bluuebunny/crossref_metadata_2025 huggingface dataset:
Genome sequence ofHydrangea macrophyllaand its application in analysis of the double flower phenotype
Authors: Nashima K , Shirasawa K , Ghelfi A , Hirakawa H , Isobe S , Suyama T , Wada T , Kurokura T , Uemachi T , Azuma M , Akutsu M , Kodama M , Nakazawa Y , Namai K
Published: June 2020

Owing to its high ornamental value, the double flower phenotype of hydrangea (Hydrangea macrophylla) is one of its most important traits. In this study, genome sequence information was obtained to explore effective DNA markers and the causative genes for double flower production in hydrangea. Single molecule real-time sequencing data followed by a HiC analysis was employed. The resultant haplotype-phased sequences consisted of 3,779 sequences (2.256 Gb in length and N50 of 1.5 Mb), and 18 pseudomolecules comprising 1.08 Gb scaffold sequences along with a high-density SNP genetic linkage map. Using the genome sequence data obtained from two breeding populations, the SNPs linked to double flower loci (DjoandDsu), were discovered for each breeding population. DNA markers J01 linked toDjoand S01 linked toDsuwere developed, and these could be used successfully to distinguish the recessive double flower allele for each locus respectively. TheLEAFYgene was suggested as the causative gene forDsu,since frameshift was specifically observed in double flower accession withdsu. The genome information obtained in this study will facilitate a wide range of genomic studies on hydrangea in the future.
Development and validation of a knowledge-driven risk calculator for critical illness in COVID-19 patients
Authors: Cahan Amos , Gottesman Tamar , Katz Michal Tzuchman , Masad Roee , Azulay Gal , Dicker Dror , Zeidman Aliza , Berkov Evgeny , Levin Gal sahaf , Tadmor Boaz , Lev Shaul
Published: June 2020

Facing the rapidly spreading novel coronavirus disease (COVID-19), evidence to inform decision-making at both the clinical and policy-making level is highly needed. Based on the results of a study by Petrilli et al, we have developed a calculator using patient data at admission to predict the risk of critical illness (intensive care unit admission, use of mechanical ventilation, discharge to hospice, or death).

We report a retrospective validation of the risk calculator on 145 consecutive patients admitted with COVID-19 to a single hospital in Israel. Of the 18 patients with critical illness, 17 were correctly identified by the model(sensitivity: 94.4%, 95% CI, 72.7% to 99.9%; specificity: 81.9%, 95% CI, 74.1% to 88.2%). Of the 127 patients with non-critical illness, 104 were correctly identified. This, despite considerable differences between the original and validation study populations.

Our results show that data from published knowledge can be used to provide reliable, patient level, automated risk assessment, potentially reducing the cognitive burden on physicians and helping policy makers better prepare for future needs.
Drivers underpinning the malignant transformation of giant cell tumour of bone
Authors: Fittall Matthew W. , Ellery Peter , Lyskjær Iben , Lombard Patrick , Ijaz Jannat , Strobl Anna-Christina , Oukrif Dahmane , Tarabichi Maxime , Sill Martin , Koelsche Christian , Demeulemeester Jonas , Collord Grace , Tirabosco Roberto , Amary Fernanda , Campbell Peter J. , Pfister Stefan , Jones David T.W. , Pillay Nischalan , Loo Peter Van , Behjati Sam , Flanagan Adrienne M.
Published: June 2020

The rare benign giant cell tumour of bone (GCTB) is defined by an almost unique G34W oncohistone mutation in the H3.3 histone gene. Here we reveal the genomic and methylation patterns underlying the rare clinical phenomena of benign metastases and malignant transformation of GCTB.
Publish or perish: reporting characteristics of peer-reviewed publications, pre-prints and registered studies on the COVID-19 pandemic
Authors: Gianola S , Jesus TS , Bargeri S , Castellini G
Published: June 2020

Background

The COVID-19 pandemic has resulted in a mass of academic papers being published in a very brief span of time. Our aim was to compare the amount and reporting characteristics of COVID-19 related peer-reviewed and pre-prints publications. We also investigated the amount of ongoing trials and systematic reviews.

Methods and findings

A cross-sectional study of publications covering the COVID-19 pandemic time frame, up to May 20, 2020 was conducted. PubMed with appropriate combinations of Medical Subject Headings and COVID-19 section of MedRxiv and BioRxiv archives were searched. We examined Clinicaltrial.gov, Chinese Clinical Trial Registry, EU Register and 15 other trial registers as well as the international prospective register of systematic reviews (PROSPERO). Characteristics of each publication source were extracted. Regression analyses and Z tests were used to analyze publication trends over the weeks and compare their relative proportions.

We found 3635 peer-reviewed publications and 3805 pre-prints, of which 8.6% (n=329) were published in indexed journals. Peer-reviewed and pre-print publications amount both increased significantly over time (p<0.001). Case reports (peer-reviewed: 6% vs pre-prints: 0.9%,p<0.001) and letters (17.4% vs 0.5%,p<0.001) accounted for a greater share of the peer-reviewed compared to pre-print publications. In turn, randomized controlled trials (0.22% vs 0.63%p<0.001) and systematic reviews (0.08% vs 5%) accounted for a significantly greater share of the pre-print publications. Clinicaltrials.gov, Chinese Clinical Trial Registry and EU register included 57.9%, 49.5 % and 98.9% trials mostly still “recruiting”. PROSPERO amounted to 962 systematic review protocols.

