bluuebunny/crossref_metadata_2025 huggingface dataset:
A Genome-based Model to Predict the Virulence ofPseudomonas aeruginosaIsolates
Authors: Pincus Nathan B. , Ozer Egon A. , Allen Jonathan P. , Nguyen Marcus , Davis James J. , Winter Deborah R. , Chuang Chih-Hsien , Chiu Cheng-Hsun , Zamorano Laura , Oliver Antonio , Hauser Alan R.
Published: June 2020

Variation in the genome ofPseudomonas aeruginosa, an important pathogen, can have dramatic impacts on the bacterium’s ability to cause disease. We therefore asked whether it was possible to predict the virulence ofP. aeruginosaisolates based upon their genomic content. We applied a machine learning approach to a genetically and phenotypically diverse collection of 115 clinicalP. aeruginosaisolates using genomic information and corresponding virulence phenotypes in a mouse model of bacteremia. We defined the accessory genome of these isolates through the presence or absence of accessory genomic elements (AGEs), sequences present in some strains but not others. Machine learning models trained using AGEs were predictive of virulence, with a mean nested cross-validation accuracy of 75% using the random forest algorithm. However, individual AGEs did not have a large influence on the algorithm’s performance, suggesting instead that the virulence prediction derives from a diffuse genomic signature. These results were validated with an independent test set of 25P. aeruginosaisolates whose virulence was predicted with 72% accuracy. Machine learning models trained using core genome single nucleotide variants and whole genome k-mers also predicted virulence. Our findings are a proof of concept for the use of bacterial genomes to predict pathogenicity inP. aeruginosaand highlight the potential of this approach for predicting patient outcomes.

IMPORTANCE

Pseudomonas aeruginosais a clinically important gram-negative opportunistic pathogen. As a species,P. aeruginosahas a large degree of heterogeneity both through variation in sequences found throughout the species (core genome) and the presence or absence of sequences in different isolates (accessory genome).P. aeruginosaisolates also differ markedly in their ability to cause disease. In this study, we used machine learning to predict the virulence level ofP. aeruginosaisolates in a mouse bacteremia model based on genomic content. We show that both the accessory and core genome are predictive of virulence. This study provides a machine learning framework to investigate relationships between bacterial genomes and complex phenotypes such as virulence.
Trajectories of depressive symptoms among vulnerable groups in the UK during the COVID-19 pandemic
Authors: Frank Philipp , Iob Eleonora , Steptoe Andrew , Fancourt Daisy
Published: June 2020

Objective

The coronavirus disease 2019 (COVID-19) pandemic has affected many aspects of the human condition, including mental health and psychological wellbeing. This study examined trajectories of depressive symptoms (DST) over time among vulnerable individuals in the UK during the COVID-19 pandemic.

Methods

The sample consisted of 51,417 adults recruited from the COVID-19 Social Study. Depressive symptoms were measured on seven occasions (21st March - 2nd April), using the Patient Health Questionnaire (PHQ-9). Sociodemographic vulnerabilities included non-white ethnic background, low socio-economic position (SEP), and type of work (keyworker versus no keyworker). Health-related and psychosocial vulnerabilities included pre-existing physical and mental health conditions, experience of psychological and/or physical abuse, and low social support. Group-based DST were derived using latent growth mixture modelling and multivariate logistic regression models were fitted to examine the association between these vulnerabilities and DSTs. Model estimates were adjusted for age, sex, and suspected COVID-19 diagnosis.

Results

Three DSTs were identified: low [N=30,850 (60%)] moderate [N=14,911 (29%)], and severe [N=5,656 (11%)] depressive symptoms. DSTs were relatively stable across the first 6 weeks of lockdown. After adjusting for covariates, experiences of physical/psychological abuse (OR 13.16, 95% CI 12.95-13.37), pre-existing mental health conditions (OR 13.00 95% CI 12.87-13.109), pre-existing physical health conditions (OR 3.41, 95% CI 3.29-3.54), low social support (OR 12.72, 95% CI 12.57-12.86), and low SEP (OR 5.22, 95% CI 5.08-5.36) were significantly associated with the severe DST. No significant association was found for ethnicity (OR 1.07, 95% 0.85-1.28). Participants with key worker roles were less likely to experience severe depressive symptoms (OR 0.66, 95% 0.53-0.80). Similar but smaller patterns of associations were found for the moderate DST.

Conclusions

People with psychosocial and health-related risk factors, as well as those with low SEP seem to be most vulnerable to experiencing moderate or severe depressive symptoms during the COVID-19 pandemic.
Detection of SARS-CoV-2 in wastewater in Japan by multiple molecular assays-implication for wastewater-based epidemiology (WBE)
Authors: Hata Akihiko , Honda Ryo , Hara-Yamamura Hiroe , Meuchi Yuno
Published: June 2020

