bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of the effects of irrigation and fertilization on tomato fruit yield and quality: a principal component analysis
Authors: Wang Xiukang , Xing Yingying 
Published: March 2017

AbstractIrrigation and fertilization are key practices for improving the fruit quality and yield of vegetables grown in greenhouses. We carried out an experiment in a solar greenhouse spanning three consecutive growing seasons to evaluate the effects of irrigation and fertilization on the fruit yield and quality, water use efficiency (WUE) and fertilizer partial factor productivity (PFP) of tomatoes. Interactions between irrigation and fertilization treatments and individual factors of irrigation and fertilization significantly (p < 0.01) affected fruit yield, WUE and PFP. WUE and fruit yield and quality were more sensitive to changes in irrigation than to changes in fertilizer, but PFP showed the opposite trend. Interestingly, the treatment with moderate irrigation (W2: 75% ET
0
) and high fertilizer level (F1: 240N−120P2O5−150K2O kg ha−1) was twice ranked first after a combinational evaluation. In conclusion, the proper application of drip fertigation (W2F1) may be a good compromise for solar greenhouse-grown tomatoes with regard to fruit yield and quality, WUE, and PFP. The present study sheds light on the contributions of these practices, clarifies their impacts, and provides a basis for evaluating and selecting better management practices for growing greenhouse vegetables.
Developmental Whole Brain White Matter Alterations in Transgenic Huntington’s Disease Monkey
Authors: Meng Yuguang , Jiang Jie , Bachevalier Jocelyne , Zhang Xiaodong , Chan Anthony W. S. 
Published: March 2017

AbstractTransgenic Huntington’s disease monkey (HD monkey) model provides great opportunity for studying disease progression that could lead to new insight for developing biomarker, early intervention and novel therapeutics. Whole brain white matter integrity of HD-monkeys was examined longitudinally from 6 to 48 months using diffusion tensor imaging (DTI) and tract-based spatial statistics (TBSS). Progressive developmental white matter alterations in HD monkeys were widespread and were observed not only in fiber bundles connecting cortical areas to the striatum (e.g. striatal bundle and external capsule), but also in long association fiber pathways, commissural fibers, and subcortical fiber bundle. In all fiber tracts, the data indicate an arrest in white matter development around 23 months followed by slight decline until adulthood in HD monkeys. The microstructural changes parallel the progressive motor, memory and cognitive decline previously reported as HD monkeys aged. The findings revealed the widespread progressive temporal-spatial microstructural changes in HD monkey brains from infancy to adulthood, suggesting differentiated degenerations across different brain areas during brain development.
Internal valence modulates the speed of object recognition
Authors: Panichello Matthew F. , Kveraga Kestutis , Chaumon Maximilien , Bar Moshe , Barrett Lisa Feldman 
Published: March 2017

AbstractBrain regions that process affect are strongly connected with visual regions, but the functional consequences of this structural organization have been relatively unexplored. How does the momentary affect of an observer influence perception? We induced either pleasant or unpleasant affect in participants and then recorded their neural activity using magnetoencephalography while they completed an object recognition task. We hypothesized, and found, that affect influenced the speed of object recognition by modulating the speed and amplitude of evoked responses in occipitotemporal cortex and regions important for representing affect. Furthermore, affect modulated functional interactions between affective and perceptual regions early during perceptual processing. These findings indicate that affect can serve as an important contextual influence on object recognition processes.
Kaposi’s sarcoma-associated herpesvirus ORF34 is essential for late gene expression and virus production
Authors: Nishimura Mayu , Watanabe Tadashi , Yagi Syota , Yamanaka Takahiro , Fujimuro Masahiro 
Published: March 2017

AbstractKaposi’s sarcoma-associated herpesvirus (KSHV) is the causative agent of Kaposi’s sarcoma, primary effusion lymphoma, and multicentric Castleman’s disease. KSHV establishes a life-long infection in its host and alternates between a latent and lytic infection state. During lytic infection, lytic-related genes are expressed in a temporal manner and categorized as immediate early, early, and late gene transcripts. ORF34 is an early-late gene that interacts with several viral transcription-associated factors, however its physiological importance remains poorly understood. Here, we investigated the role of ORF34 during KSHV infection by generating ORF34-deficient KSHV, using a bacterial artificial chromosome system. Our results reveal that ORF34-deficient KSHV exhibited significantly attenuated late gene expression and viral production but did not affect viral DNA replication. ORF34 interacted with transcription factors ORF18, ORF24, ORF31, and ORF66, and a novel ORF34-interaction partner, ORF23. The C-terminal region of ORF34 was important for interaction with ORF24 and viral production. Our data support a model, in which ORF34 serves as a hub for recruiting a viral transcription complex to ORF24 to promote late viral gene expression.
Co-expression of BirA with biotin bait achieves in vivo biotinylation of overexpressed stable N-glycosylated sRAGE in transgenic silkworms
Authors: Kumano-Kuramochi Miyuki , Tatematsu Ken-ichiro , Ohnishi-Kameyama Mayumi , Maeda-Yamamoto Mari , Kobori Toshiro , Sezutsu Hideki , Machida Sachiko 
Published: March 2017

