bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contraction-expansion dynamics of reef species in response to sea-level changes
Authors: Hoareau TB , Pretorius PC 
Published: January 2021

AbstractThe contraction-expansion model (CEM) describes the dynamics of species that survived in refugia during the last glacial maximum (LGM) and expanded their range when environmental conditions slowly improved from the Late Glacial through to the Holocene. The CEM has been proposed to describe the dynamics of reef species in response to sea-level fluctuations from a range of disciplines, but genetic inferences rather suggest stable population sizes since the last glacial period. Here, we address this paradox by providing a new model of modern reef development, by assessing the effect of LGM bottlenecks using genetic simulations, and by using a survey of the literature on reef species to compile both estimates of times to expansion and applied rates of molecular evolution. Using previously published radiocarbon dates of core data, we propose a synthetic model for the dynamics of modern coral reefs in the Indo-Pacific region. This model describes both an initiation at 9.9 ka and subsequent development that confirms a strong influence of sea-level fluctuations on reef dynamics. Simulations based on mtDNA datasets showed that pre-LGM genetic signatures of expansion are lost. Recent literature shows that, although genetic expansions of tropical marine species are frequent (>95%), the onset of these expansions is old (median ~110 ka), which indicates that most populations have remained stable since before the LGM. These pre-LGM expansions are explained by the low mutation rates (1.66% changes/site/Myr) known to be inadequate to calibrate time at population level. Specific calibrations should help solve the paradox and generalise the CEM for reef species.
Nuclear Morphometry is a superior Prognostic Predictor in comparison to Histological grading in Renal cell Carcinoma: A Retrospective Clinico-pathological study
Authors: Agrawal Shruti , Jain Nikunj 
Published: January 2021

AbstractBackgroundRenal cell carcinoma (RCC) comprises of a spectrum of clinico-pathologically distinct entities thereby making it difficult to accurately predict the clinical outcome. Though many predictive factors have been described in literature, tumor stage and nuclear grade have been established to consistently correlate with the tumor behaviour. However, tumors in the same stage have shown to behave differently. Similarly subjectivity and lack of reproducibility in nuclear grade mandates use of more objective parameters such as digital nuclear morphometry which could provide consistent and more reliable results in predicting prognosis. The study was conducted with the main objective of comparing the histological grade and the nuclear morphometric variables in RCC for predicting the clinical outcome.Material and methodsA total of 219 cases of renal tumors in adults were retrieved retrospectively from the archives of pathology department in Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow and their clinical, gross and microscopic features were noted. Nuclear grading was done in 181 cases of clear cell and papillary RCC of which computer-assisted morphometry for various nuclear parameters was done in 100 cases where a follow-up data of at least 3 years was available. Nuclear grade and morphometric parameters were correlated statistically with the clinical outcome of the patients.ResultsHistological nuclear grade did not show statistically significant correlation with progression free survival (PFS). Higher values of mean nuclear area, mean nuclear circumference, mean nuclear major diameter and mean nuclear minor diameter were significant predictors of PFS with a strong inverse correlation.ConclusionNuclear morphometry is a more reliable predictor of clinical outcome in patients of RCC when compared to histological grade and should be included in predictive model with other clinical and pathological parameters to accurately determine tumor behaviour.
Quantifying non-communicable diseases’ burden in Egypt using State-Space model
Authors: El-Saadani Somaya , Saleh Mohamed , Ibrahim Sarah A. 
Published: January 2021

