bluuebunny/crossref_metadata_2025_split huggingface dataset:
An exact method for quantifying the reliability of end-of-epidemic declarations in real time
Authors: Parag Kris V , Donnelly Christl A , Jha Rahul , Thompson Robin N 
Published: July 2020

AbstractWe derive and validate a novel and analytic method for estimating the probability that an epidemic has been eliminated (i.e. that no future local cases will emerge) in real time. When this probability crosses 0.95 an outbreak can be declared over with 95% confidence. Our method is easy to compute, only requires knowledge of the incidence curve and the serial interval distribution, and evaluates the statistical lifetime of the outbreak of interest. Using this approach, we rigorously show how the time-varying under-reporting of infected cases will artificially inflate the inferred probability of elimination and hence lead to early (false-positive) end-of-epidemic declarations. Contrastingly, we prove that incorrectly identifying imported cases as local will deceptively decrease this probability, resulting in late (false-negative) declarations. Failing to sustain intensive surveillance during the later phases of an epidemic can therefore substantially mislead policymakers on when it is safe to remove travel bans or relax quarantine and social distancing advisories. World Health Organisation guidelines recommend fixed (though disease-specific) waiting times for end-of-epidemic declarations that cannot accommodate these variations. Consequently, there is an unequivocal need for more active and specialised metrics for reliably identifying the conclusion of an epidemic.
The natural history of symptomatic COVID-19 in Catalonia, Spain: a multi-state model including 109,367 outpatient diagnoses, 18,019 hospitalisations, and 5,585 COVID-19 deaths among 5,627,520 people
Authors: Burn Edward , Tebé Cristian , Fernandez-Bertolin Sergio , Aragon Maria , Recalde Martina , Roel Elena , Prats-Uribe Albert , Prieto-Alhambra Daniel , Duarte-Salles Talita 
Published: July 2020

AbstractBackgroundThe natural history of Coronavirus Disease 2019 (COVID-19) has yet to be fully described, with most previous reports focusing on hospitalised patients. Using linked patient-level data, we set out to describe the associations between age, gender, and comorbidities and the risk of outpatient COVID-19 diagnosis, hospitalisation, and/or related mortality.MethodsA population-based cohort study including all individuals registered in Information System for Research in Primary Care (SIDIAP). SIDIAP includes primary care records covering > 80% of the population of Catalonia, Spain, and was linked to region-wide testing, hospital and mortality records. Outpatient diagnoses of COVID-19, hospitalisations with COVID-19, and deaths with COVID-19 were identified between 1st March and 6th May 2020. A multi-state model was used, with cause-specific Cox survival models estimated for each transition.FindingsA total of 5,627,520 individuals were included. Of these, 109,367 had an outpatient diagnosis of COVID-19, 18,019 were hospitalised with COVID-19, and 5,585 died after either being diagnosed or hospitalised with COVID-19. Half of those who died were not admitted to hospital prior to their death. Risk of a diagnosis with COVID-19 peaked first in middle-age and then again for oldest ages, risk for hospitalisation after diagnosis peaked around 70 years old, with all other risks highest at oldest ages. Male gender was associated with an increased risk for all outcomes other than outpatient diagnosis. The comorbidities studied (autoimmune condition, chronic kidney disease, chronic obstructive pulmonary disease, dementia, heart disease, hyperlipidemia, hypertension, malignant neoplasm, obesity, and type 2 diabetes) were all associated with worse outcomes.InterpretationThere is a continued need to protect those at high risk of poor outcomes, particularly the elderly, from COVID-19 and provide appropriate care for those who develop symptomatic disease. While risks of hospitalisation and death are lower for younger populations, there is a need to limit their role in community transmission. These findings should inform public health strategies, including future vaccination campaigns.
PROJECTING A MATURE EPIDEMIC: A SIMPLE TOOL WITH AN APPLICATION TO COVID-19 DEATHS
Authors: Artzrouni Marc , Wykoff Randy 
Published: July 2020

