bluuebunny/crossref_metadata_2025_split huggingface dataset:
Is attachment style in early childhood associated with mental health difficulties in late adolescence?
Authors: Clery Philippa , Rowe Angela , Munafò Marcus R. , Mahedy Liam 
Published: March 2021

AbstractBackgroundAlthough existing research has suggested an association between insecure attachment styles and mental health difficulties, these studies often have small sample sizes, use cross-sectional designs, and measure attachment as a discrete variable at a single point. It is also unclear whether these associations persist into late adolescence. In this prospective study we aimed to determine whether insecure attachment style in early childhood is associated with depression and self-harm at 18 years.MethodsWe used data from the Avon Longitudinal Study of Parents and Children cohort. Mothers completed attachment related questionnaires when their child was 18, 30, and 42 months old. Offspring depression and lifetime self-harm was assessed at 18 years using the Clinical Interview Schedule-Revised. Attachment was derived as a latent variable in a structural equation modelling framework. Logistic regression was performed on participants with complete attachment data (n=7032) to examine the association between attachment style and depression and self-harm, with adjustment for potential confounders. Differential dropout was accounted for using multiple imputation.ResultsWe found some evidence for an association between attachment quality and depression and self-harm. In the fully adjusted imputed model, a one standard deviation increase in insecure attachment was associated with a 13% increase in the odds of depression at age 18 (OR=1.13; 95%CI=1.00 to 1.27) and a 14% increase in the odds of self-harm at age 18 (OR=1.14; 95%CI=1.02 to 1.25).ConclusionsOur findings strengthen the evidence suggesting that an insecure attachment style assessed in early childhood is associated with mental health difficulties in late adolescence. If this association is causal, policies to support parenting or attachment-based interventions to improve attachment quality could help reduce mental health difficulties in adolescence/young adulthood.
Efficient masking of plant genomes by combining kmer counting and curated repeats
Authors: Contreras-Moreira Bruno , Filippi Carla V , Naamati Guy , Girón Carlos García , Allen James E , Flicek Paul 
Published: March 2021

Ii.Summary/AbstractThe annotation of repetitive sequences within plant genomes can help in the interpretation of observed phenotypes. Moreover, repeat masking is required for tasks such as whole-genome alignment, promoter analysis or pangenome exploration. While homology-based annotation methods are computationally expensive, k-mer strategies for masking are orders of magnitude faster. Here we benchmark a two-step approach, where repeats are first called by k-mer counting and then annotated by comparison to curated libraries. This hybrid protocol was tested on 20 plant genomes from Ensembl, using the kmer-based Repeat Detector (Red) and two repeat libraries (REdat and nrTEplants, curated for this work). We obtained repeated genome fractions that match those reported in the literature, but with shorter repeated elements than those produced with conventional annotators. Inspection of masked regions overlapping genes revealed no preference for specific protein domains. Half of Red masked sequences can be successfully classified with nrTEplants, with the complete protocol taking less than 2h on a desktop Linux box. The repeat library and the scripts to mask and annotate plant genomes can be obtained athttps://github.com/Ensembl/plant-scripts.
Revisiting the role ofToxoplasma gondiiERK7 in the maintenance and stability of the apical complex
Authors: Dos Santos Pacheco Nicolas , Tosetti Nicolò , Krishnan Aarti , Haase Romuald , Soldati-Favre Dominique 
Published: March 2021

