bluuebunny/crossref_metadata_2025 huggingface dataset:
Predicament and outlook of China's math education
Authors: Zhao Weijie
Published: April 2020

Mathematics is the foundation of science and rational thinking. Math education for the younger generation is the fundamental project to upgrade the mathematical literacy and the creativity of the whole society. China's education system has long been different from that of Western countries. China has fostered many gold medal winners of the International Mathematics Olympiad, but is also criticized as lacking creativity. In this NSR forum on math education in China, educators of high schools and universities as well as researchers of different scientific fields gather to talk about the current predicaments and future developments of China's math education.

Zenghu Li

Mathematician; Professor of the School of Mathematical Sciences, Beijing Normal University, Beijing, China

Chao Tang

Quantitative biologist; Director of the Center for Quantitative Biology, Peking University, Beijing, China

Zhihong Xia

Mathematician; Professor of Mathematics, Northwestern University, Evanston, USA and the Founding Chair of the Department of Mathematics, Southern University of Science and Technology, Shenzhen, China

Jinlong Yang

Computational chemist; Professor of the School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, China

Huawei Zhu

Headmaster of Shenzhen Middle School, Shenzhen, China; Former leader and head coach of the national team of China for the International Mathematics Olympiad, China

Gang Tian (Chair)

Mathematician; Professor of the School of Mathematical Sciences, Peking University, Beijing, China
Protein designer David Baker: I like doing things that seem like magic
Authors: Zhao Weijie , Wang Chu
Published: April 2020

Search ‘de novo protein design’ on Google and you will find the name David Baker in all results of the first page. Professor David Baker at the University of Washington and other scientists are opening up a new world of fantastic proteins. Protein is the direct executor of most biological functions and its structure and function are fully determined by its primary sequence. Baker's group developed the Rosetta software suite that enabled the computational prediction and design of protein structures. Being able to design proteins from scratch means being able to design executors for diverse purposes and benefit society in multiple ways. Recently, NSR interviewed Prof. Baker on this fast-developing field and his personal experiences.
Going Once, Going Twice: Using Willingness-to-Accept Auctions to Promote Smoking Cessation
Authors: Quisenberry Amanda J , Shaw Shreya , Ferketich Amy K , Corrigan Jay R
Published: April 2020

Introduction

Incentive-based smoking cessation interventions increase quit rates. The optimal incentive, however, is unknown. We used a willingness-to-accept (WTA) auction where smokers submitted bids indicating the incentive they would need to receive for 1 week of smoking cessation.

Aims and Methods

Smokers ready to quit (n = 35) participated in a WTA auction, naming the amount they needed to be paid to quit for 1 week. Auction winners received an incentive if they successfully quit. All smokers received nicotine replacement therapy and self-help cessation materials. Carbon monoxide concentrations were monitored remotely three times during the week and in person at the final session.

Results

Participants who smoked their first cigarette within 5 min of waking demanded a significantly larger incentive in exchange for quitting than those who waited (p < .05). About 45% of auction winners quit smoking compared to 20% of nonwinners (p < .05). The cost per quit was $466 among auction winners compared to $894 among nonwinners.

Conclusions

WTA auctions may be an effective way to determine the amount smokers need to be paid to quit, which would allow researchers to estimate the most cost-effective payment to offer as part of incentive-based smoking cessation programs. Replication evaluating longer-term cessation outcomes with larger samples is warranted.

Implications

Incentive-based smoking cessation interventions increase quit rates. However, the optimal incentive is unknown. We found that a WTA auction is a feasible technique for estimating the amount smokers need to be paid to quit. Incentives are a surprisingly cost-effective way to facilitate smoking cessation because they are only paid to those who successfully quit. WTA auctions are a promising tool for determining the incentive that strikes the optimal balance between being large enough to motivate cessation, but small enough that it can be offered to the largest possible population of smokers for a given program budget.
Harder things will stretch you further: helping first-year undergraduate students meaningfully engage with recent research papers in probability and statistics
Authors: Grindle Nicholas , Jones Elinor , Northrop Paul
Published: April 2020

Undergraduate research increasingly features in university mathematics degrees. Despite this, research papers are used infrequently in mathematics teaching, and this is especially the case for first-year undergraduates. Mathematical subjects are more likely than other STEM disciplines to pinpoint cognitive difficulty as the principal reason for not exposing undergraduate students to research papers. In this paper, we test whether first-year students can engage effectively with research papers. We describe an intervention that exposes first-year, first term undergraduate students to current research in probability and statistics by asking them to read a research paper and summarize it for a general readership following an interview with the paper’s author. Our findings show that the activity introduced students to new fields of knowledge and helped to develop a clearer understanding of scientific process, leading to a heightened sense of personal satisfaction at engaging closely with current research. We argue that structured reading of research papers can lead to productive and rewarding engagement with difficult content, recent and current research and with research processes and that this should make us reconsider the role of research papers in the undergraduate mathematics curriculum.
UPΦ phages, a new group of filamentous phages found in several members of Enterobacteriales
Authors: Shapiro Jason W , Putonti Catherine
Published: April 2020

