bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inhibition of CSF1R, a receptor involved in microglia viability, alters behavioral and molecular changes induced by cocaine
Authors: da Silva Maria Carolina Machado , Gomes Giovanni Freitas , de Barros Fernandes Heliana , da Silva Aristóbolo Mendes , Teixeira Antônio Lúcio , Moreira Fabrício A. , de Miranda Aline Silva , de Oliveira Antônio Carlos Pinheiro 
Published: August 2021

AbstractDifferent data suggest that microglia may participate in the drug addiction process as these cells respond to neurochemical changes induced by the administration of these substances. In order to study the role of microglia in drug abuse, Swiss mice aged 8–9 weeks were treated with the CSF1R inhibitor PLX3397 (40 mg/kg, p.o.) and submitted to behavioral sensitization or conditioned place preference (CPP) induced by cocaine (15 mg/kg, i.p.). Thereafter, brains were used to evaluate the effects of CSF1R inhibition and cocaine administration on morphological, biochemical and molecular changes. CSF1R inhibition attenuated behavioral sensitization, reduced the number of Iba-1+ cells and increased ramification and lengths of the branches in the remaining microglia. Additionally, both cocaine and PLX3397 increased the cell body to total cell size ratio of Iba-1+ cells, as well as CD68+ and GFAP+ stained areas, suggesting an activated pattern of the glial cells. Besides, CSF1R inhibition increased CX3CL1 levels in the striatum, prefrontal cortex and hippocampus, as well as reduced CX3CR1 expression in the hippocampus. In this region, cocaine also reduced BDNF levels, an effect that was enhanced by CSF1R inhibition. In summary, our results suggest that microglia participate in the behavioral and molecular changes induced by cocaine. This study contributes to the understanding of the role of microglia in cocaine addiction.
Mutational patterns and clonal evolution from diagnosis to relapse in pediatric acute lymphoblastic leukemia
Authors: Sayyab Shumaila , Lundmark Anders , Larsson Malin , Ringnér Markus , Nystedt Sara , Marincevic-Zuniga Yanara , Tamm Katja Pokrovskaja , Abrahamsson Jonas , Fogelstrand Linda , Heyman Mats , Norén-Nyström Ulrika , Lönnerholm Gudmar , Harila-Saari Arja , Berglund Eva C. , Nordlund Jessica , Syvänen Ann-Christine 
Published: August 2021

AbstractThe mechanisms driving clonal heterogeneity and evolution in relapsed pediatric acute lymphoblastic leukemia (ALL) are not fully understood. We performed whole genome sequencing of samples collected at diagnosis, relapse(s) and remission from 29 Nordic patients. Somatic point mutations and large-scale structural variants were called using individually matched remission samples as controls, and allelic expression of the mutations was assessed in ALL cells using RNA-sequencing. We observed an increased burden of somatic mutations at relapse, compared to diagnosis, and at second relapse compared to first relapse. In addition to 29 known ALL driver genes, of which nine genes carried recurrent protein-coding mutations in our sample set, we identified putative non-protein coding mutations in regulatory regions of seven additional genes that have not previously been described in ALL. Cluster analysis of hundreds of somatic mutations per sample revealed three distinct evolutionary trajectories during ALL progression from diagnosis to relapse. The evolutionary trajectories provide insight into the mutational mechanisms leading relapse in ALL and could offer biomarkers for improved risk prediction in individual patients.
Elimination of glutamatergic transmission from Hb9 interneurons does not impact treadmill locomotion
Authors: Koronfel Lina M. , Kanning Kevin C. , Alcos Angelita , Henderson Christopher E. , Brownstone Robert M. 
Published: August 2021

AbstractThe spinal cord contains neural circuits that can produce the rhythm and pattern of locomotor activity. It has previously been postulated that a population of glutamatergic neurons, termed Hb9 interneurons, contributes to locomotor rhythmogenesis. These neurons were identified by their expression of the homeobox gene, Hb9, which is also expressed in motor neurons. We developed a mouse line in which Cre recombinase activity is inducible in neurons expressing Hb9. We then used this line to eliminate vesicular glutamate transporter 2 from Hb9 interneurons, and found that there were no deficits in treadmill locomotion. We conclude that glutamatergic neurotransmission by Hb9 interneurons is not required for locomotor behaviour. The role of these neurons in neural circuits remains elusive.
Understanding nutrient imbalances in maize (Zea mays L.) using the diagnosis and recommendation integrated system (DRIS) approach in the Maize belt of Nigeria
Authors: Aliyu Kamaluddin T. , Huising Jeroen , Kamara Alpha Y. , Jibrin Jibrin M. , Mohammed Ibrahim B. , Nziguheba Generose , Adam Adam M. , Vanlauwe Bernard 
Published: August 2021