Presence of SARS-coronavirus-2 (SARS-CoV-2) in wastewater sample has been documented in several countries. Wastewater-based epidemiology (WBE) is potentially effective for early warning of COVID-19 outbreak. The purpose of this study was to verify the detection limit of WBE for COVID-19. In total, 27 influent wastewater samples were collected from four wastewater treatment plants in Ishikawa and Toyama prefectures in Japan. During the study period, numbers of the confirmed COVID-19 cases in these prefectures increased from almost 0 to around 20 per 100,000 peoples. SARS-CoV-2 RNA in the samples were identified by several PCR-based assays. Among the 27 samples, 7 were positive for SARS-CoV-2 by at least one out of the three quantitative RT-PCR assays. These samples were also positive by RT-nested PCR assays. The detection frequency became higher when the number of total confirmed SARS-CoV-2 cases in 100,000 peoples became above 10 in each prefecture. However, SARS-CoV-2 could also be detected with a low frequency when the number was below 1.0. Considering that the number of the confirmed cases does not necessarily reflect the actual prevalence of the infection at the time point, data on the relationship between the number of infection cases and concentration in wastewater needs to be accumulated further.
Elevated levels of hoarding in ADHD: a special link with inattention
Authors: Morein-Zamir Sharon , Kasese Michael , Chamberlain Samuel R , Trachtenberg Estherina
Published: June 2020

Hoarding Disorder (HD) is under recognised and under-treated. Though HD develops by early adulthood, patients present only later in life, resulting in research based largely on samples of predominantly older females. Whilst formerly associated with Obsessive-Compulsive Disorder (OCD), it is now recognised that individuals with HD often have inattention symptoms reminiscent of Attention Deficit/Hyperactivity Disorder (ADHD). Here, we investigated HD in adults with ADHD. Patients in an ADHD clinic (n=88) reported on ADHD, HD and OCD-related symptoms, and compared with age, gender and education matched controls (n=90). Findings were assessed independently in an online UK sample to verify replication using a dimensional approach (n=220). Clinically significant hoarding symptoms were found in ~20% versus 2% of ADHD and control groups, respectively, with those with hoarding being on average in their thirties and with approximately half being male. Greater hoarding severity was noted even in the remaining patients compared with controls (d=0.89). Inattention was the only significant statistical predictor of hoarding severity in patients. Similarly, inattention, alongside depression and anxiety were the greatest predictors of hoarding in the independent sample where 3.2% identified as having clinically significant hoarding. Patients with ADHD had a high frequency of hoarding symptoms, which were specifically linked to inattention. HD should be routinely assessed in individuals with ADHD, as they do not typically disclose associated difficulties, despite these potentially leading to impaired everyday functioning. Research in HD should also investigate adults with ADHD, who are younger and with a greater prevalence of males than typical HD samples.
COVID-19 infections and outcomes in patients with multiple myeloma in New York City: a cohort study from five academic centers
Authors: Hultcrantz Malin , Richter Joshua , Rosenbaum Cara , Patel Dhwani , Smith Eric , Korde Neha , Lu Sydney , Mailankody Sham , Shah Urvi , Lesokhin Alexander , Hassoun Hani , Tan Carlyn , Maura Francesco , Derkacs Andriy , Diamond Benjamin , Rossi Adriana , Pearse Roger N. , Madduri Deepu , Chari Ajai , Kaminetsky David , Braunstein Marc , Gordillo Christian , Davies Faith , Jagannath Sundar , Niesvizky Ruben , Lentzsch Suzanne , Morgan Gareth , Landgren Ola
Published: June 2020

Importance

New York City is a global epicenter for the SARS-CoV-2 outbreak with a significant number of individuals infected by the virus. Patients with multiple myeloma have a compromised immune system, due to both the disease and anti-myeloma therapies, and may therefore be particularly susceptible to coronavirus disease 2019 (COVID-19); however, there is limited information to guide clinical management.

Objective

To assess risk factors and outcomes of COVID-19 in patients with multiple myeloma.

Design

Case-series.

Setting

Five large academic centers in New York City.

Participants

Patients with multiple myeloma and related plasma cell disorders who were diagnosed with COVID-19 between March 10th, 2020 and April 30th,2020.

Exposures

Clinical features and risk factors were analyzed in relation to severity of COVID-19.

Main Outcomes and Measures

Descriptive statistics as well as logistic regression were used to estimate disease severity reflected in hospital admissions, intensive care unit (ICU) admission, need for mechanical ventilation, or death.

Results

Of 100 multiple myeloma patients (male 58%; median age 68, range 41-91) diagnosed with COVID-19, 74 (74%) were admitted; of these 13 (18%) patients were placed on mechanical ventilation, and 18 patients (24%) expired. None of the studied risk factors were significantly associated (P>0.05) with adverse outcomes (ICU-admission, mechanical ventilation, or death): hypertension (N=56) odds ratio (OR) 2.3 (95% confidence interval [CI] 0.9-5.9); diabetes (N=18) OR 1.1 (95% CI 0.3-3.2); age >65 years (N=63) OR 2.0 (95% CI 0.8-5.3); high dose melphalan with autologous stem cell transplant <12 months (N=7) OR 1.2 (95% CI 0.2-7.4), IgG<650 mg/dL (N=42) OR=1.2 (95% CI 0.4-3.1). In the entire series of 127 patients with plasma cell disorders, hypertension was significantly associated with the combined end-point (OR 3.4, 95% CI 1.5-8.1).