Conclusion

Pre-prints were slightly more prevalent than peer-reviewed publications, yet both are growing. To fill the void given by the absence of published primary studies, immediate opinions (i.e., letters) has virulently been published in PubMed. However, preprints has been promoted as rapid responses to give direct and promptly access at scientific findings in this pandemic.
High temperature has no impact on the reproduction number and new cases of COVID-19 in Bushehr, Iran
Authors: Sahafizadeh Ebrahim , Sartoli Samaneh
Published: June 2020

Background

COVID-19 was first reported in Iran on February 19, 2020. Bushehr, one of the warmest provinces of Iran, was the last province confirmed to be infected on March 5, 2020. In the beginning of April, Bushehr was announced as a ‘white’, coronavirus-free, province. However, increasing the temperature in the next months did not affect the spread of coronavirus and the number of confirmed cases increased during the next months, so that Bushehr was announced as a ‘Red’ province on June 13, 2020.

Methods

This paper aims 1) to estimate the reproduction number of COVID-19 in Bushehr considering COVID-19 reported cases of Bushehr from April to June 12, 2020, using exponential function and SIR epidemic model, and 2) to investigate the impact of temperature on the reproduction number and the spread of coronavirus in Bushehr using the temperature data.

Results

The reproduction number was estimated to be 2.564, 2.641 and 2.573 at the beginning of April, May and June 2020 respectively. Regarding the increase in the temperature from April to June, the results showed that not only was the spread of COVID-19 not reduced but it also increased.

Conclusion

Data analysis on this study showed that high temperature has no impact on the reproduction number and does not slow down the spread of coronavirus in Bushehr.
Clinical Characteristics and Outcomes of Venous Thromboembolism in Patients Hospitalized for COVID-19: Systematic Review and Meta-Analysis
Authors: Henrina Joshua , Santosa Putra Iwan Cahyo , Cahyadi Irvan , Hadi Gunawan Hoo Felicia , Cahyadi Alius , Suciadi Leonardo Paskah
Published: June 2020

Objective

To investigate the clinical characteristics and outcomes of Coronavirus Disease of 2019 (COVID-19) patients complicated with venous thromboembolism (VTE)

Method

We performed a comprehensive literature search of several databases to find studies that assessed VTE in hospitalized COVID-19 patients with a primary outcome of all-cause mortality and secondary outcomes of intensive care unit (ICU) admission and mechanical ventilation. We also evaluated the clinical characteristics of VTE sufferers.

Results

Eight studies have been included with a total of 1237 pooled subjects. Venous thromboembolism was associated with higher mortality (RR 2.48 (1.35, 4.55),p=0.003;I25%,p=0.35) after we performed sensitivity analysis, ICU admission (RR 2.32 (1.53, 3.52),p<0.0001;I280%,p<0.0001), and mechanical ventilation need (RR 2.73 (1.56, 4.78),p=0.0004;I277%,p=0.001). Furthermore, it was also associated to male gender (RR 1.21 (1.08, 1.35),p=0.0007;I212%,p=0.34), higher white blood cells count (MD 1.24 (0.08, 2.41), 0.04;I20%; 0.26), D-dimer (MD 4.49 (2.74, 6.25),p<0.00001;I267%,p=0.009) and LDH levels (MD 70.93 (19.33, 122.54),p<0.007;I221%, p=0.28). In addition, after sensitivity analysis was conducted, VTE also associated with older age (MD 2.79 (0.06, 5.53),p=0.05;I225%,p=0.24) and higher CRP levels (MD 2.57 (0.88, 4.26);p=0.003;I20%,p=0.96).

Conclusion

Venous thromboembolism in COVID-19 patients was associated with increased mortality, ICU admission, and mechanical ventilation requirement. Male gender, older age, higher levels of biomarkers, including WBC count, D-Dimer, and LDH were also being considerably risks for developing VTE in COVID-19 patients during hospitalization.
Clinical characteristics of Coronavirus Disease 2019 (COVID-19) patients in Kuwait
Authors: Alshukry Abdullah , Ali Hamad , Ali Yaseen , Taweel Talal Al , Abu-Farha Mohammad , AbuBaker Jehad , Devarajan Sriraman , Dashti Ali A. , Bandar Ali , Taleb Hessah , Bader Abdullah Al , Aly Nasser Y. , Al-Ozairi Ebaa , Al-Mulla Fahd , Abbas Mohammad Bu
Published: June 2020

This is a retrospective single-center study of 417 consecutive patients with coronavirus disease 2019 (COVID-19) admitted to Jaber Al-Ahmad Hospital in Kuwait between February 24, 2020 and May 24, 2020. In total, 39.3% of patients were asymptomatic, 41% were symptomatic with mild/moderate symptoms, 5.3% were admitted to the intensive care unit (ICU) and recovered, and 14.4% died. The mean age of death cases was 54.20 years (± 11.09). Comorbidities were more prevalent in patients who died compared with others. Key findings include abnormal levels of markers assicated with infection, inflammation, abnormal blood clotting, heart problems and kidney problems in patients with severe form of the disease and poor putcome. We report a rapidly deteriorating estimated glomerular filtration rate (eGFR) in deaths during ICU stay with kidney injury complications reported in 65% of deaths (p < 0.05). Our dynamic profiling of eGFR in ICU highlights the potential role of renal markers in forecasting disease outcome that could perhaps identify patients at risk of poor outcome.
Detecting space-time clusters of COVID-19 in Brazil: mortality, inequality, socioeconomic vulnerability, and the relative risk of the disease in Brazilian municipalities
Authors: Martines M. R , Ferreira R.V , Toppa R. H. , Assunção L. M. , Desjardins M.R. , Delmelle E.M.
Published: June 2020

