bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Influence of Convectively Coupled Kelvin Waves on Atlantic Niños
Authors: Zhao Siyu , Fu Rong 
Published: April 2022

AbstractAtlantic Niños dominate the equatorial Atlantic variability during boreal summer (June–August). The coupled ocean‐atmosphere processes associated with Atlantic Niños have been extensively documented. However, the role of atmospheric convectively coupled Kelvin waves (CCKWs), which are uncorrelated to those previously identified processes, in triggering Atlantic Niños has been unclear. Here we identify CCKWs using Wheeler‐Kiladis filtering based on 10°S–10°N averaged daily outgoing longwave radiation. CCKWs propagate eastward from South America and induce surface zonal wind anomalies over the equatorial Atlantic Ocean. Strong anomalous CCKWs during spring (March–May) and their associated surface westerly wind anomalies can trigger downwelling oceanic Kelvin waves that change the east–west slope of the thermocline, consequently leading to Atlantic Niño. A causal effect network reveals that interannual sea surface temperature (SST) anomalies in the Atlantic Niño Index area and CCKWs, both in spring, are uncorrelated, but both appear to influence SST anomalies over the Atlantic Niño Index area in summer. The CCKWs are also uncorrelated to other coupled ocean‐atmosphere sources, such as El Niño–Southern Oscillation and Atlantic Meridional Mode. Among a total of 15 Atlantic Niño/Niña events identified for the period of 1980–2017, two‐thirds of the events are linked to CCKWs. In particular, three Atlantic Niña events (1982, 1994, and 2005) are mainly triggered by CCKWs, under unfavorable SST preconditions. Thus, CCKWs in spring, due to atmospheric internal variability, provide another mechanism for triggering Atlantic Niños and probably weaken their predictability.
Interannual Impact of the North Atlantic Tripole SST Mode on the Surface Potential Vorticity Over the Tibetan Plateau During Boreal Summer
Authors: Sheng Chen , He Bian , Wu Guoxiong , Liu Yimin , Zhang Shaoyu , Zhang Ping 
Published: April 2022

AbstractThe Tibetan Plateau (TP) is an important forcing in the global climate system. Compared to the extensive studies on the influence of the TP on surrounding climates, the variability of the surface potential vorticity (PV) over the TP (TPSPV) in response to other forcings is seldom discussed. In this article, the influence of the interannual mode of North Atlantic tripole sea surface temperature (NAT) on the TPSPV during boreal summer is investigated. Results show that the negative (positive) anomalous TPSPV is associated with anomalous unstable (stable) surface air, cyclonic (anticyclonic) surface circulation, and rising (sinking) motion, which favors the stronger (weaker) East Asian summer monsoon and weaker (stronger) Indian summer monsoon. Further analysis indicates that the negative TPSPV is significantly correlated with a positive NAT mode with a cold center in the middle and warm centers in the subtropic and subpolar regions. This relationship is further testified by numerical experiments. The results further demonstrate that the positive NAT forcing can stimulate a Rossby wave train aloft, which passes Scandinavia, Ural and arrives at the TP and eventually triggers a low‐level positive PV over the TP. Constrained by the PV‐θmechanism, the low‐level positive PV favors a decrease in static stability near the surface and thus leads to a negative TPSPV. Under the positive feedback between TPSPV and vertical motion, the negative TPSPV could further strengthen. Therefore, the positive NAT phase could intensify the thermal and dynamic forcings of the TP in association with TPSPV during boreal summer.
Diurnal to Intraseasonal Precipitation Variation Around the Northwestern Coast of Luzon Island: Results From YMC‐BSM 2018 Field Campaign
Authors: Yokoi Satoru , Shirooka Ryuichi , Yoneyama Kunio , Cayanan Esperanza O. , Iglesia Cynthia O. 
Published: April 2022

