bluuebunny/crossref_metadata_2025 huggingface dataset:
Coalescence of Growing Bubbles in Highly Viscous Liquids
Authors: Ohashi Masatoshi , Maruishi Takafumi , Toramaru Atsushi
Published: October 2022

Bubble coalescence in ascending magma is a key process that controls the eruption violence and the texture of volcanic pyroclasts. In the present study, we performed in situ experiments to investigate the coalescence of two growing bubbles in highly viscous liquids (102 and 1,020 Pa ⋅ s). A new experimental apparatus enables us to directly observe the drainage of the film between growing bubbles in three dimensions. We combined the experimental results and a simple scaling analysis to reveal the dynamics of film drainage in terms of a capillary number depending on the liquid viscosity η, the bubble growth rate , and the surface tension σ. The capillary number represents the interplay between the viscous force arising from bubble growth and the capillary force. At Ca ≪ 1, two adjacent bubbles retain their spherical shapes until the film ruptures, and the capillary forces control the drainage timescale. In contrast, at Ca ≫ 1, bubbles largely flatten and bubble growth itself drives film drainage. We also provide a general formula for the drainage timescale over a wide range of capillary numbers (10−3 < Ca < 101). Our results highlight the importance of bubble growth in the coalescence process. The variations of bubble shape and number density during decompression can be explained by the capillary number.
Toward Next‐Generation Lava Flow Forecasting: Development of a Fast, Physics‐Based Lava Propagation Model
Authors: Hyman David M. R. , Dietterich Hannah R. , Patrick Matthew R.
Published: October 2022

During effusive volcanic crises, the eruption and propagation of lava flows pose a significant hazard to nearby populations, homes, and infrastructure. Consequently, timely lava flow forecasts are a critical need for volcano observatory and emergency management operations. Previous lava flow modeling tools are typically either too slow to produce timely forecasts, or are fast, but lack critical aspects of lava physics or important forecasting outputs. In particular, the strong thermal stratification present in laminar, high‐Prandtl number flows has generally been neglected. Bulk rheological changes have previously been computed from cell‐averaged temperatures, assuming that the flow is thermally mixed. Here, we detail the development and initial testing of Lava2d, a new two‐dimensional depth‐averaged finite volume model of lava flow propagation over natural terrain which accounts for bulk rheological changes due to thermorheological stratification. We use a novel approach to energy conservation based on tracking cooling and solidifying at the flow base and at the moving flow surface, allowing for the estimation of more realistic vertical thermorheological profiles, while maintaining computational efficiency, producing very timely model runs. We validate our approach with three examples: comparison with theoretical propagation of crust‐dominated lava flows, comparison with a large‐scale molten basalt experiment from the Syracuse University Lava Project, and efficiency testing and comparison with the initial phase of the 1984 Mauna Loa lava flows. Our model is shown to produce rapid, realistic forecasts, making it a good candidate for operationalization in active volcanic regions such as in Hawai'i.
Linkage of Equatorial Ionization Anomaly With the Day‐To‐Day Occurrence of Postsunset Irregularities and Scintillation in Low‐Latitude Region Around 110°E
Authors: Luo Weihua , Li Heng , Xiong Chao , Zhu Zhengping , Yu Xiao , Chang Shanshan
Published: October 2022

The zonal electric field and meridional wind are two major factors to affect the formation of both equatorial ionization anomaly (EIA) and plasma irregularities in equatorial and low‐latitude regions, the correlation between the EIA characteristics and the occurrence of both irregularities and the sequent scintillation is always concerned. In this study, we investigated the relationship between the day‐to‐day occurrence of scintillation based on ground‐based GPS observations at Sanya (18.3°N, 109.6°E; dip lat.: 12.8°N) and Hongkong (22.4°N, 114.2°E; dip lat.: 16.1°N), China, and day‐to‐day variations of EIA inferred from the Gravity Recovery and Climate Experiment observations in equinoctial months (March‐April and September‐October) during high solar activities (2012–2014). The results indicated that EIA strength can be linked with the day‐to‐day occurrence of post‐sunset irregularities and scintillation, and post‐sunset scintillation would be likely to occur as electron density above the EIA trough is low and EIA is strong. There are other key factors to affect the initiation and evolution of irregularities besides zonal electric field and meridional wind, such as seed perturbations or wave‐like structures. The day‐to‐day variations of electron density in EIA regions, EIA strength and EIA asymmetry were not well correlated quantitatively with the scintillation intensity representing by daily S4 maximum in low‐latitude region. These results can help us understand and predict the day‐to‐day variability of irregularities and scintillation in equatorial and low‐latitude regions.
Analog and Numerical Modeling of Rift‐Rift‐Rift Triple Junctions
Authors: Maestrelli D. , Brune S. , Corti G. , Keir D. , Muluneh A. A. , Sani F.
Published: October 2022

