bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessing trait driver theory along abiotic gradients in tropical plant communities
Authors: Lourenço Jehová , Newman Erica A. , Dias Milanez Camilla Rozindo , Thomaz Luciana Dias , Enquist Brian J.
Published: February 2020

Despite the many studies using trait-based approaches to assess the impact of environmental gradients in forest trait composition, the relative roles of (i) intraspecific variation in community assembly and (ii) microclimatic or fine scale abiotic variation in shaping local trait diversity remain poorly understood. To advance their understanding we tested several assumptions and predictions of trait driver theory (TDT). We quantified the shape of trait distributions related to tree carbon, nutrient economics and stem hydraulics across a small-scale but steep gradient of soil water availability.

We utilized a unique and steep environmental gradient in the coastal Brazilian Atlantic forest (restinga) communities that spans a very short distance (207 ±60 meters). We collected leaf and wood samples of tree species across 42 patches (or plots) ofrestingaforest. Furthermore, to detect if species directionally shift in niche space, we analyzed species composition in multidimensional hypervolume space.

Despite short geographic distances, we observed large shifts in species replacement and intraspecific variation reflected by a directional shift in plant function. Consistent with TDT, we observe (i) trait distributions that are skewed in directions consistent with a forest responding to recent hotter and drier; (ii) peaked trait distributions, indicating strong functional convergence; and (iii) conditions decreasing means and variances of several leaf carbon and nutrient economic traits as well as stem hydraulic traits.

Synthesis.Observed species replacements along the water table gradient and interspecific measures of functional diversity (community kurtosis and skewness) are consistent with strong phenotype/environmental matching of plant carbon, nutrient, and hydraulic strategies. We observe environmental filtering in both extremities of the gradient, selecting for acquisitive (wet) to conservative (dry) setup of traits. Similarly, species that span the entire water availability gradient are characterized by directional intraspecific shifts in multi-trait space that mirror interspecific shifts. Strong environmental gradients across short spatial scales provide unique systems to accurately assess assembly processes and address long-held assumptions and timely hypothesis predicted by trait driver theory.
Multivariate Analyses of Codon Usage of SARS-CoV-2 and other betacoronaviruses
Authors: Gu Haogao , Chu Daniel , Peiris Malik , Poon Leo L.M.
Published: February 2020

Coronavirus disease 2019 (COVID-19) is a global health concern as it continues to spread within China and beyond. The causative agent of this disease, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), belongs to the genusBetacoronaviruswhich also includes severe acute respiratory syndrome related coronavirus (SARSr-CoV) and Middle East respiratory syndrome related coronavirus (MERSr-CoV). Codon usage of viral genes are believed to be subjected to different selection pressures in different host environments. Previous studies on codon usage of influenza A viruses can help identify viral host origins and evolution trends, however, similar studies on coronaviruses are lacking. In this study, global correspondence analysis (CA), within-group correspondence analysis (WCA) and between-group correspondence analysis (BCA) were performed among different genes in coronavirus viral sequences. The amino acid usage pattern of SARS-CoV-2 was generally found similar to bat and human SARSr-CoVs. However, we found greater synonymous codon usage differences between SARS-CoV-2 and its phylogenetic relatives on spike and membrane genes, suggesting these two genes of SARS-CoV-2 are subjected to different evolutionary pressures.
SEIR Transmission dynamics model of 2019 nCoV coronavirus with considering the weak infectious ability and changes in latency duration
Authors: Pengpeng Shi , Shengli Cao , Peihua Feng
Published: February 2020

Pneumonia patients of 2019-ncov in latent period are not easy to be effectively quarantined, but there is evidence that they have strong infectious ability. Here, the infectious ability of patients during the latent period is slightly less than that of the infected patients was assumed. We established a new SEIR propagation dynamics model, that considered the weak transmission ability of the incubation period, the variation of the incubation period length, and the government intervention measures to track and isolate comprehensively. Based on the raw epidemic data of China from January 23, 2020 to February 10, 2020, the dynamic parameters of the new present SEIR model are fitted. Through the Euler integration algorithm to solve the model, the effect of infectious ability of incubation patients on the theoretical estimation of the present SEIR model was analyzed, and the occurrence time of peak number in China was predicted.
A SMAD4-modulated gene profile predicts disease-free survival in stage II and III colorectal cancer
Authors: Szeglin Bryan C. , Wu Chao , Marco Michael R. , Park Hyun Sung , Zhang Zeda , Zhang Bing , Garcia-Aguilar Julio , Beauchamp R. Daniel , Chen Xi , Smith J. Joshua
Published: February 2020

Objective

Loss of SMAD4 is associated with worse outcomes for colorectal cancer patients. We used gene ontology and bioinformatics to identify an RNA-based SMAD4-modulated profile and test its association with patient outcome.

Design

Using a discovery dataset of 250 colorectal cancer patients, we analyzed expression of BMP/Wnt target genes for association with SMAD4 expression. Promoters of the BMP/Wnt genes were interrogated for SMAD-binding elements. 15 genes were implicated and three tested for modulation by SMAD4 in patient-derived colorectal cancer tumoroids. Expression of the 15 genes was used for unsupervised hierarchical clustering of a training dataset and two resulting clusters modeled in a centroid model. This model was applied to an independent validation dataset of stage II and III patients. Disease-free survival was analyzed by the Kaplan-Meier method.

