bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide identification of the BASS gene family in four Gossypium species and functional characterization of GhBASSs against salt stress
Authors: Myo Thwin , Wei Fang , Zhang Honghao , Hao Jianfeng , Zhang Bin , Liu Zhixian , Cao Gangqiang , Tian Baoming , Shi Gongyao 
Published: May 2021

AbstractBile acid sodium symporter (BASS) family proteins encode a class of sodium/solute symporters. Even though the sodium transporting property of BASSs in mammals was well studied, their sodium transportability and functional roles in plant salt tolerance remained largely unknown. Here, BASS family members from 4 cotton species, as well as 30 other species were identified. Then, they were designated as members of BASS1 to BASS5 subfamilies according to their sequence similarity and phylogenetic relationships. There were 8, 11, 16 and 18 putative BASS genes in four cotton species. While whole-genome duplications (WGD) and segmental duplications rendered the expansion of the BASS gene family in cotton, BASS gene losses occurred in the tetraploid cotton during the evolution from diploids to allotetraploids. Concerning functional characterizations, the transcript profiling of GhBASSs revealed that they not only preferred tissue-specific expression but also were differently induced by various stressors and phytohormones. Gene silencing and overexpression experiments showed that GhBASS1 and GhBASS3 positively regulated, whereas GhBASS2, GhBASS4 and GhBASS5 negatively regulated plant salt tolerance. Taken together, BASS family genes have evolved before the divergence from the common ancestor of prokaryotes and eukaryotes, and GhBASSs are plastidial sodium-dependent metabolite co-transporters that can influence plant salt tolerance.
Freeze–thaw characterization process to minimize aggregation and enable drug product manufacturing of protein based therapeutics
Authors: Jain Keethkumar , Salamat-Miller Nazila , Taylor Katherine 
Published: May 2021

AbstractPhysical instabilities of proteins in the form of protein aggregation continue to be a major challenge in the development of protein drug candidates. Aggregation can occur during different stages of product lifecycle such as freeze–thaw, manufacturing, shipping, and storage, and can potentially delay commercialization of candidates. A lack of clear understanding of the underlying mechanism(s) behind protein aggregation and the potential immunogenic reactions renders the presence of aggregates in biotherapeutic products undesirable. Understanding and minimizing aggregation can potentially reduce immunogenic responses and make protein therapeutics safer. Therefore, it is imperative to identify, understand, and control aggregation during early formulation development and develop reliable and orthogonal analytical methodologies to detect and monitor levels of aggregation. Freezing and thawing are typical steps involved in the manufacturing of drug product and could result in complex physical and chemical changes, which in turn could potentially cause protein aggregation. This study provides a systematic approach in understanding and selecting the ideal freeze–thaw conditions for manufacturing of protein-based therapeutics. It identifies the importance of balancing different excipients with an overall goal of sufficiently reducing or eliminating aggregation and developing a stable and scalable formulation. The results demonstrated that the freeze–thaw damage of mAb-1 in aqueous solutions was significantly reduced by identification of optimal freeze–thaw conditions using first a small-scale model with subsequent at-scale verifications. The work provides a framework for successful transfer of drug product manufacturing process from small-scale to the manufacturing scale production environment especially for molecules that are susceptible to freeze–thaw induced degradations.
Characterization and description of Faecalibacterium butyricigenerans sp. nov. and F. longum sp. nov., isolated from human faeces
Authors: Zou Yuanqiang , Lin Xiaoqian , Xue Wenbin , Tuo Li , Chen Ming-Sheng , Chen Xiao-Hui , Sun Cheng-hang , Li Feina , Liu Shao-wei , Dai Ying , Kristiansen Karsten , Xiao Liang 
Published: May 2021

