bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of oil, dispersant, and pressure on microbial communities from the Gulf of Mexico
Authors: Noirungsee Nuttapol , Hackbusch Steffen , Viamonte Juan , Bubenheim Paul , Liese Andreas , Müller Rudolf 
Published: April 2020

AbstractTheDeepwater Horizonincident in the Gulf of Mexico in 2010 released an unprecedented amount of petroleum hydrocarbons 1500 meters below the sea surface. Few studies have considered the influence of hydrostatic pressure on bacterial community development and activity during such spills. The goal of this study was to investigate the response of indigenous sediment microbial communities to the combination of increased pressure, hydrocarbons and dispersant. Deep-sea sediment samples collected from the northern Gulf of Mexico were incubated at atmospheric pressure (0.1 MPa) and at elevated pressure (10 MPa), with and without the addition of crude oil and dispersant. After incubations at 4 °C for 7 days,ColwelliaandPsychrobiumwere highly abundant in all samples. Pressure differentially impacted members of the Alteromonadales. The influences of pressure on the composition of bacterial communities were most pronounced when dispersant was added to the incubations.MoritellaandThalassotaleawere greatly stimulated by the addition of dispersant, suggesting their roles in dispersant biodegradation. However,Moritellawas negatively impacted by increasing pressure. The presence of dispersant was shown to decrease the relative abundance of a known hydrocarbon degrader,Cycloclasticus, while increasing pressure increased its relative abundance. This study highlights the significant influence of pressure on the development of microbial communities in the presence of oil and dispersant during oil spills and related response strategies in the deep sea.
Dynamics of Global Gene Expression and Regulatory Elements in Growing Brachypodium Root System
Authors: Ogden Aaron J. , Wietsma Thomas W. , Winkler Tanya , Farris Yuliya , Myers Gabriel L. , Ahkami Amir H. 
Published: April 2020

AbstractRoot systems are dynamic and adaptable organs that play critical roles in plant development. However, how roots grow and accumulate biomass during plant life cycle and in relation to shoot growth phenology remains understudied. A comprehensive time-dependent root morphological analysis integrated with molecular signatures is then required to advance our understanding of root growth and development. Here we studiedBrachypodium distachyonrooting process by monitoring root morphology, biomass production, and C/N ratios during developmental stages. To provide insight into gene regulation that accompanies root growth, we generated comprehensive transcript profiles of Brachypodium whole-root system at four developmental stages. Our data analysis revealed that multiple biological processes including trehalose metabolism and various families of transcription factors (TFs) were differentially expressed in root system during plant development. In particular, the AUX/IAA, ERFs, WRKY, NAC, and MADS TF family members were upregulated as plant entered the booting/heading stage, while ARFs and GRFs were downregulated suggesting these TF families as important factors involved in specific phases of rooting, and possibly in regulation of transition to plant reproductive stages. We identified several Brachypodium candidate root biomass-promoting genes andcis-regulatory elements for further functional validations and root growth improvements in grasses.
Plasma Metabolic Signature of Atherosclerosis Progression and Colchicine Treatment in Rabbits
Authors: Izidoro Mario Augusto , Cecconi Alberto , Panadero María Isabel , Mateo Jesús , Godzien Joanna , Vilchez Jean Paul , López-Gonzálvez Ángeles , Ruiz-Cabello Jesús , Ibañez Borja , Barbas Coral , Rupérez Francisco J. 
Published: April 2020

AbstractBalloon catheter endothelial denudation in New Zealand white rabbits fed high cholesterol diet is a validated atherosclerosis model. Well-characterized in terms of atherosclerosis induction and progression, the metabolic changes associated with the atherosclerosis progression remain indeterminate. Non-targeted metabolomics permits to develop such elucidation and allows to evaluate the metabolic consequences of colchicine treatment, an anti-inflammatory drug that could revert these changes. 16 rabbits underwent 18 weeks of atherosclerosis induction by diet and aortic denudation. Thereafter animals were randomly assigned to colchicine treatment or placebo for 18 weeks while on diet. Plasma samples were obtained before randomization and at 36 weeks. Multiplatform (GC/MS, CE/MS, RP-HPLC/MS) metabolomics was applied. Plasma fingerprints were pre-processed, and the resulting matrixes analyzed to unveil differentially expressed features. Different chemical annotation strategies were accomplished for those significant features. We found metabolites associated with either atherosclerosis progression, or colchicine treatment, or both. Atherosclerosis was profoundly associated with an increase in circulating bile acids. Most of the changes associated with sterol metabolism could not be reverted by colchicine treatment. However, the variations in lysine, tryptophan and cysteine metabolism among others, have shown new potential mechanisms of action of the drug, also related to atherosclerosis progression, but not previously described.
Kairomone-like activity of bile and bile components: A step towards revealing the chemical nature of fish kairomone
Authors: Pijanowska Joanna , Markowska Magdalena , Ruszczyńska Anna , Bulska Ewa , Dawidowicz Piotr , Ślusarczyk Mirosław , Biesaga Magdalena 
Published: April 2020

