bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pre-Pandemic COVID-19 in New York City: A descriptive analysis of COVID-19 illness prior to February 29, 2020
Authors: Keating Page , Sell Jessica , Chen Judy , Ackelsberg Joel , Wu Winfred , Tsoi Benjamin , Weiss Don 
Published: April 2022

AbstractBackgroundOn January 30, 2020 the COVID-19 pandemic was declared a Public Health Emergency of International Concern (PHEIC) by the World Health Organization. Almost a month later on February 29, 2020, the first case in New York City (NYC) was diagnosed.MethodsThree-hundred-sixty persons with COVID-like illness was reported to the NYC Department of Health and Mental Hygiene (DOHMH) before February 29, but 37 of these tested negative and 237 were never tested for SARS-COV-2. Records of 86 persons with confirmed COVID-19 and symptom onset prior to February 29, 2020 were reviewed by four physician-epidemiologists. Case-patients were classified as likely early onset COVID-19, or insufficient evidence to determine onset. Clinical and epidemiological factors collected by DOHMH and supplemented with emergency department records were analyzed.ResultsThirty-nine likely early onset COVID-19 cases were identified. The majority had severe disease with 69% presenting to an ED visit within 2 weeks of symptom onset. The first likely COVID-19 case on record had symptom onset on January 28, 2020. Only 7 of the 39 cases (18%) had traveled internationally within 14 days of onset (none to China).ConclusionsSARS-CoV-2 and COVID-19 was in NYC before being classified as a PHEIC, and eluded surveillance for another month. The delay in recognition limited mitigation effort and by the time that city and state-wide mandates were enacted 16 and 22 days later there was already community transmission.Key PointsRecords of 86 persons with confirmed COVID-19 and symptom onset prior to February 29, 2020 were reviewed for likelihood of early onset COVID-19. Thirty-nine likely early onset COVID-19 cases were identified, suggesting that early COVID-19 transmission in NYC went undetected.
Beyond Common Outcomes: Client’s Perspectives on the Benefits of Prenatal Care Coordination
Authors: Greene Madelyne Z. , Tran-Smith Bikki , Moua Pahder 
Published: April 2022

AbstractPrenatal Care Coordination (PNCC) is a fee-for-service Medicaid benefit available in Wisconsin and several other states. It provides for home visiting, health education, care coordination and other supportive services to high-risk mothers. However, PNCC is not supported by an evidence-based model, its impact is not systematically evaluated, and the benefit is not currently reaching all eligible mothers. The purpose of this qualitative descriptive study was to describe PNCC clients’ perspectives on the experience of receiving the PNCC benefit and the value and impact of PNCC in the context of their own lives. We interviewed recent clients of PNCC programs in two PNCC sites that varied by racial/ethnic community makeup, rural/urban geography, and health department size. PNCC clients identified two major benefits of PNCC: 1) social and emotional support from the PNCC nurse; and 2) assistance with obtaining or getting connected to other resources they needed. These two program benefits were especially meaningful to PNCC clients in the context of difficult life events and circumstances. Findings from this study highlight the impact of PNCC services on social and emotional health through trusting and supportive nurse-client relationships. Our findings also suggest that a longer program period and the development of standards to assess program effectiveness would improve PNCC client outcomes and reduce disparities in maternal health.
Multiplex RT-qPCR assay (N200) to detect and estimate prevalence of multiple SARS-CoV-2 Variants of Concern in wastewater
Authors: Fuzzen Meghan , Harper Nathanael B.J. , Dhiyebi Hadi A. , Srikanthan Nivetha , Hayat Samina , Peterson Shelley W. , Yang Ivy , Sun J.X. , Edwards Elizabeth A. , Giesy John P. , Mangat Chand S. , Graber Tyson E. , Delatolla Robert , Servos Mark R. 
Published: April 2022

