bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isolation, characterization, molecular analysis and application of bacteriophage DW-EC to control Enterotoxigenic Escherichia coli on various foods
Authors: Dewanggana Marta Nisita , Evangeline Clare , Ketty Maurita Delia , Waturangi Diana Elizabeth , Yogiara  , Magdalena Stella 
Published: January 2022

AbstractAmong food preservation methods, bacteriophage treatment can be a viable alternative method to overcome the drawbacks of traditional approaches. Bacteriophages are naturally occurring viruses that are highly specific to their hosts and have the capability to lyse bacterial cells, making them useful as biopreservation agents. This study aims to characterize and determine the application of bacteriophage isolated from Indonesian traditional Ready-to-Eat (RTE) food to control EnterotoxigenicEscherichia coli(ETEC) population in various foods. Phage DW-EC isolated from Indonesian traditional RTE food called dawet with ETEC as its host showed a positive result by the formation of plaques (clear zone) in the bacterial host lawn. Transmission electron microscopy (TEM) results also showed that DW-EC can be suspected to belong to theMyoviridaefamily. Molecular characterization and bioinformatic analysis showed that DW-EC exhibited characteristics as promising biocontrol agents in food samples. Genes related to the lytic cycle, such as lysozyme and tail fiber assembly protein, were annotated. There were also no signs of lysogenic genes among the annotation results. The resulting PHACTS data also indicated that DW-EC was leaning toward being exclusively lytic. DW-EC significantly reduced the ETEC population (P ≤ 0.05) in various food samples after two different incubation times (1 day and 6 days) in chicken meat (80.93%; 87.29%), fish meat (63.78%; 87.89%), cucumber (61.42%; 71.88%), tomato (56.24%; 74.51%), and lettuce (46.88%; 43.38%).
Digital health tools for the passive monitoring of depression: a systematic review of methods
Authors: De Angel Valeria , Lewis Serena , White Katie , Oetzmann Carolin , Leightley Daniel , Oprea Emanuela , Lavelle Grace , Matcham Faith , Pace Alice , Mohr David C. , Dobson Richard , Hotopf Matthew 
Published: January 2022

AbstractThe use of digital tools to measure physiological and behavioural variables of potential relevance to mental health is a growing field sitting at the intersection between computer science, engineering, and clinical science. We summarised the literature on remote measuring technologies, mapping methodological challenges and threats to reproducibility, and identified leading digital signals for depression. Medical and computer science databases were searched between January 2007 and November 2019. Published studies linking depression and objective behavioural data obtained from smartphone and wearable device sensors in adults with unipolar depression and healthy subjects were included. A descriptive approach was taken to synthesise study methodologies. We included 51 studies and found threats to reproducibility and transparency arising from failure to provide comprehensive descriptions of recruitment strategies, sample information, feature construction and the determination and handling of missing data. The literature is characterised by small sample sizes, short follow-up duration and great variability in the quality of reporting, limiting the interpretability of pooled results. Bivariate analyses show consistency in statistically significant associations between depression and digital features from sleep, physical activity, location, and phone use data. Machine learning models found the predictive value of aggregated features. Given the pitfalls in the combined literature, these results should be taken purely as a starting point for hypothesis generation. Since this research is ultimately aimed at informing clinical practice, we recommend improvements in reporting standards including consideration of generalisability and reproducibility, such as wider diversity of samples, thorough reporting methodology and the reporting of potential bias in studies with numerous features.
Diacylglyceryl-N,N,N-trimethylhomoserine-dependent lipid remodeling in a green alga, Chlorella kessleri
Authors: Oishi Yutaro , Otaki Rie , Iijima Yukari , Kumagai Eri , Aoki Motohide , Tsuzuki Mikio , Fujiwara Shoko , Sato Norihiro 
Published: January 2022

