bluuebunny/crossref_metadata_2025 huggingface dataset:
Demonstrate, observe, assist perform (DOAP) versus structured educational video (SEV) in imparting standard skill in male urinary bladder catheterisation
Authors: Balakrishnan Santosh , Paul Lijo , Rajan Minu N , Arthungal Sherin A
Published: March 2021

Introduction

Conventional teaching and learning methods have been seen to fail to assure achievement of competencies in male bladder catherization in the Indian Medical Graduate (IMG) with wide variation noted in competencies. This could be remedied by introduction of Structured training methods.

Aims and Objective

The study aimed to investigate DOAP method of training in a Skill Lab against training through a Structured Educational Video (SEV) with the objective of comparing their efficacy in training Final MBBS Students in the psychomotor skill of performing male bladder catheterisation.

Material & Methods

Final MBBS students fulfilling selection criteria were randomly allocated into two comparable groups. One group underwent Skill lab training using DOAP method while the other group underwent training using a SEV by the same instructor. CRRI interns, regularly performing MBC at work by virtue of conventional training, with 6-8 months experience formed a control group. All participants underwent assessment of skill in MBC by skill lab OSCE evaluation, by assessors who were blinded to the participant’s method of training. Data was recorded and analysed using standard statistical software. Trial evaluation from the trial groups was obtained using Survey monkey tool.

Observation

There was no statistically significant difference in the ability of DOAP group or SEV group in being able to safely perform MBC though a higher level of confidence was expressed with their training by DOAP group. Both trial groups statistically outperformed the control group.

Conclusion

Structured training assures competence. Video-assisted Training produces comparable results though DOAP method is preferred by students. A combination of the techniques may facilitate optimal training.
Impact of previous COVID-19 on immune response after a single dose of BNT162b2 SARS-CoV-2 vaccine
Authors: Velasco María , Galán Ma Isabel , Casas Ma Luisa , Pérez-Fernández Elia , Martínez-Ponce Diana , González-Piñeiro Beatriz , Castilla Virgilio , Guijarro Carlos ,   Working Group Alcorcón COVID-19
Published: March 2021

Immune response after a single-dose of BNT162b2 vaccine is markedly increased in subjects with previous SARS-CoV-2 infection, reaching similar IgG titers to those elicited by the full two-doses in naïve cases, and increased modestly after the second dose. These data may inform the priority of the boosting dose.
Agreement between commercially available ELISA and in-house Luminex SARS-CoV-2 antibody immunoassays
Authors: Santano Rebeca , Barrios Diana , Crispi Fàtima , Crovetto Francesca , Vidal Marta , Chi Jordi , Izquierdo Luis , Gratacós Eduard , Moncunill Gemma , Dobaño Carlota
Published: March 2021

Abstract

Serological diagnostic of the severe respiratory distress syndrome coronavirus 2 (SARS-CoV-2) is a valuable tool for the determination of immunity and surveillance of exposure to the virus. In the context of an ongoing pandemic, it is essential to externally validate widely used tests to assure correct diagnostics and epidemiological estimations. We evaluated the performance of the COVID-19 ELISA IgG and IgM/A (Vircell, S.L.) against a highly specific and sensitive in-house Luminex immunoassay in a set of samples from pregnant women and cord blood. The agreement between both assays was moderate to high for IgG but low for IgM/A. Considering seropositivity by either IgG and/or IgM/A, the technical performance of the ELISA was highly imbalanced, with 96% sensitivity at the expense of 22% specificity. As for the clinical performance, the negative predictive value reached 87% while the positive predictive value was 51%. Our results stress the need for highly specific and sensitive assays and external validation of diagnostic tests with different sets of samples to avoid the clinical, epidemiological and personal disturbances derived from serological misdiagnosis.
Rapid Screening for SARS-CoV-2 Variants of Concern in Clinical and Environmental Samples Using Nested RT-PCR Assays Targeting Key Mutations of the Spike Protein
Authors: La Rosa G. , Mancini P. , Bonanno Ferraro G. , Veneri C. , Iaconelli M. , Lucentini L. , Bonadonna L. , Brusaferro S. , Brandtner D. , Fasanella A. , Pace L. , Parisi A. , Galante D. , Suffredini E.
Published: March 2021

New SARS-CoV-2 mutations are constantly emerging, raising concerns of increased transmissibility, virulence or escape from host immune response.

We describe a nested RT-PCR assay (∼1500 bps) to detect multiple key spike protein mutations distinctive of the major known circulating SARS-CoV-2 variants, including the three Variants of Concern (VOCs) 20I/501Y.V1 (United Kingdom), 20H/501Y.V2 (South Africa), and 20J/501Y.V3 (Brazil), as well as the 20E.EU1 variant (Spain), the CAL.20C recently identified in California, and the mink-associated variant (GR, lineage B.1.1.298). Prior to application to field samples, the discriminatory potential of this PCR assay was explored using GISAID and Nextclade. To extend variant detection to challenging matrices such as sewage, where the amplification of long fragments is problematic, two short nested RT-PCR assays (∼300 bps) were also designed, targeting portions of the region spanned by the long nested assay.

The three newly-designed assays were then tested on field samples, including 7 fully-sequenced viral isolates from swab samples and 34 urban wastewater samples, some of which collected in areas where circulation of VOCs had been reported.

