bluuebunny/crossref_metadata_2025 huggingface dataset:
Chromatin domains are encoded and molded by isochores: Isochores encode chromatin domains and chromosome compartments
Authors: Bernardi Giorgio
Published: December 2016

The formation of mammalian chromatin domains was investigated by analyzing the domain/isochore connection. This showed that LADs correspond to GC-poor isochores and are compositionally flat, flexible chromatin structures because of the local nucleosome depletions associated with the presence of oligo-A’s. In contrast, TADs correspond to GC-rich isochores that consist of single or (much more frequently) multiple, GC peaks that shape the single or multiple, loops of TADs. Indeed, the increasing nucleosome depletions linked to the GC gradients of isochore peaks lead to an increasing chromatin flexibility (accompanied by an increasing accessibility and decreasing supercoiling). In conclusion, isochores not only encode but also mold chromatin architecture; while architectural proteins play a role in closing and insulating TAD loops. An extension of this model concerns the encoding of open and closed chromosome compartments by alternating GC-rich and GC-poor isochores, the interactions among compartments defining the 3-D chromosome folding.
When GWAS meets the Connectivity Map: drug repositioning for seven psychiatric disorders
Authors: So Hon-Cheong , Chau Carlos K.L. , Chiu Wan-To , Ho Kin-Sang , Lo Cho-Pong , Yim Stephanie Ho-Yue , Sham Pak C.
Published: December 2016

Our knowledge of disease genetics has advanced rapidly during the past decade, with the advent of high-throughput genotyping technologies such as genome-wide association studies (GWAS). However, few methodologies were developed and systemic studies performed to identify novel drug candidates utilizing GWAS data. In this study we focus on drug repositioning, which is a cost-effective approach to shorten the developmental process of new therapies. We proposed a novel framework of drug repositioning by comparing GWAS-imputed transcriptome with drug expression profiles from the Connectivity Map. The approach was applied to 7 psychiatric disorders. We discovered a number of novel repositioning candidates, many of which are supported by preclinical or clinical evidence. We found that the predicted drugs are significantly enriched for known psychiatric medications, or therapies considered in clinical trials. For example, drugs repurposed for schizophrenia are strongly enriched for antipsychotics (p= 4.69E-06), while those repurposed for bipolar disorder are enriched for antipsychotics (p= 2.26E-07) and antidepressants (p= 1.17E-05). These findings provide support to the usefulness of GWAS signals in guiding drug discoveries and the validity of our approach in drug repositioning. We also present manually curated lists of top repositioning candidates for each disorder, which we believe will serve as a useful resource for researchers.
GeneSeqToFamily: the Ensembl Compara GeneTrees pipeline as a Galaxy workflow
Authors: Thanki Anil S. , Soranzo Nicola , Haerty Wilfried , Davey Robert P.
Published: December 2016

Background

Gene duplication is a major factor contributing to evolutionary novelty, and the contraction or expansion of gene families has often been associated with morphological, physiological and environmental adaptations. The study of homologous genes helps us to understand the evolution of gene families. It plays a vital role in finding ancestral gene duplication events as well as identifying genes that have diverged from a common ancestor under positive selection. There are various tools available, such as MSOAR, OrthoMCL and HomoloGene, to identify gene families and visualise syntenic information between species, providing an overview of syntenic regions evolution at the family level. Unfortunately, none of them provide information about structural changes within genes, such as the conservation of ancestral exon boundaries amongst multiple genomes. The Ensembl GeneTrees computational pipeline generates gene trees based on coding sequences and provides details about exon conservation, and is used in the Ensembl Compara project to discover gene families.

Findings

A certain amount of expertise is required to configure and run the Ensembl Compara GeneTrees pipeline via command line. Therefore, we have converted the command line Ensembl Compara GeneTrees pipeline into a Galaxy workflow, called GeneSeqToFamily, and provided additional functionality. This workflow uses existing tools from the Galaxy ToolShed, as well as providing additional wrappers and tools that are required to run the workflow.

Conclusions

GeneSeqToFamily represents the Ensembl Compara pipeline as a set of interconnected Galaxy tools, so they can be run interactively within the Galaxy’s user-friendly workflow environment while still providing the flexibility to tailor the analysis by changing configurations and tools if necessary. Additional tools allow users to subsequently visualise the gene families produced by the workflow, using the Aequatus.js interactive tool, which has been developed as part of the Aequatus software project.
OptiClust: Improved method for assigning amplicon-based sequence data to operational taxonomic units
Authors: Westcott Sarah L. , Schloss Patrick D.
Published: December 2016