AbstractToxoplasma gondiiERK7 is known to contribute to the integrity of the apical complex and to be involved only in the final step of the conoid biogenesis. In the absence of ERK7, mature parasites lose their conoid complex and are unable to glide, invade or egress from host cells. In contrast to a previous report, we show here that depletion of ERK7 phenocopies the depletion of the apical cap proteins AC9 or AC10. The absence of ERK7 leads to the loss of the apical polar ring, the disorganization of the basket of subpellicular microtubules and an impairment in micronemes secretion. Ultra-expansion microscopy (U-ExM) coupled to NHS-Ester staining on intracellular parasites offers an unprecedented level of resolution and highlights the disorganization of the rhoptries as well as the dilated plasma membrane at the apical pole in the absence of ERK7. Comparative proteomics analysis of wild-type and ERK7 or AC9 depleted parasites led to the disappearance of known, predicted, as well as putative novel components of the apical complex. In contrast, the absence of ERK7 led to an accumulation of microneme proteins, resulting from the defect in exocytosis of the organelles.ImportanceThe conoid is an enigmatic, dynamic organelle positioned at the apical tip of the coccidian subgroup of the Apicomplexa, close to the apical polar ring (APR) from which the subpellicular microtubules (SPTMs) emerge and at the site of microneme and rhoptry secretory organelles exocytosis. InToxoplasma gondii, the conoid protrudes concomitantly to microneme secretion, during egress, motility and invasion. The conditional depletion of the apical cap structural protein AC9 or AC10 leads to a disorganization of SPTMs as well as the loss of APR and conoid that result in microneme secretion defect and block in motility, invasion and egress. We show here that depletion of the kinase ERK7 phenocopies completely AC9 and AC10 mutants. Moreover, the combination of ultrastructure expansion microscopy with an NHS ester staining revealed that ERK7 depleted parasites exhibit a dilated apical plasma membrane and a mis-positioning of the rhoptry organelles.
Identification and characterization of novel infection associated transcripts in macrophages
Authors: Prabhakar A , Singla Mohit , Lodha Rakesh , Rao Vivek 
Published: March 2021

ABSTRACTRegulated expression of genes in response to internal and external stimuli is primarily responsible for the enormous plasticity and robustness of biological systems. Recent studies have elucidated complex regulatory non protein coding transcript (lncRNA) circuits in coordinated response of immune cells. By analysis of lncRNA expression profiles of macrophages in response to Mtb infection, we identified novel highly expressed transcripts, unique in encompassing one functional protein coding transcript- CMPK2 and a previously identified type I IFN responsive lncRNA- NRIR. While these RNA are induced by virulent Mtb early, the complete absence of expression in non-viable Mtb infected cells coupled to a more protracted expression profile in the case of BCG suggest an important role in macrophage response to mycobacteria. Moreover, enhanced expression was observed in macrophages from TB patients. The elevated expression by 1h in response to fast growing bacteria further emphasizes the importance of these RNAs in the macrophage infection response. These transcripts (TILT1, 2,3 -TLR4 andInfection inducedLongTranscript) are triggered exclusively by TLR4 stimulation (LPS) with faster and stronger kinetics in comparison to the lncRNA – NRIR. Overall, we provide evidence for the presence of numerous transcripts that is a part of the early infection response program of macrophages.
Prevalence of short interpregnancy interval and its associated factors among pregnant women in Debre Berhan town, Ethiopia
Authors: Mamo Hana , Dagnaw Abinet , Tadesse Nigussie , Berhane Kalayu , Shiferaw Kehabtimer 
Published: March 2021

AbstractBackgroundShort inter-pregnancy interval is when the time elapsed between the dates of birth of the preceding child and the conception date of the current pregnancy is < 24 months. Despite its direct effects on the perinatal and maternal outcomes, there is a paucity of evidence on its prevalence and determinant factors, particularly in Ethiopia. Therefore, this study assessed the prevalence and associated factors of short inter-pregnancy interval among pregnant women in Debre Berhan town, Northern Ethiopia.MethodsA community based cross sectional study was conducted among a randomly selected 496 pregnant women in Debre Berhan town from February 9 to March 9, 2020. The data was collected by using interviewer administered questionnaire and analyzed using STATA (14.2) statistical software. To identify the predictors of short inter-pregnancy interval, multivariable binary logistic regression was fitted and findings are presented using adjusted odds ratio (AOR) with 95% confidence interval (CI).ResultThe overall prevalence of short inter-pregnancy interval (<24 months) among pregnant women was 205 (40.9%). Being over 30 years of age at first birth (AOR=3.50; 95% CI: 2.12-6.01), non-use of modern contraceptive (AOR=2.51; 95% CI: 1.23-3.71), duration of breast feeding for less than 12 months (AOR= 2.62; 95% CI: 1.32-5.23), parity above four (AOR=0.31; 95% CI: 0.05-0.81), and unintended pregnancy (AOR= 5.42; 95% CI: 3.34-9.22) were independently associated factors with short inter-pregnancy interval.ConclusionDespite the family planning and other public health intervention tried in the country, the prevalence of short inter-pregnancy interval in this study was high. Therefore, it implies that increasing contraceptive use and encouraging optimal breast feeding might help in the efforts made to avert the problem.
Where to learn to flatten the curve: a modelling study
Authors: Silk Matthew J , Carrignon Simon , Bentley R. Alexander , Fefferman Nina H 
Published: March 2021

