bluuebunny/crossref_metadata_2025 huggingface dataset:
Perceived public health threat a key factor for willingness to get the COVID-19 vaccine in Australia
Authors: Dodd Rachael H , Pickles Kristen , Cvejic Erin , Cornell Samuel , Isautier Jennifer MJ , Copp Tessa , Nickel Brooke , Bonner Carissa , Batcup Carys , Muscat Danielle M , Ayre Julie , McCaffery Kirsten J
Published: April 2021

Background

Vaccination rollout against COVID-19 has begun across multiple countries worldwide. Although the vaccine is free, rollout might still be compromised by hesitancy or concerns about COVID-19 vaccines.

Methods

We conducted two online surveys of Australian adults in April (during national lockdown; convenience cross-sectional sample) and November (virtually no cases of COVID-19; nationally representative sample) 2020, prior to vaccine rollout. We asked about intentions to have a potential COVID-19 vaccine (If a COVID-19 vaccine becomes available, I will get it) and free-text responses (November only).

Results

After adjustment for differences in sample demographics, the estimated proportion agreeing to a COVID-19 vaccine if it became available in April (n=1146) was 76.2%. In November (n=2034) this was estimated at 71.4% of the sample; additional analyses identified that the variation was driven by differences in perceived public health threat between April and November. Across both surveys, female gender, being younger, having inadequate health literacy and lower education were associated with reluctance to be vaccinated against COVID-19. Lower perceived susceptibility to COVID-19, belief that data on the efficacy of vaccines is ‘largely made up’, having lower confidence in government, and lower perception of COVID-19 as a public health threat, were also associated with reluctance to be vaccinated against COVID-19. The top three reasons for agreeing to vaccinate (November only) were to protect myself and others, moral responsibility, and having no reason not to get it. For those who were indifferent or disagreeing to vaccinate, safety concerns were the top reason, followed by indecision and lack of trust in the vaccine respectively.

CONCLUSIONS

These findings highlight some factors related to willingness to accept a COVID-19 vaccine prior to one being available in Australia. Now that the vaccine is being offered, this study identifies key issues that can inform public health messaging to address vaccine hesitancy.

HIGHLIGHTS

Perceived public health threat is associated with intentions to vaccinate

Those believing the efficacy of vaccines is made up were less willing to get vaccinated

To protect myself and others was the top reason for getting the vaccine

Safety concerns was the top reason against getting the vaccine
Longitudinal analysis shows durable and broad immune memory after SARS-CoV-2 infection with persisting antibody responses and memory B and T cells
Authors: Cohen Kristen W. , Linderman Susanne L. , Moodie Zoe , Czartoski Julie , Lai Lilin , Mantus Grace , Norwood Carson , Nyhoff Lindsay E. , Edara Venkata Viswanadh , Floyd Katharine , De Rosa Stephen C. , Ahmed Hasan , Whaley Rachael , Patel Shivan N. , Prigmore Brittany , Lemos Maria P. , Davis Carl W. , Furth Sarah , O’Keefe James , Gharpure Mohini P. , Gunisetty Sivaram , Stephens Kathy A. , Antia Rustom , Zarnitsyna Veronika I. , Stephens David S. , Edupuganti Srilatha , Rouphael Nadine , Anderson Evan J. , Mehta Aneesh K. , Wrammert Jens , Suthar Mehul S. , Ahmed Rafi , Juliana McElrath M.
Published: April 2021

Ending the COVID-19 pandemic will require long-lived immunity to SARS-CoV-2. Here, we evaluate 254 COVID-19 patients longitudinally up to eight months and find durable broad-based immune responses. SARS-CoV-2 spike binding and neutralizing antibodies exhibit a bi-phasic decay with an extended half-life of >200 days suggesting the generation of longer-lived plasma cells. SARS-CoV-2 infection also boosts antibody titers to SARS-CoV-1 and common betacoronaviruses. In addition, spike-specific IgG+ memory B cells persist, which bodes well for a rapid antibody response upon virus re-exposure or vaccination. Virus-specific CD4+ and CD8+ T cells are polyfunctional and maintained with an estimated half-life of 200 days. Interestingly, CD4+ T cell responses equally target several SARS-CoV-2 proteins, whereas the CD8+ T cell responses preferentially target the nucleoprotein, highlighting the potential importance of including the nucleoprotein in future vaccines. Taken together, these results suggest that broad and effective immunity may persist long-term in recovered COVID-19 patients.
Machine Learning and Prediction of All-Cause Mortality among Chinese Older Adults
Authors: Jin Xurui , Sun Yiyang , Zhu Tinglong , Leng Yu , Guan Shuyi , Zhang Kehan , Li Kangshuo , Niu Zhangming , Wu Chenkai , Zeng Yi , Yao Yao , Yan Lijing L.
Published: April 2021

Background and aim

Mortality risk stratification was vital for targeted intervention. This study aimed at building the prediction model of all-cause mortality among Chinese dwelling elderly with different methods including regression models and machine learning models and to compare the performance of machine learning models with regression model on predicting mortality. Additionally, this study also aimed at ranking the predictors of mortality within different models and comparing the predictive value of different groups of predictors using the model with best performance.

Method

We used data from the 2008 and 2011 waves of Chinese Longitudinal Healthy Longevity Survey (CLHLS). The follow-up of CLHLS was conducted every 2-3 years till 2018. The analysis sample included 2,448 participants. We used totally 117 predictors to build the prediction model for survival including 61 questionnaire, 41 biomarker and 15 genetics predictors. Four models were built (XG-Boost, random survival forest [RSF], Cox regression with all variables and Cox-backward). We used C-index and integrated Brier score to evaluate the performance of those models.