AbstractDespite the efforts of a number of research groups worldwide, we still have a poor understanding of the chemical nature of the fish kairomones which induce defensive morphology, life history and behavior in their planktonic prey. Bile excreted by foraging fish play a crucial role in their signaling systems. Using high-performance liquid chromatography (HPLC), we revealed the presence of primary and secondary bile acids and bile salts in fish-conditioned water, similar as in carp bile. Upon exposure to either fish bile or commercially acquired bile salts, Daphnia demonstrated similar changes in life history and behavior as when exposed to fish kairomones. The synergic effect of the injured Daphnia alarm substance with fish bile on Daphnia life history is similar to the adaptive effect of the same alarm substance combined with fish kairomones. This strongly supports the view that fish bile or selected bile acids/salts may be responsible for the biological activity of kairomones.
Effective microtissue RNA extraction coupled with Smart-seq2 for reproducible and robust spatial transcriptome analysis
Authors: Yamazaki Miki , Hosokawa Masahito , Arikawa Koji , Takahashi Kiyofumi , Sakanashi Chikako , Yoda Takuya , Matsunaga Hiroko , Takeyama Haruko 
Published: April 2020

AbstractSpatial transcriptomics is useful for understanding the molecular organization of a tissue and providing insights into cellular function in a morphological context. In order to obtain reproducible results in spatial transcriptomics, we have to maintain tissue morphology and RNA molecule stability during the image acquisition and biomolecule collection processes. Here, we developed a tissue processing method for robust and reproducible RNA-seq from tissue microdissection samples. In this method, we suppressed RNA degradation in fresh-frozen tissue specimens by dehydration fixation and effectively collected a small amount of RNA molecules from microdissection samples by magnetic beads. We demonstrated the spatial transcriptome analysis of the mouse liver and brain in serial microdissection samples (100 μm in a diameter and 10 μm in thickness) produced by a microdissection punching system. Using our method, we could prevent RNA degradation at room temperature and effectively produce a sequencing library with Smart-seq2. This resulted in reproducible sequence read mapping in exon regions and the detection of more than 2000 genes compared to non-fixed samples in the RNA-seq analysis. Our method would be applied to various transcriptome analyses, providing the information for region specific gene expression in tissue specimens.
Greyhound racing ideal trajectory path generation for straight to bend based on jerk rate minimization
Authors: Hossain Md. Imam , Eager David , Walker Paul D. 
Published: April 2020

AbstractThis paper presents methods for modelling and designing an ideal path trajectory between straight and bend track path segments for racing greyhounds. To do this, we numerically generate clothoid and algebraic curve segments for racing quadrupeds using a sequential vector transformation method as well as using a helper equation for approaching ideal clothoid segments that would respect greyhound kinematic parameters and boundary conditions of the track. Further, we look into the limitations of using a clothoid curve for racing dog track path design and propose a smooth composite curve for track transition design which roughly maintains G3 curvature continuity for smooth jerk to overcome limitations of a clothoid transition. Finally, we show results from race data modelling and past injury data, which provide a strong indication of clothoid curve segments improving the dynamics and safety of racing greyhounds while reducing injuries.
Analysing the phenotype development of soybean plants using low-cost 3D reconstruction
Authors: Zhu Rongsheng , Sun Kai , Yan Zhuangzhuang , Yan Xuehui , Yu Jianglin , Shi Jia , Hu Zhenbang , Jiang Hongwei , Xin Dawei , Zhang Zhanguo , Li Yang , Qi Zhaoming , Liu Chunyan , Wu Xiaoxia , Chen Qingshan 
Published: April 2020