AbstractWe describe a new statistical model for the spread of a mature epidemic, i.e. one characterized by an exponentially decaying growth rate of the cumulative number of cases/deaths – the speed of this decay being measured by the growth rate’s half-life. If such a pattern is observed during the recent past, then it can be extrapolated. A spreadsheet is made available that allows users to input weekly cumulative numbers of deaths and obtain an estimate of the growth rate’s baseline half-life and the corresponding projections. These projections can be compared to those with a larger half-life (if a protracted epidemic is expected, e.g. due to second wave), or with a smaller one (if successful therapies or mitigation efforts reduce transmission). The model is applied to deaths due to COVID-19 in California in May-June 2020.
Staff testing for COVID-19 via an online pre-registration form
Authors: Moolla M. Saadiq , Parker Arifa , Parker M. Aslam , Sithole Sthembiso , Amien Leila , Chiecktey Rubeena , Bawa Tasneem , Mowlana Abdurasiet 
Published: July 2020

Structured AbstractBackgroundHealthcare workers are at increased risk of contracting SARS-CoV-2 and potentially causing institutional outbreaks. Staff testing is critical in identifying and isolating infected individuals while also reducing unnecessary workforce depletion. Tygerberg Hospital implemented an online pre-registration system to expedite staff and cluster testing.ObjectivesWe aimed to identify (1) specific presentations associated with a positive or negative result for SARS-CoV-2 and (2) staff sectors where enhanced strategies for testing might be required.MethodsRetrospective descriptive study involving all clients making use of the hospital’s pre-registration system during May 2020.ResultsOf 799 clients, most were young and female with few comorbidities. The most common occupation was nurses followed by administrative staff, doctors and general assistants. Doctors tested earlier compared to other staff (median: 1.5 vs 4 days). The most frequent presenting symptoms were headache, sore throat, cough and myalgia. Amongst those testing positive (n=105), fever, altered smell, altered taste sensation, chills and history of fever were the most common symptoms. Three or more symptoms was more predictive of a positive test, but 12/145 asymptomatic clients also tested positive.ConclusionStaff coronavirus testing using an online pre-registration form is a viable and acceptable strategy. While some presentations are less likely to be associated with SARS-CoV-2 infection, no symptom can completely exclude it. Staff testing should form part of a bundle of strategies to protect staff including wearing masks, regular hand washing, buddy screening, physical distancing, availability of PPE and special dispensation for COVID-19-related leave.Unstructured AbstractHospital staff testing is critical to identify and isolate SARS-CoV-2 infected individuals while reducing unnecessary workforce depletion. Tygerberg Hospital implemented an online pre-registration system to expedite staff testing. In a retrospective descriptive study of all clients registering during May 2020 (N=799), we found rapid and sustained uptake of the system. The most frequent presenting symptoms were headache, sore throat, cough and myalgia. Amongst those testing positive (n=105), fever, altered smell, altered taste sensation and chills were the most likely symptoms, but 12/145 asymptomatic clients also tested positive. Staff testing should form part of a bundle of strategies to protect staff.
Fluorescentin vivoediting reporter (FIVER): A novel multispectral reporter ofin vivogenome editing
Authors: Tennant Peter A. , Foster Robert G. , Dodd Daniel O. , Sou Ieng Fong , McPhie Fraser , Younger Nicholas , Murphy Laura C. , Pearson Matthew , Vernay Bertrand , Keighren Margaret A. , Budd Peter , Hart Stephen L. , Megaw Roly , Boulter Luke , Mill Pleasantine 
Published: July 2020

