bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular landscape and functional characterization of centrosome amplification in ovarian cancer
Authors: Sauer Carolin M. , Hall James A. , Couturier Dominique-Laurent , Bradley Thomas , Piskorz Anna M. , Griffiths Jacob , Sawle Ashley , Eldridge Matthew D. , Smith Philip , Hosking Karen , Reinius Marika A.V. , Gavarró Lena Morrill , Mes-Masson Anne-Marie , Ennis Darren , Millan David , Hoyle Aoisha , McNeish Iain A. , Jimenez-Linan Mercedes , Martins Filipe Correia , Tischer Julia , Vias Maria , Brenton James D. 
Published: September 2022

AbstractHigh grade serous ovarian carcinoma (HGSOC) is characterised by poor outcome and extreme chromosome instability (CIN). Therapies targeting centrosome amplification (CA), a key mediator of chromosome missegregation and CIN, may have significant clinical utility in HGSOC. However, the prevalence of CA in HGSOC, its relationship to genomic biomarkers of CIN and its potential impact on therapeutic response have not been defined. Using high-throughput multi-regional microscopy on 287 clinical HGSOC tumour tissues and 73 ovarian cancer cell lines, we show that CA through centriole overduplication is a highly recurrent and heterogeneous feature of HGSOC and is strongly associated with CIN and genome subclonality. Cell-based studies showed that high prevalence CA is phenocopied in ovarian cancer cell lines, and that high CA is associated with increased multi-treatment resistance; most notably to paclitaxel which is the most common treatment used in HGSOC. CA in HGSOC may therefore present a potential driver of tumour evolution and a powerful biomarker for response to standard-of-care treatment.
European scenarios for future biological invasions
Authors: Pérez-Granados Cristian , Lenzner Bernd , Golivets Marina , Saul Wolf-Christian , Jeschke Jonathan M. , Essl Franz , Peterson Garry D. , Rutting Lucas , Latombe Guillaume , Adriaens Tim , Aldridge David C. , Bacher Sven , Bernardo-Madrid Rubén , Brotons Lluís , Díaz François , Gallardo Belinda , Genovesi Piero , González-Moreno Pablo , Kühn Ingolf , Kutleša Petra , Leung Brian , Liu Chunlong , Pagitz Konrad , Pastor Teresa , Pauchard Aníbal , Rabitsch Wolfgang , Roy Helen E. , Robertson Peter , Seebens Hanno , Solarz Wojciech , Starfinger Uwe , Tanner Rob , Vilà Montserrat , Roura-Pascual Núria 
Published: September 2022

AbstractInvasive alien species are one of the major threats to global biodiversity, ecosystem integrity, nature’s contribution to people and human health. While scenarios about potential future developments have been available for other global change drivers for quite some time, we largely lack an understanding of how biological invasions might unfold in the future across spatial scales.Based on previous work on global invasion scenarios, we developed a workflow to downscale global scenarios to a regional and policy-relevant context. We applied this workflow at the European scale to create four European scenarios of biological invasions until 2050 that consider different environmental, socio-economic and socio-cultural trajectories, namely the European Alien Species Narratives (Eur-ASNs).We compared the Eur-ASNs with their previously published global counterparts (Global-ASNs), assessing changes in 26 scenario variables. This assessment showed a high consistency between global and European scenarios in the logic and assumptions of the scenario variables. However, several discrepancies in scenario variable trends were detected that could be attributed to scale differences. This suggests that the workflow is able to capture scale-dependent differences across scenarios.We also compared the Global- and Eur-ASNs with the widely used Global and European Shared Socioeconomic Pathways (SSPs), a set of scenarios developed in the context of climate change to capture different future socio-economic trends. Our comparison showed considerable divergences in the scenario space occupied by the different scenarios, with overall larger differences between the ASNs and SSPs than across scales (global vs. European) within the scenario initiatives.Given the differences between the ASNs and SSPs, it seems that the SSPs do not adequately capture the scenario space relevant to understanding the complex future of biological invasions. This underlines the importance of developing independent, but complementary, scenarios focused on biological invasions. The downscaling workflow we presented and implemented here provides a tool to develop such scenarios across different regions and contexts. This is a major step towards an improved understanding of all major drivers of global change including biological invasions.
Socially transmitted innovations in dynamic predator-prey systems
Authors: Kikuchi David W. , Simon Margaret W. 
Published: September 2022

