bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chest imaging representing a COVID-19 positive rural U.S. population
Authors: Desai Shivang , Baghal Ahmad , Wongsurawat Thidathip , Jenjaroenpun Piroon , Powell Thomas , Al-Shukri Shaymaa , Gates Kim , Farmer Phillip , Rutherford Michael , Blake Geri , Nolan Tracy , Sexton Kevin , Bennett William , Smith Kirk , Syed Shorabuddin , Prior Fred 
Published: November 2020

AbstractAs the COVID-19 pandemic unfolds, radiology imaging is playing an increasingly vital role in determining therapeutic options, patient management, and research directions. Publicly available data are essential to drive new research into disease etiology, early detection, and response to therapy. In response to the COVID-19 crisis, the National Cancer Institute (NCI) has extended the Cancer Imaging Archive (TCIA) to include COVID-19 related images. Rural populations are one population at risk for underrepresentation in such public repositories. We have published in TCIA a collection of radiographic and CT imaging studies for patients who tested positive for COVID-19 in the state of Arkansas. A set of clinical data describes each patient including demographics, comorbidities, selected lab data and key radiology findings. These data are cross-linked to SARS-COV-2 cDNA sequence data extracted from clinical isolates from the same population, uploaded to the GenBank repository. We believe this collection will help to address population imbalance in COVID-19 data by providing samples from this normally underrepresented population.
Factors related with sarcopenia and sarcopenic obesity among low- and middle-income settings: the 10/66 DRG study
Authors: Daskalopoulou Christina , Wu Yu-Tzu , Pan William , Giné Vázquez Iago , Prince Martin , Prina Matthew , Tyrovolas Stefanos 
Published: November 2020

AbstractSarcopenia and sarcopenic obesity research in low- and middle- income countries (LMICs) is limited. We investigated sarcopenia and sarcopenic obesity prevalence and sociodemographic, bio-clinical and lifestyle factors in LMICs settings. For the purposes of this study, the 10/66 Dementia Research Group follow-up wave information from individuals aged 65 and over in Cuba, Dominican Republic, Peru, Mexico, Puerto Rico, China, was employed and analysed (n = 8.694). Based on indirect population formulas, we calculated body fat percentage (%BF) and skeletal muscle mass index (SMI). Sarcopenia prevalence ranged from 12.4% (Dominican Republic) to 24.6% (rural Peru); sarcopenic obesity prevalence ranged from 3.0% (rural China) to 10.2% (rural Peru). Odds ratios (OR) with 95% confidence intervals (CI) for sarcopenia were higher for men 2.82 (2.22–3.57) and those with higher %BF 1.08 (1.07–1.09), whereas higher number of assets was associated with a decreased likelihood 0.93 (0.87–1.00). OR of sarcopenic obesity were higher for men 2.17 (1.70–2.76), those reporting moderate alcohol drinking 1.76 (1.21–2.57), and those with increased number of limiting impairments 1.54 (1.11–2.14). We observed heterogeneity in the prevalence of sarcopenia and sarcopenic obesity in the 10/66 settings. We also found a variety of factors to be associated with those. Our results reveal the need for more research among the older population of LMICs.
Phylogenetic analysis of cell-cycle regulatory proteins within the Symbiodiniaceae
Authors: Gorman Lucy M. , Wilkinson Shaun P. , Kitchen Sheila A. , Oakley Clinton A. , Grossman Arthur R. , Weis Virginia M. , Davy Simon K. 
Published: November 2020

