bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selective sweep for an enhancer involucrin allele identifies skin barrier adaptation out of Africa
Authors: Mathyer Mary Elizabeth , Brettmann Erin A. , Schmidt Alina D. , Goodwin Zane A. , Oh Inez Y. , Quiggle Ashley M. , Tycksen Eric , Ramakrishnan Natasha , Matkovich Scot J. , Guttman-Yassky Emma , Edwards John R. , de Guzman Strong Cristina 
Published: May 2021

AbstractThe genetic modules that contribute to human evolution are poorly understood. Here we investigate positive selection in the Epidermal Differentiation Complex locus for skin barrier adaptation in diverse HapMap human populations (CEU, JPT/CHB, and YRI). Using Composite of Multiple Signals and iSAFE, we identify selective sweeps for LCE1A-SMCP and involucrin (IVL) haplotypes associated with human migration out-of-Africa, reaching near fixation in European populations. CEU-IVL is associated with increased IVL expression and a known epidermis-specific enhancer. CRISPR/Cas9 deletion of the orthologous mouse enhancer in vivo reveals a functional requirement for the enhancer to regulate Ivl expression in cis. Reporter assays confirm increased regulatory and additive enhancer effects of CEU-specific polymorphisms identified at predicted IRF1 and NFIC binding sites in the IVL enhancer (rs4845327) and its promoter (rs1854779). Together, our results identify a selective sweep for a cis regulatory module for CEU-IVL, highlighting human skin barrier evolution for increased IVL expression out-of-Africa.
Testing the climate intervention potential of ocean afforestation using the Great Atlantic Sargassum Belt
Authors: Bach Lennart T. , Tamsitt Veronica , Gower Jim , Hurd Catriona L. , Raven John A. , Boyd Philip W. 
Published: May 2021

AbstractEnsuring that global warming remains <2 °C requires rapid CO2emissions reduction. Additionally, 100–900 gigatons CO2must be removed from the atmosphere by 2100 using a portfolio of CO2removal (CDR) methods. Ocean afforestation, CDR through basin-scale seaweed farming in the open ocean, is seen as a key component of the marine portfolio. Here, we analyse the CDR potential of recent re-occurring trans-basin belts of the floating seaweedSargassumin the (sub)tropical North Atlantic as a natural analogue for ocean afforestation. We show that two biogeochemical feedbacks, nutrient reallocation and calcification by encrusting marine life, reduce the CDR efficacy ofSargassumby 20–100%. Atmospheric CO2influx into the surface seawater, after CO2-fixation bySargassum, takes 2.5–18 times longer than the CO2-deficient seawater remains in contact with the atmosphere, potentially hindering CDR verification. Furthermore, we estimate that increased ocean albedo, due to floatingSargassum, could influence climate radiative forcing more thanSargassum-CDR. Our analysis shows that multifaceted Earth-system feedbacks determine the efficacy of ocean afforestation.
A generalized multipath delayed-choice experiment on a large-scale quantum nanophotonic chip
Authors: Chen Xiaojiong , Deng Yaohao , Liu Shuheng , Pramanik Tanumoy , Mao Jun , Bao Jueming , Zhai Chonghao , Dai Tianxiang , Yuan Huihong , Guo Jiajie , Fei Shao-Ming , Huber Marcus , Tang Bo , Yang Yan , Li Zhihua , He Qiongyi , Gong Qihuang , Wang Jianwei 
Published: May 2021

AbstractBohr’s complementarity is one central tenet of quantum physics. The paradoxical wave-particle duality of quantum matters and photons has been tested in Young’s double-slit (double-path) interferometers. The object exclusively exhibits wave and particle nature, depending measurement apparatus that can be delayed chosen to rule out too-naive interpretations of quantum complementarity. All experiments to date have been implemented in the double-path framework, while it is of fundamental interest to study complementarity in multipath interferometric systems. Here, we demonstrate generalized multipath wave-particle duality in a quantum delayed-choice experiment, implemented by large-scale silicon-integrated multipath interferometers. Single-photon displays sophisticated transitions between wave and particle characters, determined by the choice of quantum-controlled generalized Hadamard operations. We characterise particle-nature by multimode which-path information and wave-nature by multipath coherence of interference, and demonstrate the generalisation of Bohr’s multipath duality relation. Our work provides deep insights into multidimensional quantum physics and benchmarks controllability of integrated photonic quantum technology.
The transcriptome of wild-type and immortalized corneal epithelial cells
Authors: Furuya Kai , Wu Tao , Orimoto Ai , Sugano Eriko , Tomita Hiroshi , Kiyono Tohru , Kurose Takahiro , Takai Yoshihiro , Fukuda Tomokazu 
Published: May 2021