ABSTRACTIndividual behavioral variation is common, yet often we do not know how it is maintained. A potential explanation is that some behaviors must be acquired rather than genetically inherited. We investigate the social transmission of behavioral innovations, which can be key for the success of predator species, especially in contexts where environmental changes take place. We examine innovation in two classic predator-prey models. We assume that innovations increase predator attack rates or conversion efficiencies, or that innovations reduce predator mortality or prey handling time. We find that a common outcome of innovations is the destabilization of the system. Destabilizing effects include increasing oscillations or limit cycles. If either of these outcomes increases the risk of extinction, innovations that benefit individual predators may not have positive long-term effects on predator populations. Furthermore, as populations cycle, innovative individuals can be nearly eliminated, maintaining temporal behavioral variability. The destabilizing effects of behavioral innovations on predator-prey dynamics could have implications for biological invasions, urban populations, endangered species, and, more broadly, the maintenance of behavioral polymorphisms.
Phenotypic switch and reduced the growth of melanoma spheroids in the presence of mast cell-conditioned medium: potential impact of nutrient starvation effects
Authors: Grujic Mirjana , Nguyen Thanh , Héchard Tifaine , Wang Helen , Lampinen Maria , Paivandy Aida , Pejler Gunnar 
Published: September 2022

AbstractMast cells are abundant in melanoma tumors, and studies suggest that they can be either detrimental or protective for melanoma growth. However, the underlying mechanisms are not fully understood. Here, we adopted a hanging drop-established spheroid system to investigate how mast cells can influence melanoma growth and phenotype in a 3-D context. In the presence of mast cells or mast cell-conditioned medium, melanoma spheroid growth was profoundly reduced. To address the underlying mechanism, we conducted a transcriptomic analysis, which revealed that mast cell-conditioned medium had extensive effects on the melanoma gene expression patterns. Pathway analyses revealed profound effects on the expression of genes related to amino acid and protein metabolism. The conditioned medium also induced an upregulated expression of cancer-related genes, including adhesion molecules implicated in metastatic spreading. In line with this, after transfer to a Matrigel extracellular matrix milieu, spheroids that had been developed in the presence of mast cell-conditioned medium displayed enhanced elevated growth and adhesive properties. However, when assessing for possible effects of nutrient starvation, i.e., reduced nutrient content in mast cell-conditioned medium, we found that the observed effects on melanoma spheroid growth potentially could be explained by such effects. Hence, it cannot be excluded that the observed phenotypic alterations of melanoma spheroids grown in the presence of mast cells or mast cell-conditioned media are, at least partly, due to nutrient starvation rather than to the action of factors secreted by mast cells. Instead, our findings may provide insight into the effects on gene expression events that occur in melanoma tumors under nutrient stress.
Infant antibody repertoires during the first two years of influenza vaccination
Authors: Kuraoka Masayuki , Curtis Nicholas C. , Watanabe Akiko , Tanno Hidetaka , Shin Seungmin , Ye Kevin , Macdonald Elizabeth , Lavidor Olivia , Kong Susan , Holle Tarra Von , Windsor Ian , Ippolito Gregory C. , Georgiou George , Walter Emmanuel B. , Kelsoe Garnett H. , Harrison Stephen C. , Moody M. Anthony , Bajic Goran , Lee Jiwon 
Published: September 2022

