bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hunting Eagles with glass mice: revisiting the inoculum effect forStreptococcus pyogeneswith a hollow fibre infection model
Authors: Marum Darcy , Manning Laurens , Raby Edward 
Published: January 2021

AbstractBackgroundSevere, invasiveStreptococcus pyogenes(Strep A) infections result in greater than 500,000 deaths annually. First line treatment for such infections is combination benzylpenicillin and clindamycin, but treatment failure can occur with this regimen. This failure has been partially attributed to the inoculum effect, which presents as reduced antibiotic susceptibility during high bacterial density and plateau-phase growth. Hollow fibre infection models (HFIM) have been proposed as an alternative toin vivoresearch to study these effects.ObjectivesTo re-evaluate the inoculum effect for benzylpenicillin, clindamycin, linezolid and trimethoprim-sulfamethoxazole using a Strep A HFIM.MethodsDifferential antibiotic susceptibility of Strep A was measured in a HFIM starting from low- and high-density inocula. Dynamic antibiotic concentrations were delivered over 48 hours to simulate human pharmacokinetics. Differences in antibiotic susceptibility were determined at 24 and 48 hours by plate count of remaining viable colony-forming units.ResultsInoculum effects were seen in benzylpenicillin and linezolid at 24 hours, and benzylpenicillin, linezolid and clindamycin at 48 hours. The effect size was greatest for continuously infused benzylpenicillin. No inoculum effect was seen in trimethoprim-sulfamethoxazole.ConclusionsInoculum effects were seen in the HFIM model using benzylpenicillin, linezolid and clindamycin, which may predict reduced clinical efficacy following treatment delay. The model has proven robust and largely in agreeance with published data, recommending it for further Strep A study.
EdU incorporation to assess cell proliferation and drug susceptibility for the brain-eating amoeba,Naegleria fowleri
Authors: Troth Emma V. , Kyle Dennis E. 
Published: January 2021

AbstractNaegleria fowleriis a pathogenic free-living amoeba that is commonly found in warm, freshwater and can cause a rapidly fulminant disease known as primary amoebic meningoencephalitis (PAM). New drugs are urgently needed to treat PAM, as the fatality rate is >97%. Until recently, few advances have been made in the discovery of new drugs forN. fowleriand one drawback is the lack of validated tools and methods to enhance drug discovery and diagnostics research. In this study we aimed to validate alternative methods to assess cell proliferation that are commonly used for other cell types and develop a novel drug screening assay to evaluate drug efficacy onN. fowlerireplication. EdU (5-ethynyl-2′-deoxyuridine) is a pyrimidine analog of thymidine that can be used as a quantitative endpoint for cell proliferation. EdU incorporation is detected via a copper catalyzed click reaction with an Alexa Fluor linked azide. EdU incorporation in replicatingN. fowleriwas validated using fluorescence microscopy and quantitative methods for assessing EdU incorporation were developed by using an imaging flow cytometer. Currently used PAM therapeutics inhibitedN. fowlerireplication and EdU incorporationin vitro. EdA (5′ethynyl-2′-deoxyadenosine), an adenine analog, also was incorporated by N. fowleri, but was more cytotoxic than EdU. In summary, EdU incorporation could be used as a complimentary method for drug discovery for these neglected pathogens.
Quality of life and health-related utility after head&neck cancer surgery
Authors: Parimbelli Enea , Simon Christian , Soldati Federico , Duchoud Lorry , Armas Gian Luca , de Almeida John , Quaglini Silvana 
Published: January 2021

