bluuebunny/crossref_metadata_2025 huggingface dataset:
Genome-wide association study identifies seven novel loci associating with circulating cytokines and cell adhesion molecules in Finns
Authors: Sliz Eeva , Kalaoja Marita , Ahola-Olli Ari , Raitakari Olli , Perola Markus , Salomaa Veikko , Lehtimäki Terho , Karhu Toni , Viinamäki Heimo , Salmi Marko , Santalahti Kristiina , Jalkanen Sirpa , Jokelainen Jari , Keinänen-Kiukaanniemi Sirkka , Männikkö Minna , Herzig Karl-Heinz , Järvelin Marjo-Riitta , Sebert Sylvain , Kettunen Johannes
Published: December 2018

Background

Inflammatory processes contribute to the pathophysiology of multiple chronic conditions. Genetic factors play a crucial role in modulating the inflammatory load, but the exact mechanisms are incompletely understood.

Methods

To add understanding to the molecular mechanisms in inflammation, we performed a genome-wide association study (GWAS) on 16 circulating cytokines and cell adhesion molecules (inflammatory phenotypes) in Northern Finland Birth Cohort 1966 (NFBC1966, N=5,284). A subsequent meta-analysis was completed for 10 phenotypes available in a GWAS of three other Finnish population cohorts adding up to 13,577 individuals in the study. Complementary association tests were performed to study the effect of the ABO blood types on soluble adhesion molecule levels.

Results

We identified seven novel and confirmed six previously reported loci associating with at least one of the studied inflammatory phenotypes (p<3.1×10−9). We observed three loci associating with the concentration of soluble vascular cell adhesion molecule-1 (sVCAM-1), one of which is the ABO locus that has been previously associated with soluble E-selectin (sE-selectin) and intercellular adhesion molecule-1 (sICAM-1) levels. Results from the complementary analyses suggest that the blood type B associates primarily with the concentration of sVCAM-1 while the A1 subtype shows a robust effect on sE-selectin and sICAM-1 levels. Furthermore, the genotypes in the ABO locus associating with higher soluble adhesion molecule levels tend to associate with lower low-density lipoprotein cholesterol level and lower cardiovascular disease risk.

Conclusion

The present results extend the knowledge about genetic factors contributing to the inflammatory load. Our findings suggest that two distinct mechanisms contribute to the soluble adhesion molecule levels at the ABO locus. The negative correlation between the genetic effects on soluble adhesion molecule levels and cardiovascular traits in this locus further suggests that increased soluble adhesion molecule levels per se may not be a risk factor for cardiovascular disease.
Environmental enrichment on neural plasticity in juvenile Baltic sturgeon (Acipenser oxyrinchus)
Authors: Camara-Ruiz Maria , Espirito Santo Carlos , Gessner Joern , Wuertz Sven
Published: December 2018

Conservation biologists have long emphasized the importance of environmental enrichment in hatcheries which main objective is restocking. In this study, we evaluated the impact that long-term exposure of environmental enrichment in an artificial river section (surface water, ambient light and temperature) has on neural plasticity in juvenile Baltic sturgeons (Acipenser oxyrinchus) in comparison to fish that were reared in glass-fiber tanks in a recirculation system (aquaculture control group) under constant light and temperature conditions and an intermediate group reared in glass-fiber tanks with ambient water and natural photoperiod and temperature fluctuation. All expositions were carried out in triplicate. From the three markers reported to indicate neural plasticity, only an up-regulation of neurod1 in the forebrain of Baltic sturgeon (A. oxyrinchus) reared in enriched environment was observed in comparison to the semi-natural group and to the aquaculture (control) group. The two other markers (brain-derived neurotropic factor (bdnf), and proliferating cell nuclear antigen (pcna) did not reveal any significant differences between the groups. In conclusion, only minor effects of environmental enrichment on neuroplasticity were observed here.
Modular, ultra-stable, and highly parallel protein force spectroscopy in magnetic tweezers using peptide linkers
Authors: Löf Achim , Walker Philipp U , Sedlak Steffen M , Obser Tobias , Brehm Maria A , Benoit Martin , Lipfert Jan
Published: December 2018

Single-molecule force spectroscopy has provided unprecedented insights into protein folding, force-regulation, and function. Here, we present a modular magnetic tweezers force spectroscopy approach that uses elastin-like polypeptide linkers to provide a high yield of protein tethers. Our approach extends protein force spectroscopy into the low force (<1 pN) regime and enables ultra-stable measurements on many molecules in parallel. We present (un-)folding data for the single protein domain ddFLN4 and for the large multi-domain dimeric protein von Willebrand factor (VWF) that is critically involved in primary hemostasis. The measurements reveal exponential force-dependencies of unfolding and refolding rates, directly resolve the stabilization of the VWF A2 domain by Ca2+, and discover transitions in the VWF C-domain stem at low forces that likely constitute the first steps of VWF activation in vivo. Our modular attachment approach will enable precise and multiplexed force spectroscopy measurements for a wide range of proteins in the physiologically relevant force regime.
Italian norms and naming latencies for 357 high quality color images
Authors: Navarrete Eduardo , Arcara Giorgio , Mondini Sara , Penolazzi Barbara
Published: December 2018

