bluuebunny/crossref_metadata_2025_split huggingface dataset:
Millisecond-scale behaviours of plankton quantifiedin situandin vitrousing the Event-based Vision Sensor (EVS)
Authors: Takatsuka Susumu , Miyamoto Norio , Sato Hidehito , Morino Yoshiaki , Kurita Yoshihisa , Yabuki Akinori , Chen Chong , Kawagucci Shinsuke 
Published: January 2023

AbstractThe Event-based Vision Sensor (EVS) is a bio-inspired sensor that captures detailed motions of objects, developed with the applicability to become the ‘eyes’ of machines and especially self-driving cars. Compared to conventional frame-based image sensors as employed in video cameras, EVS has an extremely fast motion capture equivalent to 10,000-fps even with standard optical settings and additionally has high dynamic ranges for brightness and also lower consumption of memory and energy. These features make the EVS an ideal method to tackle questions in biology, such as the fine-scale behavioural ecology. Here, we developed 22 characteristic features for analysing the motions of aquatic particles from the raw data of the EVS, and deployed the EVS system in both natural environments and laboratory aquariums to test its applicability to filming and analysing plankton behaviour. Our EVS monitoring in turbid water at the bottom of Lake Biwa, Japan identified several particles exhibiting distinct cumulative trajectory with periodicities in their motion (up to 16 Hz), suggesting that they were living organisms with rhythmic behaviour. We also carried out EVS monitoring in the deep sea aided by infrared lighting to minimise influence on behaviour, and observed particles with active motion and periodicities over 40 Hz. Furthermore, we used the EVS to observe laboratory cultures of six species of zooplankton and phytoplankton, confirming that they have species-specific motion periodicities of up to 41 Hz. We applied machine learning to automatically classify particles into five categories (four categories of zooplankton plus passive particles), which achieved an accuracy up to 86%. Our attempts to use the EVS for biological observations, especially focusing on its millisecond-scale temporal resolution and wide dynamic range provide a new avenue to investigate rapid and periodical motion and behaviour in small organisms. Given its compact size with low consumption of battery and memory, the EVS will likely be applicable in the near future for the automated monitoring of the behaviour of plankton by edge computing on autonomous floats, as well as quantifying rapid cellular-level activities under microscopy.
The detection of brood parasitism and quasi-parasitism in the burying beetleNicrophorus quadripunctatusunder natural conditions
Authors: Niida Takuma , Yao Izumi , Nisimura Tomoyosi , Suzuki Seizi 
Published: January 2023

AbstractIntraspecific brood parasitism (IBP), where a parasitic female lays eggs in the nest of another female of the same species, occurs in insects and birds. Also, quasi-parasitism (QP), where a parasitic female copulates with a host male at his nest and lays eggs that are fertilized by the male, has been documented in a few monogamous birds, but QP has not been observed in any insects.Burying beetles, genusNicrophorus, use small vertebrate carcasses for reproducing and providing biparental care for their offspring. IBP has been observed in one burying beetle by laboratory experiments, but has not been well reported under natural conditions. IBP and QP may occur under natural conditions in burying beetles.Here we focused on a burying beetle,Nicrophorus quadripunctatus. Ten broods, consisting of larvae and their parental female and male, were collected from a deciduous forest. To investigate the kin relationship between parents and larvae, eight microsatellite DNA loci were used.We detected three types of parasitic larvae: 1) larva not related to either its parental female or male, 2) larva not related to its parental female, but unknown regarding its parental male, and 3) larva not related to its parental female, but related to its parental male. These results suggested that IBP and QP can occur with certain frequencies in the reproduction ofN. quadripunctatusunder natural conditions. QP is thought to have a benefit for a parental male to enhance his paternity within one brood in this species.
Human papillomavirus 16 E2 interaction with TopBP1 is required for E2 and viral genome stability during the viral life cycle
Authors: Prabhakar Apurva T. , James Claire D. , Fontan Christian T. , Otoa Raymonde , Wang Xu , Bristol Molly L. , Hill Ronald D. , Dubey Aanchal , Morgan Iain M. 
Published: January 2023

