bluuebunny/crossref_metadata_2025_split huggingface dataset:
Broad phylogeny and functionality of cellulosomal components in the bovine rumen microbiome
Authors: Bensoussan Lizi , Moraïs Sarah , Dassa Bareket , Friedman Nir , Henrissat Bernard , Lombard Vincent , Bayer Edward A. , Mizrahi Itzhak 
Published: October 2016

SummaryThe cellulosome is an extracellular multi‐enzyme complex that is considered one of the most efficient plant cell wall‐degrading strategies devised by nature. Its unique modular architecture, achieved by high affinity and specific interaction between protein modules (cohesins and dockerins) enables formation of various enzyme combinations. Extensive research has been dedicated to the mechanistic nature of the cellulosome complex. Nevertheless, little is known regarding its distribution and abundance among microbes in natural plant fibre‐rich environments. Here, we explored these questions in bovine rumen microbial communities, specialized in efficient degradation of lignocellulosic plant material. We bioinformatically screened for cellulosomal modules in this complex environment using a previously published ultra‐deep fibre‐adherent rumen metagenome. Intriguingly, a large portion of the functions of the dockerin‐containing proteins were related to alternative biological processes, and not necessarily to the classic fibre degradation function. Our analysis was experimentally validated by characterizing specific interactions between selected cohesins and dockerins and revealed that cellulosome is a more generalized strategy used by diverse bacteria, some of which were not previously associated with cellulosome production. Remarkably, our results provide additional proof of similarity among rumen microbial communities worldwide. This study suggests a broader and widespread role for the cellulosomal machinery in nature.
A putative 3‐hydroxyisobutyryl‐CoA hydrolase is required for efficient symbiotic nitrogen fixation in Sinorhizobium meliloti and Sinorhizobium fredii NGR234
Authors: Zamani Maryam , diCenzo George C. , Milunovic Branislava , Finan Turlough M. 
Published: October 2016

SummaryWe report that the smb20752 gene of the alfalfa symbiont Sinorhizobium meliloti is a novel symbiotic gene required for full N2‐fixation. Deletion of smb20752 resulted in lower nitrogenase activity and smaller nodules without impacting overall nodule morphology. Orthologs of smb20752 were present in all alpha and beta rhizobia, including the ngr_b20860 gene of Sinorhizobium fredii NGR234. A ngr_b20860 mutant formed Fix− determinate nodules that developed normally to a late stage of the symbiosis on the host plants Macroptilium atropurpureum and Vigna unguiculata. However an early symbiotic defect was evident during symbiosis with Leucaena leucocephala, producing Fix− indeterminate nodules. The smb20752 and ngr_b20860 genes encode putative 3‐hydroxyisobutyryl‐CoA (HIB‐CoA) hydrolases. HIB‐CoA hydrolases are required for l‐valine catabolism and appear to prevent the accumulation of toxic metabolic intermediates, particularly methacrylyl‐CoA. Evidence presented here and elsewhere (Curson et al., , PLoS ONE 9:e97660) demonstrated that Smb20752 and NGR_b20860 can also prevent metabolic toxicity, are required for l‐valine metabolism, and play an undefined role in 3‐hydroxybutyrate catabolism. We present evidence that the symbiotic defect of the HIB‐CoA hydrolase mutants is independent of the inability to catabolize l‐valine and suggest it relates to the toxicity resulting from metabolism of other compounds possibly related to 3‐hydroxybutyric acid.
Complete tooth loss as status passage
Authors: Gibson Barry John , Sussex Philip V. , Fitzgerald Ruth P. , Thomson William Murray 
Published: October 2016

AbstractThe aim of this article is to add to the literature on the sociology of oral health and dentistry by presenting the relevance of status passage to the study of complete tooth loss. The article reports on an analysis of data taken from participants residing in the Nelson region of New Zealand. In total the data include interviews from 20 participants, all of whom had their remaining natural teeth removed before 1960. In total, 12 women and eight men were interviewed. All were from a European background with an age range of 71 to 101 years. Following a narrative approach, participants were interviewed on the nature of the social factors that resulted in complete tooth loss by starting with their family history and then focusing on the factors and events leading up to their total tooth loss. Data were analysed using the methods and techniques of grounded theory. This article provides an outline of the importance of scheduling, prescribing, social factors, ‘compound awareness contexts’ and reversibility to the status passage into complete tooth loss. We conclude by arguing that the theory of status passage may enable a detailed analysis of the ‘time‐space extensionality’ of trajectories into complete tooth loss.
Relative validity of a 2‐day 24‐hour dietary recall compared with a 2‐day weighed dietary record among adults in South China
Authors: Xue Hongmei , Yang Mingzhe , Liu Yan , Duan Ruonan , Cheng Guo , Zhang Xiao 
Published: October 2016