AbstractLow nutrient use efficiency in maize as a result of imbalanced nutrition has been reported to drastically reduce yield. We implemented a nutrient omission experiment to assess the effect of nutrient application on maize yield and nutritional balance. Maize ear leaves were analyzed for nutrients, to identify nutrient balance status using the Diagnostic and Recommendation Integrated System (DRIS) approach. Results indicated that omission of N or P resulted in highly imbalanced DRIS indices respectively, and significantly lower grain yield. A strong inverse relationship between K ear leaf content with DRIS index suggests that K application negatively increases K imbalance in many situations. Imbalances of Mg, Ca and Cu were more associated with higher yielding treatments. A Which-Won-Where result show that nutrient imbalances in the diagnosis were systematically frequent when N was omitted. All the diagnosed nutrients were imbalanced even under the highest yielding NPKZn treatment; indicating further opportunity for yield increase with more balanced nutrition. Balanced nutrition of maize in the maize belt of Nigeria should target application of varying rates of N, P, K, Mg, S and Zn, depending on the soil conditions. But, because of complexities of nutrient interactions during uptake, it is hardly possible to realize a balanced nutrition. However, differentiating the application of antagonistic nutrients into foliar or soil-based methods is recommended for a more balanced maize nutrition.
Aflatoxins are natural scavengers of reactive oxygen species
Authors: Finotti E. , Parroni A. , Zaccaria M. , Domin M. , Momeni B. , Fanelli C. , Reverberi M. 
Published: August 2021

AbstractThe role of aflatoxins (AFs) in the biology of producing strains, Aspergillus sect. Flavi, is still a matter of debate. Over recent years, research has pointed to how environmental factors altering the redox balance in the fungal cell can switch on the synthesis of AF. Notably, it has been known for decades that oxidants promote AF synthesis. More recent evidence has indicated that AF synthesis is controlled at the transcriptional level: reactive species that accumulate in fungal cells in the stationary growth phase modulate the expression of aflR, the main regulator of AF synthesis—through the oxidative stress related transcription factor AP-1. Thus, AFs are largely synthesized and secreted when (i) the fungus has exploited most nutritional resources; (ii) the hyphal density is high; and (iii) reactive species are abundant in the environment. In this study, we show that AFs efficiently scavenge peroxides and extend the lifespan of E. coli grown under oxidative stress conditions. We hypothesize a novel role for AF as an antioxidant and suggest its biological purpose is to extend the lifespan of AFs-producing strains of Aspergillus sect. Flavi under highly oxidizing conditions such as when substrate resources are depleted, or within a host.
Suppression of top-down influence decreases neuronal excitability and contrast sensitivity in the V1 cortex of cat
Authors: Ding Jian , Hu Xiangmei , Xu Fei , Yu Hao , Ye Zheng , Zhang Shen , Pan Huijun , Pan Deng , Tu Yanni , Zhang Qiuyu , Sun Qingyan , Hua Tianmiao 
Published: August 2021

AbstractHow top-down influence affects neuronal activity and information encoding in the primary visual cortex (V1) remains elusive. This study examined changes of neuronal excitability and contrast sensitivity in cat V1 cortex after top-down influence of area 7 (A7) was modulated by transcranial direct current stimulation (tDCS). The neuronal excitability in V1 cortex was evaluated by visually evoked field potentials (VEPs), and contrast sensitivity (CS) was assessed by the inverse of threshold contrast of neurons in response to visual stimuli at different performance accuracy. We found that the amplitude of VEPs in V1 cortex lowered after top-down influence suppression with cathode-tDCS in A7, whereas VEPs in V1 did not change after sham-tDCS in A7 and nonvisual cortical area 5 (A5) or cathode-tDCS in A5 and lesioned A7. Moreover, the mean CS of V1 neurons decreased after cathode-tDCS but not sham-tDCS in A7, which could recover after tDCS effect vanished. Comparisons of neuronal contrast-response functions showed that cathode-tDCS increased the stimulus contrast required to generate the half-maximum response, with a weakly-correlated reduction in maximum response but not baseline response. Therefore, top-down influence of A7 enhanced neuronal excitability in V1 cortex and improved neuronal contrast sensitivity by both contrast gain and response gain.
Development of robust isothermal RNA amplification assay for lab-free testing of RNA viruses
Authors: Biyani Radhika , Sharma Kirti , Kojima Kenji , Biyani Madhu , Sharma Vishnu , Kumawat Tarun , Juma Kevin Maafu , Yanagihara Itaru , Fujiwara Shinsuke , Kodama Eiichi , Takamura Yuzuru , Takagi Masahiro , Yasukawa Kiyoshi , Biyani Manish 
Published: August 2021

