bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Combined Modeling and Measurement Approach to Assess the Nodal Tide Modulation in the North Sea
Authors: Hagen Robert , Plüß Andreas , Jänicke Leon , Freund Janina , Jensen Jürgen , Kösters Frank 
Published: February 2021

AbstractThe correct representation of the 18.61‐year nodal tide is essential for an interpretation of the evolution of mean sea level, as errors cause misleading bias. The nodal tide is currently estimated by applying correction factors in harmonic analysis, which are derived from the equilibrium tide. From the equilibrium tide, correction values f for amplitude and u for phase are determined, which alter lunar tidal constituents, depending on the nodal cycle. This approach has proven to be valid for many tide gauges, even though the impact of the nodal tide in shelf seas has been shown to differ from their theoretical correction value. Hence, tidal constituents from tide records in the North Atlantic shelf region were analyzed for their nodal amplitude and phase lag with a new multiple, nonlinear regression approach, which is able to approximate the nodal modulation quantitatively and its agreement to the theoretical equilibrium tide. Results show an overestimation of the lunar M2 and N2 constituents by the equilibrium of more than 2.7% in the Wadden Sea, while O1 and K2 are underestimated by 1–4.6%, which would produce an error of 2–5 cm for example, in the German Wadden Sea. Additionally, a process‐based model of the North Sea was applied at the diurnal minimum and maximum of the nodal cycle to calculate a spatial distribution of f and u. Results confirm the spatially varying nodal satellite modulation in friction dominated, shallow water regions.
Particulate Scattering and Backscattering in Relation to the Nature of Particles in the Red Sea
Authors: Kheireddine Malika , Brewin R. J. W. , Ouhssain M. , Jones B. H. 
Published: February 2021

AbstractMeasurements of light scattering can be used to quantify the concentration and composition of oceanic particles, and resolve biogeochemical processes spanning different time and space scales. In this paper, we analyze the first dataset, collected over wide spatial scales in the Red Sea, of particulate scattering (), particulate backscattering (), particulate absorption and chlorophyll‐a concentration [Chl_a]. We fit a three‐component conceptual model relating to [Chl_a], assuming a fixed background component (), and two additional components driven by small (<2m) and large phytoplankton (>2m) ( and , respectively). We extend the approach, for the first time, to the modeling of total particulate scattering (), allowing us to retrieve the backscattering ratio for each component in the model. We observe a high backscattering ratio for the background component which, when analyzed alongside measurements of particulate absorption, suggests it is likely dominated by non‐algal (rather than algal) particles. The high contribution of non‐algal particles to at low [Chl_a] may be related to the unique conditions in the Red Sea, or more broadly, characteristic of other oceanic conditions. The work illustrates how we can combine optical measurements with conceptual models, to understand better the composition of oceanic particles and ultimately, improve monitoring of marine biogeochemical processes. Our work will also be useful for developing regional ocean‐color models for the Red Sea.
Detectable Increases in Sequential Flood‐Heatwave Events Across China During 1961–2018
Authors: Chen Yang , Liao Zhen , Shi Yan , Tian Yangmei , Zhai Panmao 
Published: February 2021

AbstractTraditional univariate analysis on weather and climate extremes failed to consider temporally compounding events and the resulting cascading impacts. A case in point is a sequence of flood and heatwave within a week, which slows recovery and amplifies damages. We show that across China, floods and heatwaves seldom occurred serially within seven days in the past, but after 2000 the probability is five‐to‐ten times higher in southern, northwestern and northeastern sectors. It is the significant increase in heatwaves that alters the clustering of independent extremes, and facilitates the emergence of sequential extremes. Typhoon‐participating sequential extremes have also increased significantly in frequency in both inland and coastal areas, with the fastest rate at around 200% decade−1 registered within the 30–35°N latitudinal band. The observed increases in sequential flood‐heatwave events are discernibly stronger and more widespread than what would be expected from pure random variability, implying a detectable role of anthropogenic forcings.
Predator-induced defence in a dinoflagellate generates benefits without direct costs
Authors: Ryderheim Fredrik , Selander Erik , Kiørboe Thomas 
Published: February 2021