AbstractHere, we demonstrated the expression of the N-glycosylated extracellular ligand binding domain of receptor for advanced glycation end products (sRAGE) in middle silk glands (MSGs) of transgenic silkworms using the GAL4/UAS system. Over 1 mg of sRAGE was obtained from one transgenic silkworm. sRAGE purified from the silkworm exhibited good stability and maintained specific ligand-binding ability. In addition, N-glycan analysis of sRAGE revealed that N-glucan completely lacked potentially allergenic fucose. Moreover, co-expression of biotin ligase (BirA) with C-terminal BioEase-tagged sRAGE in MSGs resulted in efficient biotinylation of sRAGE after addition of biotin bait. C-terminal biotinylated sRAGE could be immobilized onto a solid surface in one direction through binding to streptavidin without any loss of ability. The dissociation constant of sRAGE with fructose-BSA, a typical RAGE ligand, was 7.25 × 10−7 M, consistent with that on the mammalian cell surface. Thus, we developed a novel, innovative silkworm expression system for efficient expression of recombinant sRAGE, which could serve as a basis for the elucidation of RAGE-ligand interactions and facilitate the search for new ligands and inhibitors.
PET Radiomics in NSCLC: state of the art and a proposal for harmonization of methodology
Authors: Sollini M. , Cozzi L. , Antunovic L. , Chiti A. , Kirienko M. 
Published: March 2017

AbstractImaging with positron emission tomography (PET)/computed tomography (CT) is crucial in the management of cancer because of its value in tumor staging, response assessment, restaging, prognosis and treatment responsiveness prediction. In the last years, interest has grown in texture analysis which provides an “in-vivo” lesion characterization, and predictive information in several malignances including NSCLC; however several drawbacks and limitations affect these studies, especially because of lack of standardization in features calculation, definitions and methodology reporting. The present paper provides a comprehensive review of literature describing the state-of-the-art of FDG-PET/CT texture analysis in NSCLC, suggesting a proposal for harmonization of methodology.
TP53 Arg72Pro, mortality after cancer, and all-cause mortality in 105,200 individuals
Authors: Kodal Jakob B. , Vedel-Krogh Signe , Kobylecki Camilla J. , Nordestgaard Børge G. , Bojesen Stig E. 
Published: March 2017

AbstractRs1042522 (Arg72Pro) is a functional polymorphism of TP53. Pro72 has been associated with lower all-cause mortality and lower mortality after cancer. We hypothesized that TP53 Pro72 is associated with lower mortality after cancer, lower all-cause mortality, and with increased cancer incidence in the general population in a contemporary cohort. We genotyped 105,200 individuals aged 20–100 years from the Copenhagen General Population Study, recruited in 2003–2013, and followed them in Danish health registries. During follow-up 5,531 individuals died and 5,849 developed cancer. Hazard ratios for mortality after cancer were 1.03 (95% confidence interval:0.93–1.15) for Arg/Pro and 0.96 (95% CI:0.79–1.18) for Pro/Pro versus Arg/Arg. Hazard ratios for all-cause mortality were 0.99 (95% CI:0.93–1.04) for Arg/Pro and 1.09 (95% CI:0.98–1.21) for Pro/Pro versus Arg/Arg. Risk of cancer specific mortality, cardiovascular mortality, and respiratory mortality were not associated with Arg72Pro genotype overall; however, in exploratory subgroup analyses, genotype-associated risks of malignant melanoma and diabetes were altered. Considering multiple comparisons the latter findings may represent play of chance. The TP53 Arg72Pro genotype was not associated with mortality after cancer, all-cause mortality, or cancer incidence in the general population in a contemporary cohort. Our main conclusion is therefore a lack of reproducing an effect of TP53 Arg72Pro genotype on mortality.
Combination of Electroencephalography and Near-Infrared Spectroscopy in Evaluation of Mental Concentration during the Mental Focus Task for Wisconsin Card Sorting Test
Authors: Chen Che-Wei , Sun Chia-Wei 
Published: March 2017