AbstractCK2 phosphorylation of HPV16 E2 at serine 23 promotes interaction with TopBP1, and this interaction is important for E2 plasmid segregation function. Here we demonstrate that the E2-TopBP1 interaction is critical for E2 and viral genome stability during the viral life cycle. Introduction of the S23A mutation into the HPV16 genome results in a loss of E2 expression and viral genome integration during organotypic rafting. Co-culture of N/Tert-1+E2-S23A cells with J2 fibroblasts results in E2-S23A degradation via the proteasome, wild-type E2 is not degraded. TopBP1 siRNA treatment of N/Tert-1+E2-WT cells results in E2 degradation only in the presence of J2 cells demonstrating the critical role for TopBP1 in maintaining E2 stability. The CK2 inhibitor CX4945 promotes E2-WT degradation in the presence of fibroblasts as it disrupts E2-TopBP1 interaction. siRNA targeting SIRT1 rescues E2-S23A stability in N/Tert-1 cells treated with J2 fibroblasts, with an increased E2-S23A acetylation. The results demonstrate that the E2-TopBP1 interaction is critical during the viral life cycle as it prevents fibroblast stimulated SIRT1 mediated deacetylation of E2 that promotes protein degradation. This means that the E2-TopBP1 complex maintains E2 and viral genome stability and that disruption of this complex can promote viral genome integration. Finally, we demonstrate that HPV11 E2 also interacts with TopBP1 and that this interaction is critical for HPV11 E2 stability in the presence of J2 cells. Treatment of N/Tert-1+11E2-WT cells with CX4945 results in 11E2 degradation. Therefore, CK2 inhibition is a therapeutic strategy for alleviating HPV11 diseases, including juvenile respiratory papillomatosis.ImportanceHuman papillomaviruses are pathogens that cause a host of diseases ranging from benign warts to cancers. There are no therapeutics available for combating these diseases that directly target viral proteins or processes, therefore we must enhance our understanding of HPV life cycles to assist with identifying novel treatments. In this report, we demonstrate that HPV16 and HPV11 E2 protein expression is dependent upon TopBP1 interaction in keratinocytes interacting with fibroblasts, which recapitulate stromal interactions in culture. The degradation of 16E2 promotes HPV16 genome integration, therefore the E2-TopBP1 interaction is critical during the viral life cycle. We demonstrate that the CK2 inhibitor CX4945 disrupts HPV11 interaction with TopBP1 and destabilizes HPV11 E2 protein in the presence of J2 fibroblasts; we propose that CX4945 could alleviate HPV11 disease burden.
Post-discharge mortality among children under 5 years admitted with suspected sepsis in Uganda: a prospective multi-site study
Authors: Wiens Matthew O , Bone Jeffrey N , Kumbakumba Elias , Businge Stephen , Tagoola Abner , Sherine Sheila Oyella , Byaruhanga Emmanuel , Ssemwanga Edward , Barigye Celestine , Nsungwa Jesca , Olaro Charles , Ansermino J Mark , Kissoon Niranjan , Singer Joel , Larson Charles P , Lavoie Pascal M , Dunsmuir Dustin , Moschovis Peter P , Novakowski Stefanie , Komugisha Clare , Tayebwa Mellon , Mwesigwa Douglas , Zhang Cherri , Knappett Martina , West Nicholas , Nguyen Vuong , Mugisha Nathan Kenya , Kabakyenga Jerome 
Published: January 2023