AbstractBackgroundIndividual behavioural decisions are responses to both a person’s perceived social norms and could be driven by both their physical and social environment. In the context of the COVID-19 pandemic, these environments correspond to epidemiological risk from contacts and the social construction of risk by communication within networks of friends. Understanding when, and under which circumstances, each modality of influence can foster the widespread adoption of protective behaviours is critical for shaping useful, practical public health messaging that will best enhance the public response.MethodsWe use a multiplex network approach to explore how information from both physical contact and social communication networks is driving a mitigating behavioural response to disease risk.FindingsWe show that maintaining focus on awareness of risk in each individual’s physical layer contacts promotes the greatest reduction in disease spread, but only when an individual is aware of the symptoms of a non-trivial proportion of their physical contacts (approximately 20% or more). Information from the communication layer was less useful when these connections matched less well with physical contacts and contributed little in combination with accurate information from the physical layer.InterpretationWe conclude that maintaining social focus on local outbreak status will allow individuals to structure their perceived social norms appropriately and respond more rapidly when risk increases. Finding ways to relay accurate local information from trusted community leaders could improve mitigation even where more intrusive/costly strategies, such as contact-tracing, are not possible.
The SARS-CoV-2 receptor angiotensin-converting enzyme 2 (ACE2) in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: analysis of high-throughput epigenetic and gene expression studies
Authors: Malato João , Sotzny Franziska , Bauer Sandra , Freitag Helma , Fonseca André , Grabowska Anna D , Graça Luís , Cordeiro Clara , Nacul Luís , Lacerda Eliana M , Castro-Marrero Jesus , Scheibenbogen Carmen , Westermeier Francisco , Sepúlveda Nuno 
Published: March 2021

AbstractPatients affected by Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) show specific epigenetic and gene expression signatures of the disease. However, it is unknown whether these signatures include abnormal levels of the human angiotensin-converting enzymes, ACE and ACE2, the latter being the main receptor described for the host-cell invasion by SARS-CoV-2. To investigate that, we first re-analyzed available case-control epigenome-wide association studies based on DNA methylation data, and case-control gene expression studies based on microarray data. From these published studies, we found an association between ME/CFS and 4 potentially hypomethylated probes located in theACElocus. We also found another disease association with one hypomethylated probe located in the transcription start site of ACE2. The same disease associations were obtained for women but not for men after performing sex-specific analyses. In contrast, a meta-analysis of gene expression levels could not provide evidence for a differentially expression ofACEandACE2in affected patients when compared to healthy controls. In line with this negative finding, the analysis of a new data set on the gene expression ofACEandACE2in peripheral blood mononuclear cells did not find any differences between a female cohort of 37 patients and 34 age-matched healthy controls. Future studies should be conducted to extend this investigation to other potential receptors used by SARS-CoV-2. These studies will help researchers and clinicians to improve the understanding of the health risk imposed by this virus when infecting patients affected by this debilitating disease.
Salted roads lead to edema and reduced locomotor function in wood frogs
Authors: Frymus Lauren E. , Goedert Debora , Zamora-Camacho Francisco Javier , Smith Peter C. , Zeiss Caroline J. , Comas Mar , Abbott Timothy A. , Basu Silvia P. , DeAndressi Jason C. , Forgione Mia E. , Maloney Michael J. , Priester Joseph L. , Senturk Faruk , Szeligowski Richard V. , Tucker Alina S. , Zhang Mason , Calsbeek Ryan , Brady Steven P. 
Published: March 2021