Filamentous phages establish chronic infections in their bacterial hosts, and new phages are secreted by infected bacteria for multiple generations, typically without causing host death. Often, these viruses integrate in their host’s genome by co-opting the host’s XerCD recombinase system. In several cases, these viruses also encode genes that increase bacterial virulence in plants and animals. Here, we describe a new filamentous phage, UPϕ901, which we originally found integrated in a clinical isolate of Escherichia coli from urine. UPϕ901 and closely related phages can be found in published genomes of over 200 other bacteria, including strains of Citrobacter koseri, Salmonella enterica, Yersinia enterocolitica, and Klebsiella pneumoniae. Its closest relatives are consistently found in urine or in the blood and feces of patients with urinary tract infections. More distant relatives can be found in isolates from other environments, including sewage, water, soil, and contaminated food. Each of these phages, which we collectively call ‘UPϕ viruses’, also harbors two or more novel genes of unknown function.
Systematics and historical biogeography of Neotropical foam-nesting frogs of theAdenomera heyericlade (Leptodactylidae), with the description of six new Amazonian species
Authors: Carvalho Thiago R D , Moraes Leandro J C L , Lima Albertina P , Fouquet Antoine , Peloso Pedro L V , Pavan Dante , Drummond Leandro O , Rodrigues Miguel T , Giaretta Ariovaldo A , Gordo Marcelo , Neckel-Oliveira Selvino , Haddad Célio F B
Published: April 2020

A large proportion of the biodiversity of Amazonia, one of the most diverse rainforest areas in the world, is yet to be formally described. One such case is the Neotropical frog genus Adenomera. We here evaluate the species richness and historical biogeography of the Adenomera heyeri clade by integrating molecular phylogenetic and species delimitation analyses with morphological and acoustic data. Our results uncovered ten new candidate species with interfluve-associated distributions across Amazonia. In this study, six of these are formally named and described. The new species partly correspond to previously identified candidate lineages ‘sp. F’ and ‘sp. G’ and also to previously unreported lineages. Because of their rarity and unequal sampling effort of the A. heyeri clade across Amazonia, conservation assessments for the six newly described species are still premature. Regarding the biogeography of the A. heyeri clade, our data support a northern Amazonian origin with two independent dispersals into the South American Dry Diagonal. Although riverine barriers have a relevant role as environmental filters by isolating lineages in interfluves, dispersal rather than vicariance must have played a central role in the diversification of this frog clade.
The relevance of gene flow with wild relatives in understanding the domestication process
Authors: Moreno-Letelier Alejandra , Aguirre-Liguori Jonás A. , Piñero Daniel , Vázquez-Lobo Alejandra , Eguiarte Luis E.
Published: April 2020

The widespread use of genomic tools has allowed for a deeper understanding of the genetics and the evolutionary dynamics of domestication. Recent studies have suggested that multiple domestications and introgression are more common than previously thought. However, the ability to correctly infer the many aspects of domestication process depends on having an adequate representation of wild relatives. Cultivated maize (Zea maysssp.mays) is one of the most important crops in the world, with a long and a relatively well-documented history of domestication. The current consensus points towards a single domestication event from teosinteZea maysssp.parviglumisfrom the Balsas Basin in Southwestern Mexico. However, the underlying diversity of teosintes fromZ. maysssp. parviglumisandZea maysssp.mexicanawas not taken into account in early studies. We used 32 739 single nucleotide polymorphisms (SNPs) obtained from 29 teosinte populations and 43 maize landraces to explore the relationship between wild and cultivated members ofZea.We then inferred the levels of gene flow among teosinte populations and maize, the degree of population structure ofZea mayssubspecies, and the potential domestication location of maize. We confirmed a strong geographic structure withinZ. maysssp.parviglumisand documented multiple gene flow events with other members of the genus, including an event betweenZ. maysssp.mexicanaand maize. Our results suggest that the likely ancestor of maize may have been domesticated in Jalisco or in the southern Pacific Coast and not in the Balsas Basin as previously thought. In this context, different populations of both teosinte subspecies have contributed to modern maize's gene pool. Our results point towards a long period of domestication marked by gene flow with wild relatives, confirming domestication as long and ongoing process.
Different laterality indexes are poorly correlated with one another but consistently show the tendency of males and females to be more left- and right-lateralized, respectively
Authors: Buenaventura Castillo Carlos , Lynch Andy G. , Paracchini Silvia
Published: April 2020

