bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractLakes 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

AbstractNumerous 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

AbstractScattering 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

AbstractEnergy 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

AbstractMarine 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

AbstractToxoplasma 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

AbstractPrior 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

AbstractColonomics 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

AbstractCorynebacterium 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

AbstractEvidence 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

AbstractThe 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

AbstractOne 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

AbstractRecent 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

AbstractThe 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.