bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Coronary Computed Tomography Angiography Image Quality With High-concentration and Low-concentration Contrast Agents
Authors: Im Dong Jin , Kim Yun-Hyeon , Choo Ki Seok , Kang Joon-Won , Jung Jung Im , Won Yoodong , Kim Hyo Rim , Chung Myung Hee , Han Kyunghwa , Choi Byoung Wook 
Published: January 2022

Purpose:
To confirm that the image quality of coronary computed tomography (CT) angiography with a low tube voltage (80 to 100 kVp), iterative reconstruction, and low-concentration contrast agents (iodixanol 270 to 320 mgI/mL) was not inferior to that with conventional high tube voltage (120 kVp) and high-concentration contrast agent (iopamidol 370 mgI/mL).

Materials and Methods:
This prospective, multicenter, noninferiority, randomized trial enrolled a total of 318 patients from 8 clinical sites. All patients were randomly assigned 1: 1: 1 for each contrast medium of 270, 320, and 370 mgI/mL. CT scans were taken with a standard protocol in the high-concentration group (370 mgI/mL) and with 20 kVp lower protocol in the low-concentration group (270 or 320 mgI/mL). Image quality and radiation dose were compared between the groups. Image quality was evaluated with a score of 1 to 4 as subject image quality.

Results:
The mean HU, signal-to-noise ratio, and contrast-to-noise ratio of the 3 groups were significantly different (all P<0.0001). The signal-to-noise ratio and contrast-to-noise ratio of the low-concentration groups were significantly lower than those of the high-concentration group (P<0.05). However, the image quality scores were not significantly different among the 3 groups (P=0.745). The dose length product and effective dose of the high-concentration group were significantly higher than those of the low-concentration group (P<0.0001 and 0.003, respectively).

Conclusions:
The CT protocol with iterative reconstruction and lower tube voltage for low-concentration contrast agents significantly reduced the effective radiation dose (mean: 3.7±2.7 to 4.1±3.1 mSv) while keeping the subjective image quality as good as the standard protocol (mean: 5.7±3.4 mSv).
Diminished antibody response against SARS-CoV-2 Omicron variant after third dose of mRNA vaccine in kidney transplant recipients
Authors: Jurdi Ayman Al , Gassen Rodrigo B. , Borges Thiago J. , Lape Isadora T. , Morena Leela , Efe Orhan , Solhjou Zhabiz , Fekih Rania El , Deban Christa , Bohan Brigid , Pattanayak Vikram , Kotton Camille N. , Azzi Jamil R. , Riella Leonardo V. 
Published: January 2022

AbstractBackgroundAvailable SARS-CoV-2 vaccines have reduced efficacy against the Omicron variant in immunocompetent individuals. Kidney transplant recipients (KTRs) have diminished antiviral responses to wild-type SARS-CoV-2 after vaccination, and data on antiviral responses to SARS-CoV-2 variants, including the Omicron variant, are limited.MethodsWe conducted a prospective, multi-center cohort study of 51 adult KTRs who received three doses of BNT162b2 or mRNA-1273. Blood and urine samples were collected before and four weeks after the third vaccine dose. The primary outcome was anti-viral antibody responses against wild-type and variants of SARS-CoV-2. Secondary objectives included occurrence of breakthrough SARS-CoV-2 infection and non-invasive monitoring for rejection using serum creatinine, proteinuria, donor-derived cell-free DNA and donor-specific antibodies. Sera from pre-pandemic healthy controls and KTRs were used for comparison.Results67% of KTRs developed anti-wild-type spike antibodies after the third vaccine dose, similar to the Alpha (51%) and Beta (53%) variants, but higher than the Gamma (39%) and Delta (25%) variants. No KTRs had neutralizing responses to the Omicron variant before the third vaccine dose. After the third dose, fewer KTRs had neutralizing responses to the Omicron variant (12%) compared to wild-type (61%) and Delta (59%) variants. Three patients (6%) developed breakthrough SARS-CoV-2 infection at a median of 89 days. No KTRs developed allograft injury, de novo donor-specific antibodies or allograft rejection.ConclusionIn KTRs, a third dose of mRNA vaccines increases antibody responses against wild-type and variants of SARS-CoV-2, while neutralizing responses to the Omicron variant remain markedly reduced.
EchinoDB: An update to the web-based application for genomic and transcriptomic data on echinoderms
Authors: Mittal Varnika , Reid Robert W. , Machado Denis Jacob , Mashanov Vladimir , Janies Daniel A. 
Published: January 2022

