bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of SARS-CoV-2 RNA in fourteen wastewater treatment systems in Uttarakhand and Rajasthan States of North India
Authors: Arora Sudipti , Nag Aditi , Rajpal Ankur , Tiwari Satya Brat , Sethi Jasmine , Sutaria Devanshi , Rajvanshi Jayana , Saxena Sonika , Srivastava Sandeep , Kazmi A. A. , Tyagi Vinay Kumar 
Published: September 2020

AbstractWe investigated the presence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) RNA at different treatment stages of 15 wastewater treatment plants (WWTPs) in two North Indian states of Rajasthan and Uttarakhand. Untreated (influent), biologically treated, and disinfected wastewater samples were collected from May to August 2020. The qualitative analysis of the wastewater for the presence of SARS-CoV-2 RNA was done using different pre-processing methods. SARS-CoV-2 RNA was detected in 11 out of 39 wastewater samples in Jaipur district and 5 out of 17 wastewater samples in Haridwar District using Reverse-Transcriptase Quantitative Polymerase Chain Reaction (RT-qPCR) for qualitative detection. None of the 56 samples tested for post-secondary or tertiary treatment were found positive for SARS-CoV-2 RNA. The findings indicate that there are no SARS-CoV-2 related risks involved with using the treated effluent for non-potable applications. In contrast, untreated wastewater may be a potential route of viral transmission to the WWTP and sanitation workers. Future studies are imperative to understand the survival rates of these viruses in wastewater.Graphical AbstractHighlightsMild to moderate genome load observed in the municipal wastewater samples.Increased patient numbers post-lockdown correspond to a decrease in the CTvalue of genes.Presence of SARS-CoV-2 genome load was observed in untreated wastewater.E gene was present in abundance in wastewaters as compared to the N gene and RdRp gene.SARS-CoV-2 genome load was absent in secondary and tertiary treated effluent.
COVerAGE-DB: A database of age-structured COVID-19 cases and deaths
Authors: Riffe Tim , Acosta Enrique ,   COVerAGE-DB project team
Published: September 2020

AbstractCOVerAGE-DB is an open access database including cumulative counts of confirmed COVID-19 cases, deaths, and tests by age and sex. Original data and sources are provided alongside data and measures in age-harmonized formats. The database is still in development, and at this writing, it includes 87 countries, and 195 subnational areas. Cumulative counts of COVID-19 cases, deaths, and tests are recorded daily (when possible) since January 2020. Many time series thus fully capture the first pandemic wave and the beginning of later waves. An international team, composed of more than 60 researchers, contributed to the collection of data and metadata in COVerAGE-DB from governmental institutions, as well as to the design and implementation of the data processing and validation pipeline. We encourage researchers interested in supporting this project to send a message to the email: coverage-db@demogr.mpg.de
Environmental risk factors for gastric cancer: a protocol for umbrella review of meta-analyses
Authors: Kim Min Seo , Kim Seungwon , Park Sungsoo 
Published: September 2020

ABSTRACTGastric cancer is the fifth most commonly diagnosed cancer globally, accounting for 5.7% of the new cancer cases in 2018[1]. Gastric cancer remains an important global concern because it is the third leading cause of cancer death[1] and its increasing incidence[2]. Therefore, it is crucial to develop prevention strategies for gastric cancer. Helicobacter pylori infection, a WHO class I carcinogen, is a significant risk factor of gastric cancer; however, only 0.5% of infected individuals would develop gastric cancer[3]. This data suggests that there are other additional risk factors for gastric cancer. A large body of research has been performed to investigate the association between various environmental factors and gastric cancer, including dietary factors, tobacco smoking, and alcohol drinking. However, the precision and strength of these existing studies need to be clarified. Umbrella review is one of the most useful tools for a clear understanding of a broad topic area. It provides a comprehensive overall picture of findings for specific questions based on high-level evidence of published systemic reviews and meta-analyses[4]. Thus, this study aimed to conduct an umbrella review of systemic reviews and meta-analyses that investigated gastric cancer risk factors.
Microfluidic Affinity Profiling reveals a Broad Range of Target Affinities for Anti-SARS-CoV-2 Antibodies in Plasma of COVID-19 Survivors
Authors: Schneider Matthias M. , Emmenegger Marc , Xu Catherine K. , Morales Itzel Condado , Meisl Georg , Turelli Priscilla , Zografou Chryssa , Zimmermann Manuela R. , Frey Beat M. , Fiedler Sebastian , Denninger Viola , Jacquat Raphaël P. B. , Madrigal Lidia , Ilsley Alison , Kosmoliaptsis Vasilis , Fiegler Heike , Trono Didier , Knowles Tuomas P. J. , Aguzzi Adriano 
Published: September 2020

