bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strategies for reducing the fertilizer application rate in the ridge and furrow rainfall harvesting system in semiarid regions
Authors: Lian Yanhao , Meng Xiangping , Yang Zhen , Wang Tianlu , Ali Shahzad , Yang Baoping , Zhang Peng , Han Qingfang , Jia Zhikuan , Ren Xiaolong 
Published: May 2017

AbstractThe ridge and furrow rainwater harvesting (RFRH) system is a promising water-saving planting technique for dryland farming, but we lack a full understanding of the effects of different fertilizer rates (N:P) on plant nutrient uptake and nutrient use efficiency (NuUE) in foxtail millet using this planting method, as well as the available nutrient residues in the soil. We conducted field studies (Loess Plateau, China) comparing RFRH planting (R) and traditional flat planting (T) at four different fertilizer rates to determine suitable fertilizer application rates for R during 2013–2015. Compared with T, R improved the soil moisture and the utilization of rainwater and fertilizer, thereby enhancing the grain yield, water use efficiency (WUE), grain nutrient uptake, and NUE in a dry year, but with no improvements in a rainy year. The grain yield and WUE exhibited parabolic increasing trends as the fertilizer application rate increased over three years, but no significant increase was found when the fertilizer rate exceeded 189:96 kg N:P ha−1 under R, which significantly reduced the NuUE and might waste nutrients. Therefore, we recommend R combined with 189:96 kg N:P ha−1 as a promising planting strategy for foxtail millet in semiarid areas.
Novel approach for accurate tissue-based protein colocalization and proximity microscopy
Authors: Lutz Mirjam I. , Schwaiger Carmen , Hochreiter Bernhard , Kovacs Gabor G. , Schmid Johannes A. 
Published: May 2017

AbstractFluorescence colocalization microscopy is frequently used to assess potential links between distinct molecules; however, this method can lead to striking false-positive results and erroneous conclusions. Here we developed a novel approach with more sophisticated mathematical colocalization analyses together with visualization of physical proximity using fluorescence resonance energy transfer (FRET). To verify our results we used the proximity ligation assay (PLA). With these methods we could demonstrate that distinct neurodegeneration-related proteins either not or only rarely interact in human brain tissue.
Node Attribute-enhanced Community Detection in Complex Networks
Authors: Jia Caiyan , Li Yafang , Carson Matthew B. , Wang Xiaoyang , Yu Jian 
Published: May 2017

AbstractCommunity detection involves grouping the nodes of a network such that nodes in the same community are more densely connected to each other than to the rest of the network. Previous studies have focused mainly on identifying communities in networks using node connectivity. However, each node in a network may be associated with many attributes. Identifying communities in networks combining node attributes has become increasingly popular in recent years. Most existing methods operate on networks with attributes of binary, categorical, or numerical type only. In this study, we introduce kNN-enhance, a simple and flexible community detection approach that uses node attribute enhancement. This approach adds the k Nearest Neighbor (kNN) graph of node attributes to alleviate the sparsity and the noise effect of an original network, thereby strengthening the community structure in the network. We use two testing algorithms, kNN-nearest and kNN-Kmeans, to partition the newly generated, attribute-enhanced graph. Our analyses of synthetic and real world networks have shown that the proposed algorithms achieve better performance compared to existing state-of-the-art algorithms. Further, the algorithms are able to deal with networks containing different combinations of binary, categorical, or numerical attributes and could be easily extended to the analysis of massive networks.
Construction of novel repeat proteins with rigid and predictable structures using a shared helix method
Authors: Youn Suk-Jun , Kwon Na-Young , Lee Ji Hyun , Kim Jin Hong , Choi Jinwoo , Lee Hayyoung , Lee Jie-Oh 
Published: May 2017

AbstractGenerating artificial protein assemblies with complex shapes requires a method for connecting protein components with stable and predictable structures. Currently available methods for creating rigid protein assemblies rely on either complicated calculations or extensive trial and error. We describe a simple and efficient method for connecting two proteins via a fused alpha helix that is formed by joining two preexisting helices into a single extended helix. Because the end-to-end ligation of helices does not guarantee the formation of a continuous helix, we superimposed 1–2 turns of pairs of connecting helices by using a molecular graphics program. Then, we chose amino acids from the two natural sequences that would stabilize the connecting helix. This “shared helix method” is highly efficient. All the designed proteins that could be produced in Escherichia coli were readily crystallized and had the expected fusion structures. To prove the usefulness of this method, we produced two novel repeat proteins by assembling several copies of natural or artificial proteins with alpha helices at both termini. Their crystal structures demonstrated the successful assembly of the repeating units with the intended curved shapes. We propose that this method could dramatically expand the available repertoire of natural repeat proteins.
Control of light absorbance using plasmonic grating based perfect absorber at visible and near-infrared wavelengths
Authors: Nguyen Duc Minh , Lee Dasol , Rho Junsuk 
Published: May 2017