AbstractHere we release a new version of EchinoDB (https://echinodb.uncc.edu). EchinoDB is a database of genomic and transcriptomic data on echinoderms. The initial database consisted of groups of 749,397 orthologous and paralogous transcripts arranged in orthoclusters by sequence similarity. The new version of EchinoDB includes RNA-seq data of the brittle star Ophioderma brevispinum and high-quality genomic assembly data of the green sea urchin Lytechinus variegatus. In addition, we enabled keyword searches for annotated data and installed an updated version of Sequenceserver to allow BLAST searches. The data are downloadable in FASTA format. The first version of EchinoDB appeared in 2016 and was implemented in GO on a local server. The new version has been updated using R Shiny to include new features and improvements in the application. Furthermore, EchinoDB now runs entirely in the cloud for increased reliability and scaling. EchinoDB enjoys a user base drawn from the fields of phylogenetics, developmental biology, genomics, physiology, neurobiology, and regeneration. As use cases, we illustrate how EchinoDB is used in discovering pathways and gene regulatory networks involved in the tissue regeneration process.
Neuropsychological and neuroanatomical features of patients with behavioral variant Alzheimer’s disease (AD): a comparison to behavioral variant frontotemporal dementia and amnestic AD groups
Authors: Perez Sophia Dominguez , Phillips Jeffrey S. , Norise Catherine , Kinney Nikolas G. , Vaddi Prerana , Halpin Amy , Rascovsky Katya , Irwin David J. , McMillan Corey T. , Xie Long , Wisse Laura E.M. , Yushkevich Paul A. , Kallogjeri Dorina , Grossman Murray , Cousins Katheryn A.Q. 
Published: January 2022

ABSTRACTAn understudied non-amnestic variant of Alzheimer’s disease (AD), behavioral variant AD (bvAD) is associated with progressive personality, behavior, or executive dysfunction and frontal atrophy. This study characterizes the neuropsychological and neuroanatomical features associated with bvAD by comparing it to behavioral variant frontotemporal dementia (bvFTD), amnestic AD (aAD), and subjects with normal cognition. Subjects included 16 bvAD, 67 bvFTD, and 18 aAD patients, and 26 healthy controls. Compared to bvFTD, bvAD showed more significant visuospatial impairments (Rey Figure copy and recall), more irritability (Neuropsychological Inventory), and equivalent verbal memory (Philadelphia Verbal Learning Test). Compared to aAD, bvAD indicated more executive dysfunction (F-letter fluency) and better visuospatial performance. Neuroimaging analysis found that bvAD showed cortical thinning relative to bvFTD posteriorly in left temporal-occipital regions; bvFTD had cortical thinning relative to bvAD in left inferior frontal cortex. bvAD had cortical thinning relative to aAD in prefrontal and anterior temporal regions. All patient groups had lower volumes than controls in both anterior and posterior hippocampus. However, bvAD patients had higher average volume than aAD patients in posterior hippocampus and higher volume than bvFTD patients in anterior hippocampus after adjustment for age and intracranial volume. Findings demonstrated that underlying pathology mediates disease presentation in bvAD and bvFTD.
Cardiovascular disease protein biomarkers are associated with kidney function: the Framingham Heart Study
Authors: Keshawarz Amena , Hwang Shih-Jen , Lee Gha Young , Yu Zhi , Yao Chen , Köttgen Anna , Levy Daniel 
Published: January 2022

