bluuebunny/crossref_metadata_2025_split huggingface dataset:
Principled Multi-Omic Analysis Reveals Gene Regulatory Mechanisms Of Phenotype Variation
Authors: Hanson Casey , Cairns Junmei , Wang Liewei , Sinha Saurabh 
Published: June 2017

AbstractRecent studies have analyzed large scale data sets of gene expression to identify genes associated with inter-individual variation in phenotypes ranging from cancer sub-types to drug sensitivity, promising new avenues of research in personalized medicine. However, gene expression data alone is limited in its ability to reveal cis-regulatory mechanisms underlying phenotypic differences. In this study, we develop a new probabilistic model, called pGENMi, that integrates multi-omics data to investigate the transcriptional regulatory mechanisms underlying inter-individual variation of a specific phenotype – that of cell line response to cytotoxic treatment. In particular, pGENMi simultaneously analyzes genotype, DNA methylation, gene expression and transcription factor (TF)-DNA binding data, along with phenotypic measurements, to identify TFs regulating the phenotype. It does so by combining statistical information about expression quantitative trait loci (eQTLs) and expression-correlated methylation marks (eQTMs) located within TF binding sites, as well as observed correlations between gene expression and phenotype variation. Application of pGENMi to data from a panel of lymphoblastoid cell lines treated with 24 drugs, in conjunction with ENCODE TF ChIP data, yielded a number of known as well as novel TF-drug associations. Experimental validations by TF knock-down confirmed 41% of the predicted and tested associations, compared to a 12% confirmation rate of tested non-associations (controls). Extensive literature survey also corroborated 62% of the predicted associations above a stringent threshold. Moreover, associations predicted only when combining eQTL and eQTM data showed higher precision compared to an eQTL-only or eQTM-only analysis with the same method, further demonstrating the value of multi-omic integrative analysis.
Overcoming the SPS concerns of the Bangladesh fisheries and aquaculture sector
Authors: Alam Shawkat , Tomossy George F. 
Published: June 2017

Purpose
The purpose of this paper is to address the challenges developing countries face in attempting to balance sanitary and phytosanitary measures (SPS) health and safety measures against concerns about protectionism, illustrated by the impact of trade barriers on the fisheries and aquaculture sector in Bangladesh. The paper then provides recommendations to overcome the effects of these trade barriers.

Design/methodology/approach
The author uses a close doctrinal approach for the first three parts of the paper by analysing the provisions of the World Trade Organisation (WTO) SPS Agreement and the effect of those provisions in creating domestic compliance gaps in the Bangladeshi fisheries and aquaculture sector. A qualitative approach is then adopted in suggesting potential reforms and future directions to assist the Bangladeshi fisheries and aquaculture sector overcome SPS trade barrier issues.

Findings
To overcome the market access issues created by SPS trade barriers, Bangladesh and other developing countries require multilateral assistance, accommodation by trading partners and internal reforms. This includes reforming internal governance structures, improving trade participation and negotiation, increasing infrastructure investment and learning from similar countries who have improved their supply chain management.

Research limitations/implications
This paper will have significant implications by contributing to law and policy reform debates involving international trade law and domestic compliance gaps. It will also assist other developing countries that experience SPS trade barriers to learn from the experience of the Bangladeshi fisheries and aquaculture sector.

Practical implications
This paper has practical implications by providing recommendations for how Bangladesh can overcome SPS trade barriers and improve its market access. This will help Bangladesh integrate into the global trading system by enhancing its participation in the SPS framework.

Social implications
By addressing and providing recommendations for the SPS trade barrier challenges faced by Bangladesh fishery and aquaculture sector, this paper provides a framework to improve the economic development and global competitiveness of the industry. This will contribute the gross domestic product growth and help increase the overall living standards of the people involved in the fisheries and aquaculture business in Bangladesh.

