bluuebunny/crossref_metadata_2025_split huggingface dataset:
Freezing Diluted Bovine Serum Albumin Standards Does Not Significantly Affect Standard Curves
Authors: Sheets Rachelle , Rajaboina Bhavik , Bromberg Caitlin E. , Curtin Liam P. , Haddock Mitchell L. , Stafford Phillip , Thomas Theresa Currier , Scheck Adrienne C. 
Published: July 2024

AbstractTotal protein isolation followed by quantitation is a common protocol in many laboratories. Quantitation is often done using a colorimetric assay such as the bicinchoninic acid (BCA) assay in which a change in the color of the BCA reagent is related to protein concentration. Extracted protein samples are compared to a standard curve made with dilutions of a protein standard such as bovine serum albumin (BSA) to determine their concentrations. A series of experiments was designed to determine the most reproducible and accurate method for quantifying protein concentrations of samples in an experimental series over time. The effect of freezing on diluted standards was investigated. Standards were frozen at −20°C or −80°C and serially thawed and refrozen up to three times prior to their use in a BCA assay. Thawing and refreezing the standards had no significant effect on protein concentration and the resulting standard curves. Inter-person and intra-person variability in the preparation of standards was also investigated. Protein concentration differences due to inter-person and intra-person variability were greater than protein concentration variability resulting from freezing and thawing, regardless of the freezing temperature. The most reproducible and accurate method for determining the protein concentration of extracted samples in an experimental series over time is diluting a large batch of BSA standards and freezing them at either −20°C or −80°C. Reproducibility was maintained with up to three freeze-thaws.HighlightsFreezing diluted BSA standards at either −20°C or −80°C and thawing and refreezing them up to three times does not significantly alter their protein concentrations.Inter-person variability in standard curves is greater than intra-person variability, and controlling for developer decreases variability in most cases.There is more consistency in standard curves when a single batch of diluted standards is aliquoted and frozen at either −20°C or −80°C and thawed up to three times than when the same investigator or different investigators make fresh standards before each assay.
Latent mitotic vulnerability of AML cells induced by therapeutic agents
Authors: Niikura Ryuta , Yabushita Tomohiro , Yamamoto Shohei , Suzuki Hiroaki , Fukuyama Masamitsu , Hata Shoji , Goyama Susumu , Kitamura Toshio , Chinen Takumi , Kitagawa Daiju 
Published: July 2024

AbstractAcute myeloid leukemia (AML) is a hematopoietic malignancy with a poor prognosis. Understanding the unidentified properties of AML cells is beneficial for the identification of novel therapeutic strategies for AML. In this study, we uncover the vulnerabilities of AML cells in mitosis when exposed to therapeutic agents. Through comparative analysis of large-scale data quantifying drug effects on cancer cell proliferation, the drug targeting the cell cycle and mitosis are predicted to possess high cytotoxicity against AML cell lines. Consistently, live-cell imaging with microwell devices demonstrates that clinical drugs targeting the cell cycle processes, such as idarubicin, pevonedistat and vincristine, potently induce mitotic cell death in AML cells. While these therapeutic agents also induce cell death through S/G2 phase arrest, the cytotoxic effects during mitosis are notably more pronounced. Furthermore, by employing additional inhibition of Chk1 to override the G2/M checkpoint, the AML cells stalled in the S/G2 phase prematurely enter mitosis, resulting in a significant increase in cell death. Collectively, these results unveiled the latent mitotic vulnerabilities of AML cells, providing a basis for developing novel therapeutic interventions.
Flexible movement kernel estimation in habitat selection analyses with generalized additive models
Authors: Arce Guillen Rafael , Pohle Jennifer , Jeltsch Florian , Roeleke Manuel , Reineking Björn , Klappstein Natasha , Schlägel Ulrike 
Published: July 2024

