bluuebunny/crossref_metadata_2025_split huggingface dataset:
MVP-VSASL: measuring MicroVascular Pulsatility using Velocity-Selective Arterial Spin Labeling
Authors: Chen Conan , Barnes Ryan A. , Bangen Katherine J. , Han Fei , Pfeuffer Josef , Wong Eric C. , Liu Thomas T. , Bolar Divya S. 
Published: June 2024

1AbstractPurposeBy leveraging the small-vessel specificity of velocity-selective arterial spin labeling (VSASL), we present a novel technique for measuring cerebral MicroVascular Pulsatility named MVP-VSASL.Theory and MethodsWe present a theoretical model relating the pulsatile, cerebral blood flow-driven VSASL signal to the microvascular pulsatility index (PI), a widely used metric for quantifying cardiac-dependent fluctuations. The model describes the dependence of PI on bolus durationτ(an adjustable VSASL sequence parameter) and provides guidance for selecting a value ofτthat maximizes the SNR of the PI measurement. The model predictions were assessed in humans using data acquired with retrospectively cardiac-gated VSASL sequences over a broad range ofτvalues. In vivo measurements were also used to demonstrate the feasibility of whole-brain voxel-wise PI mapping, assess intrasession repeatability of the PI measurement, and illustrate the potential of this method to explore an association with age.ResultsThe theoretical model showed excellent agreement to the empirical data in a gray matter region of interest (average R2value of 0.898±0.107 across six subjects). We further showed excellent intrasession repeatability of the pulsatility measurement (ICC = 0.960,p<0.001) and the potential to characterize associations with age (r= 0.554,p= 0.021).ConclusionWe have introduced a novel, VSASL-based cerebral microvascular pulsatility technique, which may facilitate investigation of cognitive disorders where damage to the microvasculature has been implicated.
Impact of increasing CD4 count threshold eligibility for antiretroviral therapy initiation on advanced HIV disease and tuberculosis prevalence and incidence in South Africa: an interrupted time series analysis
Authors: Asare Kwabena , Lewis Lara , van der Molen Johan , Sookrajh Yukteshwar , Khubone Thokozani , Ngwenya Thulani , Ntokozo Mkhize Siyabonga , Lessells Richard J , Naidoo Kogieleum , Sosibo Phelelani , Bottomley Christian , Garrett Nigel , Dorward Jienchi 
Published: June 2024

AbstractIntroductionWe investigated the impact of increasing CD4 count eligibility for antiretroviral-therapy (ART) initiation on advanced HIV and tuberculosis (TB) prevalence and incidence among people living with HIV (PLHIV) in South Africa.MethodsWe conducted an interrupted time series analysis with de-identified data of PLHIV aged ≥15 initiating ART between April-2012 and February-2020 at 65 primary healthcare clinics in KwaZulu-Natal, South Africa. Outcomes included monthly proportions of new ART initiators presenting with advanced HIV (CD4 count <200 cells/µl) and TB disease. We created a cohort of monthly ART initiators without TB and evaluated the cumulative incidence of TB within 12 months follow-up. We used segmented binomial regression models to estimate relative risks (RR) of outcomes, allowing for a step and slope change after expanding the ART initiation CD4 count eligibility from <350 to <500 cells/µl in January- 2015 and following Universal-Test-and-Treat (UTT) implementation in September-2016.ResultsAmong 187,544 participants, median age was 32 (27-39), and 125,065 (66.7%) were female. After January-2015, risk of advanced HIV at initiation decreased by 24.5% (RR=0.745, 95%CI 0.690-0.800) and further reduced by 26.2% following UTT implementation (RR=0.738, 95%CI 0.688-0.788). Risk of TB at initiation also decreased by 28.7% after January-2015 (RR=0.713, 95%CI 0.644-0.782) and further decreased by 17.6% after UTT implementation (RR=0.824, 95%CI 0.703-0.945) but remained stable among initiators with advanced HIV. Among the incidence cohort, the risk of new TB decreased by 31.9% (RR=0.681, 95%CI 0.441-0.921) following UTT implementation. Among the incidence cohort with advanced HIV, there was weak evidence of a decrease in risk of new TB (RR=0.755, 95%CI 0.489-1.021), but it gradually decreased per month (slope change per month 9.7%, RR=0.903, 95%CI 0.872-0.934) following UTT implementation.ConclusionsOur data supports the added benefit of decreased TB co-burden with expanded ART access. Early diagnosis and immediate linkage to care should be prioritised among PLHIV.
Coaching ribosome biogenesis from the nuclear periphery
Authors: Zhuang Yinyin , Guo Xiangfu , Razorenova Olga V. , Miles Christopher E. , Zhao Wenting , Shi Xiaoyu 
Published: June 2024