Results

The XG-Boost model and RSF model shows slightly better predictive performance than Cox models and Cox-backward models based on the C-index and integrated Brier score in predicting surviving. Age, activity of daily living and Mini-Mental State Examination score were identified as the top 3 predictors in the XG-Boost and RSF models. Biomarker and questionnaire predictors have a similar predictive value, while genetic predictors have no addictive predictive value when combined with questionnaire or biomarker predictors.

Conclusion

In this work, it is shown that machine learning techniques can be a useful tool for both prediction and its performance sightly outperformed the regression model in predicting survival.
A study of the clearness rate of fetal Sylvian fissure shown on different sections by prenatal ultrasound
Authors: Pingping Xu , Dirong Zhang , Yu Shi , Fengbei Kong , Chunxiao Yao , Ying She , Guoru Wu
Published: April 2021

Objective

To compare the clearness rate of fetal Sylvian fissure revealed by prenatal ultrasonography on trans-cerebellar section and trans-thalamic section, and to provide scientific basis for selecting the best section of prenatal ultrasound to evaluate the developmental parameters related to fetal Sylvian fissure.

Methods

This was a retrospective study. We analyzed all the fetal images on trans-cerebellar section and trans-thalamic section stored in the imaging system who were undergoing grade III prenatal ultrasound examination in our hospital from January 2017 to December 2018. The gestational age was divided into three groups which were 21 to 24 weeks, 25 to 28 weeks and 29 to 32 weeks respectively. The evaluation criteria for the clear appearance of the Sylvian fissure were complete morphology of the Sylvian fissure and clear apical and anteriorly edges of the Sylvian fissure. The results of showing Sylvian fissure clearly were divided into four groups: only on trans-cerebellar section shown clear, only on trans-thalamic section shown clear, both on trans-cerebellar section and trans-thalamic section shown clear, and both on trans-cerebellar section and trans-thalamic section not shown clear. The clearness rate of each group and the total clearness rate of each section were analyzed statistically.

Results

The clearness rates of showing Sylvian fissure only on trans-cerebellar section were 62.3% at 21 to 24 weeks, 70.1% at 25 to 28 weeks and 63.6% at 29 to 32 weeks. The clearness rates of showing Sylvian fissure only on trans-thalamic section were 11.1% at 21 ∼ 24 weeks, 10.5% at 25 ∼ 28 weeks and 9.1% at 29 ∼ 32 weeks. The clearness rates of showing Sylvian fissure both on trans-cerebellar and trans-thalamic sections were 22.1% at 21 to 24 weeks, 15.0% at 25 to 28 weeks and 13.0% at 29 to 32 weeks. The unclearness rates of showing Sylvian fissure both on trans-cerebellar and trans-thalamic sections were 4.5%at 21 ∼ 24 weeks, 4.4% at 25 ∼ 28 weeks and 14.3% at 29 ∼ 32 weeks. The clearness rate of showing Sylvian fissure on trans-cerebellar section was significantly higher than on trans-thalamic section (P < 0.05). The total clearness rate of showing Sylvian fissure on trans-cerebellar section and trans-thalamic section were 83.1% and 28.3% respectively.

Conclusion

In this study, it was suggested that prenatal ultrasound selection of trans-cerebellar section is better than trans-thalamic section in evaluating the developmental parameters related to the Sylvian fissure.
Informing patterns of health and social care utilisation in Irish older people according to the Clinical Frailty Scale
Authors: O’Halloran Aisling M. , Hartley Peter , Moloney David , McGarrigle Christine , Kenny Rose Anne , Romero-Ortuno Roman
Published: April 2021

There is increasing policy interest in the consideration of frailty measures (rather than chronological age alone) to inform a more equitable allocation of health and social care resources in the community. The Clinical Frailty Scale (CFS) has attracted interest for its simplicity and consideration of multiple relevant geriatric dimensions. However, a criticism of the CFS has been the possible subjectivity in the scoring, bringing the possible danger of lack of scoring consistency across agencies. For that reason, the authors of the CFS published a classification tree method to assist with routine scoring of the CFS.

The aim of the present study was to apply the CFS classification tree to data from adults aged 65 and over from The Irish Longitudinal Study on Ageing (TILDA) and correlate derived CFS categories with patterns of health and social care utilisation in Irish older people assessed in Wave 5 of the study (year 2018). In addition, we explored how CFS categories and states changed over 8 years in TILDA between Wave 1 (2010) and Wave 5.

Results showed the following prevalence of CFS categories in Wave 5: 6% ‘very fit’ (CFS1), 36% ‘fit’ (CFS2), 31% ‘managing well’ (CFS3), 16% ‘vulnerable’ (CFS4), 6% ‘mildly frail’ (CFS5), 4% ‘moderately frail’ (CFS6) and 1% ‘severely frail’ (CFS7). No participants were ‘very severely frail’ or ‘terminally ill’. In wave 5, increasing CFS categories had an association with increasing utilisation of hospital and community health services, and increasing hours of formal and informal social care provision. The transitions analyses from Wave 1 to 5 suggested a dynamic picture of CFS transitions, with 2-year probability of transitioning from ‘fit’ (CFS1-3) to ‘vulnerable’ (CFS4), and ‘fit’ to ‘frail’ (CFS5+) at 34% and 6%, respectively. ‘Vulnerable’ and ‘frail’ had a 22% and 17% probability of reversal to ‘fit’ and ‘vulnerable’, respectively.

