bluuebunny/crossref_metadata_2025_split huggingface dataset:
tuf
Gene Sequence Variation in Bifidobacterium longum subsp.
infantis
Detected in the Fecal Microbiota of Chinese Infants
Authors: Lawley Blair , Centanni Manuela , Watanabe Jun , Sims Ian , Carnachan Susan , Broadbent Roland , Lee Pheng Soon , Wong Khai Hong , Tannock Gerald W. 
Published: April 2018

ABSTRACT

Members of the bacterial genus
Bifidobacterium
generally dominate the fecal microbiota of infants. The species
Bifidobacterium longum
is prevalent, but the
B. longum
subsp.
longum
and
B. longum
subsp.
infantis
strains that are known to colonize the infant bowel are not usually differentiated in microbiota investigations. These subspecies differ in their capacities to metabolize human milk oligosaccharides (HMO) and may have different ecological and symbiotic roles in humans. Quantitative PCR provides a quick analytical method by which to accurately ascertain the abundances of target species in microbiotas and microcosms. However, amplification targets in DNA extracted from samples need to be dependably differential. We evaluated the
tuf
gene sequence as a molecular target for quantitative PCR measurements of the abundances of
B. longum
subsp.
infantis
and
B. longum
subsp.
longum
in fecal microbiotas. This approach resulted in the detection of a
tuf
gene variant (operational taxonomic unit 49 [OTU49]) in Chinese infants that has sequence similarities to both
B. longum
subsp.
infantis
and
B. longum
subsp.
longum
. We compared the genome sequence and growth and transcriptional characteristics of an OTU49 isolate cultured in HMO medium to those of other
B. longum
subsp.
infantis
cultures. We concluded from these studies that OTU49 belongs to
B. longum
subsp.
infantis
, that dependable quantitative PCR (qPCR) differentiation between the
B. longum
subspecies cannot be achieved by targeting
tuf
gene sequences, and that functional genes involved in carbohydrate metabolism might be better targets because they delineate ecological functions.

IMPORTANCE
High-throughput DNA sequencing methods and advanced bioinformatics analysis have revealed the composition and biochemical capacities of microbial communities (microbiota and microbiome), including those that inhabit the gut of human infants. However, the microbiology and function of natural ecosystems have received little attention in recent decades, so an appreciation of the dynamics of gut microbiota interactions is lacking. With respect to infants, rapid methodologies, such as quantitative PCR, are needed to determine the prevalences and proportions of different bifidobacterial species in observational and microcosm studies in order to obtain a better understanding of the dynamics of bifidobacterial nutrition and syntrophy, knowledge that might be used to manipulate the microbiota and perhaps ensure the better health of infants.
Association of serum orosomucoid with 30-min plasma glucose and glucose excursion during oral glucose tolerance tests in non-obese young Japanese women
Authors: Tsuboi Ayaka , Minato Satomi , Yano Megumu , Takeuchi Mika , Kitaoka Kaori , Kurata Miki , Yoshino Gen , Wu Bin , Kazumi Tsutomu , Fukuo Keisuke 
Published: April 2018

ObjectiveInflammatory markers are elevated in insulin resistance (IR) and diabetes. We tested whether serum orosomucoid (ORM) is associated with postload glucose, β-cell dysfunction and IR inferred from plasma insulin kinetics during a 75 g oral glucose tolerance test (OGTT).Research design and methods75 g OGTTs were performed with multiple postload glucose and insulin measurements over a 30–120 min period in 168 non-obese Japanese women (aged 18–24 years). OGTT responses, serum adiponectin and high-sensitivity C reactive protein (hsCRP) were cross-sectionally analyzed by analysis of variance and then Bonferroni’s multiple comparison procedure. Stepwise multivariate linear regression analyses were used to identify most important determinants of ORM.ResultsOf 168 women, 161 had normal glucose tolerance. Postload glucose levels and the area under the glucose curve (AUCg) increased in a stepwise fashion from the first through the third ORM tertile. In contrast, there was no or modest, if any, association with fat mass index, trunk/leg fat ratio, adiponectin, hsCRP, postload insulinemia, the Matsuda index and homeostasis model assessment IR. In multivariable models, which incorporated the insulinogenic index, the Matsuda index and HOMA-IR, 30 min glucose (standardized β: 0.517) and AUCg (standardized β: 0.495) explained 92.8% of ORM variations.ConclusionsElevated circulating orosomucoid was associated with elevated 30 min glucose and glucose excursion in non-obese young Japanese women independently of adiposity, IR, insulin secretion, adiponectin and other investigated markers of inflammation. Although further research is needed, these results may suggest a clue to identify novel pathways that may have utility in monitoring dysglycemia within normal glucose tolerance.
Residential proximity to livestock farms is associated with a lower prevalence of atopy
Authors: Borlée Floor , Yzermans C Joris , Krop Esmeralda J M , Maassen Catharina B M , Schellevis François G , Heederik Dick J J , Smit Lidwien A M 
Published: April 2018