BackgroundBiomarkers common to chronic kidney disease (CKD) and cardiovascular disease (CVD) may reflect early impairments underlying both diseases.MethodsWe evaluated associations of 71 CVD-related plasma proteins measured in 2,873 Framingham Heart Study (FHS) Offspring cohort participants with cross-sectional continuous eGFR and with longitudinal change in eGFR from baseline to follow-up (ΔeGFR). We also evaluated the associations of the 71 CVD proteins with the following dichotomous secondary outcomes: prevalent CKD stage ≥3 (cross-sectional), new-onset CKD stage ≥3 (longitudinal), and rapid decline in eGFR (longitudinal). Proteins significantly associated with eGFR and ΔeGFR were subsequently validated in 3,951 FHS Third Generation cohort participants and were tested using Mendelian randomization (MR) analysis to infer putatively causal relations between plasma protein biomarkers and kidney function.ResultsIn cross-sectional analysis, 37 protein biomarkers were significantly associated with eGFR at FDR<0.05 in the FHS Offspring cohort and 20 of these validated in the FHS Third Generation cohort at p<0.05/37. In longitudinal analysis, 27 protein biomarkers were significantly associated with ΔeGFR at FDR<0.05 and 12 of these were validated in the FHS Third Generation cohort at p<0.05/27. Additionally, 35 protein biomarkers were significantly associated with prevalent CKD, five were significantly associated with new-onset CKD, and 17 were significantly associated with rapid decline in eGFR. MR suggested putatively causal relations of melanoma cell adhesion molecule (MCAM; -0.011±0.003 mL/min/1.73m2, p=5.11E-5) and epidermal growth factor-containing fibulin-like extracellular matrix protein 1 (EFEMP1; - 0.006±0.002 mL/min/1.73m2, p=0.0001) concentration with eGFR.Discussion/ConclusionsEight protein biomarkers were consistently associated with eGFR in cross-sectional and longitudinal analysis in both cohorts and may capture early kidney impairment; others were implicated in association and causal inference analyses. A subset of CVD protein biomarkers may contribute causally to the pathogenesis of kidney impairment and should be studied as targets for CKD treatment and early prevention.
Factors Associated with COVID-19 Testing among People who Inject Drugs: Missed Opportunities for Reaching those Most at Risk
Authors: Yeager Samantha , Abramovitz Daniela , Harvey-Vera Alicia , Vera Carlos F. , Algarin Angel B. , Smith Laramie R. , Rangel Gudelia , Artamonova Irina , Patterson Thomas L. , Bazzi Angela R. , Brugman Emma L. , Strathdee Steffanie A. 
Published: January 2022

AbstractPeople who inject drugs (PWID) are vulnerable to SARS-CoV-2 infection. We examined correlates of COVID-19 testing among PWID in the U.S.-Mexico border region and described encounters with services or venues representing potential opportunities (i.e., ‘touchpoints’) where COVID-19 testing could have been offered. Between October, 2020 and September, 2021, participants aged ≥18 years from San Diego, California, USA and Tijuana, Baja California, Mexico who injected drugs within the last month completed surveys and SARS-CoV-2, HIV, and HCV serologic testing. Logistic regression was used to identify factors associated with COVID-19 testing prior to enrollment. Of 583 PWID, 30.5% previously had a COVID-19 test. Of 172 PWID who tested SARS-CoV-2 seropositive in our study (30.1%), 50.3% encountered at least one touchpoint within the prior six months where COVID-19 testing could have been offered. Factors independently associated with at least two fold higher odds of COVID-19 testing were living in San Diego (versus Tijuana), having recently been incarcerated or attending substance use disorder (SUD) treatment and having at least one chronic health condition. In addition, recent homelessness, having had at least one COVID-19 vaccine dose and having been tested for HIV or HCV since the pandemic began were independently associated with COVID-19 testing. We identified several factors independently associated with COVID-19 testing and multiple touchpoints where COVID-19 testing could be scaled up for PWID, such as SUD treatment programs and syringe service programs. Integrated health services are needed to improve access to rapid, free COVID-19 testing in this vulnerable population.
Surgical interventions targeting the nucleus caudalis for craniofacial pain: a systematic and historical review
Authors: Santyr Brendan , Abbass Mohamad , Chalil Alan , Vivekanandan Amirti , Tindale Margaret , Boulis Nicholas M. , Lau Jonathan C. 
Published: January 2022