AbstractCellular immortalization enables indefinite expansion of cultured cells. However, the process of cell immortalization sometimes changes the original nature of primary cells. In this study, we performed expression profiling of poly A-tailed RNA from primary and immortalized corneal epithelial cells expressing Simian virus 40 large T antigen (SV40) or the combination of mutant cyclin-dependent kinase 4 (CDK4), cyclin D1, and telomere reverse transcriptase (TERT). Furthermore, we studied the expression profile of SV40 cells cultured in medium with or without serum. The profiling of whole expression pattern revealed that immortalized corneal epithelial cells with SV40 showed a distinct expression pattern from wild-type cells regardless of the presence or absence of serum, while corneal epithelial cells with combinatorial expression showed an expression pattern relatively closer to that of wild-type cells.
Prevalence and risk factors of anxiety and depression among the community-dwelling elderly in Nay Pyi Taw Union Territory, Myanmar
Authors: Cho Su Myat , Saw Yu Mon , Saw Thu Nandar , Than Thet Mon , Khaing Moe , Khine Aye Thazin , Kariya Tetsuyoshi , Soe Pa Pa , Oo San , Hamajima Nobuyuki 
Published: May 2021

AbstractProviding elderly mental healthcare in Myanmar is challenging due to the growing elderly population and limited health resources. To understand common mental health problems among Myanmar elderly, this study explored the prevalence and risk factors of anxiety and depression among the elderly in the Nay Pyi Taw Union Territory, Myanmar. A cross-sectional study was conducted among 655 elderly by face-to-face interviews with a pretested questionnaire. Descriptive analysis and multiple logistic regression analyses were performed. The prevalence of anxiety and depression were 39.4% (33.5% for males and 42.4% for females) and 35.6% (33.0% for males and 36.9% for females), respectively. The adjusted odds ratio of having anxiety was significant for having low education level, having comorbidity, having BMI < 21.3, poor dental health, no social participation, and having no one to consult regarding personal problems, while that of having depression was significant for having comorbidity, having BMI < 21.3, poor vision, and having no one to consult regarding personal problems. The reported prevalence of anxiety and depression indicate the demand for mental healthcare services among Myanmar elderly. Myanmar needs to improve its elderly care, mental healthcare, and social security system to reflect the actual needs of its increasing elderly population. Screening for anxiety and depression among elderly with comorbidities should be promoted. Raising community awareness of mental health, encouraging social participation, and supportive counselling are also essential in combating anxiety and depression among Myanmar elderly.
Germinal GLT8D1, GATAD2A and SLC25A39 mutations in a patient with a glomangiopericytal tumor and five different sarcomas over a 10-year period
Authors: Beddok Arnaud , Pérot Gaëlle , Le Guellec Sophie , Thebault Noémie , Coutte Alexandre , Sevestre Henri , Chauffert Bruno , Chibon Frédéric 
Published: May 2021

