bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolomic Prediction of Human Prostate Cancer Aggressiveness: Magnetic Resonance Spectroscopy of Histologically Benign Tissue
Authors: Vandergrift Lindsey A. , Decelle Emily A. , Kurth Johannes , Wu Shulin , Fuss Taylor L. , DeFeo Elita M. , Halpern Elkan F. , Taupitz Matthias , McDougal W. Scott , Olumi Aria F. , Wu Chin-Lee , Cheng Leo L. 
Published: March 2018

AbstractProstate cancer alters cellular metabolism through events potentially preceding cancer morphological formation. Magnetic resonance spectroscopy (MRS)-based metabolomics of histologically-benign tissues from cancerous prostates can predict disease aggressiveness, offering clinically-translatable prognostic information. This retrospective study of 185 patients (2002–2009) included prostate tissues from prostatectomies (n = 365), benign prostatic hyperplasia (BPH) (n = 15), and biopsy cores from cancer-negative patients (n = 14). Tissues were measured with high resolution magic angle spinning (HRMAS) MRS, followed by quantitative histology using the Prognostic Grade Group (PGG) system. Metabolic profiles, measured solely from 338 of 365 histologically-benign tissues from cancerous prostates and divided into training-testing cohorts, could identify tumor grade and stage, and predict recurrence. Specifically, metabolic profiles: (1) show elevated myo-inositol, an endogenous tumor suppressor and potential mechanistic therapy target, in patients with highly-aggressive cancer, (2) identify a patient sub-group with less aggressive prostate cancer to avoid overtreatment if analysed at biopsy; and (3) subdivide the clinicopathologically indivisible PGG2 group into two distinct Kaplan-Meier recurrence groups, thereby identifying patients more at-risk for recurrence. Such findings, achievable by biopsy or prostatectomy tissue measurement, could inform treatment strategies. Metabolomics information can help transform a morphology-based diagnostic system by invoking cancer biology to improve evaluation of histologically-benign tissues in cancer environments.
Multilocus genetic profile in dopaminergic pathway modulates the striatum and working memory
Authors: Wang Chao , Liu Bing , Zhang Xiaolong , Cui Yue , Yu Chunshui , Jiang Tianzi 
Published: March 2018

AbstractDopamine is critical in pathophysiology and therapy of schizophrenia. Many studies have reported altered dopaminergic activity in the dorsal but not ventral striatum in schizophrenia. Based on the largest genome-wide association study of schizophrenia to date, we calculated the polygenic risk score (PGRS) of each subject in a healthy general group, including all variations in the set of functionally related genes involved in dopamine neurotransmitter system. We aimed to test whether the genetic variations in the dopaminergic pathway that have been identified as associated with schizophrenia are related to the function of the striatum and to working memory. We found that a higher PGRS was significantly associated with impairment in working memory. Moreover, resting-state functional connectivity analysis revealed that as the polygenic risk score increased, the connections between left putamen and caudate and the default mode network grew stronger, while the connections with the fronto-parietal network grew weaker. Our findings may shed light on the biological mechanism underlying the “dopamine hypothesis” of schizophrenia and provide some implications regarding the polygenic effects on the dopaminergic activity in the risk for schizophrenia.
A Poroelastic Model of a Fibrous-Porous Tissue Engineering Scaffold
Authors: Yuan Daniel , Somers Sarah M. , Grayson Warren L. , Spector Alexander A. 
Published: March 2018

AbstractTissue engineering scaffolds are used in conjunction with stem cells for the treatment of various diseases. A number of factors provided by the scaffolds affect the differentiation of stem cells. Mechanical cues that are part of the natural cellular microenvironment can both accelerate the differentiation toward particular cell lineages or induce differentiation to an alternative cell fate. Among such factors, there are externally applied strains and mechanical (stiffness and relaxation time) properties of the extracellular matrix. Here, the mechanics of a fibrous-porous scaffold is studied by applying a coordinated modeling and experimental approach. A force relaxation experiment is used, and a poroelastic model associates the relaxation process with the fluid diffusion through the fibrous matrix. The model parameters, including the stiffness moduli in the directions along and across the fibers as well as fluid diffusion time, are estimated by fitting the experimental data. The time course of the applied force is then predicted for different rates of loading and scaffold porosities. The proposed approach can help in a reduction of the technological and experimental efforts to produce 3-D scaffolds for regenerative medicine as well as in a higher accuracy of the estimation of the local factors sensed by stem cells.
Identification of highly effective target genes for RNAi-mediated control of emerald ash borer, Agrilus planipennis
Authors: Rodrigues Thais B. , Duan Jian J. , Palli Subba R. , Rieske Lynne K. 
Published: March 2018