In the domain of cognitive studies on the lexico-semantic representational system, one of the most important means of ensuring well-suited experimental designs is using ecological stimulus sets accompanied by normative data on the most relevant variables affecting the processing of their items. In the context of image sets, color photographs are particularly suited for this aim as they reduce the difficulty of visual decoding processes that may emerge with traditional image sets of line drawings, especially in clinical populations. We provide Italian norms for a set of 357 high quality image-items belonging to 23 semantic subcategories. Data from several variables affecting image processing: age of acquisition, familiarity, lexical frequency, manipulability, name agreement, typicality and visual complexity; were collected from a sample of 255 Italian-speaking participants. Lexical frequency data were derived from the CoLFIS corpus. Furthermore, we collected data with on image naming latencies aimed at exploring how much of the variance in these latencies could be explained by the above mentioned critical variables. Multiple regression analyses on the naming latencies show classical psycholinguistic phenomena, such as the effects of age of acquisition and name agreement. In addition, manipulability is also a significant predictor. The described Italian normative data and naming latencies are available for download as supplementary material.
Number of children and body composition in later life among men and women: Results from a British birth cohort study
Authors: Bridger Staatz Charis , Hardy Rebecca
Published: December 2018

Background
Although research has found associations between increasing number of children and higher body mass index (BMI), there has been limited research investigating the association with body composition despite abdominal fat being associated with cardiovascular and metabolic risk independently of general adiposity. Most existing research has focussed on women, but investigating the relationship in men can help distinguish biological effects of pregnancy from social pathways related to parenthood.
Methods
Using the MRC National Survey of Health and Development (NSHD) multiple regression models were applied to test associations between number of children and body composition at age 60-64 (N=2229) and body mass index (BMI) and waist circumference (WC) at ages 60-64 and 69 (N=2149).
Results
In adjusted models, associations were observed between increasing numbers of children and increasing fat-adjusted lean mass index in women (p=0.06). Among men, those with children had 0.59kg (95% CI: 0.15 to 1.02) greater lean mass index than those without and fat:lean mass ratio was greater in those with 4+ children because of their slightly higher mean fat mass. Weak evidence of a higher android:gynoid mass ratio in women with children (0.03, 95% CI: 0.00,0.06, p=0.1) was observed with no associations with fat mass index or android or gynoid fat mass. Increasing BMI was observed with increasing parity in women at 60-64 and more strongly at 69 years where associations among men were also observed more clearly.
Conclusion
There was little evidence of a consistent association between number of children and body composition in early old age. The strongest associations are observed for lean, rather than fat mass, and in men rather than women, suggesting little evidence of biological effects of pregnancy in women. The results indicate social pathways associated with parenthood are the likely underlying mechanisms, with suggestion there may be selection into parenthood among men.
How to Build a Fruit: Transcriptomics of a Novel Fruit Type in the Brassiceae
Authors: Carey Shane , Hall Jocelyn C , Mendler Kerrin
Published: December 2018

Comparative gene expression studies are invaluable for predicting how existing genetic pathways may be modified or redeployed to produce novel and variable phenotypes. Fruits are ecologically important organs because of their impact on plant fitness and seed dispersal, modifications in which results in morphological variation across species. A novel fruit type in the Brassicaceae known as heteroarthrocarpy enables distinct dispersal methods in a single fruit through segmentation via a lateral joint and variable dehiscence at maturity. Given the close relationship to Arabidopsis, species that exhibit heteroarthrocarpy are powerful models to elucidate how differences in gene expression of a fruit patterning pathway may result in novel fruit types. Transcriptomes of distal, joint, and proximal regions from Erucaria erucarioides and Cakile lanceolata were analyzed to elucidate within and between species differences in whole transcriptome, gene ontology, and fruit patterning expression profiles. Whole transcriptome expression profiles vary between fruit regions in patterns that are consistent with fruit anatomy. These transcriptomic variances do not correlate with changes in gene ontology, as they remain generally stable within and between both species. Upstream regulators in the fruit patterning pathway, FILAMENTOUS FLOWER and YABBY3, are expressed in the distal and proximal regions of E. erucarioides, but not in the joint, implicating alterations in the pathway in heteroarthrocarpic fruits. Downstream gene, INDEHISCENT, is significantly upregulated in the abscissing joint region of C. lanceolata, which suggests repurposing of valve margin genes for novel joint disarticulation in an otherwise indehiscent fruit. In summary, these data are consistent with modifications in fruit patterning genes producing heteroarthrocarpic fruits through different components of the pathway relative to other indehiscent, non-heteroarthrocarpic, species within the family. Our understanding of fruit development in Arabidopsis is now extended to atypical siliques within the Brassicaceae, facilitating future studies on seed shattering in important Brassicaceous crops and pernicious weeds.
Article The Genotype Diversity within the H5N8 Influenza A Subtype
Authors: Dalby Andrew R. , Tinworth Lorna , Iqbal Munir
Published: December 2018

