bluuebunny/crossref_metadata_2025 huggingface dataset:
Understanding sequencing data as compositions: an outlook and review
Authors: Quinn Thomas P. , Erb Ionas , Richardson Mark F. , Crowley Tamsyn M.
Published: October 2017

Motivation

Although seldom acknowledged explicitly, count data generated by sequencing platforms exist as compositions for which the abundance of each component (e.g., gene or transcript) is only coherently interpretable relative to other components within that sample. This property arises from the assay technology itself, whereby the number of counts recorded for each sample is constrained by an arbitrary total sum (i.e., library size). Consequently, sequencing data, as compositional data, exist in a non-Euclidean space that renders invalid many conventional analyses, including distance measures, correlation coefficients, and multivariate statistical models.

Results

The purpose of this review is to summarize the principles of compositional data analysis (CoDA), provide evidence for why sequencing data are compositional, discuss compositionally valid methods available for analyzing sequencing data, and highlight future directions with regard to this field of study.
Whole-nanoparticle atomistic modeling of the schwertmannite structure from total scattering data
Authors: Sestu M. , Navarra G. , Carrero S. , Valvidares S. M. , Aquilanti G. , Pérez-Lopez R. , Fernandez-Martinez A.
Published: October 2017

Schwertmannite is a poorly crystalline nanometric iron sulfate oxyhydroxide. This mineral shows a structural variability under different environments. Because of that, the determination of its structure and, consequently, of its physical–chemical properties is quite challenging. This article presents a detailed structural investigation of the structure of schwertmannite conducted under different approaches: X-ray absorption spectroscopy, Rietveld refinement, and a combined reverse Monte Carlo and Debye function analysis of the whole nanoparticle structure. The schwertmannite model presented here is, to the auhors' knowledge, the most complete model so far reported.
4-(4-Hydroxyphenyl)-2,2,4-trimethyl-7,8-benzothiachroman, a fused-ring counterpart ofthia-Dianin's compound
Authors: Frampton Christopher S. , McKendrick Joseph J. , MacNicol David D.
Published: October 2017

The title compound, C22H22OS [systematic name: 4-(1,3,3-trimethyl-2,3-dihydro-1H-4-thiaphenanthren-1-yl)phenol], crystallizes unsolvated from nitromethane as colourless prisms (m.p. 425–427 K) in the polar monoclinic space groupIawithZ′ = 2 (moleculesAandB). Both independent molecules possess a very similarproximalconformation, this referring to the juxtaposition of the 4-hydroxyphenyl substituent with respect to thesyn-related methyl group. In the crystal, moleculeAis linked to moleculeBby an O—H...O hydrogen bond. In turn, moleculeBexhibits a weak O—H...π interaction with the phenolic group of moleculeArelated bya-glide symmetry. Together, these lead to [100] chains.
A new lanthanum(III) complex containing acetylacetone and 1H-imidazole
Authors: Koizumi Atsuya , Hasegawa Takuya , Itadani Atsushi , Toda Kenji , Zhu Taoyun , Sato Mineo
Published: October 2017

In the title complex, diaqua(1H-imidazole-κN3)(nitrato-κ2O,O′)bis(4-oxopent-2-en-2-olato-κ2O,O′)lanthanum(III), [La(C5H7O2)2(NO3)(C3H4N2)(H2O)2], the La atom is coordinated by eight O atoms of two acetylacetonate (acac) anions acting as bidentate ligands, two water molecule as monodentate ligands, one nitrate anions as a bidentate ligand and one N atom of an imidazolate (ImH) molecule as a monodentate ligand. Thus, the coordination number of the La atom is nine in a monocapped square antiprismatic polyhedron. There are three types of intermolecular hydrogen bonds between ligands, the first involving nitrate–water O...H—O interactions running along the [001] direction, the second involving acac–water O...H—O interactions along the [010] direction and the third involving an Im–nitrate N—H...O interaction along the [100] direction (five interactions of this type). Thus, an overall one-dimensional network structure is generated. The molecular plane of an ImH molecule is almost parallel to that of a nitrate ligand, making an angle of only 6.04 (12)°. Interestingly, the ImH plane is nearly perpendicular to the planes of two neighbouring acac ligands.
Crystal structure of {2,6-bis[(dimethylamino)methyl]phenyl-κ3N,C1,N′}(bromido/chlorido)mercury(II)
Authors: Gupta Anand , Singh Harkesh B. , Butcher Ray J.
Published: October 2017

In the molecular structure of the title compound, {2,6-bis[(dimethylamino)methyl]phenyl-κ3N,C1,N′}[bromido/chlorido(0.30/0.70)]mercury(II)–{2,6-bis[(dimethylamino)methyl]phenyl-κ3N,C1,N′}[bromido/chlorido(0.24/0.76)]mercury(II) (1/1), [HgBr0.30Cl0.70(C12H19N2)]·[HgBr0.24Cl0.76(C12H19N2)], there are two molecules in the asymmetric unit of formulaLHgX{L= 2,6-bis[(dimethylamino)methyl]phenyl andX= Cl/Br}. In each molecule, the halide site is mixed Cl/Br, with occupancies of 0.699 (7):0.301 (7) and 0.763 (7):0.237 (7), respectively. The two molecules are linked into dimers by a combination of Hg...Hg [Hg...Hg = 3.6153 (3) Å] and C—H...Cl and C—H...π interactions.
4-Benzyl-1-(4-nitrophenyl)-1H-1,2,3-triazole: crystal structure and Hirshfeld analysis
Authors: Zukerman-Schpector Julio , Dallasta Pedroso Sofia , Sousa Madureira Lucas , Weber Paixão Márcio , Ali Akbar , Tiekink Edward R. T.
Published: October 2017