AimTo determine the relative validity of a 2‐day 24‐hour dietary recall (HR) designed to assess energy and nutrient intake among Chinese adults compared with a 2‐day weighed dietary record (WD).MethodsData were obtained from an ongoing population‐based, prospective cohort study of adults aged 18–65 years in South China. A total of 41 adults completing a HR and a WD within 14 days were included in the present analysis. Estimations of individual mean differences, Spearman's correlation coefficients, cross‐classifications and Bland–Altman plots were used to assess the agreement between the intakes of energy and 18 nutrients obtained from the HR and the WD.ResultsWith the exception of total fat, saturated fatty acids, thiamine, potassium and magnesium, the energy and nutrient intakes between the HR and WD showed no significant differences. All dietary intakes that were evaluated by the HR were correlated significantly with the dietary intake from the WD (de‐attenuated correlation coefficients ranged from 0.10 to 0.87). The proportion of participants classified into quartiles correctly ranged from 61% for tocopherol intake to 90% for energy intake. The weighted k values ranking the participants ranged from 0.11 for tocopherol intake to 0.41 for the intakes of energy and calcium. The Bland–Altman plots showed moderate/good agreement among all the dietary intakes that were estimated from the HR and WD, except for total fat.ConclusionsThis study suggests that an HR could be a valid tool for estimating the energy and nutrient intakes among adults in South China at the group level.
Development of food lists as a first step to develop a food frequency questionnaire for toddlers in a multi‐ethnic population
Authors: Mubarik Farya , Bhaskaran Kalpana , Kho Stephanie , Vereijken Carel , Nambiar Smita , Eussen Simone , Muhardi Leilani 
Published: October 2016

AimToddlerhood is an important stage of growth, thus understanding the food intake of children in this age group is important. In Singapore, there is currently no simple tool, such as Food Frequency Questionnaire (FFQ), to collect dietary information from this ethnically diverse age group. Generating an appropriate food list is a crucial step in the development of a FFQ and this step is not clearly documented in the literature. The purpose of this study is to generate food lists and portion sizes for toddlers from three major ethnic groups in Singapore and document the processes involved in this first stage.MethodsA total of 30 mothers (equal number of Malays, Indians and Chinese) of 11–24‐month‐old children completed three‐day food records and participated in the focus group discussion. The reported food items were then categorised into food groups.ResultsThe food lists varied by ethnic groups with the longest list obtained from Chinese toddlers. There were also other foods that were then classified as common foods for all ethnicities. Commonly used utensils among the three ethnic groups were small‐sized bowls, plates, cups and spoons. For portion sizes, these utensils were typically half‐filled for the toddlers.ConclusionsAs all Singaporeans have access to the same foods, the ethnic‐specific food lists generated in this study could be combined into one list. Together with portion sizes, this information can be used for developing a semi‐quantitative FFQ.
Accuracy and precision of estimation equations to predict net endogenous acid excretion using the Australian food database
Authors: Parmenter Benjamin H. , Slater Gary J. , Frassetto Lynda A. 
Published: October 2016

AimThe gold standard of measurement for net endogenous acid production (NEAP) is net acid excretion (NAE), a test that is not readily available, and consequently, estimative equations by Remer and Manz and Frassetto et al. are often used. These equations rely on nutrient databases and it is recommended that their validity be assessed using a country's database before their application in research in that country. We sought to delineate the accuracy and precision of these estimation equations using the Australian food database.MethodsIn a double blind, randomised, cross‐over fashion, healthy participants (n = 13) residing in regional Australia were exposed to varying net acid loads while they collected weighted food diaries and 24‐hour urine samples for measurement of NAE.ResultsIn comparison to the Frassetto et al. equations (equation one bias = −57.1 mEq/day, equation two bias = −32.8 mEq/day), only the Remer and Manz equation was accurate (bias = −5.4 mEq/day); however, all equations were imprecise.ConclusionsUsing the Australian database, the performance of these equations to predict NEAP appears equal to other databases; however, caveats apply in their application. For future research, the equation by Remer and Manz is preferential for group estimates. None of the equations are recommended for individual estimates.
Process evaluation of a patient‐centred, patient‐directed, group‐based education program for the management of type 2 diabetes mellitus
Authors: Odgers‐Jewell Kate , Isenring Elisabeth , Thomas Rae , Reidlinger Dianne P. 
Published: October 2016