AbstractWith the development of digital agriculture, 3D reconstruction technology has been widely used to analyse crop phenotypes. To date, most research on 3D reconstruction of field crops has been limited to analysis of population characteristics. Therefore, in this study, we propose a method based on low-cost 3D reconstruction technology to analyse the phenotype development during the whole growth period. Based on the phenotypic parameters extracted from the 3D reconstruction model, we identified the “phenotypic fingerprint” of the relevant phenotypes throughout the whole growth period of soybean plants and completed analysis of the plant growth patterns using a logistic growth model. The phenotypic fingerprint showed that, before the R3 period, the growth of the five varieties was similar. After the R5 period, the differences among the five cultivars gradually increased. This result indicates that the phenotypic fingerprint can accurately reveal the patterns of phenotypic changes. The logistic growth model of soybean plants revealed the time points of maximum growth rate of the five soybean varieties, and this information can provide a basis for developing guidelines for water and fertiliser application to crops. These findings will provide effective guidance for breeding and field management of soybean and other crops.
High prevalence of albuminuria amongst people who inject drugs: A cross-sectional study
Authors: McGowan C. R. , Wright T. , Nitsch D. , Lewer D. , Brathwaite R. , Scott J. , Hope V. , Ciccarone D. , Dunn J. , Gillmore J. , Story A. , Harris M. 
Published: April 2020

AbstractAlbuminuria is a key biomarker for cardiovascular disease and chronic kidney disease. Our study aimed to describe the prevalence of albuminuria amongst people who inject drugs in London and to test any potential associations with demographic characteristics, past diagnoses, and drug preparation and administration practices. We carried out a cross-sectional survey amongst people who use drugs in London. The main outcome measure was any albuminuria including both microalbuminuria and macroalbuminuria. Three-hundred and sixteen samples were tested by local laboratory services. Our study initially employed point-of-care testing methods but this resulted in a high number of false positives. Our findings suggest the prevalence of albuminuria amongst PWID is twice that of the general population at 19% (95%CI 15.3–24.0%). Risk factors associated with albuminuria were HIV (aOR 4.11 [95% CI 1.37–12.38]); followed by overuse of acidifier for dissolving brown heroin prior to injection (aOR 2.10 [95% CI 1.04–4.22]). Albuminuria is high amongst people who inject drugs compared to the general population suggesting the presence of increased cardiovascular and renal pathologies. This is the first study to demonstrate an association with acidifier overuse. Dehydration may be common amongst this population and may affect the diagnostic accuracy of point-of-care testing for albuminuria.
Clinical outcome of breast cancer in carriers of BRCA1 and BRCA2 mutations according to molecular subtypes
Authors: De Talhouet Solene , Peron Julien , Vuilleumier Aurelie , Friedlaender Alex , Viassolo Valeria , Ayme Aurélie , Bodmer Alexandre , Treilleux Isabelle , Lang Noemie , Tille Jean- Christophe , Chappuis Pierre O. , Buisson Adrien , Giraud Sophie , Lasset Christine , Bonadona Valerie , Trédan Olivier , Labidi-Galy S.Intidhar 
Published: April 2020

