bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct and indirect effects of native range expansion on soil microbial community structure and function
Authors: Collins Courtney G. , Carey Chelsea J. , Aronson Emma L. , Kopp Christopher W. , Diez Jeffrey M. 
Published: May 2016

Summary

Analogous to the spread of non‐native species, shifts in native species’ ranges resulting from climate and land use change are also creating new combinations of species in many ecosystems. These native range shifts may be facilitated by similar mechanisms that provide advantages for non‐native species and may also have comparable impacts on the ecosystems they invade.

Soil biota, in particular bacteria and fungi, are important regulators of plant community composition and below‐ground ecosystem function. Compared to non‐native plant invasions, there have been relatively few studies examining how soil biota influence – or are influenced by – native species range shifts.

Here, we examined how a native range‐expanding sagebrush species (Artemisia rothrockii) affects below‐ground abiotic conditions and microbial community structure and function using next‐generation sequencing coupled with other biotic and abiotic soil analyses. We utilized a range‐expansion gradient, together with a shrub removal experiment and structural equation models, to determine the direct and indirect drivers of these interconnected processes.

Sagebrush colonization increased bacterial and archaeal richness and diversity and altered community composition across the expansion gradient. Soil organic C and N and soil moisture increased with sagebrush presence; however, results varied across the expansion gradient. We found no relationship between sagebrush and soil pH; however, pH strongly influenced microbial richness and diversity. Microbial (substrate‐induced) respiration was influenced by soil organic N, as well as microbial diversity and functional group relative abundances, highlighting direct and indirect effects of sagebrush on microbial community structure and function. Microbial community composition of soils after 4 years of sagebrush removal was more similar to communities in shrub interspaces than underneath shrubs, suggesting microbial community resilience.

Synthesis. Our results suggest that native range expansions can have important impacts on soil biological communities, soil chemistry and hydrology which can further impact below‐ground ecosystem processes such as nutrient cycling and litter decomposition. The combination of high‐throughput sequencing and structural equation modelling used here offers an exciting yet underutilized approach to understanding how both native and non‐native species’ range expansions may affect the structure and function of soil ecosystems.
Alterations and correlations of the gut microbiome, metabolism and immunity in patients with primary biliary cirrhosis
Authors: Lv Long‐Xian , Fang Dai‐Qiong , Shi Ding , Chen De‐Ying , Yan Ren , Zhu Yi‐Xin , Chen Yan‐Fei , Shao Li , Guo Fei‐Fei , Wu Wen‐Rui , Li Ang , Shi Hai‐Yan , Jiang Xia‐Wei , Jiang Hui‐Yong , Xiao Yong‐Hong , Zheng Shu‐Sen , Li Lan‐Juan 
Published: May 2016

SummaryWe selected 42 early‐stage primary biliary cirrhosis (PBC) patients and 30 healthy controls (HC). Metagenomic sequencing of the 16S rRNA gene was used to characterize the fecal microbiome. UPLC‐MS/MS assaying of small molecules was used to characterize the metabolomes of the serum, urine and feces. Liquid chip assaying of serum cytokines was used to characterize the immune profiles. The gut of PBC patients were depleted of some potentially beneficial bacteria, such as Acidobacteria, Lachnobacterium sp., Bacteroides eggerthii and Ruminococcus bromii, but were enriched in some bacterial taxa containing opportunistic pathogens, such as γ‐Proteobacteria, Enterobacteriaceae, Neisseriaceae, Spirochaetaceae, Veillonella, Streptococcus, Klebsiella, Actinobacillus pleuropneumoniae, Anaeroglobus geminatus, Enterobacter asburiae, Haemophilus parainfluenzae, Megasphaera micronuciformis and Paraprevotella clara. Several altered gut bacterial taxa exhibited potential interactions with PBC through their associations with altered metabolism, immunity and liver function indicators, such as those of Klebsiella with IL‐2A and Neisseriaceae with urinary indoleacrylate. Many gut bacteria, such as some members of Bacteroides, were altered in their associations with the immunity and metabolism of PBC patients, although their relative abundances were unchanged. Consequently, the gut microbiome is altered and may be critical for the onset or development of PBC by interacting with metabolism and immunity.
Shelf‐Life Extension of Chill‐Stored Beef Longissimus Steaks Packaged under Modified Atmospheres with 50% O2 and 40% CO2
Authors: Yang Xiaoyin , Niu Lebao , Zhu Lixian , Liang Rongrong , Zhang Yimin , Luo Xin 
Published: May 2016