AbstractThe study aimed to model and quantify the health burden induced by four non-communicable diseases in Egypt, the first to be conducted in the context of a less developing county. The study used the State-Space model and adopted two Bayesian methods: Particle Filter and Particle Independent Metropolis-Hastings to model and estimate the NCDs’ health burden trajectories. We drew on time-series data of the International Health Metric Evaluation, CAPMAS’s Annual Bulletin of Health Services Statistics, the World Bank, and WHO data. Both Bayesian methods showed that the burden trajectories are on the rise. Most of the findings agreed with our assumptions and are in line with the literature. Previous year burden strongly predicts the burden of the current year. High prevalence of the risk factors, disease prevalence, and the disease’s severity level all increase illness burden. Years of life lost due to death has high loadings in most of the diseases. Contrary to the study assumption, results found a negative relationship between disease burden and health services utilization which can be attributed to the lack of full health insurance coverage and the pattern of health care seeking behavior in Egypt. Our study highlights that Particle Independent Metropolis-Hastings is sufficient in estimating the parameters of the study model, in the case of time-constant parameters. The study recommends using state Space models with Bayesian estimation approaches with time-series data in public health and epidemiology research.
Increased Risk of Autopsy-Proven Pneumonia with Sex, Season and Neurodegenerative Disease
Authors: Beach Thomas G. , Russell Aryck , Sue Lucia I. , Intorcia Anthony J. , Glass Michael J. , Walker Jessica E. , Arce Richard , Nelson Courtney M. , Hidalgo Tony , Chiarolanza Glenn , Mariner Monica , Scroggins Alex , Pullen Joel , Souders Leslie , Sivananthan Kimberly , Carter Niana , Saxon-LaBelle Megan , Hoffman Brittany , Garcia Angelica , Callan Michael , Fornwalt Brandon E. , Carew Jeremiah , Filon Jessica , Cutler Brett , Papa Jaclyn , Curry Jasmine R. , Oliver Javon , Shprecher David , Atri Alireza , Belden Christine , Shill Holly A. , Driver-Dunckley Erika , Mehta Shyamal H. , Adler Charles H. , Haarer Chadwick F. , Ruhlen Thomas , Torres Maria , Nguyen Steve , Schmitt Dasan , Fietz Mary , Lue Lih-Fen , Walker Douglas G. , Mizgerd Joseph P. , Serrano Geidy E. 
Published: January 2021

AbstractThere has been a markedly renewed interest in factors associated with pneumonia, a leading cause of death worldwide, due to its frequent concurrence with pandemics of influenza and Covid-19 disease. Reported predisposing factors to both bacterial pneumonia and pandemic viral lower respiratory infections are wintertime occurrence, older age, obesity, pre-existing cardiopulmonary conditions and diabetes. Also implicated are age-related neurodegenerative diseases that cause parkinsonism and dementia. We investigated the prevalence of autopsy-proven pneumonia in the Arizona Study of Aging and Neurodegenerative Disorders (AZSAND), a longitudinal clinicopathological study, between the years 2006 and 2019 and before the beginning of the Covid-19 pandemic. Of 691 subjects dying at advanced ages (mean 83.4), pneumonia was diagnosed postmortem in 343 (49.6%). There were 185 subjects without dementia or parkinsonism while clinicopathological diagnoses for the other subjects included 319 with Alzheimer’s disease dementia, 127 with idiopathic Parkinson’s disease, 72 with dementia with Lewy bodies, 49 with progressive supranuclear palsy and 78 with vascular dementia. Subjects with one or more of these neurodegenerative diseases all had higher pneumonia rates, ranging between 50 and 61%, as compared to those without dementia or parkinsonism (40%). In multivariable logistic regression models, male sex and a non-summer death both had independent contributions (ORs of 1.67 and 1.53) towards the presence of pneumonia at autopsy while the absence of parkinsonism or dementia was a significant negative predictor of pneumonia (OR 0.54). Male sex, dementia and parkinsonism may also be risk factors for Covid-19 pneumonia. The apolipoprotein E4 allele, as well as obesity, chronic obstructive pulmonary disease, diabetes, hypertension, congestive heart failure, cardiomegaly and cigarette smoking history, were not significantly associated with pneumonia, in contradistinction to what has been reported for Covid-19 disease.
Competing Health Risks Associated with the COVID-19 Pandemic and Early Response: A Scoping Review
Authors: Baral Stefan , Rao Amrita , Twahirwa Rwema Jean Olivier , Lyons Carrie , Cevik Muge , Kågesten Anna E. , Diouf Daouda , Sohn Annette H. , Phaswana-Mafuya Nancy , Kamarulzaman Adeeba , Millett Gregorio , Marcus Julia L. , Mishra Sharmistha 
Published: January 2021