Rift‐Rift‐Rift triple junctions are key features of emergent plate boundary networks during fragmentation of a continent. A key example of such a setting is the Afar triple junction where the African, Arabian and Somalian plates interact. We performed analog and numerical models simulating continental break‐up in a Rift‐Rift‐Rift setting to investigate the resulting structural pattern and evolution. We modified the ratio between plate velocities, and we performed single‐stage (with all plates moving at the same time) and two‐stage (where one plate first moves alone and then all the plates move simultaneously) models. Additionally, the direction of extension was changed to induce orthogonal extension in one of the three rift branches. Our models suggest that differential extension velocities in the rift branches determine the localization of the structural triple junction, which is located closer to the rift branch experiencing slower extension velocities. Furthermore, imposed velocities affect the deformation resulting in end‐member fault patterns. The effect of applying similar velocities in all rift arms is to induce a symmetric fault pattern (generating a Y‐shaped geometry). In contrast, a faster plate generates structures trending orthogonal to dominant velocity vectors, while faults associated with the movement of the slower plates remain subordinate (generating a T‐shaped pattern). Two‐stage models reveal high‐angle faults interacting at the triple junction, confirming that differential extension velocities strongly affect fault patterns. These latter models show large‐scale similarities with fault patterns observed in the Afar triple junction, providing insights into the factors controlling the structural evolution of this area.
PAF1 cooperates with YAP1 in metaplastic ducts to promote pancreatic cancer
Authors: Nimmakayala Rama Krishna , Ogunleye Ayoola O. , Parte Seema , Krishna Kumar Nivedeta , Raut Pratima , Varadharaj Venkatesh , Perumal Naveen Kumar , Nallasamy Palanisamy , Rauth Sanchita , Cox Jesse L. , Lele Subodh M. , Batra Surinder K. , Ponnusamy Moorthy P.
Published: October 2022

Acinar-to-ductal metaplasia (ADM) is a precursor lesion of pancreatic ductal adenocarcinoma (PDAC); however, the regulators of the ADM-mediated PDAC development and its targeting are poorly understood. RNA polymerase II-associated factor 1 (PAF1) maintains cancer stem cells leading to the aggressiveness of PDAC. In this study, we investigated whether PAF1 is required for the YAP1-mediated PDAC development and whether CA3 and verteporfin, small molecule inhibitors of YAP1/TEAD transcriptional activity, diminish pancreatic cancer (PC) cell growth by targeting the PAF1/YAP1 axis. Here, we demonstrated that PAF1 co-expresses and interacts with YAP1 specifically in metaplastic ducts of mouse cerulein- or KrasG12D-induced ADM and human PDAC but not in the normal pancreas. PAF1 knockdown (KD) reduced SOX9 in PC cells, and the PC cells showed elevated PAF1/YAP1 complex recruitment to the promoter of SOX9. The PAF1 KD reduced the 8xTEAD and SOX9 promoter-luciferase reporter activities in the mouse KC (KrasG12D; Pdx-1 Cre) cells and human PC cells, indicating that the PAF1 is required for the YAP1-mediated development of ADM and PC. Moreover, treatment with CA3 or verteporfin reduced the expressions of PAF1, YAP1, TEAD4, and SOX9 and decreased colony formation and stemness in KC and PC cells. CA3 treatment also reduced the viability and proliferation of PC cells and diminished the duct-like structures in KC acinar explants. CA3 or verteporfin treatment decreased the recruitment of the PAF1/YAP1 complex to the SOX9 promoter in PC cells and reduced the 8xTEAD and SOX9 promoter-luciferase reporter activities in KC and PC cells. Overall, PAF1 cooperates with YAP1 during ADM and PC development, and verteporfin and CA3 inhibit ADM and PC cell growth by targeting the PAF1/YAP1/SOX9 axis in vitro and ex vivo models. This study identified a regulatory axis of PDAC initiation and its targeting, paving the way for developing targeted therapeutic strategies for pancreatic cancer patients.
GSDME deficiency leads to the aggravation of UVB-induced skin inflammation through enhancing recruitment and activation of neutrophils
Authors: Chen Yujie , Lian Ni , Chen Sihan , Xiao Ta , Ke Yangying , Zhang Yiqun , Song Changjun , Yang Yong , Xu Song , Gu Heng , Chen Xu
Published: October 2022

Gasdermin E (GSDME)-mediated pyroptosis is induced in keratinocytes of UVB-challenged skin. The role of GSDME in UVB-caused skin damage remains unknown. To explore the role of GSDME in UVB-induced skin inflammation. We compared differences in skin appearance, histological features, keratinocyte death modalities, infiltration of immune cells, and levels of some inflammatory cytokines between Gsdme−/− mice and wild type (WT) mice after UVB exposure. We explored whether keratinocytes contribute to GSDME deficiency-caused aggravation of UVB-induced skin inflammation in GSDME knockdown keratinocyte cultured in vitro and keratinocyte-specific Gsdme conditional knockout mice. We used anti-Ly6G antibody to deplete neutrophils and explore their role in UVB-caused skin damage. Skin damage and neutrophils infiltration were aggravated in UVB-challenged Gsdme−/− mice, compared with UVB-challenged WT mice. Apoptosis and necroptosis, which were initiated together with GSDME-mediated pyroptosis in UVB-challenged WT mice, were not enhanced in UVB-challenged Gsdme−/− mice. Neutrophils activation indicators and its recruiting cytokines were increased in skin tissue of UVB-challenged Gsdme−/− mice. However, GSDME knockdown did not lead to the further increase of mRNA and secretion of TNF-α and IL-6 in UVB-challenged keratinocytes. Skin damage was not aggravated in UVB-challenged Gsdme cKO mice. Neutrophils depletion alleviated UVB-caused skin damage in WT mice and Gsdme−/− mice, and eliminated its aggravation in Gsdme−/− mice. This study demonstrates that GSDME plays a restrictive role in UVB-induced skin damage through inhibiting excessive recruitment and activation of neutrophils in the immune microenvironment in UVB-caused skin inflammation. However, keratinocytes might not contribute to this restrictive function.
RUNDC3A/SNAP25/Akt signaling mediates tumor progression and chemoresistance in gastric neuroendocrine carcinoma
Authors: Lin Ziqi , Kwok Hang Fai
Published: October 2022