SummarySevere invagination of the nuclear envelope is a hallmark of cancers, aging, neurodegeneration, and infections. However, the outcomes of nuclear invagination remain unclear. This work identified a new function of nuclear invagination: regulating ribosome biogenesis. With expansion microscopy, we observed frequent physical contact between nuclear invaginations and nucleoli. Surprisingly, the higher the invagination curvature, the more ribosomal RNA and pre-ribosomes are made in the contacted nucleolus. By growing cells on nanopillars that generate nuclear invaginations with desired curvatures, we can increase and decrease ribosome biogenesis. Based on this causation, we repressed the ribosome levels in breast cancer and progeria cells by growing cells on low-curvature nanopillars, indicating that overactivated ribosome biogenesis can be rescued by reshaping nuclei. Mechanistically, high-curvature nuclear invaginations reduce heterochromatin and enrich nuclear pore complexes, which promote ribosome biogenesis. We anticipate that our findings will serve as a foundation for further studies on nuclear deformation.HighlightsNuclear invaginations regulate ribosome biogenesis by physically contacting nucleoli.High-curvature nuclear tunnels increase ribosome biogenesis.Nanopillars reduce ribosome biogenesis by transforming high-curvature nuclear invaginations to low-curvature ones.
Metabolic and transcriptomic analyses of nectaries reveal differences in the mechanism of nectar production between monocots (Ananas comosus) and dicots (Nicotiana tabacum)
Authors: Göttlinger Thomas , Pirritano Marcello , Simon Martin , Fuß Janina , Lohaus Gertrud 
Published: June 2024

AbstractBackgroundNectar is offered by numerous flowering plants to attract pollinators. To date, the production and secretion of nectar have been analyzed mainly in eudicots, particularly rosids such asArabidopsis. However, due to the enormous diversity of flowering plants, further research on other plant species, especially monocots, is needed.Ananas comosus(monocot) is an economically important species and ideal for such analyses because it produce easily accessible nectar in sufficient quantities. In addition, the analyses were also carried out withNicotiana tabacum(dicot, asterids) for comparison.ResultsWe performed transcriptome sequencing (RNA-Seq) analyses of the nectaries ofAnanas comosusandNicotiana tabacum, to test whether mechanisms described for nectar production and secretion inArabidopsisare also present in these plant species. The focus of these analyses is on carbohydrate metabolism and transport (e.g., sucrose-phosphate synthases, invertases, sucrose synthases, SWEETs and further sugar transporters). In addition, the metabolites were analyzed in the nectar, nectaries and leaves of both plant species to address the question whether concentration gradients for different metabolites exist between the nectaries and nectar.The nectar ofN. tabacumcontains large amounts of glucose, fructose and sucrose, and the sucrose concentration in the nectar appears to be similar to the sucrose concentration in the nectaries. Nectar production and secretion in this species closely resembles corresponding processes in some other dicots, including sucrose synthesis in nectaries and sucrose secretion by SWEET9.The nectar ofA. comosusalso contains large amounts of glucose, fructose and sucrose and in this species the sucrose concentration in the nectar appears to be higher than the sucrose concentration in the nectaries. Furthermore, orthologs of SWEET9 appear to be generally absent inA. comosusand other monocots. Therefore, sucrose export by SWEETs from the nectaries into the nectar can be excluded, rather, other mechanisms, such as active sugar export or exocytosis, are more likely.ConclusionThe mechanisms of nectar production and secretion inN. tabacumappear to be largely similar to those in other dicots, whereas in the monocotyledonous speciesA. comosus, different synthesis and transport processes are involved.
Skull bone marrow-derived immune cells infiltrate the damaged cortex and exhibit anti-inflammatory properties
Authors: Soliman Eman , Basso Erwin Kristobal Gudenschwager , Ju Jing , Willison Andrew , Theus Michelle H. 
Published: June 2024

