bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence evolution of SARS-CoV-2 infection in the Municipality of São Paulo, 2020 - 2021
Authors: Albuquerque Jose O M , Kamioka Gabriela A , Madalosso Geraldine , Costa Selma A , Ferreira Paula B , Pino Francisco A , Sato Ana Paula S , Carvalho Ana Carolina A , Amorim Ana Beatriz P , Aires Caroline C , Kataoka Ana Paula A G , Savani Elisa S M M , Bessa Thirsa A F , Aguiar Breno S , Failla Marcelo A , Santos Edson A , Brito Edjane M T , Santos Maria C H , Silva Solange M S , Caldeira Luiz A V , Zamarco Luiz C , Fonseca Sandra M S , Lima Marcia M C , Marques Ivanilda A , Silva Fabiana E V , Glasser Paula R , Burihan Patrícia C P R , Cavazzana Cinthya L , Lara Renata C , Mello Debora S , Pellini Alessandra C G , Nishio Fernando Y , Kian Fernanda M , Braga Elza S , Bertelli Nilza M P , Fracini Wagner , Gonçalves Marcelo D A , Zular Paulete S , Piva Regiane S , de Masi Eduardo 
Published: June 2021

AbstractObjectivesTo estimate the evolution of the prevalence of SARS-CoV-2 virus infection among residents aged 18 years or over in the municipality of São Paulo.MethodsThis is a population-based household survey conducted every 15 days, between June and September 2020 and January and February 2021. In total, 11 phases were performed. The presence of antibodies against SARS-CoV-2 was identified in venous blood using a lateral flow test, Wondfo Biotech. In the last phase, it was combined with an immunoenzymatic test, Euroimmun. Participants also answered a semi-structured questionnaire on sociodemographic and economic factors and social distancing measures. Prevalence estimates and 95% confidence intervals were estimated according to the region, Human Development Index, sex, age group, ethnicity, education, income and variables associated with risk or prevention of the infection. To compare the frequencies among the categories of each variable, the chi-square test with Rao Scott correction was used, considering a 5% significance level.ResultsIn total, 23,397 individuals were interviewed and had their samples collected. The estimated prevalence of antibodies against SARS-CoV-2 ranged from 9.7% (95%CI: 7.9-11.8%) to 25.0% (95%CI: 21.7-28.7). The prevalence of individuals with antibodies against SARS-CoV-2 was higher among black and pardo people, people with lower schooling, people with lower income and among residents of regions with lower Human Development Index. The lowest prevalences were associated with recommended measures of disease protection. The proportion of asymptomatic infection was 45.1%.ConclusionThe estimated prevalence of SARS-CoV-2 infection was lower than the cumulative incidence variation, except for the last phase of the study. The differences in prevalence estimates observed among subpopulations showed the social inequality as a risk of infection. The lower prevalence observed among those who could follow prevention measures reinforce the need to maintain the social distancing measures as ways to prevent SARS-CoV-2 infection.
A Short Plus Long-Amplicon Based Sequencing Approach Improves Genomic Coverage and Variant Detection In the SARS-CoV-2 Genome
Authors: Arana Carlos , Liang Chaoying , Brock Matthew , Zhang Bo , Zhou Jinchun , Chen Li , Cantarel Brandi , SoRelle Jeffrey , Hooper Lora V. , Raj Prithvi 
Published: June 2021

AbstractHigh viral transmission in the COVID-19 pandemic has enabled SARS-CoV-2 to acquire new mutations that impact genome sequencing methods. The ARTIC.v3 primer pool that amplifies short amplicons in a multiplex-PCR reaction is one of the most widely used methods for sequencing the SARS-CoV-2 genome. We observed that some genomic intervals are poorly captured with ARTIC primers. To improve the genomic coverage and variant detection across these intervals, we designed long amplicon primers and evaluated the performance of a short (ARTIC) plus long amplicon (MRL) sequencing approach. Sequencing assays were optimized on VR-1986D-ATCC RNA followed by sequencing of nasopharyngeal swab specimens from five COVID-19 positive patients. ARTIC data covered >90% of the virus genome fraction in the positive control and four of the five patient samples. Variant analysis in the ARTIC data detected 67 mutations, including 66 single nucleotide variants (SNVs) and one deletion in ORF10. Of 66 SNVs, five were present in the spike gene, including nt22093 (M177I), nt23042 (S494P), nt23403 (D614G), nt23604 (P681H), and nt23709 (T716I). The D614G mutation is a common variant that has been shown to alter the fitness of SARS-CoV-2. Two spike protein mutations, P681H and T716I, which are represented in the B.1.1.7 lineage of SARS-CoV-2, were also detected in one patient. Long-amplicon data detected 58 variants, of which 70% were concordant with ARTIC data. Combined analysis of ARTIC +MRL data revealed 22 mutations that were either ambiguous (17) or not called at all (5) in ARTIC data due to poor sequencing coverage. For example, a common mutation in the ORF3a gene at nt25907 (G172V) was missed by the ARTIC assay. Hybrid data analysis improved sequencing coverage overall and identified 59 high confidence mutations for phylogenetic analysis. Thus, we show that while the short amplicon (ARTIC) assay provides good genomic coverage with high throughput, complementation of poorly captured intervals with long amplicon data can significantly improve SARS-CoV-2 genomic coverage and variant detection.
Awareness and Agreement with Neurofibromatosis Care Guidelines among Neurofibromatosis Specialists
Authors: Merker Vanessa L. , Knight Pamela , Radtke Heather B. , Yohay Kaleb , Ullrich Nicole J. , Plotkin Scott R. , Jordan Justin T. 
Published: June 2021

