bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hierarchical imaging and computational analysis of three-dimensional vascular network architecture in the entire postnatal and adult mouse brain
Authors: Wälchli Thomas , Bisschop Jeroen , Miettinen Arttu , Ulmann-Schuler Alexandra , Hintermüller Christoph , Meyer Eric P. , Krucker Thomas , Wälchli Regula , Monnier Philippe , Carmeliet Peter , Vogel Johannes , Stampanoni Marco 
Published: October 2020

ABSTRACTThe formation of new blood vessels and the establishment of vascular networks are crucial during brain development, in the adult healthy brain, as well as in various diseases of the central nervous system (CNS). Here, we describe a method that enables hierarchical imaging and computational analysis of vascular networks in postnatal- and adult mouse brains. Resin-based vascular corrosion casting, scanning electron microscopy, synchrotron radiation and desktop µCT imaging, and computational network analysis are used. Combining these methods enables detailed visualization and quantification of the three-dimensional (3D) brain vasculature. Network features such as vascular volume fraction, branch point density, vessel diameter, - length, -tortuosity, and -directionality as well as extravascular distance can be obtained at any developmental stage from the early postnatal to the adult brain. Our method allows characterizing brain vascular networks separately for capillaries and non-capillaries.The entire protocol, from mouse perfusion to vessel network analysis, takes approximately 10 days.Online summaryThis protocol uses vascular corrosion casting, hierarchical synchrotron radiation µCT imaging, and computational image analysis to assess the three-dimensional vascular network architecture.
SARS-CoV-2 genome-wide mapping of CD8 T cell recognition reveals strong immunodominance and substantial CD8 T cell activation in COVID-19 patients
Authors: Saini Sunil Kumar , Hersby Ditte Stampe , Tamhane Tripti , Povlsen Helle Rus , Hernandez Susana Patricia Amaya , Nielsen Morten , Gang Anne Ortved , Hadrup Sine Reker 
Published: October 2020

SummaryTo understand the CD8+T cell immunity related to viral protection and disease severity in COVID-19, we evaluated the complete SARS-CoV-2 genome (3141 MHC-I binding peptides) to identify immunogenic T cell epitopes, and determine the level of CD8+T cell involvement using DNA-barcoded peptide-major histocompatibility complex (pMHC) multimers. COVID-19 patients showed strong T cell responses, with up to 25% of all CD8+lymphocytes specific to SARS-CoV-2-derived immunodominant epitopes, derived from ORF1 (open reading frame 1), ORF3, and Nucleocapsid (N) protein. A strong signature of T cell activation was observed in COVID-19 patients, while no T cell activation was seen in the ‘non-exposed’ and ‘high exposure risk’ healthy donors. Interestingly, patients with severe disease displayed the largest T cell populations with a strong activation profile. These results will have important implications for understanding the T cell immunity to SARS-CoV-2 infection, and how T cell immunity might influence disease development.
High resolution and high throughput bacteria separation from blood using elasto-inertial microfluidics
Authors: Iyengar Sharath Narayana , Kumar Tharagan , Mårtensson Gustaf , Russom Aman 
Published: October 2020

AbstractImproved sample preparation has the potential to address a huge unmet need for fast turnaround sepsis tests that enable early administration of appropriate antimicrobial therapy. In recent years, inertial and elasto-inertial microfluidics-based sample preparation has gained substantial interest for bioparticle separation applications. However, for applications in blood stream infections the throughput and bacteria separation efficiency has thus far been limited. In this work, for the first time we report elasto-inertial microfluidics-based bacteria isolation from blood at throughputs and efficiencies unparalleled with current microfluidics-based state of the art. In the method, bacteria-spiked blood sample is prepositioned close to the outer wall of a spiral microchannel using a viscoelastic sheath buffer. The blood cells will remain fully focused throughout the length of the channel while bacteria migrate to the inner wall for effective separation. Initially, particles of different sizes were used to investigate particle focusing and the separation performance of the spiral device. A separation efficiency of 96% for the 1 µm particles was achieved, while 100% of 3 µm particles were recovered at the desired outlet at a high throughput of 1 mL/min. Following, processing blood samples revealed a minimum of 1:2 dilution was necessary to keep the blood cells fully focus at the outer wall. In experiments involving bacteria spiked in diluted blood, viableE.coliwere continuously separated at a total flow rate of 1 mL/min, with an efficiency between 82 to 90% depending on the blood dilution. Using a single spiral, it takes 40 minutes to process 1 mL of blood at a separation efficiency of 82% and 3 hours at 90% efficiency. To the best of our knowledge, this is the highest blood sample throughput per single microfluidic chip reported for the corresponding separation efficiency. As such, the label-free, passive and high throughput bacteria isolation method has a great potential for speeding up downstream phenotypic and molecular analysis of bacteria.
Allele-specific collateral and fitness effects determine the dynamics of fluoroquinolone-resistance evolution
Authors: Liakopoulos Apostolos , Aulin Linda B. S. , Buffoni Matteo , Fragkiskou Efthymia , van Hasselt J. G. Coen , Rozen Daniel E. 
Published: October 2020

