bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence and Factors Associated With Delay in Presentation of Breast Cancer Patients in Ethiopia: A Cross-Sectional Institution-Based Study
Authors: Muhammed Jabir Abdella , Kroeber Eric Sven , Deribe Bedilu , Unverzagt Susanne , Taylor Lesley , Aynalem Amdehiwot , fetene Deriba 
Published: November 2022

AbstractBackgroundIn developing countries, the high mortality of breast cancer (BC) patients is strongly related to delayed presentation and subsequent advanced stage diagnosis, pointing to the need for improved detection programs. This study aims to assess the prevalence and factors associated with delayed presentation of BC patients at Hawassa University Oncology Center (HUOC), Hawassa, Ethiopia.MethodsA cross-sectional institution-based survey was conducted among BC patients between May 1stand August 30th, 2021. BC patients attending HUOC were included by consecutive sampling. Data was collected using an interviewer-administered questionnaire and medical record data extraction. A multivariable binary logistic regression model was carried out to identify associations between delayed presentation and potential risk factors.ResultsA total of 150 BC patients participated in the study giving a response rate of 100%. Of these, 86 (57.3%) women presented with a long delay of ≥ 3 months. The median time to visit a health care provider after recognition of the first symptoms was 5.5 months. Urban residence (adjusted odds ratio (AOR) = 0.42; 95 %-CI=0.18-0.97) and not visiting of traditional healer (AOR=0.15, 95 %-CI=0.07-0.34) was associated with shorter delay time. No breast pain symptoms (AOR=8.57; 95 %-CI=3.47-21.15), no family history of BC (AOR=5.12; 95 %-CI=1.36-19.33), and travel distance ≥ 5 km (AOR=3.00, 95 %-CI=1.25-7.21) were associated with longer delay in presentation.ConclusionA substantial proportion of patients with BC in southern Ethiopia have delays in seeking medical care. Interventional programs like public BC awareness campaigns are strongly needed to reduce delayed presentation and to increase early detection of cancer cases.
High performance, large-scale multi-compartment Hodgkin-Huxley simulation of Drosophila’s whole-brain neural circuit model
Authors: Higuchi Kaoruko , Kazawa Tomoki , Sakai Buntaro , Namiki Shigehiro , Haupt Stephan Shuichi , Kanzaki Ryohei 
Published: November 2022

AbstractA major challenge in neurosciences is the elucidation of neural mechanisms in brains that are crucial for the processing of sensory information and the generation of adaptive behavior. In conjunction with the ever-growing body of experimental data, computational simulations have become crucial in integrating information and testing hypotheses, requiring fast large-scale simulators. We constructed a whole-brain neural circuit model of the fly Drosophila with biophysically detailed multi-compartment Hodgkin-Huxley models based on the morphologies of individual neurons published in open databases. Performance tuning of the simulator enabled near real-time simulation of the resting state of the Drosophila whole-brain model in the large-scale computational environment of the supercomputer Fugaku, for which we achieved in excess of 630 TFLOPS using 480k cores. In our whole-brain model, neural circuit dynamics related to a standard insect learning paradigm, the association of taste rewards with odors could be simulated.
Biochemical characterization and NMR study of a PET-hydrolyzing cutinase fromFusarium solani pisi
Authors: Hellesnes Kristina Naasen , Vijayaraj Shunmathi , Fojan Peter , Petersen Evamaria , Courtade Gaston 
Published: November 2022

ABSTRACTIn recent years, the drawbacks of plastics have become evident, with plastic pollution becoming a major environmental issue. There is an urgent need to find solutions to efficiently manage plastic waste by using novel recycling methods. Biocatalytic recycling of plastics by using enzyme-catalyzed hydrolysis is one such solution that has gained interest, in particular for recycling polyethylene terephthalate (PET). To provide insights into PET hydrolysis by cutinases, we have here characterized the kinetics of a PET-hydrolyzing cutinase fromFusarium solani pisi(FsC) at different pH values, mapped the interaction between FsC and the PET analog BHET by using NMR spectroscopy, and monitored product release directly and in real time by using time-resolved NMR experiments. We found that primarily aliphatic side chains around the active site participate in the interaction with BHET, and that pH conditions and mutation around the active site (L182A) can be used to tune the relative amounts of degradation products. Moreover, we propose that the low catalytic performance of FsC on PET is caused by poor substrate binding combined with slow MHET hydrolysis. Overall, our results provide insights into obstacles that preclude efficient PET hydrolysis by FsC and suggest future approaches for overcoming these obstacles and generating efficient PET-hydrolyzing enzymes.TOC Graphic (For Table of Contents use only)
Capsular polysaccharide inhibits vaccine-induced O-antigen antibody binding and function across both classical and hypervirulent K2:O1 strains ofKlebsiella pneumoniae
Authors: Wantuch Paeton L. , Knoot Cory J. , Robinson Lloyd S. , Vinogradov Evgeny , Scott Nichollas E. , Harding Christian M. , Rosen David A. 
Published: November 2022

