bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of commercial RT-PCR diagnostic kits for COVID-19
Authors: van Kasteren Puck B. , van der Veer Bas , van den Brink Sharon , Wijsman Lisa , de Jonge Jørgen , van den Brandt Annemarie , Molenkamp Richard , Reusken Chantal B.E.M. , Meijer Adam 
Published: April 2020

ABSTRACTThe final months of 2019 witnessed the emergence of a novel coronavirus in the human population. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has since spread across the globe and is posing a major burden on society. Measures taken to reduce its spread critically depend on timely and accurate identification of virus-infected individuals by the most sensitive and specific method available, i.e. real-time reverse transcriptase PCR (RT-PCR). Many commercial kits have recently become available, but their performance has not yet been independently assessed.The aim of this study was to compare basic analytical and clinical performance of selected RT-PCR kits from seven different manufacturers (Altona Diagnostics, BGI, CerTest Biotec, KH Medical, PrimerDesign, R-Biopharm AG, and Seegene).We used serial dilutions of viral RNA to establish PCR efficiency and estimate the 95% limit of detection (LOD95%). Furthermore, we ran a panel of SARS-CoV-2-positive clinical samples (n=16) for a preliminary evaluation of clinical sensitivity. Finally, we used clinical samples positive for non-coronavirus respiratory viral infections (n=6) and a panel of RNA from related human coronaviruses to evaluate assay specificity.PCR efficiency was ≥96% for all assays and the estimated LOD95% varied within a 6-fold range. Using clinical samples, we observed some variations in detection rate between kits. Importantly, none of the assays showed cross-reactivity with other respiratory (corona)viruses, except as expected for the SARS-CoV-1 E-gene.We conclude that all RT-PCR kits assessed in this study may be used for routine diagnostics of COVID-19 in patients by experienced molecular diagnostic laboratories.
Stroma secreted IL6 selects for “stem-like” population and alters pancreatic tumor microenvironment by reprogramming metabolic pathways
Authors: Kesh Kousik , Garrido Vanessa T , Doesch Austin , Durden Brittany , Gupta Vineet K , Sharma Nikita S , Lyle Michael , Nagathihalli Nagaraj , Merchant Nipun , Saluja Ashok , Banerjee Sulagna 
Published: April 2020

AbstractPancreatic adenocarcinoma is a devastating disease with an abysmal survival rate of 9%. A robust fibro-inflammatory and desmoplastic stroma, characteristic of pancreatic cancer, contributes to the challenges in developing viable therapeutic strategies in this disease. Apart from constricting blood vessels and preventing efficient drug delivery to the tumor, the stroma also contributes to aggressive biology of the cancer along with its immune-evasive microenvironment. In this study, we show that in pancreatic tumors, the developing stroma increases tumor initiation frequency in pancreatic cancer cells in vivo by enriching for CD133+ aggressive “stem-like” cells. Additionally, the stromal fibroblasts secrete IL6 as the major cytokine, increases glycolytic flux in the pancreatic tumor cells and increases lactate efflux in the microenvironment via activation of the STAT signaling pathway. We also show that the secreted lactate favors activation of M2 macrophages in the tumor microenvironment, which excludes CD8+ T-cells in the tumor. Our data additionally confirms that treatment of pancreatic tumors with anti-IL6 antibody results in tumor regression as well as decreased CD133+ population within the tumor. Furthermore, inhibiting the lactate efflux in the microenvironment reduces M2 macrophages, and makes pancreatic tumors more responsive to anti-PD1 therapy. This suggests that stromal IL6 driven metabolic reprogramming plays a significant role in the development of an immune evasive microenvironment. In conclusion, our study shows that targeting the metabolic pathways affected by stromal IL6 can make pancreatic tumors amenable to checkpoint inhibitor therapy.
The safety profile of Bald’s eyesalve for the treatment of bacterial infections
Authors: Anonye Blessing O , Nweke Valentine , Furner-Pardoe Jessica , Gabrilska Rebecca , Rafiq Afshan , Ukachukwu Faith , Bruce Julie , Lee Christina , Unnikrishnan Meera , Rumbaugh Kendra P. , Snyder Lori AS , Harrison Freya 
Published: April 2020

