bluuebunny/crossref_metadata_2025_split huggingface dataset:
Serological response to COVID-19 vaccination in IBD patients receiving biologics
Authors: Wong Serre-Yu , Dixon Rebekah , Pazos Vicky Martinez ,   ICARUS-IBD Working Group, Gnjatic Sacha , Colombel Jean-Frederic , Cadwell Ken 
Published: March 2021

AbstractObjectiveThe impact of medications on COVID-19 vaccine efficacy in IBD patients is unknown, as patients with immunosuppressed states and/or treated with immunosuppressants were excluded from vaccine trials. To address this, we evaluated serological responses to COVID-19 vaccination with the SARS-CoV-2 spike (S) mRNA BNT162b2 (Pfizer-BioNTech) and mRNA-1273 (NIH-Moderna) vaccines in IBD patients enrolled in an ongoing SARS-CoV-2 sero-survey at the Icahn School of Medicine at Mount Sinai in New York City.DesignWe obtained sera from 48 patients who had undergone vaccination with one or two vaccine doses. Sera were tested for SARS-CoV-2 anti-RBD total immunoglobulins and IgG (Siemens COV2T and sCOVG assays), anti-Spike IgG (in-house ELISA), and anti-nucleocapsid antibodies (Roche).ResultsAll IBD patients (15/15) who completed two-dose vaccine schedules achieved seroconversion to high levels. Two IBD patients with history of COVID-19 infections and who were seropositive at baseline seroconverted to high levels after the first dose. Concurrent biologic use was 85% (41/48), including 33% of patients (16) on TNF antagonist monotherapy, 42% (17) on vedolizumab monotherapy, 6% (3) on vedolizumab combination therapy with thiopurine, and 8% (4) ustekinumab; 1 patient was receiving guselkumab for psoriasis. Three patients (6%) were on oral steroids at the time of vaccination.ConclusionIBD patients receiving biologics can seroconvert with robust serological responses after complete Pfizer-BioNTech and NIH-Moderna COVID-19 vaccination. In IBD-patients with previous SARS-CoV-2 seroconversion, a single dose of either vaccine can induce high index values, mirroring findings from the general population.
Discrimination of non-nestmate early brood in ants: behavioural and chemical analyses
Authors: de Fouchier Arthur , Leroy Chloé , Khila Abderrahman , d’Ettorre Patrizia 
Published: March 2021

AbstractBrood is critically important in social insect colonies. It carries the colony’s fitness through delivering future reproductive adults as well as workers that will increase the colony’s workforce. Adoption of non-nestmate brood can increase the colony workforce but entails the risk of rearing unrelated sexuals or social parasites. Thus, theory would predict that ant workers will evolve the ability to discriminate between nestmate and alien brood using the chemical cues displayed at the brood’s surface. This appears especially true for eggs and first instar (L1) larvae, which require more resources before becoming adult workers compared to older brood. However, the chemical signature of ant early brood stages and its recognition by workers remains understudied. To fill this gap, we investigated the chemical basis of early brood nestmate and cross-species recognition in six ant species. We also tested the discrimination behaviour of workers in brood retrieval trials. We observed species-level cues and discrimination against hetero-specific brood. We also found that eggs and most L1 larvae displayed a colony signature. However, only some species discriminated against non-nestmate early brood. Interestingly, these species belong to genera subject to brood parasitism. We hypothesize that non-nestmate brood discrimination could arise from species adaptations against brood parasitism.
Altered transcriptome-proteome coupling indicates aberrant proteostasis in Parkinson’s disease
Authors: Dick Fiona , Tysnes Ole-Bjørn , Alves Guido Werner , Nido Gonzalo S. , Tzoulis Charalampos 
Published: March 2021