Conclusions and Relevance

Although multiple myeloma patients have a compromised immune system due to both the disease and therapy; in this largest disease specific cohort to date of patients with multiple myeloma and COVID-19, compared to the general population, we found risk factors for adverse outcome to be shared and mortality rates to be within the higher range of officially reported mortality rates.
Microsomal reductase activity in patients with thyroid neoplasms
Authors: Proskurnina Elena V. , Fedorova Maria V. , Sozarukova Madina M. , Mitichkin Aleksandr E. , Panteleev Igor V. , Svetlov Evgeny V.
Published: June 2020

Objective

Cytochrome b5 reductase (CYB5R) and cytochrome P450 reductase (CYPOR) play an important role in cell metabolism; however, their role in thyroid hormonogenesis and carcinogenesis has not been studied. The activity of CYB5R correlates with metastasizing in breast cancer, but there are no similar studies for CYB5R and CYPOR for thyroid cancer. The aim was to assess the activity of CYB5R and CYPOR in thyroid tissues in benign and malignant thyroid neoplasms.

Methods

36 patients with thyroid neoplasms participated in the study. The control euthyroid goiter group included 10 patients; the thyrotoxic nodular goiter group included 14 patients; the papillary thyroid cancer T1-2N0-1M0 (PTC) group included 12 patients. The activity of CYB5R and CYPOR was assessed with lucigenin-enhanced chemiluminescence stimulated by NADH and NADPH, respectively.

Results

The activity of CYB5R and CYPOR increased several times in thyrotoxicosis and approximately by an order of magnitude in some cases of PTC, but the activity change of CYPOR was more pronounced compared to CYB5R. For the PTC group, the subgroups with low and high activity of microsomal reductases were detected. Microsomal reductases in follicular adenoma was 2–4-fold less active compared to nontoxic goiter and the low-activity PTC group.

Conclusions

Activity of microsomal reductases varies in thyroid pathology and can serve as a diagnostic and prognostic parameter in papillary thyroid cancer.
A Diffusion tensor imaging study to compare normative fractional anisotropy values with patients suffering from Parkinson’s disease in the brain grey and white matter
Authors: Kotian Rahul P , Prakashini K , Nair N Sreekumaran
Published: June 2020

Background

Diffusion tensor imaging (DTI) appears as a sensitive method to study Parkinson’s disease (PD) pathophysiology and severity. Fractional anisotropy (FA) value is one of the scalar derivatives of DTI used to find out anisotropy within a voxel in a tissue and used for determining white matter integrity in aging and neurodegenerative diseases. We studied DTI derived FA in early PD subjects as their routine MRI scans were normal.

Methods

40 patients with early PD and 40 healthy controls were employed to evaluate changes in microstructural white and grey matter in the brain’s using DTI derived FA values. Comparison of FA values in the brain’s white and grey matter of patients with PD and age matched controls at the corpus callosum, centrum semiovale, pons, putamen, caudate nucleus, substantia nigra, cerebral peduncles and cerebellar peduncles, was done using a region of interest (ROI) technique, with b-value 1000s/mm2 and TE=100 milliseconds using 1.5T MRI system.

Results

PD patients showed differences in FA values in both the grey and white matter areas of the brain’s compared to healthy controls. Our study revealed the presence of damage in the substantia nigra, corpus callosum, putamen and cerebral peduncles mainly in the PD group.

Conclusion

Our findings indicate that DTI and region of interest (ROI) methods can be used in patients with early PD to study microstructural alterations mainly in the substantia nigra, putamen and corpus callosum.
Global RNA-seq identified FBXL8 as a novel E3 ligase which modulates tumor suppressors to promote BRCA advancement
Authors: Chang Shu-Chun , Hsu Wayne , Su Emily Chia-Yu , Hung Chin-Sheng , Ding Jeak Ling
Published: June 2020

The initiation and progression of breast cancer (BRCA) is associated with inflammation and immune-overactivation. The E3 ubiquitin ligase is known to subtly balance immune-overactivation and pro-tumorigenesis. Here, by global transcriptional profiling of BRCA patient tissues, we identified a signature expression profile of F-box factors, of which FBXL8 emerged as a novel key component of E3 ligase. Our ex vivo studies (n=1349) indicate that FBXL8 promotes tumorigenesis and its level escalates with BRCA advancement. Knockdown of FBXL8 caused: (i) accumulation of two tumor-suppressors,CCND2 and IRF5, suggesting their collaborative regulation of BRCA status, (ii) intrinsic apoptosis in BRCA, (iii) inhibition of cell migration and invasion and (iv) downregulation of cancer-promoting cytokines/ chemokines; all of these effects curtailed the tumor microenvironment and suppressed cancer progression. Our findings highlight the translational impact of exploiting FBXL8 and its interaction partners (CCND2 and IRF5) for developing anti-cancer strategies and potential therapeutics to limit BRCA progression.
Using machine learning to predict COVID-19 infection and severity risk among 4,510 aged adults: a UK Biobank cohort study
Authors: Willette Auriel A. , Willette Sara A. , Wang Qian , Pappas Colleen , Klinedinst Brandon S. , Le Scott , Larsen Brittany , Pollpeter Amy , Li Tianqi , Brenner Nicole , Waterboer Tim
Published: June 2020

Background

Many risk factors have emerged for novel 2019 coronavirus disease (COVID-19). It is relatively unknown how these factors collectively predict COVID-19 infection risk, as well as risk for a severe infection (i.e., hospitalization).

