bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic variations in the host dependency factors ALCAM and TPST2 impact HIV-1 disease progression
Authors: Kruize Zita , Maurer Irma , Boeser-Nunnink Brigitte D.M. , Booiman Thijs , Kootstra Neeltje A.
Published: April 2020

Objectives:

Recently, the activated leukocyte cell adhesion molecule (ALCAM) and tyrosylprotein sulfotransferase 2 (TPST2) have been identified as important host dependency factors (HDFs) for in-vitro HIV-1 replication. To determine whether these genes play a role in HIV-1 pathogenesis, we analysed whether naturally occurring genetic variations were associated with the clinical course of infection.

Design/methods:

Single nucleotide polymorphisms (SNPs) in ALCAM and TPST2 were analysed in a cohort of 304 HIV-1-infected men who have sex with men and survival analysis was used to determine their effect on the outcome of untreated HIV-1 infection. Flowcytometry was used to determine the effect of SNPs on CD4+ T-cell activation prior to HIV-1 infection and 1 and 5 years after infection. In-vitro HIV-1 infections were performed to analyse the effect of the SNPs on HIV-1 replication.

Results:

We observed that the minor allele of rs1344861 in ALCAM was associated with accelerated disease progression, whereas the minor allele of rs9613199 in TPST2 was associated with delayed disease progression. In-vitro infection assays did not demonstrate any differences in HIV-1 replication associated with rs9613199. However, the increase in CD4+ T-cell immune activation levels during HIV-1 infection was less pronounced in infected individuals homozygous for rs9613199, which is in agreement with delayed disease progression.

Conclusion:

Our data demonstrate that ALCAM and TPST2 play a role in HIV-1 pathogenesis. SNPs in these genes, without known functional implications, had a major effect on disease progression, and therefore, these HDFs may be attractive and effective targets for new treatment strategies.
Enhancing natural killer cell function with gp41-targeting bispecific antibodies to combat HIV infection
Authors: Ramadoss Nitya S. , Zhao Nancy Q. , Richardson Barbra A. , Grant Philip M. , Kim Peter S. , Blish Catherine A.
Published: April 2020

Objective(s):

The aim of this study was to develop and evaluate the activity of bispecific antibodies (bsAbs) to enhance natural killer (NK) cell antibody-dependent cellular cytotoxicity (ADCC) against HIV-infected cells.

Design:

These bsAbs are based on patient-derived antibodies targeting the conserved gp41 stump of HIV Env, and also incorporate a high-affinity single chain variable fragment (scFv) targeting the activating receptor CD16 on NK cells. Overall, we expect the bsAbs to provide increased affinity and avidity over their corresponding mAbs, allowing for improved ADCC activity against Env-expressing target cells.

Methods:

bsAbs and their corresponding mAbs were expressed in 293T cells and purified. The binding of bsAbs and mAbs to their intended targets was determined using Bio-Layer Interferometry, as well as flow cytometry based binding assays on in-vitro infected cells. The ability of these bsAbs to improve NK cell activity against HIV-infected cells was tested using in-vitro co-culture assays, using flow cytometry and calcein release to analyse NK cell degranulation and target cell killing, respectively.

Results:

The bsAbs-bound gp41 with similar affinity to their corresponding mAbs had increased affinity for CD16. The bsAbs also bound to primary CD4+ T cells infected in vitro with two different strains of HIV. In addition, the bsAbs induce increased NK cell degranulation and killing of autologous HIV-infected CD4+ T cells.

Conclusion:

On the basis of their in-vitro killing efficacy, bsAbs may provide a promising strategy to improve NK-mediated immune targeting of infected cells during HIV infection.
Pediatric trauma triage: A Pediatric Trauma Society Research Committee systematic review
Authors: Mora Maria Carmen , Veras Laura , Burke Rita V. , Cassidy Laura D. , Christopherson Nathan , Cunningham Aaron , Jafri Mubeen , Marion Erica , Lidsky Karen , Yanchar Natalie , Wu Lin , Gosain Ankush
Published: April 2020

BACKGROUND

Significant variability exists in the triage of injured children with most systems using mechanism of injury and/or physiologic criteria. It is not well established if existing triage criteria predict the need for intervention or impact morbidity and mortality. This study evaluated existing evidence for pediatric trauma triage. Questions defined a priori were as follows: (1) Do prehospital trauma triage criteria reduce mortality? (2) Do prehospital trauma scoring systems predict outcomes? (3) Do trauma center activation criteria predict outcomes? (4) Do trauma center activation criteria predict need for procedural or operative interventions? (5) Do trauma bay pediatric trauma scoring systems predict outcomes? (6) What secondary triage criteria for transfer of children exist?

METHODS

A structured, systematic review was conducted, and multiple databases were queried using search terms related to pediatric trauma triage. The literature search was limited to January 1990 to August 2019. Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) methodology was applied with the methodological index for nonrandomized studies tool used to assess the quality of included studies. Qualitative analysis was performed.

RESULTS

A total of 1,752 articles were screened, and 38 were included in the qualitative analysis. Twelve articles addressed questions 1 and 2, 21 articles addressed question 3 to 5, and five articles addressed question 6. Existing literature suggest that prehospital triage criteria or scoring systems do not predict or reduce mortality, although selected physiologic parameters may. In contrast, hospital trauma activation criteria can predict the need for procedures or surgical intervention and identify patients with higher mortality; again, physiologic signs are more predictive than mechanism of injury. Currently, no standardized secondary triage/transfer protocols exist.

