bluuebunny/crossref_metadata_2025_split huggingface dataset:
Agriculture in urban and peri-urban areas in the United States: Highlights from the Census of Agriculture
Authors: Rogus Stephanie , Dimitri Carolyn 
Published: March 2014

AbstractUrban agriculture, a current trend in many US cities, is purported to bring enhanced food security, reduction of food waste, community building, open green space in cities and higher property values. However, the literature lacks an understanding of whether urban farming has extended beyond a compelling concept into the practice of farming in the city and peri-urban areas. The exact definition of an urban farm is challenging, since many urban farms have a primary mission of supporting social goals rather than providing food. Use of the USDA definition of farm omits many self-identified urban farms, but the most consistent measure of agriculture is the Census of Agriculture. Using census data, this paper finds that urban farms are smaller than the typical farm, and while the amount of urban and peri-urban farmland declined between 2002 and 2007, the total number of farms increased. Growth in farmland is positively related to land values, suggesting that increases in urban farmland are more likely to take place in population dense, land scarce areas. Spatial analysis of urban and peri-urban farms in the Northeast finds fewer clusters of farms in areas with high land costs. In the most populous Northeastern cities, the farms are more likely to be located in the peri-urban area than in the urban core. Urban farms in the Northeast were more likely to produce vegetables, eggs and goats. Significant levels of vegetable farm clusters were detected surrounding Providence, Boston and Hartford Metropolitan Statistical Areas, which are regions that had no significant level of clustering of total farms. Future analysis, incorporating data from the 2012 census, should provide insight into whether local policy changes have resulted in growth in urban farms and farmland.
“What Happens in the Cabin . . .”: An Arts-Based Autoethnography of Underground Hip Hop Song Making
Authors: HARRISON ANTHONY KWAME 
Published: March 2014

AbstractTaking an autoethnographic perspective that foregrounds the interplay between the author's artist-self and researcher-self, this article explores the relationship between agency and structure in the activities surrounding underground hip hop music making within a home studio recording space. It aims to demystify the aura of in-studio music creation by focusing on the nexus of oral/written, pre-composed/improvised, and pre-recorded/live creative practices as experienced within the context of performance. Utilizing Harris Berger's notion of stance, I discuss how hip hop recording artists transcend performative self-consciousness in the pursuit of creativity. Ultimately, this article presents hip hop home recording studios as spaces that facilitate particular kinds of musical innovation through a mix of collective and individual pursuits, as well as routinized and spontaneous activities.
Paul's BoutiqueandFear of a Black Planet: Digital Sampling and Musical Style in Hip Hop
Authors: SEWELL AMANDA 
Published: March 2014

AbstractThe Beastie Boys’Paul's Boutique(1989) and Public Enemy'sFear of a Black Planet(1990) often draw comparisons because of their profuse and eclectic use of digital sampling. These two hip hop albums, however, use sampling in markedly different ways, a fact that is obscured because no well-developed language exists to differentiate how and why their sampling styles differ. To account for these differences, this article proposes a typology for sample-based hip hop, a systematic terminological and conceptual approach to this repertory. Using these two classic albums by the Beastie Boys and Public Enemy as case studies, this typology offers a way to describe and distinguish in concrete terms the richly varied musical styles that make up sample-based hip hop.
Design, simulation, and fabrication of broadband coaxial matched loads for the frequency range from 0 to 110 GHz
Authors: Tag Andreas , Leinhos Jens , Hechtfischer Gerd , Leibfritz Martin , Eibert Thomas 
Published: March 2014

Combining a theory for reflection-free termination of coaxial lines together with a novel manufacturing method results in 1-mm coaxial matched loads with an excellent absorption behavior over the frequency range from 0 to 110 GHz. Three different electromagnetic (EM) simulation approaches verify the capability of these matched loads to achieve reflection coefficients smaller than −43 dBover the entire frequency range. Matched loads with a maximum reflection coefficient of only −32 dBhave been produced. An excellent performance was achieved by exponentially tapering the outer conductor over the region of a coaxial ceramic substrate coated by a thin-film resistance and by compensation for EM wave propagation inside the resistive coating.
States' obligations to mitigate the direct and indirect health consequences of non-international armed conflicts: complementarity of IHL and the right to health
Authors: Müller Amrei 
Published: March 2014