AbstractKlebsiella pneumoniaepresents as two circulating pathotypes: classicalK. pneumoniae(cKp) and hypervirulentK. pneumoniae(hvKp). Classical isolates are considered urgent threats due to their antibiotic resistance profiles, while hvKpisolates have historically been antibiotic susceptible. Recently, however, increased rates of antibiotic resistance have been observed in both hvKpand cKp, further underscoring the need for preventive and effective immunotherapies. Two distinct surface polysaccharides have gained traction as vaccine candidates againstK. pneumoniae: capsular polysaccharide and the O-antigen of lipopolysaccharide. While both targets have practical advantages and disadvantages, it remains unclear which of these antigens included in a vaccine would provide superior protection against matchedK. pneumoniaestrains. Here, we report the production of two bioconjugate vaccines, one targeting the K2 capsular serotype and the other targeting the O1 O-antigen. Using murine models, we investigated whether these vaccines induced specific antibody responses that recognize K2:O1K. pneumoniaestrains. While each vaccine was immunogenic in mice, both cKpand hvKpstrains exhibited decreased O-antibody binding in the presence of capsule. Further, O1 antibodies demonstrated decreased killing in serum bactericidal assays with encapsulated strains, suggesting that the presence ofK. pneumoniaecapsule blocks O1-antibody binding and function. Finally, the K2 vaccine outperformed the O1 vaccine against both cKpand hvKpin two different murine infection models. These data suggest that capsule-based vaccines may be superior to O-antigen vaccines for targeting hvKpand some cKpstrains, due to capsule blocking the O-antigen.Significance StatementCurrently there are no licensed vaccines targetingK. pneumoniae, but several are in development. Two prominentK. pneumoniaesurface polysaccharides (capsule and O-antigen) represent attractive vaccine targets; however, the relative efficacy of these potential vaccines againstK. pneumoniaestrains has not been directly compared. To inform future vaccine development, we evaluate two bioconjugate vaccines (targeting either capsule or O-antigen) demonstrating that each are immunogenic in murine models. However, we find thatK. pneumoniaecapsule largely inhibits recognition by antibodies raised against O-antigen. Further, we demonstrate that a capsule-based vaccine outperforms an O-antigen vaccine against both cKpand hvKpin murine models of pneumonia and bacteremia, suggesting that capsule-based vaccines offer superior protection from someK. pneumoniaeinfections.
P bodies coat germ granules to promote transgenerational gene silencing inC. elegans
Authors: Du Zhenzhen , Shi Kun , Brown Jordan S. , He Tao , Wu Wei-Sheng , Zhang Ying , Lee Heng-Chi , Zhang Donglei 
Published: November 2022

AbstractThe formation of biomolecular condensates has emerged as a critical mechanism for compartmentation in living cells. Despite interactions between distinct condensates having been reported, the biological relevance of these interactions remains elusive. In germ cells, small RNA silencing factors are enriched in germ granule condensates, where distinct factors are organized into sub-compartments with specific functions linked to genome surveillance or transgenerational gene silencing. Here we showed that perinuclear germ granules are coated by P body condensates, which are known for housing translationally-inactive mRNAs and mRNA degradation factors. Disruption of P body factors, including CGH-1/DDX6 and CAR-1/LSM14, lead to dispersal of small RNA factors from perinuclear germ granules and disorganization of sub-compartments within germ granules. We further found that CAR-1 promotes the interaction between CGH-1 and germ granule factors, and these interactions are critical for the ability of CGH-1 to promote piRNA-mediated gene silencing. Importantly, we observed thatcgh-1mutants are competent in triggering gene silencing but exhibit defects in maintaining gene silencing in subsequent generations. Small RNA sequencing further showed thatcgh-1mutants exhibit defects in amplifying secondary small RNAs, known carriers of gene silencing memories. Together, our results uncover the function of P body factors in small RNA-mediated transgenerational gene silencing and highlight how the formation and function of one condensate can be regulated by an adjacent, interacting condensate in cells.
Prefrontal stimulation disrupts motor memory consolidation at the micro timescale
Authors: Gann Mareike A. , Dolfen Nina , King Bradley R. , Robertson Edwin M. , Albouy Geneviève 
Published: November 2022

