bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of sterol synthesis in bacteria
Authors: Wei Jeremy H. , Yin Xinchi , Welander Paula V. 
Published: April 2016

AbstractSterols are essential components of eukaryotic cells whose biosynthesis and function in eukaryotes has been studied extensively. Sterols are also recognized as the diagenetic precursors of steranes preserved in sedimentary rocks where they can function as geological proxies for eukaryotic organisms and/or aerobic metabolisms and environments. However, production of these lipids is not restricted to the eukaryotic domain as a few bacterial species also synthesize sterols. Phylogenomic studies have identified genes encoding homologs of sterol biosynthesis proteins in the genomes of several additional species, indicating that sterol production may be more widespread in the bacterial domain than previously thought. Although the occurrence of sterol synthesis genes in a genome indicates the potential for sterol production, it provides neither conclusive evidence of sterol synthesis nor information about the composition and abundance of basic and modified sterols that are actually being produced. Here, we coupled bioinformatics with lipid analyses to investigate the scope of bacterial sterol production. We identified oxidosqualene cyclase (Osc), which catalyzes the initial cyclization of oxidosqualene to the basic sterol structure, in 34 bacterial genomes from 5 phyla (Bacteroidetes, Cyanobacteria, Planctomycetes, Proteobacteria and Verrucomicrobia) and in 176 metagenomes. Our data indicate that bacterial sterol synthesis likely occurs in diverse organisms and environments and also provides evidence that there are as yet uncultured groups of bacterial sterol producers. Phylogenetic analysis of bacterial and eukaryotic Osc sequences revealed two potential lineages of the sterol pathway in bacteria indicating a complex evolutionary history of sterol synthesis in this domain. We characterized the lipids produced by Osc-containing bacteria and found that we could generally predict the ability to synthesize sterols. However, predicting the final modified sterol based on our current knowledge of bacterial sterol synthesis was difficult. Some bacteria produced demethylated and saturated sterol products even though they lacked homologs of the eukaryotic proteins required for these modifications emphasizing that several aspects of bacterial sterol synthesis are still completely unknown. It is possible that bacteria have evolved distinct proteins for catalyzing sterol modifications and this could have significant implications for our understanding of the evolutionary history of this ancient biosynthetic pathway.
Araport11: a complete reannotation of theArabidopsis thalianareference genome
Authors: Cheng Chia-Yi , Krishnakumar Vivek , Chan Agnes , Schobel Seth , Town Christopher D. 
Published: April 2016

ABSTRACTThe flowering plantArabidopsis thalianais a dicot model organism for research in many aspects of plant biology. A comprehensive annotation of its genome paves the way for understanding the functions and activities of all types of transcripts, including mRNA, noncoding RNA, and small RNA. The most recent annotation update (TAIR10) released more than five years ago had a profound impact onArabidopsisresearch. Maintaining the accuracy of the annotation continues to be a prerequisite for future progress. Using an integrative annotation pipeline, we assembled tissue-specific RNA-seq libraries from 113 datasets and constructed 48,359 transcript models of protein-coding genes in eleven tissues. In addition, we annotated various classes of noncoding RNA including small RNA, long intergenic RNA, small nucleolar RNA, natural antisense transcript, small nuclear RNA, and microRNA using published datasets and in-house analytic results. Altogether, we identified 738 novel protein-coding genes, 508 novel transcribed regions, 5051 non-coding genes, and 35846 small-RNA loci that formerly eluded annotation. Analysis on the splicing events and RNA-seq based expression profile revealed the landscapes of gene structures, untranslated regions, and splicing activities to be more intricate than previously appreciated. Furthermore, we present 692 uniformly expressed housekeeping genes, 43% of whose human orthologs are also housekeeping genes. This updated Arabidopsis genome annotation with a substantially increased resolution of gene models will not only further our understanding of the biological processes of this plant model but also of other species.
Effective Dynamic Models of Metabolic Networks
Authors: Vilkhovoy Michael , Minot Mason , Varner Jeffrey D. 
Published: April 2016

AbstractMathematical models of biochemical networks are useful tools to understand and ultimately predict how cells utilize nutrients to produce valuable products. Hybrid cybernetic models in combination with elementary modes (HCM) is a tool to model cellular metabolism. However, HCM is limited to reduced metabolic networks because of the computational burden of calculating elementary modes. In this study, we developed the hybrid cybernetic modeling with flux balance analysis or HCM-FBA technique which uses flux balance solutions instead of elementary modes to dynamically model metabolism. We show HCM-FBA has comparable performance to HCM for a proof of concept metabolic network and for a reduced anaerobicE. colinetwork. Next, HCM-FBA was applied to a larger metabolic network of aerobicE. colimetabolism which was infeasible for HCM (29 FBA modes versus more than 153,000 elementary modes). Global sensitivity analysis further reduced the number of FBA modes required to describe the aerobicE. colidata, while maintaining model fit. Thus, HCM-FBA is a promising alternative to HCM for large networks where the generation of elementary modes is infeasible.
Growth-Environment Dependent Modulation ofStaphylococcus aureusBranched-Chain to Straight-Chain Fatty Acid Ratio and Incorporation of Unsaturated Fatty Acids
Authors: Sen Suranjana , Johnson Seth R. , Song Yang , Sirobhushanam Sirisha , Tefft Ryan , Gatto Craig , Wilkinson Brian J. 
Published: April 2016