AbstractCollateral sensitivity (CS), which arises when resistance to one antibiotic increases sensitivity towards other antibiotics, offers novel treatment opportunities to constrain or reverse the evolution of antibiotic-resistance. The applicability of CS-informed treatments remains uncertain, in part because we lack an understanding of the generality of CS effects for different resistance mutations, singly or in combination. Here we address this issue in the Gram-positive pathogenStreptococcus pneumoniaeby measuring collateral and fitness effects of clinically relevantgyrAandparCalleles, and their combinations, that confer resistance to fluoroquinolones. We integrated these results in a mathematical model which allowed us to evaluate how differentin silicocombination treatments impact the dynamics of resistance evolution. We identified common and conserved CS effects of differentgyrAandparCalleles; however, the spectrum of collateral effects was unique for each allele or allelic pair. This indicated that allelic identity can impact the evolutionary dynamics of resistance evolution during monotreatment and combination treatment. Our model simulations, which included the experimentally derived antibiotic susceptibilities and fitness effects, and antibiotic specific pharmacodynamics, revealed that both collateral and fitness effects impact the population dynamics of resistance evolution. Overall, we provide evidence that allelic identity and interactions can have a pronounced impact on collateral effects to different antibiotics and suggest that these need to be considered in models examining CS-based therapies.SignificanceA promising strategy to overcome the evolution of antibiotic resistant bacteria is to use collateral sensitivity-informed antibiotic treatments that rely on cycling or mixing of antibiotics, such that that resistance towards one antibiotic confers increased sensitivity to the other. Here, focusing on multi-step fluoroquinolone resistance inStreptococcus pneumoniae, we show that antibiotic-resistance induces diverse collateral responses whose magnitude and direction are determined by allelic identity. Using mathematical simulations, we show that these effects can be exploited via combination treatment regimens to suppress thede novoemergence of resistance during treatment.
Mutational analysis and assessment of its impact on proteins of SARS-CoV-2 genomes from India
Authors: Laskar Rezwanuzzaman , Ali Safdar 
Published: October 2020

AbstractThe ongoing global pandemic of SARS-CoV-2 implies a corresponding accumulation of mutations. Herein the mutational status of 611 genomes from India along with their impact on proteins was ascertained. After excluding gaps and ambiguous sequences, a total of 493 variable sites (152 parsimony informative and 341 singleton) were observed. The most prevalent reference nucleotide was C (209) and substituted one was T (293). NSP3 had the highest incidence of 101 sites followed by S protein (74 sites), NSP12b (43 sites) and ORF3a (31 sites). The average number of mutations per sample for males and females was 2.56 and 2.88 respectively suggesting a higher contribution of mutations from females. Non-uniform geographical distribution of mutations implied by Odisha (30 samples, 109 mutations) and Tamil Nadu (31 samples, 40 mutations) suggests that sequences in some regions are mutating faster than others. There were 281 mutations (198 ‘Neutral’ and 83 ‘Disease’) affecting amino acid sequence. NSP13 has a maximum of 14 ‘Disease’ variants followed by S protein and ORF3a with 13 each. Further, constitution of ‘Disease’ mutations in genomes from asymptomatic people was mere 11% but those from deceased patients was over three folds higher at 38% indicating contribution of these mutations to the pathophysiology of the SARS-CoV-2.
Winter activity of boreal bats
Authors: Blomberg Anna S. , Vasko Ville , Meierhofer Melissa B. , Johnson Joseph S. , Eeva Tapio , Lilley Thomas M. 
Published: October 2020

ABSTRACTNatural hibernation sites used by bats in areas that lack cave features have long remained unresolved. To investigate hibernation site selection and winter activity of boreal bats, we recorded bat calls using passive acoustic monitoring on 16 sites. These sites included four rock outcrops with crevices and cave features, three glacial erratics or boulder fields, three ancient shores, three root cellars and three control sites where we did not expect bats to be overwintering. Our results revealed echolocation calls ofEptesicus nilssonii,Plecotus auritusandMyotissp. We recorded significantly more activity near rock outcrops and root cellars compared to other habitats. We also found that ambient temperature had a positive effect on bat activity and found evidence thatP. auritusmay be using low barometric pressure as a proxy for suitable foraging conditions during the winter. Our results suggest that rock outcrops may be more important to bats than previously acknowledged, highlighting the need to take these sites in account in planning of conservation measures. Furthermore, our findings underline the suitability of using acoustic monitoring in homing on hibernation sites that are not otherwise accessible.
Newly isolated sporopollenin microcages fromCedrus libaniandPinus nigrafor controlled delivery of Oxaliplatin
Authors: Mujtaba Muhammad , Yılmaz Bahar Akyauz , Cansaran-Duman Demet , Akyuz Lalehan , Yangın Sevcan , Kaya Murat , Çeter Talip , Khawar Khalid Mahmood 
Published: October 2020