AbstractBRCA1/BRCA2 genes play a central role in DNA repair and their mutations increase sensitivity to DNA-damaging agents. There are conflicting data regarding the prognostic value of BRCA germline mutations in breast cancer (BC) patients. We collected clinical, pathological and genetic data of a cohort 925 BC patients preselected for genetic screening and treated with neoadjuvant or adjuvant chemotherapy, of whom 266 were BRCA carriers. Overall, 171 women carried a BRCA1 mutation, 95 carried a BRCA2 mutation, and 659 were non-carriers. In the entire cohort, there was a prolonged disease-free survival (DFS) for BRCA carriers (hazard ratio (HR) = 0.63; 95% confidence interval (CI), 0.44–0.90 for BRCA1; HR = 0.72; 95%CI, 0.47–1.1 for BRCA2; p = 0.020) and a trend toward prolonged disease-specific survival (DSS; HR = 0.65; 95%CI, 0.40–1.1 for BRCA1; HR = 0.78; 95%CI, 0.44–1.38 for BRCA2; p = 0.19) though not statistically significant. In the TNBC group, BRCA carriers had prolonged DFS (adjusted HR = 0.50; 95%CI, 0.28–0.89 for BRCA1; adjusted HR = 0.37; 95%CI, 0.11–1.25, for BRCA2; p = 0.034) and DSS (adjusted HR = 0.42; 95%CI, 0.21–0.82 for BRCA1; adjusted HR = 0.45; 95%CI, 0.11–1.9 for BRCA2; p = 0.023). In the non-TNBC group, the BRCA1 or BRCA2 mutations did not have any impact on survival. These results suggest that BRCA1/BRCA2 germline mutations are associated with prolonged survival only if women were diagnosed with TNBC.
Occurrence and genetic diversity of CRESS DNA viruses in wild birds: a Hungarian study
Authors: Kaszab Eszter , Lengyel György , Marton Szilvia , Dán Ádám , Bányai Krisztián , Fehér Enikő 
Published: April 2020

AbstractCircoviruses, cycloviruses and other circular, replication-associated protein-encoding single stranded (CRESS) DNA viruses have been detected in a variety of animal taxa. In this study, cloacal swab samples (n = 90) were examined for CRESS DNA viruses from 31 wild bird species living at various aquatic sites in Hungary to identify possible reservoirs of viruses pathogenic to domestic poultry. A total of 30 (33.3%) specimens tested positive with pan-CRESS DNA virus specific PCR. Goose circovirus (GoCV), Duck associated cyclovirus 1 (DuACyV-1) and Garrulus glandarius associated circular virus 1 (GgaCV-1) were detected in nine, three and two different bird species, respectively. Selected specimens were subjected to whole genome sequencing. The obtained sequence data revealed conserved gene structure within the identified virus species and detected homologous (within GoCV) and possible heterologous recombination (within DuACyV-1) events. Results presented here provide new information on the genomic diversity and evolution of selected CRESS DNA viruses.
Effects of anti-PD-1 immunotherapy on tumor regression: insights from a patient-derived xenograft model
Authors: Martín-Ruiz Asunción , Fiuza-Luces Carmen , Martínez-Martínez Esther , Arias Clemente F. , Gutiérrez Lourdes , Ramírez Manuel , Martín-Acosta Paloma , Coronado Maria José , Lucia Alejandro , Provencio Mariano 
Published: April 2020

AbstractImmunotherapies, such as checkpoint blockade of programmed cell death protein-1 (PD-1), have resulted in unprecedented improvements in survival for patients with lung cancer. Nonetheless, not all patients benefit equally and many issues remain unresolved, including the mechanisms of action and the possible effector function of immune cells from non-lymphoid lineages. The purpose of this study was to investigate whether anti-PD-1 immunotherapy acts on malignant tumor cells through mechanisms beyond those related to T lymphocyte involvement. We used a murine patient-derived xenograft (PDX) model of early-stage non–small cell lung carcinoma (NSCLC) devoid of host lymphoid cells, and studied the tumor and immune non-lymphoid responses to immunotherapy with anti-PD-1 alone or in combination with standard chemotherapy (cisplatin). An antitumor effect was observed in animals that received anti-PD-1 treatment, alone or in combination with cisplatin, likely due to a mechanism independent of T lymphocytes. Indeed, anti-PD-1 treatment induced myeloid cell mobilization to the tumor concomitant with the production of exudates compatible with an acute inflammatory reaction mediated by murine polymorphonuclear leukocytes, specifically neutrophils. Thus, while keeping in mind that more research is needed to corroborate our findings, we report preliminary evidence for a previously undescribed immunotherapy mechanism in this model, suggesting a potential cytotoxic action of neutrophils as PD-1 inhibitor effector cells responsible for tumor regression by necrotic extension.
A cognitively demanding working-memory intervention enhances extinction
Authors: de Voogd Lycia D. , Phelps Elizabeth A. 
Published: April 2020