AbstractIdentifying the origins and contributions of different immune cell populations following brain injury is crucial for understanding their roles in inflammation and tissue repair. This study investigated the infiltration and phenotypic characteristics of skull bone marrow-derived immune cells in the murine brain after TBI. We performed calvarium transplantation from GFP donor mice and subjected the recipients to controlled cortical impact (CCI) injury 14 days post-transplant. Confocal imaging at 3 days post-CCI revealed GFP+ calvarium-derived cells infiltrating the ipsilateral core lesional area, expressing CD45 and CD11b immune markers. These cells included neutrophil (Ly6G+) and monocyte (Ccr2+) identities. Calvarium-derived GFP+/Iba1+ monocyte/macrophages expressed the efferocytosis receptor MerTK and displayed engulfment of NeuN+ and caspase 3+ apoptotic cells. Phenotypic analysis showed that greater calvarium-derived monocyte/macrophages disproportionately express the anti-inflammatory arginase-1 marker than pro-inflammatory CD86. To differentiate the responses of blood- and calvarium-derived macrophages, we transplanted GFP calvarium skull bone into tdTomato bone marrow chimeric mice, then performed CCI injury 14 days post-transplant. Calvarium-derived GFP+ cells predominantly infiltrated the lesion boundary, while blood-derived TdTomato+ cells dispersed throughout the lesion and peri-lesion. Compared to calvarium-derived cells, more blood-derived cells expressed pro-inflammatory CD86 and displayed altered 3D morphologic traits. These findings uniquely demonstrate that skull bone-derived immune cells infiltrate the brain after injury and contribute to the neuroinflammatory milieu, representing a novel immune cell source that may be further investigated for their causal role in functional outcomes.
Network controllability analysis reveals the antiviral potential of Etravirine against Hepatitis E Virus infection
Authors: Ansari Shabnam , Sarmah Dipanka Tanu , Verma Rohit , Chandrasekar Kannan , Chatterjee Samrat , Surjit Milan 
Published: June 2024

AbstractHepatitis E virus (HEV) is a major cause of acute viral hepatitis in lower- and middle-income countries. HEV infection may lead to acute liver failure, chronic liver disease and high mortality in pregnant women. Antiviral therapy is not a standard treatment for HEV patients. Computational biology tools promise to revolutionize the antiviral drug discovery. Here, we analyzed the transcriptome data of HEV infected primary human hepatocyte (PHH)-cells through connectivity map database and applied control theory on functional network to identify antiviral targets against HEV. The above analyses predicted PKCβ, PKB/AKT and CK1ε as potential antiviral targets against HEV. The antiviral function of PKB/AKT and CK1ε was experimentally validated by using respective biochemical inhibitors in g3 (genotype 3)-HEV replicon and Huh7 cell-based model of g3 and g1-HEV infection. Further, knockdown of CK1ε showed a similar effect. These data confirmed that CK1ε is an antiviral target for HEV. At present, there are no FDA approved drugs targeting CK1ε. Etravirine is an FDA approved non-nucleoside reverse transcriptase inhibitor drug, used for the treatment of Human immunodeficiency virus type 1 (HIV-1) infected patients. Anin silicostudy predicted Etravirine to be a potent inhibitor of CK1ε. Our experiments revealed potent antiviral activity of Etravirine against HEV, which was mediated via its ability to inhibit the activity of CK1ε. Taken together, the current study demonstrates that PKB/AKT and CK1ε are bonafide antiviral targets for HEV and paves the way for repurposing Etravirine for the treatment of HEV infected patients.ImportanceAntiviral treatment is not the standard care for acute viral hepatitis E patients. Unbiased identification of antiviral targets or large-scale screening of antiviral compounds against the hepatitis E virus (HEV) has not been reported. Here, computational biology approach was followed to unbiasedly identify antiviral targets of HEV. Transcriptome data of HEV infected primary human hepatocyte (PHH) cells were analyzed to identify modulators of the network and generate directional networks. Network controllability analysis identified PKCβ, PKB/AKT and CK1ε as potential antiviral targets against HEV. Antiviral function of PKB/AKT and CK1ε was confirmed using cell-based models of genotype 1 (g1)- and g3-HEV infection. Further experiments demonstrated the antiviral activity of Etravirine against HEV, mediated via its ability to inhibit the CK1ε activity. Etravirine is an FDA approved non-nucleoside reverse transcriptase inhibitor, used for the treatment of Human immunodeficiency virus type-1 (HIV-1)-infected patients. This study reveals the potential of repurposing Etravirine for treatment of HEV patients and illustrate the importance of computational biology in antiviral drug discovery.
Bacteriophage Treatment against Carbapenem-resistantKlebsiella pneumoniae(KPC) in a Neutropenic Murine Model of Gastrointestinal Translocation and Renal infection
Authors: Zagaliotis Panagiotis , Michalik-Provasek Jordyn , Mavridou Eleftheria , Naing Ethan , Vizirianakis Ioannis S. , Chatzidimitriou Dimitrios , Gill Jason J. , Walsh Thomas J. 
Published: June 2024

