regulating transcription, we now show that nuclear FAK regulates expression of many adhesion-related proteins that localise to the nucleus and that nuclear FAK binds to the adhesome component and nuclear protein Hic-5. FAK and Hic-5 work together in the nucleus, co-regulating a subset of genes transcriptionally. We demonstrate the principle that there are subcomplexes of nuclear adhesion proteins that cooperate to control transcription.
Mechanical forces couple bone matrix mineralization with inhibition of angiogenesis to limit adolescent bone growth
Authors: Dzamukova Maria , Brunner Tobias M. , Miotla-Zarebska Jadwiga , Heinrich Frederik , Brylka Laura , Mashreghi Mir-Farzin , Kusumbe Anjali , Kühn Ralf , Schinke Thorsten , Vincent Tonia L. , Löhning Max 
Published: June 2022

AbstractBone growth requires a specialised, highly angiogenic blood vessel subtype, so-called type H vessels, which pave the way for osteoblasts surrounding these vessels. At the end of adolescence, type H vessels differentiate into quiescent type L endothelium lacking the capacity to promote bone growth. Until now, the signals that switch off type H vessel identity and thus limit adolescent bone growth have remained ill defined. Here we show that mechanical forces, associated with increased body weight at the end of adolescence, trigger the mechanoreceptor PIEZO1 and thereby mediate enhanced production of the kinase FAM20C in osteoblasts. FAM20C, the major kinase of the secreted phosphoproteome, phosphorylates dentin matrix protein 1, previously identified as a key factor in bone mineralization. Thereupon, dentin matrix protein 1 is secreted from osteoblasts in a burst-like manner. Extracellular dentin matrix protein 1 inhibits vascular endothelial growth factor signalling by preventing phosphorylation of vascular endothelial growth factor receptor 2. Hence, secreted dentin matrix protein 1 transforms type H vessels into type L to limit bone growth activity and enhance bone mineralization. The discovered mechanism may suggest new options for the treatment of diseases characterised by aberrant activity of bone and vessels such as osteoarthritis, osteoporosis and osteosarcoma.
Nuclear Vav3 is required for polycomb repression complex-1 activity in B-cell lymphoblastic leukemogenesis
Authors: Nayak R. C. , Chang K. H. , Singh A. K. , Kotliar M. , Desai M. , Wellendorf A. M. , Wunderlich M. , Bartram J. , Mizukawa B. , Cuadrado M. , Dexheimer P. , Barski A. , Bustelo X. R. , Nassar N. N. , Cancelas J. A. 
Published: June 2022

AbstractAcute B-cell lymphoblastic leukemia (B-ALL) results from oligo-clonal evolution of B-cell progenitors endowed with initiating and propagating leukemia properties. The activation of both the Rac guanine nucleotide exchange factor (Rac GEF) Vav3 and Rac GTPases is required for leukemogenesis mediated by the oncogenic fusion protein BCR-ABL. Vav3 expression becomes predominantly nuclear upon expression of BCR-ABL signature. In the nucleus, Vav3 interacts with BCR-ABL, Rac, and the polycomb repression complex (PRC) proteins Bmi1, Ring1b and Ezh2. The GEF activity of Vav3 is required for the proliferation, Bmi1-dependent B-cell progenitor self-renewal, nuclear Rac activation, protein interaction with Bmi1, mono-ubiquitination of H2A(K119) (H2AK119Ub) and repression of PRC-1 (PRC1) downstream target loci, of leukemic B-cell progenitors. Vav3 deficiency results in de-repression of negative regulators of cell proliferation and repression of oncogenic transcriptional factors. Mechanistically, we show that Vav3 prevents the Phlpp2-sensitive and Akt (S473)-dependent phosphorylation of Bmi1 on the regulatory residue S314 that, in turn, promotes the transcriptional factor reprogramming of leukemic B-cell progenitors. These results highlight the importance of non-canonical nuclear Rho GTPase signaling in leukemogenesis.
From subcritical behavior to a correlation-induced transition in rumor models
Authors: Ferraz de Arruda Guilherme , Jeub Lucas G. S. , Mata Angélica S. , Rodrigues Francisco A. , Moreno Yamir 
Published: June 2022

AbstractRumors and information spreading emerge naturally from human-to-human interactions and have a growing impact on our everyday life due to increasing and faster access to information, whether trustworthy or not. A popular mathematical model for spreading rumors, data, or news is the Maki–Thompson model. Mean-field approximations suggested that this model does not have a phase transition, with rumors always reaching a fraction of the population. Conversely, here, we show that a continuous phase transition is present in this model. Moreover, we explore a modified version of the Maki–Thompson model that includes a forgetting mechanism, changing the Markov chain’s nature and allowing us to use a plethora of analytic and numeric methods. Particularly, we characterize the subcritical behavior, where the lifespan of a rumor increases as the spreading rate drops, following a power-law relationship. Our findings show that the dynamic behavior of rumor models is much richer than shown in previous investigations.
De novo biosynthesis of rubusoside and rebaudiosides in engineered yeasts
Authors: Xu Yameng , Wang Xinglong , Zhang Chenyang , Zhou Xuan , Xu Xianhao , Han Luyao , Lv Xueqin , Liu Yanfeng , Liu Song , Li Jianghua , Du Guocheng , Chen Jian , Ledesma-Amaro Rodrigo , Liu Long 
Published: June 2022