Results

In vitro analysis of three genes identified in the SMAD4-modulated profile (JAG1, TCF7, MYC) revealed modulation by SMAD4 consistent with the trend observed in the profile. In the training dataset (n = 553), the profile was not associated with outcome. However, among stage II and III patients (n = 461), distinct clusters were identified by unsupervised hierarchical clustering that were associated with disease-free survival (p = 0.02). The main model was applied to a validation dataset (n = 257) which confirmed the association of clustering with disease-free survival (p = 0.02).

Conclusions

A SMAD4-modulated RNA-based gene profile identified high-risk stage II and III colorectal cancer patients, can predict disease-free survival, and has prognostic potential for stage II and III colorectal cancer patients.
BioTracs: A transversal framework for computational workflow standardization and traceability
Authors: Abi-Ghanem Joséphine , Ouattara Djomangan Adama
Published: February 2020

Background

The need of digital tools for integrative analysis is today important in most scientific areas. It leads to several community-driven initiatives to standardize the sharing of data and computational workflows. However, there exists no open agnostic framework to model and implement computation workflows, in particular in bioinformatics. It is therefore difficult for data scientists to share transparently and integrate heterogeneous analysis processes coming from different scientific domains, programing languages, projects or teams.

Results

We present here BioTracs, a transversal framework for computational workflow standardization and traceability. It is based on PRISM architecture (Process Resource Interfacing SysteM), an agnostic open architecture we introduce here to standardize the way processes and resources can be modelled and interfaced in computational workflows to ensure traceability, reproducibility and facilitate sharing. BioTracs is today implemented in MATLAB and available under open source license on GitHub. Several BioTracs-derived applications are also available online. They were successfully applied to large-scale metabolomics and clinical studies and demonstrated flexibility and robustness.

Conclusions

As an implementation of the PRISM architecture, BioTracs paved the way to an open framework in which bioinformatics could specify ad model workflows. PRISM architecture is designed to provide scalability and transparency from the code to the project level we less efforts. It could also be implemented using open object-oriented languages such as Python, C++ or java.

Abstract Figure
Auditory tests for characterizing hearing deficits in listeners with various hearing abilities: The BEAR test battery
Authors: Sanchez-Lopez Raul , Nielsen Silje Grini , El-Haj-Ali Mouhamad , Bianchi Federica , Fereczkowski Michal , Cañete Oscar M , Wu Mengfan , Neher Tobias , Dau Torsten , Santurette Sébastien
Published: February 2020

The Better hEAring Rehabilitation (BEAR) project aims to provide a new clinical profiling tool – a test battery – for hearing loss characterization. Whereas the loss of sensitivity can be efficiently measured using pure-tone audiometry, the assessment of supra-threshold hearing deficits remains a challenge. In contrast to the classical ‘attenuation-distortion’ model, the proposed BEAR approach is based on the hypothesis that the hearing abilities of a given listener can be characterized along two dimensions, reflecting independent types of perceptual deficits (distortions). A data-driven approach provided evidence for the existence of different auditory profiles with different degrees of distortions. Ten tests were included in a test battery, based on their clinical feasibility, time efficiency and related evidence from the literature. The tests were divided into six categories: audibility, speech perception, binaural processing abilities, loudness perception, spectro-temporal modulation sensitivity and spectro-temporal resolution. Seventy-five listeners with symmetric, mild-to-severe sensorineural hearing loss were selected from a clinical population. The analysis of the results showed interrelations among outcomes related to high-frequency processing and outcome measures related to low-frequency processing abilities. The results showed the ability of the tests to reveal differences among individuals and their potential use in clinical settings.
The reproductive number R0 of COVID-19 based on estimate of a statistical time delay dynamical system
Authors: Shao Nian , Cheng Jin , Chen Wenbin
Published: February 2020

In this paper, we estimate the reproductive number R0 of COVID-19 based on Wallinga and Lipsitch framework [11] and a novel statistical time delay dynamic system. We use the observed data reported in CCDC’s paper to estimate distribution of the generation interval of the infection and apply the simulation results from the time delay dynamic system as well as released data from CCDC to fit the growth rate. The conclusion is: Based our Fudan-CCDC model, the growth rate r of COVID-19 is almost in [0.30, 0.32] which is larger than the growth rate 0.1 estimated by CCDC [9], and the reproductive number R0 of COVID-19 is estimated by 3.25 ≤ R0 ≤ 3.4 if we simply use R = 1 + r ∗ Tc with Tc = 7.5, which is bigger than that of SARS. Some evolutions and predictions are listed.
A quantitative framework to define the end of an outbreak: application to Ebola Virus Disease
Authors: Djaafara Bimandra A , Imai Natsuko , Hamblion Esther , Impouma Benido , Donnelly Christl A , Cori Anne
Published: February 2020