AbstractNear-infrared spectroscopy (NIRS) is a noninvasive neuroimaging tool for measuring evoked functional changes in brain oxygenation. Electroencephalography (EEG) can be used to evaluate the functionality of cortical connections and obtain information on regional cortical activity. Coregistration of EEG–NIRS is a recent technique that has been applied for measuring changes in electrical and hemodynamic activity in the human brain. EEG–NIRS coregistration facilitates the avoidance of misleading interpretations of NIRS, particularly in the diagnosis of neurological disorders. In this study, we investigated an approach for enhancing accuracy of NIRS by using EEG to monitor physiological activity during a mental focus task. Using the Wisconsin Card Sorting Test for the subjects mental focus task, we identified two trend types in the EEG and NIRS signals of normal subjects. These data can assist in understanding brain activation statuses and enable determining subjects’ degree of mental concentration. If the data can be standardized for the diagnosis of neurological disorders, they can provide a new index to improve traditional methods (e.g., questionnaires) to assist clinical doctors in diagnosing cognitive disorders.
Exploring Approaches for Detecting Protein Functional Similarity within an Orthology-based Framework
Authors: Weichenberger Christian X. , Palermo Antonia , Pramstaller Peter P. , Domingues Francisco S. 
Published: March 2017

AbstractProtein functional similarity based on gene ontology (GO) annotations serves as a powerful tool when comparing proteins on a functional level in applications such as protein-protein interaction prediction, gene prioritization, and disease gene discovery. Functional similarity (FS) is usually quantified by combining the GO hierarchy with an annotation corpus that links genes and gene products to GO terms. One large group of algorithms involves calculation of GO term semantic similarity (SS) between all the terms annotating the two proteins, followed by a second step, described as “mixing strategy”, which involves combining the SS values to yield the final FS value. Due to the variability of protein annotation caused e.g. by annotation bias, this value cannot be reliably compared on an absolute scale. We therefore introduce a similarity z-score that takes into account the FS background distribution of each protein. For a selection of popular SS measures and mixing strategies we demonstrate moderate accuracy improvement when using z-scores in a benchmark that aims to separate orthologous cases from random gene pairs and discuss in this context the impact of annotation corpus choice. The approach has been implemented in Frela, a fast high-throughput public web server for protein FS calculation and interpretation.
An Integrated H-G Scheme Identifying Areas for Soil Remediation and Primary Heavy Metal Contributors: A Risk Perspective
Authors: Zou Bin , Jiang Xiaolu , Duan Xiaoli , Zhao Xiuge , Zhang Jing , Tang Jingwen , Sun Guoqing 
Published: March 2017

AbstractTraditional sampling for soil pollution evaluation is cost intensive and has limited representativeness. Therefore, developing methods that can accurately and rapidly identify at-risk areas and the contributing pollutants is imperative for soil remediation. In this study, we propose an innovative integrated H-G scheme combining human health risk assessment and geographical detector methods that was based on geographical information system technology and validated its feasibility in a renewable resource industrial park in mainland China. With a discrete site investigation of cadmium (Cd), arsenic (As), copper (Cu), mercury (Hg) and zinc (Zn) concentrations, the continuous surfaces of carcinogenic risk and non-carcinogenic risk caused by these heavy metals were estimated and mapped. Source apportionment analysis using geographical detector methods further revealed that these risks were primarily attributed to As, according to the power of the determinant and its associated synergic actions with other heavy metals. Concentrations of critical As and Cd, and the associated exposed CRs are closed to the safe thresholds after remediating the risk areas identified by the integrated H-G scheme. Therefore, the integrated H-G scheme provides an effective approach to support decision-making for regional contaminated soil remediation at fine spatial resolution with limited sampling data over a large geographical extent.
Analysis of factors affecting the therapeutic effect of propranolol for infantile haemangioma of the head and neck
Authors: Dong Jian-Yong , Ning Jie-Xin , Li Kai , Liu Chao , Wang Xu-Xia , Li Rong-Hui , Yue Lin-Lin , Huang Ying-Ying , Liu Shao-Hua 
Published: March 2017

