bluuebunny/crossref_metadata_2025_split huggingface dataset:
Light exposure mediates circadian rhythms of rhizosphere microbial communities
Authors: Zhao Kankan , Ma Bin , Xu Yan , Stirling Erinne , Xu Jianming 
Published: March 2021

Abstract
Microbial community circadian rhythms have a broad influence on host health and even though light-induced environmental fluctuations could regulate microbial communities, the contribution of light to the circadian rhythms of rhizosphere microbial communities has received little attention. To address this gap, we monitored diel changes in the microbial communities in rice (Oryza sativa L.) rhizosphere soil under light–dark and constant dark regimes, identifying microbes with circadian rhythms caused by light exposure and microbial circadian clocks, respectively. While rhizosphere microbial communities displayed circadian rhythms under light–dark and constant dark regimes, taxa possessing circadian rhythms under the two conditions were dissimilar. Light exposure concealed microbial circadian clocks as a regulatory driver, leading to fewer ecological niches in light versus dark communities. These findings disentangle regulation mechanisms for circadian rhythms in the rice rhizosphere microbial communities and highlight the role of light-induced regulation of rhizosphere microbial communities.
The soil microbial food web revisited: Predatory myxobacteria as keystone taxa?
Authors: Petters Sebastian , Groß Verena , Söllinger Andrea , Pichler Michelle , Reinhard Anne , Bengtsson Mia Maria , Urich Tim 
Published: March 2021

Abstract
Trophic interactions are crucial for carbon cycling in food webs. Traditionally, eukaryotic micropredators are considered the major micropredators of bacteria in soils, although bacteria like myxobacteria and Bdellovibrio are also known bacterivores. Until recently, it was impossible to assess the abundance of prokaryotes and eukaryotes in soil food webs simultaneously. Using metatranscriptomic three-domain community profiling we identified pro- and eukaryotic micropredators in 11 European mineral and organic soils from different climes. Myxobacteria comprised 1.5–9.7% of all obtained SSU rRNA transcripts and more than 60% of all identified potential bacterivores in most soils. The name-giving and well-characterized predatory bacteria affiliated with the Myxococcaceae were barely present, while Haliangiaceae and Polyangiaceae dominated. In predation assays, representatives of the latter showed prey spectra as broad as the Myxococcaceae. 18S rRNA transcripts from eukaryotic micropredators, like amoeba and nematodes, were generally less abundant than myxobacterial 16S rRNA transcripts, especially in mineral soils. Although SSU rRNA does not directly reflect organismic abundance, our findings indicate that myxobacteria could be keystone taxa in the soil microbial food web, with potential impact on prokaryotic community composition. Further, they suggest an overlooked, yet ecologically relevant food web module, independent of eukaryotic micropredators and subject to separate environmental and evolutionary pressures.
Minimally invasive supratentorial neurosurgical approaches guided by Smartphone app and compass
Authors: Fernandes de Oliveira Santos Bruno , de Araujo Paz Daniel , Fernandes Victor Miranda , dos Santos José Calasans , Chaddad-Neto Feres Eduardo Aparecido , Sousa Antonio Carlos Sobral , Oliveira Joselina Luzia Menezes 
Published: March 2021

AbstractThe precise location in the scalp of specifically planned points can help to achieve less invasive approaches. This study aims to develop a smartphone app, evaluate the precision and accuracy of the developed tool, and describe a series of cases using the referred technique. The application was developed with the React Native framework for Android and iOS. A phantom was printed based on the patient's CT scan, which was used for the calculation of accuracy and precision of the method. The points of interest were marked with an "x" on the patient's head, with the aid of the app and a compass attached to a skin marker pen. Then, two experienced neurosurgeons checked the plausibility of the demarcations based on the anatomical references. Both evaluators marked the frontal, temporal and parietal targets with a difference of less than 5 mm from the corresponding intended point, in all cases. The overall average accuracy observed was 1.6 ± 1.0 mm. The app was used in the surgical planning of trepanations for ventriculoperitoneal (VP) shunts and for drainage of abscesses, and in the definition of craniotomies for meningiomas, gliomas, brain metastases, intracranial hematomas, cavernomas, and arteriovenous malformation. The sample consisted of 88 volunteers who exhibited the following pathologies: 41 (46.6%) had brain tumors, 17 (19.3%) had traumatic brain injuries, 16 (18.2%) had spontaneous intracerebral hemorrhages, 2 (2.3%) had cavernomas, 1 (1.1%) had arteriovenous malformation (AVM), 4 (4.5%) had brain abscesses, and 7 (7.9%) had a VP shunt placement. In cases approached by craniotomy, with the exception of AVM, straight incisions and minicraniotomy were performed. Surgical planning with the aid of the NeuroKeypoint app is feasible and reliable. It has enabled neurological surgeries by craniotomy and trepanation in an accurate, precise, and less invasive manner.
Versatile knowledge guided network inference method for prioritizing key regulatory factors in multi-omics data
Authors: Ogris Christoph , Hu Yue , Arloth Janine , Müller Nikola S. 
Published: March 2021

