bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design and fabrication of 3D-printed patient-specific soft tissue and bone phantoms for CT imaging
Authors: Mei Kai , Pasyar Pouyan , Geagan Michael , Liu Leening P. , Shapira Nadav , Gang Grace J. , Stayman J. Webster , Noël Peter B. 
Published: April 2023

AbstractThe objective of this study is to create patient-specific phantoms for computed tomography (CT) that have realistic image texture and densities, which are critical in evaluating CT performance in clinical settings. The study builds upon a previously presented 3D printing method (PixelPrint) by incorporating soft tissue and bone structures. We converted patient DICOM images directly into 3D printer instructions using PixelPrint and utilized stone-based filament to increase Hounsfield unit (HU) range. Density was modeled by controlling printing speed according to volumetric filament ratio to emulate attenuation profiles. We designed micro-CT phantoms to demonstrate the reproducibility and to determine mapping between filament ratios and HU values on clinical CT systems. Patient phantoms based on clinical cervical spine and knee examinations were manufactured and scanned with a clinical spectral CT scanner. The CT images of the patient-based phantom closely resembled original CT images in texture and contrast. Measured differences between patient and phantom were less than 15 HU for soft tissue and bone marrow. The stone-based filament accurately represented bony tissue structures across different X-ray energies, as measured by spectral CT. In conclusion, this study demonstrated the possibility of extending 3D-printed patient-based phantoms to soft tissue and bone structures while maintaining accurate organ geometry, image texture, and attenuation profiles.
HRSA Population Health Dashboard
Authors: Nguyen Chi 
Published: April 2023

AbstractProject PurposeTo develop a quality dashboard tool for the Health Resources and Services Administration (HRSA) community health centers to examine health center characteristics associated with performance excellence and predict future healthcare cost.BackgroundHRSA is the primary federal agency for improving health care to people who are geographically isolated, economically or medically vulnerable. HRSA-funded health centers are required to upload to Uniform Data System (UDS). HRSA health data is rich; however, their website provides limited meaningful visualization and data-driven analysis.MethodThe project reviewed data from Uniform Data System between 2017 and 2019. The data was cleaned using Excel. Visualization was displayed on Tableau, and the cost prediction modeling was completed using Python Machine Learning libraries. All the findings are available for public view on Weebly-hosted website.OutcomesThe Tableau dashboard showcases the effectiveness of the preventive intervention and chronic disease management initiatives over the years. This tool focuses on comparison between outcomes in health care programs and cost benefits in all states. The dashboard also uses the most fit Machine Learning model and the most important variables to predict the cost per patient of a health center.DiscussionThe lack of similar performance comparison dashboards by HRSA suggests a need for HRSA Population Health Dashboard to understand the performances of HRSA-funded health centers or regions through times. It shows the ineffectiveness of the current healthcare programs in reducing disease growth and healthcare cost over the course of 3 years.Next Steps/OpportunitiesThe final dashboard will be available for public use and will continue to aggregate more real-time data using Application Programming Interface (API) to improve its accuracy of prediction model. The HRSA Population Health Dashboard will be beneficial to management at both HRSA federal- and health center-level to make valuable strategies.
The effectiveness of precision supplements on depression symptoms in a US population
Authors: Julian Cristina , Shen Nan , Molusky Matthew , Hu Lan , Gopu Vishakh , Gorakshakar Anmol , Patridge Eric , Antoine Grant , Connell Janelle , Keiser Hilary , Naidoo Uma , Vuyisich Momchilo , Banavar Guruduth 
Published: April 2023

AbstractNutrition plays a pivotal role in depression, but dietary interventions are usually not personalized and do not consider patients’ microbial and human molecular functions. This preliminary study evaluated the effectiveness of precision supplements (PS) on depression symptoms as part of a personalized nutrition subscription plan that accounts for the gene expression activity of the microbiome and the human host. People with depression, 86 taking PS and 45 controls responded to the patient health questionnaire-9 (PHQ-9) at two time points an average of ∼6 months apart. Categorical changes were evaluated using the PHQ-9 score system, and clinically significant categorical differences were observed between the two groups (effect size = 0.48; p <0.001). The difference in differences was calculated using multiple group propensity score weighting adjusting for age, sex, BMI, and physical activity, and the PHQ-9 score decreased by ∼4 points (∼29%) for the intervention group (t0: 13.75+-3.80, t1: 9.78+-6.42) vs Controls (t0: 14.07+-3.64, t1: 13.59 +-6.65). Thus, precision supplement use over ∼6 months significantly reduced depression symptoms, with 69.8% of the individuals in the intervention group improving their category to no/low depression vs. 15.6% in the control group.
Deep resequencing of the 1q22 locus in non-lobar intracerebral hemorrhage
Authors: Parodi Livia , Comeau Mary E , Georgakis Marios K , Mayerhofer Ernst , Chung Jaeyoon , Falcone Guido J , Malik Rainer , Demel Stacie L , Worrall Bradford B , Koch Sebastian , Testai Fernando D , Kittner Steven J , McCauley Jacob L , Hall Christiana E , Mayson Douglas J , Elkind Mitchell SV , James Michael L , Woo Daniel , Rosand Jonathan , Langefeld Carl D , Anderson Christopher D 
Published: April 2023