AbstractWastewater-based surveillance (WBS) has become an effective tool around the globe for indirect monitoring of COVID-19 in communities. Quantities of viral fragments of SARS-CoV-2 in wastewater are related to numbers of clinical cases of COVID-19 reported within the corresponding sewershed. Variants of Concern (VOCs) have been detected in wastewater by use of reverse transcription quantitative polymerase chain reaction (RT-qPCR) or sequencing. A multiplex RT-qPCR assay to detect and estimate the prevalence of multiple VOCs, including Omicron/Alpha, Beta, Gamma, and Delta, in wastewater RNA extracts was developed and validated. The probe-based multiplex assay, named “N200” focuses on amino acids 199-202, a region of the N gene that contains several mutations that are associated with variants of SARS- CoV-2 within a single amplicon. Each of the probes in the N200 assay are specific to the targeted mutations and worked equally well in single- and multi-plex modes. To estimate prevalence of each VOC, the abundance of the targeted mutation was compared with a non- mutated region within the same amplified region. The N200 assay was applied to monitor frequencies of VOCs in wastewater extracts from six sewersheds in Ontario, Canada collected between December 1, 2021, and January 4, 2022. Using the N200 assay, the replacement of the Delta variant along with the introduction and rapid dominance of the Omicron variant were monitored in near real-time, as they occurred nearly simultaneously at all six locations. The N200 assay is robust and efficient for wastewater surveillance can be adopted into VOC monitoring programs or replace more laborious assays currently being used to monitor SARS- CoV-2 and its VOCs.
Modeling vital rates and age-sex structure of Pacific arctic phocids: influence on aerial survey correction factors
Authors: Conn Paul B. , Trukhanova Irina S. 
Published: April 2022

AbstractTo estimate abundance, surveys of marine mammals often rely on samples of satellite-tagged individuals to correct counts for the proportion of animals that are unavailable to be detected. However, naïve application of this correction relies on the key assumption that availability of the tagged sample resembles that of the population. Here, we show how matrix population models can be used to estimate the stable stage structure of bearded seals (Erignathus barbatus), ribbon seals (Histriophoca fasciata), ringed seals (Pusa hispida), and spotted seals (Phoca largha) in the Bering and Chukchi Seas, and how these proportions can be used to adjust aerial survey correction factors so that they represent population-level availability. We find that correction factors ignoring age-sex composition can positively bias spotted seal abundance by an average of 13% and negatively bias ribbon seal abundance by an average of 5%. Note that we did not examine potential bias for bearded or ringed seals due to low sample sizes; as such, we urge caution in interpretation of abundance estimates for these species.
Legacy effect of microplastics on plant-soil feedbacks
Authors: Lozano Y.M , Rillig M.C 
Published: April 2022

AbstractMicroplastics are a complex contaminant suite that are now understood to affect plants and soil biota and the processes they drive. However, the role of microplastic in plant-soil feedbacks, a key feature in plant-soil interactions, is still unknown. We address this here, using soil from a previous experiment, which has been conditioned with 12 different microplastic types including fibers, films, foams, and fragments. To evaluate the feedback effect, we grew a native and a range-expanding plant species with inocula extracted from each one of these soils. At harvest, plant biomass and root morphological traits were measured.Films gave rise to a positive feedback on shoot mass (higher mass with soil inocula conditioned with microplastics than without), likely via negative effects on harmful soil biota. Foams and fragments also caused positive feedback on shoot mass likely via effects on enzymatic activities and mutualistic soil biota. Fibers led to negative feedback on root mass as they may promote the abundance of soil pathogens.Microplastics also have a legacy effect on root traits: Daucus had thicker roots probably for promoting mycorrhizal associations while Calamagrostis had reduced root diameter probably for diminishing pathogenic infection. Microplastic legacy on plants is species-specific and may affect plant biomass primarily via root traits. Microplastics, as a function of their shape and polymer type, have a feedback effect on plant performance.
Defining tertiary sulci in lateral prefrontal cortex in chimpanzees using human predictions
Authors: Hathaway Catherine B. , Voorhies Willa I. , Sathishkumar Neha , Mittal Chahat , Yao Jewelia K. , Miller Jacob A. , Parker Benjamin J. , Weiner Kevin S. 
Published: April 2022

