bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-throughput toxicogenomic screening of chemicals in the environment using metabolically competent hepatic cell cultures
Authors: Franzosa Jill A. , Bonzo Jessica A. , Jack John , Baker Nancy C. , Kothiya Parth , Witek Rafal P. , Hurban Patrick , Siferd Stephen , Hester Susan , Shah Imran , Ferguson Stephen S. , Houck Keith A. , Wambaugh John F. 
Published: January 2021

AbstractThe ToxCast in vitro screening program has provided concentration-response bioactivity data across more than a thousand assay endpoints for thousands of chemicals found in our environment and commerce. However, most ToxCast screening assays have evaluated individual biological targets in cancer cell lines lacking integrated physiological functionality (such as receptor signaling, metabolism). We evaluated differentiated HepaRGTMcells, a human liver-derived cell model understood to effectively model physiologically relevant hepatic signaling. Expression of 93 gene transcripts was measured by quantitative polymerase chain reaction using Fluidigm 96.96 dynamic arrays in response to 1060 chemicals tested in eight-point concentration-response. A Bayesian framework quantitatively modeled chemical-induced changes in gene expression via six transcription factors including: aryl hydrocarbon receptor, constitutive androstane receptor, pregnane X receptor, farnesoid X receptor, androgen receptor, and peroxisome proliferator-activated receptor alpha. For these chemicals the network model translates transcriptomic data into Bayesian inferences about molecular targets known to activate toxicological adverse outcome pathways. These data also provide new insights into the molecular signaling network of HepaRGTMcell cultures.
Measuring the α-particle charge radius with muonic helium-4 ions
Authors: Krauth Julian J. , Schuhmann Karsten , Ahmed Marwan Abdou , Amaro Fernando D. , Amaro Pedro , Biraben François , Chen Tzu-Ling , Covita Daniel S. , Dax Andreas J. , Diepold Marc , Fernandes Luis M. P. , Franke Beatrice , Galtier Sandrine , Gouvea Andrea L. , Götzfried Johannes , Graf Thomas , Hänsch Theodor W. , Hartmann Jens , Hildebrandt Malte , Indelicato Paul , Julien Lucile , Kirch Klaus , Knecht Andreas , Liu Yi-Wei , Machado Jorge , Monteiro Cristina M. B. , Mulhauser Françoise , Naar Boris , Nebel Tobias , Nez François , dos Santos Joaquim M. F. , Santos José Paulo , Szabo Csilla I. , Taqqu David , Veloso João F. C. A. , Vogelsang Jan , Voss Andreas , Weichelt Birgit , Pohl Randolf , Antognini Aldo , Kottmann Franz 
Published: January 2021

AbstractThe energy levels of hydrogen-like atomic systems can be calculated with great precision. Starting from their quantum mechanical solution, they have been refined over the years to include the electron spin, the relativistic and quantum field effects, and tiny energy shifts related to the complex structure of the nucleus. These energy shifts caused by the nuclear structure are vastly magnified in hydrogen-like systems formed by a negative muon and a nucleus, so spectroscopy of these muonic ions can be used to investigate the nuclear structure with high precision. Here we present the measurement of two 2S–2P transitions in the muonic helium-4 ion that yields a precise determination of the root-mean-square charge radius of the α particle of 1.67824(83) femtometres. This determination from atomic spectroscopy is in excellent agreement with the value from electron scattering1, but a factor of 4.8 more precise, providing a benchmark for few-nucleon theories, lattice quantum chromodynamics and electron scattering. This agreement also constrains several beyond-standard-model theories proposed to explain the proton-radius puzzle2–5, in line with recent determinations of the proton charge radius6–9, and establishes spectroscopy of light muonic atoms and ions as a precise tool for studies of nuclear properties.
HD-EEG for tracking sub-second brain dynamics during cognitive tasks
Authors: Mheich A. , Dufor O. , Yassine S. , Kabbara A. , Biraben A. , Wendling F. , Hassan M. 
Published: January 2021