AbstractThis study was conducted to compare the shelf‐life of beef steaks stored in different packaging conditions: overwrapped (OW) packaging and 2 modified atmosphere packaging systems (MAP): 80% O2 MAP (80% O2/20% CO2) and 50% O2 MAP (50% O2/40% CO2/10% N2). Steaks were stored at 2 °C for 20 d. Headspace gas composition, microbial counts, color stability, pH, purge loss, and lipid oxidation were monitored. Among the packaging types, 50% O2 MAP was superior to OW packaging and 80% O2 MAP in delaying bacterial growth and extending shelf‐life to 20 d. 50% O2 MAP also gave steaks an acceptable color during storage. No significant differences were observed in color stability of steaks packaged in both 50% O2 MAP and 80% O2 MAP. This study reveals 50% O2 MAP is a realistic alternative to preserve beef steaks efficiently.
Analysis of Duplicated Multiple‐Samples Rank Data Using the Mack–Skillings Test
Authors: Carabante Kennet Mariano , Alonso‐Marenco Jose Ramon , Chokumnoyporn Napapan , Sriwattana Sujinda , Prinyawiwatkul Witoon 
Published: May 2016

AbstractAppropriate analysis for duplicated multiple‐samples rank data is needed. This study compared analysis of duplicated rank preference data using the Friedman versus Mack–Skillings tests. Panelists (n = 125) ranked twice 2 orange juice sets: different‐samples set (100%, 70%, vs. 40% juice) and similar‐samples set (100%, 95%, vs. 90%). These 2 sample sets were designed to get contrasting differences in preference. For each sample set, rank sum data were obtained from (1) averaged rank data of each panelist from the 2 replications (n = 125), (2) rank data of all panelists from each of the 2 separate replications (n = 125 each), (3) jointed rank data of all panelists from the 2 replications (n = 125), and (4) rank data of all panelists pooled from the 2 replications (n = 250); rank data (1), (2), and (4) were separately analyzed by the Friedman test, although those from (3) by the Mack–Skillings test. The effect of sample sizes (n = 10 to 125) was evaluated. For the similar‐samples set, higher variations in rank data from the 2 replications were observed; therefore, results of the main effects were more inconsistent among methods and sample sizes. Regardless of analysis methods, the larger the sample size, the higher the χ2 value, the lower the P‐value (testing H0: all samples are not different). Analyzing rank data (2) separately by replication yielded inconsistent conclusions across sample sizes, hence this method is not recommended. The Mack–Skillings test was more sensitive than the Friedman test. Furthermore, it takes into account within‐panelist variations and is more appropriate for analyzing duplicated rank data.
CoMuS: simulating coalescent histories and polymorphic data from multiple species
Authors: Papadantonakis S. , Poirazi P. , Pavlidis P. 
Published: May 2016

AbstractThe simultaneous analysis of intra‐ and interspecies variation is challenging mainly because our knowledge about patterns of polymorphisms where both intra‐ and interspecies samples coexist is limited. In this study, we present CoMuS (Coalescent of Multiple Species), a multispecies coalescent software that can simulate intra‐ and interspecies polymorphisms. CoMuS supports a variety of speciation models and demographic scenarios related to the history of each species. In CoMuS, speciation can be accompanied by either instant or gradual isolation between sister species. Sampling may also occur in the past, and thus, we can study simultaneously extinct and extant species. Our software supports both the infinite‐ and the finite‐site model, with substitution rate heterogeneity among sites and a user‐defined proportion of invariable sites. We demonstrate the usage of CoMuS in various applications: species delimitation, software testing, model selection and parameter inference involving present‐day and ancestral samples, comparison between gradual and instantaneous isolation models, estimation of speciation time between human and chimpanzee using both intra‐ and interspecies variation. We expect that CoMuS will be particularly useful for studies where species have been separated recently from their common ancestor and phenomena such as incomplete lineage sorting or introgression still occur.
Oral administration of recombinant Mycobacterium smegmatis expressing a tripeptide construct derived from endogenous and microbial antigens prevents atherosclerosis in ApoE−/− mice
Authors: Deshpande Vrushali , Krishnan Rameshkumar , Philip Sheena , Faludi Ildiko , Ponnusamy Thiruvelselvan , Thota Lakshmi Narasimha Rao , Endresz Valeria , Lu Xinjie , Kakkar Vijay V. , Mundkur Lakshmi A. 
Published: May 2016