ABSTRACTSimilarities and differences in brain structure and function across species is of major interest in systems neuroscience, comparative biology, and brain mapping. Recently, increased emphasis has been placed on tertiary sulci, which are shallow indentations of the cerebral cortex that appear last in gestation, continue to develop after birth, and are largely either human- or hominoid-specific. While tertiary sulcal morphology in lateral prefrontal cortex (LPFC) has been linked to functional representations and cognition in humans, it is presently unknown if LPFC tertiary sulci also exist in non-human hominoids. To fill this gap in knowledge, we leveraged two freely available multimodal datasets to address the following main question: Can LPFC tertiary sulci be defined in chimpanzee cortical surfaces from human predictions? We found that 1-3 components of the posterior middle frontal sulcus (pmfs) in the posterior middle frontal gyrus are identifiable in nearly all chimpanzee hemispheres. In stark contrast to the consistency of the pmfs components, we could only identify components of the paraintermediate frontal sulcus (pimfs) in two chimpanzee hemispheres. LPFC tertiary sulci were relatively smaller and shallower in chimpanzees compared to humans. In both species, two of the pmfs components were deeper in the right compared to the left hemisphere. As these results have direct implications for future studies interested in the functional and cognitive role of LPFC tertiary sulci across species, we share probabilistic predictions of the three pmfs components to guide the definitions of these sulci in future studies.
Genetic and potential antigenic evolution of influenza A(H1N1)pdm09 viruses circulating in Kenya during 2009-2018 influenza seasons
Authors: Owuor D. Collins , de Laurent Zaydah R. , Nyawanda Bryan O. , Emukule Gideon O. , Kondor Rebecca , Barnes John R. , Nokes D. James , Agoti Charles N. , Chaves Sandra S. 
Published: April 2022

AbstractBackgroundInfluenza viruses undergo rapid evolutionary changes, which requires continuous surveillance to monitor for genetic and potential antigenic changes in circulating viruses that can guide control and prevention decision making.MethodsWe sequenced and phylogenetically analyzed A(H1N1)pdm09 virus genome sequences obtained from specimens collected from hospitalized patients of all ages with or without pneumonia between 2009 and 2018 from seven sentinel surveillance sites across Kenya. We compared these sequences with recommended vaccine strains during the study period to infer genetic and potential antigenic changes in circulating viruses and determinants of clinical outcome.ResultsWe generated and analyzed a total of 383 A(H1N1)pdm09 virus genome sequences. Phylogenetic analyses revealed that multiple genetic groups (clades, subclades, and subgroups) of A(H1N1)pdm09 virus circulated in Kenya over the study period; these evolved away from their vaccine strain, forming clades 7 and 6, subclades 6C, 6B, and 6B.1, and subgroups 6B.1A and 6B.1A1. Several amino acid substitutions among circulating viruses were associated with continued evolution of the viruses, especially in antigenic epitopes and receptor binding sites (RBS) of circulating viruses. Disease severity reduced with increase in age among children aged <5 years.ConclusionOur study highlights the utility of genomic surveillance to monitor the evolutionary changes of influenza viruses. Routine influenza surveillance with broad geographic representation and whole genome sequencing capacity to inform on the severity of circulating strains could improve selection of influenza strains for inclusion in vaccines.
A Sepsis Treatment Algorithm to Improve Early Antibiotic De-escalation While Maintaining Adequacy of Coverage (Early-IDEAS): A Prospective Observational Study
Authors: Bucheeri Mohamed , Elligsen Marion , Lam Philip W. , Daneman Nick , MacFadden Derek 
Published: April 2022