Our results suggest that the CFS classification tree was able to stratify the TILDA population aged 65 and over into subgroups with increasing health and social care needs. The CFS classification tree could be used to aid the allocation of health and social care resources in older people in Ireland, but given the frequency of CFS transitions in the population, it is recommended that CFS status in individuals is reviewed at least every 2 years.
Impact of school-based malaria screening and treatment onP. falciparuminfection and anemia prevalence in two transmission settings in Malawi
Authors: Cohee Lauren M. , Peterson Ingrid , Coalson Jenna E. , Valim Clarissa , Chilombe Moses , Ngwira Andrew , Bauleni Andy , Schaffer-DeRoo Sarah , Seydel Karl B. , Wilson Mark L. , Taylor Terrie E. , Mathanga Don P. , Laufer Miriam K.
Published: April 2021

Background

In areas highly endemic for malaria,Plasmodium falciparum(Pf) infection prevalence peaks in school-age children, adversely affecting their health and education. School-based intermittent preventive treatment reduces this burden, however concerns about cost and widespread use of antimalarial drugs have limited enthusiasm for this approach. School-based screening-and-treatment is an attractive alternative. We conducted a school-based cohort study to evaluate the impact of screening-and-treatment on the prevalence ofPfinfection and anemia in two different transmission settings.

Methods

We screened 704 students in four Malawian primary schools forPfinfection using rapid diagnostic tests (RDTs). Those testing positive were treated with artemether-lumefantrine. Outcomes werePfinfections detected by microscopy or PCR and anemia after six weeks.

Results

Prevalence of infection by RDT at screening was 37% (range among schools 9-64%). We detected a significant reduction after six weeks in infections by microscopy (adjusted relative reduction (aRR) 47.1%, p<0.0001) and PCR (aRR 23.1%, p<0.0001), but no reduction in anemia. In low, seasonal prevalence areas, sub-patent infections at screening led to persistent infection, but not disease, during follow-up. In high transmission settings, new infections frequently occurred within six weeks after treatment.

Conclusions

School-based screening-and-treatment reducedPfinfection but not anemia. This approach could be enhanced in low transmission settings by using more sensitive screening tests and in high transmission settings by repeating the intervention or using longer acting drugs.

Malaria screening-and-treatment reducedP. falciparuminfections but not anemia. Because rapid diagnostic tests failed to detect low-density infections, screening tests with higher sensitivity may be needed in low transmission areas where low-density infections make-up a larger proportion of infections.
Estimating the false positive rate of highly automated SARS-CoV-2 nucleic acid amplification testing
Authors: Chandler Christopher M. , Bourassa Lori , Mathias Patrick C. , Greninger Alexander L.
Published: April 2021

Molecular testing for infectious diseases is generally both very sensitive and specific. Well-designed PCR primers rarely cross-react with other analytes, and specificities seen during test validation are often 100%. However, analytical specificities measured during validation may not reflect real-world performance across the entire testing process. Here, we use the unique environment of SARS-CoV-2 screening among otherwise well individuals to examine the false positivity rate of high throughput so-called “sample-to-answer” nucleic acid amplification testing (NAAT) on three commercial assays: the Hologic Panther Fusion®, Hologic Aptima® transcription mediated amplification (TMA), and Roche cobas® 6800. We used repetitive sampling of the same person as the gold standard to determine test specificity rather than retesting of the same sample. We examined 451 people repetitively sampled over 7 months via nasal swab, comprising 7,242 results. During the study period there were twelve positive tests (0.17%) from 9 people. Eight positive tests (0.11%, five individuals) were considered bona fide true positives based on repeat positives or outside testing and epidemiological data. One positive test had no follow-up testing or metadata and could not be adjudicated. Three positive tests (three individuals) did not repeat as positive on a subsequent collection, nor did the original positive specimen test positive on an orthogonal platform. We consider these three tests false positives and estimate the overall false positive rate of high-throughput automated, sample-to-answer NAAT testing to be approximately 0.041% (3/7242). These data help laboratorians, epidemiologists, and regulators understand specificity and positive predictive value associated with high-throughput NAAT testing.
T-cell responses to acute cardiorespiratory or resistance exercise in cohorts of physically active or physically inactive older adults: A randomized complete crossover
Authors: Graff Rachel M. , Jennings Kristofer , LaVoy Emily C. , Warren Victoria E. , Macdonald Brad W. , Park Yoonjung , Markofski Melissa M.
Published: April 2021

Aging is associated with many chronic diseases that are maintained and perpetuated by immune dysregulation and chronic systemic inflammation. T-cells often undergo age-related changes, including an accumulation of memory cells, which places individuals at increased risk for novel infections and may predispose them to increased inflammation. Regular exercise training has been suggested to offset age-related changes in T-cells, but the majority of literature is derived from cardiorespiratory exercise (CRE) studies. Much less is understood about the T-cell response to resistance exercise (RE). The purpose of this study was to examine the effects of acute CRE and acute RE on the T-cell response among a cohort of physically active older adults (PA) compared to a cohort of physically inactive older adults (PI).