AbstractConstantly decreasing costs of high-throughput profiling on many molecular levels generate vast amounts of multi-omics data. Studying one biomedical question on two or more omic levels provides deeper insights into underlying molecular processes or disease pathophysiology. For the majority of multi-omics data projects, the data analysis is performed level-wise, followed by a combined interpretation of results. Hence the full potential of integrated data analysis is not leveraged yet, presumably due to the complexity of the data and the lacking toolsets. We propose a versatile approach, to perform a multi-level fully integrated analysis: The Knowledge guIded Multi-Omics Network inference approach, KiMONo (https://github.com/cellmapslab/kimono). KiMONo performs network inference by using statistical models for combining omics measurements coupled to a powerful knowledge-guided strategy exploiting prior information from existing biological sources. Within the resulting multimodal network, nodes represent features of all input types e.g. variants and genes while edges refer to knowledge-supported and statistically derived associations. In a comprehensive evaluation, we show that our method is robust to noise and exemplify the general applicability to the full spectrum of multi-omics data, demonstrating that KiMONo is a powerful approach towards leveraging the full potential of data sets for detecting biomarker candidates.
Predictive olfactory learning in Drosophila
Authors: Zhao Chang , Widmer Yves F. , Diegelmann Sören , Petrovici Mihai A. , Sprecher Simon G. , Senn Walter 
Published: March 2021

AbstractOlfactory learning and conditioning in the fruit fly is typically modelled by correlation-based associative synaptic plasticity. It was shown that the conditioning of an odor-evoked response by a shock depends on the connections from Kenyon cells (KC) to mushroom body output neurons (MBONs). Although on the behavioral level conditioning is recognized to be predictive, it remains unclear how MBONs form predictions of aversive or appetitive values (valences) of odors on the circuit level. We present behavioral experiments that are not well explained by associative plasticity between conditioned and unconditioned stimuli, and we suggest two alternative models for how predictions can be formed. In error-driven predictive plasticity, dopaminergic neurons (DANs) represent the error between the predictive odor value and the shock strength. In target-driven predictive plasticity, the DANs represent the target for the predictive MBON activity. Predictive plasticity in KC-to-MBON synapses can also explain trace-conditioning, the valence-dependent sign switch in plasticity, and the observed novelty-familiarity representation. The model offers a framework to dissect MBON circuits and interpret DAN activity during olfactory learning.
Mining The Cancer Genome Atlas gene expression data for lineage markers in distinguishing bladder urothelial carcinoma and prostate adenocarcinoma
Authors: Ch’ng Ewe Seng 
Published: March 2021