AbstractInfantile haemangiomas (IHs) are the most common congenital vascular tumours of infancy. Propranolol has been demonstrated to be effective for IHs; however, the factors affecting its therapeutic effect remain unknown. We enrolled 169 infants with IHs of the head and neck region treated with oral propranolol at a dose of 2.0 mg/kg/day. We evaluated the therapeutic responses 6 months after treatment and the end of treatment, which were categorized into four grades. The type and location of the lesions and the infant age at treatment initiation were analysed. The clinical response rate (III + IV) was 91.72% at 6 months after treatment and 97.63% at the end of treatment. The average treatment duration was 9.99 (2–24) months. The group aged 4–6 months exhibited a greater therapeutic response rate (98.48%). The treatment duration was shorter (9.52 months) for mixed-type IHs. Better therapeutic responses were observed for IHs located around the parotid, periorbital, cheek, and neck regions and for multiple IH lesions. Our study indicated that propranolol is effective for IHs affecting the head and neck. The age at treatment initiation and the location of the lesions had a significant effect on the therapeutic response, whereas the lesion type might affect the treatment duration.
Determination of leaf carbon isotope discrimination in C4 plants under variable N and water supply
Authors: Yang Hao , Yu Qiang , Sheng Wen-ping , Li Sheng-gong , Tian Jing 
Published: March 2017

AbstractUnderstanding the mechanisms underlying variations in carbon isotope discrimination (Δ) in C4 plants is critical for predicting the C3/C4 ratio in C3/C4 mixed grassland. The value of Δ is determined by bundle sheath leakiness (Ф) and the ratio of intercellular to ambient CO2 concentration (C
i
/C
a
). Leaf nitrogen concentration (N
leaf
) is considered a driver of Δ in C4 plants. However, little is known about how N
leaf
affects Ф and C
i
/C
a
, and subsequently Δ. Here leaf carbon isotope composition, N
leaf
, Ф, and leaf gas exchange were measured in Cleistogenes squarrosa, a dominant C4 species in the Inner Mongolia grassland. Δ remained relatively stable under variable N and water supply. Higher N supply and lower water supply increased N
leaf
, stimulated photosynthesis and further decreased C
i
/C
a
. High N supply increased Ф, which responded weakly to water supply. N
leaf
exerted similar effects on C
i
/C
a
and on Ф in the field and pot experiments. Pooling all the data, N
leaf
explained 73% of the variation in C
i
/C
a
. Overall, both Ф and C
i
/C
a
determined Δ; however, the contribution of Ф was stronger. N
leaf
influenced Δ primarily though C
i
/C
a
, rather than Ф. Ф should be considered in estimating Δ of C4 endmember.
Reconstruction of Large-scale Defects with a Novel Hybrid Scaffold Made from Poly(L-lactic acid)/Nanohydroxyapatite/Alendronate-loaded Chitosan Microsphere: in vitro and in vivo Studies
Authors: Wu Hongwei , Lei Pengfei , Liu Gengyan , Shrike Zhang Yu , Yang Jingzhou , Zhang Longbo , Xie Jie , Niu Wanting , Liu Hua , Ruan Jianming , Hu Yihe , Zhang Chaoyue 
Published: March 2017

AbstractA chitosan-based microsphere delivery system has been fabricated for controlled release of alendronate (AL). The present study aimed to incorporate the chitosan/hydroxyapatite microspheres-loaded with AL (CH/nHA-AL) into poly(L-lactic acid)/nanohydroxyapatite (PLLA/nHA) matrix to prepare a novel microspheres-scaffold hybrid system (CM-ALs) for drug delivery and bone tissue engineering application. The characteristics of CM-ALs scaffolds containing 10% and 20% CH/nHA-AL were evaluated in vitro, including surface morphology and porosity, mechanical properties, drug release, degradation, and osteogenic differentiation. The in vivo bone repair for large segmental radius defects (1.5 cm) in a rabbit model was evaluated by radiography and histology. In vitro study showed more sustained drug release of CM-AL-containing scaffolds than these of CM/nHA-AL and PLLA/nHA/AL scaffolds, and the mechanical and degradation properties of CM-ALs (10%) scaffolds were comparable to that of PLLA/nHA control. The osteogenic differentiation of adipose-derived stem cells (ASCs) was significantly enhanced as indicated by increased alkaline phosphates (ALP) activity and calcium deposition. In vivo study further showed better performance of CM-ALs (10%) scaffolds with complete repair of large-sized bone defects within 8 weeks. A microspheres-scaffold-based release system containing AL-encapsulated chitosan microspheres was successfully fabricated in this study. Our results suggested the promising application of CM-ALs (10%) scaffolds for drug delivery and bone tissue engineering.
The gene expression profiles in response to 102 traditional Chinese medicine (TCM) components: a general template for research on TCMs
Authors: Lv Chao , Wu Xueting , Wang Xia , Su Juan , Zeng Huawu , Zhao Jing , Lin Shan , Liu Runhui , Li Honglin , Li Xuan , Zhang Weidong 
Published: March 2017