The most common way to assess handedness is based on the preferred hand for writing, leading to a binary (left or right) trait. Handedness can also be assessed as a continuous trait with laterality indexes, but these are not time- and cost-effective, and are not routinely collected. Rarely, different handedness measures are collected for the same individuals. Here, we assessed the relationship of preferred hand for writing with four laterality indexes, reported in previous literature, derived from measures of dexterity (pegboard task, marking squares and sorting matches) and strength (grip strength), available in a range of
N
= 6664–8069 children from the ALSPAC cohort. Although all indexes identified a higher proportion of individuals performing better with their right hand, they showed low correlation with each other (0.08–0.3). Left handers were less consistent compared to right handers in performing better with their dominant hand, but that varied across indexes, i.e. 13% of left handers performed better with their right hand on marking squares compared to 48% for sorting matches and grip strength. Analysis of sex effects on the laterality indexes showed that males and females tend to be, on all measures, more left- and right-lateralized, respectively. Males were also over-represented among the individuals performing equally with both hands suggesting they had a higher tendency to be weakly lateralized. This study shows that different handedness measures tap into different dimensions of laterality and cannot be used interchangeably. The trends observed across indexes for males and females suggest that sex effects should be taken into account in handedness and laterality studies.
A novel test of flexible planning in relation to executive function and language in young children
Authors: Miller Rachael , Frohnwieser Anna , Ding Ning , Troisi Camille A. , Schiestl Martina , Gruber Romana , Taylor Alex H. , Jelbert Sarah A. , Boeckle Markus , Clayton Nicola S.
Published: April 2020

In adult humans, decisions involving the choice and use of tools for future events typically require episodic foresight. Previous studies suggest some non-human species are capable of future planning; however, these experiments often cannot fully exclude alternative learning explanations. Here, we used a novel tool-use paradigm aiming to address these critiques to test flexible planning in 3- to 5-year-old children, in relation to executive function and language abilities. In the flexible planning task, children were not verbally cued during testing, single trials avoided consistent exposure to stimulus–reward relationships, and training trials provided experience of a predictable return of reward. Furthermore, unlike most standard developmental studies, we incorporated short delays before and after tool choice. The critical test choice included two tools with equal prior reward experience—each only functional in one apparatus. We tested executive function and language abilities using several standardized tasks. Our results echoed standard developmental research: 4- and 5-year-olds outperformed 3-year-olds on the flexible planning task, and 5-year-old children outperformed younger children in most executive function and language tasks. Flexible planning performance did not correlate with executive function and language performance. This paradigm could be used to investigate flexible planning in a tool-use context in non-human species.
Impact of
Seriphium plumosum
densification on Mesic Highveld Grassland biodiversity in South Africa
Authors: Graham Susannah C. , Barrett Alan S. , Brown Leslie R.
Published: April 2020

Mesic Highveld Grassland is important for biodiversity conservation, but is threatened by bush densification from
Seriphium plumosum
. This indigenous densifier spreads rapidly and outcompetes other herbaceous species, changing the species composition and structure of grasslands. This study looks at three different densities of
S. plumosum
and how these affect grassland biodiversity within Telperion, Mpumalanga, South Africa. An intermediate density of
S. plumosum
(1500 individuals (ind) ha
−1
) resulted in the highest plant species diversity (
H
= 2.26), a low density (24 ind ha
−1
) was moderately diverse (
H
= 1.96) and a high density (9500 ind ha
−1
) was least diverse (
H
= 1.78). There were differences between the three densities in terms of plant species diversity, with the intermediate density being significantly more diverse (
p
< 0.01) than both the low and high densities. Findings indicate that there was a significant difference between the sites in terms of ecological successional status (
p
< 0.01). The presence of
S. plumosum
at low densities can be considered an integral part of the environment. It is important that in areas where
S. plumosum
occurs, it should be monitored. If this species is not in balance within its environment and it starts becoming dense, it will negatively affect the biodiversity, species composition and structure of the habitat.
An individualized mosaic of maternal microbial strains is transmitted to the infant gut microbial community
Authors: Koo Hyunmin , McFarland Braden C. , Hakim Joseph A. , Crossman David K. , Crowley Michael R. , Rodriguez J. Martin , Benveniste Etty N. , Morrow Casey D.
Published: April 2020

To understand the origins of the infant gut microbial community, we have used a published metagenomic dataset of the faecal microbiome of mothers and their related infants at early (4, 7 and 21 days) and late times (6–15 months) following birth. Using strain-tracking analysis, individual-specific patterns of microbial strain sharing were found between mothers and infants following vaginal birth. Overall, three mother–infant pairs showed only related strains, while 12 infants of mother–infant pairs contained a mosaic of maternal-related and unrelated microbes. Analysis of a second dataset from nine women taken at different times of pregnancy revealed individual-specific faecal microbial strain variation that occurred in seven women. To model transmission in the absence of environmental microbes, we analysed the microbial strain transmission to F1 progenies of human faecal transplanted gnotobiotic mice bred with gnotobiotic males. Strain-tracking analysis of five different dams and their F1 progeny revealed both related and unrelated microbial strains in the mother's faeces. The results of our analysis demonstrate that multiple strains of maternal microbes, some that are not abundant in the maternal faecal community, can be transmitted during birth to establish a diverse infant gut microbial community.
Context-dependent effects of relative temperature extremes on bill morphology in a songbird
Authors: LaBarbera Katie , Marsh Kyle J. , Hayes Kia R. R. , Hammond Talisin T.
Published: April 2020