AbstractThis work provides the community with high-density Electroencephalography (HD-EEG, 256 channels) datasets collected during task-free and task-related paradigms. It includes forty-three healthy participants performing visual naming and spelling tasks, visual and auditory naming tasks and a visual working memory task in addition to resting state. The HD-EEG data are furnished in the Brain Imaging Data Structure (BIDS) format. These datasets can be used to (i) track brain networks dynamics and their rapid reconfigurations at sub-second time scale in different conditions, (naming/spelling/rest) and modalities, (auditory/visual) and compare them to each other, (ii) validate several parameters involved in the methods used to estimate cortical brain networks through scalp EEG, such as the open question of optimal number of channels and number of regions of interest and (iii) allow the reproducibility of results obtained so far using HD-EEG. We hope that delivering these datasets will lead to the development of new methods that can be used to estimate brain cortical networks and to better understand the general functioning of the brain during rest and task. Data are freely available from https://openneuro.org.
Phylogenetic analyses of distantly related clades of bent-toed geckos (genus Cyrtodactylus) reveal an unprecedented amount of cryptic diversity in northern and western Thailand
Authors: Chomdej Siriwadee , Pradit Waranee , Suwannapoom Chatmongkon , Pawangkhanant Parinya , Nganvongpanit Korakot , Poyarkov Nikolay A. , Che Jing , Gao Yangchun , Gong Shiping 
Published: January 2021

AbstractCyrtodactylus species are the most diverse of the geckos and are widely distributed in Southeast Asia, including Thailand. However, their patterns of distribution, especially in northern and western parts of Thailand, remain unknown because few Cyrtodactylus species in these regions have been described. Thus, a data set of mitochondrial NADH dehydrogenase 2 (ND2) gene and flanking tRNAs from Cyrtodactylus found in northern and western Thailand, including contiguous areas, was assembled to elucidate phylogenetic relationships and identify the distribution patterns of these geckos. The results showed four well-supported clades, a northwestern clade (A), a northern clade (B), a western clade (C), and a special clade characterized by specific morphological features (D). Clades A–C were grouped with strong support by the geography of their localities from northern Thailand (Mae Hong Son and Chiang Mai Provinces) along the Tenasserim mountain ranges to Phang-Nga Province, Thailand. Clade D is a distinct clade of Cyrtodactylus species characterized by a tuberculate and prehensile tail and distributed widely in mainland Southeast Asia. Overall, the results suggest a pattern of geographic separation and distribution of Cyrtodactylus in northern and western Thailand. Additionally, this study provides evidence of a hidden biodiversity of Cyrtodactylus in these regions.
Cell properties assessment using optimized dielectrophoresis-based cell stretching and lumped mechanical modeling
Authors: Hosseini Imman I. , Moghimi Zand Mahdi , Ebadi Amir Ali , Fathipour Morteza 
Published: January 2021

AbstractCells mechanical property assessment has been a promising label-free method for cell differentiation. Several methods have been proposed for single-cell mechanical properties analysis. Dielectrophoresis (DEP) is one method used for single-cell mechanical property assessment, cell separation, and sorting. DEP method has overcome weaknesses of other techniques, including compatibility with microfluidics, high throughput assessment, and high accuracy. However, due to the lack of a general and explicit model for this method, it has not been known as an ideal cell mechanical property evaluation method. Here we present an explicit model using the most general electromagnetic equation (Maxwell Stress Tensor) for single-cell mechanical evaluation based on the DEP method. For proof of concept, we used the proposed model for differentiation between three different types of cells, namely erythrocytes, peripheral blood mononuclear cells (PBMC), and an epithelial breast cancer cells line (T-47D). The results show that, by a lumped parameter that depends on cells' mechanical and electrical properties, the proposed model can successfully distinguish between the mentioned cell types that can be in a single blood sample. The proposed model would open up the chance to use a mechanical assessment method for cell searching in parallel with other methods.
Cytotoxic Escherichia coli strains encoding colibactin, cytotoxic necrotizing factor, and cytolethal distending toxin colonize laboratory common marmosets (Callithrix jacchus)
Authors: McCoy Colleen S. , Mannion Anthony J. , Feng Yan , Madden Carolyn M. , Artim Stephen C. , Au Gina G. , Dolan Mikayla , Haupt Jennifer L. , Burns Monika A. , Sheh Alexander , Fox James G. 
Published: January 2021