AbstractThe fatty acid composition of membrane glycerolipids is a major determinant ofStaphylococcus aureusmembrane biophysical properties that impacts key factors in cell physiology including susceptibility to membrane active antimicrobials, pathogenesis, and response to environmental stress. The fatty acids ofS. aureusare considered to be a mixture of branched-chain fatty acids (BCFAs), which increase membrane fluidity, and straight-chain fatty acids (SCFAs) that decrease it. The balance of BCFAs and SCFAs in strains USA300 and SH1000 was affected considerably by differences in the conventional laboratory medium in which the strains were grown with media such as Mueller-Hinton broth and Luria broth resulting in high BCFAs and low SCFAs, whereas growth in Tryptic Soy Broth and Brain-Heart Infusion broth led to reduction in BCFAs and an increase in SCFAs. Straight-chain unsaturated fatty acids (SCUFAs) were not detected. However, when the organism was grownex vivoin serum, the fatty acid composition was radically different with SCUFAs, which increase membrane fluidity, making up a substantial proportion of the total (<25%) with SCFAs (>37%) and BCFAs (>36%) making up the rest. Staphyloxanthin, an additional major membrane lipid component unique toS. aureus, tended to be greater in content in cells with high BCFAs or SCUFAs. Cells with high staphyloxanthin content had a lower membrane fluidity that was attributed to increased production of staphyloxanthin.S. aureussaves energy and carbon by utilizing host fatty acids for part of its total fatty acids when growing in serum. The fatty acid composition ofin vitrogrownS. aureusis likely to be a poor reflection of the fatty acid composition and biophysical properties of the membrane when the organism is growing in an infection in view of the role of SCUFAs in staphylococcal membrane composition and virulence.Funding:This work was funded in part by grant 1R15AI099977 to Brian Wilkinson and Craig Gatto and grant 1R15GM61583 to Craig Gatto from the National Institutes of Health
Pattern alteration of women’s suits based on ease distribution
Authors: Gu Bingfei , Su Junqiang , Liu Guolian , Xu Bugao 
Published: April 2016

Purpose
The goal of this study was to realize pattern alterations for women’s suits by using the spatial distribution of distance ease in the body-garment interface.

Design/methodology/approach
An unclothed mannequin and the mannequin clothed with seven suits having different ease allowances were scanned by a 3D body scanner respectively. The image of the unclothed mannequin was then superimposed on that of each clothed mannequin (suit) to exhibit the differences in ease distribution among these suits. The distance eases at ten selected body landmarks were determined by measuring the gaps between the body and suit surfaces.

Findings
The mathematical models of ease distributions were built through the regression analysis to predict the distance ease with a given ease allowance. After the verification with the actual measurements, these ease distribution models could provide localized distance eases for alternating pattern pieces to ensure a specified ease allowance.

Originality/value
In order to realize the automatic generation of garment patterns, the ease distribution between a human body and a garment is crucial because ease is one of the determinants for garment fit. This study demonstrated a new approach of automatic pattern alteration based on 3D scanned data to accelerate the pattern making process for women’s suits with customized ease allowance.
Modification of Hogarth models on the stripe costume
Authors: Zhu Xuyun , Wen Xuming , Wang Jianping , Zhang Hang 
Published: April 2016

Purpose
Beautiful and simple curves are most commonly employed in apparel design since they can not only simplify the manufacture process, but also significantly beautify the breast profile of customers. However, it is regularly difficult to choose the most suitable curve when producing the strip costume; this is due to the fact that the curve is a kind of aesthetics without any laws. The quantification and standardization to curves are necessary for fashion design. The purpose of this paper is to investigate the relationship between the stripe of costumes and the breast profiles of wearers.

Design/methodology/approach
Seven curves drawn derived from the Hogarth theory (Hogarth curves) were firstly diagrammatized by the central line technology using CorelDraw, and the format of bitmaps and quadratic functions of these selected curves were obtained respectively. Simulating formulas were subsequently used to interpret these curves. The standard of curves for apparel design was finally established after being evaluated by comparison between the different types of female breasts and the curves on the costumes.

Findings
The established models indicated that the fourth Hogarth curves was the most attractive one that combining the static state and the dynamic beauty, which could also help females to highlight the beautiful breast shapes.