The long assay successfully amplified all the previously characterized viral isolates, allowing the correct identification of variants 20I/501Y.V1 and 20E.EU1 present in the panel. The sequences obtained using the short assays were consistent with those obtained with the long assay. Mutations characteristic of VOCs (UK and Brazilian variant) and of other variant (Spanish) were detected in sewage samples. To our knowledge, this is the first evidence of the presence of sequences harboring key mutations of 20I/501Y.V1 and 20J/501Y.V3 in urban wastewaters, highlighting the potential contribution of wastewater surveillance to explore SARS-CoV-2 diversity.

The developed nested RT-PCR assays can be used as an initial rapid screening test to select clinical samples containing mutations of interest. This can speed up diagnosis and optimize resources since it allows full genome sequencing to be done only on clinically relevant specimens. The assays can be also employed for a rapid and cost-effective detection of VOCs or other variants in sewage for the purposes of wastewater-based epidemiology. The approach proposed here can be used to better understand SARS-CoV-2 variant diversity, geographic distribution and impact worldwide.
Prediction of COVID-19 mortality among hospitalized patients in Sudan
Authors: Abd El-Raheem Ghada Omer Hamad , Awad Yousif Maysoun Ahmed , Ibrahim Mohamed Doaa Salih
Published: March 2021

Background

COVID-19 was primarily reported in China. The mortality rate across countries had ranged from 1% up to more than 10% and it is underestimated in some countries. Advanced age is the most frequently reported factor associated to mortality. Other factors were the presence of comorbidities such as diabetes mellitus, hypertension and obesity. Several models for mortality prediction had been developed to assist in improving the prognosis. The aim of our study was to assess the factors related to mortality among COVID-19 patients and develop a prediction model based on these factors.

Methods

A retrospective cohort study assessed the factors related to the mortality among COVID-19 patients who attended Imperial Hospital isolation centre on November-December, 2020, Khartoum, Sudan. Statistical tests performed were chi-square test, odds ratio and regression to develop the prediction model. Tests were considered statistically significant whenp< 0.05.

Results

105 patients were studied. 29% of the patients were deceased, while, 71% were discharged alive. A statistically significant association was found between the age and severity with regards to mortality rate (p=0.034, 0.018 respectively). The model equation for mortality prediction: Mortality = −14.724+ (1.387* Age) + (−0.323* Gender) + (1.814* Admission) + (0.193* Ischemic Heart Disease) + (−0.369* Fever) + (1.595* Cough) + (1.953* Complications) + (0.149* Duration of hospitalization) + (0.999* Enoxaparin dose).

Conclusions

Age, admission ward, cough and enoxaparin dose were statistically significant predictors for COVID-19 mortality (p= 0.014, 0.011, 0.015, 0.006 respectively).
Detection of SARS-CoV-2 lineage P.1 in patients from a region with exponentially increasing hospitalization rates in February 2021, Rio Grande do Sul, Southern Brazil
Authors: Martins Andreza Francisco , Zavascki Alexandre Prehn , Wink Priscila Lamb , Volpato Fabiana Caroline Zempulski , Monteiro Francielle Liz , Rosset Clévia , De-Paris Fernanda , Ramos Álvaro Krüger , Luís Barth Afonso
Published: March 2021

The emergence SARS-CoV-2 P.1 lineage has been coincidental with a rapid growth in hospitalization in the northern region of Brazil. An exponential growth of severe COVID-19 occurred in Rio Grande do Sul state, Southern Brazil in February-2021. Whole-genome sequencing revealed that the previously undetected P.1 lineage accounted for 88.9% of specimens collected from patients at a referral COVID-19 hospital. These findings raise concerns regarding a possible association between lineage P.1 and rapid growth in cases and hospitalizations.
Topaz1, an essential gene for murine spermatogenesis, down-regulates the expression of numerous testis-specific long non-coding RNAs
Authors: Chadourne Manon , Poumerol Elodie , Jouneau Luc , Passet Bruno , Castille Johan , Sellem Eli , Pailhoux Eric , Mandon-Pépin Béatrice
Published: March 2021

Spermatogenesis involves coordinated processes, including meiosis, to produce functional gametes. We previously reportedTopaz1as a germ cell-specific gene highly conserved in vertebrates.Topaz1knockout males are sterile with testes that lack haploid germ cells because of meiotic arrest after prophase I. To better characterizeTopaz1−/−testes, we used RNA-sequencing analyses at two different developmental stages (P16 and P18). The absence of TOPAZ1 disturbed the expression of genes involved in microtubule and/or cilium mobility, which was consistent with testicular histology showing the disruption of microtubules and centrosomes. Moreover, a quarter of P18 dysregulated genes are long non-coding RNAs (lncRNAs), and three of them are testis-specific and located in spermatocytes, their expression starting between P11 and P15. The suppression of one of them,4939463O16Rik, did not alter fertility although sperm parameters were disturbed and sperm concentration fell. The transcriptome of P18-4939463O16Rik−/−testes was altered and the molecular pathways affected included microtubule-based processes, the regulation of cilium movement and spermatogenesis. The absence of TOPAZ1 protein or4930463O16Rikproduced the same enrichment clusters in mutant testes despite a contrasted phenotype on male fertility. In conclusion, TOPAZ1 appeared to stabilize the expression of numerous lncRNAs. Its suppression is not essential for fertility but required during the terminal differentiation of male gametes.