METHODS

Twenty-four healthy older adults (PA n=12; PI n=12; mean ± SD; age (yrs) PA 62 ± 5, PI 64 ± 5; height (cm) PA 170.9 ± 6.9, PI 162.9 ± 8.0; weight (kg) PA 69.3 ± 10.2, PI 68.2 ± 12.8; BMI (kg/m2) PA 23.9 ± 3.0, PI 25.6 ± 3.5) completed one bout of CRE and one bout of RE in a randomized order, both at a moderate intensity, and separated by at least 7 days. Blood samples drawn pre-exercise, post-exercise, and 1h post-exercise (recovery) were analyzed for CD4+ and CD8+ T-cells and their differentiation status using surface markers CD45RA, CD62L, and CD57, as well as for Th17 cells (CD4+ CD161+ CD196+) using flow cytometry.

RESULTS

PI had higher numbers of circulating CD57+ EMRA CD4+ T-cells (PA, mean ± SE, 1 ± 2 cells/uL; PI, 6 ± 2 cells/uL; p=0.01; z=2.32) than PA at pre-exercise. Both CRE and RE elicited a significant mobilization of highly-differentiated (CD45RA+ CD62L-; CD57+ CD45RA+ CD62L-) CD8+ T-cells into the circulation post-exercise in both PA and PI groups. Furthermore, CRE resulted in a decrease in the number of circulating Th17 cells post-exercise, while RE increased Th17 cell mobilization compared to the CRE response.

CONCLUSION

Taken together, T-cells in PA and PI respond similarly to acute CRE and support previously reported data showing a significant mobilization of highly differentiated T-cells. The present study confirms that moderate intensity RE also elicits this response, but highlights potential differences between CRE and RE on the immune responses of T-cells, particularly in PI individuals.

Clinical trial registration

This research study was registered at clinicaltrials.gov NCT03794050
Developing RT-LAMP Assays for Detection of SARS-CoV-2 in Saliva
Authors: Huang Xin , Tang Gongyu , Ismail Nahed , Wang Xiaowei
Published: April 2021

The coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has killed millions of people worldwide. The current crisis has created an unprecedented demand for rapid test of SARS-CoV-2 infection. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a fast and convenient method to amplify and identify the transcripts of a targeted pathogen. However, the sensitivity and specificity of RT-LAMP were generally regarded as inferior when compared with the gold standard RT-qPCR. To address this issue, we combined bioinformatic and experimental analyses to improve the assay performance for COVID-19 diagnosis. First, we developed an improved algorithm to design LAMP primers targeting the nucleocapsid (N), membrane (M), and spike (S) genes of SARS-CoV-2. Next, we rigorously validated these new assays for their efficacy and specificity. Further, we demonstrated that multiplexed RT-LAMP assays could directly detect as low as a few copies of SARS-CoV-2 RNA in saliva, without the need of RNA isolation. Importantly, further testing using saliva samples from COVID-19 patients indicated that the new RT-LAMP assays were in total agreement in sensitivity and specificity with standard RT-qPCR. In summary, our new LAMP primer design algorithm along with the validated assays provide a fast and reliable method for the diagnosis of COVID-19 cases.
Risk factors for long covid in previously hospitalised children using the ISARIC Global follow-up protocol: A prospective cohort study
Authors: Osmanov Ismail M , Spiridonova Ekaterina , Bobkova Polina , Gamirova Aysylu , Shikhaleva Anastasia , Andreeva Margarita , Blyuss Oleg , El-Taravi Yasmin , DunnGalvin Audrey , Comberiati Pasquale , Peroni Diego G , Apfelbacher Christian , Genuneit Jon , Mazankova Lyudmila , Miroshina Alexandra , Chistyakova Evgeniya , Samitova Elmira , Borzakova Svetlana , Bondarenko Elena , Korsunskiy Anatoliy A , Konova Irina , Hanson Sarah Wulf , Carson Gail , Sigfrid Louise , Scott Janet T , Greenhawt Matthew , Whittaker Elizabeth A , Garralda Elena , Swann Olivia , Buonsenso Danilo , Nicholls Dasha E , Simpson Frances , Jones Christina , Semple Malcolm G , Warner John O , Vos Theo , Olliaro Piero , Munblit Daniel ,   Sechenov StopCOVID Research Team
Published: April 2021

Background The long-term sequelae of coronavirus disease 2019 (Covid-19) in children remain poorly characterised. This study aimed to assess long-term outcomes in children previously hospitalised with Covid-19 and associated risk factors.

Methods This is a prospective cohort study of children (18 years old and younger) admitted with confirmed Covid-19 to Z.A. Bashlyaeva Children's Municipal Clinical Hospital in Moscow, Russia. Children admitted to the hospital during the first wave of the pandemic, between April 2, 2020 and August 26, 2020, were included. Telephone interview using the International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) Covid-19 Health and Wellbeing paediatric follow up survey. Persistent symptoms (>5 months) were further categorised by system(s) involved.

Findings Overall, 518 of 853 (61%) of eligible children were available for the follow-up assessment and included in the study. Median age was 10.4 years (IQR, 3-15.2) and 270 (52.1%) were girls; median follow-up since hospital discharge was 256 (223-271) days. At the time of the follow-up interview 126 (24.3%) participants reported persistent symptoms among which fatigue (53, 10.7%), sleep disturbance (36, 6.9%,) and sensory problems (29, 5.6%) were the most common. Multiple symptoms were experienced by 44 (8.4%) participants. Risk factors for persistent symptoms were: age "6-11 years" (odds ratio 2.74 (95% confidence interval 1.37 to 5.75) and "12-18 years" (2.68, 1.41 to 5.4), and a history of allergic diseases (1.67, 1.04 to 2.67).