The molecule in the title compound, C15H12N4O2, has a twistedL-shape with the dihedral angle between the aromatic rings of the N-bound benzene and C-bound benzyl groups being 70.60 (9)°. The nitro group is co-planar with the benzene ring to which it is connected [C—C—N—O torsion angle = 0.4 (3)°]. The three-dimensional packing is stabilized by a combination of methylene-C—H...O(nitro), methylene-C—H...π(phenyl), phenyl-C—H...π(triazolyl) and nitro-O...π(nitrobenzene) interactions, along with weak π(triazolyl)–π(nitrobenzene) contacts [inter-centroid distance = 3.8386 (10) Å]. The importance of the specified intermolecular contacts has been verified by an analysis of the calculated Hirshfeld surface.
Crystal structure of a CoIIcoordination polymer with a dipyridyl ligand:catena-poly[[bis(nitrato-κ2O,O′)cobalt(II)]-μ-N-(pyridin-2-ylmethyl)pyridine-3-amine-κ3N,N′:N′′]
Authors: Moon Suk-Hee , Kang Youngjin , Park Ki-Min
Published: October 2017

The asymmetric unit of the title compound, [Co(NO3)2L]n,L=N-(pyridine-2-ylmethyl)pyridine-3-amine (C11H11N3), contains one CoIIcentre, two nitrate anions and oneLligand in which the Cpy—C—N—Cpymoiety adopts atransconformation with a torsion angle of −173.1 (3) Å. The coordination geometry of the CoIIatom is a distorted pentagonal bipyramid. One amine N atom from theLligand and four O atoms from two η2-nitrato ligands form the basal plane and two pyridyl N atoms from two symmetry-relatedLligands occupy the apical positions [N—Co—N = 171.86 (11)°]. The displacement of the central CoIIatom from the basal plane (r.m.s. deviation = 0.085 Å) is 0.1491 (12) Å. Each bidentate nitrate group is bonded asymmetrically to the cobalt atom in an chelating fashion. The CoIIions are linked by theLligands to form a zigzag chain propagating along thec-axis direction. Within the zigzag chain, C—H...O hydrogen bonds between the ligands and the nitrate anions are observed. Adjacent zigzag chains are connectedviaintermolecular π–π stacking interactions [centroid-to-centroid distance = 3.844 (2) Å] between the pyridine rings together with N/C—H...O hydrogen bonds.
Prevalence of somatisation as a determinant of burnout amongst staff working in drug and alcohol services
Authors: Mazoruk Sabina , Huxley Adam , Alexis-Garsee Camille , Schifano Fabrizio
Published: October 2017

Purpose

The purpose of this paper is to explore the prevalence of somatisation as a determinant of burnout amongst drug and alcohol staff in the UK.

Design/methodology/approach

The study employed a cross-sectional design utilising a self-completion online questionnaire. Data were collected from substance misuse workers across England and Wales. In total, 165 responses were eligible for analysis, yielding a response rate of 5 per cent. Burnout and somatization were measured with Maslach’s Burnout Inventory and the Physical Symptoms Inventory.

Findings

The prevalence of somatic symptoms was relatively low in the sample studied. The reported levels of burnout were moderate. Personal accomplishment remained high in the sample. There was a strong association between burnout and incidence of stress-related somatic symptoms, with higher levels of burnout correlating with multiple symptoms.

Research limitations/implications

It was not possible to determine the extent of non-response bias, as at the time of the study there was no information available relating to the characteristics of drug and alcohol staff in the selected services. Therefore, as the response rate was very low (5 per cent) it was recognised that non-response bias might have affected the findings, in such way that non-respondents may have differed in their experiences of work stress, satisfaction, burnout and health outcomes.

Practical implications

Despite the limitations, the study provided practical information relating to burnout vulnerability and associated physical symptoms in this specific occupational group. These findings can support employers to address staff wellbeing with a view to prevent burnout and reduce existing levels of burnout and related somatic symptoms, and improve job performance, job satisfaction and staff retention through making appropriate adjustments, such as developing staff-wellbeing programmes. These adjustments could potentially contribute to improvement in substance misuse practice, through maintenance of healthy and satisfied workforce.

Originality/value

There are very few studies looking at burnout in drug and alcohol staff. This study is also novel in a way that it reveals correlations between a variety of specific stress-related physical symptoms and the three components of burnout.
A letter to teacher candidates at the dawn of the Trump Presidency
Authors: Smagorinsky Peter , Brasley Andie , Johnson Rebekah , Shurtz Lisa
Published: October 2017

Purpose

This paper aims to describe a letter written to undergraduate students before their enrollment in a required foundations course, Service-Learning in English Education, taken before admission to the English education program at [the university]. The course, offered in the spring of 2017, came on the heels of Donald Trump’s election to the US Presidency, an event that followed from a campaign that raged against “politically correct” social developments that respect the dignity of people historically marginalized in US society.