AbstractConventional metamaterial absorbers have multilayer designs, where the dielectric interlayer is sandwiched between a top patterned metallic structure and bottom metallic film. Here, we demonstrate that a highly polarization-sensitive perfect absorber canbe realized by replacing the bottom metallic film with a plasmonic grating. Designs for broadband and narrowband of wavelength are proposed and numerically investigated. The designed absorbers perform high light absorption, which is above 90% over the wavelength range of 0.4–1.4 µm for the broadband absorber and 98% for the absorption peak in case of the narrowband design, with a specific polarization of incident light. We find that the absorption is tunable by changing the polarization. Such absorbers offer new approach for active control of light absorbance with strong impacts for solar energy harvesting, light emitting and sensing.
Environmentally driven sexual segregation in a marine top predator
Authors: Paiva Vitor H. , Pereira Justin , Ceia Filipe R. , Ramos Jaime A. 
Published: May 2017

AbstractSexual segregation in foraging occurs in many animal species, resulting in the partitioning of resources and reduction of competition between males and females, yet the patterns and drivers of such segregation are still poorly understood. We studied the foraging movements (GPS-tracking), habitat use (habitat modelling) and trophic ecology (stable isotope analysis) of female and male Cory’s shearwatersCalonectris borealisduring the mid chick-rearing period of six consecutive breeding seasons (2010–2015). We found a clear sexual segregation in foraging in years of greater environmental stochasticity, likely years of lower food availability. When food became scarce, females undertook much longer foraging trips, exploited more homogeneous water masses, had a larger isotopic niche, fed on lower trophic level prey and exhibited a lower body condition, when compared to males. Sexual competition for trophic resources may be stronger when environmental conditions are poor. A greater foraging success of one sex may result in differential body condition of pair mates when enduring parental effort, and ultimately, in an increased probability of breeding failure.
Oncopig Soft-Tissue Sarcomas Recapitulate Key Transcriptional Features of Human Sarcomas
Authors: Schachtschneider Kyle M. , Liu Yingkai , Mäkeläinen Suvi , Madsen Ole , Rund Laurie A. , Groenen Martien A. M. , Schook Lawrence B. 
Published: May 2017

AbstractHuman soft-tissue sarcomas (STS) are rare mesenchymal tumors with a 5-year survival rate of 50%, highlighting the need for further STS research. Research has been hampered by limited human sarcoma cell line availability and the large number of STS subtypes, making development of STS cell lines and animal models representative of the diverse human STS subtypes critical. Pigs represent ideal human disease models due to their similar size, anatomy, metabolism, and genetics compared to humans. The Oncopig encodes inducible KRAS
G12D
and TP53
R167H
transgenes, allowing for STS modeling in a spatial and temporal manner. This study utilized Oncopig STS cell line (fibroblast) and tumor (leiomyosarcoma) RNA-seq data to compare Oncopig and human STS expression profiles. Altered expression of 3,360 and 7,652 genes was identified in Oncopig STS cell lines and leiomyosarcomas, respectively. Transcriptional hallmarks of human STS were observed in Oncopig STS, including altered TP53 signaling, Wnt signaling activation, and evidence of epigenetic reprogramming. Furthermore, master regulators of Oncopig STS expression were identified, including FOSL1, which was previously identified as a potential human STS therapeutic target. These results demonstrate the Oncopig STS model’s ability to mimic human STS transcriptional profiles, providing a valuable resource for sarcoma research and cell line development.
β-lapachone suppresses tumour progression by inhibiting epithelial-to-mesenchymal transition in NQO1-positive breast cancers
Authors: Yang Yang , Zhou Xianchun , Xu Ming , Piao Junjie , Zhang Yuan , Lin Zhenhua , Chen Liyan 
Published: May 2017

