bluuebunny/crossref_metadata_2025_split huggingface dataset:
Model Based Comparison of Covid-19 Cases in Two Counties in the Silicon Valley
Authors: Basu Santanu 
Published: May 2020

ABSTRACTA recently developed model to analyze Covid-19 case data has been applied to compare the Covid-19 cases and hospital bed usage in Santa Clara county and San Mateo county which are in the Silicon Valley region of California. The model gives prediction for number of cases and deaths and number of hospital beds six weeks in advance. The model is versatile and can be applied to other countries and regions as well.
The global explosion of eukaryotic algae: the potential role of phosphorus?
Authors: Eckford-Soper Lisa K , Canfield Donald E. 
Published: May 2020

AbstractThere arose one of the most important ecological transitions in Earth’s history approximately 750 million years ago during the middle Neoproterozoic Era (1000 to 541 million years ago, Ma). Biomarker evidence suggests that around this time there was a rapid shift from a predominantly bacterial-dominated world to more complex ecosystems governed by eukaryotic primary productivity. The resulting ‘Rise of the algae’ led to dramatically altered food webs that were much more efficient in terms of nutrient and energy transfer. Yet, what triggered this ecological shift? In this study we examined the theory that it was the alleviation of phosphorus (P) deficiency that gave eukaryotic alga the prime opportunity to flourish. We performed laboratory experiments on the cyanobacteriumSynochystis salinaand the eukaryotic algaeTetraselmis sueciaand examined their ability to compete for phosphorus. Both these organisms co-occur in modern European coastal waters and are not known to have any allelopathic capabilities. The strains were cultured in mono and mixed cultures in chemostats across a range of dissolved organic phosphorus (DIP) conditions to reflect modern and ancient oceanic conditions of 0.2 μM P and 2 μM P, respectively. Our results show that the cyanobacteria outcompete the algae at the low input (0.2 μM P) treatment, yet the eukaryotic algae were not completely excluded and remained a constant background component in the mixed-culture experiments. Also, despite it’s relatively large cell size, the algaeT. sueciahad a high affinity for DIP. With DIP input concentrations resembling modern-day levels (2 μM), the eukaryotic algae could effectively compete against the cyanobacteria in terms of total biomass production. These results suggest that the availability of phosphorus could have influenced the global expansion of eukaryotic algae. However, P limitation does not seem to explain the complete absence of eukaryotic algae in the biomarker record before ca. 750 Ma.
Functional reconstitution of a bacterial CO2concentrating mechanism inE. coli
Authors: Flamholz Avi I. , Dugan Eli , Blikstad Cecilia , Gleizer Shmuel , Ben-Nissan Roee , Amram Shira , Antonovsky Niv , Ravishankar Sumedha , Noor Elad , Bar-Even Arren , Milo Ron , Savage David F. 
Published: May 2020

AbstractMany photosynthetic organisms employ a CO2concentrating mechanism (CCM) to increase the rate of CO2fixation via the Calvin cycle. CCMs catalyze ≈50% of global photosynthesis, yet it remains unclear which genes and proteins are required to produce this complex adaptation. We describe the construction of a functional CCM in a non-native host, achieved by expressing genes from an autotrophic bacterium in an engineeredE. colistrain. Expression of 20 CCM genes enabledE. colito grow by fixing CO2from ambient air into biomass, with growth depending on CCM components. Bacterial CCMs are therefore genetically compact and readily transplanted, rationalizing their presence in diverse bacteria. Reconstitution enabled genetic experiments refining our understanding of the CCM, thereby laying the groundwork for deeper study and engineering of the cell biology supporting CO2assimilation in diverse organisms.One Sentence SummaryA bacterial CO2concentrating mechanism enablesE. colito fix CO2from ambient air.
Contribution of segment 3 to the acquisition of virulence in contemporary H9N2 avian influenza viruses
Authors: Clements Anabel L. , Sealy Joshua E. , Peacock Thomas P. , Sadeyen Jean-Remy , Hussain Saira , Lycett Samantha J. , Shelton Holly , Digard Paul , Iqbal Munir 
Published: May 2020