Design/methodology/approach

The letter lays out the perils of teaching a diversity-oriented course in an era of disdain for diverse people and cultures. The letter explains how the course design attempts to give all interpretive authority to the students through their selection of course books and the book club design of promoting discussion outside professorial surveillance.

Findings

The paper includes the comments of three students regarding their response to the letter and course, and concludes that teaching a politicized course in a tempestuous time is risky yet possible.

Originality/value

This paper looks at one teacher educator’s approach to introducing diversity-related ideas in a Red State during an anti-diversity presidency.
Exploring #BlackLivesMatter and sociopolitical relationships through kinship writing
Authors: Muhammad Gholnecsar E. , Mason Chisholm Glenda , Starks Francheska D.
Published: October 2017

Purpose

This study aims to explore the textual and sociopolitical relationships of kinship writing as 15 youth wrote politically charged poetry while participating in a four-week summer writing program grounded in a Black studies curriculum.

Design/methodology/approach

The authors explore the following research questions: How do youth writers draw upon each other’s writing to compose sociopolitical kinship poems when writing about critical issues affecting Black lives? What topics and oppressions do youth choose to write about and how do they write about these topics?

Findings

The authors found that the youth wrote across multiple topics affecting Black lives in their kinship poems. These include the appropriation of black beauty, gun violence and police brutality, love and Black lives, the need for equality, negative depictions and misrepresentations of Black people, the neglect and omission of Black lives and suppression of freedom. The youth took up various critical issues in their poems, which addressed what they deemed as most urgent in the lives of Black people, and these selected topics were highly historicized. We also found that the youth used the content, styles and audience of the original poems to pen their own pieces.

Research limitations/implications

Writing with another peer afforded collaborative writing and spaces for youth to read and interrogate the world while building criticality through their writing.

Originality/value

Kinship writing is a genre in which one piece of writing has a relationship with another piece of writing. Kinship writing carries significance in the Black literary community as the history of Black education has been interlaced with ideals of social learning, community, family and kinship. This literary approach contributes to ways Black people used each other’s writings to offer healing, comfort and care in a turmoil filled world.
Numerical solution of Stefan problem with variable space grid method based on mixed finite element/finite difference approach
Authors: Ivanovic Milos , Svicevic Marina , Savovic Svetislav
Published: October 2017

Purpose

The purpose of this paper is to improve the accuracy and stability of the existing solutions to 1D Stefan problem with time-dependent Dirichlet boundary conditions. The accuracy improvement should come with respect to both temperature distribution and moving boundary location.

Design/methodology/approach

The variable space grid method based on mixed finite element/finite difference approach is applied on 1D Stefan problem with time-dependent Dirichlet boundary conditions describing melting process. The authors obtain the position of the moving boundary between two phases using finite differences, whereas finite element method is used to determine temperature distribution. In each time step, the positions of finite element nodes are updated according to the moving boundary, whereas the authors map the nodal temperatures with respect to the new mesh using interpolation techniques.

Findings

The authors found that computational results obtained by proposed approach exhibit good agreement with the exact solution. Moreover, the results for temperature distribution, moving boundary location and moving boundary speed are more accurate than those obtained by variable space grid method based on pure finite differences.

Originality/value

The authors’ approach clearly differs from the previous solutions in terms of methodology. While pure finite difference variable space grid method produces stable solution, the mixed finite element/finite difference variable space grid scheme is significantly more accurate, especially in case of high alpha. Slightly modified scheme has a potential to be applied to 2D and 3D Stefan problems.
Working around it
Authors: Naweed Anjum , Trigg Joshua , Allan Matthew , Chapman Janine
Published: October 2017

Purpose

The rail driver workplace is full of challenges for effective health management. The purpose of this paper is to investigate how known barriers in rail driving may be overcome by seeking enablers of positive health status and lifestyle.

Design/methodology/approach

Five focus groups were conducted with 29 rail drivers from four rail organisations across three Australian states. Transcribed data were analysed using directed content analysis and thematic coding to develop health enabler themes and categories.

Findings

Formal initiatives to manage health were piecemeal. Efforts to maintain health involved countering deteriorative, and promoting restorative, health factors. Themes systematically illustrated work environmental, adaptational, and autonomous features of health management. Participants expressed many different approaches to enabling positive health status, and how these connected to known barriers.

Research limitations/implications

Discussion of personal health issues within the rail industry is considered a taboo topic by some, therefore participants who took part in this study data may be more representative of health-conscious drivers.

Practical implications

Occupational health in rail can be enabled in multiple ways, including: improving social support, scheduling certainty, and cross-communication around health behaviours; increasing flexibility and environmental support for health behaviours; and directly promoting dietary control and physical activity engagement. Given the diversity and global representativeness of rail systems found within Australia, the findings have international application.

Originality/value

This study uses a strength-focussed approach to highlight multiple leverage points for organisational rail-driver health interventions across three levels of the system, helping improve health intervention efficacy despite the intractable nature of their environments.
Tackling workplace bullying
Authors: Georgakopoulos Alexia , Kelly Michael P.
Published: October 2017

Purpose

The purpose of this paper is to raise awareness of the benefits of wellness programs for contemporary organizations and aids in tackling workplace bullying.

Design/methodology/approach

This study used a qualitative design and employs a new empirical approach to tackle workplace bullying. With over a hundred working professionals engaged in focus groups and facilitation methodologies for a total of five workshops and 60 hours, this study suggests a new framework for intervening in workplace bullying that considers workplace wellness as a system.