AbstractThis study investigates multiscale variability of summer‐time precipitation around the northwestern coast of Luzon Island, the Philippines, by analyzing in situ observation data of a field campaign in summer 2018 conducted under the Years of the Maritime Continent‐Boreal Summer Monsoon study in 2018 (YMC‐BSM 2018) project. It is found that boreal summer intraseasonal oscillation modulates activity of precipitation diurnal cycle, with active diurnal cycle observed only under easterly (offshore) wind conditions in the free troposphere. On the other hand, in the period of westerly winds, quasi‐biweekly fluctuation is observed, with two heavy precipitation events. These events are associated with further intensified westerly winds caused by westward‐propagating quasi‐biweekly oscillations. Day‐to‐day precipitation variability over land during the two events is associated with the strength of monsoon winds blowing toward the mountain range, which is modulated cooperatively by the quasi‐biweekly oscillations and tropical depressions over the South China Sea.
PPARγ phase separates with RXRα at PPREs to regulate target gene expression
Authors: Li Zhean , Luo Lingling , Yu Wenxia , Li Ping , Ou Danfeng , Liu Jia , Ma Hanhui , Sun Qinhu , Liang Aibin , Huang Cheng , Chi Tian , Huang Xingxu , Zhang Yu 
Published: April 2022

AbstractPeroxisome proliferator-activated receptor (PPAR)-γ is a key transcription activator controlling adipogenesis and lipid metabolism. PPARγ binds PPAR response elements (PPREs) as the obligate heterodimer with retinoid X receptor (RXR) α, but exactly how PPARγ orchestrates the transcriptional response is unknown. This study demonstrates that PPARγ forms phase-separated droplets in vitro and solid-like nuclear condensates in cell, which is intriguingly mediated by its DNA binding domain characterized by the zinc finger motif. Furthermore, PPARγ forms nuclear condensates at PPREs sites through phase separation to compartmentalize its heterodimer partner RXRα to initiate PPARγ-specific transcriptional activation. Finally, using an optogenetic approach, the enforced formation of PPARγ/RXRα condensates leads to preferential enrichment at PPREs sites and significantly promotes the expression of PPARγ target genes. These results define a novel mechanism by which PPARγ engages the phase separation principles for efficient and specific transcriptional activation.
Exome sequencing in individuals with cardiovascular laterality defects identifies potential candidate genes
Authors: Breuer Katinka , Riedhammer Korbinian M. , Müller Nicole , Schaidinger Birthe , Dombrowsky Gregor , Dittrich Sven , Zeidler Susanne , Bauer Ulrike M. M. , Westphal Dominik S. , Meitinger Thomas , Dakal Tikam Chand , Hitz Marc-Phillip , Breuer Johannes , Reutter Heiko , Hilger Alina C. , Hoefele Julia 
Published: April 2022

AbstractThe birth prevalence of laterality defects is about 1.1/10,000 comprising different phenotypes ranging from situs inversus totalis to heterotaxy, mostly associated with complex congenital heart defects (CHD) and situs abnormalities such as intestinal malrotation, biliary atresia, asplenia, or polysplenia. A proportion of laterality defects arise in the context of primary ciliary dyskinesia (PCD) accompanied by respiratory symptoms or infertility. In this study, exome sequencing (ES) was performed in 14 case-parent trios/quattros with clinical exclusion of PCD prior to analysis. Moreover, all cases and parents underwent detailed clinical phenotyping including physical examination, echocardiography by a skilled paediatric cardiologist and abdominal ultrasound examinations not to miss mildly affected individuals. Subsequent survey of the exome data comprised filtering for monoallelic de novo, rare biallelic, and X-linked recessive variants. In two families, rare variants of uncertain significance (VUS) in PKD1L1 and ZIC3 were identified. Both genes have been associated with laterality defects. In two of the remaining families, biallelic variants in LMBRD1 and DNAH17, respectively, were prioritized. In another family, an ultra-rare de novo variant in WDR47 was found. Extensive exome survey of 2,109 single exomes of individuals with situs inversus totalis, heterotaxy, or isolated CHD identified two individuals with novel monoallelic variants in WDR47, but no further individuals with biallelic variants in DNAH17 or LMBRD1. Overall, ES of 14 case-parent trios/quattros with cardiovascular laterality defects identified rare VUS in two families in known disease-associated genes PKD1L1 and ZIC3 and suggests DNAH17, LMBRD1, and WDR47 as potential genes involved in laterality defects.
Network- and enrichment-based inference of phenotypes and targets from large-scale disease maps
Authors: Hoch Matti , Smita Suchi , Cesnulevicius Konstantin , Lescheid David , Schultz Myron , Wolkenhauer Olaf , Gupta Shailendra 
Published: April 2022