AbstractRecent study has shown that RNA interference (RNAi) is efficient in emerald ash borer (EAB), Agrilus planipennis, and that ingestion of double-stranded RNA (dsRNA) targeting specific genes causes gene silencing and mortality in neonates. Here, we report on the identification of highly effective target genes for RNAi-mediated control of EAB. We screened 13 candidate genes in neonate larvae and selected the most effective target genes for further investigation, including their effect on EAB adults and on a non-target organism, Tribolium castaneum. The two most efficient target genes selected, hsp (heat shock 70-kDa protein cognate 3) and shi (shibire), caused up to 90% mortality of larvae and adults. In EAB eggs, larvae, and adults, the hsp is expressed at higher levels when compared to that of shi. Ingestion of dsHSP and dsSHI caused mortality in both neonate larvae and adults. Administration of a mixture of both dsRNAs worked better than either dsRNA by itself. In contrast, injection of EAB.dsHSP and EAB.dsSHI did not cause mortality in T. castaneum. Thus, the two genes identified cause high mortality in the EAB with no apparent phenotype effects in a non-target organism, the red flour beetle, and could be used in RNAi-mediated control of this invasive pest.
An integrated flow cytometry-based platform for isolation and molecular characterization of circulating tumor single cells and clusters
Authors: Bhagwat Neha , Dulmage Keely , Pletcher Charles H. , Wang Ling , DeMuth William , Sen Moen , Balli David , Yee Stephanie S. , Sa Silin , Tong Frances , Yu Liping , Moore Jonni S. , Stanger Ben Z. , Dixon Eric P. , Carpenter Erica L. 
Published: March 2018

AbstractComprehensive molecular analysis of rare circulating tumor cells (CTCs) and cell clusters is often hampered by low throughput and purity, as well as cell loss. To address this, we developed a fully integrated platform for flow cytometry-based isolation of CTCs and clusters from blood that can be combined with whole transcriptome analysis or targeted RNA transcript quantification. Downstream molecular signature can be linked to cell phenotype through index sorting. This newly developed platform utilizes in-line magnetic particle-based leukocyte depletion, and acoustic cell focusing and washing to achieve >98% reduction of blood cells and non-cellular debris, along with >1.5 log-fold enrichment of spiked tumor cells. We could also detect 1 spiked-in tumor cell in 1 million WBCs in 4/7 replicates. Importantly, the use of a large 200μm nozzle and low sheath pressure (3.5 psi) minimized shear forces, thereby maintaining cell viability and integrity while allowing for simultaneous recovery of single cells and clusters from blood. As proof of principle, we isolated and transcriptionally characterized 63 single CTCs from a genetically engineered pancreatic cancer mouse model (n = 12 mice) and, using index sorting, were able to identify distinct epithelial and mesenchymal sub-populations based on linked single cell protein and gene expression.
Tracing intensive fish and meat consumption using Zn isotope ratios: evidence from a historical Breton population (Rennes, France)
Authors: Jaouen Klervia , Colleter Rozenn , Pietrzak Anita , Pons Marie-Laure , Clavel Benoît , Telmon Norbert , Crubézy Éric , Hublin Jean-Jacques , Richards Michael P. 
Published: March 2018

AbstractHere we report Sr and Zn isotope ratios of teeth of medieval to early modern Breton people a population whose diet is known from historical, archeological and collagen isotope data. Most of the population, buried in the Dominican convent of Rennes, France, consists of parliamentary nobles, wealthy commoners and ecclesiastics, who had a diet rich in animal products. Our aim is to assess how the Zn isotope ratios of their teeth compare to those of other French historical populations previously studied, which were characterized by cereal-based diets, and those of modern French individuals, who daily eat animal products. We describe a clear offset (∼0.35‰) between local and non-local human individuals in Zn isotope ratios. The δ66Zntooth values of local individuals overlap that of modern French people, and are lower than those of local carnivores. Non-local δ66Zn values are similar to those of historical individuals analyzed previously. We conclude the lower Zn isotope ratios of local humans relative to the associated fauna can be explained by the consumption of carnivorous fish and pork, in agreement with historical, zooarchaeological and collagen (C, N, S) isotope data. Zn isotopes could therefore be a tracer of fish and/or substantial meat consumption in ancient populations.
Quantifying the propagation of distress and mental disorders in social networks
Authors: Scatà Marialisa , Di Stefano Alessandro , La Corte Aurelio , Liò Pietro 
Published: March 2018

