bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of null models to compare the assembly of northeast Atlantic bacterial community in the presence of crude oil with either chemical dispersant or biosurfactant
Authors: Nikolova Christina , Ijaz Umer Zeeshan , Gutierrez Tony 
Published: December 2020

AbstractThe compositions of marine microbial communities in response to crude oil in the presence of biosurfactant or synthetic dispersants have been extensively studied in the last decade. Assembly processes, however, in such communities are poorly understood. In this study, we used seven different but complementing null model approaches, such as elements of metacommunity structure, Raup-Crick beta-diversity, normalised stochasticity ratio, Tucker’s null model, quantitative process estimates, lottery assembly, and phylogenetic dispersion models, to quantify the relative importance of ecological process that drive the community assembly. We found that the presence of chemical dispersant in the oil-amended microcosms induced significant temporal changes in the assembly processes that were different from the oil-only or biogenic dispersant-amended microcosms. The assembly processes in all microcosms were neither purely deterministic nor stochastic, but increasingly deterministic in dispersant-amended microcosms. Furthermore, the relative importance of determinisms varied over time and was strongest during the middle phase of incubation. Tucker’s null model revealed that phylogenetically distinct taxa might have shaped the bacterial community assembly in the different microcosms towards more niche or neutral processes. Moreover, there was faster recruitment of phylogenetically distant species in the dispersant-amended community. Drift, homogenising selection and dispersal limitation were the dominant assembly processes in all microcosms, but variable selection was only important in dispersant-amended microcosms. In conclusion, our study highlights that the assembly processes in marine bacterial communities are not static but rather dynamic, and the chemical dispersant can cause significantly different patterns of community assembly compared to non-amended or biosurfactant-amended microcosms.ImportanceThe null model strategy is designed to intentionally exclude an ecological or evolutionary process of interest and create a beta diversity pattern that would be expected in the absence of this particular process – i.e. the community structure is random in respect to the process being tested. Recent advancements of bioinformatics and statistical tools have made it possible to apply theoretical macroecological concepts to microbial metagenomics in order to better understand and quantify the mechanisms and patterns controlling the complexity of microbial ecology. The conclusions from the null models can help predict the changes in microbial biodiversity and ecosystem services in oil polluted environments and therefore assist in making effective decisions with regards to what would be the best oil spill response option for similar environmental conditions.
Circular Economy of Anaerobic Biofilm Microbiomes: A Meta-Analysis Framework for Re-exploration of Amplicon Sequencing Data
Authors: Keating Ciara , Trego Anna Christine , Sloan William , O’Flaherty Vincent , Ijaz Umer Zeeshan 
Published: December 2020

AbstractUse of high-throughput sequencing is widespread in efforts to understand the microbial communities in natural and engineered systems. Many built ecosystems, in particular those used for engineered wastewater treatment, have harnessed the metabolic capacity of complex microbial communities for the effective removal and recovery of organic pollutants. Recent efforts to better understand and precisely engineer such systems have increasingly used high-throughput sequencing to map the structure and function of wastewater treatment microbiomes. An enormous amount of data is readily available on online repositories such as the National Center for Biotechnology Information Short Read Archive (NCBI SRA). Here, we describe and provide an optimised meta-analysis workflow to utilise this resource to collate heterogenous studies together for anaerobic digestion research. We analysed 16S rRNA gene Illumina Miseq amplicon sequencing data from 31 anaerobic digestion studies (from high-rate digesters), including >1,300 samples. Additionally, we compare several methodological choices: extraction method, v-region, taxonomical database, and the classifier. We demonstrate that collation of data from multiple v-regions can be achieved by using only the taxa for which sequences are available in the reference databases, without losses in diversity trends. This is made possible by focusing on alternative strategies for taxonomic assignments, namely, bayesian lowest common ancestor (BLCA) algorithm which offers increased resolution to the traditional naïve bayesian classifier (NBC). While we demonstrate this using an anaerobic digestion wastewater treatment dataset, this methodology can be translated to perform meta-analysis on amplicon sequences in any field. These findings not only provide a roadmap for meta-analysis in any field, but additionally provide an opportunity to reuse extensive data resources to ultimately advance knowledge of wastewater treatment systems.ImportanceIn this study, we have combined sequencing data from 31 individual studies with the purpose of identifying a meta-analysis workflow which can accurately collate data derived from sequencing different v-regions with minimal data loss and more accurate diversity patterns. While we have used Anaerobic Digestion (AD) communities for our proof-of-concept, our workflow (Fig 1) can be translated to any Illumina MiSeq meta-analysis study, in any field. Thereby, we provide the foundation for intensive data mining of existing amplicon sequencing resources. Such data-mining can provide a global perspective on complex microbial communities.Graphical Abstract
Coalescent-based species delimitation meets deep learning: Insights from a highly fragmented cactus system
Authors: Perez Manolo F. , Bonatelli Isabel A. S. , Romeiro-Brito Monique , Franco Fernando F. , Taylor Nigel P. , Zappi Daniela C. , Moraes Evandro M. 
Published: December 2020

