bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection and quantification of SARS-CoV-2 RNA in wastewater influent in relation to reported COVID-19 incidence in Finland
Authors: Tiwari Ananda , Lipponen Anssi , Hokajärvi Anna-Maria , Luomala Oskari , Sarekoski Anniina , Rytkönen Annastiina , Österlund Pamela , Al-Hello Haider , Juutinen Aapo , Miettinen Ilkka T. , Savolainen-Kopra Carita , Pitkänen Tarja 
Published: October 2021

AbstractWastewater-based surveillance is a cost-effective concept for monitoring COVID-19 pandemics at a population level. Here, SARS-CoV-2 RNA was monitored from a total of 693 wastewater (WW) influent samples from 28 wastewater treatment plants (WWTP, N = 21–42 samples per WWTP) in Finland from August 2020 to May 2021, covering WW of ca. 3.3 million inhabitants (∼ 60% of the Finnish population). The relative quantity of SARS-CoV-2 RNA fragments in the 24h-composite samples was determined by using the ultrafiltration method followed by nucleic acid extraction and RT-qPCR assay targeted with N2-assay. SARS-CoV-2 RNA signals at each WWTP were compared over time to the numbers of new and confirmed COVID-19 cases in the sewer network area.Over the 10-month surveillance period, the detection rate of SARS-CoV-2 RNA in WW was 79% (including 6% uncertain results), while only 24% of all samples exhibited gene copy (GC) numbers above the quantification limit. The range of the SARS-CoV-2 detection rate in WW varied from 33% (including 10% uncertain results) in Pietarsaari to 100% in Espoo. Only six out of 693 WW samples were positive with SARS-COV-2 RNA when the reported COVID-19 case number from the preceding 14 days was zero. Overall, the 14-day COVID-19 incidence was 7, 18 and 36 cases within the sewer network area when the probability to detect SARS-CoV-2 RNA in wastewater samples was 50%, 75% and 95%, respectively. The quantification of SARS-CoV-2 GC required significantly more COVID-19 cases: the quantification rate was 50%, 75% and 95% when the 14-day incidence was 110, 152 and 223 COVID-19 cases, respectively, per 100 000 persons. Multiple linear regression confirmed the relationship between the COVID-19 incidence and the SARS-CoV-2 GC quantified in WW at 15 out of 28 WWTPs (overall R2 = 0.36, p < 0.001). At four of the 13 WWTPs where a significant relationship was not found, the GC of SARS-CoV-2 RNA remained below the quantification limit during the whole study period. In the five other WWTPs, the sewer coverage was less than 80% of the total population in the area and thus the COVID-19 cases may have been inhabitants from the areas not covered.Based on the results obtained, WW-based surveillance of SARS-CoV-2 could be used as an indicator for local and national COVID-19 incidence trends. Importantly, the determination of SARS-CoV-2 RNA fragments from WW is a powerful and non-invasive public health surveillance measure, independent of possible changes in the clinical testing strategies or in the willingness of individuals to be tested for COVID-19.
Atypical influence of biomechanical knowledge in Complex Regional Pain Syndrome-Towards a different perspective on body representation
Authors: Filbrich L. , Verfaille C. , Vannuscorps G. , Berquin A. , Barbier O. , Libouton X. , Fraselle V. , Mouraux D. , Legrain V. 
Published: October 2021