The H5N8 influenza subtype has been involved in the global spread of the Guangdong variant of the H5 hemagglutinin. The sequence data from all of the complete genomes from the H5N8 subtype was used to analyse the genotype diversity. Clustering analysis was used to assign lineages to each of the segments where different lineages were present. The results show that there have been multiple reassortment events both within the Guangdong and non-Guangdong H5 hemagglutinin containing variants. The Guangdong H5 variants can be subdivided further into two sub-lineages 2.3.4.4.A and 2.3.4.4.B that have undergone reassortment in both the far east and the United States.
Stytra: an open-source, integrated system for stimulation, tracking and closed-loop behavioral experiments
Authors: Štih Vilim , Petrucco Luigi , Kist Andreas M , Portugues Ruben
Published: December 2018

We present Stytra, a flexible, open-source software package, written in Python, that we designed to cover all the general requirements involved in larval zebrafish behavioral experiments. It allows timed stimulus presentation, interfacing with external devices and simultaneous real-time tracking of position, tail and eye motion in both freely-swimming and head-restrained preparations.
It logs in standardized formats all recorded quantities, metadata, and code version to allow full provenance tracking, from data acquisition through analysis to publication. The package is modular and expandable for different experimental protocols and setups. Current releases can be found at https://github.com/portugueslab/stytra.
We also provide complete documentation with examples for extending the package to new stimuli and hardware, as well as a schema and parts list for behavioral setups.
We showcase Stytra by reproducing two previously behavioral protocols, one with head-restrained and the other with freely-swimming larvae, as well as an experiment in which the software is used in the context of a calcium imaging experiment, where it can trigger and communicate with other acquisition devices.
Our aims are to help laboratories with little or no experience in the field to start implementing behavioral experiments and to provide a platform for sharing stimulus protocols to enable easy reproduction of experiments and straightforward validation. In addition, Stytra can easily serve as a base platform to design behavioral experiments in other model organisms.
A genome-wide screen identifies genes that suppress the accumulation of spontaneous mutations in young and aged yeast cells
Authors: Novarina Daniele , Janssens Georges , Bokern Koen , Schut Tim , van Oerle Noor , Kazemier Hinke , Veenhoff Liesbeth , Chang Michael
Published: December 2018

To ensure proper transmission of genetic information, cells need to preserve and faithfully replicate their genome, and failure to do so leads to genome instability, a hallmark of both cancer and aging. Defects in genes involved in guarding genome stability cause several human progeroid syndromes, and an age-dependent accumulation of mutations has been observed in different organisms, from yeast to mammals. However, it is unclear if the spontaneous mutation rate changes during aging, and if specific pathways are important for genome maintenance in old cells. We developed a high-throughput replica-pinning approach to screen for genes important to suppress the accumulation of spontaneous mutations during yeast replicative aging. We found 13 known mutation suppression genes, and 31 genes that had no previous link to spontaneous mutagenesis, and all acted independently of age. Importantly, we identified PEX19, encoding an evolutionarily conserved peroxisome biogenesis factor, as an age-specific mutation suppression gene. While wild-type and pex19Δ young cells have similar spontaneous mutation rates, aged cells lacking PEX19 display an elevated mutation rate. This finding suggests that functional peroxisomes are important to preserve genome integrity specifically in old cells, possibly due to their role in reactive oxygen species metabolism.
SPIND: a reference-based auto-indexing algorithm for sparse serial crystallography data
Authors: Li Chufeng , Li Xuanxuan , Kirian Richard , Spence John C. H. , Liu Haiguang , Zatsepin Nadia A.
Published: December 2018

SPIND (sparse-pattern indexing) is an auto-indexing algorithm for sparse snapshot diffraction patterns (`stills') that requires the positions of only five Bragg peaks in a single pattern, when provided with unit-cell parameters. The capability of SPIND is demonstrated for the orientation determination of sparse diffraction patterns using simulated data from microcrystals of a small inorganic molecule containing three iodines, 5-amino-2,4,6-triiodoisophthalic acid monohydrate (I3C) [Beck & Sheldrick (2008), Acta Cryst. E64, o1286], which is challenging for commonly used indexing algorithms. SPIND, integrated with CrystFEL [White et al. (2012), J. Appl. Cryst.
45, 335–341], is then shown to improve the indexing rate and quality of merged serial femtosecond crystallography data from two membrane proteins, the human δ-opioid receptor in complex with a bi-functional peptide ligand DIPP-NH2 and the NTQ chloride-pumping rhodopsin (CIR). The study demonstrates the suitability of SPIND for indexing sparse inorganic crystal data with smaller unit cells, and for improving the quality of serial femtosecond protein crystallography data, significantly reducing the amount of sample and beam time required by making better use of limited data sets. SPIND is written in Python and is publicly available under the GNU General Public License from https://github.com/LiuLab-CSRC/SPIND.
Key performance indicators for the evaluation of academic and research laboratory facilities
Authors: Mahmoud Abubakar Sadiq , Sanni-Anibire Muizz O. , Hassanain Mohammad A. , Ahmed Wahhaj
Published: December 2018

Purpose

The purpose of this paper is to develop a comprehensive list of key performance indicators (KPIs) that can be employed in determining the functional performance of academic and research laboratory facilities.