AbstractObjectiveGenome-wide association studies have identified1q22as a susceptibility locus for cerebral small vessel diseases (CSVDs), including non-lobar intracerebral hemorrhage (ICH) and lacunar stroke. In the present study we performed targeted high-depth sequencing of1q22in ICH cases and controls to further characterize this locus and prioritize potential causal mechanisms, which remain unknown.Methods95,000 base pairs spanning1q22, includingSEMA4A, SLC25A44andPMF1/PMF1-BGLAPwere sequenced in 1,055 spontaneous ICH cases (534 lobar and 521 non-lobar) and 1,078 controls. Firth regression and RIFT analysis were used to analyze common and rare variants, respectively. Chromatin interaction analyses were performed using Hi-C, ChIP-Seq and ChIA-PET databases. Multivariable Mendelian randomization (MVMR) assessed whether alterations in gene-specific expression relative to regionally co-expressed genes at1q22could be causally related to ICH risk.ResultsCommon and rare variant analyses prioritized variants inSEMA4A5’-UTR andPMF1intronic regions, overlapping with active promoter and enhancer regions based on ENCODE annotation. Hi-C data analysis determined that1q22is spatially organized in a single chromatin loop and that the genes therein belong to the same Topologically Associating Domain. ChIP-Seq and ChIA-PET data analysis highlighted the presence of long-range interactions between theSEMA4A-promoter andPMF1-enhancer regions prioritized by association testing. MVMR analyses demonstrated thatPMF1overexpression could be causally related to non-lobar ICH risk.InterpretationAltered promoter-enhancer interactions leading toPMF1overexpression, potentially dysregulating polyamine catabolism, could explain demonstrated associations with non-lobar ICH risk at1q22, offering a potential new target for prevention of ICH and CSVD.
Risk Factors for Spontaneous Preterm Birth are Mediated through Changes in Cervical Length
Authors: Wolf Hope M. , Latendresse Shawn J. , Strauss Jerome F. , Tarca Adi L. , Romero Roberto , Hassan Sonia S. , Webb Bradley T. , York Timothy P. 
Published: April 2023

ABSTRACTAlthough short cervical length in the mid-trimester of pregnancy is a one of the strongest predictors of preterm birth (i.e., parturition before 37 completed weeks), there is limited understanding of how the dynamics of cervical remodeling (i.e., changes in cervical length) leading up to labor and delivery can inform obstetrical risk. In this study, latent growth curve analysis was applied to serial cervical length measurements across pregnancy (median of 6; IQR = 3-8) to quantify characteristics of cervical change in a cohort of 5,111 singleton pregnancies consisting predominantly of Black women. A conditional mediation model including nine common maternal risk factors for spontaneous preterm birth as exogenous predictors accounted for 26.5% of the variability in gestational age at delivery (P< 0.001). This model provides insight into distinct mechanisms by which specific maternal risk factors influence preterm birth. For instance, effects of maternal parity and smoking status were fully mediated through cervical change parameters, whereas the influence of previous preterm birth was only partially explained, suggesting alternative pathways could be involved. This study provides the first account of the intermediary role of cervical dynamics in associations between known maternal risk factors and gestational age at delivery.
Menopausal vasomotor symptoms and subclinical atherosclerotic cardiovascular disease – a population-based study
Authors: Nilsson Sigrid , Qvick Angelika , Henriksson Moa , Sederholm Lawesson Sofia , Spetz Holm Anna-Clara , Leander Karin 
Published: April 2023