Declaring the end of an outbreak is an important step in controlling infectious disease outbreaks. An objective estimation of the probability of cases arising in the future is important to reduce the risk of post-declaration flare-ups. We developed a simulation-based model to quantify that probability. We tested it on simulated Ebola Virus Disease (EVD) data and found this probability was most sensitive to the instantaneous reproduction number, the reporting rate, and the delay between symptom onset and recovery or death of the last detected case. For EVD, our results suggest that the current WHO criterion of 42 days since the outcome of the last detected case is too short and very sensitive to underreporting. The 90 days of enhanced surveillance period after the end-of-outbreak declaration is therefore crucial to capture potential flare-ups of cases. Hence, we suggest a shift to a preliminary end-of-outbreak declaration after 63 days from the symptom onset day of the last detected case. This should be followed by a 90-day enhanced surveillance, after which the official end-of-outbreak can be declared. This corresponds to less than 5% probability of flare ups in most of the scenarios examined. Our quantitative framework could be adapted to define end-of-outbreak criteria for other infectious diseases.
Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual through variant-to-gene mapping
Authors: Cousminer Diana L. , Wagley Yadav , Pippin James A. , Elhakeem Ahmed , Way Gregory P. , McCormack Shana E. , Chesi Alessandra , Mitchell Jonathan A. , Kindler Joseph M. , Baird Denis , Hartley April , Howe Laura , Kalkwarf Heidi J. , Lappe Joan M. , Lu Sumei , Leonard Michelle , Johnson Matthew E. , Hakonarson Hakon , Gilsanz Vicente , Shepherd John A. , Oberfield Sharon E. , Greene Casey S. , Kelly Andrea , Lawlor Deborah , Voight Benjamin F. , Wells Andrew D. , Zemel Babette S. , Hankenson Kurt , Grant Struan F. A.
Published: February 2020

Introductory paragraph

Bone accrual impacts lifelong skeletal health, but genetic discovery has been hampered by cross-sectional study designs and uncertainty about target effector genes. Here, we captured this dynamic phenotype by modeling longitudinal bone accrual across 11,000 bone scans followed by genome-wide association studies (GWAS). We revealed 40 loci (35 novel), half residing in topological associated domains harboring known bone genes. Variant-to-gene mapping identified contacts between GWAS loci and nearby gene promoters, and siRNA knockdown of gene expression clarified the putative effector gene at three specific loci in two osteoblast cell models. The resulting target genes highlight the cell fate decision between osteogenic and adipogenic lineages as important in normal bone accrual.
The Epidemiology of Plasmodium vivax Among Adults in the Democratic Republic of the Congo: A Nationally-Representative, Cross-Sectional Survey
Authors: Brazeau Nicholas F. , Mitchell Cedar L. , Morgan Andrew P. , Deutsch-Feldman Molly , Watson Oliver John , Thwai Kyaw L. , Waltmann Andreea , Emch Michael , Gartner Valerie , Redelings Ben , Wray Gregory A. , Mwandagalirwa Melchior K. , Tshefu Antoinette K. , Likwela Joris L. , Edwards Jess K. , Verity Robert , Parr Jonathan B. , Meshnick Steven R. , Juliano Jonathan J.
Published: February 2020

Background

Reports of P. vivax infections among Duffy-negative hosts have begun to accumulate throughout sub-Saharan Africa. Despite this growing body of evidence, no nationally representative epidemiological surveys of P. vivax in sub-Saharan Africa nor population genetic analyses to determine the source of these infections have been performed.

Methods

To overcome this critical gap in knowledge, we screened nearly 18,000 adults in the Democratic Republic of the Congo (DRC) for P. vivax using samples from the 2013-2014 Demographic Health Survey. Infections were identified by quantitative PCR and confirmed with nested-PCR. P. vivax mitochondrial genomes were constructed after short-read sequencing. Risk factors, spatial distributions and population genetic analyses were explored.

Findings

Overall, we found a 2.96% (95% CI: 2.28%, 3.65%) prevalence of P. vivax infections across the DRC. Nearly all infections were among Duffy-negative adults (486/489). Infections were not associated with typical malaria risk-factors and demonstrated small-scale heterogeneity in prevalence across space. Mitochondrial genomes suggested that DRC P. vivax is an older clade that shares its most recent common ancestor with South American isolates.

Interpretation

P. vivax is more prevalent across the DRC than previously believed despite widespread Duffy-negativity. Comparison to global and historical P. vivax sequences suggests that historic DRC P. vivax may have been transported to the New World on the wave of European expansion. Our findings suggest congolese P. vivax is an innocuous threat given its relatively flat distribution across space, lack of malaria risk factors, and potentially ancestral lineage.

Funding

National Institutes of Health and the Wellcome Trust.
Identifying candidate detoxification genes in the ecdysteroid kinase-like (EcKL) and cytochrome P450 gene families inDrosophila melanogasterby integrating evolutionary and transcriptomic data
Authors: Scanlan Jack L. , Gledhill-Smith Rebecca S. , Battlay Paul , Robin Charles
Published: February 2020

