bluuebunny/crossref_metadata_2025 huggingface dataset:
Association between plasma phosphorus and renal outcome: A prospective cohort of patients majorly with glomerulonephritis
Authors: Xu Damin , Lv Jicheng , Wang Jinwei , Zhang Luxia , Zhang Hong
Published: January 2016

Aim

Studies investigating the association between blood phosphorus and renal outcomes yielded inconsistent results, and studies from Asian population are extremely limited. We initiated the present cohort study, aiming to prospectively examine the association between blood phosphorus and adverse renal outcomes in a prospective chronic kidney disease (CKD) cohort of Chinese patients majorly with glomerulonephritis.

Methods

A total of 1430 patients were involved in the study. Linear regression analyses were used to assess the relationship between phosphorus and the slope of estimated glomerular filtration rate (eGFR). Cox regression analyses were used to assess the association between phosphorus and composite outcomes, which were defined as the presence of at least one of: eGFR halving, end stage renal disease, or death.

Results

During follow‐up for an average of 41.4 months, 196 patients developed composite outcomes. The time‐average plasma phosphorus was independently associated with the slope of eGFR (β = –0.18, 95% CI: –4.42 to –2.19, P < 0.001). Each 1 mg/dL increases of baseline and time‐average phosphorus were respectively associated with a 1.33 (95% confidence interval (CI): 1.09–1.63; P = 0.005) and 2.79 (95%CI: 2.21–3.52; P < 0.001) fold higher risk of composite outcomes. Compared with participants in the bottom quartile of time‐average phosphorus, those in the top quartile were at increased risk of composite outcomes, with a hazard ratio of 6.52 (95% CI: 3.05–13.90; P < 0.001).

Conclusion

Plasma phosphorus level is an independent risk factor of adverse renal outcomes in Chinese CKD patients majorly with glomerulonephritis. Compared with baseline value, time‐average phosphorus has a stronger relationship with renal prognosis.
Root structure–function relationships in 74 species: evidence of a root economics spectrum related to carbon economy
Authors: Roumet Catherine , Birouste Marine , Picon‐Cochard Catherine , Ghestem Murielle , Osman Normaniza , Vrignon‐Brenas Sylvain , Cao Kun‐fang , Stokes Alexia
Published: January 2016

Although fine roots are important components of the global carbon cycle, there is limited understanding of root structure–function relationships among species. We determined whether root respiration rate and decomposability, two key processes driving carbon cycling but always studied separately, varied with root morphological and chemical traits, in a coordinated way that would demonstrate the existence of a root economics spectrum (RES).

Twelve traits were measured on fine roots (diameter ≤ 2 mm) of 74 species (31 graminoids and 43 herbaceous and dwarf shrub eudicots) collected in three biomes.

The findings of this study support the existence of a RES representing an axis of trait variation in which root respiration was positively correlated to nitrogen concentration and specific root length and negatively correlated to the root dry matter content, lignin : nitrogen ratio and the remaining mass after decomposition. This pattern of traits was highly consistent within graminoids but less consistent within eudicots, as a result of an uncoupling between decomposability and morphology, and of heterogeneity of individual roots of eudicots within the fine‐root pool.

The positive relationship found between root respiration and decomposability is essential for a better understanding of vegetation–soil feedbacks and for improving terrestrial biosphere models predicting the consequences of plant community changes for carbon cycling.
Seedling root responses to soil moisture and the identification of a belowground trait spectrum across three growth forms
Authors: Larson Julie E. , Funk Jennifer L.
Published: January 2016

Root trait variation and plasticity could be key factors differentiating plant performance under drought. However, water manipulation and root measurements are rarely coupled empirically across growth forms to identify whether belowground strategies are generalizable across species.

We measured seedling root traits across three moisture levels in 18 Mediterranean forbs, grasses, and woody species.

Drought increased the root mass fraction (RMF) and decreased the relative proportion of thin roots (indicated by increased root diameters and decreased specific root length (SRL)), rates of root elongation and growth, plant nitrogen uptake, and plant growth. Although responses varied across species, plasticity was not associated with growth form. Woody species differed from forbs and grasses in many traits, but herbaceous groups were similar. Across water treatments, trait correlations suggested a single spectrum of belowground trade‐offs related to resource acquisition and plant growth. While effects of SRL and RMF on plant growth shifted with drought, root elongation rate consistently represented this spectrum.

