bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct observation of DNA alterations induced by a DNA disruptor
Authors: Ohshiro Takahito , Asai Ayumu , Konno Masamitsu , Ohkawa Mayuka , Komoto Yuki , Ofusa Ken , Ishii Hideshi , Taniguchi Masateru 
Published: April 2022

AbstractDNA alterations, such as base modifications and mutations, are closely related to the activity of transcription factors and the corresponding cell functions; therefore, detection of DNA alterations is important for understanding their relationships. Particularly, DNA alterations caused by exposure to exogenous molecules, such as nucleic acid analogues for cancer therapy and the corresponding changes in cell functions, are of interest in medicine for drug development and diagnosis purposes. However, detection of comprehensive direct evidence for the relationship of DNA modifications/mutations in genes, their effect on transcription factors, and the corresponding cell functions have been limited. In this study, we utilized a single-molecule electrical detection method for the direct observation of DNA alterations on transcription factor binding motifs upon exposure to a nucleic acid analogue, trifluridine (FTD), and evaluated the effects of the DNA alteration on transcriptional activity in cancer cell line cells. We found ~ 10% FTD incorporation at the transcription factor p53 binding regions in cancer cells exposed to FTD for 5 months. Additionally, through single-molecule analysis of p53-enriched DNA, we found that the FTD incorporation at the p53 DNA binding regions led to less binding, likely due to weaken the binding of p53. This work suggests that single-molecule detection of DNA sequence alterations is a useful methodology for understanding DNA sequence alterations.
Alterations in intestinal microbiota in ultramarathon runners
Authors: Sato Mika , Suzuki Yoshio 
Published: April 2022

AbstractTo date, only one study has reported changes in the gut microbiome of an ultramarathon runner before and after competing in the race. Herein we aimed to investigate changes in intestinal microbiota in nine ultramarathon runners. Eight of the nine participants ran 96.102 km (up 8062 m, down 6983 km) and one ran 99.12 km (up 8448 m, down 7369 m) within 38–44 h. Intestinal microbiota alterations were examined at three timepoints: before (Pre), after (Post), and 10 days after (Recovery) the race. The α- and β-diversity of intestinal microbiota were unaffected by the race. Six of the nine participants showed the B-type enterotype, while the remaining three showed the P-type enterotype; however, significant difference between enterotypes was not observed in the influence of the ultramarathon on intestinal microbiota. The abundance of mean Faecalibacterium prausnitzii, was significantly decreased from 2.9% (Pre) to 1.6% (Post), as well as other three butyrate producing bacteria. One participant with the largest decrease in F. prausnitzii abundance (− 85.7%) reported sluggishness and shallow sleep from Post to Recovery. Our findings revealed that the abundance of butyrate-producing bacteria is decreased in ultramarathon runners, which consequently decreases butyrate levels in the intestine and affects host immune function.
Protein and antigen profiles of third-stage larvae of Gnathostoma spinigerum assessed with next-generation sequencing transcriptomic information
Authors: Nogrado Kathyleen , Thiangtrongjit Tipparat , Adisakwattana Poom , Dekumyoy Paron , Muangnoicharoen Sant , Thawornkuno Charin , Reamtong Onrapak 
Published: April 2022

AbstractGnathostomiasis is a food-borne zoonotic disease that can affect humans who eat improperly cooked meat containg infective third-stage larvae. Definitive diagnosis is through larval recovery. However, this is an invasive technique and is impractical if the larvae have encysted in inaccessible areas of the body. Antigen or antibody detection might be more interesting techniques for diagnosis. Proteomic could elucidate diagnostic markers and improve our understanding of parasite biology. However, proteomic studies on Gnathostoma spinigerum are hampered by the lack of a comprehensive database for protein identification. This study aimed to explore the protein and antigen profiles of advanced third-stage G. spinigerum larvae (aL3Gs) using interrogation of mass spectrometry data and an in-house transcriptomic database for protein identification. Immunoproteomic analysis found 74 proteins in 24-kDa SDS-PAGE bands, which is size-specific for the immunodiagnosis of gnathostomiasis. Moreover, 13 proteins were found in 2-DE 24-kDa bands. The data suggest that collagenase 3, cathepsin B, glutathione S-transferase 1, cuticle collagen 14, major antigen, zinc metalloproteinase nas-4, major egg antigen, peroxiredoxin, and superoxide dismutase [Cu–Zn] may be good candidates for novel human gnathostomiasis diagnostic assays. These findings improve our understanding of the parasite’s biology and provide additional potential targets for novel therapeutics, diagnostics, and vaccines.
Development of biodegradable films using sunflower protein isolates and bacterial nanocellulose as innovative food packaging materials for fresh fruit preservation
Authors: Efthymiou Maria-Nefeli , Tsouko Erminta , Papagiannopoulos Aristeidis , Athanasoulia Ioanna-Georgia , Georgiadou Maria , Pispas Stergios , Briassoulis Demetres , Tsironi Theofania , Koutinas Apostolis 
Published: April 2022