Species increasingly face environmental extremes. Morphological responses to changes in average environmental conditions are well documented, but responses to environmental extremes remain poorly understood. We used museum specimens to investigate relationships between a thermoregulatory morphological trait, bird bill surface area (SA) and a measure of short-term relative temperature extremity (RTE), which quantifies the degree that temperature maxima or minima diverge from the 5-year norm. Using a widespread, generalist species,
Junco hyemalis
, we found that SA exhibited different patterns of association with RTE depending on the overall temperature regime and on precipitation. While thermoregulatory function predicts larger SA at higher RTE, we found this only when the RTE existed in an environmental context that opposed it: atypically cold minimum temperature in a warm climate, or atypically warm maximum temperature in a cool climate. When environmental context amplified the RTE, we found a negative relationship between SA and RTE. We also found that the strength of associations between SA and RTE increased with precipitation. Our results suggest that trait responses to environmental variation may qualitatively differ depending on the overall environmental context, and that environmental change that extremifies already-extreme environments may produce responses that cannot be predicted from observations in less-extreme contexts.
On the use of random graphs in analysing resource utilization in urban systems
Authors: Arbabi Hadi , Punzo Giuliano , Meyers Gregory , Tan Ling Min , Li Qianqian , Densley Tingley Danielle , Mayfield Martin
Published: April 2020

Urban resource models increasingly rely on implicit network formulations. Resource consumption behaviours documented in the existing empirical studies are ultimately by-products of the network abstractions underlying these models. Here, we present an analytical formulation and examination of a generic demand-driven network model that accounts for the effectiveness of resource utilization and its implications for policy levers in addressing resource management in cities. We establish simple limiting boundaries to systems' resource effectiveness. These limits are found not to be a function of system size and to be simply determined by the system's average ability to maintain resource quality through its transformation processes. We also show that resource utilization in itself does not enjoy considerable size efficiencies with larger and more diverse systems only offering increased chances of finding matching demand and supply between existing sectors in the system.
aNMJ-morph: a simple macro for rapid analysis of neuromuscular junction morphology
Authors: Minty Gavin , Hoppen Alex , Boehm Ines , Alhindi Abrar , Gibb Larissa , Potter Ellie , Wagner Boris C. , Miller Janice , Skipworth Richard J. E. , Gillingwater Thomas H. , Jones Ross A.
Published: April 2020

Large-scale data analysis of synaptic morphology is becoming increasingly important to the field of neurobiological research (e.g. ‘connectomics’). In particular, a detailed knowledge of neuromuscular junction (NMJ) morphology has proven to be important for understanding the form and function of synapses in both health and disease. The recent introduction of a standardized approach to the morphometric analysis of the NMJ—‘NMJ-morph’—has provided the first common software platform with which to analyse and integrate NMJ data from different research laboratories. Here, we describe the design and development of a novel macro—‘automated NMJ-morph’ or ‘aNMJ-morph’—to update and streamline the original NMJ-morph methodology. ImageJ macro language was used to encode the complete NMJ-morph workflow into seven navigation windows that generate robust data for 19 individual pre-/post-synaptic variables. The aNMJ-morph scripting was first validated against reference data generated by the parent workflow to confirm data reproducibility. aNMJ-morph was then compared with the parent workflow in large-scale data analysis of original NMJ images (240 NMJs) by multiple independent investigators. aNMJ-morph conferred a fourfold increase in data acquisition rate compared with the parent workflow, with average analysis times reduced to approximately 1 min per NMJ. Strong concordance was demonstrated between the two approaches for all 19 morphological variables, confirming the robust nature of aNMJ-morph. aNMJ-morph is a freely available and easy-to-use macro for the rapid and robust analysis of NMJ morphology and offers significant improvements in data acquisition and learning curve compared to the original NMJ-morph workflow.
Brevity is not a universal in animal communication: evidence for compression depends on the unit of analysis in small ape vocalizations
Authors: Clink Dena J. , Ahmad Abdul Hamid , Klinck Holger
Published: April 2020

Evidence for compression, or minimization of code length, has been found across biological systems from genomes to human language and music. Two linguistic laws—Menzerath's Law (which states that longer sequences consist of shorter constituents) and Zipf's Law of abbreviation (a negative relationship between signal length and frequency of use)—are predictions of compression. It has been proposed that compression is a universal in animal communication, but there have been mixed results, particularly in reference to Zipf's Law of abbreviation. Like songbirds, male gibbons (Hylobates muelleri) engage in long solo bouts with unique combinations of notes which combine into phrases. We found strong support for Menzerath's Law as the longer a phrase, the shorter the notes. To identify phrase types, we used state-of-the-art affinity propagation clustering, and were able to predict phrase types using support vector machines with a mean accuracy of 74%. Based on unsupervised phrase type classification, we did not find support for Zipf's Law of abbreviation. Our results indicate that adherence to linguistic laws in male gibbon solos depends on the unit of analysis. We conclude that principles of compression are applicable outside of human language, but may act differently across levels of organization in biological systems.
In-host Modelling of COVID-19 in Humans
Authors: Hernandez-Vargas Esteban A. , Velasco-Hernandez Jorge X.
Published: April 2020

COVID-19 pandemic has underlined the impact of emergent pathogens as a major threat for human health. The development of quantitative approaches to advance comprehension of the current outbreak is urgently needed to tackle this severe disease. In this work, several mathematical models are proposed to represent SARS-CoV-2 dynamics in infected patients. Considering different starting times of infection, parameters sets that represent infectivity of SARS-CoV-2 are computed and compared with other viral infections that can also cause pandemics.