Findings

The findings revealed that these professionals perceived workplace wellness as a formidable component of the health and success of employees, organizations, and community, and perceived workplace bullying as a serious threat to physical and mental wellness. Employee participation and involvement in the design of workplace wellness programs was viewed as essential to the success of these programs in organizations.

Research limitations/implications

This research has implications as it expands understanding and discovery into what aids employees to reduce their stress, fatigue, anxiety, and other conditions that lead to conflict or bullying in workplaces. It gives attention to a system of wellness that is vital to people and their organizations.

Practical implications

Study participants consistently asserted their desire to be active participants in establishing workplace wellness programs that effectively address workplace bullying, systems that enhance safety, and health.

Social implications

This study highlights the role organizations play in shaping individual and community physical and mental well-being, health, and safety through effective workplace wellness programs.

Originality/value

This study should be helpful to organizations and researchers looking to address workplace wellness, safety, and bullying in a context broader than just liability and the cost savings of employee physical health, and may further add to the discussions of workplace wellness policy and regulation.
Comprehensive functional characterization of the glycoside hydrolase family 3 enzymes from Cellvibrio japonicus reveals unique metabolic roles in biomass saccharification
Authors: Nelson Cassandra E. , Attia Mohamed A. , Rogowski Artur , Morland Carl , Brumer Harry , Gardner Jeffrey G.
Published: October 2017

Lignocellulose degradation is central to the carbon cycle and renewable biotechnologies. The xyloglucan (XyG), β(1→3)/β(1→4) mixed‐linkage glucan (MLG) and β(1→3) glucan components of lignocellulose represent significant carbohydrate energy sources for saprophytic microorganisms. The bacterium Cellvibrio japonicus has a robust capacity for plant polysaccharide degradation, due to a genome encoding a large contingent of Carbohydrate‐Active enZymes (CAZymes), many of whose specific functions remain unknown. Using a comprehensive genetic and biochemical approach, we have delineated the physiological roles of the four C. japonicus glycoside hydrolase family 3 (GH3) members on diverse β‐glucans. Despite high protein sequence similarity and partially overlapping activity profiles on disaccharides, these β‐glucosidases are not functionally equivalent. Bgl3A has a major role in MLG and sophorose utilization, and supports β(1→3) glucan utilization, while Bgl3B underpins cellulose utilization and supports MLG utilization. Bgl3C drives β(1→3) glucan utilization. Finally, Bgl3D is the crucial β‐glucosidase for XyG utilization. This study not only sheds the light on the metabolic machinery of C. japonicus, but also expands the repertoire of characterized CAZymes for future deployment in biotechnological applications. In particular, the precise functional analysis provided here serves as a reference for informed bioinformatics on the genomes of other Cellvibrio and related species.
From vineyard to winery: a source map of microbial diversity driving wine fermentation
Authors: Morrison‐Whittle Peter , Goddard Matthew R.
Published: October 2017

Humans have been making wine for thousands of years and microorganisms play an integral part in this process as they not only drive fermentation, but also significantly influence the flavour, aroma and quality of finished wines. Since fruits are ephemeral, they cannot comprise a permanent microbial habitat; thus, an age‐old unanswered question concerns the origin of fruit and ferment associated microbes. Here we use next‐generation sequencing approaches to examine and quantify the roles of native forest, vineyard soil, bark and fruit habitats as sources of fungal diversity in ferments. We show that microbial communities in harvested juice and ferments vary significantly across regions, and that while vineyard fungi account for ∼40% of the source of this diversity, uncultivated ecosystems outside of vineyards also prove a significant source. We also show that while communities in harvested juice resemble those found on grapes, these increasingly resemble fungi present on vine bark as the ferment proceeds.
Providing Family Planning Services at Primary Care Organizations after the Exclusion of Planned Parenthood from Publicly Funded Programs in Texas: Early Qualitative Evidence
Authors: White Kari , Hopkins Kristine , Grossman Daniel , Potter Joseph E.
Published: October 2017

Objective

To explore organizations’ experiences providing family planning during the first year of an expanded primary care program in Texas.

Data Sources

Between November 2014 and February 2015, in‐depth interviews were conducted with program administrators at 30 organizations: 7 women's health organizations, 13 established primary care contractors (e.g., community health centers, public health departments), and 10 new primary care contractors.

Study Design

Interviews addressed organizational capacities to expand family planning and integrate services with primary care.

Data Extraction

Interview transcripts were analyzed using a theme‐based approach. Themes were compared across the three types of organizations.

Principal Findings

Established and new primary care contractors identified several challenges expanding family planning services, which were uncommon among women's health organizations. Clinicians often lacked training to provide intrauterine devices and contraceptive implants. Organizations often recruited existing clients into family planning services, rather than expanding their patient base, and new contractors found family planning difficult to integrate because of clients’ other health needs. Primary care contractors frequently described contraceptive provision protocols that were not evidence‐based.

