bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of rhizome transcriptome and identification of a rhizomatous ER body in the clonal plant Cardamine leucantha
Authors: Araki Kiwako S. , Nagano Atsushi J. , Nakano Ryohei Thomas , Kitazume Tatsuya , Yamaguchi Katsushi , Hara-Nishimura Ikuko , Shigenobu Shuji , Kudoh Hiroshi 
Published: August 2020

AbstractThe rhizome is a plant organ that develops from a shoot apical meristem but penetrates into belowground environments. To characterize the gene expression profile of rhizomes, we compared the rhizome transcriptome with those of the leaves, shoots and roots of a rhizomatous Brassicaceae plant, Cardamine leucantha. Overall, rhizome transcriptomes were characterized by the absence of genes that show rhizome-specific expression and expression profiles intermediate between those of shoots and roots. Our results suggest that both endogenous developmental factors and external environmental factors are important for controlling the rhizome transcriptome. Genes that showed relatively high expression in the rhizome compared to shoots and roots included those related to belowground defense, control of reactive oxygen species and cell elongation under dark conditions. A comparison of transcriptomes further allowed us to identify the presence of an ER body, a defense-related belowground organelle, in epidermal cells of the C. leucantha rhizome, which is the first report of ER bodies in rhizome tissue.
Association between admission criteria and body composition among young children with moderate acute malnutrition, a cross-sectional study from Burkina Faso
Authors: Fabiansen Christian , Cichon Bernardette , Yaméogo Charles W. , Iuel-Brockdorf Ann-Sophie , Phelan Kevin P. Q. , Wells Jonathan C. , Ritz Christian , Filteau Suzanne , Briend André , Christensen Vibeke B. , Ashorn Per , Michaelsen Kim F. , Shepherd Susan , Friis Henrik 
Published: August 2020

AbstractChildren with moderate acute malnutrition (MAM) are treated based on low weight-for-length z-score (WLZ), low mid-upper arm circumference (MUAC) or both. This study aimed to assess associations of admission criteria and body composition (BC), to improve treatment of MAM. We undertook a cross-sectional study among 6–23 months old Burkinabe children with MAM. Fat-free (FFM) and fat mass (FM) were determined by deuterium dilution and expressed as FFM (FFMI) and FM index (FMI). Of 1,489 children, 439 (29.5%) were recruited by low MUAC only (MUAC-O), 734 (49.3%) by low WLZ and low MUAC (WLZ-MUAC) and 316 (21.2%) by low WLZ only (WLZ-O). Thus, 1,173 (78.8%) were recruited by low MUAC, with or without low WLZ (ALL-MUAC). After adjustments, WLZ-O had 89 g (95% confidence interval (CI) 5; 172) lower FFM compared to MUAC-O. Similarly, WLZ-O had 0.89 kg/m2 (95% CI 0.77; 1.01) lower FFMI compared to MUAC-O, whereas there was no difference for FMI. However, boys included by WLZ-O compared to MUAC-O had 0.21 kg/m2 (95% CI 0.05; 0.38) higher FMI. In contrast, girls included by WLZ-O had 0.17 (95% CI 0.01; 0.33) kg/m2 lower FMI compared to MUAC-O (interaction, p = 0.002). We found that different criteria for admission into MAM treatment programmes select children with differences in BC, especially FFMI.Trial registration: ISRCTN42569496.
Anodes for Li-ion batteries prepared from microcrystalline silicon and enabled by binder’s chemistry and pseudo-self-healing
Authors: Foss Carl Erik Lie , Müssig Stephan , Svensson Ann Mari , Vie Preben J. S. , Ulvestad Asbjørn , Mæhlen Jan Petter , Koposov Alexey Y. 
Published: August 2020