Originality/value
This work provided the fundamentally understanding of the application of Hogarth curves in fashion design and the improvement on the effectiveness of the garment industry.
Analysis of surface metal fiber arrangement of electromagnetic shielding fabric and its influence on shielding effectiveness
Authors: Liu Zhe , Wang Xiuchen , Zhang Yongheng , Zhou Zhong 
Published: April 2016

Purpose
No adequate study on scientific analysis of surface metal fiber (SMF) arrangement of electromagnetic shielding fabric (EMSF) and influence on shielding effectiveness (SE) is available at present.

Design/methodology/approach
This paper recognizes the SMF region and constructs a binary feature matrix according to edge condition, width condition and gray condition using the computer image analysis technique based on the construction of the surface digitized image of the EMSF. Three parameters of coverage, dispersion and uniformity are proposed to describe the SMF arrangement. Then experiments and testing samples are designed to analyze the relationship between the three parameters and the SE.

Findings
Results show that the proposed method can accurately recognize the SMF of the EMSF, the coverage, dispersion and uniformity can describe three aspects of the SMF arrangement of percentage content, porosity and orientation, and the three parameters are positively, negatively and positively correlated to the SE, respectively.

Originality/value
The research in this paper provides the basis for further description of the SMF arrangement of the EMSF, possesses the significance for the study of the shielding mechanism, transmission model, electromagnetic performance and rapid non-destructive evaluation of the EMSF and provide a new idea for the study on the shielding theory and application of the EMSF.
Design preferences on wearable e-nose systems for diabetes
Authors: Koo Helen S. , Michaelson Dawn , Teel Karla , Kim Dong-Joo , Park Hyejin , Park Minseo 
Published: April 2016

Purpose
The purpose of this study is to investigate potential users’ preferences and expectations for fabric-based wearable e-nose system designs in order to develop painless and non-invasive monitoring systems for diabetes.

Design/methodology/approach
After developing a fabric-based wearable sensor, this study used an online survey with a mixture of closed- and open-ended questions about people’s desires and preferences for use-contexts, product types, design styles, and other key design factors.

Findings
This study investigated the preferences and expectations on designs of wearable e-nose systems for diabetes. The results showed that designers and developers need to consider important design components including sizes, shapes, and colors for practical wearable e-nose system designs. There were strong positive and significant correlations between participant characteristics and preferred wearable e-nose system design factors.

Research limitations/implications
Future research could compare differences between different age groups with different types of diabetes.

Practical implications
Understanding these differences will help designers and marketers target consumers and create diverse designs with different versions for success in the market.

Originality/value
There is lack of research for considering designs of wearable monitoring systems for diabetes. This research will be the first research to understand design preferences and expectations for developing wearable e-nose monitoring systems for diabetes.
The impact of FGM on Shangani women in Zimbabwe
Authors: Mutanda Darlington , Rukondo Howard 
Published: April 2016

Purpose
– The purpose of this paper is to discuss the practice of female genital mutilation (FGM) in the context of gender and HIV/AIDS among the Shangani people in Zimbabwe. Broadly, the discussion ais to fcus on how FGM has been used as tool to maintain the subordinate position of women in the Shangani community.

Design/methodology/approach
– In addition to secondary material, the paper hugely benefited from interviews with Shangani women in order to appreciate the challenges of eradicating FGM in their society. The sources pointed to the fact that in addition to being exploitative, FGM has no direct health benefits to women.

Findings
– The paper confirms that eliminating FGM is difficult because it is deeply entrenched in the patriarchal establishment of the Shangani society. As a result of the patriarchal nature of the society, women find themselves subjected to positions of powerlessness as compared to their male counterparts.

Originality/value
– The paper confirms that FGM is a widespread practice in many African communities including Zimbabwe. As communities grapple with the challenges of eradicating or minimising the practice, it is important in the meantime to modernise cultural practices like FGM as a way of doing away with the spreading of HIV/AIDS. Indonesia has already taken that route. FGM as a cultural practice exposes young women to HIV infection because of blood conduct.
Diversified
mcr-1
-Harbouring Plasmid Reservoirs Confer Resistance to Colistin in Human Gut Microbiota
Authors: Ye Huiyan , Li Yihui , Li Zhencui , Gao Rongsui , Zhang Han , Wen Ronghui , Gao George F. , Hu Qinghua , Feng Youjun 
Published: April 2016

ABSTRACT

Colistin is an ultimate line of refuge against multidrug-resistant Gram-negative pathogens. Very recently, the emergence of plasmid-mediated
mcr-1
colistin resistance has become a great challenge to global public health, raising the possibility that dissemination of the
mcr-1
gene is underestimated and diversified. Here, we report three cases of plasmid-carried MCR-1 colistin resistance in isolates from gut microbiota of diarrhea patients. Structural and functional analyses determined that the colistin resistance is conferred purely by the single
mcr-1
gene. Genetic and sequence mapping revealed that
mcr-1
-harbouring plasmid reservoirs are present in diversity. Together, the data represent the first evidence of diversity in
mcr-1
-harbouring plasmid reservoirs of human gut microbiota.