Design/methodology/approach

The study employed a two-phase approach. First, a thorough literature review was conducted to identify potential KPIs specific to the performance of laboratory facilities. This was followed by an assessment of the KPIs by 12 respondents including 6 professionals and 6 users. The KPIs were arranged in the form of a questionnaire survey containing response columns for agree/disagree, and importance rating scales for evaluation. The relative importance index values were also computed.

Findings

The result of the study was a comprehensive list of 161 KPIs classified into nine categories including: space, access/circulation, utilities and waste, environmental conditions, furniture, appearance/finishes/image, communications, storage within the space and special building features. These KPIs were perceived to be at varying levels of importance by the respondents.

Originality/value

Though previous studies developed KPIs for the performance of facilities, these KPIs are not universal. Thus, the originality of this study is in its identification of a comprehensive set of KPIs unique to the design, evaluation and management of research and academic laboratory facilities.
Exploring the social structure of strategic management research with a hospitality industry focus
Authors: Koseoglu Mehmet Ali , Law Rob , Dogan Ismail Cagri
Published: December 2018

Purpose

This paper aims to investigate the social structure of strategic management research in the hospitality management field to determine whether a strong social structure is needed and, if so, how this structure can be enriched within the hospitality field.

Design/methodology/approach

A total of 1,652 articles related to hospitality strategic management published in leading hospitality and tourism as well as business journals were analyzed using co-authorship analysis combined with social network analysis.

Findings

The study’s findings demonstrate a progressive growth in collaboration. Leading authors, institutions and countries in the collaboration networks are identified. Network analysis shows that the ties in the network are too weak to build a strong social identity, although the community is broad.

Practical implications

This study provides solutions for building a strong social identity related to strategic management in the hospitality field. Moreover, this study helps leaders and managers, who need to know whom to speak to within academia to get industry-based advice, as well as scholars, junior researchers and graduate students, who must recognize the individuals producing knowledge in the academic field, to identify the key actors within the field.

Originality/value

As one of the first studies in this field, this research discusses why a strong social identity is necessary and how it can be built further while also looking at the potential for expansion in future studies.
The roles of emerging multinational companies’ technology-driven FDIs in their learning processes for innovation
Authors: Liu Ju
Published: December 2018

Purpose

The purpose of this paper is to contextually theorise the different patterns of emerging multinational companies’ (EMNCs’) learning processes for innovation and the different influences of their technology-driven FDIs (TFDIs) on the processes.

Design/methodology/approach

A comparative case study method and process tracing technique are employed to investigate how and why firms’ learning processes for innovation took place, how and why the TFDIs emerged and influenced the firms’ learning processes in different ways.

Findings

The paper identifies two different patterns of learning process for innovation (Glider model vs Helicopter model) and two different roles of the case firms’ TFDIs (accelerator vs starter) in the different contexts of their learning processes. It is found that the capability building of the domestic wind energy industry has an important influence on the case of EMNCs’ learning processes and thus on the roles of their TFDIs.

Research limitations/implications

The limitation of the paper lies in its small number of cases in a specific industry of a specific country. The two contextually identified learning models and roles of TFDIs may not be applied to other industries or other countries. Future research should investigate more cases in broader sectoral and geographic scope to test the models and also to identify new models.

Practical implications

For EMNCs, who wants to use the Helicopter model to rapidly gain production and innovation capability, cross-cultural management and integration management are crucial to practitioners. For emerging countries with ambitions to explore the global knowledge and technology pool, besides of the EMNC’s capability building, the capability building in the domestic industries should not be overlooked by policy makers.

Originality/value

The paper develops a dynamic and contextual analytical framework which helps to answer the important questions about how and under what context a TFDI emerges and influences firm’s learning process for innovation. It theorises the EMNCs’ learning process and TFDIs in the context of the development of the domestic industry. It strengthens the explanatory power of the learning-based view and adds new knowledge to the current FSA/CSA discourse in the international business literature.
Degradation index construction methodology for mechanical transmission based on fusion of multispectral oil data
Authors: Yan Shufa , Ma Biao , Zheng Changsong
Published: December 2018

Purpose

The purpose of constructing a degradation index (DI) is to better characterize the degradation degree of mechanical transmission compared with relying solely on spectral oil data, which leads to an accurate estimation of the failure time when the transmission no longer fulfills its function.

