bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic determinants of daytime napping and effects on cardiometabolic health
Authors: Dashti Hassan S. , Daghlas Iyas , Lane Jacqueline M. , Huang Yunru , Udler Miriam S. , Wang Heming , Ollila Hanna M. , Jones Samuel E. , Kim Jaegil , Wood Andrew R. ,   23andMe Research Team, Agee Michelle , Auton Adam , Bell Robert K. , Bryc Katarzyna , Clark Sarah K. , Elson Sarah L. , Fletez-Brant Kipper , Fontanillas Pierre , Furlotte Nicholas A. , Gandhi Pooja M. , Heilbron Karl , Hicks Barry , Hinds David A. , Huber Karen E. , Jewett Ethan M. , Jiang Yunxuan , Kleinman Aaron , Lin Keng-Han , Litterman Nadia K. , Luff Marie K. , McCreight Jennifer C. , McIntyre Matthew H. , McManus Kimberly F. , Mountain Joanna L. , Mozaffari Sahar V. , Nandakumar Priyanka , Noblin Elizabeth S. , Northover Carrie A. M. , O’Connell Jared , Petrakovitz Aaron A. , Pitts Steven J. , Poznik G. David , Sathirapongsasuti J. Fah , Shastri Anjali J. , Shelton Janie F. , Shringarpure Suyash , Tian Chao , Tung Joyce Y. , Tunney Robert J. , Vacic Vladimir , Wang Xin , Zare Amir S. , Weedon Michael N. , Aslibekyan Stella , Garaulet Marta , Saxena Richa
Published: February 2021

Daytime napping is a common, heritable behavior, but its genetic basis and causal relationship with cardiometabolic health remain unclear. Here, we perform a genome-wide association study of self-reported daytime napping in the UK Biobank (n = 452,633) and identify 123 loci of which 61 replicate in the 23andMe research cohort (n = 541,333). Findings include missense variants in established drug targets for sleep disorders (HCRTR1,HCRTR2), genes with roles in arousal (TRPC6,PNOC), and genes suggesting an obesity-hypersomnolence pathway (PNOC, PATJ). Association signals are concordant with accelerometer-measured daytime inactivity duration and 33 loci colocalize with loci for other sleep phenotypes. Cluster analysis identifies three distinct clusters of nap-promoting mechanisms with heterogeneous associations with cardiometabolic outcomes. Mendelian randomization shows potential causal links between more frequent daytime napping and higher blood pressure and waist circumference.
Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria
Authors: Sun Zhe , Yakhnin Alexander V. , FitzGerald Peter C. , Mclntosh Carl E. , Kashlev Mikhail
Published: February 2021

Promoter-proximal pausing regulates eukaryotic gene expression and serves as checkpoints to assemble elongation/splicing machinery. Little is known how broadly this type of pausing regulates transcription in bacteria. We apply nascent elongating transcript sequencing combined with RNase I footprinting for genome-wide analysis of σ70-dependent transcription pauses in Escherichia coli. Retention of σ70 induces strong backtracked pauses at a 10−20-bp distance from many promoters. The pauses in the 10−15-bp register of the promoter are dictated by the canonical −10 element, 6−7 nt spacer and “YR+1Y” motif centered at the transcription start site. The promoters for the pauses in the 16−20-bp register contain an additional −10-like sequence recognized by σ70. Our in vitro analysis reveals that DNA scrunching is involved in these pauses relieved by Gre cleavage factors. The genes coding for transcription factors are enriched in these pauses, suggesting that σ70 and Gre proteins regulate transcription in response to changing environmental cues.
Imaging low-mass planets within the habitable zone of α Centauri
Authors: Wagner K. , Boehle A. , Pathak P. , Kasper M. , Arsenault R. , Jakob G. , Käufl U. , Leveratto S. , Maire A.-L. , Pantin E. , Siebenmorgen R. , Zins G. , Absil O. , Ageorges N. , Apai D. , Carlotti A. , Choquet É. , Delacroix C. , Dohlen K. , Duhoux P. , Forsberg P. , Fuenteseca E. , Gutruf S. , Guyon O. , Huby E. , Kampf D. , Karlsson M. , Kervella P. , Kirchbauer J.-P. , Klupar P. , Kolb J. , Mawet D. , N’Diaye M. , Orban de Xivry G. , Quanz S. P. , Reutlinger A. , Ruane G. , Riquelme M. , Soenke C. , Sterzik M. , Vigan A. , de Zeeuw T.
Published: February 2021

Giant exoplanets on wide orbits have been directly imaged around young stars. If the thermal background in the mid-infrared can be mitigated, then exoplanets with lower masses can also be imaged. Here we present a ground-based mid-infrared observing approach that enables imaging low-mass temperate exoplanets around nearby stars, and in particular within the closest stellar system, α Centauri. Based on 75–80% of the best quality images from 100 h of cumulative observations, we demonstrate sensitivity to warm sub-Neptune-sized planets throughout much of the habitable zone of α Centauri A. This is an order of magnitude more sensitive than state-of-the-art exoplanet imaging mass detection limits. We also discuss a possible exoplanet or exozodiacal disk detection around α Centauri A. However, an instrumental artifact of unknown origin cannot be ruled out. These results demonstrate the feasibility of imaging rocky habitable-zone exoplanets with current and upcoming telescopes.
Recent African strains of Zika virus display higher transmissibility and fetal pathogenicity than Asian strains
Authors: Aubry Fabien , Jacobs Sofie , Darmuzey Maïlis , Lequime Sebastian , Delang Leen , Fontaine Albin , Jupatanakul Natapong , Miot Elliott F. , Dabo Stéphanie , Manet Caroline , Montagutelli Xavier , Baidaliuk Artem , Gámbaro Fabiana , Simon-Lorière Etienne , Gilsoul Maxime , Romero-Vivas Claudia M. , Cao-Lormeau Van-Mai , Jarman Richard G. , Diagne Cheikh T. , Faye Oumar , Faye Ousmane , Sall Amadou A. , Neyts Johan , Nguyen Laurent , Kaptein Suzanne J. F. , Lambrechts Louis
Published: February 2021

