bluuebunny/crossref_metadata_2025 huggingface dataset:
Perceptions of partial gland ablation for prostate cancer among men on active surveillance: A qualitative study
Authors: Hur Sonia S. , Tzeng Michael , Cricco-Lizza Eliza , Yu Miko , Ancker Jessica , Abramson Erika , Saigal Christopher , Ross Ashley , Hu Jim C.
Published: September 2020

Objectives

Partial gland ablation (PGA) therapy is an emerging treatment modality that targets specific areas of biopsy proven prostate cancer (PCa) to minimize treatment-related morbidity by sparing benign prostate. This qualitative study aims to explore and characterize perceptions and attitudes toward PGA in men with very-low-risk, low-risk, and favorable intermediate-risk PCa on active surveillance (AS).

Design

92 men diagnosed with very-low-risk, low-risk, and favorable intermediate-risk PCa on AS were invited to participate in semi-structured telephone interviews on PGA.

Setting

Single tertiary care center located in New York City.

Participants

20 men with very-low-risk, low-risk, and favorable intermediate-risk PCa on AS participated in the interviews.

Main outcome measures

Emerging themes on perceptions and attitudes toward PGA were developed from transcripts inductively coded and analyzed under standardized methodology.

Results

Four themes were derived from twenty interviews that represent the primary considerations in treatment decision-making: (1) the feeling of psychological safety associated with low risk disease; (2) preference for minimally invasive treatments; (3) the central role of the physician; (4) and the pursuit of treatment options that align with disease severity. Eleven men (55%) expressed interest in pursuing PGA only if their cancer were to progress, while 9 men (45%) expressed interest at the current moment.

Conclusions

Though an emerging treatment modality, patients were broadly accepting of PGA for PCa with men primarily debating the risks versus benefits of proactively treating low-risk disease. Additional research on men’s preferences and attitudes toward PGA will further guide counseling and shared decision-making for PGA.

Key Messages

What is already known about this subject?

Partial gland ablation (PGA) is an emerging treatment option for prostate cancer (PCa) that allows for the targeting of areas of biopsy proven PCa with the goal of minimizing treatment-related morbidity by avoiding treatment of non-cancerous areas of the prostate. We sought to explore patients’ beliefs and attitudes toward partial gland ablation.

What are the new findings?

We define treatment attributes that are significant to men with localized PCa, and one important theme is of the treatment intensity matching the severity of the disease. PGA appeals to men as middle ground that encompasses the duality of curative treatment and preservation of quality of life.

How might these results affect future research or surgical practice?

The exploratory themes need further exploration and may be incorporated into shared decision-making discussions in men with low-risk disease, as PGA emerges as a treatment option.
A COVID-19 Nursing Home Transmission Study: sequence and metadata from weekly testing in an extensive nursing home outbreak
Authors: van den Besselaar Judith H. , Sikkema Reina S. , Koene Fleur M.H.P.A , van Buul Laura W. , Munnink Bas B. Oude , Frénay Ine , Witt René te , Koopmans Marion P.G. , Hertogh Cees M.P.M. , Buurman Bianca M.
Published: September 2020

Background

This study aimed to assess the contribution of asymptomatic and presymptomatic residents and staff in SARS-CoV-2 transmission during a large outbreak in a Dutch nursing home.

Methods

Observational study in a 185-bed nursing home with two consecutive testing strategies: testing of symptomatic cases only, and weekly facility-wide testing of staff and residents regardless of symptoms. Nasopharyngeal and oropharyngeal testing with RT-PCR for SARs-CoV-2 was conducted with a standardized symptom assessment. Positive samples with a cycle threshold (CT) value below 32 were selected for sequencing.

Results

185 residents and 244 staff participated. Sequencing identified one cluster. In the symptom-based test strategy period 3/39 residents were presymptomatic versus 38/74 residents in the period of weekly facility-wide testing (p-value<0.001). In total, 51/59 (91.1%) of SARS-CoV-2 positive staff was symptomatic, with no difference between both testing strategies (p-value 0.763). Loss of smell and taste, sore throat, headache or myalga was hardly reported in residents compared to staff (p-value <0.001). Median Ct-value of presymptomatic residents was 21.3, which did not differ from symptomatic (20.8) or asymptomatic (20.5) residents (p-value 0.624).

Conclusions

The frequency of a/presymptomatic residents compared to staff suggests that a/presymptomatic residents could be unrecognized symptomatic cases. However, symptomatic and presymptomatic/unrecognized symptomatic residents both have the same potential for viral shedding. The high prevalence symptomatic staff found in facility-wide testing suggests that staff has difficulty attributing their symptoms to possible SARS-CoV-2 infection. Weekly testing was an effective strategy for early identification of SARS-Cov-2 cases, resulting in fast isolation and mitigation of this outbreak.
SARS-CoV-2 genomes from Oklahoma, USA
Authors: Narayanan Sai , Ritchey John C , Patil Girish , Narasaraju Teluguakula , More Sunil , Malayer Jerry , Saliki Jeremiah , Kaul Anil , Ramachandran Akhilesh
Published: September 2020

Genomic sequencing has played a major role in understanding the pathogenicity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). With the current pandemic, it is essential that SARS-CoV-2 viruses are sequenced regularly to determine mutations and genomic modifications in different geographical locations. In this study we sequenced SARS-CoV-2 from 5 clinical samples obtained in Oklahoma, USA during different time points of pandemic presence in the state. One sample from the initial days of the pandemic in the state and 4 during the peak in Oklahoma were sequenced. Previously reported mutations including D614G in S gene, P4715L in ORF1ab, S194L, R203K and G204R in N gene were identified in the genomes sequenced in this study. Possible novel mutations were also detected such as G1167V in S gene, A6269S and P3371S in ORF1ab, T28I in ORF7b, G96R in ORF8. Phylogenetic analysis of the genomes showed similarity to viruses from across the globe. These novel mutations and phylogenetic analysis emphasize the contagious nature of the virus.
Identification of potential biomarkers and inhibitors for SARS-CoV-2 infection
Authors: Gu Hanming , Yuan Gongsheng
Published: September 2020

