bluuebunny/crossref_metadata_2025_split huggingface dataset:
qPCR in a suitcase for rapid Plasmodium falciparum and Plasmodium vivax surveillance in Ethiopia
Authors: Carlier Lise , Baker Sarah Cate , Huwe Tiffany , Yewhalaw Delenasaw , Haileselassie Werissaw , Koepfli Cristian 
Published: April 2022

AbstractMany Plasmodium spp. infections, both in clinical and asymptomatic patients, are below the limit of detection of light microscopy or rapid diagnostic test (RDT). Molecular diagnosis by qPCR can be valuable for surveillance, but is often hampered by absence of laboratory capacity in endemic countries. To overcome this limitation, we optimized and tested a mobile qPCR laboratory for molecular diagnosis in Ziway, Ethiopia, where transmission intensity is low. Protocols were optimized to achieve high throughput and minimize costs and weight for easy transport. 899 samples from febrile patients and 1021 samples from asymptomatic individuals were screened by local microscopy, RDT, and qPCR within a period of six weeks. 34/52 clinical Plasmodium falciparum infections were missed by microscopy and RDT. Only 4 asymptomatic infections were detected. No hrp2 deletions were observed among 25 samples typed, but 19/24 samples carried hrp3 deletions. The majority (25/41) of Plasmodium vivax infections (1371 samples screened) were found among asymptomatic individuals. All asymptomatic P. vivax infections were negative by microscopy and RDT. In conclusion, the mobile laboratory described here can identify hidden parasite reservoirs within a short period of time, and thus inform malaria control activities.
Protective efficacy of holed and aging PBO-pyrethroid synergist-treated nets on malaria infection prevalence in north-western Tanzania
Authors: Lukole Eliud , Cook Jackie , Mosha Jacklin F. , Messenger Louisa A , Rowland Mark , Kleinschmidt Immo , Charlwood Jacques D , Mosha Franklin W , Manjurano Alphaxard , Wright Alexandra , Protopopoff Natacha 
Published: April 2022

AbstractTwo billion pyrethroid long-lasting insecticidal nets (LLINs) have been distributed since 2010 for malaria prevention in Sub-Saharan Africa. Current malaria control strategies rely on an assumed effective 3-year lifespan for LLINs. PBO synergist LLINs are a newly recommended class but there is limited information on their life span and long-term protective efficacy in communities. To assess their operational survival, a cohort of 390 PBO LLINs (Olyset Plus) and 367 standard pyrethroid LLIN (Olyset net) from 396 households were followed for 36 months in Western Tanzania. To assess the association between the condition of the LLIN and malaria infection, nets from at least 480 randomly selected households were assessed during malaria prevalence cross-sectional surveys at 4, 9, 16, 21, 28, and 33 months post-distribution. Information on the presence and condition of nets, and demographic information from the household, were collected to evaluate factors influencing net durability. After 3 years less than 17% of nets distributed were available for sleeping. The fabric condition was not associated with malaria infection in either type of net. The difference between the net types was highest when nets were between 1-2 years old, when PBO nets appeared to be similarly protective as nets less than a year old, whereas standard nets were considerably less protective as they aged, regardless of fabric condition. There was no statistical difference in the estimated median functional survival time between net types with 1.6 years (95% CI 1.38-1.87) for PBO LLIN and 1.9 years (95% CI 1.67-2.06) for standard LLINs. After 3 years, there was a loss of 55% of permethrin content for both nets, and 97% of PBO content was lost in PBO LLIN. These results highlight that functional survival is less than the recommended 3 years for both net types. However, even as the nets age, the PBO nets remained more protective than standard nets, regardless of their condition.
Elucidating the genetic architecture of DNA methylation to identify promising molecular mechanisms of disease
Authors: Ma Jiantao , Joehanes Roby , Liu Chunyu , Keshawarz Amena , Shih-Jen Hwang , Bui Helena , Tejada Brandon , Sooda Meera , Munson Peter J. , Cumhur Demirkale Y. , Courchesne Paul , Heard-Costa Nancy L. , Pitsillides Achilleas N. , Feolo Mike , Sharopova Nataliya , Vasan Ramachandran S. , Huan Tianxiao , Levy Daniel 
Published: April 2022