CONCLUSION

Evidence supporting the utility of prehospital triage criteria for injured children is insufficient, while physiology-based trauma system activation criteria do appropriately stratify injured children. The absence of strong evidence supports the need for further prehospital and secondary transfer triage-related research.

LEVEL OF EVIDENCE

Systematic review study, level II.
A comprehensive economic optimization methodology of divided wall columns for biopolyol separation
Authors: Chen Tao , Lv Lingjuan , Chen Yuanzhi , Bai Peng
Published: April 2020

Global energetic and environmental crises have attracted worldwide attention in recent years. Biomass is an important direction of development for limiting greenhouse gas emissions and replacing fossil fuel. As downstream products of biomass, some industrially valuable polyols are costly to separate via conventional distillation due to their near volatility. The use of fully heat-integrated divided wall columns (DWCs), which carry energy and equipment investment savings, is a promising technique for purifying biopolyol products. However, the design of DWCs is complex because of the greater freedom of units, so the optimization of all variables is essential to minimize the cost of separation. A response surface methodology (RSM)-based Box–Behnken design (BBD) was proposed and applied to study the interactions between groups of factors and the effects of variables on total annual cost (TAC) savings. The optimization of global variables with RSM was confirmed to be a powerful and reliable method, and the TAC savings reached 41.09% compared to conventional distillation. In short, efficient design, lower costs and energy savings for polyol separation will promote the wide application of environmentally friendly biopolyol.
Re-imaging the intentional stance
Authors: Abu-Akel Ahmad M. , Apperly Ian A. , Wood Stephen J. , Hansen Peter C.
Published: April 2020

The commonly used paradigm to investigate Dennet's ‘intentional stance’ compares neural activation when participants compete with a human versus a computer. This paradigm confounds whether the opponent is natural or artificial and whether it is intentional or an automaton. This functional magnetic resonance imaging study is, to our knowledge, the first to investigate the intentional stance by orthogonally varying perceptions of the opponents' intentionality (responding actively or passively according to a script) and embodiment (human or a computer). The mere perception of the opponent (whether human or computer) as intentional activated the mentalizing network: the temporoparietal junction (TPJ) bilaterally, right temporal pole, anterior paracingulate cortex (aPCC) and the precuneus. Interacting with humans versus computers induced activations in a more circumscribed right lateralized subnetwork within the mentalizing network, consisting of the TPJ and the aPCC, possibly reflective of the tendency to spontaneously attribute intentionality to humans. The interaction between intentionality (active versus passive) and opponent (human versus computer) recruited the left frontal pole, possibly in response to violations of the default intentional stance towards humans and computers. Employing an orthogonal design is important to adequately capture Dennett's conception of the intentional stance as a mentalizing strategy that can apply equally well to humans and other intentional agents.
Genetic variability in the expression of the SARS-CoV-2 host cell entry factors across populations
Authors: Ortiz-Fernández Lourdes , Sawalha Amr H
Published: April 2020

The entry of SARS-CoV-2 into host cells is dependent upon angiotensin-converting enzyme 2 (ACE2), which serves as a functional attachment receptor for the viral spike glycoprotein, and the serine protease TMPRSS2 which allows fusion of the viral and host cell membranes. We devised a quantitative measure to estimate genetic determinants ofACE2andTMPRSS2expression and applied this measure to >2,500 individuals. Our data show significant variability in genetic determinants ofACE2andTMPRSS2expression among individuals and between populations, and demonstrate a genetic predisposition for lower expression levels of both key viral entry genes in African populations. These data suggest that genetic factors might lead to lower susceptibility for SARS-CoV-2 infection in African populations and that host genetics might help explain inter-individual variability in disease susceptibility and severity of COVID-19.
Nonmedical Masks in Public for Respiratory Pandemics: Droplet Retention by Two-Layer Textile Barrier Fully Protects Germ-free Mice from Bacteria in Droplets
Authors: Rodriguez-Palacios Alex , Conger Mathew , Cominelli Fabio
Published: April 2020

Due to the shortage of masks during the pandemic, we recently demonstrated that household textiles are effective environmental droplet barriers (EDBs) with identical droplet retention potential as medical masks. To further promote the implementation of auniversal community droplet reduction solutionbased on a synchronized encouragement/enforcement of mask utilization by the public based on widely available textiles (mask fabrication without the need for sewing machines), here we conducted a study using germ-free mice to determine to what extent textiles were effectivein vivo. Using a bacterial-suspension spray simulation model of droplet ejection (mimicking a sneeze), we quantified the extent by which 100% cotton textile prevented the contamination of germ-free animals on the other side of the textile-barrier (simulating a properly worn mask). Of relevance, all mice protected with textiles remained germ-free after two sprays (inoculation dose: >600 bacterial droplet units per 56.75cm2) compared to the contamination of mice not protected by a textile (0/12 vs 6/6, Fisher’s exact, p<0.0001). In a second phase of the experiment with 12 germ-free mice exposed again to 10-fold more droplets remained germ-free, while 100% of mice at 180cm became colonized with a single spray (0/8 vs 4/4, Fisher exact, p=0.002). Collectively, barriers protected all mice (even with low-density textiles, heavy vs. light fabric, T-test, p=0.0028) when using textile-EDB to cover the cages (0/20 vs 10/10, Fisher exact, p<0.0001). This study demonstrated, in vivo, that widely available household textiles are 100% effective at preventing contamination of the environment and the exposed animals by microbe-carrying droplets.
Towards biomarkers for outcomes after pancreatic ductal adenocarcinoma and ischemic stroke, with focus on (co-)morbidity and aging / cellular senescence (SASKit): protocol for a prospective cohort study
Authors: Henze Larissa , Walter Uwe , Escobar Hugo Murua , Junghanß Christian , Jaster Robert , Köhling Rüdiger , Lange Falko , Salehzadeh-Yazdi Ali , Wolkenhauer Olaf , Hamed Mohamed , Barrantes Israel , Palmer Daniel , Möller Steffen , Kowald Axel , Heussen Nicole , Fuellen Georg
Published: April 2020

