bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiomics interrogation into HBV (Hepatitis B virus)-host interaction reveals novel coding potential in human genome, and identifies canonical and non-canonical proteins as host restriction factors against HBV
Authors: Yuan Shilin , Liao Guanghong , Zhang Menghuan , Zhu Yuanfei , Xiao Weidi , Wang Kun , Li Chuanyin , Jia Caiwei , Sun Na , Walch Axel , Gao Daming , Xu Ping , Deng Qiang , Zhang Jian , Wang He , Hu Ronggui 
Published: November 2021

AbstractHepatitis B Virus (HBV) constitutes a major threat to global public health. Current understanding of HBV-host interaction is yet limited. Here, ribosome profiling, quantitative mass spectrometry and RNA-sequencing were conducted on a recently established HBV replication system, through which we identified multiomic differentially expressed genes (DEGs) that HBV orchestrated to remodel host proteostasis networks. Our multiomics interrogation revealed that HBV induced significant changes in both transcription and translation of 35 canonical genes including PPP1R15A, PGAM5 and SIRT6, as well as the expression of at least 15 non-canonical open reading frames (ncORFs) including ncPON2 and ncGRWD1, thus revealing an extra coding potential of human genome. Overexpression of these five genes but not the enzymatically deficient SIRT6 mutants suppressed HBV replication while knockdown of SIRT6 had opposite effect. Furthermore, the expression of SIRT6 was down-regulated in patients, cells or animal models of HBV infection. Mechanistic study further indicated that SIRT6 directly binds to mini-chromosome and deacetylates histone H3 lysine 9 (H3K9ac) and histone H3 lysine 56 (H3K56ac), and chemical activation of endogenous SIRT6 with MDL800 suppressed HBV infection in vitro and in vivo. By generating the first multiomics landscape of host-HBV interaction, our work is thus opening a new avenue to facilitate therapeutic development against HBV infection.
Surface Laplacian of interfacial thermochemical potential: its role in solid-liquid pattern formation
Authors: Glicksman Martin E. , Wu Peichen , Ankit Kumar 
Published: November 2021

AbstractSteady-state solid-liquid interfaces allow both analytic description as sharp-interface profiles, and numerical simulation via phase-field modeling as stationary diffuse-interface microstructures. Profiles for sharp interfaces reveal their exact shapes and allow identification of the thermodynamic origin of all interfacial capillary fields, including distributions of curvature, thermochemical potential, gradients, fluxes, and surface Laplacians. By contrast, simulated diffuse interface images allow thermodynamic evolution and measurement of interfacial temperatures and fluxes. Quantitative results using both approaches verify these capillary fields and their divergent heat flow, to provide insights into interface energy balances, dynamic pattern formation, and novel methods for microstructure control. The microgravity environment of low-Earth orbit was proven useful in past studies of solidification phenomena. We suggest that NASA’s ISS National Lab can uniquely accommodate aspects of experimental research needed to explore these novel topics.
Oscillations of a soft viscoelastic drop
Authors: Tamim Saiful I. , Bostwick Joshua B. 
Published: November 2021

AbstractA soft viscoelastic drop has dynamics governed by the balance between surface tension, viscosity, and elasticity, with the material rheology often being frequency dependent, which are utilized in bioprinting technologies for tissue engineering and drop-deposition processes for splash suppression. We study the free and forced oscillations of a soft viscoelastic drop deriving (1) the dispersion relationship for free oscillations, and (2) the frequency response for forced oscillations, of a soft material with arbitrary rheology. We then restrict our analysis to the classical cases of a Kelvin–Voigt and Maxwell model, which are relevant to soft gels and polymer fluids, respectively. We compute the complex frequencies, which are characterized by an oscillation frequency and decay rate, as they depend upon the dimensionless elastocapillary and Deborah numbers and map the boundary between regions of underdamped and overdamped motions. We conclude by illustrating how our theoretical predictions for the frequency-response diagram could be used in conjunction with drop-oscillation experiments as a “drop vibration rheometer”, suggesting future experiments using either ultrasonic levitation or a microgravity environment.
4 Day in dry immersion reproduces partially the aging effect on the arteries as observed during 6 month spaceflight or confinement
Authors: Greaves Danielle , Guillon Laurent , Besnard Stephane , Navasiolava Nastassia , Arbeille Philippe 
Published: November 2021

