bluuebunny/crossref_metadata_2025_split huggingface dataset:
Illusory occlusion affects stereoscopic depth perception
Authors: Chen Zhimin , Denison Rachel N. , Whitney David , Maus Gerrit W. 
Published: March 2018

AbstractWhen occlusion and binocular disparity cues conflict, what visual features determine how they combine? Sensory cues, such as T-junctions, have been suggested to be necessary for occlusion to influence stereoscopic depth perception. Here we show that illusory occlusion, with no retinal sensory cues, interacts with binocular disparity when perceiving depth. We generated illusory occlusion using stimuli filled in across the retinal blind spot. Observers viewed two bars forming a cross with the intersection positioned within the blind spot. One of the bars was presented binocularly with a disparity signal; the other was presented monocularly, extending through the blind spot, with no defined disparity. When the monocular bar was perceived as filled in through the blind spot, it was perceived as occluding the binocular bar, generating illusory occlusion. We found that this illusory occlusion influenced perceived stereoscopic depth: depth estimates were biased to be closer or farther, depending on whether a bar was perceived as in front of or behind the other bar, respectively. Therefore, the perceived relative depth position, based on filling-in cues, set boundaries for interpreting metric stereoscopic depth cues. This suggests that filling-in can produce opaque surface representations that can trump other depth cues such as disparity.
Factors associated with cognitive impairment in elderly versus nonelderly patients with metabolic syndrome: the different roles of FGF21
Authors: Phrommintikul Arintaya , Sa-nguanmoo Piangkwan , Sripetchwandee Jirapas , Vathesatogkit Prin , Chattipakorn Nipon , Chattipakorn Siriporn C. 
Published: March 2018

AbstractIncreased fibroblast growth factor 21 (FGF21) levels have been found in patients with metabolic syndrome (MetS). MetS is also associated with cognitive decline. However, the correlation between FGF21 and cognitive decline in elderly and nonelderly MetS patients has not been investigated. 116 non-elderly patients (age <65 years old) and 96 elderly patients (≥65 years old) with MetS were enrolled. Blood samples for FGF21 were collected from all participants after 12-hour fasting. Cognitive function was assessed using the Montreal cognitive assessment (MoCA) test. The MoCA score was negatively associated with age and was different among different levels of education in these MetS patients. In the non-elderly group, body mass index (BMI) showed positively correlated with MoCA score while, FGF21 level and HbA1C were negatively associated with the MoCA score in non-elderly MetS patients. BMI was the only factor which showed a negative correlation with the MoCA score in elderly MetS patients. This study demonstrated that FGF21 level was independently associated with cognitive impairment in non-elderly patients but not in elderly patients. The possible role of FGF21 level in cognitive impairment in non-elderly should be confirmed in a prospective study.
Occupational and leisure time physical inactivity and the risk of type II diabetes and hypertension among Mexican adults: A prospective cohort study
Authors: Medina C. , Janssen I. , Barquera S. , Bautista-Arredondo S. , González M. E. , González C. 
Published: March 2018

AbstractThere is a lack of longitudinal data linking physical inactivity and chronic diseases among Mexicans. Objective. To examine the relationship between total, leisure and occupational moderate-to-vigorous physical activity (MVPA) and incidence of type II diabetes (T2D) and hypertension in the Mexico City Diabetes Study. Study design and population. A prospective cohort study was conducted from 1989 to 2009 among 2282 men and non-pregnant women residing in six low-income neighborhoods in Mexico City. Main outcome. Incidence of T2D and hypertension. Results. After controlling for confounders, <1 MET/min/week of MVPA during leisure time was associated with higher risk of hypertension (HR 1.29, CI 95% 1.01, 1.66) and T2D (HR 1.31 CI 95% 1.00, 1.74). In addition, accumulating <1 MET/min/week of occupational MVPA was associated with higher risk of hypertension (HR 1.47, CI 95% 1.13, 1.90). Conclusion. The absence of leisure and occupational MVPA was associated with an increased risk of hypertension. However, no associations were found between occupational MVPA and T2D.
Spin density wave instability in a ferromagnet
Authors: Wu Yan , Ning Zhenhua , Cao Huibo , Cao Guixin , Benavides Katherine A. , Karna S. , McCandless Gregory T. , Jin R. , Chan Julia Y. , Shelton W. A. , DiTusa J. F. 
Published: March 2018