SummaryIntroductionImmunotherapy by inducing oral tolerance to atherogenic self‐antigens is gaining importance as an alternative treatment modality for atherosclerosis. The use of live bacterial vectors to express the recombinant antigen in vivo will obviate the need for large‐scale purification of recombinant protein and may also augment the efficacy of oral tolerance induction.AimThe objective of the study was to explore the use of recombinant Mycobacterium smegmatis as a live vector for oral delivery of antigens to induce immune tolerance.Method and ResultsWe developed a M. smegmatis vector to secrete a recombinant tripeptide construct (AHC; peptides from Apolipoprotein B, Heat‐shock protein 60 and Chlamydia pneumoniae outer membrane protein) expressed in a dendroaspin protein scaffold in pJH154 background. Immune response and oral tolerance to the cloned peptides were studied in C57/BL6 mice. The efficacy of this live vaccine to control atherosclerosis was studied in ApoE−/− knockout mice in C57/BL6 background. Oral administration of M. smegmatis secreting the cloned AHC antigen was found to induce tolerance to cloned protein and reduce the development of atherosclerosis by 24.0% compared to control. Protection against atherosclerosis was associated with increase in expression of regulatory T cell‐associated markers including CTLA4 (1.8‐fold), Foxp3 (2.6‐fold), TGF‐β (2.8‐fold), IL10 (2.9‐fold), and reduction in lipids, macrophage infiltration, and expression of inflammatory mediators in aorta.ConclusionsOur results suggest that M. smegmatis can be developed as an oral carrier of recombinant proteins to treat inflammatory autoimmune diseases.
Proton pump inhibitors use and change in bone mineral density
Authors: Arj Abbas , Razavi Zade Mohsen , Yavari Maryam , Akbari Hossein , Zamani Batol , Asemi Zatollah 
Published: May 2016

AbstractObjectiveLimited data are available reporting the effect of proton pump inhibitor (PPI) use on changes in bone mineral density (BMD). The aim of this study was to investigate the relationship between PPI use and BMD.MethodsThe current cross‐sectional study included 80 patients (31 male and 49 female) aged 20–45 years old without history of hip fracture with a follow‐up of at least 2 years. The study was carried out in 40 daily PPI users and 40 PPI non‐users. Femur and posterior‐anterior spine BMD were quantified by dual‐energy X‐ray absorptiometry in all participants. The relationship between use of PPI and BMD was tested by multivariate linear regression analysis adjusted for age, sex, BMI and serum vitamin D levels.ResultsOur study demonstrated that mean femoral T‐scores were significant between PPI and non‐user groups (−0.44 ± 1.11 vs. +0.19 ± 0.95, P = 0.007). In addition, the frequency of femoral osteoporosis and osteopenia in the exposed group was significantly more in the control group (P = 0.04). Mean femoral Z‐scores, lumbar spine T‐score and lumbar spine Z‐score were not statistically different between PPI and non‐user groups. The linear regression analysis revealed that there was no association between PPI and non‐users, and lumbar spine T‐score.ConclusionOverall, the results of this study showed that PPI use in subjects without risk factors of osteoporosis determined by the femoral T‐score compared with the control group was associated with increased risk of developing osteoporosis and osteopenia in the femur bones.
Association between depression and anemia in otherwise healthy adults
Authors: Vulser H. , Wiernik E. , Hoertel N. , Thomas F. , Pannier B. , Czernichow S. , Hanon O. , Simon T. , Simon J‐M , Danchin N. , Limosin F. , Lemogne C. 
Published: May 2016

ObjectiveIt remains debated whether anemia is associated with depression, independently of physical health factors. We report a large‐scale cross‐sectional study examining this association in adults free of chronic disease and medication from the general population.MethodHemoglobin levels were measured among 44 173 healthy participants [63% men; mean [standard deviation] age = 38.4 (11.1) years] from the ‘Investigations Préventives et Cliniques’ (IPC) cohort study. Depression was measured with the Questionnaire of Depression 2nd version, Abridged. Logistic regression analyses were performed to examine the association between anemia and depression, while adjusting for a wide range of sociodemographic characteristics and health‐related factors (i.e., sex, age, living status, education level, occupational status, alcohol intake, smoking status, physical activity, and body mass index).ResultsDepressed participants were significantly more likely to have anemia compared to non‐depressed participants, even after adjustment for sociodemographic and health‐related variables [odds ratio = 1.36; 95% confidence interval = (1.18; 1.57)]. Anemia prevalence increased with depression severity, suggesting a dose–response relationship (P for trend <0.001).ConclusionIn healthy adults from the general population, we found a significant and robust association between depression and anemia. Further studies are needed to assess the longitudinal relationship between both conditions and determine the mechanisms underlying this association.
Prevalence of obesity in paediatric psoriasis and its impact on disease severity and progression
Authors: Ergun Tulin , Seckin Gencosmanoglu Dilek , Karakoc‐Aydiner Elif , Salman Andac , Tekin Burak , Bulbul‐Baskan Emel , Alpsoy Erkan , Cakıroglu Aylin , Onsun Nahide 
Published: May 2016