Design/methodology/approach

The DI is modeled using a weighted average function with two desirable properties: maximizing the monotonic trend and minimizing the variance of failure threshold between different transmissions. The method includes concentration modification, data selection and data fusion steps that lead to a reasonable mechanical transmission degradation model. The proposed methodology was verified through a case study involving multispectral oil data sampled from several power-shift steering transmissions.

Findings

The results show that the DI outperforms all spectral oil data. Compared with the existing spectral oil data-based degradation modeling approach for mechanical transmissions, the present methodology provides an accurate RUL prediction.

Research limitations/implications

There are several important directions for future research: First, more degradation data (i.e. ferrography) that are tailored to the degradation modeling of mechanical transmission need to be involved. Second, more effective degradation data selection methodologies that are applicable for multiple data types need to be developed. Third, kernel methods that can fuse the nonlinear degradation data need to be investigated.

Originality/value

The novelty of this methodology lies in integrating the multiple degradation data in a unified DI. And the main contribution of this paper is to establish a new direction in degradation modeling and RUL prediction of mechanical transmission.
Metadata categorization for identifying search patterns in a digital library
Authors: Bogaard Tessel , Hollink Laura , Wielemaker Jan , van Ossenbruggen Jacco , Hardman Lynda
Published: December 2018

Purpose

For digital libraries, it is useful to understand how users search in a collection. Investigating search patterns can help them to improve the user interface, collection management and search algorithms. However, search patterns may vary widely in different parts of a collection. The purpose of this paper is to demonstrate how to identify these search patterns within a well-curated historical newspaper collection using the existing metadata.

Design/methodology/approach

The authors analyzed search logs combined with metadata records describing the content of the collection, using this metadata to create subsets in the logs corresponding to different parts of the collection.

Findings

The study shows that faceted search is more prevalent than non-faceted search in terms of number of unique queries, time spent, clicks and downloads. Distinct search patterns are observed in different parts of the collection, corresponding to historical periods, geographical regions or subject matter.

Originality/value

First, this study provides deeper insights into search behavior at a fine granularity in a historical newspaper collection, by the inclusion of the metadata in the analysis. Second, it demonstrates how to use metadata categorization as a way to analyze distinct search patterns in a collection.
The stepped model of peer provision practice: capturing the dynamics of peer support work in action
Authors: Zeng Grace , Chung Donna
Published: December 2018

Purpose

In recent years, the employment of peer providers (PPs) has grown with the wider acceptance of lived experience expertise in recovery-oriented service provision. Although its effectiveness, theoretical foundations and factors influencing outcomes have been studied, a framework accounting for the dynamics of the PP–peer relationship has yet to be formulated. The purpose of this paper is to employ a qualitative approach to explore the journeys undertaken by PPs with their peers and form it into a cohesive framework of understanding.

Design/methodology/approach

In-depth interviews were conducted with PPs who were employed specifically to use their lived experience in supporting someone through mental distress. These interviews were recorded, transcribed and coded using a framework approach. To enhance rigour, this framework was verified with the latter author and three other participants recruited after data analysis.

Findings

A stepped model of peer provision practice was crafted to capture the non-linearity of recovery, as well as the PP–peer relationship. This model is founded upon trust in the milieu of shared experience and involves: creating a safe place – a stage of building trust and rapport to a point where a PP is given permission to enter into their peer’s headspace; a working partnership – stage of setting and working towards goals collaboratively; and stepping out – a stage marked by the termination of the PP–peer relationship.

Originality/value

This paper proposes a tangible framework underpinning the dynamics of peer provision practice, which furthers our understanding and complements current practice models in peer provision services.
The effectiveness of applied learning: an empirical evaluation using role playing in the classroom
Authors: Acharya Harneel , Reddy Rakesh , Hussein Ahmed , Bagga Jaspreet , Pettit Timothy
Published: December 2018

Purpose

The purpose of this paper is to evaluate the effectiveness of role playing as an applied learning technique for enhanced classroom experiences as compared to traditional lecture methods.

Design/methodology/approach

This study uses the pre-test/post-test design to conduct experiments with several control and experimental groups. Subjects are graduate students in an MBA program at a private, non-profit university in a traditional classroom setting.

Findings

Students in the experimental group gained significantly more knowledge (post-test minus pre-test scores) – 45 percent higher – through participation in the role playing exercise as compared to the control group.

Research limitations/implications

This study represents only a single educational discipline explored using a single role playing learning activity. Impacts on the long-term retention of the knowledge should be studied further.

Practical implications

Educators should enhance their classroom experience with more applied learning activities such as role playing in order to increase knowledge gain and potentially longer knowledge retention.