AbstractDue to its cooperative nature, magnetic ordering involves a complex interplay between spin, charge, and lattice degrees of freedom, which can lead to strong competition between magnetic states. Binary Fe3Ga4is one such material that exhibits competing orders having a ferromagnetic (FM) ground state, an antiferromagnetic (AFM) behavior at intermediate temperatures, and a conspicuous re-entrance of the FM state at high temperature. Through a combination of neutron diffraction experiments and simulations, we have discovered that the AFM state is an incommensurate spin-density wave (ISDW) ordering generated by nesting in the spin polarized Fermi surface. These two magnetic states, FM and ISDW, are seldom observed in the same material without application of a polarizing magnetic field. To date, this unusual mechanism has never been observed and its elemental origins could have far reaching implications in many other magnetic systems that contain strong competition between these types of magnetic order. Furthermore, the competition between magnetic states results in a susceptibility to external perturbations allowing the magnetic transitions in Fe3Ga4to be controlled via temperature, magnetic field, disorder, and pressure. Thus, Fe3Ga4has potential for application in novel magnetic memory devices, such as the magnetic components of tunneling magnetoresistance spintronics devices.
Innate immune system activation in zebrafish and cellular models of Diamond Blackfan Anemia
Authors: Danilova Nadia , Wilkes Mark , Bibikova Elena , Youn Min-Young , Sakamoto Kathleen M. , Lin Shuo 
Published: March 2018

AbstractDeficiency of ribosomal proteins (RPs) leads to Diamond Blackfan Anemia (DBA) associated with anemia, congenital defects, and cancer. While p53 activation is responsible for many features of DBA, the role of immune system is less defined. The Innate immune system can be activated by endogenous nucleic acids from non-processed pre-rRNAs, DNA damage, and apoptosis that occurs in DBA. Recognition by toll like receptors (TLRs) and Mda5-like sensors induces interferons (IFNs) and inflammation. Dying cells can also activate complement system. Therefore we analyzed the status of these pathways in RP-deficient zebrafish and found upregulation of interferon, inflammatory cytokines and mediators, and complement. We also found upregulation of receptors signaling to IFNs including Mda5, Tlr3, and Tlr9. TGFb family member activin was also upregulated in RP-deficient zebrafish and in RPS19-deficient human cells, which include a lymphoid cell line from a DBA patient, and fetal liver cells and K562 cells transduced with RPS19 shRNA. Treatment of RP-deficient zebrafish with a TLR3 inhibitor decreased IFNs activation, acute phase response, and apoptosis and improved their hematopoiesis and morphology. Inhibitors of complement and activin also had beneficial effects. Our studies suggest that innate immune system contributes to the phenotype of RPS19-deficient zebrafish and human cells.
Sample-Index Misassignment Impacts Tumour Exome Sequencing
Authors: Vodák Daniel , Lorenz Susanne , Nakken Sigve , Aasheim Lars Birger , Holte Harald , Bai Baoyan , Myklebost Ola , Meza-Zepeda Leonardo A. , Hovig Eivind 
Published: March 2018

AbstractSample pooling enabled by dedicated indexes is a common strategy for cost-effective and robust high-throughput sequencing. Index misassignment leading to mutual contamination between pooled samples has however been described as a general problem of the latest Illumina sequencing instruments utilizing exclusion amplification. Using real-life data from multiple tumour sequencing projects, we demonstrate that index misassignment can induce artefactual variant calls closely resembling true, high-quality somatic variants. These artefactual calls potentially impact cancer applications utilizing low allelic frequencies, such as in clonal analysis of tumours. We discuss the available countermeasures with an emphasis on improved library indexing methods, and provide software that can assist in the identification of variants that may be consequences of index misassignment.
Identification of Urinary Activin A as a Novel Biomarker Reflecting the Severity of Acute Kidney Injury
Authors: Takahashi Shunsuke , Nakasatomi Masao , Takei Yoshinori , Ikeuchi Hidekazu , Sakairi Toru , Kaneko Yoriaki , Hiromura Keiju , Nojima Yoshihisa , Maeshima Akito 
Published: March 2018