The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has overwhelmed many health systems globally. Here, we aim to identify biological markers and associated biological processes of COVID-19 using a bioinformatics approach to elucidate their potential pathogenesis. The gene expression profile of the GSE152418 dataset was originally produced by using the high-throughput Illumina NovaSeq 6000. Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) and Gene Ontology (GO) enrichment analyses were applied to identify functional categories and biochemical pathways. KEGG and GO results suggested that biological pathways such as “Cancer pathways” and “Insulin pathways” were mostly affected in the development of COVID-19. Moreover, we identified several genes including EP300, CREBBP, and POLR2A were involved in the virus activities in COVID-19 patients. We further predicted that some inhibitors may have the potential to block the SARS-CoV-2 infection based on the L1000FWD analysis. Therefore, our study provides further insights into the underlying pathogenesis of COVID-19.
Cost-effective serological test to determine exposure to SARS-CoV-2: ELISA based on the receptor-binding domain of the spike protein (Spike-RBDN318-V510) expressed in Escherichia coli
Authors: Márquez-Ipiña Alan Roberto , González-González Everardo , Rodríguez-Sánchez Iram Pablo , Lara-Mayorga Itzel Montserrat , Mejía-Manzano Luis Alberto , González-Valdez José , Ortiz-Lopez Rocio , Rojas-Martinez Augusto , Santiago Grissel Trujillo-de , Moisés Alvarez Mario
Published: September 2020

Massive worldwide serological testing for SARS-CoV-2 is needed to determine the extent of virus exposure in a particular region, the ratio of symptomatic to asymptomatic infected persons, and the duration and extent of immunity after infection. To achieve this aim, the development and production of reliable and cost-effective SARS-CoV-2 antigens is critical.

Here, we report the bacterial production of the peptide S-RBDN318-V510, which contains the receptor binding domain of the SARS-CoV-2 spike protein. We purified this peptide using a straightforward approach involving bacterial lysis, his-tag mediated affinity chromatography, and imidazole-assisted refolding. The antigen performances of S-RBDN318-V510 and a commercial full-length spike protein were compared in two distinct ELISAs. In direct ELISAs, where the antigen was directly bound to the ELISA surface, both antigens discriminated sera from non-exposed and exposed individuals. However, the discriminating resolution was better in ELISAs that used the full-spike antigen than the S-RBDN318-V510. Attachment of the antigens to the ELISA surface using a layer of anti-histidine antibodies gave equivalent resolution for both S-RBDN318-V510 and the full length spike protein.

Our results demonstrate that ELISA-functional SARS-CoV-2 antigens can be produced in bacterial cultures. S-RBDN318-V510 is amenable to massive production and may represent a cost-effective alternative to the use of structurally more complex antigens in serological COVID-19 testing.
Parents’ and guardians’ views on the acceptability of a future Covid-19 vaccine: a multi-methods study in England
Authors: Bell Sadie , Clarke Richard , Mounier-Jack Sandra , Walker Jemma L , Paterson Pauline
Published: September 2020

Background

The availability of a COVID-19 vaccine has been heralded as key to controlling the COVID-19 pandemic. COVID-19 vaccination programme success will rely on public willingness to be vaccinated.

Methods

We used a multi-methods approach – involving an online cross-sectional survey and semi-structured interviews - to investigate the views of parents’ and guardians’ on the acceptability of a future COVID-19 vaccine. 1252 parents and guardians (aged 16+ years) who reported living in England with a child aged 18 months or under completed the survey. Nineteen survey respondents were interviewed.

Findings

Most participants reported they would definitely accept or were unsure but leaning towards accepting a COVID-19 vaccine for themselves (Definitely 55.8%; Unsure but leaning towards yes 34.3%) and their child/children (Definitely 48.2%; Unsure but leaning towards yes 40.9%). Participants were more likely to accept a COVID-19 vaccine for themselves than for their child/children. Less than 4% of participants reported that they would definitely not accept a COVID-19 vaccine for themselves or their children. Participants that self-reported as Black, Asian, Chinese, Mixed or Other ethnicity were almost 3 times more likely to reject a COVID-19 vaccine for themselves and their children than White British, White Irish and White Other participants. Respondents from lower income households were also more likely to reject a COVID-19 vaccine.

The main reason for vaccine acceptance was for self-protection from COVID-19. Common concerns were around COVID-19 vaccine safety and effectiveness, which were largely prompted by the newness and rapid development of the vaccine.

Conclusion

To alleviate concerns, information on how COVID-19 vaccines are developed and tested, including their safety and efficacy, must be communicated clearly to the public. To prevent Inequalities in uptake, it is crucial to understand and address factors that may affect COVID-19 vaccine acceptability in ethnic minority lower-income groups who are disproportionately affected by COVID-19.
The case series of 34 patients with COVID-19 diagnosed with HIV infection from Central and Eastern European Countries – Euroguidelines in Central and Eastern Europe Network Group data
Authors: Kase Kerstin , Skrzat-Klapaczyńska Agata , Vassilenko Anna , Harxhi Arjan , Lakatos Botond , Lukić Gordana Dragović , Jilich David , Verhaz Antonija , Yancheva Nina , Dumitrescu Florentina , Matulionyte Raimonda , Horban Andrzej , Kowalska Justyna D.
Published: September 2020

Background

A novel coronavirus (SARS-CoV-2) causing coronavirus disease (COVID-19) was detected at the end of 2019 in China. There are many COVID-19 studies in progress however, little is known about the course of COVID-19 in people living with HIV (PLWH). The aim of our study was to describe epidemiology and clinical characteristics of PLWH diagnosed with COVID-19 reported form Central and Eastern European Countries.