AbstractThe rise in antimicrobial resistance has prompted the development of alternatives, such as plant-derived compounds, to combat bacterial infections. Bald’s eyesalve, a remedy used in the Early Medieval period, has previously been shown to have efficacy againstStaphylococcus aureusgrown in anin vitromodel of soft tissue infection. This remedy also had bactericidal activity against methicillin-resistantS. aureus(MRSA) in a chronic mouse wound. However, the safety profile of Bald’s eyesalve has not yet been demonstrated, and this is vital before testing in humans. Here, we determined the safety potential of Bald’s eyesalve usingin vitro,ex vivo, andin vivomodels representative of skin or eye infections. We also confirmed that Bald’s eyesalve is active against an important eye pathogen,Neisseria gonorrhoeae. Low levels of cytotoxicity were observed in eyesalve-treated cell lines representative of skin and immune cells. Results from a bovine corneal opacity and permeability test demonstrated slight irritation to the cornea that resolved within 10 minutes. The slug mucosal irritation assay revealed that a low level of mucus was secreted by slugs exposed to eyesalve, indicating mild mucosal irritation. We obtained promising results from mouse wound closure experiments; no visible signs of irritation or inflammation were observed. Our results suggest that Bald’s eyesalve could be tested further on human volunteers to assess safety for topical application against bacterial infections.ImportanceAlternative treatment for bacterial infections are needed to combat the ever increasing repertoire of bacteria resistant to antibiotics. A medieval plant-based remedy, Bald’s eyesalve, shows promise as a substitute for the treatment of these infections. For any substance to be effective in the treatment of bacterial infections in humans, it is important to consider the safety profile. This is a key consideration in order to have the necessary regulatory approval. We demonstrate the safety profile of Bald’s eyesalve using a variety of models, including whole-organ and whole-animal models. Our results show that Bald’s eyesalve is mildly toxic to cultured human cells, but potentially suitable for patch tests on healthy human volunteers to assess safety for later clinical trials. Our work has the potential to transform the management of diseases caused by bacterial infections, such as diabetic foot ulcers, through topical application of a natural product cocktail based on Bald’s eyesalve.
Modular output circuits of the fastigial nucleus mediate diverse motor and nonmotor functions of the cerebellar vermis
Authors: Fujita Hirofumi , Kodama Takashi , Lac Sascha du 
Published: April 2020

AbstractThe cerebellar vermis, long associated with axial motor control, has been implicated in a surprising range of neuropsychiatric disorders and cognitive and affective functions. Remarkably little is known, however, about the specific cell types and neural circuits responsible for these diverse functions. Here, using single-cell gene expression profiling and anatomical circuit analyses of vermis output neurons in the mouse fastigial (medial cerebellar) nucleus, we identify five major classes of glutamatergic projection neurons distinguished by gene expression, morphology, distribution, and input-output connectivity. Each fastigial cell type is connected with a specific set of Purkinje cells and inferior olive neurons and in turn innervates a distinct collection of downstream targets. Transsynaptic tracing indicates extensive disynaptic links with cognitive, affective, and motor forebrain circuits. These results indicate that diverse cerebellar vermis functions are mediated by modular synaptic connections of distinct fastigial cell types which differentially coordinate posturomotor, oromotor, positional-autonomic, orienting, and vigilance circuits.
Physiology of PNS axons relies on glycolytic metabolism in myelinating Schwann cells
Authors: Deck Marie , Van Hameren Gerben , Campbell Graham , Bernard-Marissal Nathalie , Devaux Jérôme , Berthelot Jade , Lattard Alise , Médard Jean-Jacques , Gautier Benoît , Quintana Patrice , Chao de la Barca Juan Manuel , Reynier Pascal , Lenaers Guy , Chrast Roman , Tricaud Nicolas 
Published: April 2020