Originality/value
This paper is an original work that has not been published elsewhere. It is the first time a paper has dealt with the legal, policy and compliance challenges faced by the fisheries and aquaculture sector in Bangladesh.
Story composition, mental state language and self‐regulated strategy instruction for writers with autism spectrum conditions
Authors: Mourgkasi Vasiliki , Mavropoulou Sofia 
Published: June 2017

In this single‐subject study, we evaluated the effects of an intervention using a modified version of the Self‐Regulated Strategy Development (SRSD) approach on the story composition skills and the use of mental state language in three writers with autism spectrum conditions (ASC). Interestingly, the intervention was not found to be effective in increasing the number of words, sentences and advanced words for all participants, while only two participants used more story elements and improved the holistic quality of their compositions. Nevertheless, all participants used more mental state terms, spent more time for story planning, transferred their new skills to different writing tasks and maintained them 4 weeks post‐intervention. These findings demonstrate the effectiveness of the extended version of the SRSD approach on the use of mental state language in the writings of children with ASC.
Luther's Schem Hamphoras
Authors: Schramm Brooks 
Published: June 2017

AbstractThis article provides a concise summary of Luther's anti‐Jewish treatise, On the Schem Hamphoras and On the Lineage of Christ (March 1543) and describes its purpose, interworkings, and scatological rhetoric. The treatise is interpreted as Luther's defense of the Second Commandment over against Jewish superstitions regarding the name of God; his attempt to undermine the credibility of the rabbis and their influence on the Christian Hebraists; and his further strengthening of his platform for the expulsion of the Jews as initially articulated in On the Jews and Their Lies (January 1543).
Relationships, Human Nature, and the Four “Words” of Inspector Gamache1
Authors: Largen Kristin Johnston 
Published: June 2017

AbstractThe Inspector Gamache mysteries by Louise Penny are very popular, in no small part because of the appeal of the main character, Chief Inspector Armand Gamache. However, another main draw of the series is the small set of recurring main characters. In this article, I delve deeply into their lives and relationships, using as a lens the four sayings of Gamache as a means of illuminating both the brokenness and grace that characterize human relationality.
“These Things Continue”: Violence as Contamination in Everyday Life After War in Northern Uganda
Authors: Meinert Lotte , Whyte Susan Reynolds 
Published: June 2017

AbstractAfter decades of violent war, families are rebuilding their lives in the Acholi subregion of Northern Uganda. The return to normal order is marked by problems people see as consequences of the years of insecurity: mental illness, alcoholism, domestic violence, marital instability, and land conflicts that sometimes turn vicious. The ravages of war and years of constraint have left a legacy of troubles that is contagious and contaminating. The war is over, but people say that “these things continue.” In this article, we follow the case of one family and explore the social contagion and contamination of “these things.” We relate Acholi ideas ofcen, the spirits of the vengeful dead, to Post‐Traumatic Stress Disorder (PTSD) and phenomenological conceptions of violence and “the alien” in human experience.
The Shareholder Base Hypothesis of Stock Return Volatility: Empirical Evidence
Authors: Jankensgård Håkan , Vilhelmsson Anders 
Published: June 2017

AbstractWe use Swedish ownership data to explore whether a large and diversified shareholder base leads to lower volatility by improving the information content of stock prices. We find that volatility increases in the number of shareholders with respect to both the number of relatively large shareholders and the fraction of shares held by investors with stakes below 0.1%. Volatility is also positively related to the number of institutional owners but negatively related to the number of large and underdiversified institutional owners. Foreign investors have no impact. Our results suggest that a large shareholder base does not lower volatility.
Topical equol preparation improves structural and molecular skin parameters
Authors: Magnet U. , Urbanek C. , Gaisberger D. , Tomeva E. , Dum E. , Pointner A. , Haslberger A.G. 
Published: June 2017