Aging-related processes such as cellular senescence are believed to underlie the accumulation of diseases in time, causing (co-)morbidity, including cancer, thromboembolism and stroke. Intervening into these processes may delay, stop or reverse morbidity. To study the link between (co-)morbidity and aging, by exploring biomarkers and molecular mechanisms of disease-triggered deterioration, we will recruit 50 patients with pancreatic ductal adenocarcinoma, 50 patients with (thromboembolic) ischemic stroke and 50 controls, at Rostock University Medical Center. We will gather routine blood data, clinical performance measurements and patient-reported outcomes at up to 9 points in time, and in-depth transcriptomics & proteomics at two early time points. Aiming for clinically relevant biomarkers, the primary outcome is a composite of probable sarcopenia, clinical performance (described by ECOG Performance Status for patients with pancreatic ductal adenocarcinoma and the Modified Rankin Scale for patients with stroke) and quality of life. Further outcomes cover other aspects of morbidity such as cognitive decline, and of comorbidity such as vascular or cancerous events. The data analysis is comprehensive in that it includes biostatistics & machine learning, both following standard role models & additional explorative approaches. Predictive biomarkers for interventions addressing senescence may become available if the biomarkers that we find are predominantly related to aging / cellular senescence. Similarly, diagnostic biomarkers will be explored for their relationship to aging / cellular senescence. Our findings will require validation in independent studies, and our dataset shall be useful to validate the findings of other studies. In some of the explorative analyses, we shall include insights from systems biology modeling as well as insights from preclinical animal models. We humbly suggest that our detailed study protocol and data analysis plan may also guide other biomarker exploration trials.

In Brief

The SASKit (“Senescence-Associated Systems diagnostics Kit for cancer and stroke”) study primarily aims to discover novel biomarkers for deterioration of health and (co-)morbidities triggered by pancreatic ductal adenocarcinoma or ischemic stroke.
Neutrophil extracellular traps (NETs) as markers of disease severity in COVID-19
Authors: Zuo Yu , Yalavarthi Srilakshmi , Shi Hui , Gockman Kelsey , Zuo Melanie , Madison Jacqueline A. , Blair Christopher , Weber Andrew , Barnes Betsy J. , Egeblad Mikala , Woods Robert J. , Kanthi Yogendra , Knight Jason S.
Published: April 2020

In severe cases of coronavirus disease 2019 (COVID-19), viral pneumonia progresses to respiratory failure. Neutrophil extracellular traps (NETs) are extracellular webs of chromatin, microbicidal proteins, and oxidant enzymes that are released by neutrophils to contain infections. However, when not properly regulated, NETs have potential to propagate inflammation and microvascular thrombosis—including in the lungs of patients with acute respiratory distress syndrome. While elevated levels of blood neutrophils predict worse outcomes in COVID-19, the role of NETs has not been investigated. We now report that sera from patients with COVID-19 (n=50 patients, n=84 samples) have elevated levels of cell-free DNA, myeloperoxidase(MPO)-DNA, and citrullinated histone H3 (Cit-H3); the latter two are highly specific markers of NETs. Highlighting the potential clinical relevance of these findings, cell-free DNA strongly correlated with acute phase reactants including C-reactive protein, D-dimer, and lactate dehydrogenase, as well as absolute neutrophil count. MPO-DNA associated with both cell-free DNA and absolute neutrophil count, while Cit-H3 correlated with platelet levels. Importantly, both cell-free DNA and MPO-DNA were higher in hospitalized patients receiving mechanical ventilation as compared with hospitalized patients breathing room air. Finally, sera from individuals with COVID-19 triggered NET release from control neutrophils in vitro. In summary, these data reveal high levels of NETs in many patients with COVID-19, where they may contribute to cytokine release and respiratory failure. Future studies should investigate the predictive power of circulating NETs in longitudinal cohorts, and determine the extent to which NETs may be novel therapeutic targets in severe COVID-19.
An Objective Structural and Functional Reference Standard for Diagnostic Studies in Glaucoma
Authors: Mariottoni Eduardo B. , Jammal Alessandro A. , Berchuck Samuel I. , Tavares Ivan M. , Medeiros Felipe A.
Published: April 2020

Purpose

To propose a reference standard for the definition of glaucomatous optic neuropathy (GON) consisting of objective parameters from spectral-domain optical coherence tomography (SDOCT) and standard automated perimetry (SAP), and to apply it to the development and evaluation of a deep learning (DL) algorithm to detect glaucomatous damage on fundus photographs.