AbstractDelimiting species boundaries is a major goal in evolutionary biology. An increasing body of literature has focused on the challenges of investigating cryptic diversity within complex evolutionary scenarios of speciation, including gene flow and demographic fluctuations. New methods based on model selection, such as approximate Bayesian computation, approximate likelihoods, and machine learning are promising tools arising in this field. Here, we introduce a framework for species delimitation using the multispecies coalescent model coupled with a deep learning algorithm based on convolutional neural networks (CNNs). We compared this strategy with a similar ABC approach. We applied both methods to test species boundary hypotheses based on current and previous taxonomic delimitations as well as genetic data (sequences from 41 loci) inPilosocereus aurisetus, a cactus species complex with a sky-island distribution and taxonomic uncertainty. To validate our method, we also applied the same strategy on data from widely accepted species from the genusDrosophila. The results show that our CNN approach has high capacity to distinguish among the simulated species delimitation scenarios, with higher accuracy than ABC. For the cactus dataset, a splitter hypothesis without gene flow showed the highest probability in both CNN and ABC approaches, a result agreeing with previous taxonomic classifications and in line with the sky-island distribution and low dispersal features ofP. aurisetus. Our results highlight the cryptic diversity within theP. aurisetuscomplex and show that CNNs are a promising approach for distinguishing complex evolutionary histories, even outperforming the accuracy of other model-based approaches such as ABC.
Daily electrical activity in the master circadian clock of a diurnal mammal
Authors: Bano-Otalora Beatriz , Moye Matthew J. , Brown Timothy M. , Lucas Robert J. , Diekman Casey O. , Belle Mino D. C. 
Published: December 2020

AbstractDaily or circadian rhythms in mammals are orchestrated by a master circadian clock within the hypothalamic suprachiasmatic nuclei (SCN). Here, cell-autonomous oscillations in gene expression, intrinsic membrane properties, and synaptic communication shape the electrical landscape of the SCN across the circadian day, rendering SCN neurons overtly more active during the day than at night. This well-accepted hallmark bioelectrical feature of the SCN has overwhelmingly emerged from studies performed on a small number of nocturnal rodent species. Therefore, for the first time, we investigate the spontaneous and evoked electrical activity of SCN neurons in a diurnal mammal. To this end, we measured the electrical activity of individual SCN neurons during the day and at night in brain slices prepared from the diurnal murid rodentRhabdomys pumilioand then developed cutting-edge data assimilation and mathematical modelling approaches to uncover the underlying ionic mechanisms. We find thatR. pumilioSCN neurons were more excited in the day than at night, recapitulating the prototypical pattern of SCN neuronal activity previously observed in nocturnal rodents. By contrast, the evoked activity ofR. pumilioneurons included a prominent suppressive response that is not present in the SCN of nocturnal rodents. Our computational modelling approaches reveal transient subthreshold A-type potassium channels as the primary determinant of the suppressive response and highlight a key role for this ionic mechanism in tuning excitability of clock neurons and optimising SCN function to accommodateR. pumilio’sdiurnal niche.
Overexpression of human alpha-Synuclein leads to dysregulated microbiome/metabolites with ageing in a rat model of Parkinson disease
Authors: Singh Yogesh , Trautwein Christoph , Romani Joan , Salker Madhuri S , Neckel Peter H , Fraccaroli Isabel , Abeditashi Mahkameh , Woerner Nils , Admard Jakob , Dhariwal Achal , Dueholm Morten S , Schäfer Karl-Herbert , Lang Florian , Otzen Daniel , Lashuel Hilal A , Riess Olaf , Casadei Nicolas 
Published: December 2020