AbstractBackgroundCOVID-19 has rapidly emerged as a global public health threat with infections recorded in nearly every country. Responses to COVID-19 have varied in intensity and breadth, but generally have included domestic and international travel limitations, closure of non-essential businesses, and repurposing of health services. While these interventions have focused on testing, treatment, and mitigation of COVID-19, there have been reports of interruptions to diagnostic, prevention, and treatment services for other public health threats.ObjectivesWe conducted a scoping review to characterize the early impact of COVID-19 on HIV, tuberculosis, malaria, sexual and reproductive health, and malnutrition.MethodsA scoping literature review was completed using searches of PubMed and preprint servers (medRxiv/bioRxiv) from January 1st to October 31st, 2020, using Medical Subject Headings (MeSH) terms related to SARS-CoV-2 or COVID-19 and HIV, tuberculosis, malaria, sexual and reproductive health, and malnutrition. Empiric studies reporting original data collection or mathematical models were included, and available data synthesized by region. Studies were excluded if they were not written in English.ResultsA total of 1604 published papers and 205 preprints met inclusion criteria, including 8.2% (132/1604) of published studies and 10.2% (21/205) of preprints: 7.3% (68/931) on HIV, 7.1% (24/339) on tuberculosis, 11.6% (26/224) on malaria, 7.8% (13/166) on sexual and reproductive health, and 9.8% (13/132) on malnutrition. Thematic results were similar across competing health risks, with substantial indirect effects of the COVID-19 pandemic and response on diagnostic, prevention, and treatment services for HIV, tuberculosis, malaria, sexual and reproductive health, and malnutrition.DiscussionCOVID-19 emerged in the context of existing public health threats that result in millions of deaths every year. Thus, effectively responding to COVID-19 while minimizing the negative impacts of COVID-19 necessitates innovation and integration of existing programs that are often siloed across health systems. Inequities have been a consistent driver of existing health threats; COVID-19 has worsened disparities, reinforcing the need for programs that address structural risks. The data reviewed here suggest that effective strengthening of health systems should include investment and planning focused on ensuring the continuity of care for both rapidly emergent and existing public health threats.
Corynebacterium glutamicumregulation beyond transcription: Organizing principles and reconstruction of an extended regulatory network incorporating regulations mediated by small RNA and protein-protein interactions
Authors: Escorcia-Rodríguez Juan M. , Tauch Andreas , Freyre-González Julio A. 
Published: January 2021

AbstractCorynebacterium glutamicumis a Gram-positive bacterium found in soil where the condition changes demand plasticity of the regulatory machinery. The study of such machinery at the global scale has been challenged by the lack of data integration. Here, we report three regulatory network models forC. glutamicum:strong(3040 interactions) constructed solely with regulations previously supported by directed experiments;all evidence(4665 interactions) containing thestrongnetwork, regulations previously supported by non-directed experiments, and protein-protein interactions with a direct effect on gene transcription; andsRNA(5222 interactions) containing theall evidencenetwork and sRNA-mediated regulations. Compared to the previous version (2018), thestrongandall evidencenetworks increased by 75 and 1225 interactions, respectively. We analyzed the system-level components of the three networks to identify how they differ and compared their structures against those for the networks of more than 40 species. The inclusion of the sRNAs regulations changed the proportions of the system-level components and increased the number of modules but decreased their size. TheC. glutamicumregulatory structure contrasted with other bacterial regulatory networks. Finally, we used thestrongnetworks of three model organisms to provide insights and future directions of theC. glutamicumregulatory network characterization.
Commercial vaccines do not confer protection against two genetic strains ofPiscirickettsia salmonis, LF-89-like and EM-90-like, in Atlantic salmon
Authors: Figueroa Carolina , Torrealba Débora , Morales-Lange Byron , Mercado Luis , Dixon Brian , Conejeros Pablo , Silva Gabriela , Soto Carlos , Gallardo José A. 
Published: January 2021