Methods

On-line survey was sent to Euroguidelines in Central and Eastern Europe (ECEE) Network Group. Analysis included all confirmed COVID-19 cases between March 11 and June 26 2020 among PLWH in 12 countries: Albania, Belarus, Bosnia and Herzegovina, Bulgaria, Czech Republic, Estonia, Hungary, Lithuania, Poland, Romania, Russia, and Serbia.

Results

In total 34 cases were reported. The mean age of those patients was 42.7 years (IQR = 35.8-48.5) and most of the patients were male (70.6% vs 29.4%). The mean CD4+ T-cell count prior COVID-19 diagnosis was 558 cells/mm3(IQR = 312-719) and HIV RNA viral load (VL) was undetectable in 18 of 34 (53%) cases, the data about most recent HIV RNA VL was not available in three cases (8,8%). Comorbidities were observed in 19 (55.9%) patients, mostly cardiovascular disease (27,8%), and in 10 (29.4%) patients had coinfection, mostly chronic hepatitis C (87.5%). The clinical course of COVID-19 was asymptomatic in 4 (12%) cases, mild disease without hospitalization was reported in 11 (32%) cases. Stable patients with respiratory and/or systemic symptoms have been documented in 14 (41%) cases; 5 (15%) patients were clinically unstable with respiratory failure. Full recovery was reported in 31 (91%) cases, two patients died. In one case the data was not available.

Conclusion

This study from 12 countries in Central and Eastern Europe region indicates no alarming signals of increased morbidity or mortality from COVID-19 among HIV-positive persons there is a need for further research.
Inexpensive, versatile and open-source methods for SARS-CoV-2 detection
Authors: Graham Thomas G.W. , Dugast-Darzacq Claire , Dailey Gina M. , Nguyenla Xammy H. , Dis Erik Van , Esbin Meagan N. , Abidi Abrar , Stanley Sarah A. , Darzacq Xavier , Tjian Robert
Published: September 2020

Re-opening of communities in the midst of the ongoing COVID-19 pandemic has ignited a second wave of infections in many places around the world. Mitigating the risk of reopening will require widespread SARS-CoV-2 testing, which would be greatly facilitated by simple, rapid, and inexpensive testing methods. To this end, we evaluated several protocols for RNA extraction and RT-qPCR that are simpler and less expensive than prevailing methods. First, we show that isopropanol precipitation provides an effective means of RNA extraction from nasopharyngeal (NP) swab samples. Second, we evaluate direct addition of NP swab samples to RT-qPCR reactions without an RNA extraction step. We describe a simple, inexpensive swab collection solution suitable for direct addition, which we validate using contrived swab samples. Third, we describe an open-source master mix for RT-qPCR and show that it permits detection of viral RNA in NP swab samples. Lastly, we show that an end-point fluorescence measurement provides an accurate diagnostic readout without requiring a qPCR thermocycler. Adoption of these simple, inexpensive methods has the potential to significantly reduce the time and expense of COVID-19 testing.
Graphene nanoplatelet and Graphene oxide functionalization of face mask materials inhibits infectivity of trapped SARS-CoV-2
Authors: Maio Flavio De , Palmieri Valentina , Babini Gabriele , Augello Alberto , Palucci Ivana , Perini Giordano , Salustri Alessandro , De Spirito Marco , Sanguinetti Maurizio , Delogu Giovanni , Rizzi Laura Giorgia , Cesareo Giulio , Soon-Shiong Patrick , Sali Michela , Papi Massimiliano
Published: September 2020

Recent advancements in bidimensional nanoparticles such as Graphene nanoplatelets (G) and the derivative Graphene oxide (GO) have the potential to meet the need for highly functional personal protective equipment (PPE) that confers increased protection against SARS-CoV-2 infection and the spread COVID-19. The ability of G and GO to interact with and bind microorganisms as well as RNA and DNA provides an opportunity to develop engineered textiles for use in PPE. The face masks widely used in health care and other high-risk settings for COVID transmission provide only a physical barrier that decreases likelihood of infection and do not inactivate the virus. Here, we show pre-incubation of viral particles with free GO inhibits SARS-CoV-2 infection of VERO cells. Highly relevant to PPE materials, when either polyurethane or cotton material was loaded with G or GO and culture medium containing SARS-CoV-2 viral particles either filtered through or incubated with the functionalized materials, the infectivity of the medium was nearly completely inhibited. The findings presented here constitute an important nanomaterials-based strategy to significantly increase face mask and other PPE efficacy in protection against the SARS-CoV-2 virus and COVID-19 that may be applicable to additional anti-SARS-CoV-2 measures including water filtration, air purification, and diagnostics.