AimThe present study developed and evaluated a patient‐centred, patient‐directed, group‐based education program for the management of type 2 diabetes mellitus.MethodsTwo frameworks, the Medical Research Council (MRC) framework for developing and evaluating complex interventions and the RE‐AIM framework were followed. Data to develop the intervention were sourced from scoping of the literature and formative evaluation. Program evaluation comprised analysis of primary recruitment of participants through general practitioners, baseline and end‐point measures of anthropometry, four validated questionnaires, contemporaneous facilitator notes and telephone interviews with participants.ResultsA total of 16 participants enrolled in the intervention. Post‐intervention results were obtained from 13 participants, with an estimated mean change from baseline in weight of −0.72 kg (95%CI −1.44 to −0.01), body mass index of −0.25 kg/m2 (95%CI −0.49 to −0.01) and waist circumference of −1.04 cm (95%CI −4.52 to 2.44). The group education program was acceptable to participants. The results suggest that recruitment through general practitioners is ineffective, and alternative recruitment strategies are required.ConclusionsThis patient‐centred, patient‐directed, group‐based intervention for the management of type 2 diabetes mellitus was both feasible and acceptable to patients. Health professionals should consider the combined use of the MRC and RE‐AIM frameworks in the development of interventions to ensure a rigorous design process and to enable the evaluation of all phases of the intervention, which will facilitate translation to other settings. Further research with a larger sample trialling additional recruitment strategies, evaluating further measures of effectiveness and utilising lengthier follow‐up periods is required.
Daily Ingestion ofAloe VeraGel Powder Containing Aloe Sterols Prevents Skin Photoaging in OVX Hairless Mice
Authors: Yao Ruiqing , Tanaka Miyuki , Misawa Eriko , Saito Marie , Nabeshima Kazumi , Yamauchi Koji , Abe Fumiaki , Yamamoto Yuki , Furukawa Fukumi 
Published: October 2016

AbstractEstrogen deficiencies associated with menopause accelerate spontaneous skin aging and stimulate the ultraviolet (UV) irradiation‐induced photoaging of skin. However, food compositions with the potential to ameliorate the UV irradiation‐induced acceleration of skin aging with menopause have not yet been investigated in detail. In the present study, we examined the ability of plant sterols derived fromAloe veragel to prevent the UV irradiation‐induced acceleration of skin aging in ovariectomized mice. Skin transepidermal water loss (TEWL) was significantly higher in the ovariectomy group than in the sham operation group following UVB irradiation, whereas skin elasticity was significantly lower. Ultraviolet B (UVB) irradiation induced greater reductions in skin hyaluronic acid levels and more severe collagen fiber damage in the derims in the ovariectomy group than in the sham group. The intake of AVGP significantly ameliorated this acceleration in skin aging by reducing the expression of matrix metalloproteinases (MMPs) and increasing that of epidermal growth factor (EGF) and hyaluronan synthase (HAS) in the skin. These results indicate that AVGP supplementation prevents skin damage induced by UVB irradiation and ovariectomy in part by inhibiting damage to the extracellular matrix.
Glycemic status and chronic kidney disease in Chinese adults: Findings from the REACTION study
Authors: Lin Lin , Lu Jieli , Chen Lulu , Mu Yiming , Ye Zhen , Liu Chao , Chen Gang , Shi Lixin , Zhao Jiajun , Li Qiang , Yang Tao , Yan Li , Wan Qin , Wu Shengli , Liu Yan , Wang Guixia , Luo Zuojie , Tang Xulei , Huo Yanan , Gao Zhengnan , Su Qing , Wang Youmin , Qin Guijun , Deng Huacong , Yu Xuefeng , Shen Feixia , Chen Li , Zhao Liebin , Xu Yu , Xu Min , Peng Kui , Du Rui , Dai Meng , Li Mian , Wang Tiange , Zhao Zhiyun , Lai Shenghan , Li Donghui , Bi Yufang , Wang Weiqing , Ning Guang ,   on behalf of the REACTION Study Group
Published: October 2016