The global emergence of Zika virus (ZIKV) revealed the unprecedented ability for a mosquito-borne virus to cause congenital birth defects. A puzzling aspect of ZIKV emergence is that all human outbreaks and birth defects to date have been exclusively associated with the Asian ZIKV lineage, despite a growing body of laboratory evidence pointing towards higher transmissibility and pathogenicity of the African ZIKV lineage. Whether this apparent paradox reflects the use of relatively old African ZIKV strains in most laboratory studies is unclear. Here, we experimentally compare seven low-passage ZIKV strains representing the recently circulating viral genetic diversity. We find that recent African ZIKV strains display higher transmissibility in mosquitoes and higher lethality in both adult and fetal mice than their Asian counterparts. We emphasize the high epidemic potential of African ZIKV strains and suggest that they could more easily go unnoticed by public health surveillance systems than Asian strains due to their propensity to cause fetal loss rather than birth defects.
Multifunctional evolution of B and AGL6 MADS box genes in orchids
Authors: Hsu Hsing-Fun , Chen Wei-Han , Shen Yi-Hsuan , Hsu Wei-Han , Mao Wan-Ting , Yang Chang-Hsien
Published: February 2021

We previously found that B and AGL6 proteins form L (OAP3-2/OAGL6-2/OPI) and SP (OAP3-1/OAGL6-1/OPI) complexes to determine lip/sepal/petal identities in orchids. Here, we show that the functional L’ (OAP3-1/OAGL6-2/OPI) and SP’ (OAP3-2/OAGL6-1/OPI) complexes likely exist and AP3/PI/AGL6 genes have acquired additional functions during evolution. We demonstrate that the presumed L’ complex changes the structure of the lower lateral sepals and helps the lips fit properly in the center of the flower. In addition, we find that OAP3-1/OAGL6-1/OPI in SP along with presumed SP’ complexes regulate anthocyanin accumulation and pigmentation, whereas presumed L’ along with OAP3-2/OAGL6-2/OPI in L complexes promotes red spot formation in the perianth. Furthermore, the B functional proteins OAP3-1/OPI and OAGL6-1 in the SP complex could function separately to suppress sepal/petal senescence and promote pedicel abscission, respectively. These findings expand the current knowledge behind the multifunctional evolution of the B and AGL6 genes in plants.
Genotyping cognate Plasmodium falciparum in humans and mosquitoes to estimate onward transmission of asymptomatic infections
Authors: Sumner Kelsey M. , Freedman Elizabeth , Abel Lucy , Obala Andrew , Pence Brian W. , Wesolowski Amy , Meshnick Steven R. , Prudhomme-O’Meara Wendy , Taylor Steve M.
Published: February 2021

Malaria control may be enhanced by targeting reservoirs of Plasmodium falciparum transmission. One putative reservoir is asymptomatic malaria infections and the scale of their contribution to transmission in natural settings is not known. We assess the contribution of asymptomatic malaria to onward transmission using a 14-month longitudinal cohort of 239 participants in a high transmission site in Western Kenya. We identify P. falciparum in asymptomatically- and symptomatically-infected participants and naturally-fed mosquitoes from their households, genotype all parasites using deep sequencing of the parasite genes pfama1 and pfcsp, and use haplotypes to infer participant-to-mosquito transmission through a probabilistic model. In 1,242 infections (1,039 in people and 203 in mosquitoes), we observe 229 (pfcsp) and 348 (pfama1) unique parasite haplotypes. Using these to link human and mosquito infections, compared with symptomatic infections, asymptomatic infections more than double the odds of transmission to a mosquito among people with both infection types (Odds Ratio: 2.56; 95% Confidence Interval (CI): 1.36–4.81) and among all participants (OR 2.66; 95% CI: 2.05–3.47). Overall, 94.6% (95% CI: 93.1–95.8%) of mosquito infections likely resulted from asymptomatic infections. In high transmission areas, asymptomatic infections are the major contributor to mosquito infections and may be targeted as a component of transmission reduction.
Descriptive multi-agent epidemiology via molecular screening on Atlantic salmon farms in the northeast Pacific Ocean
Authors: Bateman Andrew W. , Schulze Angela D. , Kaukinen Karia H. , Tabata Amy , Mordecai Gideon , Flynn Kelsey , Bass Arthur , Di Cicco Emiliano , Miller Kristina M.
Published: February 2021

Rapid expansion of salmon aquaculture has resulted in high-density populations that host diverse infectious agents, for which surveillance and monitoring are critical to disease management. Screening can reveal infection diversity from which disease arises, differential patterns of infection in live and dead fish that are difficult to collect in wild populations, and potential risks associated with agent transmission between wild and farmed hosts. We report results from a multi-year infectious-agent screening program of farmed salmon in British Columbia, Canada, using quantitative PCR to assess presence and load of 58 infective agents (viruses, bacteria, and eukaryotes) in 2931 Atlantic salmon (Salmo salar). Our analysis reveals temporal trends, agent correlations within hosts, and agent-associated mortality signatures. Multiple agents, most notablyTenacibaculum maritimum, were elevated in dead and dying salmon. We also report detections of agents only recently shown to infect farmed salmon in BC (Atlantic salmon calicivirus, Cutthroat trout virus-2), detection in freshwater hatcheries of two marine agents (Kudoa thyrsitesandTenacibaculum maritimum), and detection in the ocean of a freshwater agent (Flavobacterium psychrophilum). Our results provide information for farm managers, regulators, and conservationists, and enable further work to explore patterns of multi-agent infection and farm/wild transmission risk.
Submicron spatial resolution optical coherence tomography for visualising the 3D structures of cells cultivated in complex culture systems
Authors: Tsai Chia-Ying , Shih Cheng-Hung , Chu Hsiao-Sang , Hsieh Yi-Ting , Huang Sheng-Lung , Chen Wei-Li
Published: February 2021