AbstractIntroductionGiven the wide range of neurofibromatoses (NF) symptoms and medical specialties involved in NF care, we sought to evaluate the level of awareness of, and agreement with, published NF clinical guidelines among United States NF specialists.MethodsAn anonymous, cross-sectional online survey was distributed to attendees of a large NF research conference. Respondents self-reported demographics, practice characteristics, awareness of seven NF guideline publications, and level of agreement with up to 40 individual guidelines using a 5-point Likert scale. We calculated the proportion of guidelines that each clinician rated “strongly agree”, and assessed for differences in guideline awareness and agreement by respondent characteristics.ResultsSixty-three clinicians (49% female; 80% academic practice) across >8 medical specialties completed the survey. Awareness of each guideline publication ranged from 53%-79% of respondents; specialists had higher awareness of publications endorsed by their medical professional organization (p<0.05). The proportion of respondents who “strongly agree” with individual guidelines ranged from 17%-83%; for 16 guidelines, less than 50% of respondents “strongly agree”. There were no significant differences in overall agreement with guidelines based on clinicians’ gender, race, specialty, years in practice, practice type (academic/private practice/other), practice location (urban/suburban/rural), or involvement in NF research (p>0.05 for all).ConclusionsWe identified wide variability in both awareness of, and agreement with, published NF care guidelines among NF experts. Future efforts should focus on evidence-based, consensus-driven methods to update and disseminate guidelines across this multi-specialty group. Patients and caregivers should also be consulted to anticipate barriers to accessing and implementing guideline-driven care.
Rapid spread of the SARS-CoV-2 δ variant in French regions in June 2021
Authors: Alizon Samuel , Haim-Boukobza Stéphanie , Foulongne Vincent , Verdurme Laura , Trombert-Paolantoni Sabine , Lecorche Emmanuel , Roquebert Bénédicte , Sofonea Mircea T. 
Published: June 2021

AbstractAnalysing 9,030 variant-specific tests performed on SARS-CoV-2 positive samples collected in France between 31 May and 21 June 2021 reveals a rapid growth of the δ variant in 3 French regions. The next weeks will prove decisive but the magnitude of the estimated transmission advantages could represent a major challenge for public health authorities.
FAMILY’S RESILIENCE IN CAREGIVING ELDERLY WITH DEMENTIA: A SYSTEMATIC REVIEW
Authors: Pradana Anung Ahadi , Rohayati  
Published: June 2021

AbstractObjectiveDementia patients have complex needs that may become a burden to those who caregive them. They are treated at home by family members due to financial limitations and lack of support from health services. Therefore, the measurement of self-resilience in caregivers needs special attention from professionals.MethodThis study used a systematic review method from 4 databases consisting of the CINAHL, ProQuest, PubMed, and Google Scholar between 2015 till 2020; 17 articles were considered to meet the inclusion criteria.ResultsCaregiver of elderly with dementia has a tendency to experience burdens that affect the quality of the care performed. The level of resilience that caregivers have can help reduce the level of burden they experience and improve their quality of life.ConclusionsSocial support and formal support by health workers for caregivers have a significantly positive effect in increasing the level of resilience of caregivers.
Evidence for a serotonergic subtype of major depressive disorder: A NeuroPharm-1 study
Authors: Köhler-Forsberg Kristin , Ozenne Brice , Landman Elizabeth B. , Larsen Søren V. , Poulsen Asbjørn S. , Dam Vibeke H. , Ip Cheng-Teng , Jørgensen Anders , Meyer Michal , Eiberg Hans R. L. , Svarer Claus , Jørgensen Martin B. , Frokjaer Vibe G. , Knudsen Gitte M. 
Published: June 2021