ABSTRACTBackgroundCarbapenemase producingKlebsiella pneumoniae(KPC) are globally emerging pathogens which that cause life-threatening infections. Novel treatment alternatives are urgently needed.MethodsWe therefore investigated the effectiveness of three novel bacteriophages (Spivey, Pharr and Soft) in a neutropenic murine model of KPC gastrointestinal colonization, translocation, and disseminated infection. Bacteriophage efficacy was determined by residual bacterial burden of KPC in kidneys. Parallel studies were conducted of bacteriophage pharmacokinetics and resistance..ResultsTreatment of mice with 5×109PFU of phage cocktail via intraperitoneal injection was effective in significantly reducing renal KPC burden by 102CFU (p<0.01) when administered every 24 hours and 103CFU (p<0.01) every 12 hours. Moreover, a combination of bacteriophage and ceftazidime-avibactam produced a synergistic effect, resulting in a 105reduction in bacterial burden in caecum and kidney (p<0.001 in both tissues). Prophylactic administration of bacteriophages via oral gavage did not prevent KPC translocation to the kidneys. Bacteriophage decay determined by linear regression of the ln of mean concentrations demonstrated R2values in plasma of 0.941, kidney 0.976, and caecum 0.918, with half-lives of 2.5h < t1/2< 3.5 h. Furthermore, a phage-resistant mutant displayed increased sensitivity to serum killingin vitro, but did not show significant defects in renal infectionin vivo.ConclusionsA combination of bacteriophages demonstrated significant efficacy alone and synergy with ceftazidime/avibactam in treatment of experimental disseminated KPC infection in neutropenic mice.
Precise measurement of molecular phenotypes with barcode-based CRISPRi systems
Authors: Lobel Joseph H. , Ingolia Nicholas T. 
Published: June 2024

SummaryGenome-wide CRISPR-Cas9 screens have untangled regulatory networks and revealed the genetic underpinnings of diverse biological processes. Their success relies on experimental designs that interrogate specific molecular phenotypes and distinguish key regulators from background effects. Here, we realize these goals with a generalizable platform for CRISPR interference with barcoded expression reporter sequencing (CiBER-seq) that dramatically improves the sensitivity and scope of genome-wide screens. We systematically address technical factors that distort phenotypic measurements by normalizing expression reporters against closely-matched control promoters, integrated together into the genome at single copy. To test our ability to capture post-transcriptional and post-translational regulation through sequencing, we screened for genes that affected nonsense-mediated mRNA decay and Doa10-mediated cytosolic protein decay. Our optimized CiBER-seq screens accurately capture the known components of well-studied RNA and protein quality control pathways with minimal background. These results demonstrate the precision and versatility of CiBER-seq for dissecting the genetic networks controlling cellular behaviors.
Structural basis of bulk lipid transfer by bridge-like lipid transfer protein LPD-3
Authors: Kang Yunsik , Lehmann Katherine S. , Vanegas Juan , Long Hannah , Jefferson Amanda , Freeman Marc , Clark Sarah 
Published: June 2024