AbstractAdvances in genome editing technologies have created opportunities to treat rare genetic diseases, which are often overlooked in terms of therapeutic development. Nonetheless, substantial challenges remain: namely, achieving therapeutically beneficial levels and kinds of editing in the right cell type(s). Here we describe the development of FIVER (fluorescentin vivoediting reporter) — a modular toolkit forin vivodetection of genome editing with distinct fluorescent read-outs for non-homologous end-joining (NHEJ), homology-directed repair (HDR) and homology-independent targeted integration (HITI). We demonstrate that fluorescent outcomes reliably report genetic changes following editing with diverse genome editors in primary cells, organoids andin vivo. We show the potential of FIVER for high-throughput unbiased screens, from small molecule modulators of genome editing outcomes in primary cells through to genome-widein vivoCRISPR cancer screens. Importantly, we demonstrate itsin vivoapplication in postnatal organ systems of interest for genetic therapies — retina and liver. FIVER will broadly help expedite the development of therapeutic genome surgery for many genetic disorders.
Direct visualization of four diffusive LexA states controlling SOS response strength during antibiotic treatment
Authors: Schärfen Leonard , Tišma Miloš , Hartmann Andreas , Schlierf Michael 
Published: July 2020

AbstractIn bacteria, the key mechanism governing mutation, adaptation and survival upon DNA damage is the SOS response. Through autoproteolytic digestion triggered by single-stranded DNA caused by most antibiotics, the transcriptional repressor LexA controls over 50 SOS genes including DNA repair pathways and drivers of mutagenesis. Efforts to inhibit this response and thereby combat antibiotic resistance rely on a broad understanding of its behaviorin vivo, which is still limited. Here, we develop a single-molecule localization microscopy assay to directly visualize LexA mobility inEscherichia coliand monitor the SOS response on the level of transcription factor activity. We identify four diffusive populations and monitor their temporal evolution upon ciprofloxacin-induced continuous DNA damage. With LexA mutants, we assign target bound, non-specifically DNA bound, freely diffusing and cleaved repressors. We develop a strategy to count LexA in fixed cells at different time points after antibiotic stress and combine the time-evolution of LexA sub-populations and the repressor’s overall abundance. Through fitting a detailed kinetic model we obtainin vivosynthesis, cleavage and binding rates and determined that the regulatory feedback system reaches a new equilibrium in ∼100 min. LexA concentrations showed non-constant heterogeneity during SOS response and designate LexA expression, and thereby regulation of downstream SOS proteins, as drivers of evolutionary adaptation. Even under low antibiotic stress, we observed a strong SOS response on the LexA level, suggestion that small amounts of antibiotics can trigger adaptation inE. coli.
Improving vaccine efficacy based on non-covalent photoinactivation of microorganisms - sources vaccine antigens (MSVA)
Authors: Martynov Artur , Farber Boris , Osolodchenko Tatyana , Klein Ilya 
Published: July 2020

AbstractOne of the most promising methods for non-covalent inactivation of vaccine-producing microorganisms is the use of photoinactivation using riboflavin derivatives. The study used a dynamic combinatorial derivative of riboflavin - succinyl-maleinyl riboflavin. Corpuscular vaccines are divided into the following groups: from 2AB to 5AB - bacteria were inactivated by riboflavin derivative and blue light, and groups from 6AB to 9AB were inactivated by formalin (0.1% formalin in 9 log CFU was kept for 2 weeks in an thermostat and then sterility was determined - bacterial growth was not observed). A dynamic derivative of riboflavin at a final concentration of 0.02% can photo inactivate 6 time more bacteria P. Aeruginosa and E. coli than riboflavin. The minimum effective blue light emitter power (450 nm) for the photodynamic inactivation of both P. aeruginosa and E. coli is 1024.2 mW / cm2. In groups of mice pre-vaccinated intraperitoneally with corpuscular photo inactivated vaccines based on suspensions of and E. coli at doses of 0.5-1.0 ml 4 log (CFU) / mL, 100% survival of all animals was observed, whereas in control group with the same type of vaccines but formalin-treated vaccines, it failed to achieve a 100% protective effect.
Lox’d in translation: Contradictions in the nomenclature surrounding common lox site mutants and their implications in experiments
Authors: Shaw Daniel , Serrano Luis , Lluch-Senar Maria 
Published: July 2020