Assignment of 16S rRNA gene sequences to operational taxonomic units (OTUs) is a computational bottleneck in the process of analyzing microbial communities. Although this has been an active area of research, it has been difficult to overcome the time and memory demands while improving the quality of the OTU assignments. Here we developed a new OTU assignment algorithm that iteratively reassigns sequences to new OTUs to optimize the Matthews correlation coefficient (MCC), a measure of the quality of OTU assignments. To assess the new algorithm, OptiClust, we compared it to ten other algorithms using 16S rRNA gene sequences from two simulated and four natural communities. Using the OptiClust algorithm, the MCC values averaged 15.2 and 16.5% higher than the OTUs generated when we used the average neighbor and distance-based greedy clustering with VSEARCH, respectively. Furthermore, on average, OptiClust was 94.6-times faster than the average neighbor algorithm and just as fast as distance-based greedy clustering with VSEARCH. An empirical analysis of the efficiency of the algorithms showed that the time and memory required to perform the algorithm scaled quadratically with the number of unique sequences in the dataset. The significant improvement in the quality of the OTU assignments over previously existing methods will significantly enhance downstream analysis by limiting the splitting of similar sequences into separate OTUs and merging of dissimilar sequences into the same OTU. The development of the OptiClust algorithm represents a significant advance that is likely to have numerous other applications.
Generation of heritable germline mutations in the jewel waspNasonia vitripennisusing CRISPR/Cas9
Authors: Li Ming , Cook Au Lauren Yun , Douglah Deema , Chong Abigail , White Bradley J. , Ferree Patrick M. , Akbari Omar S.
Published: December 2016

The revolutionary RNA-guided endonuclease CRISPR/Cas9 system has proven to be a powerful tool for gene editing in a plethora of organisms. Here, utilizing this system we developed an efficient protocol for the generation of heritable germline mutations in the parasitoid jewel wasp,Nasonia vitripennis, a rising insect model organism for the study of evolution, development of axis pattern formation, venom production, haplo-diploid sex determination, and host–symbiont interactions. To establish CRISPR-directed gene editing inN. vitripennis,we targeted a conserved eye pigmentation genecinnabar, generating several independent heritable germline mutations in this gene. Briefly, to generate these mutants, we developed a protocol to efficiently collectN. vitripenniseggs from a parasitized flesh fly pupa,Sarcophaga bullata, inject these eggs with Cas9/guide RNA mixtures, and transfer injected eggs back into the host to continue development. We also describe a flow for screening mutants and establishing stable mutant strains through genetic crosses. Overall, our results demonstrate that the CRISPR/Cas9 system is a powerful tool for genome manipulation inN. vitripennis, with strong potential for expansion to target critical genes, thus allowing for the investigation of a number of important biological phenomena in this organism.
Structural characterization of theStreptococcus pneumoniaecarbohydrate substrate-binding protein SP0092
Authors: Culurgioni Simone , Tang Minzhe , Walsh Martin Austin
Published: December 2016

Streptococcus pneumoniaeis an opportunistic respiratory pathogen that remains a major cause of morbidity and mortality globally, with infants and the elderly at the highest risk.S. pneumoniaerelies entirely on carbohydrates as a source of carbon and dedicates a third of all uptake systems to carbohydrate import. The structure of the carbohydrate-free substrate-binding protein SP0092 at 1.61 Å resolution reveals it to belong to the newly proposed subclass G of substrate-binding proteins, with a ligand-binding pocket that is large enough to accommodate complex oligosaccharides. SP0092 is a dimer in solution and the crystal structure reveals a domain-swapped dimer with the monomer subunits in a closed conformation but in the absence of carbohydrate ligand. This closed conformation may be induced by dimer formation and could be used as a mechanism to regulate carbohydrate uptake.
On human correspondence
Authors: Ingold Tim
Published: December 2016

In this article I offer an overture to social life, starting from the premise that every living being should be envisaged not as a blob but as a bundle of lines. I show that in joining with one another, these lines comprise a meshwork, in which every node is a knot. And in answering to one another, lifelines co‐respond. I propose the term ‘correspondence’ to connote their affiliation, and go on to show that correspondence rests on three essential principles: of habit (rather than volition), ‘agencing’ (rather than agency), and attentionality (rather than intentionality). I explain habit as ‘doing undergoing’, agencing as a process in which the ‘I’ emerges as a question, and attention as a resonant coupling of concurrent movements. I discuss the ethical and imaginative dimensions of correspondence under the respective rubrics of care and longing. Finally, I spell out the implications of a theory of correspondence for the way we approach classic themes of anthropological inquiry, including kinship and affinity, ecology and economy, ritual and religion, and politics and law. In a coda, I suggest that anthropology, too, must be a discipline of correspondence.
Flexible kinship: shaping transnational families among the Chinese in Tahiti
Authors: Trémon Anne‐Christine
Published: December 2016

This article examines the practices of ‘flexible kinship’ used by Chinese migrants in colonial Tahiti. ‘Flexible kinship’ draws attention to the strategic uses that are made of kinship in the context of migration and diaspora: the adjustments to cultural, political, and legal borders that lead to changes in family forms and in the relations between kin. Using a multi‐generational perspective, I examine how families were shaped by successive changes and reversals in legal‐political and economic events and conjunctures over the long twentieth century. I argue for the importance of addressing transnational border‐crossing practices that involve not just a spatial extension of networks but also legal strategies within the host locality. I further show that if it is true that the Confucian hierarchical order has conditioned transnational practices of flexible kinship, then this hierarchy has not only bent to the circumstances, it has to a great extent been weakened. Finally, I argue that the history of familial adjustments has shaped a habitus that maximizes economic and legal security, especially among women.
Unfitness for Detention Among Arrestees with Suspected Mental Disorders in Paris, France
Authors: Lepresle Aude , Vidal Camille , Mairesse Eric , Chariot Patrick
Published: December 2016