ABSTRACTBACKGROUNDMenopausal vasomotor symptoms (VMS) have been associated with subclinical and manifest atherosclerotic cardiovascular disease (ASCVD) but have not been studied in relation to image-detected coronary atherosclerosis. We assessed the association between VMS and subclinical ASCVD in peri- and postmenopausal women, considering a wide range of cardiovascular related risk factors that could potentially influence the relationship.METHODSThis cross-sectional population-based study was conducted on a subset of participants from the Swedish CArdioPulmonary BioImage Study (SCAPIS), including women 50-65 years of age. The women underwent comprehensive cardiovascular assessments and completed an extensive questionnaire, which included questions about current and previous menopause-related symptoms. VMS was assessed on a 4-point scale and analyzed in relation to subclinical ASCVD, detected via coronary computed tomography angiography (CCTA), coronary artery calcium score (CACS) and carotid ultrasound using logistic regression analyses.RESULTSOf 2995 women included, 14.2% reported previous or on-going severe VMS (n=425), 18.1% moderate VMS (n=543), and 67.7% no or mild VMS (n=2027). Women who had ever experienced severe VMS, but not those with ever moderate VMS, had higher prevalence of CCTA-detected coronary atherosclerosis (34.1 vs 27.8%, p=0.017), but not segmental involvement score (SIS) >3 (4.5 vs 5.1%, p=0.332), CACS>100 (5.8 vs 6.8%, p=0.166) or any carotid plaque (47.6% vs 46.6%, p=249) than women with never or ever mild VMS. Using the same reference, ever severe but not moderate VMS was significantly associated with CCTA-detected coronary atherosclerosis, odds ratio (OR) after multivariable adjustment 1.33, 95% CI 1.02–1.72. This association was only present for durations of severe VMS of more than 5 years (multivariable adjusted OR 1.53 95% CI 1.09-2.14) or when the onset of severe VMS occurred before menopause (multivariable adjusted OR 1.60 95% CI 1.06-2.42). Additional adjustment for menopausal hormone therapy strengthened the associations whereas additional adjustment for physical activity did not. No significant association with SIS>3, CACS>100, nor with any carotid plaque was observed.CONCLUSIONSPrevious or on-going severe but not moderate VMS were significantly associated with CCTA-detected coronary atherosclerosis, independent of a broad range of cardiovascular risk factors. No corresponding associations was observed for SIS>3, CACS>100 or carotid atherosclerosis.
GAN-MAT: Generative Adversarial Network-based Microstructural Profile Covariance Analysis Toolbox
Authors: Park Yeong Jun , Lee Mi Ji , Yoo Seulki , Kim Chae Yeon , Namgung Jong Young , Park Yunseo , Park Hyunjin , Lee Eun-Chong , Yun Yeo Dong , Paquola Casey , Bernhardt Boris C. , Park Bo-yong 
Published: April 2023

AbstractMultimodal magnetic resonance imaging (MRI) provides complementary information for investigating brain structure and function; for example, anin vivomicrostructure-sensitive proxy can be estimated using the ratio between T1- and T2-weighted structural MRI. However, acquiring multiple imaging modalities is challenging in patients with inattentive disorders. In this study, we proposed a comprehensive framework to provide multiple imaging features related to the brain microstructure using only T1-weighted MRI. Our toolbox consists of (i) synthesizing T2-weighted MRI from T1-weighted MRI using a conditional generative adversarial network; (ii) estimating microstructural features, including intracortical covariance and moment features of cortical layer-wise microstructural profiles; and (iii) generating a microstructural gradient, which is a low-dimensional representation of the intracortical microstructure profile. We trained and tested our toolbox using T1- and T2-weighted MRI scans of 1,104 healthy young adults obtained from the Human Connectome Project database. We found that the synthesized T2-weighted MRI was very similar to the actual image and that the synthesized data successfully reproduced the microstructural features. The toolbox was validated using an independent dataset containing healthy controls and patients with episodic migraine as well as the atypical developmental condition of autism spectrum disorder. Our toolbox may provide a new paradigm for analyzing multimodal structural MRI in the neuroscience community, and is openly accessible athttps://github.com/CAMIN-neuro/GAN-MAT.
Evaluation of ATNPDframework and biofluid markers to predict cognitive decline in early Parkinson’s disease
Authors: Cousins Katheryn A.Q. , Irwin David J. , Tropea Thomas F. , Rhodes Emma , Phillips Jeffrey S. , Chen-Plotkin Alice S. , Brumm Michael C. , Coffey Christopher S. , Kang Ju Hee , Simuni Tanya , Foroud Tatiana , Toga Arthur W. , Tanner Caroline M. , Kieburtz Karl , Mollenhauer Brit , Galasko Douglas R. , Hutten Samantha , Weintraub Daniel , Siderowf Andrew , Marek Kenneth , Kollmorgen Gwendlyn , Poston Kathleen L. , Shaw Leslie M. ,   The Parkinson’s Progression Marker Initiative
Published: April 2023