AbstractSilicon, while suffering from major degradation issues, has been recognized as a next promising material to replace currently used graphite in the anodes of Li-ion batteries. Several pathways to mitigate the capacity fading of silicon has been proposed, including optimization of the electrode composition. Within the present work we evaluated different binder formulations to improve the long-term performance of the Li-ion batteries’ anodes based on industrial grade silicon (Si) which is typically characterized by a particle sizes ranging from 100 nm to 5.5 microns. The decrease of pH in a binder formulation was found to detrimental for the cycling performance of Si due to enhanced formation of an ester-type bonding between the carboxylic group of the binder and hydroxyl group on the Si surface as well as cross-linking. Furthermore, the present work was focused on the use of the industrial grade Si with very high loading of Si material (up to 80% by weight) to better highlight the effects of the surface chemistry of Si and its influence on the performance of Si-based anodes in Li-ion batteries. The tested system allowed to establish a pseudo self-healing effect that manifests itself through the restoration of the anode capacity by approximately 25% and initiates after approximately 20 cycles. The stabilization of the capacity is attributed to self-limiting lithiation process. Such effect is closely related to SEI formation and transport properties of an electrode prepared from silicon of industrial grade.
An idealised approach of geometry and topology to the diffusion of cations in honeycomb layered oxide frameworks
Authors: Kanyolo Godwill Mbiti , Masese Titus 
Published: August 2020

AbstractHoneycomb layered oxides are a novel class of nanostructured materials comprising alkali or coinage metal atoms intercalated into transition metal slabs. The intricate honeycomb architecture and layered framework endows this family of oxides with a tessellation of features such as exquisite electrochemistry, unique topology and fascinating electromagnetic phenomena. Despite having innumerable functionalities, these materials remain highly underutilised as their underlying atomistic mechanisms are vastly unexplored. Therefore, in a bid to provide a more in-depth perspective, we propose an idealised diffusion model of the charged alkali cations (such as lithium, sodium or potassium) in the two-dimensional (2D) honeycomb layers within the multi-layered crystal of honeycomb layered oxide frameworks. This model not only explains the correlation between the excitation of cationic vacancies (by applied electromagnetic fields) and the Gaussian curvature deformation of the 2D surface, but also takes into consideration, the quantum properties of the cations and their inter-layer mixing through quantum tunnelling. Through this work, we offer a novel theoretical framework for the study of multi-layered materials with 2D cationic diffusion currents, as well as providing pedagogical insights into the role of topological phase transitions in these materials in relation to Brownian motion and quantum geometry.
Neutrophil to lymphocyte ratio and breast cancer risk: analysis by subtype and potential interactions
Authors: Gago-Dominguez Manuela , Matabuena Marcos , Redondo Carmen M. , Patel Sandip Pravin , Carracedo Angel , Ponte Sara Miranda , Martínez María Elena , Castelao J. Esteban 
Published: August 2020

AbstractMultiple studies have found the neutrophil to lymphocyte ratio (NLR) to be associated with adverse breast cancer (BC) prognosis and survival. Very limited data exist on the role of NLR and risk of BC. The BREOGAN study is a population-based case–control study conducted in Galicia, Spain. We examined the WBC- and NLR-BC relationships. The risk of BC increased with increasing levels of neutrophils percentage (NE%) (multivariable OR for the highest category (95% CI) = 2.14 (1.39–3.32), P-trend < 0.001) and of the NLR (multivariable OR for the highest category (95% CI) = 1.93 (1.26–2.97), P-trend < 0.001). Lymphocytes absolute (L#) and percentage (L%) were associated with a decreased risk of BC (multivariable OR for the highest category (95% CI) = 0.54 (0.35–0.83), and 0.51 (0.33–0.79), P-trend = 0.001 and < 0.001, respectively). The NLR-BC association was more pronounced among Luminal A BC (multivariable OR for the highest category (95% CI) = 2.00 (1.17–3.45), P-trend < 0.001), HER2-negative BC (multivariable OR for the highest category (95% CI) = 1.87 (1.16–3.02), P-trend < 0.001), and those with high total cholesterol and low H2O2 levels.
Genetic variability of the U5 and downstream sequence of major HIV-1 subtypes and circulating recombinant forms
Authors: Mbondji-Wonje Christelle , Dong Ming , Zhao Jiangqin , Wang Xue , Nanfack Aubin , Ragupathy Viswanath , Sanchez Ana M. , Denny Thomas N. , Hewlett Indira 
Published: August 2020