AbstractHabitat selection analysis includes resource selection analysis (RSA) and step selection analysis (SSA). These frameworks are used in order to understand space use of animals. Particularly, the SSA approach specifies the space availability of sequential locations through a movement kernel. This movement kernel is typically defined as the product of independent parametric distributions of step lengths (SLs) and turning angles (TAs). However, this assumption may not always be plausible for real data where short SLs are often correlated with large TAs and vice versa.The objective of this paper is to relax the need for parametric distributions usinggeneralized additive models(GAMs) and the R-package mgcv, based on the work of Klappstein et al. (2024). For this, we propose to specify the movement kernel as a bivariate tensor product, rather than independent distributions of SLs and TAs. In addition, we account for residual spatial autocorrelation in this GAM-approach.Using simulations, we show that the tensor product approach accurately estimates the underlying movement kernel and that the fixed effects of the model are not biased. In particular, if the data are simulated with a copula distribution for SL and TA, i.e. if the independence assumption for SL and TA does not hold, the GAM approach produces better estimates than the classical approach. In addition, including a bivariate tensor product in the model leads to a better uncertainty estimation of the model parameters and a higher predictive quality of the model.Incorporating a bivariate tensor product solves the problem of assuming parametric distributions and independence between SLs and TAs. This offers greater flexibility and makes the analysis of real data more reliable.
Ecologically and economically sustainable level of timber harvesting in boreal forests – defining the safe operating space for forest use
Authors: Mönkkönen Mikko , Blattert Clemens , Cours Jérémy , Duflot Rémi , Elo Merja , Eyvindson Kyle , Kouki Jari , Triviño María , Burgas Daniel 
Published: July 2024

AbstractPlanetary-level analyses indicate that we are exceeding the ecological limits. However, we need approaches to implement global sustainability frameworks regionally, using natural resources at levels that allow for their regeneration. We present a framework to define limits beyond which ecosystems are threatened to collapse, to answer how much we can extract from ecosystems, and to manage natural resources for both human and ecosystem wellbeing. We exemplify this approach with the heath forest habitat types in Finland, which provide most of the national timber production. We use the IUCN Red List of Habitats to set favourable reference values for volume of deadwood, proportion of old-growth forest cover and proportion of deciduous trees. Through forest growth simulations and management optimization, we found that the proportion of old-growth forest is the most challenging criteria to be reached only by 2100. This would require not only a larger use of extensive forest management practices than hitherto but also to drastically reduce the maximum economic sustainable harvest level from the current 96% to 60%. By combining threat assessments with ecosystem modelling and management planning, this approach can support regional decision makers to make informed decisions to stay within safe limits of use of natural resources.
Detecting branching rate heterogeneity in multifurcating trees with applications in lineage tracing data
Authors: Gao Yingnan , Feder Alison F 
Published: July 2024

AbstractUnderstanding cellular birth rate differences is crucial for predicting cancer progression and interpreting tumor-derived genetic data. Lineage tracing experiments enable detailed reconstruction of cellular genealogies, offering new opportunities to measure branching rate heterogeneity. However, the lineage tracing process can introduce complex tree features that complicate this effort. Here, we examine tree characteristics in lineage tracing-derived genealogies and find that editing window placement leads to multifurcations at a tree’s root or tips. We propose several ways in which existing tree topology-based metrics can be extended to test for rate heterogeneity on trees even in the presence of lineage-tracing associated distortions. Although these methods vary in power and robustness, a test based on theJ1statistic effectively detects branching rate heterogeneity in simulated lineage tracing data. Tests based on other common statistics (ŝand the Sackin index) show interior performance toJ1. We apply our validated methods to xenograft experimental data and find widespread rate heterogeneity across multiple study systems. Our results demonstrate the potential of tree topology statistics in analyzing lineage tracing data, and highlight the challenges associated with adapting phylogenetic methods to these systems.
An efficient method for immortalizing mouse embryonic fibroblasts
Authors: Srinivasan Srisathya , Ho Hsin-Yi Henry 
Published: July 2024