The first case of COVID-19 in South America occurred in Brazil on February 25th, 2020. By June 7th, 2020, there were 691,758 confirmed cases, 36,455 confirmed deaths, and a mortality rate of 5.3%. To assist with the establishment of measures for the strategic planning to combat the COVID-19 pandemic in Brazil, we present the first Brazilian geographic study with the aims to examine “active” hand “emerging” space-time clusters of COVID-19. We examine the associations between clusters and mortality rate, vulnerability, and social inequality. We used the prospective space-time scan statistic to detect daily COVID-19 clusters and examine the relative risk from February 25th - June 7th, 2020 in 5,570 Brazilian municipalities. We apply a Spearman’s statistic to measure correlation between the relative risk of each cluster and mortality rate, GINI index, and social inequality. We detected 11 emerging space-time clusters of COVID-19 occurring in all Brazilian regions, with seven of them with a relative risk greater than one, and the highest in the Amapá state in the northern region of Brazil. We observed a positive and significant correlation between the relative risk and mortality rate, Brazilian Social Vulnerability Index, and GINI Index. The results can be utilized to improve COVID-19 response and planning in all Brazilian states.
Hypokalemia in Patients with COVID-19
Authors: Gaetano Alfano , Annachiara Ferrari , Francesco Fontana , Perrone Rossella , Mori Giacomo , Elisabetta Ascione , Riccardo Magistroni , Giulia Venturi , Pederzoli Simone , Margiotta Gianlulca , Romeo Marilina , Piccinini Francesca , Giacomo Franceschi , Sara Volpi , Matteo Faltoni , Giacomo Ciusa , Erica Bacca , Marco Tutone , Alessandro Raimondi , Marianna Menozzi , Erica Franceschini , Gianluca Cuomo , Gabriella Orlando , Antonella Santoro , Margherita Di Gaetano , Cinzia Puzzolante , Federica Carli , Andrea Bedini , Jovana Milic , Marianna Meschiari , Cristina Mussini , Gianni Cappelli , Giovanni Guaraldi ,   Modena Covid-19 Working Group (MoCo19)
Published: June 2020

Patients with COVID-19 may experience multiple conditions (e.g., fever, hyperventilation, anorexia, gastroenteritis, acid-base disorder) that may cause electrolyte imbalances. Hypokalemia is a concerning electrolyte disorder that may increase the susceptibility to various kinds of arrhythmia. This study aimed to estimate prevalence, risk factors and outcome of hypokalemia in a cohort of non-critically ill patients. A retrospective analysis was conducted on 290 hospitalized patients with confirmed COVID-19 infection at the tertiary teaching hospital of Modena, Italy.

Hypokalemia (<3.5 mEq/L) was detected in 119 patients (41%). The decrease of serum potassium level was of mild entity (3-3.4 mEq/L) and occurred in association with hypocalcemia (P=0.001) and lower level of serum magnesium (P=0.028) compared to normokaliemic patients. Urine K: creatinine ratio, measured in a small subset of patients (n=45; 36.1%), showed an increase of urinary potassium excretion in the majority of the cases (95.5%). Causes of kaliuria were diuretic therapy (53.4%) and corticosteroids (23.3%). In the remaining patients, urinary potassium loss was associated with normal serum magnesium, low sodium excretion (FENa< 1%) and metabolic alkalosis. Risk factors for hypokalemia were female gender (P=0.002; HR 0.41, 95%CI 0.23-0.73) and diuretic therapy (P=0.027; HR 1.94, 95%CI 1.08-3.48). Hypokalemia, adjusted for sex, age and SOFA score, resulted not associated with ICU admission (P=0.131, 95% CI 0.228-1.212) and in-hospital mortality (P=0.474; 95% CI 0,170-1,324) in our cohort of patients.

Hypokalemia is a frequent disorder in COVID-19 patients and urinary potassium loss may be the main cause of hypokalemia. The disorder was mild in the majority of the patients and was unrelated to poor outcomes. Nevertheless, hypokalemic patients required potassium supplements to dampen the risk of arrhythmias.
Evidence for a pervasive autobiographical memory impairment in Logopenic Progressive Aphasia: clinical and neural correlates
Authors: Ramanan Siddharth , Foxe David , El-Omar Hashim , Ahmed Rebekah M. , Hodges John R. , Piguet Olivier , Irish Muireann
Published: June 2020

Logopenic Progressive Aphasia is a rare language disorder characterised by repetition and naming difficulties, reflecting the progressive degeneration of left-lateralized peri-sylvian temporal and inferior parietal regions. Mounting evidence suggests that cognitive impairments in this syndrome extend beyond the language domain to include episodic encoding and retrieval disturbances. To date, it remains unknown whether autobiographical memories from across the lifespan are also subject to decline, yet this information is critical to arrive at a comprehensive understanding of the Logopenic syndrome. The objective of this study was to provide the first in depth examination of autobiographical memory function in Logopenic Progressive Aphasia using the Autobiographical Interview, a validated semi-structured interview which assesses recollection of the past under free and probed recall conditions. Autobiographical memory performance in 10 well-characterised Logopenic Progressive Aphasia patients was contrasted with that of 18 typical amnestic Alzheimer’s disease and 16 healthy Control participants. Relative to Controls, Logopenic Progressive Aphasia cases showed marked impairment in the free recall of episodic details, scoring comparably to disease-matched cases of Alzheimer’s disease. This impairment was evident across all time periods and persisted even when formal structured probing was provided. Importantly, controlling for overall level of language disruption failed to ameliorate the autobiographical memory impairment in the Logopenic Progressive Aphasia group, suggesting a genuine amnesia spanning recent and remote memories. Whole-brain voxel-based morphometry analyses revealed that total episodic information retrieved in Logopenic Progressive Aphasia was associated with decreased grey matter intensity predominantly in a bilateral posterior parietal network. Taken together, our findings reveal for the first time the presence of marked remote and recent autobiographical memory impairments in Logopenic Progressive Aphasia, that cannot be explained solely due to their language difficulties or disease staging. Our findings hold important clinical implications for the accurate characterization of Logopenic Progressive Aphasia, and suggest that episodic memory difficulties should be considered as one of the core clinical features of this syndrome.
Pre-existing immunity provides a barrier to airborne transmission of influenza viruses
Authors: Le Sage Valerie , Jones Jennifer E. , Kormuth Karen A. , Fitzsimmons William J. , Nturibi Eric , Padovani Gabriella H. , Arevalo Claudia P. , French Andrea J. , Avery Annika J. , Manivanh Richard , McGrady Elizabeth E. , Bhagwat Amar R. , Lauring Adam S. , Hensley Scott E. , Lakdawala Seema S.
Published: June 2020