AbstractThis study presents the valorization of side streams from the sunflower-based biodiesel industry for the production of bio-based and biodegradable food packaging following circular economy principles. Bacterial cellulose (BC) was produced via fermentation in 6 L static tray bioreactors using nutrient-rich supplements derived from the enzymatic hydrolysis of sunflower meal (SFM) combined with crude glycerol as carbon source. Novel biofilms were produced using either matrices of protein isolates extracted from sunflower meal (SFMPI) alone or SFMPI matrices reinforced with nanocellulose biofillers of commercial or bacterial origin. Acid hydrolysis was employed for ex-situ modification of BC to nanostructures (56 nm). The biofilms reinforced with bacterial nanocellulose structures (SFMPI-BNC) showed 64.5% higher tensile strength, 75.5% higher Young’s modulus, 131.5% higher elongation at break, 32.5% lower water solubility and 14.1% lower water vapor permeability than the biofilms produced only with SFMPI. The biofilms were evaluated on fresh strawberries packaging showing that the SFMPI-BNC-based films lead to effective preservation at 10 °C considering microbial growth and physicochemical profile (weight loss, chemical characterization, color, firmness and respiration activity). The SFMPI-BNC-based films could be applied in fresh fruit packaging applications.
Increased emergency cardiovascular events among under-40 population in Israel during vaccine rollout and third COVID-19 wave
Authors: Sun Christopher L. F. , Jaffe Eli , Levi Retsef 
Published: April 2022

AbstractCardiovascular adverse conditions are caused by coronavirus disease 2019 (COVID-19) infections and reported as side-effects of the COVID-19 vaccines. Enriching current vaccine safety surveillance systems with additional data sources may improve the understanding of COVID-19 vaccine safety. Using a unique dataset from Israel National Emergency Medical Services (EMS) from 2019 to 2021, the study aims to evaluate the association between the volume of cardiac arrest and acute coronary syndrome EMS calls in the 16–39-year-old population with potential factors including COVID-19 infection and vaccination rates. An increase of 25% was detected in both call types during January–May 2021, compared with the years 2019–2020. Using Negative Binomial regression models, the weekly emergency call counts were significantly associated with the rates of 1st and 2nd vaccine doses administered to this age group but were not with COVID-19 infection rates. While not establishing causal relationships, the findings raise concerns regarding vaccine-induced undetected severe cardiovascular side-effects and underscore the already established causal relationship between vaccines and myocarditis, a frequent cause of unexpected cardiac arrest in young individuals. Surveillance of potential vaccine side-effects and COVID-19 outcomes should incorporate EMS and other health data to identify public health trends (e.g., increased in EMS calls), and promptly investigate potential underlying causes.
Speed management across road environments of varying complexities and self-regulation behaviors in drivers with cataract
Authors: Ortiz-Peregrina Sonia , Ortiz Carolina , Martino Francesco , Casares-López Miriam , Castro-Torres José J. , Anera Rosario G. 
Published: April 2022

AbstractEvidence suggests that drivers with cataract self-regulate their driving, but there is a lack of objective information. This study compared speed behavior in older drivers with and without cataract and how the parameter is influenced by road traffic complexity and driver characteristics. The study included 15 drivers with cataract and a control group of 20 drivers. Visual status was assessed using visual acuity, contrast sensitivity, and intraocular straylight. Speed management was studied using a driving simulator. Driving difficulty and self-regulation patterns were evaluated by means of the Driver Habits Questionnaire (DHQ). The cataract group showed a significant decrease in visual function in all the parameters evaluated (p < 0.05). These drivers tended to drive at lower speeds than the control group. Road characteristics, gender, and intraocular straylight in the better eye were identified as significant predictors of speed management. Drivers with cataract experience greater driving difficulty, particularly when driving at night (p < 0.05). Drivers with cataract reduce their driving speed more than older drivers without visual impairment. The straylight parameter may be a good indicator of each driver’s subjective perception of their own visual ability to drive. This work helps shed light on the mechanisms through which age-related visual impairment influences driving behavior.
Nutritional value and bioaccumulation of heavy metals in nine commercial fish species from Dachen Fishing Ground, East China Sea
Authors: Huang Hong , Li Yingdong , Zheng Xinyun , Wang Zuanyi , Wang Zhenhua , Cheng Xiaopeng 
Published: April 2022