AbstractHeterogeneity of human beings leads to think and react differently to social phenomena. Awareness and homophily drive people to weigh interactions in social multiplex networks, influencing a potential contagion effect. To quantify the impact of heterogeneity on spreading dynamics, we propose a model of coevolution of social contagion and awareness, through the introduction of statistical estimators, in a weighted multiplex network. Multiplexity of networked individuals may trigger propagation enough to produce effects among vulnerable subjects experiencing distress, mental disorder, which represent some of the strongest predictors of suicidal behaviours. The exposure to suicide is emotionally harmful, since talking about it may give support or inadvertently promote it. To disclose the complex effect of the overlapping awareness on suicidal ideation spreading among disordered people, we also introduce a data-driven approach by integrating different types of data. Our modelling approach unveils the relationship between distress and mental disorders propagation and suicidal ideation spreading, shedding light on the role of awareness in a social network for suicide prevention. The proposed model is able to quantify the impact of overlapping awareness on suicidal ideation spreading and our findings demonstrate that it plays a dual role on contagion, either reinforcing or delaying the contagion outbreak.
Cold Atmospheric Plasma Induces ATP-Dependent Endocytosis of Nanoparticles and Synergistic U373MG Cancer Cell Death
Authors: He Zhonglei , Liu Kangze , Manaloto Eline , Casey Alan , Cribaro George P. , Byrne Hugh J. , Tian Furong , Barcia Carlos , Conway Gillian E. , Cullen Patrick J. , Curtin James F. 
Published: March 2018

AbstractGold nanoparticles (AuNP) have potential as both diagnostic and therapeutic vehicles. However, selective targeting and uptake in cancer cells remains challenging. Cold atmospheric plasma (CAP) can be combined with AuNP to achieve synergistic anti-cancer cytotoxicity. To explore synergistic mechanisms, we demonstrate both rate of AuNP uptake and total amount accumulated in U373MG Glioblastoma multiforme (GBM) cells are significantly increased when exposed to 75 kV CAP generated by dielectric barrier discharge. No significant changes in the physical parameters of AuNP were caused by CAP but active transport mechanisms were stimulated in cells. Unlike many other biological effects of CAP, long-lived reactive species were not involved, and plasma-activated liquids did not replicate the effect. Chemical effects induced by direct and indirect exposure to CAP appears the dominant mediator of enhanced uptake. Transient physical alterations of membrane integrity played a minor role. 3D-reconstruction of deconvoluted confocal images confirmed AuNP accumulation in lysosomes and other acidic vesicles, which will be useful for future drug delivery and diagnostic strategies. Toxicity of AuNP significantly increased by 25-fold when combined with CAP. Our data indicate that direct exposure to CAP activates AuNP-dependent cytotoxicity by increasing AuNP endocytosis and trafficking to lysosomes in U373MG cells.
Whole Genome Resequencing of Capsicum baccatum and Capsicum annuum to Discover Single Nucleotide Polymorphism Related to Powdery Mildew Resistance
Authors: Ahn Yul-Kyun , Manivannan Abinaya , Karna Sandeep , Jun Tae-Hwan , Yang Eun-Young , Choi Sena , Kim Jin-Hee , Kim Do-Sun , Lee Eun-Su 
Published: March 2018

AbstractThe present study deals with genome wide identification of single-nucleotide polymorphism (SNP) markers related to powdery mildew (PM) resistance in two pepper varieties. Capsicum baccatum (PRH1- a PM resistant line) and Capsicum annuum (Saengryeg- a PM susceptible line), were resequenced to develop SNP markers. A total of 6,213,009 and 6,840,889 SNPs for PRH1 and Saengryeg respectively have been discovered. Among the SNPs, majority were classified as homozygous type SNPs, particularly in the resistant line. Moreover, the SNPs were differentially distributed among the chromosomes in both the resistant and susceptible lines. In total, 4,887,031 polymorphic SNP loci were identified between the two lines and 306,871 high-resolution melting (HRM) marker primer sets were designed. In order to understand the SNPs associated with the vital genes involved in diseases resistance and stress associated processes, chromosome-wise gene ontology analysis was performed. The results revealed the occurrence that SNPs related to diseases resistance genes were predominantly distributed in chromosome 4. In addition, 6281 SNPs associated with 46 resistance genes were identified. Among the lines, PRH1 consisted of maximum number of polymorphic SNPs related to NBS-LRR genes. The SNP markers were validated using HRM assay in 45 F4 populations and correlated with the phenotypic disease index.
Incongruent pitch cues are associated with increased activation and functional connectivity in the frontal areas
Authors: Lin Jo-Fu Lotus , Imada Toshiaki , Kuhl Patricia K. , Lin Fa-Hsuan 
Published: March 2018