Three-dimensional (3D) configuration of in vitro cultivated cells has been recognised as a valuable tool in developing stem cell and cancer cell therapy. However, currently available imaging approaches for live cells have drawbacks, including unsatisfactory resolution, lack of cross-sectional and 3D images, and poor penetration of multi-layered cell products, especially when cells are cultivated on semitransparent carriers. Herein, we report a prototype of a full-field optical coherence tomography (FF-OCT) system with isotropic submicron spatial resolution in en face and cross-sectional views that provides a label-free, non-invasive platform with high-resolution 3D imaging. We validated the imaging power of this prototype by examining (1) cultivated neuron cells (N2A cell line); (2) multilayered, cultivated limbal epithelial sheets (mCLESs); (3) neuron cells (N2A cell line) and mCLESs cultivated on a semitransparent amniotic membrane (stAM); and (4) directly adherent colonies of neuron-like cells (DACNs) covered by limbal epithelial cell sheets. Our FF-OCT exhibited a penetrance of up to 150 μm in a multilayered cell sheet and displayed the morphological differences of neurons and epithelial cells in complex coculture systems. This FF-OCT is expected to facilitate the visualisation of cultivated cell products in vitro and has a high potential for cell therapy and translational medicine research.
MEF2C shapes the microtranscriptome during differentiation of skeletal muscles
Authors: Piasecka Agnieszka , Sekrecki Michał , Szcześniak Michał Wojciech , Sobczak Krzysztof
Published: February 2021

Myocyte enhancer factor 2C (MEF2C) is a transcription factor that regulates heart and skeletal muscle differentiation and growth. Several protein-encoding genes were identified as targets of this factor; however, little is known about its contribution to the microtranscriptome composition and dynamics in myogenic programs. In this report, we aimed to address this question. Deep sequencing of small RNAs of human muscle cells revealed a set of microRNAs (miRNAs), including several muscle-specific miRNAs, that are sensitive to MEF2C depletion. As expected, in cells with knockdown of MEF2C, we found mostly downregulated miRNAs; nevertheless, as much as one-third of altered miRNAs were upregulated. The majority of these changes are driven by transcription efficiency. Moreover, we found that MEF2C affects nontemplated 3′-end nucleotide addition of miRNAs, mainly oligouridylation. The rate of these modifications is associated with the level of TUT4 which mediates RNA 3′-uridylation. Finally, we found that a quarter of miRNAs which significantly changed upon differentiation of human skeletal myoblasts is inversely altered in MEF2C deficient cells. We concluded that MEF2C is an essential factor regulating both the quantity and quality of the microtranscriptome, leaving an imprint on the stability and perhaps specificity of many miRNAs during the differentiation of muscle cells.
Multiple objects interacting with a solidification front
Authors: Tyagi Sidhanth , Monteux Cécile , Deville Sylvain
Published: February 2021

The interaction of objects suspended in a liquid melt with an advancing solidification front is of special interest in nature and engineering sciences. The front can either engulf the object into the growing crystal or repel it. Therefore, the object-front confrontation can have a strong influence on the microstructure and mechanical or functional properties of the solidified material. The past theoretical models and experimental studies have mostly investigated the interaction of isolated, spherical, and hard objects in pure melts. However, the outcome of object-front interactions in complex (more realistic) systems, where multiple objects and solutes are present, is still poorly understood. Here we show the interaction of multiple oil droplets with an ice-water front in the absence and presence of solute effects using in situ cryo-confocal microscopy. We report on how the object size, number of objects, and bulk solute concentration influence the the object-front interaction and the front morphology, as well as the subsequent object spatial distribution. We suggest that the volume fraction of objects suspended in a liquid melt in conjunction with the amount of bulk solute concentration are two important parameters to be incorporated in the development of object-front interaction models.
Traffic signal optimization on a square lattice with quantum annealing
Authors: Inoue Daisuke , Okada Akihisa , Matsumori Tadayoshi , Aihara Kazuyuki , Yoshida Hiroaki
Published: February 2021

The spread of intelligent transportation systems in urban cities has caused heavy computational loads, requiring a novel architecture for managing large-scale traffic. In this study, we develop a method for globally controlling traffic signals arranged on a square lattice by means of a quantum annealing machine, namely the D-Wave quantum annealer. We first formulate a signal optimization problem that minimizes the imbalance of traffic flows in two orthogonal directions. Then we reformulate this problem as an Ising Hamiltonian, which is compatible with quantum annealers. The new control method is compared with a conventional local control method for a large 50-by-50 city, and the results exhibit the superiority of our global control method in suppressing traffic imbalance over wide parameter ranges. Furthermore, the solutions to the global control method obtained with the quantum annealing machine are better than those obtained with conventional simulated annealing. In addition, we prove analytically that the local and the global control methods converge at the limit where cars have equal probabilities for turning and going straight. These results are verified with numerical experiments.
Comparative study of generalized couette flow of couple stress fluid using optimal homotopy asymptotic method and new iterative method
Authors: Farooq Muhammad , Khan Alamgeer , Nawaz Rashid , Islam Saeed , Ayaz Muhammad , Chu Yu-Ming
Published: February 2021