Gastric neuroendocrine carcinoma (GNEC), a heterogeneous group of neuroendocrine neoplasms (NENs) derived from gastric neuroendocrine cells, has been shown to be more aggressive and chemoresistant in gastric cancer, which contributes to the poor prognosis. We analysed transcriptome profiles of tumor/non-tumor tissue from GNEC patients and GNEC cell lines to explore the underlying mechanisms. Our results suggest a critical role for synaptosomal-associated protein 25 kDa (SNAP25) in GNEC. SNAP25 was found to stabilize Akt via modulating its monoubiquitination. We further identified RUN domain containing 3A (RUNDC3A) as an upstream molecule that regulates SNAP25 expression, which is associated with tumor progression and chemoresistance in GNECs. Moreover, these findings were extended into multiple NENs including neuroendocrine carcinomas in the intestinal tract, lungs and pancreas. Identifying the RUNDC3A/SNAP25/Akt axis in NENs may provide a novel insight into the potential therapeutic target for patients with NENs.
Mapping global lake dynamics reveals the emerging roles of small lakes
Authors: Pi Xuehui , Luo Qiuqi , Feng Lian , Xu Yang , Tang Jing , Liang Xiuyu , Ma Enze , Cheng Ran , Fensholt Rasmus , Brandt Martin , Cai Xiaobin , Gibson Luke , Liu Junguo , Zheng Chunmiao , Li Weifeng , Bryan Brett A.
Published: October 2022

Lakes are important natural resources and carbon gas emitters and are undergoing rapid changes worldwide in response to climate change and human activities. A detailed global characterization of lakes and their long-term dynamics does not exist, which is however crucial for evaluating the associated impacts on water availability and carbon emissions. Here, we map 3.4 million lakes on a global scale, including their explicit maximum extents and probability-weighted area changes over the past four decades. From the beginning period (1984–1999) to the end (2010–2019), the lake area increased across all six continents analyzed, with a net change of +46,278 km2, and 56% of the expansion was attributed to reservoirs. Interestingly, although small lakes (<1 km2) accounted for just 15% of the global lake area, they dominated the variability in total lake size in half of the global inland lake regions. The identified lake area increase over time led to higher lacustrine carbon emissions, mostly attributed to small lakes. Our findings illustrate the emerging roles of small lakes in regulating not only local inland water variability, but also the global trends of surface water extent and carbon emissions.
Exportin 4 depletion leads to nuclear accumulation of a subset of circular RNAs
Authors: Chen Liang , Wang Yucong , Lin Jiamei , Song Zhenxing , Wang Qinwei , Zhao Wenfang , Wang Yan , Xiu Xiaoyu , Deng Yuqi , Li Xiuzhi , Li Qiqi , Wang Xiaolin , Li Jingxin , Liu Xu , Liu Kunpeng , Zhou Jincong , Li Kuan , Liu Yuchan , Liao Shanhui , Deng Qin , Xu Chao , Sun Qianwen , Wu Shengzhou , Zhang Kaiming , Guan Min-Xin , Zhou Tianhua , Sun Fei , Cai Xiujun , Huang Chuan , Shan Ge
Published: October 2022

Numerous RNAs are exported from the nucleus, abnormalities of which lead to cellular complications and diseases. How thousands of circular RNAs (circRNAs) are exported from the nucleus remains elusive. Here, we provide lines of evidence to demonstrate a link between the conserved Exportin 4 (XPO4) and nuclear export of a subset of circRNAs in metazoans. Exonic circRNAs (ecircRNAs) with higher expression levels, larger length, and lower GC content are more sensitive to XPO4 deficiency. Cellular insufficiency of XPO4 leads to nuclear circRNA accumulation, circRNA:DNA (ciR-loop) formation, linear RNA:DNA (liR-loop) buildup, and DNA damage. DDX39 known to modulate circRNA export can resolve ciR-loop, and splicing factors involved in the biogenesis of circRNAs can also affect the levels of ciR-loop. Testis and brain are two organs with high abundance of circRNAs, and insufficient XPO4 levels are detrimental, as Xpo4 heterozygous mice display male infertility and neural phenotypes. Increased levels of ciR-loop, R-loop, and DNA damage along with decreased cell numbers are observed in testis and hippocampus of Xpo4 heterozygotes. This study sheds light on the understandings of mechanism of circRNA export and reveals the significance of efficient nuclear export of circRNAs in cellular physiology.
Tracking moving objects through scattering media via speckle correlations
Authors: Jauregui-Sánchez Y. , Penketh H. , Bertolotti J.
Published: October 2022

Scattering can rapidly degrade our ability to form an optical image, to the point where only speckle-like patterns can be measured. Truly non-invasive imaging through a strongly scattering obstacle is difficult, and usually reliant on a computationally intensive numerical reconstruction. In this work we show that, by combining the cross-correlations of the measured speckle pattern at different times, it is possible to track a moving object with minimal computational effort and over a large field of view.
The weather affects air conditioner purchases to fill the energy efficiency gap
Authors: He Pan , Liu Pengfei , Qiu Yueming , Liu Lufan
Published: October 2022

Energy efficiency improvement is often hindered by the energy efficiency gap. This paper examines the effect of short-run temperature fluctuations on the Energy Star air conditioner purchases in the United States from 2006 to 2019 using transaction-level data. Results show that the probability of purchasing an Energy Star air conditioner increases as the weekly temperature before the transaction deviates from 20–22 °C. A larger response is related to fewer cooling degree days in the previous years, higher electricity prices/income/educational levels/age/rate of owners, more common use of electricity, and stronger concern about climate change. 1 °C increase and decrease from 21 °C would lead to a reduction of total energy expenditure by 35.46 and 17.73 million dollars nationwide (0.13% and 0.06% of the annual total energy expenditure on air conditioning), respectively. Our findings have important policy implications for demand-end interventions to incorporate the potential impact of the ambient physical environment.
Hydrogen-bonds mediate liquid-liquid phase separation of mussel derived adhesive peptides
Authors: Guo Qi , Zou Guijin , Qian Xuliang , Chen Shujun , Gao Huajian , Yu Jing
Published: October 2022

