bluuebunny/crossref_metadata_2025_split huggingface dataset:
Autophagy inhibition elicits emergence from metastatic dormancy by inducing and stabilizing Pfkfb3 expression
Authors: La Belle Flynn Alyssa , Calhoun Benjamin C. , Sharma Arishya , Chang Jenny C. , Almasan Alexandru , Schiemann William P. 
Published: August 2019

AbstractBreast cancer stem cells (BCSCs) are unique in their ability to undergo unlimited self-renewal, an essential process in breast cancer recurrence following metastatic dormancy. Emergent metastatic lesions were subjected to microarray analysis, which identified 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (Pfkfb3) as a differentially expressed gene coupled to metastatic recurrence. Here, we report that elevated Pfkfb3 expression correlates with the appearance of aggressive breast cancers and reduces relapse-free survival, as well as enhances BCSC self-renewal and metastatic outgrowth. We observe an inverse relationship between Pfkfb3 expression and autophagy, which reduces Pfkfb3 expression and elicits cellular dormancy. Targeted depletion of Atg3, Atg7, or p62/sequestosome-1 to inactivate autophagy restores aberrant Pfkfb3 expression in dormant BCSCs, leading to their reactivation of proliferative programs and outgrowth. Moreover, Pfkfb3 interacts physically with autophagy machinery, specifically the UBA domain of p62/sequestosome-1. Importantly, disrupting autophagy and this event enables Pfkfb3 to drive dormant BCSCs and metastatic lesions to recur.
Rainfall drives variation in rates of change in intrinsic water use efficiency of tropical forests
Authors: Adams Mark A. , Buckley Thomas N. , Turnbull Tarryn L. 
Published: August 2019

AbstractRates of change in intrinsic water use efficiency (W) of trees relative to those in atmospheric [CO2] (ca) have been mostly assessed via short-term studies (e.g., leaf analysis, flux analysis) and/or step increases in ca (e.g., FACE studies). Here we use compiled data for abundances of carbon isotopes in tree stems to show that on decadal scales, rates of change (dW/dca) vary with location and rainfall within the global tropics. For the period 1915–1995, and including corrections for mesophyll conductance and photorespiration, dW/dca for drier tropical forests (receiving ~ 1000 mm rainfall) were at least twice that of the wettest (receiving ~ 4000 mm). The data also empirically confirm theorized roles of tropical forests in changes in atmospheric 13C/12C ratios (the 13C Suess Effect). Further formal analysis of geographic variation in decade-to-century scale dW/dca will be needed to refine current models that predict increases in carbon uptake by forests without hydrological cost.
Whole-exome and whole-transcriptome sequencing of canine mammary gland tumors
Authors: Kim Ka-Kyung , Seung Byung-Joon , Kim Dohyun , Park Hee-Myung , Lee Sejoon , Song Doo-Won , Lee Gunho , Cheong Jae-Ho , Nam Hojung , Sur Jung-Hyang , Kim Sangwoo 
Published: August 2019

AbstractStudies of naturally occurring cancers in dogs, which share many genetic and environmental factors with humans, provide valuable information as a comparative model for studying the mechanisms of human cancer pathogenesis. While individual and small-scale studies of canine cancers are underway, more generalized multi-omics studies have not been attempted due to the lack of large-scale and well-controlled genomic data. Here, we produced reliable whole-exome and whole-transcriptome sequencing data of 197 canine mammary cancers and their matched controls, annotated with rich clinical and biological features. Our dataset provides useful reference points for comparative analysis with human cancers and for developing novel diagnostic and therapeutic technologies for cancers in pet dogs.
HENA, heterogeneous network-based data set for Alzheimer’s disease
Authors: Sügis Elena , Dauvillier Jerome , Leontjeva Anna , Adler Priit , Hindie Valerie , Moncion Thomas , Collura Vincent , Daudin Rachel , Loe-Mie Yann , Herault Yann , Lambert Jean-Charles , Hermjakob Henning , Pupko Tal , Rain Jean-Christophe , Xenarios Ioannis , Vilo Jaak , Simonneau Michel , Peterson Hedi 
Published: August 2019