AbstractObjectiveEquol has been shown to improve skin health and regeneration, due to its antioxidative, phytoestrogenic and epigenetic characteristics. The effects of a topical intervention on skin structure, telomere length and epigenetic markers in skin cells were analysed.MethodsSixty‐four participants were divided in four groups and three of them treated topically with the following: emulsion with Equol powder (Isoflavandiol‐E‐55‐RS®); emulsion with microencapsulated Equol (Vesisorb® Isoflavandiol‐E‐55‐RS®) and an emulsion with lecithin (Vesisorb® placebo). A control group of 6 volunteers did not receive any intervention. The active compound was a 0.5% equol‐racemate. For 58 participants, all samples were collected. Structural analysis, molecular analysis and questionnaires were performed at the start of the study and after 8 weeks of intervention, twice a day. Structural skin parameters were analysed by Visioscan® VC 98 and Cutometer® dual MPA 580. Molecular analyses from epidermal cells collected by skin stripping of the forehead included telomere length and LINE‐1 methylation, following DNA extraction, bisulfite conversion and qPCR as well as high‐resolution melting curve analysis. Effects of nutrition and lifestyle habits were evaluated with a standardized food and lifestyle questionnaire.Results and discussionThe surface analysis showed significant improvements in skin roughness, skin texture and skin smoothness after both interventions. Cutometer® dual MPA 580 measurement revealed improvement of skin firmness and elasticity parameters for both preparations. A decrease in mean LINE‐1 methylation (n.s.) and telomere length (sign. P < 0.05) was observed in the sample group with age. In the treated groups, significantly longer telomeres were observed after intervention. Whether changes in telomere length reflect changes in the regulation of telomerase, epigenetic interactions or turnover of keratinocytes needs further research. Stability and availability of preparations in skin seems to be high as not many significant differences in the activity of pure or encapsulated substances were seen.ConclusionThe results of this study indicate that equol has beneficial effects on structural as well as molecular skin parameters and encourages further investigations to decipher the epigenetic regulation of skin ageing and interactions of equol.
Life of Martha Entwistle: Australia's first convict mental health nurse
Authors: Raeburn Toby , Liston Carol , Hickmott Jarrad , Cleary Michelle 
Published: June 2017

AbstractThe present position paper provides an account of the life of Martha Entwistle, the earliest recorded convict nurse who worked within the Castle Hill Asylum. In our review of primary historical sources, Australia's first convict mental health nurse was found to be a resilient woman who endured several traumatic life experiences. Her nursing within Australia's first mental health asylum was highly valued by the superintendent of the service. She nursed in a harsh colonial environment, short of adequate resources, during an era of fast‐paced industrial and technological a change. Martha Entwistle's experiences provide a historical account of the role of the early convict mental health nurse. Her life story enables modern‐day nurses to reflect on the advances made in mental health nursing and contexts of care for nurses today.
A worldwide phylogenetic classification of the Poaceae (Gramineae) II: An update and a comparison of two 2015 classifications
Authors: Soreng Robert J. , Peterson Paul M. , Romaschenko Konstantin , Davidse Gerrit , Teisher Jordan K. , Clark Lynn G. , Barberá Patricia , Gillespie Lynn J. , Zuloaga Fernando O. 
Published: June 2017

AbstractWe present a new worldwide phylogenetic classification of 11 506 grass species in 768 genera, 12 subfamilies, seven supertribes, 52 tribes, five supersubtribes, and 90 subtribes; and compare two phylogenetic classifications of the grass family published in 2015 (Soreng et al. and Kellogg). The subfamilies (in descending order based on the number of species) are Pooideae with 3968 species in 202 genera, 15 tribes, and 30 subtribes; Panicoideae with 3241 species in 247 genera, 13 tribes, and 19 subtribes; Bambusoideae with 1670 species in 125 genera, three tribes, and 15 subtribes; Chloridoideae with 1602 species in 124 genera, five tribes, and 26 subtribes; Aristidoideae with 367 species in three genera, and one tribe; Danthonioideae with 292 species in 19 genera, and one tribe; Micrairoideae with 184 species in eight genera, and three tribes; Oryzoideae with 115 species in 19 genera, four tribes, and two subtribes; Arundinoideae with 40 species in 14 genera, two tribes, and two subtribes; Pharoideae with 12 species in three genera, and one tribe; Puelioideae with 11 species in two genera, and two tribes; and the Anomochlooideae with four species in two genera, and two tribes. We also include a radial tree illustrating the hierarchical relationships among the subtribes, tribes, and subfamilies. Newly described taxa include: supertribes Melicodae and Nardodae; supersubtribes Agrostidodinae, Boutelouodinae, Gouiniodinae, Loliodinae, and Poodinae; and subtribes Echinopogoninae and Ventenatinae.
Anatomy, microstructure, and endogenous hormone changes in Gnetum parvifolium during anthesis
Authors: Lan Qian , Liu Jian‐Feng , Shi Sheng‐Qing , Deng Nan , Jiang Ze‐Ping , Chang Er‐Mei 
Published: June 2017