AbstractDistinguishing bladder urothelial carcinomas from prostate adenocarcinomas for poorly differentiated carcinomas derived from the bladder neck entails the use of a panel of lineage markers to help make this distinction. Publicly available The Cancer Genome Atlas (TCGA) gene expression data provides an avenue to examine utilities of these markers. This study aimed to verify expressions of urothelial and prostate lineage markers in the respective carcinomas and to seek the relative importance of these markers in making this distinction. Gene expressions of these markers were downloaded from TCGA Pan-Cancer database for bladder and prostate carcinomas. Differential gene expressions of these markers were analyzed. Standard linear discriminant analyses were applied to establish the relative importance of these markers in lineage determination and to construct the model best in making the distinction. This study shows that all urothelial lineage genes except for the gene for uroplakin III were significantly expressed in bladder urothelial carcinomas (p < 0.001). In descending order of importance to distinguish from prostate adenocarcinomas, genes for uroplakin II, S100P, GATA3 and thrombomodulin had high discriminant loadings (> 0.3). All prostate lineage genes were significantly expressed in prostate adenocarcinomas(p < 0.001). In descending order of importance to distinguish from bladder urothelial carcinomas, genes for NKX3.1, prostate specific antigen (PSA), prostate-specific acid phosphatase, prostein, and prostate-specific membrane antigen had high discriminant loadings (> 0.3). Combination of gene expressions for uroplakin II, S100P, NKX3.1 and PSA approached 100% accuracy in tumor classification both in the training and validation sets. Mining gene expression data, a combination of four lineage markers helps distinguish between bladder urothelial carcinomas and prostate adenocarcinomas.
Poliovirus-nonsusceptible Vero cell line for the World Health Organization global action plan
Authors: Okemoto-Nakamura Yuko , Someya Kenji , Yamaji Toshiyuki , Saito Kyoko , Takeda Makoto , Hanada Kentaro 
Published: March 2021

AbstractPolio or poliomyelitis is a disabling and life-threatening disease caused by poliovirus (PV). As a consequence of global polio vaccination efforts, wild PV serotypes 2 and 3 have been eradicated around the world, and wild PV serotype 1-transmitted cases have been largely eliminated except for limited regions. However, vaccine-derived PV, pathogenically reverted live PV vaccine strains, has become a serious issue. For the global eradication of polio, the World Health Organization is conducting the third edition of the Global Action Plan, which is requesting stringent control of potentially PV-infected materials. To facilitate the mission, we generated a PV-nonsusceptible Vero cell subline, which may serve as an ideal replacement of standard Vero cells to isolate emerging/re-emerging viruses without the risk of generating PV-infected materials.
Long read, isoform aware sequencing of mouse nucleus accumbens after chronic cocaine treatment
Authors: Estill Molly , Ribeiro Efrain , Francoeur Nancy J. , Smith Melissa L. , Sebra Robert , Yeh Szu-Ying , Cunningham Ashley M. , Nestler Eric J. , Shen Li 
Published: March 2021

AbstractTo better understand the full-length transcriptome of the nucleus accumbens (NAc)—a key brain reward region—in chronic cocaine treatment, we perform the first single molecule, long-read sequencing analysis using the Iso-seq method to detect 42,114 unique transcripts from mouse NAc polyadenylated RNA. Using GENCODE annotation as a reference, we find that over half of the Iso-seq derived transcripts are annotated, while 46% of them harbor novel splicing events in known genes; around 1% of them correspond to other types of novel transcripts, such as fusion, antisense and intergenic. Approximately 34% of the novel transcripts are matched with a compiled transcriptome assembled from published short-read data from various tissues, with the remaining 69% being unique to NAc. These data provide a more complete picture of the NAc transcriptome than existing annotations and can serve as a comprehensive reference for future transcriptomic analyses of this important brain reward region.
Relaxation damage control via fatigue-hydraulic fracturing in granitic rock as inferred from laboratory-, mine-, and field-scale experiments
Authors: Zang Arno , Zimmermann Günter , Hofmann Hannes , Niemz Peter , Kim Kwang Yeom , Diaz Melvin , Zhuang Li , Yoon Jeoung Seok 
Published: March 2021

AbstractThe ability to control induced seismicity in energy technologies such as geothermal heat and shale gas is an important factor in improving the safety and reducing the seismic hazard of reservoirs. As fracture propagation can be unavoidable during energy extraction, we propose a new approach that optimises the radiated seismicity and hydraulic energy during fluid injection by using cyclic- and pulse-pumping schemes. We use data from laboratory-, mine-, and field-scale injection experiments performed in granitic rock and observe that both the seismic energy and the permeability-enhancement process strongly depend on the injection style and rock type. Replacing constant-flow-rate schemes with cyclic pulse injections with variable flow rates (1) lowers the breakdown pressure, (2) modifies the magnitude-frequency distribution of seismic events, and (3) has a fundamental impact on the resulting fracture pattern. The concept of fatigue hydraulic fracturing serves as a possible explanation for such rock behaviour by making use of depressurisation phases to relax crack-tip stresses. During hydraulic fatigue, a significant portion of the hydraulic energy is converted into rock damage and fracturing. This finding may have significant implications for managing the economic and physical risks posed to communities affected by fluid-injection-induced seismicity.
The encoding of stochastic regularities is facilitated by action-effect predictions
Authors: Korka Betina , Schröger Erich , Widmann Andreas 
Published: March 2021