Interpretation A quarter of children experienced persistent symptoms months after hospitalization with acute covid-19 infection, with almost one in ten experiencing multi-system involvement. Older age and allergic diseases were associated with higher risk of persistent symptoms at follow-up. Our findings highlight the need for replication and further investigation of potential mechanisms as well as clinical support to improve long term outcomes in children.

Funding None.
The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models
Authors: Rozowsky Joel , Drenkow Jorg , Yang Yucheng T , Gursoy Gamze , Galeev Timur , Borsari Beatrice , Epstein Charles B , Xiong Kun , Xu Jinrui , Gao Jiahao , Yu Keyang , Berthel Ana , Chen Zhanlin , Navarro Fabio , Liu Jason , Sun Maxwell S , Wright James , Chang Justin , Cameron Christopher JF , Shoresh Noam , Gaskell Elizabeth , Adrian Jessika , Aganezov Sergey , Aguet François , Balderrama-Gutierrez Gabriela , Banskota Samridhi , Corona Guillermo Barreto , Chee Sora , Chhetri Surya B , Cortez Martins Gabriel Conte , Danyko Cassidy , Davis Carrie A , Farid Daniel , Farrell Nina P , Gabdank Idan , Gofin Yoel , Gorkin David U , Gu Mengting , Hecht Vivian , Hitz Benjamin C , Issner Robbyn , Kirsche Melanie , Kong Xiangmeng , Lam Bonita R , Li Shantao , Li Bian , Li Tianxiao , Li Xiqi , Lin Khine Zin , Luo Ruibang , Mackiewicz Mark , Moore Jill E , Mudge Jonathan , Nelson Nicholas , Nusbaum Chad , Popov Ioann , Pratt Henry E , Qiu Yunjiang , Ramakrishnan Srividya , Raymond Joe , Salichos Leonidas , Scavelli Alexandra , Schreiber Jacob M , Sedlazeck Fritz J , See Lei Hoon , Sherman Rachel M , Shi Xu , Shi Minyi , Sloan Cricket Alicia , Strattan J Seth , Tan Zhen , Tanaka Forrest Y , Vlasova Anna , Wang Jun , Werner Jonathan , Williams Brian , Xu Min , Yan Chengfei , Yu Lu , Zaleski Christopher , Zhang Jing , Ardlie Kristin , Cherry J Michael , Mendenhall Eric M , Noble William S , Weng Zhiping , Levine Morgan E , Dobin Alexander , Wold Barbara , Mortazavi Ali , Ren Bing , Gillis Jesse , Myers Richard M , Snyder Michael P , Choudhary Jyoti , Milosavljevic Aleksandar , Schatz Michael C , Guigó Roderic , Bernstein Bradley E , Gingeras Thomas R , Gerstein Mark
Published: April 2021

Understanding how genetic variants impact molecular phenotypes is a key goal of functional genomics, currently hindered by reliance on a single haploid reference genome. Here, we present the EN-TEx resource of personal epigenomes, for ∼25 tissues and >10 assays in four donors (>1500 open-access functional genomic and proteomic datasets, in total). Each dataset is mapped to a matched, diploid personal genome, which has long-read phasing and structural variants. The mappings enable us to identify >1 million loci with allele-specific behavior. These loci exhibit coordinated epigenetic activity along haplotypes and less conservation than matched, non-allele-specific loci, in a fashion broadly paralleling tissue-specificity. Surprisingly, they can be accurately modelled just based on local nucleotide-sequence context. Combining EN-TEx with existing genome annotations reveals strong associations between allele-specific and GWAS loci and enables models for transferring known eQTLs to difficult-to-profile tissues. Overall, EN-TEx provides rich data and generalizable models for more accurate personal functional genomics.
Eye movements reveal spatiotemporal dynamics of visually-informed planning in navigation
Authors: Zhu Seren L. , Lakshminarasimhan Kaushik J. , Arfaei Nastaran , Angelaki Dora E.
Published: April 2021

Goal-oriented navigation is widely understood to depend upon internal maps. Although this may be the case in many settings, humans tend to rely on vision in complex, unfamiliar environments. To study the nature of gaze during visually-guided navigation, we tasked humans to navigate to transiently visible goals in virtual mazes of varying levels of difficulty, observing that they took near-optimal trajectories in all arenas. By analyzing participants’ eye movements, we gained insights into how they performed visually-informed planning. The spatial distribution of gaze revealed that environmental complexity mediated a striking trade-off in the extent to which attention was directed towards two complimentary aspects of the world model: the reward location and task-relevant transitions. The temporal evolution of gaze revealed rapid, sequential prospection of the future path, evocative of neural replay. These findings suggest that the spatiotemporal characteristics of gaze during navigation are significantly shaped by the unique cognitive computations underlying real-world, sequential decision making.
Trypanosoma bruceiTim50 Plays a Critical Role in Cell Cycle Regulation and Parasite Infectivity
Authors: Tripathi Anuj , Singha Ujjal K , Cooley Ayorinde , Gillyard Taneisha , Krystofiak Evan , Pratap Siddharth , Davis Jamaine , Chaudhuri Minu
Published: April 2021