AbstractIn oligotrophic waters, cnidarian hosts rely on symbiosis with their photosynthetic dinoflagellate partners (family Symbiodiniaceae) to obtain the nutrients they need to grow, reproduce and survive. For this symbiosis to persist, the host must regulate the growth and proliferation of its symbionts. One of the proposed regulatory mechanisms is arrest of the symbiont cell cycle in the G1phase, though the cellular mechanisms involved remain unknown. Cell-cycle progression in eukaryotes is controlled by the conserved family of cyclin-dependent kinases (CDKs) and their partner cyclins. We identified CDKs and cyclins in different Symbiodiniaceae species and examined their relationship to homologs in other eukaryotes. Cyclin proteins related to eumetazoan cell-cycle-related cyclins A, B, D, G/I and Y, and transcriptional cyclin L, were identified in the Symbiodiniaceae, alongside several alveolate-specific cyclin A/B proteins, and proteins related to protist P/U-type cyclins and apicomplexan cyclins. The largest expansion of Symbiodiniaceae cyclins was in the P/U-type cyclin groups. Proteins related to eumetazoan cell-cycle-related CDKs (CDK1) were identified as well as transcription-related CDKs. The largest expansion of CDK groups was, however, in alveolate-specific groups which comprised 11 distinct CDK groups (CDKA-J) with CDKB being the most widely distributed CDK protein. As a result of its phylogenetic position, conservation across Symbiodiniaceae species, and the presence of the canonical CDK motif, CDKB emerged as a likely candidate for aSaccharomyces cerevisiaeCdc28/Pho85-like homolog in Symbiodiniaceae. Similar to cyclins, two CDK-groups found in Symbiodiniaceae species were solely associated with apicomplexan taxa. A comparison ofBreviolum minutumCDK and cyclin gene expression between free-living and symbiotic states showed that several alveolate-specific CDKs and two P/U-type cyclins exhibited altered expressionin hospite, suggesting that symbiosis influences the cell cycle of symbionts on a molecular level. These results highlight the divergence of Symbiodiniaceae cell-cycle proteins across species. These results have important implications for host control of the symbiont cell cycle in novel cnidarian–dinoflagellate symbioses.
Metabolomics and psychological features in fibromyalgia and electromagnetic sensitivity
Authors: Piras Cristina , Conte Stella , Pibiri Monica , Rao Giacomo , Muntoni Sandro , Leoni Vera Piera , Finco Gabriele , Atzori Luigi 
Published: November 2020

AbstractFibromyalgia (FM) as Fibromyalgia and Electromagnetic Sensitivity (IEI-EMF) are a chronic and systemic syndrome. The main symptom is represented by strong and widespread pain in the musculoskeletal system. The exact causes that lead to the development of FM and IEI-EMF are still unknown. Interestingly, the proximity to electrical and electromagnetic devices seems to trigger and/or amplify the symptoms. We investigated the blood plasma metabolome in IEI-EMF and healthy subjects using1H NMR spectroscopy coupled with multivariate statistical analysis. All the individuals were subjected to tests for the evaluation of psychological and physical features. No significant differences between IEI-EMF and controls relative to personality aspects, Locus of Control, and anxiety were found. Multivariate statistical analysis on the metabolites identified by NMR analysis allowed the identification of a distinct metabolic profile between IEI-EMF and healthy subjects. IEI-EMF were characterized by higher levels of glycine and pyroglutamate, and lower levels of 2-hydroxyisocaproate, choline, glutamine, and isoleucine compared to healthy subjects. These metabolites are involved in several metabolic pathways mainly related to oxidative stress defense, pain mechanisms, and muscle metabolism. The results here obtained highlight possible physiopathological mechanisms in IEI-EMF patients to be better defined.
Immortalisation of primary human alveolar epithelial lung cells using a non-viral vector to study respiratory bioreactivity in vitro
Authors: Katsumiti Alberto , Ruenraroengsak Pakatip , Cajaraville Miren P. , Thorley Andrew J. , Tetley Teresa D. 
Published: November 2020