AbstractThe objectives of this study were to determine whether 4 days of dry immersion (DI) induced similar arterial aging as spaceflight and to test the impact of thigh cuffs. Eighteen subjects underwent DI; nine wore thigh cuffs. Cardiac and arterial targets were assessed by ultrasound. No significant differences were found between the groups. The left ventricle volume, stroke volume (SV), and ejection fraction decreased with DI (p < 0.001). Carotid distensibility reduced (p < 0.05), carotid to femoral arterial tree became stiffer in 33% of the subjects, and femoral artery intima media thickness increased (p < 0.05). A reduction in plasma volume is likely to have caused the observed cardiac changes, whereas the arterial wall changes are probably best explained by hypokinesia and/or environmental stress. These changes are similar but lower in amplitude than those observed in spaceflight and mimic the natural aging effect on earth. The daytime-worn thigh cuffs had no acute or chronic impact on these arterial-focused measurements.
An integrative analysis of genomic and exposomic data for complex traits and phenotypic prediction
Authors: Zhou Xuan , Lee S. Hong 
Published: November 2021

AbstractComplementary to the genome, the concept of exposome has been proposed to capture the totality of human environmental exposures. While there has been some recent progress on the construction of the exposome, few tools exist that can integrate the genome and exposome for complex trait analyses. Here we propose a linear mixed model approach to bridge this gap, which jointly models the random effects of the two omics layers on phenotypes of complex traits. We illustrate our approach using traits from the UK Biobank (e.g., BMI and height for N ~ 35,000) with a small fraction of the exposome that comprises 28 lifestyle factors. The joint model of the genome and exposome explains substantially more phenotypic variance and significantly improves phenotypic prediction accuracy, compared to the model based on the genome alone. The additional phenotypic variance captured by the exposome includes its additive effects as well as non-additive effects such as genome–exposome (gxe) and exposome–exposome (exe) interactions. For example, 19% of variation in BMI is explained by additive effects of the genome, while additional 7.2% by additive effects of the exposome, 1.9% by exe interactions and 4.5% by gxe interactions. Correspondingly, the prediction accuracy for BMI, computed using Pearson’s correlation between the observed and predicted phenotypes, improves from 0.15 (based on the genome alone) to 0.35 (based on the genome and exposome). We also show, using established theories, that integrating genomic and exposomic data can be an effective way of attaining a clinically meaningful level of prediction accuracy for disease traits. In conclusion, the genomic and exposomic effects can contribute to phenotypic variation via their latent relationships, i.e. genome-exposome correlation, and gxe and exe interactions, and modelling these effects has a potential to improve phenotypic prediction accuracy and thus holds a great promise for future clinical practice.
A preliminary study on the evaluation of left atrial function of rheumatoid arthritis by two dimensional speckle tracking imaging
Authors: Ji Xiang , Zhang Xia , Li Guojie 
Published: November 2021

AbstractTo evaluate the changes of left atrial (LA) geometry and function in patients with rheumatoid arthritis (RA) by conventional echocardiography and two-dimensional speckle tracking imaging (2D-STI). We enrolled 46 RA patients with a duration of < 5 years as Group I, 40 RA patients with a duration of ≥ 5 years as Group II, and 40 normal subjects as the control group. Conventional echocardiography was conducted to measure traditional parameters. The LA strain during reservoir phase (LASr), LA strain during conduit phase (LAScd), LA strain during contraction phase (LASct), and LA global longitudinal strain (LAGLS) were obtained from 2D-STI. Related ultrasound results were compared. The LASct was significantly higher in Group I than in control group (P < 0.05). The LASr, LAScd, and LAGLS were significantly lower in Group I than in control group (all P < 0.05). The LASr, LAScd, LASct, and LAGLS were significantly lower in Group II than in control group and Group I (all P < 0.05). The function of LA impaired in RA patients, and the impairment aggravated with the clinical course of RA patients. 2D-STI technology can early and accurately evaluate the LA function of RA patients by evaluating LASr, LAScd, LASct, and LAGLS.
Assessment of the plasmidome of an extremophilic microbial community from the Diamante Lake, Argentina
Authors: Perez María Florencia , Saona Luis Alberto , Farías María Eugenia , Poehlein Anja , Meinhardt Friedhelm , Daniel Rolf , Dib Julián Rafael 
Published: November 2021