One Sentence Summary

Cotton and polyurethane materials functionalized with bidimensional Graphene nanoplatelets trap SARS-CoV-2 and have the potential to reduce spread of COVID-19.
Pathologic and molecular responses to neoadjuvant trastuzumab and/or lapatinib from a phase II randomized trial in HER2-positive breast cancer (TRIO-US B07)
Authors: Hurvitz Sara A. , Caswell-Jin Jennifer L. , McNamara Katherine L. , Zoeller Jason J. , Bean Gregory R. , Dichmann Robert , Perez Alejandra , Patel Ravindranath , Zehngebot Lee , Allen Heather , Bosserman Linda , DiCarlo Brian , Kennedy April , Giuliano Armando , Calfa Carmen , Molthrop David , Mani Aruna , Chen Hsiao-Wang , Dering Judy , Adams Brad , Kotler Eran , Press Michael F. , Brugge Joan S. , Curtis Christina , Slamon Dennis J.
Published: September 2020

In this neoadjuvant trial (TRIO-US B07), participants with early-stage HER2-positive breast cancer (N=128) were randomized to receive trastuzumab (T), lapatinib (L), or both (TL) as HER2-targeted therapy, with each participant given one cycle of this designated anti-HER2 therapy alone followed by six cycles of standard combination chemotherapy with the same anti-HER2 therapy. We observed similar pathologic complete response (pCR) rates between T and TL, and a lower pCR rate with L. Higher-level amplification of HER2 and hormone receptor-negative status were associated with a higher pCR rate. Higher pre-treatment immune infiltrate trended toward higher pCR rate in T-treated groups, and greater HR expression correlated with lower immune infiltrate. Large shifts in tumor, immune, and stromal gene expression occurred after one cycle of HER2-targeted therapy. In contrast to pCR rates, the L-containing arms exhibited greater proliferation reduction than T at this timepoint. Immune expression signatures increased in all arms after one cycle of HER2-targeted therapy, decreasing again by the time of surgery. Our results inform approaches to early assessment of sensitivity to anti-HER2 therapy and shed light on the role of the immune microenvironment in response to HER2-targeted agents.
THE REMOTE ANALYSIS OF BREATH SOUND IN COVID-19 PATIENTS: A SERIES OF CLINICAL CASES
Authors: Furman E. , Charushin A. , Eirikh E. , Furman G. , Sokolovsky V. , Malinin S. , Sheludko V.
Published: September 2020

Background

Respiratory sounds have been recognized as a possible indicator of behavior and health. Computer analysis of these sounds can indicate of characteristic sound changes caused by COVID-19 and can be used for diagnosis of this illness.

Purpose

The communication aim is development of fast remote computer-assistance diagnosis of COVID-19, based on analysis of respiratory sounds.

Materials and Methods

Fast Fourier transform (FFT) was applied for analyses of respiratory sounds recorded near the mouth of 9 COVID-19 patients and 4 healthy volunteers. Sampling rate was 48 kHz.

Results

Comparing of FFT spectrums of the respiratory sounds of the patients and volunteers we proposed numerical healthy-ill criterions.

Conclusions

The proposed computer method, based on analysis of the FFT spectrums of respiratory sounds of the patients and volunteers, allows one to automatically diagnose COVID-19 with sufficiently high diagnostic values. This method can be applied at development of noninvasive self-testing kits for COVID-19.
E-cigarette use and combustible tobacco cigarette smoking uptake among non-smokers, including relapse in former smokers: umbrella review, systematic review and meta-analysis
Authors: Baenziger Olivia Nina , Ford Laura , Yazidjoglou Amelia , Joshy Grace , Banks Emily
Published: September 2020

Combustible tobacco smoking is a leading cause of death and disability worldwide. E-cigarettes are promoted for smoking cessation, but evidence on how their use relates to smoking uptake is limited. We searched PubMed, Scopus, Web of Science, PsychINFO (Ovid), Medline (Ovid) and Wiley Cochrane Library in April 2020. Studies of non-smokers - never, not current, and former smokers - with a baseline measure of e-cigarette use and an outcome measure of combustible smoking uptake were included. Of 6,225 studies identified, 3 systematic reviews (incorporating 13 primary research studies) and 12 additional studies were included in umbrella and top-up systematic reviews, respectively. All 25 studies found increased risk of smoking uptake with e-cigarette exposure, although magnitude varied substantially. Using a random-effects model, comparing e-cigarette users versus non-e-cigarette users, among never-smokers at baseline the odds ratio (OR) for smoking initiation was 3.25 (95%CI 2.61-4.05, I2 85.7%) and among non-smokers at baseline the OR for current smoking was 2.87 (95%CI 1.97-4.19, I2 90.1%). Among former smokers, smoking relapse was higher in e-cigarette users versus non-users (OR=2.40, 95% CI 1.50-3.83, I2 12.3%). Across multiple settings, non-smokers who use e-cigarettes are consistently more likely than non-e-cigarettes users to initiate combustible cigarette smoking and become current smokers; risk magnitude varied, with an average of around three times the odds. Former smokers using e-cigarettes have over twice the odds of relapse as non-e-cigarettes users. This study is the first to our knowledge to review and pool data on the latter topic.
High-throughput quantitation of SARS-CoV-2 antibodies in a single-dilution homogeneous assay
Authors: Kainulainen Markus H. , Bergeron Eric , Chatterjee Payel , Chapman Asheley P. , Lee Joo , Chida Asiya , Tang Xiaoling , Wharton Rebekah E. , Mercer Kristina B. , Petway Marla , Jenks Harley M. , Flietstra Timothy D. , Schuh Amy J. , Satheshkumar Panayampalli S. , Chaitram Jasmine M. , Owen S. Michele , Finn M. G. , Goldstein Jason M. , Montgomery Joel M. , Spiropoulou Christina F.
Published: September 2020

SARS-CoV-2 emerged in late 2019 and has since spread around the world, causing a pandemic of the respiratory disease COVID-19. Detecting antibodies against the virus is an essential tool for tracking infections and developing vaccines. Such tests, primarily utilizing the enzyme-linked immunosorbent assay (ELISA) principle, can be either qualitative (reporting positive/negative results) or quantitative (reporting a value representing the quantity of specific antibodies). Quantitation is vital for determining stability or decline of antibody titers in convalescence, efficacy of different vaccination regimens, and detection of asymptomatic infections. Quantitation typically requires two-step ELISA testing, in which samples are first screened in a qualitative assay and positive samples are subsequently analyzed as a dilution series. To overcome the throughput limitations of this approach, we developed a simpler and faster system that is highly automatable and achieves quantitation in a single-dilution screening format with sensitivity and specificity comparable to those of ELISA.

