bluuebunny/crossref_metadata_2025_split huggingface dataset:
Culex pipiensL. andCulex restuansegg rafts harbor diverse bacterial communities compared to their midgut tissues
Authors: Juma Elijah O. , Kim Chang-Hyun , Dunlap Christopher , Allan Brian F. , Stone Chris M. 
Published: May 2020

AbstractBackgroundThe bacterial communities associated with mosquito eggs are an essential component of the mosquito microbiota, yet there are few studies characterizing and comparing the microbiota of mosquito eggs to other host tissues.MethodsWe sampled gravid femaleCulex pipiensandCulex restuansfrom the field, allowed them to oviposit in the laboratory, and characterized the microbiota associated with their egg rafts and midguts for comparison through MiSeq sequencing of the 16S rRNA gene.ResultsBacterial richness was higher in egg rafts than in midguts for both species, and higher inCx pipiensL. thanCx. restuans. The midgut samples ofCx. pipiensandCx. restuanswere dominated byProvidencia. Culex pipiensL. andCx. restuansegg rafts samples were dominated byRalstoniaandNovosphingobium, respectively. NMDS ordination based on Bray-Curtis distance matrix revealed that egg raft samples, or midgut tissues harbored similar bacterial communities regardless of the mosquito species. Within each mosquito species, there were distinct clustering of bacterial communities between egg raft and midgut tissues.ConclusionThese findings expand the list of described bacterial communities associated withCx. pipiensL. andCx. restuans and the additional characterization of the egg raft bacterial communities facilitates comparative analysis of mosquito host tissues, providing a basis for future studies seeking to understand any functional role of microbiota in mosquito biology.
Lifestyle acquired immunity, decentralized intelligent infrastructures and revised healthcare expenditures may limit pandemic catastrophe: a lesson from COVID-19
Authors: Ahmed Asif , Haque Tasnima , Rahman Mohammad Mahmudur 
Published: May 2020

AbstractHuman race has often faced pandemic with substantial number of fatalities. As COVID-19 pandemic reached and endured in every corner on earth, countries with moderate to strong healthcare support and expenditure seemed to struggle in containing disease transmission and casualties. COVID-19 affected countries have variability in demographic, socioeconomic and life style health indicators. At this context it is important to find out at what extent these parametric variations are actually modulating disease outcomes. To answer this, we have selected demographic, socioeconomic and health indicators e.g. population density, percentage of urban population, median age, health expenditure per capita, obesity, diabetes prevalence, alcohol intake, tobacco use, case fatality of non communicable diseases (NCDs) as independent variables. Countries were grouped according to these variables and influence on dependent variables e.g. COVID-19 test positive, case fatality and case recovery rates were statistically analyzed. The results suggest that countries with variable median age has significantly different outcome on test positive rate (P<0.01). Both median age (P=0.0397) and health expenditure per capita (P=0.0041) has positive relation with case recovery. Increasing number of test per 100K population showed positive and negative relation with number of positives per 100K population (P=0.0001) and percentage of test positives (P<0.0001) respectively. Alcohol intake per capita in liter (P=0.0046), diabetes prevalence (P=0.0389) and NCDs mortalities (P=0.0477) also showed statistical relation with case fatality rate. Further analysis revealed that countries with high healthcare expenditure along with high median age and increased urban population showed more case fatality but also had better recovery rate. Investment in health sector alone is insufficient in controlling pandemic severity. Intelligent and sustainable healthcare both in urban and rural settings and healthy lifestyle acquired immunity may reduce disease transmission and comorbidity induced fatalities respectively.
Estimating Household Transmission of SARS-CoV-2
Authors: Curmei Mihaela , Ilyas Andrew , Evans Owain , Steinhardt Jacob 
Published: May 2020