AbstractBackgroundSubstantial mortality occurs after hospital discharge in children under 5 years old with suspected sepsis. A better understanding of its epidemiology is needed for effective interventions aimed at reducing child mortality in resource limited settings.MethodsIn this prospective observational cohort study, we recruited 0-60-month-old children admitted with suspected sepsis from the community to the paediatric wards of six Ugandan hospitals. The primary outcome was six-month post-discharge mortality among those discharged alive. We evaluated the interactive impact of age, time of death, and location of death on risk factors for mortality.Findings6,545 children were enrolled, with 6,191 discharged alive. The median (interquartile range) time from discharge to death was 32 (10–92) days, with a six-month post-discharge mortality rate of 5·5%, constituting 51% of total mortality. Deaths occurred at home (45%), intransit to care (18%), or in hospital (37%) during a subsequent readmission. Post-discharge death was strongly associated with weight-for-age z-scores < -3 (adjusted hazard ratio [aHR] 5·04; 95%CI: 3·97–6·37), referral for further care (aHR 9·08; 95%CI 6·68–12·34), and unplanned discharge (aHR 3·36; 95%CI 2·64–4·28). The hazard ratio of those with severe anaemia increased with time since discharge, while the hazard ratios of discharge vulnerabilities (unplanned, poor feeding) decreased with time. Children with severe anaemia (<7 g/dL) died 35 days (95%CI 19·4–51·9) later than those without anaemia. Age influenced the effect of several variables, including anthropometric indices (less impact with increasing age), anaemia (greater impact), and admission temperature (greater impact).InterpretationPaediatric post-discharge mortality following suspected sepsis is common, with diminishing, though persistent, risk over the 6 months after discharge. Efforts to improve post-discharge outcomes are critical to achieving Sustainable Development Goal 3.2 (ending preventable childhood deaths under 5 years of age).FundingGrand Challenges Canada (#TTS-1809-1939), Thrasher Research Fund (#13878), BC Children’s Hospital Foundation, and Mining4Life.
Evaluation of two red cell inclusion staining methods for assessing spleen function among sickle cell disease patients in North-East Nigeria
Authors: Ladu Adama I , Satumari Ngamariju A , Abba Aisha M , Abulfathi Fatima A , Jeffery Caroline , Adekile Adekunle , Bates Imelda 
Published: January 2023

AbstractIntroductionThe loss of splenic function is associated with an increased risk of infection in sickle cell disease (SCD); however, spleen function is rarely documented among SCD patients in Africa, due partly to the non-availability of sophisticated techniques such as scintigraphy. Methods of assessing splenic function which may be achievable in resource-poor settings include counting red blood cells (RBC) containing Howell Jolly Bodies (HJB) and RBC containing silver-staining (argyrophilic) inclusions (AI) using a light microscope. We evaluated the presence of HJB - and AI - containing RBC as markers of splenic dysfunction among SCD patients in Nigeria.MethodsWe prospectively enrolled children and adults with SCD in steady state attending outpatient clinics at a tertiary hospital in North-East Nigeria. The percentages of HJB- and AI-containing red cells were estimated from peripheral blood smears and compared to normal controls.ResultsThere were 182 SCD patients and 102 healthy controls. Both AI- and HJB-containing red cells could be easily identified in the participants blood smears. SCD patients had a significantly higher proportion of red cells containing HJB (1.5%; IQR 0.7% - 3.1%) compared to controls (0.3%; IQR 0.1% - 0.5%) (P= 0.0001). The AI red cell counts were also higher among the SCD patients (47.4%; IQR 34.5% - 66.0%) than the control group (7.1%; IQR 5.1% - 8.7%) (P= 0.0001). The intra-observer reliability for assessment of HJB-(R = 0.92; R2= 0.86) and AI-containing red cells (R = 0.90; R2= 0.82) was high. The estimated intra-observer agreement was better with the HJB count method (95% limits of agreement, −4.5 to 4.3;P= 0.579).ConclusionWe have demonstrated the utility of light microscopy in the assessment of red cells containing - HJB and AI inclusions as indices of splenic dysfunction in Nigerian SCD patients. These methods can be easily applied in the routine evaluation and care of patients with SCD to identify those at high risk of infection and initiate appropriate preventive measures.
Cross-sectional Ct distributions from qPCR tests can provide an early warning signal for the spread of COVID-19 in communities
Authors: Sharmin Mahfuza , Manivannan Mani , Woo David , Sorel Océane , Auclair Jared , Gandhi Manoj , Mujawar Imran 
Published: January 2023

