bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stress–response relationships related to ageing and death of orthodox seeds: a study comparing viability and RNA integrity in soya bean (Glycine max) cv. Williams 82
Authors: Walters Christina , Fleming Margaret B. , Hill Lisa M. , Dorr Emma J. , Richards Christopher M. 
Published: September 2020

AbstractCharacterizing non-lethal damage within dry seeds may allow us to detect early signs of ageing and accurately predict longevity. We compared RNA degradation and viability loss in seeds exposed to stressful conditions to quantify relationships between degradation rates and stress intensity or duration. We subjected recently harvested (‘fresh’) ‘Williams 82’ soya bean seeds to moisture, temperature and oxidative stresses, and measured time to 50% viability (P50) and rate of RNA degradation, the former using standard germination assays and the latter using RNA Integrity Number (RIN). RIN values from fresh seeds were also compared with those from accessions of the same cultivar harvested in the 1980s and 1990s and stored in the refrigerator (5°C), freezer (−18°C) or in vapour above liquid nitrogen (−176°C). Rates of viability loss (P50−1) and RNA degradation (RIN⋅d−1) were highly correlated in soya bean seeds that were exposed to a broad range of temperatures [holding relative humidity (RH) constant at about 30%]. However, the correlation weakened when fresh seeds were maintained at high RH (holding temperature constant at 35°C) or exposed to oxidizing agents. Both P50−1 and RIN⋅d−1 parameters exhibited breaks in Arrhenius behaviour near 50°C, suggesting that constrained molecular mobility regulates degradation kinetics of dry systems. We conclude that the kinetics of ageing reactions at RH near 30% can be simulated by temperatures up to 50°C and that RNA degradation can indicate ageing prior to and independent of seed death.
Photon and photon–neutron experimental dosimetry in Grid therapy with 18 MV photon beams
Authors: Tajiki Sareh , Gholami Somayeh , Esfahani Mahbod , Rastjoo Ali , Hakimi Amir , Beheshti Amir K. , Meigooni Ali 
Published: September 2020

AbstractPropose:Spatially fractionated Grid radiation therapy (SFGRT) in an effective technique for bulky and radio-sensitive tumours. SFGRT using a constructed block has been used to evaluate the photon and photo-neutron (PN) dose measurement in 18-MV photon beam energy.Methods and materials:A mounted Grid block on to a Varian Clinac 2100c linear accelerator was used to perform photon dosimetry. The percentage depth dose, in-plane and cross-plane beam profile and output factor was measured by ionization chamber in water. The PN contamination was measured after photon dosimetry using the combination of thermoluminescence dosimetry types 600 and 700, and Polycarbonate Film dosimeters on the surface and in the maximum depth dose (dmax) of solid water™ slabs.Results:The valley-to-peak ration for 6 and 18 MV photon beams obtained from the beam profiles was ~35 and 72%, respectively. Fast and thermal PN equivalent dose decreased in the Grid field compared to an open field (without Grid).Conclusion:The Grid therapy dosimetry compared to the conventional radiotherapy (without the grid) the production of fast and thermal neutrons were reduced. Using of a Grid block in high-energy photon beams for a long period of the treatment continuously might be a new source of contamination due to the interaction of photon beam resulting the activation of the Grid block
Single-cell sequencing techniques from individual to multiomics analyses
Authors: Kashima Yukie , Sakamoto Yoshitaka , Kaneko Keiya , Seki Masahide , Suzuki Yutaka , Suzuki Ayako 
Published: September 2020

AbstractHere, we review single-cell sequencing techniques for individual and multiomics profiling in single cells. We mainly describe single-cell genomic, epigenomic, and transcriptomic methods, and examples of their applications. For the integration of multilayered data sets, such as the transcriptome data derived from single-cell RNA sequencing and chromatin accessibility data derived from single-cell ATAC-seq, there are several computational integration methods. We also describe single-cell experimental methods for the simultaneous measurement of two or more omics layers. We can achieve a detailed understanding of the basic molecular profiles and those associated with disease in each cell by utilizing a large number of single-cell sequencing techniques and the accumulated data sets.
Single-cell multiomics: technologies and data analysis methods
Authors: Lee Jeongwoo , Hyeon Do Young , Hwang Daehee 
Published: September 2020