AbstractSelective serotonin reuptake inhibitors (SSRIs) are the first line pharmacological treatment of Major Depressive Disorder (MDD), but only about half of patients benefit from it. Cerebral serotonin 4 receptor (5-HT4R) binding measured with positron emission tomography (PET) is inversely related to serotonin levels and can serve as a proxy for brain serotonin levels. We here determine if 5-HT4R differs between healthy and MDD individuals and if it is associated with successful outcomes of serotonergic treatment of MDD. We [11C]-SB207145 PET-scanned 100 (71 F) untreated patients with moderate to severe MDD and 91 (55 F) healthy controls; 40 patients were re-scanned after 8 weeks treatment. All patients started treatment with the SSRI escitalopram and were followed clinically after 1, 2, 4, 8 and 12 weeks. Treatment response was measured as change from baseline.Before treatment, patients with MDD had 8% lower global 5-HT4R binding than controls (95%CI[-13.1%;-2.5%], p<0.001). Non-responders did not differ from controls, whereas remitters had 9% lower binding than controls ([-16.1%;-2.7%], p=0.004). Independent of treatment outcomes, patients reduced their neostriatal 5-HT4R binding (−9%, [-12.8%;-5.0%], p<0.001) after serotonergic intervention.Overall, patients with MDD have lower cerebral 5-HT4R binding than controls, suggesting that 5-HT4R is a biomarker for MDD. The observation that SSRI treatment leads to reduced neostriatal 5-HT4R binding supports that the treatment does indeed increase brain 5-HT levels. Patients who remit to SSRIs have lower cerebral 5-HT4R prior to treatment than controls whereas non-responders do not differ. We propose that non-responders to SSRI’s constitute a subgroup with non-serotonergic depression.ClinicalTrials.gov Identifier: NCT02869035Registry name: Treatment Outcome in Major Depressive DisorderURL: https://clinicaltrials.gov/ct2/show/NCT02869035?term=NCT02869035&draw=2&rank=1
WHotLAMP: A simple, inexpensive, and sensitive molecular test for the detection of SARS-CoV-2 in saliva
Authors: Ng David , Pinharanda Ana , Vogt Merly C. , Litwin-Kumar Ashok , Stearns Kyle , Thopte Urvashi , Cannavo Enrico , Enikolopov Armen , Fiederling Felix , Kosmidis Stylianos , Noro Barbara , Rodrigues-Vaz Ines , Shayya Hani , Andolfatto Peter , Peterka Darcy S. , Tabachnik Tanya , D’Armiento Jeanine , Goldklang Monica , Bendesky Andres 
Published: June 2021

AbstractDespite the development of effective vaccines against SARS-CoV-2, epidemiological control of the virus is still challenging due to slow vaccine rollouts, incomplete vaccine protection to current and emerging variants, and unwillingness to get vaccinated. Therefore, frequent testing of individuals to identify early SARS-CoV-2 infections, contact-tracing and isolation strategies remain crucial to mitigate viral spread. Here, we describe WHotLAMP, a rapid molecular test to detect SARS-CoV-2 in saliva. WHotLAMP is simple to use, highly sensitive (3.6 viral RNA copies per microliter of saliva) and specific, as well as inexpensive, making it ideal for frequent screening. Moreover, WHotLAMP does not require toxic chemicals or specialized equipment and thus can be performed in point-of-care settings, and may also be adapted for resource-limited environments or home use. While applied here to SARS-CoV-2, WHotLAMP can be modified to detect other pathogens, making it adaptable for other diagnostic assays, including for use in future outbreaks.
Seroprevalence of COVID-19 in HIV Population
Authors: Naik Shivdas Rajaram , Kumar Swasthi S , Mittal Ankit , Swain Satish , Ranjan Sanjay , Soneja Manish , Sinha Sanjeev , Nischal Neeraj , Jorwal Pankaj , Chaturvedi Pradeep , Wig Naveet 
Published: June 2021

