bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correlation between cervical HPV DNA detection and HPV16 seroreactivity measured with L1-only and L1+L2 viral capsid antigens
Authors: Trevisan Andrea , Candeias João M.G. , Thomann Patrícia , Villa Luisa L. , Franco Eduardo L. , Trottier Helen ,   the Ludwig-McGill Study Group
Published: June 2020

Introduction.Persistent human papillomavirus (HPV) type 16 infection is the main causal agent of cervical cancer. Most HPV infections clear spontaneously within 1–2 years. Although not all infected women develop detectable HPV antibodies, about 60–70 % seroconvert and retain their antibodies at low levels.Aim.We investigated if cervical HPV16 DNA positivity was associated with HPV16 seroreactivity measured with two different antigen formulations. We assessed if associations were influenced by co-infection with other HPV types and HPV16 viral load.Methodology.We used baseline data for women participating in the Ludwig–McGill cohort, a longitudinal investigation of the natural history of HPV infection and cervical neoplasia. The study enrolled 2462 Brazilian women from 1993 to 1997 (pre-vaccination). ELISA assays were based on L1-only or L1+L2 virus-like particles (VLPs). Seroreactivity was expressed as normalized absorbance ratios. HPV genotyping and viral load were evaluated by PCR protocols. Pearson’srwas used to measure correlations between interval-scaled variables. Serological accuracy in HPV16 DNA detection was assessed using receiver operating characteristic (ROC) curves. We analysed the association between HPV DNA positivity and HPV16 seroreactivity by linear regression.Results.Correlations between L1+L2 and L1-only VLPs for detection of HPV16 were poor (r=0.43 and 0.44 for dilutions 1 : 10 and 1 : 50, respectively). The protocol with the best accuracy was L1+L2 VLPs at serum dilution 1 : 10 (ROC area=0.73, 95 % CI: 0.65–0.85). HPV16 DNA positivity was correlated with HPV16 seroreactivity and was not influenced by co-infection or viral load. To a lesser degree, HPV16 seroreactivity was correlated with infection by other Alpha-9 papillomavirus species.Conclusion.HPV16 DNA positivity and HPV16 seroreactivity are strongly correlated. L1+L2 VLPs perform better than L1-only VLPs for detecting IgG antibodies to HPV16 in women infected with HPV16 or other Alpha-9 HPV species. This study advances our understanding of humoral immune responses against HPV16 by providing insights about the influence of VLP antigen composition to measure humoral immune response against naturally acquired HPV infection.
A how-to-guide to building a robust SARS-CoV-2 testing program at a university-based health system
Authors: Nimer Stephen D. , Chapman Jennifer , Reidy Lisa , Alencar Alvaro , Wu Yanyun , Williams Sion , Pagan Lazara , Gjolaj Lauren , MacIntyre Jessica , Triana Melissa , Vance Barbara , Andrews David , Fan Yao-Shan , Zhou Yi , Martinez Octavio , Garcia-Buitrago Monica , Cray Carolyn , Tekin Mustafa , McCauley Jacob , Ruiz Philip , Pagan Paola , Lamar Walter , Alencar Maritza , Bilbao Daniel , Prieto Silvia , Polania Maritza , Suarez Maritza , Lujardo Melissa , Campos Gloria , Morris Michele , Shukla Bhavarth , Caban-Martinez Alberto , Kobetz Erin , Parekh Dipen , Jorda Merce 
Published: June 2020

AbstractWhen South Florida became a hotspot for COVID-19 disease in March 2020, we faced an urgent need to develop test capability to detect SARS-CoV-2 infection. We assembled a transdisciplinary team of knowledgeable and dedicated physicians, scientists, technologists and administrators, who rapidly built a multi-platform, PCR- and serology-based detection program, established drive-thru facilities and drafted and implemented guidelines that enabled efficient testing of our patients and employees. This process was extremely complex, due to the limited availability of needed reagents, but outreach to our research scientists and to multiple diagnostic laboratory companies and government officials enabled us to implement both FDA authorized and laboratory developed testing (LDT)-based testing protocols. We analyzed our workforce needs and created teams of appropriately skilled and certified workers, to safely process patient samples and conduct SARS-CoV-2 testing and contact tracing. We initiated smart test ordering, interfaced all testing platforms with our electronic medical record, and went from zero testing capacity, to testing hundreds of healthcare workers and patients daily, within three weeks. We believe our experience can inform the efforts of others, when faced with a crisis situation.
SARS-CoV-2 in wastewater treatment plants
Authors: Collivignarelli Maria Cristina , Collivignarelli Carlo , Carnevale Miino Marco , Abbà Alessandro , Pedrazzani Roberta , Bertanza Giorgio 
Published: June 2020