Author Summary

TheTopaz1gene was initially characterized during the initiation of meiosis in the sheep fetal ovary. In order to determine its function, a KO of the murine gene was performed. In this species, only males were sterile and spermatogenesis was blocked before the first meiotic division. Here, we show that cytoskeletal elements are markedly disturbed in mutant testes, indicating that these elements play an important function in spermatogenesis. While the mitotic spindle of spermatogonia was normal, the meiotic spindle of spermatocytes was hemi-spindle-shaped and the homologous chromosome pairs could position themselves on the equatorial plate. In addition, lncRNAs account for 25% of genes whose expression in testes varies significantly in the absence ofTopaz1. This suggests a key role for these factors in spermatogenesis. Largely testis-specific, they may be involved in spermatogenesis and play a more or less critical role in mouse fertility, which probably also depends on their redundancies.
The neural basis of creative production: A cross-modal ALE meta-analysis
Authors: Brown Steven , Kim Eunseon
Published: March 2021

One of the central questions about the cognitive neuroscience of creativity is the extent to which creativity depends on either domain-specific or domain-general mechanisms. To address this question, we carried out two parallel activation likelihood estimation meta-analyses of creativity: 1) a motoric analysis that combined studies across five domains of creative production (verbalizing, music, movement, writing, and drawing), and 2) an analysis of the Alternate Uses divergent-thinking task. All experiments contained a contrast between a creative task and a matched non-creative or less-creative task that controlled for the sensorimotor demands of task performance. The activation profiles of the two meta-analyses were non-overlapping, but both pointed to a domain-specific interpretation in which creative production is, at least in part, an enhancement of sensorimotor brain areas involved in non-creative production. The most concordant areas of activation in the motoric meta-analysis were high-level motor areas such as the pre-supplementary motor area and inferior frontal gyrus that interface motor planning and executive control, suggesting a means of uniting domain-specificity and -generality in creative production.
Robotic Antimicrobial Susceptibility Platform (RASP): A Next Generation Approach to One-Health Surveillance of Antimicrobial Resistance
Authors: Truswell Alec , Abraham Rebecca , O’Dea Mark , Lee Zheng Zhou , Lee Terence , Laird Tanya , Blinco John , Kaplan Shai , Turnidge John , Trott Darren J. , Jordan David , Abraham Sam
Published: March 2021

Background

Surveillance of antimicrobial resistance (AMR) is critical to reducing its wide-reaching impact. Its reliance on sample size invites solutions to longstanding constraints regarding scalability. A robotic platform (RASP) was developed for high-throughput AMR surveillance in accordance with internationally recognised standards (CLSI and ISO 20776-1:2019) and validated through a series of experiments.

Methods

Experiment A compared RASP’s ability to achieve consistent MICs to that of a human technician across eight replicates for fourE. coliisolates. Experiment B assessed RASP’s agreement with human performed MICs across 91E. coliisolates with a diverse range of AMR profiles. Additionally, to demonstrate its real-world applicability, the RASP workflow was then applied to five faecal samples where a minimum of 47E. coliper animal (239 total) were evaluated using an AMR indexing framework.

Results

For each drug-rater-isolate combination in experiment A, there was a clear consensus of the MIC and deviation from the consensus remained within one doubling-dilution (the exception being gentamicin at two dilutions). Experiment B revealed a concordance correlation coefficient of 0.9670 (95%CI: 0.9670 - 0.9670) between the robot and human performed MICs. RASP’s application to the five faecal samples highlighted the intra-animal diversity of gut commensalE. coli,identifying between five and nine unique isolate AMR phenotypes per sample.

Conclusions

While adhering to internationally accepted guidelines, RASP was superior in throughput, cost and data resolution when compared to an experienced human technician. Integration of robotics platforms in the microbiology laboratory is a necessary advancement for future One-Health AMR endeavours.
Mechanisms of transforming DNA uptake to the periplasm ofBacillus subtilis
Authors: Hahn Jeanette , DeSantis Micaela , Dubnau David
Published: March 2021

We demonstrate here that the acquisition of DNAase resistance by transforming DNA, often assumed to indicate transport to the cytoplasm, actually reflects uptake to the periplasm, requiring a re-evaluation of conclusions about the roles of several proteins in transformation. The new evidence suggests that the transformation pilus is needed for DNA binding to the cell surface near the cell poles and for the initiation of uptake. The cellular distribution of the membrane-anchored ComEA ofB. subtilisdoes not noticeably change during DNA uptake as does the unanchored ComEA ofVibrioandNeisseria. Instead, our evidence suggests that ComEA stabilizes the attachment of transforming DNA at localized regions in the periplasm and then mediates uptake, probably by a Brownian ratchet mechanism. Following that, the DNA is transferred to periplasmic portions of the channel protein ComEC, which plays a previously unsuspected role in uptake to the periplasm. We show that the transformation endonuclease NucA also facilitates uptake to the periplasm and that the previously demonstrated role of ComFA in the acquisition of DNAase resistance actually derives from the instability of ComGA when ComFA is deleted. These results prompt a new understanding of the early stages of DNA uptake for transformation.