AbstractMouse embryonic fibroblasts (MEFs) derived from genetically modified mice are a valuable resource for studying gene function and regulation. The MEF system can also be combined with rescue studies to characterize the function of mutant genes/proteins, such as disease-causing variants. However, primary MEFs undergo senescence soon after isolation and passaging, making long-term genetic manipulations difficult. Previously described methods for MEF immortalization are often inefficient or alter the physiological properties of the cells. Here, we describe an optimized protocol for immortalizing MEFs via CRISPR-mediated deletion of theTp53gene. This method is highly efficient and consistently generates immortalized MEFs, or iMEFs, within 14 days. Importantly, iMEFs closely resemble the parent cell populations, and individual iMEFs can be cloned and expanded for subsequent genetic manipulation and characterization. We envision that this protocol can be adopted to immortalize other mouse primary cell types.Key FeaturesCRISPR-based knockout of theTp53gene enables efficient immortalization of mouse embryonic fibroblasts (MEFs) in under 2 weeks.Immortalization requires a Neon electroporator or another comparable electroporation system to transfect cells with theTp53CRISPR constructs.
Transmission is a key driver of extensively drug-resistant tuberculosis
Authors: Goig Galo A. , Loiseau Chloé , Maghradze Nino , Mchedlishvili Kakha , Avaliani Teona , Brites Daniela , Borrell Sonia , Aspindzelashvili Rusudan , Avaliani Zaza , Kipiani Maia , Tukvadze Nestani , Jugheli Levan , Gagneux Sebastien 
Published: July 2024

AbstractMultidrug-resistant tuberculosis (MDR-TB) and extensively drug-resistant (XDR) TB are threatening global TB control. The World Health Organization has recently endorsed new regimens for the treatment of MDR-TB that rely on the new and repurposed drugs bedaquiline, pretomanid and linezolid with or without moxifloxacin (BPaL(M)). As BPaL(M) is being rolled-out, resistance to these new drugs is already emerging, leading to acquired XDR-TB. Importantly, instances of transmitted XDR-TB have been reported. The spread of highly drug-resistantM. tuberculosis(MTB) strains pose at risk novel TB treatments that took decades to develop. In this study, we analyzed 6,926 MTB genomes from a 13-year nationwide study in Georgia, a known geographical hotspot of MDR-TB, together with more than 80,000 MTB genomes from public sources to estimate the relative contribution of transmission to the burden of XDR-TB. We show that XDR-TB is already geographically widespread, occurring in at least 27 countries across four continents. Moreover, we estimated that a quarter of the XDR-TB cases identified are likely the consequence of transmission. Our findings call for urgent improvements in the global diagnostic capacity, infection control, and surveillance of XDR-TB.
The COVID-19 pandemic in Canada’s provinces: mitigation measures and outcomes
Authors: Grootendorst Paul 
Published: July 2024

AbstractThe rapid spread of SARS-CoV-2 in early 2020 forced provincial health authorities across Canada to quickly institute infection control measures. It is now four years since the start of the global pandemic, and an opportune time to consider how Canada’s provinces compared in their SARS-CoV-2 containment policies and the resulting impacts on mortality and economic activity. I compare provincial exposure to SARS-CoV-2 using data on the number out-of-province arrivals into each province. I compare the key containment measures used in each province, the length of time that these measures were imposed, and the uptake of COVID-19 vaccines by province. Using Statistics Canada data, I also estimate the impact of the COVID-19 pandemic on provincial crude death rates during 2020-2023, and life expectancy and gross domestic product during 2020-2022. I find substantial provincial variation in pandemic responses and outcomes. The provinces varied in their use of the most stringent public health measures. Uptake of the primary COVID vaccinations varied from 76% to 92%; booster vaccination uptake varied even more. There was also marked provincial variation in mortality and economic outcomes. While this study does not estimate the impacts of provincial response stringency and COVID vaccine uptake on mortality and other outcomes, it does provide suggestive evidence that can be formally assessed in future research.
Knowledge and occupational practices of beauticians and barbers in the transmission of viral hepatitis: a mixed-methods study in Volta Region of Ghana
Authors: Adjei-Gyamfi Silas , Korang Felix Kwame , Asirifi Abigail , Asobuno Clotilda 
Published: July 2024