In this retrospective study (11/2013–04/2014), we aimed to identify the factors associated with psychiatric hospitalization among detainees in police custody. We included 137 patients (M/F, 74%/26%; median age, 37 years), and 125 (91%) had a mental disorder. Seventy‐seven patients (56%) had involuntary hospitalization. Sixty patients (44%) were declared fit for detention, and 48 (80%) of these patients had a mental disorder. All patients who required urgent psychiatric care and could not provide valid consent for care were declared as requiring involuntary hospitalization. Forty‐nine of the 62 patients (79%) who required urgent psychiatric care and were suspected to have committed serious crimes were involuntarily admitted. In conclusion, we commonly found that some individuals with mental disorders were considered fit for detention in police cells.
Policy Dilemmas in Financing Long‐term Care in Europe
Authors: Costa‐Font Joan , Courbage Christophe , Zweifel Peter
Published: December 2016

Long‐term care (LTC) is the largest insurable risk facing the elderly in most high‐income countries. Paradoxically, institutional responses to the need to insure ex ante (i.e. before the contingency occurs) the financial risks of needing LTC, either through social, private, or self insurance, exhibit limited development. In contrast, mechanisms to finance LTC ex post continue to develop, primarily those supported by the public sector (i.e. subsidies or tax deductions) and the family (i.e. intergenerational transfers). Both ex ante and ex post types of financing mechanisms are found to be subject to shortcomings which give rise to dilemmas for public policy. Governments confront these dilemmas in different ways, causing a great deal of heterogeneity in the financing and provision of LTC services across Europe.
‘I miss my family, it's been a while…’ A qualitative study of clinicians who live and work in rural/remote Australian Aboriginal communities
Authors: Irving Michelle , Short Stephanie , Gwynne Kylie , Tennant Marc , Blinkhorn Anthony
Published: December 2016

Objectives

Dental issues are more prevalent for Aboriginal Australians, especially those living in rural/remote locations, but distribution of clinicians is favoured towards metropolitan areas and are not always culturally competent. This study aimed to document the experiences of dental clinicians who relocated to rural/remote communities to provide dental services to Aboriginal communities in an effort to redress these gaps.

Setting

Clinicians working in a new rural/remote dental service strategy to Aboriginal communities in Northern NSW.

Design

Qualitative semi‐structured face‐to‐face interviews and reflective diaries were analysed qualitatively.

Participants

Relocating dental clinicians and their support team.

Results

Three major themes emerged: Theme one: Mastering the clinical environment through professional experiences: Increasing professional capabilities, clinical environment, valuing team work and gaining community respect. Theme two: Development and growth of the individual through personal and social experiences: culture shock, developing cultural competence, social impact, economic cost and personal adjustments and growth. Theme three: An overarching sense of achievement and advice to new clinicians.

Conclusion

Relocation to rural and remote communities to provide health services is a complex but rewarding process. Providing personal and professional support, to relocating clinicians resulted in an overall positive experience for the participants, where they increased their professional skills and developed personally. Living and working in the community increased their cultural competence. Barriers were overcome through effective communication, flexibility and teamwork. Funding for rural placements, such as these, is critical for rural and remote health services and should include long‐term appropriate funding for mentoring and support.
Evaluating distribution of the left branch of the middle colic artery and the left colic artery by CT angiography and colonography to classify blood supply to the splenic flexure
Authors: Fukuoka Asako , Sasaki Takahiro , Tsukikawa Satoshi , Miyajima Nobuyoshi , Ostubo Takehito
Published: December 2016

Introduction

CT angiography has gained widespread acceptance for preoperative evaluation of blood supply in patients with colorectal cancer. However, there have been few reports that pertain to the splenic flexure, for which surgery is technically difficult. We used preoperative CT angiography and CT colonography to evaluate blood supply to the splenic flexure.

Methods

We defined the splenic flexure as the junction of the distal third of the transverse colon and the proximal third of the descending colon. We reviewed 191 cases and considered the descending colon as divided into the proximal third and the distal two‐thirds; we then determined which part of the descending colon the left colic artery (LCA) entered. We also considered the transverse colon as divided into the proximal two‐thirds and the distal third, and evaluated which part of the transverse colon the left branch of the middle colic artery entered.

Result

We classified blood supply to the splenic flexure into six types, described by the feeder vessels: type 1, the LCA (39.7%); type 2, the left branch of the middle colic artery (17.8%); type 3, the LCA and the left branch of the middle colic artery (9.9%); type 4, the accessory left colic artery (4.1%); type 5, the LCA and the accessory left colic artery (2.6%); and type 6, the marginal artery (25.6%).