Introduction and GoalsSARS-CoV-2 is transmitted both in the community and within households. Social distancing and lockdowns reduce community transmission but do not directly address household transmission. We provide quantitative measures of household transmission based on empirical data, and estimate the contribution of households to overall spread. We highlight policy implications from our analysis of household transmission, and more generally, of changes in contact patterns under social distancing.MethodsWe investigate the household secondary attack rate (SAR) for SARS-CoV-2, as well as Rh, which is the average number of within-household infections caused by a single index case. We identify previous works that estimated the SAR. We correct these estimates based on the false-negative rate of PCR testing and the failure to test asymptomatics. Results are pooled by a hierarchical Bayesian random-effects model to provide a meta-analysis estimate of the SAR. We estimate Rh using results from population testing in Vo’, Italy and contact tracing data that we curate from Singapore. The code and data behind our analysis are publicly available1.ResultsWe identified nine studies of the household secondary attack rate. Our modeling suggests the SAR is heterogeneous across studies. The pooled central estimate of the SAR is 30% but with a posterior 95% credible interval of (0%, 67%) reflecting this heterogeneity. This corresponds to a posterior mean for the SAR of 30% (18%, 43%) and a standard deviation of 15% (9%, 27%). If results are not corrected for false negatives and asymptomatics, the pooled central estimate for the SAR is 20% (0%, 43%). From the same nine studies, we estimate Rh to be 0.47 (0.13, 0.77). Using contact tracing data from Singapore, we infer an Rh value of 0.32 (0.22, 0.42). Population testing data from Vo’ yields an Rh estimate of 0.37 (0.34, 0.40) after correcting for false negatives and asymptomatics.InterpretationOur estimates of Rh suggest that household transmission was a small fraction (5%-35%) of R before social distancing but a large fraction after (30%-55%). This suggests that household transmission may be an effective target for interventions. A remaining uncertainty is whether household infections actually contribute to further community transmission or are contained within households. This can be estimated given high-quality contact tracing data.More broadly, our study points to emerging contact patterns (i.e., increased time at home relative to the community) playing a role in transmission of SARS-CoV-2. We briefly highlight another instance of this phenomenon (differences in contact between essential workers and the rest of the population), provide coarse estimates of its effect on transmission, and discuss how future data could enable a more reliable estimate.
COVIEdb: A database for potential immune epitopes of coronaviruses
Authors: Wu Jingcheng , Chen Wenfan , Zhou Jingjing , Zhao Wenyi , Chen Shuqing , Zhou Zhan 
Published: May 2020

Abstract2019 novel coronavirus (2019-nCoV) has caused large-scale pandemic COVID-19 all over the world. It’s essential to find out which parts of the 2019-nCoV sequence are recognized by human immune system for vaccine development. And for the prevention of the potential outbreak of similar coronaviruses in the future, vaccines against immunogenic epitopes shared by different human coronaviruses are essential. Here we predict all the potential B/T-cell epitopes for SARS-CoV, MERS-CoV, 2019-nCoV and RaTG13-CoV based on the protein sequences. We found YFKYWDQTY in ORF1ab protein, VYDPLQPEL and TVYDPLQPEL in spike (S) protein might be pan-coronavirus targets for vaccine development. All the predicted results are stored in a database COVIEdb (http://biopharm.zju.edu.cn/coviedb/).
Decoding music-evoked emotions in the auditory and motor cortex
Authors: Putkinen Vesa , Nazari-Farsani Sanaz , Seppälä Kerttu , Karjalainen Tomi , Sun Lihua , Karlsson Henry K. , Hudson Matthew , Heikkilä Timo T. , Hirvonen Jussi , Nummenmaa Lauri 
Published: May 2020

AbstractMusic can induce strong subjective experience of emotions, but it is debated whether these responses engage the same neural circuits as emotions elicited by biologically significant events. We examined the functional neural basis of music-induced emotions in a large sample (n=102) of subjects who listened to emotionally engaging (happy, sad, fearful, and tender) pieces of instrumental music while their haemodynamic brain activity was measured with functional magnetic resonance imaging (fMRI). Ratings of the four categorical emotions and liking were used to predict haemodynamic responses in general linear model (GLM) analysis of the fMRI data. Multivariate pattern analysis (MVPA) was used to reveal discrete neural signatures of the four categories of music-induced emotions. To map neural circuits governing non-musical emotions, the subjects were scanned while viewing short emotionally evocative film clips. The GLM revealed that most emotions were associated with activity in the auditory, somatosensory and motor cortices, cingulate gyrus, insula, and precuneus. Fear and liking also engaged the amygdala. In contrast, the film clips strongly activated limbic and cortical regions implicated in emotional processing. MVPA revealed that activity in the auditory cortex in particular as well as in the primary motor cortices reliably discriminated the emotion categories. Our results indicate that different music-induced basic emotions have distinct representations in regions supporting auditory processing, motor control, somatosensation and interoception but do not strongly rely on limbic and medial prefrontal regions critical for emotions with survival value.
NK cells and CTLs are required to clear solid tumor in a novel model of patient-derived-xenograft
Authors: Le Duy Tri , Burt Bryan , Van Buren George , Abeynaike Shawn , Zalfa Cristina , Nikzad Rana , Kheradmand Farrah , Paust Silke 
Published: May 2020