AbstractPitch plays a crucial role in music and speech perception. Pitch perception is characterized by multiple perceptual dimensions, such as pitch height and chroma. Information provided by auditory signals that are related to these perceptual dimensions can be either congruent or incongruent. To create conflicting cues for pitch perception, we modified Shepard tones by varying the pitch height and pitch chroma dimensions in either the same or opposite directions. Our behavioral data showed that most listeners judged pitch changes based on pitch chroma, instead of pitch height, when incongruent information was provided. The reliance on pitch chroma resulted in a stable percept of upward or downward pitch shift, rather than alternating between two different percepts. Across the incongruent and congruent conditions, consistent activation was found in the bilateral superior temporal and inferior frontal areas. In addition, significantly stronger activation was observed in the inferior frontal areas during the incongruent compared to congruent conditions. Enhanced functional connectivity was found between the left temporal and bilateral frontal areas in the incongruent than congruent conditions. Increased intra-hemispheric and inter-hemispheric connectivity was also observed in the frontal areas. Our results suggest the involvement of the frontal lobe in top-down and bottom-up processes to generate a stable percept of pitch change with conflicting perceptual cues.
NF-kB2 Genetic Variations are Significantly Associated with Non-Small Cell Lung Cancer Risk and Overall Survival
Authors: Dimitrakopoulos Foteinos-Ioannis D. , Antonacopoulou Anna G. , Kottorou Anastasia E. , Maroussi Stella , Panagopoulos Nikolaos , Koukourikou Ioulia , Scopa Chrisoula , Kalofonou Melpomeni , Koutras Angelos , Makatsoris Thomas , Papadaki Helen , Dougenis Dimitrios , Brock Malcolm , Kalofonos Haralabos P. 
Published: March 2018

AbstractDuring the last decade, a growing number of publications implicate NF-kB2 in NSCLC pathogenesis. Here, we investigated the clinical relevance of NF-kB2 single nucleotide polymorphisms (SNPs) rs7897947, rs11574852 and rs12769316 in NSCLC and their association with NF-kB2 protein and mRNA levels. Our data show that TT (rs7897947T >G) and AA (rs12769316G >A) genotypes were strongly associated with an increased risk for NSCLC (P = 0.019 and P = 0.003, respectively). Additionally, in multivariate analysis, TT (rs7897947T >G) homozygosity was associated with worse 2- and 3-year survival rates (P = 0.030 and P = 0.028, respectively), especially among patients with stages III/IV, who had worse 2, 3 and 5-year survival (P = 0.001, P = 0.022 and P = 0.035, respectively). In chemotherapy-treated patients, TT (rs12769316G >A) homozygosity was also associated with worse 2- and 3-year survival compared to G allele carriers (P = 0.006 and P = 0.014, respectively). Furthermore, rs12769316 was correlated with survival outcome of stage I and II patients (P = 0.031 and P = 0.006, respectively). Interestingly, amongst the patients who developed metastases, A allele carriers had better 5-year survival (P = 0.020). In addition, rs12769316 was associated with NF-kB2 protein (P = 0.001) and mRNA expression (P = 0.017) as well as with tumor maximum diameter (P = 0.025). Overall, this study suggests that rs7897947 and rs12769316 are involved in NSCLC susceptibility, in treatment response and in clinical outcome.
First adequately-known quadrupedal sirenian from Eurasia (Eocene, Bay of Biscay, Huesca, northeastern Spain)
Authors: Díaz-Berenguer Ester , Badiola Ainara , Moreno-Azanza Miguel , Canudo José Ignacio 
Published: March 2018