IMPORTANCE

Transformation is a widely distributed mechanism of bacterial horizontal gene transfer that plays a role in the spread of antibiotic resistance and virulence genes and more generally in evolution. Although transformation was discovered nearly a century ago and most, if not all of the proteins required have been identified in several bacterial species, much remains poorly understood about the molecular mechanism of DNA uptake. This study uses epifluorescence microscopy to investigate the passage of labeled DNA into the compartment between the cell wall and the cell membrane ofBacillus subtilis, a necessary early step in transformation. The roles of individual proteins in this process are identified, and their modes of action are clarified.
Impedance scaling for gold and platinum microelectrodes
Authors: Fan Bo , Wolfrum Bernhard , Robinson Jacob T.
Published: March 2021

Objective

Electrical measurement of the activity of individual neurons is a primary goal for many invasive neural electrodes. Making these “single unit” measurements requires that we fabricate electrodes small enough so that only a few neurons contribute to the signal, but not so small that the impedance of the electrode creates overwhelming noise or signal attenuation. Thus, neuroelectrode design often must strike a balance between electrode size and electrode impedance, where the impedance is often assumed to scale linearly with electrode area.

Approach and main results

Here we study how impedance scales with neural electrode area and find that the 1 kHz impedance of Pt electrodes (but not Au electrodes) transitions from scaling with area (r-2) to scaling with perimeter (r-1) when the electrode radius falls below 10 microns. This effect can be explained by the transition from planar to spherical diffusion behavior previously reported for electrochemical microelectrodes.Significance:These results provide important intuition for designing small, single unit recording electrodes. Specifically, for materials where the impedance is dominated by a pseudo-capacitance that is associated with a diffusion limited process, the total impedance will scale with perimeter rather than area when the electrode size becomes comparable with the diffusion layer thickness. For Pt electrodes this transition occurs around 10 um radius electrodes. At even lower frequencies (1 Hz) impedance approaches a constant. This transition to r-1scaling implies that electrodes with a pseudo-capacitance can be made smaller than one might expect before thermal noise or voltage division limits the ability to acquire high-quality single-unit recordings.
Unplanned Hospital Visits after Ambulatory Surgical Care
Authors: Bongiovanni Tasce , Parzynski Craig , Ranasinghe Isuru , Steinman Michael A , Ross Joseph S.
Published: March 2021

Structured Abstract

Objectives

We sought to assess the rate of unplanned hospital visits among patients undergoing ambulatory surgery.

Summary Background Data

The majority of surgeries performed in the United States now take place in outpatient settings. Post-discharge hospital visit rates have been shown to vary widely, suggesting variation in surgical or discharge care quality. Complicating efforts to address quality, most facilities and surgeons are unaware of their patients’ hospital visits after surgery since patients may present to a different hospital.

Methods

We used state-level, administrative data from the Agency for Healthcare Research and Quality’s Healthcare Cost and Utilization Project from California to assess unplanned hospital visits after ambulatory surgery. To compare rates across centers, we determined the age, sex, and procedure-adjusted rates of hospital visits for each facility using 2-level, hierarchical, generalized linear models using methods similar to existing Centers for Medicare and Medicaid Services measures.

Results

Among a total of 1,260,619 ambulatory same-day surgeries from 440 surgical facilities, the risk adjusted 30-day rate of unplanned hospital visits was 4.8%, with emergency department visits of 3.1% and hospital admissions of 1.7%. Several patient characteristics were associated with increased risk of unplanned hospitals visits, including increased age, increased number of comorbidities (using the Elixhauser score), and type of procedure (p<0.001).

Conclusions

The overall rate unplanned hospital visits within 30 days after same-day surgery is low but variable, suggesting a difference in the quality of care provided. Further, these rates are higher among specific patient populations and procedure types, suggesting areas for targeted improvement.

Mini-Abstract

The majority of surgeries performed in the United States now take place in outpatient settings with wide variation of post-discharge hospital visit rates. We used state-level, administrative data to assess the rate of unplanned hospital visits after ambulatory surgery and found a risk adjusted 30-day rate of 4.8%. Increased age, increased number of comorbidities (using the Elixhauser score), and type of procedure were associated with increased risk of unplanned hospitals visits, suggesting areas for targeted improvement.
Spread and sources of information and misinformation about COVID-19 early during the pandemic in a U.S. national cohort study
Authors: Westmoreland Drew A. , Berry Amanda , Zimba Rebecca , Kulkarni Sarah , Parcesepe Angela , Maroko Andrew R , Poehlein Emily , You William , Mirzayi Chloe , Kochhar Shivani , Robertson McKaylee , Waldron Levi , Grov Christian , Nash Denis
Published: March 2021

Background

Early in the pandemic, misinformation about COVID-19 was spread on social media. The purpose of this study was to describe trusted sources of COVID-19 information and claims seen and believed about COVID-19 early in the pandemic among U.S. adults. Then, we assessed the impact of believing such claims on engaging in personal protective actions (PPA).

Methods

We used baseline data from the CHASING COVID Cohort (n = 7,070) collected March 28, 2020 to April 20, 2020 to describe trusted sources of COVID-19 information as well as claims circulating on social media that had been seen and believed. We used Poisson regression to determine the association of believing certain claims with engaging in a higher number of PPA.

Results

The top three trusted sources of COVID-19 information were the CDC (67.9%), the WHO (53.7%), and State Health Departments (53.0%). Several COVID-19 claims circulated on social media had been seen, e.g., that the virus was created in a laboratory (54.8%). Moreover, substantial proportions of participants indicated agreement with some of these claims. In multivariable regression, we found that belief in certain claims was associated with engaging in a higher number of PPA. For example, believing that paper masks would prevent transmission of the virus was associated with engaging in a higher number of protective actions (β = 0.02, 95% CI: 0.004 – 0.046).