AbstractThe critical role of the regulatory elements at the 5′ end of the HIV-1 genome in controlling the life cycle of HIV-1 indicates that this region significantly influences virus fitness and its biological properties. In this study, we performed a detailed characterization of strain-specific variability of sequences from the U5 to upstream of the gag gene start codon of diverse HIV-1 strains by using next-generation sequencing (NGS) techniques. Overall, we found that this region of the HIV-1 genome displayed a low degree of intra-strain variability. On the other hand, inter-strain variability was found to be as high as that reported for gag and env genes (13–17%). We observed strain-specific single point and clustered mutations in the U5, PBS, and gag leader sequences (GLS), generating potential strain-specific transcription factor binding sites (TFBS). Using an infrared gel shift assay, we demonstrated the presence of potential TFBS such as E-box in CRF22_01A, and Stat 6 in subtypes A and G, as well as in their related CRFs. The strain-specific variation found in the sequence corresponding at the RNA level to functional domains of the 5ʹ UTR, could also potentially impact the secondary/tertiary structural rearrangement of this region. Thus, the variability observed in this 5′ end of the genomic region of divergent HIV-1 strains strongly suggests that functions of this region might be affected in a strain-specific manner. Our findings provide new insights into DNA–protein interactions that regulate HIV-1 replication and the influence of strain characterization on the biology of HIV-1 infection.
Pharmacological activation of the circadian component REV-ERB inhibits HIV-1 replication
Authors: Borrmann Helene , Davies Rhianna , Dickinson Matthew , Pedroza-Pacheco Isabela , Schilling Mirjam , Vaughan-Jackson Alun , Magri Andrea , James William , Balfe Peter , Borrow Persephone , McKeating Jane A. , Zhuang Xiaodong 
Published: August 2020

AbstractHuman immunodeficiency virus 1 (HIV-1) is a life-threatening pathogen that still lacks a curative therapy or vaccine. Despite the reduction in AIDS-related deaths achieved by current antiretroviral therapies, drawbacks including drug resistance and the failure to eradicate infection highlight the need to identify new pathways to target the infection. Circadian rhythms are endogenous 24-h oscillations which regulate physiological processes including immune responses to infection, and there is an emerging role for the circadian components in regulating viral replication. The molecular clock consists of transcriptional/translational feedback loops that generate rhythms. In mammals, BMAL1 and CLOCK activate rhythmic transcription of genes including the nuclear receptor REV-ERBα, which represses BMAL1 and plays an essential role in sustaining a functional clock. We investigated whether REV-ERB activity regulates HIV-1 replication and found REV-ERB agonists inhibited HIV-1 promoter activity in cell lines, primary human CD4 T cells and macrophages, whilst antagonism or genetic disruption of REV-ERB increased promoter activity. The REV-ERB agonist SR9009 inhibited promoter activity of diverse HIV-subtypes and HIV-1 replication in primary T cells. This study shows a role for REV-ERB synthetic agonists to inhibit HIV-1 LTR promoter activity and viral replication, supporting a role for circadian clock components in regulating HIV-1 replication.
Temperature-dependent life history and transcriptomic responses in heat-tolerant versus heat-sensitive Brachionus rotifers
Authors: Paraskevopoulou Sofia , Dennis Alice B. , Weithoff Guntram , Tiedemann Ralph 
Published: August 2020

AbstractThermal stress response is an essential physiological trait that determines occurrence and temporal succession in nature, including response to climate change. We compared temperature-related demography in closely related heat-tolerant and heat-sensitive Brachionus rotifer species. We found significant differences in heat response, with the heat-sensitive species adopting a strategy of long survival and low population growth, while the heat-tolerant followed the opposite strategy. In both species, we examined the genetic basis of physiological variation by comparing gene expression across increasing temperatures. Comparative transcriptomic analyses identified shared and opposing responses to heat. Interestingly, expression of heat shock proteins (hsps) was strikingly different in the two species and mirrored differences in population growth rates, showing that hsp genes are likely a key component of a species’ adaptation to different temperatures. Temperature induction caused opposing patterns of expression in further functional categories including energy, carbohydrate and lipid metabolism, and in genes related to ribosomal proteins. In the heat-sensitive species, elevated temperatures caused up-regulation of genes related to meiosis induction and post-translational histone modifications. This work demonstrates the sweeping reorganizations of biological functions that accompany temperature adaptation in these two species and reveals potential molecular mechanisms that might be activated for adaptation to global warming.
Near-isogenic soybean lines carrying Asian soybean rust resistance genes for practical pathogenicity validation
Authors: Kashiwa Takeshi , Muraki Yukie , Yamanaka Naoki 
Published: August 2020