AbstractMembrane lipid remodeling contributes to the environmental acclimation of plants. In the green lineage, a betaine lipid, diacylglyceryl-N,N,N-trimethylhomoserine (DGTS), is included exclusively among green algae and nonflowering plants. Here, we show that the green alga Chlorella kessleri synthesizes DGTS under phosphorus-deficient conditions through the eukaryotic pathway via the ER. Simultaneously, phosphatidylcholine and phosphatidylethanolamine, which are similar to DGTS in their zwitterionic properties, are almost completely degraded to release 18.1% cellular phosphorus, and to provide diacylglycerol moieties for a part of DGTS synthesis. This lipid remodeling system that substitutes DGTS for extrachloroplast phospholipids to lower the P-quota operates through the expression induction of the BTA1 gene. Investigation of this lipid remodeling system is necessary in a wide range of lower green plants for a comprehensive understanding of their phosphorus deficiency acclimation strategies.
Primordial mimicry induces morphological change in Escherichia coli
Authors: Lu Hui , Aida Honoka , Kurokawa Masaomi , Chen Feng , Xia Yang , Xu Jian , Li Kai , Ying Bei-Wen , Yomo Tetsuya 
Published: January 2022

AbstractThe morphology of primitive cells has been the subject of extensive research. A spherical form was commonly presumed in prebiotic studies but lacked experimental evidence in living cells. Whether and how the shape of living cells changed are unclear. Here we exposed the rod-shaped bacterium Escherichia coli to a resource utilization regime mimicking a primordial environment. Oleate was given as an easy-to-use model prebiotic nutrient, as fatty acid vesicles were likely present on the prebiotic Earth and might have been used as an energy resource. Six evolutionary lineages were generated under glucose-free but oleic acid vesicle (OAV)-rich conditions. Intriguingly, fitness increase was commonly associated with the morphological change from rod to sphere and the decreases in both the size and the area-to-volume ratio of the cell. The changed cell shape was conserved in either OAVs or glucose, regardless of the trade-offs in carbon utilization and protein abundance. Highly differentiated mutations present in the genome revealed two distinct strategies of adaption to OAV-rich conditions, i.e., either directly targeting the cell wall or not. The change in cell morphology of Escherichia coli for adapting to fatty acid availability supports the assumption of the primitive spherical form.
DAF-2c signaling promotes taste avoidance after starvation in Caenorhabditis elegans by controlling distinct phospholipase C isozymes
Authors: Tomioka Masahiro , Jang Moon Sun , Iino Yuichi 
Published: January 2022

AbstractPreviously, we reported that DAF-2c, an axonal insulin receptor isoform in Caenorhabditis elegans, acts in the ASER gustatory neuron to regulate taste avoidance learning, a process in which worms learn to avoid salt concentrations experienced during starvation. Here, we show that secretion of INS-1, an insulin-like peptide, after starvation conditioning is sufficient to drive taste avoidance via DAF-2c signaling. Starvation conditioning enhances the salt-triggered activity of AIA neurons, the main sites of INS-1 release, which potentially promotes feedback signaling to ASER to maintain DAF-2c activity during taste avoidance. Genetic studies suggest that DAF-2c–Akt signaling promotes high-salt avoidance via a decrease in PLCβ activity. On the other hand, the DAF-2c pathway promotes low-salt avoidance via PLCε and putative Akt phosphorylation sites on PLCε are essential for taste avoidance. Our findings imply that animals disperse from the location at which they experience starvation by controlling distinct PLC isozymes via DAF-2c.
Viscoelastic parameterization of human skin cells characterize material behavior at multiple timescales
Authors: Parvini Cameron H. , Cartagena-Rivera Alexander X. , Solares Santiago D. 
Published: January 2022

AbstractCountless biophysical studies have sought distinct markers in the cellular mechanical response that could be linked to morphogenesis, homeostasis, and disease. Here, an iterative-fitting methodology visualizes the time-dependent viscoelastic behavior of human skin cells under physiologically relevant conditions. Past investigations often involved parameterizing elastic relationships and assuming purely Hertzian contact mechanics, which fails to properly account for the rich temporal information available. We demonstrate the performance superiority of the proposed iterative viscoelastic characterization method over standard open-search approaches. Our viscoelastic measurements revealed that 2D adherent metastatic melanoma cells exhibit reduced elasticity compared to their normal counterparts—melanocytes and fibroblasts, and are significantly less viscous than fibroblasts over timescales spanning three orders of magnitude. The measured loss angle indicates clear differential viscoelastic responses across multiple timescales between the measured cells. This method provides insight into the complex viscoelastic behavior of metastatic melanoma cells relevant to better understanding cancer metastasis and aggression.
Interannual temperature variability is a principal driver of low-frequency fluctuations in marine fish populations
Authors: van der Sleen Peter , Zuidema Pieter A. , Morrongiello John , Ong Jia Lin J. , Rykaczewski Ryan R. , Sydeman William J. , Di Lorenzo Emanuele , Black Bryan A. 
Published: January 2022