AbstractBackgroundAlthough Ghana is endemic for hepatitis B virus (HBV) and hepatitis C virus (HCV) infections, the National Policy on Viral Hepatitis stipulates that there is unreliable data, limited knowledge, and deficiency in research on viral hepatitis, especially among high-risk workers in the eastern part of the country. This study therefore assessed the knowledge level and occupational practices of beauticians and barbers in the transmission of HBV and HCV in the Volta Region of Ghana.MethodsA cross-sectional mixed methods study was conducted in Volta Ghana from April to June 2021. While an in-depth interview was used to collect data from five environmental health officers who were selected as key informants in the qualitative stage, structured questionnaires/checklists, and direct observations were employed to collect data from 340 beauticians and barbers in the quantitative stage. During the qualitative stage, the process of coding, and mind mapping via thematic analysis was carried out. Furthermore, descriptive and inferential analyses were performed using Stata version 17.0 at a 95% significance level in the quantitative stage.ResultsMost beauticians and barbers reported poor knowledge levels about HBV and HCV (67.0%), although the awareness of this viral hepatitis was high (88.2%). While almost one-third of the observed participants practiced safe occupational activities (31.5%), 29.0%, 49.4%, and 55.3% of them observed hand hygiene, wore protective clothes/gloves, and sterilized or disinfected tools after use respectively. Beauticians and barbers with higher (tertiary) education (AOR=11.4; 95%CI=1.44–27.5; p=0.021) and those with heavy workload per day (AOR=4.34; 95%CI=1.31– 14.4; p=0.016) were more likely to report good knowledge level about HBV and HCV. Additionally, beauticians were more likely to practice safe occupational activities as compared to barbers (AOR=14.2; 95%CI=4.11–28.8; p<0.001). The key informant interviews revealed that there was little or no licensing, monitoring, and training organized for beauticians and barbers.ConclusionParticipants showed high awareness but limited knowledge about HBV and HCV. The general safety practices among the participants were poor. Our study results suggest possible viral transmission through the activities of beauticians and barbers which could be attributed to the lack of regulatory systems and training of beauticians and barbers.
COVID-19 severity and risk of SARS-CoV-2-associated asthma exacerbation by time since booster vaccination: a longitudinal analysis of data from the COVIDENCE UK study
Authors: Vivaldi Giulia , Talaei Mohammad , Pfeffer Paul E , Shaheen Seif O , Martineau Adrian R 
Published: July 2024

AbstractBackgroundIn several countries, COVID-19 booster vaccinations are offered annually to priority groups, but many people have not been vaccinated in over a year. We aimed to assess the association between time since booster vaccination and characteristics of breakthrough infection. We also assessed whether incident COVID-19 continued to associate with asthma exacerbations in boosted individuals, and whether risk of COVID-19-associated exacerbation was affected by time since vaccination.MethodsCOVIDENCE UK is a prospective, longitudinal, population-based study of COVID-19. We included adult participants who had received ≥1 booster vaccination. Time since vaccination was binarised at 6 months or 12 months according to vaccine eligibility subgroup. We used logistic, Cox, and linear regression to obtain adjusted estimates for the association between time since vaccination and breakthrough infection severity, symptom duration, and acute changes to health-related quality of life (measured by the EQ-5D-3L Index). We then assessed the association of incident COVID-19 with asthma exacerbations using multilevel mixed models, by time since vaccination.Results7391 boosted participants reported a breakthrough infection. Across all eligibility subgroups, greater time since vaccination associated with increased odds of infection requiring bedrest (vsmilder symptoms), with the highest odds for adults aged 65–75 years (1.83 [95% CI 1.51–2.23] when vaccinated >6 monthsvs≤6 months prior). However, we observed little evidence of association between time since vaccination and symptom duration. Vaccination >12 months prior (vs≤12 months) was associated with a small decrease in EQ-5D-3L Index among participants younger than 65 years (-0.03 points [-0.04 to -0.01]). Among 2100 participants with asthma, incident COVID-19 associated with increased risk of asthma exacerbation, both ≤12 months after vaccination (OR 5.31 [4.36–6.48]) and later (6.06 [3.23–11.38]), with a greater difference in point estimates when specifically considering severe asthma exacerbations (6.82 [4.88–9.54] for ≤12 monthsvs10.06 [3.90–25.92] for >12 months).ConclusionLonger time since booster vaccination consistently associates with more severe breakthrough infections, and may potentially increase risk of severe asthma exacerbations. These findings highlight the importance of ensuring those currently eligible receive their booster vaccinations, and the need for research on further vaccinations in people with asthma no longer eligible for boosters.
The effect of artificial oocyte activation on blastocysts rate in patients with low blastocyst rates: A retrospective cohort study
Authors: Sendy Feras , Hemmings Robert , Kadoch Isaac-Jacques , Jamal Wael , Phillips Simon 
Published: July 2024