Abstract
Inducible defences in phytoplankton are often assumed to come at a cost to the organism, but trade-offs have proven hard to establish experimentally. A reason for this may be that some trade-off costs only become evident under resource-limiting conditions. To explore the effect of nutrient limitation on trade-offs in toxin-producing dinoflagellates, we induced toxin production in Alexandrium minutum by chemical cues from copepods under different levels of nitrogen limitation. The effects were both nitrogen- and grazer-concentration dependent. Induced cells had higher cellular toxin content and a larger fraction of the cells was rejected by a copepod, demonstrating the clear benefits of toxin production. Induced cells also had a higher carbon and nitrogen content, despite up to 25% reduction in cell size. Unexpectedly, induced cells seemed to grow faster than controls, likely owing to a higher specific nutrient affinity due to reduced size. We thus found no clear trade-offs, rather the opposite. However, indirect ecological costs that do not manifest under laboratory conditions may be important. Inducing appropriate defence traits in response to threat-specific warning signals may also prevent larger cumulative costs from expressing several defensive traits simultaneously.
Myeloma-specific superenhancers affect genes of biological and clinical relevance in myeloma
Authors: Jia Yunlu , Zhou Jianbiao , Tan Tze King , Chung Tae-Hoon , Wong Regina Wan Ju , Chooi Jing-Yuan , Lim Julia Sze Lynn , Sanda Takaomi , Ooi Melissa , De Mel Sanjay , Soekojo Cinnie , Chen Yongxia , Zhang Enfan , Cai Zhen , Shen Peng , Ruan Jian , Chng Wee-Joo 
Published: February 2021

AbstractMultiple myeloma (MM) is an aggressive plasma cell neoplasm characterized by genomic heterogeneity. Superenhancers (SEs) are defined as large clusters of enhancers in close genomic proximity, which regulate genes for maintaining cellular identity and promote oncogenic transcription to which cancer cells highly addicted. Here, we analyzed cis-regulatory elements in MM samples with H3K27ac ChIP-seq, to identify novel SE-associated genes involved in the myeloma pathogenesis. SEs and their associated genes in cancerous tissue were compared with the control samples, and we found SE analysis alone uncovered cell-lineage-specific transcription factors and well-known oncogenes ST3GAL6 and ADM. Using a transcriptional CDK7 inhibitor, THZ1, coupled with H3K27ac ChlP-seq, we identified MAGI2 as a novel SE-associated gene of myeloma cells. Elevated MAGI2 was related to myelomagenesis with gradual increased expression from MGUS, SMM to newly diagnosed and relapsed MM. High prevalence of MAGI2 was also associated with poor survival of MM patients. Importantly, inhibition of the SE activity associated with MAGI2 decreased MAGI2 expression, inhibited cell growth and induced cell apoptosis. Mechanistically, we revealed that the oncogenic transcription factor, MAF, directly bound to the SE region and activated gene transcription. In summary, the discoveries of these acquired SEs-associated genes and the novel mechanism by which they are regulated provide new insights into MM biology and MAGI2-MAF-SE regulatory circuit offer potential novel targets for disease treatment.
A distinct metabolic response characterizes sensitivity to EZH2 inhibition in multiple myeloma
Authors: Nylund Patrick , Atienza Párraga Alba , Haglöf Jakob , De Bruyne Elke , Menu Eline , Garrido-Zabala Berta , Ma Anqi , Jin Jian , Öberg Fredrik , Vanderkerken Karin , Kalushkova Antonia , Jernberg-Wiklund Helena 
Published: February 2021

AbstractMultiple myeloma (MM) is a heterogeneous haematological disease that remains clinically challenging. Increased activity of the epigenetic silencer EZH2 is a common feature in patients with poor prognosis. Previous findings have demonstrated that metabolic profiles can be sensitive markers for response to treatment in cancer. While EZH2 inhibition (EZH2i) has proven efficient in inducing cell death in a number of human MM cell lines, we hereby identified a subset of cell lines that despite a global loss of H3K27me3, remains viable after EZH2i. By coupling liquid chromatography-mass spectrometry with gene and miRNA expression profiling, we found that sensitivity to EZH2i correlated with distinct metabolic signatures resulting from a dysregulation of genes involved in methionine cycling. Specifically, EZH2i resulted in a miRNA-mediated downregulation of methionine cycling-associated genes in responsive cells. This induced metabolite accumulation and DNA damage, leading to G2 arrest and apoptosis. Altogether, we unveiled that sensitivity to EZH2i in human MM cell lines is associated with a specific metabolic and gene expression profile post-treatment.
Magneto-optical diagnosis of symptomatic malaria in Papua New Guinea
Authors: Arndt L. , Koleala T. , Orbán Á. , Ibam C. , Lufele E. , Timinao L. , Lorry L. , Butykai Á. , Kaman P. , Molnár A. P. , Krohns S. , Nate E. , Kucsera I. , Orosz E. , Moore B. , Robinson L. J. , Laman M. , Kézsmárki I. , Karl S. 
Published: February 2021