AbstractArmed conflicts have numerous adverse health consequences for the affected populations, many of which occur in the long-term. This article analyses in detail how international humanitarian law (IHL) and the right to health complement each other in obliging states to mitigate the direct and indirect health consequences of non-international armed conflicts. With its historical origin and purpose of protecting wounded and sick combatants of standing governmental armies, IHL focuses on the protection of the wounded and sick suffering from the direct health consequences of armed conflicts, such as injuries resulting from ongoing hostilities. The right to health is more expansive: it obliges states to prioritise the provision of primary health care through creating and maintaining an accessible basic health system. This focus enables it to highlight and address the indirect health consequences of armed conflicts, such as the spreading of epidemic and endemic diseases and rising child and maternal mortality and morbidity.
Damaging Effects of Multi-walled Carbon Nanotubes on Pregnant Mice with Different Pregnancy Times
Authors: Qi Wei , Bi Juanjuan , Zhang Xiaoyong , Wang Jing , Wang Jianjun , Liu Peng , Li Zhan , Wu Wangsuo 
Published: March 2014

AbstractThe mechanism by which nanoparticles cross the placental barrier was studied by using isotopic tracers. The abortion rates and other related data were counted and analysed in pregnant mice with different pregnancy times. Results showed that oxidised multi-walled carbon nanotubes (oMWCNTs) crossed the placental barrier and entered the foetus body. The abortion rates in the pregnant mice depended on pregnancy times. The abortion rates in the first-time, second-time and fourth-time pregnant mice were 70%, 40% and 50%, respectively. The maternal body weight gain was inhibited until gestational ages of 13, 10 and 11 d. oMWCNTs decreased the serum progesterone level and increased the serum oestradiol level in a dose- and time-dependent manner. However, this effect decreased with gestational age. The histology and vascular endothelial growth factor/reactive oxygen species content in the placenta showed that oMWCNTs narrowed the blood vessel and decreased the number of blood vessels in the placenta.
A personalized committee classification approach to improving prediction of breast cancer metastasis
Authors: Jahid Md Jamiul , Huang Tim H. , Ruan Jianhua 
Published: March 2014

Abstract
Motivation: Metastasis prediction is a well-known problem in breast cancer research. As breast cancer is a complex and heterogeneous disease with many molecular subtypes, predictive models trained for one cohort often perform poorly on other cohorts, and a combined model may be suboptimal for individual patients. Furthermore, attempting to develop subtype-specific models is hindered by the ambiguity and stereotypical definitions of subtypes.
Results: Here, we propose a personalized approach by relaxing the definition of breast cancer subtypes. We assume that each patient belongs to a distinct subtype, defined implicitly by a set of patients with similar molecular characteristics, and construct a different predictive model for each patient, using as training data, only the patients defining the subtype. To increase robustness, we also develop a committee-based prediction method by pooling together multiple personalized models. Using both intra- and inter-dataset validations, we show that our approach can significantly improve the prediction accuracy of breast cancer metastasis compared with several popular approaches, especially on those hard-to-learn cases. Furthermore, we find that breast cancer patients belonging to different canonical subtypes tend to have different predictive models and gene signatures, suggesting that metastasis in different canonical subtypes are likely governed by different molecular mechanisms.
Availability and implementation: Source code implemented in MATLAB and Java available at www.cs.utsa.edu/∼jruan/PCC/ .
Contact: jianhua.ruan@utsa.edu
Supplementary information: Supplementary data are available at Bioinformatics online .
Characterization of p38 MAPK isoforms for drug resistance study using systems biology approach
Authors: Peng Huiming , Peng Tao , Wen Jianguo , Engler David A. , Matsunami Risë K. , Su Jing , Zhang Le , Chang Chung-Che (Jeff) , Zhou Xiaobo 
Published: March 2014