AbstractPurposeThis work describes the methodology adopted and the results obtained in a utility elicitation task. The purpose was to elicit utility coefficients (UCs) needed to calculate quality-adjusted life years for a cost/utility analysis of TORS (Trans-Oral robotic Surgery) versus TLM (Trans-oral Laser Microsurgery), which are two minimally-invasive trans-oral surgery techniques for head & neck cancers.MethodsSince the economic evaluation would be conducted from the point of view of the Swiss healthcare system, Swiss people (healthy volunteers) have been interviewed in order to tailor the model to that specific country. The utility elicitation was performed using a computerized tool (UceWeb). Standard gamble and rating scale methods were used.ResultsUCs have been elicited from 47 individuals, each one providing values for 18 health states, for a total of 1692 expected values. Health states, described using graphical factsheets, ranged from remission to palliative care. Elicited UCs were different among states, ranging from 0.980 to 0.213. Those values were comparable to previously published results from a Canadian population, except for states related to recurrent disease (local, regional, and distant), and palliation, where the Swiss population showed lower utility values.ConclusionFrom a methodological point of view, our study shows that the UceWeb tool can be profitably used for utility elicitation from healthy volunteers. From an application point of view, the study provides utility values that can be used not only for a specific cost-utility analysis, but for future studies involving health states following trans-oral head & neck surgery. Moreover, the study confirms that some UCs vary among countries, demanding for tailored elicitation tasks.
The incremental value of computed tomography of COVID-19 pneumonia in predicting ICU admission
Authors: Bartolucci Maurizio , Benelli Matteo , Betti Margherita , Bicchi Sara , Fedeli Luca , Giannelli Federico , Aquilini Donatella , Baldini Alessio , Consales Guglielmo , Di Natale Massimo Edoardo , Lotti Pamela , Vannucchi Letizia , Trezzi Michele , Mazzoni Lorenzo Nicola , Santini Sandro , Carpi Roberto , Matarrese Daniela , Bernardi Luca , Mascalchi Mario ,   COVID Working Group USL Toscana Centro and Azienda Ospedaliero-Universitaria Careggi,   members of the Working Group USL Toscana Centro and Azienda Ospedaliero-Universitaria Careggi, Allescia Germana , Busoni Simone , Bindi Alessandra , Cavigli Edoardo , Cozzi Diletta , Dedola Giovanni Luca , Mazzocchi Silvia , Miele Vittorio , Pozzessere Chiara , Taddeucci Adriana , Viviani Adriano , Zini Chiara 
Published: January 2021

AbstractRationaleTriage is crucial for patient’s management and estimation of the required Intensive Care Unit (ICU) beds is fundamental for Health Systems during the COVID-19 pandemic.ObjectiveTo assess whether chest Computed Tomography (CT) of COVID-19 pneumonia has an incremental role in predicting patient’s admission to ICU.MethodsWe performed volumetric and texture analysis of the areas of the affected lung in CT of 115 outpatients with COVID-19 infection presenting to the Emergency Room with dyspnea and unresponsive hypoxyemia. Admission blood laboratory including lymphocyte count, serum lactate dehydrogenase, D-dimer and C-Reactive Protein and the ratio between the arterial partial pressure of oxygen and inspired oxygen were collected. By calculating the areas under the receiver-operating characteristic curves (AUC), we compared the performance of blood laboratory-arterial gas analyses features alone and combined with the CT features in two hybrid models (Hybrid radiological and Hybrid radiomics)for predicting ICU admission. Following a machine learning approach, 63 patients were allocated to the training and 52 to the validation set.Measurements and Main ResultsTwenty-nine (25%) of patients were admitted to ICU. The Hybrid radiological model comprising the lung %consolidation performed significantly (p=0.04) better in predicting ICU admission in the validation (AUC=0.82; 95%Confidence Interval 0.68-0.95) set than the blood laboratory-arterial gas analyses features alone (AUC=0.71; 95%Confidence Interval 0.56-0.86). A risk calculator for ICU admission was derived and is available at:https://github.com/cgplab/covidappConclusionsThe volume of the consolidated lung in CT of patients with COVID-19 pneumonia has a mild but significant incremental value in predicting ICU admission.
Levels of SARS-CoV-2 population exposure are considerably higher than suggested by seroprevalence surveys
Authors: Chen Siyu , Flegg Jennifer A , White Lisa J , Aguas Ricardo 
Published: January 2021

AbstractAccurate knowledge of accurate levels of prior population exposure has critical ramifications for preparedness plans of subsequent SARS-CoV-2 epidemic waves and vaccine prioritization strategies. Serological studies can be used to estimate levels of past exposure and thus position populations in their epidemic timeline. To circumvent biases introduced by decaying antibody titers over time, population exposure estimation methods should account for seroreversion, to reflect that changes in seroprevalence measures over time are the net effect of increases due to recent transmission and decreases due to antibody waning. Here, we present a new method that combines multiple datasets (serology, mortality, and virus positivity ratios) to estimate seroreversion time and infection fatality ratios and simultaneously infer population exposure levels. The results indicate that the average time to seroreversion is six months, and that true exposure may be more than double the current seroprevalence levels reported for several regions of England.
COVID-19 seroprevalence among healthcare workers of a large COVID Hospital in Rome reveals strengths and limits of two different serological tests
Authors: Vetrugno Giuseppe , La Milia Daniele Ignazio , D’Ambrosio Floriana , Di Pumpo Marcello , Pastorino Roberta , Boccia Stefania , Ricci Rosalba , De-Giorgio Fabio , Cicconi Michela , Foti Federica , Pascucci Domenico , Castrini Francesco , Carini Elettra , Cambieri Andrea , D’Alfonso Maria Elena , Capalbo Gennaro , Fantoni Massimo , Moscato Umberto , Staiti Domenico , De Simone Francesco Maria , Berloco Filippo , Zega Maurizio , Cattani Paola , Posteraro Brunella , Sanguinetti Maurizio , Laurenti Patrizia 
Published: January 2021