AbstractAs for the SARS coronavirus in the 2003 epidemic, the presence of SARS-CoV-2 has been demonstrated in faeces and, in some cases, urine of infected people, as well as in wastewater. This paper proposes a critical review of the state of the art regarding studies on the presence of SARS-CoV-2 in wastewater and sewage sludge, the factors affecting its inactivation and the main proposed treatments, with the aim to provide useful information at operative level in order to better and safer manage wastewater and sewage sludge. Given the lack of literature on SARS-CoV-2, studies involving other HCoVs such as SARS-CoV and HCoV-229E have been also considered. In wastewater, the resistance of SARS-CoV has proven to be very limited, especially at temperatures above 20 °C, and the virus has been easily removed with the use of chlorine (> 0.5 mg L−1 for 30 min). For sewage sludge, based on in vitro experiments, it is suggested to increase the retention times before a possible reuse in agriculture only for precautionary purposes, since SARS-CoV-2 is unlikely to occur in the sludge. SARS-CoV-2 in wastewater might track the epidemic trends: although being extremely promising, an effective and wide application of this approach requires a deeper knowledge of the amounts of viruses excreted through the faeces and the actual detectability of viral RNA in sewage.
Asymmetry of auditory-motor speech processing is determined by language experience
Authors: Tang Ding-lan , Möttönen Riikka , Asaridou Salomi S. , Watkins Kate E. 
Published: June 2020

AbstractSpeech processing relies on interactions between auditory and motor systems and is asymmetrically organized in the human brain. The left auditory system is specialized for processing of phonemes, whereas the right is specialized for processing of pitch changes in speech that affect prosody. In speakers of tonal languages, however, processing of pitch (i.e., tone) changes that alter word meaning is left-lateralized. This indicates that linguistic function and language experience shape auditory speech processing asymmetries; their effect on auditory-motor speech processing remains unknown, however. Here, we investigated the asymmetry of motor contributions to auditory speech processing in speakers of tonal and non-tonal languages. We temporarily disrupted the left or right speech motor cortex using repetitive transcranial magnetic stimulation (rTMS) and measured the impact of these disruptions on auditory processing of phoneme and tone changes in sequences of syllables using electroencephalography (EEG). We found that disruption of the speech motor cortex in the left, but not the right hemisphere, impaired processing of phoneme changes in both language groups equally. In contrast, the effect of motor disruptions on processing of tone changes differed in tonal and non-tonal language groups: disruption of the left speech motor cortex significantly impaired processing of tone changes in tonal language speakers, whereas disruption of the right speech motor cortex modulated processing of tone changes in non-tonal speakers. We conclude that the contribution of the left and right speech motor cortex to auditory speech processing is determined by the functional role of the acoustic cues in the listener’s native language.Significance StatementThe principles underlying hemispheric asymmetries of auditory speech processing remain debated. The asymmetry of auditory speech processing is affected by the low-level acoustic cues, but also by their linguistic function. By combining TMS and EEG, we investigated the asymmetry of motor contributions to auditory speech processing in tonal and non-tonal language speakers. For the first time, we provide causal evidence that auditory-motor speech processing asymmetries are shaped by the functional role of the acoustic cues in the listener’s native language. The lateralised top-down motor influences are likely to affect asymmetry of speech processing in the auditory system.
Network Analysis and Human Single Cell Brain Transcriptomics Reveal Novel Aspects of Alpha-Synuclein (SNCA) Biology
Authors: Teeple Erin , Jindal Khushboo , Kiragasi Beril , Annaldasula Siddharth , Byrne Ann , Chai Lilly , Sadeghi Mahdiar , Kayatekin Can , Shankara Srinivas , Klinger Katherine W. , Sardi S. Pablo , Madden Stephen L. , Kumar Dinesh 
Published: June 2020