AbstractExisting patient-derived-xenograft (PDX) mouse models of solid tumors lack a fully tumor-donor matched “syngeneic” and functional immune system. We developed such a model by engrafting lymphopenic recipient mice with a fresh undisrupted piece of solid tumor, whereby tumor-infiltrating lymphocytes (TIL) expanded in the recipient mice for several weeks. Tumors engrafted in about seventy to eighty percent ofsyngeneic-immune-system-PDX (SIS-PDX) mice, which harbored tumor-exhausted immune-effector and functional immune-regulatory cells persisting for at least six-months post-engraftment. Interleukin-15 (IL-15)-stimulation in addition to immune checkpoint inhibition (ICI), prevented resistance, resulting in complete or partial response to combined treatment. Further, the depletion of Cytotoxic T lymphocytes (CTLs) and/or Natural Killer (NK) cells from combined immunotherapy in SIS-PDX mice revealed that both cell types are required for the maximal response to tumor. Our novel SIS-PDX model provides a valuable resource for powerful mechanistic and therapeutic studies designed to eradicate solid tumors.
CCM signaling complex (CSC) coupling both classic and non-classic progesterone receptor signaling
Authors: Abou-Fadel Johnathan , Jiang Xiaoting , Grajeda Brian , Padarti Akhil , Ellis Cameron C. , Zhang Jun 
Published: May 2020

AbstractExcessive progesterone (PRG) may increase breast cancer risk under hormone therapy during postmenopause or hormonal contraception. As a sex steroid hormone, PRG exerts its cellular responses through signaling cascades involving classic (genomic), non-classic (non-genomic), or both combined responses by binding to either classic nuclear PRG receptors or non-classic membrane PRG receptors. Currently, the intricate balance and switch mechanisms between these two signaling cascades remain elusive. Three genes, KRIT1 (CCM1), MGC4607 (CCM2), and PDCD10 (CCM3), have been demonstrated to form a CCM signaling complex (CSC). In this report, we discover that the CSC plays an essential role in coupling both classic and non-classic PRG signaling pathways by mediating crosstalk between them. The coupled signaling pathways were detailed through high throughput omics.One Sentence SummaryWe discover a novel signaling network among the CCM signaling complex (CSC), classic and non-classic progesterone receptors, and their ligands-progesterone/mifepristone, is dynamically modulated and fine-tuned with a series of feedback regulations; perturbation of this intricate balance, such as hormone therapy in the postmenopause or hormonal contraception regimen, or perturbed CSC signaling could result in increased risks in breast cancer or compromising tumor therapy.
Mass Spectrometric detection of SARS-CoV-2 virus in scrapings of the epithelium of the nasopharynx of infected patients via Nucleocapsid N protein
Authors: Nikolaev EN , Indeykina MI , Brzhozovskiy AG , Bugrova AE , Kononikhin AS , Starodubtseva NL , Petrotchenko EV , Kovalev G , Borchers CH , Sukhikh GT 
Published: May 2020