Human-to-human transmission of influenza viruses is a serious public health threat, yet the precise role of immunity from previous infections on the susceptibility to airborne viruses is still unknown. Using human seasonal influenza viruses in a ferret model, we examined the roles of exposure duration and heterosubtypic immunity on influenza transmission. We found that airborne transmission of seasonal influenza strains is abrogated in recipient animals with pre-existing non-neutralizing immunity, indicating that transmissibility of a given influenza virus strain should be examined in the context of ferrets that are not immunologically naïve.
Spindle scaling is governed by cell boundary regulation of microtubule nucleation
Authors: Rieckhoff Elisa Maria , Berndt Frederic , Golfier Stefan , Decker Franziska , Elsner Maria , Ishihara Keisuke , Brugués Jan
Published: June 2020

Cellular organelles such as the mitotic spindle adjust their size to the dimensions of the cell. It is widely understood that spindle scaling is governed by regulation of microtubule polymerization. Here we use quantitative microscopy in living zebrafish embryos andXenopusegg extracts in combination with theory to show that microtubule polymerization dynamics are insufficient to scale spindles and only contribute below a critical cell size. In contrast, microtubule nucleation governs spindle scaling for all cell sizes. We show that this hierarchical regulation arises from the partitioning of a nucleation inhibitor to the cell membrane. Our results reveal that cells differentially regulate microtubule number and length using distinct geometric cues to maintain a functional spindle architecture over a large range of cell sizes.
Control of fluid flow by Adgrd1 is essential for mammalian oviductal embryo transport
Authors: Bianchi Enrica , Sun Yi , Almansa-Ordonez Alexandra , Woods Michael , Goulding David , Martinez-Martin Nadia , Wright Gavin J.
Published: June 2020

Dysfunction of oviductal embryo transport can lead to ectopic pregnancy which affects 1 to 2% of all conceptions in the United States and Europe, and is the most common cause of pregnancy-related death in the first trimester1, 2. Ectopic pregnancies almost always occur in the Fallopian tube, emphasizing the critical role of oviductal transport in human reproduction3. Oviductal transit is regulated and involves a valve-like “tubal-locking” phenomenon that temporarily arrests oocytes at the ampullary-isthmic junction (AIJ) where fertilization occurs4. Here, we show that female mice lacking the orphan adhesion G-protein coupled receptorAdgrd1are sterile because they are unable to unlock the restraining mechanism at the AIJ, inappropriately retaining embryos within the oviduct.Adgrd1is expressed on the oviductal epithelium and the post-ovulatory attenuation of tubal fluid production is dysregulated inAdgrd1-deficient mice. We identified Plxdc2 as an activating ligand for Adgrd1 displayed on the surface of cumulus cells. Our findings suggest that regulating oviductal luminal fluid production by Adgrd1 controls embryo transit, and provides important insights into the genetic regulation and molecular mechanisms involved embryo tubal transport.
Hospital outbreak of carbapenem-resistant Enterobacteriales associated with an OXA-48 plasmid carried mostly byEscherichia coliST399
Authors: Ledda Alice , Cummins Martina , Shaw Liam P. , Jauneikaite Elita , Cole Kevin , Lasalle Florent , Barry Deborah , Rosmarin Caryn , Anaraki Sudy , Wareham David , Stoesser Nicole , Paul John , Manuel Rohini , Cherian Benny P , Didelot Xavier
Published: June 2020

A hospital outbreak of carbapenem-resistant Enterobacteriales was detected by routine surveillance. Whole genome sequencing and subsequent analysis revealed a conserved promiscuous OXA-48 carrying plasmid as the defining factor within this outbreak. Four different species of Enterobacteriales were involved in the outbreak.Escherichia coliST399 accounted for 20/55 of all the isolates. Comparative genomics with publicly availableE. coliST399 sequence data showed that the outbreak isolates formed a unique clade. The OXA-48 plasmid identified in the outbreak differed from other known plasmids by an estimated five homologous recombination events. We estimated a lower bound to the plasmid conjugation rate to be 0.23 conjugation events per lineage per year. Our analysis suggests co-evolution between the plasmid and its main bacterial host to be a key driver of the outbreak. This is the first study to report carbapenem-resistantE. coliST399 carrying OXA48 as the main cause of a plasmid-borne outbreak within a hospital setting. This study supports complementary roles for both plasmid conjugation and clonal expansion in the emergence of this outbreak.
Selective REM-Sleep Suppression Increases Next-Day Negative Affect and Amygdala Responses to Social Exclusion
Authors: Glosemeyer Robert W , Diekelmann Susanne , Cassel Werner , Kesper Karl , Koehler Ulrich , Westermann Stefan , Steffen Armin , Borgwardt Stefan , Wilhelm Ines , Müller-Pinzler Laura , Paulus Frieder M , Krach Sören , Stolz David S
Published: June 2020