AbstractBackground/ObjectivesThe current literature suggests there is a possible connection between paediatric psoriasis and obesity. However, there is a paucity of research on the influence of increased adiposity on the severity of paediatric psoriasis and disease progression. We aimed to compare the prevalence of being overweight or obese in paediatric psoriasis patients and controls and assess the potential impact of being overweight/obese on disease severity and progression of disease.MethodsThis multicentre prospective case‐control study included 289 psoriasis patients (aged < 18 years) treated and followed up by one of the four university hospitals in Turkey. The control group consisted of 151 consecutive age‐matched and sex‐matched children who lacked a personal or family history of psoriasis. The participants' characteristics, psoriasis‐related parametres (e.g., initial subtype, psoriasis area and severity index, presence of psoriatic arthritis) and body mass index were determined.ResultsThe difference between the prevalence of being overweight/obese among psoriatics (28%) and the control group (19%) was significant (P = 0.024). Being overweight/obese had no significant impact on disease severity and unresponsiveness to topical treatment. Within a median follow‐up time of 12 months, 23% of our patients with localised disease at disease onset progressed to generalised disease. The impact of being overweight/obese on disease progression was found to be non‐significant; however, disease duration was found to have a significant impact on disease progression (P = 0.026).ConclusionsAlthough it is not associated with disease severity and course, increased bodyweight may be a health problem for psoriatic children.
Formal training in general movement assessment is required to effectively evaluate infants with perinatal asphyxia in outpatient settings
Authors: Brown Annemette K. , Greisen Gorm , Haugsted Ulla , Jonsbo Finn 
Published: May 2016

AbstractAimGeneral movement assessment (GMA) can help to identify children with a high risk of developing neurological dysfunction, such as cerebral palsy, and certified training is provided in this specialism. The aim of this study was to investigate the feasibility and reliability of using video recordings to assess GMA, in a busy Danish outpatient clinic.MethodsThe study comprised 30‐term infants born with perinatal asphyxia, who were video recorded at three months. They were assessed by two certified GMA observers and re‐assessed two weeks later. Interobserver and intra‐observer agreements were analysed using proportional agreement, and nominal kappa statistics were used to calculate 95% confidence intervals (95% CI).ResultsWe found substantial and almost perfect interobserver and intra‐observer reliability. Intra‐observer agreement was 0.85 (95% CI: 0.65–1.00; p < 0.0001) and 0.85 (95% CI: 0.62–1.00; p < 0.0001), and interobserver agreement was 0.71 (95% CI: 0.45–0.96; p < 0.0001) at time point one and 0.85 (95% CI: 0.63–1.00; p < 0.0001) two weeks later. All video recordings were completed within our multidisciplinary outpatient clinic without delay.ConclusionThis study demonstrated the reliability of the GMA method in a busy multidisciplinary Danish paediatric outpatient setting, when assessors had been formally trained in the method and used it regularly.
Investigating a Longitudinal Trajectory of Child Obesity and Its Association with Child Maltreatment in South Korea
Authors: Park Aely , Kim Youngmi 
Published: May 2016

This study investigated the association between child maltreatment and body mass index (BMI) using data from four waves (wave 2 in 2011 through 5 in 2014) of the Korean Children & Youth Panel Survey collected by the South Korean National Youth Policy Institute. We employed a latent growth curve modeling approach to estimate an unobserved latent trajectory and to test the longitudinal effects of child abuse and neglect on BMI. Our results indicate that child abuse is significantly associated with BMI and children who report higher levels of abuse tend to have higher rates of increase in their BMI. This study addresses a gap in the literature by demonstrating that a parent's maltreatment of their child has a long‐term effect on the rate of change in their BMI over time.
Evaluation of the factors contributing to long‐term survival in canine tonsillar squamous cell carcinoma
Authors: Grant J , North S 
Published: May 2016