Conclusions

Results suggest the need for public health leadership on social media platforms to combat misinformation and supports social media as a tool to further public health interventions.
Acceptability of contact management and care of simple cases of COVID-19 at home: a mixed-method study in Senegal
Authors: Ba Mouhamadou Faly , Ridde Valéry , Diallo Amadou Ibra , Tine Jean Augustin Diégane , Kane Babacar , Gaye Ibrahima , Traoré Zoumana , Bonnet Emmanuel , Faye Adama
Published: March 2021

Introduction

In mid-2020, due to the health system challenges from increased COVID-19 cases, the Ministry of Health and Social Action in Senegal opted for contact management and care of simple cases at home. The study’s objective was to determine the acceptability of contact management, home care of simple cases of COVID-19, and its associated factors.

Method

This was a sequential mixed-method study. We collected data from June 11, 2020, to July 10, 2020, for the quantitative survey (N=813) and from August 24 to September 16, 2020, for the qualitative survey (N=30). We carried out a sampling strategy using marginal quotas at the national level. We collected data using a structured questionnaire in a telephone interview for the quantitative survey and using an interview guide formulated from the quantitative survey’s initial results for the qualitative data. We assessed acceptability using binomial logistic regression combined with content analysis.

Results

The care of simple cases of COVID-19 at home was well accepted (78.5%). This result was justified for some (saturation of the health system) but not for others (risk of contamination). The use of home contact management was less accepted (51.4%), with risk limitation as the main reason given. The acceptability of home-based care for simple cases was positively associated with knowledge of the modes of transmission of the virus (ORaj: 1.55 [95%CI: 1.04,2.28]), regular research into COVID-19 (ORaj: 2.12 [95%CI: 1.45,3.12]), belief in the existence of treatment (ORaj: 1.82 [95%CI: 1.19,2.83]), and confidence in institutional information (ORaj: 2.10 [95%CI: 1.43,3.10]). The acceptability of home-based contact management was positively associated with knowledge of the modes of transmission of the virus (ORaj: 1.77 [95%CI: 1.27,2.48]), regular research for information on COVID-19 (ORaj: 2.39 [95%CI: 1.76,3.26]), and confidence in the government in the fight against the epidemic (ORaj: 1.51 [95%CI: 1.10,2.08]).

Conclusion

Regular information on the disease, knowledge of its mode of transmission and trust in institutions are factors in accepting COVID-19 management at the community level. Authorities should take these factors into account for better communication to improve the acceptability of home-based care.
Individual’s daily behaviour and intergenerational mixing in different social contexts of Kenya
Authors: Del Fava Emanuele , Adema Irene , Kiti Moses C. , Poletti Piero , Merler Stefano , Nokes D. James , Manfredi Piero , Melegaro Alessia
Published: March 2021

Which are the characteristics of contact patterns in diverse social contexts in sub-Saharan Africa, and which types of individuals and daily behaviours may play a pivotal role in infection transmission to the most vulnerable, such as older adults? We address these questions using novel survey data on social contacts and time use from a sample of 1407 individuals from rural, urban, and slum settings in Kenya. In the rural setting, we observed the highest number of daily social contacts (11.56, SD = 0.23) and the highest share of intergenerational mixing with older adults (7.5% vs. around 4% in the urban settings). Intergenerational mixing with older adults was mainly reported by individuals spending their day mostly in the general community (around 8%) or at home (5.1%), rather than at work (1.5%) or at school (3.6%). These results are essential to define effective interventions to control infection transmission in the African context.
The Burden of and Factors Associated with Age-Related Eye Diseases in Arab American Adults
Authors: Yaldo Luke M. , Dallo Florence J. , Ruterbusch Julie J. , Schwartz Kendra , Jamil Hikmet J.
Published: March 2021

Purpose

To estimate the age- and sex-adjusted proportions of cataract, diabetic retinopathy, glaucoma, and macular degeneration among the Arab American community, a notably understudied minority that is aggregated under whites.

Methods

The Arab American Eye Study is a multicenter retrospective chart review involving ten years of electronic medical records (1/1/2010 through 1/1/2020). The study sample included 1,390 Arab Americans and 4,950 whites 45 years of age and older, totaling 6,340 subjects. Arab Americans were identified using an Arab American name algorithm. Subjects with race variables other than white or Arab American or those under age 45 were excluded from the study. Age- and sex-adjusted proportions of cataract, diabetic retinopathy, glaucoma, and macular degeneration were determined. Odds ratios with 95% confidence intervals were used to examine the association between race/ethnicity and eye diseases.

Results

Of the 6,340 participants (4,950 whites and 1,390 Arab Americans), males comprised 46.3% and the median age group was 55-64 years. Arab Americans displayed higher age- and sex-adjusted proportions of cataracts (45.4% versus 40.7%), dry age-related macular degeneration (10% versus 8.9%), glaucoma (8% vs 6%), and diabetic retinopathy (11.7% versus 4.2%). Fully adjusted logistic regression revealed that Arab Americans were 19% more likely to have cataracts (OR = 1.19; 95% CI = 1.05, 1.35) and 272% more likely to have diabetic retinopathy (OR = 2.72; 95% CI = 2.17; 3.41).