One sentence summary

Protein complementation enables mix-and-read SARS-CoV-2 serology that rivals sensitivity and specificity of ELISA but excels in throughput and quantitation.
Review of evidence regarding attributes and behaviours of smokers as smoking prevalence falls, including evidence relevant to the ‘hardening hypothesis’
Authors: Harris Miranda , Martin Melonie , Yazidjoglou Amelia , Ford Laura , Lucas Robyn M , Banks Emily
Published: September 2020

To review evidence relevant to Australia and similar high-income countries regarding continuing smokers’ motivation, dependence and quitting behaviour as smoking prevalence declines, to assess whether population “hardening” (decreasing propensity to quit) or “softening” (the converse) is occurring. MEDLINE, PsychINFO, Scopus, Web of Science and Cochrane Library were searched to July 2019, using terms related to smoking and hardening, for reviews and large, population-based repeat cross-sectional studies. There were additional searches of reference lists and citations of key research articles. Two reviewers screened half the titles and abstracts each, and two reviewers screened all full texts independently using tested criteria. Four reviewers independently and systematically extracted data from eligible publications, with one reviewer per study, checked by another reviewer. Of 265 titles identified, three reviews and ten repeat cross-sectional studies (not included in the reviews) were included. All three reviews concluded that hardening has not occurred among the general smoking population over time. Of the ten repeated cross-sectional studies, five examined motivation, nine examined dependence, five examined hardcore smoking, and two examined quit outcomes over time. All found a lack of hardening and most found softening within the smoking population, consistent across hardening indicators, definitions, countries (and tobacco control environments) and time periods examined. Declining smoking prevalence has been accompanied by softening within the population of smokers, characterised by increasing motivation to quit and reduced dependency. Based on the weight of the available evidence from high-income countries, the “hardening hypothesis” should be rejected.
Risk assessment of vector-borne disease transmission using spatiotemporal network model and climate data with an application of dengue in Bangladesh
Authors: Riad Mahbubul H , Cohnstaedt Lee W , Scoglio Caterina M
Published: September 2020

Vector-borne disease risk assessment is crucial to optimize surveillance, preventative measures (vector control), and resource allocation (medical supplies). High arthropod abundance and host interaction strongly correlate to vector-borne pathogen transmission. Increasing host density and movement increases the possibility of local and long-distance pathogen transmission. Therefore, we developed a risk assessment framework using climate (average temperature and rainfall) and host demographic (host density and movement) data, particularly suitable for regions with unreported or under-reported incidence data. This framework consisted of a spatiotemporal network-based approach coupled with a compartmental disease model and a non-homogeneous Gillespie algorithm. One-month and two-month lagged temperature and rainfall data have been used to develop the correlation of climate data with vector abundance and host-vector interactions. This correlation can be expressed as vectorial capacity— a parameter, which governs the spreading of infection from an infected host to a susceptible via vectors. As an example, the novel risk assessment framework is applied for dengue in Bangladesh. Vectorial capacity is inferred for each week throughout a year using average monthly temperature and rainfall data, while the whole country is divided into some spatial locations (upazilas). Long-distance pathogen transmission is expressed with human movement data in the spatiotemporal network. We have identified the spatiotemporal suitability of dengue spreading in Bangladesh as well as the significant-incidence window and peak incidence period. Analysis of yearly dengue data variation suggests the possibility of a significant outbreak with a new serotype introduction. The outcome of the framework comprises of weather-dependent spatiotemporal suitability maps and probabilistic risk maps for spatial infection spreading. This framework is capable of vector-borne disease risk assessment without historical incidence data and can be a useful tool for preparedness with accurate human movement data.
Trabeculae microstructure parameters serve as effective predictors for marginal bone loss of dental implant in the mandible
Authors: Zhang Hengguo , Shan Jie , Zhang Ping , Chen Xin , Jiang Hongbing
Published: September 2020

Marginal bone loss (MBL) is one of the leading causes of dental implant failure. This study aimed to investigate the feasibility of machine learning (ML) algorithms based on trabeculae microstructure parameters to predict the occurrence of severe MBL. Eighty-one patients (41 severe MBL cases and 40 normal controls) were involved in the current study. Four ML models, including support vector machine (SVM), artificial neural network (ANN), logistic regression (LR), and random forest (RF), were employed to predict severe MBL. The area under the receiver operating characteristic (ROC) curve (AUC), sensitivity, and specificity were used to evaluate the performance of these models. At the early stage of functional loading, severe MBL cases showed a significant increase of structure model index and trabecular pattern factor in peri-implant alveolar bone. The SVM model exhibited the best outcome in predicting MBL (AUC = 0.967, sensitivity = 91.67%, specificity=100.00%), followed by ANN (AUC = 0.928, sensitivity = 91.67%, specificity=93.33%), LR (AUC = 0.906, sensitivity = 91.67%, specificity = 93.33%), RF (AUC = 0.842, sensitivity = 75.00%, specificity = 86.67%). Together, ML algorithms based on the morphological variation of trabecular bone can be used to predict severe MBL.
Evaluation of Serum Zinc Concentration in Vitiligo, A Case-Control Study
Authors: Ahmed Ahmed Abdul-Aziz , Ahmed Hayder Saad , Abdulqader Ahmed Talib
Published: September 2020

Background

Vitiligo is an acquired autoimmune pigmentary disorder characterized by ivory white patches. Zinc is proposed to have an immune modulatory, antioxidant and antiapoptotic properties in vitiligo patients.The aim of this study is to evaluate serum zinc in vitiligo patients.