AbstractThe first encounter with influenza virus biases later immune responses. This “immune imprinting”, formerly from infection within a few years of birth, is in the U.S. now largely from immunization with a quadrivalent, split vaccine (IIV4). In a pilot study of IIV4 imprinting, we characterized, by single-B-cell cultures, NextGen sequencing, and plasma antibody proteomics, the primary antibody responses to influenza in two infants during their first two years of seasonal influenza vaccination. One infant, who received only a single vaccination in Year 1, contracted an influenza B (IBV) infection between the two years, allowing us to compare imprinting by infection and vaccination. That infant had a shift in hemagglutinin (HA)-reactive B-cell specificity from largely influenza A (IAV)-specific in Year 1 to IBV-specific in Year 2, both before and after vaccination. HA-reactive B cells from the other infant maintained a more evenly distributed specificity. In Year 2, class-switched HA-specific B cell IGHV somatic hypermutation (SHM) levels reached average levels seen in adults. The HA-reactive plasma antibody repertoires of both infants comprised a relatively small number of antibody clonotypes, with one or two very abundant clonotypes. Thus, after the Year 2 boost, both infants had overall B cell profiles that resembled those of adult controls.ImportanceInfluenza virus is a moving target for the immune system. Variants emerge that escape protection from antibodies elicited by a previously circulating variant (“antigenic drift”). The immune system usually responds to a drifted influenza virus by mutating existing antibodies rather than by producting entirely new ones. Thus, immune memory of the earliest influenza exposure has a major influence on later responses to infection or vaccination (“immune imprinting”). In the many studies of influenza immunity in adult subjects, imprinting has been from an early infection, since only in the past two decades have infants received influenza immunizations. The work reported in this paper is a pilot study of imprinting in two infants by the flu vaccine, which they received before experiencing an influenza infection. The results suggest that a quadrivalent (four-subtype) vaccine may provide an immune imprint less dominated by one subtype than does a monovalent infection.
Diversification of the Ruminant Skull Along an Evolutionary Line of Least Resistance
Authors: Rhoda Daniel , Haber Annat , Angielczyk Kenneth D. 
Published: September 2022

AbstractMorphological integration is relevant to evolutionary biology and paleontology because the structure of variation within populations determines the ways in which a population can respond to selective pressures. However, understanding the macroevolutionary consequences of morphological integration is elusive because the adaptive landscape is dynamic and population-level constraints themselves evolve. By analyzing a previously published dataset of 2859 ruminant crania with 3D geometric morphometrics and phylogenetic comparative methods, we find that variation within and between ruminant species is biased by a highly conserved mammalian-wide allometric pattern, CREA, where larger species have proportionally longer faces. More tightly integrated species and species more biased towards CREA have diverged farther from their ancestors, and Ruminantia as a clade diversified farther than expected in the direction anticipated by CREA. Our analyses indicate that CREA acts as an evolutionary ‘line of least resistance’ and facilitates morphological diversification due to its alignment with the browser-grazer continuum. These results demonstrate that biological processes constraining variation at the microevolutionary level can produce highly directional phenotypic evolution over macroevolutionary timescales.
A bioinformatics pipeline for the assessment of the evolutionary relationship of some Drosophila species based on class II transposons mapping
Authors: Constantin Nicoleta-Denisa , Bologa Alexandru Marian , Ratiu Attila Cristian , Ecovoiu Alexandru Al. 
Published: September 2022

AbstractTransposons are mobile DNA sequences, known for their ability to insert into other locations in the genome. Genome sequencing allowed the identification of the high content of transposons in various model organisms. Here, we present a bioinformatics pipeline developed to estimate the evolutionary relationship between Drosophila melanogaster and other Drosophilidae based on the comparative analysis of the presence and distribution of class II transposons. Our study reveals that the presence and distribution of transposons hobo, HB, Tc1, Tc1-2, hopper and Bari1 points to close evolutionary relationship among D. melanogaster, D. simulans, D. sechellia and D. yakuba, which is in accordance with other data available in literature.
Droplet microfluidics forward for tracing target cells at single-cell transcriptome resolution
Authors: Liu Yang , Wang Shiyu , Lyu Menghua , Xie Run , Guo Weijin , He Ying , Shi Xuyang , Wang Yang , Qi Jingyu , Zhu Qianqian , Zhang Hui , Luo Tao , Chen Huaying , Zhu Yonggang , Dong Xuan , Li Zida , Gu Ying , Mu Feng , Liu Longqi , Xu Xun , Liu Ya 
Published: September 2022