Conclusions

Results from the Arab American Eye Study suggest that the burden of cataract and diabetic retinopathy is significantly higher among Arab Americans in comparison to whites.
Are vaccines safe in patients with Long COVID? A prospective observational study
Authors: Arnold DT , Milne A , Samms E , Stadon L , Maskell NA , Hamilton FW
Published: March 2021

Introduction

Although the efficacy of SARS-CoV-2 vaccination to prevent symptomatic COVID-19 is well established, there are no published studies on the impact on symptoms in patients with Long Covid. Anecdotal reports have suggested both a potential benefit and worsening of symptoms post vaccination with the uncertainty leading to some vaccine hesitancy amongst affected individuals.

Methods

Patients initially hospitalised with COVID-19 were prospectively recruited to an observational study with clinical follow-up at 3 months (June-July 2020) and 8 months (Dec 2020-Jan 2021) post-admission. Participants who received the Pfizer-BioNTech (BNT162b2) or Oxford-AstraZeneca (ChAdOx1 nCoV-19) vaccine between January to February 2021 were identified and matched 2:1 (in terms of 8-month symptoms) with participants from the same cohort who were unvaccinated. All were re-assessed at 1 month post vaccination (or matched timepoint for unvaccinated cohort). Validated quality of life (SF-36), mental wellbeing (WEMWBS) and ongoing symptoms were assessed at all timepoints. Formal statistical analysis compared the effect of vaccination on recent quality of life using baseline symptoms, age, and gender in linear regression.

Results

Forty-four vaccinated participants were assessed at a median of 32 days (IQR 20-41) post vaccination with 22 matched unvaccinated participants. Most were highly symptomatic of Long Covid at 8 months (82% in both groups had at least 1 persistent symptom), with fatigue (61%), breathlessness (50%) and insomnia (38%) predominating. There was no significant worsening in quality-of-life or mental wellbeing metrics pre versus post vaccination. Nearly two-thirds (n=27) reported transient (<72hr duration) systemic effects (including fever, myalgia and headache).

When compared to matched unvaccinated participants from the same cohort, those who had receive a vaccine had a small overall improvement in Long Covid symptoms, with a decrease in worsening symptoms (5.6% vaccinated vs 14.2% unvaccinated) and increase in symptom resolution (23.2% vaccinated vs 15.4% unvaccinated) (p=0.035). No difference in response was identified between Pfizer-BioNTech or Oxford-AstraZeneca vaccines.

Conclusions

Receipt of vaccination with either an mRNA or adenoviral vector vaccine was not associated with a worsening of Long Covid symptoms, quality of life, or mental wellbeing. Individuals with prolonged COVID-19 symptoms should receive vaccinations as suggested by national guidance.
Comparison of SARS-CoV-2 detection in Saliva by real-time RT-PCR and RT-PCR/MALDI-TOF Methods
Authors: Hernandez Matthew M. , Banu Radhika , Shrestha Paras , Patel Armi , Chen Feng , Cao Liyong , Fabre Shelcie , Tan Jessica , Lopez Heidi , Chiu Numthip , Shifrin Biana , Zapolskaya Inessa , Flores Vanessa , Lee Pui Yiu , Castañeda Sergio , Ramírez Juan David , Jhang Jeffrey , Osorio Giuliana , Gitman Melissa R. , Nowak Michael D. , Reich David L. , Cordon-Cardo Carlos , Sordillo Emilia Mia , Paniz-Mondolfi Alberto E.
Published: March 2021

The coronavirus disease 2019 (COVID-19) pandemic has accelerated the need for rapid implementation of diagnostic assays for detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in respiratory specimens. While multiple molecular methods utilize nasopharyngeal specimens, supply chain constraints and need for easier and safer specimen collection warrant alternative specimen types, particularly saliva. Although saliva has been found to be a comparable clinical matrix for detection of SARS-CoV-2, evaluations of diagnostic and analytic performance across platforms for this specimen type are limited. Here, we compared two methods for SARS-CoV-2 detection in saliva: the Roche cobas® 6800/8800 SARS-CoV-2 real-time RT-PCR Test and the Agena Biosciences MassARRAY® SARS-CoV-2 Panel/MassARRAY® System. Overall, both systems had high agreement with one another, and both demonstrated high diagnostic sensitivity and specificity when compared to matched patient upper respiratory specimens. We also evaluated the analytical sensitivity of each platform and determined the limit of detection of the Roche assay was four times lower than that of Agena for saliva specimens (390.6 v. 1,562.5 copies/mL). Furthermore, across individual target components of each assay, T2 and N2 targets had the lowest limits of detection for each platform, respectively. Together, we demonstrate that saliva represents an appropriate specimen for SARS-CoV-2 detection in two technologies that have high agreement and differ in analytical sensitivities overall and across individual component targets. The addition of saliva as an acceptable specimen and understanding the sensitivity for testing on these platforms can further inform public health measures for screening and detection to combat the COVID-19 pandemic.
DIP: Natural History Model for Major Depression with Incidence and Prevalence
Authors: Yildirim Melike , Gaynes Bradley N , Keskinocak Pinar , Pence Brian W , Swann Julie
Published: March 2021

Background

Major depression is a treatable disease, and untreated depression can lead to serious health complications. Therefore, prevention, early identification, and treatment efforts are essential. Natural history models can be utilized to make informed decisions about interventions and treatments of major depression.