The capacity to detoxify toxic compounds is essential for adaptation to the ecological niches of many organisms, especially insects. However, detoxification in insects is often viewed through the lens of mammalian detoxification research, even though the organ and enzyme systems involved have diverged for over half a billion years. Phosphorylation is a non-canonical phase II detoxification reaction that, among animals, occurs near exclusively in insects, but the enzymes responsible have never been cloned or otherwise identified. We propose the hypothesis that members of the arthropod-specific ecdysteroid kinase-like (EcKL) gene family encode detoxicative kinases. To test this hypothesis, we annotated the EcKL gene family in 12 species ofDrosophilaand explored their evolution within the genus. Many ancestral EcKL clades are evolutionarily unstable and have experienced repeated gene gain and loss events, while others are conserved as single copy orthologs. Leveraging multiple published gene expression datasets fromD. melanogaster, and using the cytochrome P450s—a canonical detoxification family—as a test case, we demonstrate relationships between xenobiotic induction, detoxification tissue-enriched expression and evolutionary instability in the EcKLs and the P450s. We also found previously unreported genomic and transcriptomic variation in a number of EcKLs and P450s associated with toxic stress phenotypes using a targeted phenome-wide association study (PheWAS) approach. Lastly, we devised a systematic method for identifying candidate detoxification genes in large gene families that is concordant with experimentally determined functions of P450 genes inD. melanogaster. Applying this method to the EcKLs suggested a significant proportion of these genes play roles in detoxification, and that the EcKLs may constitute a detoxification gene family in insects. Additionally, we estimate that between 11–16 uncharacterisedD. melanogasterP450s are strong detoxification candidates.

Highlights

The poorly characterised ecdysteroid kinase-like (EcKL) gene family is hypothesised to encode enzymes responsible for detoxification by phosphorylation in insects.

An integrative ‘detoxification score’ method accurately categorises the known functions of a canonical detoxification family, the cytochrome P450s, and suggests many EcKLs are also involved in detoxification.

A targeted phenome-wide association study finds novel associations between EcKL/P450 variation and a number of toxic stress phenotypes, such as two unlinked EcKL paralogs that are both associated with developmental methylmercury resistance.
Height differences in clonal stands ofTussilago farfarapromote outcrossing by influencing pollinator behaviour
Authors: Dolezal Aleksandra J.
Published: February 2020

Plants with mixed mating systems balance the advantages of selfing and the costs of inbreeding. Previous studies have shown that plant species with the ability to self-pollinate and cross pollinate have strategies to promote outcrossing to increase genetic diversity. Various features of floral morphology are thought to be deliberate mechanisms to manipulate plant mating systems. I hypothesized that within-plant variation in flower stem height is a morphological trait that can reduce geitonogamy by increasing pollinator movement among plants. This hypothesis was tested using coltsfoot (Tussilago farfara); coltsfoot plants host several flowering stems that differ in height, with each stem having a single, terminal flowerhead. I used cut flowers to create ‘populations’ of coltsfoot in which each plant had four inflorescences with equal or unequal flower stalk lengths and measured frequency of insect pollinators that would stay among flowers within a plant or move to other plants. All pollinators (bee flies, hover flies, solitary bees and wasps) showed a marked discrimination in favor of leaving plants with flowers of different heights and stayed when plants had flowers of the same height. This study shows that variation in flower heights is important for reducing geitonogamy in coltsfoot and suggests that the evolution of this morphological trait should be considered in studies of mating systems.
Trait plasticity and covariance along a continuous soil moisture gradient
Authors: Monroe J. Grey , Cai Haoran , Des Marais David L.
Published: February 2020

Water availability is perhaps the greatest environmental determinant of plant yield and fitness. However, our understanding of plant-water relations is limited because it is primarily informed by experiments considering soil moisture variability at two discrete levels – wet and dry – rather than as a continuously varying environmental gradient. Here we used experimental and statistical methods based on function-valued traits to explore responses to a continuous soil moisture gradient in physiological and morphological traits in two species and five genotypes each of the model grassBrachypodium.We find that most traits exhibit non-linear responses to soil moisture variability. We also observe differences in the shape of these non-linear responses between traits, species, and genotypes. Emergent phenomena arise from this variation including changes in trait correlations and evolutionary constraints as a function of soil moisture. These results point to the importance of considering non-linearity in plant-water relations to understand plastic and evolutionary responses to changing climates.
Investigating the dynamics of microbial consortia in spatially structured environments
Authors: Gupta Sonali , Ross Tyler D. , Gomez Marcella M. , Grant Job L. , Romero Philip A. , Venturelli Ophelia S.
Published: February 2020

The spatial organization of microbial communities arises from a complex interplay of biotic and abiotic interactions and is a major determinant of ecosystem functions. We design a microfluidic platform to investigate how the spatial arrangement of microbes impacts gene expression and growth. We elucidate key biochemical parameters that dictate the mapping between spatial positioning and gene expression patterns. We show that distance can establish a low-pass filter to periodic inputs, and can enhance the fidelity of information processing. Positive and negative feedback can play disparate roles in the synchronization and robustness of a genetic oscillator distributed between two strains to spatial separation. Quantification of growth and metabolite release in an amino-acid auxotroph community demonstrates that the interaction network and stability of the community are highly sensitive to temporal perturbations and spatial arrangements. In sum, our microfluidic platform can quantify spatiotemporal parameters influencing diffusion-mediated interactions in microbial consortia.
Kidney impairment is associated with in-hospital death of COVID-19 patients
Authors: Cheng Yichun , Luo Ran , Wang Kun , Zhang Meng , Wang Zhixiang , Dong Lei , Li Junhua , Yao Ying , Ge Shuwang , Xu Gang
Published: February 2020

Background

Information on kidney impairment in patients with coronavirus disease 2019 (COVID-19) is limited. This study aims to assess the prevalence and impact of abnormal urine analysis and kidney dysfunction in hospitalized COVID-19 patients in Wuhan.