AbstractThe correlation between mRNA and protein levels has been shown to decline in the ageing brain, possibly reflecting age-dependent changes in the proteostasis. It is thought that impaired proteostasis may be implicated in the pathogenesis of Parkinson’s disease (PD), but evidence derived from the patient brain is currently limited. Here, we hypothesized that if impaired proteostasis occurs in PD, this should be reflected in the form of altered correlation between transcriptome and proteome compared to healthy ageing.To test this hypothesis, we integrated transcriptomic data with proteomics from prefrontal cortex tissue of 17 PD patients and 11 demographically matched healthy controls and assessed gene-specific correlations between RNA and protein level. To control for the effects of ageing, brain samples from 4 infants were included in the analyses.In the healthy aged brain, we observed a genome-wide decreased correlation between mRNA and protein levels. Moreover, a group of genes encoding synaptic vesicle proteins exhibited inverse correlations. This phenomenon likely reflects the spatial separation of mRNA and protein into the neuronal soma and synapsis, respectively, commonly characterizing these genes. Most genes showed a significantly lower correlation between mRNA and protein levels in PD compared to neurologically healthy ageing, consistent with a proteome-wide decline in proteostasis. Genes showing an inverse correlation in PD were enriched for proteasome subunits, suggesting that these proteins show accentuated spatial separation of transcript and protein between the soma and axon/synapses in PD neurons. Moreover, the PD brain was characterized by increased positive mRNA-protein correlation for some genes encoding components of the mitochondrial respiratory chain, suggesting these may require tighter regulation in the face of mitochondrial pathology characterizing the PD brain.Our results are highly consistent with a proteome-wide impairment of proteostasis in the PD brain and strongly support the hypothesis that aberrant proteasomal function is implicated in the pathogenesis of PD. Moreover, our findings have important implications for the correct interpretation of differential gene expression studies in PD. In the presence of disease-specific altered coupling of transcriptome and proteome, measured differences in mRNA levels cannot be used to infer changes at the protein-level and should be supplemented with direct determination of proteins nominated by the analyses.
Respiratory and Cardiovascular Health Effects of E-Cigarette Substitution: Protocol for Two Living Systematic Reviews
Authors: O’Leary Renée , Qureshi Maria Ahmed , La Rosa Giusy Rita Maria , Vernooij Robin W. M. , Odimegwu Damian Chukwu , Bertino Gaetano , Polosa Riccardo 
Published: March 2021

ABSTRACTBackgroundDespite the clear risks of tobacco use, millions of people continue to smoke. Electronic nicotine delivery systems (ENDS), commonly called e-cigarettes, have been proposed as a substitute for those who are unwilling or unable to quit. Current systematic and narrative reviews on the health effects of ENDS use, respiratory and cardiovascular effects in particular, have come to differing conclusions.ObjectiveThe purpose of our two systematic reviews is to critically assess and synthesize the available human studies on the respiratory and cardiovascular health effects of ENDS substitution for people who smoke. The primary goal is to provide clinicians with evidence on the health effects of ENDS substitution to inform their treatment recommendations and plans. The twin goal is to promote the health literacy of ENDS users with facts on the health effects of ENDS. A secondary goal is to develop policy briefs to provide governmental bodies with a preliminary assessment of the potential public health impacts of ENDS.MethodsThese two reviews will be living systematic reviews. The systematic reviews will be initiated with a baseline review. Studies will be evaluated with the JBI quality assessment tools and a checklist of biases drawn from the Centre for Evidence Based Medicine’s Catalogue of Bias. A narrative synthesis is planned due to the heterogeneity of data. A search for recently published studies will be conducted every three months, and an updated review published every six months for the duration of the project or possibly longer.ResultsThe baseline and updated reviews will be published in a peer review journal. The review findings will be reported in a white paper for clinicians, a fact sheet for people who use ENDS, and country-specific policy briefs.ConclusionsThe substitution of ENDS for cigarettes is one of the ways to potentially reduce the risks of smoking. Clinicians and their patients need to understand the potential benefits and possible risks of substituting ENDS for cigarettes. Our living systematic reviews seek to highlight the best and most up-to-date evidence in this highly contentious and fast-moving field of research.
Temperature at conception and pregnancy loss in rural KwaZulu-Natal Province, South Africa: Implications for climate change policy in sub-Saharan African settings
Authors: Moodley Yoshan , Tanser Frank , Tomita Andrew 
Published: March 2021