Methods

Among aged adults (69.3 ± 8.6 years) in UK Biobank, COVID-19 data was downloaded for 4,510 participants with 7,539 test cases. We downloaded baseline data from 10-14 years ago, including demographics, biochemistry, body mass, and other factors, as well as antibody titers for 20 common to rare infectious diseases. Permutation-based linear discriminant analysis was used to predict COVID-19 risk and hospitalization risk. Probability and threshold metrics included receiver operating characteristic curves to derive area under the curve (AUC), specificity, sensitivity, and quadratic mean.

Results

The “best-fit” model for predicting COVID-19 risk achieved excellent discrimination (AUC=0.969, 95% CI=0.934-1.000). Factors included age, immune markers, lipids, and serology titers to common pathogens like human cytomegalovirus. The hospitalization “best-fit” model was more modest (AUC=0.803, 95% CI=0.663-0.943) and included only serology titers.

Conclusions

Accurate risk profiles can be created using standard self-report and biomedical data collected in public health and medical settings. It is also worthwhile to further investigate if prior host immunity predicts current host immunity to COVID-19.
Predicting future cognitive decline from non-brain and multimodal brain imaging data in healthy and pathological aging
Authors: Liem Franziskus , Dadi Kamalaker , Engemann Denis A. , Gramfort Alexandre , Bellec Pierre , Craddock R. Cameron , Damoiseaux Jessica S. , Steele Christopher J. , Yarkoni Tal , Margulies Daniel S. , Varoquaux Gaël
Published: June 2020

Cognitive decline occurs in healthy and pathological aging, and both may be preceded by subtle changes in the brain — offering a basis for cognitive predictions. Previous work has largely focused on predicting a diagnostic label from structural brain imaging. Our study broadens the scope of applications to cognitive decline in healthy aging by predicting future decline as a continuous trajectory, rather than a diagnostic label. Furthermore, since brain structure as well as function changes in aging, it is reasonable to expect predictive gains when using multiple brain imaging modalities. Here, we tested whether baseline multimodal neuroimaging data improve the prediction of future cognitive decline in healthy and pathological aging. Non-brain data (including demographics and clinical and neuropsychological scores) were combined with structural and functional connectivity MRI data from the OASIS-3 project (N = 662; age = 46 – 96y). The combined input data was entered into cross-validated multi-target random forest models to predict future cognitive decline (measured by the Clinical Dementia Rating and the Mini-Mental State Examination), on average 5.8y into the future. The analysis was preregistered and all analysis code is publicly available. We found that combining non-brain with structural data improved the continuous prediction of future cognitive decline (best test-set performance: R2= 0.42) and that cognitive performance, daily functioning, and subcortical volume drove the performance of our model. In contrast, including functional connectivity did not improve predictive accuracy. In the future, the prognosis of age-related cognitive decline may enable earlier and more effective cognitive, pharmacological, and behavioral interventions to be tailored to the individual.
Neuroinflammation in the normal appearing white matter of multiple sclerosis brain causes abnormalities at the node of Ranvier
Authors: Delgado Patricia Gallego , James Rachel , Browne Eleanor , Meng Joanna , Umashankar Swetha , Picon Carmen , Mazarakis Nicholas D. , Faisal A. Aldo , Howell Owain W. , Reynolds Richard
Published: June 2020

Changes to the structure of nodes of Ranvier in the normal-appearing white matter (NAWM) of MS brains are associated with chronic inflammation. We show that the paranodal domains in MS NAWM are longer on average than control, with Kv1.2 channels dislocated into the paranode. These pathological features are reproduced in a model of chronic meningeal inflammation generated by the injection of lentiviral vectors for the lymphotoxin-α (LTα) and interferon-γ (IFNγ) genes. We show that tumour necrosis factor (TNF), IFNγ and glutamate can provoke paranodal elongation in cerebellar slice cultures, which could be reversed by an NMDA blocker. When these changes were inserted into a computational model to simulate axonal conduction, a rapid decrease in velocity was observed, reaching conduction failure in small diameter axons. We suggest that glial cells activated by proinflammatory cytokines can produce high levels of glutamate, which triggers paranodal pathology, contributing to axonal damage and conduction deficits.
Genome modularization reveals overlapped gene topology is necessary for efficient viral reproduction
Authors: Wright Bradley W , Ruan Juanfang , Molloy Mark P , Jaschke Paul R
Published: June 2020