AbstractOur brains continuously build and update predictive models of the world, sources of prediction being drawn for example from sensory regularities and/or our own actions. Yet, recent results in the auditory system indicate that stochastic regularities may not be easily encoded when a rare medium pitch deviant is presented between frequent high and low pitch standard sounds in random order, as reflected in the lack of sensory prediction error event-related potentials [i.e., mismatch negativity (MMN)]. We wanted to test the implication of the predictive coding theory that predictions based on higher-order generative models—here, based on action intention, are fed top-down in the hierarchy to sensory levels. Participants produced random sequences of high and low pitch sounds by button presses in two conditions: In a “specific” condition, one button produced high and the other low pitch sounds; in an “unspecific” condition, both buttons randomly produced high or low-pitch sounds. Rare medium pitch deviants elicited larger MMN and N2 responses in the “specific” compared to the “unspecific” condition, despite equal sound probabilities. These results thus demonstrate that action-effect predictions can boost stochastic regularity-based predictions and engage higher-order deviance detection processes, extending previous notions on the role of action predictions at sensory levels.
Uncovering genomic regions controlling plant architectural traits in hexaploid wheat using different GWAS models
Authors: Muhammad Ali , Li Jianguo , Hu Weichen , Yu Jinsheng , Khan Shahid Ullah , Khan Muhammad Hafeez Ullah , Xie Guosheng , Wang Jibin , Wang Lingqiang 
Published: March 2021

AbstractWheat is a major food crop worldwide. The plant architecture is a complex trait mostly influenced by plant height, tiller number, and leaf morphology. Plant height plays a crucial role in lodging and thus affects yield and grain quality. In this study, a wheat population was genotyped by using Illumina iSelect 90K single nucleotide polymorphism (SNP) assay and finally 22,905 high-quality SNPs were used to perform a genome-wide association study (GWAS) for plant architectural traits employing four multi-locus GWAS (ML-GWAS) and three single-locus GWAS (SL-GWAS) models. As a result, 174 and 97 significant SNPs controlling plant architectural traits were detected by ML-GWAS and SL-GWAS methods, respectively. Among these SNP makers, 43 SNPs were consistently detected, including seven across multiple environments and 36 across multiple methods. Interestingly, five SNPs (Kukri_c34553_89, RAC875_c8121_1490, wsnp_Ex_rep_c66315_64480362, Ku_c5191_340, and tplb0049a09_1302) consistently detected across multiple environments and methods, played a role in modulating both plant height and flag leaf length. Furthermore, candidate SNPs (BS00068592_51, Kukri_c4750_452 and BS00022127_51) constantly repeated in different years and methods associated with flag leaf width and number of tillers. We also detected several SNPs (Jagger_c6772_80, RAC875_c8121_1490, BS00089954_51, Excalibur_01167_1207, and Ku_c5191_340) having common associations with more than one trait across multiple environments. By further appraising these GWAS methods, the pLARmEB and FarmCPU models outperformed in SNP detection compared to the other ML-GWAS and SL-GWAS methods, respectively. Totally, 152 candidate genes were found to be likely involved in plant growth and development. These finding will be helpful for better understanding of the genetic mechanism of architectural traits in wheat.
Strain-induced yellow to blue emission tailoring of axial InGaN/GaN quantum wells in GaN nanorods synthesized by nanoimprint lithography
Authors: Avit Geoffrey , Robin Yoann , Liao Yaqiang , Nan Hu , Pristovsek Markus , Amano Hiroshi 
Published: March 2021