AbstractFunctional brain responses in hippocampo- and striato-cortical networks during initial motor sequence learning (MSL) are critical for memory consolidation. We have recently shown that prefrontal stimulation applied prior to initial MSL can alter these learning-related responses. In the present study, we investigated whether such stimulation-induced modulations of brain responses can influence motor memory consolidation at different timescales. Specifically, we examined the effect of prefrontal stimulation on the behavioral and neural responses associated to (i) fast consolidation processes occurring during short rest episodes interspersed with practice during initial learning (i.e., micro timescale) and (ii) slow consolidation process taking place across practice sessions separated by 24h (i.e., macro timescale). To do so, we applied active (inhibitory or facilitatory) or control theta-burst stimulation to the prefrontal cortex of young healthy participants before they were trained on an MSL task while their brain activity was recorded using functional magnetic resonance imaging (fMRI). Motor performance was retested, in the MRI scanner, after a night of sleep. Both our behavioral and brain imaging results indicate that while stimulation did not modulate consolidation at the macro timescale, it disrupted the micro-offline consolidation process. Specifically, our behavioral data indicate that active - as compared to control - stimulation resulted in a decrease in micro-offline gains in performance over the short rest intervals. At the brain level, stimulation disrupted activity in the caudate nucleus and the hippocampus during the micro-offline intervals. Additionally, multivariate pattern persistence from task into inter-practice rest episodes - which is thought to reflect the reactivation of learning-related patterns - was hindered by active prefrontal stimulation in the hippocampus and caudate nucleus. Importantly, stimulation also altered the link between the brain and the behavioral markers of the micro-offline consolidation process. These results collectively suggest that active prefrontal stimulation prior to MSL disrupted both the behavioral and neural correlates of motor memory consolidation at the micro timescale.
Bax Forms a Membrane Surface Protein-Lipid Complex as it Initiates Apoptosis
Authors: Clifton Luke A. , Wacklin-Knecht Hanna P. , Ådén Jörgen , Mushtaq Ameeq Ul , Sparrman Tobias , Gröbner Gerhard 
Published: November 2022

AbstractCellular clearance by apoptosis is essential in life. In its intrinsic (mitochondrial) pathway apoptotic members of the Bcl-2 (B cell CLL/lymphoma-2) protein family, such as Bax (Bcl-2-associated X) protein, perforate the mitochondrial outer membrane (MOM), which causes release of apoptotic factors and final cell death. How those apoptotic proteins mechanistically exert their action at the membrane level still however remains elusive. Upon internal stress signals Bax is massively recruited to the MOM, where it oligomerizes and partially penetrates into the membrane. Using neutron reflectometry (NR) and attenuated total reflection Fourier-Transform infrared spectroscopy (ATR-FTIR) spectroscopy we unraveled key molecular steps of this membrane-affiliation process of Bax on a spatial and temporal scale. By titrating intact human Bax to MOM-like bilayers containing cardiolipin, essential for protein recruitment, we could identify different functional phases. Initially, there is a fast adsorption event to the membrane surface with high affinity. Thereafter, a kinetically slower (minutes to hours) event occurs with Bax penetration, thereby triggering a major reorganizing of the mitochondrial bilayer. Finally, a membrane-Bax complex is generated, with a minor Bax population remaining membrane-inserted, while the main population is relocated to the membrane surface upon lipid redistribution into a complex with Bax; a process enabling membrane perforation. We propose a comprehensive molecular model of mitochondrial membrane penetration by formation of complex Bax/lipid clusters; a concept which provides a new foundation to understand the cell-killing activity of Bax and its apoptotic relatives in human cells.Significance StatementThe apoptotic Bax protein is a key player in the mitochondrial apoptotic pathway. Here, neutron reflectometry (NR) unravels the mechanism by which Bax is targeting and perforating mitochondria to release apoptotic factors for final cell death. We found that this cardiolipin driven process of the outer mitochondrial membrane system has two main phases. Upon a fast (10-20 min) phase of membrane association Bax initiates the formation of pores by removing lipids and depositing them as Bax/lipid complexes on top of the bilayer on a time scale of several hours similar toin vivoapoptotic cell death. Our results provide a mechanistic rationale for cell-killing processes driven by apoptotic Bcl-2 proteins; and their molecular inhibition in many cancers.
HAND1 knockdown disrupts trophoblast global gene expression
Authors: Fresch Robert , Courtney Jennifer , Brockway Heather , Wilson Rebecca L. , Jones Helen 
Published: November 2022