Sequence overlap between two genes is common across all genomes, with viruses having high proportions of these gene overlaps. The biological function and fitness effects of gene overlaps are not fully understood, and their effects on gene cluster and genome-level refactoring are unknown. The bacteriophage ϕX174 genome has ∼26% of nucleotides involved in encoding more than one gene. In this study we use an engineered ϕX174 phage containing a genome with all gene overlaps removed, to show that gene overlap is critical to maintaining optimal viral fecundity. Through detailed phenotypic measurements we reveal that genome modularization in ϕX174 causes virion replication, stability, and attachment deficiencies. Quantitation of the complete phage proteome across an infection cycle reveals almost half the proteins display abnormal expression patterns. Taken together, we have for the first time comprehensively demonstrated that gene modularization severely perturbs the coordinated functioning of a bacteriophage replication cycle. This work highlights the biological importance of gene overlap in natural genomes and that reducing gene overlap disruption should be an integral part of future genome engineering projects.
Discovery of cryptic plant diversity in one of the harshest environments: the rooftops of the Alps
Authors: Boucher Florian C. , Dentant Cédric , Ibanez Sébastien , Capblancq Thibaut , Boleda Martí , Boulangeat Louise , Smyčka Jan , Roquet Cristina , Noûs Camille , Lavergne Sébastien
Published: June 2020

High altitude temperate mountains have long been considered devoid of life owing to high extinction or low speciation rates during the Pleistocene. We performed a phylogenetic and population genomic investigation of an emblematic high-altitude plant clade (Androsacesect.Aretia, 31 currently recognized species), based on plant surveys conducted during alpinism expeditions. Surprisingly, we inferred that this clade originated in the Miocene and continued diversifying through Pleistocene glaciations, and discovered three novel species ofAndrosacedwelling on different bedrock types on the rooftops of the Alps. This suggests that temperate high mountains have been cradles of plant diversity even during the Pleistocene, with in-situ speciation driven by the combined action of geography and geology. Our findings have an unexpected historical relevance: H.-B. de Saussure likely observed one of these species during his 1788 expedition to the Mont Blanc and we describe it here, over two hundred years after its first sighting.
Anatomical correlates of face patches in macaque inferotemporal cortex
Authors: Arcaro Michael J. , Mautz Theodora , Livingstone Margaret S.
Published: June 2020

Primate brains typically have regions within the ventral visual stream that are selectively responsive to faces. These face patches are located in similar parts of macaque inferotemporal (IT) cortex across individuals though correspondence with particular anatomical features has not been previously reported. Here, using high resolution functional and anatomical imaging, we show that small “bumps” along the lower bank of the superior temporal sulcus are predictive of the location of face-selective regions. Recordings from implanted multi-electrode arrays verified that these bumps contain face-selective neurons. These bumps were present in monkeys raised without seeing faces and that lack face patches, indicating that these anatomical landmarks are predictive, of but not sufficient for, the presence of face selectivity. These bumps are found across primate species, indicating common evolutionary developmental mechanisms.
Assembly intermediates of orthoreovirus captured in the cell
Authors: Sutton Geoff , Sun Dapeng , Fu Xiaofeng , Kotecha Abhay , Hecksel Corey W. , Clare Daniel K. , Zhang Peijun , Stuart David I. , Boyce Mark
Published: June 2020

Traditionally molecular assembly pathways for viruses have been inferred from high resolution structures of stable intermediates purifiedin vitro, and from low resolution images of cell sections as well as from genetic approaches including conditionally lethal mutants. Here, we directly visualise a previously unsuspected ‘single shelled’ icosahedral intermediate for a mammalian orthoreovirus, in addition to the expected virions, in cryo-preserved infected cells by cryo-electron tomography of cellular lamellae1,2. Particle classification and averaging yielded structures at resolutions as high as 5.6 Å, sufficient to identify secondary structural elements and place known molecular structures, allowing us to produce an atomic model of the intermediate, comprising 120 copies of protein λ1 and 120 copies of σ2. This λ1 shell is in a ‘collapsed’ form compared to the mature virions, with the molecules pushed inwards at the icosahedral 5-folds by ~100 Å. This grossly indented shell, although produced by a mammalian reovirus, is reminiscent of the first assembly intermediate of prokaryotic dsRNA viruses belonging to a different virus family3, adding weight to the supposition that these diverse viruses share a common ancestor, and suggesting mechanisms for the assembly of viruses of theReoviridae. Such methodology holds enormous promise for the dissection of the replication cycle of many viruses.
A cautionary note on the use of haplotype callers in Phylogenomics
Authors: Duchen Pablo , Salamin Nicolas
Published: June 2020

Next-generation-sequencing haplotype callers are commonly used in studies to call variants from newly-sequenced species. However, due to the current availability of genomic resources, it is still common practice to use only one reference genome for a given genus, or even one reference for an entire clade of a higher taxon. The problem with traditional haplotype callers such as the one from GATK, is that they are optimized for variant calling at the population level, but not at the phylogenetic level. Thus, the consequences for downstream analyses can be substantial. Here, through simulations, we compare the performance between the haplotype callers of GATK and ATLAS, and present their differences at various phylogenetic scales. We show how the haplotype caller of GATK substantially underestimates the number of variants at the phylogenetic level, but not at the population level. We also quantified the level at which the accuracy of heterozygote calls declines with increasing distance to the reference genome. Such decrease is very sharp in GATK, while ATLAS maintains a high accuracy in variant calling, even at moderately-divergent species from the reference. We further suggest that efforts should be taken towards acquiring more reference genomes per species, before pursuing high-scale phylogenomic studies.
Laboratory based surveillance of SARS-CoV-2 in Pakistan
Authors: Badar Nazish , Ikram Aamer , Mirza Hamza Ahmad , Ahad Abdul , Alam Muhammad Masroor , Arshad Yasir , Umair Massab , Sharif Salmaan , Hassan Afreenish , Salman Muhammad
Published: June 2020