Patients and methods

This is case–control study conducted from December 2019 to May 2020. The study included 50 patient with vitiligo and 50 age- and sex-matched controls.A 2 ml venous blood sample was taken from patients and controls by zinc-free syringe and was measured by atomic absorption spectrophotometry.

Results

The mean serum zinc level was 73.14±19.32 in patients group and 85.36±14.14 in controls group (p-value=0.005). It also was 77.65±22.07 and 82.84±14.32 in male patients and controls, respectively. In female patients, it was 70.82±17.65and in female controls was 82.88±13.79(p-value=0.02). Regarding the residence, the mean serum zinc level in patients group was 70.13±21.4 in urban and 76.39±17.73 in rural area. In controls group, mean serum zinc was 83.25±14.12 and 89.11±13.77 in urban and rural area, respectively (p-value=0.003). According to the clinical patterns of vitiligo, the mean serum zinc observed was 75.32±19.64 in vitiligo vulgaris, 70.45±21.23 in acrofacial vitiligo and 68.7±17.61 in segmental vitiligo (p-value=0.68).

Conclusion

Serum zinc level was significantly low in patients with vitiligo but not associated with the type of vitiligo or family history of autoimmune diseases. It was even lower when vitiligo is associated with nail changes than vitiligo without any nail abnormalities.
Genetic association studies of fibromuscular dysplasia identify new risk loci and shared genetic basis with more common vascular diseases
Authors: Georges Adrien , Yang Min-Lee , Berrandou Takiy-Eddine , Bakker Mark , Dikilitas Ozan , Kiando Soto Romuald , Ma Lijiang , Satterfield Benjamin A. , Sengupta Sebanti , Yu Mengyao , Deleuze Jean-François , Dupré Delia , Hunker Kristina L. , Kyryachenko Sergiy , Liu Lu , Amar Laurence , Brummett Chad M. , Coleman Dawn M. , d’Escamard Valentina , de Leeuw Peter , Fendrikova-Mahlay Natalia , Kadian-Dodov Daniella , Li Jun Z. , Lorthioir Aurélien , Pappaccogli Marco , Prejbisz Aleksander , Smigielski Witold , Stanley James C. , Zawistowski Matthew , Zhou Xiang , Zoellner Sebastian ,   FEIRI investigators,   International stroke genetics consortium (ISGC) intracranial aneurysm working group,   Megastroke, De Buyzere Marc L. , Debette Stéphanie , Dobrowolski Piotr , Drygas Wojciech , Gornik Heather L. , Olin Jeffrey W. , Piwonski Jerzy , Rietzschel Ernst R. , Ruigrok Ynte , Vikkula Miikka , Celinska Ewa Warchol , Januszewicz Andrzej , Kullo Iftikhar J. , Azizi Michel , Jeunemaitre Xavier , Persu Alexandre , Kovacic Jason C. , Ganesh Santhi K. , Bouatia-Naji Nabila
Published: September 2020

Fibromuscular dysplasia (FMD) is an arteriopathy that presents clinically by hypertension and stroke, mostly in early middle-aged women. We report results from the first genome-wide association meta-analysis of FMD including 1962 FMD cases and 7100 controls. We confirmedPHACTR1and identified three new loci (LRP1, ATP2B1, andLIMA1)associated with FMD. Transcriptome-wide association analysis in arteries identified one additional locus (SLC24A3). FMD associated variants were located in arterial-specific enhancers active in vascular smooth muscle cells and fibroblasts. Target genes are broadly involved in mechanisms related to actin cytoskeleton and intracellular calcium homeostasis, central to vascular contraction. Cross-trait linkage disequilibrium analyses identified positive genetic correlations with blood pressure, migraine and intracranial aneurysm, and an inverse correlation with coronary artery disease, independent from the genetics of blood pressure.
Association between corticosteroids and intubation or death among patients with COVID-19 pneumonia in non-ICU settings: an observational study using of real-world data from 51 hospitals in France and Luxembourg
Authors:   The COCORICO Collaborative Group, Tran Viet-Thi , Mahévas Matthieu , Bani-Sadr Firouze , Robineau Olivier , Perpoint Thomas , Perrodeau Elodie , Gallay Laure , Ravaud Philippe , Goehringer François , Lescure François-Xavier
Published: September 2020

Objective

To assess the effectiveness of corticosteroids on outcomes of patients with mild COVID-19 pneumonia.

Methods

We used routine care data from 51 hospitals in France and Luxembourg to assess the effectiveness of corticosteroids at 0.8 mg/kg/day eq. prednisone (CTC group) vs standard of care (no-CTC group) among patients ≤ 80 years old with COVID-19 pneumonia requiring oxygen without mechanical ventilation. The primary outcome was intubation or death at Day 28. Baseline characteristics of patients were balanced using propensity score inverse probability of treatment weighting.