AbstractIn several hospitals worldwide, healthcare workers are currently at the forefront against coronavirus disease 2019 (COVID-19). Since Fondazione Policlinico Universitario A. Gemelli (FPG) IRCCS has been enlisted as a COVID hospital, healthcare workers deployed to COVID wards were separated from those with limited or no exposure, whereas administrative staff was destined to work-from-home. Between June 4 and July 3 2020, an investigation was carried out to evaluate seroprevalence of SARS-CoV-2 IgG antibodies among employees of the FPG using point-of-care (POC) and venous blood tests. Sensitivity, specificity and predictive values were determined with reverse-transcription polymerase chain reaction (RT-PCR) on nasal/oropharyngeal swabs as gold standard.Four thousand, seven hundred seventy-seven participants were enrolled. Seroprevalence was 3.66% using the POC test and 1.19% using venous blood test, with a significant difference between the two (p < 0.05).POC sensitivity and specificity were, respectively, 63.64% (95% confidence interval (CI): 62.20% to 65.04%) and 96.64% (95% CI: 96.05% to 97.13%), while those of the venous blood test were, respectively, 78.79% (95% CI: 77.58% to 79.94%) and 99.36% (95% CI: 99.07% to 99.55%). Among low-risk population, point-of-care’s predictive values were 58.33% (positive) and 98.23% (negative) whereas venous blood test’s were 92.86% (positive) and 98.53% (negative). In conclusion, point-of-care tests have low diagnostic accuracy, while venous blood tests seem to show an overall poor reliability.
The Effect of Temperature on Covid-19 Confirmed Cases: Evidence from US Counties
Authors: NoghaniBehambari Hamid , Salari Mahmoud , Noghani Farzaneh , Tavassoli Nahid 
Published: January 2021

AbstractThis paper studies the effect of air temperature on the transmission of COVID-19 in the U.S. using daily observations across counties. This study uses various ordinary least squares (OLS) models with a comprehensive set of fixed effects to overcome unobserved heterogeneity issues across counties as well as the generalized method of moments (GMM) estimators as dynamic models to address endogeneity issue. Our main results indicate that an increase of one degree in temperature is associated with a reduction of 0.041 cases per 100,000 population at the county-level. We run several robustness tests and all the models confirm the impact of temperature on COVID-19 confirmed new cases. These results help policymakers and economists in optimizing decisions and investments to reduce COVID- 19 new cases.JEL CodesI10; Q51; Q54; H12
Whole-Cell Dissociated Suspension Analysis in Human Brain Neurodegenerative Disease: A Pilot Study
Authors: Serrano Geidy E. , Walker Jessica E. , Intorcia Anthony J. , Glass Michael J. , Arce Richard A. , Piras Ignazio S. , Talboom Joshua S. , Nelson Courtney M. , Cutler Brett D. , Sue Lucia I. , Lue Lih-Fen , Huentelman Matthew , Beach Thomas G. 
Published: January 2021