AbstractThe clinical outcome of SARS-CoV-2 infections, which can range from asymptomatic to lethal, is crucially shaped by the concentration of antiviral antibodies and by their affinity to their targets. However, the affinity of polyclonal antibody responses in plasma is difficult to measure. Here we used Microfluidic Antibody Affinity Profiling (MAAP) to determine the aggregate affinities and concentrations of anti-SARS-CoV-2 antibodies in plasma samples of 42 seropositive individuals, 19 of which were healthy donors, 20 displayed mild symptoms, and 3 were critically ill. We found that dissociation constants, Kd, of anti-receptor binding domain antibodies spanned 2.5 orders of magnitude from sub-nanomolar to 43 nM. Using MAAP we found that antibodies of seropositive individuals induced the dissociation of pre-formed spike-ACE2 receptor complexes, which indicates that MAAP can be adapted as a complementary receptor competition assay. By comparison with cytopathic-effect based neutralisation assays, we show that MAAP can reliably predict the cellular neutralisation ability of sera, which may be an important consideration when selecting the most effective samples for therapeutic plasmapheresis and tracking the success of vaccinations.
Maintenance Electroconvulsive Therapy and hospital re-admission days among patients with mental illness in Malaysia
Authors: Francis Benedict , Han Ng Yit , Ip Julian Wong Joon , Thin Ling Shiau , Gill Jesjeet Singh , Hui Koh Ong , Petrus Chiara Francine , Sulaiman Ahmad Hatim 
Published: September 2020

AbstractBackgroundRelapse prevention strategies are important as part of optimal patient care. As such, maintenance electroconvulsive therapy (mECT) is an important treatment modality to keep patients in remission longer. However, the practice of mECT in Malaysia, specifically and Asia generally, is still scarce.AimsOur study aimed to explore the characteristics of patients receiving maintenance ECT (mECT) and further investigate whether this treatment modality reduces re-admission days in patients with severe mental illness.MethodsA retrospective chart review study design was employed. The medical records of 22 patients followed up at University Malaya Medical Centre, Malaysia were analysed with regards to the outcome measures, which was days of re-admission post mECT, Potential confounders were controlled for via stratification analysis.ResultsThere was a significant reduction in re-admission days post mECT (p<0.001, r:0.85) across all the variables analysed. The variable with the biggest effect size were patients younger than 60 years old (p:0.01, r:0.70), followed by medication with polypharmacy (p:0.002, r: 0.65). The magnitude of reduction in re-admissions was greater in the schizophrenia spectrum group compared to the affective disorders group (r: 0.64 vs. 0.57).ConclusionOur study provides data regarding the efficacy of mECT in significantly reducing days of re-admission in patients with treatment resistant schizophrenia spectrum illness and affective disorders. As widespread usage of mECT is still lacking in Asia, our results is encouraging for more practitioners to prescribe mECT for their patients in order to reduce rates of hospital re-admission.
Molecular diagnosis of non-syndromic hearing loss patients using a stepwise approach
Authors: Wang Jing , Xiang Jiale , Chen Lisha , Luo Hongyu , Xu Xiuhua , Li Nan , Cui Chunming , Xu Jingjing , Song Nana , Peng Jiguang , Peng Zhiyu 
Published: September 2020