ObjectivesExposure to farm environments during childhood and adult life seems to reduce the risk of atopic sensitisation. Most studies have been conducted among farmers, but people living in rural areas may have similar protective effects for atopy. This study aims to investigate the association between residential proximity to livestock farms and atopy among non-farming adults living in a rural area in the Netherlands.MethodsWe conducted a cross-sectional study among 2443 adults (20–72 years). Atopy was defined as specific IgE to common allergens and/or total IgE ≥100 IU/mL. Residential proximity to livestock farms was assessed as 1) distance to the nearest pig, poultry, cattle or any farm, 2) number of farms within 500 m and 1000 m, and 3) modelled annual average fine dust emissions from farms within 500 m and 1000 m. Data were analysed with multiple logistic regression and generalised additive models.ResultsThe prevalence of atopy was 29.8%. Subjects living at short distances from farms (<327 m, first tertile) had a lower odds for atopy compared with subjects living further away (>527 m, third tertile) (OR 0.79, 95% CI 0.63 to 0.98). Significant associations in the same direction were found with distance to the nearest pig or cattle farm. The associations between atopy and livestock farm exposure were somewhat stronger in subjects who grew up on a farm.ConclusionsLiving in close proximity to livestock farms seems to protect against atopy. This study provides evidence that protective effects of early-life and adult farm exposures may extend beyond farming populations.
Anisotropy effects on baryogenesis in f(R) theories of gravity
Authors: Aghamohammadi A. , Hossienkhani H. , Saaidi Kh. 
Published: April 2018

We study the f(R) theory of gravity in an anisotropic metric and its effect on the baryon number-to-entropy ratio. The mechanism of gravitational baryogenesis based on the CPT-violating gravitational interaction between derivative of the Ricci scalar curvature and the baryon-number current is investigated in the context of the f(R) gravity. The gravitational baryogenesis in the Bianchi type I (BI) Universe is examined. We survey the effect of anisotropy of the Universe on the baryon asymmetry from the point of view of the f(R) theories of gravity and its effect on [Formula: see text] for radiation dominant regime.
Statistical description of massless excitations within a sphere with a linear equation of state and the dark energy case
Authors: Viaggiu S. 
Published: April 2018

In this paper, we continue the investigations present in Refs. 1–3. In particular, we extend the theorem proved in Ref. 3 to any massless excitation in a given spherical box. As a first interesting result, we show that it is possible, contrary to the black hole case studied in detail in Refs. 1–3, to build macroscopic configurations with a dark energy equation of state. To this purpose, by requiring a stable configuration, a macroscopic dark fluid is obtained with an internal energy [Formula: see text] scaling as the volume [Formula: see text], but with a fundamental correction looking like [Formula: see text] motivated by quantum fluctuations. Thanks to the proposition in Sec. 3 (and in Ref. 3 for gravitons), one can depict the dark energy in terms of massless excitations with a discrete spectrum. This fact opens the possibility to test a possible physical mechanism converting usual radiation into dark energy in a macroscopic configuration, also in a cosmological context. In fact, for example, in a Friedmann flat universe with a cosmological constant, particles are marginally trapped at the Hubble horizon for any given comoving observer.
Identification of a Small Molecule That Selectively Inhibits ERG-Positive Cancer Cell Growth
Authors: Mohamed Ahmed A. , Xavier Charles P. , Sukumar Gauthaman , Tan Shyh-Han , Ravindranath Lakshmi , Seraj Nishat , Kumar Vineet , Sreenath Taduru , McLeod David G. , Petrovics Gyorgy , Rosner Inger L. , Srivastava Meera , Strovel Jeffrey , Malhotra Sanjay V. , LaRonde Nicole A. , Dobi Albert , Dalgard Clifton L. , Srivastava Shiv 
Published: April 2018