AbstractComplex diseases are inherently multifaceted, and the associated data are often heterogeneous, making linking interactions across genes, metabolites, RNA, proteins, cellular functions, and clinically relevant phenotypes a high-priority challenge. Disease maps have emerged as knowledge bases that capture molecular interactions, disease-related processes, and disease phenotypes with standardized representations in large-scale molecular interaction maps. Various tools are available for disease map analysis, but an intuitive solution to perform in silico experiments on the maps in a wide range of contexts and analyze high-dimensional data is currently missing. To this end, we introduce a two-dimensional enrichment analysis (2DEA) approach to infer downstream and upstream elements through the statistical association of network topology parameters and fold changes from molecular perturbations. We implemented our approach in a plugin suite for the MINERVA platform, providing an environment where experimental data can be mapped onto a disease map and predict potential regulatory interactions through an intuitive graphical user interface. We show several workflows using this approach and analyze two RNA-seq datasets in the Atlas of Inflammation Resolution (AIR) to identify enriched downstream processes and upstream transcription factors. Our work improves the usability of disease maps and increases their functionality by facilitating multi-omics data integration and exploration.
Whole-genome sequences of 37 breeding line Bombyx mori strains and their phenotypes established since 1960s
Authors: Kim Seong-Wan , Kim Min Jee , Kim Seong-Ryul , Park Jeong Sun , Kim Kee-Young , Kim Ki Hwan , Kwak Woori , Kim Iksoo 
Published: April 2022

AbstractBombyx mori is a key insect in the sericulture industry and one of the very important economic animals that are responsible for not only the livelihood of many farmers internationally but also expended biomedical use. The National Institute of Agricultural Sciences of the Rural Development Administration of Korea (NIAS, RDA, Korea) has been collecting silkworm resources with various phenotypic traits from the 1960s and established breeding lines for using them as genetic resources. And these breeding line strains have been used to develop suitable F1 hybrid strains for specific use. In this study, we report the whole-genome sequences of 37 breeding line B. mori strains established over the past 60 years, along with the description of their phenotypic characteristics with photos of developmental stages. In addition, we report the example phenotypic characteristics of the F1-hybrid strain using these breeding line strains. We hope this data will be used as valuable resources to the related research community for studying B. mori and similar other insects.
Modeling and characterization of stochastic resistive switching in single Ag2S nanowires
Authors: Frick Nikolay , Hosseini Mahshid , Guilbaud Damien , Gao Ming , LaBean Thomas H. 
Published: April 2022

AbstractChalcogenide resistive switches (RS), such as Ag2S, change resistance due to the growth of metallic filaments between electrodes along the electric field gradient. Therefore, they are candidates for neuromorphic and volatile memory applications. This work analyzed the RS of individual Ag2S nanowires (NWs) and extended the basic RS model to reproduce experimental observations. The work models resistivity of the device as a percolation of the conductive filaments. It also addressed continuous fluctuations of the resistivity with a stochastic change in volume fractions of the filaments in the device. As a result, these fluctuations cause unpredictable patterns in current-voltage characteristics and include a spontaneous change in resistance of the device during the linear sweep that conventional memristor models with constant resistivity cannot represent. The parameters of the presented stochastic model of a single Ag2S NW were fitted to the experimental data and reproduced key features of RS in the physical devices. Moreover, the model suggested a non-core shell structure of the Ag2S NWs. The outcome of this work is aimed to aid in simulating large self-assembled memristive networks and help to extend existing RS models.
A novel liver cancer diagnosis method based on patient similarity network and DenseGCN
Authors: Zhang Ge , Peng Zhen , Yan Chaokun , Wang Jianlin , Luo Junwei , Luo Huimin 
Published: April 2022

AbstractLiver cancer is the main malignancy in terms of mortality rate, accurate diagnosis can help the treatment outcome of liver cancer. Patient similarity network is an important information which helps in cancer diagnosis. However, recent works rarely take patient similarity into consideration. To address this issue, we constructed patient similarity network using three liver cancer omics data, and proposed a novel liver cancer diagnosis method consisted of similarity network fusion, denoising autoencoder and dense graph convolutional neural network to capitalize on patient similarity network and multi omics data. We compared our proposed method with other state-of-the-art methods and machine learning methods on TCGA-LIHC dataset to evaluate its performance. The results confirmed that our proposed method surpasses these comparison methods in terms of all the metrics. Especially, our proposed method has attained an accuracy up to 0.9857.
A machine learning algorithm for electrocardiographic fQRS quantification validated on multi-center data
Authors: Villa Amalia , Vandenberk Bert , Kenttä Tuomas , Ingelaere Sebastian , Huikuri Heikki V , Zabel Markus , Friede Tim , Sticherling Christian , Tuinenburg Anton , Malik Marek , Van Huffel Sabine , Willems Rik , Varon Carolina 
Published: April 2022