Based on the target cell model, SARS-CoV-2 infecting time between susceptible cells (mean of 30 days approximately) is much slower than those reported for Ebola (about 3 times slower) and influenza (60 times slower). The within-host reproductive number for SARS-CoV-2 is consistent to the values of influenza infection (1.7-5.35). The best model to fit the data was including immune responses, which suggest a slow cell response peaking between 5 to 10 days post onset of symptoms. The model with eclipse phase, time in a latent phase before becoming productively infected cells, was not supported. Interestingly, both, the target cell model and the model with immune responses, predict that virus may replicate very slowly in the first days after infection, and it could be below detection levels during the first 4 days post infection. A quantitative comprehension of SARS-CoV-2 dynamics and the estimation of standard parameters of viral infections is the key contribution of this pioneering work.
ACE 2 Coding Variants: A Potential X-linked Risk Factor for COVID-19 Disease
Authors: Gibson William T. , Evans Daniel M , An Jianghong , Jones Steven JM
Published: April 2020

Viral genetic variants are widely known to influence disease progression among infected humans. Given the recent and rapid emergence of pandemic SARS-CoV-2 infection, the cause of COVID-19 disease, viral protein variants have attracted research interest. However, little has yet been written about genetic risk factors among human hosts. Human genetic variation has proven to affect disease progression and outcome for important diseases such as HIV infection and malaria infestation. The fact that the human ACE2 protein is encoded on the X chromosome means that males who carry rare ACE2 coding variants will express those variants in all ACE2-expressing cells, whereas females will typically express those variants in a mosaic distribution determined by early X-inactivation events. This sex-based difference in ACE2 expression has unique implications for epidemiological studies designed to assess host genetic factors influencing progression from asymptomatic SARS-coV-2 infection to COVID-19. Here we present theoretical modelling of rare ACE2 coding variants documented to occur naturally in several human superpopulations and subpopulations, and show that rare variants predicted to affect the binding of ACE2 to the SARS-CoV-2 spike protein exist in people. Though the rs4646116 (p.Lys26Arg) allele is found in 1 in 70 Ashkenazi Jewish males, and in 1 in 172 non-Finnish European males, this allele is found at higher frequencies in females. Furthermore, the class of missense ACE2 alleles predicted to affect SARS-CoV-2 binding are found in aggregate among 1.43% and 2.16% of Ashkenazi males and females, respectively, as well as in 0.58% and 1.24% of European males and females outside of Finland. These alleles are rarer in other population groups, and almost absent from East Asians genotyped to date.

Though we are aware that full genome-wide and exome-wide sequencing studies may ultimately be required to assess human genetic susceptibility to SARS-CoV-2 fully, we argue on the basis of strong prior probabilities that genotyping of this class of alleles is justified in cases of atypical SARS-CoV-2 diseases, such as asymptomatic super-spreaders (if any are identified), and in neonatal/paediatric-onset COVID-19 disease. Even relatively rare susceptibility factors (1% or fewer carriers) may become quantitatively important in the context of hundreds of thousands of infections. A small number of asymptomatic carriers, or a small number of super-spreaders, or a small segment of the population that is disproportionately likely to require intensive care, can magnify the medical, social and economic impacts of a pandemic of this size. The speed of the pandemic and the large number of affected cases worldwide justify efforts to identify all possible risk factors for adverse outcomes, including efforts to identify genetic susceptibility factors in human hosts.
Yeast FIT2 homolog is necessary to maintain cellular proteostasis by regulating lipid homeostasis
Authors: Shyu Peter , Yap Wei Sheng , Gaspar Maria L. , Jesch Stephen A. , Marvalim Charlie , Prinz William A. , Henry Susan A. , Thibault Guillaume
Published: April 2020

Lipid droplets (LDs) have long been regarded as inert cytoplasmic organelles with the primary function of housing excess intracellular lipids. More recently, LDs have been strongly implicated in conditions of lipid and protein dysregulation. The fat storage inducing transmembrane (FIT) family of proteins comprises of evolutionarily conserved endoplasmic reticulum (ER)-resident proteins that have been reported to induce LD formation. Here, we establish a model system to study the role ofS. cerevisiae FIThomologues (ScFIT),SCS3andYFT2, in proteostasis and stress response pathways. While LD biogenesis and basal ER stress-induced unfolded protein response (UPR) remain unaltered inScFITmutants,SCS3was found to be essential for proper stress-induced UPR activation and for viability in the absence of the sole yeast UPR transducer IRE1. Devoid of a functional UPR,scs3mutants exhibited accumulation of triacylglycerol within the ER along with aberrant LD morphology, suggesting a UPR-dependent compensatory mechanism for LD maturation. Additionally,SCS3was necessary to maintain phospholipid homeostasis. Strikingly, the absence of the ScFIT proteins results in the downregulation of the closely-related Heat Shock Response (HSR) pathway. In line with this observation, global protein ubiquitination and the turnover of both ER and cytoplasmic misfolded proteins is impaired inScFITcells, while a screen for interacting partners of Scs3 identifies components of the proteostatic machinery as putative targets. Taken together, these suggest that ScFIT proteins may modulate proteostasis and stress response pathways with lipid metabolism at the interface between the two cellular processes.
Analysis of Effective Dose at Computed Tomography in a Modern 64 slice Multidetector CT System in an Irish Tertiary Care Centre with Local and International Reference Standards
Authors: Curran Tadhg-Iarla , Maher Michael , McLaughlin Patrick , Coffey Fíona , O’Neill Siobhan
Published: April 2020

Background

Computed tomography (CT), by its nature, imparts a high dose of ionising radiation to patients being imaged. Diagnostic Reference Levels (DRLs) are used extensively in research but are also used in practice to establish if local imaging protocols have been optimised.