AbstractBackground and ObjectivesIn Parkinson’s disease (PD), Alzheimer’s disease (AD) co-pathology is common and clinically relevant. However, the longitudinal progression of AD cerebrospinal fluid (CSF) biomarkers – β-amyloid 1-42 (Aβ42), phosphorylated tau 181 (p-tau181) and total tau (t-tau) – in PD is poorly understood, and may be distinct from clinical AD. Moreover, it is unclear if CSF p-tau181and serum neurofilament light (NfL) have added prognostic utility in PD, when combined with CSF Aβ42. First, we describe longitudinal trajectories of biofluid markers in PD. Second, we modified the AD β-amyloid/tau/neurodegeneration (ATN) framework for application in PD (ATNPD) using CSF Aβ42(A), p-tau181(T), and serum NfL (N), and tested ATNPDprediction of longitudinal cognitive decline in PD.MethodsParticipants were selected from the Parkinson’s Progression Markers Initiative (PPMI) cohort, clinically-diagnosed with sporadic PD or as normal Controls, and followed annually for 5 years. Linear mixed effects models (LMEM) tested the interaction of diagnosis with longitudinal trajectories of analytes (log-transformed, FDR-corrected). In PD, LMEMs tested how baseline ATNPDstatus (AD [A+T+N±]vs. not) predicted clinical outcomes, including Montreal Cognitive Assessment (MoCA; rank-transformed, FDR-corrected).ResultsParticipants were 364 PD and 168 Controls, with comparable baseline mean (±SD) age (PD=62±10; Control=61±11]; Mann-Whitney-Wilcoxon:p=0.40) and gender distribution (PD=231 males [63%]; Control=107 males [64%]; chi-square:p=1.0). PD had overall lower CSF p-tau181(β=-0.16, 95%CI=-0.23 – -0.092,p=2.2e-05) and t-tau than Controls (β=-0.13, 95%CI=-0.19 – -0.065,p=4.0e-04), but not Aβ42(p=0.061) or NfL (p=0.32). Over time, PD had greater increases in serum NfL than Controls (β=0.035, 95%CI=0.022 – 0.048,p=9.8e-07); PD slopes did not differ from controls for CSF Aβ42(p=0.18), p-tau181(p=1.0) or t-tau (p=0.96). Using ATNPD, PD classified as A+T+N± (n=32; 9%) had consistently worse cognitive decline, including on global MoCA (β=-73, 95%CI=-110 – -37,p=0.00077), than all other ATNPDstatuses including A+ alone (A+T-N-; n=75; 21%).DiscussionIn early PD, CSF p-tau181and t-tau were low compared to Controls and did not increase over 5 year follow-up. Even so, classification using modified ATNPD(incorporating CSF p-tau181with CSF Aβ42and serum NfL) may identify biologically-relevant subgroups of PD to improve prediction of cognitive decline in early PD.
The Structures of Secretory IgA in complex withStreptococcus pyogenesM4 and human CD89 provide insights on mucosal host-pathogen interactions
Authors: Liu Qianqiao , Stadtmueller Beth M. 
Published: April 2023

ABSTRACTImmunoglobulin (Ig) A functions as monomeric IgA in the serum and Secretory (S) IgA in mucosal secretions. Host IgA Fc receptors (FcαRs), including human FcαR1/CD89, mediate IgA effector functions; however human pathogenStreptococcus pyogeneshas evolved surface-protein virulence factors, including M4, that also engage the CD89 binding site on IgA. Despite human mucosa serving as a reservoir for pathogens, SIgA interactions with CD89 and M4 remain poorly understood. Here we report cryo-EM structures of M4-SIgA and CD89-SIgA complexes, which unexpectedly reveal different SIgA-binding stoichiometry for M4 and CD89. Structural data, supporting experiments, and modeling indicate that copies of SIgA bound toS. pyogenesM4 will adopt similar orientations on the bacterium surface and leave one host FcαR binding site open. Results suggest unappreciated functional consequences associated with SIgA binding to host and bacterial FcαRs relevant to understanding host-microbe co-evolution, IgA effector functions and to improving the outcomes of group AStreptococcusinfection.
Enhancing the Applied Force and Range of Axial Optical Tweezers
Authors: Zhang Zheng , Milstein Joshua N. 
Published: April 2023