ABSTRACTAlpha-synuclein (SNCA) aggregates are pathological hallmarks of synucleinopathies, neurodegenerative disorders including Parkinson’s Disease (PD) and Lewy Body Dementia (LBD). Functional networks are not yet well-characterized for SNCA by CNS cell type. We investigated cell-specific differences in SNCA expression using Allen Brain Database single-nucleus RNA-seq data from human Middle Temporal Gyrus (MTG, 15,928 nuclei) and Anterior Cingulate Cortex (ACC, 7,258 nuclei). Weighted gene co-expression analysis (WGCNA) and hierarchical clustering identified a conserved SNCA co-expression module. Module genes were highly conserved (p < 10−10) and most highly expressed in excitatory neurons versus inhibitory neurons and other glial cells. SNCA co-expression module genes from ACC and MTG regions were then used to construct a protein-protein interaction (PPI) network, with SNCA empirically top hub. Genes in the SNCA PPI network were compared with genes nearest single nucleotide polymorphisms linked with PD risk in genome-wide association studies. 16 genes in our PPI network are nearest genes to PD risk loci (p < 0.0006) and 55 genes map within 100kb. Selected SNCA PPI network genes nearest PD risk loci were disrupted by CRISPR knock out gene editing for validation of network functional significance; disruption of STK39, GBA, and MBNL2 resulted in significantly elevated intracellularSNCAexpression.
Associations between COVID-19 infection, tobacco smoking and nicotine use, common respiratory conditions and inhaled corticosteroids: a prospective QResearch-Case Mix Programme data linkage study January-May 2020
Authors: Lindson Nicola , Gao Min , Hartmann-Boyce Jamie , Smith Margaret , Aveyard Paul , Young Duncan , Coupland Carol , Tan Pui San , Clift Ashley K. , Harrison David , Gould Doug , Pavord Ian D , Watkinson Peter , Hippisley-Cox Julia 
Published: June 2020

AbstractIntroductionEpidemiological and laboratory research seems to suggest that smoking and perhaps nicotine alone could reduce the severity of COVID-19. Likewise, there is some evidence that inhaled corticosteroids could also reduce its severity, opening the possibility that nicotine and inhaled steroids could be used as treatments.MethodsIn this prospective cohort study, we will link English general practice records from the QResearch database to Public Health England’s database of SARS-CoV-2 positive tests, Hospital Episode Statistics, admission to intensive care units, and death from COVID-19 to identify our outcomes: hospitalisation, ICU admission, and death due to COVID. Using Cox regression, we will perform sequential adjustment for potential confounders identified by separate directed acyclic graphs to:Assess the association between smoking and COVID-19 disease severity, and how that changes on adjustment for smoking-related comorbidity.More closely characterise the association between smoking and severe COVID-19 disease by assessing whether the association is modified by age (as a proxy of length of smoking), gender, ethnic group, and whether people have asthma or COPD.Assess for evidence of a dose-response relation between smoking intensity and disease severity, which would help create a case for causality.Examine the association between former smokers who are using NRT or are vaping and disease severity.Examine whether pre-existing respiratory disease is associated with severe COVID-19 infection.Assess whether the association between chronic obstructive pulmonary disease (COPD) and asthma and COVID-19 disease severity is modified by age, gender, ethnicity, and smoking status.Assess whether the use of inhaled corticosteroids is associated with severity of COVID-19 disease.To assess whether the association between use of inhaled corticosteroids and severity of COVID-19 disease is modified by the number of other airways medications used (as a proxy for severity of condition) and whether people have asthma or COPD.ConclusionsThis representative population sample will, to our knowledge, present the first comprehensive examination of the association between smoking, nicotine use without smoking, respiratory disease, and severity of COVID-19. We will undertake several sensitivity analyses to examine the potential for bias in these associations.
COVID 19 Pandemic: A Real-time Forecasts & Prediction of Confirmed Cases, Active Cases using the ARIMA model & Public Health in West Bengal, India
Authors: Sarkar Dibash , Biswas Moinak 
Published: June 2020