AbstractSporopollenin-mediated controlled drug delivery has been studied extensively owing to its physicochemical and biological charachteristics. In the present study, sporopollenin was successfully extracted from pollen grains ofC. libaniandP. nigrafollowed by the loading of a commonly known anticancer drug Oxaliplatin. Both the drug loading and physicochemical features were confirmed by using light microscopy, FT-IR, SEM and TGA. For the first time, real-time cell analyzer system, xCELLigence, was employed to record the Oxaliplatin-loaded and sporopollenin-mediated cell death (CaCo-2 and Vero cells) in real time. Both the assays confirmed the slow release of Oxaliplatin from sporopollenin for around 40–45 h. The expression of MYC andFOXO-3genes significantly increased in CaCo2 cell and decreased non-cancerous Vero cell confirming that sporopollenin-mediated controlled release of Oxaliplatin was promoting apoptosis cell death preventing the spread of its negative effects to nearby healthy cells. All the results suggested thatC. libaniandP. nigracould be suitable candidates for slow delivery of drugs.
Chlorophyll content and chlorophyll fluorescence as physiological parameters for monitoringOrobanche foetidaPoir. infestation on faba bean (Vicia fabaL.)
Authors: Amri Moez , Abbes Zouhaier , Trabelsi Imen , Ghanem Michel Edmond , Mentag Rachid , Kharrat Mohamed 
Published: October 2020

AbstractIn total, 39 faba bean (Vicia fabaL.) advanced lines were evaluated for resistance to broomrapeOrobanche foetidaunder highly infested field conditions. The trials were conducted during two consecutive copping seasons at Oued-Beja Research Station in Tunisia. The advanced lines XAR-VF00.13-1-2-1-2-1 and XBJ90.04-2-3-1-1-1-2A expressed high resistance level toO. foetidaexceeding those recorded for resistance checks Najeh and Baraca. Results showed thatO. foetidasignificantly affected the biomass, grain yield, chlorophyll content index (CCI) and the maximum quantum efficiency (Fv/Fmratio). No significant effect ofO. foetidaparasitism was observed on host plant water content (WC).O. foetidaparasitism significantly affected both CCI and Fv/Fmratio. CCI decreases varied from 46.4% for the susceptible check Badi and 4.2% and 9.3% observed for the genotypes Baraca and XBJ90.04-2-3-1-1-1-2A. Compared to susceptible check, slight decreases of Fv/Fmratio were observed for both advanced lines XBJ90.04-2-3-1-1-1-2A and XAR-VF00.13-1-2-1-2-1. Correlation between CCI and Fv/Fmwith the resistance to broomrape makes this, easy-to-measure, parameter very useful as a practical screening tool for early parasitism detection, diagnosis and identification and selection of high resistant plants against this pathogen.
Persistence of the ground beetle (Coleoptera: Carabidae) microbiome to diet manipulation
Authors: Silver Anita , Perez Sean , Gee Melanie , Xu Bethany , Garg Shreeya , Will Kipling , Gill Aman 
Published: October 2020

ABSTRACTHost-associated microbiomes can play important roles in the ecology and evolution of their insect hosts, but bacterial diversity in many insect groups remains poorly understood. Here we examine the relationship between host environment, host traits, and microbial diversity in three species in the ground beetle family (Coleoptera: Carabidae), a group of roughly 40,000 species that synthesize a wide diversity of defensive compounds. This study found that the ground beetle microbiome is consistent across different host food sources. We used 16S amplicon sequencing to profile three species that are phylogenetically distantly related, trophically distinct, and whose defensive chemical secretions differ:Anisodactylus similisLeConte, 1851,Pterostichus serripes(LeConte, 1875), andBrachinus elongatulusChaudoir, 1876. Wild-caught beetles were compared to individuals maintained in the lab for two weeks on carnivorous, herbivorous, or starvation diets. Soil environment but not diet had a significant effect on bacterial diversity and composition. The three carabid species have patterns of microbial diversity similar to those previously found in other insect hosts. Metagenomic samples from two highly active tissue types — guts, and pygidial gland secretory cells (which produce defensive compounds) — were processed and sequenced separately from those of the remaining body. The observed similarity of the pygidial gland secretory cell microbiome across hosts suggests the possibility that it may be a conserved community, possibly due to functional interactions related to defensive chemistry. These results provide a baseline for future studies of the role of microbes in the diversification of defensive chemical biosynthesis in carabids.
Species composition and dynamics of aphids and parasitoid wasps in maize fields in Northeastern China
Authors: Zhang Ying , Zhao Min-chi , Cheng Jia , Liu Shuo , Yuan Hai-bin 
Published: October 2020