AbstractSince Braak’s hypothesis stating that sporadic Parkinson’s disease follows a specific progression of the pathology from the peripheral to the central nervous system and can be monitored by detecting accumulation of the alpha-Synuclein protein. There is growing interest in understanding how the gut (commensal) microbiome can regulate alpha-Synuclein accumulation which can lead to PD. We studied a transgenic rat model overexpressing the human alpha-Synuclein and found that the protein overexpression resulted in gut alpha-Synuclein expression and aggregation in the gut neurons with advancing age. A progressive gut microbial composition alteration characterized by the reduction of Firmicutes to Bacteroidetes ratio could be detected in the young transgenic rat model and interestingly this ratio was then increased with aging. This observation was accompanied in older animals by intestinal inflammation, increase gut permeability and a robust alteration in metabolites production characterized by the increase of succinate level in the feces and serum. Manipulation of the gut bacteria by short-term antibiotics treatment revealed a complete loss of short-chain fatty acids (SCFAs) and reduction in succinate levels. Although antibiotics treatment did not change alpha-synuclein expression in the enteric nervous system of the colon, it can reduce alpha-synuclein expression in the olfactory bulb of the transgenic rats. In summary, synchronous with ageing, our data emphasize that the gut microbiome dysbiosis leads to a specific alteration of gut metabolites which are reflected in the serum and can be modulated by the environment.
Differential Expression ofNPAS4in the Dorsolateral Prefrontal Cortex Following Acute Opioid Intoxication
Authors: Sosnowski David W. , Jaffe Andrew E. , Tao Ran , Deep-Soboslay Amy , Kleinman Joel E. , Hyde Thomas M. , Shu Chang , Sabunciyan Sarven , Maher Brion S. 
Published: December 2020

AbstractBackground and AimsThe physical, emotional, and social impacts of opioid abuse are well known; although preclinical models reveal the neurobiological pathways altered through opioid abuse, comprehensive assessments of gene expression in human brain samples are lacking. The goals of the present study were to compare gene expression in the prefrontal cortex between brain samples of individuals who died of acute opioid intoxication and group-matched controls, and to test if differential gene expression was enriched in gene sets related to opioid use.DesignCross-sectional study using human brains donated to the Lieber Institute for Brain Development. Study groups included 72 brain samples from individuals who died of acute opioid intoxication, 53 group-matched psychiatric control samples, and 28 group-matched normal control samples.SettingMaryland, USA.ParticipantsPostmortem tissue samples of the dorsolateral prefrontal cortex from 153 deceased individuals(Mage= 35.42,SD= 9.43 years; 62% male; 77% White).MeasurementsWhole transcriptome RNA sequencing was used to generate exon counts, and differential expression was tested usinglimma-voom.Analyses controlled for relevant sociodemographic characteristics, technical covariates, and cryptic relatedness and batch effects using quality surrogate variable analysis. Gene set enrichment analyses (GSEA) also were conducted.FindingsSixteen genes were differentially expressed (i.e., FDR-correctedp< .10) in opioid samples compared to control samples. The top differentially expressed gene,NPAS4(FDR adjustedp= .005), was downregulated in opioid samples and has previously been implicated in cocaine use. Enrichment analyses did not provide evidence for enrichment in pathways obviously related to opioid use.ConclusionsNPAS4is differentially expressed in the prefrontal cortex of subjects that died of an opioid overdose, providing evidence for another gene with functional relevance to opioid use and overdose.
Genome-wide Copy Number Variations in a Large Cohort of Bantu African Children
Authors: Yilmaz Feyza , Null Megan , Astling David , Yu Hung-Chun , Cole Joanne , Santorico Stephanie A. , Hallgrimsson Benedikt , Manyama Mange , Spritz Richard A. , Hendricks Audrey E. , Shaikh Tamim H. 
Published: December 2020