AbstractHigh-sugar diet causes health problems, many of which can be addressed with the use of sugar substitutes. Rubusoside and rebaudiosides are interesting molecules, considered the next generation of sugar substitutes due to their low-calorie, superior sweetness and organoleptic properties. However, their low abundance in nature makes the traditional plant extraction process neither economical nor environmental-friendly. Here we engineer baker’s yeast Saccharomyces cerevisiae as a chassis for the de novo production of rubusoside and rebaudiosides. In this process, we identify multiple issues that limit the production, including rate-liming steps, product stress on cellular fitness and unbalanced metabolic networks. We carry out a systematic engineering strategy to solve these issues, which produces rubusoside and rebaudiosides at titers of 1368.6 mg/L and 132.7 mg/L, respectively. The rubusoside chassis strain here constructed paves the way towards a sustainable, large-scale fermentation-based manufacturing of diverse rebaudiosides.
Droplets in underlying chemical communication recreate cell interaction behaviors
Authors: Pizarro Agustin D. , Berli Claudio L. A. , Soler-Illia Galo J. A. A. , Bellino Martín G. 
Published: June 2022

AbstractThe sensory-motor interaction is a hallmark of living systems. However, developing inanimate systems with “recognize and attack” abilities remains challenging. On the other hand, controlling the inter-droplet dynamics on surfaces is key in microengineering and biomedical applications. We show here that a pair of droplets can become intelligently interactive (chemospecific stimulus-response inter-droplet autonomous operation) when placed on a nanoporous thin film surface. We find an attacker-victim-like non-reciprocal interaction between spatially separated droplets leading to an only-in-one shape instability that triggers a drop projection to selectively couple, resembling cellular phenomenologies such as pseudopod emission and phagocytic-like functions. The nanopore-driven underlying communication and associated chemical activity are the main physical ingredients behind the observed behavior. Our results reveal that basic features found in many living cell types can emerge from a simple two-droplet framework. This work is a promising step towards the design of microfluidic smart robotics and for origin-of-life protocell models.
Magnetotactic bacteria and magnetofossils: ecology, evolution and environmental implications
Authors: Goswami Pranami , He Kuang , Li Jinhua , Pan Yongxin , Roberts Andrew P. , Lin Wei 
Published: June 2022

AbstractMagnetotactic bacteria (MTB) are a group of phylogenetically diverse and morphologically varied microorganisms with a magnetoresponsive capability called magnetotaxis or microbial magnetoreception. MTB are a distinctive constituent of the microbiome of aquatic ecosystems because they use Earth’s magnetic field to align themselves in a north or south facing direction and efficiently navigate to their favored microenvironments. They have been identified worldwide from diverse aquatic and waterlogged microbiomes, including freshwater, saline, brackish and marine ecosystems, and some extreme environments. MTB play important roles in the biogeochemical cycling of iron, sulphur, phosphorus, carbon and nitrogen in nature and have been recognized from in vitro cultures to sequester heavy metals like selenium, cadmium, and tellurium, which makes them prospective candidate organisms for aquatic pollution bioremediation. The role of MTB in environmental systems is not limited to their lifespan; after death, fossil magnetosomal magnetic nanoparticles (known as magnetofossils) are a promising proxy for recording paleoenvironmental change and geomagnetic field history. Here, we summarize the ecology, evolution, and environmental function of MTB and the paleoenvironmental implications of magnetofossils in light of recent discoveries.
The sanitary indoor environment—a potential source for intact human-associated anaerobes
Authors: Pausan Manuela-Raluca , Blohs Marcus , Mahnert Alexander , Moissl-Eichinger Christine 
Published: June 2022

AbstractA healthy human microbiome relies on the interaction with and exchange of microbes that takes place between the human body and its environment. People in high-income countries spend most of their time indoors and for this reason, the built environment (BE) might represent a potent source of commensal microbes. Anaerobic microbes are of particular interest, as researchers have not yet sufficiently clarified how the human microbiome acquires oxygen-sensitive microbes. We sampled the bathrooms in ten households and used propidium monoazide (PMA) to assess the viability of the collected prokaryotes. We compared the microbiome profiles based on 16S rRNA gene sequencing and confirmed our results by genetic and cultivation-based analyses. Quantitative and qualitative analysis revealed that most of the microbial taxa in the BE samples are human-associated. Less than 25% of the prokaryotic signatures originate from intact cells, indicating that aerobic and stress resistant taxa display an apparent survival advantage. However, we also confirmed the presence of intact, strictly anaerobic taxa on bathroom floors, including methanogenic archaea. As methanogens are regarded as highly sensitive to aerobic conditions, oxygen-tolerance experiments were performed with human-associated isolates to validate their survival. These results show that human-associated methanogens can survive oxic conditions for at least 6 h. We collected strong evidence that supports the hypothesis that obligate anaerobic taxa can survive in the BE for a limited amount of time. This suggests that the BE serves as a potential source of anaerobic human commensals.
Unfolding the structural stability of nanoalloys via symmetry-constrained genetic algorithm and neural network potential
Authors: Han Shuang , Barcaro Giovanni , Fortunelli Alessandro , Lysgaard Steen , Vegge Tejs , Hansen Heine Anton 
Published: June 2022

AbstractThe structural stability of nanoalloys is a challenging research subject due to the complexity of size, shape, composition, and chemical ordering. The genetic algorithm is a popular global optimization method that can efficiently search for the ground-state nanoalloy structure. However, the algorithm suffers from three significant limitations: the efficiency and accuracy of the energy evaluator and the algorithm’s efficiency. Here we describe the construction of a neural network potential intended for rapid and accurate energy predictions of Pt-Ni nanoalloys of various sizes, shapes, and compositions. We further introduce a symmetry-constrained genetic algorithm that significantly improves the efficiency and viability of the algorithm for realistic size nanoalloys. The combination of the two allows us to explore the space of homotops and compositions of Pt-Ni nanoalloys consisting of up to 4033 atoms and quantitatively report the interplay of shape, size, and composition on the dominant chemical ordering patterns.