Tim50 is a receptor subunit of the preprotein-translocase of the mitochondrial inner membrane, TIM23.Trypanosoma brucei, the infective agent for African trypanosomiasis, possesses a homologue of Tim50 (TbTim50) with a pair of characteristic DXDX(T/V) phosphatase signature motifs. Here, we demonstrated that besides its protein phosphatase activity, the recombinant TbTim50 binds and hydrolyzes phosphatidic acid in a concentration-dependent manner.In silicostructural homology models identify the putative binding interfaces that may accommodate different phospho-substrates. Interestingly, TbTim50 depletion in the bloodstream form (BF) ofT. bruceireduced cardiolipin (CL) levels and decreased mitochondrial membrane potential (ΔΨ). TbTim50 knockdown (KD) also reduced the population of G2 phase and increased G1 phase; thus, BF cell growth was reduced. Confocal and electron microscopy revealed a defect in regulation of kinetoplast (kDNA) replication due to TbTim50 KD. Depletion of TbTim50 increased the levels of AMPK phosphorylation, and parasite morphology was changed to stumpy-like with upregulation of few stumpy marker gene expressions. Importantly, we observed that TbTim50-depleted parasites were unable to establish infection in mice and rats. Proteomics analysis showed reductions of the translation factors, flagellar transport proteins, and many proteasomal subunits, including the mitochondrial HslVU that is known to play a role in kDNA replication. Reduction of the level of HslV in TbTim50 KD cells was further validated by immunoblot analysis. Altogether, our results showed that TbTim50 is essential for mitochondrial function, regulation of kDNA replication, and cell cycle in the BF. Therefore, TbTim50 is an important target for structure-based drug design to combat African trypanosomiasis.

Importance

African trypanosomiasis, a neglected tropical disease caused by parasitic protozoanTrypanosoma brucei, is transmitted by the tsetse fly prevalent in sub-Saharan Africa. During its digenetic life cycle,T. bruceiundergoes multiple developmental changes to adapt in different environments.T. bruceiBF, dwelling in mammalian blood, generates ATP from glycolysis and hydrolyzes ATP in mitochondria for inner membrane potential. We found that TbTim50, a HAD-family phosphatase, is critical forT. bruceiBF survivalin vitroandin vivo. Depletion of TbTim50 in BF reduced CL levels and mitochondrial ΔΨ and caused a detrimental effect on many cellular functions. Cells accumulated in G1-S phase, and kinetoplast was over-replicated due to depletion of mitochondrial proteasomes, HslVU, a master-regulator of kDNA replication. Cell growth inhibition was accompanied by changes in morphology, AMPK phosphorylation, and upregulation of stumpy-specific gene expression. TbTim50 is essential forT. bruceisurvival and an importantT. bruceitherapeutic target.
Relative Mutant N501Y SARS-CoV-2 Spike Protein RBD Inhibition of Anti-Spike Protein IgG and ACE-2 Binding to Spike Protein Species
Authors: Klegerman Melvin E. , Cirillo Jeffrey D. , McPherson David D.
Published: April 2021

In the SARS-CoV-2 coronavirus pandemic of 2019 (COVID-19), it has become evident that the ACE-2 receptor-binding domain (RBD) of the viral spike protein (SP) is the target of neutralizing antibodies that comprise a critical element of protective immunity to the virus. The most definitive confirmation of this contention is that the two mRNA COVID-19 vaccines in general use, which elicit antibodies specific for the RBD, exhibit approximately 95% protective efficacy against COVID-19. A potential challenge to vaccine efficacy is the emergence of SARS-CoV-2 variants possessing multiple mutations affecting amino acid residues in the RBD. Of concern are variants that arose in the United Kingdom, Brazil and South Africa. One of the variants, designated B.1.351, has shown a higher transmissibility due to greater affinity for the ACE-2 receptor and decreased neutralization by convalescent plasma, therapeutic monoclonal antibodies, and post-vaccination plasma. Common to several of the variants is the N501Y mutation in the RBD, which may be responsible for at least part of the observed variant properties. To test this hypothesis, we measured the ability of the Y501 RBD to inhibit binding of the wild type RBD and full SP (S1 + S2) to the ACE-2 protein and a human monoclonal IgG antibody elicited to the wild type RBD, relative to the wild type RBD in two enzyme-linked immunosorbent assays (ELISAs). We found no significant difference in the IC50of the two RBD species’ inhibition of ACE-2 binding, but unexpectedly found that the IC50of the wild type RBD inhibition of antibody binding was nearly twice that of the Y501 RBD, reflecting a lower affinity. These results suggest that the individual N501Y mutation does not contribute to altered viral properties by itself, but may contribute to a collective conformational shift produced by multiple mutations.
Understanding double descent through the lens of principal component regression
Authors: Lind Christine H. , Yu Angela J.
Published: April 2021

A number of recent papers have studied the double-descent phenomenon: as the number of parameters in a supervised learning model increasingly exceeds that of data points (“second-descent”), the empirical risk curve has been observed to not overfit, instead decreasing monotonically, sometimes to a level even better than the best “first-descent” model (using a subset of features not exceeding the number of data points). Understanding exactly when this happens and why it happens is an important theoretical problem. Focusing on the over-parameterized linear regression setting, a commonly chosen case study in the double-descent literature, we present two theoretical results: 1) final second-descent (regression using all of the predictor variables) and principal component (PC) regression without dimensionality reduction are equivalent; 2) the PCR risk curve can be expected to lower bound not only all linearly transformed first-descent models, but also all linearly transformed second-descent models (including the elimination of features as a special case); 3) if the smallest singular value of the design matrix is “large enough” (we will define mathematically), final second-descent can be expected to outperform any first-descent or second-descent model. These insights have important ramifications for a type of semi-supervised learning problem, a scenario which can explain why a face representation trained on unlabeled faces from one race would be better for later supervised-learning tasks on the same race of faces than for faces from another race – this can both provide a scientific explanation for the other-race effect seen in humans and give hints for how to mitigate similar issues in the domain of ethical AI.
A novel fragmented mitochondrial genome in the protist pathogen Toxoplasma gondii and related tissue coccidia
Authors: Namasivayam Sivaranjani , Baptista Rodrigo P. , Xiao Wenyuan , Hall Erica M. , Doggett Joseph S. , Troell Karin , Kissinger Jessica C.
Published: April 2021