Aim

To audit effective dose (ED) at CT for four commonly performed examinations performed with a modern multidectector 64 slice CT (MDCT) system at large tertiary care centre by comparison with current international reference standards

Methods

800 consecutive studies of CT brain, cervical spine, thorax and abdomen-pelvis were examined. All patients were imaged on 64-slice MDCT with study-specific protocols. Dose descriptors were extracted from image dose reports. ED was calculated using dose-length product conversion coefficients for all patients. Data was collated with Irish national and local DRLs, and published international point values.

Results

ED range at CT abdomen-pelvis of 2.03-26.04 mSv (mean 8.041 mSv) was 28.5% above the national DRL (9 mSv) and 26% above the local DRL (9.75 mSv). ED at CT thorax of 2.46-10.09 mSv (5.061 mSv) was 3.5% greater than local DRL (8.4mSv) and 42.5% greater than the national DRL (5.46 mSv). ED at CT brain of 2.25-8.08 mSv (3.075 mSv) was 100% above both the local (1.98 mSv) and national (2.06 mSv) DRLs. CT cervical spine ED of 1.49-21.94 mSv (5.14 mSv) was 79% greater than the local (3.07 mSv) and 100% greater than the national DRL (1.42 mSv).

Conclusions

All studies exceed national DRLs. A significant optimisation potential is noted, in particular, for studies involving the head and cervical spine. A further review of study protocols is necessary to facilitate optimisation of total study radiation dose.
Using surgical wrapping material for the fabrication of respirator masks
Authors: Meijer Johanna H , Vrielink Joric Oude
Published: April 2020

Given the current shortage of respirator masks and the resulting lack of personal protective equipment for use by clinical staff, we examined bottom-up solutions that would allow hospitals to fabricate respirator masks that: (i) meet requirements in terms of filtering capacities, (ii) are easy to produce rapidly and locally, and (iii) can be constructed using materials commonly available in hospitals worldwide. We found that Halyard H300 material used for wrapping of surgical instruments and routinely available in hospitals, met these criteria. Specifically, three layers of material achieved a filter efficiency of 94%, 99%, and 100% for 0.3 μm, 0.5 μm, and 3.0 μm particles, respectively; importantly, these values are close to the efficiency provided by FFP2 and N95 masks. After re-sterilization up to 5 times, the filter’s efficiency remains sufficiently high for use as an FFP1 respirator mask. Finally, using only one layer of the material satisfies the criteria for use as a ‘surgical mask’. This material can therefore be used to help protect hospital staff and other healthcare professionals who require access to suitable masks but lack commercially available solutions.
An epidemiologic profile of COVID-19 patients in Vietnam
Authors: Nguyen Huy G. , Nguyen Tuan V.
Published: April 2020

Background and Aim

There is a paucity of data on the COVID-19 pandemic in Vietnam. In this paper, we sought to provide an epidemiologic description of patients who were infected with SARS-Cov-2 in Vietnam.

Methods

Data were abstracted from the wikipedia’s COVID-19 information resource and Johns Hopkins University Dashboard. Demographic data and treatment status were obtained for each patient in each day. The coverage period was from 23/1/2020 to 10/4/2020. Descriptive analyses of incident cases were stratified by gender and age group. The estimation of the reproduction ratio was done with a bootstrap method using the R statistical environment.

Results

During the coverage period, Vietnam has recorded 257 cases of COVID-19. Approximately 54% of the cases were women. The median age of patients was 30 years (range: 3 months to 88 years), with 78% of patients aged 49 or younger. About 66% (n = 171) of patients were overseas tourists (20%) and Vietnamese students or workers returning from overseas (46%). Approximately 57% (n = 144) of patients have been recovered and discharged from hospitals. There have been no mortality. The reproduction ratio was estimated to range between 0.95 and 1.24.

Conclusion

These data indicate that a majority of COVID-19 patients in Vietnam was imported cases in overseas tourists and young students and workers who had returned from overseas.
Undergraduate medical students in India are underprepared to be the young-taskforce against Covid-19 amid prevalent fears
Authors: Agarwal Vishwesh , Gupta Latika , Davalbhakta Samira , Misra Durga , Agarwal Vikas , Goel Ashish
Published: April 2020

Background

The healthcare system in India faces an acute shortage of front-line doctors to fight the Covid-19. Thus, the recruitment of undergraduate medical students into the health care force is being considered by many state governments. A survey was conducted amongst undergraduate medical students to understand their knowledge, attitude, and preparedness towards the ongoing pandemic.