AbstractDNA methylation commonly occurs at cytosine-phosphate-guanine sites (CpGs) that can serve as biomarkers for many diseases. We analyzed whole genome sequencing data to identify DNA methylation quantitative trait loci (mQTLs) in 4,126 Framingham Heart Study participants. Our mQTL mapping identified 94,362,817 cis-mQTLvariant-CpG pairs (for 210,156 unique autosomal CpGs) at P<1e-7 and 33,572,145 trans-mQTL variant-CpG pairs (for 213,606 unique autosomal CpGs) at P<1e-14. Using cis-mQTL variants for 1,258 CpGs associated with seven cardiovascular disease risk factors, we found 104 unique CpGs that colocalized with at least one cardiovascular disease trait. For example, cg11554650 (PPP1R18) colocalized with type 2 diabetes, driven by a single nucleotide polymorphism (rs2516396). We performed Mendelian randomization (MR) analysis and demonstrated 58 putatively causal relations of CVD risk factor-associated CpGs to one or more risk factors (e.g., cg05337441 [APOB] with LDL; MR P=1.2e-99, and 17 causal associations with coronary artery disease (e.g. cg08129017 [SREBF1] with coronary artery disease; MR P=5e-13). We also showed that three CpGs, e.g., cg14893161 (PM20D1), are putatively causally associated with COVID-19 severity. To assist in future analyses of the role of DNA methylation in disease pathogenesis, we have posted a comprehensive summary data set in the National Heart, Lung, and Blood Institute’s BioData Catalyst.
Unlocking the multiphasic nature of intracellular calcium signatures triggered by fungal signals inLotus japonicusroots
Authors: Binci Filippo , Offer Elisabetta , Crosino Andrea , Sciascia Ivan , Kleine-Vehn Jürgen , Genre Andrea , Giovannetti Marco , Navazio Lorella 
Published: April 2022

AbstractThe recognition of different microbe-associated molecular patterns in the rhizosphere triggers in the plant root the activation of either an immune response or an accommodation program. In both types of responses, Ca2+is a crucial intracellular messenger, mediating the early stages of the respective signalling pathways. In this work, we analysed the cytosolic and nuclear Ca2+changes activated by a set of chitin-related oligomers in different genetic backgrounds ofLotus japonicusroots by using specifically targeted aequorin-based Ca2+reporters. By means of pharmacological and genetic approaches, we dissected the Ca2+signal into two temporally distinct components: a rapid initial transient, followed by a longer and milder elevation in Ca2+concentration. Taking advantage of a complementary analysis using a cameleon-based bioassay inMedicago truncatularoot organ cultures, we showed that the second phase can be interpreted as the Ca2+spiking that is widely described in response to the perception of symbiotic signals. By contrast, the rapid first phase, critically dependent on elicitor concentration, was found to correlate with the activation of plant immunity marker genes. Overall, our study provides novel clues to a better understanding of the subtle boundaries between symbiotic and immunity responses in root-fungus interactions.HighlightIntracellular calcium changes induced inLotus japonicusroots by fungal signals were dissected in two separate phases, relying on distinct genetic programs and differentially mediating plant symbiotic or immunity responses.
Effects of local versus global competition on reproductive skew and sex differences in social dominance behaviour
Authors: Leimar Olof , Bshary Redouan 
Published: April 2022

AbstractSocial hierarchies are often found in group-living animals. The hierarchy position can influence reproductive success (RS), with a skew towards high-ranking individuals. The amount of aggression in social dominance varies greatly, both between species and between males and females within species. Using game theory we study this variation by taking into account the degree to which reproductive competition in a social group is mainly local to the group, emphasising within-group relative RS, or global to a larger population, emphasising an individual’s absolute RS. Our model is similar to recent approaches in that reinforcement learning is used as a behavioural mechanism allowing social-hierarchy formation. We test two hypotheses. The first is that local competition should favour the evolution of mating or foraging interference, and thus of reproductive skew. Second, decreases in reproductive output caused by an individual’s accumulated fighting damage, such as reduced parenting ability, will favour less intense aggression but should have little influence on reproductive skew. From individual-based simulations of the evolution of social dominance and interference, we find support for both hypotheses. We discuss to what extent our results can explain observed sex differences in reproductive skew and social dominance behaviour.
A quantitative and spatial analysis of cell cycle regulators during the fission yeast cycle
Authors: Curran Scott , Dey Gautam , Rees Paul , Nurse Paul 
Published: April 2022