Marine mussels achieve strong underwater adhesion by depositing mussel foot proteins (Mfps) that form coacervates during the protein secretion. However, the molecular mechanisms that govern the phase separation behaviors of the Mfps are still not fully understood. Here, we report that GK-16*, a peptide derived from the primary adhesive protein Mfp-5, forms coacervate in seawater conditions. Molecular dynamics simulations combined with point mutation experiments demonstrate that Dopa- and Gly- mediated hydrogen-bonding interactions are essential in the coacervation process. The properties of GK-16* coacervates could be controlled by tuning the strength of the electrostatic and Dopa-mediated hydrogen bond interactions via controlling the pH and salt concentration of the solution. The GK-16* coacervate undergoes a pH induced liquid-to-gel transition, which can be utilized for the underwater delivery and curing of the adhesives. Our study provides useful molecular design principles for the development of mussel-inspired peptidyl coacervate adhesives with tunable properties.
A unique Toxoplasma gondii haplotype accompanied the global expansion of cats
Authors: Galal Lokman , Ariey Frédéric , Gouilh Meriadeg Ar , Dardé Marie-Laure , Hamidović Azra , Letourneur Franck , Prugnolle Franck , Mercier Aurélien
Published: October 2022

Toxoplasma gondii is a cyst-forming apicomplexan parasite of virtually all warm-blooded species, with all true cats (Felidae) as definitive hosts. It is the etiologic agent of toxoplasmosis, a disease causing substantial public health burden worldwide. Few intercontinental clonal lineages represent the large majority of isolates worldwide. Little is known about the evolutionary forces driving the success of these lineages, the timing and the mechanisms of their global dispersal. In this study, we analyse a set of 156 genomes and we provide estimates of T. gondii mutation rate and generation time. We elucidate how the evolution of T. gondii populations is intimately linked to the major events that have punctuated the recent history of cats. We show that a unique haplotype, whose length represents only 0.16% of the whole T. gondii genome, is common to all intercontinental lineages and hybrid populations derived from these lineages. This haplotype has accompanied wildcats (Felis silvestris) during their emergence from the wild to domestic settlements, their dispersal in the Old World, and their expansion in the last five centuries to the Americas. The selection of this haplotype is most parsimoniously explained by its role in sexual reproduction of T. gondii in domestic cats.
Understanding change in COVID-19 vaccination intention with network analysis of longitudinal data from Dutch adults
Authors: Chambon Monique , Kammeraad Wesley G. , van Harreveld Frenk , Dalege Jonas , Elberse Janneke E. , van der Maas Han L. J.
Published: October 2022

Prior research into the relationship between attitudes and vaccination intention is predominantly cross-sectional and therefore does not provide insight into directions of relations. During the COVID-19 vaccines development and enrollment phase, we studied the temporal dynamics of COVID-19 vaccination intention in relation to attitudes toward COVID-19 vaccines and the pandemic, vaccination in general, social norms and trust. The data are derived from a longitudinal survey study with Dutch participants from a research panel (N = 744; six measurements between December 2020 and May 2021; age 18–84 years [M = 53.32]) and analyzed with vector-autoregression network analyses. While cross-sectional results indicated that vaccination intention was relatively strongly related to attitudes toward the vaccines, results from temporal analyses showed that vaccination intention mainly predicted other vaccination-related variables and to a lesser extent was predicted by variables. We found a weak predictive effect from social norm to vaccination intention that was not robust. This study underlines the challenge of stimulating uptake of new vaccines developed during pandemics, and the importance of examining directions of effects in research into vaccination intention.
COLONOMICS - integrative omics data of one hundred paired normal-tumoral samples from colon cancer patients
Authors: Díez-Villanueva Anna , Sanz-Pamplona Rebeca , Solé Xavier , Cordero David , Crous-Bou Marta , Guinó Elisabet , Lopez-Doriga Adriana , Berenguer Antoni , Aussó Susanna , Paré-Brunet Laia , Obón-Santacana Mireia , Moratalla-Navarro Ferran , Salazar Ramon , Sanjuan Xavier , Santos Cristina , Biondo Sebastiano , Diez-Obrero Virginia , Garcia-Serrano Ainhoa , Alonso Maria Henar , Carreras-Torres Robert , Closa Adria , Moreno Víctor
Published: October 2022