Abstract
Motivation: p38 mitogen-activated protein kinase activation plays an important role in resistance to chemotherapeutic cytotoxic drugs in treating multiple myeloma (MM). However, how the p38 mitogen-activated protein kinase signaling pathway is involved in drug resistance, in particular the roles that the various p38 isoforms play, remains largely unknown.
Method: To explore the underlying mechanisms, we developed a novel systems biology approach by integrating liquid chromatography–mass spectrometry and reverse phase protein array data from human MM cell lines with computational pathway models in which the unknown parameters were inferred using a proposed novel algorithm called modularized factor graph.
Results: New mechanisms predicted by our models suggest that combined activation of various p38 isoforms may result in drug resistance in MM via regulating the related pathways including extracellular signal-regulated kinase (ERK) pathway and NFкB pathway. ERK pathway regulating cell growth is synergistically regulated by p38δ isoform, whereas nuclear factor kappa B (NFкB) pathway regulating cell apoptosis is synergistically regulated by p38α isoform. This finding that p38δ isoform promotes the phosphorylation of ERK1/2 in MM cells treated with bortezomib was validated by western blotting. Based on the predicted mechanisms, we further screened drug combinations in silico and found that a promising drug combination targeting ERK1/2 and NFκB might reduce the effects of drug resistance in MM cells. This study provides a framework of a systems biology approach to studying drug resistance and drug combination selection.
Availability and implementation: RPPA experimental Data and Matlab source codes of modularized factor graph for parameter estimation are freely available online at http://ctsb.is.wfubmc.edu/publications/modularized-factor-graph.php
Contact: xizhou@wakehealth.edu or zhanglcq@swu.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
FISH: fast and accurate diploid genotype imputation via segmental hidden Markov model
Authors: Zhang Lei , Pei Yu-Fang , Fu Xiaoying , Lin Yong , Wang Yu-Ping , Deng Hong-Wen 
Published: March 2014

Abstract
Motivation: Fast and accurate genotype imputation is necessary for facilitating gene-mapping studies, especially with the ever increasing numbers of both common and rare variants generated by high-throughput-sequencing experiments. However, most of the existing imputation approaches suffer from either inaccurate results or heavy computational demand.
Results: In this article, aiming to perform fast and accurate genotype-imputation analysis, we propose a novel, fast and yet accurate method to impute diploid genotypes. Specifically, we extend a hidden Markov model that is widely used to describe haplotype structures. But we model hidden states onto single reference haplotypes rather than onto pairs of haplotypes. Consequently the computational complexity is linear to size of reference haplotypes. We further develop an algorithm ‘merge-and-recover (MAR)’ to speed up the calculation. Working on compact representation of segmental reference haplotypes, the MAR algorithm always calculates an exact form of transition probabilities regardless of partition of segments. Both simulation studies and real-data analyses demonstrated that our proposed method was comparable to most of the existing popular methods in terms of imputation accuracy, but was much more efficient in terms of computation. The MAR algorithm can further speed up the calculation by several folds without loss of accuracy. The proposed method will be useful in large-scale imputation studies with a large number of reference subjects.
Availability: The implemented multi-threading software FISH is freely available for academic use at https://sites.google.com/site/lzhanghomepage/FISH .
Contact: zlbio12@gmail.com ; pyf0419@gmail.com ; hdeng2@tulane.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
SDSS J114657.79+403708.6: the third most distant blazar at z = 5.0
Authors: Ghisellini G. , Sbarrato T. , Tagliaferri G. , Foschini L. , Tavecchio F. , Ghirlanda G. , Braito V. , Gehrels N. 
Published: March 2014

Abstract
The radio-loud quasar SDSS J114657.79+403708.6 at a redshift z = 5.0 is one of the most distant radio-loud objects. The IR-optical luminosity and spectrum suggest that its black hole has a very large mass: M = (5 ± 1) × 109 M⊙. The radio-loudness (ratio of the radio to optical flux) of the source is large (around 100), suggesting that the source is viewed at small angles from the jet axis, and could be a blazar. The X-ray observations fully confirm this hypothesis, due to the high level and hardness of the flux. This makes SDSS J114657.79+403708.6 the third most distant blazar known, after Q0906+693 (z = 5.47) and B2 1023+25 (z = 5.3). Among those, SDSS J114657.79+403708.6 has the largest black hole mass, setting interesting constraints on the mass function of heavy (&gt;109 M⊙) black holes at high redshifts.
Inhibition of p38 Mitogen‐Activated Protein Kinase Attenuates Butyrate‐Induced Intestinal Barrier Impairment in a Caco‐2 Cell Monolayer Model
Authors: Huang Xiao‐Zhong , Li Zhong‐Rong , Zhu Li‐Bin , Huang Hui‐Ya , Hou Long‐Long , Lin Jing 
Published: March 2014