AbstractAcute kidney injury (AKI) is a common but complex condition that is associated with increased morbidity and mortality. In the present study, we examined whether urinary activin A, a member of the TGF-beta superfamily, is present in mice with ischemia-reperfusion injury and in humans with AKI, as well as its potential as a biomarker for AKI. Expression of activin A was markedly increased in ischemic mouse kidneys. In situ hybridization demonstrated that activin mRNA was expressed in tubular cells of ischemic kidneys but not of normal kidneys. Immunoreactive activin A, which was absent in normal kidneys, was detected in the cytoplasm of proximal tubular cells in ischemic kidneys. Activin A was undetectable in the urine of normal mice. In contrast, activin A was significantly increased in the urine of ischemic mice at 3 h after reperfusion. Urinary activin A levels increased according to the period of ischemia. In humans, urinary activin A was almost undetectable in healthy volunteers and in patients with pre-renal AKI, but was significantly increased in patients with renal AKI. There was no significant correlation between urinary activin A and serum activin A. Collectively, urinary activin A might be a useful biomarker reflecting the severity of AKI.
Furin inhibitor protects against neuronal cell death induced by activated NMDA receptors
Authors: Yamada Mariko , Hayashi Hideki , Yuuki Moe , Matsushima Nahoko , Yuan Bo , Takagi Norio 
Published: March 2018

AbstractThe proprotein convertases (PCs) act as serine proteases and are known to convert diverse precursor proteins into their active forms. Among the PCs, furin has been considered to play a crucial role not only in embryogenesis, but also in the initiation and progression of certain pathologic conditions. However, the roles played by furin with respect to neuronal cell injuries remain to be determined. An excessive influx of Ca2+ through the N-methyl-d-aspartate (NMDA) receptor has been associated with diverse neurological and neurodegenerative disorders. The aim of this study was to achieve further insight into the pathophysiologic roles of furin in cultured cortical neurons. We demonstrated that furin inhibitors dose-dependently prevented neuronal injury induced by NMDA treatment. Neuronal injury induced by NMDA treatment was attenuated by the calpain inhibitor calpeptin. And the increase observed in the activity of calpain after NMDA treatment was significantly inhibited by these furin inhibitors. Furthermore, calpain-2 activity, which was evaluated by means of the immunoblotting assay, was increased by NMDA treatment. It was noteworthy that this increased activity was almost completely inhibited by a furin inhibitor. Our findings suggested that furin is involved in NMDA-induced neuronal injury by acting upstream of calpain.
Dynamic Evolution of α-Gliadin Prolamin Gene Family in Homeologous Genomes of Hexaploid Wheat
Authors: Huo Naxin , Zhu Tingting , Altenbach Susan , Dong Lingli , Wang Yi , Mohr Toni , Liu Zhiyong , Dvorak Jan , Luo Ming-Cheng , Gu Yong Q. 
Published: March 2018

AbstractWheat Gli-2 loci encode complex groups of α-gliadin prolamins that are important for breadmaking, but also major triggers of celiac disease (CD). Elucidation of α-gliadin evolution provides knowledge to produce wheat with better end-use properties and reduced immunogenic potential. The Gli-2 loci contain a large number of tandemly duplicated genes and highly repetitive DNA, making sequence assembly of their genomic regions challenging. Here, we constructed high-quality sequences spanning the three wheat homeologous α-gliadin loci by aligning PacBio-based sequence contigs with BioNano genome maps. A total of 47 α-gliadin genes were identified with only 26 encoding intact full-length protein products. Analyses of α-gliadin loci and phylogenetic tree reconstruction indicate significant duplications of α-gliadin genes in the last ~2.5 million years after the divergence of the A, B and D genomes, supporting its rapid lineage-independent expansion in different Triticeae genomes. We showed that dramatic divergence in expression of α-gliadin genes could not be attributed to sequence variations in the promoter regions. The study also provided insights into the evolution of CD epitopes and identified a single indel event in the hexaploid wheat D genome that likely resulted in the generation of the highly toxic 33-mer CD epitope.
Microbiota Composition May Predict Anti-Tnf Alpha Response in Spondyloarthritis Patients: an Exploratory Study
Authors: Bazin Thomas , Hooks Katarzyna B. , Barnetche Thomas , Truchetet Marie-Elise , Enaud Raphaël , Richez Christophe , Dougados Maxime , Hubert Christophe , Barré Aurélien , Nikolski Macha , Schaeverbeke Thierry 
Published: March 2018