AbstractH9N2 avian influenza viruses circulate in poultry throughout much of Asia, the Middle East and Africa. These viruses cause huge economic damage to poultry production systems and pose a zoonotic threat both in their own right as well as in the generation of novel zoonotic viruses, for example H7N9. In recent years it has been observed that H9N2 viruses have further adapted to poultry, becoming more highly transmissible and causing higher morbidity and mortality. Here, we investigate the molecular basis for this increased virulence, comparing a virus from the 1990s and a contemporary field strain. The modern virus replicated to higher titres in various systems and this difference mapped to a single amino acid polymorphism at position 26 of the endonuclease domain shared by the PA and PA-X proteins. This change was responsible for the virulent phenotype and extended tissue tropism seen in chickens. Although the PA K26E change correlated with increased host cell shutoff activity of the PA-X proteinin vitro, it could not be overridden by frameshift site mutations that block PA-X expression and therefore increased PA-X activity could not explain the differences in replication phenotype. Instead, this indicates these differences are due to subtle effects on PA function. This work gives insight into the ongoing evolution and poultry adaptation of H9N2 and other avian influenza viruses and helps us understand the soaring morbidity and mortality rates in the field, as well as rapidly expanding geographical range seen in these viruses.Author SummaryAvian influenza viruses, such as H9N2, cause huge economic damage to poultry production worldwide and are additionally considered potential pandemic threats. Understanding how these viruses evolve in their natural hosts is key to effective control strategies. In the Middle East and South Asia an older H9N2 virus strain has been replaced by a new reassortant strain with greater fitness. Here we take representative viruses and investigate the genetic basis for this ‘fitness’. A single mutation in the virus was responsible for greater fitness, enabling high growth of the contemporary H9N2 virus in cells, as well as in chickens. The genetic mutation that modulates this change is within the viral PA protein, a part of the virus polymerase gene that contributes in viral replication as well as contribute in the virus accessory functions – however we find that the fitness effect is specifically due to changes in the protein polymerase activity.
Automated and partially-automated contact tracing: a rapid systematic review to inform the control of COVID-19
Authors: Braithwaite Isobel , Callender Tom , Bullock Miriam , Aldridge Robert W 
Published: May 2020

AbstractBackgroundAutomated or partially-automated contact tracing tools are being deployed by many countries to contain SARS-CoV-2; however, the evidence base for their use is not well-established.MethodsWe undertook a rapid systematic review of automated or partially-automated contact tracing, registered with PROSPERO (CRD42020179822). We searched PubMed, EMBASE, OVID Global Health, EBSCO COVID Portal, Cochrane Library, medRxiv, bioRxiv, arXiv and Google Advanced for articles relevant to COVID-19, SARS, MERS, influenza or Ebola from 1/1/200014/4/2020. Two authors reviewed all full-text manuscripts. One reviewer extracted data using a pre-piloted form; a second independently verified extracted data. Primary outcomes were the number or proportion of contacts (and/or subsequent cases) identified; secondary outcomes were indicators of outbreak control, app/tool uptake, resource use, cost-effectiveness and lessons learnt. The Effective Public Health Practice Project tool or CHEERS checklist were used in quality assessment.Findings4,033 citations were identified and 15 were included. No empirical evidence of automated contact tracing’s effectiveness (regarding contacts identified or transmission reduction) was identified. Four of seven included modelling studies suggested that controlling COVID-19 requires high population uptake of automated contact-tracing apps (estimates from 56% to 95%), typically alongside other control measures. Studies of partially-automated contact tracing generally reported more complete contact identification and follow-up, and greater intervention timeliness (0.5-5 hours faster), than previous systems. No meta-analyses were possible.InterpretationAutomated contact tracing has potential to reduce transmission with sufficient population uptake and usage. However, there is an urgent need for well-designed prospective evaluations as no studies provided empirical evidence of its effectiveness.
Climate change education in school: knowledge, behavior and attitude
Authors: Tibola da Rocha Vanessa , Brandli Luciana Londero , Kalil Rosa Maria Locatelli 
Published: May 2020

Purpose
The purpose of this paper is to present an experience of inclusion of the theme “climate change” in a Brazilian public school through training conducted with teachers.

Design/methodology/approach
The methodology was based on three specific phases: reflection, focusing on the application of a pretest with 45 questions directed to three domains (knowledge, attitude and behavior); climate change education (CCE) training; and application of a post-test and action, regarding the insertion in the school space.