BackgroundSARS-CoV-2 PCR testing data has been widely used for COVID-19 surveillance. Existing COVID-19 forecasting models mainly rely on case counts, even though the binary PCR results provide a limited picture of the pandemic trajectory. Most forecasting models have failed to accurately predict the COVID-19 waves before they occur. Recently a model utilizing cross-sectional population cycle threshold (Ct) values obtained from PCR tests (Ct-based model) was developed to overcome the limitations of using only binary PCR results. In this study, we aimed to improve on COVID-19 forecasting models using features derived from the Ct-based model, to detect epidemic waves earlier than case-based trajectories.MethodsPCR data was collected weekly at Northeastern University (NU) between August 2020 and January 2022. The NU campus epidemic trajectories were generated from the campus incidence rates. In addition, epidemic trajectories were generated for Suffolk County, where NU is located, based on publicly available case-counts. A novel forecasting approach was developed by enhancing a recent deep learning model with Ct-based features, along with the model’s default features. For this, cross-sectional Ct values from PCR data were used to generate Ct-based epidemic trajectories, including effective reproductive rate (Rt) and incidence. The improvement in forecasting performance was compared using absolute errors and residual squared errors with respect to actual observed cases at the 7-day and 14-day forecasting horizons. The model was also tested prospectively over the period January 2022 to April 2022.ResultsRt estimates from the Ct-based model preceded NU campus and Suffolk County cases by 12 and 14 days respectively, with a three-way synched Spearman correlation of 0.57. Enhancing the forecasting models with Ct-based information significantly decreased absolute error and residual squared error compared to the original model without Ct features (p-value <0.001 for both 7 and 14-days forecasting horizons).ConclusionCt-based epidemic trajectories can herald an earlier signal for impending epidemic waves in the community and forecast transmission peaks. Moreover, COVID-19 forecasting models can be enhanced using these Ct features to improve their forecasting accuracy.Policy implicationsWe make the case that public health agencies should publish Ct values along with the binary positive/negative PCR results. Early and accurate forecasting of epidemic waves can inform public health policies and countermeasures which can mitigate spread.
Assessing spontaneous sensory neuron activity usingin vivocalcium imaging
Authors: Ingram Sonia L , Chisholm Kim I , Wang Feng , De Koninck Yves , Denk Franziska , Goodwin George L 
Published: January 2023

AbstractHeightened spontaneous activity in sensory neurons is often reported in individuals living with chronic pain. It is possible to study this activity in rodents using electrophysiology, but these experiments require great skill and can be prone to bias. Here, we have examined whetherin vivocalcium imaging with GCaMP6s can be used as an alternative approach. We show that spontaneously active calcium transients can be visualised in the fourth lumbar dorsal root ganglion (L4 DRG) viain vivoimaging in a mouse model of pain. Application of lidocaine to the nerve, between the inflamed site and the DRG, silenced spontaneous firing and revealed the true baseline level of calcium for spontaneously active neurons. We used this data to train a machine leaning algorithm to predict when a neuron is spontaneously active. We show that our algorithm is accurate in two different models of pain: intraplantar Complete Freund’s Adjuvant and antigen-induced arthritis, with accuracies of 90.0% +/-1.2 and 85.9 % +/-2.1, respectively, assessed against visual inspection by an experienced observer. The algorithm can also detect neuronal activity in imaging experiments generated in a different lab using a different microscope configuration (Accuracy = 94.0 % +/2.2). We provide a Google Colaboratory Notebook to allow anyone easy access to this novel tool, for assessment of peripheral neuron activity in their own calcium imaging setups.
Bovine blood and milk T-cell subsets in distinct states of activation and differentiation during subclinicalStaphylococcus aureusmastitis
Authors: Tucker Nisha , Cunha Patricia , Gilbert Florence B. , Rambault Marion , Santos Kamila Reis , Remot Aude , Germon Pierre , Rainard Pascal , Martins Rodrigo Prado 
Published: January 2023

AbstractT-lymphocytes are key mediators of adaptive cellular immunity and knowledge about distinct subsets of these cells in healthy and infected mammary gland secretions remains limited. In this study, we used a multiplex cytometry panel to show that staphylococcal mastitis causes the activation of CD4+, CD8+and γδ T-cells found in bovine milk. We also highlight remarkable differences in the proportions of naïve and memory T-cells subsets found in blood and milk. These observations will contribute to a better understanding of cell-mediated immune mechanisms in the udder and to the development of new therapeutic and preventive strategies targeting mastitis.
From methylation to myelination: epigenomic and transcriptomic profiling of chronic inactive demyelinated multiple sclerosis lesions
Authors: Tiane Assia , Schepers Melissa , Reijnders Rick A. , van Veggel Lieve , Chenine Sarah , Rombaut Ben , Dempster Emma , Verfaillie Catherine , Wasner Kobi , Grünewald Anne , Prickaerts Jos , Pishva Ehsan , Hellings Niels , van den Hove Daniel , Vanmierlo Tim 
Published: January 2023