AbstractCongenital heart disease (CHD) affects nearly 1% of births annually, and CHD pregnancies carry increased risk of developing pathologies of abnormal placentation. We previously reported significant developmental impacts of disruptingHand1, a gene associated with CHD, expression in placenta trophoblast and endothelial cells in multiple mouse models. In this study, we aimed to build upon this knowledge and characterize the mechanistic impacts of disruptingHAND1on human placenta trophoblast and vascular endothelial cell gene expression.HAND1gene expression was silenced in BeWo cells, a choriocarcinoma model of human cytotrophoblasts, (n=3-9 passages) and isolated human placental microvascular endothelial cells (HPMVEC; n=3 passages), withHAND1siRNA for 96 h. Cells were harvested, mRNA isolated and RNA sequencing performed using the Illumina NextSeq 550 platform. Normalization and differential gene expression analyses were conducted using general linear modeling in edgeR packages. Statistical significance was determined using a log2 fold change of >1.0 or <−1.0 and unadjusted p-value ≤0.05. Panther DB was used for overrepresentation analysis, and String DB for protein association network analysis. There was downregulation of 664 genes, and upregulation of 59 genes in BeWo cells with directHAND1knockdown. Overrepresentation analysis identified disruption to pathways including cell differentiation, localization, and cell projection organization. In contrast, only 7 genes were changed with directHAND1knockdown in HPMVECs. Disruption toHAND1expression significantly alters gene expression profile in trophoblast but not endothelial cells. This data provides further evidence that future studies on genetic perturbations in CHDs should consider the extra-embryonic tissue in addition to the fetal heart.
Skeletal muscle DNA methylation and mRNA responses to a bout of higher versus lower load resistance exercise in previously trained men
Authors: Sexton Casey L. , Godwin Joshua S. , McIntosh Mason C. , Ruple Bradley A. , Osburn Shelby C. , Hollingsworth Blake R. , Kontos Nicholas J. , Agostinelli Philip J. , Kavazis Andreas N. , Ziegenfuss Tim N. , Lopez Hector L. , Smith Ryan , Young Kaelin C. , Dwaraka Varun B. , Fruge Andrew D. , Mobley Christopher B. , Sharples Adam P. , Roberts Michael D. 
Published: November 2022

ABSTRACTWe sought to determine the skeletal muscle genome-wide DNA methylation and mRNA responses to one bout of lower-load (LL) versus higher-load (HL) resistance exercise. Trained college-aged males (n=11, 23±4 years old, 4±3 years self-reported training) performed LL or HL bouts to failure separated by one week. The HL bout (i.e., 80 Fail) consisted of four sets of back squats and four sets of leg extensions to failure using 80% of participants estimated one-repetition maximum (i.e., est. 1-RM). The LL bout (i.e., 30 Fail) implemented the same paradigm with 30% of est. 1-RM. Vastus lateralis muscle biopsies were collected before, 3 hours, and 6 hours after each bout. Muscle DNA and RNA were batch-isolated and analyzed using the 850k Illumina MethylationEPIC array and Clariom S mRNA microarray, respectively. Performed repetitions were significantly greater during the 30 Fail versus 80 Fail (p<0.001), although total training volume (sets x reps x load) was not significantly different between bouts (p=0.571). Regardless of bout, more CpG site methylation changes were observed at 3-versus 6-hours post exercise (239,951 versus 12,419, respectively; p<0.01), and nuclear global ten-eleven translocation (TET) activity, but not global DNA methyltransferase activity, increased 3- and 6-hours following exercise regardless of bout. The percentage of genes significantly altered at the mRNA level that demonstrated opposite DNA methylation patterns was greater 3- versus 6-hours following exercise (~75% versus ~15%, respectively). Moreover, high percentages of genes that were up- or downregulated 6 hours following exercise also demonstrated significantly inversed DNA methylation patterns across one or more CpG sites 3 hours following exercise (65% and 82%, respectively). While 30 Fail decreased DNA methylation across various promoter regions versus 80 Fail, transcriptome-wide mRNA and bioinformatics indicated that gene expression signatures were largely similar between bouts. Bioinformatics overlay of DNA methylation and mRNA expression data indicated that genes related to “Focal adhesion”, “MAPK signaling”, and “PI3K-Akt signaling” were significantly affected at the 3- and 6-hour time points, and again this was regardless of bout. In conclusion, extensive molecular profiling suggests that post-exercise alterations in the skeletal muscle DNA methylome and mRNA transcriptome elicited by LL and HL training bouts to failure are largely similar, and this could be related to equal volumes performed between bouts.
ImprintedDlk1dosage as a size determinant of the mammalian pituitary gland
Authors: Scagliotti Valeria , Vignola Maria Lillina , Willis Thea , Howard Mark , Marinelli Eugenia , Gaston-Massuet Carles , Andoniadou Cynthia , Charalambous Marika 
Published: November 2022