ABSTRACTObjectives:Butyrate is well known to induce apoptosis in differentiating intestinal epithelial cells. The present study was designed to examine the role of p38 mitogen‐activated protein kinase (MAPK) in butyrate‐induced intestinal barrier impairment.Methods:The intestinal barrier was determined by measuring the transepithelial electrical resistance (TER) in a Caco‐2 cell monolayer model. The permeability was determined by measuring transepithelial passage of fluorescein isothiocyanate‐conjugated inulin (inulin‐FITC). The morphology of the monolayers was examined with scanning electron microscopy. The apoptosis status was determined by annexin V–FITC labeling and flow cytometry. The activity of p38 MAPK was determined by the phosphorylation status of p38 with Western blotting.Results:Butyrate at 5 mM increases the apoptosis rate of Caco‐2 cells and induces impairment of intestinal barrier functions as determined by decreased TER and increased inulin‐FITC permeability. Butyrate treatment activates p38 MAPK in a concentration‐ and time‐dependent manner. SB203580, a specific p38 inhibitor, inhibits butyrate‐induced Caco‐2 cell apoptosis. Treatment of SB203580 significantly attenuates the butyrate‐induced impairment of barrier functions in the Caco‐2 cell monolayer model.Conclusions:p38 MAPK can be activated by butyrate and is involved in the butyrate‐induced apoptosis and impairment of intestinal barrier function. Inhibition of p38 MAPK can significantly attenuate butyrate‐induced intestinal barrier dysfunction.
Hidradenoma papilliferum of the vulva in association with an anogenital mammary‐like gland
Authors: Kurashige Yuta , Kishida Kosuke , Kurashige Kumiko , Minemura Tokuya , Nagatani Tetsuo 
Published: March 2014

AbstractHidradenoma papilliferum (HP) is a benign adnexal neoplasm which preferentially develops in the anogenital region of women. Although the origin of HP was previously thought to be an apocrine sweat gland, recent studies have suggested that it may derive from the anogenital mammary‐like gland (MLG). In this paper, we present a 43‐year‐old Japanese woman with hidradenoma papilliferum of the vulva. The lesion developed 7 years prior to her visit, and clinically appeared as a skin‐colored cystic nodule. Histopathological examination revealed that the neoplasm was formed by the tubular structures consisting of two types of pleomorphic cells, columnar cells in the luminal layer and cuboidal cells in the basal layer. Further, the surgical specimen contained a wide, divergent, lobular ductal structure located in the vicinity of the neoplastic lesion, which was consistent with MLG.
Systemic sclerosis with sarcoidosis: Case report and review of the published work
Authors: Senda Satoko , Igawa Ken , Nishioka Megumi , Murota Hiroyuki , Katayama Ichiro 
Published: March 2014

AbstractSarcoidosis and systemic sclerosis (SSc) rarely coexist. Here, we report a Japanese female SSc patient who developed systemic sarcoidosis. Her SSc was a limited type negative for anti‐Scl‐70 antibody and positive for anticentromere antibody (ACA). Moreover, we performed a review of the English‐language published work that described cases of concurrent SSc and sarcoidosis. Then, we found that most SSc and sarcoidosis concurrent patients positive for anti‐Scl‐70 antibody were male (77.8%). On the other hand, most patients positive for ACA were female (87.5%). These results suggest some relationships between autoantibody profiles and sex in SSc and sarcoidosis concurrence.
Grazing intensity affects insect diversity via sward structure and heterogeneity in a long‐term experiment
Authors: Jerrentrup Jana Sabrina , Wrage‐Mönnig Nicole , Röver Klaus‐Ulrich , Isselstein Johannes 
Published: March 2014