AbstractHuman activities have caused massive losses of natural populations across the globe. Like many groups, amphibians have experienced substantial declines worldwide, driven by environmental changes such as habitat conversion, pollution, and disease emergence. Each of these drivers is often found in close association with the presence of roads. Here we report a novel consequence of roads affecting an amphibian native to much of North America, the wood frog (Rana sylvatica). Across 38 populations distributed from southern to central New England, we found that adult wood frogs living adjacent to roads had higher incidence and severity of edema (bloating caused by fluid accumulation) during the breeding season than frogs living away from the influence of roads. This effect was best explained by increased conductivity of breeding ponds, caused by runoff pollution from road salt used for de-icing. Edema severity was negatively correlated with locomotor performance in more northerly populations. Interestingly, northern populations experience more intense winters, which tends to result in more de-icing salt runoff and increased energetic demands associated with overwintering cryoprotection needs. Thus, this emerging consequence of roads appears to impose potential fitness costs associated with locomotion, and these effects might be most impactful on populations living in regions where de-icing is most intense.
Mycenaspecies can be opportunist-generalist plant root invaders
Authors: Harder Christoffer Bugge , Hesling Emily , Botnen Synnøve S. , Dima Bálint , von Bonsdorff-Salminen Tea , Niskanen Tuula , Jarvis Susan G. , Lorberau Kelsey E. , Ouimette Andrew , Hester Alison , Hobbie Erik A. , Taylor Andy F.S. , Kauserud Håvard 
Published: March 2021

SummaryRecently, several saprotrophic genera have been found to invade/interact with plant roots in laboratory growth experiments, and this coincides with reports of abundant saprotrophic fungal sequences in plant roots. However, it is uncertain if this reflects field phenomena, and if reports on coincidentally amplified saprotrophs are simply coincidental.We investigated root invasion by presumed saprotrophic fungi by focusing on the large genusMycenain1)a systematic analysis of the occurrence of saprotrophic fungi in new and previously published ITS1/ITS2 datasets generated from roots of 10 mycorrhizal plant species, and2)we analysed natural abundances of13C/15N stable isotope signatures of fungal/plant communities from five comparable field locations to examine the trophic status ofMycenaspecies.Mycenawas the only saprotrophic genus consistently found in 9 of 10 plant host roots, with high within-host variation inMycenasequence proportions (0-80%) recovered.Mycenacarpophores displayed isotopic signatures consistent with published13C/15N profiles of both saprotrophic or mutualistic lifestyles, with considerable intraspecific variation, resembling the patterns seen in growth experiments. These results indicate that multipleMycenaspecies opportunistically invade the roots of a range of plant species, possibly forming a spectrum of interactions. This potentially challenges our general understanding of fungal ecology.Originality significance statementThis is the first study to apply a dual approach of systematic metabarcoding of plant roots and stable isotope signatures on dried field material to the large and common saprotrophic fungal genusMycena. This is significant as it shows that members of this genus, normally not expected to be found inside plant roots at all, are in fact associated eith multiple plant hosts. The study furthermore shows that species in this genus may occupy different ecological roles in the field besides being saprotrophic. That a large and common fungal genus known to be a quantitatively important litter decayer can be an opportunistic root invader and interact with host plants is of interest to all mycologists and ecologists working on plant-fungus/microb symbiosis.
PRIMATE LIMB CONFORMATION: IMPLICATIONS FOR MECHANICAL ENERGY CONSERVATION*
Authors: Catalino Michael P. 
Published: March 2021