Methods

An anonymized survey on a cloud-based website (Survey Monkey®) comprising 33 questions was served to medical students.

Results

Of 616 (24.6%) respondents among 2500 invitees across six medical schools in India, most (54.1%) were in the final year of their undergraduate training program. Knowledge regarding viral transmission, clinical features, laboratory diagnosis, and drugs being tried out in Covid-19 was adequate among most students. However, understanding of the incubation period 123 (20%) and time to symptoms 30 (4.8%) was less than satisfactory. Three-fourths (75%) were unaware of the treatment guidelines for Covid-19, and one-quarter (155, 25.1%) were unaware of the required precautions during management. Moreover, 179 (29.1%) were unaware that Covid-19 causes an asymptomatic or minor illness in young individuals. Nearly 70% were reluctant to attend clinics from fear of getting infected or passing on to others. Besides, 250 (40.6%) were not updated on Covid-19, and most (486, 78.9%) resorted to social media for information on Covid-19.

Conclusion

Prevalent fears and inadequate understanding of Covid-19 suggest that undergraduate medical students are not prepared to be the front-line taskforce in the current pandemic.
Modeling COVID-19: Forecasting and analyzing the dynamics of the outbreak in Hubei and Turkey
Authors: Aslan Ibrahim Halil , Demir Mahir , Wise Michael Morgan , Lenhart Suzanne
Published: April 2020

As the pandemic of Coronavirus Disease 2019 (COVID-19) rages throughout the world, accurate modeling of the dynamics thereof is essential. However, since the availability and quality of data varies dramatically from region to region, accurate modeling directly from a global perspective is difficult, if not altogether impossible. Nevertheless, via local data collected by certain regions, it is possible to develop accurate local prediction tools, which may be coupled to develop global models.

In this study, we analyze the dynamics of local outbreaks of COVID-19 via a coupled system of ordinary differential equations (ODEs). Utilizing the large amount of data available from the ebbing outbreak in Hubei, China as a testbed, we estimate the basic reproductive number, ℛ0 of COVID-19 and predict the total cases, total deaths, and other features of the Hubei outbreak with a high level of accuracy. Through numerical experiments, we observe the effects of quarantine, social distancing, and COVID-19 testing on the dynamics of the outbreak. Using knowledge gleaned from the Hubei outbreak, we apply our model to analyze the dynamics of outbreak in Turkey. We provide forecasts for the peak of the outbreak and the total number of cases/deaths in Turkey, for varying levels of social distancing, quarantine, and COVID-19 testing.
Rapid diagnosis of SARS-CoV-2 infection by detecting IgG and IgM antibodies with an immunochromatographic device: a prospective single-center study
Authors: Pérez-García Felipe , Pérez-Tanoira Ramón , Romanyk Juan , Arroyo Teresa , Gómez-Herruz Peña , Cuadros-González Juan
Published: April 2020

Objectives

SARS-CoV-2 infection diagnosis is challenging in patients from 2-3 weeks after the onset of symptoms, due to the low positivity rate of the PCR. Serologic tests could be complementary to PCR in these situations. The aim of our study was to analyze the diagnostic performance of one serologic rapid test in COVID-19 patients.

Methods

We evaluated an immunochromatographic test (AllTest COVID-19 IgG / IgM) which detects IgG and IgM antibodies. We validated the serologic test using serum samples from 45 negative patients (group 1) and 55 patients with COVID-19 confirmed by PCR (group 2). Then, we prospectively evaluated the test in 63 patients with clinical diagnosis of pneumonia of unknown etiology that were COVID-19 negative by PCR (group 3).

Results

All 45 patients from group 1 were negative for the serologic test (specificity = 100%). Regarding group 2 (PCR-positive), the median time from their symptom onset until testing was 11 days. For these 55 group-2 patients, the test was positive for either IgM or IgG in 26 (overall sensitivity = 47%), and in patients tested 14 days or more after the onset of symptoms, the sensitivity was 74%. Regarding the 63 group-3 patients, median time after symptom onset was 17 days, and the test was positive in 56 (89% positivity).

Conclusions

Our study shows that serologic rapid tests could be used as a complement of PCR to diagnose SARS-CoV-2 infection after 14 days from the onset of symptoms and in patients with pneumonia and negative PCR for SARS-CoV-2.
Estimating the real-time case fatality rate of COVID-19 using Poisson mixtures model
Authors: Lee Paul H.
Published: April 2020

We proposed using Poisson mixtures model that utilized data of deaths, recoveries, and total confirmed cases in each day since the outbreak. We demonstrated that our CFR estimates for Hubei Province and other parts of China were superior to the simple CFR estimators in the early stage of COVID-19 outbreak.
The origin and underlying driving forces of the SARS-CoV-2 outbreak
Authors: Chaw Shu-Miaw , Tai Jui-Hung , Chen Shi-Lun , Hsieh Chia-Hung , Chang Sui-Yuan , Yeh Shiou-Hwei , Yang Wei-Shiung , Chen Pei-Jer , Wang Hurng-Yi
Published: April 2020