In this research work, we have studied the steady generalized Couette flow of couple stress fluid between two parallel plates considering the non-isothermal effects. The governing equations that are, continuity, momentum and energy equations are reduced to ordinary differential equations. The Optimal Homotopy Asymptotic Method (OHAM) and New Iterative Method (NIM) are used to solve this coupled system of differential equations. Using the said methods, we have obtained expressions for velocity profile, temperature distribution, volume flux, average velocity and shear stress. The results of OHAM and NIM are compared numerically as well as graphically and a tremendous agreement is attained.
Rat in vitro spermatogenesis promoted by chemical supplementations and oxygen-tension control
Authors: Matsumura Takafumi , Sato Takuya , Abe Takeru , Sanjo Hiroyuki , Katagiri Kumiko , Kimura Hiroshi , Fujii Teruo , Tanaka Hiromitsu , Hirabayashi Masumi , Ogawa Takehiko
Published: February 2021

In vitro spermatogenesis (IVS) using air–liquid interphase organ culture method is possible with mouse testis tissues. The same method, however, has been hardly applicable to animals other than mice, only producing no or limited progression of spermatogenesis. In the present study, we challenged IVS of rats with modifications of culture medium, by supplementing chemical substances, including hormones, antioxidants, and lysophospholipids. In addition, reducing oxygen tension by placing tissues in an incubator of lower oxygen concentration and/or applying silicone cover ceiling on top of the tissue were effective for improving the spermatogenic efficiency. Through these modifications of the culture condition, rat spermatogenesis up to round spermatids was maintained over 70 days in the cultured tissue. Present results demonstrated a significant progress in rat IVS, revealing conditions commonly favorable for mice and rats as well as finding rat-specific optimizations. This is an important step towards successful IVS in many animal species, including humans.
Diversification of OmpA and OmpF of Yersinia ruckeri is independent of the underlying species phylogeny and evidence of virulence-related selection
Authors: Ormsby Michael J. , Davies Robert L.
Published: February 2021

Yersinia ruckeri is the causative agent of enteric redmouth disease (ERM) which causes economically significant losses in farmed salmonids, especially Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss, Walbaum). However, very little is known about the genetic relationships of disease-causing isolates in these two host species or about factors responsible for disease. Phylogenetic analyses of 16 representative isolates based on the nucleotide sequences of 19 housekeeping genes suggests that pathogenic Atlantic salmon and rainbow trout isolates represent distinct host-specific lineages. However, the apparent phylogenies of certain isolates has been influenced by horizontal gene transfer and recombinational exchange. Splits decomposition analysis demonstrated a net-like phylogeny based on the housekeeping genes, characteristic of recombination. Comparative analysis of the distribution of individual housekeeping gene alleles across the isolates demonstrated evidence of genomic mosaicism and recombinational exchange involving certain Atlantic salmon and rainbow trout isolates. Comparative nucleotide sequence analysis of the key outer membrane protein genes ompA and ompF revealed that the corresponding gene trees were both non-congruent with respect to the housekeeping gene phylogenies providing evidence that horizontal gene transfer has influenced the evolution of both these surface protein-encoding genes. Analysis of inferred amino acid sequence variation in OmpA identified a single variant, OmpA.1, that was present in serotype O1 and O8 isolates representing typical pathogenic strains in rainbow trout and Atlantic salmon, respectively. In particular, the sequence of surface-exposed loop 3 differed by seven amino acids to that of other Y. ruckeri isolates. These findings suggest that positive selection has likely influenced the presence of OmpA.1 in these isolates and that loop 3 may play an important role in virulence. Amino acid sequence variation of OmpF was greater than that of OmpA and was similarly restricted mainly to the surface-exposed loops. Two OmpF variants, OmpF.1 and OmpF.2, were associated with pathogenic rainbow trout and Atlantic salmon isolates, respectively. These OmpF proteins had very similar amino acid sequences suggesting that positive evolutionary pressure has also favoured the selection of these variants in pathogenic strains infecting both species.
Elucidating the involvement of apoptosis in postmortem proteolysis in porcine muscles from two production cycles using metabolomics approach
Authors: Ma Danyi , Suh Dong Ho , Zhang Jiaying , Chao Yufan , Duttlinger Alan W. , Johnson Jay S. , Lee Choong Hwan , Kim Yuan H. Brad
Published: February 2021

Apoptosis has been suggested as the first step in the process of conversion of muscle into meat. While a potential role of apoptosis in postmortem proteolysis has been proposed, the underlying mechanisms by which metabolome changes in muscles would influence apoptotic and proteolytic process, leading to meat quality variation, has not been determined. Here, apoptotic and proteolytic attributes and metabolomics profiling of longissimus dorsi (LD) and psoas major (PM) muscles in pigs from two different production cycles (July–Jan vs. Apr–Sep) were evaluated. PM showed higher mitochondrial membrane permeability (MMP), concurrent with less extent of calpain-1 autolysis and troponin T degradation and higher abundance of HSP27 and αβ-crystallin compared to LD (P < 0.05). Apr–Sep muscles showed concurrence of extended apoptosis (indicated by higher MMP), calpain-1 autolysis and troponin T degradation, regardless of muscle effects (P < 0.05). Metabolomics profiling showed Apr–Sep muscles to increase in oxidative stress-related macronutrients, including 6-carbon sugars, some branched-chain AA, and free fatty acids. Antioxidant AA (His and Asp) and ascorbic acid were higher in July–Jan (P < 0.05). The results of the present study suggest that early postmortem apoptosis might be positively associated with pro-oxidant macronutrients and negatively associated with antioxidant metabolites, consequently affecting meat quality attributes in a muscle-specific manner.
MC4R mutant mice develop ovarian teratomas
Authors: Naser Abdullah An , Miyazaki Takehiro , Wang Jun , Takabayashi Shuji , Pachoensuk Theeranukul , Tokumoto Toshinobu
Published: February 2021