AbstractSoft tissue sarcoma represents about 1% of all adult cancers. Occurrence of multiple sarcomas in a same individual cannot be fortuitous. A 72-year-old patient had between 2007 and 2016 a glomangiopericytal tumor of the right forearm and a succession of sarcomas of the extremities: a leiomyosarcoma of the left buttock, a myxofibrosarcoma (MFS) of the right forearm, a MFS of the left scapula, a left latero-thoracic MFS and two undifferentiated sarcomas on the left forearm. Pathological examination of the six locations was not in favor of disease with local/distant recurrences but could not confirm different diseases. An extensive molecular analysis including DNA-array, RNA-sequencing and DNA-Sanger-sequencing, was thus performed to determine the link between them. The genomic profile of the glomangiopericytal tumor and the six sarcomas revealed that five sarcomas were different diseases and one was the local recurrence of the glomangiopericytal tumor. While the chromosomal alterations in the six tumors were different, a common somatic CDKN2A/CDKN2B deletion was identified. RNA-sequencing of five tumors identified mutations in GLT8D1, GATAD2A and SLC25A39 in all samples. The germline origin of these mutations was confirmed by Sanger-sequencing. Innovative molecular analysis methods have made possible a better understanding of the complex tumorigenesis of multiple sarcomas.
Changes in soil water holding capacity and water availability following vegetation restoration on the Chinese Loess Plateau
Authors: Zhang Yong-wang , Wang Kai-bo , Wang Jun , Liu Changhai , Shangguan Zhou-ping 
Published: May 2021

AbstractChanges in land use type can lead to variations in soil water characteristics. The objective of this study was to identify the responses of soil water holding capacity (SWHC) and soil water availability (SWA) to land use type (grassland, shrubland and forestland). The soil water characteristic curve describes the relationship between gravimetric water content and soil suction. We measured the soil water characteristic parameters representing SWHC and SWA, which we derived from soil water characteristic curves, in the 0–50 cm soil layer at sites representing three land use types in the Ziwuling forest region, located in the central part of the Loess Plateau, China. Our results showed that the SWHC was higher at the woodland site than the grassland and shrubland, and there was no significant difference between the latter two sites, the trend of SWA was similar to the SWHC. From grassland to woodland, the soil physical properties in the 0–50 cm soil layer partially improved, BD was significantly higher at the grassland site than at the shrubland and woodland sites, the clay and silt contents decreased significantly from grassland to shrubland to woodland and sand content showed the opposite pattern, the soil porosity was higher in the shrubland and woodland than that in the grassland, the soil physical properties across the 0–50 cm soil layer improved. Soil texture, porosity and bulk density were the key factors affecting SWHC and SWA. The results of this study provide insight into the effects of vegetation restoration on local hydrological resources and can inform soil water management and land use planning on the Chinese Loess Plateau.
DNA barcodes using a double nanopore system
Authors: Seth Swarnadeep , Bhattacharya Aniket 
Published: May 2021

AbstractThe potential of a double nanopore system to determine DNA barcodes has been demonstrated experimentally. By carrying out Brownian dynamics simulation on a coarse-grained model DNA with protein tag (barcodes) at known locations along the chain backbone, we demonstrate that due to large variation of velocities of the chain segments between the tags, it is inevitable to under/overestimate the genetic lengths from the experimental current blockade and time of flight data. We demonstrate that it is the tension propagation along the chain’s backbone that governs the motion of the entire chain and is the key element to explain the non uniformity and disparate velocities of the tags and DNA monomers under translocation that introduce errors in measurement of the length segments between protein tags. Using simulation data we further demonstrate that it is important to consider the dynamics of the entire chain and suggest methods to accurately decipher barcodes. We introduce and validate an interpolation scheme using simulation data for a broad distribution of tag separations and suggest how to implement the scheme experimentally.
Elevated dimethylarginine, ATP, cytokines, metabolic remodeling involving tryptophan metabolism and potential microglial inflammation characterize primary open angle glaucoma
Authors: Pulukool Sujith Kumar , Bhagavatham Sai Krishna Srimadh , Kannan Vishnu , Sukumar Piruthivi , Dandamudi Rajesh Babu , Ghaisas Shamika , Kunchala Haripriya , Saieesh Darshan , Naik Ashwin Ashok , Pargaonkar Ashish , Sharma Anuj , Sivaramakrishnan Venketesh 
Published: May 2021