AbstractMarine fish populations commonly exhibit low-frequency fluctuations in biomass that can cause catch volatility and thus endanger the food and economic security of dependent coastal societies. Such variability has been linked to fishing intensity, demographic processes and environmental variability, but our understanding of the underlying drivers remains poor for most fish stocks. Our study departs from previous findings showing that sea surface temperature (SST) is a significant driver of fish somatic growth variability and that life-history characteristics mediate population-level responses to environmental variability. We use autoregressive models to simulate how fish populations integrate SST variability over multiple years depending on fish life span and trophic position. We find that simulated SST-driven population dynamics can explain a significant portion of observed low-frequency variability in independent observations of fisheries landings around the globe. Predictive skill, however, decreases with increasing fishing pressure, likely due to demographic truncation. Using our modelling approach, we also show that increases in the mean and variance of SST could amplify biomass volatility and lessen its predictability in the future. Overall, biological integration of high-frequency SST variability represents a null hypothesis with which to explore the drivers of low-frequency population change across upper-trophic marine species.
UVC inactivation of pathogenic samples suitable for cryo-EM analysis
Authors: Depelteau Jamie S. , Renault Ludovic , Althof Nynke , Cassidy C. Keith , Mendonça Luiza M. , Jensen Grant J. , Resch Guenter P. , Briegel Ariane 
Published: January 2022

AbstractCryo-electron microscopy has become an essential tool to understand structure and function of biological samples. Especially for pathogens, such as disease-causing bacteria and viruses, insights gained by cryo-EM can aid in developing cures. However, due to the biosafety restrictions of pathogens, samples are often treated by chemical fixation to render the pathogen inert, affecting the ultrastructure of the sample. Alternatively, researchers use in vitro or ex vivo models, which are non-pathogenic but lack the complexity of the pathogen of interest. Here we show that ultraviolet-C (UVC) radiation applied at cryogenic temperatures can be used to eliminate or dramatically reduce the infectivity of Vibrio cholerae and the bacterial virus, the ICP1 bacteriophage. We show no discernable structural impact of this treatment of either sample using two cryo-EM methods: cryo-electron tomography followed by sub-tomogram averaging, and single particle analysis (SPA). Additionally, we applied the UVC irradiation to the protein apoferritin (ApoF), which is a widely used test sample for high-resolution SPA studies. The UVC-treated ApoF sample resulted in a 2.1 Å structure indistinguishable from an untreated published map. This research demonstrates that UVC treatment is an effective and inexpensive addition to the cryo-EM sample preparation toolbox.
Fluorescence lifetime DNA-PAINT for multiplexed super-resolution imaging of cells
Authors: Oleksiievets Nazar , Sargsyan Yelena , Thiele Jan Christoph , Mougios Nikolaos , Sograte-Idrissi Shama , Nevskyi Oleksii , Gregor Ingo , Opazo Felipe , Thoms Sven , Enderlein Jörg , Tsukanov Roman 
Published: January 2022

AbstractDNA point accumulation for imaging in nanoscale topography (DNA-PAINT) is a powerful super-resolution technique highly suitable for multi-target (multiplexing) bio-imaging. However, multiplexed imaging of cells is still challenging due to the dense and sticky environment inside a cell. Here, we combine fluorescence lifetime imaging microscopy (FLIM) with DNA-PAINT and use the lifetime information as a multiplexing parameter for targets identification. In contrast to Exchange-PAINT, fluorescence lifetime PAINT (FL-PAINT) can image multiple targets simultaneously and does not require any fluid exchange, thus leaving the sample undisturbed and making the use of flow chambers/microfluidic systems unnecessary. We demonstrate the potential of FL-PAINT by simultaneous imaging of up to three targets in a cell using both wide-field FLIM and 3D time-resolved confocal laser scanning microscopy (CLSM). FL-PAINT can be readily combined with other existing techniques of multiplexed imaging and is therefore a perfect candidate for high-throughput multi-target bio-imaging.
Selective control of synaptically-connected circuit elements by all-optical synapses
Authors: Prakash Mansi , Murphy Jeremy , St Laurent Robyn , Friedman Nina , Crespo Emmanuel L. , Bjorefeldt Andreas , Pal Akash , Bhagat Yuvraj , Kauer Julie A. , Shaner Nathan C. , Lipscombe Diane , Moore Christopher I. , Hochgeschwender Ute 
Published: January 2022