Results

Among the 891 patients included in the analysis, 203 were assigned to the CTC group. At day 28, corticosteroids did not reduce the rate of the primary outcome (wHR 0.92, 95% CI 0.61 to 1.39) nor the cumulative death rate (wHR 1.03, 95% CI 0.54 to 1.98). Corticosteroids significantly reduced the rate of the primary outcome for patients requiring oxygen ≥ at 3L/min (wHR 0.50, 95% CI 0.30 to 0.85) or C-Reactive Protein (CRP) ≥ 100mg/L (wHR 0.44, 95%CI 0.23 to 0.85). We found a higher number of hyperglycaemia events among patients who received corticosteroids, but number of infections were similar across the two groups.

Conclusions

We found no association between the use of corticosteroids and intubation or death in the broad population of patients ≤80 years old with COVID-19 hospitalized in non-ICU settings. However, the treatment was beneficial for patients with ≥ 3L/min oxygen or CRP ≥ 100mg/L at baseline. These data support the need to confirm the right timing of corticosteroids for patients with mild COVID.

Short summary

We assessed the effectiveness of corticosteroids among patients ≤ 80 years old with COVID-19, in non-ICU settings. Our results support the use of corticosteroids for patients receiving oxygen at ≥3L/min or with a C-reactive protein ≥ 100mg/L at baseline.
Modeling the Spread and Control of COVID-19
Authors: Trivedi Ashutosh , Sreenivas Nanda Kishore , Rao Shrisha
Published: September 2020

Data-centric models of COVID-19 have been tried, but have certain
limitations. In this work, we propose an agent-based model of the epidemic in a
confined space of agents representing humans. An extension to the SEIR model
allows us to consider the difference between the appearance (black-box view) of
the spread of disease, and the real situation (glass-box view). Our model allows
for simulations of lockdowns, social distancing, personal hygiene, quarantine,
and hospitalization, with further considerations of different parameters such as
the extent to which hygiene and social distancing are observed in a population.
Our results give qualitative indications of the effects of various policies and
parameters; for instance, that lockdowns by themselves are extremely unlikely to
bring an end to an epidemic and may indeed make things worse, that social
distancing matters more than personal hygiene, and that the growth of infection
comes down significantly for moderately high levels of social distancing and
hygiene, even in the absence of herd immunity.

The code and documentation for this work can be accessed from
https://github.com/ABM-for-Covid/ABM-for-Covid-19. We
have also created an interactive application (https://abmforcovid.org) for anyone to run experiments
and test with their own strategies.
Digital Health Interventions in Palliative Care: A Systematic Meta-Review and Evidence Synthesis
Authors: Finucane Anne M. , O’Donnell Hannah , Lugton Jean , Swenson Connie , Pagliari Claudia
Published: September 2020

Digital health interventions (DHIs) have the potential to improve the accessibility and effectiveness of palliative care but heterogeneity amongst existing systematic reviews presents a challenge for evidence synthesis. This rigorous meta-review applied a structured search of 10 databases from 2006 to 2020, revealing 21 relevant systematic reviews, encompassing 332 unique publications. Most reviews were moderate quality. Interventions delivered via videoconferencing (17%), electronic healthcare records (16%) and phone (13%) were most frequently described. DHIs were typically used in palliative care for education (20%), symptom management (15%), decision-making support (13%), information provision or management (13%), and communication (9%). Positive impacts were reported on education, decision-making, information-sharing, communication, and costs. Impacts on symptom management were either positive or showed no harmful effects. However often DHIs were described but not evaluated. Responsive pragmatic research designs are now needed to guide further evaluation, implementation and to inform future service innovation.
Meta-analysis of the clinical performance of commercial SARS-CoV-2 nucleic acid, antigen and antibody tests up to 22 August 2020
Authors: Van Walle I , Leitmeyer K , Broberg E K
Published: September 2020

We reviewed the clinical performance of SARS-CoV-2 nucleic acid, viral antigen and antibody tests based on 94739 test results from 157 published studies and 20205 new test results from 12 EU/EEA Member States. Pooling the results and considering only results with 95% confidence interval width ≤5%, we found 4 nucleic acid tests, among which 1 point of care test, and 3 antibody tests with a clinical sensitivity ≥95% for at least one target population (hospitalised, mild or asymptomatic, or unknown). Analogously, 9 nucleic acid tests and 25 antibody tests, among which 12 point of care tests, had a clinical specificity of ≥98%. Three antibody tests achieved both thresholds. Evidence for nucleic acid and antigen point of care tests remains scarce at present, and sensitivity varied substantially. Study heterogeneity was low for 8/14 (57.1%) sensitivity and 68/84 (81.0%) specificity results with confidence interval width ≤5%, and lower for nucleic acid tests than antibody tests. Manufacturer reported clinical performance was significantly higher than independently assessed in 11/32 (34.4%) and 4/34 (11.8%) cases for sensitivity and specificity respectively, indicating a need for improvement in this area. Continuous monitoring of clinical performance within more clearly defined target populations is needed.
Physiological Effect of Prone Positioning in Mechanically Ventilated SARS- CoV-2 Infected Patients with Severe ARDS: Preliminary Analysis of an Observational Study
Authors: Roy Avishek , Behera Srikant , Pande Aparna , Bhattacharjee Anirban , Bhattacharyya Amrita , Baidya Dalim K , Anand Rahul K , Ray Bikash R , Subramaniam Rajeshwari , Maitra Souvik
Published: September 2020