Methods

We conducted a consecutive cohort study of COVID-19 patients admitted in a tertiary teaching hospital with 3 branches following a major outbreak in Wuhan in 2020. Hematuria, proteinuria, serum creatinine concentration and other clinical parameters were extracted from the electronic hospitalization databases and laboratory databases. Incidence rate for acute kidney injury (AKI) was examined during the study period. Association between kidney impairment and in-hospital death was analyzed.

Results

We included 710 consecutive COVID-19 patients, 89 (12.3%) of whom died in hospital. The median age of the patients was 63 years (inter quartile range, 51-71), including 374 men and 336 women. On admission, 44% of patients have proteinuria hematuria and 26.9% have hematuria, and the prevalence of elevated serum creatinine and blood urea nitrogen were 15.5% and 14.1% respectively. During the study period, AKI occurred in 3.2% patients. Kaplan–Meier analysis demonstrated that patients with kidney impairment have higher risk for in-hospital death. Cox proportional hazard regression confirmed that elevated serum creatinine, elevated urea nitrogen, AKI, proteinuria and hematuria was an independent risk factor for in-hospital death after adjusting for age, sex, disease severity, leukocyte count and lymphocyte count.

Conclusions

The prevalence of kidney impairment (hematuria, proteinuria and kidney dysfunction) in hospitalized COVID-19 patients was high. After adjustment for confounders, kidney impairment indicators were associated with higher risk of in-hospital death. Clinicians should increase their awareness of kidney impairment in hospitalized COVID-19 patients.
Reduction and Functional Exhaustion of T Cells in Patients with Coronavirus Disease 2019 (COVID-19)
Authors: Diao Bo , Wang Chenhui , Tan Yingjun , Chen Xiewan , Liu Ying , Ning Lifen , Chen Li , Li Min , Liu Yueping , Wang Gang , Yuan Zilin , Feng Zeqing , Wu Yuzhang , Chen Yongwen
Published: February 2020

BACKGROUND

The outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed great threat to human health, which has been declared a public health emergency of international concern (PHEIC) by the WHO. T cells play a critical role in antiviral immunity but their numbers and functional state in COVID-19 patients remain largely unclear.

METHODS

We retrospectively reviewed the counts of total T cells, CD4+, CD8+T cell subsets, and serum cytokine concentration from inpatient data of 522 patients with laboratory-confirmed COVID-19, admitted into two hospitals in Wuhan from December 2019 to January 2020, and 40 healthy controls, who came to the hospitals for routine physical examination. In addition, the expression of T cell exhaustion markers PD-1 and Tim-3 were measured by flow cytometry in the peripheral blood of 14 COVID-19 cases.

RESULTS

The number of total T cells, CD4+and CD8+T cells were dramatically reduced in COVID-19 patients, especially among elderly patients (⩾60 years of age) and in patients requiring Intensive Care Unit (ICU) care. Counts of total T cells, CD8+T cells or CD4+T cells lower than 800/μL, 300/μL, or 400/μL, respectively, are negatively correlated with patient survival. Statistical analysis demonstrated that T cell numbers are negatively correlated to serum IL-6, IL-10 and TNF-α concentration, with patients in decline period showing reduced IL-6, IL-10 and TNF-α concentrations and restored T cell counts. Finally, T cells from COVID-19 patients have significantly higher levels of the exhausted marker PD-1 as compared to health controls. Moreover, increasing PD-1 and Tim-3 expression on T cells could be seen as patients progressed from prodromal to overtly symptomatic stages, further indicative of T cell exhaustion.

CONCLUSIONS

T cell counts are reduced significantly in COVID-19 patients, and the surviving T cells appear functionally exhausted. Non-ICU patients, with total T cells, CD8+T cells CD4+T cells counts lower than 800/μL, 300/μL, and 400/μL, respectively, may still require aggressive intervention even in the immediate absence of more severe symptoms due to a high risk for further deterioration in condition.
Psychological responses, behavioral changes and public perceptions during the early phase of the COVID-19 outbreak in China: a population based cross-sectional survey
Authors: Qian Mengcen , Wu Qianhui , Wu Peng , Hou Zhiyuan , Liang Yuxia , Cowling Benjamin J. , Yu Hongjie
Published: February 2020

Objective

To investigate psychological and behavioral responses to the threat of SARS-CoV-2 infections and their associations with public perceptions in China

Design

Cross sectional population-based telephone survey via random digital dialing between 1 and 10 February, 2020

Setting

Wuhan (the epicentre and quarantined city), and Shanghai (a typical major city with close transportation link with Wuhan)

Participants

Random sample of 510 residents in Wuhan and 501 residents in Shanghai aged above 18

Main outcome measures

Anxiety (measured by the 7-item generalized anxiety disorder [GAD-7] scale), recommended and avoidance behaviors (engaged in all six behaviors such as increasing surface cleaning and reducing going out).