AbstractIntroductionPhysiological oocyte activation requires a synergy between the oocyte and sperm to release calcium (Ca2+) through oscillations. The absence of such synergy between the oocyte and sperm leads to a negative impact on oocyte activation. Studies have shown that Artificial oocyte activation (AOA) is helpful in cases with failed or low fertilization rates. Studies present mixed opinions about increasing blastocyst rate.MethodsA retrospective cohort single-center study was performed between January 2018 and October 2023, including 54 couples with suboptimal blastocyst development. The study compared intracytoplasmic sperm injection (ICSI) AOA cycles with previous conventional ICSI cycles and conventional ICSI without AOA cycles with previous conventional ICSI cycles in couples with failed or low blastocyst rates (< 30%) in the original ICSI cycle.ResultsWe compared 22 AOA cycles to previous conventional ICSI cycles in the same patients and 32 conventional ICSI cycles without AOA to previous conventional ICSI cycles in the same patients. After AOA, the blastocyst rate was not significantly higher than the control group (48% vs 29% p=0.19). Conversely, the blastocyst rate was significantly higher in the conventional ICSI without AOA cycles than in the control group (48% vs 24% p=0.04). The fertilization rate was not statistically significant between the first and second cycles in both groups.ConclusionThe literature still lacks strong evidence for AOA overcoming impaired embryonic development. Therefore, AOA remains reserved for couples with a failed or low fertilization history to improve fertilization results. Optimal laboratory conditions and ovarian stimulation modifications without AOA may improve blastocyst rates.
MUC1andMUC4expression are inversely correlated and trigger immunological response and transport pathways in gliomas
Authors: Machado Gabriel Cardoso , Ferrer Valéria Pereira 
Published: July 2024

AbstractDiffuse gliomas are tumors that arise from glial or glial progenitor cells. They are currently classified as astrocytoma isocitrate dehydrogenase (IDH)-mutant or oligodendroglioma IDH-mutant, and chromosome arms 1p/19q-codeleted, both slower-growing tumors, or glioblastoma (GBM), a more aggressive tumor. Despite advances in the diagnosis and treatment of gliomas, the median survival time after diagnosis of GBM remains low, approximately 15 months, with a 5-year overall survival rate of only 6.8%. Therefore, new biomarkers and therapy targets that could support better prognosis of these tumors would be of great value. MUC1 and MUC4, membrane-bound mucins, has been identified as a potential biomarker in several tumors. However, the role of these mucins in adult gliomas has not yet been well explored. Here, we show for the first time, in a retrospective study and byin silicoanalysis, the relevance and correlation of these genes in adult gliomas. Analysis of adult diffuse glioma patient cohorts revealed differential methylation and expression patterns of MUC1 and MUC4 across GBM and non-GBM subtypes. GBM patients exhibited decreased MUC1 methylation and elevated expression (r-0.25, p < 0.0001) whereas increased MUC4 methylation and its lower expression (r-0.13, p = 0.1344). Conversely, in non-GBM patients, MUC1 showed higher methylation levels and low expression (r-0.27, p < 0.0001) whereas MUC4 showed lower methylation levels and high expression (r-0.32, p < 0.0001). The expression levels of these genes influenced overall survival (OS) in gliomas patients (p = 0.0344), with high MUC1 and low MUC4 expression associated with worse OS. MUC1 and MUC4 correlated with MUC20 in both GBM (r = 0.54) and non-GBM (r = 0.53) patients (p < 0.0001). Functional enrichment analysis revealed distinct biological roles for co-expressed genes with MUC1 involvement in innate immunity, antigen processing, pro-inflammatory responses in both non-GBM and GBM cohorts, and integrin-based signaling pathways in GBM patients. MUC4 co-expressed genes were involved in ion transport in GBM patients. Using molecular docking, we observed that MUC1 has domains that are physically capable of interacting with immune response-related proteins such as Receptor for Advanced Glycation End-products (RAGE), Major Histocompatibility Complex II (MHCII), and extracellular matrix receptor integrin alpha 2 (ITGA2). These findings shed light on the molecular mechanisms underlying glioma progression and highlight MUC1 and MUC4 as potential prognostic markers and therapeutic targets in glioma management.