AbstractFragmented QRS (fQRS) is an electrocardiographic (ECG) marker of myocardial conduction abnormality, characterized by additional notches in the QRS complex. The presence of fQRS has been associated with an increased risk of all-cause mortality and arrhythmia in patients with cardiovascular disease. However, current binary visual analysis is prone to intra- and inter-observer variability and different definitions are problematic in clinical practice. Therefore, objective quantification of fQRS is needed and could further improve risk stratification of these patients. We present an automated method for fQRS detection and quantification. First, a novel robust QRS complex segmentation strategy is proposed, which combines multi-lead information and excludes abnormal heartbeats automatically. Afterwards extracted features, based on variational mode decomposition (VMD), phase-rectified signal averaging (PRSA) and the number of baseline-crossings of the ECG, were used to train a machine learning classifier (Support Vector Machine) to discriminate fragmented from non-fragmented ECG-traces using multi-center data and combining different fQRS criteria used in clinical settings. The best model was trained on the combination of two independent previously annotated datasets and, compared to these visual fQRS annotations, achieved Kappa scores of 0.68 and 0.44, respectively. We also show that the algorithm might be used in both regular sinus rhythm and irregular beats during atrial fibrillation. These results demonstrate that the proposed approach could be relevant for clinical practice by objectively assessing and quantifying fQRS. The study sets the path for further clinical application of the developed automated fQRS algorithm.
Characterizing tuberculosis transmission dynamics in high-burden urban and rural settings
Authors: Smith Jonathan P. , Oeltmann John E. , Hill Andrew N. , Tobias James L. , Boyd Rosanna , Click Eleanor S. , Finlay Alyssa , Mondongo Chawangwa , Zetola Nicola M. , Moonan Patrick K. 
Published: April 2022

AbstractMycobacterium tuberculosistransmission dynamics in high-burden settings are poorly understood. Growing evidence suggests transmission may be characterized by extensive individual heterogeneity in secondary cases (i.e., superspreading), yet the degree and influence of such heterogeneity is largely unknown and unmeasured in high burden-settings. We conducted a prospective, population-based molecular epidemiology study of TB transmission in both an urban and rural setting of Botswana, one of the highest TB burden countries in the world. We used these empirical data to fit two mathematical models (urban and rural) that jointly quantified both the effective reproductive number,$$R$$R, and the propensity for superspreading in each population. We found both urban and rural populations were characterized by a high degree of individual heterogeneity, however such heterogeneity disproportionately impacted the rural population: 99% of secondary transmission was attributed to only 19% of infectious cases in the rural population compared to 60% in the urban population and the median number of incident cases until the first outbreak of 30 cases was only 32 for the rural model compared to 791 in the urban model. These findings suggest individual heterogeneity plays a critical role shaping local TB epidemiology within subpopulations.
3D-printed model and osteotomy template technique compared with conventional closing-wedge osteotomy in cubitus varus deformity
Authors: Li Jin , Wang Jing , Rai Saroj , Ze RenHao , Hong Pan , Wang ShangYu , Tang Xin 
Published: April 2022