AbstractCyclomodulins are virulence factors that modulate cellular differentiation, apoptosis, and proliferation. These include colibactin (pks), cytotoxic necrotizing factor (cnf), and cytolethal distending toxin (cdt). Pathogenic pks+, cnf+, and cdt+ E. coli strains are associated with inflammatory bowel disease (IBD) and colorectal cancer in humans and animals. Captive marmosets are frequently afflicted with IBD-like disease, and its association with cyclomodulins is unknown. Cyclomodulin-encoding E. coli rectal isolates were characterized using PCR-based assays in healthy and clinically affected marmosets originating from three different captive sources. 139 E. coli isolates were cultured from 122 of 143 marmosets. The pks gene was detected in 56 isolates (40%), cnf in 47 isolates (34%), and cdt in 1 isolate (0.7%). The prevalences of pks+ and cnf+ E. coli isolates were significantly different between the three marmoset colonies. 98% of cyclomodulin-positive E. coli belonged to phylogenetic group B2. Representative isolates demonstrated cyclomodulin cytotoxicity, and serotyping and whole genome sequencing were consistent with pathogenic E. coli strains. However, the presence of pks+, cnf+, or cdt+ E. coli did not correlate with clinical gastrointestinal disease in marmosets. Cyclomodulin-encoding E. coli colonize laboratory common marmosets in a manner dependent on the source, potentially impacting reproducibility in marmoset models.
Welwitschia: Phylogeography of a living fossil, diversified within a desert refuge
Authors: Jürgens Norbert , Oncken Imke , Oldeland Jens , Gunter Felicitas , Rudolph Barbara 
Published: January 2021

AbstractWelwitschia mirabilisis one of the most extraordinary plant species on earth. With a fossil record of 112 My and phylogenetically isolated within the order Gnetales, the monotypic genusWelwitschiahas survived only in the northern Namib Desert in Angola and Namibia. Despite its iconic role, the biogeography, ecological niche, and evolutionary history of the species remain poorly understood. Here we present the first comprehensive map of the strongly disjunct species range, and we explore the genetic relationships among all range fragments based on six SSR markers. We also assess the variation of the environmental niche and habitat preference. Our results confirm genetic divergence, which is consistent with the hypothetical existence of two subspecies withinWelwitschia. We identify an efficient geographical barrier separating two gene pools at 18.7°S in northern Namibia. We also identify further diversification within each of the two subspecies, with several different gene pools in ten isolated range fragments. Given the presence of well-isolated populations with unique gene pools and the association with different bioclimatic variables, rock types, and habitats within arid river catchments, we can hypothesize that the present intraspecific diversity may have evolved at least in part within the present refuge of the northern Namib Desert.
Evolving determinants of carotid atherosclerosis vulnerability in asymptomatic patients from the MAGNETIC observational study
Authors: Catalano Oronzo , Bendotti Giulia , Mori Alessia , De Salvo Maria , Falconi Marialuisa , Aloi Teresa L. , Tibollo Valentina , Bellazzi Riccardo , Bardile Alberto Ferrari , Montagna Stefano , Pesarin Clara , Poggi Paolo , Pedretti Roberto F. E. , Priori Silvia G. 
Published: January 2021

AbstractMRI can assess plaque composition and has demonstrated an association between some atherosclerotic risk factors (RF) and markers of plaque vulnerability in naive patients. We aimed at investigating this association in medically treated asymptomatic patients. This is a cross-sectional interim analysis (August 2013–September 2016) of a single center prospective study on carotid plaque vulnerability (MAGNETIC study). We recruited patients with asymptomatic carotid atherosclerosis (US stenosis > 30%, ECST criteria), receiving medical treatments at a tertiary cardiac rehabilitation. Atherosclerotic burden and plaque composition were quantified with 3.0 T MRI. The association between baseline characteristics and extent of lipid-rich necrotic core (LRNC), fibrous cap (CAP) and intraplaque hemorrhage (IPH) was studied with multiple regression analysis. We enrolled 260 patients (198 male, 76%) with median age of 71-y (interquartile range: 65–76). Patients were on antiplatelet therapy, ACE-inhibitors/angiotensin receptor blockers and statins (196–229, 75–88%). Median LDL-cholesterol was 78 mg/dl (59–106), blood pressure 130/70 mmHg (111–140/65–80), glycosylated hemoglobin 46 mmol/mol (39–51) and BMI 25 kg/m2 (23–28); moreover, 125 out of 187 (67%) patients were ex-smokers. Multivariate analysis of a data-set of 487 (94%) carotid arteries showed that a history of hypercholesterolemia, diabetes, hypertension or smoking did not correlate with LRNC, CAP or IPH. Conversely, maximum stenosis was the strongest independent predictor of LRNC, CAP and IPH (p < 0.001). MRI assessment of plaque composition in patients on treatment for asymptomatic carotid atherosclerosis shows no correlation between plaque vulnerability and the most well-controlled modifiable RF. Conversely, maximum stenosis exhibits a strong correlation with vulnerable features despite treatment.
Salicylic diamines selectively eliminate residual undifferentiated cells from pluripotent stem cell-derived cardiomyocyte preparations
Authors: Burkert Karsten , Taheri Hadiseh , Hamad Sarkawt , Oliverio Matteo , Peinkofer Gabriel , Kornfeld Jan-Wilhelm , Harnying Wacharee , Pfannkuche Kurt , Hescheler Jürgen , Berkessel Albrecht , Šarić Tomo 
Published: January 2021