Results

The prevalence rates of moderate or severe anxiety (score ≥10 on GAD-7) were 32.7% (n=167) among Wuhan participants and 20.4% (n=102) among Shanghai participants. 78.6% (n=401) of Wuhan participants and 63.9% (n=320) of Shanghai participants had carried out all six precautionary behaviors. For both measures, Wuhan participants were more responsive to the outbreak (p<0.001). Controlling for personal characteristics, logistic regression results suggested that risks of moderate or severe anxiety were positively associated with perceived susceptibility (odds ratio 1.6, 95% confidence interval 1.3-1.8) and severity of the disease (1.6, 1.4-1.9) and confusion about information reliability (1.6, 1.5-1.9). Having confidence in taking measures to protect oneself against the disease was associated with a lower risk (0.6, 0.5-0.7). The strongest predictor of behavioral change was perceived severity (1.2, 1.1-1.4), followed by confusion about information reliability (1.1, 1.0-1.3).

Conclusions

Psychological and behavioral responses to COVID-19 have been dramatic during the rising phase of the outbreak. Our results support efforts for timely dissemination of accurate and reliable information to address the high anxiety level.
Geometric Semi-automatic Analysis of Colles’ Fractures
Authors: Reyes-Aldasoro Constantino Carlos , Ngan Kwun Ho , Ananda Ananda , Garcez Artur d’Avila , Appelboam Andy , Knapp Karen M.
Published: February 2020

Fractures of the wrist are common in Emergency Departments, where some patients are treated with a procedure called Manipulation under Anaesthesia. In some cases this procedure is unsuccessful and patients need to visit the hospital again where they undergo surgery to treat the fracture. This work describes a geometric semi-automatic image analysis algorithm to analyse and compare the x-rays of healthy controls and patients with dorsally displaced wrist fractures (Colles’ fractures) who were treated with Manipulation under Anaesthesia. A series of 161 posterior-anterior radiographs from healthy controls and patients with Colles’ fractures were acquired and analysed. The patients’ group was further subdivided according to the outcome of the procedure (successful/unsuccessful) and pre- or post-intervention creating five groups in total (healthy, pre-successful, pre-unsuccessful, post-successful, post-unsuccessful). The semi-automatic analysis consisted of manual location of three landmarks (finger, lunate and radial styloid) and automatic processing to generate 32 geometric and texture measurements, which may be related to conditions such as osteoporosis and swelling of the wrist. Statistical differences were found between patients and controls and pre- and post-intervention, but not between the procedures. The most distinct measurements were those of texture. Although the study includes a relatively low number of cases and measurements, the statistical differences are encouraging.
Modeling and Prediction of the 2019 Coronavirus Disease Spreading in China Incorporating Human Migration Data
Authors: Zhan Choujun , Tse Chi K. , Fu Yuxia , Lai Zhikang , Zhang Haijun
Published: February 2020

This study integrates the daily intercity migration data with the classic Susceptible-Exposed-Infected-Removed (SEIR) model to construct a new model suitable for describing the dynamics of epidemic spreading of Coronavirus Disease 2019 (COVID-19) in China. Daily intercity migration data for 367 cities in China are collected from Baidu Migration, a mobile-app based human migration tracking data system. Historical data of infected, recovered and death cases from official source are used for model fitting. The set of model parameters obtained from best data fitting using a constrained nonlinear optimization procedure is used for estimation of the dynamics of epidemic spreading in the coming weeks. Our results show that the number of infections in most cities in China will peak between mid February to early March 2020, with about 0.8%, less than 0.1% and less than 0.01% of the population eventually infected in Wuhan, Hubei Province and the rest of China, respectively.
Views about integrating smoking cessation treatment within psychological services for patients with common mental illness: a multi-perspective qualitative study
Authors: Taylor Gemma , Sawyer Katherine , Kessler David , Munafò Marcus , Aveyard Paul , Shaw Alison
Published: February 2020

Background

Smoking rates are significantly higher in people with mental health problems, compared to those without. Negative attitudes towards smoking cessation are widespread in inpatient settings towards patients with severe and enduring mental illness. It is not clear if the same attitudes operate in psychological services towards people with common mental illness. We aimed to understand the concerns and views that patients, therapists, and smoking cessation practitioners may have about integrating smoking cessation treatment into psychological treatment for common mental illness and how these concerns may be overcome.

Methods

Thematic analysis of 23 in-depth interviews. Interviews took place in Improving Access to Psychological Therapies (IAPT) and smoking cessation services in England. Participants were 11 psychological wellbeing practitioners (PWPs), six IAPT patients with common mental illness, and six smoking cessation advisors.

Outcomes

None.

Findings

IAPT patients reported psychological benefits from smoking, but also described smoking as a form of therapeutic self-harm. PWPs seem positive towards smoking cessation treatment for people with common mental illness. IAPT PWPs and patients accept evidence that smoking tobacco may harm mental health, and quitting might benefit mental health. PWPs report expertise in helping people with common mental illness to make behavioural changes in the face of mood disturbances and poor motivation. IAPT appears to be a natural environment for smoking cessation intervention. PWPs felt confident to offer smoking cessation treatments to IAPT patients, but thought that a reduction in caseload was required to deliver smoking cessation support in an already pressed service.
Association of Population migration and Coronavirus Disease 2019 epidemic control
Authors: Ding Yu , Luo Sihui , Zheng Xueying , Ling Ping , Yue Tong , Liu Zhirong , Weng Jianping
Published: February 2020

Background and Objective

To analyze the impact of different patterns of migration flow in two cities, Hefei and Shenzhen, on the epidemic and disease control of Coronavirus Disease 2019 (COVID-19), in order to provide insight for making differentiated controlling policies.