AbstractWe have carried out a systems-level analysis of the spatial and temporal dynamics of cell cycle regulators in the fission yeastSchizosaccharomyces pombe. In a comprehensive single cell analysis we have precisely quantified the levels of 38 proteins previously identified as regulators of the G2 to mitosis transition, and of 7 proteins acting at the G1 to S-phase transition. Only two of the 38 mitotic regulators exhibit changes in concentration at the whole cell level, the mitotic B-type cyclin Cdc13 which accumulates continually throughout the cell cycle, and the regulatory phosphatase Cdc25 which exhibits a complex cell cycle pattern. Both proteins show similar patterns of change within the nucleus as in the whole cell but at higher concentrations. In addition, the concentrations of the major fission yeast cyclin dependent kinase (CDK) Cdc2, the CDK regulator Suc1 and the inhibitory kinase Wee1 also increase in the nucleus peaking at mitotic onset but are constant in the whole cell. The significant increase in concentration with size for Cdc13 supports the model that mitotic B-type cyclin accumulation acts as a cell size sensor. We propose a two-step process for the control of mitosis. First, Cdc13 accumulates in a size-dependent manner which drives increasing CDK activity. Second, from mid G2 the increasing nuclear accumulation of Cdc25 and the counteracting Wee1 introduces a bistability switch that results in a rapid rise of CDK activity at the end of G2 and thus brings about an orderly progression into mitosis.Significance StatementAcross eukaryotes the increasing level of cyclin dependent kinase (CDK) activity drives progression through the cell cycle. As most cells divide at specific sizes, information responding to the size of the cell must feed into the regulation of CDK activity. In this study, we use fission yeast to precisely measure how proteins that have been previously identified in genome wide screens as cell cycle regulators change in their levels with cell cycle progression. We identify the mitotic B-type cyclin Cdc13 and mitotic inhibitory phosphatase Cdc25 as the only two proteins that change in both whole cell and nuclear concentration through the cell cycle, making them candidates for universal cell size sensors at the onset of mitosis and cell division.
Resolving subcellular pH with a quantitative fluorescent lifetime biosensor
Authors: Rennick Joshua J. , Nowell Cameron J. , Pouton Colin W. , Johnston Angus P.R. 
Published: April 2022

AbstractChanges in sub-cellular pH play a key role in metabolism, cell growth, membrane transport, and can also be exploited to control cargo release from therapeutic delivery systems. Most methods to measure pH rely on intensity changes of pH sensitive fluorophores, however these measurements are hampered by high uncertainty in the inferred pH and the need for multiple fluorophores. To address this, we have developed a method to accurately quantify sub-cellular pH in individual vesicles using fluorescent lifetime imaging microscopy (pHLIM). pHLIM exploits the linear pH dependant lifetime of the fluorescent protein mApple and uses deep learning models to automatically identify and measure the pH of subcellular compartments. We have engineered mApple fusion proteins to measure the pH of the cytosol, endosomes, lysosomes and demonstrated the utility of pHLIM by measuring pH changes induced by drugs (bafilomycin A1) and polyethylenimine (a common transfection reagent). pHLIM is a simple and quantitative method to measure sub-cellular pH that has the potential to help with the design of the next generation of controlled drug release systems and to understand drug action and disease progression.
The transcription factor RXRA regulates lipid metabolism in duck myoblasts by the CD36 network
Authors: Pan Ziyi , Li Guoyu , Du Guoqing , Wu Dongsheng , Li Xuewen , Wang Yu , Zhao Junxian , Zhang Xiran , Chen Xingyong , Zhang Chen , Jing Sihua , Geng Zhaoyu 
Published: April 2022