AbstractExploiting a pure culture strategy to investigate the composition of the human gut microbiota, two novel anaerobes, designated strains AF52-21T and CM04-06T, were isolated from faeces of two healthy Chinese donors and characterized using a polyphasic approach. The two strains were observed to be gram-negative, non-motile, and rod-shaped. Both strains grew optimally at 37 °C and pH 7.0. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the two strains clustered with species of the genus Faecalibacterium and were most closely related to Faecalibacterium prausnitzii ATCC 27768T with sequence similarity of 97.18% and 96.87%, respectively. The two isolates shared a 16S rRNA gene sequence identity of 98.69%. Draft genome sequencing was performed for strains AF52-21T and CM04-06T, generating genome sizes of 2.85 Mbp and 3.01 Mbp. The calculated average nucleotide identity values between the genomes of the strains AF52-21T and CM04-06T compared to Faecalibacterium prausnitzii ATCC 27768T were 83.20% and 82.54%, respectively, and 90.09% when comparing AF52-21T and CM04-06T. Both values were below the previously proposed species threshold (95–96%), supporting their recognition as novel species in the genus Faecalibacterium. The genomic DNA G + C contents of strains AF52-21T and CM04-06T calculated from genome sequences were 57.77 mol% and 57.51 mol%, respectively. Based on the phenotypic, chemotaxonomic and phylogenetic characteristics, we conclude that both strains represent two new Faecalibacterium species, for which the names Faecalibacterium butyricigenerans sp. nov. (type strain AF52-21T = CGMCC 1.5206T = DSM 103434T) and Faecalibacterium longum sp. nov. (type strain CM04-06T = CGMCC 1.5208T = DSM 103432T) are proposed.
Comparative and evolutionary analyses reveal conservation and divergence of the notch pathway in lophotrochozoa
Authors: He Xin , Wu Fucun , Zhang Linlin , Li Li , Zhang Guofan 
Published: May 2021

AbstractLophotrochozoan species exhibit wide morphological diversity; however, the molecular basis underlying this diversity remains unclear. Here, we explored the evolution of Notch pathway genes across 37 metazoan species via phylogenetic and molecular evolutionary studies with emphasis on the lophotrochozoans. We displayed the components of Notch pathway in metazoans and found that Delta and Hes/Hey-related genes, as well as their functional domains, are duplicated in lophotrochozoans. Comparative transcriptomics analyses allow us to pinpoint sequence divergence of multigene families in the Notch signalling pathway. We identified the duplication mechanism of a mollusc-specific gene, Delta2, and found it displayed complementary expression throughout development. Furthermore, we found the functional diversification not only in expanded genes in the Notch pathway (Delta and Hes/Hey-related genes), but also in evolutionary conservative genes (Notch, Presenilin, and Su(H)). Together, this comprehensive study demonstrates conservation and divergence within the Notch pathway, reveals evolutionary relationships among metazoans, and provides evidence for the occurrence of developmental diversity in lophotrochozoans, as well as a basis for future gene function studies.
Crystal growth of clathrate hydrate formed with H2 + CO2 mixed gas and tetrahydropyran
Authors: Maruyama Meku , Matsuura Riku , Ohmura Ryo 
Published: May 2021

AbstractHydrate-based gas separation technology is applicable to the CO2 capture and storage from synthesis gas mixture generated through gasification of fuel sources including biomass. This paper reports visual observations of crystal growth dynamics and crystal morphology of hydrate formed in the H2 + CO2 + tetrahydropyran (THP) + water system with a target for developing the hydrate-based CO2 separation process design. Experiments were conducted at a temperature range of 279.5–284.9 K under the pressure of 4.9–5.3 MPa. To simulate the synthesis gas, gas composition in the gas phase was maintained around H2:CO2 = 0.6:0.4 in mole fraction. Hydrate crystals were formed and extended along the THP/water interface. After the complete coverage of the interface to shape a polycrystalline shell, hydrate crystals continued to grow further into the bulk of liquid water. The individual crystals were identified as hexagonal, tetragonal and other polygonal-shaped formations. The crystal growth rate and the crystal size varied depending on thermodynamic conditions. Implications from the obtained results for the arrangement of operating conditions at the hydrate formation-, transportation-, and dissociation processes are discussed.
A practice of using five-colour chart to guide the control of COVID-19 and resumption of work in Zhejiang Province, China
Authors: He Fan , Shang Xiaopeng , Ling Feng , Chen Zhiping , Fu Tiehong , Lin Junfen , Wang Zhen 
Published: May 2021