ABSTRACTBackgroundEmpiric antibiotic treatment selection should provide adequate coverage for potential pathogens while minimizing unnecessary broad-spectrum antibiotic use. We sought to pilot a rule- and model-based early sepsis treatment algorithm (Early-IDEAS) to make optimal individualized antibiotic recommendations.MethodsThe Early-IDEAS decision support algorithm was derived from previous Gram-negative and Gram-positive prediction rules and models. The Gram-negative prediction consists of multiple parametric regression models which predict the likelihood of susceptibility for each commonly used antibiotic for Gram-negative pathogens, based on epidemiologic predictors and prior culture results and recommends the narrowest spectrum agent that exceeds a predefined threshold of adequate coverage. The Gram-positive rules direct the addition or cessation of vancomycin based on prior culture results. We applied the algorithm to prospectively identified consecutive adults within 24-hours of suspected sepsis. The primary outcome was the proportion of patients for whom the algorithm recommended de-escalation of the primary antibiotic regimen. Secondary outcomes included: (1) the proportion of patients for whom escalation was recommended; (2) the number of recommended de-escalation steps along a pre-specified antibiotic cascade; and (3) the adequacy of therapy in the subset of patients with culture-confirmed infection.ResultsWe screened 578 patients, of whom 107 eligible patients with sepsis were included. The Early-IDEAS treatment recommendation was informed by Gram-negative models in 76 (71%) of patients, Gram-positive rules in 66 (61.7%), and local guidelines in 27 (25%). Antibiotic de-escalation was recommended by the algorithm in almost half of all patients (n=50, 47%), no treatment change was recommended in 48 patients (45%), and escalation was recommended in 9 patients (8%). Amongst the patients where de-escalation was recommended, the median number of steps down the a priori antibiotic treatment cascade was 2. Among the 17 patients with relevant culture-positive blood stream infection, the clinician prescribed regimen provided adequate coverage in 14 (82%) and the algorithm recommendation would have provided adequate coverage in 13 (76%), p=1. Among the 25 patients with positive relevant (non-blood) cultures, the clinician prescribed regimen provided adequate coverage in 22 (88%) and the algorithm recommendation would have provided adequate coverage in 21 (84%), p=1.ConclusionsAn individualized decision support algorithm in early sepsis could lead to substantial antibiotic de-escalation without compromising adequate antibiotic coverage.
Stimulated emission depletion microscopy with a single depletion laser using five fluorochromes and fluorescence lifetime phasor separation
Authors: Pisfil Mariano Gonzalez , Nadelson Iliya , Bergner Brigitte , Rottmeier Sonja , Thomae Andreas W. , Dietzel Steffen 
Published: April 2022

AbstractStimulated emission depletion (STED) microscopy achieves super-resolution by exciting a diffraction-limited volume and then suppressing fluorescence in its outer parts by depletion. Multiple depletion lasers may introduce misalignment and bleaching. Hence, a single depletion wavelength is preferable for multi-color analyses. However, this limits the number of usable spectral channels. Using cultured cells, common staining protocols, and commercially available fluorochromes and microscopes we exploit that the number of fluorochromes in STED or confocal microscopy can be increased by phasor based fluorescence lifetime separation of two dyes with similar emission spectra but different fluorescent lifetimes. In our multi-color FLIM-STED approach two fluorochromes in the near red (exc. 594 nm, em. 600-630) and two in the far red channel (633/641-680), supplemented by a single further redshifted fluorochrome (670/701-750) were depleted with 775 nm. To the best of our knowledge, these are the first published five color STED images. Generally, this approach doubles the number of fully distinguishable colors in laser scanning microscopy. We provide evidence that eight color FLIM-STED with a single depletion laser would be possible if suitable fluorochromes were identified and we confirm that a fluorochrome may have different lifetimes depending on the molecules to which it is coupled.
Mutations in DNA polymerase δ subunit 1 mediate CMD2-type resistance to Cassava Mosaic Geminiviruses
Authors: Lim Y.W. , Mansfeld B.N. , Schläpfer P. , Gilbert K.B. , Narayanan N.N. , Qi W. , Wang Q. , Zhong Z. , Boyher A. , Gehan J. , Beyene G. , Lin Z.D. , Esuma W. , Feng S. , Chanez C. , Eggenberger N. , Adiga G. , Alicai T. , Jacobsen S.E. , Taylor N.J , Gruissem W. , Bart R.S. 
Published: April 2022

ABSTRACTCassava mosaic disease suppresses cassava yields across the tropics. The dominant CMD2 locus confers resistance to the cassava mosaic geminiviruses. It has been reported that CMD2-type landraces lose resistance after regeneration through de novo morphogenesis. As full genome bisulfite sequencing failed to uncover an epigenetic mechanism for loss of resistance, we performed whole genome sequencing and genetic variant analysis and fine-mapped the CMD2 locus to a 190 kilobase interval. Data suggest that CMD2-type resistance is caused by a nonsynonymous, single nucleotide polymorphism in DNA polymerase δ subunit 1 (MePOLD1) located within this region. Virus-induced gene silencing of MePOLD1 in a Cassava mosaic disease-susceptible cassava variety produced a recovery phenotype typical of CMD2-type resistance. Analysis of other CMD2-type cassava varieties identified additional resistance alleles within MePOLD1. MePOLD1 resistance alleles represent important genetic resources for resistance breeding or genome editing, and elucidating mechanisms of resistance to geminiviruses.
A systems approach reveals species differences in hepatic stress response capacity
Authors: Russomanno Giusy , Sison-Young Rowena , Livoti Lucia A. , Coghlan Hannah , Jenkins Rosalind E. , Kunnen Steven J. , Fisher Ciarán P. , Reddyhoff Dennis , Gardner Iain , Rehman Adeeb H. , Fenwick Stephen W. , Jones Andrew R. , De Conchard Guy Vermeil , Simonin Gilles , Bertheux Helene , Weaver Richard J. , Liguori Michael J. , Clausznitzer Diana , Stevens James L. , Goldring Christopher E. , Copple Ian M. 
Published: April 2022