Originality/value

This study uses a customized role playing activity within a business curriculum as one of many applied learning techniques. The value to students was shown by significantly higher gain in knowledge while simultaneously enhancing their enjoyment of the classroom experience to potentially encourage further lifelong learning.
Gut microbiota in patients after surgical treatment for colorectal cancer
Authors: Jin Ye , Liu Yang , Zhao Lei , Zhao Fuya , Feng Jing , Li Shengda , Chen Huinan , Sun Jiayu , Zhu Biqiang , Geng Rui , Wei Yunwei
Published: December 2018

Colorectal cancer (CRC) is a common disease worldwide that is strongly associated with the gut microbiota. However, little is known regarding the gut microbiota after surgical treatment. 16S rRNA gene sequencing was used to evaluate differences in gut microbiota among colorectal adenoma patients, CRC patients, CRC postoperative patients and healthy controls by comparing gut microbiota diversity, overall composition and taxonomic signature abundance. The gut microbiota of CRC patients, adenoma patients and healthy controls developed in accordance with the adenoma‐carcinoma sequence, with impressive shifts in the gut microbiota before or during the development of CRC. The gut microbiota of postoperative patients and CRC patients differed significantly. Subdividing CRC postoperative patients according to the presence or absence of newly developed adenoma which based on the colonoscopy findings revealed that the gut microbiota of newly developed adenoma patients differed significantly from that of clean intestine patients and was more similar to the gut microbiota of carcinoma patients than to the gut microbiota of healthy controls. The alterations of the gut microbiota between the two groups of postoperative patients corresponded to CRC prognosis. More importantly, we used the different gut microbiota as biomarkers to distinguish postoperative patients with or without newly developed adenoma, achieving an AUC value of 0.72. These insights on the changes in the gut microbiota of CRC patients after surgical treatment may allow the use of the microbiota as non‐invasive biomarkers for the diagnosis of newly developed adenomas and to help prevent cancer recurrence in postoperative patients.
Engagement and literacy: reading between the lines
Authors: Alexander Patricia A.
Published: December 2018

In this commentary, several core principles underlying the editorial and articles comprising the Special Issue on improving literacy engagement are identified and discussed. Those principles pertain to the multidimensional nature of literacy engagement, the explicit or implicit definitions offered for the construct, the positive contributions that engagement makes to improve reading and writing, the positive characteristics of engaged readers and writers and the consequences that academic or economic disadvantages have on engagement and literacy development. There are also lingering questions that are posed about literacy engagement and about engaged readers and writers. Those questions inquire as to whether one definition of literacy engagement suffices, if the forms of literacy engagement are truly separable in practice and measurable in research, whether totally disengaged students actually exist and what precise nature of the relation between literacy engagement and literacy competence is.
Forensic Comparison of Automotive Aluminum Wheel Fragments Using Synchrotron Radiation X‐ray Fluorescence with 18‐ and 116‐keV Excitation X‐rays
Authors: Nishiwaki Yoshinori , Takekawa Tomohiro
Published: December 2018

The performance of synchrotron radiation X‐ray fluorescence (SR‐XRF) spectrometry for nondestructive discrimination of small fragments of automotive aluminum wheels was studied. Fragments (< 500 × 500 μm2) of 45 kinds of wheels were first analyzed by scanning electron microscopy–energy dispersive spectroscopy (SEM‐EDS) and then by SR‐XRF. Despite the Mg/Al intensity ratio being a useful identification index, SEM‐EDS was not efficient enough because of the absence of other meaningful indicators of comparison. Conversely, pairwise comparison was conducted and a 92.9% identification was achieved via SR‐XRF using 18‐keV X‐rays. Trace heavy elements in the high‐energy region were detected by SR‐XRF using 116‐keV X‐rays, and an 82.9% identification was obtained. Combined use of 18‐ and 116‐keV X‐rays allowed 98.2% identification. Hence, SR‐XRF is a powerful tool for nondestructive discrimination of automotive aluminum wheels with high precision using trace elements in a wide energy region.
Marshaling Adaptive Capacities within an Adaptive Management Framework to Enhance the Resiliency of Wastewater Systems
Authors: Mullin Cristina A. , Kirchhoff Christine J.
Published: December 2018

We assess adaptive capacity and adaptive management as measures of wastewater (WW) system resiliency using data from interviews with WW system managers (hereafter managers) impacted by past storms. Results suggest the most resilient WW systems are those with high adaptive capacities that employ an adaptive management approach to make ongoing adaptation investments over time. Greater amounts of generic adaptive capacities (i.e., skilled staff and good leadership) help smooth both day‐to‐day and emergency operations and provide a foundation for adaptive management. In turn, adaptive management helps managers both build more generic adaptive capacities, and develop and employ greater amounts and diversity of specific adaptive capacities (i.e., soft and/or hard adaptations) that are especially important for enhancing and sustaining resiliency. Adaptive management also enables managers to better understand their system's vulnerabilities, how those vulnerabilities change over time, and what specific actions may reduce those vulnerabilities. Finally, our work suggests WW system resilience critically depends on the capacities of the human systems for building resilience as much as or more so than relying only on physical infrastructure resilience. Our work contributes to filling an important gap in the literature by advancing our understanding of the human dimensions of infrastructure resilience and has practical implications for advancing resilience in the WW sector.
Reduced Prevalence of Alcoholic Gastritis in Hospitalized Individuals Who Consume Cannabis
Authors: Adejumo Adeyinka Charles , Li Jingjing , Akanbi Olalekan , Adejumo Kelechi Lauretta , Bukong Terence Ndonyi
Published: December 2018

Background

Alcoholic gastritis, a superficial erosive disease of the stomach, is a common manifestation of risky alcohol use. In contrast, cannabis which is frequently co‐used with alcohol suppresses gastric acidity and might counteract the deleterious effect of alcohol on the gastric mucosa. However, no clinical study has examined the impact of cannabis use on the development of alcoholic gastritis among risky alcohol users.