AbstractImproving extinction learning has the potential to optimize psychotherapy for persistent anxiety-related disorders. Recent findings show that extinction learning can be improved with a cognitively demanding eye-movement intervention. It is, however, unclear whether [1] any cognitively-demanding task can enhance extinction, or whether it is limited to eye movements, and [2] the effectiveness of such an intervention can be enhanced by increasing cognitive load. Participants (n = 102, n = 75 included in the final sample) completed a Pavlovian threat conditioning paradigm across two days. One group underwent standard extinction (Control), a second group underwent extinction paired with a 1-back working memory task (Low-Load), and a third group underwent extinction paired with a 2-back working memory task (High-Load). We found that the conditioned response during extinction was reduced for both the Low-Load and the High-Load groups compared to the Control group. This reduction persisted during recovery the following day when no working memory task was executed. Finally, we found that within the High-Load group, participants with lower accuracy scores on the 2-back task (i.e., for who the task was more difficult) had a stronger reduction in the conditioned response. We did not observe this relationship within the Low-Load group. Our findings suggest that cognitive load induced by a working memory intervention embedded during extinction reduces persistent threat responses.
Expected spatial patterns of alien woody plants in South Africa’s protected areas under current scenario of climate change
Authors: Bezeng Bezeng S. , Yessoufou Kowiyou , Taylor Peter J. , Tesfamichael Solomon G. 
Published: April 2020

AbstractAlthough protected areas (PAs) are declared to provide sanctuaries for biodiversity, they are increasingly threatened by the synergistic effects of anthropic factors, invasive alien species and climate change. Consequently, interventions are required to minimize the impacts of these threats on PAs’ integrity. To inform these interventions in the South African context and under the current climate change scenario, we tested for geographic patterns of alien woody species across the network of 1,453 PAs using three alien invasion indices – alien species abundance, invaded area ratio and alien species richness. Our analysis shows that, under current climate change scenario, none of the PAs would be effective in shielding against alien plants and PAs that are geographically close tend to share similar invasion patterns. In addition, PAs that are hotspots of alien species are also geographically clustered but these findings are biome-dependent. Our outlier analysis reveals not only an island of disproportionately rich PAs in alien species, but also identifies some alien-poor PAs. We suggest that PAs that are hotspots of alien species as well as outliers of disproportionately rich PAs in alien species should be priority in monitoring and invasion control programmes in the context of the ongoing climate change.
The Effect of Planning, Strategy Learning, and Working Memory Capacity on Mental Workload
Authors: Radüntz Thea 
Published: April 2020

AbstractIn our modern society, planning and problem solving are crucial for handling a wide range of situations. Investigation of the experienced mental workload connected to planning, strategy learning, and working memory capacity is of particular interest for adjusting conditions according to the mental state of the individual. In our study, we examined 21 subjects during a planning and a working memory task. We applied the method of Dual Frequency Head Maps (DFHM) from the electroencephalogram for capturing mental workload objectively. We evaluated the DFHM-workload index and performance data during the learning and main phase of the planning task and linked the results to subjects’ working memory capacity. The DFHM-workload index indicated that subjects with higher working memory capacity experienced a gradual decrease in mental workload during strategy learning of the planning task. However, the effect of learning on mental workload disappeared during the main phase.
Sub-lattice of Jahn-Teller centers in hexaferrite crystal
Authors: Gudkov V. V. , Sarychev M. N. , Zherlitsyn S. , Zhevstovskikh I. V. , Averkiev N. S. , Vinnik D. A. , Gudkova S. A. , Niewa R. , Dressel M. , Alyabyeva L. N. , Gorshunov B. P. , Bersuker I. B. 
Published: April 2020

AbstractA novel type of sub-lattice of the Jahn-Teller (JT) centers was arranged in Ti-doped barium hexaferrite BaFe12O19. In the un-doped crystal all iron ions, sitting in five different crystallographic positions, are Fe3+ in the high-spin configuration (S = 5/2) and have a non-degenerate ground state. We show that the electron-donor Ti substitution converts the ions to Fe2+ predominantly in tetrahedral coordination, resulting in doubly-degenerate states subject to the $$E\otimes e$$
E
⊗
e
problem of the JT effect. The arranged JT complexes, Fe2+O4, their adiabatic potential energy, non-linear and quantum dynamics, have been studied by means of ultrasound and terahertz-infrared spectroscopies. The JT complexes are sensitive to external stress and applied magnetic field. For that reason, the properties of the doped crystal can be controlled by the amount and state of the JT complexes.