The spread of SARS-CoV-2 since December 2019 has become a pandemic and impacted many aspects of human society. Here, we analyzed genetic variation of SARS-CoV-2 and its related coronavirus and found the evidence of intergenomic recombination. After correction for mutational bias, analysis of 137 SARS-CoV-2 genomes as of 2/23/2020 revealed the excess of low frequency mutations on both synonymous and nonsynonymous sites which is consistent with recent origin of the virus. In contrast to adaptive evolution previously reported for SARS-CoV in its brief epidemic in 2003, our analysis of SARS-CoV-2 genomes shows signs of relaxation of selection. The sequence similarity of the spike receptor binding domain between SARS-CoV-2 and a sequence from pangolin is probably due to an ancient intergenomic introgression. Therefore, SARS-CoV-2 might have cryptically circulated within humans for years before being recently noticed. Data from the early outbreak and hospital archives are needed to trace its evolutionary path and reveal critical steps required for effective spreading. Two mutations, 84S in orf8 protein and 251V in orf3 protein, occurred coincidentally with human intervention. The 84S first appeared on 1/5/2020 and reached a plateau around 1/23/2020, the lockdown of Wuhan. 251V emerged on 1/21/2020 and rapidly increased its frequency. Thus, the roles of these mutations on infectivity need to be elucidated. Genetic diversity of SARS-CoV-2 collected from China was two time higher than those derived from the rest of the world. In addition, in network analysis, haplotypes collected from Wuhan city were at interior and have more mutational connections, both of which are consistent with the observation that the outbreak of cov-19 was originated from China.

In contrast to adaptive evolution previously reported for SARS-CoV in its brief epidemic, our analysis of SARS-CoV-2 genomes shows signs of relaxation of selection. The sequence similarity of the spike receptor binding domain between SARS-CoV-2 and a sequence from pangolin is probably due to an ancient intergenomic introgression. Therefore, SARS-CoV-2 might have cryptically circulated within humans for years before being recently noticed. Data from the early outbreak and hospital archives are needed to trace its evolutionary path and reveal critical steps required for effective spreading. Two mutations, 84S in orf8 protein and 251V in orf3 protein, occurred coincidentally with human intervention. The 84S first appeared on 1/5/2020 and reached a plateau around 1/23/2020, the lockdown of Wuhan. 251V emerged on 1/21/2020 and rapidly increased its frequency. Thus, the roles of these mutations on infectivity need to be elucidated.
COVID-19 outbreak at a large homeless shelter in Boston: Implications for universal testing
Authors: Baggett Travis P. , Keyes Harrison , Sporn Nora , Gaeta Jessie M.
Published: April 2020

The circumstances of homelessness create the potential for rapid transmission of SARS-CoV-2 in this vulnerable population. Upon observing a cluster of COVID-19 cases from a single large homeless shelter in Boston, Boston Health Care for the Homeless Program conducted symptom assessments and polymerase chain reaction (PCR) testing for SARS-CoV-2 among all guests residing at the shelter over a 2-day period. Of 408 participants, 147 (36.0%) were PCR-positive for SARS-CoV-2. COVID-positive individuals were more likely to be male (p<0.001) but did not differ significantly from COVID-negative individuals with respect to other demographic and clinical characteristics. Cough (7.5%), shortness of breath (1.4%), and fever (0.7%) were all uncommon among COVID-positive individuals. Our findings illustrate the rapidity with which COVID-19 can be widely transmitted in a homeless shelter setting and suggest that universal PCR testing, rather than a symptom triggered approach, may be a better strategy for identifying and mitigating COVID-19 among people experiencing homelessness.
Identification of potential vaccine candidates againstSARS-CoV-2, A step forward to fight COVID-19: A Reverse Vaccinology Approach
Authors: Gupta Ekta , Mishra Rupesh Kumar , Niraj Ravi Ranjan Kumar
Published: April 2020

The recent Coronavirus Disease 2019 (COVID-19) causes an immense health crisis to global public health. The COVID-19 is the etiologic agent of a recently arose disease caused by the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).Presently, there is no vaccine available against this emerged viral disease. Therefore, it is indeed a need of the hour to develop an effectual and safe vaccine against this decidedly pandemic disease. In the current study, we collectedSARS-CoV-2genome which is prominent in India against human host, further more using reverse vaccinology here we claim effective vaccine candidates that can be mile stone in battle against COVID19. This novel study divulged one promising antigenic peptide GVYFASTEK from surface glycoprotein (protein accession no. - QIA98583.1) ofSARS-CoV-2,which was predicated to be interacted with MHC alleles and showed up to 90% conservancy and high value of antigenicity. Subsequently, the molecular docking and simulation studies were verified molecular interaction of this prime antigenic peptide with the residues of HLA-A*11–01 allele for MHC Class I. After vigorous analysis, this peptide was predicted to be suitable epitope which is capable to induce the strong cell-mediated immune response against theSARS-CoV-2.Consequences from the current study could facilitate selectingSARS-CoV-2epitopes for vaccine production pipelines in the immediate future. This novel research will certainly pave the way for a fast, reliable and virtuous platform to provide timely countermeasure of this dangerous pandemic disease, COVID-19.