AbstractSpondyloarthritis (SpA) pathophysiology remains largely unknown. While the association with genetic factors has been established for decades, the influence of gut microbiota is only an emerging direction of research. Despite the remarkable efficacy of anti-TNF-α treatments, non-responders are frequent and no predictive factors of patient outcome have been identified. Our objective was to investigate the modifications of intestinal microbiota composition in patients suffering from SpA three months after an anti-TNF-α treatment. We performed 16S rDNA sequencing of 38 stool samples from 19 spondyloarthritis patients before and three months after anti-TNF-α treatment onset. SpA activity was assessed at each time using ASDAS and BASDAI scores. Some modifications of the microbiota composition were observed after three months of anti-TNF-α treatment, but no specific taxon was modified, whatever the clinical response. We identified a particular taxonomic node before anti-TNF-α treatment that can predict the clinical response as a biomarker, with a higher proportion of Burkholderiales order in future responder patients. This study suggests a cross-influence between anti-TNF-α treatment and intestinal microbiota. If its results are confirmed on larger groups of patients, it may pave the way to the development of predictive tests suitable for clinical practices.
Improvement of physical properties of calcium phosphate cement by elastin-like polypeptide supplementation
Authors: Jang Ji-Hyun , Shin Sumi , Kim Hyun-Jung , Jeong Jinyoung , Jin Hyo-Eon , Desai Malav S. , Lee Seung-Wuk , Kim Sun-Young 
Published: March 2018

AbstractCalcium phosphate cements (CPCs) are synthetic bioactive cements widely used as hard tissue substitutes. Critical limitations of use include their poor mechanical properties and poor anti-washout behaviour. To address those limitations, we combined CPC with genetically engineered elastin-like polypeptides (ELPs). We investigated the effect of the ELPs on the physical properties and biocompatibility of CPC by testing ELP/CPC composites with various liquid/powder ratios. Our results show that the addition of ELPs improved the mechanical properties of the CPC, including the microhardness, compressive strength, and washout resistance. The biocompatibility of ELP/CPC composites was also comparable to that of the CPC alone. However, supplementing CPC with ELPs functionalized with octaglutamate as a hydroxyapatite binding peptide increased the setting time of the cement. With further design and modification of our biomolecules and composites, our research will lead to products with diverse applications in biology and medicine.
Antidepressant drug-specific prediction of depression treatment outcomes from genetic and clinical variables
Authors: Iniesta Raquel , Hodgson Karen , Stahl Daniel , Malki Karim , Maier Wolfgang , Rietschel Marcella , Mors Ole , Hauser Joanna , Henigsberg Neven , Dernovsek Mojca Zvezdana , Souery Daniel , Dobson Richard , Aitchison Katherine J. , Farmer Anne , McGuffin Peter , Lewis Cathryn M. , Uher Rudolf 
Published: March 2018

AbstractIndividuals with depression differ substantially in their response to treatment with antidepressants. Specific predictors explain only a small proportion of these differences. To meaningfully predict who will respond to which antidepressant, it may be necessary to combine multiple biomarkers and clinical variables. Using statistical learning on common genetic variants and clinical information in a training sample of 280 individuals randomly allocated to 12-week treatment with antidepressants escitalopram or nortriptyline, we derived models to predict remission with each antidepressant drug. We tested the reproducibility of each prediction in a validation set of 150 participants not used in model derivation. An elastic net logistic model based on eleven genetic and six clinical variables predicted remission with escitalopram in the validation dataset with area under the curve 0.77 (95%CI; 0.66-0.88; p = 0.004), explaining approximately 30% of variance in who achieves remission. A model derived from 20 genetic variables predicted remission with nortriptyline in the validation dataset with an area under the curve 0.77 (95%CI; 0.65-0.90; p < 0.001), explaining approximately 36% of variance in who achieves remission. The predictive models were antidepressant drug-specific. Validated drug-specific predictions suggest that a relatively small number of genetic and clinical variables can help select treatment between escitalopram and nortriptyline.
Urinary CE-MS peptide marker pattern for detection of solid tumors
Authors: Belczacka Iwona , Latosinska Agnieszka , Siwy Justyna , Metzger Jochen , Merseburger Axel S. , Mischak Harald , Vlahou Antonia , Frantzi Maria , Jankowski Vera 
Published: March 2018