Healthy sleep, positive general affect, and the ability to regulate emotional experiences are fundamental for well-being. In contrast, various mental disorders are associated with altered rapid eye movement (REM) sleep, negative affect, and diminished emotion regulation abilities. However, the neural processes mediating the relationship between these different phenomena are still not fully understood. In the present study of 42 healthy volunteers, we investigated the effects of selective REM sleep suppression (REMS) on general affect, as well as on feelings of social exclusion, emotion regulation, and their neural underpinnings. Using functional magnetic resonance imaging we show that REMS increases amygdala responses to experimental social exclusion, as well as negative affect on the morning following sleep deprivation. There was no evidence that emotional responses to experimentally induced social exclusion or their regulation using cognitive reappraisal were impacted by diminished REM sleep. Our findings indicate that general affect and amygdala activity depend on REM sleep, while specific emotional experiences possibly rely on additional psychological processes and neural systems that are less readily influenced by REMS.
In vivo imaging of swimming micromotors using hybrid high-frequency ultrasound and photoacoustic imaging
Authors: Aziz Azaam , Holthof Joost , Meyer Sandra , Schmidt Oliver G. , Medina-Sánchez Mariana
Published: June 2020

The fast evolution of medical micro- and nanorobots in the endeavor to perform non-invasive medical operations in living organisms boosted the use of diverse medical imaging techniques in the last years. Among those techniques, photoacoustic (PA) tomography has shown to be promising for the imaging of microrobots in deep-tissue (ex vivo and in vivo), as it possesses the molecular specificity of optical techniques and the penetration depth of ultrasound imaging. However, the precise maneuvering and function control of microrobots, in particular in living organisms, demand the combination of both anatomical and functional imaging methods. Therefore, herein, we report the use of a hybrid High-Frequency Ultrasound (HFUS) and PA imaging system for the real-time tracking of magnetically driven micromotors (single and swarms) in phantoms, ex vivo, and in vivo (in mice bladder and uterus), envisioning their application for targeted drug-delivery.
Discovery of molecular features underlying morphological landscape by integrating spatial transcriptomic data with deep features of tissue image
Authors: Bae Sungwoo , Choi Hongyoon , Lee Dong Soo
Published: June 2020

Profiling molecular features associated with the morphological landscape of tissue is crucial to interrogate structural and spatial patterns that underlie biological function of tissues. Here, we present a new method, SPADE, to identify important genes associated with morphological contexts by combining spatial transcriptomic data with co-registered images. SPADE incorporates deep learning-derived image patterns with spatially resolved gene expression data to extract morphological context markers. Morphological features that correspond to spatial maps of transcriptome were extracted by image patches surrounding each spot, and then, represented by image latent features. The molecular profiles correlated with the image latent features were identified. The extracted genes could be further analyzed to discover functional terms and also exploited to extract clusters maintaining morphological contexts. We apply our approach to spatial transcriptomic data of three different tissues to suggest an unbiased method capable of offering image-integrated gene expression trends.
The SARS-CoV-2 spike protein alters barrier function in 2D static and 3D microfluidic in vitro models of the human blood–brain barrier
Authors: Buzhdygan Tetyana P. , DeOre Brandon J. , Baldwin-Leclair Abigail , McGary Hannah , Razmpour Roshanak , Galie Peter A. , Potula Raghava , Andrews Allison M. , Ramirez Servio H.
Published: June 2020

As researchers across the globe have focused their attention on understanding SARS-CoV-2, the picture that is emerging is that of a virus that has serious effects on the vasculature in multiple organ systems including the cerebral vasculature. Observed effects on the central nervous system includes neurological symptoms (headache, nausea, dizziness), fatal microclot formation and in rare cases encephalitis. However, our understanding of how the virus causes these mild to severe neurological symptoms and how the cerebral vasculature is impacted remains unclear. Thus, the results presented in this report explored whether deleterious outcomes from the SARS-COV-2 viral spike protein on primary human brain microvascular endothelial cells (hBMVECs) could be observed. First, using postmortem brain tissue, we show that the angiotensin converting enzyme 2 or ACE2 (a known binding target for the SARS-CoV-2 spike protein), is expressed throughout various caliber vessels in the frontal cortex. Additionally, ACE2 was also detectable in primary human brain microvascular endothelial (hBMVEC) maintained under cell culture conditions. Analysis for cell viability revealed that neither the S1, S2 or a truncated form of the S1 containing only the RBD had minimal effects on hBMVEC viability within a 48hr exposure window. However, when the viral spike proteins were introduced into model systems that recapitulate the essential features of the Blood-Brain Barrier (BBB), breach to the barrier was evident in various degrees depending on the spike protein subunit tested. Key to our findings is the demonstration that S1 promotes loss of barrier integrity in an advanced 3D microfluid model of the human BBB, a platform that most closely resembles the human physiological conditions at this CNS interface. Subsequent analysis also showed the ability for SARS-CoV-2 spike proteins to trigger a pro-inflammatory response on brain endothelial cells that may contribute to an altered state of BBB function. Together, these results are the first to show the direct impact that the SARS-CoV-2 spike protein could have on brain endothelial cells; thereby offering a plausible explanation for the neurological consequences seen in COVID-19 patients.
Lack of mucosal cholinergic innervation is associated with increased risk of enterocolitis in Hirschsprung’s disease
Authors: Keck Simone , Galati-Fournier Virginie , Kym Urs , Moesch Michèle , Usemann Jakob , Subotic Ulrike , Tharakan Sasha J. , Krebs Thomas , Stathopoulos Eleuthere , Schmittenbecher Peter , Cholewa Dietmar , Romero Philipp , Reingruber Bertram , Bruder Elisabeth ,   NIG study Group, Holland-Cunz Stefan
Published: June 2020