AbstractBackgroundCOVID-19 is an emerging infectious disease which has been declared a Pandemic by the World Health Organization (WHO) on March 11 2020. This pandemic has spread over the world in more than 200 countries. India is also adversely affected by this pandemic, and there are no signs of slowing down of the virus in coming time. The absence of a vaccine for COVID-19 is making the situation worse for the already overstretched Indian public health care system. As economic burden makes it increasingly difficult for our country to continue imposing control measures, it is vital for states like West Bengal to make predictions using time series forecasting for the upcoming cases, test kits, health care and estimated the requirement of Quarantine centers, isolation beds, ICU beds and ventilators for COVID-19 patients.ObjectiveThis study is forecasting the confirmed and active cases for COVID-19 until August, using time series ARIMA model & Public Health in West Bengal, India.MethodsWe used ARIMA model, and Auto ARIMA model for forecasting confirmed and active cases till the end of August month using time series data of COVID-19 cases in West Bengal, India from March 1, 2020, to June 4, 2020.ResultsWe are expecting that West Bengal will have around62279 ± 5000Cases by the end of August based on our forecasts. Meanwhile Maharashtra, Punjab, Gujarat and Delhi (UT) will be the most affected states, having the highest number of active and confirmed cases at the end of August.Discussion and ConclusionThis forecasts show a very crucial situation for West Bengal in coming days and, the actual numbers can go higher than our estimates of confirmed case as Lockdown 5.0 & Unlock 1.0 will be implemented from 1stJune 2020 in India, West Bengal will be observing a partial lift of the lockdown and in that case, there will be a surge in the number of daily confirmed and active cases. The requirement of Health care sector needs to be further improved isolation beds, ICUs and ventilators will also be needed to increase in that scenario. Inter State & Intra State Movement restrictions are lifted. Hence, Migrants returning to their homes due to loss of livelihood and income in the lockdown period may lead to a rise in the number of cases, which could not be accounted for in our projections. We suggest more of Public-Private Partnership (PPP) model in the health sector to accommodate COVID-19 patients adequately and reduce the burden of the already overstretched Indian public health care system, which will directly or indirectly affect the States in the time of crisis.
Predictors of Mental Health during the Covid-19 Pandemic in the US: role of economic concerns, health worries and social distancing
Authors: Kämpfen Fabrice , Kohler Iliana V. , Ciancio Alberto , de Bruin Wändi Bruine , Maurer Jürgen , Kohler Hans-Peter 
Published: June 2020

ObjectiveTo assess mental health in the US adult population in the Covid-19 pandemic and explore the roles of economic concerns, health worries and social distancing in shaping mental health outcomes.MethodsWe analyze online survey data from the “Understanding America Study” (UAS) that is representative of the US adult population and covers the period of March 10-31st 2020 (sample size: 6436).ResultsAbout 29% (CI:27.4-.30.4%) of the US adult population reported some depression/anxiety symptoms osver the study period, with symptoms deteriorating over the month of March. Worsening mental health was most strongly associated with concerns about the economic consequences of the pandemic, while concerns about the potential impact of the virus on respondents’ own health and the practice of social distancing also predicted the presence of depression and anxiety symptoms, albeit less strongly.ConclusionsOur findings point towards a major mental health crisis unfolding simultaneously with the pandemic in the US. They also highlight the importance of economic countermeasures and social policy for mitigating the impact of Covid-19 on adult mental health in the US over and above an effective public health response.
Training residents in underwater colonoscopies is more effective than in air colonoscopies
Authors: Vyas Dinesh , Chang Josiah , Goyal Megha , Obad Nashwan , Ramdass Prakash , Sodavarapu Soujanya 
Published: June 2020

AbstractBackgroundColonoscopy screenings are the most valuable tool in preventing colorectal mortalities. The traditional technique uses air-insufflation, but water-infusion is a newer colonoscopy technique which is rapidly becoming standard of care, as it may decrease patient discomfort and the need for analgesics and anesthetics. Research is still ongoing as to the comparability of detection rates between the two techniques. The purpose of this study was to determine if training residents in underwater colonoscopies is more effective than training them in traditional air-insufflation colonoscopies.MethodsThis study was a retrospective, single-institution study that compared the patient-related and procedure-related variables of 183 colonoscopies performed by two cohorts of physicians. In the first cohort, the gastroenterologist with a resident trainee performed an air colonoscopy. In the second, the gastroenterologist and resident trainee performed an underwater colonoscopy.ResultsFor patient-related variables, there was no significant difference in age, previous abdominal surgeries, or bowel preparation. There were more females in the underwater group, which is significant as females tend to be harder to scope due to the increased tortuosity of their colon. For procedural outcomes, there was no significant difference in adenoma detection rate, cecal intubation rate, or procedural complications (hypotension, bradycardia). On average, the water colonoscopies required less midazolam and fentanyl, although they did have a longer procedural time.ConclusionsOverall, these findings suggest that training residents in underwater colonoscopies may increase patient comfort and decrease complications with comparable success rates.
Th17 cells contribute to combination MEK inhibitor and anti-PD-L1 therapy resistance inKRAS/p53mutant lung cancers
Authors: Peng David H. , Rodriguez B. Leticia , Diao Lixia , Gaudreau Pierre-Olivier , Padhye Aparna , Kapere Joshua Ochieng , Class Caleb A. , Fradette Jared J. , Gibson Laura , Chen Limo , Wang Jing , Byers Lauren A. , Gibbons Don. L 
Published: June 2020