AbstractLipid metabolism is a highly complex metabolic process regulated at multiple levels. RXRA is a well-characterized factor that regulates lipid metabolism. To explore the function and mechanism of the transcription factor RXRA in myoblasts, and to further explore the key factors that RXRA regulates the target gene CD36 signaling network to regulate lipid metabolism. We found that the transcription factor RXRA inhibited the accumulation of triglycerides (TGs), cholesterol (CHOL) and non-esterified fatty acids (NEFA) in CS2 cells by regulating CD36 as well as the fatty acid beta oxidation pathway. CD36 functions similar to RXRA in myoblasts. CD36 overexpression reduced the levels of TGs, CHOL, NEFAs and saturated fatty acids (SFAs) in these cells, while CD36 knockout increased the levels of TGs, CHOL, NEFAs, SFAs and monounsaturated fatty acids (MUPAs) in these cells. GRB2, MAP1B, SLC38A1, SLC4A7, NCOA3, PKIA, MOB2, SAA2 and RXRA are involved in the CD36 promotion of lipid efflux through lipid metabolism, endocytosis and amino acid metabolism. Considering these results, we propose that RXRA regulates lipid metabolism in myoblasts by regulating the CD36 signaling network.
N-terminal helices and A domain of archaeal FtsY facilitate SRP54 binding and the association with cell membrane
Authors: Gupta Sayandeep , Sinha Souvik , Bhakta Koustav , Bhowmick Arghya , Ghosh Abhrajyoti 
Published: April 2022

AbstractThe process of protein translocation is essential to the maintenance of cellular life and has been critically addressed in eukaryotes and bacteria. However, little information is available regarding protein translocation across archaeal membranes. The signal recognition particle (SRP) plays an important role in this process. It binds the signal peptide at the N-terminus of the polypeptide chain and interacts with the cognate SRP receptor (FtsY) located on the target membrane to form a targeting complex (TC). Concomitant GTP hydrolysis by SRP and FtsY delivers the polypeptide to the adjacent protein-conducting channel. The present study aims to characterize the structural domains of FtsY contributing to the targeting complex (TC) formation in Sulfolobus acidocaldarius, a thermo-acidophilic crenarchaeon. The contacting residues between SRP54 and FtsY were mapped along the αN1-N3 helices. Interestingly, the previously reported crystal structure did not take the N-terminal A domain into account – a region rich in negatively charged residues. Such observation led us to investigate the contribution of each of the three participating helices (αN1-3) in terms of membrane association and functional TC formation. Through biophysical analyses of SRP-FtsY and FtsY-membrane interaction, and biochemical characterization of the reciprocal GTPase activity, this work sought to elucidate the minimal structural motif controlling the archaeal TC assembly.
A bug’s tale: revealing the history, biogeography and ecological patterns of 500 years of insect introductions
Authors: López Daniela N. , Fuentes-Contreras Eduardo , Ruiz Cecilia , Ide Sandra , Estay Sergio A. 
Published: April 2022

AbstractThe arrival of Europeans to the Americas triggered a massive exchange of organisms on a continental scale. This exchange was accelerated by the amazing increase in the movement of people and goods during the 20th century. In Chile, scientific and technical literature contains hundreds of records of exotic insect species in different parts of the territory, from the hyperarid Atacama Desert to the Magallanes Region. Here, we analyze the biological patterns obtained from the database of introductions of exotic insects to Chile from the European arrival to the present. Our task includes a review of old records in museums, libraries, collections, expedition records and catalogs. Almost 600 species of exotic insects have been reported in Chile. Introductions started at the very arrival of Europeans to the central valley of Chile and underwent a huge acceleration in the second half of the 20th century. The order Hemiptera was the most prevalent among introduced insects. Most species are linked to agriculture and forestry. Species are of Palearctic origin in more than 50% of the records. In terms of temporal trends, the rate of introduced species shows an abrupt increase at the beginning of the 1950s. This change may be associated with the strong development in agriculture and forestry in Chile after World War II and the increase in intercontinental air traffic. We believe that the understanding of past patterns of introductions is an important component in the design of current policies to minimize the impact of invasive insects.
Cycling for climate and public health: a missed opportunity for France
Authors: Schwarz Emilie , Leroutier Marion , Quirion Philippe , Jean Kévin 
Published: April 2022