Findings
The survey results highlight the difficulty teachers have in understanding and applying CCE in the classroom and it underscores the importance of this approach.

Research limitations/implications
The research approach is related to a specific case in a school located in south of Brazil. Although the school has its own context, the reported experience can be considered elsewhere.

Practical implications
This case study reinforces that CCE presents broad challenges for the scientific community. For the reason that the understanding of the topic (CCE) is complex, considering the global context and the divergent opinions on the subject.

Social implications
The paper reinforces that for today’s society, sustainable development is no longer a choice but a necessity, underpinned by global Agenda 2030 discussions. In this context, teachers are essential to the transformation toward a better future.

Originality/value
The difficulties and facilities encountered during the experience serve to enhance new actions at national or even global level, respecting each new context of study and insertion of research directed to the theme – CCE.
Organizing professionalism: integrating institutional logics in Brazilian law firms
Authors: Tureta César , Castelo Júnior Clóvis 
Published: May 2020

PurposeThe purpose of this study is to analyse organizing professionalism and its consequences for the work of lawyers in large Brazilian corporate law firms.Design/methodology/approachThe study used qualitative interviews with lawyers linked to six of the Brazilian’s leading law firms. The focus of the interviews was to explore the work organization form considering the changes to the legal profession in recent years.FindingsThe results indicate that the institutional changes had substantial consequences for lawyers: a need to organize work, to integrate professional and management logic and to develop typical managerial skills to be more connective when performing tasks in work teams.Research limitations/implicationsSocio-economic changes that gave rise to more flexible forms of work organization have imposed professional restructuring and leading law firms to adopt a business model of organizing. The study is based on qualitative interviews, meaning that the findings cannot be generalized.Practical implicationsLawyers need to develop typical managerial skills to align their competencies with the management logic incorporated by law firms.Originality/valueDespite the increase of studies on professions, the integration of professional and managerial logic and its consequences to lawyers has been underdeveloped. Furthermore, research has focussed mainly on macro-level changes and given less attention to how institutional changes impact individual level.
High expression of KITLG is a new hallmark activating the MAPK pathway in type A and AB thymoma
Authors: Yang Zhaoyu , Liu Shinan , Wang Yuanguo , Chen Yuan , Zhang Peng , Liu Yimei , Zhang Hui , Zhang Peng , Tao Ziyou , Xiong Kai 
Published: May 2020

BackgroundKIT proto‐oncogene ligand (KITLG) is a pleiotropic factor which is found in diverse cancers and is involved in cell proliferation, differentiation, and survival. However, the value of KITLG in thymoma remains unclear.MethodsA total of 121 thymoma samples from The Cancer Genome Atlas Thymoma (TCGA‐THYM) dataset were used to analyze KITLG related genome‐wide expression profiles, and microRNA profiles and methylation alterations and a GEO dataset‐GSE29695, including 37 samples was used as verification. For cell‐based studies, specific small interfering RNA targeting KITLG or a KITLG overexpression vector were used to clarify the changes of the MAPK pathway in an AB thymoma cell line Thy0517.ResultsBoth datasets showed that high expression of KITLG was significantly associated with type A and AB thymoma. Through multiomic analysis of the TCGA‐THYM, it was found that with the high expression of KITLG, there were 220 upregulated and 72 downregulated genes at the mRNA level, 79 positive and 78 negative miRNAs, 28 hypermethylation and 163 hypomethylation regions. In the thymoma cell line Thy0517, it was found that the expression of GRB2 and the phosphorylation levels of BRAF, MEK1/2, and ERK1/2 in the MAPK pathway were positively correlated with the change in KITLG.ConclusionsHigh expression of KITLG is a new hallmark of WHO type A and AB thymomas in which it might play a critical role through the activation of the MAPK signaling pathway. Additionally, it is hoped that KITLG will become a potential target for the diagnosis of type A and AB thymoma through further research in the future.Key pointsSignificant findings of the studyKIT proto‐oncogene ligand (KITLG) is a new hallmark of type A and AB thymomas which induce a series of aberrant alteration of mRNA, miRNA and DNA methylation. The expression of KITLG is significantly higher in type A and AB than other subtypes of thymoma.What this study addsKITLG activated the MAPK signaling pathway to promote type A and AB thymoma which might be a potential diagnostic biomarker or target.
Sepsis is underreported in Swedish intensive care units: A retrospective observational multicentre study
Authors: Lengquist Maria , Lundberg Oscar H. M. , Spångfors Martin , Annborn Martin , Levin Helena , Friberg Hans , Frigyesi Attila 
Published: May 2020