AbstractAlzheimer’s disease and other types of dementia are the top cause for disabilities in later life and various types of experiments have been performed to understand the underlying mechanisms of the disease with the aim of coming up with potential drug targets. These experiments have been carried out by scientists working in different domains such as proteomics, molecular biology, clinical diagnostics and genomics. The results of such experiments are stored in the databases designed for collecting data of similar types. However, in order to get a systematic view of the disease from these independent but complementary data sets, it is necessary to combine them. In this study we describe a heterogeneous network-based data set for Alzheimer’s disease (HENA). Additionally, we demonstrate the application of state-of-the-art graph convolutional networks, i.e. deep learning methods for the analysis of such large heterogeneous biological data sets. We expect HENA to allow scientists to explore and analyze their own results in the broader context of Alzheimer’s disease research.
Intrinsic tryptophan fluorescence spectroscopy reliably determines galectin-ligand interactions
Authors: Sindrewicz Paulina , Li Xiaoxin , Yates Edwin A. , Turnbull Jeremy E. , Lian Lu-Yun , Yu Lu-Gang 
Published: August 2019

AbstractGalectins are involved in the regulation of divergent physiological and pathological processes and are increasingly recognized to play important roles in a number of diseases. However, a simple and effective way in assessing galectin-ligand interactions is lacking. Our examination of the sequence of all 12 human galectin members reveals the presence of one or more tryptophan residues in the carbohydrate-recognition domains of each galectin. This led us to investigate the possibility that alteration of the galectin intrinsic tryptophan fluorescence could be used in determining the strength of galectin-ligand interactions. One representative member from each of the three subtype galectins, galectin-2 (proto-), galectin-3 (chimera-) and galectin-4 (tandem repeat-type), was selected and analysed for galectin interaction with three ligands of different affinities: galactose, lactose and N-acetyl-lactosamine using tryptophan fluorescence spectroscopy (TFS) and, as a comparison, isothermal titration calorimetry (ITC). Good agreement between TFS and ITC measurements were revealed in ligand bindings of all galectin members. Moreover, TFS detected very weak galectin binding where ITC could not reliably do so. The reliability of TFS in determining galectin-ligand interactions was further validated by analysis of galectin-3 interaction with a semisynthetic ligand, F3. Thus, TFS can be used as a simple, sensitive and reliable way to determine galectin-ligand interactions and also as a drug-discovery platform in developing galectin-targeted therapeutic drugs.
The application of poorly crystalline silicotitanate in production of 225Ac
Authors: Fitzsimmons Jonathan , Abraham Alyson , Catalano Demetra , Younes Ali , Cutler Cathy S. , Medvedev Dmitri 
Published: August 2019

AbstractActinium-225 (225Ac) can be produced from a Thorium-229/Radium-225 (229Th/225Ra) generator, from high/low energy proton irradiated natural Thorium or Radium-226 target. Titanium based ion exchanger were evaluated for purification of 225Ac. Poorly crystalline silicotitanate (PCST) ion exchanger had high selectivity for Ba, Ag and Th. 225Ac was received with trace amounts of 227Ac, 227Th and 223Ra, and the solution was used to evaluate the retention of the isotopes on PCST ion exchanger. Over 90% of the 225Ac was recovered from PCST, and the radiopurity was >99% (calculated based on 225Ac, 227Th, and 223Ra). The capacity of the PCST inorganic ion exchange for Barium and 232Th was determined to be 24.19 mg/mL for Barium and 5.05 mg/mL for Thorium. PCST ion exchanger could separate 225Ac from isotopes of Ra and Th, and the process represents an interesting one step separation that could be used in an 225Ac generator from 225Ra and/or 229Th. Capacity studies indicated PCST could be used to separate 225Ac produced on small 226Ra targets (0.3–1 g), but PCST did not have a high enough capacity for production scale Th targets (50–100 g).
Competitive percolation strategies for network recovery
Authors: Smith Andrew M. , Pósfai Márton , Rohden Martin , González Andrés D. , Dueñas-Osorio Leonardo , D’Souza Raissa M. 
Published: August 2019