AbstractTo overcome the scarcity of primary human alveolar epithelial cells for lung research, and the limitations of current cell lines to recapitulate the phenotype, functional and molecular characteristics of the healthy human alveolar epithelium, we have developed a new method to immortalise primary human alveolar epithelial lung cells using a non-viral vector to transfect the telomerase catalytic subunit (hTERT) and the simian virus 40 large-tumour antigen (SV40). Twelve strains of immortalised cells (ICs) were generated and characterised using molecular, immunochemical and morphological techniques. Cell proliferation and sensitivity to polystyrene nanoparticles (PS) were evaluated. ICs expressed caveolin-1, podoplanin and receptor for advanced glycation end-products (RAGE), and most cells were negative for alkaline phosphatase staining, indicating characteristics of AT1-like cells. However, most strains also contained some cells that expressed pro-surfactant protein C, classically described to be expressed only by AT2 cells. Thus, the ICs mimic the cellular heterogeneity in the human alveolar epithelium. These ICs can be passaged, replicate rapidly and remain confluent beyond 15 days. ICs showed differential sensitivity to positive and negatively charged PS nanoparticles, illustrating their potential value as an in vitro model to study respiratory bioreactivity. These novel ICs offer a unique resource to study human alveolar epithelial biology.
Subtype specific expression and survival prediction of pivotal lncRNAs in muscle invasive bladder cancer
Authors: Rinaldetti Sebastien , Worst Thomas Stefan , Rempel Eugen , Kriegmair Maximilian C. , Hartmann Arndt , Porubsky Stefan , Bolenz Christian , Erben Philipp 
Published: November 2020

AbstractComprehensive transcriptome expression analyses of bladder cancer revealed distinct lncRNA clusters with differential molecular and clinical characteristics. In this study, pivotal lncRNAs were assessed for their impact on survival and their differential expression between the molecular bladder cancer subtypes. FFPE samples from chemotherapy-naïve patients with muscle invasive bladder cancer (MIBC) were analyzed on the Nanostring nCounter platform for absolute quantification. An established 36-gene panel was used for molecular subtype classification into basal, luminal and infiltrated MIBC. In a second step, 14 pivotal lncRNAs were assessed for their molecular subtype attribution, and their predictive value in disease-specific survival. In silico validation was performed on a total of 487 MIBC patients (MDA, TGCA and Chungbuk cohort). Several pivotal lncRNAs showed a distinct molecular subtype attribution: e.g. MALAT1 showed a downregulation in the basal subtype (p = 0.009), TUG1 and CBR3AS1 showed an upregulation in the luminal subtype (p ≤ 0.001). High transcript levels of SNHG16, CBR3AS1 and H19 appeared to be predictive for a shorter disease-specific survival. Patients overexpressing putative oncogenes MALAT1 and TUG1 in MIBC tissue presented prolonged survival, suggesting tumor suppressive effects of both lncRNAs. The Nanostring nCounter proved to be a valid platform for the quantification of low-abundance transcripts including lncRNAs.
Effect of membrane fusion protein AdeT1 on the antimicrobial resistance of Escherichia coli
Authors: Barlow Victoria L. , Lai Shu-Jung , Chen Chia-Yu , Tsai Cheng-Han , Wu Shih-Hsiung , Tsai Yu-Hsuan 
Published: November 2020

AbstractAcinetobacter baumannii is a prevalent pathogen that can rapidly acquire resistance to antibiotics. Indeed, multidrug-resistant A. baumannii is a major cause of hospital-acquired infections and has been recognised by the World Health Organization as one of the most threatening bacteria to our society. Resistance-nodulation-division (RND) type multidrug efflux pumps have been demonstrated to convey antibiotic resistance to a wide range of pathogens and are the primary resistance mechanism employed by A. baumannii. A component of an RND pump in A. baumannii, AdeT1, was previously demonstrated to enhance the antimicrobial resistance of Escherichia coli. Here, we report the results of experiments which demonstrate that wild-type AdeT1 does not confer antimicrobial resistance in E. coli, highlighting the importance of verifying protein production when determining minimum inhibitory concentrations (MICs) especially by broth dilution. Nevertheless, using an agar-based MIC assay, we found that propionylation of Lys280 on AdeT1 renders E. coli cells more resistant to erythromycin.
Impact of carbon monoxide poisoning on the risk of breast cancer
Authors: Huang Chien-Cheng , Ho Chung-Han , Chen Yi-Chen , Hsu Chien-Chin , Lin Hung-Jung , Tian Yu-Feng , Wang Jhi-Joung , Guo How-Ran 
Published: November 2020