Conclusion

We classified blood supply to the splenic flexure into more complex types than previous reports had. Because we dissect the lymph nodes according to the type of blood supply, knowing the type before splenic flexure surgery is crucial.
Phase 2 study of tabalumab, a human anti‐B‐cell activating factor antibody, with bortezomib and dexamethasone in patients with previously treated multiple myeloma
Authors: Raje Noopur S. , Moreau Philippe , Terpos Evangelos , Benboubker Lotfi , Grząśko Norbert , Holstein Sarah A. , Oriol Albert , Huang Shang‐Yi , Beksac Meral , Kuliczkowski Kazimierz , Tai Datchen F. , Wooldridge James E. , Conti Ilaria , Kaiser Christopher J. , Nguyen Tuan S. , Cronier Damien M. , Palumbo Antonio
Published: December 2016

In this double‐blind, Phase 2 study, 220 patients with relapsed/refractory multiple myeloma were randomly assigned 1:1:1 to receive placebo (N = 72), tabalumab 100 mg (N = 74), or tabalumab 300 mg (N = 74), each in combination with dexamethasone 20 mg and subcutaneous bortezomib 1·3 mg/m2on a 21‐day cycle. No significant intergroup differences were observed among primary (median progression‐free survival [mPFS]) or secondary efficacy outcomes. ThemPFSwas 6·6, 7·5 and 7·6 months for the tabalumab 100, 300 mg and placebo groups, respectively (tabalumab 100 mg vs. placebo Hazard ratio (HR) [95% confidence interval (CI)] = 1·13 [0·80–1·59],P = 0·480; tabalumab 300 mg vs. placeboHR[95%CI] = 1·03 [0·72–1·45],P = 0·884). The most commonly‐reported treatment‐emergent adverse events were thrombocytopenia (37%), fatigue (37%), diarrhoea (35%) and constipation (32%). Across treatments, patients with low baselineBAFF(also termedTNFSF13B) expression (n = 162) had significantly longermPFSthan those with highBAFFexpression (n = 55), using the 75th percentile cut‐off point (mPFS[95%CI] = 8·3 [7·0–9·3] months vs. 5·8 [3·7–6·6] months;HR[95%CI] = 1·59 [1·11–2·29],P = 0·015). Although generally well tolerated,PFSwas not improved during treatment with tabalumab compared to placebo. A higher dose of 300 mg tabalumab did not improve efficacy compared to the 100 mg dose. Nonetheless,BAFFappears to have some prognostic value in patients with multiple myeloma.
Internal structure and significance of ice‐marginal moraine in the Kebnekaise Mountains, northern Sweden
Authors: Tonkin Toby N. , Midgley Nicholas G. , Graham David J. , Labadz Jillian C.
Published: December 2016

Despite a long history of glaciological research, the palaeo‐environmental significance of moraine systems in the Kebnekaise Mountains, Sweden, has remained uncertain. These landforms offer the potential to elucidate glacier response prior to the period of direct monitoring and provide an insight into the ice‐marginal processes operating at polythermal valley glaciers. This study set out to test existing interpretations of Scandinavian ice‐marginal moraines, which invoke ice stagnation, pushing, stacking/dumping and push‐deformation as important moraine forming processes. Moraines at Isfallsglaciären were investigated using ground‐penetrating radar to document the internal structural characteristics of the landform assemblage. Radar surveys revealed a range of substrate composition and reflectors, indicating a debris‐ice interface and bounding surfaces within the moraine. The moraine is demonstrated to contain both ice‐rich and debris‐rich zones, reflecting a complex depositional history and a polygenetic origin. As a consequence of glacier overriding, the morphology of these landforms provides a misleading indicator of glacial history. Traditional geochronological methods are unlikely to be effective on this type of landform as the fresh surface may post‐date the formation of the landform following reoccupation of the moraine rampart by the glacier. This research highlights that the interpretation of geochronological data sets from similar moraine systems should be undertaken with caution.
A small‐scale qualitative scoping study into the experiences of looked after children and care leavers who are parents in Wales
Authors: Roberts Louise
Published: December 2016

This paper presents the findings of a scoping study into looked after children and care leavers who are parents in Wales. Eight parents engaged in a qualitative interview. Thirty‐one pregnancies were discussed during the interviews: 16 live births, two ongoing pregnancies, one stillbirth, one termination and 11 miscarriages. At the point of interview, two parents continued to care for their children, but six had experienced the permanent removal of their child/ren as a result of social services intervention. Twelve of the 16 children discussed in the interviews were ‘looked after’ or adopted.

Despite its small‐scale nature, the study highlights important considerations before, during and after participants became parents. Broadly categorized, these relate to the influence of parents' childhood experiences on their capacity to be parents, the availability and adequacy of support during parenting and the ensuing impact of parenting ‘success’ or ‘failure’. For parents who had experienced the loss of a child, some were resigned to having no further children, some continued to hope for a family in the future, while others had experienced cycles of repeated pregnancies and compulsory removals. The findings are considered in the context of related literature and suggest that increased attention is required in this under‐researched but highly emotive area.
Recommendations and consensus on the treatment of peritoneal metastases of colorectal origin: a systematic review of national and international guidelines
Authors: Klaver C. E. L. , Groenen H. , Morton D. G. , Laurberg S. , Bemelman W. A. , Tanis P. J. ,   the research committee of the European Society of Coloproctology
Published: December 2016

Aim

This systematic review aimed to provide an overview of (inter)national guidelines on the treatment of peritoneal metastases of colorectal cancer origin (PMCRC) and to determine the degree of consensus and available evidence with identification of topics for future research.

Method

A systematic search of MEDLINE, Embase, PubMed as well as Tripdatabase, National Guideline Clearinghouse, BMJ Best Practice and Guidelines International Network was performed to identify (inter)national guidelines and consensus statements from oncological or surgical societies on PMCRC. The quality of guidelines was assessed using the AGREE‐II score. Topics followed by recommendations were extracted from the guidelines. The recommendations, highest level of supporting evidence and the degree of consensus were determined for each topic.