Teratomas in mice, composed of different tissue types, are derived from primordial germ cells (PGCs) in the foetal gonads. The strongest candidate gene in the testicular teratoma locus (Ter) responsible for testicular teratoma formation was identified as mutation in Dnd1, Dnd1R178*. However, the phenotype of mice with a mutated Dnd1 gene was germ cell loss. This suggests that other genes are involved in teratoma formation. Testicular teratomas can also be induced experimentally (experimentally testicular teratomas: ETTs) in 129/Sv mice by transplanting E12.5 foetal testes into adult testes. Previously, we mapped the ett1 locus, which is the locus responsible for ETT formation on chromosome 18. By exome sequence analysis of the 129 and LTXBJ (LT) strains, we identified a missense mutation in the melanocortin 4 receptor (MC4R) gene among 8 genes in the ett1 region. The missense mutation causes a substitution of glycine 25 by serine. Thus, this gene is a candidate for ETT formation. We established the LT-ett1 congenic strain, which introduced the locus responsible for ETT formation genetically into the genomes of a testicular teratoma non-susceptible strain. In this study, we crossed LT-ett1 and a previously established LT-Ter strain to establish the double congenic strain LT-Ter-ett1. Also, we established a strain with a point mutation in the MC4R gene of the LT strain by genome editing, LT-MC4RG25S. Furthermore, double genetically modified strain LT-Ter-MC4RG25S was established to address the relation between Ter and MC4R. Surprisingly, highly developed ovarian teratomas (OTs), instead of testicular teratomas, appeared not only in the LT-Ter-MC4RG25S and LT-MC4RG25S strains but also in the LT-ett1 and LT-Ter-ett1 strains. The incidence of OT formation was high in double genetically modified strains. The results demonstrated that MC4R is one of the genes responsible for OT formation. It was suggested that the effect of the missense mutation in MC4R on teratoma formation was promoted by abnormal germ cell formation by the mutation in DND1.
Cavitation bubble dynamics in a vicinity of a thin membrane wetted by different fluids
Authors: Lokar Žiga , Petkovšek Rok , Dular Matevž
Published: February 2021

Understanding and controlling the interaction of cavitation bubbles and nearby material is becoming essential optimization of various processes. We examined the interaction of a single bubble with a membrane with different fluids on each side of it. Significant differences in bubble behavior depending on the fluid properties were observed, while the influence of membrane properties was less pronounced. The study has important implications, such as optimization of sonoporation (targeted drug delivery) where the mechanism, by which the permeability of the membrane is increased, is still not well understood. These results show that the focus of the optimization process should, in the first place, lie on the properties of liquids, rather than the mechanical properties of the membrane itself.
Flagellin-based electrochemical sensing layer for arsenic detection in water
Authors: Jankovics Hajnalka , Szekér Patrik , Tóth Éva , Kakasi Balázs , Lábadi Zoltán , Saftics András , Kalas Benjamin , Fried Miklós , Petrik Péter , Vonderviszt Ferenc
Published: February 2021

Regular monitoring of arsenic concentrations in water sources is essential due to the severe health effects. Our goal was to develop a rapidly responding, sensitive and stable sensing layer for the detection of arsenic. We have designed flagellin-based arsenic binding proteins capable of forming stable filament structures with high surface binding site densities. The D3 domain of Salmonella typhimurium flagellin was replaced with an arsenic-binding peptide motif of different bacterial ArsR transcriptional repressor factors. We have shown that the fusion proteins developed retain their polymerization ability and have thermal stability similar to that of wild-type filament. The strong arsenic binding capacity of the monomeric proteins was confirmed by isothermal titration calorimetry (ITC), and dissociation constants (Kd) of a few hundred nM were obtained for all three variants. As-binding fibers were immobilized on the surface of a gold electrode and used as a working electrode in cyclic voltammetry (CV) experiments to detect inorganic arsenic near the maximum allowable concentration (MAC) level. Based on these results, it can be concluded that the stable arsenic-binding flagellin variant can be used as a rapidly responding, sensitive, but simple sensing layer in a field device for the MAC-level detection of arsenic in natural waters.
Influence of ultrasound on selected microorganisms, chemical and structural changes in fresh tomato juice
Authors: Starek Agnieszka , Kobus Zbigniew , Sagan Agnieszka , Chudzik Barbara , Pawłat Joanna , Kwiatkowski Michał , Terebun Piotr , Andrejko Dariusz
Published: February 2021

The paper presents the possibility of applying ultrasonic technology for inactivation of mesophilic aerobic microorganisms, lactic acid bacteria, coliform bacteria, and yeast with the maintenance of the chemical and structural properties of tomato juice. The research was conducted on fresh tomato juice obtained from the Apis F1 variety. Pressed juice was exposed to high power ultrasound and frequency 20 kHz with three operational parameters: ultrasound intensity (28 and 40 W cm−2), treatment time (2, 5, and 10 min), and product storage time (1, 4, 7 and 10 days). The temperature of the juice during the sonication ranged from 37 to 52 °C depending on the intensity of ultrasound and time of treatment. Effectiveness of the tested microorganisms eradication in the juice depended on the amplitude and duration of the ultrasound treatment. It was shown that the juice exposed to an ultrasonic field with an intensity of 40 W cm−2 for 10 min was microbiologically pure and free from spoilage microorganism even after 10 storage days. No statistically significant differences in pH were found between the untreated juice and the sonicated samples. The ultrasonic treatment was found to change the content of lycopene in small degree (both an increase and a decrease, depending on the processing time) and to induce a small decrease in the vitamin C content. The study suggests that the ultrasonic treatment can be successfully implemented on an industrial scale for the production of not-from-concentrate (NFC) tomato juice.
Optimal control of the COVID-19 pandemic: controlled sanitary deconfinement in Portugal
Authors: Silva Cristiana J. , Cruz Carla , Torres Delfim F. M. , Muñuzuri Alberto P. , Carballosa Alejandro , Area Iván , Nieto Juan J. , Fonseca-Pinto Rui , Passadouro Rui , Santos Estevão Soares dos , Abreu Wilson , Mira Jorge
Published: February 2021