COVID-19 cases are alarmingly increasing in Pakistan since May 2020. Laboratory based surveillance system has been in place since the start of the pandemic. The genomic surveillance of SARS-CoV-2 strains isolated locally has been conducted based on partial ORF1b. The sequences were classified to show the phylogenetic correlation and showed 100% homology with those detected in neighboring countries India and China. The rapid increase in cases has led to development of robust strategies to enhance the laboratory testing capacity. We are currently meeting the country requirement to diagnose the virus in the community. Nonetheless, factors like recent ease in lockdown measures has led to massive rise in number of cases in few weeks time.
Correlation between meteorological factors and COVID-19 infection in the Belém Metropolitan Region
Authors: da Silva Félix Lélis , Gomes Maryjane Diniz A. , da Silva Andréa P. Lélis , de Sousa Samio Costa , de Souza Marcos Francisco Serafim , da Silva Gabriel Lélis P.
Published: June 2020

Many factors can influence the spread of viruses and respiratory infections. Studies have suggested that there is a direct relationship between environmental issues and population density with cases of COVID-19. In this sense, this research aims to analyze, through correlational study and Krigagem, the relationship of meteorological and demographic variables with cases of COVID-19 in regions of subtropical climate in Brazil. The results suggest that population and demographic density (hab/km2) are risk factors for the spread of SAR-Cov-2 and an increase in the daily case record of COVID-19. The distribution of cases according to age group did not present a significant disparity between men and women. Relative humidity (RH)%, average temperature °C, minimum temperature °C, maximum temperature °C, wind speed m/s and daily precipitation (rain) mm show negative relationships with cases of COVID-19 in regions of humid equatorial climate. Analysis between associations of environmental factors, wind, temperature and HR in a region is extremely important to understand the dynamics of SARS-Cov-2 in the environment. In the northern region of Brazil, low wind speed, high temperatures and high RH are observed, environmental factors that, when associated, reduce the transmission process because it hinders the movement of the virus in the environment. In this sense, it is suggested that the transmission of SARS-CoV-2 in this region is disseminated through fluids in the air between man/man and by contact between objects/men. Therefore, strategic public policies to combat the pandemic must consider the environmental factors of the regions involved and control and/or blocking the transit of people.
Effect of social distancing on COVID-19 incidence and mortality in the US
Authors: VoPham Trang , Weaver Matthew D. , Hart Jaime E. , Ton Mimi , White Emily , Newcomb Polly A.
Published: June 2020

Social distancing policies were implemented in most US states as a containment strategy against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The effectiveness of these policy interventions on morbidity and mortality remains unknown. Our analysis examined the associations between statewide policies and objective measures of social distancing, and objective social distancing and COVID-19 incidence and mortality. We used nationwide, de-identified smartphone GPS data to estimate county-level social distancing. COVID-19 incidence and mortality data were from the Johns Hopkins Coronavirus Resource Center. Generalized linear mixed models were used to estimate incidence rate ratios (IRRs) and 95% confidence intervals (CIs) for the association between objective social distancing and COVID-19 incidence and mortality. Stay-at-home orders were associated with a 35% increase in social distancing. Higher social distancing was associated with a 29% reduction in COVID-19 incidence (adjusted IRR 0.71; 95% CI 0.57-0.87) and a 35% reduction in COVID-19 mortality (adjusted IRR 0.65; 95% CI 0.55-0.76). These findings provide evidence to inform ongoing national discussions on the effectiveness of these public health measures and the potential implications of returning to normal social activity.
Diatom Modulation of Microbial Consortia Through Use of Two Unique Secondary Metabolites
Authors: Shibl Ahmed A. , Isaac Ashley , Ochsenkühn Michael A. , Cárdenas Anny , Fei Cong , Behringer Gregory , Arnoux Marc , Drou Nizar , Santos Miraflor P. , Gunsalus Kristin C. , Voolstra Christian R. , Amin Shady A.
Published: June 2020