AbstractAdvances in single-cell isolation and barcoding technologies offer unprecedented opportunities to profile DNA, mRNA, and proteins at a single-cell resolution. Recently, bulk multiomics analyses, such as multidimensional genomic and proteogenomic analyses, have proven beneficial for obtaining a comprehensive understanding of cellular events. This benefit has facilitated the development of single-cell multiomics analysis, which enables cell type-specific gene regulation to be examined. The cardinal features of single-cell multiomics analysis include (1) technologies for single-cell isolation, barcoding, and sequencing to measure multiple types of molecules from individual cells and (2) the integrative analysis of molecules to characterize cell types and their functions regarding pathophysiological processes based on molecular signatures. Here, we summarize the technologies for single-cell multiomics analyses (mRNA-genome, mRNA-DNA methylation, mRNA-chromatin accessibility, and mRNA-protein) as well as the methods for the integrative analysis of single-cell multiomics data.
Human Cell Atlas and cell-type authentication for regenerative medicine
Authors: Panina Yulia , Karagiannis Peter , Kurtz Andreas , Stacey Glyn N. , Fujibuchi Wataru 
Published: September 2020

AbstractIn modern biology, the correct identification of cell types is required for the developmental study of tissues and organs and the production of functional cells for cell therapies and disease modeling. For decades, cell types have been defined on the basis of morphological and physiological markers and, more recently, immunological markers and molecular properties. Recent advances in single-cell RNA sequencing have opened new doors for the characterization of cells at the individual and spatiotemporal levels on the basis of their RNA profiles, vastly transforming our understanding of cell types. The objective of this review is to survey the current progress in the field of cell-type identification, starting with the Human Cell Atlas project, which aims to sequence every cell in the human body, to molecular marker databases for individual cell types and other sources that address cell-type identification for regenerative medicine based on cell data guidelines.
Prognostic value of tertiary lymphoid structure and tumour infiltrating lymphocytes in oral squamous cell carcinoma
Authors: Li Qunxing , Liu Xiangqi , Wang Dikan , Wang Yanqiong , Lu Huanzi , Wen Shuqiong , Fang Juan , Cheng Bin , Wang Zhi 
Published: September 2020

AbstractTertiary lymphoid structures (TLS) are ectopic lymphoid structures in cancers that are largely associated with favourable prognosis. However, the prognostic value of TLSs in oral squamous cell carcinoma (OSCC) is largely unknown, and the association between tumour infiltrating lymphocytes (TILs) and TLSs has been rarely explored in OSCC. In this study, associated markers of TLS, including peripheral node address (PNAd) in high endothelial venules, CD20 in B cells and CD3 in T cells, were examined in 168 OSCC patients, and survival analysis was performed between TLS-positive and TLS-negative cohorts. We detected the presence of TILs by staining CD8+ cytotoxic T cells and CD57+ NK cells as well. TLSs appeared as highly organized structures in 45 (26.8%) cases. TLS-positive patients had a better 5-year overall survival (OS) rate (88.9% vs. 56.1%, P < 0.001) and relapse-free survival (RFS) rate (88.9% vs. 63.4%, P = 0.002). Moreover, the presence of TLS was an independent prognostic factor for both the 5-year OS rate (hazard ratio [HR] = 3.784; 95% confidence interval [CI], 1.498–9.562) and RFS rate (HR = 3.296; 95% CI, 1.279–8.490) in multivariate analysis. Furthermore, a higher density of CD8+ T cells and CD57+ NK cells was found in TLS-positive sections than in TLS-negative counterparts (P < 0.001), and their combination provided a higher predictive accuracy (AUC = 0.730; 95% CI, 0.654–0.805). In conclusion, our results suggest that TLS is an independent positive prognostic factor for OSCC patients. These findings provide a theoretical basis for the future diagnostic and therapeutic value of TLSs in OSCC treatment.
Cytotoxic CD8+ T cells in cancer and cancer immunotherapy
Authors: Raskov Hans , Orhan Adile , Christensen Jan Pravsgaard , Gögenur Ismail 
Published: September 2020

AbstractThe functions of, and interactions between, the innate and adaptive immune systems are vital for anticancer immunity. Cytotoxic T cells expressing cell-surface CD8 are the most powerful effectors in the anticancer immune response and form the backbone of current successful cancer immunotherapies. Immune-checkpoint inhibitors are designed to target immune-inhibitory receptors that function to regulate the immune response, whereas adoptive cell-transfer therapies use CD8+ T cells with genetically modified receptors—chimaeric antigen receptors—to specify and enhance CD8+ T-cell functionality. New generations of cytotoxic T cells with genetically modified or synthetic receptors are being developed and evaluated in clinical trials. Furthermore, combinatory regimens might optimise treatment effects and reduce adverse events. This review summarises advances in research on the most prominent immune effectors in cancer and cancer immunotherapy, cytotoxic T cells, and discusses possible implications for future cancer treatment.
TET2 directs mammary luminal cell differentiation and endocrine response
Authors: Kim Mi Ran , Wu Meng-Ju , Zhang Yingsheng , Yang Jer-Yen , Chang Chun Ju 
Published: September 2020