BackgroundSepsis is a common indication for admission to the intensive care unit (ICU). Since definitions vary across studies, comparisons of prevalence and outcomes have been challenging. We aimed to compare sepsis according to ICU discharge codes with sepsis according to Sepsis‐3 criteria and to investigate the epidemiology of sepsis in the ICU. We hypothesized that sepsis using discharge codes is underreported.MethodsAdult ICU admissions to four ICUs in Sweden between 2015 and 2017 were screened for sepsis according to the Sepsis‐3 criteria. Medical records were reviewed and data extracted from the Swedish Intensive Care Registry.ResultsOf 5990 adult ICU patients, 28% fulfilled the Sepsis‐3 criteria on admission, but only 31% of them had sepsis as the registered main diagnosis at ICU discharge. Of the 1654 Sepsis‐3 patients, 38% met the septic shock criteria. The Sepsis‐3 in‐hospital mortality was 26% compared to 33% in patients with septic shock. The incidence rate for ICU‐treated sepsis was 81 cases per 100 000 person‐years. One in four had a positive blood culture, and 44% were culture negative.ConclusionThis large Swedish multicentre study showed that 28% of adult ICU patients fulfilled the Sepsis‐3 criteria, but only one third of them had sepsis according to ICU discharge codes. We could confirm our hypothesis, that sepsis is severely underreported in Swedish ICUs, and we conclude that discharge codes should not be used for quality control or research purposes.
Smicridea (Smicridea) nigripennis species group (Trichoptera: Hydropsychidae) from Brazil: new species, new distributional records and an identification key
Authors: Desidério Gleison R , Rázuri‐Gonzales Ernesto , Pes Ana M , Hamada Neusa 
Published: May 2020

AbstractThree new species in the Smicridea (Smicridea) nigripennis species group are described and illustrated based on specimens collected in Serra da Mocidade National Park and Serra do Tepequém in the northern mountain range of Brazilian Amazonia, Roraima State, and in Rio Formosinho located in Cerrado biome of midwestern Brazil, Mato Grosso do Sul State. Smicridea (Smicridea) mocidade Desidério & Rázuri‐Gonzales, sp. nov., Smicridea (Smicridea) santosi Desidério & Rázuri‐Gonzales, sp. nov. and Smicridea (Smicridea) tepequensis Desidério & Rázuri‐Gonzales, sp. nov. can be recognised mainly by the morphology of the phallic apparatus. New distributional records are provided for Smicridea (Smicridea) caatinga Alves et al., 2018, Smicridea (Smicridea) franciscana Rocha et al., 2016, Smicridea (Smicridea) mirnae Almeida & Flint, 2002 and Smicridea (Smicridea) palifera Flint, 1981. Smicridea (Smicridea) cornuta Flint, 1974 is recorded for the first time from Brazil. Additionally, a key to identify males of the 10 species in the Smicridea (Smicridea) nigripennis species group known from Brazil is provided.
Anaphylaxis in pregnancy: a population‐based multinational European study
Authors: McCall S. J. , Bonnet M.‐P. , Äyräs O. , Vandenberghe G. , Gissler M. , Zhang W.‐H. , Van Leeuw V. , Deneux‐Tharaux C. , Kurinczuk J. J. , Knight M. ,   the INOSS collaboration
Published: May 2020