We demonstrate that general patterns of root morphology and plasticity are identifiable across diverse species. Root trait measurements should enhance our understanding of belowground strategy and performance across growth forms, but it will be critical to incorporate plasticity and additional aspects of root function into these efforts.
Can ketones compensate for deteriorating brain glucose uptake during aging? Implications for the risk and treatment of Alzheimer's disease
Authors: Cunnane Stephen C. , Courchesne‐Loyer Alexandre , St‐Pierre Valérie , Vandenberghe Camille , Pierotti Tyler , Fortier Mélanie , Croteau Etienne , Castellano Christian‐Alexandre
Published: January 2016

Brain glucose uptake is impaired in Alzheimer's disease (AD). A key question is whether cognitive decline can be delayed if this brain energy defect is at least partly corrected or bypassed early in the disease. The principal ketones (also called ketone bodies), β‐hydroxybutyrate and acetoacetate, are the brain's main physiological alternative fuel to glucose. Three studies in mild‐to‐moderate AD have shown that, unlike with glucose, brain ketone uptake is not different from that in healthy age‐matched controls. Published clinical trials demonstrate that increasing ketone availability to the brain via moderate nutritional ketosis has a modest beneficial effect on cognitive outcomes in mild‐to‐moderate AD and in mild cognitive impairment. Nutritional ketosis can be safely achieved by a high‐fat ketogenic diet, by supplements providing 20–70 g/day of medium‐chain triglycerides containing the eight‐ and ten‐carbon fatty acids octanoate and decanoate, or by ketone esters. Given the acute dependence of the brain on its energy supply, it seems reasonable that the development of therapeutic strategies aimed at AD mandates consideration of how the underlying problem of deteriorating brain fuel supply can be corrected or delayed.
Prenatal vitamin A supplementation associated with adverse child behavior at 3 years in a prospective birth cohort in Japan
Authors: Ishikawa Yohei , Tanaka Haruka , Akutsu Taisuke , Koide Kentaro , Sakuma Mio , Okazaki Minoru , Ida Hiroyuki , Urashima Mitsuyoshi
Published: January 2016

Background

Many pregnant women take vitamin supplements during pregnancy. The aim of this paper was to clarify the effects of dietary supplementation prior to and/or during pregnancy on child behavior.

Methods

A prospective birth cohort study from pregnancy to 3 years of age involving 1271 pairs of Japanese pregnant women and their newborns, was carried out. The women completed a self‐administered questionnaire during the third trimester of pregnancy. To evaluate deviations in child behavior as an endpoint, each mother completed the Japanese Child Behavior Checklist for ages 2–3 years after 3 years of birth. Participant characteristics were compared between supplement takers and non‐takers.

Results

Among many kinds of supplements, intake of supplemental vitamin A/β‐carotene prior to and/or during pregnancy was associated with hazardous effects on child behavior at 3 years of age (total t‐score, P = 0.003; internal t‐score, P = 0.027; external t‐score, P = 0.013). This association held true even after adjusting for age, number of deliveries, infertility treatment, consumption of fast food, smoking status, maternal and paternal education, maternal and paternal income, gestational age at birth, anthropometry at birth (weight, height, head circumference and body circumference), and the State–Trait Anxiety Inventory at 3 years of age by means of multiple imputation.

Conclusions

Intake of supplemental vitamin A prior to and/or during pregnancy may worsen child behavior at 3 years of age.
Large‐scale molecular phylogeny of Cryptorhynchinae (Coleoptera, Curculionidae) from multiple genes suggests American origin and later Australian radiation
Authors: RIEDEL ALEXANDER , TÄNZLER RENE , PONS JOAN , SUHARDJONO YAYUK R. , BALKE MICHAEL
Published: January 2016

The monophyly of the highly diverse weevil subfamily Cryptorhynchinae is tested with a dataset of 203 taxa representing 159 genera of Curculionoidea, 105 of them Cryptorhynchinae s.l. We construct a phylogeny based on an alignment of 5523 bp, consisting of fragments from two mitochondrial genes (two fragments of COI, 16S) and seven nuclear genes (ArgK, CAD, EF1α, enolase, H4, 18S, 28S). Analyses of maximum likelihood and Bayes inference recovered largely congruent results. Groups with different morphology of the rostral furrow (e.g. Aedemonini, Camptorhinini, Cryptorhynchini, Ithyporini) are not closely related to each other. However, most taxa with a mesosternal receptacle are monophyletic and here defined as Cryptorhynchinae s.s., comprising Cryptorhynchini, Gasterocercini, Torneumatini and Psepholacini, but also Arachnopodini and Idopelma Faust. The genus Phyrdenus LeConte is excluded from Cryptorhynchinae and transferred to Conotrachelini of Molytinae. Thus defined, the group still comprises several thousand species with centres of its diversity in South America and Australia. The early lineages we find in America and the Palearctic, while the extremely diverse faunas of Australia and neighbouring islands mainly belong to a more recent, species‐rich radiation. This also includes a clade comprising the majority of litter‐inhabiting species of New Zealand and the genus Miocalles Pascoe. Flightlessness was attained repeatedly and resulted in convergent evolution of a similar habitus in different zoogeographic regions, mainly exhibited by the polyphyletic genus Acalles Schoenherr.
The Effects of a Crosslinked, Modified Hyaluronic Acid (xCMHA‐S) Gel on Equine Tendon Healing
Authors: Jann Henry W. , Hart James C. A. , Stein Larry E. , Ritchey Jerry , Blaik Margaret , Payton Mark , Fackelman Gustave E. , Rezabek Grant B. , Mann Brenda K.
Published: January 2016

Objective

To assess the effects of a crosslinked, modified hyaluronic acid (xCMHA‐S) gel on equine tendon healing using an in vivo surgical model.