Colonomics is a multi-omics dataset that includes 250 samples: 50 samples from healthy colon mucosa donors and 100 paired samples from colon cancer patients (tumor/adjacent). From these samples, Colonomics project includes data from genotyping, DNA methylation, gene expression, whole exome sequencing and micro-RNAs (miRNAs) expression. It also includes data from copy number variation (CNV) from tumoral samples. In addition, clinical data from all these samples is available. The aims of the project were to explore and integrate these datasets to describe colon cancer at molecular level and to compare normal and tumoral tissues. Also, to improve screening by finding biomarkers for the diagnosis and prognosis of colon cancer. This project has its own website including four browsers allowing users to explore Colonomics datasets. Since generated data could be reuse for the scientific community for exploratory or validation purposes, here we describe omics datasets included in the Colonomics project as well as results from multi-omics layers integration.
A manually curated compendium of expression profiles for the microbial cell factory Corynebacterium glutamicum
Authors: Kranz Angela , Polen Tino , Kotulla Christian , Arndt Annette , Bosco Graziella , Bussmann Michael , Chattopadhyay Ava , Cramer Annette , Davoudi Cedric-Farhad , Degner Ursula , Diesveld Ramon , Freiherr von Boeselager Raphael , Gärtner Kim , Gätgens Cornelia , Georgi Tobias , Geraths Christian , Haas Sabine , Heyer Antonia , Hünnefeld Max , Ishige Takeru , Kabus Armin , Kallscheuer Nicolai , Kever Larissa , Klaffl Simon , Kleine Britta , Kočan Martina , Koch-Koerfges Abigail , Kraxner Kim J. , Krug Andreas , Krüger Aileen , Küberl Andreas , Labib Mohamed , Lange Christian , Mack Christina , Maeda Tomoya , Mahr Regina , Majda Stephan , Michel Andrea , Morosov Xenia , Müller Olga , Nanda Arun M. , Nickel Jens , Pahlke Jennifer , Pfeifer Eugen , Platzen Laura , Ramp Paul , Rittmann Doris , Schaffer Steffen , Scheele Sandra , Spelberg Stephanie , Schulte Julia , Schweitzer Jens-Eric , Sindelar Georg , Sorger-Herrmann Ulrike , Spelberg Markus , Stansen Corinna , Tharmasothirajan Apilaasha , Ooyen Jan van , van Summeren-Wesenhagen Philana , Vogt Michael , Witthoff Sabrina , Zhu Lingfeng , Eikmanns Bernhard J. , Oldiges Marco , Schaumann Georg , Baumgart Meike , Brocker Melanie , Eggeling Lothar , Freudl Roland , Frunzke Julia , Marienhagen Jan , Wendisch Volker F. , Bott Michael
Published: October 2022

Corynebacterium glutamicum is the major host for the industrial production of amino acids and has become one of the best studied model organisms in microbial biotechnology. Rational strain construction has led to an improvement of producer strains and to a variety of novel producer strains with a broad substrate and product spectrum. A key factor for the success of these approaches is detailed knowledge of transcriptional regulation in C. glutamicum. Here, we present a large compendium of 927 manually curated microarray-based transcriptional profiles for wild-type and engineered strains detecting genome-wide expression changes of the 3,047 annotated genes in response to various environmental conditions or in response to genetic modifications. The replicates within the 927 experiments were combined to 304 microarray sets ordered into six categories that were used for differential gene expression analysis. Hierarchical clustering confirmed that no outliers were present in the sets. The compendium provides a valuable resource for future fundamental and applied research with C. glutamicum and contributes to a systemic understanding of this microbial cell factory.

Measurement(s)
Gene Expression Analysis

Technology Type(s)
Two Color Microarray

Factor Type(s)
WT condition A vs. WT condition B • Plasmid-based gene overexpression in parental strain vs. parental strain with empty vector control • Deletion mutant vs. parental strain

Sample Characteristic - Organism
Corynebacterium glutamicum

Sample Characteristic - Environment
laboratory environment

Sample Characteristic - Location
Germany
Cooking methods are associated with inflammatory factors, renal function, and other hormones and nutritional biomarkers in older adults
Authors: Rodríguez-Ayala Montserrat , Banegas José Ramón , Ortolá Rosario , Gorostidi Manuel , Donat-Vargas Carolina , Rodríguez-Artalejo Fernando , Guallar-Castillón Pilar
Published: October 2022

Evidence of the role of cooking methods on inflammation and metabolic health is scarce due to the paucity of large-size studies. Our aim was to evaluate the association of cooking methods with inflammatory markers, renal function, and other hormones and nutritional biomarkers in a general population of older adults. In a cross sectional analysis with 2467 individuals aged ≥ 65, dietary and cooking information was collected using a validated face-to-face dietary history. Eight cooking methods were considered: raw, boiling, roasting, pan-frying, frying, toasting, sautéing, and stewing. Biomarkers were analyzed in a central laboratory following standard procedures. Marginal effects from generalized linear models were calculated and percentage differences (PD) of the multivariable-adjusted means of biomarkers between extreme sex-specific quintiles (Q) of cooking methods consumption were computed ([Q5 − Q1/Q1] × 100). Participants’ mean age was 71.6 years (53% women). Significant PD for the highest vs lowest quintile of raw food consumption was − 54.7% for high sensitivity-C reactive protein (hs-CRP), − 11.9% for neutrophils, − 11.9% for Growth Differentiation Factor-15, − 25.0% for Interleukin-6 (IL-6), − 12.3% for urinary albumin, and − 10.3% for uric acid. PD for boiling were − 17.8% for hs-CRP, − 12.4% for urinary albumin, and − 11.3% for thyroid-stimulating hormone. Concerning pan-frying, the PD was − 23.2% for hs-CRP, − 11.5% for IL-6, − 16.3% for urinary albumin and 10.9% for serum vitamin D. For frying, the PD was a 25.7% for hs-CRP, and − 12.6% for vitamin D. For toasting, corresponding figures were − 21.4% for hs-CRP, − 11.1% for IL-6 and 10.6% for vitamin D. For stewing, the PD was 13.3% for hs-CRP. Raw, boiling, pan-frying, and toasting were associated with healthy profiles as for inflammatory markers, renal function, thyroid hormones, and serum vitamin D. On the contrary, frying and, to a less extent, stewing showed unhealthier profiles. Cooking methods not including added fats where healthier than those with added fats heated at high temperatures or during longer periods of time.
The human splenic microcirculation is entirely open as shown by 3D models in virtual reality
Authors: Steiniger Birte S. , Pfeffer Henriette , Gaffling Simone , Lobachev Oleg
Published: October 2022