Methods

We propose a natural history model of major depression. We use steady-state analysis to study the discrete-time Markov chain model. For this purpose, we solved differential equations and tested the parameter and transition probabilities empirically.

Results

We showed that bias in parameters might collectively cause a significant mismatch in a model. If incidence is correct, then lifetime prevalence is 33.2% for females and 20.5% for males, which is higher than reported values. If prevalence is correct, then incidence is .0008 for females and .00065 for males, which is lower than reported values. The model can achieve feasibility if incidence is at low levels and recall bias of the lifetime prevalence is quantified to be 31.9% for females and 16.3% for males.

Limitations

Model is limited to major depression, and patients who have other types of depression are assumed healthy. We assume that transition probabilities (except incidence rates) are correct.

Conclusion

We constructed a preliminary model for the natural history of major depression. We determine the lifetime prevalence are underestimated. We conclude that the average incidence rates may be underestimated for males. Our findings mathematically prove the arguments around the potential discordance between reported incidence and lifetime prevalence rates.
Oxygen provision to severely ill COVID-19 patients at the peak of the 2020 pandemic in a Swedish district hospital
Authors: Hvarfner Anna , Al-Djaber Ahmed , Ekström Hampus , Enarsson Malin , Castegren Markus , Baker Tim , Schell Carl Otto
Published: March 2021

Oxygen is a low-cost and life-saving therapy for patients with COVID-19. Yet, it is a limited resource in many hospitals in low income countries and in the 2020 pandemic even hospitals in richer countries reported oxygen shortages. An accurate understanding of oxygen requirements is needed for capacity planning. The World Health Organization estimates the average flow-rate of oxygen to severe COVID-19-patients to be 10 l/min. However, there is a lack of empirical data about the oxygen provision to patients. This study aimed to estimate the oxygen provision to COVID-19 patients with severe disease in a Swedish district hospital.

A retrospective, medical records-based cohort study was conducted in March to May 2020 in a Swedish district hospital. All adult patients with severe COVID-19 – those who received oxygen in the ward and had no ICU-admission during their hospital stay – were included. Data were collected on the oxygen flow-rates provided to the patients throughout their hospital stay, and summary measures of oxygen provision calculated.

One-hundred and twenty six patients were included, median age was 70 years and 43% were female. On admission, 27% had a peripheral oxygen saturation of ≤91% and 54% had a respiratory rate of ≥25/min. The mean oxygen flow-rate to patients while receiving oxygen therapy was 3.0 l/min (SD 2.9) and the mean total volume of oxygen provided per patient admission was 16,000 l (SD 23,000).

In conclusion, the provision of oxygen to severely ill COVID-19-patients was lower than previously estimated. Further research is required before global estimates are adjusted.
Real-time Updating of Dynamic Social Networks for COVID-19 Vaccination Strategies
Authors: Cheng Sibo , Pain Christopher C. , Guo Yi-Ke , Arcucci Rossella
Published: March 2021

Vaccination strategy is crucial in fighting the COVID-19 pandemic. Since the supply is still limited in many countries, contact network-based interventions can be most powerful to set an efficient strategy by identifying high-risk individuals or communities. However, due to the high dimension, only partial and noisy network information can be available in practice, especially for dynamic systems where contact networks are highly time-variant. Furthermore, the numerous mutations of SARS-CoV-2 have a significant impact on the infectious probability, requiring real-time network updating algorithms. In this study, we propose a sequential network updating approach based on data assimilation techniques to combine different sources of temporal information. We then prioritise the individuals with high-degree or high-centrality, obtained from assimilated networks, for vaccination. The assimilation-based approach is compared with the standard method (based on partially observed networks) and a random selection strategy in terms of vaccination effectiveness in a SIR model. The numerical comparison is first carried out using real-world face-to-face dynamic networks collected in a high school, followed by sequential multi-layer networks generated relying on the Barabasi-Albert model emulating large-scale social networks with several communities.
Acceptability of COVID-19 vaccination among health care workers in Ghana
Authors: Agyekum Martin Wiredu , Afrifa-Anane Grace Frempong , Kyei-Arthur Frank , Addo Bright
Published: March 2021

The acceptance or otherwise of the COVID-19 vaccine by health care workers can influence the uptake of COVID-19 vaccines among the general population as they are a reliable source of health information. In this study, we sought to determine the acceptability of COVID-19 vaccines among health care workers in Ghana. Using a cross-sectional design, we collected data from 234 health care workers through a self-administered online survey from 16 January to 15 February 2021. Descriptive, bivariate and multivariate analyses using binary logistic regression were performed using STATA version 15. The results showed that 39.3% of health care workers had the intention of receiving the COVID-19 vaccine. Factors such as sex, category of health care workers, relative being diagnosed with COVID-19, and trust in the accuracy of the measures taken by the government in the fight against COVID-19 proved to be significant predictors of the acceptability of the COVID-19 vaccine. Concerns about the safety of vaccines and the adverse side effects of the vaccine were identified as the main reasons why health care workers would decline uptake of the COVID-19 vaccine in Ghana. The self-reported low intention of health care workers to accept the COVID-19 vaccine in Ghana requires the urgent call of the Government of Ghana and other stakeholders to critically address health care workers’ concerns about the safety and adverse side effects of COVID-19 vaccines, as this would increase vaccine uptake. Interventions must also take into consideration sex and the category of health care workers to achieve the desired results.
Comprehensive evaluation of the impact of sociodemographic inequalities on adverse outcomes and excess mortality during the COVID-19 pandemic in Mexico City
Authors: Antonio-Villa Neftali Eduardo , Fernandez-Chirino Luisa , Pisanty-Alatorre Julio , Mancilla-Galindo Javier , Kammar-García Ashuin , Vargas-Vázquez Arsenio , González-Díaz Armando , Fermín-Martínez Carlos A. , Márquez-Salinas Alejandro , Cañedo-Guerra Enrique , Bahena-López Jessica Paola , Villanueva-Reza Marco , Márquez-Sánchez Jessica , Jaramillo-Molina Máximo Ernesto , Gutiérrez-Robledo Luis Miguel , Bello-Chavolla Omar Yaxmehen
Published: March 2021