AbstractClinical translation of pluripotent stem cell (PSC) derivatives is hindered by the tumorigenic risk from residual undifferentiated cells. Here, we identified salicylic diamines as potent agents exhibiting toxicity to murine and human PSCs but not to cardiomyocytes (CMs) derived from them. Half maximal inhibitory concentrations (IC50) of small molecules SM2 and SM6 were, respectively, 9- and 18-fold higher for human than murine PSCs, while the IC50 of SM8 was comparable for both PSC groups. Treatment of murine embryoid bodies in suspension differentiation cultures with the most effective small molecule SM6 significantly reduced PSC and non-PSC contamination and enriched CM populations that would otherwise be eliminated in genetic selection approaches. All tested salicylic diamines exerted their toxicity by inhibiting the oxygen consumption rate (OCR) in PSCs. No or only minimal and reversible effects on OCR, sarcomeric integrity, DNA stability, apoptosis rate, ROS levels or beating frequency were observed in PSC-CMs, although effects on human PSC-CMs seemed to be more deleterious at higher SM-concentrations. Teratoma formation from SM6-treated murine PSC-CMs was abolished or delayed compared to untreated cells. We conclude that salicylic diamines represent promising compounds for PSC removal and enrichment of CMs without the need for other selection strategies.
How neurons exploit fractal geometry to optimize their network connectivity
Authors: Smith Julian H. , Rowland Conor , Harland B. , Moslehi S. , Montgomery R. D. , Schobert K. , Watterson W. J. , Dalrymple-Alford J. , Taylor R. P. 
Published: January 2021

AbstractWe investigate the degree to which neurons are fractal, the origin of this fractality, and its impact on functionality. By analyzing three-dimensional images of rat neurons, we show the way their dendrites fork and weave through space is unexpectedly important for generating fractal-like behavior well-described by an ‘effective’ fractal dimension D. This discovery motivated us to create distorted neuron models by modifying the dendritic patterns, so generating neurons across wide ranges of D extending beyond their natural values. By charting the D-dependent variations in inter-neuron connectivity along with the associated costs, we propose that their D values reflect a network cooperation that optimizes these constraints. We discuss the implications for healthy and pathological neurons, and for connecting neurons to medical implants. Our automated approach also facilitates insights relating form and function, applicable to individual neurons and their networks, providing a crucial tool for addressing massive data collection projects (e.g. connectomes).
Large-scale systematic analysis of exposure to multiple cancer risk factors and the associations between exposure patterns and cancer incidence
Authors: Steinberg Julia , Yap Sarsha , Goldsbury David , Nair-Shalliker Visalini , Banks Emily , Canfell Karen , O’Connell Dianne L. 
Published: January 2021

AbstractExposures to cancer risk factors such as smoking and alcohol are not mutually independent. We aimed to identify risk factor exposure patterns and their associations with sociodemographic characteristics and cancer incidence. We considered 120,771 female and, separately, 100,891 male participants of the Australian prospective cohort 45 and Up Study. Factor analysis grouped 36 self-reported variables into 8 combined factors each for females (largely representing ‘smoking’, ‘alcohol’, ‘vigorous exercise’, ‘age at childbirth’, ‘Menopausal Hormone Therapy’, ‘parity and breastfeeding’, ‘standing/sitting’, ‘fruit and vegetables’) and males (largely representing ‘smoking’, ‘alcohol’, ‘vigorous exercise’, ‘urology and health’, ‘moderate exercise’, ‘standing/sitting’, ‘fruit and vegetables’, ‘meat and BMI’). Associations with cancer incidence were investigated using multivariable logistic regression (4–8 years follow-up: 6193 females, 8749 males diagnosed with cancer). After multiple-testing correction, we identified 10 associations between combined factors and cancer incidence for females and 6 for males, of which 14 represent well-known relationships (e.g. bowel cancer: females ‘smoking’ factor Odds Ratio (OR) 1.16 (95% Confidence Interval (CI) 1.08–1.25), males ‘smoking’ factor OR 1.15 (95% CI 1.07–1.23)), providing evidence for the validity of this approach. The catalogue of associations between exposure patterns, sociodemographic characteristics, and cancer incidence can help inform design of future studies and targeted prevention programmes.
Growth, lifetime, directional movement and myosin-dependent motility of mutant keratin granules in cultured cells
Authors: Lehmann S. M. , Leube R. E. , Windoffer R. 
Published: January 2021