The human spleen is equipped with an organ-specific microcirculation. The initial part of the venous circulation is formed by spleen-specific large microvessels, the sinuses. Sinuses eventually fuse to form venules and veins. For more than 170 years there have been debates, whether splenic red pulp capillaries join sinuses, i.e., whether the microcirculation is closed or open—or even simultaneously closed and open. We have now solved this question by three-dimensional reconstruction of a limited number of immunostained serial sections of red and white pulp areas, which were visualized in virtual reality. Splenic capillaries have special end structures exhibiting multiple small diverging endothelial cell processes, which always keep a certain distance to the walls of sinuses. Only very few capillary ends were difficult to diagnose. Positive identification of these end structures permits to conclude that the human splenic microcirculation is entirely open. This is also true for the perifollicular capillary network and for capillaries close to red pulp venules. Follicles are supplied by a relatively dense open perifollicular capillary net, which is primarily, but not exclusively, fed by sheathed and few non-sheathed capillaries from the surrounding red pulp network.
Higher off-target amplicon detection rate in MiSeq v3 compared to v2 reagent kits in the context of 16S-rRNA-sequencing
Authors: Odendaal Mari-Lee , Groot James A. , Hasrat Raiza , Chu Mei Ling J. N. , Franz Eelco , Bogaert Debby , Bosch Thijs , de Steenhuijsen Piters Wouter A. A.
Published: October 2022

One of the most widely used techniques in microbiota research is 16S-rRNA-sequencing. Several laboratory processes have been shown to impact sequencing results, especially in low biomass samples. Low biomass samples are prone to off-target amplification, where instead of bacterial DNA, host DNA is erroneously amplified. Knowledge on the laboratory processes influencing off-target amplification and detection is however scarce. We here expand on previous findings by demonstrating that off-target amplification is not limited to invasive biopsy samples, but is also an issue in low bacterial biomass respiratory (mucosal) samples, especially when below 0.3 pg/μL. We show that off-target amplification can partly be mitigated by using gel-based library purification methods. Importantly, we report a higher off-target amplicon detection rate when using MiSeq reagent kit v3 compared to v2 (mean 13.3% vs 0.1% off-target reads/sample, respectively), possibly as a result of differences in reagents or sequencing recipes. However, since after bioinformatic removal of off-target reads, MiSeq reagent kit v3 still results in a twofold higher number of reads when compared to v2, v3 is still preferred over v2. Together, these results add to the growing knowledge base on off-target amplification and detection, allowing researchers to anticipate this problem in 16S-rRNA-based microbiome studies involving low biomass samples.
Comprehensive experimental investigation of the effective parameters on stability of silica nanoparticles during low salinity water flooding with minimum scale deposition into sandstone reservoirs
Authors: Bijani Masoud , Khamehchi Ehsan , Shabani Mehdi
Published: October 2022

Recent studies showed the high potential of nanofluids as an enhanced oil recovery (EOR) agent in oil reservoirs. This study aimed to investigate the effects of salts and ions, the salinity of aqueous solution, total dissolved solids (TDS), scale deposition of mixing brines, surface charge as zeta potential (ZP) value, and pH of injected brines as low salinity water (LSW) on the stability of silica nanoparticles (NPs). The experiments were conducted on the stability of silica NPs at different concentrations and brines to determine optimum salinity, dilution, cations, and anions concentrations. The results showed that 10 times diluted seawater (SW#10D) was optimum low salinity water (OLSW) as injected LSW and water-based nanofluids. Results showed that by decreasing the salinity, increasing seawater dilution, and removing Mg2+ and Ca2+ cations, the amount of scale deposition decreased, and the brine's brine's brine stability of NPs in brine improved. At the optimum salinity and dilution conditions, compared with other salinities, there was less scale formation with more nanofluid stability. Obtained results from ZP measurements and dynamic light scattering (DLS) showed that by removing divalent ions (Mg2+ and Ca2+) of water-based nanofluid (low salinity hard water (LSHW) composition), more NPs were attached to the surface due to the reduction in repulsive forces between the NPs. Therefore, at optimum low salinity soft water (OLSSW), more wettability alteration occurred compared with optimum low salinity hard water (OLSHW) due to the more stability of NPs in OLSSW. The obtained results from the contact angle measurements, surface adsorption of the NPs by FESEM images, and ZP measurements showed that the predominant mechanism in enhancing oil recovery by nanofluid was the wettability alteration by disjoining pressure. According to wettability alteration results, the silica NPs with an optimized concentration in the optimized LSHW and LSSW compositions could be improved the wettability alteration by up to 23.37% and 55.81% compared with the without NPs. The optimized LSSW compared with LSHW composition could be improved the wettability alteration by up to 11.69%. In addition, OLSSW-based nanofluid compared with OLSHW could be increased wettability alteration toward strongly water-wet by up to 33.44%.
LZS-1, Lanzarote (Canary Island, Spain) lunar (Apollo 14) basaltic soil simulant
Authors: Alberquilla Fernando , Martínez-Frías Jesús , García-Baonza Valentín , Lunar Rosario
Published: October 2022