AbstractUnderstanding resistance mechanisms to targeted therapies and immune checkpoint blockade in mutant KRAS lung cancers is critical to developing novel combination therapies and improving patient survival. Here, we show that MEK inhibition enhanced PD-L1 expression while PD-L1 blockade upregulated MAPK signaling in mutant KRAS lung tumors. Combined MEK inhibition with anti-PD-L1 synergistically reduced lung tumor growth and metastasis, but tumors eventually developed resistance to sustained combinatorial therapy. Multi-platform profiling revealed that resistant lung tumors have increased infiltration of Th17 cells, which secrete IL-17 and IL-22 cytokines to promote lung cancer cell invasiveness and MEK inhibitor resistance. Antibody depletion of IL-17A in combination with MEK inhibition and PD-L1 blockade markedly reduced therapy-resistancein vivo. Clinically, increased expression of Th17-associated genes in melanoma patients treated with PD-1 blockade predicted poorer overall survival and response. Our study validates a triple combinatorial therapeutic strategy to overcome resistance to combined MEK inhibitor and PD-L1 blockade.
Characterizing the growing microorganisms at species level in 46 anaerobic digesters at Danish wastewater treatment plants: A six-year survey on microbiome structure and key drivers
Authors: Jiang Chenjing , Peces Miriam , Andersen Martin H. , Kucheryavskiy Sergey , Nierychlo Marta , Yashiro Erika , Andersen Kasper S. , Kirkegaard Rasmus H. , Hao Liping , Høgh Jan , Hansen Aviaja A. , Dueholm Morten S. , Nielsen Per H. 
Published: June 2020

AbstractAnaerobic digestion (AD) is a key technology at many wastewater treatment plants (WWTPs) for converting surplus activated sludge to methane-rich biogas. However, the limited number of surveys and the lack of comprehensive data sets have hindered a deeper understanding of the characteristics and associations between key variables and the microbiome composition. Here, we present a six-year survey of 46 anaerobic digesters, located at 22 WWTPs in Denmark, which is the largest known study of the microbial ecology of AD at WWTPs at a regional scale. For three types of AD (mesophilic, mesophilic with thermal hydrolysis pretreatment, and thermophilic), we present the typical value range of 12 key parameters including operational variables and performance parameters. The bacterial and archaeal microbiomes were analyzed at species-level resolution using amplicon sequencing in >1,000 samples and the new ecosystem-specific MiDAS 3 reference database. We detected 42 phyla, 1,600 genera and 3,584 species in the bacterial microbiome, where 70% of the genera and 93% of the species represented uncultivated taxa that were only classified based on MiDAS 3denovoplaceholder taxonomy. More than 40% of the 100 most abundant bacterial species did not grow in the digesters and were only present due to immigration with the feed sludge. Temperature, ammonium concentration, and pH were the main drivers shaping the microbiome clusters of the three types of ADs for both bacteria and for archaea. Within mesophilic digesters, feed sludge composition and other key parameters (organic loading rate, biogas yield, and ammonium concentration) correlated with the growing bacterial microbiome. Furthermore, correlation analysis revealed the main drivers for specific species among growing bacteria and archaea, and revealed the potential ecological function of many novel taxa. Our study highlights the influence of immigration on bacterial AD microbiome. Subsetting the growing microbes improves the understanding of the diversity and main drivers of microbiome assembly, and elucidates functionality of specific species-level microorganisms. This six-year survey provides a comprehensive insight into microbiome structure at species level, engineering and ecological performance, and a foundation for future studies of the ecological significance/characteristics and function of the novel taxa.