Methods

We analyzed hospital discharge records of adults (age ≥ 18 years), from 2014 of the Nationwide Inpatient Sample, with a diagnosis of risky alcohol use (n = 316,916). We used a propensity‐based matching algorithm to match cannabis users to nonusers on 1:1 ratio (30,713: 30,713). We then measured the adjusted relative risk (aRR) for having alcoholic gastritis using conditional Poisson regression models with generalized estimating equations.

Results

Our study revealed that among risky alcohol users, cannabis co‐users have a lower prevalence of alcoholic gastritis compared to noncannabis users (1,289 [1,169 to 1,421] vs. 1,723 [1,583 to 1,875] per 100,000 hospitalizations for risky alcohol use), resulting in a 25% decreased probability of alcoholic gastritis (aRR: 0.75 [0.66 to 0.85]; p‐value <0.0001). Furthermore, dependent cannabis usage resulted in a lower prevalence of alcoholic gastritis when compared to both nondependent cannabis users (0.72 [0.52 to 0.99]) and to noncannabis users (0.56 [0.41 to 0.76]).

Conclusions

We reveal that risky alcohol drinking combined with cannabis use is associated with reduced prevalence of alcohol‐associated gastritis in patients. Given increased cannabis legislation globally, understanding whether and how the specific ingredients in cannabis plant extract can be used in the treatment of alcoholic gastritis is paramount. In this regard, further molecular mechanistic studies are needed to delineate the mechanisms of our novel findings not only for alcoholic gastritis but also for gastritis from other causes.
A clinical trial with protracted infusion 5‐fluorouracil and mitomycin C for localized squamous cell carcinoma of the anus
Authors: Ngan David , Chu Julie , Chander Sarat , Michael Michael , Heriot Alexander G. , Ngan Samuel Y. , Rischin Danny , Leong Trevor
Published: December 2018

Purpose

Mitomycin C (MMC) plus standard 5‐fluorouracil (FU) infusion in weeks 1 and 5 often contributes to radiotherapy interruptions and possibly less‐than‐ideal outcomes in anal cancer. This study was to evaluate alternative strategies for chemotherapy delivery that might be less toxic or more efficacious, and outcomes of patient‐initiated treatment interruption for severe acute toxicity.

Materials and methods

This was a prospective, nonrandomized study for patients with T1‐4N0‐3M0 anal squamous carcinoma. Radiotherapy of 54 Gy in 30 fractions over 6 weeks was given with infusion FU 300 mg/m2/day for 96 hours/week for 6 weeks plus bolus MMC at 10 mg/m2 on D1.

Results

Fifty patients were recruited (72% female). Median age was 60.5 years (35–84). Forty‐seven patients (94%) received 54 Gy. Median duration of chemoradiation was 39 days (37–105). Grade 3 and 4 acute toxicity were observed in 66%. Thirty‐one percent with severe acute toxicity developed severe late toxicity. Of those who experienced severe late skin toxicity, 29% did not have severe acute toxicity.

Disease‐free survival at 5 years was 74% (95% confidence interval [CI], 60–84), and at 9 years 61% (95% CI, 46–74). Overall survival at 5 years was 84% (95% CI, 71–92), and at 9 years 67% (95% CI, 50–81). Colostomy‐free survival at 5 years was 70% (95% CI, 56–81), and at 9 years 57% (95% CI, 40–72).

Conclusion

It is feasible to deliver chemoradiation with bolus MMC and protracted infusion FU for anal cancer. Efficacy and toxicity of this regimen seem similar to conventional chemoradiation with FU/MMC. Acute skin toxicity is not a reliable predictor of severe late skin toxicity.
Artificial shear stress effects on leukocytes at a biomaterial interface
Authors: Radley Gemma , Laura Pieper Ina , Thomas Bethan R. , Hawkins Karl , Thornton Catherine A.
Published: December 2018