AbstractThe study of the sexual systems of plants is very important for understanding their evolutionary process. Gnetum is a pivotal species in comprehending the seed plant phylogeny. However, the sexual systems of this genus are not fully understood. To investigate the sexual system of Gnetum, the anatomical structure, microstructure, and endogenous hormones were investigated from the differentiation of flower buds to fertilization in the floral organs of female and male of G. parvifolium (Warb.) C.Y. Cheng, widely distributed in the north of China. After 2 years of field investigations, the staminate strobili were observed on female plants for the first time and the abortive ovules were also found on male plants. In addition, high levels of gibberellin A3 and zeatin riboside led to masculinization, whereas a high level of indole‐3‐acetic acid favored feminization. A comprehensive analysis of the results indicates that G. parvifolium may not be completely dioecious on morphology, but female and male plants can only perform their own gender function, which would provide a better understanding of the diversity of sexual systems in Gnetum, and reproductive structures of seed plants.
On Proprioception in Action: Multimodality versus Deafferentation
Authors: Wong Hong Yu 
Published: June 2017

AbstractRecent research on proprioception reveals that it relies on a systematically distorted model of bodily dimensions. This generates a puzzle about proprioception in action control: action requires accurate bodily parameters. Proprioception is crucial for ordinary action, but if it relies on a systematically distorted body model, then proprioception should contain systematic errors. But we cannot respond by discarding proprioception from motor control, since we know from the severe problems deafferented agents face in acting that ordinary action requires proprioception. The solution is that the possibility of bodily action is provided for by multimodal body representations for action (the ‘body schema’).
Is the Quarter of Birth Endogenous? New Evidence from Taiwan, the US, and Indonesia
Authors: Fan Elliott , Liu Jin‐Tan , Chen Yen‐Chien 
Published: June 2017

AbstractRecent evidence based on US data suggests that the quarter or month of birth (QOB or MOB) may be endogenous, since family characteristics can explain up to 50% of the effects of QOB on the education outcomes and earnings of adult males. In this study, based on a sample of one million Taiwanese siblings, we examine university admission at age 18 as our outcome variable and find that at school entry, the oldest (September born) children are 31–38% more likely to be admitted into university at age 18 than the youngest (August born) children, indicating strong seasonality in university admission. The inclusion of controls for family background is found to explain only a small portion of these effects, particularly for males. Given that such results are at odds with the recent US evidence, we revisit the US Census data and find that when racial differences are properly controlled for in the estimation, even a rich set of family characteristics is capable of explaining only a minor proportion of the QOB effects. Furthermore, using data from the US and Indonesia, we find that seasonal temperature variation is unlikely to be an important contributor to the US‐Taiwan disparity. Our findings imply that the validity of using QOB or MOB as an instrumental variable may be dependent on the population being studied and the sample selected.
Structure Mapping and Vocabularies for Thinking
Authors: Loewenstein Jeffrey 
Published: June 2017

AbstractWhile extremes tend to capture attention, the ordinary is often most of the story. So it may be with the structure‐mapping process. The structure‐mapping process can account for such pinnacles of thinking as analogy and metaphor, which can lead to overlooking the mundane, incremental use of structure mapping. Consequently, the current discussion shifts focus to the value of close comparisons between literally similar items for the development of knowledge. The intent is to foster greater integration between process and content as well as between individuals and collectives. The payoff is identifying some undue simplifications and some promising new directions.
Removal of 17α‐ethinylestradiol, salicylic acid, trimethoprim, carbamazepine and nonylphenol through biological carbon and nitrogen removal processes
Authors: Odize Victory , Rahman Arifur , Jones Kimberly , Khunjar Wendell , Murthy Sudhir 
Published: June 2017