Design

Retrospective, cross-sectional study.

Methods

Data were extracted from the Duke Glaucoma Registry and included 2,927 eyes of 2,025 participants with fundus photos, SDOCT and SAP acquired within six months. Eyes were classified as GON versus normal based on a combination of objective SDOCT and SAP criteria. A DL convolutional neural network was trained to predict the probability of GON from fundus photos. The algorithm was tested on an independent sample with performance assessed by sensitivity, specificity, area under the receiver operating characteristic curve (AUC), and likelihood ratios (LR).

Results

The test sample included 585 eyes of 405 participants. The median DL probability of glaucoma in eyes with GON was 99.8% versus 0.03% for normal eyes (P < 0.001), with an AUC of 0.92 and sensitivity of 77% at 95% specificity. LRs indicated that the DL algorithm provided large changes in the post-test probability of disease for the majority of eyes.

Conclusions

The DL algorithm had high performance to discriminate eyes with GON from normal. The newly proposed objective definition of GON used as reference standard may increase the comparability of diagnostic studies of glaucoma across devices and populations, helping to improve the development and assessment of tests in clinical practice.
Single Nucleus Multiomic Profiling Reveals Age-Dynamic Regulation of Host Genes Associated with SARS-CoV-2 Infection
Authors: Wang Allen , Chiou Joshua , Poirion Olivier B , Buchanan Justin , Valdez Michael J , Verheyden Jamie M , Hou Xiaomeng , Guo Minzhe , Newsome Jacklyn M , Kudtarkar Parul , Faddah Dina A , Zhang Kai , Young Randee E , Barr Justinn , Misra Ravi , Huyck Heidie , Rogers Lisa , Poole Cory , Whitsett Jeffery A. , Pryhuber Gloria , Xu Yan , Gaulton Kyle J , Preissl Sebastian , Sun Xin ,   NHLBI LungMap Consortium
Published: April 2020

Respiratory failure is the leading cause of COVID-19 death and disproportionately impacts adults more than children. Here, we present a large-scale snATAC-seq dataset (90,980 nuclei) of the human lung, generated in parallel with snRNA-seq (46,500 nuclei), from healthy donors of ~30 weeks, ~3 years and ~30 years of age. Focusing on genes implicated in SARS-CoV-2 cell entry, we observed an increase in the proportion of alveolar epithelial cells expressingACE2andTMPRSS2in adult compared to young lungs. Consistent with expression dynamics, 10 chromatin peaks linked toTMPRSS2exhibited significantly increased activity with age and harbored IRF and STAT binding sites. Furthermore, we identified 14 common sequence variants in age-increasing peaks with predicted regulatory function, including several associated with respiratory traits andTMPRSS2expression. Our findings reveal a plausible contributor to why children are more resistant to COVID-19 and provide an epigenomic basis for transferring this resistance to older populations.
Laparoscopic vs open gastrectomy- An updated metanalysis of randomized control trials for short term outcomes
Authors: Vasavada Bhavin , Patel Hardik
Published: April 2020

Introduction

Aim of this metanalysis was to compare short term outcomes of laparoscopic and open gastrectomy for gastric cancer.

Material and methods

EMBASE, MEDLINE, PubMed and the Cochrane Database were searched for randomized control trials comparing outcomes in patients undergoing laparoscopic gastrectomies with those patients undergoing open gastrectomies. The primary outcome was 30 days morbidity and mortality. Secondary outcomes studied included length of stay, blood loss, d2gastrectomies, lymph node retrieval, operative time, distal gastrectomy, wound complications and intraabdominal complications Systemic review and Metanalysis were done according to MOOSE and PRISMA guidelines.

Results

Morbidity was significantly low in laparoscopic group (P=0.003).There was no significant difference between mortality between the two groups. (P=0.75). There fewer wound complications in laparoscopic group, no difference intra-abdominal complications in both the groups. Blood loss was significantly lesser in laparoscopic group.(p <0.001). Hospital stay was similar in laparoscopic group. (P=0.30). Operative time was significantly higher in laparoscopic group. (P< 0.001). Laparoscopic group patients had less number of lymph node retrieval compared to laparoscopic group.(p = 0.002). Laparoscopic group also contained similar advanced staged gastric cancer than open gastrectomies. (p= 0.64)

Conclusions

Laparoscopic gastrectomies were associated with better short term outcomes.
Novel BRAF fusions in pediatric histiocytic neoplasms define distinct therapeutic responsiveness to RAF paradox breakers
Authors: Jain Payal , Surrey Lea F. , Straka Joshua , Russo Pierre , Womer Richard , Li Marilyn M. , Storm Phillip B. , Waanders Angela , Hogarty Michael D. , Resnick Adam , Picarsic Jennifer
Published: April 2020