Summary

In the past, insect diversity in grasslands showed a severe decline due to management intensification or abandonment. In this study, we investigate the long‐term influence of grazing and the potential for spatial patterns created by different grazing intensities to enhance insect diversity.
In a long‐term experiment (2002–2011), three grazing intensities were applied to 1‐ha paddocks in a triplicate block design: moderate grazing (MC), lenient grazing (LC) and very lenient grazing (VLC, since 2005). The experiment was conducted in a moderately species‐rich grassland at the edge of the Solling Uplands in Lower Saxony, Germany. Orthoptera (grasshoppers) and Lepidoptera (butterflies) on three 50‐m transects per paddock were counted in 2002–2004 and again in 2010 and 2011. Statistics were performed using linear mixed modelling.
Grasshopper diversity measures (species richness and abundance) were significantly affected by grazing intensity; abundance increased from 2002 to 2011 more strongly in the LC than in the MC treatment. Butterfly species richness response to grazing intensity varied among years. Data from 2010 and 2011 did not reveal any advantage of the lowest grazing intensity (VLC) compared to the intermediate grazing intensity treatment (LC) in either insect group.
Multiple regressions were used to investigate diversity patterns. Along with compressed sward height, spatial patchiness was important for grasshopper species richness and abundance as well as for butterfly species numbers. Butterfly abundance was mainly influenced by vertical sward height heterogeneity in addition to the significant effects of thistle abundance and number of nectar plant species.
Synthesis and applications. Cattle grazing intensity affects the proportions and spatial heterogeneity of short and tall sward patches on pastures. The less mobile grasshoppers particularly benefitted from the structural modifications created by cattle at lenient grazing levels (stocking rate 1·14 SLU ha−1, standard livestock unit (SLU) = 500 kg). In the final study years, areas with intermediate grazing intensity revealed high diversity indices and the most distinct patchiness, therefore a further reduction in grazing intensity is not recommended. This indicates that commercial livestock production may be compatible with conservation targets.
Evaluation of Allium and its Seasoning on Toxigenic, Nutritional, and Sensorial Profiles of Groundnut Oil
Authors: Murugan Kasi , Anandaraj K. , Al‐Sohaibani Saleh A. 
Published: March 2014

AbstractMitigation of xerophilic storage fungi‐associated aflatoxin threat in culinary oil will be a new technology advantage to food industries. Groundnut oil isolate Aspergillus flavus MTCC 10680 susceptibility to Allium species (A. sativum L., A. cepa L., and A. cepa var. aggregatum) extracts, composition, and in silico confirmation of extract's phytoconstituent aflatoxin synthesis inhibition were determined. The behavior of seasoning carrier medium groundnut oil in the presence of Allium was also determined. All the Allium species extracts exhibited concentration dependent in vitro inhibition on mycelial biomass, radial growth, and toxin elaboration. The gas chromatography‐mass spectrometry revealed the presence of 28, 16, and 9 compounds in the extracts of A. sativum, A. cepa, A. cepa var. aggregatum, respectively. The Allium phytocostituents‐like hexadecanoic acid, 5‐Octanoyl‐2,4,6(1H,3H,5H)‐pyrimidinetrione, Guanosine, and so on, showed higher binding energy with aflatoxin synthesis key enzyme ver1. Allium seasoning increased the typical nutty odor of the groundnut oil with sweet aroma note as well as intensification of pale yellow color. Allium seasoning exhibited the highest aflatoxin detoxification and aroma development without any nutritional loss. Culinary oil Allium seasoning has anti‐aflatoxin and food additive potential for use in food industries.
Rapid Detection of Acetamiprid in Foods using Surface‐Enhanced Raman Spectroscopy (SERS)
Authors: Wijaya Wisiani , Pang Shintaro , Labuza Theodore P. , He Lili 
Published: March 2014

AbstractAcetamiprid is a neonicotinoid pesticide that is commonly used in modern farming. Acetamiprid residue in food commodities can be a potential harm to human and has been implicated in the honey bee hive die off crisis. In this study, we developed rapid, simple, and sensitive methods to detect acetamiprid in apple juice and on apple surfaces using surface‐enhanced Raman spectroscopy (SERS). No pretreatment of apple juice sample was performed. A simple surface swab method was used to recover acetamiprid from the apple surface. Samples were incubated with silver dendrites for several minutes and SERS spectra were taken directly from the silver surface. Detection of a set of 5 apple juice samples can be done within 10 min. The swab‐SERS method took 15 min for a set of 5 samples. Resulting spectral data were analyzed using principal component analysis. The highest acetamiprid peak at 634 cm−1 was used to detect and quantify the amount of acetamiprid spiked in 1:1 water–methanol solvent, apple juice, and on apple surface. The SERS method was able to successfully detect acetamiprid at 0.5 μg/mL (0.5 ppm) in solvent, 3 μg/mL (3 ppm) in apple juice, and 0.125 μg/cm2 on apple surfaces. The SERS methods provide simple, rapid, and sensitive ways to detect acetamiprid in beverages and on the surfaces of thick skinned fruits and vegetables.