The COVID-19 pandemic has forced policy makers to decree urgent confinements to stop a rapid and massive contagion. However, after that stage, societies are being forced to find an equilibrium between the need to reduce contagion rates and the need to reopen their economies. The experience hitherto lived has provided data on the evolution of the pandemic, in particular the population dynamics as a result of the public health measures enacted. This allows the formulation of forecasting mathematical models to anticipate the consequences of political decisions. Here we propose a model to do so and apply it to the case of Portugal. With a mathematical deterministic model, described by a system of ordinary differential equations, we fit the real evolution of COVID-19 in this country. After identification of the population readiness to follow social restrictions, by analyzing the social media, we incorporate this effect in a version of the model that allow us to check different scenarios. This is realized by considering a Monte Carlo discrete version of the previous model coupled via a complex network. Then, we apply optimal control theory to maximize the number of people returning to “normal life” and minimizing the number of active infected individuals with minimal economical costs while warranting a low level of hospitalizations. This work allows testing various scenarios of pandemic management (closure of sectors of the economy, partial/total compliance with protection measures by citizens, number of beds in intensive care units, etc.), ensuring the responsiveness of the health system, thus being a public health decision support tool.
Role of PDK1 in skeletal muscle hypertrophy induced by mechanical load
Authors: Kuramoto Naoki , Nomura Kazuhiro , Kohno Daisuke , Kitamura Tadahiro , Karsenty Gerard , Hosooka Tetsuya , Ogawa Wataru
Published: February 2021

Phosphatidylinositol 3-kinase (PI3K) plays an important role in protein metabolism and cell growth. We here show that mice (M-PDK1KO mice) with skeletal muscle–specific deficiency of 3′-phosphoinositide–dependent kinase 1 (PDK1), a key component of PI3K signaling pathway, manifest a reduced skeletal muscle mass under the static condition as well as impairment of mechanical load–induced muscle hypertrophy. Whereas mechanical load-induced changes in gene expression were not affected, the phosphorylation of ribosomal protein S6 kinase (S6K) and S6 induced by mechanical load was attenuated in skeletal muscle of M-PDK1KO mice, suggesting that PDK1 regulates muscle hypertrophy not through changes in gene expression but through stimulation of kinase cascades such as the S6K-S6 axis, which plays a key role in protein synthesis. Administration of the β2-adrenergic receptor (AR) agonist clenbuterol activated the S6K-S6 axis in skeletal muscle and induced muscle hypertrophy in mice. These effects of clenbuterol were attenuated in M-PDK1KO mice, and mechanical load–induced activation of the S6K-S6 axis and muscle hypertrophy were inhibited in mice with skeletal muscle–specific deficiency of β2-AR. Our results suggest that PDK1 regulates skeletal muscle mass under the static condition and that it contributes to mechanical load–induced muscle hypertrophy, at least in part by mediating signaling from β2-AR.
Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus)
Authors: Nguyen Thanh Thi , Pathirana Pubudu N. , Nguyen Thin , Nguyen Quoc Viet Hung , Bhatti Asim , Nguyen Dinh C. , Nguyen Dung Tien , Nguyen Ngoc Duy , Creighton Douglas , Abdelrazek Mohamed
Published: February 2021

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly pathogenic virus that has caused the global COVID-19 pandemic. Tracing the evolution and transmission of the virus is crucial to respond to and control the pandemic through appropriate intervention strategies. This paper reports and analyses genomic mutations in the coding regions of SARS-CoV-2 and their probable protein secondary structure and solvent accessibility changes, which are predicted using deep learning models. Prediction results suggest that mutation D614G in the virus spike protein, which has attracted much attention from researchers, is unlikely to make changes in protein secondary structure and relative solvent accessibility. Based on 6324 viral genome sequences, we create a spreadsheet dataset of point mutations that can facilitate the investigation of SARS-CoV-2 in many perspectives, especially in tracing the evolution and worldwide spread of the virus. Our analysis results also show that coding genes E, M, ORF6, ORF7a, ORF7b and ORF10 are most stable, potentially suitable to be targeted for vaccine and drug development.
Genetic structure of a remnant Acropora cervicornis population
Authors: Canty Steven W. J. , Fox Graeme , Rowntree Jennifer K. , Preziosi Richard F.
Published: February 2021

Amongst the global decline of coral reefs, hope spots such as Cordelia Bank in Honduras, have been identified. This site contains dense, remnant thickets of the endangered species Acropora cervicornis, which local managers and conservation organizations view as a potential source population for coral restoration projects. The aim of this study was to determine the genetic diversity of colonies across three banks within the protected area. We identified low genetic diversity (FST = 0.02) across the three banks, and genetic similarity of colonies ranged from 91.3 to 95.8% between the banks. Clonality rates were approximately 30% across the three banks, however, each genotype identified was unique to each bank. Despite the low genetic diversity, subtle genetic differences within and among banks were demonstrated, and these dense thickets were shown not to be comprised of a single or a few genotypes. The presence of multiple genotypes suggests A. cervicornis colonies from these banks could be used to maintain and enhance genetic diversity in restoration projects. Management of hope spots, such as Cordelia Bank, and the incorporation of genetic information into restoration projects to ensure genetic diversity within out-planted populations, will be critical in the ongoing challenge of conserving and preserving coral reefs.
DeepACSON automated segmentation of white matter in 3D electron microscopy
Authors: Abdollahzadeh Ali , Belevich Ilya , Jokitalo Eija , Sierra Alejandra , Tohka Jussi
Published: February 2021