ABSTRACTDetection of viral RNA by PCR is currently the main diagnostic tool for COVID-19 [1]. The PCR-based test, however, shows limited sensitivity, especially at early and late stages of the disease development [2,3], and is relatively time consuming. Fast and reliable complementary methods for detecting the viral infection would be of help in the current pandemia conditions. Mass-spectrometry is one of such possibilities. We have developed a mass-spectrometry based method for the detection of the SARS CoV-2 virus in nasopharynx epithelial swabs, based on the detection of the viral nucleocapsid N protein. The N protein of the SARS-COV-2 virus, the most abundant protein in the virion, is the best candidate for mass-spectrometric detection of the infection, and MS-based detection of several peptides from the SARS-COoV-2 nucleoprotein has been reported earlier by the Sinz group [4]. Our approach shows confident identification of the N protein in patient samples even with the lowest viral loads and a much simpler preparation procedure. Our main protocol consists of virus inactivation by heating and adding of isopropanol, and tryptic digestion of the proteins sedimented from the swabs followed by MS analysis. A set of unique peptides, produced as a result of proteolysis of the nucleocapsid phosphoprotein of SARS-CoV-2, is detected. The obtained results can further be used to create fast parallel mass-spectrometric approaches for the detection of the virus in the nasopharyngeal mucosa, saliva, sputum and other physiological fluids.
Early Recovery Protocols Effect the Opioid Prescriptions at Discharge After Major Urologic Cancer Surgery
Authors: Carnes Kevin M. , Ata Ashar , Cangero Theodore , Mian Badar M. 
Published: May 2020

ABSTRACTIntroductionEarly recovery after surgery (ERAS) protocols are designed limit the use of opioids during in-patient stay to facilitate recovery and early discharge. However, there are conflicting reports of opioids prescribed at discharge to these patients. We wished to evaluate the effect of early recovery efforts on the opioid prescriptions given at discharge after major urologic cancer surgery.MethodsWe reviewed opioid prescription data from patients discharged from our facility after major urologic cancer surgery from 2016 to 2018, including cystectomy, nephrectomy (total, partial) and prostatectomy. The opioid prescriptions were normalized to hydrocodone-5 mg tablet equivalents. Multivariable analysis was performed to evaluate the effect of various factors on opioid prescriptions at discharge.Results409 patients met the inclusion criteria, with 207 without ERAS and 202 on ERAS protocol. Potent opioid (oxycodone or hydrocodone) use was reduced from 92% to 43% and tramadol use increased from 8% to 57% (p < 0.001). Following ERAS, we noted reduction in opioid prescriptions for prostatectomy (30%, p < 0.001), cystectomy (27%, p = 0.02) and all nephrectomy procedures (32%, p < 0.001). On multivariable analysis for each procedure, ERAS protocol was a significant predictor of opioid prescriptions at discharge.ConclusionsA significant decrease in the opioid prescriptions given at discharge was noted after major urologic cancer surgery with the use of ERAS protocols. There was a significant shift towards the use of less potent opioids. These findings provides a benchmark for further interventions and reduction in the outpatient opioid prescriptions after major urologic surgery.
Contributions of insula and superior temporal sulcus to interpersonal guilt and responsibility in social decisions
Authors: Gädeke Maria , Willems Tom , Ahmed Omar Salah , Weber Bernd , Hurlemann René , Schultz Johannes 
Published: May 2020

AbstractThis study investigated the neural mechanisms involved in feelings of interpersonal guilt and responsibility evoked by social decisions. In two studies (one during fMRI), participants repeatedly chose between safe and risky monetary outcomes in social contexts. Across conditions, each participant chose for both themselves and a partner (Socialcondition), or the partner chose for both themselves and the participant (Partnercondition), or the participant chose just for themselves (Solocondition, control). If the risky option was chosen in theSocialorPartnercondition, participant and partner could each receive either the high or the low outcome of a lottery with 50% probability, independently of each other. Participants were shown the outcomes for themselves and for their partner on each trial, and reported their momentary happiness every few trials. As expected, participant happiness decreased following both low lottery outcomes for themselves and for the partner. Crucially, happiness decreases following low outcomes for the partner were larger when the participant rather than their partner had made the choice, which fits an operational definition of guilt. This guilt effect was associated with BOLD signal increase in the left anterior insula. Connectivity between this region and the right inferior frontal gyrus varied depending on choice and experimental condition, suggesting that this part of prefrontal cortex is sensitive to guilt-related information during social choices. Variations in happiness were well explained by computational models based on participant’s and partner’s rewards and reward prediction errors. A model-based analysis revealed a left superior temporal sulcus cluster that tracked partner reward prediction errors that followed participant choices. Our findings identify neural mechanisms of guilt and social responsibility during social decisions under risk.
A developmental analysis of juxtavascular microglia dynamics and interactions with the vasculature
Authors: Mondo Erica , Becker Shannon C. , Kautzman Amanda G. , Schifferer Martina , Baer Christina E. , Chen Jiapei , Huang Eric J. , Simons Mikael , Schafer Dorothy P. 
Published: May 2020