AbstractSimple tests of infectiousness that return results in minutes and directly from samples even with low viral loads could be a potential game-changer in the fight against COVID-19. Here, we describe an improved isothermal nucleic acid amplification assay, termed the RICCA (RNAIsothermalCo-assisted andCoupledAmplification) reaction, that consists of a simple one-pot format of ‘sample-in and result-out’ with a primary focus on the detection of low copy numbers of RNA virus directly from saliva without the need for laboratory processing. We demonstrate our assay by detecting 16S rRNA directly fromE. colicells with a sensitivity as low as 8 CFU/μL and RNA fragments from a synthetic template of SARS-CoV-2 with a sensitivity as low as 1740 copies/μL. We further demonstrate the applicability of our assay for real-time testing at the point of care by designing a closed format for paper-based lateral flow assay and detecting heat-inactivated SARS-COV-2 virus in human saliva at concentrations ranging from 28,000 to 2.8 copies/μL with a total assay time of 15–30 min.
Fully-automated root image analysis (faRIA)
Authors: Narisetti Narendra , Henke Michael , Seiler Christiane , Junker Astrid , Ostermann Jörn , Altmann Thomas , Gladilin Evgeny 
Published: August 2021

AbstractHigh-throughput root phenotyping in the soil became an indispensable quantitative tool for the assessment of effects of climatic factors and molecular perturbation on plant root morphology, development and function. To efficiently analyse a large amount of structurally complex soil-root images advanced methods for automated image segmentation are required. Due to often unavoidable overlap between the intensity of fore- and background regions simple thresholding methods are, generally, not suitable for the segmentation of root regions. Higher-level cognitive models such as convolutional neural networks (CNN) provide capabilities for segmenting roots from heterogeneous and noisy background structures, however, they require a representative set of manually segmented (ground truth) images. Here, we present a GUI-based tool for fully automated quantitative analysis of root images using a pre-trained CNN model, which relies on an extension of the U-Net architecture. The developed CNN framework was designed to efficiently segment root structures of different size, shape and optical contrast using low budget hardware systems. The CNN model was trained on a set of 6465 masks derived from 182 manually segmented near-infrared (NIR) maize root images. Our experimental results show that the proposed approach achieves a Dice coefficient of 0.87 and outperforms existing tools (e.g., SegRoot) with Dice coefficient of 0.67 by application not only to NIR but also to other imaging modalities and plant species such as barley and arabidopsis soil-root images from LED-rhizotron and UV imaging systems, respectively. In summary, the developed software framework enables users to efficiently analyse soil-root images in an automated manner (i.e. without manual interaction with data and/or parameter tuning) providing quantitative plant scientists with a powerful analytical tool.
Mortality and risk factors associated with pulmonary embolism in coronavirus disease 2019 patients: a systematic review and meta-analysis
Authors: Gómez Carlos Andrés , Sun Cheuk-Kwan , Tsai I-Ting , Chang Yang-Pei , Lin Ming-Chung , Hung I-Yin , Chang Ying-Jen , Wang Li-Kai , Lin Yao-Tsung , Hung Kuo-Chuan 
Published: August 2021