Axial optical tweezers provide a natural geometry for performing biomechanical assays such as rupture force measurements of protein binding. Axial traps, however, are typically weaker than their lateral counterparts requiring high laser power to maintain a well calibrated, linear restoring force. Here we show how to extend the spatial range over which well calibrated forces can be applied by considering aberration effects and extend the range of applied forces by accounting for the nonlinear response that appears when an optically trapped bead is moved far from the trap center. These refinements to the force calibration can be used to apply higher axial forces at reduced laser powers deeper into a sample. To illustrate the method, we reproduce both the linear extension regime and overstretching transition observed in dsDNA at significantly reduced laser powers.http://dx.doi.org/10.1364/ao.XX.XXXXXX
Adaptation to bile and anaerobicity limitsVibrio choleraephage adsorption
Authors: Netter Zoe , Dunham Drew T. , Seed Kimberley D. 
Published: April 2023

AbstractBacteriophages (viruses of bacteria) play a pivotal role in shaping both the evolution and dynamics of bacterial populations. Bacteria employ arsenals of genetically encoded phage defense systems, but can alternatively achieve protection by changing the availability of cellular resources that phages rely on for propagation. These physiological changes are often adaptive responses to unique environmental signals. The facultative pathogenVibrio choleraeadapts to both aquatic and intestinal environments with niche-specific physiological changes that ensure its evolutionary success in such disparate settings. In both niches,V. choleraeis susceptible to predation by lytic phages like ICP1. However, both phages and susceptible bacterial hosts coexist in nature, indicating that environmental cues may modulateV. choleraecell state to protect against phage infection. This work explores one such modification in response to the intestine-specific signals of bile and anaerobicity. We found thatV. choleraegrown in these conditions reduces O1-antigen decoration on its outer membrane lipopolysaccharide. Because the O1-antigen is an essential moiety for ICP1 phage infection, we investigated the effect of partial O1-antigen depletion as a mechanism of phage defense and observed that O1-depletion limits phage adsorption. We identified mechanistic contributions to O1-depletion, including the essentiality of a weak acid tolerance system for O1 production at low pH, and alterations in transcriptional profiles indicating limitations in resources for O1-biosynthesis. This analysis illustrates a complex interplay between signals relevant to the intestinal environment and bacterial physiology that provideV. choleraewith protection from phage predation.
HBV prevalence in Sub-continental countries: a systematic review and meta-analysis
Authors: Hogan Sam , Page Andrew , Dixit Sameer , McBride Kate 
Published: April 2023

ABSTRACTBackgroundHepatitis B virus (HBV) is a major source of disease burden worldwide, especially in developing nations. Although vaccine programs exist to control infections, certain sub-populations around the world continue to have very high prevalence of HBV infection.MethodsA systematic search of studies of HBV published after 2010 was conducted for India, Pakistan, Bangladesh, Nepal, Sri Lanka and Bhutan. Each paper was independently screened for risk of bias and inclusion. Data were extracted from included studies before being analysed to estimate pooled prevalence, and to conduct sub-group analyses. Random-effects models were used for estimating summary prevalence due to a high level of heterogeneity between studies, and funnel plots were combined with Egger’s test to assess publication bias. Meta-regression was conducted to investigate sources of between-study heterogeneity.ResultsThe pooled prevalence of HBV across all studies was 4% (95% CI 0.02, 0.06). For countries with multiple studies, the pooled prevalence of HBV was 3% (95% CI 0.02, 0.05) for India, 6% (95% CI 0.04, 0.10) for Pakistan, 5% (95% CI of 0.02, 0.12) for Bangladesh, and 1% (95% CI 0.00, 0.08) for Nepal. There was some evidence of publication bias, and a high level of heterogeneity across studies. Risk of bias analysis found most studies to be of fair or moderate quality.ConclusionsThe prevalence of HBV among sub-continental countries was higher than the global average but was not as high as some other regions. Countries with greater numbers of displaced persons had higher prevalence of HBV, with a wide range of prevalence between subpopulations likely reflecting differential uptake, and implementation, of vaccination programs.