AbstractThe Cre-Lox system is a highly versatile and powerful DNA recombinase mechanism, mainly used in genetic engineering to insert or remove desired DNA sequences. It is widely utilised across multiple fields of biology, with applications ranging from plants, to mammals, to microbes. A key feature of this system is its ability to allow recombination between mutant lox sites, traditionally named lox66 and lox71, to create a functionally inactive double mutant lox72 site. However, a large portion of the published literature has incorrectly annotated these mutant lox sites, which in turn can lead to difficulties in replication of methods, design of proper vectors, and confusion over the proper nomenclature. Here, we demonstrate common errors in annotations, the impacts they can have on experimental viability, and a standardised naming convention. We also show an example of how this incorrect annotation can induce toxic effects in bacteria that lack optimal DNA repair systems, exemplified byMycoplasma pneumoniae.Data SummaryThe authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.
Hippocampal dentate gyrus coordinates brain-wide communication and memory updating through an inhibitory gating
Authors: Caramés José María , Pérez-Montoyo Elena , Garcia-Hernandez Raquel , Canals Santiago 
Published: July 2020

AbstractDistinct forms of memory processing are often causally identified with specific brain regions, but a key facet of memory processing includes linking separated neuronal populations. Using cell-specific manipulations of inhibitory neuronal activity, we discovered a key role of the dentate gyrus (DG) in coordinating dispersed neuronal populations during memory formation. In whole-brain fMRI and electrophysiological experiments, we found that parvalbumin (PV) interneurons in the DG control the functional coupling of the hippocampus within a wider network of neocortical and subcortical structures including the prefrontal cortex (PFC) and the nucleus accumbens (NAc). In a novel object-location task, regulation of PV interneuron activity enhanced or prevented memory encoding and, without effect upon the total number of task activated c-Fos+ cells, revealed a correlation between activated neuronal populations in the hippocampus-PFC-NAc network. These data suggest a critical regulatory role of PV interneurons in the dentate gyrus in brain-wide polysynaptic communication channels and the association of cell assemblies across multiple brain regions.
A ray-tracing algorithm for ab initio calculation of thermal load in undulator-based synchrotron beamlines
Authors: Rebuffi Luca , Shi Xianbo , Sanchez del Rio Manuel , Reininger Ruben 
Published: July 2020

The OASYS suite and its powerful integration features are used to implement a ray-tracing algorithm to accurately calculate the thermal load in any component of an undulator-based synchrotron beamline. This is achieved by sampling and converting the SRW source of a given energy into a Shadow source and using the latter code to ray trace the full beamline. The accuracy of the algorithm is proved by reconstructing the full undulator radiation distribution through an aperture and comparing the result with direct calculaton of the total power using SRW. The algorithm is particularly suited to analyze cases with complex beamline layouts and optical elements, such as crystals, multilayers, and compound refractive lenses. Examples of its use to calculate the power load on elements of two of the feature beamlines at the Advanced Photon Source Upgrade Project and a comparison of the results with analytical calculations are presented.
The role of national culture in the relationship between microfinance outreach and sustainability: a correlated random effects approach
Authors: Zainuddin Mohammad , Mahi Masnun , Akter Shabiha , Yasin Ida Md. 
Published: July 2020

PurposeThis study investigates the role of national culture between outreach and sustainability of microfinance institutions (MFIs). Despite microfinance's deep embeddedness in cultural contexts, research on the influence of national culture on MFI performance is rather sparse. This paper seeks to fill this gap and, based on cross-country microfinance data, attempts to explain the outreach-sustainability relationship in reference to cultural factors.Design/methodology/approachAn unbalanced panel, consisting of 5,741 MFI-year observations of 1,232 MFIs from 43 countries in six regions, is drawn from the Microfinance Information Exchange (MIX) Market database. Two different econometric models are tested. Model 1 estimates the direct effect of outreach on sustainability, using a fixed-effects estimator. Model 2 examines the moderation effect of national culture on outreach-sustainability relationship, employing correlated random effects approach.FindingsThe results show that depth of outreach and financial sustainability of MFIs are negatively related, and the relationship is moderated by national culture. Power distance and uncertainty avoidance positively moderate the outreach-sustainability relationship, whereas individualism and masculinity negatively moderate the relationship.Originality/valueThe findings suggest that the national culture where MFIs are located plays an important contingent role in their performance and that the magnitude of the trade-off effect varies from culture to culture. The research thus provides further insight in the trade-off debate and contributes to literatures of both microfinance and cross-cultural management.
Hardware simulation of lane keeping assist based on sensor fusion
Authors: Cholis Basjaruddin Noor , Rakhman Edi , Adinugraha Fazrin 
Published: July 2020