AbstractRestoring operation of critical infrastructure systems after catastrophic events is an important issue, inspiring work in multiple fields, including network science, civil engineering, and operations research. We consider the problem of finding the optimal order of repairing elements in power grids and similar infrastructure. Most existing methods either only consider system network structure, potentially ignoring important features, or incorporate component level details leading to complex optimization problems with limited scalability. We aim to narrow the gap between the two approaches. Analyzing realistic recovery strategies, we identify over- and undersupply penalties of commodities as primary contributions to reconstruction cost, and we demonstrate traditional network science methods, which maximize the largest connected component, are cost inefficient. We propose a novel competitive percolation recovery model accounting for node demand and supply, and network structure. Our model well approximates realistic recovery strategies, suppressing growth of the largest connected component through a process analogous to explosive percolation. Using synthetic power grids, we investigate the effect of network characteristics on recovery process efficiency. We learn that high structural redundancy enables reduced total cost and faster recovery, however, requires more information at each recovery step. We also confirm that decentralized supply in networks generally benefits recovery efforts.
A BAC Transgene Expressing Human CFTR under Control of Its Regulatory Elements Rescues Cftr Knockout Mice
Authors: Gawenis Lara R. , Hodges Craig A. , McHugh Daniel R. , Valerio Dana M. , Miron Alexander , Cotton Calvin U. , Liu Jinghua , Walker Nancy M. , Strubberg Ashlee M. , Gillen Austin E. , Mutolo Michael J. , Kotzamanis George , Bosch Jürgen , Harris Ann , Drumm Mitchell L. , Clarke Lane L. 
Published: August 2019

AbstractSmall-molecule modulators of cystic fibrosis transmembrane conductance regulator (CFTR) biology show promise in the treatment of cystic fibrosis (CF). A Cftr knockout (Cftr KO) mouse expressing mutants of human CFTR would advance in vivo testing of new modulators. A bacterial artificial chromosome (BAC) carrying the complete hCFTR gene including regulatory elements within 40.1 kb of DNA 5′ and 25 kb of DNA 3′ to the gene was used to generate founder mice expressing hCFTR. Whole genome sequencing indicated a single integration site on mouse chromosome 8 (8qB2) with ~6 gene copies. hCFTR+ offspring were bred to murine Cftr KO mice, producing hCFTR+/mCftr− (H+/m−) mice, which had normal survival, growth and goblet cell function as compared to wild-type (WT) mice. Expression studies showed hCFTR protein and transcripts in tissues typically expressing mCftr. Functionally, nasal potential difference and large intestinal short-circuit (Isc) responses to cAMP stimulation were similar in magnitude to WT mice, whereas small intestinal cAMP ΔIsc responses were reduced. A BAC transgenic mouse with functional hCFTR under control of its regulatory elements has been developed to enable the generation of mouse models of hCFTR mutations by gene editing for in vivo testing of new CF therapies.
Muscle satellite cells and impaired late stage regeneration in different murine models for muscular dystrophies
Authors: Ribeiro Antonio F. , Souza Lucas S. , Almeida Camila F. , Ishiba Renata , Fernandes Stephanie A. , Guerrieri Danielle A. , Santos André L. F. , Onofre-Oliveira Paula C. G. , Vainzof Mariz 
Published: August 2019

AbstractSatellite cells (SCs) are the main muscle stem cells responsible for its regenerative capacity. In muscular dystrophies, however, a failure of the regenerative process results in muscle degeneration and weakness. To analyze the effect of different degrees of muscle degeneration in SCs behavior, we studied adult muscle of the dystrophic strains: DMDmdx, Largemyd, DMDmdx/Largemyd, with variable histopathological alterations. Similar results were observed in the dystrophic models, which maintained normal levels of PAX7 expression, retained the Pax7-positive SCs pool, and their proliferation capacity. Moreover, elevated expression of MYOG, an important myogenic factor, was also observed. The ability to form new fibers was verified by the presence of dMyHC positive regenerating fibers. However, those fibers had incomplete maturation characteristics, such as small and homogenous fiber caliber, which could contribute to their dysfunction. We concluded that dystrophic muscles, independently of their degeneration degree, retain their SCs pool with proliferating and regenerative capacities. Nonetheless, the maturation of these new fibers is incomplete and do not prevent muscle degeneration. Taken together, these results suggest that the improvement of late muscle regeneration should better contribute to therapeutic approaches.
First determination of Pu isotopes (239Pu, 240Pu and 241Pu) in radioactive particles derived from Fukushima Daiichi Nuclear Power Plant accident
Authors: Igarashi Junya , Zheng Jian , Zhang Zijian , Ninomiya Kazuhiko , Satou Yukihiko , Fukuda Miho , Ni Youyi , Aono Tatsuo , Shinohara Atsushi 
Published: August 2019