AbstractBackgroundDiagnosed diabetes has been associated with chronic kidney disease (CKD). However, the association between non‐diabetic hyperglycemia and CKD remained uncertain. The aim of the present study was to investigate the association between different glycemic status and CKD in Chinese adults and to assess the prevalence and control of diabetes among individuals with CKD.MethodsIn all, 250 752 adults aged ≥40 years were selected from the baseline cohort of the Risk Evaluation of cAncers in Chinese diabeTic Individuals: a lONgitudinal (REACTION) study. Plasma glucose concentrations and biochemical and other clinical data were collected; CKD was defined as an estimated glomerular filtration rate (eGFR) <60 mL/min per 1.73 m2.ResultsThe prevalence of CKD increased gradually with deterioration of glucose metabolic status in both men and women (
P

trend < 0.001 for both). Compared with individuals with normal glucose regulation, men with prediabetes and diabetes had higher risks of prevalent CKD (prediabetes odds ratio [OR] 1.15, 95% confidence interval [CI] 1.02–1.32; newly diagnosed diabetes OR 1.27, 95% CI 1.08–1.49; previously diagnosed diabetes OR 2.05, 95% CI 1.78–2.35). Similar results were observed in women, but not among those with prediabetes. In male CKD patients with diabetes, 52.1% received antidiabetic treatment and 41.8% of those treated had effective glycemic control, higher than values for females.ConclusionsPrediabetes and diabetes were associated with an increased risk of CKD in Chinese men. Control of diabetes among Chinese CKD patients is far from optimal.
PSMC (pairwise sequentially Markovian coalescent) analysis of RAD (restriction site associated DNA) sequencing data
Authors: Liu Shenglin , Hansen Michael M. 
Published: October 2016

AbstractThe pairwise sequentially Markovian coalescent (PSMC) method uses the genome sequence of a single individual to estimate demographic history covering a time span of thousands of generations. Although originally designed for whole‐genome data, we here use simulations to investigate its applicability to reference genome‐aligned restriction site associated DNA (RAD) data. We find that RAD data can potentially be used for PSMC analysis, but at present with limitations. The key factor is the proportion (p) of the genome that the RAD data covers. In our simulations, a proportion of 10% can still retain a substantial amount of coalescent information, whereas for 1% estimation becomes unreliable. The performance depends strongly on mutation rate (μ) and recombination rate (r) and is proportional to μ*p/r. When the value of this term is low, increasing the amount of data and number of iterations helps restoring the power of the estimation. We subsequently analyse one whole‐genome‐sequenced and 17 RAD‐sequenced three‐spined sticklebacks (Gasterosteus aculeatus) from a lake in Greenland. The whole‐genome sequence suggests a relatively recent expansion and decline within ca. 4000–40 000 generations ago, possibly reflecting postglacial expansion and founding of the lake population. RAD data, where chromosomes from 10 individuals are combined, identify a similar pattern. Our study provides guidance about the use of PSMC analysis and suggests measures that can improve its utility for RAD data. Finally, the study shows that RAD loci in general contain coalescent information that can be used for developing more targeted methods.
RNA‐Seq identifies redox balance related gene expression alterations under acute cadmium exposure in yeast
Authors: Huang Xinhe , Li Yuxing , Pan Jingmei , Li Ming , Lai Yongqin , Gao Jie , Li Xueru 
Published: October 2016