AbstractIntroductionCraniofacial pain is a prevalent group of conditions and when refractory to conventional treatments poses a significant burden. The last decade has seen a renewed interest in the multimodal management of pain. Interventions targeting the nucleus caudalis (NC) of the trigeminocervical complex have been available as a treatment option since the 1930s, yet evidence for efficacy remains limited.MethodsWe present a systematic review of the literature providing a historical perspective on interventions targeting the NC leading up to the present. We examine the various intervention techniques, clinical indications, and procedural efficacy. A novel outcome reporting scheme was devised to enable comparison among studies due to historically variable reporting methods.ResultsA review of the literature revealed 33 retrospective studies published over the last 80 years reporting on 827 patients. The most common technique was the open NC dorsal root entry zone nucleotomy/tractotomy; however, there has been an emergence of novel approaches such as endoscopic and spinal cord stimulation in the last 10 years. Regardless of intervention technique or preoperative diagnosis, 87% of patients demonstrated improvement with treatment.ConclusionThe literature surrounding NC intervention techniques is reviewed. Recent advancements and the wide range of craniofacial pain syndromes for which these interventions show potential efficacy is discussed. New and less invasive techniques continue to emerge as putative therapeutic options. However, prospective studies are lacking. Furthermore, the evidence supporting even well-established techniques remain of poor quality. Future work should be prospective, utilize standard outcome reporting, and address efficacy comparisons between intervention type and preoperative diagnosis.
Unraveling membrane properties at the organelle-level with LipidDyn
Authors: Scrima Simone , Tiberti Matteo , Campo Alessia , Corcelle-Termeau Elisabeth , Judith Delphine , Foged Mads Møller , Clemmensen Knut Kristoffer Bundgaard , Tooze Sharon , Jäättelä Marja , Maeda Kenji , Lambrughi Matteo , Papaleo Elena 
Published: January 2022

AbstractCellular membranes are formed from many different lipids in various amounts and proportions depending on the subcellular localization. The lipid composition of membranes is sensitive to changes in the cellular environment, and their alterations are linked to several diseases, including cancer. Lipids not only form lipid-lipid interactions but also interact with other biomolecules, including proteins, profoundly impacting each other.Molecular dynamics (MD) simulations are a powerful tool to study the properties of cellular membranes and membrane-protein interactions on different timescales and at varying levels of resolution. Over the last few years, software and hardware for biomolecular simulations have been optimized to routinely run long simulations of large and complex biological systems. On the other hand, high-throughput techniques based on lipidomics provide accurate estimates of the composition of cellular membranes at the level of subcellular compartments. The community needs computational tools for lipidomics and simulation data effectively interacting to better understand how changes in lipid compositions impact membrane function and structure. Lipidomic data can be analyzed to design biologically relevant models of membranes for MD simulations. Similar applications easily result in a massive amount of simulation data where the bottleneck becomes the analysis of the data to understand how membrane properties and membrane-protein interactions are changing in the different conditions. In this context, we developed LipidDyn, an in silico pipeline to streamline the analyses of MD simulations of membranes of different compositions. Once the simulations are collected, LipidDyn provides average properties and time series for several membrane properties such as area per lipid, thickness, diffusion motions, the density of lipid bilayers, and lipid enrichment/depletion. The calculations exploit parallelization and the pipelines include graphical outputs in a publication-ready form. We applied LipidDyn to different case studies to illustrate its potential, including membranes from cellular compartments and transmembrane protein domains. LipidDyn is implemented in Python and relies on open-source libraries. LipidDyn is available free of charge under the GNU General Public License from https://github.com/ELELAB/LipidDyn.
SPITFIR(e): A supermaneuverable algorithm for restoring 2D-3D fluorescence images and videos, and background subtraction
Authors: Prigent Sylvain , Nguyen Hoai-Nam , Leconte Ludovic , Valades-Cruz Cesar Augusto , Hajj Bassam , Salamero Jean , Kervrann Charles 
Published: January 2022

AbstractWhile fluorescent microscopy imaging has become the spearhead of modern biology as it is able to generate long-term videos depicting 4D nanoscale cell behaviors, it is still limited by the optical aberrations and the photon budget available in the specimen and to some extend to photo-toxicity. A direct consequence is the necessity to develop flexible and “off-road” algorithms in order to recover structural details and improve spatial resolution, which is critical when pushing the illumination to the low levels in order to limit photo-damages. Moreover, as the processing of very large temporal series of images considerably slows down the analysis, special attention must be paid to the feasibility and scalability of the developed restoration algorithms. To address these specifications, we present a very flexible method designed to restore 2D-3D+Time fluorescent images and subtract undesirable out-of-focus background. We assume that the images are sparse and piece-wise smooth, and are corrupted by mixed Poisson-Gaussian noise. To recover the unknown image, we consider a novel convex and non-quadratic regularizer Sparse Hessian Variation) defined as the mixed norms which gathers image intensity and spatial second-order derivatives. This resulting restoration algorithm named SPITFIR(e) (SParse fIT for Fluorescence Image Restoration) utilizes the primal-dual optimization principle for energy minimization and can be used to process large images acquired with varied fluorescence microscopy modalities. It is nearly parameter-free as the practitioner needs only to specify the amount of desired sparsity (weak, moderate, high). Experimental results in lattice light sheet, stimulated emission depletion, multifocus microscopy, spinning disk confocal, and wide-field microscopy demonstrate the generic ability of the SPITFIR(e) algorithm to efficiently reduce noise and blur, and to subtract undesirable fluorescent background, while avoiding the emergence of deconvolution artifacts.
RNA-mediated nucleosome depletion is required for elimination of transposon-derived DNA
Authors: Singh Aditi , Maurer-Alcalá Xyrus X. , Solberg Therese , Gisler Silvan , Ignarski Michael , Swart Estienne C. , Nowacki Mariusz 
Published: January 2022