AbstractGaN nanorods (NRds) with axial InGaN/GaN MQWs insertions are synthesized by an original cost-effective and large-scale nanoimprint-lithography process from an InGaN/GaN MQWs layer grown on c-sapphire substrates. By design, such NRds exhibit a single emission due to the c-axis MQWs. A systematic study of the emission of the NRds by time-resolved luminescence (TR-PL) and power dependence PL shows a diameter-controlled luminescence without significant degradation of the recombination rate thanks to the diameter-controlled strain tuning and QSCE. A blueshift up to 0.26 eV from 2.28 to 2.54 eV (543 nm to 488 nm) is observed for 3.2 nm thick InGaN/GaN QWs with an In composition of 19% when the NRds radius is reduced from 650 to 80 nm. The results are consistent with a 1-D based strain relaxation model. By combining state of the art knowledge of c-axis growth and the strong strain relieving capability of NRds, this process enables multiple and independent single-color emission from a single uniform InGaN/GaN MQWs layer in a single patterning step, then solving color mixing issue in InGaN based nanorods LED devices.
Arm movement adaptation to concurrent pain constraints
Authors: Kühn Johannes , Bagnato Carlo , Burdet Etienne , Haddadin Sami 
Published: March 2021

AbstractHow do humans coordinate their movements in order to avoid pain? This paper investigates a motor task in the presence of concurrent potential pain sources: the arm must be withdrawn to avoid a slap on the hand while avoiding an elbow obstacle with an electrical noxious stimulation. The results show that our subjects learned to control the hand retraction movement in order to avoid the potential pain. Subject-specific motor strategies were used to modify the joint movement coordination to avoid hitting the obstacle with the elbow at the cost of increasing the risk of hand slap. Furthermore, they used a conservative strategy as if assuming an obstacle in 100% of the trials.
Genetic basis and identification of candidate genes for wooden breast and white striping in commercial broiler chickens
Authors: Lake Juniper A. , Dekkers Jack C. M. , Abasht Behnam 
Published: March 2021

AbstractWooden breast (WB) and white striping (WS) are highly prevalent and economically damaging muscle disorders of modern commercial broiler chickens characterized respectively by palpable firmness and fatty white striations running parallel to the muscle fiber. High feed efficiency and rapid growth, especially of the breast muscle, are believed to contribute to development of such muscle defects; however, their etiology remains poorly understood. To gain insight into the genetic basis of these myopathies, a genome-wide association study was conducted using a commercial crossbred broiler population (n = 1193). Heritability was estimated at 0.5 for WB and WS with high genetic correlation between them (0.88). GWAS revealed 28 quantitative trait loci (QTL) on five chromosomes for WB and 6 QTL on one chromosome for WS, with the majority of QTL for both myopathies located in a ~ 8 Mb region of chromosome 5. This region has highly conserved synteny with a portion of human chromosome 11 containing a cluster of imprinted genes associated with growth and metabolic disorders such as type 2 diabetes and Beckwith-Wiedemann syndrome. Candidate genes includepotassium voltage-gated channel subfamily Q member 1(KCNQ1), involved in insulin secretion and cardiac electrical activity,lymphocyte-specific protein 1(LSP1), involved in inflammation and immune response.
Total body irradiation causes a chronic decrease in antioxidant levels
Authors: Sun Lue , Inaba Yohei , Sogo Yu , Ito Atsuo , Bekal Mahesh , Chida Koichi , Moritake Takashi 
Published: March 2021

AbstractIonizing radiation exposure may not only cause acute radiation syndrome, but also an increased risk of late effects. It has been hypothesized that induction of chronic oxidative stress mediates the late effects of ionizing radiation. However, only a few reports have analyzed changes in long-term antioxidant capacity after irradiation in vivo. Our previous study demonstrated changes in whole-blood antioxidant capacity and red blood cell (RBC) glutathione levels within 50 days after total body irradiation (TBI). In this study, seven-week-old, male, C57BL/6J mice exposed to total body irradiation by X-ray and changes in whole-blood antioxidant capacity and RBC glutathione levels at ≥ 100 days after TBI were investigated. Whole-blood antioxidant capacity was chronically decreased in the 5-Gy group. The RBC reduced glutathione (GSH) level and the GSH/oxidative glutathione (GSSG) ratio were chronically decreased after ≥ 1 Gy of TBI. Interestingly, the complete blood counts (CBC) changed less with 1-Gy exposure, suggesting that GSH and the GSH/GSSG ratio were more sensitive radiation exposure markers than whole-blood antioxidant capacity and CBC counts. It has been reported that GSH depletion is one of the triggers leading to cataracts, hypertension, and atherosclerosis, and these diseases are also known as radiation-induced late effects. The present findings further suggest that chronic antioxidant reduction may contribute to the pathogenesis of late radiation effects.