AbstractBackgroundGlobal warming is projected to cause a substantial rise in temperatures with serious health implications across sub-Saharan Africa. Although South African policy makers have drafted a climate change adaptation plan, potential health threats posed by increasing temperatures on women’s reproductive health are overlooked due to the lack of local population-based evidence. We sought to address the gap in the evidence around global warming and women’s reproductive health in sub-Saharan Africa by using one of the continent’s largest prospective cohorts from rural KwaZulu-Natal Province, South Africa to investigate the relationship between temperature at conception and pregnancy loss.MethodsOur study sample consisted of 36341 pregnancies from 16765 women from the uMkhanyakude District of KwaZulu-Natal, South Africa between 2000-2017. Average monthly temperatures for the study locale during the study period were obtained from the South African Weather Services. An adjusted logistic regression model was used to investigate the relationship between temperature at conception and pregnancy loss (miscarriage or stillbirth).ResultsThe rate of pregnancy loss in the study sample was 1.9 (95% Confidence interval [CI]: 1.7-2.0) per 100 pregnancies. We observed a 4% higher odds of pregnancy loss for each 1°C increase in temperature (Adjusted Odds Ratio: 1.04, 95% CI: 1.01-1.08).ConclusionThere is a clear relationship between temperature and pregnancy loss in our sub-Saharan African setting. The effects of global warming will likely exacerbate the existing challenges for women’s reproductive health in this region. Pregnancy outcomes should be given adequate attention when sub-Saharan African governments draft policies in response to global warming.
COVID-19 Implications of the Physical Interaction of Artificial Fog on Respiratory Aerosols
Authors: Loss Matthew , Katchen Mark , Arvelo Ilan , Arnold Phil , Shum Mona 
Published: March 2021

AbstractIntroductionArtificial fog is used in the film, television, and live entertainment industries to enhance lighting, as a visual effect, and to create a specific sense of mood or atmosphere. This study investigated whether the suspension time of respiratory aerosols spiked with tagged DNA tracers would change in the presence of glycerin- or glycol-containing artificial fogs.Methods & MaterialsRespiratory aerosols with tagged DNA tracers were sprayed into a closed environment without and with glycerin- or glycol-containing artificial fog, with air samples taken at regular intervals to determine the decay of tagged DNA tracer over time. The study treatments included Control (no fog), Glycerin Low (3 mg/m3), Glycerin High (∼15 mg/m3), Glycol Low (∼5 mg/m3), and Glycol High (∼40 mg/m3).ResultsAll artificial fog treatments had lower mean log reduction curves compared to the Control treatment. Compared to the Control and Glycerin Low treatments, the differences in mean log reduction for nearly all other artificial fog treatments were statistically significant (p<0.001); the difference between Control and Glycerin Low treatments was not statistically significant (p=0.087). The differences in mean log reduction between treatments using the same artificial fog type were not statistically significant.ConclusionArtificial fog use does not increase suspension time of respiratory aerosols, and therefore does not appear to increase the risk of airborne transmission of diseases from respiratory aerosols, such as COVID-19. Of the two types of artificial fogs investigated, that containing glycol decreased suspension time more than that containing glycerin. In practice, the additional reduction in suspension time provided by the physical interaction of respiratory aerosols with artificial fog does not suggest any practical benefit for using artificial fog as a control measure.
Development and validation of the long covid symptom and impact tools, a set of patient-reported instruments constructed from patients’ lived experience
Authors: Tran Viet-Thi , Riveros Caroline , Clepier Bérangère , Desvarieux Moïse , Collet Camille , Yordanov Youri , Ravaud Philippe 
Published: March 2021