AbstractSmall RNAs are known to mediate silencing of transposable elements and other genomic loci, increasing nucleosome density and preventing undesirable gene expression. Post-zygotic development of the Paramecium somatic genome requires elimination of thousands of transposon remnants (IESs) and transposable elements that are scattered throughout the germline genome (Garnier et al. 2004). The elimination process is guided by Piwi-associated small RNAs and leads to precise cleavage at IES boundaries (Bouhouche et al. 2011; Furrer et al. 2017). Previous research suggests that small RNAs induce heterochromatin formation within IESs, which, in turn, is required for DNA elimination (Liu et al. 2007). Here we show that IES recognition and precise excision is facilitated by recruitment of a homolog of a chromatin remodeler ISWI, which depletes target genomic regions of nucleosomes, making the chromatin accessible for DNA cleavage. ISWI knockdown in Paramecium leads to pronounced inhibition of DNA elimination. Furthermore, nucleosome profiling indicates that ISWI is required for IES elimination in nucleosome-dense genomic regions, while other IESs do not require small RNAs or ISWI for excision. ISWI silencing notably also reduces DNA elimination precision, resulting in aberrant excision at alternative IES boundaries. In summary, we demonstrate that chromatin remodeling that increases DNA accessibility together with small RNAs are necessary for efficient and precise DNA elimination in Paramecium.
Sleep slow-wave oscillations trigger seizures in a genetic epilepsy model of Dravet syndrome
Authors: Catron Mackenzie A. , Howe Rachel K. , Besing Gai-Linn K. , John Emily K. St. , Potesta Cobie Victoria , Gallagher Martin J. , Macdonald Robert L. , Zhou Chengwen 
Published: January 2022

AbstractSleep is the brain state when cortical activity decreases and memory consolidates. However, in human epileptic patients, including genetic epileptic seizures such as Dravet syndrome, sleep is the preferential period when epileptic spike-wave discharges (SWDs) appear, with more severe epileptic symptoms in female patients than male patients, which influencing patient sleep quality and memory. Currently, seizure onset mechanisms during sleep period still remain unknown. Our previous work has shown that the sleep-like state-dependent synaptic potentiation mechanism can trigger epileptic SWDs(Zhang et al., 2021). In this study, using one heterozygous (het) knock-in (KI) transgenic mice (GABAA receptor γ2 subunit Gabrg2Q390X mutation) and an optogenetic method, we hypothesized that slow-wave oscillations (SWOs) themselves in vivo could trigger epileptic seizures. We found that epileptic SWDs in het Gabrg2+/Q390X KI mice exhibited preferential incidence during NREM sleep period, accompanied by motor immobility/ facial myoclonus/vibrissal twitching, with more frequent incidence in female het KI mice than male het KI mice. Optogenetic induced SWOs in vivo significantly increased epileptic seizure incidence in het Gabrg2+/Q390X KI mice with increased duration of NREM sleep or quiet-wakeful states. Furthermore, suppression of SWO-related homeostatic synaptic potentiation by 4- (diethylamino)-benzaldehyde (DEAB) injection (i.p.) greatly decreased seizure incidence in het KI mice, suggesting that SWOs did trigger seizure activity in het KI mice. In addition, EEG delta-frequency (0.1-4 Hz) power spectral density during NREM sleep was significantly larger in female het Gabrg2+/Q390X KI mice than male het Gabrg2+/Q390X KI mice, which likely contributes to the gender difference in seizure incidence during NREM sleep/quiet-wake as that in human patients.