Abstract
Oncogenic activation of the ETS-related gene (ERG) by recurrent gene fusions (predominantly TMPRSS2–ERG) is one of the most validated and prevalent genomic alterations present in early stages of prostate cancer. In this study, we screened small-molecule libraries for inhibition of ERG protein in TMPRSS2–ERG harboring VCaP prostate cancer cells using an In-Cell Western Assay with the highly specific ERG-MAb (9FY). Among a subset of promising candidates, 1-[2-Thiazolylazo]-2-naphthol (NSC139021, hereafter ERGi-USU) was identified and further characterized. ERGi-USU selectively inhibited growth of ERG-positive cancer cell lines with minimal effect on normal prostate or endothelial cells or ERG-negative tumor cell lines. Combination of ERGi-USU with enzalutamide showed additive effects in inhibiting growth of VCaP cells. A screen of kinases revealed that ERGi-USU directly bound the ribosomal biogenesis regulator atypical kinase RIOK2 and induced ribosomal stress signature. In vivo, ERGi-USU treatment inhibited growth of ERG-positive VCaP tumor xenografts with no apparent toxicity. Structure-activity–based derivatives of ERGi-USU recapitulated the ERG-selective activity of the parental compound. Taken together, ERGi-USU acts as a highly selective inhibitor for the growth of ERG-positive cancer cells and has potential for further development of ERG-targeted therapy of prostate cancer and other malignancies.
Significance: A highly selective small-molecule inhibitor of ERG, a critical driver of early stages of prostate cancer, will be imperative for prostate cancer therapy. Cancer Res; 78(13); 3659–71. ©2018 AACR.
A new species of Malenchus (Nematoda: Tylenchomorpha) with an updated phylogeny of the Tylenchidae
Authors: Qing Xue , Pereira Tiago J. , Slos Dieter , Couvreur Marjolein , Bert Wim 
Published: April 2018

Summary
The family Tylenchidae is one of most abundant and diverse nematode groups found in soil habitats. In this study, a new species named Malenchus cylindricus sp. n. is described based on light and scanning electron microscopy and molecular data. The new species is characterised by elongate-cylindrical vulva-anus body shape and a narrow annulation. We updated the phylogeny of Tylenchidae by including molecular data for the rare genera Miculenchus and Tenunemellus and by improving the morphological characterisation of the genus Lelenchus. Additionally, we compared the effect of alignment methods on the tree topologies and branch support values. The results suggest that the position of subfamily Ecphyadophorinae within Tylenchidae needs to be further revised. Phylogenies inferred from different sequence-based alignments were relatively more similar (i.e., tree topology and branch support) to one another than to secondary structure-aided methods. Finally, conflicting branch support values can be reconciled by properly selecting the alignment method.
Modeling the Dynamic Vegetation–Climate System over China Using a Coupled Regional Model
Authors: Shi Ying , Yu Miao , Erfanian Amir , Wang Guiling 
Published: April 2018