ABSTRACTMicroglia, the resident macrophages of the central nervous system (CNS), are dynamic cells, constantly extending and retracting their processes as they contact and functionally regulate neurons and other glial cells. There is far less known about microglia-vascular interactions, particularly under healthy steady-state conditions. Here, we use the male and female mouse cerebral cortex to show that a higher percentage of microglia associate with the vasculature during the first week of postnatal development compared to older ages and the timing of these associations are dependent on the fractalkine receptor (CX3CR1). Similar developmental microglia-vascular associations were detected in the prenatal human brain. Using live imaging in mice, we found that juxtavascular microglia migrated when microglia are actively colonizing the cortex and became stationary by adulthood to occupy the same vascular space for nearly 2 months. Further, juxtavascular microglia at all ages contact vascular areas void of astrocyte endfeet and the developmental shift in microglial migratory behavior along vessels corresponded to when astrocyte endfeet more fully ensheath vessels. Together, our data provide a comprehensive assessment of microglia-vascular interactions. They support a mechanism by which microglia use the vasculature to migrate within the developing brain parenchyma. This migration becomes restricted upon the arrival of astrocyte endfeet when juxtavascular microglia then establish a long-term, stable contact with the vasculature.SIGNIFICANCE STATEMENTWe report the first extensive analysis of juxtavascular microglia in the healthy, developing and adult brain. Live imaging revealed that juxtavascular microglia within the cortex are highly motile and migrate along vessels as they are colonizing cortical regions. Using confocal, expansion, super-resolution, and electron microscopy, we determined that microglia associate with the vasculature at all ages in areas lacking full coverage astrocyte endfoot coverage and motility of juxtavascular microglia ceases as astrocyte endfeet more fully ensheath the vasculature. Our data lay the fundamental groundwork to investigate microglia-astrocyte crosstalk and juxtavascular microglial function in the healthy and diseased brain. They further provide a potential vascular-dependent mechanism by which microglia colonize the brain to later regulate neural circuit development.
Influence of the culture media on the aspect and growth of oilseed rape fungal pathogens
Authors: Ermel Magali , Jumel Stéphane , Bousset Lydia 
Published: May 2020

AbstractWhile culturing fungal pathogens on artificial media, the phenotype, i.e. colony aspect, growth kinetics and in some case the pigment production can be used as discrimination criteria. Our aim was to enable the comparison between the growth kinetics of 8 fungal species, cultured simultaneously on 3 different media, and imaged under standardised conditions. Using a camera stand, taking pictures was quick and easy, producing homogeneous pictures, facilitating their comparison. The colony growth kinetics varied widely across the 8 species. The mycelium aspect and pigment production depended on the media and changed over time. Having standardised the imaging setup and grown species simultaneously allows proposing reference sets of pictures.
Ebola and Marburg virus matrix layers are locally ordered assemblies of VP40 dimers
Authors: Wan W. , Clarke M. , Norris M. , Kolesnikova L. , Koehler A. , Bornholdt Z. , Becker S. , Saphire E.O. , Briggs J.A.G. 
Published: May 2020

AbstractA key step in the life cycle of enveloped viruses is the budding of nascent virions from the host membrane. In filoviruses such as Ebola and Marburg virus, this process is achieved by the matrix protein VP40. When expressed alone, VP40 induces the budding of filamentous virus-like particles, suggesting that localization to the plasma membrane, oligomerization into a matrix layer, and the generation of membrane curvature are intrinsic properties of VP40. While a number of crystal structures of VP40 have been determined in various oligomerization states, there has been no direct information on the structure of assembled VP40 matrix layers within viruses or virus-like particles. Here, we present structures of Ebola and Marburg VP40 matrix layers in intact virus-like particles, as well as within intact Marburg viruses. We find that the matrix layers are formed from VP40 dimers which assemble into extended chains via C-terminal domain interactions. These chains stack into layers, forming a 2D lattice below the membrane surface. However, these 2D lattices are only locally ordered, forming a patchwork assembly across the membrane surfaces and suggesting that assembly may begin at multiple points. These observations define the structure and arrangement of the matrix protein layer that mediates the formation of filamentous filovirus particles.