AbstractBackgroundSeroprevalence helps us to estimate the exact prevalence of a disease in a population. Although the world has been battling this pandemic for more than a year now, we still do not know about the burden of this disease in people living with HIV/AIDS (PLHA). Seroprevalence data in this population subset is scarce in most parts of the world, including India. The current study aimed to estimate the seroprevalence of anti-SARS-CoV-2 IgG antibody among PLHA.AimTo determine the seroprevalence of SARS-CoV-2 antibodies in PLHA.MethodThis was a cross-sectional study conducted at a tertiary care hospital in North India. We recruited HIV positive patients following at the ART centre of the institute. Anti-SARS-CoV-2 IgG antibody levels targeting recombinant spike receptor-binding domain (RBD) protein of SARS CoV-2 were estimated in serum sample by the chemiluminescent immunoassay method.ResultsA total of 164 patients were recruited in the study with a mean age (±SD) of 41.2 (±15.4) years, of which 55% were male. Positive serology against SARS CoV-2 was detected in 14% patients (95% CI: 9.1-20.3%).ConclusionThe seroprevalence of COVID-19 infection in PLHA was lower than the general population in the same region, which ranged from 23.48% to 28.3% around the study period.
Knowledge and use of lactational amenorrhea as a family planning method among adolescent mothers in Uganda: a secondary analysis of Demographic and Health Surveys between 2006 and 2016
Authors: Birabwa Catherine , Bakkabulindi Pamela , Wafula Solomon T , Waiswa Peter , Benova Lenka 
Published: June 2021

ABSTRACTObjectiveTo assess the level of knowledge and use of lactational amenorrhea method (LAM) among adolescents in Uganda between 2006 and 2016 using nationally representative data from Demographic and Health Surveys (DHS).DesignCross-sectional design involving analysis of three DHS (2006, 2011, and 2016) in Uganda.SettingThe data was collected in Uganda. The DHS are nationally representative surveys on a wide range of indicators including contraception knowledge and use.ParticipantsA total of 8,250 adolescents (15-19 years) and 7,110 young women (20-24 years) were included.Primary outcome measureUse of LAM among adolescents and young women with a livebirth within six months before each survey.ResultsIn 2016, less than 1% of eligible adolescents correctly used LAM and 56% were passively benefitting from LAM. The median duration of postpartum amenorrhea (PPA) among adolescents in 2016 was 6.9 months, declining from 8.3 months in 2006. Compared to adolescents, eligible young women had higher knowledge of LAM and higher medianPPA duration in 2016. The percentage of eligible adolescents who met the LAM criteria irrespective of whether they reported LAM use (protected by LAM) decreased from 76% in 2006 to 57% in 2016. More than 50% of eligible adolescents were aware of LAM in 2016, increasing from 6% in 2006, potentially in part due to change in survey question.ConclusionDespite increasing awareness of LAM, reported and correct use of LAM was low among adolescents who could benefit from this method in Uganda, and declining over time. Support for adolescents to harness the benefits of correct LAM use should be increased. Additional research is needed to better understand the dynamics of LAM use in adolescents, including the transition to use of other modern contraceptive methods.Strengths and limitations of this study➢Lactational amenorrhea method has the potential to promote healthy timing and spacing of pregnancies and to reduce repeat adolescent births, yet, its use among Ugandan adolescents has not been examined.➢This study provides useful insights into the behavior of adolescents mothers which can be targeted to improve their reproductive knowledge and wellbeing.➢The study used data from three standardised nationally representative surveys, thus findings are generalizable and comparable over time and across age groups.➢Assessment of knowledge of LAM was affected by a change in the phrasing of the question in 2016, thus providing limited comparability with previous surveys.➢The measurement of LAM use was based on self-report.
Molecular epidemiology and antimicrobial resistance phenotype of paediatric bloodstream infections caused by Gram-negative bacteria in Oxfordshire, UK
Authors: Lipworth Sam , Vihta Karina-Doris , Davies Tim , Wright Sarah , Tabirao Merline , Chau Kevin , Vaughan Alison , Kavanagh James , Barker Leanne , George Sophie , Segal Shelley , Paulus Stephane , Barrett Lucinda , Oakley Sarah , Jeffery Katie , Butcher Lisa , Peto Tim , Crook Derrick , Walker Sarah , Kadambari Seilesh , Stoesser Nicole 
Published: June 2021