AbstractCarbon monoxide (CO) is a toxic gas and an endogenous signaling molecule. Some studies involving cell lines have revealed the potential antibreast cancer effects of CO. Data on such effects in humans, however, are limited. Thus, we conducted a study on patients with CO poisoning (COP) to evaluate the effects of CO on the risk of breast cancer. We identified female patients who were diagnosed with COP over the period of 2002 and 2009 from the Nationwide Poisoning Database of Taiwan. For comparison, we selected females without COP from the National Health Insurance Research Database. Participants in the COP and comparison cohorts were matched on the index year, age, monthly income, and geographic region of residence at a 1:6 ratio. We followed up the two cohorts until the end of 2014 and compared their risks of developing breast cancer. We included 7053 participants with COP and 42,318 participants without COP. Participants with COP were at a lower risk of developing breast cancer than those without COP (0.7% vs. 1.0%, p < 0.001). Cox proportional hazard regression analyses revealed that COP was associated with a hazard ratio of 0.67 (95% confidence interval [95% CI] 0.50–0.90) for breast cancer after we adjusted for age, monthly income, geographic region, and comorbidities of hypertension, diabetes, and hyperlipidemia. Our result provides evidence for the potential protective effects of CO against breast cancer in humans. Further studies that directly evaluate the potential effects are warranted.
Multiple gene substitution by Target-AID base-editing technology in tomato
Authors: Hunziker Johan , Nishida Keiji , Kondo Akihiko , Kishimoto Sanae , Ariizumi Tohru , Ezura Hiroshi 
Published: November 2020

AbstractThe use of Target activation-induced cytidine deaminase (Target-AID) base-editing technology with the CRISPR-Cas 9 system fused with activation-induced cytidine deaminase (AID) resulted in the substitution of a cytidine with a thymine. In previous experiments focusing on a single target gene, this system has been reported to work in several plant species, including tomato (Solanum lycopersicum L.). In this research, we used Target-AID technology to target multiple genes related to carotenoid accumulation in tomato. We selected 3 genes, SlDDB1, SlDET1 and SlCYC-B, for their roles in carotenoid accumulation. Among 12 edited T0 lines, we obtained 10 independent T0 lines carrying nucleotide substitutions in the three targeted genes, with several allelic versions for each targeted gene. The two edited lines showed significant differences in carotenoid accumulation. These results demonstrate that Target-AID technology is a highly efficient tool for targeting multiple genes with several allelic versions.
α-Synuclein promotes IAPP fibril formation in vitro and β-cell amyloid formation in vivo in mice
Authors: Mucibabic Marija , Steneberg Pär , Lidh Emmelie , Straseviciene Jurate , Ziolkowska Agnieszka , Dahl Ulf , Lindahl Emma , Edlund Helena 
Published: November 2020

AbstractType 2 diabetes (T2D), alike Parkinson’s disease (PD), belongs to the group of protein misfolding diseases (PMDs), which share aggregation of misfolded proteins as a hallmark. Although the major aggregating peptide in β-cells of T2D patients is Islet Amyloid Polypeptide (IAPP), alpha-synuclein (αSyn), the aggregating peptide in substantia nigra neurons of PD patients, is expressed also in β-cells. Here we show that αSyn, encoded by Snca, is a component of amyloid extracted from pancreas of transgenic mice overexpressing human IAPP (denoted hIAPPtg mice) and from islets of T2D individuals. Notably, αSyn dose-dependently promoted IAPP fibril formation in vitro and tail-vein injection of αSyn in hIAPPtg mice enhanced β-cell amyloid formation in vivo whereas β-cell amyloid formation was reduced in hIAPPtg mice on a Snca −/− background. Taken together, our findings provide evidence that αSyn and IAPP co-aggregate both in vitro and in vivo, suggesting a role for αSyn in β-cell amyloid formation.
No modulation of postprandial metabolism by transcutaneous auricular vagus nerve stimulation: a cross-over study in 15 healthy men
Authors: Vosseler Andreas , Zhao Dongxing , Fritsche Louise , Lehmann Rainer , Kantartzis Konstantinos , Small Dana M. , Peter Andreas , Häring Hans-Ulrich , Birkenfeld Andreas L. , Fritsche Andreas , Wagner Robert , Preißl Hubert , Kullmann Stephanie , Heni Martin 
Published: November 2020