AbstractBridge-like lipid transport proteins (BLTPs) are an evolutionarily conserved family of proteins that localize to membrane contact sites and are thought to mediate the bulk transfer of lipids from a donor membrane, typically the endoplasmic reticulum (ER), to an acceptor membrane, such as a that of the cell or an organelle1. Despite the fundamental importance of BLTPs for cellular function, the architecture, composition, and lipid transfer mechanisms remain poorly characterized. Here, we present the subunit composition and the cryo-electron microscopy structure of the native LPD-3 BLTP complex isolated from transgenicC. elegans. LPD-3 folds into an elongated, rod-shaped tunnel whose interior is filled with ordered lipid molecules that are coordinated by a track of ionizable residues that line one side of the tunnel. LPD-3 forms a complex with two previously uncharacterized proteins, here named “Intake” and “Spigot”, both of which interact with the N-terminal end of LPD-3 where lipids enter the tunnel. Intake has three transmembrane helices, one of which borders the entrance to the tunnel; Spigot has one transmembrane helix and extends 80 Å along the cytosolic surface of LPD-3. Experiments in multiple model systems indicate that Spigot plays a conserved role in ER-PM contact site formation. Our LPD-3 complex structural data, together with molecular dynamics simulations of the transmembrane region in a lipid bilayer, reveal protein-lipid interactions that suggest a model for how the native LPD-3-complex mediates bulk lipid transport and provide a foundation for mechanistic studies of BLTPs.
Mammographic density assessed using deep learning in women at high risk of developing breast cancer: the effect of weight change on density
Authors: Squires Steven , Harvie Michelle , Howell Anthony , Evans D. Gareth , Astley Susan M. 
Published: June 2024

AbstractObjectivesHigh mammographic density (MD) and excess weight are associated with increased risk of breast cancer. Weight loss interventions could reduce risk, but classically defined percentage density measures may not reflect this due to disproportionate loss of breast fat. We investigate an artificial intelligence-based density method, reporting density changes in 46 women enrolled in a weight-loss study in a family history breast cancer clinic, using a volumetric density method as a comparison.MethodsWe analysed data from women who had weight recorded and mammograms taken at the start and end of the 12-month weight intervention study. MD was assessed at both time points using a deep learning model, pVAS, trained on expert estimates of percent density, and Volpara ™ density software.ResultsThe Spearman rank correlation between reduction in weight and change in density was 0.17 (−0.13 to 0.43) for pVAS and 0.59 (0.36 to 0.75) for Volpara volumetric percent density.ConclusionspVAS percent density measurements were not significantly affected by change in weight. Percent density measured with Volpara increased as weight decreased, driven by changes in fat volume.Advances in knowledgeThe effect of weight change on pVAS mammographic density predictions has not previously been published.
Assessing Antimicrobial Use Patterns in Christian Health Association of Malawi (CHAM) Health Facilities: A Cross-Sectional Study Protocol
Authors: Chirambo Evans Chimayi , Nkhoma Dumisani , Chiumia Francis , Odeo Sharon , Khomani Patience , Chibwe Innocent , Matchado Simon , Matchere Pacharo , Chiweza Beatrice , Mwenyekonde Elled , Kampira Elizabeth , Mitambo Collins , Makala Happy 
Published: June 2024

AbstractIntroductionThe threat of antimicrobial resistance (AMR) in Malawi is high with reported mortality of 19,300 annually, the 23rd highest age-standardised mortality. One of the drivers of AMR is misuse of antibiotics, a phenomenon that has not been adequately researched in Malawi. This study aims to investigate antimicrobial use patterns using prescribing, patient and facility indicators Christian Health Association of Malawi (CHAM) health facilities.MethodsThis will be a multiple cross-sectional study which will collect data from facility (194), patients (388), and prescriptions (3,104). Data will be collected using KoboToolbox v2021, and exported into Microsoft Excel version 2016 for cleaning and coding. Variables will be categorized according to the antimicrobial use indicators. The study will use STATA Version 14 statistical software for data analysis. Subsequently, facilities will be put in GPS map to show hotspots of irrational antimicrobial use. The study will run from January 2024 to December 2025.DiscussionThis study will provide detailed information on frequently used antimicrobials, the cost of antimicrobials relative to medicine budget, the intensity of exposure to antimicrobials, the availability of antimicrobials, patients’ understanding of antimicrobials use, and availability of important documents for antimicrobial use. Secondarily, the study will unravel the prevalence of irrational antimicrobial use, the main factors contributing to it, and location where irrational use is most prevalent. These findings will inform the national antimicrobial stewardship action plan, aiming to safeguard the available antimicrobials.Ethics and DisseminationThe protocol has been approved by Malawi’s College of Medicine Research Ethics Committee (COMREC) [Protocol # P.04/24-0651]. Participation in the study will be voluntary, and consent and assent will be sought during data collection. Data will be handled confidentially, with findings disseminated in conferences, to key AMR focused stakeholders, and finally through manuscript publication in a peer reviewed journal.