AbstractAsian soybean rust caused by the fungal pathogen Phakopsora pachyrhizi is the most devastating disease of soybean. The host cultivar specificity of the pathogen shows considerable differentiation depending on the area and season of its emergence. Although resistance genes for P. pachyrhizi (Rpp) have been reported in several soybean varieties, the genetic background of these varieties is highly differentiated. Furthermore, some of the varieties harbor unknown genetic factors in addition to Rpp that could influence resistance reactions against the pathogen. In order to gain a comprehensive understanding of Rpp–P. pachyrhizi interactions, homogenous plant material harboring Rpp genes is necessary. In this study, we bred Rpp-near isogenic lines (Rpp-NILs), which retained identical plant characters originating from a single genetic background, and accordingly showed low-variant compatible/incompatible reactions against the pathogen. These Rpp-NILs can be used as genetic resources for studying P. pachyrhizi epidemiology and elucidating resistance mechanisms. Compatible/incompatible relationships between the soybean rust resistance gene Rpp and isolates of the pathogen P. pachyrhizi are clearly distinguishable using the Rpp-NILs bred in this study.
Forensic validation of a panel of 12 SNPs for identification of Mongolian wolf and dog
Authors: Jiang Hong Hui , Li Bo , Ma Yue , Bai Su Ying , Dahmer Thomas D. , Linacre Adrian , Xu Yan Chun 
Published: August 2020

AbstractWolf (Canis lupus) is a species included in appendices of CITES and is often encountered in cases of alleged poaching and trafficking of their products. When such crimes are suspected, those involved may attempt to evade legal action by claiming that the animals involved are domestic dogs (C. l. familiaris). To respond effectively to such claims, law enforcement agencies require reliable and robust methods to distinguish wolves from dogs. Reported molecular genetic methods are either unreliable (mitogenome sequence based), or operationally cumbersome and require much DNA (un-multiplexed microsatellites), or financially expensive (genome wide SNP genotyping). We report on the validation of a panel of 12 ancestral informative single nucleotide polymorphism (SNP) markers for discriminating wolves from dogs. A SNaPshot multiplex genotyping system was developed for the panel, and 97 Mongolian wolves (C. l. chanco) and 108 domestic dogs were used for validation. Results showed this panel had high genotyping success (0.991), reproducibility (1.00) and origin assignment accuracy (0.97 ± 0.05 for dogs and 1.00 ± 0.03 for wolves). Species-specificity testing suggested strong tolerance to DNA contamination across species, except for Canidae. The minimum DNA required for reliable genotyping was 6.25 pg/μl. The method and established gene frequency database are available to support identification of wolves and dogs by law enforcement agencies.
Ascorbate peroxidase 4 plays a role in the tolerance of Chlamydomonas reinhardtii to photo-oxidative stress
Authors: Kuo Eva YuHua , Cai Meng-Siou , Lee Tse-Min 
Published: August 2020

AbstractAscorbate peroxidase (APX; EC 1.11.1.11) activity and transcript levels of CrAPX1, CrAPX2, and CrAPX4 of Chlamydomonas reinhardtii increased under 1,400 μE·m−2·s−1 condition (HL). CrAPX4 expression was the most significant. So, CrAPX4 was downregulated using amiRNA technology to examine the role of APX for HL acclimation. The CrAPX4 knockdown amiRNA lines showed low APX activity and CrAPX4 transcript level without a change in CrAPX1 and CrAPX2 transcript levels, and monodehydroascorbate reductase (MDAR), dehydroascorbate reductase (DHAR), and glutathione reductase (GR) activities and transcript levels. Upon exposure to HL, CrAPX4 knockdown amiRNA lines appeared a modification in the expression of genes encoding the enzymes in the ascorbate–glutathione cycle, including an increase in transcript level of CrVTC2, a key enzyme for ascorbate (AsA) biosynthesis but a decrease in MDAR and DHAR transcription and activity after 1 h, followed by increases in reactive oxygen species production and lipid peroxidation after 6 h and exhibited cell death after 9 h. Besides, AsA content and AsA/DHA (dehydroascorbate) ratio decreased in CrAPX4 knockdown amiRNA lines after prolonged HL treatment. Thus, CrAPX4 induction together with its association with the modulation of MDAR and DHAR expression for AsA regeneration is critical for Chlamydomonas to cope with photo-oxidative stress.
Oral and vaginal microbiota in selected field mice of the genus Apodemus: a wild population study
Authors: Matějková Tereza , Hájková Petra , Stopková Romana , Stanko Michal , Martin Jean-François , Kreisinger Jakub , Stopka Pavel 
Published: August 2020