AbstractCubitus varus deformity is the most common late complication of malunited supracondylar fracture that requires corrective osteotomy and fixation. From 2009 to 2017, 40 consecutive patients with cubitus varus deformity were included. Twenty patients underwent the conventional closing-wedge osteotomy (conventional group), while the other twenty patients underwent the 3D-printed model and osteotomy template osteotomy (3D-printed template group). The functional outcome was evaluated using the Mayo Elbow Performance Index (MEPI) Score and Flynn criteria. There were no statistically significant differences were observed regarding the humerus-elbow-wrist angle and tilting angle between the two groups, both preoperatively and postoperatively at 24 months. No statistically significant differences were observed regarding the elbow ROM (127.0 ± 4.7° VS 128.9 ± 3.8°) and MEPI score (93.5 ± 3.3 VS 94.3 ± 4.1) between the groups. All patients were satisfied both cosmetically and functionally as per the Flynn criteria and MEPI score. The conventional osteotomy and 3D-printed model and osteotomy template techniques both met the treatment requirements of cubitus varus deformity. The 3D-printed template technique showed better osteotomy accuracy, but no significant advantage regarding the functional and cosmetic results than conventional osteotomy.
Imaging furcation defects with low-dose cone beam computed tomography
Authors: Ruetters Maurice , Gehrig Holger , Kim Ti-Sun , Bartha Valentin , Bruckner Thomas , Schwindling Franz Sebastian , Felten Anna , Lux Christopher , Sen Sinan 
Published: April 2022

AbstractDifferent cone beam computed tomography (CBCT) protocols have shown promising results for imaging furcation defects. This study evaluates the suitability of low-dose (LD)-CBCT for this purpose. Fifty-nine furcation defects of nine upper and 16 lower molars in six human cadavers were measured by a high-dose (HD)-CBCT protocol, a LD-CBCT protocol, and a surgical protocol. HD-CBCT and LD-CBCT measurements were made twice by two investigators and were compared with the intrasurgical measurements, which served as the reference. Furcation defect volumes generated from HD-CBCT and LD-CBCT imaging were segmented by one rater. Cohen’s kappa and intraclass correlation coefficient (ICC) values were calculated to determine intra- and interrater reliability. The level of significance was set at α = 0.05. In total, 59 furcation defects of nine upper and 16 lower human molars were assessed. Comparing CBCT furcation defect measurements with surgical measurements revealed a Cohen’s kappa of 0.5975 (HD-and LD-CBCT), indicating moderate agreement. All furcation defects identified by HD-CBCT were also detected by LD-CBCT by both raters, resulting in a Cohen’s kappa of 1. For interrater agreement, linear furcation defect measurements showed an ICC of 0.992 for HD-CBCT and 0.987 for LD-CBCT. The intrarater agreement was 0.994(r1)/0.992(r2) for HD-CBCT and 0.987(r1)/0.991(r2) for LD-CBCT. The intermodality agreement was 0.988(r1)/0.991(r2). Paired t-test showed no significant differences between HD-CBCT and LD-CBCT measurements. LD-CBCT is a precise and reliable method for detecting and measuring furcation defects in mandibular and maxillary molars in this experimental setting. It has the potential to improve treatment planning and treatment monitoring with a far lower radiation dose than conventional HD-CBCT.
Controlling unequal surface energy results caused by test liquids: the case of UV/O3 Treated PET
Authors: Altay Bilge Nazli , Fleming Paul D. , Rahman Md Arifur , Pekarovicova Alexandra , Myers Bruce , Aydemir Cem , Karademir Arif 
Published: April 2022

AbstractUltraviolet/ozone (UV/O3) treatment has been reported to be an effective method to modify properties such as wettability, adhesion or adsorption of plastic surfaces. The change in the surface is measured by contact angle analysis, which employs liquids and their surface tensions (ST) to estimate the surface energy (SE). We found two different practices in the scientific community: (1) the majority of researchers adopted the ST value of liquids from the literature, while (2) other researchers conducted real-time measurements in the lab under ambient conditions prior to SE estimation. To the best of our knowledge, there is no study that compares the difference between the two practices. One study was found to show different SE methods generating unequal SE values for the same substrate. However, there was no definitive conclusion backed by general thermodynamics rules. In this study, we presented (1) a statistical significance test that showed the literature and experimental ST values are significantly different, and studied (2) the effect of different liquid pairs on the SE estimation for UV/O3 treated poly(ethylene terephthalate) (PET) substrate. Modification techniques such as atmospheric pressure plasma or chemical modification were studied previously to examine PET’s wettability and the SE. The UV/O3 treatment was studied to improve adhesion and to modify its chemical properties for adsorption. In contrast, we studied (3) the effect of UV/O3 on wettability at different timeframes and addressed (4) how to control unequal SE based on a method that was refined on a rigorous thermodynamic three-phase system. It must be noted that this method can be generalized to other types of solid surfaces to estimate thermodynamically self-consistent SE values. This work also provides (5) a web-based calculator that complements computational findings available to the readership in the data availability section.