Background & Aims

Hirschsprung’s disease (HSCR) is a congenital intestinal motility disorder defined by the absence of enteric nervous cells (ganglia). The development of HSCR-associated enterocolitis remains a life-threatening complication. Absence of enteric ganglia implicates extramural innervation of acetylcholine-secreting (cholinergic) nerve fibers. Cholinergic signals have been reported to control excessive inflammation, but the impact on HSCR-associated enterocolitis is unknown.

Methods

We enrolled 44 HSCR patients in a prospective multicenter study and grouped them according to their degree of colonic mucosal cholinergic innervation using immunohistochemistry. The fiber phenotype was correlated with the tissue cytokine profile as well as immune cell frequencies using quantitative reverse-transcribed real-time polymerase chain reaction (qRT-PCR) of whole colonic tissue and fluorescence-activated cell sorting (FACS) analysis of isolated colonic immune cells. Fiber-associated immune cells were identified using confocal immunofluorescence microscopy and characterized by RNA-seq analysis. Microbial dysbiosis was analyzed in colonic patient tissue using 16S rDNA gene sequencing. Finally, the fiber phenotype was correlated with postoperative enterocolitis manifestation.

Results

We provided evidence that extrinsic mucosal innervation correlated with reduced interleukin (IL)-17 cytokine levels and T-helper-17 (Th17) cell frequencies. Bipolar CD14highmacrophages colocalized with neurons and expressed significantly less interleukin-23, a Th17-promoting cytokine. HSCR patients lacking mucosal cholinergic nerve fibers showed microbial dysbiosis and had a higher incidence of postoperative enterocolitis.

Conclusion

The mucosal fiber phenotype might serve as a new prognostic marker for enterocolitis development in HSCR patients and may offer an approach to personalized patient care and new future therapeutic options. (www.clinicaltrials.govaccessing numberNCT03617640)
Naturally mutated spike proteins of SARS-CoV-2 variants show differential levels of cell entry
Authors: Ozono Seiya , Zhang Yanzhao , Ode Hirotaka , Tan Toong Seng , Imai Kazuo , Miyoshi Kazuyasu , Kishigami Satoshi , Ueno Takamasa , Iwatani Yasumasa , Suzuki Tadaki , Tokunaga Kenzo
Published: June 2020

The causative agent of the coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is steadily mutating during continuous transmission among humans. Such mutations can occur in the spike (S) protein that binds to the angiotensin-converting enzyme-2 (ACE2) receptor and is cleaved by transmembrane protease serine 2 (TMPRSS2). However, whether S mutations affect SARS-CoV-2 infectivity remains unknown. Here, we show that naturally occurring S mutations can reduce or enhance cell entry via ACE2 and TMPRSS2. A SARS-CoV-2 S-pseudotyped lentivirus exhibits substantially lower entry than SARS-CoV S. Among S variants, the D614G mutant shows the highest cell entry, as supported by structural observations. Nevertheless, the D614G mutant remains susceptible to neutralization by antisera against prototypic viruses. Taken together, these data indicate that the D614G mutation enhances viral infectivity while maintaining neutralization susceptibility.
CD40 and CD80/86 signaling in cDC1s mediate effective neoantigen vaccination and generation of antigen-specific CX3CR1+CD8+T cells in mice
Authors: Yamauchi Takayoshi , Hoki Toshifumi , Oba Takaaki , Attwood Kristopher , Cao Xuefang , Ito Fumito
Published: June 2020

The use of tumor mutation-derived neoantigen represents a promising approach for cancer vaccines. Preclinical and early-phase human clinical studies have shown the successful induction of tumor neoepitope-directed responses; however, overall clinical efficacy of neoantigen vaccines has been limited. One major obstacle of this strategy is the prevailing lack of sufficient understanding of the mechanism underlying the generation of neoantigen-specific CD8+T cells. Here, we report a correlation between antitumor efficacy of neoantigen/toll-like receptor 3 (TLR3)/CD40 vaccination and the generation of antigen-specific CD8+T cells expressing CX3C chemokine receptor 1 (CX3CR1) in a preclinical model. Mechanistic studies using mixed bone marrow chimeras identified that CD40 and CD80/86, but not CD70 signaling in Batf3-dependent conventional type 1 dendritic cells (cDC1s) is required for antitumor efficacy of neoantigen vaccine and generation of neoantigen-specific CX3CR1+CD8+T cells. Although CX3CR1+CD8+T cells exhibited robustin vitroeffector function, depletion of this subset did not alter the antitumor efficacy of neoantigen/TLR3/CD40 agonists vaccination, suggesting that the expanded CX3CR1+CD8+T cell subset represents the post-differentiatedin vivoeffective CX3CR1-negative CD8+T cell subset. Taken together, our results reveal a critical role of CD40 and CD80/86 signaling in cDC1s in antitumor efficacy of neoantigen-based therapeutic vaccines, and implicate the potential utility of CX3CR1 as a circulating predictive T-cell biomarker in vaccine therapy.
Multi Locus View : An Extensible Web Based Tool for the Analysis of Genomic Data
Authors: Sergeant Martin J , Hughes Jim R , Hentges Lance , Lunter Gerton , Downes Damien J , Taylor Stephen
Published: June 2020