Conclusions

Many primary care organizations in Texas initially lacked the capacity to provide evidence‐based family planning services that women's health organizations already provided.
The Impact of the 2013 CAP Reform on the Decoupled Payments’ Capitalisation into Land Values
Authors: Ciaian Pavel , Kancs d'Artis , Espinosa Maria
Published: October 2017

We assess the effects of the 2013 CAP reform on the capitalisation of decoupled payments in land rental values. Our estimates suggest that the reform leads to an increase in the capitalisation of decoupled payments by an additional 18 cents for each Euro of decoupled payments relative to the pre‐reform situation. However, there is an important variation in the reform effects between Member States (MS) particularly between Old Member States (OMS) and New MS (NMS). In NMS, the capitalisation rate slightly reduces from 83% in the pre‐reform period to 79% in the post‐reform period. Although, the rate is significantly lower in OMS, it doubles (from 21% to 43%) due to the reform. The main sources of the post‐reform capitalisation in the European Union (EU) are the pre‐reform capitalisation accounting for 69% of the total post‐reform capitalisation, followed by the entitlement stock change with 19%, by the internal convergence of payments with 18%, the budget change (including external convergence) with 1%, and the differentiation of payments (redistributive payment) with −7%. Overall, our estimates suggest that on average in the EU, the non‐farming landowners’ policy gains are 27% of the total decoupled payments in the post‐reform period compared to 18% in the pre‐reform period.
Identification of Thiols in Yellow Onion (Allium cepa L.) Using Solvent Vented Large Volume Injection GC‐MS
Authors: Wermes Clint , Cannon Robert , Haasnoot Sytze , Colstee Hans , Niedeveld Cor , Koopmanschap Gijs , Da Costa Neil C.
Published: October 2017

Thiols are often highly odor active molecules and as such can significantly contribute to aroma while being present at extremely low concentrations. This paper details the identification of thiols in yellow onion juice by solvent extraction followed by thiol enrichment using a mercuric agarose gel column. Due to the inherent thermal instability and low concentrations of thiols in onion, chromatographic analysis utilized larger volume solvent elimination injections. New sulfur compounds in onion included 1,1‐propanedithiol, bis‐(1‐sulfanylpropyl)‐sulfide, 1‐methylsulfanyl‐1‐propanethiol, 1‐propylsulfanyl‐1‐propanethiol, and 1‐allylsulfanyl‐1‐propanethiol. A discussion on the potential route of formation for each compound is included along with the orthonasal and retronasal evaluations of the synthesized molecules. This work investigated and identified 5 newly identified compounds present in onions that can impart onion character at low concentrations levels.
Differential expression of the three Alcanivorax borkumensis SK2 genes coding for the P450 cytochromes involved in the assimilation of hydrocarbons
Authors: Sevilla Emma , Yuste Luis , Moreno Renata , Rojo Fernando
Published: October 2017

Alcanivorax borkumensis, a marine bacterium highly specialized in degrading linear and branched alkanes, plays a key ecological role in the removal of marine oil spills. It contains several alternative enzyme systems for terminal hydroxylation of alkanes, including three P450 cytochromes (P450‐1, P450‐2 and P450‐3). The present work shows cytochrome P450‐1 to be expressed from the promoter of the upstream gene fdx. Promoter Pfdx was more active when C8‐C18 n‐alkanes or pristane were assimilated than when pyruvate was available. The product of ABO_0199 (named CypR) was identified as a transcriptional activator of Pfdx. The inactivation of cypR impaired growth on tetradecane, showing the importance of the fdx‐P450‐1 and/or cypR genes. P450‐2 expression was low‐level and constitutive under all conditions tested, while that of P450‐3 from promoter P450‐3 was much higher when cells assimilated pristane than when n‐alkanes or pyruvate were available. However, the inactivation of P450‐3 had no visible impact on pristane assimilation. Cyo terminal oxidase, a component of the electron transport chain, was found to stimulate promoter PP450‐3 activity, but it did not affect promoters Pfdx or PP450‐2. A. borkumensis, therefore, appears to carefully coordinate the expression of its multiple hydrocarbon degradation genes using both specific and global regulatory systems.
Treatment and outcomes of melanoma in Asia: Results from the National Cancer Centre Singapore
Authors: Teh Yi Lin , Goh Wei Lin , Tan Sze Huey , Yong Grace , Sairi Alisa Noor Hidayah , Soo Khee Chee , Ong Johnny , Chia Claramae , Tan Grace , Soeharno Henry , Tan Mann Hong , Chan Michelle , Sathiyamoorthy Selvarajan , Sittampalam Kesavan , Teh Jonathan , Chin Francis , Sethi Vijay , Teo Melissa , Quek Richard , Farid Mohamad
Published: October 2017

Background

Acral melanoma (AM) and mucosal melanoma (MM) make up more than half of melanomas in Asia but comprise only 5% of cases in Caucasians, where cutaneous melanoma (CM) predominates. AM and MM are thought to be genetically and biologically distinct from CM. We report the characteristics and outcomes of melanoma patients from the National Cancer Centre Singapore.

Methods

Case records of 210 patients treated between 2002 and 2014 were reviewed.

Results

Median follow‐up was 2.5 years. CM, AM and MM made up of 37.6%, 33.8% and 16.2% of cases, respectively, with 6.2% each having ocular melanoma and unknown primary. Caucasians made up 16.2% of patients, accounting for 36.7% of CM but only 2.8 of AM and 2.9% of MM. Patients with MM (2.9% stage I, 14.7% stage IV) presented with higher American Joint Committee on Cancer (AJCC) stage than those with AM (16.9% stage I, 5.6% stage IV) or CM (24.1% stage I, 8.9% stage IV) (P = 0.01). Median overall survival (OS) was 5.7 years for all patients, and 1.0 year for metastatic disease. Considering stage I–III disease, multivariable Cox regression analysis demonstrated age ≥60 years and higher stage to be independent adverse prognostic factors for RFS and OS. Sentinel lymph node biopsy, undertaken for 56 stage I–III patients (25 AM, 31 CM) did not influence outcome.