Results

Twenty‐one guidelines were included, in most (15) of which cytoreductive surgery with hyperthermic intraperitoneal chemotherapy (CRS/HIPEC) was recommended in selected patients based on level 1b evidence. Substantial consensus was also reached on the benefit of multidisciplinary team discussion and the achievability of a (near) complete cytoreduction (CC0‐1) without supporting evidence. Both evidence and consensus were lacking regarding other aspects including preoperative positron emission tomography/CT, second look surgery in high risk patients, the optimal patient selection for CRS/HIPEC, procedural aspects of HIPEC and (perioperative) systemic therapy.

Conclusion

In currently available guidelines, evidence and consensus on the treatment strategy for PMCRC are lacking. Updates of guidelines are ongoing and future (randomized) clinical trials should contribute to multidisciplinary and international consensus on treatment strategies for PMCRC.
Determinants of pre‐transplantation pectoralis muscle area (PMA) and post‐transplantation change in PMA in lung transplant recipients
Authors: Hoang Van , Li Gloria W. , Kao Christina C. , Dronavalli Goutham , Parulekar Amit D.
Published: December 2016

Background

This study aimed to determine predictors of pectoralis muscle area (PMA) and assess change in PMA following lung transplantation and its relationship to outcomes.

Methods

A retrospective review of 88 lung transplant recipients at a single center was performed. PMA was determined on a single axial slice from chest computerized tomography. Pectoralis muscle index (PMI) was calculated from the PMA divided by the height squared.

Results

PMI decreased post‐transplantation (8.1±2.8 cm2/m2 pre‐transplantation, 7.5±2.9 cm2/m2 at 6 months, and 7.6±2.7 cm2/m2 at 12 months, P<.05). Chronic obstructive pulmonary disease (COPD) and interstitial lung disease (ILD) were predictors of pre‐transplant PMI (β=−2.3, P=.001 for COPD; β=2.1, P<.001 for ILD) and percent change in PMI at 12 months post‐transplantation relative to baseline (β=19.2, P=.04 for COPD; β=−20.1, P=.01 for ILD). Patients in the highest quartile for PMI change at 12 months had fewer ventilator days compared with patients in the other quartiles (P=.03).

Conclusions

Underlying diagnosis was a significant predictor of both pre‐transplantation PMI and change in PMI post‐transplantation. Further studies of PMI are needed to determine its clinical utility in predicting outcomes following lung transplantation.
Immunoglobulin heavy and light chains and T‐cell receptor beta and gamma chains PCR assessment on cytological samples. A study comparing FTA cards and cryopreserved lymph node fine‐needle cytology
Authors: Peluso A. L. , Cozzolino I. , Bottiglieri A. , Lucchese L. , Di Crescenzo R. M. , Langella M. , Selleri C. , Zeppa P.
Published: December 2016

Objectives

To evaluate and compare the DNA yield and quality extracted from lymph node fine needle cytology (FNC) samples stored on FTA cards to those cryopreserved, and to assess the immunoglobulin heavy and light chains (IGHK) and T‐Cell receptor beta and gamma chains (TCRBG) PCR tests.

Methods

DNA extractions were performed on FNC of 80 non‐Hodgkin lymphomas (NHL), four myelomas and 56 benign reactive hyperplasias (BRH) cryopreserved and stored on FTA cards. The JAK2 gene was amplified to assess the DNA integrity and the IGHK/TCRBG clonality status was tested.

Results

IGHK monoclonality was found in 99% of B‐cell NHL and 100% of myeloma. TCRBG monoclonality was found in 100% of T‐cell NHL. TCRBG polyclonality was detected in 97% of B‐cell NHL, 100% of myeloma and 96% of BRH. IGHK/TCRBG PCR data were confirmed by histological and/or follow‐up controls. No differences were found in the DNA quality between cryopreservation and FTA cards storage methods.

Conclusions

IGHK/TCRBG PCR of the lymphoproliferative process on FTA cards is comparable to those cryopreserved. FTA cards can be used to store lymph node FNC for further molecular investigations.
Application of Ethical Principles to Research using Public Health Data in The Global South: Perspectives from Africa
Authors: Anane‐Sarpong Evelyn , Wangmo Tenzin , Sankoh Osman , Tanner Marcel , Elger Bernice Simone
Published: December 2016

Existing ethics guidelines, influential literature and policies on ethical research generally focus on real‐time data collection from humans. They enforce individual rights and liberties, thereby lowering need for aggregate protections. Although dependable, emerging public health research paradigms like research using public health data (RUPD) raise new challenges to their application. Unlike traditional research, RUPD is population‐based, aligned to public health activities, and often reliant on pre‐collected longitudinal data. These characteristics, when considered in relation to the generally lower protective ethico‐legal frameworks of the Global South, including Africa, highlight ethical gaps. Health and demographic surveillance systems are examples of public health programs that accommodate RUPD in these contexts. We set out to explore the perspectives of professionals with a working knowledge of these systems to determine practical ways of appropriating the foundational principles of health research to advance the ever growing opportunities in RUPD. We present their perspectives and in relation to the literature and our ethical analysis, make context relevant recommendations. We further argue for the development of a framework founded on the discussions and recommendations as a minimum base for achieving optimal ethics for optimal RUPD in the Global South.
The importance of canopy complexity in shaping seasonal spider and beetle assemblages in saltmarsh habitats
Authors: FORD HILARY , EVANS BEN , Van KLINK ROEL , SKOV MARTIN W. , GARBUTT ANGUS
Published: December 2016

1. Habitat structure, including vegetation structural complexity, largely determines invertebrate assemblages in semi‐natural grasslands. The importance of structural complexity to the saltmarsh invertebrate community, where the interplay between vegetation characteristics and tidal inundation is key, is less well known.