AbstractSince the outbreak of COVID-19 in December 2019 in Wuhan, Zhejiang has become the province with the largest number of cases. The aim of this article is to present Zhejiang province’s experience of establishing an accurate and smart control mechanism for epidemic prevention and control and resumption of work and production using a ‘five-colour epidemic chart’. The number of confirmed cases, proportion of local cases, and occurrence of clustered outbreaks were used as evaluation indicators to calculate the county-level epidemic risk and were assigned different weight coefficients; the absence of cases for 3 and 7 consecutive days was used as the adjustment index. When the first chart was published on February 9, there were 1 very-high-risk, 12 high-risk, and 12 low-risk counties. Under the five-colour chart, Zhejiang began to adopt precise measures to prevent and control the epidemic and resume work and production. By February 24, the low-risk counties had expanded to 82, with no high-risk and very-high-risk counties. The epidemic situation in Zhejiang province has been effectively controlled. The experience of epidemic prevention and control in Zhejiang is worthy to be emulated and learned by other countries and regions.
Intensity correlation OCT is a classical mimic of quantum OCT providing up to twofold resolution improvement
Authors: Kolenderska Sylwia M. , Kolenderski Piotr 
Published: May 2021

AbstractQuantum Optical Coherence Tomography (Q-OCT) uses quantum properties of light to provide several advantages over its classical counterpart, OCT: it achieves a twice better axial resolution with the same spectral bandwidth and it is immune to even orders of dispersion. Since these features are very sought-after in OCT imaging, many hardware and software techniques have been created to mimic the quantum behaviour of light and achieve these features using traditional OCT systems. The most recent, purely algorithmic scheme—an improved version of Intensity Correlation Spectral Domain OCT named ICA-SD-OCT—showed even-order dispersion cancellation and reduction of artefacts. The true capabilities of this method were unfortunately severely undermined, both in terms of its relation to Q-OCT and its main performance parameters. In this work, we provide experimental demonstrations as well as numerical and analytical arguments to show that ICA-SD-OCT is a true classical equivalent of Q-OCT, more specifically its Fourier domain version, and therefore it enables a true two-fold axial resolution improvement. We believe that clarification of all the misconceptions about this very promising algorithm will highlight the great value of this method for OCT and consequently lead to its practical applications for resolution- and quality-enhanced OCT imaging.
Differential gene expression in Drosophila melanogaster and D. nigrosparsa infected with the same Wolbachia strain
Authors: Detcharoen Matsapume , Schilling Martin P. , Arthofer Wolfgang , Schlick-Steiner Birgit C. , Steiner Florian M. 
Published: May 2021

AbstractWolbachiaare maternally inherited endosymbionts that infect nearly half of all arthropod species.Wolbachiamanipulate their hosts to maximize their transmission, but they can also provide benefits such as nutrients and resistance against viruses to their hosts. TheWolbachiastrainwMel was recently found to increase locomotor activities and possibly trigger cytoplasmic incompatibility in the transinfected flyDrosophilanigrosparsa. Here, we investigated, in females of bothD.melanogasterandD.nigrosparsa, the gene expression between animals uninfected and infected withwMel, using RNA sequencing to see if the twoDrosophilaspecies respond to the infection in the same or different ways. A total of 2164 orthologous genes were used. The two fly species responded to the infection in different ways. Significant changes shared by the fly species belong to the expression of genes involved in processes such as oxidation–reduction process, iron-ion binding, and voltage-gated potassium-channel activity. We discuss our findings also in the light of howWolbachiasurvive within both the native and the novel host.
A randomized controlled trial of two diets enriched with protein or fat in patients with type 2 diabetes treated with dapagliflozin
Authors: Watanabe Yasuhiro , Suzuki Daisuke , Kuribayashi Nobuichi , Uchida Daigaku , Kato Mitsutoshi , Ohashi Hiroshi , Nagayama Daiji , Yamaguchi Takashi , Ohira Masahiro , Saiki Atsuhito , Tatsuno Ichiro 
Published: May 2021