AbstractThe rapid promotion of single-cell omics in various fields has begun to help solve many problems encountered in research including precision medicine, prenatal diagnosis, and embryo development. Meanwhile, single-cell techniques are also constantly updated with increasing demand. For some specific target cells, the workflow from droplet screening to single-cell sequencing is a preferred option, which also should reduce the impact of operation steps such as demulsification and cell recovery. We developed an all-in-droplet method integrating cell encapsulation, target sorting, droplet picoinjection, and single-cell transcriptome profiling on chips to achieve a labor-saving monitor of TCR-T cells. As a proof of concept, in this research, TCR-T cells were encapsulated, sorted, and performed single-cell transcriptome sequencing (scRNA-seq) by injecting reagents into droplet. It avoided the tedious operation of droplet breakage and re-encapsulation between droplet sorting and scRNA-seq. Moreover, convenient device operation will accelerate the progress of chip marketization. The strategy achieved an excellent recovery performance of single cell transcriptome with a median gene number over 4000 and a cross-contamination rate of 8.2 ± 2%. Furthermore, this strategy allows us to develop a device with high integrability to monitor infused TCR-T cells, which will promote the development of adoptive T cell immunotherapy and their clinical application.
Kangaroo mother care for preterm or low birth weight infants: A systematic review and meta-analysis
Authors: Sivanandan Sindhu , Sankar Mari Jeeva 
Published: September 2022

ABSTRACTImportanceThe Cochrane review (2016) on kangaroo mother care (KMC) demonstrated a significant reduction in the risk of mortality in low birth weight (LBW) infants. New evidence from large multi-center randomized trials has been available since its publication.ObjectiveThe objective of the systematic review was to compare the effects of KMC vs. conventional care and early (i.e., within 24 hours of birth) vs. late initiation of KMC on critical outcomes such as neonatal mortality.MethodsEight electronic databases, including PubMed, Embase, and Cochrane CENTRAL, until March 2022, were searched. All randomized trials comparing KMC versus conventional care or early vs. late initiation of KMC in LBW or preterm infants were included.Data extraction and synthesisThe review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines and was registered with PROSPERO.Main outcomes and measuresThe primary outcome was mortality by 28 days of life. Other outcomes included severe infection, hypothermia, exclusive breastfeeding rates, and neurodevelopmental impairment. Results were pooled using fixed-effect and random-effects meta-analyses in RevMan 5.4 or Stata 15.1 (StataCorp, College Station, TX).ResultsIn total, 31 trials with 15,559 infants were included in the review; 27 studies compared KMC with conventional care, while 4 compared early vs. late initiation of KMC. Compared to conventional care, KMC significantly reduced the risks of mortality (relative risk [RR] 0.68; 95% CI 0.53 to 0.86; 11 trials, 10505 infants; high certainty evidence) at discharge or 28 days of age and severe infection till the latest follow-up (RR 0.85, 95% CI 0.79 to 0.92; 9 trials; moderate certainty evidence). On subgroup analysis, KMC provided for a duration of at least 8 hours per day had more significant benefits compared to lesser duration KMC. Studies comparing early vs. late-initiated KMC demonstrated a significant reduction in neonatal mortality (RR 0.77, 95% CI 0.66 to 0.91; 3 trials, 3693 infants; high certainty evidence) and clinical sepsis till 28-days (RR 0.85, 95% CI 0.76 to 0.96; 2 trials; low certainty evidence) favoring early initiation of KMC.Conclusions and RelevanceThe review provides updated evidence on the effects of KMC on mortality and other critical outcomes in low birth weight infants. The findings suggest that KMC should preferably be initiated within 24 hours of birth and provided for at least 8 hours daily.
Rationale, Design, and Baseline Characteristics of the VALIANT (COVID-19 in Older Adults: A Longitudinal Assessment) Cohort
Authors: Cohen Andrew B. , McAvay Gail J. , Geda Mary , Chattopadhyay Sumon , Lee Seohyuk , Acampora Denise , Araujo Katy , Charpentier Peter , Gill Thomas M. , Hajduk Alexandra M. , Ferrante Lauren E. 
Published: September 2022