Medical devices, such as ventricular assist devices (VADs), introduce both foreign materials and artificial shear stress to the circulatory system. The effects these have on leukocytes and the immune response are not well understood. Understanding how these two elements combine to affect leukocytes may reveal why some patients are susceptible to recurrent device‐related infections and provide insight into the development of pump thrombosis. Biomaterials—DLC: diamond‐like carbon‐coated stainless steel; Sap: single‐crystal sapphire; and Ti: titanium alloy (Ti6Al4V) were attached to the parallel plates of a rheometer. Whole human blood was left between the two discs for 5 minutes at +37°C with or without the application of shear stress (0 s–1 or 1000 s–1). Blood was removed and used for complete blood cell counts, flow cytometry (leukocyte activation, cell death, microparticle generation, phagocytic ability, and reactive oxygen species [ROS] production), and the production of pro‐inflammatory cytokines. L‐selectin expression on monocytes was decreased when blood was exposed to the biomaterials both with and without shear. Applying shear stress to blood on a Sap and Ti surface led to activation of neutrophils shown as decreased L‐selectin expression. Sap and Ti blunted the LPS‐stimulated macrophage migration inhibitory factor (MIF) production, most notably when sheared on Ti. The biomaterials used here have been shown to activate leukocytes in a static environment. The introduction of shear appears to exacerbate this activation. Interestingly, a widely accepted biocompatible material (Ti) utilized in many different types of devices has the capacity for immune cell activation and inhibition of MIF secretion when combined with shear stress. These findings contribute to our understanding of the contribution of biomaterials and shear stress to recurrent infections and vulnerability to sepsis in some VAD patients as well as pump thrombosis.
Sex‐by‐formulation interaction in bioequivalence studies: the importance of formulations and experimental conditions
Authors: Ibarra Manuel , Vázquez Marta , Fagiolino Pietro
Published: December 2018

In a recently published investigation, the authors argued against the likelihood of sex‐based subject‐by‐formulation interactions in bioequivalence studies, i.e. male and female subjects exhibiting different discriminatory potential to detect bioavailability differences between formulations. The researchers performed a strong methodological study showing the increased probability of false‐positive findings in exploratory subgroup analysis, a well‐known and documented statistical issue. Indeed, the main limitation of assessing a sex‐by‐formulation interaction in average bioequivalence studies lies in the fact that these clinical trials are not designed for this purpose. In this commentary, we further discuss on why the impact of sex differences in gastrointestinal physiology over in vivo drug dissolution and absorption rate cannot remain hidden behind statistical limitations, particularly when average bioequivalence conclusions could be affected. Regulatory agencies should encourage and support these important issues related to biopharmaceutical quality of drug products in both sexes. In addition, a sex‐based analysis of bioequivalence results will enhance the representativeness of conclusions and provide important information regarding formulation performance, thereby promoting the efficacy and safety of generic drugs and reducing consumer risk. The extrapolation of study conclusions from one sex to another is far away from being scientifically proven.
Guidelines for reporting of statistics for clinical research in urology
Authors: Assel Melissa , Sjoberg Daniel , Elders Andrew , Wang Xuemei , Huo Dezheng , Botchway Albert , Delfino Kristin , Fan Yunhua , Zhao Zhiguo , Koyama Tatsuki , Hollenbeck Brent , Qin Rui , Zahnd Whitney , Zabor Emily C. , Kattan Michael W. , Vickers Andrew J.
Published: December 2018

In an effort to improve the quality of statistics in the clinical urology literature, statisticians at European Urology, The Journal of Urology, Urology and BJU International came together to develop a set of guidelines to address common errors of statistical analysis, reporting, and interpretation. Authors should ‘break any of the guidelines if it makes scientific sense to do so’, but would need to provide a clear justification. Adoption of the guidelines will in our view not only increase the quality of published papers in our journals but improve statistical knowledge in our field in general.
Pharmacogenetics of angiotensin‐converting enzyme inhibitor‐induced angioedema
Authors: Liau Yusmiati , Chua Ignatius , Kennedy Martin A. , Maggo Simran
Published: December 2018

Angioedema is a rare adverse effect of the commonly used angiotensin‐converting enzyme inhibitors (ACEi) and is reported to occur with a prevalence of 0.1%‐0.7%. Although most ACEi‐induced angioedema (ACEi‐A) cases are mild, severe cases requiring intensive care and even resulting in death have been reported in the literature. The mechanisms underlying ACEi‐A are not yet fully understood, but bradykinin and/or substance P accumulation resulting from inhibition of ACE is believed to play a crucial role. ACEi‐A occurs at variable frequencies across different racial groups, suggesting a genetic association with the development of ACEi‐A. To date, one genome‐wide association study and several candidate gene studies have been published on the association of genetic variation with ACEi‐A. Genetic associations reported have been attributed to several distinct mechanisms: (a) genes coding for alternative enzymes responsible for the degradation of bradykinin and/or substance P in the diminution of ACE activity (b) ACE gene function, (c) bradykinin receptor genes, (d) genes implicated in immune and inflammation regulation and (e) genes in the fibrinolytic and coagulation pathway. Despite several plausible genetic associations, there are currently no genetic variants with sufficient effect to be clinically useful. The low incidence of ACEi‐A suggests that a combination of genomic approaches with the capability to detect potentially important variants might be required to shed light on the mechanism of this adverse reaction. Additionally, many non‐genetic risk factors associated with ACEi‐A suggest the potential contribution of epigenetic dysregulation.