AbstractImproved methods for malaria diagnosis are urgently needed. Here, we evaluate a novel method named rotating-crystal magneto-optical detection (RMOD) in 956 suspected malaria patients in Papua New Guinea. RMOD tests can be conducted within minutes and at low cost. We systematically evaluate the capability of RMOD to detect infections by directly comparing it with expert light microscopy, rapid diagnostic tests and polymerase chain reaction on capillary blood samples. We show that compared to light microscopy, RMOD exhibits 82% sensitivity and 84% specificity to detect any malaria infection and 87% sensitivity and 88% specificity to detect Plasmodium vivax. This indicates that RMOD could be useful in P. vivax dominated elimination settings. Parasite density correlates well with the quantitative magneto-optical signal. Importantly, residual hemozoin present in malaria-negative patients is also detectable by RMOD, indicating its ability to detect previous infections. This could be exploited to reveal transmission hotspots in low-transmission settings.
The acquisition of molecular drivers in pediatric therapy-related myeloid neoplasms
Authors: Schwartz Jason R. , Ma Jing , Kamens Jennifer , Westover Tamara , Walsh Michael P. , Brady Samuel W. , Robert Michael J. , Chen Xiaolong , Montefiori Lindsey , Song Guangchun , Wu Gang , Wu Huiyun , Branstetter Cristyn , Hiltenbrand Ryan , Walsh Michael F. , Nichols Kim E. , Maciaszek Jamie L. , Liu Yanling , Kumar Priyadarshini , Easton John , Newman Scott , Rubnitz Jeffrey E. , Mullighan Charles G. , Pounds Stanley , Zhang Jinghui , Gruber Tanja , Ma Xiaotu , Klco Jeffery M. 
Published: February 2021

AbstractPediatric therapy-related myeloid neoplasms (tMN) occur in children after exposure to cytotoxic therapy and have a dismal prognosis. The somatic and germline genomic alterations that drive these myeloid neoplasms in children and how they arise have yet to be comprehensively described. We use whole exome, whole genome, and/or RNA sequencing to characterize the genomic profile of 84 pediatric tMN cases (tMDS: n = 28, tAML: n = 56). Our data show that Ras/MAPK pathway mutations, alterations in RUNX1 or TP53, and KMT2A rearrangements are frequent somatic drivers, and we identify cases with aberrant MECOM expression secondary to enhancer hijacking. Unlike adults with tMN, we find no evidence of pre-existing minor tMN clones (including those with TP53 mutations), but rather the majority of cases are unrelated clones arising as a consequence of cytotoxic therapy. These studies also uncover rare cases of lineage switch disease rather than true secondary neoplasms.
Pd-catalyzed formal Mizoroki–Heck coupling of unactivated alkyl chlorides
Authors: Lee Geun Seok , Kim Daeun , Hong Soon Hyeok 
Published: February 2021

AbstractThe use of alkyl chlorides in Pd-catalyzed Mizoroki–Heck coupling reactions remains an unsolved problem despite their significant potential for synthetic utility and applicability. The combination of the high thermodynamic barrier of alkyl chloride activation and kinetic propensity of alkylpalladium complexes to undergo undesired β-hydride elimination provides significant challenges. Herein, a variety of alkyl chlorides, even tertiary chlorides, are shown to efficiently participate in Mizoroki–Heck cross-coupling reactions with excellent functional group compatibility under mild reaction conditions via photoinduced Pd catalysis. The reaction is applied to late-stage functionalizations of diverse biologically significant scaffolds and iterative double Mizoroki–Heck annulations, affording high molecular complexity in a single step. Notably, studies on the kinetic isotope effects in combination with density functional theory (DFT)-computations completely exclude the involvement of a previously proposed β-hydride elimination in the catalytic cycle, revealing that the chlorine atom transfer process is the key catalytic turnover step. This distinctive single-electron transfer mediated reaction pathway resolves a longstanding challenge in traditional two-electron based Pd-catalyzed Mizoroki–Heck cross-coupling with alkyl electrophiles, wherein the β-hydride elimination is involved in the formation of both the desired product and undesired by-products.
Multiple mechanisms drive genomic adaptation to extreme O2 levels in Drosophila melanogaster
Authors: Iranmehr Arya , Stobdan Tsering , Zhou Dan , Zhao Huiwen , Kryazhimskiy Sergey , Bafna Vineet , Haddad Gabriel G. 
Published: February 2021