Pediatric histiocytic neoplasms are clonal hematopoietic disorders driven by mutations activating the mitogen-activated protein kinase (MAPK) pathway, such as BRAF-V600E. In non-BRAFV600E cases, we investigated alternative MAPK mutations and found two novel BRAF gene fusions. We investigated the distinct responsiveness of novel BRAF fusions to RAFi therapies and explored the mechanistic basis of such differential responses compared to other BRAF fusions. Two histiocytic patient tumors were analyzed using the CHOP Comprehensive Next-Gen Sequencing Solid Tumor Panel and a targeted RNA-seq panel for 106 fusion partner genes. In the two M- and L-type histiocytic neoplasms assessed, we found novel and rare BRAF gene fusions, MTAP-BRAF and MS4A6A-BRAF, respectively. Both BRAF fusions activated the MAPK/ PI3K pathways and showed homo- and hetero-dimerization with BRAF and the respective N-terminal fusion partner. In contrast to common BRAF fusions, MTAP-BRAF and MS4A6A-BRAF did not respond to PLX8394 due to a lack of disruption of active fusion homo- and hetero-dimers, which was in turn due to the untargeted, stable dimerization mediated by the N-terminal fusion partners. Conversely, we observed robust suppression with LY3009120 that bound fusion dimers and kept them in an inactivate confirmation. MEKi were found to successfully suppress fusion driven signaling and oncogenic phenotypes. Our finding that PLX8394 does not disrupt MTAP-BRAF or MS4A6A-BRAF dimerization due to contribution of N-terminal partners defines a novel paradigm for the distinct mechanisms sought by BRAF fusions in response to RAFi therapy. Overall, this study highlights the unique and differential biology hijacked by BRAF fusions in response to RAFi and further warrants detailed mechanistic classification of BRAF fusions based on their responsiveness to targeted agents.
Marburg and Ebola virus infections elicit a complex, muted inflammatory state in bats
Authors: Jayaprakash Anitha D. , Ronk Adam J. , Prasad Abhishek N. , Covington Michael F. , Stein Kathryn R. , Schwarz Toni M. , Hekmaty Saboor , Fenton Karla A. , Geisbert Thomas W. , Basler Christopher F. , Bukreyev Alexander , Sachidanandam Ravi
Published: April 2020

The Marburg and Ebola filoviruses cause a severe, often fatal, disease in humans and nonhuman primates but have only subclinical effects in bats, including Egyptian rousettes, which are a natural reservoir of Marburg virus. A fundamental question is why these viruses are highly pathogenic in humans but fail to cause disease in bats. To understand how bats resist the disease caused by filoviruses, we infected one cohort of Egyptian rousette bats with Marburg virus and another cohort with Ebola virus and harvested multiple tissues for mRNA expression analysis. While virus transcripts were found primarily in the liver, Principal component analysis (PCA) revealed coordinated changes across multiple tissues. Gene signatures in kidney and liver pointed at induction of vasodilation, reduction of coagulation and changes in the regulation of iron metabolism. Signatures of immune response detected in spleen and liver indicated a robust anti-inflammatory state signified by macrophages in the M2 state and an active T cell response. Many of the responsive genes were found to be evolutionarily divergent, providing a framework for understanding the differences in outcomes of filovirus infections between bats and humans. In this study, we outline multiple interconnected pathways that respond to infection by MARV and EBOV, providing insights into the complexity of the mechanisms that enable bats to resist the disease caused by filoviral infections. The results have the potential to aid in the development of new strategies to effectively mitigate and treat the disease caused by these viruses in humans.
High-surety isothermal amplification and detection of SARS-CoV-2, including with crude enzymes
Authors: Bhadra Sanchita , Riedel Timothy E. , Lakhotia Simren , Tran Nicholas D. , Ellington Andrew D.
Published: April 2020

Isothermal nucleic acid amplification tests (iNAT), such as loop-mediated isothermal amplification (LAMP), are good alternatives to polymerase chain reaction (PCR)-based amplification assays, especially for point-of-care and low resource use, in part because they can be carried out with relatively simple instrumentation. However, iNATs can generate spurious amplicons, especially in the absence of target sequences, resulting in false positive results. This is especially true if signals are based on non-sequence-specific probes, such as intercalating dyes or pH changes. In addition, pathogens often prove to be moving, evolving targets, and can accumulate mutations that will lead to inefficient primer binding and thus false negative results. Internally redundant assays targeting different regions of the target sequence can help to reduce such false negatives. Here we describe rapid conversion of three previously described SARS-CoV-2 LAMP assays that relied on non-sequence-specific readout into assays that can be visually read using sequence-specific fluorogenic oligonucleotide strand exchange (OSD) probes. We evaluate one-pot operation of both individual and multiplex LAMP-OSD assays and demonstrate detection of SARS-CoV-2 virions in crude human saliva.
Nairobi Sheep Disease Virus: a historical and epidemiological perspective
Authors: Krasteva Stephanie , Jara Manuel , Frias-De-Diego Alba , Machado Gustavo
Published: April 2020

Nairobi Sheep Disease virus (NSDv) is a zoonotic and tick-borne disease that can cause over 90% mortality in small ruminants. NSDv has historically circulated in East Africa and has recently emerged in the Asian continent. Despite efforts to control the disease, some regions, mostly in warmer climates, persistently report disease outbreaks. Consequently, it is necessary to understand how environmental tolerances and factors that influence transmission may shed light on its possible emergence in other regions. In this study, we quantified the available literature of NSDv from which occurrence data was extracted. In total, 308 locations from Uganda, Kenya, Tanzania, Somalia, India, Sri Lanka and China were coupled with landscape conditions to reconstruct the ecological conditions for NSDv circulation and identify areas of potential disease transmission risk. Our results identified areas suitable for NSDv in Ethiopia, Malawi, Zimbabwe, Southeastern China, Taiwan, and Vietnam. Unsuitable areas included Democratic Republic of Congo, Zambia, and Southern Somalia. In summary, soil moisture, livestock density, and precipitation predispose certain areas to NSDv circulation. It is critical to investigate the epidemiology of NSDv in order to promote better allocation of resources to control its spread in regions that are more at risk. This will help reduce disease impact worldwide as climate change will favor emergence of such vector-borne diseases in areas with dense small ruminant populations.
Association of common genetic variants in theCPSF7andSDHAF2genes with Canine Idiopathic Pulmonary Fibrosis in the West Highland White Terrier
Authors: Piras Ignazio S. , Bleul Christiane , Siniard Ashley , Wolfe Amanda J. , De Both Matthew D. , Hernandez Alvaro G. , Huentelman Matthew J.
Published: April 2020