Mitochondrial genome content and structure vary widely across the eukaryotic tree of life, with protists displaying extreme examples. Apicomplexan and dinoflagellate protists have evolved highly reduced mitochondrial genome sequences, mtDNA, consisting of only three cytochrome genes and fragmented rRNA genes. Here, we report the independent evolution of fragmented cytochrome genes in Toxoplasma and related tissue coccidia and evolution of a novel genome architecture consisting minimally of 21 sequence blocks (SBs) totaling 5.9 kb that exist as nonrandom concatemers. Single-molecule Nanopore reads consisting entirely of SBs ranging from 0.1 to 23.6 kb reveal both whole and fragmented cytochrome genes. Full-length cytochrome transcripts including a divergent coxIII are detected. The topology of the mitochondrial genome remains an enigma. Analysis of a cob point mutation reveals that homoplasmy of SBs is maintained. Tissue coccidia are important pathogens of man and animals, and the mitochondrion represents an important therapeutic target. The mtDNA sequence has been elucidated, but a definitive genome architecture remains elusive.
Socio-demographic influences on various consumer food safety indices: an empirical study of ethnic Goan pork sausage consumers
Authors: Rajkumar Solomon , Nayar Renuka , Rajagopal Kavitha , Chakurkar Eaknath B. , Venkatesh Vismitha Shree , Nambiar Prejit , Paramesh Venkatesh
Published: April 2021

Purpose

The purpose of this paper is to assess food safety knowledge, choice behavior and health hazard concerns of ethnic Goan pork sausage consumers through various consumer food safety indices and also to evaluate socio-demographic influences on various consumer food safety indices.

Design/methodology/approach

Primary data in the form of 210 questionnaire responses were collected from Goan pork sausage consumers. Based on the responses, seven various consumer food safety indices were derived. The cumulative score of all the indices were normalized (0–1). The association between socio-demographic variables and consumer indices were evaluated using linear regression analysis, Pearson's correlation matrix, principal component analysis (PCA) and correspondence analysis (CA).

Findings

The results of the analysis indicate that the consumption of Goan pork sausages is most prevalent amongst younger people with high education having higher income. A majority of consumers have high score for the four consumer indices. The results of correlation analysis, regression analysis, PCA and CA revealed a significant association of consumer indices with socio-demographic variables.

Originality/value

The results of this study will provide a way forward for the evaluation of existing overall food safety concerns in the target population and in the future would be used for the promotion of good handling practices and health of Goan pork sausage consumers.
Developing a framework for sacred grove management using stakeholder analysis: evidence from sacred groves in Gujarat, India
Authors: Pandey Amit , Sardana Kavita , Gupta Sandeep Kumar
Published: April 2021

Purpose

The purpose of this study is to use the framework of stakeholder analysis in a participatory democracy, used in forest management planning, for arriving at the best management option for selected sacred groves of Kachchh. This is achieved by accounting for economic, cultural and ecological values and the resulting outcomes in the complex institutional mechanism. Additionally, this study provides a framework for complex decision-making that characterizes the management of sacred groves involving multiple criteria and options accounting for multiple stakeholders that involve conflicting interests.

Design/methodology/approach

The analytical hierarchy process was used to calculate the global priorities of management options using the relative importance of stakeholders, weights of different decision criteria to arrive at the best management practice for selected groves of Kachchh. The global priorities of management options rank management practices based on stakeholders' values and their effects on the choice of management strategy as well as on the potential to attain a compromise between competing interests. For this purpose, survey responses of 141 individuals belonging to seven different stakeholder categories were analyzed. Along with focus group discussions, and personal interviews, a stratified random sampling technique was used to survey respondents.

Findings

Based on the global priority weights of the alternatives, it is determined that the restoration management option (guggal is restored by planting new guggal sapplings, cattle grazing is prohibited and high levels of ecosystem goods and services are provided) had the highest score, followed by the preservation management option (grazing is allowed on the periphery, juvenile guggal is preserved and moderate ecosystem goods and services are provided). Therefore, restoration of sacred groves is the best management practice of sacred groves in West Kachchh, offering a compromise between maximizing provision of ecosystem services and economic benefits in terms of allowing cattle grazing.

Originality/value

Though there are several studies on best management practices for community-owned forests, irrigation systems, and pasture lands, and the role of local institutions in sustaining these common-pool resources; such studies for sacred groves are absent, despite sacred groves being one of the longest surviving common-pool resources that has sustained it over several decades. This is the first study that uses the framework of stakeholder analysis to arrive at the best management practice for sacred groves. The uniqueness of the study lies in a comprehensive evaluation of ecological–economic–cultural interests of multiple stakeholders toward management of sacred groves.
Working with emotions: cultural employee perspectives to service management expectations
Authors: Babatunde Akanji , Mordi Chima , Ajonbadi Hakeem Adeniyi , Oruh Emeka Smart
Published: April 2021

Purpose

Drawing on the emotional labour theory, the purpose of this paper is to explore the effects of cultural orientation on emotion regulation and display processes for service employees.