AbstractRadioactive particles were released into the environment during the Fukushima Dai-ichi Nuclear Power Plant (FDNPP) accident. Many studies have been conducted to elucidate the chemical composition of released radioactive particles in order to understand their formation process. However, whether radioactive particles contain nuclear fuel radionuclides remains to be investigated. Here, we report the first determination of Pu isotopes in radioactive particles. To determine the Pu isotopes (239Pu, 240Pu and 241Pu) in radioactive particles derived from the FDNPP accident which were free from the influence of global fallout, radiochemical analysis and inductively coupled plasma-mass spectrometry measurements were conducted. Radioactive particles derived from unit 1 and unit 2 or 3 were analyzed. For the radioactive particles derived from unit 1, activities of 239+240Pu and 241Pu were (1.70–7.06) × 10−5 Bq and (4.10–8.10) × 10−3 Bq, respectively and atom ratios of 240Pu/239Pu and 241Pu/239Pu were 0.330–0.415 and 0.162–0.178, respectively. These ratios were consistent with the simulation results from ORIGEN code and measurements from various environmental samples. In contrast, Pu was not detected in the radioactive particles derived from unit 2 or 3. The difference in Pu contents is clear evidence towards different formation processes of radioactive particles, and detailed formation processes can be investigated from Pu analysis.
High rates of maternal depression amongst Syrian refugees in Lebanon - a pilot study
Authors: Stevenson Kerrie , Alameddine Reina , Rukbi Ghaith , Chahrouri Mario , Usta Jinan , Saab Bassem , Bennett Phillip , Glover Vivette , Reynolds Rebecca M. 
Published: August 2019

AbstractThis pilot study compares symptoms of depression and risk factors amongst Syrian refugees and low-income Lebanese mothers accessing a primary care centre in Beirut between January and June 2018. Women who gave birth in the previous two years or who were currently pregnant were included in the study. Depressive symptoms were assessed using the Arabic Edinburgh Postnatal Depression Scale (EPDS). Correlations between EPDS score and sociodemographic and mental health variables were analysed using Pearson’s coefficient and ANOVA. 35 Syrian and 25 Lebanese women were recruited, 15 of whom were pregnant. EPDS scores were high in the whole group (mean 16.12 (SD 7.72), n = 60). Scores were higher amongst Syrian refugees than Lebanese mothers (17.77, SD 7.66 vs, 13.80, SD 7.34, p < 0.05). Illegal residence (p < 0.001), domestic violence (p < 0.05) and a history of mental illness (p < 0.01) were associated with higher scores. This pilot study demonstrates high rates of symptoms of depression amongst mothers in this population. Symptoms were particularly prevalent amongst Syrian refugees; three-quarters were ‘probably depressed’ and would warrant psychiatric assessment. This highlights the importance of improved mental healthcare for refugee mothers, the importance of addressing the social determinants of maternal mental health and further research into the effects of depression on these women and their children.
A New Clevosaurid from the Triassic (Carnian) of Brazil and the Rise of Sphenodontians in Gondwana
Authors: Hsiou Annie S. , Nydam Randall L. , Simões Tiago R. , Pretto Flávio A. , Onary Silvio , Martinelli Agustín G. , Liparini Alexandre , Martínez Paulo R. Romo de Vivar , Soares Marina B. , Schultz Cesar L. , Caldwell Michael W. 
Published: August 2019

AbstractThe early evolution of lepidosaurs is marked by an extremely scarce fossil record during the Triassic. Importantly, most Triassic lepidosaur specimens are represented by disarticulated individuals from high energy accretion deposits in Laurasia, thus greatly hampering our understanding of the initial stages of lepidosaur evolution. Here, we describe the fragmentary remains of an associated skull and mandible of Clevosaurus hadroprodon sp. nov., a new taxon of sphenodontian lepidosaur from the Late Triassic (Carnian; 237–228 Mya) of Brazil. Referral to Sphenodontia is supported by the combined presence of a marginal dentition ankylosed to the apex of the dentary, maxilla, and premaxilla; the presence of ‘secondary bone’ at the bases of the marginal dentition; and a ventrally directed mental process at the symphysis of the dentary. Our phylogenetic analyses recover Clevosaurus hadroprodon as a clevosaurid, either in a polytomy with the Late Triassic to Early Jurassic Clevosaurus and Brachyrhinodon (under Bayesian inference), or nested among different species of Clevosaurus (under maximum parsimony). Clevosaurus hadroprodon represents the oldest known sphenodontian from Gondwana, and its clevosaurid relationships indicates that these sphenodontians achieved a widespread biogeographic distribution much earlier than previously thought.
Natural Frequencies of seiches in Lake Chapala
Authors: Avalos Cueva David , Monzón Cesar O. , Filonov Anatoliy , Tereshchenko Iryna , Limón Covarrubias Pedro , Galaviz González José Roberto 
Published: August 2019