AbstractEpigenetic regulation plays an important role in governing stem cell fate and tumorigenesis. Lost expression of a key DNA demethylation enzyme TET2 is associated with human cancers and has been linked to stem cell traits in vitro; however, whether and how TET2 regulates mammary stem cell fate and mammary tumorigenesis in vivo remains to be determined. Here, using our recently established mammary specific Tet2 deletion mouse model, the data reveals that TET2 plays a pivotal role in mammary gland development and luminal lineage commitment. We show that TET2 and FOXP1 form a chromatin complex that mediates demethylation of ESR1, GATA3, and FOXA1, three key genes that are known to coordinately orchestrate mammary luminal lineage specification and endocrine response, and also are often silenced by DNA methylation in aggressive breast cancers. Furthermore, Tet2 deletion-PyMT breast cancer mouse model exhibits enhanced mammary tumor development with deficient ERα expression that confers tamoxifen resistance in vivo. As a result, this study elucidates a role for TET2 in governing luminal cell differentiation and endocrine response that underlies breast cancer resistance to anti-estrogen treatments.
Environmental variability supports chimpanzee behavioural diversity
Authors: Kalan Ammie K. , Kulik Lars , Arandjelovic Mimi , Boesch Christophe , Haas Fabian , Dieguez Paula , Barratt Christopher D. , Abwe Ekwoge E. , Agbor Anthony , Angedakin Samuel , Aubert Floris , Ayimisin Emmanuel Ayuk , Bailey Emma , Bessone Mattia , Brazzola Gregory , Buh Valentine Ebua , Chancellor Rebecca , Cohen Heather , Coupland Charlotte , Curran Bryan , Danquah Emmanuel , Deschner Tobias , Dowd Dervla , Eno-Nku Manasseh , Michael Fay J. , Goedmakers Annemarie , Granjon Anne-Céline , Head Josephine , Hedwig Daniela , Hermans Veerle , Jeffery Kathryn J. , Jones Sorrel , Junker Jessica , Kadam Parag , Kambi Mohamed , Kienast Ivonne , Kujirakwinja Deo , Langergraber Kevin E. , Lapuente Juan , Larson Bradley , Lee Kevin C. , Leinert Vera , Llana Manuel , Marrocoli Sergio , Meier Amelia C. , Morgan Bethan , Morgan David , Neil Emily , Nicholl Sonia , Normand Emmanuelle , Ormsby Lucy Jayne , Pacheco Liliana , Piel Alex , Preece Jodie , Robbins Martha M. , Rundus Aaron , Sanz Crickette , Sommer Volker , Stewart Fiona , Tagg Nikki , Tennie Claudio , Vergnes Virginie , Welsh Adam , Wessling Erin G. , Willie Jacob , Wittig Roman M. , Yuh Yisa Ginath , Zuberbühler Klaus , Kühl Hjalmar S. 
Published: September 2020

AbstractLarge brains and behavioural innovation are positively correlated, species-specific traits, associated with the behavioural flexibility animals need for adapting to seasonal and unpredictable habitats. Similar ecological challenges would have been important drivers throughout human evolution. However, studies examining the influence of environmental variability on within-species behavioural diversity are lacking despite the critical assumption that population diversification precedes genetic divergence and speciation. Here, using a dataset of 144 wild chimpanzee (Pan troglodytes) communities, we show that chimpanzees exhibit greater behavioural diversity in environments with more variability — in both recent and historical timescales. Notably, distance from Pleistocene forest refugia is associated with the presence of a larger number of behavioural traits, including both tool and non-tool use behaviours. Since more than half of the behaviours investigated are also likely to be cultural, we suggest that environmental variability was a critical evolutionary force promoting the behavioural, as well as cultural diversification of great apes.
Characterization and mitigation of gene expression burden in mammalian cells
Authors: Frei Timothy , Cella Federica , Tedeschi Fabiana , Gutiérrez Joaquín , Stan Guy-Bart , Khammash Mustafa , Siciliano Velia 
Published: September 2020