AbstractPart of the multifaceted pathophysiology of Complex Regional Pain syndrome (CRPS) has been ascribed to a lateralized maladaptive neuroplasticity in sensorimotor cortices, a finding that has been corroborated by behavioral studies indicating that CRPS patients indeed present difficulties in mentally representing their painful limb. Hand laterality judgment tasks (HLT) are widely used to measure such difficulties, with the laterality of hand stimuli corresponding to the affected hand judged more slowly than the one of hand stimuli corresponding to the unaffected hand. Importantly, the HLT is also regularly used in the rehabilitation of CRPS and other chronic pain disorders, with the aim to activate motor imagery and, consequently, restoring the cortical representation of the limb. The potential of these tasks to elicit motor imagery is thus critical to their use in therapy. Yet, the influence of the biomechanical constraints (BMC) on HLT reaction time, supposed to reflect the activation of motor imagery, is rarely verified. In the present study we investigated the influence of the BMC on the perception of hand postures and movements. The results of a first experiment, in which a HLT was used, showed that CRPS patients were significantly slower than controls in judging hand stimuli, whether or not the depicted hand corresponded to their affected hand, but that their performance did not differ from controls when they judged non-body stimuli. Results regarding reaction time patterns reflecting the BMC were inconclusive in CRPS and controls, questioning the validity of the task in activating motor imagery processes. In a second experiment we therefore directly investigated the influence of implicit knowledge of upper-limb BMC on perceptual judgments of hand movements with the apparent body movement perception task. Participants judge the perceived path of movement between two depicted hand positions, with only one of the two proposed paths that is biomechanically plausible. While the controls chose the biomechanically plausible path most of the time, CRPS patients did not, indicating that the perception and/or use of the BMC seems to be disturbed in CRPS. These findings show a non-lateralized body representation impairment in CRPS, which might be related to difficulties in using correct knowledge of the body’s biomechanics. Most importantly however, our results, in agreement with previous studies, indicate that it seems highly challenging to measure motor imagery and the indexes of BMC with the classical HLT task, which has important implications for the rehabilitation of chronic pain with these tasks.
The association of infectious mononucleosis and breast cancer in The Health of Women (HOW) Study®
Authors: Heng Yujing J. , Love Susan , DeHart Jessica Clague , Fingeroth Joyce D. , Wulf Gerburg M. 
Published: October 2021

AbstractBackgroundThe link between Epstein-Barr Virus (EBV) and breast cancer (BC) remains unclear. Infectious mononucleosis (IM) is a clinical manifestation of delayed onset of EBV infection in early adulthood. We utilized the Health of Women (HOW) Study® to understand the association between IM and BC risk.Subjects and methodsThe HOW Study® was a web-based survey of BC risk factors with >40,000 participants who answered seven modules between 2012 and 2015; 3,654 women had IM between the ages of 10 and 22 years (16.8%) and 17,026 never developed IM (78.5%). Of these 20,680 women, 1,997 (9.7%) had Stages I-III BC and 13,515 (65.4%) were cancer-free. Multivariable binary logistic regression ascertained the association between IM and BC risk by controlling for ethnicity, family history, age at menarche, oral contraceptive use, tobacco use, birthplace, parity, age at first birth, body mass index, and breast biopsy. Secondary analyses stratified cancer cases into those who had BC at <50 or ≥50 years old and by estrogen receptor (ER) subtype.ResultsParticipants were mostly white, middle-aged women born in the United States or Canada. Women who had IM were less likely to develop BC than those who did not develop IM (adjusted odds ratio (OR)=0.83, 95% confidence interval (CI) 0.71-0.96). Findings were similar when stratifying women into <50 or ≥50 years old at BC diagnosis (<50 years old, adjusted OR=0.82, 95% CI 0.67-0.998; ≥50 years old, adjusted OR=0.83, 95% CI 0.69-1.00). Women who had IM were less likely to develop ER positive BC (adjusted OR=0.84, 95% CI 0.71-0.997); there was no association between IM and ER negative BC (adjusted OR=0.88, 95% CI 0.65-1.16).ConclusionIn the HOW Study®, women diagnosed with IM between the ages of 10 and 22 had lower breast cancer risk compared to women who never developed IM.
Tuning DO:DM ratios modulates MHC class II immunopeptidomes
Authors: Olsson Niclas , Jiang Wei , Adler Lital N. , Mellins Elizabeth D. , Elias Joshua E. 
Published: October 2021