AbstractTo detect the genomic mechanisms underlying evolutionary dynamics of adaptation in sexually reproducing organisms, we analyze multigenerational whole genome sequences of Drosophila melanogaster adapting to extreme O2 conditions over an experiment conducted for nearly two decades. We develop methods to analyze time-series genomics data and predict adaptive mechanisms. Here, we report a remarkable level of synchronicity in both hard and soft selective sweeps in replicate populations as well as the arrival of favorable de novo mutations that constitute a few asynchronized sweeps. We additionally make direct experimental observations of rare recombination events that combine multiple alleles on to a single, better-adapted haplotype. Based on the analyses of the genes in genomic intervals, we provide a deeper insight into the mechanisms of genome adaptation that allow complex organisms to survive harsh environments.
Interpenetrating interfaces for efficient perovskite solar cells with high operational stability and mechanical robustness
Authors: Dong Qingshun , Zhu Chao , Chen Min , Jiang Chen , Guo Jingya , Feng Yulin , Dai Zhenghong , Yadavalli Srinivas K. , Hu Mingyu , Cao Xun , Li Yuqian , Huang Yizhong , Liu Zheng , Shi Yantao , Wang Liduo , Padture Nitin P. , Zhou Yuanyuan 
Published: February 2021

AbstractThe perovskite solar cell has emerged rapidly in the field of photovoltaics as it combines the merits of low cost, high efficiency, and excellent mechanical flexibility for versatile applications. However, there are significant concerns regarding its operational stability and mechanical robustness. Most of the previously reported approaches to address these concerns entail separate engineering of perovskite and charge-transporting layers. Herein we present a holistic design of perovskite and charge-transporting layers by synthesizing an interpenetrating perovskite/electron-transporting-layer interface. This interface is reaction-formed between a tin dioxide layer containing excess organic halide and a perovskite layer containing excess lead halide. Perovskite solar cells with such interfaces deliver efficiencies up to 22.2% and 20.1% for rigid and flexible versions, respectively. Long-term (1000 h) operational stability is demonstrated and the flexible devices show high endurance against mechanical-bending (2500 cycles) fatigue. Mechanistic insights into the relationship between the interpenetrating interface structure and performance enhancement are provided based on comprehensive, advanced, microscopic characterizations. This study highlights interface integrity as an important factor for designing efficient, operationally-stable, and mechanically-robust solar cells.
Chromatin accessibility of circulating CD8+ T cells predicts treatment response to PD-1 blockade in patients with gastric cancer
Authors: Shin Hyun Mu , Kim Gwanghun , Kim Sangjib , Sim Ji Hyun , Choi Jiyeob , Kim Minji , Kwon Minsuk , Ye Sang-Kyu , Lee Dong-Sup , Cho Seung Woo , Kim Seung Tae , Lee Jeeyun , Kim Hang-Rae 
Published: February 2021

AbstractAlthough tumor genomic profiling has identified small subsets of gastric cancer (GC) patients with clinical benefit from anti-PD-1 treatment, not all responses can be explained by tumor sequencing alone. We investigate epigenetic elements responsible for the differential response to anti-PD-1 therapy by quantitatively assessing the genome-wide chromatin accessibility of circulating CD8+ T cells in patients’ peripheral blood. Using an assay for transposase-accessible chromatin using sequencing (ATAC-seq), we identify unique open regions of chromatin that significantly distinguish anti-PD-1 therapy responders from non-responders. GC patients with high chromatin openness of circulating CD8+ T cells are significantly enriched in the responder group. Concordantly, patients with high chromatin openness at specific genomic positions of their circulating CD8+ T cells demonstrate significantly better survival than those with closed chromatin. Here we reveal that epigenetic characteristics of baseline CD8+ T cells can be used to identify metastatic GC patients who may benefit from anti-PD-1 therapy.
Towards plant resistance to viruses using protein-only RNase P
Authors: Gobert Anthony , Quan Yifat , Arrivé Mathilde , Waltz Florent , Da Silva Nathalie , Jomat Lucile , Cohen Mathias , Jupin Isabelle , Giegé Philippe 
Published: February 2021