Conclusion

Our study reinforces the known unique clinicopathologic features of melanomas in Asians where AM and MM predominate. Age and stage remain the most critical prognostic factors across all subtypes.
Editorial: rifaximin in cirrhosis ‐ is it what we've been waiting for?
Authors: Huang J.
Published: October 2017

Linked Content

This article is linked to Kang et al papers. To view these articles visit https://doi.org/10.1111/apt.14343 and https://doi.org/10.1111/apt.14275.
Letter: the risk of cancer in patients with gastric intestinal metaplasia
Authors: Ponzetto A. , Figura N.
Published: October 2017

Linked Content

This article is linked to Kuipers and Pittayanon et al papers. To view these articles visit https://doi.org/10.1111/apt.14155 and https://doi.org/10.1111/apt.14082.
Letter: enteral nutrition therapy for the induction of remission in paediatric Crohn's disease
Authors: Dai C. , Cao Q. , Jiang M.
Published: October 2017

Linked Content

This article is linked to Feathers et al and Swaminath et al papers. To view these articles visit https://doi.org/10.1111/apt.14359 and https://doi.org/10.1111/apt.14253.
Editorial: rifaximin in cirrhosis—is this what we've been waiting for? Authors’ reply
Authors: Kang S. H. , Lee Y. B. , Lee J.‐H.
Published: October 2017

Linked Content

This article is linked to Huang and Kang et al papers. To view these articles visit https://doi.org/10.1111/apt.14325 and https://doi.org/10.1111/apt.14275.
Letter: low‐FODMAP diet for exercise‐induced gastrointestinal syndrome—Authors’ reply
Authors: Costa R. J. S. , Snipe R. M. J. , Kitic C. M. , Gibson P. R.
Published: October 2017

Linked Content

This article is linked to Uno and Costa et al papers. To view these articles visit https://doi.org/10.1111/apt.14330 and https://doi.org/10.1111/apt.14157.
Single‐incision laparoscopic cholecystectomy for gallbladder torsion: A case report and literature review
Authors: Matsubara Keiso , Urushihara Takashi , Oshita Akihiko , Itamoto Toshiyuki
Published: October 2017

We present a case of preoperatively diagnosed gallbladder torsion (GT) that was successfully treated by single‐incision laparoscopic cholecystectomy. An 80‐year‐old woman presented with sudden pain and a palpable mass in the right upper quadrant. Contrast‐enhanced CT revealed ischemic changes, a swollen gallbladder with a V‐shaped distortion of the extrahepatic ducts, and the gallbladder in an abnormal anatomical position; clinical findings indicated GT. We performed single‐incision laparoscopic cholecystectomy and intraoperatively found that the floating gallbladder was twisted counterclockwise by 180° around the cystic duct. After an uneventful postoperative course, the patient was discharged on postoperative day 7. Laparoscopic cholecystectomy for a GT was first performed in 1994, and since then, 28 cases, including ours, have been treated laparoscopically. Laparoscopic cholecystectomy for GT could be the standard treatment for this condition, and single‐incision laparoscopic cholecystectomy may be a good surgical option for patients with GT because of its anatomical characteristics.
A method for extracting carboxy‐myoglobin from beef
Authors: Waga Masahiro , Takeda Shiro , Sakata Ryoichi
Published: October 2017

The present study was conducted to devise a method for the effective extraction of carboxy‐myoglobin (COMb) from beef without carbon monoxide dissociation. The ratio of COMb to myoglobin was computed at absorptions of wavelengths 541 and 551 nm, which characterize COMb and the isosbestic point between COMb and deoxy‐myoglobin, respectively. The COMb extraction rate was found to vary with temperature, pH and oxygen conditions. The decrease observed in this rate was inversely proportional to the rise in extraction temperature. The COMb extraction rate was also affected by pH, and the stability of COMb in the extract solution was the highest at pH 8.0–9.0. Moreover, the presence of oxygen was found to disturb COMb extraction. According to these results, nearly all COMb could be extracted from carbon‐monoxide‐treated beef under stirring conditions in pH 8.5 deoxidized buffer, at 1°C, and under N2 flow with the improved extraction method in this study (98.1 ± 2.7%). The decrement of COMb in the extract was accelerated by light, and the COMb was stable for 20 min in the dark, at 1°C. The extraction conditions for COMb described above should allow the accurate evaluation of COMb in meat tissue.
Perspective of landscape change following early settlement (landnám) in Svalbarðstunga, northeastern Iceland
Authors: Roy Natasha , Woollett James , Bhiry Najat , Haemmerli Guillaume , Forbes Véronique , Pienitz Reinhard
Published: October 2017