AbstractBackgroundCopy number variations (CNVs) account for a substantial proportion of inter-individual genomic variation. However, a majority of genomic variation studies have focused on single-nucleotide variations (SNVs), with limited genome-wide analysis of CNVs in large cohorts, especially in populations that are under-represented in genetic studies including people of African descent.ResultsIn this study, we carried out a genome-wide analysis in > 3400 healthy Bantu Africans from Tanzania using high density (> 2.5 million probes) genotyping arrays. We identified over 400000 CNVs larger than 1 kilobase (kb), for an average of 120 CNVs (SE = 2.57) per individual. We detected 866 large CNVs (≥ 300 kb), some of which overlapped genomic regions previously associated with multiple congenital anomaly syndromes, including Prader-Willi/Angelman syndrome (Type1) and 22q11.2 deletion syndrome. Furthermore, several of the common CNVs seen in our cohort (≥ 5%) overlap genes previously associated with developmental disorders.ConclusionThese findings may help refine the phenotypic outcomes and penetrance of variations affecting genes and genomic regions previously implicated in diseases. Our study provides one of the largest datasets of CNVs from individuals of African ancestry, enabling improved clinical evaluation and disease association of CNVs observed in research and clinical studies in African populations.
ace2expression is higher in intestines and liver while being tightly regulated in development and disease in zebrafish
Authors: Keskus Ayse Gokce , Tombaz Melike , Arici Burcin I. , Dincaslan Fatma B. , Nabi Afshan , Shehwana Huma , Konu Ozlen 
Published: December 2020

AbstractHuman Angiotensin I Converting Enzyme 2 (ACE2) that acts as a receptor for SARS-CoV-2 entry is highly expressed in human type II pneumocytes and enterocytes and similarly in other mammals and zebrafish (Danio rerio). The zebrafish genome has a highly conserved, one-to-one ortholog ofACE2, i.e.,ace2, whose expression profile however has not yet been studied during development or in pathologies relevant to COVID-19. Herein, we identified significant development-, tissue- and gender-specific modulations inace2expression based on meta-analysis of zebrafish Affymetrix transcriptomics datasets (ndatasets=107, GPL1319 in GEO database). Co-expression network analysis oface2revealed distinct positively correlated (carboxypeptidase activity and fibrin clot formation), and negatively correlated (cilia biogenesis/transport and chromatin modifications) STRING network modules. Using additional transcriptomics datasets, we showed zebrafish embryos before 3 days post fertilization (dpf) exhibited low levels oface2that increased significantly until 4 dpf implicating a role forace2in organogenesis. Re-analysis of RNA-seq datasets from zebrafish adult tissues demonstratedace2was expressed highly in intestines, variably in liver, and at lower levels in other organs. In addition, zebrafish females and males showed significant dimorphism in their age-dependent expression oface2, and between ovary and testis where the latter had higher levels. Moreover, we demonstratedace2expression was significantly modulated under different physiological and pathological conditions associated with development, diet, infection, and inflammation. Our findings implicate a novel translational role for zebrafishace2in differentiation and pathologies predominantly found in intestines and liver, in which the effects of SARS-CoV-2 could be detrimental.
Broadband X-ray ptychography using multi-wavelength algorithm
Authors: Yao Yudong , Jiang Yi , Klug Jeffrey , Nashed Youssef , Roehrig Christian , Preissner Curt , Marin Fabricio , Wojcik Michael , Cossairt Oliver , Cai Zhonghou , Vogt Stefan , Lai Barry , Deng Junjing 
Published: December 2020