AbstractGlaucoma of which primary open angle glaucoma (POAG) constitutes 75%, is the second leading cause of blindness. Elevated intra ocular pressure and Nitric oxide synthase (NOS) dysfunction are hallmarks of POAG. We analyzed clinical data, cytokine profile, ATP level, metabolomics and GEO datasets to identify features unique to POAG. N9 microglial cells are used to gain mechanistic insights. Our POAG cohort showed elevated ATP in aqueous humor and cytokines in plasma. Metabolomic analysis showed changes in 21 metabolites including Dimethylarginine (DMAG) and activation of tryptophan metabolism in POAG. Analysis of GEO data sets and previously published proteomic data sets bins genes into signaling and metabolic pathways. Pathways from reanalyzed metabolomic data from literature significantly overlapped with those from our POAG data. DMAG modulated purinergic signaling, ATP secretion and cytokine expression were inhibited by N-Ethylmaleimide, NO donors, BAPTA and purinergic receptor inhibitors. ATP induced elevated intracellular calcium level and cytokines expression were inhibited by BAPTA. Metabolomics of cell culture supernatant from ATP treated sets showed metabolic deregulation and activation of tryptophan metabolism. DMAG and ATP induced IDO1/2 and TDO2 were inhibited by N-Ethylmaleimide, sodium nitroprusside and BAPTA. Our data obtained from clinical samples and cell culture studies reveal a strong association of elevated DMAG, ATP, cytokines and activation of tryptophan metabolism with POAG. DMAG mediated ATP signaling, inflammation and metabolic remodeling in microglia might have implications in management of POAG.
Two-photon GCaMP6f imaging of infrared neural stimulation evoked calcium signals in mouse cortical neurons in vivo
Authors: Kaszas Attila , Szalay Gergely , Slézia Andrea , Bojdán Alexandra , Vanzetta Ivo , Hangya Balázs , Rózsa Balázs , O’Connor Rodney , Moreau David 
Published: May 2021

AbstractInfrared neural stimulation is a promising tool for stimulating the brain because it can be used to excite with high spatial precision without the need of delivering or inserting any exogenous agent into the tissue. Very few studies have explored its use in the brain, as most investigations have focused on sensory or motor nerve stimulation. Using intravital calcium imaging with the genetically encoded calcium indicator GCaMP6f, here we show that the application of infrared neural stimulation induces intracellular calcium signals in Layer 2/3 neurons in mouse cortex in vivo. The number of neurons exhibiting infrared-induced calcium response as well as the amplitude of those signals are shown to be both increasing with the energy density applied. By studying as well the spatial extent of the stimulation, we show that reproducibility of the stimulation is achieved mainly in the central part of the infrared beam path. Stimulating in vivo at such a degree of precision and without any exogenous chromophores enables multiple applications, from mapping the brain’s connectome to applications in systems neuroscience and the development of new therapeutic tools for investigating the pathological brain.
Collagen fiber regulation in human pediatric aortic valve development and disease
Authors: Clift Cassandra L. , Su Yan Ru , Bichell David , Jensen Smith Heather C. , Bethard Jennifer R. , Norris-Caneda Kim , Comte-Walters Susana , Ball Lauren E. , Hollingsworth M. A. , Mehta Anand S. , Drake Richard R. , Angel Peggi M. 
Published: May 2021

AbstractCongenital aortic valve stenosis (CAVS) affects up to 10% of the world population without medical therapies to treat the disease. New molecular targets are continually being sought that can halt CAVS progression. Collagen deregulation is a hallmark of CAVS yet remains mostly undefined. Here, histological studies were paired with high resolution accurate mass (HRAM) collagen-targeting proteomics to investigate collagen fiber production with collagen regulation associated with human AV development and pediatric end-stage CAVS (pCAVS). Histological studies identified collagen fiber realignment and unique regions of high-density collagen in pCAVS. Proteomic analysis reported specific collagen peptides are modified by hydroxylated prolines (HYP), a post-translational modification critical to stabilizing the collagen triple helix. Quantitative data analysis reported significant regulation of collagen HYP sites across patient categories. Non-collagen type ECM proteins identified (26 of the 44 total proteins) have direct interactions in collagen synthesis, regulation, or modification. Network analysis identified BAMBI (BMP and Activin Membrane Bound Inhibitor) as a potential upstream regulator of the collagen interactome. This is the first study to detail the collagen types and HYP modifications associated with human AV development and pCAVS. We anticipate that this study will inform new therapeutic avenues that inhibit valvular degradation in pCAVS and engineered options for valve replacement.
Illustrating changes in landscapes of passing opportunities along a set of competitive football matches
Authors: Gómez-Jordana Luis Ignacio , Amaro e Silva Rodrigo , Milho João , Ric Angel , Passos Pedro 
Published: May 2021