AbstractThe study evaluated the nutritional quality in muscle tissues of nine commercially important marine fish species. And the concentrations of trace metals (i.e. As, Hg, Cu, Pb, Cr, Cd and Zn) in the muscles (edible part) and tissues (gill and liver) of fishes caught from Dachen fishing ground, the coast of Zhejiang Province, East China Sea, were determined, and the values of target hazard quotient (THQ) and the carcinogenic risk (TR) were calculated for assessing human health risk. Significant differences(P < 0.05) were observed in the proximate chemical composition of fish muscles in these species. The muscle protein content of fish species ranged from 12.36 to 23.41%. The muscle lipid content of fishes ranged from 0.48 to 2.54%. The accumulation capacity of heavy metals (except Cr) in livers and gills was higher than that in muscles. In addition, the accumulation ability of most fishes is related to the water layer they live, the fishes living in the demersal layer showed more accumulation of heavy metals than the middle-upper layer(except Cu). Estimated daily intake (EDI), target hazard quotient (THQ), hazard index (HI) and the carcinogenic risk (TR) assessed for potential human health risk implications suggest that the values were within the acceptable threshold for human. However, the carcinogenic risk(TR) of As and Cr was close to the critical limit (10–4). Therefore, in order to ensure the health and safety of human consumption, the continuous monitoring of heavy metals in Dachen fishing ground area is suggested.
Impact of temperature on dengue and chikungunya transmission by the mosquito Aedes albopictus
Authors: Mercier Aurélien , Obadia Thomas , Carraretto Davide , Velo Enkelejda , Gabiane Gaelle , Bino Silvia , Vazeille Marie , Gasperi Giuliano , Dauga Catherine , Malacrida Anna R. , Reiter Paul , Failloux Anna-Bella 
Published: April 2022

AbstractThe mosquito Aedes albopictus is an invasive species first detected in Europe in Albania in 1979, and now established in 28 European countries. Temperature is a limiting factor in mosquito activities and in the transmission of associated arboviruses namely chikungunya (CHIKV) and dengue (DENV). Since 2007, local transmissions of CHIKV and DENV have been reported in mainland Europe, mainly in South Europe. Thus, the critical question is how far north transmission could occur. In this context, the Albanian infestation by Ae. albopictus is of interest because the species is present up to 1200 m of altitude; this allows using altitude as a proxy for latitude. Here we show that Ae. albopictus can transmit CHIKV at 28 °C as well as 20 °C, however, the transmission of DENV is only observed at 28 °C. We conclude that if temperature is the key environmental factor limiting transmission, then transmission of CHIKV, but not DENV is feasible in much of Europe.
Proof of concept for the use of trained sniffer dogs to detect osteosarcoma
Authors: Ortal Agustín , Rodríguez Aida , Solis-Hernández María Pilar , de Prado Miguel , Rey Verónica , Tornín Juan , Estupiñán Óscar , Gallego Borja , Murillo Dzohara , Huergo Carmen , García-Llano Juan Luis , Costilla Serafín , Rodríguez René 
Published: April 2022