Ptychography is a rapidly developing scanning microscopy which is able to view the internal structures of samples at a high resolution beyond the illumination size. The achieved spatial resolution is theoretically dose-limited. A broadband source can provide much higher flux compared with a monochromatic source; however, it conflicts with the necessary coherence requirements of this coherent diffraction imaging technique. In this paper, a multi-wavelength reconstruction algorithm has been developed to deal with the broad bandwidth in ptychography. Compared with the latest development of mixed-state reconstruction approach, this multi-wavelength approach is more accurate in the physical model, and also considers the spot size variation as a function of energy due to the chromatic focusing optics. Therefore, this method has been proved in both simulation and experiment to significantly improve the reconstruction when the source bandwidth, illumination size and scan step size increase. It is worth mentioning that the accurate and detailed information of the energy spectrum for the incident beam is not required in advance for the proposed method. Further, we combine multi-wavelength and mixed-state approaches to jointly solve temporal and spatial partial coherence in ptychography so that it can handle various disadvantageous experimental effects. The significant relaxation in coherence requirements by our approaches allows the use of high-flux broadband X-ray sources for high-efficient and high-resolution ptychographic imaging.
Flooding in mega-cities: using structural equation modeling to assess flood impact in Dhaka
Authors: Fatemi Md. Nawrose , Okyere Seth Asare , Diko Stephen Kofi , Abunyewah Matthew , Kita Michihiro , Rahman Tahmina 
Published: December 2020

PurposeThis paper aims to bring the more recent discourse on the multilayered and interconnected dimensions of flood vulnerability, damage and risk reduction at the microlevel of global south cities to Dhaka, by looking at multiple factors and their relationships.Design/methodology/approachA cross-sectional research design was used to generate data from 315 respondents in five neighborhoods in Eastern Dhaka, located in high flood damage zones with previous flood experience, using a structural equation model to test nine hypothetical relationships.FindingsThe model confirms that low socioeconomic conditions often lead households to use social capital to traverse flood vulnerabilities in cities. It also advances this notion to show that flood impact unleashes social capital through collective activities in responding to flooding. Further, it reveals that while socioeconomic conditions influence flood impacts, these also engender the necessary mechanisms to unleash collective responses to flooding.Practical implicationsThis paper suggests the need for context-specific interventions that transcend physical and infrastructural responses to integrate socioeconomic conditions as a basis of understanding and addressing flood vulnerabilities. To achieve this requires transcending generic participatory mechanisms to use frameworks that encourage genuine participation and partnerships using coproduction.Originality/valueThis paper engages both the inner city and peri-urban areas of Dhaka to extend current conversations on the various conditions underlying flood impact to offer entry points for integrated flood management interventions at the microlevel. This paper contributes to fill the research gap in Dhaka where very few studies have examined flood damages to residential buildings and its driving factors at the neighborhood level.
Supporting students with coaching or training depending on their basic psychological needs
Authors: Diller Sandra Julia , Muehlberger Christina , Braumandl Isabell , Jonas Eva 
Published: December 2020

PurposeThis study aims to investigate how university students' basic psychological needs (autonomy, competence and relatedness) determine whether coaching or training is more supportive for them.Design/methodology/approachReal-life coaching (N1 = 110) and training (N2 = 176) processes with students as clients were examined, measuring the students' needs before the coaching/training, their need fulfilment after the coaching/training and their satisfaction and goal attainment/intrinsic motivation after the coaching/training.FindingsThe results show that university students with a higher autonomy need had this need fulfilled to a greater extent through coaching, while university students with a higher competence need had this need fulfilled to a greater extent through training.Research limitations/implicationsThe research focused on university students and was conducted at German-speaking universities, so it is unclear to what extent the findings are transferable to other contexts. In addition, future research is needed to further compare other personal development tools, such as mentoring or consulting.Practical implicationsThe results depict the relevance of the most appropriate personal development tool (coaching or training) depending on students' needs. Furthermore, coaches should be autonomy-supportive, while trainers should be competence-supportive.Originality/valueSupporting students with the most appropriate personal development tool is essential for the effectiveness of this tool. Thus, the personal development tool used should reflect students' needs: students with a high autonomy need should receive coaching, while students with a high competence need should receive training.