AbstractDiamante Lake located at 4589 m.a.s.l. in the Andean Puna constitutes an extreme environment. It is exposed to multiple extreme conditions such as an unusually high concentration of arsenic (over 300 mg L−1) and low oxygen pressure. Microorganisms thriving in the lake display specific genotypes that facilitate survival, which include at least a multitude of plasmid-encoded resistance traits. Hence, the genetic information provided by the plasmids essentially contributes to understand adaptation to different stressors. Though plasmids from cultivable organisms have already been analyzed to the sequence level, the impact of the entire plasmid-borne genetic information on such microbial ecosystem is not known. This study aims at assessing the plasmidome from Diamante Lake, which facilitates the identification of potential hosts and prediction of gene functions as well as the ecological impact of mobile genetic elements. The deep-sequencing analysis revealed a large fraction of previously unknown DNA sequences of which the majority encoded putative proteins of unknown function. Remarkably, functions related to the oxidative stress response, DNA repair, as well as arsenic- and antibiotic resistances were annotated. Additionally, all necessary capacities related to plasmid replication, mobilization and maintenance were detected. Sequences characteristic for megaplasmids and other already known plasmid-associated genes were identified as well. The study highlights the potential of the deep-sequencing approach specifically targeting plasmid populations as it allows to evaluate the ecological impact of plasmids from (cultivable and non-cultivable) microorganisms, thereby contributing to the understanding of the distribution of resistance factors within an extremophilic microbial community.
Comparative assessment of nutritional, thermal, rheological and functional properties of nine Australian lupin cultivars
Authors: Mazumder Kishor , Biswas Biswajit , Kerr Philip G. , Blanchard Christopher , Nabila Afia , Golder Mimi , Aziz Mohammad Gulzarul , Farahnaky Asgar 
Published: November 2021

AbstractLupin holds an important place among the legumes and the utilization of lupin as a dietary protein source is an excellent environmentally friendly alternative to animal-based products for human nutrition. In the present study, nutritional, thermal, rheological and functional properties of nine Australian lupin cultivars have been assayed in order to find the most valuable one, both nutritiously and industrially. The set comprised six Lupinus angustifolius L. viz., Barlock, Gunyadi, Jenabillup, Jindalee, Jurien, Mandelup and three Lupinus albus L. viz., Luxor, Rosetta, WK388 cultivars. The tests included analysis of color, macronutrient and micronutrient composition, pasting, textural and thermal properties, electrophoretic profile of protein isolates, swelling power, water and oil absorption capacity, emulsifying capacity, emulsion stability, creaming stability, foaming capacity and stability of the cultivars’ dehulled seed flours. The results indicated substantial variation in macro and micro-nutritional value as well as satisfactory swelling ability, solubility, surface hydrophobicity, foaming ability, emulsifying capacity and gelation property of lupin flours. Superior nutritional, thermal, rheological and functional potential was demonstrated by the L. albus cultivars compared to the L. angustifolius cultivars with the exception of Mandelup.
Assessment of four organophosphorus pesticides as inhibitors of human acetylcholinesterase and butyrylcholinesterase
Authors: Čadež Tena , Kolić Dora , Šinko Goran , Kovarik Zrinka 
Published: November 2021