ABSTRACTMajor histocompatibility complex class II (MHC-II) antigen presentation underlies a wide range of immune responses in health and disease. However, how MHC-II antigen presentation is regulated by the peptide-loading catalyst HLA-DM (DM), its associated modulator, HLA-DO (DO), is incompletely understood. This is due largely to technical limitations: model antigen presenting cell (APC) systems that express these MHC-II peptidome regulators at physiologically variable levels have not been described. Likewise, computational prediction tools that account for DO and DM activities are not presently available. To address these gaps, we created a panel of single MHC-II allele, HLA-DR4-expressing APC lines that cover a wide range of DO:DM ratio states. Using a combined immunopeptidomic and proteomic discovery strategy, we measured the effects DO:DM ratios have on peptide presentation by surveying over 10,000 unique DR4-presented peptides. The resulting data provide insight into peptide characteristics that influence their presentation with increasing DO:DM ratios. These include DM-sensitivity, peptide abundance, binding affinity and motif, peptide length and register positioning on the source protein. These findings have implications for designing improved HLA-II prediction algorithms and research strategies for dissecting the variety of functions that different APCs serve in the body.IN BRIEFPeptides presented by MHC-II are critical to adaptive immune function. The non-canonical MHC molecules HLA-DM and HLA-DO cooperatively regulate MHC-II function, but how varied DO-to-DM ratios across different APCs and cellular contexts might influence their immunopeptide repertoires is unclear. We address this by measuring cell lines expressing these two proteins spanning a range of relative abundances. We found that peptides could be categorized according to how robustly they were presented at different DO:DM ratios. Importantly, this presentation was only partially linked to predicted affinity to the MHC-II molecule.HIGHLIGHTSDescribe MHC-class II peptide repertoires from a unique HLA-DR4 cell line panel with increasing DO:DM ratios.Demonstrate striking and divergent changes in MHC-II immunopeptidomes that result from the tuning function of DO:DM.These findings bridge gap in understanding and predicting MHC-II antigen presentation.GRAPHICAL ABSTRACT
Single cell profiling in COVID-19 associated acute kidney injury reveals patterns of tubule injury and repair in human
Authors: Legouis David , Rinaldi Anna , Arnoux Gregoire , Verissimo Thomas , Scotti-Gerber Jennifer , Faivre Anna , Schibler Manuel , Rinaldi Andrea , Naesens Maarten , Koppitch Kari , Pugin Jerome , McMahon Andrew P , Moll Solange , de Seigneux Sophie , Cippà Pietro E 
Published: October 2021

AbstractThe cellular mechanisms of kidney tubule repair are poorly characterized in human. Here, we applied single-nucleus RNA sequencing to analyze the kidney in the first days after acute injury in 5 critically ill patients with COVID-19. We identified abnormal proximal tubule cell states associated with injury, characterized by altered functional and metabolic profiles and by pro-fibrotic properties. Tubule repair involved the plasticity of mature tubule cells in a process of cell de-differentiation and re-differentiation, which displayed substantial similarities between mouse and man. In addition, in man we identified a peculiar tubule reparative response determining the expansion of progenitor-like cells marked by PROM1 and following a differentiation program characterized by the sequential activation of the WNT, NOTCH and HIPPO signaling pathways. Taken together, our analyses reveal cell state transitions and fundamental cellular hierarchies underlying kidney injury and repair in critically ill patients.
Green fluorescent protein-like pigments optimize the internal light environment in symbiotic reef building corals
Authors: Bollati Elena , Lyndby Niclas H. , D’Angelo Cecilia , Kühl Michael , Wiedenmann Jörg , Wangpraseurt Daniel 
Published: October 2021

AbstractPigments homologous to the Green Fluorescent Protein (GFP) have been proposed to fine-tune the internal light microclimate of corals, facilitating photoacclimation of photosynthetic coral symbionts (Symbiodiniaceae) to life in different reef habitats and environmental conditions. However, direct measurements of the in vivo light conditions inside the coral tissue supporting this conclusion are lacking. Here, we quantified the intra-tissue spectral light environment of corals expressing GFP-like proteins from widely different light regimes. We focus on (1) photoconvertible red fluorescent proteins (pcRFPs), thought to enhance photosynthesis in mesophotic habitats via wavelength conversion, and (2) chromoproteins (CPs), which provide photoprotection to the symbionts in shallow water via light absorption. Optical microsensor measurements indicated that both pigment groups strongly alter the coral tissue light environment. Estimates derived from light spectra measured in pcRFP-containing corals showed that fluorescence emission can contribute to >50% of orange-red light available to the photosynthetic symbionts at mesophotic depths. We further show that upregulation of pink CPs in shallow-water corals during bleaching leads to a reduction of orange light by 10-20% compared to low-CP tissue. Thus, screening by CPs has an important role in mitigating the light-enhancing effect of coral tissue scattering during bleaching. Our results provide the first experimental quantification of the importance of GFP-like proteins in fine-tuning the light microclimate of corals during photoacclimation.
The effects of age, sex, weight and breed on canid methylomes
Authors: Rubbi Liudmilla , Zhang Haoxuan , Feng Junxi , He Christopher , Kurnia Patrick , Ratan Prashansa , Tammana Aakash , Thompson Michael , Stahler Daniel , Ostrander Elaine A. , vonHoldt Bridgett , Pellegrini Matteo 
Published: October 2021