AbstractBiochemical analysis of human brain tissue is typically done by homogenizing whole pieces of brain and separately characterizing the proteins, RNA, DNA, and other macromolecules within. While this has been sufficient to identify substantial changes, there is little ability to identify small changes or alterations that may occur in subsets of cells. To effectively investigate the biochemistry of disease in the brain, with its different cell types, we must first separate the cells and study them as phenotypically defined populations or even as individuals. In this project, we developed a new method for the generation of whole-cell-dissociated-suspensions (WCDS) in fresh human brain tissue that could be shared as a resource with scientists to study single human cells or populations. Characterization of WCDS was done in paraffin-embedded sections stained with H&E, and by phenotyping with antibodies using immunohistochemistry and fluorescence-activated cell sorting (FACS). Additionally, we compared extracted RNA from WCDS with RNA from adjacent intact cortical tissue, using RT-qPCR for cell-type-specific RNA for the same markers as well as whole transcriptome sequencing. More than 11,626 gene transcripts were successfully sequenced and classified using an external database either as being mainly expressed in neurons, astrocytes, microglia, oligodendrocytes, endothelial cells, or mixed (in two or more cell types). This demonstrates that we are currently capable of producing WCDS with a full representation of different brain cell types combined with RNA quality suitable for use in biochemical analysis.
HIV-infected patients on combined antiretroviral treatment had similar level of arterial stiffness to the patients with ST-segment elevation myocardial infarction
Authors: Mikuła Tomasz , Suchacz Magdalena M. , Peller Michał , Balsam Paweł , Kołtowski Łukasz , Główczyńska Renata , Filipiak Krzysztof J. , Opolski Grzegorz , Wiercińska-Drapało Alicja 
Published: January 2021

AbstractPurposeThe cardiovascular disease has become very common among HIV-infected patients. The aim was to compare the arterial stiffness and the endothelial dysfunction in HIV-infected patients to non-HIV-infected patients in week 4 after ST-segment elevation myocardial infarction (STEMI).MethodsThe arterial stiffness was calculated by Endo-PAT 2000(ITAMAR®) and the endothelial function by Peripheral Arterial Tonometry(PAT®). The correct endothelial function was defined for natural logarithm of reactive hyperaemia index (lnRHI)>0.51. Arterial stiffness was assessed as the AI and corrected for heart rate of 75 bpm (AI@75).ResultsSixty-three patients were recruited to this study, n=34 patients with HIV infection (n=18 on cART) and n=29 HIV-negative patients after recent STEMI. No statistically significant differences for AI and AI@75 were found in STEMI and in HIV on cART group. We observed p<0.05 for AI and AI@75 for patients without cART compared to STEMI and on cART patients. The observed lnRHI results were significantly different p<0.05 in STEMI and on cART patients. We get similar endothelial dysfunction p>0.05 for patients without cART compared to STEMI and on cART patients.ConclusionsAssessing cardiovascular risk also with non-invasive methods among HIV-infected patients is very important especially in HIV-patients on cART. Endothelial dysfunction is connected with HIV infection and can be similar for STEMI and HIV-infected without cART.
Structural and mechanistic insights into the Artemis endonuclease and strategies for its inhibition
Authors: Yosaatmadja Yuliana , Baddock Hannah T , Newman Joseph A , Bielinski Marcin , Gavard Angeline E , Mukhopadhyay Shubhashish M M , Dannerfjord Adam A , Schofield Christopher J , McHugh Peter J , Gileadi Opher 
Published: January 2021

ABSTRACTArtemis (DCLRE1C) is an endonuclease that plays a key role in development of B- and T-lymphocytes and in DNA double-strand break repair by non-homologous end-joining (NHEJ). Artemis is phosphorylated by DNA-PKcs and acts to open DNA hairpin intermediates generated during V(D)J and class-switch recombination. Consistently, Artemis deficiency leads to radiosensitive congenital severe immune deficiency (RS-SCID). Artemis belongs to a structural superfamily of nucleases that contain conserved metallo-β-lactamase (MBL) and β-CASP (CPSF-Artemis-SNM1-Pso2) domains. Here, we present crystal structures of the catalytic domain of wild type and variant forms of Artemis that cause RS-SCID Omenn syndrome. The truncated catalytic domain of the Artemis is a constitutively active enzyme that with similar activity to a phosphorylated full-length protein. Our structures help explain the basis of the predominantly endonucleolytic activity of Artemis, which contrast with the predominantly exonuclease activity of the closely related SNM1A and SNM1B nucleases. The structures also reveal a second metal binding site in its β-CASP domain that is unique to Artemis. By combining our structural data that from a recently reported structure we were able model the interaction of Artemis with DNA substrates. Moreover, co-crystal structures with inhibitors indicate the potential for structure-guided development of inhibitors.
Shear-Mediated Platelet Activation is Accompanied by Unique Alterations of Platelet Lipid Profile
Authors: Sweedo Alice , Wise Lisa M. , Roka-Moiia Yana , Arce Fernando Teran , Saavedra S. Scott , Sheriff Jawaad , Bluestein Danny , Slepian Marvin J. , Purdy John G. 
Published: January 2021