AbstractExperimental evidence suggests a crucial role of the autonomic nervous system in whole body metabolism with major regulatory effects of the parasympathetic branch in postprandial adaptation. However, the relative contribution of this mechanism is still not fully clear in humans. We therefore compared the effects of transcutaneous auricular vagus nerve stimulation (taVNS, Cerbomed Nemos) with sham stimulation during an oral glucose tolerance test in a randomized, single-blind, cross-over design in 15 healthy lean men. Stimulation was performed for 150 min, 30 min before and during the entire oral glucose tolerance test with stimulation cycles of 30 s of on-phase and 30 s of off-phase and a 25 Hz impulse. Heart rate variability and plasma catecholamine levels were assessed as proxies of autonomic tone in the periphery. Neither analyzed heart rate variability parameters nor plasma catecholamine levels were significantly different between the two conditions. Plasma glucose, insulin sensitivity and insulin secretion were also comparable between conditions. Thus, the applied taVNS device or protocol was unable to achieve significant effects on autonomic innervation in peripheral organs. Accordingly, glucose metabolism remained unaltered. Therefore, alternative approaches are necessary to investigate the importance of the autonomic nervous system in postprandial human metabolism.
Platform- and label-free detection of lead ions in environmental and laboratory samples using G-quadraplex probes by circular dichroism spectroscopy
Authors: Kim Raeyeong , Youn Young-Sang , Kang Misook , Kim Eunjoo 
Published: November 2020

AbstractGuanine-rich quadruplex (G-QD) are formed by conversion of nucleotides with specific sequences by stabilization of positively charged K+ or Na+. These G-QD structures differentially absorb two-directional (right- and left-handed) circularly polarized light, which can discriminate the parallel or anti-parallel structures of G-QDs. In this study, G-QDs stabilized by Pb2+ were analyzed by a circular dichroism (CD) spectroscopy to determine Pb2+ concentration in water samples. Thrombin aptamer (TBA), PS2.M, human telomeric DNA (HTG), AGRO 100, and telomeric related sequence (T2) were studied to verify their applicability as probes for platform- and label-free detection of Pb2+ in environmental as well as laboratory samples. Among these nucleotides, TBA and PS2.M exhibited higher binding constants for Pb2+, 1.20–2.04 × 106/M at and 4.58 × 104–1.09 × 105/M at 100 micromolar and 100 mM K+ concentration, respectively. They also exhibited excellent selectivity for Pb2+ than for Al3+, Cu2+, Ni2+, Fe3+, Co2+, and Cr2+. When Pb2+ was spiked into an effluent sample from a wastewater treatment plant (WWTP), its existence was detected by CD spectroscopy following a simple addition of TBA or PS2.M. By the addition of TBA and PS2.M, the Pb2+ signals were observed in effluent samples over 0.5 micromolar (100 ppb) concentration. Furthermore, PS2.M caused a Pb2+-specific absorption band in the effluent sample without spiking of Pb2+, and could be induced to G-QD structure by the background Pb2+ concentration in the effluent, 0.159 micromolar concentration (3.30 ppb). Taken together, we propose that TBA and PS2.M are applicable as platform- and label-free detection probes for monitoring Pb2+ in environmental samples such as discharged effluent from local WWTPs, using CD spectroscopy.
Relationship between oral health impacts and personality profiles among orthodontic patients treated with Invisalign clear aligners
Authors: Al Nazeh Abdullah A. , Alshahrani Ibrahim , Badran Serene A. , Almoammar Salem , Alshahrani Abdulaziz , Almomani Bashar A. , AL-Omiri Mahmoud K. 
Published: November 2020