AbstractIn Atlantic salmon, vaccines have failed to control and prevent Piscirickettsiosis, for reasons that remain elusive. In this study, we report the efficacy of a commercial vaccine developed with thePiscirickettsia salmonisisolate AL100005 against other two isolates which are considered highly and ubiquitously prevalent in Chile: LF-89-like and EM-90-like. Two cohabitation trials were performed to mimic real-life conditions and vaccine performance: 1) post smolt fish were challenged with a single infection of LF-89-like, 2) adults were coinfected with EM-90-like and a low coinfection of sea lice. In the first trial, the vaccine delayed smolt mortalities by two days; however, unvaccinated and vaccinated fish did not show significant differences in survival (unvaccinated: 60.3%, vaccinated: 56.7%; p = 0.28). In the second trial, mortality started three days later for vaccinated fish than unvaccinated fish. However, unvaccinated and vaccinated fish did not show significant differences in survival (unvaccinated: 64.6%, vaccinated: 60.2%, p= 0.58). Thus, we found no evidence that the evaluated vaccines confer effective protection against of LF-89-like or EM-90-like with estimated relative survival proportions (RPSs) of −9% and −12%, respectively. More studies are necessary to evaluate whether pathogen heterogeneity is a key determinant of the vaccine efficacy againstP. salmonis.
ConVarT: a search engine for matching human genetic variants with variants from non-human species
Authors: Pir Mustafa S. , Bilgin Halil I. , Sayici Ahmet , Coşkun Fatih , Torun Furkan M. , Zhao Pei , Kang Yahong , Cevik Sebiha , Kaplan Oktay I. 
Published: January 2021

ABSTRACTThe availability of genetic variants, together with phenotypic annotations from model organisms, facilitates comparing these variants with equivalent variants in humans. However, existing databases and search tools do not make it easy to scan for equivalent variants, namely “matching variants” (MatchVars) between humans and other organisms. Therefore, we developed an integrated search engine called ConVarT (http://www.convart.org/) for matching variants between humans, mice, andC. elegans. ConVarT incorporates annotations (including phenotypic and pathogenic) into variants, and these previously unexploited phenotypic MatchVars from mice andC. eleganscan give clues about the functional consequence of human genetic variants. Our analysis shows that many phenotypic variants in different genes from mice andC. elegans, so far, have no counterparts in humans, and thus, can be useful resources when evaluating a relationship between a new human mutation and a disease.
Neural correlates of orbital telorism
Authors: Pawlak Mikolaj A. , Knol Maria J. , Vernooij Meike W. , Ikram M. Arfan , Adams Hieab H.H. , Evans T. E. 
Published: January 2021

ABSTRACTOrbital telorism, the interocular distance, is a clinically informative and in extremes is considered a minor physical anomaly. While its extremes, hypo- and hypertelorism, have been linked to disorders often related to cognitive ability, little is known about the neural correlates of normal variation of telorism within the general population. We derived measures of orbital telorism from cranial magnetic resonance imaging (MRI) by calculating the distance between the eyeball center of gravity in two population-based datasets (N=5,653, N=29,824, Mean age 64.66, 63.75 years). This measure was found to be related grey matter tissue density within numerous regions of the brain, including, but surprisingly not limited to, the frontal regions, in both positive and negative directions. Additionally, telorism was related to several cognitive functions, such as Perdue Pegboard test (Beta, P-value, (CI95%) −0.02, 1.63×10-7(−0.03;-0.01)) and fluid intelligence (0.02, 4.75×10-06(0.01:0.02)), with some relationships driven by individuals with a smaller orbital telorism. This is reflective of the higher prevalence of hypo-telorism in developmental disorders, specifically those that accompany lower cognitive lower functioning. This study suggests, despite previous links only made in clinical extremes, that orbital telorism holds some relation to structural brain development and cognitive function in the general population. This relationship is likely driven by shared developmental periods.
The renal inflammatory network of nephronophthisis
Authors: Quatredeniers Marceau , Bienaimé Frank , Ferri Giulia , Isnard Pierre , Porée Esther , Billot Katy , Birgy Eléonore , Ceccarelli Salomé , Silbermann Flora , Braeg Simone , Nguyen-Khoa Thao , Salomon Rémi , Gubler Marie-Claire , Wolfgang Kuehn E. , Saunier Sophie , Viau Amandine 
Published: January 2021