ABSTRACTPlatelet activation by mechanical means such as shear stress, is a vital driver of thrombotic risk in implantable blood-contacting devices used in treatment of heart failure. Lipids are essential in platelets activation and have been studied following biochemical activation. However, little is known regarding lipid alterations occurring with mechanical – shear mediated platelet activation. Here, we determined if shear-activation of platelets induced lipidome changes that differ from those associated with biochemically-mediated platelet activation. We performed high-resolution lipidomic analysis on purified platelets from four healthy human donors. For each donor, we compared the lipidome of platelets that were non-activated or activated by shear, ADP, or thrombin treatment. We found that shear activation altered cell-associated lipids and led to the release of lipids into the extracellular environment. Shear-activated platelets released 21 phospholipids and sphingomyelins at levels statistically higher than platelets activated by biochemical stimulation. Many of the released phospholipids contained an arachidonic acid tail or were phosphatidylserine lipids, which have procoagulant properties. We conclude that shear-mediated activation of platelets alters the basal platelet lipidome. Further, these alterations differ and are unique in comparison to the lipidome of biochemically activated platelets. Our findings suggest that lipids released by shear-activated platelets may contribute to altered thrombosis in patients with implanted cardiovascular therapeutic devices.
Wide distribution of alternatively coded Lak megaphages in animal microbiomes
Authors: Crisci Marco A. , Chen Lin-Xing , Devoto Audra E. , Borges Adair L. , Bordin Nicola , Sachdeva Rohan , Tett Adrian , Sharrar Allison M. , Segata Nicola , Debenedetti Francesco , Bailey Mick , Burt Rachel , Wood Rhiannon M. , Rowden Lewis J. , Corsini Paula M. , Holmes Mark A. , Lei Shufei , Banfield Jillian F. , Santini Joanne M. 
Published: January 2021

AbstractLak phages with alternatively coded ~540 kbp genomes were recently reported to replicate in Prevotella in the gut microbiomes of humans that consume a non-western diet, baboons and some pigs. Here, we investigate the diversity and broader distribution of Lak phages in human and animal microbiomes using diagnostic PCR and genome-resolved metagenomics. Lak phages were detected in 13 different animal types and are particularly prevalent in pigs, with significant enrichment in the hindgut compared to foregut. We reconstructed 34 new Lak genomes, including six curated complete genomes, all of which are alternatively coded. The most deeply branched Lak is from a horse faecal sample and is the largest phage genome from an animal microbiome (~660 kbp). From the Lak genomes, we identified families of hypothetical proteins associated with specific animal types. Overall, we substantially expanded Lak phage diversity and demonstrate their occurrence in a variety of human and animal microbiomes.
Moving patronin foci and growing microtubule plus ends direct the spatiotemporal dynamics of Rho signaling and myosin during apical constriction
Authors: Guru Anwesha , Saravanan Surat , Sharma Deepanshu , Narasimha Maithreyi 
Published: January 2021

SummaryThe contraction of the amnioserosa by apical constriction provides the major force for Drosophila dorsal closure. The nucleation, movement and dispersal of apicomedial actomyosin complexes generate pulsed constrictions during early dorsal closure whereas persistent apicomedial and circumapical actomyosin complexes drive the unpulsed constrictions that follow. What governs the spatiotemporal assembly of these distinct complexes, endows them with their pulsatile dynamics, and directs their motility remains unresolved. Here we identify an essential role for microtubule growth in regulating the timely contraction of the amnioserosa. We show that a symmetric cage of apical microtubules forms around the coalescing apicomedial myosin complex. An asymmetric tail of microtubules then trails the moving myosin complex and disperses as the myosin complex dissolves. Perturbing microtubule growth reduced the coalescence and movement of apicomedial myosin complexes and redistributed myosin and its activator, Rho kinase to the circumapical pool and altered the cell constriction and tissue contraction dynamics of the amnioserosa. We show that RhoGEF2, the activator of the Rho1 GTPase, is transiently associated with microtubule plus end binding protein EB1 and the apicomedial actomyosin complex. Our results suggest that microtubule growth from moving patronin platforms modulates actomyosin contractility through the spatiotemporal regulation of Rho1 activity. We propose that microtubule reorganisation enables a self-organising, mechanosensitive feedback loop that buffers the tissue against mechanical stresses by modulating actomyosin contractility.