AbstractMaize,Zea maysL., is the most abundant field crop in China. Aphids are the most economically damaging pest on maize, particularly in the cotton agri-ecosystems of Jilin Province, northern China. Parasitic wasps are important natural enemies of aphids, but limited information exists about their species composition, richness and seasonal dynamics in northern China. In this study, the population dynamics of maize aphids and parasitoid wasps were assessed in relation to each other during the summer seasons of two consecutive years, 2018 and 2019. We selected maize fields in the Changchun, Songyuan, Huinan and Gongzhuling areas of Jilin Province. Four species of aphids were recorded from these maize fields:Rhopalosiphum padi(L), Rhopalosiphum maidis(Fitch), Aphis gossypiiGlover andMacrosiphum miscanthi(Takahashi). The dominant species in each of the four areas wereR. maids(Filch) andR. padiin Changchun,R. padiin Songyuan,A. gossypiiandR. padiin Huinan, andA.gossypiiandR. padiin Gongzhuling. We delineated a species complex made up of primary parasitoids and hyperparasitoids associated with maize aphids. The primary parasitoidsLysiphlebus testaceipes, Binodoxys communisandAphelinus albipodustogether formed approximately 85.3% of the parasitoid complex.Pachyneuron aphidis, Phaenoglyphis villosa, Syrphophagus taeniatusandAsaphes suspensusmade up the hyperparasitoids. Of the primary parasitoids,L. testaceipeswas the dominant species (81.31%). Of the hyperparasitoid group,P. villosawas the dominant species (68.42%). Parasitism rates followed the fluctuation of the aphid population. The highest parasitic rate was observed during the peak period of cotton aphids. In this paper, the occurrence dynamics and dominant species of aphids and the dynamics of parasitic natural enemies of aphids in maize fields in Jilin Province are, for the first time, systematically reported. This study provides important information for the establishment and promotion of aphid biological control in maize fields.
Utilization and prospectus of non-timber forest products as livelihood materials
Authors: Das Atanu Kumar , Asaduzzaman Md. , Islam Md Nazrul 
Published: October 2020

AbstractA study was conducted to find out the present utilization of non-timber forest products of the Sundarbans and tries to find out the alternative uses of these resources. The Sundarbans is the largest mangrove forest in the world and proper utilization of all resources can get a chance to manage this forest in sustainable way. A questionnaire survey was conducted to get information about the utilization of non-timber forest products. It has been found that about 87% of the people are fully dependent and 13% of the people are partially dependent on the Sundarbans. Among minor forest products, golpata, honey and fish were used by 92%, 93% and 82% of people, respectively. Most of the people are unknown about the alternative use of minor forest products but there is a great chance to use them for better purposes. Alternative uses of these products will help to improve the forest conditions as well as the socio-economic conditions of the people adjacent to the Sundarbans.
Facial expressions of emotional stress in horses
Authors: Lundblad Johan , Rashid Maheen , Rhodin Marie , Andersen Pia Haubro 
Published: October 2020

AbstractHorses have the ability to generate a remarkable repertoire of facial expressions, some which have been linked to certain emotional states, for example pain. Studies suggest that facial expressions may be a more ‘honest’ expression of emotional state in horses than behavioral or physiological parameters. This study sought to describe the facial expressions during stress of healthy horses free of pain, using a standardized method of recording facial expressions in video. Stress was induced in 28 horses by subjecting them to road transport and 10 of these horses were also subjected to social isolation. The horses served as their own control. A body-mounted, remote controlled heart rate monitor provided continuous heart rate measurements during the interventions. The horses’ facial expressions were video-recorded during the interventions. Frequency and duration of each facial expression were then determined, according to the Equine Facial Action Coding System. Heart rate increased during the stressful interventions (p=0.01), confirming that the interventions were stressful. Using both the human investigation- and the co-occurrence methods, the following facial traits could be observed during stress:eye white increase(p<0.001),nostril dilator(p<0.001),upper eyelid raiser(p<0.001),inner brow raiser(p=0.042),tongue show(p<0.001) along with an increase in ‘ear flicker’ (p<0.001) and blink frequency (p<0.001). The facial actions were successfully used to train a machine-learning classifier to discriminate between stressed and calm horses, with an accuracy of 74.2 %. Most of the facial features identified correspond well with previous research on the subject, for example flared nostrils, repetitive mouth behaviors, increased eye white, tongue show and ear movements. Some features selected as indicative of emotional pain-free stress are used in face-based pain assessment tools, such as dilated nostrils, eye white increase or inner brow raiser. The relation between facial expressions of stress and pain should therefore further be studied.