ABSTRACTBackgroundHearing loss is one of the most common birth disorders in humans with an estimated prevalence of 1-3 in every 1000 newborns. This study has investigated the molecular etiology of a deaf cohort using a stepwise strategy to effectively diagnose patients and the challenges faced to verify genetic heterogenicity and the variable mutation spectrums of hearing loss.MethodsIn order to target known pathogenic variants, multiplex PCR plus next-generation sequencing was applied in the first tier, while undiagnosed cases were further referred to exome sequencing. A total of 92 unrelated patients with nonsyndromic hearing loss were enrolled.ResultsIn total, 64% (59/92) of patients were molecularly diagnosed, 44 of which were identified in the first tier by multiplex PCR plus sequencing. Of 48 undiagnosed patients from the first tier, exome sequencing identified eleven diagnoses (23%, 11/48) and four probably diagnoses (8%, 4/48). The rate of secondary findings of exome sequencing in our cohort is 3.4%.ConclusionThe research presented a molecular diagnosis spectrum of 92 non-syndromic hearing loss patients and demonstrated the benefits of using the stepwise diagnostic approach in the genetic test of the non-syndromic hearing loss patient cohort.
Urban versus rural prevalence of intestinal parasites using multi-parallel qPCR in Colombia
Authors: Bryan Patricia E. , Romero Marcela , Sánchez Miryan , Torres Giovanny , Gómez Wilber , Restrepo Marcos , Restrepo Alejandro , Mejia Rojelio 
Published: September 2020

AbstractStool samples from 122 children from urban slum (n = 72) and rural (n = 50) areas were analyzed using multi-parallel real-time qPCR to determine the prevalence of intestinal parasites from two communities in Colombia. Findings indicated a prevalence of 86.1% Blastocystis spp., 62.5% Giardia intestinalis, 19.4% Cryptosporidium spp., 19.4% Ascaris lumbricoides, and 5.6% Trichuris trichiura in an urban slum; and 76% Blastocystis spp., 68% Giardia intestinalis, 20% Entamoeba histolytica, 50% Ascaris lumbricoides, 46% Trichuris trichiura and 2% Strongyloides stercoralis in rural areas. Polyparasitism was higher in rural (58%) compared to urban (25%) areas (p = 0.001). Trichuris trichiura burden was higher in the rural area (p = 0.002). Over 40% of helminth infections in rural areas had a heavy parasite burden by WHO classification. Over half of urban and rural children were infected with Giardia intestinalis and Blastocystis spp. Our data provides accurate epidemiologic surveillance for public health interventions.
First quarter chronicle of COVID-19: an attempt to measure governments’ response
Authors: Şahin Şule , del Carmen Boado-Penas María , Constantinescu Corina , Eisenberg Julia , Henshaw Kira , Hu Maoqi , Wang Jing , Zhu Wei 
Published: September 2020

AbstractThe crisis caused by COVID-19 revealed the global unpreparedness for handling the impact of a pandemic. In this paper, we present a first quarter chronicle of COVID-19 in Hubei China, Italy and Spain, specifically their infection speed, death and fatality rates. By fitting distributions to these rates, we look for the effectiveness of government measures during the pandemic through a number of statistical approaches.
Putting (Big) Data in Action: Saving Lives with Countrywide Population Movement Monitoring Using Mobile Devices during the COVID‐19 Crisis
Authors: Szocska Miklos , Pollner Peter , Schiszler Istvan , Joo Tamas , Palicz Tamas , McKee Martin , Telekom Nyrt. Magyar , Magyarorszag Zrt. Telenor , Sohonyai Adam , Szoke Jozsef , Toth Adam , Gaal Peter 
Published: September 2020

AbstractMany countries have implemented strict social distancing measures in the hope of reducing transmission of SARS-CoV-2 but the effectiveness of these measures is determined by the willingness of populations to comply with restrictions. Consequently, a system of monitoring population movement using existing data sources can inform those making decisions about policy responses to the COVID-19 pandemic.We describe a collaboration with all 3 major domestic telecommunication companies in Hungary to use aggregated anonymous mobile phone usage data to calculate two indices for assessing the effect of movement restrictions: a “mobility-index” and a “stay-at-home (or resting) index”. The strengths and weaknesses of this approach are compared with the smartphone-based, COVID-19 Community Mobility Reports from Google.Data generated by mobile phones have long been identified as a potential means to analyse mass population movement, but its operationalisation raises several technical questions, such as making sense of Call Detail Records, collation of data from different mobile network providers, and personal data protection concerns. The method described here addresses these issues and offers an effective and inexpensive tool to monitor the impact of social distancing measures, achieving high levels of accuracy and resolution. Especially in populations where uptake of smartphones is modest, this method has certain advantages over app-based solutions, with greater population coverage, but it is not an alternative to smartphone-based solutions used for contact tracing and quarantine monitoring. We believe that this method can easily be adapted by other countries.
Downregulation of Defensin genes in SARS-CoV-2 infection
Authors: Idris Mohammed M , Banu Sarena , Siva Archana B , Nagaraj Ramakrishnan 
Published: September 2020