Unicellular eukaryotic phytoplankton, such as diatoms, rely on microbial communities for survival despite lacking specialized compartments to house microbiomes (e.g., animal gut). Microbial communities have been widely shown to benefit from diatom excretions that accumulate within the microenvironment surrounding phytoplankton cells, known as the phycosphere. However, mechanisms that enable diatoms and other unicellular eukaryotes to nurture specific microbiomes by fostering beneficial bacteria and repelling harmful ones are mostly unknown. We hypothesized that diatom exudates may attune microbial communities and employed an integrated multi-omics approach using the ubiquitous diatom Asterionellopsis glacialis to reveal how it modulates its naturally associated bacteria. We show that A. glacialis reprograms its transcriptional and metabolic profiles in response to bacteria to secrete a suite of central metabolites and two unusual secondary metabolites, rosmarinic acid and azelaic acid. While central metabolites are utilized by potential bacterial symbionts and opportunists alike, rosmarinic acid promotes attachment of beneficial bacteria to the diatom and simultaneously suppresses the attachment of opportunists. Similarly, azelaic acid enhances growth of beneficial bacteria, while simultaneously inhibiting growth of opportunistic ones. We further show that the bacterial response to azelaic acid is widespread in the world’s oceans and taxonomically restricted to a handful of bacterial genera. Our results demonstrate the innate ability of an important unicellular eukaryotic group to modulate their microbial consortia, similar to higher eukaryotes, using unique secondary metabolites that regulate bacterial growth and behavior inversely in different bacterial populations.
Biosynthesis and chemical characterization of an intracellular red pigment ofTalaromyces islandicusT101
Authors: Pimentel Rodrigues Igor Vinícius , Assunção Borges Katia Regina , da Cruz Neurene , Teles Amanda Mara , Neto da Silva Marcos Antonio Custódio , de Nazaré Silva Alves Rita , de Andrade Marcelo Souza , Khayat André Salim , Pinho Jaqueline Diniz , Marques Vale André Alvares , Araújo Guimarães Sulayne Janayna , Ruiz Jerônimo Conceição , Soares Brandão Nascimento Maria do Desterro , de Barros Bezerra Geusa Felipa
Published: June 2020

The interest in red colorants by the food industry has been increasing recently due to its wide application in many foods and beverages, and also to the carcinogenic and teratogenic effects of some synthetic dyes. Many ascomycetous fungi are able to synthesize and produce pigments, rendering them as alternative sources of natural dyes that are independent of environmental conditions.Talaromyces islandicusTI01 was isolated from a marine-influenced environment that has been suffering for decades from anthropogenic actions in its body of water. Broth microdilution technique was performed to analyze the antimicrobial activity. For analysis of the cytotoxic activity, the MTT [3-(4,5-dimethylthiazol-2-yl) -2,5-diphenyltetrazolium bromide] assay was conducted. The chemical analysis of the extract was performed by LC/MS (liquid chromatography coupled to mass spectrometry). The minimum bactericidal concentration (MBC) ofT. islandicus’intracellular red pigmented extract (IRPE) forE. coliATCC 25922 andS. aureusATCC 25923 was 1000 μg/ml. The minimum inhibitory concentration (MIC) forE. coliwas 250 μg/mL and forS. aureus500 μg/mL, respectively, whereas forC. tropicalisATCC 1369 was 62.5 μg/mL. IC50 for breast cancer cell line (MCF-7) was 45.43 ± 1.657 μg / mL. The major compounds present in the extract were: Luteoskyrin(1)and N-GABA-PP-V (6-[(Z)-2-Carboxyvinyl]-N-GABA-PP-V)(2). The results show that IRPE fromT. islandicusTI01 has a prominent antibacterial activity againstE. coliandS. aureus, making this pigment interesting for development of new food colorants and/or conservative agents, since these bacteria are food-borne pathogens.
COVID-19: Comparison between 8-days and extended 4weeks outbreak periods through socioeconomic and natural factors
Authors: Ullah Sana , Zheng Jianghua , Zuo Zhengkang , Zhang Feizhou , Shang Ke , Yu Wenjie , Fu Yu , Han Chuqiao , Lin Yi , Jiang Kaiwen , Sun Shanlin , Sun Yiyuan , Zhao Shoujiang , Yan Lei
Published: June 2020

Since mid-March 2020, global COVID-19 pandemic has experienced an exponential growth in process from sporadic to sudden outbreaks. This paper selects the 8-day surge data of daily cases, death and recovery rates (March 19-26, 2020) from 18 countries with severe pandemic situation to discuss the impact of 9 factors of both socioeconomic and natural on the pathogen outbreak. Moreover, the paper also elaborates analysis and comparison of relatively slow 4-week (February 1-29, 2020) data of China’s surge cases to determine the relationship between social and natural factors and on the spread of pandemic, which provides an effective reference for delaying and controlling the pandemic development.
A Model Based Analysis for COVID-19 Pandemic in India: Implications for Health Systems and Policy for Low- and Middle-Income Countries
Authors: Prinja Shankar , Bahuguna Pankaj , Chugh Yashika , Vassal Anna , Pandey Arvind , Aggarwal Sumit , Arora Narendra Kumar
Published: June 2020

Disclaimer statement

The authors have withdrawn this manuscript because they do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Readiness assessment of public–private partnerships (PPPs) adoption in developing countries: the case of Tanzania
Authors: Chileshe Nicholas , Kavishe Neema
Published: June 2020

Purpose

The purpose of this paper is to examine the Tanzanian practitioner’s readiness assessment for public–private partnership (PPP) adoption. This study is important as the readiness assessment enables the stakeholders to assess their capability and current status quo to implement new ideas such as PPPs.

Design/methodology/approach

Underpinned by the theoretical lenses of innovation diffusion theory (IDT), this research undertakes semi-structured interviews with PPP practitioners within the Tanzanian affordable housing sector. The content analysis was used for the data as collected.

Findings

“Lack of awareness and usage of PPPs framework models during the feasibility and subsequent implementation process”, “Limited knowledge and skills required for PPP practitioners”, “Poor capacity building”, “Lack of engagement of experts during the viability and assessment process” and “Poor selection process of private partners giving rising to unsolicited proposals” are the main PPP features influencing the readiness process and fostering of innovation.