ABSTRACTIn order to understand the energy implications of primate limb conformation, the biomechanics of swing phase and the vertical movements of limb center of gravity were examined in the arboreal rhesus macaque (Macaca mulatta) and the semi-terrestrial long-tailed macaque (Macaca fascicularis). The objective was to better understand the potential variation in locomotor adaptations in these two macaque species within different ecological environments. In particular, the objective of this study was to identify the implications that these movements have on the internal energy costs of locomotion. I show that the biomechanics of swing phase for these two species have important effects on their limb center of gravity, although they may have similar limb segment mass distributions. This study suggests that mechanical energy conservation during swing phase is important in mammalian locomotion.
Aggregated Mycobacterium tuberculosis enhances the inflammatory response
Authors: Rodel Hylton E. , Ferreira Isabella Markham , Ziegler Carly G.K , Ganga Yashica , Bernstein Mallory , Hwa Shi-Hsia , Nargan Kievershen , Lustig Gila , Kaplan Gilla , Noursadeghi Mahdad , Shalek Alex K. , Steyn Adrie , Sigal Alex 
Published: March 2021

AbstractMycobacterium tuberculosis (Mtb) readily aggregates in culture and Mtb aggregates in the lung were observed in experimental Mtb infection. However, the physiological consequences of Mtb aggregation are incompletely understood. Here we examined the human macrophage transcriptional response to aggregated Mtb relative to infection with non-aggregated single or multiple bacilli per host cell. Infection with aggregated Mtb led to an early upregulation of pro-inflammatory associated genes and enhanced TNFα signaling via the NFκB pathway. Both these pathways were significantly upregulated relative to infection with single bacilli, and TNFα signaling was also significantly elevated relative to infection with multiple non-aggregated Mtb. Secretion of TNFα and downstream cytokines were also enhanced. On a longer timescale, aggregate infection led to overall increased acidification per macrophage and a high proportion of death in these cells after aggregate phagocytosis. Host cell death did not occur when Mtb aggregates were heat killed despite such clumps being readily picked up. To validate that Mtb aggregates do occur in the human lung, we document Mtb aggregates surrounding a cavity in a human TB lesion. Aggregates may therefore be present in some lesions and elicit a stronger inflammatory response resulting in recruitment of additional phagocytes and their subsequent death, potentially leading to necrosis and transmission.
Mechanical influences onin silicotumor evolution
Authors: Rosenbauer Jakob , Berghoff Marco , Glazier James A. , Schug Alexander 
Published: March 2021

AbstractExperimental insight and conceptual understanding of tumor growth are steadily growing and leading to new therapeutic interventions. Experiments and clinical studies are able to link single-cell properties to macroscopic tumor attributes. The development of cellular subpopulations in heterogeneous tumors can be understood as an evolutionary system with different cell types competing over both space and nutrients. However, to predict the growth trajectory and development of a tumor, fitness and trade-offs of cell properties in the context of the surroundings are required and often inaccessible. The optimum of the evolutionary trajectory provides a target for intervention, but can mostly not be identified. We propose that the optimal value of cellular properties is influenced by the tumor surrounding. Computational multiscale-modeling of tissue enables the observation of the trajectory of each cell while modeling the tumor surrounding. We model a 3D spheroid tumor and the fitness of individual cells and the evolutionary behavior of the tumor are quantified and linked to global parameters. Cell–cell adhesion and cell motility are two important mechanical properties for cell development and used as free parameters. Mechanical properties alone are able to drive the tumor towards low adhesion.We implement a dynamically changing nutrient surrounding representing the fluctuating blood-supply through blood vessel collapse and angiogenesis. We find that the evolutionary speed depends on the frequency of the fluctuations. We identify a frequency domain in which the evolutionary speed is significantly increased over a tumor with constant nutrient supply. The findings suggest that mechanically-induced fluctuations can accelerate tumor evolution.Author summaryLimited space and nutrients together with competing cell types drive an evolutionary process inside tumors. This process selects for the fittest cell types and optimizes the growing behavior for its local surroundings. An expanding tumor exerts mechanical forces on its cells and its surroundings, leading to a fluctuating nutrient supply through collapsing blood vessels. Here, we observe the influence of a dynamically changing surrounding on the evolutionary behavior of heterogeneous tumors in a high-resolution computational model. We find that the evolutionary speed depends on the frequency of the fluctuations and a fitness advantage of low-adhesion cells.