AbstractNQO1 is a FAD-binding protein that can form homodimers and reduce quinones to hydroquinones, and a growing body of evidence currently suggests that NQO1 is dramatically elevated in solid cancers. Here, we demonstrated that NQO1 was elevated in breast cancer and that its expression level was positively correlated with invasion and reduced disease free survival (DFS) and overall survival (OS) rates. Next, we found that β-lapachone exerted significant anti-proliferation and anti-metastasis effects in breast cancer cell lines due to its effects on NQO1 expression. Moreover, we revealed that the anti-cancer effects of β-lapachone were mediated by the inactivation of the Akt/mTOR pathway. In conclusion, these results demonstrated that NQO1 could be a useful prognostic biomarker for patients with breast cancer, and its bioactivatable drug, β-lapachone represented a promising new development and an effective strategy for indicating the progression of NQO1-positive breast cancers.
Fiber-utilizing capacity varies in Prevotella- versus Bacteroides-dominated gut microbiota
Authors: Chen Tingting , Long Wenmin , Zhang Chenhong , Liu Shuang , Zhao Liping , Hamaker Bruce R. 
Published: May 2017

AbstractThe gut microbiota of individuals are dominated by different fiber-utilizing bacteria, which ferment dietary fiber into short chain fatty acids (SCFAs) known to be important for human health. Here, we show that the dominance of Prevotella versus Bacteroides in fecal innocula, identified into two different enterotypes, differentially impacts in vitro fermentation profiles of SCFAs from fibers with different chemical structures. In a microbiome of the Prevotella enterotype, fructooligosaccharides, and sorghum and corn arabinoxylans significantly promoted one single Prevotella OTU with equally high production of total SCFAs with propionate as the major product. Conversely, in the Bacteroides-dominated microbiota, the three fibers enriched different OTUs leading to different levels and ratios of SCFAs. This is the first report showing how individual differences in two enterotypes cause distinctly different responses to dietary fiber. Microbiota dominated by different fiber-utilizing bacteria may impact host health by way of producing different amounts and profiles of SCFAs from the same carbohydrate substrates.
Generation of a planar direct-current glow discharge in atmospheric pressure air using rod array electrode
Authors: Li Xuechen , Zhang Panpan , Jia Pengying , Chu Jingdi , Chen Junying 
Published: May 2017

AbstractScaling up atmospheric pressure glow discharge to large volume is desirable for low-temperature plasma applications. In this paper, an approach to generate a glow discharge in a planar shape with a fairly large volume is proposed in atmospheric pressure air through utilizing a direct-current excited rod array electrode. The planar discharge with a wide gap originates from three discrete discharges with a narrow gap. Based on electrical method and optical emission spectroscopy, it is found that gap voltage increases, while discharge current remains constant with increasing the gap width. Temperature and electron density of the discharge decrease with increasing the gap width.
Identification and characterization of two types of amino acid-regulated acetyltransferases in actinobacteria
Authors: Lu Yu-Xing , Liu Xin-Xin , Liu Wei-Bing , Ye Bang-Ce 
Published: May 2017

Abstract
One hundred and fifty GCN5-like acetyltransferases with amino acid-binding (ACT)-GCN5-related N-acetyltransferase (GNAT) domain organization have been identified in actinobacteria. The ACT domain is fused to the GNAT domain, conferring amino acid-induced allosteric regulation to these protein acetyltransferases (Pat) (amino acid sensing acetyltransferase, (AAPatA)). Members of the AAPatA family share similar secondary structure and are divided into two groups based on the allosteric ligands of the ACT domain: the asparagine (Asn)-activated PatA and the cysteine (Cys)-activated PatA. The former are mainly found in Streptomyces; the latter are distributed in other actinobacteria. We investigated the effect of Asn and Cys on the acetylation activity of Sven_0867 (SvePatA, from Streptomyces venezuelae DSM 40230) and Amir_5672 (AmiPatA, from Actinosynnema mirum strain DSM 43827), respectively, as well as the relationship between the structure and function of these enzymes. These findings indicate that the activity of PatA and acetylation level of proteins may be closely correlated with intracellular concentrations of Asn and Cys in actinobacteria. Amino acid-sensing signal transduction in acetyltransferases may be a mechanism that regulates protein acetylation in response to nutrient availability. Future work examining the relationship between protein acetylation and amino acid metabolism will broaden our understanding of post-translational modifications (PTMs) in feedback regulation.
In-Hospital Outcomes Following Extracorporeal Membrane Oxygenation in a Retrospective Cohort of Infants
Authors: Schueller Maya , Greenberg Rachel , Smith P. , Laughon Matthew , Clark Reese , Hornik Christoph 
Published: May 2017