AbstractUsing the Regional Climate Model (RegCM) coupled with the Community Land Model (CLM) including modules of carbon–nitrogen cycling (CN) and vegetation dynamics (DV), this study evaluates the performance of the model with different capacity of representing vegetation processes in simulating the present-day climate over China based on three 21-yr simulations driven with boundary conditions from the ERA-Interim reanalysis data during 1989–2009. For each plant functional type (PFT), the plant pheonology, density, and fractional coverage in RegCM-CLM are all prescribed as static from year to year; RegCM-CLM-CN prescribes static fractional coverage but predicts plant phenology and density, and RegCM-CLM-CN-DV predicts plant phenology, density, and fractional coverage. Compared against the observational data, all three simulations reproduce the present-day climate well, including the wind fields, temperature and precipitation seasonal cycles, extremes, and interannual variabilities. Relative to RegCM-CLM, both RegCM-CLM-CN and RegCM-CLM-CN-DV perform better in simulating the interannual variability of temperature and spatial distribution of mean precipitation, but produce larger biases in the mean temperature field. RegCM-CLM-CN overestimates leaf area index (LAI), which enhances the cold biases and alleviates the dry biases found in RegCM-CLM. RegCM-CLM-CN-DV underestimates vegetation cover and/or stature, and hence overestimates surface albedo, which enhances the wintertime cold and dry biases found in RegM-CLM. During summer, RegCM-CLM-CN-DV overestimates LAI in south and east China, which enhances the cold biases through increased evaporative cooling; in the west where evaporation is low, the albedo effect of the underestimated vegetation cover is still dominant, leading to enhanced cold biases relative to RegCM-CLM.
Sex, Race, and Place
Authors: Boggess Lyndsay N. , Powers Ráchael A. , Chamberlain Alyssa W. 
Published: April 2018

Objectives: We draw upon theories of social disorganization, strain, and subculture of violence to examine how sex and race/ethnicity intersect to inform nonlethal violent offending at the macrolevel. Methods: Using neighborhood-level incidents, we examine (1) the structural correlates of male and female nonlethal violence and (2) whether ecological conditions have variable impacts on the prevalence of White, Black, and Latino male and female offenses above and beyond differential exposure to disadvantage. We use multivariate negative binomial regression within a structural equation modeling framework which allows for the examination of the same set of indicator variables on more than one dependent variable simultaneously while accounting for covariance between the dependent variables. Results: We find few significant differences in the salience of disadvantage on female and male violence across race and ethnicity although some differences emerge for White men and women. Structural factors are largely sex invariant within race and ethnicity. Conclusions: Despite expectations that disadvantage would have differential effects across sex and race/ethnicity, we uncover only minor differences. This suggests that structural effects are more invariant than variant across subgroups and highlights the importance of investigating both similarities and differences when examining neighborhood structure, intersectionality, and criminal behavior.
The effects of spiritual care on quality of life and spiritual well-being among patients with terminal illness: A systematic review
Authors: Chen Jingyi , Lin Yazhu , Yan Jie , Wu Yong , Hu Rong 
Published: April 2018

Background: Terminal illness not only causes physical suffering but also spiritual distress. Spiritual care has been widely implemented by healthcare professionals to assist patients coping with spiritual distress. However, the effects of spiritual care need to be clear. Aim: To evaluate the effects of spiritual care on quality of life and spiritual well-being among patients with terminal illness. Design: Systematic review according to the recommendations of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidance. Data sources: A comprehensive search was conducted in nine electronic databases from date of inception to May 2017. Hand searches of the bibliographies of relevant articles were also performed. The studies were independently reviewed by two investigators who scored them for methodological quality using the Cochrane Risk of Bias Tool. Results: No statistical pooling of outcomes was performed and a narrative summary was chosen to describe the included studies. A total of 19 studies with 1548 participants were identified in the systematic review, corresponding to seven kinds of interventions. The risk of bias for these studies were all rated as moderate. A majority of studies indicated that spiritual care had a potential beneficial effect on quality of life and spiritual well-being among patients with terminal illness. Conclusion: It is suggested that healthcare professionals integrate spiritual care with usual care in palliative care. When providing spiritual care, healthcare professionals should take into consideration patients’ spiritual needs, preference, and cultural background. More multicenter and disciplinary studies with rigorous designs are needed in the future.
Surviving the Storm: Factors Determining Party Survival in Central and Eastern Europe
Authors: Deegan-Krause Kevin , Haughton Tim 
Published: April 2018