Canine Idiopathic Pulmonary Fibrosis (CIPF) is a chronic fibrotic lung disease that is observed at a higher frequency in the West Highland White Terrier dog breed (WHWT) and may have molecular pathological overlap with human lung fibrotic disease. We conducted a Genome-Wide Association Study (GWAS) in the WHWT using Whole Genome Sequencing (WGS) to discover genetic variants associated with CIPF. Saliva-derived DNA samples were sequenced using the Riptide™ DNA library prep kit. After quality controls, 28 affected, 44 unaffected and 1,843,695 informative Single Nucleotide Polymorphisms (SNPs) were included in the GWAS. Data were analyzed both at the single SNP and gene levels using the GEMMA and GATES methods, respectively. We detected significant signals at the gene level in both theCPSF7andSDHAF2genes (adjusted p = 0.016 and p = 0.025, respectively), two overlapping genes located on chromosome 18. The top SNP for both genes was rs22669389, however it did not reach genome-wide significance in the GWAS (adjusted p = 0.078). Our studies provide, for the first time, candidate loci for CIPF in the WHWT.CPSF7was recently associated with lung adenocarcinoma further highlighting the potential relevance of our results since IPF and lung cancer share several pathological mechanisms.
Global trends in biodiversity and ecosystem services from 1900 to 2050
Authors: Pereira Henrique M. , Rosa Isabel M.D. , Martins Inês S. , Kim HyeJin , Leadley Paul , Popp Alexander , van Vuuren Detlef P. , Hurtt George , Anthoni Peter , Arneth Almut , Baisero Daniele , Chaplin-Kramer Rebecca , Chini Louise , Di Fulvio Fulvio , Di Marco Moreno , Ferrier Simon , Fujimori Shinichiro , Guerra Carlos A. , Harfoot Michael , Harwood Thomas D. , Hasegawa Tomoko , Haverd Vanessa , Havlík Petr , Hellweg Stefanie , Hilbers Jelle P. , Hill Samantha L. L. , Hirata Akiko , Hoskins Andrew J. , Humpenöder Florian , Janse Jan H. , Jetz Walter , Johnson Justin A. , Krause Andreas , Leclère David , Matsui Tetsuya , Meijer Johan R. , Merow Cory , Obsersteiner Michael , Ohashi Haruka , Poulter Benjamin , Purvis Andy , Quesada Benjamin , Rondinini Carlo , Schipper Aafke M. , Settele Josef , Sharp Richard , Stehfest Elke , Strassburg Bernardo B. N. , Takahashi Kiyoshi , Talluto Matthew V. , Thuiller Wilfried , Titeux Nicolas , Visconti Piero , Ware Christopher , Wolf Florian , Alkemade Rob
Published: April 2020

Despite the scientific consensus on the extinction crisis and its anthropogenic origin, the quantification of historical trends and of future scenarios of biodiversity and ecosystem services has been limited, due to the lack of inter-model comparisons and harmonized scenarios. Here, we present a multi-model analysis to assess the impacts of land-use and climate change from 1900 to 2050. During the 20th century provisioning services increased, but biodiversity and regulating services decreased. Similar trade-offs are projected for the coming decades, but they may be attenuated in a sustainability scenario. Future biodiversity loss from land-use change is projected to keep up with historical rates or reduce slightly, whereas losses due to climate change are projected to increase greatly. Renewed efforts are needed by governments to meet the 2050 vision of the Convention on Biological Diversity.

One Sentence Summary

Development pathways exist that allow for a reduction of the rates of biodiversity loss from land-use change and improvement in regulating services but climate change poses an increasing challenge.
Contrasting effects of chronic lithium, haloperidol and olanzapine exposure on synaptic clusters in the rat prefrontal cortex
Authors: Halff Els F. , Cotel Marie-Caroline , Natesan Sridhar , McQuade Richard , Ottley Chris J. , Srivastiva Deepak P. , Howes Oliver D. , Vernon Anthony C.
Published: April 2020