Tracing the entirety of ultrastructures in large three-dimensional electron microscopy (3D-EM) images of the brain tissue requires automated segmentation techniques. Current segmentation techniques use deep convolutional neural networks (DCNNs) and rely on high-contrast cellular membranes and high-resolution EM volumes. On the other hand, segmenting low-resolution, large EM volumes requires methods to account for severe membrane discontinuities inescapable. Therefore, we developed DeepACSON, which performs DCNN-based semantic segmentation and shape-decomposition-based instance segmentation. DeepACSON instance segmentation uses the tubularity of myelinated axons and decomposes under-segmented myelinated axons into their constituent axons. We applied DeepACSON to ten EM volumes of rats after sham-operation or traumatic brain injury, segmenting hundreds of thousands of long-span myelinated axons, thousands of cell nuclei, and millions of mitochondria with excellent evaluation scores. DeepACSON quantified the morphology and spatial aspects of white matter ultrastructures, capturing nanoscopic morphological alterations five months after the injury.
SARS-CoV-2 and tissue damage: current insights and biomaterial-based therapeutic strategies
Authors: Roy Himadri Shekhar , Singh Rupali , Ghosh Deepa
Published: February 2021

Schematic representation of use of biomaterials in tissue regeneration for SARS-CoV-2-affected organs.
Towards the development of safer by design TiO2-based photocatalytic paint: impacts and performances
Authors: Rosset A. , Bartolomei V. , Laisney J. , Shandilya N. , Voisin H. , Morin J. , Michaud-Soret I. , Capron I. , Wortham H. , Brochard G. , Bergé V. , Carriere M. , Dussert F. , Le Bihan O. , Dutouquet C. , Benayad A. , Truffier-Boutry D. , Clavaguera S. , Artous S.
Published: February 2021

Safer by design approaches for TiO2 based photocatalytic paints.
Salt reduction in bread via enrichment of dietary fiber containing sodium and calcium
Authors: Li Yan-Lei , Han Kai-Ning , Feng Guang-Xin , Wan Zhi-Li , Wang Gao-Shang , Yang Xiao-Quan
Published: February 2021

A novel salt reduction strategy in bread via the enrichment of dietary fiber-contained sodium and calcium.
Trust is good, control is better: a review on monitoring and characterization techniques for flow battery electrolytes
Authors: Nolte Oliver , Volodin Ivan A. , Stolze Christian , Hager Martin D. , Schubert Ulrich S.
Published: February 2021

This review article summarizes the state-of-the-art techniques for the characterization and monitoring of flow battery electrolytes highlighting in particular the importance of the electrolyte state-of-charge and state-of-health assessment.
The effects of DOPO modified Co-based metalorganic framework on flame retardancy, stiffness and thermal stability of epoxy resin
Authors: Cai Liyun , Xin Fei , Zhai Congcong , Chen Yu , Xu Bo , Li Xiangmei
Published: February 2021

The DOPO@ZIF-67 promoted the carbonization process of the EP flame retardant composites, and the rigidity and damping coefficient of EP composites are also improved compared with pure EP.
Preparation of ashless cellulose paper standards for rapid determination of multi-element concentrations in airborne fine particulate matter using laser ablation inductively coupled plasma mass spectrometry
Authors: Qiao Lei , Zhang Ruijie , Qiao Jing , He Xiaoyan , Wu Zhiwei
Published: February 2021

A simple procedure for the rapid determination of multi-element concentrations in PM2.5 samples using LA-ICP-MS was developed. The direct solid sampling method can also be expanded to study element spatial distributions in airborne filter materials.
Aligned carbon nanotube fibers for fiber-shaped solar cells, supercapacitors and batteries
Authors: Cao Yufang , Zhou Tao , Wu Kunjie , Yong Zhenzhong , Zhang Yongyi
Published: February 2021

Aligned CNT fibers emerge as the promising electrodes for fiber energy harvesting/storage devices due to their lightweight, high specific surface areas, outstanding mechanical and electrical property.
Highly flexible and free-standing carbon nanotube/hollow carbon nanocage hybrid films for high-performance supercapacitors
Authors: Shi Qiang Qiang , Zhan Hang , Zhang Yu , Wang Jian Nong
Published: February 2021

A carbon nanotube-hollow carbon nanocage hybrid film is fabricated via a facile layer-by-layer strategy. The in situ addition of hollow carbon nanocages to the film is beneficial for preventing CNT stacking and thus promoting electrolyte transport.
Using Adinandra nitida leaf extract to prevent heterocyclic amine formation in fried chicken patties
Authors: Zhao Tianpei , Xi Jun , Zhang Chenxia , Ma Yuxiang , Wang Xuede
Published: February 2021

Adinandra nitida leaf extract, rich in polyphenols and flavonoids, can effectively prevent the formation of heterocyclic amines in fried chicken patties.
Kinetics and reaction mechanism of photochemical degradation of diclofenac by UV-activated peroxymonosulfate
Authors: Peng Yunlan , Shi Hongle , Wang Zhenran , Fu Yongsheng , Liu Yiqing
Published: February 2021

Compared to UV alone and PMS alone systems, diclofenac was removed more efficiently in UV/PMS system at pH 7.0 due to the contribution of SO4˙− and HO˙ and its degradation followed the pseudo-first order kinetic model.
Growth factor loading on aliphatic polyester scaffolds
Authors: Shen Hong , Hu Xixue
Published: February 2021