SummaryDespite the lactate shuttle theory, how glial cells support axonal metabolism and function remains unclear. Lactate production is a common occurrence following anaerobic glycolysis in muscles. However, several other cell types, including some stem cells, activatezd macrophages and tumor cells, can produce lactate in presence of oxygen and cellular respiration, using Pyruvate Kinase 2 (PKM2) to divert pyruvate to lactate dehydrogenase. We show here that PKM2 is also upregulated in mature myelinating Schwann cells (mSC) of mouse sciatic nerve. Deletion of this isoform in PLP-expressing cells in mice leads to a deficit of lactate in mSC and in peripheral nerves. This had no detectable consequences on the myelin sheath. However, mutant mice developed a peripheral neuropathy. Peripheral nerve axons of mutant mice failed to maintain lactate homeostasis upon activity, resulting in an impaired production of mitochondrial ATP. Action potential propagation was not altered but axonal mitochondria transport was slowed down, muscle axon terminals retracted and motor neurons displayed cellular stress. Additional reduction of lactate availability through dichloroacetate treatment, which diverts pyruvate to mitochondrial oxidative phosphorylation, further aggravated motor dysfunction in mutant mice. Thus, lactate production through aerobic glycolysis is essential in mSC for the long-term maintenance of peripheral nerve axon physiology and function.
3D SYNAPTIC ORGANIZATION OF THE RAT CA1 AND ALTERATIONS INDUCED BY COCAINE SELF-ADMINISTRATION
Authors: Blazquez-Llorca L. , Miguéns M. , Montero-Crespo M. , Selvas A. , Gonzalez-Soriano J. , Ambrosio E. , DeFelipe J. 
Published: April 2020

ABSTRACTThe hippocampus plays a key role in contextual conditioning and has been proposed as an important component of the cocaine addiction brain circuit. To gain knowledge about cocaine-induced alterations in this circuit, we used Focused Ion Beam milling/Scanning Electron Microscopy (FIB/SEM) to reveal and quantify the 3D synaptic organization of thestratum radiatumof rat CA1, under normal circumstances and after cocaine-self administration (SA). Most synapses are asymmetric (excitatory), macular-shaped, and in contact with spine heads. After cocaine-SA, the size and complexity of both asymmetric and symmetric (inhibitory) synapses increased but no changes were observed in the synaptic density.This work constitutes the first detailed report on the 3D synaptic organization in thestratum radiatumof the CA1 field of cocaine-SA rats. Our data contribute to the elucidation of the normal and altered synaptic organization of the hippocampus, which is crucial for better understanding the neurobiological mechanisms underlying cocaine addiction.
Detection of Gray Mold Infection in Plants Using a Multispectral Imaging System
Authors: Scarboro Clifton G. , Ruzsa Stephanie M. , Doherty Colleen J. , Kudenov Michael W. 
Published: April 2020

AbstractGray mold disease caused by the fungusBotrytis cinereadamages many crop hosts worldwide and is responsible for heavy economic losses. Early diagnosis and detection of the disease would allow for more effective crop management practices to prevent outbreaks in field or greenhouse settings. Furthermore, having a simple, non-invasive way to quantify the extent of gray mold disease is important for plant pathologists interested in quantifying infection rates. In this paper, we design and build a multispectral imaging system for discriminating between leaf regions, infected with gray mold, and those that remain unharmed on a lettuce (Lactuca spp.)host. First, we describe a method to select two optimal (high contrast) spectral bands from continuous hyperspectral imagery (450-800 nm). We then built a system based on these two spectral bands, located at 540 and 670 nm. The resultant system uses two cameras, with a narrow band-pass spectral filter mounted on each, to measure the multispectral reflectance of a lettuce leaf. The two resulting images are combined using a normalized difference calculation that produces a single image with high contrast between the leaves’ infected and healthy regions. A classifier was then created based on the thresholding of single pixel values. We demonstrate that this simple classification produces a true positive rate of 95.25% with a false positive rate of 9.316%.
The Mechanics of Temporal Interference Stimulation
Authors: Cao Jiaming , Doiron Brent , Goswami Chaitanya , Grover Pulkit 
Published: April 2020