IMPORTANCE
The plasmid-mediated mobile colistin resistance gene (
mcr-1
) challenged greatly the conventional idea mentioned above that colistin is an ultimate line of refuge against lethal infections by multidrug-resistant Gram-negative pathogens. It is a possibility that diversified dissemination of the
mcr-1
gene might be greatly underestimated. We report three cases of plasmid-carried MCR-1 colistin resistance in isolates from gut microbiota of diarrhea patients and functionally define the colistin resistance conferred purely by the single
mcr-1
gene. Genetic and sequence mapping revealed unexpected diversity among the
mcr-1
-harbouring plasmid reservoirs of human gut microbiota.
The Importance of First Impressions: Early Events in Mycobacterium tuberculosis Infection Influence Outcome
Authors: Cadena Anthony M. , Flynn JoAnne L. , Fortune Sarah M. 
Published: April 2016

ABSTRACTTuberculosis remains a major health threat in much of the world. New vaccines againstMycobacterium tuberculosisare essential for preventing infection, disease, and transmission. However, the host immune responses that need to be induced by an effective vaccine remain unclear. Increasingly, it has become clear that early events in infection are of major importance in the eventual outcome of the infection. Studying such events in humans is challenging, as they occur within the lung and thoracic lymph nodes, and any clinical signs of early infection are relatively nonspecific. Nonetheless, clinical studies and animal models of tuberculosis have provided new insights into the local events that occur in the first few weeks of tuberculosis. Development of an effective vaccine requires a clear understanding of the successful (and detrimental) early host responses againstM. tuberculosis, with the goal to improve upon natural immune responses and prevent infection or disease.
New index of social deprivation during pregnancy: results from a national study in France
Authors: Opatowski Marion , Blondel Béatrice , Khoshnood Babak , Saurel-Cubizolles Marie-Josèphe 
Published: April 2016

ObjectivesTo identify precariousness markers in pregnant women that differ from the usual socioeconomic variables.MethodsData were obtained from the National Perinatal Survey, a representative sample of women giving birth in France in 2010. From six indicators of social vulnerability, four were selected by multiple correspondence analysis. The first axis of this analysis was used, characterised by the following contributory variables: receiving RSA (Revenu de Solidarité Active) allowance; benefitting from the CMU (Couverture Maladie Universelle) system (French social security) or not being insured; not living in own accommodation; and not living with a partner. These four variables were summed to create a deprivation index.ResultsThis index was strongly associated with social maternal characteristics and correctly identified women who were socially vulnerable. Furthermore, it was highly related to the psychosocial context, access to care, behaviours during pregnancy, and pregnancy outcomes. These associations remained significant after adjustment for social variables: compared with no deprivation (no factors), a high level of deprivation (≥3 factors) was associated with late prenatal care (OR 5.8, 95% CI 4.6 to 7.2) and small for gestational age (OR 1.5, 95% CI 1.1 to 1.9).ConclusionsThis index of social deprivation was associated with health issues and behaviours during pregnancy, even after adjustment for social variables, revealing a dimension not measured by the usual variables. Moreover, it is simple to use and easily reproducible.
Health and social consequences of an alcohol-related admission to critical care: a qualitative study
Authors: McPeake Joanne , Forrest Ewan , Quasim Tara , Kinsella John , O'Neill Anna 
Published: April 2016

ObjectiveTo examine the impact of critical care on future alcohol-related behaviour. Further, it aimed to explore patterns of recovery for patients with and without alcohol use disorders beyond the hospital environment.DesignIn-depth, semistructured interviews with participants (patients) 3–7 months post intensive care discharge.SettingThe setting for this study was a 20-bedded mixed intensive care unit (ICU), in a large teaching hospital in Scotland. On admission, patients were allocated to one of the three alcohol groups: low risk, harmful/hazardous and alcohol dependency.Participants21 participants who received mechanical ventilation for greater than 3 days were interviewed between March 2013 and June 2014.InterventionsNone.Measurements and main resultsFour themes which impacted on recovery from ICU were identified in this patient group: psychological resilience, support for activities of daily living, social support and cohesion and the impact of alcohol use disorders on recovery. Participants also discussed the importance of personalised goal setting and appropriate and timely rehabilitation for alcohol-related behaviours during the critical care recovery period.ConclusionsThere is a significant interplay between alcohol misuse and recovery from critical illness. This study has demonstrated that at present, there is a haphazard approach to rehabilitation for patients after ICU. A more targeted rehabilitation pathway for patients leaving critical care, with specific emphasis on alcohol misuse if appropriate, requires to be generated.