AbstractSarcomas are mesenchymal cancers which often show an aggressive behavior and patient survival largely depends on an early detection. In last years, much attention has been given to the fact that cancer patients release specific odorous volatile organic compounds (VOCs) that can be efficiently detected by properly trained sniffer dogs. Here, we have evaluated for the first time the ability of sniffer dogs (n = 2) to detect osteosarcoma cell cultures and patient samples. One of the two dogs was successfully trained to discriminate osteosarcoma patient-derived primary cells from mesenchymal stem/stromal cells (MSCs) obtained from healthy individuals. After the training phase, the dog was able to detect osteosarcoma specific odor cues in a different panel of 6 osteosarcoma cell lines with sensitivity and specificity rates between 95 and 100%. Moreover, the same VOCs were also detected by the sniffer dog in saliva samples from osteosarcoma patients (n = 2) and discriminated from samples from healthy individuals with a similar efficacy. Altogether, these results indicate that there are common odor profiles shared by cultures of osteosarcoma cells and body fluid samples from patients and provide a first proof of concept about the potential of canine odor detection as a non-invasive screening method to detect osteosarcomas.
Morphology of subsurface cracks in glass-ceramics induced by Vickers indentation observed by synchrotron X-ray multiscale tomography
Authors: Okuma Gaku , Maeda Kei , Yoshida Satoshi , Takeuchi Akihisa , Wakai Fumihiro 
Published: April 2022

AbstractThe characterization of subsurface cracks induced by indentation is a challenge for understanding contact damage, impact, wear, erosion, and abrasion of brittle materials, because the crack pattern observable on the surface is only a part of the total crack system. Here we applied synchrotron X-ray multiscale tomography to observe the morphology of subsurface cracks produced by Vickers indentation in a novel CaO–Al2O3–SiO2 glass-ceramic with plate-like crystals forming a house-of-cards microstructure. It revealed a diverse type of crack systems around the semispherical microcrack zone beneath the indent, including a new mode II inclined lateral crack driven by the maximum shear stress. Tomography images provided knowledge on how the heterogeneous microstructure affected the toughening processes such as crack deflection, crack bridging, and microcracking.
Sequence-based evaluation of promoter context for prediction of transcription start sites in Arabidopsis and rice
Authors: Hiratsuka Tosei , Makita Yuko , Yamamoto Yoshiharu Y. 
Published: April 2022

AbstractGenes are transcribed from transcription start sites (TSSs), and their position in a genome is strictly controlled to avoid mis-expression of undesired regions. In this study, we designed and developed a methodology for the evaluation of promoter context, which detects proximal promoter regions from − 200 to − 60 bp relative to a TSS, in Arabidopsis and rice genomes. The method positively evaluates spacer sequences and Regulatory Element Groups, but not core promoter elements like TATA boxes, and is able to predict the position of a TSS within a width of 200 bp. An important feature of the evaluation/prediction method is its independence of the core promoter elements, which was demonstrated by successful prediction of all the TATA, GA, and coreless types of promoters without notable differences in the accuracy of prediction. The positive relationship identified between the evaluation scores and gene expression levels suggests that this method is useful for the evaluation of promoter maturity.
DNA-based copy number analysis confirms genomic evolution of PDX models
Authors: Hoge Anna C. H. , Getz Michal , Zimmer Anat , Ko Minjeong , Raz Linoy , Beroukhim Rameen , Golub Todd R. , Ha Gavin , Ben-David Uri 
Published: April 2022

AbstractGenomic evolution of patient-derived xenografts (PDXs) may lead to their gradual divergence away of their tumors of origin. We previously reported the genomic evolution of the copy number (CN) landscapes of PDXs during their engraftment and passaging1. However, whether PDX models are highly stable throughout passaging2, or can evolve CNAs rapidly1,3, remains controversial. Here, we reassess the genomic evolution of PDXs using DNA-based CN profiles. We find strong evidence for genomic evolution in the DNA-based PDX data: a median of ~10% of the genome is differentially altered between matched primary tumors (PTs) and PDXs across cohorts (range, 0% to 73% across all models). In 24% of the matched PT-PDX samples, over a quarter of the genome is differentially affected by CN alterations. Moreover, in matched analyses of PTs and their derived PDXs at multiple passages, later-passage PDXs are significantly less similar to their parental PTs than earlier-passage PDXs, indicative of genomic divergence. We conclude that PDX models indeed evolve throughout their derivation and propagation, and that the phenotypic consequences of this evolution ought to be assessed in order to determine its relevance to the proper application of these valuable cancer models.
Atomically resolved TEM imaging of covalently functionalised graphene
Authors: Dolle Christian , Schweizer Peter , Dasler Daniela , Gsänger Sebastian , Maidl Robert , Abellán Gonzalo , Hauke Frank , Meyer Bernd , Hirsch Andreas , Spiecker Erdmann 
Published: April 2022