Methods

We collected demographic and epidemiological information of confirmed COVID-19 cases in Hefei and Shenzhen between January 19 and February 11, 2020, from data officially published by the provincial and municipal Centers for Disease Control and Prevention (CDC). From these data we calculated basic reproduction number R0 to reflect the rate of spread of COVID-19 in these cities. Aggregated data of population migration during the same period was extracted from Baidu Migration. The change of R0 in the two cites were analyzed and compared. Spearman correlation analysis between R0 and population inflow from epidemic focus were performed.

Results

A total of 157 confirmed cases was identified in Hefei by 24:00 February 11, 2020, with an average age of 44.4±15.6 years, 74 female (47.1%) and 386 confirmed cases were identified in Shenzhen, with an average age of 45.15±17.99 years, 202 female (52.3%). Significant difference in the proportion of imported cases between the two cities was observed (Hefei vs Shenzhen, 24.2% vs 74.9%, p=0.000). Before January 31 2020, during the initial stage of the Level 1 Response to Major Public Health Emergencies, there was no significant association observed in Shenzhen between R0 and the proportion of population inflow from the epidemic focus (P =0.260, r=-0.452); meanwhile in Hefei, such association was strong (P =0.000, r=1.0). However, after the initial stage of response, the situation reversed. A weak association was observed in Shenzhen between be R0 and the proportion of population inflow from the epidemic focus (P=0.073, r=0.536) but not in Hefei (P =0.498, r=0.217).

Conclusion

Following Level 1 Response, consistent decline of R0 of COVID-19 was observed in both Hefei and Shenzhen. Different patterns of disease spread were observed in the two cities, driven by different patterns of population migration. This indicated that population migration should be taken into consideration when we set controlling policy of a novel infectious disease.
Fly wing evolution explained by a neutral model with mutational pleiotropy
Authors: Jiang Daohan , Zhang Jianzhi
Published: February 2020

To what extent the speed of mutational production of phenotypic variation determines the rate of long-term phenotypic evolution is a central question in evolutionary biology. In a recent study, Houleet al.addressed this question by studying the mutational variation, microevolution, and macroevolution of locations of vein intersections on fly wings, reporting very slow phenotypic evolution relative to the rates of mutational input, high phylogenetic signals of these traits, and a strong, linear correlation between the mutational variance of a trait and its rate of evolution. Houleet al. examined multiple models of phenotypic evolution but found none consistent with all these observations. Here we demonstrate that the purported linear correlation between mutational variance and evolutionary divergence is an artifact. More importantly, patterns of fly wing evolution are explainable by a simple model in which the wing traits are neutral or neutral within a range of phenotypic values but their evolutionary rates are reduced because most mutations affecting these traits are purged owing to their pleiotropic effects on other traits that are under stabilizing selection. We conclude that the evolutionary patterns of fly wing morphologies are explainable under the existing theoretical framework of phenotypic evolution.
Efficient coding of numbers explains decision bias and noise
Authors: Prat-Carrabin Arthur , Woodford Michael
Published: February 2020

Human subjects differentially weight different stimuli in averaging tasks, which has been interpreted as reflecting encoding bias. We examine the alternative hypothesis that stimuli are encoded with noise, then optimally decoded. Under a model of efficient coding, the amount of noise should vary across stimuli, and depend on statistics of the stimuli. We investigate these predictions through a task in which participants are asked to compare the averages of two series of numbers, each sampled from a prior distribution that varies across blocks of trials. Subjects encode numbers with a bias and a noise that both depend on the number. Infrequently occurring numbers are encoded with more noise. We show how an efficient-coding, Bayesian-decoding model accounts for these patterns, and best captures subjects’ behaviour. Finally, our results suggest that Wei and Stocker’s “law of human perception”, which relates the bias and variability of sensory estimates, also applies to number cognition.
Vitamin D receptor protects against dysbiosis and tumorigenesis via the JAK/STAT pathway in intestine
Authors: Zhang Yong-Guo , Lu Rong , Wu Shaoping , Chatterjee Ishita , Zhou David , Xia Yinglin , Sun Jun
Published: February 2020

Background

Vitamin D exerts regulatory roles via vitamin D receptor (VDR) in mucosal immunity, host defense, and inflammation involving host factors and microbiome. HumanVdrgene variation shapes the microbiome and VDR deletion leads to dysbiosis. Low VDR expression and diminished vitamin D/VDR signaling are observed in colon cancer. Nevertheless, how intestinal epithelial VDR is involved in tumorigenesis through gut microbiota remains unknown. We hypothesized that intestinal VDR protects mice against dysbiosis via modulating the JAK/STAT pathway in tumorigenesis. To test our hypothesis, we used an azoxymethane/Dextran Sulfate Sodium-induced cancer model in intestinal VDR conditional knockout (VDRΔIEC) mice, cell cultures, stem-cell derived colonoids, and human colon cancer samples.