Objective We sought to characterize associations between infant characteristics and extracorporeal membrane oxygenation (ECMO) survival using electronic health records data.
Study Design We examined a cohort study of infants ≥32 weeks of gestational age and ≥1,800 g birth weight supported with ECMO in a Pediatrix Medical Group neonatal intensive care unit from 1998 to 2013.
Results We identified 268 infants, of which 45 (17%) were <37 weeks of gestational age. Survival to discharge was 87% but was lower in premature compared with term infants (76 vs. 89%, p = 0.03). In multivariable analysis, acute kidney injury (odds ratio [OR] = 4.00; 95% confidence interval [CI] = 1.05, 15.24), postnatal age at cannulation of 7 to 13 days (OR = 5.86; 95% CI = 1.21, 28.44), and venoarterial ECMO cannulation (OR = 4.33; 95% CI = 1.77, 10.60) were associated with lower survival.
Conclusion ECMO cannulation type, postnatal age, and acute kidney injury were associated with lower ECMO survival, while prematurity was not. Future studies are needed to identify risk factors and strategies to improve outcomes.
Temporal regulation of epithelium formation mediated by FoxA, MKLP1, MgcRacGAP, and PAR-6
Authors: Von Stetina Stephen E. , Liang Jennifer , Marnellos Georgios , Mango Susan E. 
Published: May 2017

To establish the animal body plan, embryos link the external epidermis to the internal digestive tract. In Caenorhabditis elegans, this linkage is achieved by the arcade cells, which form an epithelial bridge between the foregut and epidermis, but little is known about how development of these three epithelia is coordinated temporally. The arcade cell epithelium is generated after the epidermis and digestive tract epithelia have matured, ensuring that both organs can withstand the mechanical stress of embryo elongation; mistiming of epithelium formation leads to defects in morphogenesis. Using a combination of genetic, bioinformatic, and imaging approaches, we find that temporal regulation of the arcade cell epithelium is mediated by the pioneer transcription factor and master regulator PHA-4/FoxA, followed by the cytoskeletal regulator and kinesin ZEN-4/MKLP1 and the polarity protein PAR-6. We show that PHA-4 directly activates mRNA expression of a broad cohort of epithelial genes, including junctional factor dlg-1. Accumulation of DLG-1 protein is delayed by ZEN-4, acting in concert with its binding partner CYK-4/MgcRacGAP. Our structure–function analysis suggests that nuclear and kinesin functions are dispensable, whereas binding to CYK-4 is essential, for ZEN-4 function in polarity. Finally, PAR-6 is necessary to localize polarity proteins such as DLG-1 within adherens junctions and at the apical surface, thereby generating arcade cell polarity. Our results reveal that the timing of a landmark event during embryonic morphogenesis is mediated by the concerted action of four proteins that delay the formation of an epithelial bridge until the appropriate time. In addition, we find that mammalian FoxA associates with many epithelial genes, suggesting that direct regulation of epithelial identity may be a conserved feature of FoxA factors and a contributor to FoxA function in development and cancer.
HEROD: a human ethnic and regional specific omics database
Authors: Zeng Xian , Tao Lin , Zhang Peng , Qin Chu , Chen Shangying , He Weidong , Tan Ying , Xia Liu Hong , Yang Sheng Yong , Chen Zhe , Jiang Yu Yang , Chen Yu Zong 
Published: May 2017

Abstract

Motivation
Genetic and gene expression variations within and between populations and across geographical regions have substantial effects on the biological phenotypes, diseases, and therapeutic response. The development of precision medicines can be facilitated by the OMICS studies of the patients of specific ethnicity and geographic region. However, there is an inadequate facility for broadly and conveniently accessing the ethnic and regional specific OMICS data.

Results
Here, we introduced a new free database, HEROD, a human ethnic and regional specific OMICS database. Its first version contains the gene expression data of 53 070 patients of 169 diseases in seven ethnic populations from 193 cities/regions in 49 nations curated from the Gene Expression Omnibus (GEO), the ArrayExpress Archive of Functional Genomics Data (ArrayExpress), the Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC). Geographic region information of curated patients was mainly manually extracted from referenced publications of each original study. These data can be accessed and downloaded via keyword search, World map search, and menu-bar search of disease name, the international classification of disease code, geographical region, location of sample collection, ethnic population, gender, age, sample source organ, patient type (patient or healthy), sample type (disease or normal tissue) and assay type on the web interface.