AbstractThis study investigated five different trace organic contaminants (TOrCs) (one hormone: 17α‐ethinylestradiol (EE2), two pharmaceuticals: salicylic acid (SA) and trimethoprim (TMP), one analgesic drug: carbamazepine (CBZ), and one surfactant metabolite: nonylphenol (NP)) removal efficiency at a full‐scale Advanced Wastewater Treatment Plant (AWTP). The AWTP achieved average EE2, SA and NP removal over 80% at the biological carbon removal stages. The results also showed a 66% removal of TMP at the nitrogen removal stages. CBZ was recalcitrant throughout the plant, due to its high solubility and low distribution coefficient between wastewater and sludge. Batch experiments were conducted on active and inactive secondary, nitrification and denitrification sludge by adding TOrCs to understand the removal mechanism through sorption and biodegradation. Sorption was the dominant mechanism to remove EE2, SA and NP in secondary treatment processes. In nitrification and denitrification processes, higher percentage of TOrCs removal through biodegradation were observed compared to removal through sorption.
Anaerobic Copper Toxicity and Iron-Sulfur Cluster Biogenesis in Escherichia coli
Authors: Tan Guoqiang , Yang Jing , Li Tang , Zhao Jin , Sun Shujuan , Li Xiaokang , Lin Chuxian , Li Jianghui , Zhou Huaibin , Lyu Jianxin , Ding Huangen 
Published: June 2017

ABSTRACT

While copper is an essential trace element in biology, pollution of groundwater from copper has become a threat to all living organisms. Cellular mechanisms underlying copper toxicity, however, are still not fully understood. Previous studies have shown that iron-sulfur proteins are among the primary targets of copper toxicity in
Escherichia coli
under aerobic conditions. Here, we report that, under anaerobic conditions, iron-sulfur proteins in
E. coli
cells are even more susceptible to copper in medium. Whereas addition of 0.2 mM copper(II) chloride to LB (Luria-Bertani) medium has very little or no effect on iron-sulfur proteins in wild-type
E. coli
cells under aerobic conditions, the same copper treatment largely inactivates iron-sulfur proteins by blocking iron-sulfur cluster biogenesis in the cells under anaerobic conditions. Importantly, proteins that do not have iron-sulfur clusters (e.g., fumarase C and cysteine desulfurase) in
E. coli
cells are not significantly affected by copper treatment under aerobic or anaerobic conditions, indicating that copper may specifically target iron-sulfur proteins in cells. Additional studies revealed that
E. coli
cells accumulate more intracellular copper under anaerobic conditions than under aerobic conditions and that the elevated copper content binds to the iron-sulfur cluster assembly proteins IscU and IscA, which effectively inhibits iron-sulfur cluster biogenesis. The results suggest that the copper-mediated inhibition of iron-sulfur proteins does not require oxygen and that iron-sulfur cluster biogenesis is the primary target of anaerobic copper toxicity in cells.

IMPORTANCE
Copper contamination in groundwater has become a threat to all living organisms. However, cellular mechanisms underlying copper toxicity have not been fully understood up to now. The work described here reveals that iron-sulfur proteins in
Escherichia coli
cells are much more susceptible to copper in medium under anaerobic conditions than they are under aerobic conditions. Under anaerobic conditions,
E. coli
cells accumulate excess intracellular copper, which specifically targets iron-sulfur proteins by blocking iron-sulfur cluster biogenesis. Since iron-sulfur proteins are involved in diverse and vital physiological processes, inhibition of iron-sulfur cluster biogenesis by copper disrupts multiple cellular functions and ultimately inhibits cell growth. The results from this study illustrate a new interplay between intracellular copper toxicity and iron-sulfur cluster biogenesis in bacterial cells under anaerobic conditions.
Complete Genome Sequence of Bacillus subtilis GQJK2, a Plant Growth-Promoting Rhizobacterium with Antifungal Activity
Authors: Ma Jinjin , Liu Hu , Wang Chengqiang , Xia Zhilin , Liu Kai , Hou Qihui , Li Yuhuan , Zhang Tongrui , Wang Haide , Wang Beibei , Wang Yun , Ge Ruofei , Xu Baochao , Yao Gan , Jiang Zhensheng , Hou Wentong , Ding Yanqin , Du Binghai 
Published: June 2017

ABSTRACT

Bacillus subtilis
GQJK2 is a plant growth-promoting rhizobacterium with antifungal activity which was isolated from
Lycium barbarum
L. rhizosphere. Here, we report the complete genome sequence of
B. subtilis
GQJK2. Ten gene clusters involved in the biosynthesis of antagonistic compounds were predicted.