A series of peat monoliths was collected from Hjálmarvík, Kúðá and Bægístaðir, three abandoned farm sites located on a transect extending from the coast to 18 km inland in the Svalbarðstunga region (northeastern Iceland) in order to document the impact of human occupation and patterns of land use on landscape change and vegetation. Svalbarðstunga is of considerable interest because of the geographical and ecological features that distinguish it from other regions of Iceland, in particular by the more direct influence of the cold East Greenland Current (EGC). Plant and insect macrofossils and diatoms identified in peat monoliths provided proxy indicators of human settlement and land use that in some cases corroborate, and in others expand upon, existing archaeological and historical dates. Based on the presence of ecofacts (calcined bones, fish bones and charcoal), synanthropic insects and some anthropogenic plant‐indicators (e.g. weeds), we showed that there was a consistent occupation and use of the coastal site of Hjálmarvík sinceAD970. At Kúðá, the scenario is quite different. Two periods of occupation or land use were identified: from prior toc.AD960 to 1190 and fromc.AD1650 to 1870. In the 15th and into the 16th centuries, the decrease in the deposition of traces of fuel wastes around the inland farm sites (Kúðá and Bægístaðir) suggests that they were used much less frequently. The decline of such proxies for human occupation occurred shortly before the occurrence of the coldest conditions from the 16th to the 17th centuries as well as prior to the V1477 eruption, suggesting that these natural factors may not have been the primary or unique driver of changing modes of tenancy. A scenario of famine‐related depopulation would have played a significant role in this decrease in the human impact on vegetation.
FL‐926‐16, a novel bioavailable carnosinase‐resistant carnosine derivative, prevents onset and stops progression of diabetic nephropathy in db/db mice
Authors: Iacobini Carla , Menini Stefano , Blasetti Fantauzzi Claudia , Pesce Carlo M , Giaccari Andrea , Salomone Enrica , Lapolla Annunziata , Orioli Marica , Aldini Giancarlo , Pugliese Giuseppe
Published: October 2017

Background and Purpose

The advanced glycation end products (AGEs) participate in the pathogenesis of diabetic nephropathy (DN) by promoting renal inflammation and injury. L‐carnosine acts as a quencher of the AGE precursors reactive carbonyl species (RCS), but is rapidly inactivated by carnosinase. In this study, we evaluated the effect of FL‐926‐16, a carnosinase‐resistant and bioavailable carnosine derivative, on the onset and progression of DN in db/db mice.

Experimental Approach

Adult male db/db mice and coeval db/m controls were left untreated or treated with FL‐926‐16 (30 mg·kg−1 body weight) from weeks 6 to 20 (prevention protocol) or from weeks 20 to 34 (regression protocol).

Key Results

In the prevention protocol, FL‐926‐16 significantly attenuated increases in creatinine (−80%), albuminuria (−77%), proteinuria (−75%), mean glomerular area (−34%), fractional (−40%) and mean (−42%) mesangial area in db/db mice. This protective effect was associated with a reduction in glomerular matrix protein expression and cell apoptosis, circulating and tissue oxidative and carbonyl stress, and renal inflammatory markers, including the NLRP3 inflammasome. In the regression protocol, the progression of DN was completely blocked, although not reversed, by FL‐926‐16. In cultured mesangial cells, FL‐926‐16 prevented NLRP3 expression induced by RCS but not by the AGE Nε‐carboxymethyllysine.

Conclusion and Implications

FL‐926‐16 is effective at preventing the onset of DN and halting its progression in db/db mice by quenching RCS, thereby reducing the accumulation of their protein adducts and the consequent inflammatory response. In a future perspective, this novel compound may represent a promising AGE‐reducing approach for DN therapy.
Transient receptor potential vanilloid 4 channel regulates vascular endothelial permeability during colonic inflammation in dextran sulphate sodium‐induced murine colitis
Authors: Matsumoto Kenjiro , Yamaba Riho , Inoue Ken , Utsumi Daichi , Tsukahara Takuya , Amagase Kikuko , Tominaga Makoto , Kato Shinichi
Published: October 2017

Background and Purpose

The transient receptor potential vanilloid 4 (TRPV4) channel is a non‐selective cation channel involved in physical sensing in various tissue types. The present study aimed to elucidate the function and expression of TRPV4 channels in colonic vascular endothelial cells during dextran sulphate sodium (DSS)‐induced colitis.

Experimental Approach

The role of TRPV4 channels in the progression of colonic inflammation was examined in a murine DSS‐induced colitis model using immunohistochemical analysis, Western blotting and Evans blue dye extrusion assay.

Key Results

DSS‐induced colitis was significantly attenuated in TRPV4‐deficient (TRPV4 KO) as compared to wild‐type mice. Repeated intrarectal administration of GSK1016790A, a TRPV4 agonist, exacerbated the severity of DSS‐induced colitis. Bone marrow transfer experiments demonstrated the important role of TRPV4 in non‐haematopoietic cells for DSS‐induced colitis. DSS treatment up‐regulated TRPV4 expression in the vascular endothelia of colonic mucosa and submucosa. DSS treatment increased vascular permeability, which was abolished in TRPV4 KO mice. This DSS‐induced increase in vascular permeability was further enhanced by i.v. administration of GSK1016790A, and this effect was abolished by the TRPV4 antagonist RN1734. TRPV4 was co‐localized with vascular endothelial (VE)‐cadherin, and VE‐cadherin expression was decreased by repeated i.v. administration of GSK1016790A during colitis. Furthermore, GSK106790A decreased VE‐cadherin expression in mouse aortic endothelial cells exposed to TNF‐α.