The pathophysiology of the majority of neuropsychiatric disorders, including schizophrenia and mood disorders, involves synaptic dysfunction and/or loss, manifesting as lower levels of several presynaptic and postsynaptic marker proteins. Whether chronic exposure to antipsychotic drugs may contribute to this pattern of synaptic loss remains controversial. In contrast, the mood stabiliser lithium has shown to exhibit neurotrophic actions and is thought to enhance synapse formation. Whilst these data are not unequivocal, they suggest that antipsychotic drugs and lithium have contrasting effects on synapse density. We therefore investigated the effect of chronic exposure to lithium and to two different antipsychotics, haloperidol and olanzapine, on presynaptic Synaptic Vesicle glycoprotein 2A (SV2A) and postsynaptic Neuroligin (NLGN) clusters in the rat frontal cortex. Chronic exposure (28 days) to haloperidol (0.5 mg/kg/d) or olanzapine (7.5 mg/kg/d) had no effect on either SV2A or NLGN clusters and no overall effect on synaptic clusters. In contrast, chronic lithium exposure (2 mmol/L eq./d) significantly increased NLGN cluster density as compared to vehicle, but did not affect either SV2A or total synaptic clusters. These data are consistent with and extend our prior work, confirming no effect of either antipsychotics or lithium on SV2A clustering, but suggest contrasting effects of these drugs on the post-synapse. Although caution needs to be exerted when extrapolating results from animals to patients, these data provide clarity with regard to the effect of antipsychotics and lithium on synaptic markers, thus facilitating discrimination of drug from illness effects in human studies of synaptic pathology in psychiatric disorders.
Synchronized cardiac impulses emerge from multi-scale, heterogeneous local calcium signals within and among cells of heart pacemaker tissue
Authors: Bychkov Rostislav , Juhaszova Magdalena , Tsutsui Kenta , Coletta Christopher , Stern Michael D. , Maltsev Victor A. , Lakatta Edward G.
Published: April 2020

Background

The current paradigm of Sinoatrial Node (SAN) impulse generation: (i) is that full-scale action potentials (APs) of a common frequency are initiated at one site and are conducted within the SAN along smooth isochrones; and (ii) does not feature fine details of Ca2+signalling present in isolated SAN cells, in which small subcellular, subthreshold local Ca2+releases (LCRs) self-organize to generate cell-wide APs.

Objectives

To study subcellular Ca2+signals within and among cells comprising the SAN tissue.

Methods

We combined immunolabeling with a novel technique to detect the occurrence of LCRs and AP-induced Ca2+transients (APCTs) in individual pixels (chonopix) across the entire mouse SAN images.

Results

At high magnification, Ca2+signals appeared markedly heterogeneous in space, amplitude, frequency, and phase among cells comprising an HCN4+/CX43-cell meshwork. The signalling exhibited several distinguishable patterns of LCR/APCT interactions within and among cells. Apparently conducting rhythmic APCTs of the meshwork were transferred to a truly conducting HCN4-/CX43+network of straited cells via narrow functional interfaces where different cell types intertwine, i.e. the SAN anatomical/functional unit. At low magnification, the earliest APCT of each cycle occurred within a small area of the HCN4 meshwork and subsequent APCT appearance throughout SAN pixels was discontinuous.

Conclusions

We have discovered a novel, microscopic Ca2+signalling paradigm of SAN operation that has escaped detection using low-resolution, macroscopic tissue isochrones employed in prior studies: APs emerge from heterogeneous subcellular subthreshold Ca2+signals, resembling multiscale complex processes of impulse generation within clusters of neurons in neuronal networks.

Condensed abstract

By combining immunolabeling with a novel optical technique we detected markedly heterogenous Ca2+signals within and among cell clusters of an HCN4+/CX43-meshwork in mouse sinoatrial node. These Ca2+signals self-organized and transferred, throughout the node, to projections from an HCN4-/CX43+network connected to a highly organized, rapidly conducting part of the CX43+network. Thus, APs emerge from heterogeneous, subthreshold Ca2+signaling not detected in low-resolution macroscopic isochrones. Our discovery requires a fundamental paradigm shift from concentric impulse propagation initiated within a leading site, to a multiscale/complex process, resembling the emergence of organized signals from heterogeneous local signals within neuronal networks.
Leveraging Fungal Calcineurin-Inhibitor Structures, Biophysics and Dynamics to Design Selective and Non-Immunosuppressive FK506 Analogs
Authors: Gobeil Sophie M.-C. , Bobay Benjamin G. , Juvvadi Praveen R. , Cole D. Christopher , Heitman Joseph , Steinbach William J. , Venters Ronald A. , Spicer Leonard D.
Published: April 2020

Calcineurin is a critical enzyme in fungal pathogenesis and antifungal drug tolerance and, therefore, an attractive antifungal target. Current clinically-accessible calcineurin inhibitors, such as FK506, are immunosuppressive to humans, so exploiting calcineurin inhibition as an antifungal strategy necessitates fungal-specificity in order to avoid inhibiting the human pathway. Harnessing fungal calcineurin-inhibitor crystal structures, we recently developed a less immunosuppressive FK506 analog, APX879, with broad-spectrum antifungal activity and demonstrable efficacy in a murine model of invasive fungal infection. Our overarching goal is to better understand, at a molecular level, the interaction determinants of the human and fungal FK506-binding proteins (FKBP12) required for calcineurin inhibition in order to guide the design of fungal-selective, non-immunosuppressive FK506 analogs. To this end, we characterized high-resolution structures of theM. circinelloidesFKBP12 bound to FK506, and of theA. fumigatus, M. circinelloidesand human FKBP12 proteins bound to the FK506 analog, APX879, which exhibits enhanced selectivity for fungal pathogens. Combining structural, genetic and biophysical methodologies with molecular dynamics simulations, we identify critical variations in these structurally similar FKBP12-ligand complexes that will guide the rational design of inhibitors with enhanced fungal-selectivity.