Results

VDRΔIECmice have higher numbers of tumors with location shifted from distal to proximal colon. Fecal microbiota analysis showed that VDR deletion leads to bacterial profile shift from normal to susceptible carcinogenesis. We found enhanced bacterial staining in mouse and human tumors. Microbial metabolites from VDRΔIECmice showed elevated secondary bile acids, consistent with the observations in human CRC. We further identified that VDR protein bound to the Jak2 promoter, suggesting that VDR transcriptionally regulated Jak2. The JAK/STAT pathway is critical in intestinal and microbial homeostasis. Fecal samples from VDRΔIECmice activate the STAT3 activation in human and mouse organoids. Lack of VDR led to hyperfunction of Jak2 in respond to intestinal dysbiosis. A JAK/STAT inhibitor abolished the microbiome-induced activation of STAT3.

Conclusion

We provide insights into the mechanism of VDR dysfunction leading to dysbiosis and tumorigenesis. It indicates a new target — microbiome and VDR for prevention of cancer.
A generalizable method for false-discovery rate estimation in mass spectrometry-based lipidomics
Authors: Fujimoto Grant M. , Kyle Jennifer E. , Lee Joon-Yong , Metz Thomas O. , Payne Samuel H.
Published: February 2020

Mass spectrometry (MS)-based lipidomics is revolutionizing lipid research with high throughput identification and quantification of hundreds to thousands of lipids with the goal of elucidating lipid metabolism and function. Estimates of statistical confidence in lipid identification are essential for downstream data interpretation in a biological context. In the related field of proteomics, a variety of methods for estimating false-discovery are available, and understanding the statistical confidence of identifications is typically required for data analysis and hypothesis testing. However, there is no current method for estimating the false discovery rate (FDR) or statistical confidence for MS-based lipid identifications. This has slowed the adoption of MS-based lipidomics research, as all identifications require manual inspection and validation to ensure their accuracy. We present here the first generalizable method for FDR estimation, a target/decoy approach, that allows those conducting MS-based lipidomics research to confidently adjust spectral score thresholds to minimize false discovery and to enable full automation of data analysis.
Influence of Energy Deficiency on the Molecular Processes ofSubstantia Nigra Pars CompactaCell for Understanding Parkinsonian Neurodegeneration: A Comprehensive Biophysical Computational Model
Authors: Muddapu Vignayanandam R. , Chakravarthy V. Srinivasa
Published: February 2020

Parkinson’s disease (PD) is the second most prominent neurodegenerative disease around the world. Although it is known that PD is caused by the loss of dopaminergic cells in substantia nigra pars compacta (SNc), the decisive cause of this inexorable cell loss is not clearly elucidated. We hypothesize that “Energy deficiency at a sub-cellular/cellular/systems level can be a common underlying cause for SNc cell loss in PD.” Here, we propose a comprehensive computational model of SNc cell which helps us to understand the pathophysiology of neurodegeneration at subcellular level in PD. The proposed model incorporates a rich vein of molecular dynamics related to SNc neurons such as ion channels, active pumps, ion exchangers, dopamine turnover processes, energy metabolism pathways, calcium buffering mechanisms, alpha-synuclein aggregation, Lewy body formation, reactive oxygen species (ROS) production, levodopa uptake, and apoptotic pathways. The proposed model was developed and calibrated based on experimental data. The influx of glucose and oxygen into the model was controlled, and the consequential ATP variations were observed. Apart from this, the dynamics of other molecular players (alpha-synuclein, ROS, calcium, and dopamine) known to play an important role in PD pathogenesis are also studied. The aim of the study was to see how deficits in supply of energy substrates (glucose and oxygen) lead to a deficit in ATP, and furthermore, deficits in ATP are the common factor underlying the pathological molecular-level changes including alpha-synuclein aggregation, ROS formation, calcium elevation, and dopamine dysfunction. The model suggests that hypoglycemia plays a more crucial role in leading to ATP deficits than hypoxia. We believe that the proposed model provides an integrated modelling framework to understand the neurodegenerative processes underlying PD.
Frequency of mispackaging ofProchlorococcusDNA by cyanophage
Authors: Laurenceau Raphaël , Raho Nicolas , Forget Mathieu , Arellano Aldo , Chisholm Sallie W.
Published: February 2020

Prochlorococcuscells are the numerically dominant phototrophs in the open ocean. Cyanophages that infect them are thus a notable fraction of the total viral population in the euphotic zone, and, as vehicles of horizontal gene transfer, appear to drive their evolution. Here we examine the propensity of three cyanophages – a podovirus, a siphovirus, and a myovirus – to mispackage host DNA in their capsids while infectingProchlorococcus,the first step in phage-mediated horizontal gene transfer. We find the mispackaging frequencies are distinctly different among the three phages. Myoviruses mispackage host DNA at low and stable frequencies, while podo- and siphoviruses vary in their mispackaging frequencies by orders of magnitude depending on growth light intensity. We attribute this difference to the concentration of intracellular reactive oxygen species and protein synthesis rates. Based on our findings, we propose a model of mispackaging frequency determined by the imbalance between the production of capsids and the number of phage genome copies during infection.