AbstractToxicity of organophosphorus compounds (OPs) remains a major public health concern due to their widespread use as pesticides and the existence of nerve agents. Their common mechanism of action involves inhibition of enzymes acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) which are crucial for neurotransmission. Both chronic and acute poisoning by OPs can leave long-lasting health effects even when the patients are treated with standard medical therapy. Therefore, an increasing urgency exists to find more effective oxime reactivators for compounds which are resistant to reactivation, especially phosphoramidates. Here, we investigated in silico and in vitro interactions and kinetics of inhibition for human cholinesterases with four organophosphate pesticides—ethoprophos, fenamiphos, methamidophos and phosalone. Overall, ethoprophos and fenamiphos displayed higher potency as inhibitors for tested cholinesterases. Our results show that methamidophos-inhibited hAChE was more susceptible to reactivation than hAChE inhibited by fenamiphos by selected oximes. Molecular modelling enabled an evaluation of interactions important for specificity and selectivity of both inhibition and reactivation of cholinesterases. Two newly developed reactivators—bispyridinium triazole oxime 14A and zwitterionic oxime RS194B possess remarkable potential for further development of antidotes directed against pesticides and related phosphoramidate exposures, such as nerve agents tabun or Novichoks.
Proteins related to ictogenesis and seizure clustering in chronic epilepsy
Authors: Lee Woo-Jin , Moon Jangsup , Lim Jung-Ah , Jeon Daejong , Yoo Jung-Suk , Park Dong-Kyu , Han Dohyun , Lee Soon-Tae , Jung Keun-Hwa , Park Kyung-Il , Lee Sang Kun , Chu Kon 
Published: November 2021

AbstractSeizure clustering is a common phenomenon in epilepsy. Protein expression profiles during a seizure cluster might reflect the pathomechanism underlying ictogenesis. We performed proteomic analyses to identify proteins with a specific temporal expression pattern in cluster phases and to demonstrate their potential pathomechanistic role. Pilocarpine epilepsy model mice with confirmed cluster pattern of spontaneous recurrent seizures by long-term video-electroencpehalography were sacrificed at the onset, peak, or end of a seizure cluster or in the seizure-free period. Proteomic analysis was performed in the hippocampus and the cortex. Differentially expressed proteins (DEPs) were identified and classified according to their temporal expression pattern. Among the five hippocampal (HC)-DEP classes, HC-class 1 (66 DEPs) represented disrupted cell homeostasis due to clustered seizures, HC-class 2 (63 DEPs) cluster-onset downregulated processes, HC-class 3 (42 DEPs) cluster-onset upregulated processes, and HC-class 4 (103 DEPs) consequences of clustered seizures. Especially, DEPs in HC-class 3 were hippocampus-specific and involved in axonogenesis, synaptic vesicle assembly, and neuronal projection, indicating their pathomechanistic roles in ictogenesis. Key proteins in HC-class 3 were highly interconnected and abundantly involved in those biological processes. This study described the seizure cluster-associated spatiotemporal regulation of protein expression. HC-class 3 provides insights regarding ictogenesis-related processes.
Nucleolar translocation of human DNA topoisomerase II by ATP depletion and its disruption by the RNA polymerase I inhibitor BMH-21
Authors: Morotomi-Yano Keiko , Yano Ken-ichi 
Published: November 2021

AbstractDNA topoisomerase II (TOP2) is a nuclear protein that resolves DNA topological problems and plays critical roles in multiple nuclear processes. Human cells have two TOP2 proteins, TOP2A and TOP2B, that are localized in both the nucleoplasm and nucleolus. Previously, ATP depletion was shown to augment the nucleolar localization of TOP2B, but the molecular details of subnuclear distributions, particularly of TOP2A, remained to be fully elucidated in relation to the status of cellular ATP. Here, we analyzed the nuclear dynamics of human TOP2A and TOP2B in ATP-depleted cells. Both proteins rapidly translocated from the nucleoplasm to the nucleolus in response to ATP depletion. FRAP analysis demonstrated that they were highly mobile in the nucleoplasm and nucleolus. The nucleolar retention of both proteins was sensitive to the RNA polymerase I inhibitor BMH-21, and the TOP2 proteins in the nucleolus were immediately dispersed into the nucleoplasm by BMH-21. Under ATP-depleted conditions, the TOP2 poison etoposide was less effective, indicating the therapeutic relevance of TOP2 subnuclear distributions. These results give novel insights into the subnuclear dynamics of TOP2 in relation to cellular ATP levels and also provide discussions about its possible mechanisms and biological significance.
Association between behavioral phenotypes and sustained use of smartphones and wearable devices to remotely monitor physical activity
Authors: Fendrich Sarah J. , Balachandran Mohan , Patel Mitesh S. 
Published: November 2021