Practical implications

The identification of the readiness approaches would support PPP policymakers and stakeholders with the government mechanisms for identifying the key areas needed to be addressed to improve the PPP implementation performance.

Originality/value

Outputs of this study provide insights on how to foster a better understanding of the readiness assessment strategies and approaches for successfully implementing PPP in affordable housing projects.
The skill of discipline – measuring F.I.R.S.T discipline principles in higher education
Authors: Krskova Hana , Baumann Chris , Breyer Yvonne , Wood Leigh Norma
Published: June 2020

Purpose

Human capital theory suggests that any increase in skills translates into greater productivity of the workforce. Non-cognitive skills, in particular, play a critical role in many domains in life. The aim of this study is to gain a greater understanding of one such skill, discipline. Viewing discipline as a tool for enhancing learning, personal development and increasing overall achievement, this study offers an alternative way to measure discipline in higher education.

Design/methodology/approach

This paper presents the results of an online survey of 537 current students and recent graduates from the United States, South Korea and China. Principal component analysis was used to test the overarching assumption that student discipline is composed of five dimensions. Multiple analysis of variance (ANOVA) with post hoc analyses andt-tests were applied to test for country and gender-related differences between the three country groups. Cluster analysis was used to profile the respondent groups based on similarities across the samples.

Findings

The results confirm that student discipline is a construct comprising five discipline dimensions – focus, intention, responsibility, structure and time (F.I.R.S.T). In addition, the identification of low, medium and high discipline levels among the respondents provides support for the recently introduced concept of a layered “threshold of Discipline”.

Originality/value

A F.I.R.S.T. discipline measurement questionnaire for capturing student discipline – underpinned by a conceptual model encompassing self-determination, goal setting, self-efficacy, self-regulation and time management principles – was developed and tested. Suggestions for enhancing graduate work readiness through increasing levels of the skill of discipline are outlined.
Finite element analysis of gradient lattice structure patterns for bone implant design
Authors: Seharing Asliah , Azman Abdul Hadi , Abdullah Shahrum
Published: June 2020

Purpose

The objective of this paper is to identify suitable lattice structure patterns for the design of porous bone implants manufactured using additive manufacturing.

Design/methodology/approach

The study serves to compare and analyse the mechanical behaviours between cubic and octet-truss gradient lattice structures. The method used was uniaxial compression simulations using finite element analysis to identify the translational displacements.

Findings

From the simulation results, in comparison to the cubic lattice structure, the octet-truss lattice structure showed a significant difference in mechanical behaviour. In the same design space, the translational displacement for both lattice structures increased as the relative density decreased. Apart from the relative density, the microarchitecture of the lattice structure also influenced the mechanical behaviour of the gradient lattice structure.

Research limitations/implications

Gradient lattice structures are suitable for bone implant applications because of the variation of pore sizes that mimic the natural bone structures. The complex geometry that gradient lattice structures possess can be manufactured using additive manufacturing technology.

Originality/value

The results demonstrated that the cubic gradient lattice structure has the best mechanical behaviour for bone implants with appropriate relative density and pore size.
Promoting an emotional connection to nature and other animals via forest school: disrupting the spaces of neoliberal performativity
Authors: Cudworth Dave
Published: June 2020

Purpose

The concept of children's alienation from, and reconnection to, nature has gained international interest. The purpose of this paper is to explore how forest school as a growing phenomenon in the UK is promoting this reconnection to nature as well as benefiting children's well-being. At the same time, forest school is providing children and young people with a more divergent learning experience, away from the structural pressures of the neoliberal classroom. With its emphasis on play-based learning in wooded areas, and the freedom to make connections and spatially engage with what is around them at their own pace, such engagement in these “alternative” learning spaces can support the development of a post-human discourse and sensibilities. This is fundamental in developing children's emotional connection in promoting pro-environmental behaviours and their attitudes towards valuing and protecting the non-human.

Design/methodology/approach

This paper draws on field notes documented during forest school leader training undertook by the author from April 2017 to May 2018. Further data were collected in the form of participant observations of forest school sessions in three schools; semi-structured interviews with the head teachers of these schools and two forest school practitioners. Supplementary data will also draw on the experiences of a group of second-year education studies university students after completing a module on forest school and outdoor learning, led by the author.

Findings

This article finds that the more children engage with wooded areas and interact with the natural environment and other creatures within that space, the more it affords meaning to them. This in turn promotes a sense of belonging and environmental stewardship, particularly in relation to non-human creatures. This article also finds that where schools provide forest school opportunities on their sites, such provision is conducive to supporting more creative practices within the “spatialities” of the neoliberal classroom.

Originality/value

Neoliberal education policy with its focus on high stakes testing and performance outcomes increasingly shapes the spatial practices of school life. Consequently, time spent outdoors and its relationship with intrinsic learning has declined in many schools. With many schools placing less importance on outdoor learning, children and young people have become further alienated from engaging in different ways with their environments. Further, data highlighting the link between forest school and children's interest in plants and other animals have not been the subject of much research.