AbstractWe utilize single neuron models to understand mechanisms behind Temporal Interference (TI) stimulation (also called “Interferential Stimulation”). We say that a neuron exhibits TI stimulation if it does not fire for a high-frequency sinusoidal input, but fires when the input is a low-frequency modulation of the high-frequency sinusoid (specifically that generated by addition of two high frequency sinusoids with a small difference in their frequencies), while the maximum amplitude is kept the same in both cases. Our key observation – that holds for both FitzHugh-Nagumo and Hodgkin-Huxley neuron models – is that for neuron models that do exhibit TI stimulation, a high frequency pure sinusoidal input results in a current balance between inward and outward currents. This current balance leads to a subthreshold periodic orbit that keeps the membrane potential from spiking for sinusoidal inputs. However, the balance is disturbed when the envelope of the sinusoids is modulated with a high slope: the fast-changing envelope activates fast depolarizing currents without giving slow outward currents time to respond. This imbalance causes the membrane potential to build up, causing the neuron to fire. This mechanistic understanding can help design current waveforms for neurons that exhibit TI stimulation, and also help classify which neuron-types may or may not exhibit TI stimulation.
In silicodesign of Multi-epitope-based peptide vaccine against SARS-CoV-2 using its spike protein
Authors: Mitra Debarghya , Pandey Janmejay , Jain Alok , Swaroop Shiv 
Published: April 2020

AbstractSARS-CoV-2 has been efficient in ensuring that many countries are brought to a standstill. With repercussions ranging from rampant mortality, fear, paranoia, and economic recession, the virus has brought together countries to look at possible therapeutic countermeasures. With prophylactic interventions possibly months away from being particularly effective, a slew of measures and possibilities concerning the design of vaccines are being worked upon. We attempted a structure-based approach utilizing a combination of epitope prediction servers and Molecular dynamic (MD) simulations to develop a multi-epitope-based subunit vaccine that involves the two subunits of the spike glycoprotein of SARS-CoV-2 (S1 and S2) coupled with a substantially effective chimeric adjuvant to create stable vaccine constructs. The designed constructs were evaluated based on their docking with Toll-Like Receptor (TLR) 4. Our findings provide an epitope-based peptide fragment that can be a potential candidate for the development of a vaccine against SARS-CoV-2. Recent experimental studies based on determining immunodominant regions across the spike glycoprotein of SARS-CoV-2 indicate the presence of the predicted epitopes included in this study.
Identification of Plitidepsin as Potent Inhibitor of SARS-CoV-2-Induced Cytopathic Effect after a Drug Repurposing Screen
Authors: Rodon Jordi , Muñoz-Basagoiti Jordana , Perez-Zsolt Daniel , Noguera-Julian Marc , Paredes Roger , Mateu Lourdes , Quiñones Carles , Erkizia Itziar , Blanco Ignacio , Valencia Alfonso , Guallar Víctor , Carrillo Jorge , Blanco Julià , Segalés Joaquim , Clotet Bonaventura , Vergara-Alert Júlia , Izquierdo-Useros Nuria 
Published: April 2020

ABSTRACTThere is an urgent need to identify therapeutics for the treatment of Coronavirus diseases 2019 (COVID-19). Although different antivirals are given for the clinical management of SARS-CoV-2 infection, their efficacy is still under evaluation. Here, we have screened existing drugs approved for human use in a variety of diseases, to compare how they counteract SARS-CoV-2-induced cytopathic effect and viral replicationin vitro.Among the potential 72 antivirals tested herein that were previously proposed to inhibit SARS-CoV-2 infection, only 18% had an IC50below 25 μM or 102IU/mL. These included plitidepsin, novel cathepsin inhibitors, nelfinavir mesylate hydrate, interferon 2-alpha, interferon-gamma, fenofibrate, camostat along the well-known remdesivir and chloroquine derivatives. Plitidepsin was the only clinically approved drug displaying nanomolar efficacy. Four of these families, including novel cathepsin inhibitors, blocked viral entry in a cell-type specific manner. Since the most effective antivirals usually combine therapies that tackle the virus at different steps of infection, we also assessed several drug combinations. Although no particular synergy was found, inhibitory combinations did not reduce their antiviral activity. Thus, these combinations could decrease the potential emergence of resistant viruses. Antivirals prioritized herein identify novel compounds and their mode of action, while independently replicating the activity of a reduced proportion of drugs which are mostly approved for clinical use. Combinations of these drugs should be tested in animal models to inform the design of fast track clinical trials.
Within-population sperm competition intensity does not predict asymmetry in conpopulation sperm precedence
Authors: Garlovsky Martin D. , Yusuf Leeban H. , Ritchie Michael G. , Snook Rhonda R. 
Published: April 2020