AbstractSmartphones and wearable devices can be used to remotely monitor health behaviors, but little is known about how individual characteristics influence sustained use of these devices. Leveraging data on baseline activity levels and demographic, behavioral, and psychosocial traits, we used latent class analysis to identify behavioral phenotypes among participants randomized to track physical activity using a smartphone or wearable device for 6 months following hospital discharge. Four phenotypes were identified: (1) more agreeable and conscientious; (2) more active, social, and motivated; (3) more risk-taking and less supported; and (4) less active, social, and risk-taking. We found that duration and consistency of device use differed by phenotype for wearables, but not smartphones. Additionally, “at-risk” phenotypes 3 and 4 were more likely to discontinue use of a wearable device than a smartphone, while activity monitoring in phenotypes 1 and 2 did not differ by device type. These findings could help to better target remote-monitoring interventions for hospitalized patients.
Estimating and evaluating the rice cluster distribution uniformity with UAV-based images
Authors: Wang Xiaohui , Tang Qiyuan , Chen Zhaozhong , Luo Youyi , Fu Hongyu , Li Xumeng 
Published: November 2021

AbstractThe uniformity of the rice cluster distribution in the field affects population quality and the precise management of pesticides and fertilizers. However, there is no appropriate technical system for estimating and evaluating the uniformity at present. For that reason, a method based on unmanned aerial vehicle (UAV images) is proposed to estimate and evaluate the uniformity in this present study. This method includes rice cluster recognition and location determination based on the RGB color characteristics of the seedlings of aerial images, region segmentation considering the rice clusters based on Voronoi Diagram, and uniformity index definition for evaluating the rice cluster distribution based on the variation coefficient. The results indicate the rice cluster recognition attains a high precision, with the precision, accuracy, recall, and F1-score of rice cluster recognition reaching > 95%, 97%, 97%, 95%, and 96%, respectively. The rice cluster location error is small and obeys the gamma (3.00, 0.54) distribution (mean error, 1.62 cm). The uniformity index is reasonable for evaluating the rice cluster distribution verified via simulation. As a whole process, the estimating method is sufficiently high accuracy with relative error less than 0.01% over the manual labeling method. Therefore, this method based on UAV images is feasible, convenient, technologically advanced, inexpensive, and highly precision for the estimation and evaluation of the rice cluster distribution uniformity. However, the evaluation application indicates that there is much room for improvement in terms of the uniformity of mechanized paddy field transplanting in South China.
A comparative study of pleural effusion in water area, water temperature and postmortem interval in forensic autopsy cases of drowning
Authors: Ishigami Akiko , Kashiwagi Masayuki , Ishida Yuko , Hara Kenji , Nosaka Mizuho , Matsusue Aya , Yamamoto Hiroki , Waters Brian , Kondo Toshikazu , Kubo Shin-ichi 
Published: November 2021

AbstractJapan is surrounded by the sea and is also a mountainous country with many rivers. Japan has the second- highest rate of deaths caused by drowning in the world. Pleural effusion (PE) is one of the major findings at autopsy. It is found in approximately 80% of drowning mortalities and is observable for a relatively long postmortem interval (PMI). We focused on the amount of pleural fluid in drowning cases, discussed the relationship of PE with the drowning environment, water temperature, and postmortem interval, and established more simple and practical criteria for the diagnosis of drowning. We measured the weight of the lungs, PE, and their sum as the intrathoracic (IT) weight (total weight of lungs + pleural effusion), and calculated the PE ratio [(PE weight/IT weight) × 100]. A total of 130 drowning deaths diagnosed through forensic autopsies were investigated in this study. The cases were classified by drowning environment (freshwater, brackish water, and seawater), water temperature (under 20 °C, more than 20 °C), and postmortem interval (less than 1 day, 1–3 days, more than 3 days). The present study demonstrated that the PE ratio may be more effective for the diagnosis of drowning. Moreover, the accumulation of PE is affected by drowning environment, water temperature, and PMI. Collectively, it is important to assess the PE ratio and consider these factors in autopsy cases of victims found in water.