Motivation

Tracking and understanding data quality, analysis and reproducibility are critical concerns in the biological sciences. This is especially true in genomics where Next Generation Sequencing (NGS) based technologies such as ChIP-seq, RNA-seq and ATAC-seq are generating a flood of genome-scale data. These data-types are extremely high level and complex with single experiments capable of mapping ten to hundreds of thousands of biologically meaningful events across the genome. However, such data are usually processed with automated tools and pipelines, generating tabular outputs and static visualizations. These are difficult to interact with and require substantial bioinformatic skills to manipulate and query. Similarly, interpretation is normally made at a high level without the ability to visualise the underlying data in detail and so the complexity and quality of the real underlying biological signal is lost. Also genomics datasets require integration with other genomics datasets to be properly interpreted and this integration with multiple tracks again requires substantial bioinformatics skills and is difficult to visualise across multiple pertinent datasets. Conventional genome browsers do allow for the detailed visualisation of multiple tracks but are limited to browsing single locations and do not allow for interactions with the dataset as a whole. MLV has been developed to allow users to fluidly interact with genomics datasets at multiple scales, from complete metadata labelled and clustered populations to detailed representations of individual elements. It has inbuilt tools to integrate signals across multiple datasets and to perform dimensionality reduction and clustering analysis based on the extracted signal, allowing for the high-level analysis of complex datasets while maintaining visualisation of the fine grain structure of the data. MLV’s ability to visualise clustering within the data combined with efficient tools for large-scale tagging of individual elements makes it a unique tool for the generation of annotated datasets for modern machine learning approaches.

Results

Multi Locus View (MLV) is a web based tool for the visualisation, analysis and annotation of Next Generation Sequencing data sets. The user is able to browse the raw data, cluster, and combine the data with other analysis. Intuitive filtering and visualisation then enables the user to quickly locate and annotate regions of interest. User datasets can then be shared with other users or made public for quick assessment from the academic community. MLV is publically available athttps://mlv.molbiol.ox.ac.ukand the source code is available athttps://github.com/Hughes-Genome-Group/mlv
Linear-time cluster ensembles of large-scale single-cell RNA-seq and multimodal data
Authors: Do Van Hoan , Ringeling Francisca Rojas , Canzar Stefan
Published: June 2020

A fundamental task in single-cell RNA-seq (scRNA-seq) analysis is the identification of transcriptionally distinct groups of cells. Numerous methods have been proposed for this problem, with a recent focus on methods for the cluster analysis of ultra-large scRNA-seq data sets produced by droplet-based sequencing technologies. Most existing methods rely on a sampling step to bridge the gap between algorithm scalability and volume of the data. Ignoring large parts of the data, however, often yields inaccurate groupings of cells and risks overlooking rare cell types. We propose methodSpecterthat adopts and extends recent algorithmic advances in (fast) spectral clustering. In contrast to methods that cluster a (random) subsample of the data, we adopt the idea of landmarks that are used to create a sparse representation of thefulldata from which a spectral embedding can then be computed in linear time. We exploit Specter’s speed in a cluster ensemble scheme that achieves a substantial improvement in accuracy over existing methods and that is sensitive to rare cell types. Its linear time complexity allows Specter to scale to millions of cells and leads to fast computation times in practice. Furthermore, on CITE-seq data that simultaneously measures gene and protein marker expression we demonstrate that Specter is able to utilize multimodal omics measurements to resolve subtle transcriptomic differences between subpopulations of cells. Specter is open source and available athttps://github.com/canzarlab/Specter.
Bacterial flagellins: does only size matter?
Authors: Shchyogolev Sergei Yu. , Burygin Gennady L. , Matora Larisa Yu.
Published: June 2020

The protein sequences of a number ofAzospirillaceaestrains were investigated that contain the pf00669 domain and belong to a variety of bacterial flagellum systems with unusually large flagellin sizes. A set of tools for the homologous and template-based modeling of protein structures was used to reveal the probability of alternative folding, i.e., generation of two protein models with significantly different 3D structures and functions (flagellin or S-layer protein) for a single amino acid sequence.
Beta2 oscillations in the hippocampal-cortical novelty detection circuit
Authors: França Arthur S C , Borgesius Nils Z. , Souza Bryan C. , Cohen Mike X
Published: June 2020

Novelty detection is a core feature of behavioral adaptation, and involves cascades of neuronal responses – from initial evaluation of the stimulus to the encoding of new representations – resulting in the behavioral ability to respond to unexpected inputs. In the past decade, a new important novelty detection feature, beta2 (~20 - 30 Hz) oscillations, has been described in the hippocampus. However, the interactions between beta2 and the hippocampal network are unknown, as well as the role – or even the presence – of beta2 in other areas involved with novelty detection. In this work, we used behavioral tasks that modulate novelty in combination with multisite local field potential (LFP) recordings targeting regions involved with novelty detection processing in mice – the CA1 region of the hippocampus, parietal cortex and mid-prefrontal cortex – to describe the oscillatory dynamics associated with novelty. We found that transient beta2 power increases were observed only during interaction with novel contexts and objects, but not with familiar contexts and objects. Also, robust theta-gamma phase-amplitude coupling was observed during the exploration of novel environments. Surprisingly, bursts of beta2 power had strong coupling with the phase of delta-range oscillations. Finally, the parietal and mid-frontal cortices had strong coherence with the hippocampus in both theta and beta2. These results highlight the importance of beta2 oscillations in a larger hippocampal-cortical circuit, suggesting that beta2 is a mechanism for detecting and modulating behavioral adaptation to novelty.
Structural Determinants of Cholesterol Recognition in Helical Integral Membrane Proteins
Authors: Marlow B. , Kuenze G. , Li B. , Sanders C. , Meiler J.
Published: June 2020