ObjectivesTo identify any prognostic factors that may be associated with the long‐term survival of dogs diagnosed with tonsillar squamous cell carcinoma (TSCC).MethodsThe medical records of 15 dogs treated for TSCC were reviewed retrospectively. The signalment, presenting signs, clinical stage, treatments and outcome were documented.ResultsThe overall median survival time (MST) of the dogs in the study was 243 days. There was a 1‐and 2‐year survival of 40% and 20%, respectively. The results of initial staging had a significant effect on survival, as dogs with only one tonsil affected and no evidence of metastatic disease had a longer MST (637.5 days) than the dogs with local (MST: 134 days) or distant (MST: 75 days) metastatic disease or bilateral tonsillar involvement at the time of initial presentation. Prolonged survival times were reported for dogs undergoing surgery and adjunctive chemotherapy (MST: 464.5 days) for treatment of their TSCC.Clinical significanceThis is the first veterinary study demonstrating an association between prognosis of patients with TSCC and stage at the time of presentation, with long survival times demonstrated for dogs with early‐stage disease following an initial treatment protocol that included surgery and chemotherapy. There was no clear association between long survival and additional surgeries for progressive disease; however; further investigation is warranted.
High‐quality care improves outcome in recumbent dairy cattle
Authors: Poulton PJ , Vizard AL , Anderson GA , Pyman MF 
Published: May 2016

ObjectiveTo investigate the influence of the quality of care on outcome and occurrence of secondary damage in recumbent dairy cows.MethodsRecumbent dairy cows were monitored during their recumbency under field conditions in South Gippsland, Victoria, Australia. The cause of the original recumbency of 218 downer cows was determined and any secondary damage, day 7 status, final outcome and the nursing conditions of the cows were recorded. A four‐tiered grading system describing nursing quality was developed to allow analysis of its influence on outcome and on the occurrence of secondary damage.ResultsDay 7 outcome, final outcome and occurrence of important secondary damage were very strongly associated with the level of overall care provided to the recumbent cows. There was a decrease in the percentage of cows recovering by day 7 from 33% to 0%, a decrease from 45% to 0% of cows eventually recovering and an increase from 68% to 100% of cows with clinically important secondary damage as overall care decreased.ConclusionManagement of recumbent cattle is potentially a significant animal welfare issue for the dairy industry and their care is a very important but often under‐appreciated aspect of their management. Recovery is positively influenced by high‐quality care by improving the chances of recovery from the initial cause of recumbency and by reducing the occurrence of secondary damage. Recumbent cows must either be nursed at a high level of care or euthanased promptly.
Severe hyponatraemia in foals: clinical findings, primary diagnosis and outcome
Authors: Collins NM , Axon JE , Carrick JB , Russell CM , Palmer JE 
Published: May 2016

ObjectiveTo evaluate severe hyponatraemia in foals presenting as medical emergencies to an intensive care unit (ICU) in order to determine the prevalence, clinical findings, primary diagnosis and outcome.DesignRetrospective case study of records from Thoroughbred foals aged less than 3 months presenting to anICUas medical emergencies in 2002–12; foals with severe hyponatraemia (serum sodium<122 mmol/L) on admission laboratory data were identified. Data retrieved included signalment, clinical findings, laboratory results, primary diagnosis, treatment and outcome.ResultsSevere hyponatraemia was identified in 69/1718 Thoroughbred foals (4%) presenting to theICUduring the study period. Of the 69 foals, 11 (15.9%) presented with neurological signs attributable to hyponatraemic encephalopathy and 7 of these foals had seizures; other neurological signs included obtundation, ataxia and apparent blindness. The three most common primary diagnoses of the 69 foals with severe hyponatraemia were renal disease (18/69, 26.1%), enterocolitis (16/69, 23.2%) and uroperitoneum (15/69, 21.7%). Treatment was directed at the primary disease and correction of the hyponatraemia. A total of 50 of the 69 foals (72.5%) with severe hyponatraemia survived to hospital discharge and 38 of them (76%) survived at least 12 months following discharge.ConclusionThe prevalence of severe hyponatraemia in this study population was 4%. The majority of foals with severe hyponatraemia did not demonstrate direct clinical manifestations as a result of the low serum sodium concentration. The outcome of foals with severe hyponatraemia was mostly favourable.