AbstractSodium-glucose cotranspsorter-2 (SGLT2) inhibitors (SGLT2i) involve loss of skeletal muscle mass, potentially leading to inadequate HbA1c reduction in type 2 diabetes (T2DM), since muscle mass is related to insulin sensitivity. The benefit of protein-enriched diet for improving HbA1c in SGLT2i-treated T2DM patients remains unclear. We conducted a multicenter, double-blind, randomized, controlled, investigator-initiated clinical trial. 130 T2DM patients treated with dapagliflozin (5 mg) were randomized to isoenergic protein-rich formula diet (P-FD) or fat-rich FD (F-FD) (1:1 allocation) to replace one of three meals/day for 24 weeks. Primary outcome was change in HbA1c. Secondary outcomes were changes in serum insulin, body composition and other metabolic parameters. Although HbA1c decreased significantly in both groups [mean (95% confidence interval) − 0.7% (− 0.9 to − 0.5) in P-FD, − 0.6% (− 0.8 to − 0.5) in F-FD], change in HbA1c was not significantly different between the two groups (P = 0.4474). Fasting insulin and body fat mass decreased, while HDL-cholesterol increased significantly in P-FD, and these changes were significantly greater compared with F-FD (all, P < 0.05). In T2DM treated with dapagliflozin, protein-enriched diet does not contribute to HbA1c reduction, although it decreases serum insulin and body fat mass, and increases HDL-cholesterol compared with fat-enriched diet with identical calories and carbohydrate ratio.
Analyzing the relationship between the cytokine profile of invasive breast carcinoma, its histopathological characteristics and metastasis to regional lymph nodes
Authors: Autenshlyus Alexander , Arkhipov Sergey , Mikhaylova Elena , Marinkin Igor , Arkhipova Valentina , Varaksin Nikolay , Vavilin Valentin , Lyahovich Vyacheslav 
Published: May 2021

AbstractThis study was aimed at analyzing the relations of metastasis to regional lymph nodes (RLNs) with histopathological indicators of invasive breast carcinoma of no special type (IC-NST) and its cytokine profile. Enzyme-linked immunosorbent assays were performed to determine concentrations of IL-2, IL-6, IL-8, IL-10, IL-17, IL-18, IL-1β, IL-1Ra, TNF-α, IFN-γ, G-CSF, GM-CSF, VEGF-A, and MCP-1 in the culture supernatant of IC-NST samples from 48 female patients. Histopathological indicators (degree of tumor cell differentiation, mitoses, and others) and ER, PR, Her2/neu, Ki-67, and CD34 expression levels were determined. By means of three types of neural network models, it was shown that for different parameters of the output layer, different groups of parameters are involved that have predictive value regarding metastasis to RLNs. As a result of multi-dimensional cluster analysis, three clusters were formed with different cytokines profiles of IC-NST. Different correlations between indicators of cytokine production by IC-NST and its histopathological parameters were revealed in groups with different cytokine profiles. It was shown that at simultaneous evaluation of the production of even two cytokines, the importance of which relationship with metastasis was revealed by neural network modeling, can increase the probability of determining the presence of metastasis in the RLNs.
Dynamic causal modelling of immune heterogeneity
Authors: Parr Thomas , Bhat Anjali , Zeidman Peter , Goel Aimee , Billig Alexander J. , Moran Rosalyn , Friston Karl J. 
Published: May 2021

AbstractAn interesting inference drawn by some COVID-19 epidemiological models is that there exists a proportion of the population who are not susceptible to infection—even at the start of the current pandemic. This paper introduces a model of the immune response to a virus. This is based upon the same sort of mean-field dynamics as used in epidemiology. However, in place of the location, clinical status, and other attributes of people in an epidemiological model, we consider the state of a virus, B and T-lymphocytes, and the antibodies they generate. Our aim is to formalise some key hypotheses as to the mechanism of resistance. We present a series of simple simulations illustrating changes to the dynamics of the immune response under these hypotheses. These include attenuated viral cell entry, pre-existing cross-reactive humoral (antibody-mediated) immunity, and enhanced T-cell dependent immunity. Finally, we illustrate the potential application of this sort of model by illustrating variational inversion (using simulated data) of this model to illustrate its use in testing hypotheses. In principle, this furnishes a fast and efficient immunological assay—based on sequential serology—that provides a (1) quantitative measure of latent immunological responses and (2) a Bayes optimal classification of the different kinds of immunological response (c.f., glucose tolerance tests used to test for insulin resistance). This may be especially useful in assessing SARS-CoV-2 vaccines.
Visual impairment increases the risk of dementia, especially in young males in a 12-year longitudinal follow-up study of a national cohort
Authors: Lee Ga-In , Chi Sang Ah , Kim Kyunga , Seo Sang Won , Kim Hee Jin , Chung Tae-Young , Lim Dong Hui 
Published: May 2021