AbstractCo-regulated genes of the Imprinted Gene Network are involved in the control of growth and body size, and imprinted gene dysfunction underlies human paediatric disorders involving the endocrine system. Imprinted genes are highly expressed in the pituitary gland, among them,Dlk1, a paternally expressed gene whose membrane-bound and secreted protein products can regulate proliferation and differentiation of multiple stem cell populations. Dosage of circulating DLK1 has been previously implicated in the control of growth through unknown molecular mechanisms. Here we generate a series of mouse genetic models to modify levels ofDlk1expression in the pituitary gland and demonstrate that the dosage of DLK1 modulates the process of stem cell commitment with lifelong impact on pituitary gland size. We establish that stem cells are a critical source of DLK1, where embryonic disruption alters proliferation in the anterior pituitary, leading to long-lasting consequences on growth hormone secretion later in life.
Validation of species-specificity of two commercial antibodies directed against RILP (Rab-interacting lyosomal protein)
Authors: Yap Chan Choo , Digilio Laura , Winckler Bettina 
Published: November 2022

AbstractRILP is one of many effectors of RAB7 which bind to RAB7 in its activated GTP-bound state. The exact mechanism by which RAB7 effectors interact with RAB7 in time and space is not well understood. One of the known functions of RILP is to recruit dynein to RAB7-positive late endosomes. Dynein has been shown to be responsible for retrograde transport of RAB7-positive late endosomes in neuronal dendrites. We thus became interested in studying RILP in cultured neurons. We herein validate two commonly used anti-RILP antibodies which are commercially available. We find that both recognize only human RILP, but not mouse or rat RILP. These antibodies are thus not suitable for experiments carried out in mouse or rat cells. Furthermore, we find an unexpected difference between neurons and HEK293 cells in their ability to recruit overexpressed RILP to endosomes and cluster them in the cell center.
Multiplex DNA fluorescence in situ hybridization to analyze maternal vs. paternalC. eleganschromosomes
Authors: Gutnik Silvia , Sawh Ahilya , Mango Susan E. 
Published: November 2022

AbstractRecent advances in high-throughput microscopy have paved the way to study chromosome organization at the single-molecule level and have led to a better understanding of genome organization in space and time. During development, distinct maternal and paternal contributions ensure the formation of an embryo proper, yet little is known about the organization of chromosomes inherited from mothers versus fathers. To tackle this question, we have modified single-molecule chromosome tracing to distinguish between the chromosomes of two well-studied strains ofC. eleganscalled Bristol and Hawai’ian. We find that chromosomes from these two strains have similar folding patterns in homozygous hermaphrodites. However, crosses between Bristol and Hawai’ian animals reveal that the paternal chromosome adopts the folding parameters of the maternal chromosome in embryos. This is accomplished by an increase in the polymer step size and decompaction of the chromosome. The data indicate that factors from the mother impact chromosome folding in trans. We also characterize the degree of intermixing between homologues within the chromosome territories. Sister chromosomes overlap frequently inC. elegansembryos, but pairing between homologues is rare, suggesting that transvection is unlikely to occur. This method constitutes a powerful tool to investigate chromosome architecture from mothers and fathers.