ABSTRACTPostcopulatory sexual selection can generate coevolutionary arms races between the sexes resulting in the rapid coevolution of reproductive phenotypes. As traits affecting fertilisation success diverge between populations postmating prezygotic barriers to gene flow may evolve. Conspecific sperm precedence is a form of such isolation thought to evolve early during speciation yet has mostly been studied between species. Here we show conpopulation sperm precedence betweenDrosophila montanapopulations. Using genomic data to estimate divergence times and patterns of gene flow between populations, we show gene flow has played a considerable role during divergence. We find conpopulation sperm precedence is asymmetric and is concordant with asymmetry in non-competitive postmating prezygotic reproductive isolation. These results suggest these phenomena have a shared mechanism, but we show that this asymmetry is unrelated to the strength of postcopulatory sexual selection acting within populations. We tested whether overlapping foreign and coevolved ejaculates within the female reproductive tract altered fertilisation success but found no effect. Our results show that neither time since divergence nor sperm competitiveness predicts the strength of postmating prezygotic reproductive isolation. We suggest that divergence of postcopulatory phenotypes resulting in postmating prezygotic isolation is potentially driven by cryptic female choice, or mutation order divergence.
Universality of cell differentiation trajectories revealed by a reconstruction of transcriptional uncertainty landscapes from single-cell transcriptomic data
Authors: Gao Nan Papili , Gandrillon Olivier , Páldi András , Herbach Ulysse , Gunawan Rudiyanto 
Published: April 2020

ABSTRACTWe employed our previously-described single-cell gene expression analysis CALISTA (Clustering And Lineage Inference in Single-Cell Transcriptional Analysis) to evaluate transcriptional uncertainty at the single-cell level using a stochastic mechanistic model of gene expression. We reconstructed a transcriptional uncertainty landscape during cell differentiation by visualizing single-cell transcriptional uncertainty surface over a two dimensional representation of the single-cell gene expression data. The reconstruction of transcriptional uncertainty landscapes for ten publicly available single-cell gene expression datasets from cell differentiation processes with linear, single or multi-branching cell lineage, reveals universal features in the cell differentiation trajectory that include: (i) a peak in single-cell uncertainty during transition states, and in systems with bifurcating differentiation trajectories, each branching point represents a state of high transcriptional uncertainty; (ii) a positive correlation of transcriptional uncertainty with transcriptional burst size and frequency; (iii) an increase in RNA velocity preceeding the increase in the cell transcriptional uncertainty. Finally, we provided biological interpretations of the universal rise-then-fall profile of the transcriptional uncertainty landscape, including a link with the Waddington’s epigenetic landscape, that is generalizable to every cell differentiation system.
Mosquitoes (Diptera:Culicidae) in an indigenous settlement of the Magdalena State, Colombia
Authors: Parra-Henao Gabriel , Perdomo Erick , Carrasquilla Deibys , Torres Emy , Perez Celenny , Molina Jose Luis 
Published: April 2020

AbstractStudies directed to investigate ecological parameters of mosquitoes populations allows to establish the risk of vector borne diseases transmission and to bring recommendations for health authorities about prevention, surveillance and control. We report some ecological aspects of mosquitoes populations in a region of Colombia. Quarterly sampling was done. For mosquito catching CDC and Shannon traps were used. Diversity and abundance indexes estimation was done. A total of 1071 mosquitoes belonging to four genera and 10 species were collected. The most abundant species wereCx quinquefasciatus(22.6%),Ae. aegypti(20.08%),Ae. scapularis(12.3%),Ae. angustivittatus(9%) andAn. albimanus(8.0%). The finding ofCx pedroi, Ae. scapularis,,Cx. nigripalpus, Cx. quinquefasciatus, Cx. declarator, Ma. titillans, andPs. feroxpreviously reported as arbovirus vectors warns about the possibility of transmission in the zone and the finding ofAn. albimanus, also warns about the risk for malaria transmission in the area.