This article is part of the special cluster titled Parties and Democratic Linkage in Post-Communist Europe, guest edited by Lori Thorlakson, and will be published in the August 2018 issue of EEPS Political parties in Central and Eastern Europe come and go quite rapidly, giving the region a reputation for electoral chaos, but amid the change, some parties survive for many electoral cycles. A brief examination of the party systems in the region shows a high rate of party collapse but also indicates the robustness of certain parties in the face of crisis. Closer comparisons of the collapsed and surviving parties indicates a significant role for three factors: organization on the ground, a clear position on an enduring issue dimension, and ability to change party leadership. The finding is particularly important for explaining the dynamics of Central and East European party systems because the same characteristics that contribute to longevity are found in lower levels among new parties in the region. Only a small subset of new parties have made choices that would contribute to long-term survival, and such cases are largely confined to those with strong ties to previous long-surviving parties.
Birth Prevalence of Orofacial Clefts in Kuwait From Hospital-Based Registration
Authors: Alhayyan Wasmiya A. , Pan Sharat C. , AlQatami Fawzi M. 
Published: April 2018

Introduction: Cleft lip and palate (CLAP) are the most common craniofacial anomalies and birth defects globally. Despite the fact that a tertiary care registry of clefts has existed in Kuwait since 2008, to date there is no published data regarding the prevalence of orofacial clefts in this population. Objective: To tabulate the pattern of orofacial clefts from tertiary care center registration during 2009 through 2014 and to estimate the prevalence and trend using population-based records. Methodology: Data from all CLAP cases (born in Kuwait) registered in the central cleft center registry of the Al-Amiri hospital, Kuwait City, Kuwait, from January 2009 to December 2014 were obtained. Data regarding the type, severity, gender as well as nationality, parental consanguinity, and associated syndrome were obtained from medical records. Birth prevalence was tabulated against the population statistics for the period obtained from the central department of statistics. Result: A total of 202 CLAP patients were recorded in the study period with a mean birth prevalence of 0.57 per 1000 live births (95% confidence interval [CI] .57 ± .23). The registry recorded 108 (53.2%) males and 94 (47.8%) females. Children born to Kuwaitis represented 53.7% of cases while those born to non-Kuwaitis represented 45.3%. The most common oral cleft was CLAP (47.3%), followed by cleft palate (30.5%), cleft lip (20.2%), and other facial clefts (2%). Other congenital anomalies were recognized in 33% of all cases. There were no statistically significant differences in oral cleft prevalence across gender or nationality. Conclusion: The prevalence of oral cleft in Kuwait appears to be similar to those of other Middle Eastern populations.
Normal feline behaviour: … and why problem behaviours develop
Authors: Bradshaw John 
Published: April 2018

Practical relevance: Cats are descended from a solitary, territorial ancestor, and while domestication has reduced their inherited tendency to be antagonistic towards all animals larger than their typical prey, they still place more reliance on the security of their territory than on psychological attachments to people or other cats, the exact opposite to dogs. Many feline problem behaviours stem from perceived threats to this security, often due to conflicts with other cats. Others are more developmental in origin, often caused by inadequate exposure to crucial stimuli, especially people, during the socialisation period. Strongly aversive events experienced at any age can also contribute. A third category comprises normal behaviour that owners deem unacceptable, such as scratching of furniture. Evidence base: This review identifies three areas in which basic research is inadequate to support widely employed concepts and practices in feline behavioural medicine. First, classification of cats’ problem behaviours relies heavily on approaches derived from studies of their behavioural ecology and, to some extent, extrapolation from canine studies. Few studies have focused on cats in the home, the environment in which most behavioural disorders are expressed. Secondly, cats’ chemical senses (olfactory and vomeronasal) are far more sensitive than our own, making it difficult for owners or clinicians to fully comprehend the sensory information upon which they base their behaviour. Thirdly, although the concept of psychological distress is widely invoked as an intervening variable in behavioural disorders, there are still no reliable measures of distress for pet cats in the home. Global importance: Psychological distress of some kind is the primary cause of many of the behavioural problems presented to clinicians, but surveys indicate that many more cats display the same clinical signs without their owners ever seeking help. The welfare of this ‘invisible’ group could be improved by veterinarians taking a more proactive approach to educating their clients about the behavioural needs of pet cats.