2. It was hypothesised that canopy complexity would be a more important predictor of spider and beetle assemblages than simple vegetation attributes (e.g. height, community type) and environmental variables (e.g. elevation) alone, measured in two saltmarsh regions, south‐east (Essex) and north‐west (Morecambe Bay) U.K. Canopy complexity (number of non‐vegetated ‘gaps’ in canopy ≥ 1 mm wide) was assessed using side‐on photography. Over 1500 spiders and beetles were sampled via suction sampling, winter and summer combined.

3. In summer, saltmarshes with abundant spider and beetle populations were characterised by high scores for canopy complexity often associated with tussocky grass or shrub cover. Simple vegetation attributes (plant cover, height) accounted for 26% of variation in spider abundance and 14% in spider diversity, rising to 46% and 41%, respectively, with the addition of canopy complexity score. Overwintering spider assemblages were associated with elevation and vegetation biomass. Summer beetle abundance, in particular the predatory and zoophagous group, and diversity were best explained by elevation and plant species richness.

4. Summer canopy complexity was identified as a positive habitat feature for saltmarsh spider communities (ground‐running hunters and sheet weavers) with significant ‘added value’ over more commonly measured attributes of vegetation structure.
Relationship Quality with Parents: Implications for Own and Partner Well‐Being in Middle‐Aged Couples
Authors: Polenick Courtney A. , Fredman Steffany J. , Birditt Kira S. , Zarit Steven H.
Published: December 2016

Relationships with parents have significant implications for well‐being throughout the lifespan. At midlife, these ties are situated within both developmental and family contexts that often involve the adult offspring's spouse. Yet, it is not known how ties with aging parents are related to psychological well‐being within middle‐aged couples. This study examined how middle‐aged wives’ and husbands’ views of the current quality of relationships with their own parents (positive and negative) are linked to their own and their partner's psychological well‐being. Using a sample of 132 middle‐aged couples from Wave 1 of the Family Exchanges Study, we estimated actor–partner interdependence models to evaluate these dyadic associations while controlling for each spouse's marital satisfaction. Both actor and partner effects were observed. With respect to actor effects, wives who reported more negative relationship quality with their own parents had elevated depressive symptoms and lower life satisfaction. Husbands who reported more negative relationship quality with their own parents had lower life satisfaction. In terms of partner effects, husbands had lower depressive symptoms and greater life satisfaction when wives reported more positive relationship quality with their own parents. Finally, the link between wives’ positive ties with parents and husbands’ lower depressive symptoms was intensified when husbands had less positive relationships with their own parents. Findings suggest that relationship quality with wives’ aging parents has implications for both spouses’ well‐being and may serve as a critical social resource for husbands.
In situ study on microwave sintering of ZTA ceramic: Effect of ZrO2 content on densification, hardness, and toughness
Authors: Meunier Christophe , Zuo Fei , Peillon Nathalie , Saunier Sébastien , Marinel Sylvain , Goeuriot Dominique
Published: December 2016

Better understanding of the effect of multimode‐microwave sintering of zirconia‐toughened alumina (ZTA) was investigated. A comparative dilatometric analysis was conducted between conventional and microwave heating processes, to clarify the influence of zirconia on the densification of ZTA under electromagnetic field. The thermal gradient on sample measurements indicates the change to the microwave volumetric heating is improved by zirconia which adsorbs microwave energy better, thus acting as a susceptor. The most beneficial effect on microstructure, toughness, and hardness were observed at the optimal zirconia content of 10 vol%. The results with both microwave and conventional sintering illustrate the strengthening effect on the composite by zirconia. Of special interest, multimode microwave sintering creates a finer homogeneous microstructure, with resulting hardness and toughening comparable to those obtained for conventional sintering, as well as improved densification, and at lower cost.
Technology‐enhanced storytelling stimulating parent–child interaction and preschool children's vocabulary knowledge
Authors: Teepe R.C. , Molenaar I. , Verhoeven L.
Published: December 2016