Conclusion and Implications

These findings indicate that an up‐regulation of TRPV4 channels in vascular endothelial cells contributes to the progression of colonic inflammation by increasing vascular permeability. Thus, TRPV4 is an attractive target for the treatment of inflammatory bowel diseases.
Sedimentation in a foreland basin within synorogenic orocline: Palaeogene of the Isparta Bend, Taurides, SW Turkey
Authors: Nemec Wojciech , Alçiçek M. Cihat , Özaksoy Volkan
Published: October 2017

The Palaeogene Isparta Basin of southwestern Anatolia formed between two convergent arms of the Isparta Bend orocline of the Tauride orogen. The origin of this tightening orocline is hypothetically explained in plate‐tectonic terms. Basin sedimentation commenced on a down‐warped Mesozoic carbonate platform of a crustal block accreted at the end of Cretaceous to the southern margin of the Anatolian plate. The basin earliest deposits are Palaeocene reddish mudstones with a fossil‐barren condensed basal part and increasingly interspersed with thin calcarenitic turbidites towards the top. The supply of turbiditic sediment to the basin plain subsequently increased, as the upper‐bathyal basin plain became surrounded from both sides by a narrow littoral shelf with an advancing turbiditic slope ramp. A major forced regression occurred at the end of Bartonian, causing incision of subaerial to submarine valleys up 600 m deep, filled in with gravelly to sandy turbidites and debrisflow deposits during the subsequent rise of relative sea level. The half‐filled valleys were re‐incised due to a Rupelian forced regression and were fully filled with fluvio‐deltaic bayhead deposits during a final marine transgression that re‐established the basin‐margin biocalcarenitic shelf. The littoral environment then expanded across the shallowing basin, as the basin axial zone was up‐domed and eroded to bedrock level at the end of Oligocene and the basin was tectonically inverted in Miocene. The pattern of intra‐orocline foreland sedimentation documented by this case study provides tentative criteria for the recognition of synorogenic oroclines and for their distinction from post‐orogenic oroclines.
Basement suites: Demand, supply, space, and technology
Authors: Suttor Greg
Published: October 2017

Key Messages

The emergence of the basement suite sector reflected the historical evolution of housing demand, supply, and home technology.

Basement suites emerged as a distinct sector in the 1970s in a context of high rental demand, declining apartment production, and shortfalls in other low‐rent supply.

Basement suites were facilitated by post‐war innovations in housing spaces, equipment, and materials, such as natural gas heating, drywall, cheap appliances, and recreation rooms.
Amphiphilic small peptides for delivery of plasmid DNAs and siRNAs
Authors: Bang Eun‐Kyoung , Cho Hanna , Jeon Sean S.‐H. , Tran Na Ly , Lim Dong‐Kwon , Hur Wooyoung , Sim Taebo
Published: October 2017

Although various delivery systems for nucleic acids have been reported, development of an efficient and non‐toxic delivery carrier is still a key subject for gene therapy. To find new efficient delivery carriers for nucleic acids, we synthesized amphiphilic peptides composed of a guanidino group, an oleyl group, and a cysteine. We prepared both linear and branched types of peptides and found that the linear peptides were superior to the branched peptides as nucleic acid carriers. Our study also suggested that the intermolecular cysteine disulfides might allow the linear peptides to form the optimal particle sizes with nucleic acids for cellular uptake. The incorporation of a benzoyl group to the linear peptide gave rise to smaller, less suitable particle size with plasmid DNA, which greatly reduced the efficiency of plasmid DNA delivery. On the other hand, the benzoyl modification maintained the optimal particle size with siRNA, and interestingly it significantly enhanced the siRNA delivery. The higher efficiency is because the hydrophobicity from the benzoyl group might assist in interacting with the hydrophobic cell membrane. This demonstrates that a small structural change can modulate the preference of the carriers. Our study may provide an insight designing efficient delivery carriers.
The Development of Regional Dialect Locality Judgments and Language Attitudes Across the Life Span
Authors: McCullough Elizabeth A. , Clopper Cynthia G. , Wagner Laura
Published: October 2017

The development of language attitudes and perception of talker regional background was investigated across the life span (N = 240, age range = 4–75 years). Participants rated 12 talkers on dimensions of geographic locality, status, and solidarity. Children could classify some dialects by locality by age 6–7 years and showed adult‐like patterns by age 8 years. Children showed adult‐like status ratings for some dialects by age 4–5 years but were not fully adult‐like until age 12 years. Solidarity ratings were more variable and did not exhibit a clear developmental trajectory, although some adult‐like patterns were in place by age 6–7 years. Locality ratings were a significant but modest predictor of attitude ratings, suggesting that geographic knowledge is one contributor to language attitudes throughout development.
An investigation of foster parent training needs
Authors: Hebert Corie G. , Kulkin Heidi
Published: October 2017

The training foster parents receive in America, pass the initial training required to certify them to take children into their homes, is not standardized. The Foster Care Independence Act of 1999 (H.R. 3443) requires prospective foster parents to be trained, but it provides only general guidelines for the training content. The training offered differs by state. This research examines what a group of foster parents attending a state foster parent association conference felt they needed in the area of training, to help them fulfil their role. Quantitative and qualitative data were collected. Foster parents were surveyed and ranked their training needs based on 10 pre‐identified needs. They also responded to an open‐ended question about their training needs. Foster parents ranked training to enhance their ability to help the child adjust in their homes and manage challenging behaviours as most needed. The qualitative data suggested that foster parents have additional needs and some are not related to training, such as the need for respite services.