AbstractObjectivesTo develop and validate patient-reported instruments, based on patients’ lived experiences, for monitoring the symptoms and impact of long covid.DesignThe long covid Symptom and Impact Tools (ST and IT) were constructed from the answers to a survey with open-ended questions to 492 patients with long covid. Validation of the tools involved adult patients with suspected or confirmed covid-19 and symptoms extending over three weeks after onset. Construct validity was assessed by examining the relations of the ST and IT scores with health related quality of life (EQ-5D-5L), function (PCFS, post-covid functional scale), and perceived health (MYMOP2). Reliability was determined by a test-retest. The “patient acceptable symptomatic state” (PASS) was determined by the percentile method.ResultsValidation involved 1022 participants (55% with confirmed covid-19, 79% female and 12.5% hospitalised for covid-19). The long covid ST and IT scores were strongly correlated with the EQ-5D-5L (rs = −0.45 and rs = −0.59 respectively), the PCFS (rs = −0.39 and rs = −0.55), and the MYMOP2 (rs = −0.40 and rs = −0.59). Reproducibility was excellent with an interclass correlation coefficient of 0.83 (95% confidence interval 0.80 to 0.86) for the ST score and 0.84 (0.80 to 0.87) for the IT score. In total, 793 (77.5%) patients reported an unacceptable symptomatic state, thereby setting the PASS for the long covid IT score at 30 (28 to 33).ConclusionsThe long covid ST and IT tools, constructed from patients’ lived experiences, provide the first validated and reliable instruments for monitoring the symptoms and impact of long covid.Short summaryWe developed the long covid Symptom and Impact Tools (ST and IT) from the experiences of 492 patients, captured during a survey with open-ended questions, and assessed their validity and reliability in a sample of 1022 patients with long covid.
Equitable Vaccine Access within an Age-Based Framework
Authors: Cobo-Lewis Alan B 
Published: March 2021

AbstractObjectivesSeveral states have adopted age-based prioritization for COVID-19 vaccine eligibility (also prioritizing teachers and child care workers) because it is simple (especially when age is quantized by decade) and age is strongly associated with COVID-19 mortality. But this approach raises equity concerns based in law and ethics. This study proposes data-driven solutions for equitable policy that retains the advantages of an age-based approach.MethodsUsing data from CDC and U.S. Census Bureau, I analyzed 507,227 COVID-19 deaths in the U.S. by age and race-ethnicity and compared the risk ratios to published data on risk ratios for other conditions.ResultsCOVID-19 mortality in the U.S. rose 2.59-fold per decade of life [95% confidence interval (2.52, 2.66)]. Down syndrome, organ transplantation, and intellectual/developmental disability have risk ratios for COVID-19 mortality that exceed that.ConclusionsPeople with specific conditions (including certain disabilities and certain medical conditions) associated with a risk ratio of 2.59 or 6.71 should be granted vaccine eligibility along with people 10 or 20 years older, respectively. Along with additional recommendations on data collection and reporting, this could help address equity within an age-based framework.3-Question Summary BoxSome states have adopted age-only prioritization for COVID-19 vaccine access, quantized by decade of life, because it is simple, and age has a strong association with COVID-19 mortality. But this raises concerns based in law and ethics.This study quantifies the age effect and documents that COVID-19 mortality increases 2.59-fold per decade of life—a smaller increase than some conditions.People with conditions associated with at least 2.59-fold COVID-19 mortality should be granted vaccine eligibility along with people at least 10 years older.
Depressive rumination is correlated with brain responses during self-related processing
Authors: Hsu Tzu-Yu , Liu Tzu-Ling , Cheng Paul Z. , Lee Hsin-Chien , Lane Timothy J. , Duncan Niall W. 
Published: March 2021

AbstractBackgroundRumination, a tendency to focus on negative self-related thoughts, is a central symptom of depression. Studying the self-related aspect of such symptoms is challenging due to the need to distinguish self effects per se from the emotional content of task stimuli. This study employs an emotionally neutral self-related paradigm to investigate possible altered self processing in depression and its link to rumination.MethodsPeople with unipolar depression (MDD; n = 25) and controls (n = 25) underwent task-based EEG recording. Late event-related potentials were studied along with low frequency oscillatory power. EEG metrics were compared between groups and correlated with depressive symptoms and reported rumination.ResultsThe MDD group displayed a difference in late potentials across fronto-central electrodes between self-related and non-self-related conditions. No such difference was seen in controls. The magnitude of this difference was positively related with depressive symptoms and reported rumination. MDD also had elevated theta oscillation power at central electrodes in self-related conditions, which was not seen in controls.ConclusionsRumination appears linked to altered self-related processing in depression, independently of stimuli-related emotional confounds. This connection between self-related processing and depression may point to self-disorder being a core component of the condition.
Parthanatos-inducing zinc agent C010DS-Zn elicits anti-tumor immune responses involving T cells and macrophagesin vivo
Authors: Chung Jinhyuk Fred , Her Zhisheng , Kong Wai Mun , Chen Qingfeng 
Published: March 2021