AbstractUnderstanding percepts, engrams and actions requires methods for selectively modulating synaptic communication between specific subsets of interconnected cells. Here, we develop an approach to control synaptically connected elements using bioluminescent light: Luciferase-generated light, originating from a presynaptic axon terminal, modulates an opsin in its postsynaptic target. Vesicular-localized luciferase is released into the synaptic cleft in response to presynaptic activity, creating a real-time Optical Synapse. Light production is under experimenter-control by introduction of the small molecule luciferin. Signal transmission across this optical synapse is temporally defined by the presence of both the luciferin and presynaptic activity. We validate synaptic Interluminescence by multi-electrode recording in cultured neurons and in mice in vivo. Interluminescence represents a powerful approach to achieve synapse-specific and activity-dependent circuit control in vivo.
Independent control of amplitude and period in a synthetic oscillator circuit with modified repressilator
Authors: Zhang Fengyu , Sun Yanhong , Zhang Yihao , Shen Wenting , Wang Shujing , Ouyang Qi , Luo Chunxiong 
Published: January 2022

AbstractSynthetic Biology aims to create predictable biological circuits and fully operational biological systems. Although there are methods to create more stable oscillators, such as repressilators, independently controlling the oscillation of reporter genes in terms of their amplitude and period is only on theoretical level. Here, we introduce a new oscillator circuit that can be independently controlled by two inducers in Escherichia coli. Some control components, including σECF11 and NahR, were added to the circuit. By systematically tuning the concentration of the inducers, salicylate and IPTG, the amplitude and period can be modulated independently. Furthermore, we constructed a quantitative model to forecast the regulation results. Under the guidance of the model, the expected oscillation can be regulated by choosing the proper concentration combinations of inducers. In summary, our work achieved independent control of the oscillator circuit, which allows the oscillator to be modularized and used in more complex circuit designs.
RegEnrich gene regulator enrichment analysis reveals a key role of the ETS transcription factor family in interferon signaling
Authors: Tao Weiyang , Radstake Timothy R. D. J. , Pandit Aridaman 
Published: January 2022

AbstractChanges in a few key transcriptional regulators can lead to different biological states. Extracting the key gene regulators governing a biological state allows us to gain mechanistic insights. Most current tools perform pathway/GO enrichment analysis to identify key genes and regulators but tend to overlook the gene/protein regulatory interactions. Here we present RegEnrich, an open-source Bioconductor R package, which combines differential expression analysis, data-driven gene regulatory network inference, enrichment analysis, and gene regulator ranking to identify key regulators using gene/protein expression profiling data. By benchmarking using multiple gene expression datasets of gene silencing studies, we found that RegEnrich using the GSEA method to rank the regulators performed the best. Further, RegEnrich was applied to 21 publicly available datasets on in vitro interferon-stimulation of different cell types. Collectively, RegEnrich can accurately identify key gene regulators from the cells under different biological states, which can be valuable in mechanistically studying cell differentiation, cell response to drug stimulation, disease development, and ultimately drug development.
Structural insights into the potency and selectivity of covalent pan-FGFR inhibitors
Authors: Qu Lingzhi , Chen Xiaojuan , Wei Hudie , Guo Ming , Dai Shuyan , Jiang Longying , Li Jun , Yue Sitong , Chen Zhuchu , Chen Yongheng 
Published: January 2022

AbstractFIIN-2, TAS-120 (Futibatinib) and PRN1371 are highly potent pan-FGFR covalent inhibitors targeting the p-loop cysteine of FGFR proteins, of which TAS-120 and PRN1371 are currently in clinical trials. It is critical to analyze their target selectivity and their abilities to overcome gatekeeper mutations. In this study, we demonstrate that FIIN-2 and TAS-120 form covalent adducts with SRC, while PRN1371 does not. FIIN-2 and TAS-120 inhibit SRC and YES activities, while PRN1371 does not. Moreover, FIIN-2, TAS-120 and PRN1371 exhibit different potencies against different FGFR gatekeeper mutants. In addition, the co-crystal structures of SRC/FIIN-2, SRC/TAS-120 and FGFR4/PRN1371 complexes reveal structural basis for kinase targeting and gatekeeper mutations. Taken together, our study not only provides insight into the potency and selectivity of covalent pan-FGFR inhibitors, but also sheds light on the development of next-generation FGFR covalent inhibitors with high potency, high selectivity, and stronger ability to overcome gatekeeper mutations.
Robust separation of topological in-plane and out-of-plane waves in a phononic crystal
Authors: Lee Myung-Joon , Oh Il-Kwon 
Published: January 2022