The search for Terrestrial Analogues is essential for the development of future permanent or semi-permanent lunar bases. Terrestrial Analogues are zones where it is possible to probe not only scientific instruments, but also other astronaut capabilities in an environment that is similar to the geological context, geomorphology, mineralogy, geochemistry, etc. that we can find on Mars, the Moon and even asteroids. This work has focused on a multi-analytical characterization of Peñas de Tao geosite basalts in Lanzarote (Canary Islands, Spain). This characterization starts from a field campaign in which 3000 g of basalt rocks were selected. Subsequently, they were analysed by different techniques to determine their composition at a mineralogical and geochemical level, and the results were compared with data from other lunar simulants and from the Apollo 14 mission. After that, a set of petrophysical tests was carried out in order to determine its physical properties and evaluate its capacity as an analogous material for use in situ as a resource for further geological and astrobiological (future lunar habitability) essays.
Exploring the over-time, multifaceted impacts of three COVID-19 lockdowns on aspects of capability, wellbeing and mental health across vulnerabilities in Austria
Authors: Helter Timea M. , Łaszewska Agata , Simon Judit
Published: October 2022

The Austrian government imposed multiple major lockdowns during the COVID-19 pandemic, but the relevant measures and their perceptions varied over time. The aim of this study was to compare the over-time impacts of the three COVID-19 lockdowns between March 2020 and December 2021 for (capability) wellbeing and mental health in Austria. Adult Austrian residents (n = 87) completed an online survey about their experiences during three COVID-19 lockdowns, including capabilities (OxCAP-MH), depression and anxiety (HADS), and general wellbeing (WHO-5). Differences across the baseline and follow-up scores of these instruments were summarised by demographic/socioeconomic characteristics. Longitudinal comparisons of the impacts of the lockdowns were conducted using random effect models on panel data for overall instrument scores and individual capability items. The levels of (capability) wellbeing and mental health decreased for most respondents across the three lockdowns: average 2.4% reduction in OxCAP-MH scores, 18.8% and 9% increases in HADS depression and anxiety subscale scores respectively, and 19.7% reduction in WHO-5 score between the first and third lockdowns. Mental health treatment prior to the pandemic, social support and satisfaction with government measures were the most influential characteristics that determine the association with impacts of the chain of lockdowns. Our study is the first to assess the differential capability limiting aspects of lockdowns over time alongside their impacts on mental health and general wellbeing and calls for special attention for mental health patients, isolation and satisfaction with government measures.
Drug resistance and population structure of Plasmodium falciparum and Plasmodium vivax in the Peruvian Amazon
Authors: Villena Fredy E. , Sanchez Juan F. , Nolasco Oscar , Braga Greys , Ricopa Leonila , Barazorda Keare , Salas Carola J. , Lucas Carmen , Lizewski Stephen E. , Joya Christie A. , Gamboa Dionicia , Delgado-Ratto Christopher , Valdivia Hugo O.
Published: October 2022

Malaria is a major health problem in Peru despite substantial progress achieved by the ongoing malaria elimination program. This study explored the population genetics of 63 Plasmodium falciparum and 170 P. vivax cases collected in the Peruvian Amazon Basin between 2015 and 2019. Microscopy and PCR were used for malaria detection and positive samples were genotyped at neutral and drug resistance-associated regions. The P. falciparum population exhibited a low nucleotide diversity (π = 0.02) whereas the P. vivax population presented a higher genetic diversity (π = 0.34). All P. falciparum samples (n = 63) carried chloroquine (CQ) resistant mutations on Pfcrt. Most P. falciparum samples (53 out of 54) carried sulfadoxine (SD) resistant mutations on Pfdhfr and Pfdhps. No evidence was found of artemisinin resistance mutations on kelch13. Population structure showed that a single cluster accounted for 93.4% of the P. falciparum samples whereas three clusters were found for P. vivax. Our study shows a low genetic diversity for both species with significant differences in genetic sub-structuring. The high prevalence of CQ-resistance mutations could be a result of indirect selection pressures driven by the P. vivax treatment scheme. These results could be useful for public health authorities to safeguard the progress that Peru has achieved towards malaria elimination.
Metabolic, physiological and anatomical responses of soybean plants under water deficit and high temperature condition
Authors: Vital Roberto Gomes , Müller Caroline , Freire Francisco Bruno Silva , Silva Fábia Barbosa , Batista Priscila Ferreira , Fuentes David , Rodrigues Arthur Almeida , Moura Luciana Minervina Freitas , Daloso Danilo Menezes , Silva Adinan Alves , Merchant Andrew , Costa Alan Carlos
Published: October 2022

Water deficit (WD) combined with high temperature (HT) is the major factor limiting agriculture worldwide, and it is predicted to become worse according to the current climate change scenario. It is thus important to understand how current cultivated crops respond to these stress conditions. Here we investigated how four soybean cultivars respond to WD and HT isolated or in combination at metabolic, physiological, and anatomical levels. The WD + HT increased the level of stress in soybean plants when compared to plants under well-watered (WW), WD, or HT conditions. WD + HT exacerbates the increases in ascorbate peroxidase activity, which was associated with the greater photosynthetic rate in two cultivars under WD + HT. The metabolic responses to WD + HT diverge substantially from plants under WW, WD, or HT conditions.Myo-inositol and maltose were identified as WD + HT biomarkers and were connected to subnetworks composed of catalase, amino acids, and both root and leaf osmotic potentials. Correlation-based network analyses highlight that the network heterogeneity increased and a higher integration among metabolic, physiological, and morphological nodes is observed under stress conditions. Beyond unveiling biochemical and metabolic WD + HT biomarkers, our results collectively highlight that the mechanisms behind the acclimation to WD + HT cannot be understood by investigating WD or HT stress separately.
Visual odometry of Rhinecanthus aculeatus depends on the visual density of the environment
Authors: Karlsson Cecilia , Willis Jay , Patel Matishalin , de Perera Theresa Burt
Published: October 2022