AbstractBackgroundMost older adults hospitalized with COVID-19 survive their acute illness. The impact of COVID-19 hospitalization on patient-centered outcomes, such as physical function, cognitive function, and symptoms, is not well understood. We sought to address this knowledge gap by collecting longitudinal data about these issues from a cohort of older adult survivors of COVID-19 hospitalization.MethodsWe undertook a prospective study of community-living persons age ≥60 years who were hospitalized with COVID-19 from June 2020 to June 2021. A baseline interview was conducted during or up to two weeks after hospitalization. Follow-up interviews occurred at one, three, and six months post-discharge. In interviews, participants completed comprehensive assessments of physical and cognitive function, symptoms, and psychosocial factors. If a participant was too impaired to complete an interview, an abbreviated assessment was performed with a proxy. Additional information was collected from the electronic health record. Baseline characteristics of the cohort are reported here.ResultsAmong 341 participants, the mean age was 71.4 (SD 8.4) years, 51% were women, and 37% were of Black race or Hispanic ethnicity. Median length of hospitalization was 8 (IQR 6-12) days. All but 4% of participants required supplemental oxygen and 21% required a higher level of care in an intensive care unit or stepdown unit. Nearly half (47%) reported at least one disability in physical function, 45% demonstrated cognitive impairment, and 67% were pre-frail or frail. Participants reported a mean of 9 of 14 (SD 3) COVID-19-related symptoms.ConclusionsOlder adults hospitalized with COVID-19 demonstrated high rates of baseline physical and cognitive impairment as well as high symptom burden. Longitudinal findings from this cohort will advance our understanding of outcome trajectories of great importance to older survivors of COVID-19.
Mind The Gap: Data availability, accessibility, transparency, and credibility during the COVID-19 pandemic, an international comparative appraisal
Authors: Rotulo Arianna , Kondilis Elias , Thwe Thaint , Gautam Sanju , Torcu Özgün , Vera-Montoya Maira , Marjan Sharika , Gazi Md Ismail , Putri Alifa Syamantha , Hasan Rubyath Binte , Mone Fabia Hannan , Rodríguez-Castillo Kenya , Tabassum Arifa , Parcharidi Zoi , Sharma Beverly , Islam Fahmida , Amoo Babatunde , Lemke Lea , Gallo Valentina 
Published: September 2022

AbstractBackgroundData transparency has played a key role in this pandemic. The aim of this paper is to map COVID-19 data availability and accessibility, and to rate their transparency and credibility in selected countries, by the source of information. This is used to identify knowledge gaps, and to analyse policy implications.MethodsThe availability of a number of COVID-19 metrics (incidence, mortality, number of people tested, test positive rate, number of patients hospitalised, number of patients discharged, the proportion of population who received at least one vaccine, the proportion of population fully vaccinated) was ascertained from selected countries for the full population, and for few of stratification variables (age, sex, ethnicity, socio-economic status) and subgroups (residents in nursing homes, inmates, students, healthcare and social workers, and residents in refugee camps).ResultsNine countries were included: Bangladesh, Indonesia, Iran, Nigeria, Turkey, Panama, Greece, the UK, and the Netherlands. All countries reported periodically most of COVID-19 metrics on the total population. Data were more frequently broken down by age, sex, and region than by ethnic group or socio-economic status. Data on COVID-19 is partially available for special groups.ConclusionsThis exercise highlighted the importance of a transparent and detailed reporting of COVID-19 related variables. The more data is publicly available the more transparency, accountability, and democratisation of the research process is enabled, allowing a sound evidence-based analysis of the consequences of health policies.FundingThis study was conducted as part of the Summer School “Sustainable Health: designing a new, better normal after COVID-19”. It is a researchers/student collaboration.
Pathology of African Swine Fever in wild boar naturally infected with German virus variants
Authors: Sehl-Ewert Julia , Deutschmann Paul , Breithaupt Angele , Blome Sandra 
Published: September 2022

AbstractIn 2020, African swine fever (ASF) was first notified in German wild boar, reaching a case number of about 4200 to date. Upon experimental infection, pathology is well-documented, however, data on field infections are very scarce in domestic pigs and not available from wild boar, respectively. Although ASF viral genome is considered exceptionally stable, a total of five lineages with 10 distinct virus variants of genotype II have emerged in Eastern Germany. To investigate the pathology in naturally infected wild boar and to evaluate virus variants II, III and IV for their virulence, wild boar carcasses were obtained from three different outbreak areas. The cadavers underwent virological and pathomorphological investigation. Regardless of the virus variant all wild boar revealed characteristic lesions of highest severity indicative for ASF. However, wild boar infected with variant IV from Spree-Neiße (SN) district showed lower viral genome loads and a lower total viral antigen score, but simultaneously revealed more chronic lesions. Our findings indicate a protracted course of the disease at least after infection with variant IV, but need confirmation under standardized experimental conditions. There is a strong need to monitor differences in the virulence among variants to identify potential attenuation that might complicate diagnosis.