SummaryThe nonessential metal cadmium can cause cell toxicity and is associated with a range of human diseases including cardiovascular diseases, neurodegenerative diseases and cancers. In this study, cadmium‐induced global gene expression profile of yeast was obtained using RNA Sequencing (RNA‐Seq) and further analyzed by means of informatics and experiments. A total of 912 Differentially Expressed Genes (DEGs) (FDR of q < 0.01), including 415 Cd‐inducible and 497 Cd‐repressed genes were identified. Based on the DEGs, 25 cadmium responsive Clusters of Orthologous Group (COG) and three types of cadmium‐induced Gene Ontology (GO) including cellular components, molecular functions and biological processes were analyzed in details. Thereafter, 79 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways under cadmium exposure were assigned. Collectively, 108 redox balance related genes were extracted under cadmium exposure. Meanwhile, cadmium exposure lowered cellular Mitochondrial Membrane Potential (MMP) and increased Reactive Oxygen Species (ROS) levels significantly in the context of mitochondrial dysfunction. Furthermore, cadmium exposure increased cellular GSH levels and decreased GSSG levels and also lowered GSSG/GSH ratio of cells, which supports experimentally our claim that the redox balance is the primary mechanism for cadmium toxicity. The results present in this study may provide new strategies for cadmium detoxification and prevention or therapies of cadmium‐associated diseases.
Two‐current choice flumes for testing avoidance and preference in aquatic animals
Authors: Jutfelt Fredrik , Sundin Josefin , Raby Graham D. , Krång Anna‐Sara , Clark Timothy D. 
Published: October 2016

Summary

Aquatic chemical ecology is an important and growing field of research that involves understanding how organisms perceive and respond to chemical cues in their environment. Research assessing the preference or avoidance of a water source containing specific chemical cues has increased in popularity in recent years, and a variety of methods have been described in the scientific literature. Two‐current choice flumes have seen the greatest increase in popularity, perhaps because of their potential to address the broadest range of research questions.

Here, we review the literature on two‐current choice flumes and show that there is a clear absence of standardized methodologies that make comparisons across studies difficult. Some of the main issues include turbulent flows that cause mixing of cues, inappropriate size of choice arenas for the animals, short experiments with stressed animals, failure to report how experiment and researcher biases were eliminated, general underreporting of methodological details, underutilization of collected data and inappropriate data analyses.

In this review, we present best practice guidelines on how to build, test and use two‐current choice flumes to measure the behavioural responses of aquatic animals to chemical cues, and provide blueprints for flume construction. The guidelines include steps that can be taken to avoid problems commonly encountered when using two‐current choice flumes and analysing the resulting data.

This review provides a set of standards that should be followed to ensure data quality, transparency and replicability in future studies in this field.
Mechanistic description of population dynamics using dynamic energy budget theory incorporated into integral projection models
Authors: Smallegange Isabel M. , Caswell Hal , Toorians Marjolein E. M. , de Roos André M. 
Published: October 2016

Summary

Integral projection models (IPMs) provide a powerful approach to investigate ecological and rapid evolutionary change in quantitative life‐history characteristics and population dynamics. IPMs are constructed from functions that describe the demographic rates – survival, growth and reproduction – in relation to the characteristics of individuals and their environment. Currently, however, demographic rates are estimated using phenomenological regression models that lack a mechanistic representation of the biological processes that give rise to observed demographic variation. This lack of mechanistic underpinning limits the ability of the model to predict future dynamics under novel environmental conditions because the model ingredients pertain to current environmental conditions only.

Here, we use dynamic energy budget (DEB) theory to construct DEB‐IPMs based on a mechanistic representation of individual life‐history trajectories. We derive the demographic functions describing growth and reproduction from a simple DEB growth model. The functions describing mortality and the association between parent and offspring characteristics do not follow DEB theory and hence are estimated from individual‐level observations.

We apply the DEB‐IPM to two contrasting systems: the small, fast‐reproducing bulb mite Rhizoglyphus robini and the large, slow‐reproducing reef manta ray Manta alfredi. In both cases, predictions of population growth rate, lifetime reproductive success and generation time agree with empirical observations. In case of the bulb mite, predictions and observations even agree across different feeding conditions.

If the DEB energetics model is accepted as describing growth and reproduction, DEB‐IPMs can be parameterised using easy‐to‐collect life cycle information (growth rate, length at birth, maturation and old age) making them suitable for data‐deficient species. Because species differ only in these DEB parameters, comparative studies of character and population dynamics between species are straightforward, particularly since DEB‐IPMs can be extended to include population feedback on resources, of which we give an example. Most crucially, because DEB theory specifies growth and reproduction rates as explicitly dependent on environmental conditions such as food availability or temperature, DEB‐IPMs provide a mechanistic platform to investigate the biological processes that determine joint change in phenotypic characters, life‐history traits, population size and community structure.