Availability and implementation
The HEROD database is freely accessible at http://bidd2.nus.edu.sg/herod/index.php. The database and web interface are implemented in MySQL, PHP and HTML with all major browsers supported.
ABC/2 Method Does not Accurately Predict Cerebral Arteriovenous Malformation Volume
Authors: Roark Christopher , Vadlamudi Venu , Chaudhary Neeraj , Gemmete Joseph J , Seinfeld Joshua , Thompson B Gregory , Pandey Aditya S 
Published: May 2017

Abstract

BACKGROUND
Stereotactic radiosurgery (SRS) is a treatment option for cerebral arteriovenous malformations (AVMs) to prevent intracranial hemorrhage. The decision to proceed with SRS is usually based on calculated nidal volume. Physicians commonly use the ABC/2 formula, based on digital subtraction angiography (DSA), when counseling patients for SRS.

OBJECTIVE
To determine whether AVM volume calculated using the ABC/2 method on DSA is accurate when compared to the exact volume calculated from thin-cut axial sections used for SRS planning.

METHODS
Retrospective search of neurovascular database to identify AVMs treated with SRS from 1995 to 2015. Maximum nidal diameters in orthogonal planes on DSA images were recorded to determine volume using ABC/2 formula. Nidal target volume was extracted from operative reports of SRS. Volumes were then compared using descriptive statistics and paired t-tests.

RESULTS
Ninety intracranial AVMs were identified. Median volume was 4.96 cm3 [interquartile range (IQR) 1.79-8.85] with SRS planning methods and 6.07 cm3 (IQR 1.3-13.6) with ABC/2 methodology. Moderate correlation was seen between SRS and ABC/2 (r = 0.662; P < .001). Paired sample t-tests revealed significant differences between SRS volume and ABC/2 (t = –3.2; P = .002). When AVMs were dichotomized based on ABC/2 volume, significant differences remained (t = 3.1, P = .003 for ABC/2 volume < 7 cm3; t = –4.4, P < .001 for ABC/2 volume > 7 cm3).

CONCLUSION
The ABC/2 method overestimates cerebral AVM volume when compared to volumetric analysis from SRS planning software. For AVMs > 7 cm3, the overestimation is even greater. SRS planning techniques were also significantly different than values derived from equations for cones and cylinders.
Acetaminophen Metabolite N-Acylphenolamine Induces Analgesia via Transient Receptor Potential Vanilloid 1 Receptors Expressed on the Primary Afferent Terminals of C-fibers in the Spinal Dorsal Horn
Authors: Ohashi Nobuko , Uta Daisuke , Sasaki Mika , Ohashi Masayuki , Kamiya Yoshinori , Kohno Tatsuro 
Published: May 2017

Abstract

Background
The widely used analgesic acetaminophen is metabolized to N-acylphenolamine, which induces analgesia by acting directly on transient receptor potential vanilloid 1 or cannabinoid 1 receptors in the brain. Although these receptors are also abundant in the spinal cord, no previous studies have reported analgesic effects of acetaminophen or N-acylphenolamine mediated by the spinal cord dorsal horn. We hypothesized that clinical doses of acetaminophen induce analgesia via these spinal mechanisms.

Methods
We assessed our hypothesis in a rat model using behavioral measures. We also used in vivo and in vitro whole cell patch-clamp recordings of dorsal horn neurons to assess excitatory synaptic transmission.

Results
Intravenous acetaminophen decreased peripheral pinch-induced excitatory responses in the dorsal horn (53.1 ± 20.7% of control; n = 10; P < 0.01), while direct application of acetaminophen to the dorsal horn did not reduce these responses. Direct application of N-acylphenolamine decreased the amplitudes of monosynaptic excitatory postsynaptic currents evoked by C-fiber stimulation (control, 462.5 ± 197.5 pA; N-acylphenolamine, 272.5 ± 134.5 pA; n = 10; P = 0.022) but not those evoked by stimulation of Aδ-fibers. These phenomena were mediated by transient receptor potential vanilloid 1 receptors, but not cannabinoid 1 receptors. The analgesic effects of acetaminophen and N-acylphenolamine were stronger in rats experiencing an inflammatory pain model compared to naïve rats.

Conclusions
Our results suggest that the acetaminophen metabolite N-acylphenolamine induces analgesia directly via transient receptor potential vanilloid 1 receptors expressed on central terminals of C-fibers in the spinal dorsal horn and leads to conduction block, shunt currents, and desensitization of these fibers.