Significance statement

Invasive fungal infections are a leading cause of death in the immunocompromised patient population. The rise in drug resistance to current antifungals highlights the urgent need to develop more efficacious and highly selective agents. Numerous investigations of major fungal pathogens have confirmed the critical role of the calcineurin pathway for fungal virulence, making it an attractive target for antifungal development. Although FK506 inhibits calcineurin, it is immunosuppressive in humans and cannot be used as an antifungal. By combining structural, genetic, biophysical, andin silicomethodologies, we pinpoint regions of FK506 and a less immunosuppressive analog, APX879, that could be altered to enhance fungal selectivity. This work represents a significant advancement toward realizing calcineurin as a viable target for antifungal drug discovery.
Efficient phasing and imputation of low-coverage sequencing data using large reference panels
Authors: Rubinacci S. , Ribeiro D.M. , Hofmeister R. , Delaneau O.
Published: April 2020

Low-coverage whole genome sequencing followed by imputation has been proposed as a cost-effective genotyping approach for disease and population genetics studies. However, its competitiveness against SNP arrays is undermined as current imputation methods are computationally expensive and unable to leverage large reference panels.

Here, we describe a method, GLIMPSE, for phasing and imputation of low-coverage sequencing datasets from modern reference panels. We demonstrate its remarkable performance across different coverages and human populations. It achieves imputation of a full genome for less than $1, outperforming existing methods by orders of magnitude, with an increased accuracy of more than 20% at rare variants. We also show that 1x coverage enables effective association studies and is better suited than dense SNP arrays to access the impact of rare variations. Overall, this study demonstrates the promising potential of low-coverage imputation and suggests a paradigm shift in the design of future genomic studies.
Temporal ordering of omics and multiomic events inferred from time series data
Authors: Kaur Sandeep , Peters Timothy J. , Yang Pengyi , Luu Laurence Don Wai , Vuong Jenny , Krycer James R. , O’Donoghue Seán I.
Published: April 2020

Temporal changes in omics events can now be routinely measured, however current analysis methods are often inadequate, especially for multiomics experiments. We report a novel analysis method that can infer event ordering at better temporal resolution than the experiment, and integrates omic events into two concise visualizations (event maps and sparklines). Testing our method gave results well-correlated with prior knowledge and indicated it streamlines analysis of time-series data.
Subtypes of functional connectivity associate robustly with ASD diagnosis
Authors: Urchs Sebastian G. , Tam Angela , Orban Pierre , Moreau Clara , Benhajali Yassine , Nguyen Hien Duy , Evans Alan C. , Bellec Pierre
Published: April 2020

Our understanding of the changes in functional brain organization in autism is hampered by the extensive heterogeneity that characterizes this neurodevelopmental disorder. Data driven clustering offers a straightforward way to decompose this heterogeneity into subtypes of distinguishable connectivity types and promises an unbiased framework to investigate behavioural symptoms and causative genetic factors. Yet the robustness and generalizability of these imaging subtypes is unknown. Here, we show that unsupervised functional connectivity subtypes are moderately associated with the clinical diagnosis of autism, and that these associations generalize to independent replication data. We found that subtypes identified robust patterns of functional connectivity, but that a discrete assignment of individuals to these subtypes was not supported by the data. Our results support the use of data driven subtyping as a data dimensionality reduction technique, rather than to establish clinical categories.
Substrate binding and turnover modulate the affinity landscape of dihydrofolate reductase to increase its catalytic efficiency
Authors: Galenkamp Nicole Stéphanie , Maglia Giovanni
Published: April 2020

It is generally accepted that enzymes structures evolved to stabilize the transition-state of a catalyzed reaction. Here, observing single molecules with a multi-turnover resolution, we provide experimental evidence for a more sophisticated narrative. We found that the binding of the NADPH cofactor to DHFR induces a first allosteric change that increases the affinity of the enzyme for the substrate. Then the enthalpy generated by the chemical step provides a power stroke that switches the enzyme to the product-bound conformations and promotes the release of the oxidized cofactor NADP+. The subsequent binding of NADPH to the vacated site provides the free energy for the recovery stroke, which induces the allosteric release of the product and resets the initial configuration. Intriguingly, the cycle is not perfect. Occasionally, DHFR undergoes second-long catalytic pauses, most likely reflecting the occupancy of an off-path conformation induced by excess energy liberated by the chemical step. This catalytic remodeling of the affinity landscape of DHFR is likely to have evolved to improve the efficiency of the reaction to cope with the high concentration of NADP+ inE. coli.And might be a general feature for complex enzymatic reaction where the binding and release of the products must be tightly controlled.
Two-dimensional reward evaluation in mice
Authors: Nachev Vladislav , Rivalan Marion , Winter York
Published: April 2020

When choosing among multi-attribute options, integrating the full information may be computationally costly and time-consuming. So-called non-compensatory decision rules only rely on partial information, for example when a difference on a single attribute overrides all others. Such rules may be ecologically more advantageous, despite being economically suboptimal. Here we present a study that investigates to what extent animals rely on integrative rules (using the full information) versus non-compensatory rules when choosing where to forage. Groups of mice were trained to obtain water from dispensers varying along two reward dimensions: volume and probability. The mice’s choices over the course of the experiment suggested an initial reliance on integrative rules, later displaced by a sequential rule, in which volume was evaluated before probability. Our results also demonstrate that while the evaluation of probability differences may depend on the reward volumes, the evaluation of volume differences is seemingly unaffected by the reward probabilities.