PurposeSafety is one of the most crucial factors in transportation due to so many factors, including human-error, that might result in various small to fatal accidents. This is why lane keeping assist (LKA) is an important system that needs to be developed. LKA will prevent the vehicle from moving to another lane because the driver is negligent to maintain the direction of the vehicle.Design/methodology/approachIn this study, LKA works using camera and ultrasonic sensors. The data coming from these two types of sensors are then fused to determine how should the car reacts to some certain situation so that it stays on the lane. The sensor fusion method was used to further ensure the car's safety.FindingsThe results of the hardware simulation show that LKA can successfully avoid the car from getting off the lane with safety index of 95% for high-speed mode and 100% for medium and low-speed mode; meanwhile on the use of ultrasonic sensor, the speed of the car is adjusted to the distance of the car's side disturbance.Originality/valueThis research has succeeded in simulating a sensor fusion–based LKA system.
Teacher trainees' understandings of mentoring within a Middle Eastern BEd program
Authors: Pattisson Joy 
Published: July 2020

PurposThe purpose of this study was to explore young Arab women's understandings of mentoring as part of a pre-service teacher training program both before and after an extended internship throughout which a collaborative approach to mentoring was practiced. It aimed to identify the opportunities and challenges such an approach would bring in the quest to support trainee teachers' professional development.Design/methodology/approachData for this small-scale qualitative study were collected using a brainstorming class-based activity, semi-structured interviews and reflective journals. Data were analyzed using word clouds, and the identification of themes through the coding of transcripts.FindingsThe dominant findings in this study were that mentoring was perceived as emotional support, pedagogic and professional support, evaluation and relationship. While understandings of mentoring amongst participants did shift as a result of mentors adopting a collaborative approach, data indicated that the strength of cultural assumptions held by the participants hindered the rate of change, creating an obstacle to the desired outcome of increasing trainees' agency.Originality/valueWhile perceptions of mentoring reported within this study indicate considerable overlap with those in other geographical and cultural contexts, closer examination of the data identified differences also. Without an understanding of the nature and influence of the social assumptions that underlie these differences, mentors who participate in culturally diverse mentor–trainee pairings can misinterpret an unwillingness of trainees to fully engage with the mentoring process and thus fail to provide the required scaffolding and support needed to maximize professional development.
The effects of indoor plants on customers' shopping decisions in a restaurant environment
Authors: Yildirim Kemal , Yildirim Kaya Nazlı Nazende , Olmus Ferdi 
Published: July 2020

PurposeThe purpose of this paper is to focus on the effects of indoor plants on customers' shopping decisions in the restaurant environment.Design/methodology/approachThe assumption of the research is that there is a relationship between restaurants where indoor plants are used and the customers' shopping decisions (restaurant entry and purchase). A hypothetical study was performed to test this assumption that was based on the digital images of two different restaurants (restaurant with and restaurant without indoor plants) modelled in a virtual environment. The Likert scale questionnaire used in this study was completed by 335 participants.FindingsResults indicated that restaurants designed with indoor plants had a more positive effect on the shopping decisions of participants than restaurants designed without indoor plants. The statistically significant results between evaluations of customers and their demographic backgrounds were determined. The male participants with a 26–35 age range showed more positive opinions about the plant designed restaurants than female participants with a 36–55 age range. Also, higher education graduate participants showed more positive opinions about the plant designed restaurant than secondary education graduate participants.Originality/valueThis paper reveals a significant relationship between restaurant design and shopping decisions. Results of the study suggest that retailers and designers may be able to make easily stores more appealing for customers by designing them with indoor plants.