AbstractTo determine, in patients with coronavirus disease 2019 (COVID-19) infection, the associations of pulmonary embolism (PE) with mortality and risk factors for PE as well as the therapeutic benefit of anticoagulant prophylaxis. Embase, PubMed, Cochrane controlled trials register, and Web of Science databases were searched from inception to October 10, 2020. We included all published trials on PE in patients diagnosed with COVID-19 with eligibility of the trials assessed following the PRISMA guidelines. Sixteen clinical trials with 5826 patients were eligible. There were significant associations of PE with the male gender [odd ratio (OR) = 1.59, 95% CI 1.28–1.97], mechanical ventilation (OR = 3.71, 95% CI 2.57–5.36), intensive care unit admission (OR = 2.99, 95% CI 2.11–4.23), circulating D-dimer [mean difference (MD) = 5.04 µg/mL, 95% CI 3.67–6.42) and CRP (MD = 1.97 mg/dL, 95% CI 0.58– 3.35) concentrations without significant correlation between PE and mortality (OR = 1.31, 95% CI 0.82–2.08) as well as other parameters or comorbidities. After omitting one trial with strict patient selection criteria for anticoagulant prophylaxis, significant prophylactic benefit was noted (OR = 0.31, 95% CI 0.1–0.91). Our findings identified the risk factors associated with PE in COVID-19 patients and supported the therapeutic benefit of anticoagulant prophylaxis against PE in this patient population.
Support vector machine and deep-learning object detection for localisation of hard exudates
Authors: Kurilová Veronika , Goga Jozef , Oravec Miloš , Pavlovičová Jarmila , Kajan Slavomír 
Published: August 2021

AbstractHard exudates are one of the main clinical findings in the retinal images of patients with diabetic retinopathy. Detecting them early significantly impacts the treatment of underlying diseases; therefore, there is a need for automated systems with high reliability. We propose a novel method for identifying and localising hard exudates in retinal images. To achieve fast image pre-scanning, a support vector machine (SVM) classifier was combined with a faster region-based convolutional neural network (faster R-CNN) object detector for the localisation of exudates. Rapid pre-scanning filtered out exudate-free samples using a feature vector extracted from the pre-trained ResNet-50 network. Subsequently, the remaining samples were processed using a faster R-CNN detector for detailed analysis. When evaluating all the exudates as individual objects, the SVM classifier reduced the false positive rate by 29.7% and marginally increased the false negative rate by 16.2%. When evaluating all the images, we recorded a 50% reduction in the false positive rate, without any decrease in the number of false negatives. The interim results suggested that pre-scanning the samples using the SVM prior to implementing the deep-network object detector could simultaneously improve and speed up the current hard exudates detection method, especially when there is paucity of training data.
Effect of saliva fluid properties on pathogen transmissibility
Authors: Reyes Jonathan , Fontes Douglas , Bazzi Alexander , Otero Michelle , Ahmed Kareem , Kinzel Michael 
Published: August 2021

AbstractWith an increasing body of evidence that SARS-CoV-2 is an airborne pathogen, droplet character formed during speech, coughs, and sneezes are important. Larger droplets tend to fall faster and are less prone to drive the airborne transmission pathway. Alternatively, small droplets (aerosols) can remain suspended for long time periods. The small size of SARS-CoV-2 enables it to be encapsulated in these aerosols, thereby increasing the pathogen’s ability to be transmitted via airborne paths. Droplet formation during human respiratory events relates to airspeed (speech, cough, sneeze), fluid properties of the saliva/mucus, and the fluid content itself. In this work, we study the fluidic drivers (fluid properties and content) and their influence on factors relating to transmissibility. We explore the relationship between saliva fluid properties and droplet airborne transmission paths. Interestingly, the natural human response appears to potentially work with these drivers to mitigate pathogen transmission. In this work, the saliva is varied using two approaches: (1) modifying the saliva with colloids that increase the viscosity/surface tension, and (2) stimulating the saliva content to increased/decreased levels. Through modern experimental and numerical flow diagnostic methods, the character, content, and exposure to droplets and aerosols are all evaluated. The results indicate that altering the saliva properties can significantly impact the droplet size distribution, the formation of aerosols, the trajectory of the bulk of the droplet plume, and the exposure (or transmissibility) to droplets. High-fidelity numerical methods used and verify that increased droplet size character enhances droplet fallout. In the context of natural saliva response, we find previous studies indicating natural human responses of increased saliva viscosity from stress and reduced saliva content from either stress or illness. These responses both favorably correspond to reduced transmissibility. Such a finding also relates to potential control methods, hence, we compared results to a surgical mask. In general, we find that saliva alteration can produce fewer and larger droplets with less content and aerosols. Such results indicate a novel approach to alter SARS-CoV-2’s transmission path and may act as a way to control the COVID-19 pandemic, as well as influenza and the common cold.
Genotypic identification of Panicum spp. in New South Wales, Australia using DNA barcoding
Authors: Chen Yuchi , Zhu Xiaocheng , Loukopoulos Panayiotis , Weston Leslie A. , Albrecht David E. , Quinn Jane C. 
Published: August 2021