AbstractUnlike genomes, which are static throughout the lifespan of an organism, DNA methylomes are dynamic. To study these dynamics we developed quantitative models that measure the effect of multiple factors on DNA methylomes including, age, sex, weight and genetics. We conducted our study in canids, which prove to be an ideal species to assess epigenetic moderators due to their extreme variability in size and well-characterized genetic structure. We collected buccal swabs from 217 canids (207 domestic dogs and 10 gray wolves) and used targeted bisulfite sequencing to measure methylomes. We also measured genotypes at over one thousand single nucleotide polymorphisms (SNPs). We found that DNA methylomes are strongly associated with age, enabling the construction of epigenetic clocks. We also show that methylomes are strongly impacted by sex, weight and sterilization status, leading to accurate predators of these factors. Methylomes are also affected by genetics and we observe multiple associations between SNP loci and methylated CpGs. Finally, we show that several factors moderate the relationship between epigenetic ages and real ages, such as body weight, which increases epigenetic aging. In conclusion, we demonstrate that the plasticity of DNA methylomes is impacted by myriad genetic and physiological factors, and that DNA methylation biomarkers are accurate predictors of age, sex and sterilization status.
Predicting increases in COVID-19 incidence to identify locations for targeted testing in West Virginia: A machine learning enhanced approach
Authors: Price Bradley S. , Khodaverdi Maryam , Halasz Adam , Hendricks Brian , Kimble Wesley , Smith Gordon S. , Hodder Sally L. 
Published: October 2021

AbstractDuring the COVID-19 pandemic, West Virginia developed an aggressive SARS-CoV-2 testing strategy which included utilizing pop-up mobile testing in locations anticipated to have near-term increases in SARS-CXoV-2 infections. In this study, we describe and compare two methods for predicting near-term SARS-CoV-2 incidence in West Virginia counties. The first method, Rt Only, is solely based on producing forecasts for each county using the daily instantaneous reproductive numbers, Rt. The second method, ML+ Rt, is a machine learning approach that uses a Long Short-Term Memory network to predict the near-term number of cases for each county using epidemiological statistics such as Rt, county population information, and time series trends including information on major holidays, as well as leveraging statewide COVID-19 trends across counties and county population size. Both approaches used daily county-level SARS-CoV-2 incidence data provided by the West Virginia Department Health and Human Resources beginning April 2020. The methods are compared on the accuracy of near-term SARS-CoV-2 increases predictions by county over 17 weeks from January 1, 2021-April 30, 2021. Both methods performed well (correlation between forecasted number of cases and the actual number of cases week over week is 0.872 for the ML+Rt method and 0.867 for the Rt Only method) but differ in performance at various time points. Over the 17-week assessment period, the ML+Rt method outperforms the Rt Only method in identifying larger spikes. We also find that both methods perform adequately in both rural and non-rural predictions. Finally, we provide a detailed discussion on practical issues regarding implementing forecasting models for public health action based on Rt, and the potential for further development of machine learning methods that are enhanced by Rt.
A persistent behavioral state enables sustained predation of humans by mosquitoes
Authors: Sorrells Trevor R. , Pandey Anjali , Rosas-Villegas Adriana , Vosshall Leslie B. 
Published: October 2021