ABSTRACTIn addition to its potential contribution to reaching climate targets, cycling may generate substantial population-level health benefits through the physical activity it requires. Due to the lack of nationally representative mobility data, the health impact of current levels of cycling is still unknown for France. Relying on a health impact assessment framework and using recent nationally-representative data on mobility, we assessed the health and related economic benefits of cycling in 2018-2019 in France. We show that such benefits remain moderated and fall short when compared to those estimated in other countries with high cycling levels. We argue that cycling in France did not receive the attention and investments it deserves over the past decade and thus represents a missed opportunity for climate action and public health.
Art therapy as treatment modality for persons living with dementia- a protocol for a scoping review of systematic reviews
Authors: Guseva Elena , Wilchesky Machelle 
Published: April 2022

AbstractObjectiveTo establish a robust understanding of the state of the evidence on the effectiveness and/or efficacy of art therapy (AT) as a non-pharmacological treatment (NPT) modality for persons living with dementia (PLWD).BackgroundOver the past decade, AT has received increased attention from health care professionals and researchers as having a potential role to play within treatment plans for PLWD.(1-4)Inclusion criteriaThis scoping review will include systematic reviews from health-related disciplines conducted within the last 20 years that report the effectiveness and/or efficacy of AT as an NPT modality for PLWD and Mild Cognitive Impairment (MCI) as their main objective. Study outcomes must include cognition, quality of life, emotional and psychological well-being, and/or neuropsychiatric symptoms (NPS).MethodsA scoping review of systematic reviews was selected to outline different types of evidence and to identify gaps in the literature. The proposed review will be guided by the methodological framework proposed by the Joanna Briggs Institute. We will therefore specify the research question, identify relevant studies, select eligible studies, extract, collate, and summarize our results. We will not conduct a quality appraisal of the included studies as this review aims to explore the general scope of research conducted that assesses AT effectiveness and efficacy in PLWD.
MOSAIC (MOthers’ AdvocateS In the Community) for Pregnant Women and Mothers of Children Under 5 with Experience of Intimate Partner Violence: A pilot randomized trial study protocol
Authors: Hailemariam Maji , Zlotnick Caron , Taft Angela , Johnson Jennifer E. 
Published: April 2022

AbstractBackgroundPregnancy and motherhood increase the risk for long-term exposure to physical, psychological and sexual intimate partner violence (IPV; sexual or physical violence by current or former partners). Pregnant women and mothers with children under 5 who have experienced IPV exhibit poor physical and mental health and obstetric outcomes. Depression and posttraumatic stress disorder (PTSD) are the two most common mental health consequences of IPV. There is good evidence that women with good social support have better mental health and IPV outcomes.MethodsThis study will develop MOthers’ AdvocateS In the Community (MOSAIC) Plus intervention for pregnant women and mothers with children under the age of 5. MOSAIC uses trained mentor mothers and has been found to reduce subsequent IPV. This study will blend the original MOSAIC intervention with principles of interpersonal psychotherapy (IPT) to address symptoms of depression, PTSD, and prevent subsequent risk of IPV. We will conduct a pilot randomized trial of the MOSAIC Plus intervention compared to the traditional MOSAIC intervention to determine its feasibility and acceptability. Study samples include focus groups (n=36), open trial (n=15), and a randomized pilot trial including 40 pregnant women and mothers with children under 5 who report current/recent of IPV and elevated symptoms of maternal depression and/or PTSD. The study’s primary outcome will be changes in maternal depressive and PTSD symptoms. Secondary outcomes will include reduction in subsequent IPV, improvement in functioning, changes in social support and effectiveness in obtaining resources.DiscussionThis is a formative study evaluating the feasibility and acceptability of a mentor mother intervention for pregnant women and mothers with children under 5. Promising results of this study will be used for a larger, fully-powered randomized trial evaluating the effectiveness of a mentor mother intervention in preventing subsequent IPV and reducing depressive and PTSD symptoms in this population.Strengths and limitations of this studyThe study is informed by a robust qualitative approach to intervention development that involves a series of focus group discussions.This study aims to develop an intervention that reduces future intimate partner violence, while also addressing related maternal mental health outcomes.A rigorous and reproducible design includes randomization, clear inclusion criteria, manualized treatment protocols and fidelity assessments.The study will use reliable and validated measures.Given the small sample size, results from the pilot randomized trial are underpowered to draw firm conclusions about effectiveness.