AbstractThis research presents an analysis of the frequencies and vibration modes of the structure of the superficial seiches of Lake Chapala using mathematical modelling and measurements. The HAMSOM model was run with wind fields from coastal meteorological stations and for different lake storage levels. The lake water level measurements were carried out in two campaigns in 2003. An analysis of the surface seiches in the lake was performed using the fast Fourier transform method. A spectral analysis of lake water level measurements reveals seiches with periods close to 5.9, 3, 2, and 1.5 h. A comparison with the periods calculated by the HAMSOM model indicates that these periods correspond to superficial seiches of the fundamental longitudinal mode of the lake and the subsequent three modes. The lake has undergone important changes in its storage level over time. Therefore, we modelled it with storage levels from the isobaths 90 to 95 m and found that surface seiche periods decreased to 5.2 h.
Linking type 2 diabetes mellitus, cardiac hypertrophy and depression in a diurnal animal model
Authors: Bilu Carmel , Einat Haim , Barak Orly , Zimmet Paul , Vishnevskia-Dai Vicktoria , Govrin Amanda , Agam Galila , Kronfeld-Schor Noga 
Published: August 2019

AbstractIt was recently suggested that the Metabolic Syndrome should be renamed to “Circadian Syndrome”. In this context, we explored the effects of living under standard laboratory conditions, where light is the only cycling variable (relevant to human modern life), in a diurnal mammal, on the relationships between affective-like pathology, type 2 diabetes mellitus (T2DM), and cardiac hypertrophy. After 20 weeks, some of the animals spontaneously developed T2DM, depressive and anxiety-like behavior and cardiac hypertrophy. There were significant correlations between levels of anxiety-like behavior and glucose tolerance, and between heart/total body weight ratio and glucose tolerance. Our data suggest a relationship between the development of T2DM, emotional and cardiac pathology as seen in diurnal humans. Furthermore, our data show a possible relationship between reduced daily cycling cues in the laboratory and what has been regularly termed “Metabolic Syndrome” and recently proposed by us to be renamed to “Circadian Syndrome”.
Suppression of gut dysbiosis by Bifidobacterium longum alleviates cognitive decline in 5XFAD transgenic and aged mice
Authors: Lee Hae-Ji , Lee Kyung-Eon , Kim Jeon-Kyung , Kim Dong-Hyun 
Published: August 2019

AbstractTo understand the role of commensal gut bacteria on the progression of cognitive decline in Alzheimer’s disease via the microbiota-gut-brain axis, we isolated anti-inflammatory Bifidobacterium longum (NK46) from human gut microbiota, which potently inhibited gut microbiota endotoxin production and suppressed NF-κB activation in lipopolysaccharide (LPS)-stimulated BV-2 cells, and examined whether NK46 could simultaneously alleviate gut dysbiosis and cognitive decline in male 5xFAD-transgenic (5XFAD-Tg, 6 months-old) and aged (18 months-old) mice. Oral administration of NK46 (1 × 109 CFU/mouse/day for 1 and 2 months in aged and Tg mice, respectively) shifted gut microbiota composition, particularly Proteobacteria, reduced fecal and blood LPS levels, suppressed NF-κB activation and TNF-α expression, and increased tight junction protein expression in the colon of 5XFAD-Tg and aged mice. NK46 treatment also alleviated cognitive decline in 5XFAD-Tg and aged mice. Furthermore, NK46 treatment suppressed amyloid-β, β/γ-secretases, and caspase-3 expression and amyloid-β accumulation in the hippocampus of 5XFAD-Tg mice. NK46 treatment also reduced Iba1+, LPS+/CD11b+, and caspase-3+/NeuN+ cell populations and suppressed NF-κB activation in the hippocampus of 5XFAD-Tg and aged mice, while BDNF expression was increased. These findings suggest that the suppression of gut dysbiosis and LPS production by NK46 can mitigate cognitive decline through the regulation of microbiota LPS-mediated NF-κB activation.