AbstractObjectivesGram-negative organisms are common causes of bloodstream infection (BSI) during the neonatal period and early childhood. Whilst several large studies have characterised these isolates in adults, equivalent data (particularly incorporating whole genome sequencing) is lacking in the paediatric population.MethodsWe performed an epidemiological and sequencing based analysis of Gram-negative bloodstream infections in children <18 years old between 2008 and 2018 in Oxfordshire, UK.Results327 isolates (296 successfully sequenced) from 287 patients were included. The burden of infection was predominantly in neonates (124/327[38%]). Most infections were caused byEscherichia coli (149/327[46%])/Klebsiellaspp. (69/327[21%]) andEnterobacter hormaechei (34/327[10%]). There was no evidence of an increasing incidence ofE. coliBSIs (IRRy 0.96, 95%CI 0.90-1.30, p=0.30) and forKlebsiellaspp. there was some evidence that the incidence decreased slightly (IRRy 0.91, 95%CI 0.83-1.00, p=0.06). Similarly the proportion of antimicrobial resistant (across all antimicrobial classes evaluated) isolates did not change over time, though we did identify some evidence of sub-breakpoint increases in gentamicin resistance IRRy 1.86, 95%CI 1.33-2.58, pheterogeneity=0.002. The population structure ofE. coliBSI isolates in neonates and children mirrors that in adults with a predominance of STs 131/95/73/69 and the same proportion of O-antigen serotypes covered by the ExPEC-4V vaccine. In most cases there was no evidence of transmission/point-source acquisition and whole genome sequencing was able to refute a previously suspectedSerratia marcescensoutbreak.ConclusionOur findings support continued use of current empirical treatment guidelines and suggest that O-antigen targeted vaccines may have a role in reducing the incidence of neonatal sepsis.
Determination of IgG1 and IgG3 SARS-CoV-2 spike protein and nucleocapsid binding – Who is binding who and why?
Authors: IIes Jason K , Zmuidinaite Raminta , Sadée Christoph , Gardiner Anna , Lacey Jonathan , Harding Stephen , Wallis Gregg , Patel Roshani , Roblett Debra , Heeney Jonathan , Baxendale Helen , Iles Ray K 
Published: June 2021

AbstractThe involvement of IgG3 in the humoral immune response to SARS-CoV2 infection has been implicated in the pathogenesis of ARDS in COVID-19. The exact molecular mechanism is unknown but may be due to the differential ability of IgG3 Fc region to fix complement and stimulate cytokine release. We examined convalescent patients’ antibodies binding to immobilised nucleocapsid and spike protein by MALDI-ToF mass spectrometry. IgG3 was a major immunoglobulin found in all samples. Differential analysis of the spectral signatures found for nucleocapsid versus spike protein demonstrated that the predominant humoral immune response to nucleocapsid was IgG3, whilst against spike it was IgG1. However, the spike protein displayed a strong affinity for IgG3 itself which it would bind from control plasma samples as well as from those previously infected with SARS-CoV2, much in the way Protein-G binds IgG1. Furthermore, detailed spectral analysis indicated a mass shift consistent with hyper-glycosylation or glycation was a characteristic of the IgG3 captured by the spike protein.
NATURAL HISTORY OF LAFORA DISEASE A Prognostic Systematic Review and Individual Participant Data Meta-Analysis
Authors: Pondrelli Federica , Muccioli Lorenzo , Licchetta Laura , Mostacci Barbara , Zenesini Corrado , Tinuper Paolo , Vignatelli Luca , Bisulli Francesca 
Published: June 2021

ABSTRACTObjectiveTo describe the clinical course of Lafora Disease (LD) and identify predictors of outcome by means of a prognostic systematic review with individual participant data meta-analysis.MethodsA search was conducted on MEDLINE and Embase with no restrictions on publication date. Only studies reporting genetically confirmed LD cases were included. Kaplan-Meier estimate was used to assess probability of death and of loss of autonomy. Univariable and multivariable Cox regression models with mixed effects (clustered survival data) were performed to evaluate prognostic factors.ResultsSeventy-three papers describing 298 genetically confirmed LD cases were selected. Mean age at disease onset was 13.4 years (SD 3.7), with 9.1% aged≥ 18 years. Overall survival rates in 272 cases were 93% [95% CI 89-96] at 5 years, 62% [95% CI 54-69] at 10 years and 57% [95% CI 49-65] at 15 years. Median survival time was 11 years. The probability of loss of autonomy in 110 cases was 45% [95% CI 36-55] at 5 years, 75% [95% CI 66-84] at 10 years, and 83% [95% CI 74-90] at 15 years. Median loss of autonomy time was 6 years. Asian origin and age at onset <18 years emerged as negative prognostic factors, while type of mutated gene and symptoms at onset were not related to survival or disability.ConclusionsThis study documented that half of patients survived at least 11 years. The notion of actual survival rate and prognostic factors is crucial to design studies on the effectiveness of upcoming new disease-modifying therapies.