AbstractTraditional Chinese medicines (TCMs) have important therapeutic value in long-term clinical practice. However, because TCMs contain diverse ingredients and have complex effects on the human body, the molecular mechanisms of TCMs are poorly understood. In this work, we determined the gene expression profiles of cells in response to TCM components to investigate TCM activities at the molecular and cellular levels. MCF7 cells were separately treated with 102 different molecules from TCMs, and their gene expression profiles were compared with the Connectivity Map (CMAP). To demonstrate the reliability and utility of our approach, we used nitidine chloride (NC) from the root of Zanthoxylum nitidum, a topoisomerase I/II inhibitor and α-adrenoreceptor antagonist, as an example to study the molecular function of TCMs using CMAP data as references. We successfully applied this approach to the four ingredients in Danshen and analyzed the synergistic mechanism of TCM components. The results demonstrate that our newly generated TCM data and related methods are valuable in the analysis and discovery of the molecular actions of TCM components. This is the first work to establish gene expression profiles for the study of TCM components and serves as a template for general TCM research.
Molecular Classification of Lobular Carcinoma of the Breast
Authors: Fu Denggang , Zuo Qi , Huang Qi , Su Li , Ring Huijun Z. , Ring Brian Z. 
Published: March 2017

AbstractThe morphology of breast tumors is complicated and diagnosis can be difficult. We present here a novel diagnostic model which we validate on both array-based and RNA sequencing platforms which reliably distinguishes this tumor type across multiple cohorts. We also examine how this molecular classification predicts sensitivity to common chemotherapeutics in cell-line based assays. A total of 1845 invasive breast cancer cases in six cohorts were collected, split into discovery and validation cohorts, and a classifier was created and compared to pathological diagnosis, grade and survival. In the validation cohorts the concordance of predicted diagnosis with a pathological diagnosis was 92%, and 97% when inconclusively classified cases were excluded. Tumor-derived cell lines were classified with the model as having predominantly ductal or lobular-like molecular physiologies, and sensitivity of these lines to relevant compounds was analyzed. A diagnostic tool can be created that reliably distinguishes lobular from ductal carcinoma and allows the classification of cell lines on the basis of molecular profiles associated with these tumor types. This tool may assist in improved diagnosis and aid in explorations of the response of lobular type breast tumor models to different compounds.
Total Extracellular Small RNA Profiles from Plasma, Saliva, and Urine of Healthy Subjects
Authors: Yeri Ashish , Courtright Amanda , Reiman Rebecca , Carlson Elizabeth , Beecroft Taylor , Janss Alex , Siniard Ashley , Richholt Ryan , Balak Chris , Rozowsky Joel , Kitchen Robert , Hutchins Elizabeth , Winarta Joseph , McCoy Roger , Anastasi Matthew , Kim Seungchan , Huentelman Matthew , Van Keuren-Jensen Kendall 
Published: March 2017

AbstractInterest in circulating RNAs for monitoring and diagnosing human health has grown significantly. There are few datasets describing baseline expression levels for total cell-free circulating RNA from healthy control subjects. In this study, total extracellular RNA (exRNA) was isolated and sequenced from 183 plasma samples, 204 urine samples and 46 saliva samples from 55 male college athletes ages 18–25 years. Many participants provided more than one sample, allowing us to investigate variability in an individual’s exRNA expression levels over time. Here we provide a systematic analysis of small exRNAs present in each biofluid, as well as an analysis of exogenous RNAs. The small RNA profile of each biofluid is distinct. We find that a large number of RNA fragments in plasma (63%) and urine (54%) have sequences that are assigned to YRNA and tRNA fragments respectively. Surprisingly, while many miRNAs can be detected, there are few miRNAs that are consistently detected in all samples from a single biofluid, and profiles of miRNA are different for each biofluid. Not unexpectedly, saliva samples have high levels of exogenous sequence that can be traced to bacteria. These data significantly contribute to the current number of sequenced exRNA samples from normal healthy individuals.