Cells, scaffolds and growth factors are three elements of tissue engineering. Growth factors precisely controlled by a scaffold will be used in conjunction with the scaffolds and cells to repair and regenerate defect tissue.
Bonding and stability of donor ligand-supported heavier analogues of cyanogen halides (L′)PSi(X)(L)
Authors: Gorantla Sai Manoj N. V. T. , Francis Maria , Roy Sudipta , Mondal Kartik Chandra
Published: February 2021

The bonding and stability of elusive heavier cyanogen halide analogues (L′)PSi(X)(L) have been theoretically investigated using EDA-NOCV method. Variation of ligands and halogen on Si atom had a significant effect on the stability of these species.
Structures and impact strength variation of chemically crosslinked high-density polyethylene: effect of crosslinking density
Authors: Ren Yueqing , Sun Xiaojie , Chen Lanlan , Li Yafei , Sun Miaomiao , Duan Xuelei , Liang Wenbin
Published: February 2021

Crosslinking significantly improves the toughness and impact strength of HDPE and extends its application, especially at low temperature.
Synthesis and biological evaluation of the new ring system benzo[f]pyrimido[1,2-d][1,2,3]triazolo[1,5-a][1,4]diazepine and its cycloalkane and cycloalkene condensed analogues
Authors: El Haimer Mohamed , Palkó Márta , Haukka Matti , Gajdács Márió , Zupkó István , Fülöp Ferenc
Published: February 2021

Derivatives of the new ring system benzo[f]pyrimido[1,2-d][1,2,3]triazolo[1,5-a][1,4]diazepinone and its cycloalkane and cycloalkene condensed analogues have been conveniently synthesized through a three-step reaction sequence.
Synthesis and evaluation of porphyrin glycoconjugates varying in linker length: preliminary effects on the photodynamic inactivation ofMycobacterium smegmatis
Authors: Dixon Charlie F. , Nottingham Ana N. , Lozano Ana Frances , Sizemore J. Alexander , Russell Logan A. , Valiton Chelsea , Newell Kimberly L. , Babin Dominique , Bridges William T. , Parris Matthew R. , Shchirov David V. , Snyder Nicole L. , Ruppel Joshua V.
Published: February 2021

Carbohydrate–porphyrin conjugates varying in the nature of the carbohydrate and the distance between the porphyrin macrocycle and the carbohydrate are reported. First studies of the impact of linker length on photodynamic inactivation are reported.
Bright sky-blue fluorescence with high color purity: assembly of luminescent diphenyl-anthracene lutetium-based coordination polymer
Authors: Kitagawa Yuichi , Naito Ayu , Fushimi Koji , Hasegawa Yasuchika
Published: February 2021

Pure sky-blue fluorescence (FWHM: 50 nm) from lutetium-based coordination polymer with diphenyl-anthracene derivative is demonstrated for the first time.
Coloring ultrasensitive MRI with tunable metal–organic frameworks
Authors: Yang Yuqi , Zhang Yingfeng , Wang Baolong , Guo Qianni , Yuan Yaping , Jiang Weiping , Shi Lei , Yang Minghui , Chen Shizhen , Lou Xin , Zhou Xin
Published: February 2021

Metal organic frameworks with tunable pore structures are able to provide varied chemical environments for hyperpolarized129Xe atom hosting, which results in distinguishing magnetic resonance signals, and stains ultra-sensitive magnetic resonance imaging (MRI) with diverse colors.
Directly visualizing carrier transport and recombination at individual defects within 2D semiconductors
Authors: Hill Joshua W. , Hill Caleb M.
Published: February 2021

Probe-based electrochemical techniques can be used to map carrier transport and recombination within two-dimensional semiconductors.
Benzocyclobutene polymer as an additive for a benzocyclobutene-fullerene: application in stable p–i–n perovskite solar cells
Authors: Tremblay Marie-Hélène , Schutt Kelly , Pulvirenti Federico , Schultz Thorsten , Wegner Berthold , Jia Xiaojia , Zhang Yadong , Longhi Elena , Dasari Raghunath R. , Fuentes-Hernandez Canek , Kippelen Bernard , Koch Norbert , Snaith Henry J. , Barlow Stephen , Marder Seth R.
Published: February 2021

Solar cells with undoped PCBCB:CL extraction layers exhibit higher power conversion efficiencies than their PCBM and PCBCB counterparts, as well as excellent thermal stability.
Ni-based bimetallic nano-catalysts anchored on BaZr0.4Ce0.4Y0.1Yb0.1O3−δ for internal steam reforming of methane in a low-temperature proton-conducting ceramic fuel cell
Authors: Hong Kyungpyo , Sutanto Stephanie Nadya , Lee Jeong A. , Hong Jongsup
Published: February 2021

Ni–Rh and Ni–Co nano-scale alloys exhibit high methane conversion, hydrogen yield, resistance to carbon formation, and long-term stability at low temperatures, allowing them to cope with the various operating conditions of direct methane-fueled PCFCs.
The high enrichment of Geobacter by TiN nanoarray anode catalyst for efficient microbial fuel cells
Authors: Liu Da , Huang Weicheng , Chang Qinghuan , Zhang Lu , Wang Ruiwen , Yan Mei , Meng Hongxue , Yang Bin , Guo Chongshen
Published: February 2021

TiN nanoarrays, in situ grown on carbon cloth gather 97.2% of the model exoelectrogen Geobacter, greatly enhancing the MFCs' performance. The experimental results and DFT calculation certify the importance of the micro–nano-hierarchical structure.
Controlling surface chemistry and mechanical properties of metal ionogels through Lewis acidity and basicity
Authors: Clarke Coby J. , Matthews Richard P. , Brogan Alex P. S. , Hallett Jason P.
Published: February 2021

Gels prepared from metal containing ionic liquids with cross-linked poly(ethylene glycol) have surface compositions and mechanical properties that can be controlled by Lewis basicity and acidity of the metal species.