Preschool children's vocabulary mainly develops verbal through interaction. Therefore, the technology‐enhanced storytelling (TES) activity Jeffy's Journey is developed to support parent–child interaction and vocabulary in preschool children. TES entails shared verbal storytelling supported by a story structure and real‐time visual, auditory and textual prompts on a tablet computer. In this exploratory study, we investigated how TES influenced parent–child interaction and vocabulary. An experimental pretest‐intervention‐posttest design was followed with 44 3‐year‐old children and their parents in the experimental group and 27 peers in the control group. Results revealed that TES stimulated active child involvement and generated parent–child interaction, yet a great variety in TES characteristics both in time spent and usage of prompts was found among participants. Dyads that spent more time on story phases showed more and higher quality parent–child interaction. The usage of prompts was associated with improved parent–child interaction quality. Finally, an effect of TES was evidenced on children's productive vocabulary knowledge. To conclude, this study demonstrates that TES can be considered as a promising context for fostering parent–child interaction and children's vocabulary development.
The First Isolation and Characterisation of the Protist Labyrinthula sp. in Southeastern Australia
Authors: Sullivan Brooke K. , Robinson Katie L. , Trevathan‐Tackett Stacey M. , Lilje Erna S. , Gleason Frank H. , Lilje Osu
Published: December 2016

As a result of anthropogenic influences and global climate change, emerging infectious marine diseases are thought to be increasingly more common and more severe than in the past. The aim of our investigation was to confirm the presence of Labyrinthula, the aetiological agent of the seagrass wasting disease, in Southeastern Australia and provide the first isolation and characterisation of this protist, in Australia. Colonies and individual cells were positively identified as Labyrinthula using published descriptions, diagrams, and photographs. Their identity was then confirmed using DNA barcoding of a region of the 18S rRNA gene. Species level identification of isolates was not possible as the taxonomy of the Labyrinthula is still poorly resolved. Still, a diversity of Labyrinthula was isolated from small sections of the southeast coast of Australia. The isolates were grouped into three haplotypes that are biogeographically restricted. These haplotypes are closely related to previously identified saprotrophic clades. The study highlights the need for further investigation into the global distribution of Labyrinthula, including phylogenetic pathogenicity and analysis of host‐parasite interactions in response to stressors. Given the results of our analyses, it is prudent to continue research into disease and epidemic agents to better prepare researchers for potential future outbreaks.
Hepatic stellate cells secreting WFA+‐M2BP: Its role in biological interactions with Kupffer cells
Authors: Bekki Yuki , Yoshizumi Tomoharu , Shimoda Shinji , Itoh Shinji , Harimoto Norifumi , Ikegami Toru , Kuno Atsushi , Narimatsu Hisashi , Shirabe Ken , Maehara Yoshihiko
Published: December 2016

Background and Aim

Hepatic stellate cells (HSCs) play a central role in hepatic fibrosis and are regulated by Kupffer cells (KCs). Wisteria floribunda agglutinin‐positive Mac‐2 binding protein (WFA+‐M2BP) was recently identified as a serum marker for hepatic fibrosis. Although WFA+‐M2BP was identified as a ligand of Mac‐2, the function of WFA+‐M2BP in hepatic fibrosis remains unclear.

Methods

Liver specimens were obtained from five patients with cirrhosis, five with chronic hepatitis, and five without hepatic fibrosis. WFA+‐M2BP kinetics were evaluated histologically and in subpopulations of liver cells such as HSCs, KCs, endothelial cells, biliary epithelial cells, and hepatocytes in in vitro culture. The function of WFA+‐M2BP in activated HSCs was evaluated using immunoblot analysis.

Results

Numbers of WFA+‐M2BP‐positive cells in liver tissues increased with fibrosis stage. There were significant differences in WFA+‐M2BP levels between fibrosis stages F0 and F1–2 (P = 0.012) and between fibrosis stages F1–2 and F3–4 (P < 0.001). HSCs were the source of WFA+‐M2BP secretion in in vitro cultures of liver cells, as determined by sandwich immunoassay. Cells of the human HSC line LX‐2 also secreted WFA+‐M2BP. Histologically, tissue sections showed that WFA+‐M2BP was located in Mac‐2‐expressing KCs. In vitro assays showed that exogenous WFA+‐M2BP stimulation enhanced Mac‐2 expression in KCs and that HSCs co‐cultured with KCs increased α‐smooth muscle actin expression. Finally, Mac‐2‐depleted KCs with short interfering RNA had reduced α‐smooth muscle actin expression following co‐culturing with HSCs.

Conclusions

WFA+‐M2BP from HSCs induces Mac‐2 expression in KCs, which in turn activates HSCs to be fibrogenic.
Test–retest reliability of quantitative sensory testing for mechanical somatosensory and pain modulation assessment of masticatory structures
Authors: Costa Y. M. , Morita‐Neto O. , de Araújo‐Júnior E. N. S. , Sampaio F. A. , Conti P. C. R. , Bonjardim L. R.
Published: December 2016

Assessing the reliability of medical measurements is a crucial step towards the elaboration of an applicable clinical instrument. There are few studies that evaluate the reliability of somatosensory assessment and pain modulation of masticatory structures. This study estimated the test–retest reliability, that is over time, of the mechanical somatosensory assessment of anterior temporalis, masseter and temporomandibular joint (TMJ) and the conditioned pain modulation (CPM) using the anterior temporalis as the test site. Twenty healthy women were evaluated in two sessions (1 week apart) by the same examiner. Mechanical detection threshold (MDT), mechanical pain threshold (MPT), wind‐up ratio (WUR) and pressure pain threshold (PPT) were assessed on the skin overlying the anterior temporalis, masseter and TMJ of the dominant side. CPM was tested by comparing PPT before and during the hand immersion in a hot water bath. anova and intra‐class correlation coefficients (ICCs) were applied to the data (α = 5%). The overall ICCs showed acceptable values for the test–retest reliability of mechanical somatosensory assessment of masticatory structures. The ICC values of 75% of all quantitative sensory measurements were considered fair to excellent (fair = 8·4%, good = 33·3% and excellent = 33·3%). However, the CPM paradigm presented poor reliability (ICC = 0·25). The mechanical somatosensory assessment of the masticatory structures, but not the proposed CPM protocol, can be considered sufficiently reliable over time to evaluate the trigeminal sensory function.
Daily antecedents and consequences of nightly sleep
Authors: Lee Soomi , Crain Tori L. , McHale Susan M. , Almeida David M. , Buxton Orfeu M.
Published: December 2016