AbstractIntermediate filament polypeptides (IFPs) are prominent components of cytoplasmic aggregates, which are pathognomonic for multiple diseases. Recent observations in cultured cells suggest that they are dynamic and subject to regulated turnover. The emerging concept is that multiple factors contribute to motility and turnover of IFP-containing aggregates. To understand their relative contribution, quantitative tools are needed. The current study addresses this need using epithelial cells producing mutant keratin IFPs that have been identified as the cause of the hereditary blister-forming skin disease epidermolysis bullosa simplex. Digital image analysis of individual granules allowed mapping of their complete life cycle, with information on multiple characteristics at any given time-point. The deduced signet features revealed rapid granule fusion and directed transport from the periphery towards the cell centre, and a limited, ~ 30 min lifetime with a slow, continuous growth phase followed by fast disassembly. As paradigmatic proof-of-principle, we demonstrate that inhibition of myosin II selectively reduces granule movement, linking keratin granule motility to retrograde cortical acto-myosin flow. The newly developed methods and established parameters will help in the characterization of known and the identification of novel regulators of IFP-containing aggregates.
Characterizing the impact of pyrite addition on the efficiency of Fe0/H2O systems
Authors: Hu Rui , Cui Xuesong , Xiao Minhui , Gwenzi Willis , Noubactep Chicgoua 
Published: January 2021

AbstractThe role of pyrite (FeS2) in the process of water treatment using metallic iron (Fe0) was investigated. FeS2 was used as a pH-shifting agent while methylene blue (MB) and methyl orange (MO) were used as an indicator of reactivity and model contaminant, respectively. The effect of the final pH value on the extent of MB discoloration was characterized using 5 g L−1 of a Fe0 specimen. pH variation was achieved by adding 0 to 30 g L−1 of FeS2. Quiescent batch experiments with Fe0/FeS2/sand systems (sand loading: 25 g L−1) and 20 mL of MB were performed for 41 days. Final pH values varied from 3.3 to 7.0. Results demonstrated that MB discoloration is only quantitative when the final pH value was larger than 4.5 and that adsorption and co-precipitation are the fundamental mechanisms of decontamination in Fe0/H2O systems. Such mechanisms are consistent with the effects of the pH value on the decontamination process.
Comprehensive somatosensory and neurological phenotyping of NCS1 knockout mice
Authors: Nguyen Lien D. , Nolte Luca G. , Tan Winston J. T. , Giuvelis Denise , Santos-Sacchi Joseph , Bilsky Edward , Ehrlich Barbara E. 
Published: January 2021

AbstractNeuronal calcium sensor 1 (NCS1) regulates a wide range of cellular functions throughout the mammalian nervous systems. Altered NCS1 expression is associated with neurodevelopmental and neurodegenerative diseases. Previous studies focused on affective and cognitive behaviors in NCS1 knockout (KO) mice, but little is known about the physiological and pathological states associated with the loss of NCS1 in the peripheral nervous system. We previously reported that NCS1 expression was reduced following paclitaxel-induced peripheral neuropathy. Here, we comprehensively investigated the phenotypes of NCS1-KO mice through a battery of behavioral tests examining both central and peripheral nervous systems. Generally, only mild differences were observed in thermal sensation and memory acquisition between NCS1-WT and -KO male mice, but not in female mice. No differences were observed in motor performance, affective behaviors, and hearing in both sexes. These results suggest that NCS1 plays a modulatory role in sensory perceptions and cognition, particularly in male mice. NCS1 has been proposed as a pharmacological target for various diseases. Therefore, the sex-specific effects of NCS1 loss may be of clinical interest. As we examined a constitutive KO model, future studies focusing on various conditional KO models will further elucidate the precise physiological significance of NCS1.