Distance travelled is a crucial metric that underpins an animal’s ability to navigate in the short-range. While there is extensive research on how terrestrial animals measure travel distance, it is unknown how animals navigating in aquatic environments estimate this metric. A common method used by land animals is to measure optic flow, where the speed of self-induced visual motion is integrated over the course of a journey. Whether freely-swimming aquatic animals also measure distance relative to a visual frame of reference is unclear. Using the marine fish Rhinecanthus aculeatus, we show that teleost fish can use visual motion information to estimate distance travelled. However, the underlying mechanism differs fundamentally from previously studied terrestrial animals. Humans and terrestrial invertebrates measure the total angular motion of visual features for odometry, a mechanism which does not vary with visual density. In contrast, the visual odometer used by Rhinecanthus acuelatus is strongly dependent on the visual density of the environment. Odometry in fish may therefore be mediated by a movement detection mechanism akin to the system underlying the optomotor response, a separate motion-detection mechanism used by both vertebrates and invertebrates for course and gaze stabilisation.
Protist impacts on marine cyanovirocell metabolism
Authors: Howard-Varona Cristina , Roux Simon , Bowen Benjamin P , Silva Leslie P , Lau Rebecca , Schwenck Sarah M , Schwartz Samuel , Woyke Tanja , Northen Trent , Sullivan Matthew B , Floge Sheri A
Published: October 2022

The fate of oceanic carbon and nutrients depends on interactions between viruses, prokaryotes, and unicellular eukaryotes (protists) in a highly interconnected planktonic food web. To date, few controlled mechanistic studies of these interactions exist, and where they do, they are largely pairwise, focusing either on viral infection (i.e., virocells) or protist predation. Here we studied population-level responses of Synechococcus cyanobacterial virocells (i.e., cyanovirocells) to the protist Oxyrrhis marina using transcriptomics, endo- and exo-metabolomics, photosynthetic efficiency measurements, and microscopy. Protist presence had no measurable impact on Synechococcus transcripts or endometabolites. The cyanovirocells alone had a smaller intracellular transcriptional and metabolic response than cyanovirocells co-cultured with protists, displaying known patterns of virus-mediated metabolic reprogramming while releasing diverse exometabolites during infection. When protists were added, several exometabolites disappeared, suggesting microbial consumption. In addition, the intracellular cyanovirocell impact was largest, with 4.5- and 10-fold more host transcripts and endometabolites, respectively, responding to protists, especially those involved in resource and energy production. Physiologically, photosynthetic efficiency also increased, and together with the transcriptomics and metabolomics findings suggest that cyanovirocell metabolic demand is highest when protists are present. These data illustrate cyanovirocell responses to protist presence that are not yet considered when linking microbial physiology to global-scale biogeochemical processes.
Fast charge transfer kinetics in an inorganic–organic S-scheme heterojunction photocatalyst for cooperative hydrogen evolution and furfuryl alcohol upgrading
Authors: Sun Lijuan , Wang Weikang , Kong Tingting , Jiang Haopeng , Tang Hua , Liu Qinqin
Published: October 2022

Inorganic Znln2S4 nanosheets were grown in situ on organic Tp-Tta COF nanoplates to construct an inorganic–organic S-scheme photocatalyst for synergetic hydrogen precipitation and furfuryl alcohol upgrading oxidation.
Stable phase‐centre horn antenna using 3D printed dielectric rod for aperture efficiency improvement of space‐fed antennas
Authors: Bagheri Mohammad Omid , Hassani Hamid Reza , Sebak Abdel Razik
Published: October 2022

The design strategy to stabilise the phase centre (PC) of the conventional horn antenna using a shaped dielectric rod is presented for aperture efficiency improvement of space‐fed antennas. In most practical horn antennas, PC location has significant variations with frequency leading to phase error loss and aperture efficiency reduction over the bandwidth of interest. To overcome this drawback, based on physical reasoning, shaped dielectric rods with appropriate excitation mode are designed and placed on the aperture of conventional rectangular and conical horn antennas. The simulation results show that using a shaped dielectric rod inside the horn antenna leads to a decrease in phase‐centre variations versus frequency without disturbing the radiation pattern and reflection coefficient. To investigate the performance, a conical corrugated horn antenna loaded by a conical tapered dielectric rod is used as a feed of the transmitarray antenna. Using a shaped dielectric rod fabricated by 3D printing technology, the PC variations of the proposed horn decrease from 1.06 λ to 0.08 λ over the X‐band (λ at 8 GHz). The measurement of the fabricated transmitarray antenna shows an improvement of maximum aperture efficiency from 55% to 64.7% at 10 GHz. The aperture efficiency bandwidth above 50% level is also increased from 1 to 2.2 GHz.
Joint optimisation of transmit beamspace and receive filter in frequency diversity array‐multi‐input multi‐output radar
Authors: Zhou Changlin , Wang Chunyang , Gong Jian , Tan Ming , Bao Lei , Liu Mingjie
Published: October 2022

Frequency diversity array (FDA) radar provides more degrees of freedom and can generate range‐angle‐time‐dependent beampattern. Furthermore, based on the receiver's multi‐input multi‐output (MIMO) scheme, the frequency diversity array‐multi‐input multi‐output (FDA‐MIMO) radar can develop a range‐dependent but time‐independent beampattern. Taking advantage of this feature, this article improves the signal‐to‐interference‐plus‐noise ratio and the effective suppression of interference by jointly optimising the transmit beamspace and the receive filter. Since the optimisation problem is a non‐convex problem with constant energy constraints, we transform it into two convex subproblems with restrictions. The whole algorithm follows the alternate optimisation over receive filter and transmit beamspace. By simulating challenging scenarios, we confirmed the effectiveness and superiority of the method.