AbstractThis study aims to illustrate the landscape of passing opportunities of a football team across a set of competitive matches. To do so positional data of 5 competitive matches was used to create polygons of pass availability. Passes were divided into three types depending on the hypothetical threat they may pose to the opposing defense (penetrative, support, and backwards passes). These categories were used to create three heatmaps per match. Moreover, the mean time of passing opportunities was calculated and compared across matches and for the three categories of passes. Due to the specificity of player’s interactive behavior, results showed heatmaps with a variety of patterns. Specifically the fifth match was very dissimilar to the other four. However, characterizing a football match in terms of passing opportunities with a single heatmap dismisses the variety of dynamics that occur throughout a match. Therefore, three temporal heatmaps over windows of 10 min were presented highlighting on-going dynamical changes in pass availability. Results also display that penetrative passes were available over shorter periods of time than backward passes that were available shorter than support passes. The results highlight the sensibility of the model to different task constrains that emerge within football matches.
Mesoscale and wind-driven intra-annual variability in the East Auckland Current
Authors: Santana Rafael , Suanda Sutara H. , Macdonald Helen , O’Callaghan Joanne 
Published: May 2021

AbstractIntra-annual variability in the East Auckland Current (EAuC) was studied using a year-long timeseries of in situ and remotely-sensed velocity, temperature and salinity observations. Satellite-derived velocities correlated well ($$\hbox {r} > 0.75$$

r
>
0.75

) with in situ observations and well-represent the long-term ($$> 30$$

>
30

days) variability of the upper ocean circulation. Four mesoscale eddies were observed during the year (for 260 days) which generated distinct flows between the continental slope and rise. The EAuC dominated the circulation in the continental shelf break, slope and rise for 110 days and generated the most energetic events associated with wind forcing. Current variability on the continental slope was coherent with along-slope wind stress (wind stress curl) at periods between 4 and 12 days (16 and 32 days). We suggest that along-slope winds generated offshore Ekman transport, uplift on the shelf-break, and a downwind geostrophic jet on the slope. In contrast, positive wind stress curl caused convergence of water, downwelling, and increased the current speed in the region. Bottom Ekman transport, generated by the EAuC, was suggested to have caused the largest temperature anomaly ($$-1.5 ^{\circ }\hbox {C}$$

-
1
.

5
∘

C

) at the continental shelf-break.
Neuroticism is positively associated with leptin/adiponectin ratio, leptin and IL-6 in young adults
Authors: Syk Mikaela , Isaksson Johan , Rasmusson Annica J. , Ekselius Lisa , Cunningham Janet L. 
Published: May 2021

AbstractHigh neuroticism is related to cardiovascular morbidity. Early detection of metabolic and cardiovascular risk is important in high-risk groups to enable preventive measures. The aim of this study was therefore to explore if neuroticism is associated with early biomarkers for cardiovascular and metabolic disease in young adults from a psychiatry cohort. Blood samples and self-ratings on neuroticism with the Swedish universities Scales of Personality (SSP) questionnaire were collected from 172 psychiatric outpatients and 46 healthy controls. The blood samples were analysed for plasma leptin, adiponectin, CRP, IL-6 and TNF-α. Associations between neuroticism and biomarkers were assessed using Spearman’s correlation coefficients and generalized linear models adjusting for confounders. In the adjusted generalized linear models, neuroticism predicted the leptin/adiponectin ratio (p = 0.003), leptin (p = 0.004) and IL-6 (p = 0.001). These associations were not better explained by current major depressive disorder and/or anxiety disorder. Adiponectin, CRP and TNF-α were not associated with neuroticism. In conclusion, the findings suggest that high neuroticism is related to elevated levels of plasma leptin/adiponectin ratio, leptin and IL-6 in young adults. Young adults with high neuroticism may therefore benefit from preventive interventions to decrease the risk for future metabolic and cardiovascular morbidity, but more research is required to test this hypothesis.