Prone position ventilation has been shown to decrease mortality and improve oxygenation in ARDS patients. With best of our knowledge, no study reported physiological effect of prone position in SARS-CoV-2 infected ARDS patients. In this prospective observational study, data of n=20 consecutive laboratory confirmed SARS-CoV-2 patients with severe ARDS as per Berlin definition was included. Data of 20 patients analyzed with a median (Interquartile range, IQR) age of 56 (45.5-67) y and median (IQR) P/F ratio of 56 (54-66) with a median (IQR) PEEP of 12 (12-14) before initiation of prone position. Seventy-five percentage (95% CI 53.1-88.8) patients were prone responders at 16h prone session and 50 (95% CI 29.9-70.1) % patients were sustained responders. There was a significant decrease in plateau airway pressure (p<0.0001), peak airway pressure (p<0.0001) and driving pressure(p<0.0001) and increase in static compliance (p=0.001), P/F ratio (p<0.0001), PaO2 (p=0.0002)and SpO2 (p=0.0004) at 4h and 16h since initiation of prone session and also after return of supine position. Prone position in SARS-CoV-2 infected severe ARDS patients is associated with improvement in lung compliance and oxygenation in two-third of the patients and persisted in half of the patients.
Influenza season 2019: analysis of 143 hospitalized cases
Authors: Bisso Indalecio Carboni , Prado Eduardo , Cantos Joaquin , Massó Agustín , Staneloni Inés , Román Eduardo San , Huespe Iván , Heras Marcos Las
Published: September 2020

Introduction

Influenza virus infection is a latent public health problem, affecting millions of people through the planet, and it is an important cause of morbidity and mortality. In Argentina, there is a significant absence of data regarding influenza severe respiratory disease and, therefore, a lack of knowledge about the impact of this disease at health institutions.

Objectives

Analysis of clinical characteristics, image findings and laboratory variables in patients with influenza viruses during 2019.

Methods

Retrospective, single-centre study, we analyzed all confirmed cases of influenza in a high complexity hospital from Buenos Aires.

Results

143 patients with influenza virus were hospitalized in this period of time. The 98.6% were infected by type A influenza, and most of them 61.5% were H1N1 subtype.

Median age was 71 years (IQR 60 - 82), 77.6% were older than 70 years, and 88.1% had at least one coexisting illness. 39.1% of the patients required intensive care, 11.1% invasive mechanical ventilation and 4.1% died during hospitalization.

Conclusion

Mortality and severity were similar to previous series of non-pandemic influenza. Analysis of annual data would be valuable in order to document the severity of influenza hospitalizations by ageJgroup and comorbidities according to the circulating influenza viruses.
Variation of SARS-CoV-2 viral loads by sample type, disease severity and time: a systematic review
Authors: Edwards Thomas , Santos Victor S. , Wilson Anne L. , Cubas-Atienzar Ana I. , Kontogianni Konstantina , Williams Christopher T. , Adams Emily R. , Cuevas Luis E.
Published: September 2020

Background

To describe whether SARS-CoV-2 viral loads (VLs) and cycle thresholds (CTs) vary by sample type, disease severity and symptoms duration.

Methods

Systematic searches were conducted in MEDLINE, EMBASE, BioRxiv and MedRxiv. Studies reporting individual SARS-CoV-2 VLs and/or CT values from biological samples. Paired reviewers independently screened potentially eligible articles. CT values and VLs distributions were described by sample type, disease severity and time from symptom onset. Differences between groups were examined using Kruskal-Wallis and Dunn ‘s tests (post-hoc test). The risk of bias was assessed using the Joanna Briggs Critical Appraisal Tools.

Results

14 studies reported CT values, 8 VLs and 2 CTs and VLs, resulting in 432 VL and 873 CT data points. VLs were higher in saliva and sputum (medians 4.7×108 and 6.5×104 genomes per ml, respectively) than in nasopharyngeal and oropharyngeal swabs (medians 1.7×102 and 4.8×103). Combined naso/oropharyngeal swabs had lower CT values (i.e. higher VLs) than single site samples (p=<0.0001). CT values were also lower in asymptomatic individuals and patients with severe COVID-19 (median CT 30 for both) than among patients with moderate and mild symptoms (31.4 and 31.3, respectively). Stool samples were reported positive for a longer period than other specimens.

Conclusion

VLs are higher in saliva and sputum and in individuals who are asymptomatic of with severe COVID-19. Diagnostic testing strategies should consider that VLs vary by sample type, disease severity and time since symptoms onset.

This systematic review found a higher viral load in saliva and sputum than in nasopharyngeal swabs, in asymptomatic individuals and patients with severe COVID-19. Diagnostic testing strategies should consider the type of sample, disease severity and the time since symptoms onset.
Deep Learning Approach to Parse Eligibility Criteria in Dietary Supplements Clinical Trials Following OMOP Common Data Model
Authors: Bompelli Anusha , Li Jianfu , Xu Yiqi , Wang Nan , Wang Yanshan , Adam Terrence , He Zhe , Zhang Rui
Published: September 2020

Dietary supplements (DSs) have been widely used in the U.S. and evaluated in clinical trials as potential interventions for various diseases. However, many clinical trials face challenges in recruiting enough eligible patients in a timely fashion, causing delays or even early termination. Using electronic health records to find eligible patients who meet clinical trial eligibility criteria has been shown as a promising way to assess recruitment feasibility and accelerate the recruitment process. In this study, we analyzed the eligibility criteria of 100 randomly selected DS clinical trials and identified both computable and non-computable criteria. We mapped annotated entities to OMOP Common Data Model (CDM) with novel entities (e.g., DS). We also evaluated a deep learning model (Bi-LSTM-CRF) for extracting these entities on CLAMP platform, with an average F1 measure of 0.601. This study shows the feasibility of automatic parsing of the eligibility criteria following OMOP CDM for future cohort identification.