AbstractWe investigated the effect of visual impairment (VI) on dementia development in a national cohort. In this 12-year nationwide population-based retrospective cohort study, national data were collected from National Health Insurance Cooperation of South Korea from 2002 to 2017, comprising 799,074 subjects selected from the dementia-free cohort representative of the Korean population. Crude hazard ratios (HRs) as well as age- and sex-adjusted HRs and confidence intervals (CIs) for the development of dementia were estimated using multivariable Cox regression models. VI significantly increased the risk of dementia with a HR of 2.726 (95% CI 2.251–3.300, p < 0.0001) after adjusting for age, sex, and interaction between age, sex, and VI. HR of interaction between VI and age for dementia was 0.539 (95% CI 0.436–0.667, p < 0.0001). In the sensitivity analysis after adjustment for age, sex, household income level, BMI and other comorbidities, VI showed higher risk for all the type of dementia (p < 0.0001). In subgroup analysis of VI, young males showed the highest risk for development of dementia with a HR of 2.687 (95% CI 2.219–3.254, p < 0.0001). VI significantly increased the risk of dementia in the study cohort, and young males with VI appeared to be the most susceptible to the development of dementia.
The effects of combined environmental factors on the intestinal flora of mice based on ground simulation experiments
Authors: Sun Peiming , Yang Jiaqi , Wang Bo , Ma Huan , Zhang Yin , Guo Jinhu , Chen Xiaoping , Zhao Jianwei , Sun Hongwei , Yang Jianwu , Yang Heming , Cui Yan 
Published: May 2021

AbstractThe composition and function of intestinal microbial communities are important for human health. However, these intestinal floras are sensitive to changes in the environment. Adverse changes to intestinal flora can affect the health of astronauts, resulting in difficulties in implementing space missions. We randomly divided mice into three groups and placed each group in either a normal environment, simulated microgravity environment or a combined effects environment, which included simulated microgravity, low pressure and noise. Fecal samples of the mice were collected for follow-up analysis based on metagenomics technology. With the influence of different space environmental factors, the species composition at the phylum and genus levels were significantly affected by the combined effects environment, especially the abundance of the Firmicutes and Bacteroidetes. Furthermore, screening was conducted to identify biomarkers that could be regarded as environmental markers. And there have also been some noticeable changes in the function of intestinal floras. Moreover, the abundance of antibiotic resistance genes (ARGs) was also found to be changed under different environmental conditions, such as bacitracin and vancomycin. The combined effects environment could significantly affect the species composition, function, and the expression of ARGs of intestinal flora of mice which may provide a theoretical basis for space medical supervision and healthcare.
WDR62 is required for centriole duplication in spermatogenesis and manchette removal in spermiogenesis
Authors: Ho Uda Y. , Feng Chun-Wei Allen , Yeap Yvonne Y. , Bain Amanda L. , Wei Zhe , Shohayeb Belal , Reichelt Melissa E. , Homer Hayden , Khanna Kum Kum , Bowles Josephine , Ng Dominic C. H. 
Published: May 2021

AbstractWDR62 is a scaffold protein involved in centriole duplication and spindle assembly during mitosis. Mutations in WDR62 can cause primary microcephaly and premature ovarian insufficiency. We have generated a genetrap mouse model deficient in WDR62 and characterised the developmental effects of WDR62 deficiency during meiosis in the testis. We have found that WDR62 deficiency leads to centriole underduplication in the spermatocytes due to reduced or delayed CEP63 accumulation in the pericentriolar matrix. This resulted in prolonged metaphase that led to apoptosis. Round spermatids that inherited a pair of centrioles progressed through spermiogenesis, however, manchette removal was delayed in WDR62 deficient spermatids due to delayed Katanin p80 accumulation in the manchette, thus producing misshapen spermatid heads with elongated manchettes. In mice, WDR62 deficiency resembles oligoasthenoteratospermia, a common form of subfertility in men that is characterised by low sperm counts, poor motility and abnormal morphology. Therefore, proper WDR62 function is necessary for timely spermatogenesis and spermiogenesis during male reproduction.
A natural constant predicts survival to maximum age
Authors: Dureuil Manuel , Froese Rainer 
Published: May 2021

AbstractInformation about the survival of species is important in many ecological applications. Yet, the estimation of a species’ natural mortality rate M remains a major problem in the management and conservation of wild populations, often circumvented by applying empirical equations that relate mortality to other traits that are more easily observed. We show that mean adult M can be approximated from the general law of decay if the average maximum age reached by individuals in a cohort is known. This is possible because the proportion P of individuals surviving to the average maximum age in a cohort is surprisingly similar across a wide range of examined species at 1.5%. The likely reason for the narrow range of P is a universal increase in the rate of mortality near the end of life, providing strong evidence that the evolutionary theories of ageing are the norm in natural populations.