AbstractThis within subject clinical experiment assessed oral health impacts before and after Invisalign orthodontic treatment and their relationships with personality characteristics. 50 patients (26 females and 24 males; mean age = 27.62 ± 8.25 years, SE = 1.17, 95% CI = 24.71–29.89 years) were assessed before and after treatment with Invisalign orthodontic treatment. Treatment clinical success was evaluated according defined clinical guidelines. Oral health impacts before and after Invisalign orthodontic treatment were measured via the Oral Health Impact Profile (OHIP). Personality features were measured via the NEO Five-Factor Inventory (NEO-FFI). Probability of α = .05 was utilized to identify significant findings. Females scored less OHIP scores after treatment (had less negative impacts) in comparison to baseline OHIP scores (t = 3.782, df = 25, P = .001, 95% CI of mean difference = 2.750–9.327). Among males, openness scores (R2 = .911, B = 5.235, 95% CI for B = 0.062–10.407, t = 2.601, P = .048) were able to predict OHIP scores before treatment; meanwhile, extraversion (R2 = .959, B = − 8.224, 95% CI for B = − 14.605–1.843, t = − 3.313, P = .021), openness (R2 = .959, B = 21.795, 95% CI for B = 10.737–32.853, t = 5.067, P = .004), and conscientiousness (R2 = .959, B = 10.293, 95% CI for B = 4.796–15.790, t = 4.813, P = .005) scores were useful to predict OHIP scores after treatment (R2 = .959, P < .05). NEO-FFI scores were not useful to predict OHIP scores before or after treatment among females (P > .05). These findings demonstrate that oral health impacts of Invisalign orthodontic treatment and personality profiles contribution to oral health impacts were different between genders.
Species, sex and geographic variation in chlamydial prevalence in abundant wild Australian parrots
Authors: Stokes Helena S. , Martens Johanne M. , Walder Ken , Segal Yonatan , Berg Mathew L. , Bennett Andrew T. D. 
Published: November 2020

AbstractChlamydia psittaci (order: Chlamydiales) is a globally distributed zoonotic bacterium that can cause potentially fatal disease in birds and humans. Parrots are a major host, yet prevalence and risk factors for infection in wild parrots are largely unknown. Additionally, recent research suggests there is a diverse range of novel Chlamydiales circulating in wildlife. We therefore sampled seven abundant parrot species in south-eastern Australia, taking cloacal swabs and serum from n = 132 wild adults. We determined C. psittaci and Chlamydiales prevalence and seroprevalence, and tested for host species, sex, geographical and seasonal differences, and temporal changes in individual infection status. Across all species, Chlamydiales prevalence was 39.8% (95% CI 31.6, 48.7), C. psittaci prevalence was 9.8% (95% CI 5.7, 16.3) and C. gallinacea prevalence was 0.8% (95% CI 0.1, 4.5). Other Chlamydiales species were not identified to species level. We identified two C. psittaci strains within the 6BC clade, which is highly virulent in humans. Seroprevalence was 37.0% (95% CI 28.5, 46.4). Host species (including crimson rosellas, galahs, sulphur-crested cockatoos and blue-winged parrots) differed in seroprevalence and Chlamydiales prevalence. Galahs had both highest Chlamydiales prevalence (54.8%) and seroprevalence (74.1%). Seroprevalence differed between sites, with a larger difference in males (range 20–63%) than females (29–44%). We reveal a higher chlamydial prevalence than previously reported in many wild parrots, with implications for potential reservoirs, and transmission risks to humans and other avian hosts.