AbstractDespite recent advances in circuit engineering, the design of genetic networks in mammalian cells is still painstakingly slow and fraught with inexplicable failures. Here, we demonstrate that transiently expressed genes in mammalian cells compete for limited transcriptional and translational resources. This competition results in the coupling of otherwise independent exogenous and endogenous genes, creating a divergence between intended and actual function. Guided by a resource-aware mathematical model, we identify and engineer natural and synthetic miRNA-based incoherent feedforward loop (iFFL) circuits that mitigate gene expression burden. The implementation of these circuits features the use of endogenous miRNAs as elementary components of the engineered iFFL device, a versatile hybrid design that allows burden mitigation to be achieved across different cell-lines with minimal resource requirements. This study establishes the foundations for context-aware prediction and improvement of in vivo synthetic circuit performance, paving the way towards more rational synthetic construct design in mammalian cells.
High-efficiency electroporation of chytrid
fungi
Authors: Swafford Andrew J. M. , Hussey Shane P. , Fritz-Laylin Lillian K. 
Published: September 2020

AbstractTwo species of parasitic fungi from the phylum Chytridiomycota (chytrids)
are annihilating global amphibian populations. These chytrid species—Batrachochytrium dendrobatidis and B. salamandrivorans—have high rates of mortality and transmission. Upon
establishing infection in amphibians, chytrids rapidly multiply within the skin and
disrupt their hosts’ vital homeostasis mechanisms. Current disease models suggest that
chytrid fungi locate and infect their hosts during a motile, unicellular ‘zoospore’ life
stage. Moreover, other chytrid species parasitize organisms from across the tree of
life, making future epidemics in new hosts a likely possibility. Efforts to mitigate the
damage and spread of chytrid disease have been stymied by the lack of knowledge about
basic chytrid biology and tools with which to test molecular hypotheses about disease
mechanisms. To overcome this bottleneck, we have developed high-efficiency delivery of
molecular payloads into chytrid zoospores using electroporation. Our electroporation
protocols result in payload delivery to between 75 and 97% of living cells of three
species: B. dendrobatidis, B. salamandrivorans, and a
non-pathogenic relative, Spizellomyces punctatus.
This method lays the foundation for molecular genetic tools needed to establish
ecological mitigation strategies and answer broader questions in evolutionary and cell
biology.
Fine scale spatial investigation of multiple insecticide resistance and underlying target-site and metabolic mechanisms in Anopheles gambiae in central Côte d’Ivoire
Authors: Oumbouke Welbeck A. , Pignatelli Patricia , Barreaux Antoine M. G. , Tia Innocent Z. , Koffi Alphonsine A. , Ahoua Alou Ludovic P. , Sternberg Eleanore D. , Thomas Matthew B. , Weetman David , N’Guessan Raphael 
Published: September 2020

AbstractRoutine monitoring of occurrence, levels and mechanisms of insecticide resistance informs effective management strategies, and should be used to assess the effect of new tools on resistance. As part of a cluster randomised controlled trial evaluating a novel insecticide-based intervention in central Côte d’Ivoire, we assessed resistance and its underlying mechanisms in Anopheles gambiae populations from a subset of trial villages. Resistance to multiple insecticides in An. gambiae s.s. and An. coluzzii was detected across villages, with dose–response assays demonstrating extremely high resistance intensity to the pyrethroid deltamethrin (> 1,500-fold), and mortality following exposure to pyrethroid-treated bednets was low (< 30% mortality in cone bioassays). The 1014F kdr mutation was almost fixed (≥ 90%) in all villages but the 1575Y kdr-amplifying mutation was relatively rare (< 15%). The carbamate and organophosphate resistance-associated Ace-1 G119S mutation was also detected at moderate frequencies (22–43%). Transcriptome analysis identified overexpression of P450 genes known to confer pyrethroid resistance (Cyp9K1, Cyp6P3, and Cyp6M2), and also a carboxylesterase (COEAE1F) as major candidates. Cyp6P3 expression was high but variable (up to 33-fold) and correlated positively with deltamethrin resistance intensity across villages (r2 = 0.78, P = 0.02). Tools and strategies to mitigate the extreme and multiple resistance provided by these mechanisms are required in this area to avoid future control failures.
Magnon magic angles and tunable Hall conductivity in 2D twisted ferromagnetic bilayers
Authors: Ghader Doried 
Published: September 2020