AbstractDefensins, crucial components of the innate immune system, play a vital role against infection as part of frontline immunity. Association of SARS-CoV-2 infection with defensins has not been investigated till date. In this study, we have investigated the expression of defensin genes in the buccal cavity during COVID-19 infection. Nasopharyngeal/Oropharyngeal swab samples collected for screening SARS-CoV-2 infection were analyzed for the expression of major defensin genes by the quantitative real-time reverse transcription polymerase chain reaction, qRT-PCR. 40 SARS-CoV-2 infected positive and 40 negative swab samples were selected for the study. Based on the RT-PCR analysis involving gene specific primer for defensin genes, 10 defensin genes were found to be expressed in the Nasopharyngeal/Oropharyngeal cavity. Six defensin genes were further found to be significantly downregulated in SARS-CoV-2 infected patients as against the control, negative samples based on differential expression analysis. The genes significantly downregulated were defensin beta 4A, 4B, 106B, 107B, 103A and defensin alpha 1B. Downregulation of several defensin genes suggests that innate immunity provided by defensins is or may be compromised in SARS-CoV-2 infection resulting in progression of the disease caused by the virus. Upregulation of defensin gene expression and use of defensin peptides could be attractive therapeutic interventions.
Sharing a household with children and risk of COVID-19: a study of over 300,000 adults living in healthcare worker households in Scotland
Authors: Wood Rachael , Thomson Emma C , Galbraith Robert , Gribben Ciara , Caldwell David , Bishop Jennifer , Reid Martin , Shah Anoop S V , Templeton Kate , Goldberg David , Robertson Chris , Hutchinson Sharon , Colhoun Helen , McKeigue Paul , McAllister David A 
Published: September 2020

AbstractBackgroundChildren are relatively protected from novel coronavirus infection (COVID-19). The reasons for this protection are not well understood but differences in the immune response to Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) have been implicated. If such differences are due to differential exposure to non-SARS-CoV-2 infectious agents, adults who are close contacts of children may partly share in this protection. Such a protective effect would have important implications for the lives of children, not least in terms of schooling.MethodsUsing a Scotland-wide record-linkage based occupational cohort comprising healthcare workers and members of their households, we examined whether sharing a household with young children (aged 0 to 11) attenuated the risk of hospitalisation with COVID-19, and/or testing positive for COVID-19 infection of any severity (any case of Covid-19). All healthcare workers directly employed by the National health Service (NHS) in Scotland, or contracted to provide general practice services, were included. Outcome and covariate data were obtained via linkage to Scotland-wide microbiology, drug prescribing, hospitalisation and death data.Results241,266 adults did not share a household with young children; 41,198, 23,783 and 3,850 shared a household with 1, 2 and 3 or more young children respectively. The risk of hospitalisation with COVID-19 was lower in those with one child and lower still in those with two or more children, adjusting for age the hazard ratio (HR) was 0.83 per child (95% CI 0.70-0.99). On additionally adjusting for sex, socioeconomic deprivation, occupation, professional role, staff/non-staff status, the number of adults and adolescents in each household, and comorbidity, the HR was 0.89 per child (95% CI 0.74-1.06). An association of the same magnitude, but more precisely estimated, was obtained for any case of COVID-19 (fully adjusted model, HR per child 0.89; 95% CI 0.84-0.95).ConclusionIncreased household exposure to young children was associated with an attenuated risk of testing positive for SARS-CoV-2 and appeared to also be associated with an attenuated risk of COVID-19 disease severe enough to require hospitalisation.
Transcriptomic Signaling Pathways involved in a naturalistic model of Inflammation-related Depression and its remission
Authors: Moisan Marie-Pierre , Foury Aline , Dexpert Sandra , Cole Steve W , Beau Cédric , Forestier Damien , Ledaguenel Patrick , Magne Eric , Capuron Lucile 
Published: September 2020