AbstractValley degree of freedom, associated with the valley topological phase, has propelled the advancement of the elastic waveguide by offering immunity to backscattering against bending and weak perturbations. Despite many attempts to manipulate the wave path and working frequency of the waveguide, internal characteristic of an elastic wave such as rich polarization has not yet been utilized with valley topological phases. Here, we introduce the rich polarization into the valley degree of freedom, to achieve topologically protected in-plane and out-of-plane mode separation of an elastic wave. Accidental degeneracy proves its real worth of decoupling the in-plane and out-of-plane polarized valley Hall phases. We further demonstrate independent and simultaneous control of in-plane and out-of-plane waves, with intact topological protection. The presenting procedure for designing the topologically protected wave separation based on accidental degeneracy will widen the valley topological physics in view of both generation mechanism and application areas.
All-optical quasi-monoenergetic GeV positron bunch generation by twisted laser fields
Authors: Zhao Jie , Hu Yan-Ting , Lu Yu , Zhang Hao , Hu Li-Xiang , Zhu Xing-Long , Sheng Zheng-Ming , Turcu Ion Cristian Edmond , Pukhov Alexander , Shao Fu-Qiu , Yu Tong-Pu 
Published: January 2022

AbstractGeneration of energetic electron-positron pairs using multi-petawatt (PW) lasers has recently attracted increasing interest. However, some previous laser-driven positron beams have severe limitations in terms of energy spread, beam duration, density, and collimation. Here we propose a scheme for the generation of dense ultra-short quasi-monoenergetic positron bunches by colliding a twisted laser pulse with a Gaussian laser pulse. In this scheme, abundant γ-photons are first generated via nonlinear Compton scattering and positrons are subsequently generated during the head-on collision of γ-photons with the Gaussian laser pulse. Due to the unique structure of the twisted laser pulse, the positrons are confined by the radial electric fields and experience phase-locked-acceleration by the longitudinal electric field. Three-dimensional simulations demonstrate the generation of dense sub-femtosecond quasi-monoenergetic GeV positron bunches with tens of picocoulomb (pC) charge and extremely high brilliance above 1014 s−1 mm−2 mrad−2 eV−1, making them promising for applications in laboratory physics and high energy physics.
Substitutional transition metal doping in MoSi2N4 monolayer: structural, electronic and magnetic properties
Authors: Abdelati Mohamed A. , Maarouf Ahmed A. , Fadlallah Mohamed M. 
Published: January 2022

We find that the Sc-, Y-, Ti-, and Zr–MoSi2N4 are metallic systems, while Mn-, Tc-, and Ru–MoSi2N4 are n-type conducting. The Fe–MoSi2N4 is a dilute magnetic semiconductor.
Applications smartphones pour l’analyse de la performance : un laboratoire dans votre poche
Authors: Morin Jean-Benoît 
Published: January 2022

La performance sportive est influencée par les capacités musculaires et physiques des athlètes. Les mesures de référence en laboratoire permettent d’évaluer les productions de force, vitesse, puissance dans des mouvements de saut, de sprint et de musculation, ou encore de biomécanique de la foulée de course, qui comptent parmi les déterminants biomécaniques de la performance sportive. Cependant, bien qu’historiquement développées « sur le terrain » notamment par les travaux d’Étienne-Jules Marey, ces techniques n’étaient pas accessibles au plus grand nombre de pratiquants et praticiens. Grâce au développement récent d’appareils photos et caméras haute fréquence (240 images/s) intégrés dans les smartphones et tablettes du fabricant Apple, des applications ont été inventées et validées par comparaison avec des mesures de référence. Elles utilisent des modèles biomécaniques validés par ailleurs pour calculer force, vitesse, puissance mécanique et performance en saut, lors d’une accélération en sprint, estimer la force maximale lors de mouvement de musculation ou des variables biomécaniques de la foulée de course et leur asymétrie. Le ratio coût/précision/simplicité élevé de ces applications a permis de générer des connaissances sur la performance sportive, mais également des avancées dans l’entraînement sportif qui auraient été impossibles sans la levée de ce verrou technologique.