The impact of the COVID-19 pandemic in Mexico City has been sharp, as several social inequalities coexist with chronic comorbidities. Here, we conducted an in-depth evaluation of the impact of social, municipal, and individual factors on the COVID-19 pandemic in working-age population living in Mexico City. To this end, we used data from the National Epidemiological Surveillance System; furthermore, we used a multidimensional metric, the social lag index (DISLI), to evaluate its interaction with mean urban population density (MUPD) and its impact on COVID-19 rates. Influence DISLI and MUPD on the effect of vehicular mobility policies on COVID-19 rates were also tested. Finally, we assessed the influence of MUPD and DISLI on discrepancies of COVID-19 and non-COVID-19 excess mortality compared with death certificates from the General Civil Registry. We detected vulnerable groups who belonged to economically active sectors and who experienced increased risk of adverse COVID-19 outcomes. The impact of social inequalities transcends individuals and has significant effects at a municipality level, with and interaction between DISLI and MUPD. Marginalized municipalities with high population density experienced an accentuated risk for adverse COVID-19 outcomes. Additionally, policies to reduce vehicular mobility had differential impacts across marginalized municipalities. Finally, we report an under-registry of COVID-19 deaths and significant excess mortality associated with non-COVID-19 deaths closely related to MUPD/DISLI in an ambulatory setting, which could be a negative externality of hospital reconversion. In conclusion, social, individual, and municipality-wide factors played a significant role in shaping the course of the COVID-19 pandemic in Mexico City.
Mendelian Randomization for causal inference accounting for pleiotropy and sample structure using genome-wide summary statistics
Authors: Hu Xianghong , Zhao Jia , Lin Zhixiang , Wang Yang , Peng Heng , Zhao Hongyu , Wan Xiang , Yang Can
Published: March 2021

Mendelian Randomization (MR) is a valuable tool for inferring causal relationships among a wide range of traits using summary statistics from genome-wide association studies (GWASs). Existing summary-level MR methods often rely on strong assumptions, resulting in many false positive findings. To relax MR assumptions, ongoing research has been primarily focused on accounting for confounding due to pleiotropy. Here we show that sample structure is another major confounding factor, including population stratification, cryptic relatedness, and sample overlap. We propose a unified MR approach, MR-APSS, which (i) accounts for pleiotropy and sample structure simultaneously by leveraging genome-wide information; and (ii) allows to include more genetic variants with moderate effects as instrument variables (IVs) to improve statistical power without inflating type I errors. We first evaluated MR-APSS using comprehensive simulations and negative controls, and then applied MR-APSS to study the causal relationships among a collection of diverse complex traits. The results suggest that MR-APSS can better identify plausible causal relationships with high reliability. In particular, MR-APSS can perform well for highly polygenic traits, where the IV strengths tend to be relatively weak and existing summary-level MR methods for causal inference are vulnerable to confounding effects.
Structure of human Mediator-RNA polymerase II transcription pre-initiation complex
Authors: Rengachari Srinivasan , Schilbach Sandra , Aibara Shintaro , Dienemann Christian , Cramer Patrick
Published: March 2021

Mediator is a conserved coactivator that enables regulated transcription initiation from eukaryotic protein-coding genes1-3. Mediator is recruited by transcriptional activators and binds the pre-initiation complex (PIC) to stimulate RNA polymerase II (Pol II) phosphorylation and promoter escape1-6. Here we prepare a 20-subunit recombinant human Mediator, reconstitute a 50-subunit Mediator-PIC complex, and resolve the complex structure by cryo-EM at an overall resolution of 4.5 Å. Mediator binds with its head module to the Pol II stalk and the general transcription factors TFIIB and TFIIE, resembling the Mediator-PIC interactions in the corresponding yeast complex7-9. One end of Mediator contains the metazoan-specific subunits MED27-MED30, which associate with exposed regions in MED14 and MED17 to form the proximal part of the tail module that binds activators. The opposite end of Mediator positions the flexibly linked CDK-activating kinase (CAK) of the general transcription factor TFIIH near the C-terminal repeat domain (CTD) of Pol II. The Mediator shoulder domain holds the CAK subunit CDK7, whereas the hook domain contacts a CDK7 element that flanks the kinase active site. The shoulder and hook reside in the Mediator head and middle modules, respectively, which can move relative to each other and may induce an active conformation of CDK7 to allosterically stimulate CTD phosphorylation and Pol II escape from the promoter.