AbstractImmune checkpoint inhibitors opened a new horizon in cancer therapy by enabling durable and complete responses in patients, but their wider application against general solid cancers has been hampered by the lack of a broadly acting anti-cancer immune response initiating agents. Parthanatos is a previously unexplored immunogenic programmed necrosis mechanism that is triggered by the hyperactivation of PARP DNA repair and executed by an efficient DNA-fragmentation mechanism. We developed a proprietary macromolecular zinc complex agent C010DS-Zn that efficiently induced parthanatos against 4T1 murine cancer cellsin vitro, which was characterized as PARP-mediated necrotic death with massive DNA damages.Ex vivoscreening of its cytotoxicity against a panel of 53 low-passage human solid cancer PDX tumor fragments demonstrated its consistent delivery of characteristically DNA-damaging cell death that was unseen in the corresponding apoptosis positive controls. Further characterization of itsin vivotreatment effects versus the immunosuppressive 4T1-Balb/c and immunogenic CT26-Balb/c syngeneic cancer models showed that sufficiently high intravenous C010DS-Zn treatments led to robust initiation of the tumor-suppressed antitumor immune compartments such as T cells and macrophages. At lower non-anticancer doses, C010DS-Zn treatment still led to significantly reduced macrophage content and inflammation in the 4T1 tumor, suggesting its potential utility against macrophage-mediated inflammations such as those seen in MIS-C or COVID19. Given the observation of its low serum bioavailability in a rat pharmacokinetic study, these results suggest potential development opportunities for C010DS-Zn to become a widely applicable immune initiation agent with chemo-like broad applicability upon its pharmacokinetic improvements.
Single-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell states
Authors: Triana Sergio H. , Vonficht Dominik , Jopp-Saile Lea , Raffel Simon , Lutz Raphael , Leonce Daniel , Antes Magdalena , Hernández-Malmierca Pablo , Ordoñez-Rueda Diana , Ramasz Beáta , Boch Tobias , Jann Johann-Christoph , Nowak Daniel , Hofmann Wolf-Karsten , Müller-Tidow Carsten , Hübschmann Daniel , Alexandrov Theodore , Benes Vladimir , Trumpp Andreas , Paulsen Malte , Velten Lars , Haas Simon 
Published: March 2021

ABSTRACTSingle-cell genomics has transformed our understanding of complex cellular systems. However, excessive costs and a lack of strategies for the purification of newly identified cell types impede their functional characterization and large-scale profiling. Here, we have generated high content single-cell proteo-genomic reference maps of human blood and bone marrow that quantitatively link the expression of up to 197 surface markers to cellular identities and biological processes across all major hematopoietic cell types in healthy aging and leukemia. These reference maps enable the automatic design of cost-effective high-throughput cytometry schemes that outperform state-of-the-art approaches, accurately reflect complex topologies of cellular systems, and permit the purification of precisely defined cell states. The systematic integration of cytometry and proteo-genomic data enables measuring the functional capacities of precisely mapped cell states at the single-cell level. Our study serves as an accessible resource and paves the way for a data-driven era in cytometry.
Genomic taxonomic assignment of individual root-knot nematodes
Authors: Sellers Graham S , Jeffares Daniel C , Lawson Bex , Prior Tom , Lunt David H 
Published: March 2021

AbstractRoot-knot nematodes (RKN; genusMeloidogyne) are polyphagous plant pathogens of great economic importance to agriculturalists globally. These species are small, diverse, and can be challenging for accurate taxonomic identification. Many of the most important crop pests confound analysis with simple genetic marker loci as they are polyploids of likely hybrid origin. Here we take a low-coverage, long-read genome sequencing approach to characterisation of individual root-knot nematodes. We demonstrate library preparation for Oxford Nanopore Technologies Flongle sequencing of low input DNA from individual juveniles and immature females, multiplexing up to twelve samples per flow cell. Taxonomic identification with Kraken 2 (ak-mer-based taxonomic assignment tool) is shown to reliably identify individual nematodes to species level, even within the very closely relatedMeloidogyne incognitagroup. Our approach forms a robust, low-cost, and scalable method for accurate RKN species diagnostics.