Cholesterol (CLR) is an integral component of mammalian membranes. It has been shown to modulate membrane dynamics and alter integral membrane protein (IMP) function. However, understanding the molecular mechanisms of these processes is complicated by limited and conflicting structural data: Specifically, in co-crystal structures of CLR-IMP complexes it is difficult to distinguish specific and biologically relevant CLR-IMP interactions from a nonspecific association captured by the crystallization process. The only widely recognized search algorithm for CLR-IMP interaction sites is sequence-based, i.e. searching for the so-called ‘CRAC’ or ‘CARC’ motifs. While these motifs are present in numerous IMPs, there is inconclusive evidence to support their necessity or sufficiency for CLR binding. Here we leverage the increasing number of experimental CLR-IMP structures to systematically analyze putative interaction sites based on their spatial arrangement and evolutionary conservation. From this analysis we create three-dimensional representations of general CLR interaction sites that form clusters across multiple IMP classes and classify them as being either specific or nonspecific. Information gleaned from our characterization will eventually enable a structure-based approach for prediction and design of CLR-IMP interaction sites.

SIGNIFICANCE

CLR plays an important role in composition and function of membranes and often surrounds and interacts with IMPs. It is a daunting challenge to disentangle CLRs dual roles as a direct modulator of IMP function through binding or indirect actor as a modulator of membrane plasticity. Only recently studies have delved into characterizing specific CLR-IMP interactions. We build on this previous work by using a combination of structural and evolutionary characteristics to distinguish specific from nonspecific CLR interaction sites. Understanding how CLR interacts with IMPs will underpin future development towards detecting and engineering CLR-IMP interaction sites.
Identification of mtROS-sensitive processes in activated CD4+T cells
Authors: Meston Daniel , Bi Wenjie , Rietschel Tina , van Ham Marco , Leichert Lars I. , Jänsch Lothar
Published: June 2020

T lymphocytes are key components in adaptive immunity and their activation naturally involves mitochondrial-derived oxygen species (mtROS). In particular, H2O2has been implicated as an important signaling molecule regulating major T cell functions. H2O2targets the oxidation status of functional cysteine residues but knowledge if and where this happens in T cell signaling networks is widely missing. This study aimed to identify mtROS-sensitive processes in activated primary human CD4+T cells. By using a thiol-specific redox proteomic approach we examined the oxidation state of 4784 cysteine-containing peptides ofex vivostimulated T cells from healthy individuals. Upon activation, a shift in oxidation was observed at catalytic cysteine residues of peroxiredoxins (PRDX5 & PRDX6), and T cells were found to maintain their global thiol-redox homeostasis. In parallel, a distinct set of 88 cysteine residues were found to be differentially oxidized upon T cell activation suggesting novel functional thiol switches. In mitochondria, cysteine oxidations selectively modified regulators of respiration (NDUFA2, NDUFA8, and UQCRH) confirming electron leakage from electron transport complexes I and III. The majority of oxidations occurred outside mitochondria and enriched sensitive thiols at regulators of cytoskeleton dynamics (e.g. CYFIP2 and ARPC1B) and known immune functions including the non-receptor tyrosine phosphatase PTPN7. Conversely, cysteine reduction occurred predominantly at transcriptional regulators and sites that coordinate zinc-binding in zinc-finger motifs. Indeed, fluorescence microscopy revealed a colocalization of zinc-rich microenvironments and mitochondria in T cells suggesting mtROS-dependent zinc-release of identified transcriptional regulators including ZFP36, RPL37A and CRIP2. In conclusion, this study complements knowledge on the mtROS signaling network and suggests zinc-dependent thiol switches as a mechanism of how mtROS affects transcription and translation in T cells.
Novel ACE2-IgG1 fusions with improvedin vitroandin vivoactivity against SARS-CoV2
Authors: Iwanaga Naoki , Cooper Laura , Rong Lijun , Beddingfield Brandon , Crabtree Jackelyn , Tripp Ralph A. , Qin Xuebin , Kolls Jay K.
Published: June 2020

SARS-CoV2, the etiologic agent of COVID-19, uses ACE2 as a cell entry receptor. Soluble ACE2 has been shown to have neutralizing antiviral activity but has a short half-life and no active transport mechanism from the circulation into the alveolar spaces of the lung. To overcome this, we constructed an ACE2-human IgG1 fusion protein with mutations in the catalytic domain of ACE2. This fusion protein contained a LALA mutation that abrogates Fcrγ binding, but retains FcRN binding to prolong the half-life, as well as achieve therapeutic concentrations in the lung lavage. Interestingly, a mutation in the catalytic domain of ACE2, MDR504, completely abrogated catalytic activity, but significantly increased binding to SARS-CoV2 spike proteinin vitro. This feature correlated with more potent viral neutralization in a plaque assay. Parental administration of the protein showed stable serum concentrations with a serum half-life of ∼ 145 hours with excellent bioavailability in the epithelial lining fluid of the lung. Prophylactic administration of MDR504 significantly attenuated SARS-CoV2 infection in a murine model. These data support that the MDR504 hACE2-Fc is an excellent candidate for pre or post-exposure prophylaxis or treatment of COVID-19.