Sleep can serve as both cause and consequence of individuals’ everyday experiences. We built upon prior studies of the correlates of sleep, which have relied primarily on cross‐sectional data, to examine the antecedents and consequences of sleep using a daily diary design. Specifically, we assessed the temporal sequence between nightly sleep and daily psychosocial stressors. Parents employed in a US information technology company (n = 102) completed eight consecutive daily diaries at both baseline and 1 year later. In telephone interviews each evening, participants reported on the previous night's sleep hours, sleep quality and sleep latency. They also reported daily work‐to‐family conflict and time inadequacy (i.e. perceptions of not having enough time) for their child and for themselves to engage in exercise. Multi‐level models testing lagged and non‐lagged effects simultaneously revealed that sleep hours and sleep quality were associated with next‐day consequences of work‐to‐family conflict and time inadequacy, whereas psychosocial stressors as antecedents did not predict sleep hours or quality that night. For sleep latency, the opposite temporal order emerged: on days with more work‐to‐family conflict or time inadequacy for child and self than usual, participants reported longer sleep latencies than usual. An exception to this otherwise consistent pattern was that time inadequacy for child also preceded shorter sleep hours and poorer sleep quality that night. The results highlight the utility of a daily diary design for capturing the temporal sequences linking sleep and psychosocial stressors.
Homozygous PPT1 Splice Donor Mutation in a Cane Corso Dog With Neuronal Ceroid Lipofuscinosis
Authors: Kolicheski A. , Barnes Heller H.L. , Arnold S. , Schnabel R.D. , Taylor J.F. , Knox C.A. , Mhlanga‐Mutangadura T. , O'Brien D.P. , Johnson G.S. , Dreyfus J. , Katz M.L.
Published: December 2016

A 10‐month‐old spayed female Cane Corso dog was evaluated after a 2‐month history of progressive blindness, ataxia, and lethargy. Neurologic examination abnormalities indicated a multifocal lesion with primarily cerebral and cerebellar signs. Clinical worsening resulted in humane euthanasia. On necropsy, there was marked astrogliosis throughout white matter tracts of the cerebrum, most prominently in the corpus callosum. In the cerebral cortex and midbrain, most neurons contained large amounts of autofluorescent storage material in the perinuclear area of the cells. Cerebellar storage material was present in the Purkinje cells, granular cell layer, and perinuclear regions of neurons in the deep nuclei. Neuronal ceroid lipofuscinosis (NCL) was diagnosed. Whole genome sequencing identified a PPT1c.124 + 1G>A splice donor mutation. This nonreference assembly allele was homozygous in the affected dog, has not previously been reported in dbSNP, and was absent from the whole genome sequences of 45 control dogs and 31 unaffected Cane Corsos. Our findings indicate a novel mutation causing the CLN1 form of NCL in a previously unreported dog breed. A canine model for CLN1 disease could provide an opportunity for therapeutic advancement, benefiting both humans and dogs with this disorder.
Nutrient composition of premixed and packaged complementary foods for sale in low‐ and middle‐income countries: Lack of standards threatens infant growth
Authors: Masters William A. , Nene Marc D. , Bell Winnie
Published: December 2016

Premixed flours for infant porridge are increasingly produced and sold in developing countries to complement continued breastfeeding. Such complementary food (CF) products have known efficacy against malnutrition in children from 6 to 24 months of age, but ingredient ratios and production processes may vary. This study provides the first systematic measurement of their actual nutrient composition. We purchased samples of 108 premixed CF products in 22 low‐ and middle‐income countries, and commissioned blind laboratory measurement of each product's macronutrients and micronutrients. We compared measured contents to nutrient claims on their packaging and to CF standards from the Codex Alimentarius, the Super Cereal Plus product used in nutrition assistance programs, and the Lutter and Dewey (2003) recommendations, as well as our own modeled nutrient requirements for a healthy breastfed child. Actual densities are significantly different from nutrient claims for protein (p = .013) and fat (p = .000). Only 15% of samples met two of the three benchmarks for fat, 32% met the most stringent protein standard, while only 22% met them for iron, and 21% for zinc. The median healthy child consuming breast milk plus enough of these solid foods to meet energy needs would experience deficits of zinc at 6 months, iron at 6 and 9 months, and dietary fat from 12 months of age. In summary, premixed CF products can provide adequate nutrient density but usually do not, revealing the need and opportunity for independent monitoring and quality assurance to help grain millers making premixed foods maintain uniform ingredient ratios and production practices.