Design/methodology/approach

Based on a Nigerian study where literature is scarce, data were gathered from semi-structured interviews conducted with 40 call centre service agents.

Findings

The findings identified three key values around reinforcing social cohesion, anticipated self-curtailment, hierarchy and expressions of servility based on broader societal needs to promote relational harmony when managing customer relations during inbound calls into the call centre.

Research limitations/implications

The extent to which the findings can be generalised is constrained by the limited and selected sample size. However, the study makes contributions to the service work theory by identifying the extent to which communication of emotions is informed in large parts by local culture and seeks to incite scholarly awareness on the differences of emotional display rules from a developing country other than western contexts.

Originality/value

This paper is among the first to focus on the interface between culture and emotional labour from a Sub-Saharan African context.
Face mask effects during COVID-19: perspectives of managers, practitioners and customers in the hotel industry
Authors: Kong Anthony , Oh Jae-Eun , Lam Terry
Published: April 2021

Purpose

The novel coronavirus (COVID-19) has completely changed the landscape of the hospitality industry. The World Health Organization does not officially recommend wearing face masks in the workplace. Wearing face masks is controversial worldwide, however it has been widely adopted in Hong Kong society. Hospitality practitioners have worn face masks to work and serve customers for almost a year long, matching the duration of the COVID-19 pandemic. This paper proposes a conceptual model of face mask effects and also discusses and evaluates the effects of wearing face masks during the pandemic.

Design/methodology/approach

A convenience sampling method is employed to investigate hospitality operators using in-depth and focus group interviews with managers, front-line staff and customers.

Findings

The perspectives of both hospitality practitioners and customers are included in this study. The concepts of (1) invisible care, (2) sense of safety and (3) service trust have been introduced in this study. These provide valuable insights for the service industry when facing a large-scale health crisis, now and in the future.

Research limitations/implications

This paper analyzes interview data collected from 35 respondents – 14 managers, 6 practitioners and 15 customers – in order to understand the critical effects of wearing face masks during the pandemic and the perspectives of both hospitality practitioners and customers.

Practical implications

For the hospitality industry, wearing face mask in service has already become a “new normal”, face mask effects might create an impact on service design, service delivery and service quality.

Originality/value

The findings show that wearing face masks turns hygiene and safety into a form of invisible care in the Asian hospitality industry. Practitioners' perspective regarding the necessity of a smile is less important to Asian customers, showing a discrepancy between the two parties. Customers do not believe that service quality has dropped due to the wearing of masks, but that the level of hygiene has risen. Unlike customers, practitioners are more concerned about not providing good quality service. However, the interview data show that respondents generally agree that mask wearing is a gesture and symbol for the hospitality industry to make tangible a new form of caring, professionalism, safety concern and communication.
Analysis of progeny–parents family travel process from perspective filial piety: driving factors, intergenerational interaction and tourism evaluation
Authors: Fu Guoqun , Zhang Chenghu , Hu Jia'jing
Published: April 2021

Purpose

This paper attempts to explore why adult progeny initiate progeny–parents family travel, how two generations interact and deal with intergenerational conflicts during travel and how they evaluate their travel experiences from the perspective of filial piety.

Design/methodology/approach

Based on in-depth interviews with both parents and their adult progeny, it is found that “repayment” or “compensation” of filial piety is the most important driving force to family travel with parents, and in many cases an adult child exhibits “overspending” by showing filial obedience. On the other hand, parents occasionally utilize filial piety as cultural resources to fulfill their personal goals and to evaluate their interactions with adult children. Finally, the authors offer an exploratory explanation to why filial generation has a relatively low evaluation while parent generation has a higher evaluation of family trip.

Findings

The authors suggest that future study in this particular area should attach much more importance to the “filial piety tool boxes” paradigm, which is in parallel with the paradigm of “concept (values) affecting behavior”.

Originality/value

The contribution of this study is to investigate the family travel process of “taking the elderly people to travel” from the perspective of interaction and filial piety.
Vulnerability toward the development of diabetes mellitus type 2 among adults from a rural community of West Bengal, India
Authors: Gupta Shibaji , Chakraborty Arup
Published: April 2021

Purpose

India has over half a million diabetics, with many others at risk. The Indian Diabetes Risk Score (IDRS) is a simple and validated tool used for mass screening of diabetes mellitus type 2 at the community level. This study assessed the vulnerability of developing diabetes in adults of a rural community of West Bengal using the IDRS and finds out the relationship of the risk of developing diabetes with socioclinical variables.

Design/methodology/approach

Multi-stage sampling was employed to select one eligible nondiabetic adult from selected families residing in the rural field practice area of a medical college in West Bengal. They were interviewed with a predesigned and pretested data collection schedule and examined.

Findings

Among 197 participants, 83.8% were female, 51.8% were illiterate and 57.4% came from Class IV of Prasad's socioeconomic scale. Of participants, 22.8% had existing known morbidities, and 23.9% had some form of substance addiction. In total, 46.8% of the participants on whom the IDRS could be applied (n = 175) were at high risk of developing diabetes (Score = 60). Gender and existing comorbidities significantly predicted a high risk of diabetes.

Originality/value

A large proportion of the Indian population yet to be diagnosed with diabetes are at a high risk of having the disease. Early detection of the disease can help curtail its complications and reduce its clinical, social and economic burden. Mass screening tools like the IDRS thus become a very important tool in India's attempts to fight diabetes.