AbstractPredatory animals pursue prey in a noisy sensory landscape, deciding when to continue or abandon their chase. The mosquito Aedes aegypti is a micropredator that first detects humans at a distance through sensory cues such as carbon dioxide. As a mosquito nears its target it senses more proximal cues such as body heat that guides it to a meal of blood. How long the search for blood continues after initial detection of a human is not known. Here we show that a 5-second optogenetic pulse of fictive carbon dioxide induced a persistent behavioral state in female mosquitoes that lasted for more than 10 minutes. This state is highly specific to females searching for a blood meal and was not induced in recently blood-fed females or in males, who do not feed on blood. In males that lack the gene fruitless, which controls persistent social behaviors in other insects, fictive carbon dioxide induced a long-lasting behavior response resembling the predatory state of females. Finally, we show that the persistent state triggered by detection of fictive carbon dioxide enabled females to engorge on a blood meal mimic offered up to 14 minutes after the initial 5-second stimulus. Our results demonstrate that a persistent internal state allows female mosquitoes to integrate multiple human sensory cues over long timescales, an ability that is key to their success as an apex micropredator of humans.
Cellular composition of human early and advanced coronary atherosclerotic lesions
Authors: Sharysh Diana , Markov Anton V. , Grigoryeva Evgeniya S. , Savelieva Olga E. , Sleptcov Aleksei A. , Zarubin Aleksei A. , Nazarenko Maria S. 
Published: October 2021

AbstractObjectiveHere, we identify and quantify leukocytes, macrophages, endothelial cells (ECs), and vascular smooth muscle cells (VSMCs) with contractile and macrophage-like phenotypes by flow cytometry to compare human early and advanced coronary atherosclerotic plaques.Approach and ResultsSixteen coronary atherosclerotic lesions of 6 patients (3 women, 3 men, age 82 ± 9 years), including one case of restenosis after coronary stenting, were collected at autopsy. The cause of death of all patients was acute myocardial infarction. The lesions were categorized into early (EALs, n = 5) and advanced (AALs, n = 11) atherosclerotic stages. We analyzed a cell suspension stained with antibodies against CD45, CD68, CD31, and αSMA (ACTA2). We noted a decrease in the number of CD45+ cells and an increase in the CD45+CD68+ subpopulation of leukocytes from EALs to AALs. Numbers of CD45−αSMA+CD68+ cells positively correlated with the CD45+CD68+ macrophage number (r = 0.81; ρ = 0.64; p < 0.05) and the histological type of an atherosclerotic lesion (r = 0.81; ρ = 0.87; p < 0.05). As an interesting case, we analyzed cellular composition of the stented coronary artery and revealed significantly greater numbers of macrophages, αSMA+CD68+ VSMCs, and ECs in comparison with nonstented plaques.ConclusionsHuman early and advanced coronary atherosclerotic lesions differ in their counts of leukocytes and leukocyte subpopulations. For the first time, αSMA+CD68+ VSMCs were identified in early atherosclerotic stages of coronary arteries. Additionally, the restenotic coronary lesion contains mostly cells and is enriched in ECs, macrophages, and αSMA+CD68+ VSMCs in particular.
In pursuit of happiness at work: exploring the role of psychological capital and coping in managing COVID-19 stress among Indian employees
Authors: Pradhan Rabindra Kumar , Jandu Kailash , Panda Madhusmita , Hati Lopamudra , Mallick Manolina 
Published: October 2021

Purpose
Employee happiness is crucial in any organization as happy employees are said to be more committed in their work. However, COVID-19 stress in the current situation is a major problem for employees and it can negatively influence their happiness level. Therefore, it is critical to understand how the stressful nature of the current pandemic threatens workplace happiness. Based on conservation of resources theory (Hobfoll, 1989), this study aims to examine the resources to be protected (i.e. psychological capital) and resource investment (i.e. coping) to ensure the happiness of the employees amidst a bio-psycho-socioeconomic crisis like COVID-19 pandemic. The study explores the mediating role of psychological capital and the moderating effect of coping on the relationship between COVID-19 stress and employee happiness.

Design/methodology/approach
Data were collected from the Indian working population by means of purposive sampling (N = 336). Standardized instruments were used to measure the variables under study. Data analysis were done using Statistical Package for Social Sciences 20.0 and Analysis of Moment Structure 20.0 software tools and PROCESS macro was used for mediation and moderation analysis.

Findings
Structural equation modelling analysis showed that COVID-19 stress negatively influenced employee happiness; whereas psychological capital partially mediated the relationship between these two variables. Further, coping was found to buffer against the harmful implications of COVID-19 stress on employee happiness.

Originality/value
In an effort to respond timely to the present pandemic scenario, the current study provides an account of the harmful effects of COVID-19-related stress on the workplace happiness of the Indian service sector employees. The study also offers insights into the possible mediating and moderating mechanisms in this relationship.