AbstractThis study aimed at identifying molecular biomarkers of inflammation-related depression in order to improve diagnosis and treatment. We performed whole-genome expression profiling from peripheral blood in a naturalistic model of inflammation-associated major depressive disorder (MDD) represented by comorbid depression in obese patients. We took advantage of the marked reduction of depressive symptoms and inflammation following bariatric surgery to test the robustness of the identified biomarkers. Depression was assessed during a clinical interview using Mini-International Neuropsychiatric Interview and the 10-item, clinician administered, Montgomery-Asberg Depression Rating Scale. From a cohort of 100 massively obese patients we selected 33 of them for transcriptomic analysis. Twenty-four of them were again analyzed 4-12 months after bariatric surgery. We conducted differential gene expression analyses before and after surgery in unmedicated MDD and non-depressed obese subjects. We found that TP53 (Tumor Protein 53), GR (Glucocorticoid Receptor) and NFκB (Nuclear Factor kappa B) pathways were the most discriminating pathways associated with inflammation-related MDD. These signaling pathways were processed in composite z-scores of gene expression that were used as biomarkers in regression analyses. Results showed that these transcriptomic biomarkers highly predicted depressive symptom intensity at baseline and their remission after bariatric surgery. While inflammation was present in all patients, GR signaling overactivation was found only in depressed ones where it may further increase inflammatory and apoptosis pathways. In conclusion, using an original model of inflammation-related depression and its remission without antidepressants, we provide molecular predictors of inflammation-related MDD and new insights in the molecular pathways involved.
Estimate of the actual number of COVID-19 cases from the analysis of deaths
Authors: Etchenique Roberto , Quiroga Rodrigo 
Published: September 2020

AbstractUsing the calculated values for the Infection Fatality Rate (IFR) of COVID-19 it is possible to estimate the prevalence of cases of infection in the city of Buenos Aires, Argentina, throughout the pandemic. The use of confirmed cases as a metric and their replacement by more reliable parameters such as death figures are discussed. The results are analyzed according to age ranges and possible sources of error in the estimates are established.
“We can’t just wish this thing away”: Caregiver perspectives on a child’s diagnosis of 3q29 deletion
Authors: Glassford Megan R. , Purcell Ryan H. , Pass Sarah , Murphy Melissa M. ,   The Emory 3q29 Project, Bassell Gary J. , Mulle Jennifer G. 
Published: September 2020

ABSTRACTObjectiveGenetic diagnoses are increasingly common in cases of intellectual disability and developmental delay. While ascertainment of a relatively common, well-studied variant may provide guidance related to treatments and developmental expectations, it is less clear how the diagnosis of a rare variant impacts caregivers, especially when the phenotype may include later onset manifestations such as psychosis. In the current study, we sought to identify caregiver concerns in the first qualitative study to assess the psychosocial impact of diagnosis on caregivers of individuals with 3q29 deletion syndrome (3q29Del), which is associated with a 40-fold increase in risk for psychosis.MethodParticipants were recruited from the national 3q29Del registry housed at Emory University (3q29deletion.org). Fifteen participants completed a semi-structured phone interview during which they were asked about their experiences before, during, and after their child received a diagnosis of 3q29Del. Interview responses were analyzed using the general inductive approach, and overarching themes were identified.ResultsWe identified the following overarching themes: difficult “diagnostic odyssey,” mixed feelings about diagnosis, frustration with degree of uncertainty, and importance of resources. Importantly, our data suggest that future risk for psychosis is often not disclosed by medical professionals, consistent with the experience of individuals with 22q11.2 deletion syndrome.ConclusionThese results highlight potential gaps in how caregivers are informed of risk for adult-onset conditions and point to key caregiver concerns for consideration in diagnosis of 3q29Del.