ABSTRACTTo minimise unexpected toxicities in early phase clinical studies of new drugs, it is vital to understand fundamental similarities and differences between preclinical test species and humans. We have used physiologically-based pharmacokinetic modelling to identify doses of the model hepatotoxin acetaminophen yielding similar hepatic burdens of the reactive metabolite N-acetyl-p-benzoquinoneimine in mice and rats, to enable comparison of tissue adaptive responses under conditions of equivalent chemical insult. Mice exhibited a greater degree of liver injury than rats, despite the equivalent hepatic NAPQI burden. Transcriptomic and proteomic analyses highlighted the stronger activation of stress response pathways (including the Nrf2 oxidative stress response and autophagy) in the livers of rats. Components of these pathways were also found to be expressed at a higher basal level in the livers of rats compared with both mice and humans. Our findings exemplify a systems approach to understanding differential species sensitivity to hepatotoxicity, and have important implications for species selection and human translation in the safety testing of new drug candidates.
Bacillus thuringiensis Cry1A toxins divert progenitor cells toward enteroendocrine fate by decreasing cell adhesion with intestinal stem cells
Authors: Jneid Rouba , Loudhaief Rihab , Zucchini-Pascal Nathalie , Nawrot-Esposito Marie-Paule , Fichant Arnaud , Rousset Raphaël , Bonis Mathilde , Osman Dani , Gallet Armel 
Published: April 2022

AbstractBacillus thuringiensis subsp. kurstaki (Btk) is a strong pathogen toward lepidopteran larvae thanks to specific Cry toxins causing leaky gut phenotypes. Hence, Btk and its toxins are used worldwide as microbial insecticide and in genetically modified crops, respectively, to fight crop pests. However, Btk belongs to the B. cereus group, some strains of which are well known human opportunistic pathogens. Therefore, ingestion of Btk along with food may threaten organisms not susceptible to Btk infection. Here we show that Cry1A toxins induce enterocyte death and intestinal stem cell (ISC) proliferation in the midgut of Drosophila melanogaster, an organism non-susceptible to Btk. Surprisingly, a high proportion of the ISC daughter cells differentiate into enteroendocrine cells instead of their initial enterocyte destiny. We show that Cry1A toxins weaken the Cadherin-dependent adherens junction between the ISC and its immediate daughter progenitor, leading the latter to adopt an enteroendocrine fate. Hence, though not lethal to non-susceptible organisms, Cry toxins can interfere with conserved cell adhesion mechanisms, thereby disrupting intestinal homeostasis and enteroendocrine functions.
Perceptual expectations and false percepts generate stimulus-specific activity in distinct layers of the early visual cortex
Authors: Haarsma Joost , Deveci Narin , Corbin Nadège , Callaghan Martina F. , Kok Peter 
Published: April 2022

AbstractPerception has been proposed to result from the integration of feedforward sensory signals with internally generated feedback signals. The latter are believed to play an important role in driving false percepts, i.e., seeing things that are not actually there. Feedforward and feedback influences on perception can be studied using layer-specific fMRI, which we used here to interrogate neural activity underlying high confidence false percepts while healthy participants (N=25) performed a perceptual orientation discrimination task. Orientation-specific BOLD activity in the deep and superficial layers of V2 reflected perceptual expectations induced by predictive auditory cues. However, these expectations did not influence participants’ perception. Instead, high confidence false percepts were reflected by orientation-specific activity in the middle input layers of V2, suggesting a feedforward signal contributing to false percepts. The prevalence of high confidence false percepts was related to everyday hallucination severity in a separate online sample (N=100), suggesting a possible link with abnormal perceptual experiences. These results reveal a feedforward mechanism underlying false percepts, reflected by spontaneous stimulus-like activity in the input layers of the visual cortex, independent of top-down perceptual expectations.