AbstractTwistronics is currently one of the most active research fields in condensed matter physics, following the discovery of correlated insulating and superconducting phases in twisted bilayer graphene (tBLG). Here, we present a magnonic analogue of tBLG. We study magnons in twisted ferromagnetic bilayers (tFBL) with collinear magnetic order, including exchange and weak Dzyaloshinskii-Moriya interactions (DMI). For negligible DMI, tFBL presents discrete magnon magic angles and flat moiré minibands analogous to tBLG. The DMI, however, changes the picture and renders the system much more exotic. The DMI in tFBL induces a rich topological magnon band structure for any twist angle. The twist angle turns to a control knob for the magnon valley Hall and Nernst conductivities. Gapped flat bands appear in a continuum of magic angles in tFBL with DMI. In the lower limit of the continuum, the band structure reconstructs to form several topological flat bands. The luxury of twist-angle control over band gaps, topological properties, number of flat bands, and valley Hall and Nernst conductivities renders tFBL a novel device from fundamental and applied perspectives.
Heat stress as an innovative approach to enhance the antioxidant production in Pseudooceanicola and Bacillus isolates
Authors: Hassan Abdelrahim H. A. , Hozzein Wael N. , Mousa Ahmed S. M. , Rabie Walaa , Alkhalifah Dalal Hussien M. , Selim Samy , AbdElgawad Hamada 
Published: September 2020

AbstractIt is well known that the quality and quantity of bioactive metabolites in plants and microorganisms are affected by environmental factors. We applied heat stress as a promising approach to stimulate the production of antioxidants in four heat-tolerant bacterial strains (HT1 to HT4) isolated from Aushazia Lake, Qassim Region, Saudi Arabia. The phylogenetic analysis of the 16S rRNA sequences indicated that HT1, HT3 and HT4 belong to genusBacillus. While HT2 is closely related toPseudooceanicola marinuswith 96.78% similarity. Heat stress differentially induced oxidative damage i.e., high lipid peroxidation, lipoxygenase and xanthine oxidase levels in HT strains. Subsequently, heat stress induced the levels of flavonoids and polyphenols in all strains and glutathione (GSH) in HT2. Heat stress also improved the antioxidant enzyme activities, namely, CAT, SOD and POX in all strains and thioredoxin activity in HT3 and HT4. While GSH cycle (GSH level and GPX, GR, Grx and GST activities) was only detectable and enhanced by heat stress in HT2. The hierarchical cluster analysis of the antioxidants also supported the strain-specific responses. In conclusion, heat stress is a promising approach to enhance antioxidant production in bacteria with potential applications in food quality improvement and health promotion.
Experimental study and parameters optimization of microalgae based heavy metals removal process using a hybrid response surface methodology-crow search algorithm
Authors: Sultana N. , Hossain S. M. Zakir , Mohammed M. Ezzudin , Irfan M. F. , Haq B. , Faruque M. O. , Razzak S. A. , Hossain M. M. 
Published: September 2020

AbstractThis study investigates the use of microalgae as a biosorbent to eliminate heavy metals ions from wastewater. TheChlorella kesslerimicroalgae species was employed to biosorb heavy metals from synthetic wastewater specimens. FTIR, and SEM/XRD analyses were utilized to characterize the microalgal biomass (the adsorbent). The experiments were conducted with several process parameters, including initial solution pH, temperature, and microalgae biomass dose. In order to secure the best experimental conditions, the optimum parameters were estimated using an integrated response surface methodology (RSM), desirability function (DF), and crow search algorithm (CSA) modeling approach. A maximum lead(II) removal efficiency of 99.54% was identified by the RSM–DF platform with the following optimal set of parameters: pH of 6.34, temperature of 27.71 °C, and biomass dosage of 1.5 g L−1. The hybrid RSM–CSA approach provided a globally optimal solution that was similar to the results obtained by the RSM–DF approach. The consistency of the model-predicted optimum conditions was confirmed by conducting experiments under those conditions. It was found that the experimental removal efficiency (97.1%) under optimum conditions was very close (less than a 5% error) to the model-predicted value. The lead(II) biosorption process was better demonstrated by the pseudo-second order kinetic model. Finally, simultaneous removal of metals from wastewater samples containing a mixture of multiple heavy metals was investigated. The removal efficiency of each heavy metal was found to be in the following order: Pb(II) > Co(II) > Cu(II) > Cd(II) > Cr(II).
Sinter-resistant Rh nanoparticles supported on γ-Al2O3nanosheets as an efficient catalyst for dry reforming of methane
Authors: Chu Shasha , Cai Zhengmiao , Wang Mingzhi , Zheng Yanping , Wang Yongke , Zhou Zhaohui , Weng Weizheng 
Published: September 2020

The unique surface structure of γ-Al2O3 nanosheets plays a key role in increasing the dispersion of Rh species in the catalyst and preventing it from sintering at high temperature under both oxidizing and reducing atmospheres.