AbstractSirenians are the only extant herbivorous mammals fully adapted to an aquatic lifestyle. They originated in Africa during the Paleocene from an undetermined clade of afrotherian mammals, and by the end of the Eocene they were widely distributed across the tropical latitudes. Here we introduce Sobrarbesiren cardieli gen. et sp. nov. It is the first adequately-known quadrupedal sirenian from Eurasia and the oldest record of this clade from western Europe. Fossils have been recovered from the middle Lutetian (SBZ15) site of Castejón de Sobrarbe-41 (Huesca, Spain), and comprise many cranial and postcranial remains, including pelvic girdle and hind limb bones, from at least six sirenian individuals of different ontogenetic stages. Sobrarbesiren shows a suite of characters previously considered synapomorphies of different clades of derived sirenians, such as the presence of the processus retroversus of the squamosal and the pterygoid fossa, combined with ancestral characters such as the presence of an alisphenoid canal, a permanent P5, at least two sacral vertebrae, a primitive pelvis and functional femora and fibulae. Sobrarbesiren is recovered as the sister taxon of Dugongidae and represents a transitional stage of adaptation to aquatic life between the amphibious quadrupedal prorastomids and the aquatic quadrupedal protosirenids.
Coherent all-optical transistor based on frustrated total internal reflection
Authors: Goodarzi A. , Ghanaatshoar M. 
Published: March 2018

AbstractThis study aims to design an all-optical transistor based on tunneling of light through frustrated total internal reflection. Under total internal reflection, the electromagnetic wave penetrates into the lower index medium. If a medium with high refractive index is placed close to the boundary of the first one, a portion of light leaks into the second medium. The penetrated electromagnetic field distribution can be influenced by another coherent light in the low refractive index medium via interference, leading to light amplification. Upon this technique, we introduce coherent all-optical transistors based on photonic crystal structures. Subsequently, we inspect the shortest pulse which is amplified by the designed system and also its terahertz repetition rate. We will show that such a system can operate in a cascade form. Operating in terahertz range and the amplification efficiency of around 20 are of advantages of this system.
RNA-Seq identifies genes whose proteins are transformative in the differentiation of cytotrophoblast to syncytiotrophoblast, in human primary villous and BeWo trophoblasts
Authors: Azar Christopher , Valentine Mark , Trausch-Azar Julie , Druley Todd , Nelson D. Michael , Schwartz Alan L. 
Published: March 2018

AbstractThe fusion of villous cytotrophoblasts into the multinucleated syncytiotrophoblast is critical for the essential functions of the mammalian placenta. Using RNA-Seq gene expression and quantitative protein expression, we identified genes and their cognate proteins which are coordinately up- or down-regulated in two cellular models of cytotrophoblast to syncytiotrophoblast development, human primary villous and human BeWo cytotrophoblasts. These include hCGβ, TREML2, PAM, CRIP2, INHA, FLRG, SERPINF1, C17orf96, KRT17 and SAA1. These findings provide avenues for further understanding the mechanisms underlying mammalian placental synctiotrophoblast development.
Mesoproterozoic juvenile crust in microcontinents of the Central Asian Orogenic Belt: evidence from oxygen and hafnium isotopes in zircon
Authors: He Zhen-Yu , Klemd Reiner , Yan Li-Li , Lu Tian-Yu , Zhang Ze-Ming 
Published: March 2018

AbstractWe report in situ O and Hf isotope data of zircon grains from coeval Mesoproterozoic (ca. 1.4 Ga) igneous metamafic (amphibolite) and granitic rocks of the Chinese Central Tianshan microcontinent (CTM) in the southern Central Asian Orogenic Belt (CAOB). Zircon grains from amphibolite have mantle-like δ18OVSMOW values of 4.7–5.6‰ and juvenile Hf isotopic compositions (εHf(t) = 8.4–15.3; TDMC = 1.57–1.22 Ga), whereas those from granitic rocks have δ18OVSMOW values of 5.6–7.0‰ and evolved Hf isotopic compositions (εHf(t) = −1.0–8.2; TDMC = 2.09–1.62 Ga). Zircon O–Hf isotopic compositions of the metamafic and granitic rocks provide evidence for Mesoproterozoic (ca. 1.4 Ga) crustal growth and a substantial Palaeoproterozoic supracrustal component in the CTM. These findings and previous studies, reporting ca. 1.4 Ga magmatic rocks from other microcontinents of the CAOB, suggest that a large belt of Mesoproterozoic (ca. 1.4 Ga) juvenile continental crust formed in a continental terrane, fragments of which now occur over a distance of more than a thousand kilometres in the southern CAOB.