SummaryAnaphylaxis in pregnancy is a rare but severe complication for both mother and infant. Population‐based data on anaphylaxis in pregnancy are lacking from mainland European countries. This multinational study presents the incidence, causative agents, management and maternal and infant outcomes of anaphylaxis in pregnancy. This descriptive multinational study used a combination of retrospective (Finnish medical registries) and prospective population‐based studies (UK, France, Belgium and the Netherlands) to identify cases of anaphylaxis. Sixty‐five cases were identified among 4,446,120 maternities (1.5 per 100,000 maternities; 95%CI 1.1–1.9). The incidence did not vary between countries. Approximately three‐quarters of reactions occurred at the time of delivery. The most common causes were antibiotics in 27 women (43%), and anaesthetic agents in 11 women (17%; including neuromuscular blocking drugs, 7), which varied between countries. Anaphylaxis had very poor outcomes for one in seven mothers and one in seven babies; the maternal case fatality rate was 3.2% (95%CI 0.4–11.0) and the neonatal encephalopathy rate was 14.3% (95%CI 4.8–30.3). Across Europe, anaphylaxis related to pregnancy is rare despite having a multitude of causative agents and different antibiotic prophylaxis protocols.
Age‐dependent changes in glutathione metabolism pathways in the lens: New insights into therapeutic strategies to prevent cataract formation—A review
Authors: Lim Julie C. , Grey Angus C. , Zahraei Ali , Donaldson Paul J. 
Published: May 2020

AbstractOcular tissues possess a robust antioxidant defence system to minimize oxidative stress and preserve tissue structure and function. Glutathione (GSH) is a powerful antioxidant and in the lens exists at unusually high concentrations. However, with advancing age, GSH levels deplete specifically in the lens centre initiating a chain of biochemical events that ultimately result in protein aggregation, light scattering and age‐related nuclear cataract. However, antioxidant supplementation has been shown to be ineffective in preventing or delaying cataract indicating that a better understanding of the delivery, uptake and metabolism of GSH in the different regions of the lens is required. This information is essential for the development of scientifically informed approaches that target the delivery of GSH to the lens nucleus, the region of the lens most affected by age‐related cataract.
Adding a second skin prick test reading and modifying the cut‐off for beta‐lactam–specificIgEenhances the sensitivity in the routine diagnostic workup for immediate beta‐lactam hypersensitivity
Authors: Rosti Bernadette , Mahler Vera 
Published: May 2020

AbstractBackgroundBeta‐lactam (BL)–antibiotics are the most frequent reason for drug‐induced hypersensitivity reactions. Because they are more efficient, less toxic, and less costly than other antibiotics, confirmation or exclusion of BL allergy is worthwhile. However, allergy tests for drug allergies are often false‐negative.ObjectivesTo evaluate the components of a stepwise diagnostic algorithm for immediate BL hypersensitivity with regard to sensitivity (SENS).MethodsConsecutive patients with suspected allergy to BL antibiotics were retrospectively analyzed with regard to increasing sensitivity (plausible history of immediate BL hypersensitivity serving as external criterion) of (i) skin prick test (SPT) by adding a second reading (n = 746), (ii) BL‐specific IgE‐determination in vitro at two cut‐offs (n = 539), and (iii) adding in vivo testing of minor and major BL determinants (n = 288).ResultsIn the history‐based population indicative of immediate BL hypersensitivity (n = 457), SPT with a sole 20‐minute reading identified 99 (SENS: 0.21) and SPT with 20‐ and 40‐minute‐reading identified 133 cases (SENS: 0.29). in vitro specific IgE‐examination identified 31 positives at a cut‐off ≥0.35 kUA/L (5.8% of tested) and 99 at cut‐off ≥0.11 kUA/L (18.4% of tested). In 203 SPT‐negative individuals, immediate BL hypersensitivity was identified by additional tests: in 79 by specific IgE (cut‐off ≥0.11 kUA/L) (thereof 53 identified solely by this test) and in 150 by in vivo testing of BL determinants in combination with Penicillin and Ampicillin intradermally (thereof 124 solely by this test); in 26 individuals both additional tests were positive. The combination of the three outpatient‐based test modalities—(i) optimized SPT, (ii) specific IgE at optimized cut‐off, and (iii) in vivo testing of BL determinants/Penicillin/Ampicillin—identified altogether 336/457 individuals with immediate BL‐hypersensitivity (SENS: 0.73), whereas the combination of the two (i) + (ii) identified 212/457 (SENS: 0.46); (i) + (iii) 283/457 (SENS: 0.61).ConclusionsTo overcome the low sensitivity of allergological tests, optimized reading times of the SPT of BL, a lower cut‐off for in vitro detection of BL‐specific IgE, and intradermal testing of Penicillin, Ampicillin, and BL‐determinants contribute to overall sensitivity under real life conditions to diagnose immediate BL‐hypersensitivity.