AbstractUrinary profiling datasets, previously acquired by capillary electrophoresis coupled to mass-spectrometry were investigated to identify a general urinary marker pattern for detection of solid tumors by targeting common systemic events associated with tumor-related inflammation. A total of 2,055 urinary profiles were analyzed, derived from a) a cancer group of patients (n = 969) with bladder, prostate, and pancreatic cancers, renal cell carcinoma, and cholangiocarcinoma and b) a control group of patients with benign diseases (n = 556), inflammatory diseases (n = 199) and healthy individuals (n = 331). Statistical analysis was conducted in a discovery set of 676 cancer cases and 744 controls. 193 peptides differing at statistically significant levels between cases and controls were selected and combined to a multi-dimensional marker pattern using support vector machine algorithms. Independent validation in a set of 635 patients (293 cancer cases and 342 controls) showed an AUC of 0.82. Inclusion of age as independent variable, significantly increased the AUC value to 0.85. Among the identified peptides were mucins, fibrinogen and collagen fragments. Further studies are planned to assess the pattern value to monitor patients for tumor recurrence. In this proof-of-concept study, a general tumor marker pattern was developed to detect cancer based on shared biomarkers, likely indicative of cancer-related features.
Two-dimensional analysis provides molecular insight into flower scent of Lilium ‘Siberia’
Authors: Shi Shaochuan , Duan Guangyou , Li Dandan , Wu Jie , Liu Xintong , Hong Bo , Yi Mingfang , Zhang Zhao 
Published: March 2018

AbstractLily is a popular flower around the world not only because of its elegant appearance, but also due to its appealing scent. Little is known about the regulation of the volatile compound biosynthesis in lily flower scent. Here, we conducted an approach combining two-dimensional analysis and weighted gene co-expression network analysis (WGCNA) to explore candidate genes regulating flower scent production. In the approach, changes of flower volatile emissions and corresponding gene expression profiles at four flower developmental stages and four circadian times were both captured by GC-MS and RNA-seq methods. By overlapping differentially-expressed genes (DEGs) that responded to flower scent changes in flower development and circadian rhythm, 3,426 DEGs were initially identified to be candidates for flower scent production, of which 1,270 were predicted as transcriptional factors (TFs). The DEGs were further correlated to individual flower volatiles by WGCNA. Finally, 37, 41 and 90 genes were identified as candidate TFs likely regulating terpenoids, phenylpropanoids and fatty acid derivatives productions, respectively. Moreover, by WGCNA several genes related to auxin, gibberellins and ABC transporter were revealed to be responsible for flower scent production. Thus, this strategy provides an important foundation for future studies on the molecular mechanisms involved in floral scent production.
Evaluation of TRMM 3B43 data over the Yangtze River Delta of China
Authors: Cao Yueqian , Zhang Wu , Wang Wenjing 
Published: March 2018

AbstractTropical Rainfall Measuring Mission (TRMM) 3B43 rainfall products during the period of 1998~2016 are evaluated via monthly and yearly precipitation data from 56 observational stations over the Yangtze River Delta (YRD). The results are as follows: (1) annual rainfall increases gradually from northwest to southwest and monthly precipitation surges sharply, owing to rainband’s abrupt pushing north caused by the westward and northward extension of Western Pacific Subtropical High, to 200 mm/month in July; (2) only seized by the TRMM, the developing process of ChunAn precipitation center synchronizes with monthly precipitation series that may recycle throughout the year; (3) 3B43 data are inclined to overestimate precipitation but performs the best (relative bias ranging within −10~10%) at most parts of the YRD zone; and its correlation coefficient with observation is 0.88 in annual scale; for monthly scale, CC peaks in March (0.96) and reaches the bottom (0.79) in August; (4) no evident connection between CC and elevation is found in the 3B43 annual rainfall products which estimate precipitation better upon urban land. This paper is of importance in understanding the impacts of complex topography and landcovers on the precipitation assessment in a river delta scale.