AbstractPlant viruses cause massive crop yield loss worldwide. Most plant viruses are RNA viruses, many of which contain a functional tRNA-like structure. RNase P has the enzymatic activity to catalyze the 5′ maturation of precursor tRNAs. It is also able to cleave tRNA-like structures. However, RNase P enzymes only accumulate in the nucleus, mitochondria, and chloroplasts rather than cytosol where virus replication takes place. Here, we report a biotechnology strategy based on the re-localization of plant protein-only RNase P to the cytosol (CytoRP) to target plant viruses tRNA-like structures and thus hamper virus replication. We demonstrate the cytosol localization of protein-only RNase P in Arabidopsis protoplasts. In addition, we provide in vitro evidences for CytoRP to cleave turnip yellow mosaic virus and oilseed rape mosaic virus. However, we observe varied in vivo results. The possible reasons have been discussed. Overall, the results provided here show the potential of using CytoRP for combating some plant viral diseases.
Laser-induced layers peeling of sputtering coatings at 1064 nm wavelength
Authors: Guo Kesheng , Wang Yanzhi , Chen Ruiyi , Zhang Yuhui , Sytchkova Anna , Zhu Meiping , Yi Kui , He Hongbo , Shao Jianda 
Published: February 2021

AbstractLarge-scale layers peeling after the laser irradiation of dual ion beam sputtering coatings is discovered and a model is established to explain it. The laser damage morphologies relate to the laser fluence, showing thermomechanical coupling failure at low energy and coating layers separation at high energy. High-pressure gradients appear in the interaction between laser and coatings, resulting in large-scale layer separation. A two-step laser damage model including defect-induced damage process and ionized air wave damage process is proposed to explain the two phenomena at different energy. At relatively high energies (higher than 20 J/cm2), ionization of the air can be initiated, leading to a peeling off effect. The peeling effect is related to the thermomechanical properties of the coating materials.
Topographical mapping of the mechanical characteristics of the human neurocranium considering the role of individual layers
Authors: Zwirner Johann , Safavi Sarah , Scholze Mario , Li Kai Chun , Waddell John Neil , Busse Björn , Ondruschka Benjamin , Hammer Niels 
Published: February 2021

AbstractThe site-dependent load-deformation behavior of the human neurocranium and the load dissipation within the three-layered composite is not well understood. This study mechanically investigated 257 human frontal, temporal, parietal and occipital neurocranial bone samples at an age range of 2 to 94 years, using three-point bending tests. Samples were tested as full-thickness three-layered composites, as well as separated with both diploë attached and removed. Right temporal samples were the thinnest samples of all tested regions (median < 5 mm; p < 0.001) and withstood lowest failure loads (median < 762 N; p < 0.001). Outer tables were thicker and showed higher failure loads (median 2.4 mm; median 264 N) than inner tables (median 1.7 mm, p < 0.001; median 132 N, p = 0.003). The presence of diploë attached to outer and inner tables led to a significant reduction in bending strength (with diploë: median < 60 MPa; without diploë: median > 90 MPa, p < 0.001). Composites (r = 0.243, p = 0.011) and inner tables with attached diploë (r = 0.214, p = 0.032) revealed positive correlations between sample thickness and age. The three-layered composite is four times more load-resistant compared to the outer table and eight times more compared to the inner table.
Homologous laminar organization of the mouse and human subiculum
Authors: Bienkowski Michael S. , Sepehrband Farshid , Kurniawan Nyoman D. , Stanis Jim , Korobkova Laura , Khanjani Neda , Clark Kristi , Hintiryan Houri , Miller Carol A. , Dong Hong-Wei 
Published: February 2021

AbstractThe subiculum is the major output component of the hippocampal formation and one of the major brain structures most affected by Alzheimer’s disease. Our previous work revealed a hidden laminar architecture within the mouse subiculum. However, the rotation of the hippocampal longitudinal axis across species makes it unclear how the laminar organization is represented in human subiculum. Using in situ hybridization data from the Allen Human Brain Atlas, we demonstrate that the human subiculum also contains complementary laminar gene expression patterns similar to the mouse. In addition, we provide evidence that the molecular domain boundaries in human subiculum correspond to microstructural differences observed in high resolution MRI and fiber density imaging. Finally, we show both similarities and differences in the gene expression profile of subiculum pyramidal cells within homologous lamina. Overall, we present a new 3D model of the anatomical organization of human subiculum and its evolution from the mouse.