AbstractAnimal-associated microbiota is expected to impose crucial effects on the host’s fitness-related performance, including reproduction. Most research to date has focused on interactions between the host with its gut microbiota; however, there remain considerable gaps in knowledge regarding microbial consortia in other organs, including interspecific divergence, temporal stability, variation drivers, and their effects on the host. To fill these gaps, we examined oral and vaginal microbiota composition in four free-living mouse species of the genus Apodemus, each varying in the degree of female promiscuity. To assess temporal stability and microbiota resistance to environmental change, we exposed one of the species, Apodemus uralensis, to standardized captive conditions and analyzed longitudinal changes in its microbiota structure. Our results revealed the existence of a “core” oral microbiota that was not only shared among all four species but also persisted almost unchanged in captivity. On the other hand, vaginal microbiota appears to be more plastic in captive conditions and less species-specific in comparison with oral microbiota. This study is amongst the first to describe oral microbiota dynamics. Furthermore, the vaginal microbiota results are especially surprising in light of the well-known role of stable vaginal microbiota as a defense against pathogens. The results indicate the existence of diverse mechanisms that shape each microbiota. On the other hand, our data provides somewhat ambiguous support for the systematic effect of phylogeny and social system on both oral and vaginal microbiota structures.
Tip cross-sectional geometry predicts the penetration depth of stone-tipped projectiles
Authors: Sitton Jase , Story Brett , Buchanan Briggs , Eren Metin I. 
Published: August 2020

AbstractUnderstanding prehistoric projectile weaponry performance is fundamental to unraveling past humans’ survival and the evolution of technology. One important debate involves how deeply stone-tipped projectiles penetrate a target. Theoretically, all things being equal, projectiles with smaller tip cross-sectional geometries should penetrate deeper into a target than projectiles with larger tip cross-sectional geometries. Yet, previous experiments have both supported and questioned this theoretical premise. Here, under controlled conditions, we experimentally examine fourteen types of stone-tipped projectile each possessing a different cross-sectional geometry. Our results show that both tip cross-sectional area (TCSA) and tip cross-sectional perimeter (TCSP) exhibit a strong, significant inverse relationship with target penetration depth, although TCSP’s relationship is stronger. We discuss why our experimental results support what is mathematically predicted while previous experiments have not. Our results are consistent with the hypothesis that when stone tip cross-sectional geometries become smaller over time in particular contexts, this evolution may be due to the selection of these attributes for increased penetration.
Factors determining speed management during distracted driving (WhatsApp messaging)
Authors: Ortiz-Peregrina Sonia , Oviedo-Trespalacios Oscar , Ortiz Carolina , Casares-López Miriam , Salas Carlos , Anera Rosario G. 
Published: August 2020

AbstractThe objective of this work was to investigate self-regulation behaviours, particularly speed management, under distracted conditions due to WhatsApp use. We also studied the influence of different environments and driver characteristics, introducing visual status (i.e., visual acuity and contrast sensitivity) as one of them. Seventy-five drivers were evaluated in a simulator study involving two test sessions under baseline and texting conditions. A cluster analysis was used to identify two groups with different visual capacity. Lastly, possible predictors of speed management were studied developing a generalised linear mixed model. Our results show that drivers reduced their speeds in the presence of more demanding driving conditions; while replying to a WhatsApp message, on curved road segments and when parked cars are present. Driving speed also correlated with driver characteristics such as age or dual task experience and human factors such as self-perceived risk of texting while driving. Finally, although there were significant differences in visual capacity between the two groups identified, the model did not identify visual capacity membership as a significant predictor of speed management. This study could provide a better understanding of the mechanisms drivers use when WhatsApp messaging and which environments and driver conditions influence how speed is managed.