AbstractIntroductionIn the progressive phase of multiple sclerosis (MS), the hampered differentiation capacity of oligodendrocyte precursor cells (OPCs) eventually results in remyelination failure. We have previously shown that DNA methylation ofId2/Id4is highly involved in OPC differentiation and remyelination. In this study, we took an unbiased approach by determining genome-wide DNA methylation patterns within chronically demyelinated MS lesions and investigated how certain epigenetic signatures relate to OPC differentiation capacity.MethodsWe compared genome-wide DNA methylation and transcriptional profiles between chronically demyelinated MS lesions and matched normal-appearing white matter (NAWM), making use of post-mortem brain tissue (n=9/group). DNA methylation differences that inversely correlated with mRNA expression of their corresponding genes were validated for their cell-type specificity in laser-captured OPCs using pyrosequencing. The CRISPR-dCas9-DNMT3a/TET1 system was used to epigenetically edit human-iPSC-derived oligodendrocytes to assess the effect on cellular differentiation.ResultsOur data show hypermethylation of CpGs within genes that cluster in gene ontologies related to myelination and axon ensheathment. Cell type-specific validation indicates a region-dependent hypermethylation ofMBP, encoding for myelin basic protein, in OPCs obtained from white matter lesions compared to NAWM-derived OPCs. By altering the DNA methylation state of specific CpGs within the promotor region ofMBP, using epigenetic editing, we show that cellular differentiation can be bidirectionally manipulated using the CRISPR-dCas9-DNMT3a/TET1 systemin vitro.ConclusionOur data indicate that OPCs within chronically demyelinated MS lesions acquire an inhibitory phenotype, which translates into hypermethylation of crucial myelination related genes. Altering the epigenetic status ofMBPcan restore the differentiation capacity of OPCs and possibly boost (re)myelination.
A human iPSC-basedin vitroneural network formation assay to investigate neurodevelopmental toxicity of pesticides
Authors: Bartmann Kristina , Bendt Farina , Dönmez Arif , Haag Daniel , Keßel Eike , Masjosthusmann Stefan , Noel Christopher , Wu Ji , Zhou Peng , Fritsche Ellen 
Published: January 2023

AbstractProper brain development is based on the orchestration of key neurodevelopmental processes, including the formation and function of neural networks. If at least one key neurodevelopmental process is affected by a chemical, an adverse outcome is expected. To allow a higher testing throughput than the guideline animal experiments, a developmental neurotoxicity (DNT)in vitrotesting battery (DNT IVB) has been set up that includes a variety of assays, which model several key neurodevelopmental processes. Gap analyses of the DNT IVB revealed the need of a human-based assay to assess neural network formation and function (NNF). Therefore, here we established the human NNF (hNNF) assay. A co-culture comprised of human-induced pluripotent stem cell (hiPSC)- derived excitatory and inhibitory neurons, as well as primary human astroglia, was differentiated for 35 days on micro-electrode arrays (MEA) and spontaneous electrical activity, together with cytotoxicity, was assessed on a weekly basis after washout of the compounds 24 h prior to measurements. In addition to the characterization of the test system, the assay was challenged with 28 compounds, mainly pesticides, identifying their DNT potential by evaluation of specific spike-, burst- and network parameters. This approach confirmed the suitability of the assay for screening environmental chemicals. Comparison of benchmark concentrations (BMC) with an NNFin vitroassay (rNNF) based on primary rat cortical cells, revealed differences in sensitivity. Together with the successful implementation of hNNF data into a postulated stressor-specific adverse outcome pathway (AOP) network associated with a plausible molecular initiating event for deltamethrin, this study suggests the hNNF assay as a useful complement to the current DNT IVB.