STRUCTURED ABSTRACTBACKGROUNDThe majority of genetic kidney disease leading to kidney failure is caused by mutations in ciliary genes. How cilia malfunction leads to progressive kidney damage is poorly understood, but recent evidence links ciliopathy genes to CCL2 dependent macrophage recruitment in autosomal dominant polycystic kidney disease (ADPKD), the most studied renal ciliopathy. Whether or not renal inflammation is involved in other renal ciliopathies is unclear.METHODSWe combined mice models with kidney biopsies and renal epithelial cells sampled from human urine to characterize the renal inflammatory network of nephronophthisis (NPH), the most frequent renal ciliopathy in children.RESULTSIn human, mutations in cilia genes involved in NPH enhance urine excretion of the chemokine CCL2, causing abnormal macrophage recruitment in kidney tissues from NPH patients. Differing from ADPKD, inactivatingCcl2specifically in mouse tubular cells does not rescue the NPH phenotype, suggesting that other inflammatory mediators are involved. Using transcriptional data from 2 NPH models, we identify a set of pro-inflammatory cytokines upregulated in this disease, independently of CCL2. The majority of detectable transcripts from this set are specifically upregulated in kidney cells from NPH patients. In line with the function of these cytokines, NPH kidneys show disproportionate neutrophils and T cells infiltrates compared to healthy subject or hypertensive and diabetic chronic kidney disease patients.CONCLUSIONSThis study reveals that inflammation is a central aspect in human NPH and delineates a specific set of inflammatory mediators that regulates immune cell recruitment in human NPH.SIGNIFICANCE STATEMENTMutations in genes encoding primary cilia proteins are the leading cause of genetic kidney failure. In autosomal dominant polycystic kidney disease (ADPKD), deregulated cilia signaling leads to kidney infiltration by macrophages through the chemokine CCL2. Little is known about renal inflammation in nephronophthisis (NPH), the most frequent pediatric renal ciliopathy. Using NPH mice models, tissues and cells from NPH patients, we unveil renal inflammation as preeminent feature of NPH. Remarkably, the renal inflammatory evoked by ciliary gene mutations in NPH does not overlap with ADPKD: it is CCL2 independent, involves a prominent recruitment of neutrophils and T cells and a specific cytokine signature. This unforeseen findings strengthen the link between primary cilia and renal inflammation.
Social Reactivation of Fear Engrams Enhances Memory Recall
Authors: Finkelstein Abby Basya , Leblanc Héloïse , Cole Rebecca H. , Gallerani Troy , Vieira Anahita , Zaki Yosif , Ramirez Steve 
Published: January 2021

AbstractFor group-living species such as humans and rodents, conspecific interactions pervasively shape emotion (1–3), attention (4), and cognitive ability (5–8). Higher-order cognitive processes such as memory within a social brain are thus interlaced with social influences. Traditional laboratory rodent cages offer a limited but nonetheless rich multi-modal landscape of communication, including auditory calls (9–12), chemical signaling (13, 14), and tactile stimulation (15, 16). The absence of such social encounters in singly housed animals results in cognitive impairments and depression-like phenotypes (17), likely obscuring how the social brain has evolved to function. It is thus important to understand the relationship between social context and how individuals process memories. As social interaction recruits hippocampal (18) and amygdalar (19) circuitry that also serves as hubs for non-social memory traces(20–24), we hypothesized that pre-existing ensembles in these regions can be modulated by social experiences and lead to changes in memory expression. Here we show that stressful social experiences enhance the recall of previously acquired fear memories in male but not female mice. Activity-dependent tagging of cells in the dentate gyrus (DG) during fear learning revealed that these ensembles were endogenously reactivated during the social experiences in males. These reactivated cells were shown to be functional components of engrams, as optogenetic stimulation of the cells active during the social experience in previously fear conditioned animals was sufficient to drive fear-related behaviors. Our findings suggest that social encounters can reactivate pre-existing DG engrams and thereby strengthen discrete memories.Significance StatementSocial environments can bolster and protect cognitive abilities. However, the relationship between social stimuli and individually learned memories remains enigmatic. Our work reveals that exposure to a stressed, naïve non-familiar conspecific or to the ambient olfactory-auditory cues of a recently stressed familiar conspecific induces reactivation of the cellular ensembles associated with a fear memory in the hippocampus. Artificially activating the hippocampal ensemble active during the social experience induces fearful behaviors only in animals that have previously acquired a negative memory, suggesting a fear-driving function of the reactivated ensembles and demonstrating the interaction between individual history and social experience. The neural resurgence of fear-driving ensembles during social experiences leads to a context-specific enhancement of fear recall. Our findings provide evidence that unlike directly physical stressors, ambient social stimuli can reactivate and amplify an individual’s memories.