AbstractCovalent functionalisation can be a powerful lever to tune the properties and processability of graphene. After overcoming the low chemical reactivity of graphene, covalent functionalisation led to the generation of new hybrid materials, applicable in a broad variation of fields. Although the process of functionalising graphene is nowadays firmly established, fundamental aspects of the produced hybrid materials remain to be clarified. Especially the atomically resolved imaging is only scarcely explored. Here we show aberration corrected in situ high resolution TEM imaging of dodecyl functionalised monolayer graphene at atomic resolution after an effective mechanical filtering approach. The mechanical filtering allows to separate adsorbed contamination from the covalently bound functional molecules and thus opens the possibility for the observation of this hybrid material. The obtained data is validated by DFT calculations and by a novel image simulation approach based on molecular dynamics (MD) simulations at room temperature.
Mycelium chemistry differs markedly between ectomycorrhizal and arbuscular mycorrhizal fungi
Authors: Huang Weilin , van Bodegom Peter M. , Declerck Stéphane , Heinonsalo Jussi , Cosme Marco , Viskari Toni , Liski Jari , Soudzilovskaia Nadejda A. 
Published: April 2022

AbstractThe chemical quality of soil carbon (C) inputs is a major factor controlling litter decomposition and soil C dynamics. Mycorrhizal fungi constitute one of the dominant pools of soil microbial C, while their litter quality (chemical proxies of litter decomposability) is understood poorly, leading to major uncertainties in estimating soil C dynamics. We examined litter decomposability of arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) fungal species using samples obtained from in vitro cultivation. We showed that the chemical composition of AM and EM fungal mycelium differs significantly: EM fungi have higher concentrations of labile (water-soluble, ethanol-soluble) and recalcitrant (non-extractable) chemical components, while AM fungi have higher concentrations of acid-hydrolysable components. Our results imply that differences in decomposability traits among mycorrhizal fungal guilds represent a critically important driver of the soil C cycle, which could be as vital as is recognized for differences among aboveground plant litter.
Density fluctuations, homeostasis, and reproduction effects in bacteria
Authors: Nemati Shahla , Singh Abhyudai , Dhuey Scott D. , McDonald Armando , Weinreich Daniel M. , Vasdekis Andreas. E. 
Published: April 2022

AbstractSingle-cells grow by increasing their biomass and size. Here, we report that while mass and size accumulation rates of singleEscherichia colicells are exponential, their density and, thus, the levels of macromolecular crowding fluctuate during growth. As such, the average rates of mass and size accumulation of a single cell are generally not the same, but rather cells differentiate into increasing one rate with respect to the other. This differentiation yields a density homeostasis mechanism that we support mathematically. Further, we observe that density fluctuations can affect the reproduction rates of single cells, suggesting a link between the levels of macromolecular crowding with metabolism and overall population fitness. We detail our experimental approach and the “invisible” microfluidic arrays that enabled increased precision and throughput. Infections and natural communities start from a few cells, thus, emphasizing the significance of density-fluctuations when taking non-genetic variability into consideration.
First-principles theory of the rate of magnetic reconnection in magnetospheric and solar plasmas
Authors: Liu Yi-Hsin , Cassak Paul , Li Xiaocan , Hesse Michael , Lin Shan-Chang , Genestreti Kevin 
Published: April 2022

AbstractThe rate of magnetic reconnection is of the utmost importance in a variety of processes because it controls, for example, the rate energy is released in solar flares, the speed of the Dungey convection cycle in Earth’s magnetosphere, and the energy release rate in harmful geomagnetic substorms. It is known from numerical simulations and satellite observations that the rate is approximately 0.1 in normalized units, but despite years of effort, a full theoretical prediction has not been obtained. Here, we present a first-principles theory for the reconnection rate in non-relativistic electron-ion collisionless plasmas, and show that the same prediction explains why Sweet-Parker reconnection is considerably slower. The key consideration of this analysis is the pressure at the reconnection site (i.e., the x-line). We show that the Hall electromagnetic fields in antiparallel reconnection cause an energy void, equivalently a pressure depletion, at the x-line, so the reconnection exhaust opens out, enabling the fast rate of 0.1. If the energy can reach the x-line to replenish the pressure, the exhaust does not open out. In addition to heliospheric applications, these results are expected to impact reconnection studies in planetary magnetospheres, magnetically confined fusion devices, and astrophysical plasmas.