AbstractAustralia has over 30 Panicum spp. (panic grass) including several non-native species that cause crop and pasture loss and hepatogenous photosensitisation in livestock. It is critical to correctly identify them at the species level to facilitate the development of appropriate management strategies for efficacious control of Panicum grasses in crops, fallows and pastures. Currently, identification of Panicum spp. relies on morphological examination of the reproductive structures, but this approach is only useful for flowering specimens and requires significant taxonomic expertise. To overcome this limitation, we used multi-locus DNA barcoding for the identification of ten selected Panicum spp. found in Australia. With the exception of P. buncei, other native Australian Panicum were genetically separated at the species level and distinguished from non-native species. One nuclear (ITS) and two chloroplast regions (matK and trnL intron-trnF) were identified with varying facility for DNA barcode separation of the Panicum species. Concatenation of sequences from ITS, matK and trnL intron-trnF regions provided clear separation of eight regionally collected species, with a maximum intraspecific distance of 0.22% and minimum interspecific distance of 0.33%. Two of three non-native Panicum species exhibited a smaller genome size compared to native species evaluated, and we speculate that this may be associated with biological advantages impacting invasion of non-native Panicum species in novel locations. We conclude that multi-locus DNA barcoding, in combination with traditional taxonomic identification, provides an accurate and cost-effective adjunctive tool for further distinguishing Panicum spp. at the species level.
Structural network topology and microstructural alterations of the anterior insula associate with cognitive and affective impairment in Parkinson’s disease
Authors: Jonkman L. E. , Fathy Y. Y. , Berendse H. W. , Schoonheim M. M. , van de Berg W. D. J. 
Published: August 2021

AbstractThe aim of the current study was to assess the structural centrality and microstructural integrity of the cortical hubs of the salience network, the anterior insular cortex (AIC) subregions and anterior cingulate cortex (ACC), and their relationship to cognitive and affective impairment in PD. MRI of 53 PD patients and 15 age-matched controls included 3D-T1 for anatomical registration, and diffusion tensor imaging for probabilistic tractography. Network topological measures of eigenvector and betweenness centrality were calculated for ventral (vAI) and dorsal (dAI) AIC. Microstructural tract integrity between vAI, dAI and the ACC was quantified with fractional anisotrophy (FA) and mean diffusivity (MD). Structural integrity and connectivity were related to cognitive and affective scores. The dAI had significantly higher eigenvector centrality in PD than controls (p < 0.01), associated with higher depression scores (left dAI only, rs = 0.28, p < 0.05). Tracts between dAI and ACC showed lower FA and higher MD in PD (p < 0.05), and associated with lower semantic fluency, working memory and executive functioning, and higher anxiety scores (range 0.002 < p < 0.05). This study provides evidence for clinically relevant structural damage to the cortical hubs of the salience network in PD, possibly due to extensive local neuropathology and loss of interconnecting AIC-ACC tracts.
Customized eye modeling for optical quality assessment in myopic femto-LASIK surgery
Authors: Lan Gongpu , Zeng Jun , Li Wenjie , Ma Guoqin , Shi Qun , Shi Yue , Wang Yicheng , Xu Jingjiang , Huang Yanping , Qin Jia , Feng Jinping , Tan Haishu , An Lin , Wei Xunbin 
Published: August 2021

AbstractRefractive surgery is recognized as an effective method for myopia treatment, but it can induce night vision disturbances such as glare. We present an eye modeling method for the optical quality assessment in response to the structural changes in the eyes by femto-LASIK surgery. Customized eye models were built from the measurements of 134 right eyes pre- and post-operatively. Optical performance was evaluated using spot diagrams, point spread functions (PSFs), modulation transfer functions (MTFs), and chromatic aberrations at various fields (0°–30°), different pupil diameters (2–6 mm), and initial myopias (− 1.25 to − 10.5 D). Pupil size and initial myopia are the two major factors that affect visual performance of post-operative eyes. The results of spot diagrams, PSFs, and MTFs indicated that post-operative visual performance deteriorated as the visual field and pupil size increased, and it was significantly influenced by initial myopia. Post-operative chromatic aberrations were also affected by initial myopia. As pupil size increased, the post-operative longitudinal chromatic aberrations tended to decrease slightly, while the transverse chromatic aberrations remained similar. The use of eye modeling for refractive surgery assessment could possibly provide a more personalized surgical approach, could improve the prediction accuracy of refractive surgery outcomes, and promote the invention and development of better surgical methods.