Study Design

In vivo experimental study.

Animals

Adult horses (n = 5).

Methods

Full thickness bilateral forelimb window tenectomies were surgically created in both forelimb superficial digital flexor tendons and xCMHA‐S gel was implanted intraoperatively into the right forelimb lesion of each horse whereas the left forelimb served as the untreated control. Healing was monitored by serial ultrasound examinations every 14 days over the course of the 84 day study. In addition, gross pathology, scanning electron microscopy for fiber diameter, and histological scoring were completed on tendon samples harvested after euthanasia at 84 days.

Results

Ultrasound assessment demonstrated a significant decrease in mean lesion size of treated (0%) compared to control (30%) tendons at 84 days. Mean (±SD) cumulative histologic tendon scores for control tendons (17.7 ± 2.7) were significantly higher than treated tendons (13.6 ± 1.9), indicating less advanced healing in the control group. Tendon cell density was increased and neovascularization, intensity of inflammation, and uniformity of fiber diameter were increased in control compared to treated tendons. There were no differences in fibroblast shape, levels of intralesional hemorrhage, linearity of collagen fibers, or collagen fiber diameter or distribution between treated and control tendons.

Conclusion

Tendons treated with xCMHA‐S gel at the time of model induction had superior histologic healing scores and sonographically smaller lesions compared to controls, suggesting that xCMHA‐S gel may aid the natural healing process.
The Appraising Evidence Game
Authors: Mick JoAnn
Published: January 2016

This column shares the best evidence‐based strategies and innovative ideas on how to facilitate the learning of EBP principles and processes by clinicians as well as nursing and interprofessional students. Guidelines for submission are available at http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1741‐6787
The Influence of Component Alignment and Ligament Properties on Tibiofemoral Contact Forces in Total Knee Replacement
Authors: Smith Colin R. , Vignos Michael F. , Lenhart Rachel L. , Kaiser Jarred , Thelen Darryl G.
Published: January 2016

The study objective was to investigate the influence of coronal plane alignment and ligament properties on total knee replacement (TKR) contact loads during walking. We created a subject-specific knee model of an 83-year-old male who had an instrumented TKR. The knee model was incorporated into a lower extremity musculoskeletal model and included deformable contact, ligamentous structures, and six degrees-of-freedom (DOF) tibiofemoral and patellofemoral joints. A novel numerical optimization technique was used to simultaneously predict muscle forces, secondary knee kinematics, ligament forces, and joint contact pressures from standard gait analysis data collected on the subject. The nominal knee model predictions of medial, lateral, and total contact forces during gait agreed well with TKR measures, with root-mean-square (rms) errors of 0.23, 0.22, and 0.33 body weight (BW), respectively. Coronal plane component alignment did not affect total knee contact loads, but did alter the medial–lateral load distribution, with 4 deg varus and 4 deg valgus rotations in component alignment inducing +17% and −23% changes in the first peak medial tibiofemoral contact forces, respectively. A Monte Carlo analysis showed that uncertainties in ligament stiffness and reference strains induce ±0.2 BW uncertainty in tibiofemoral force estimates over the gait cycle. Ligament properties had substantial influence on the TKR load distributions, with the medial collateral ligament and iliotibial band (ITB) properties having the largest effects on medial and lateral compartment loading, respectively. The computational framework provides a viable approach for virtually designing TKR components, considering parametric uncertainty and predicting the effects of joint alignment and soft tissue balancing procedures on TKR function during movement.
Effect of Fiber Crimp on the Elasticity of Random Fiber Networks With and Without Embedding Matrices
Authors: Ban Ehsan , Barocas Victor H. , Shephard Mark S. , Picu Catalin R.
Published: January 2016

Fiber networks are assemblies of one-dimensional elements representative of materials with fibrous microstructures such as collagen networks and synthetic nonwovens. The mechanics of random fiber networks has been the focus of numerous studies. However, fiber crimp has been explicitly represented only in few cases. In the present work, the mechanics of cross-linked networks with crimped athermal fibers, with and without an embedding elastic matrix, is studied. The dependence of the effective network stiffness on the fraction of nonstraight fibers and the relative crimp amplitude (or tortuosity) is studied using finite element simulations of networks with sinusoidally curved fibers. A semi-analytic model is developed to predict the dependence of network modulus on the crimp amplitude and the bounds of the stiffness reduction associated with the presence of crimp. The transition from the linear to the nonlinear elastic response of the network is rendered more gradual by the presence of crimp, and the effect of crimp on the network tangent stiffness decreases as strain increases. If the network is embedded in an elastic matrix, the effect of crimp becomes negligible even for very small, biologically relevant matrix stiffness values. However, the distribution of the maximum principal stress in the matrix becomes broader in the presence of crimp relative to the similar system with straight fibers, which indicates an increased probability of matrix failure.
Motorcycle Tire Modeling for the Study of Tire–Rim Interaction
Authors: Ballo Federico , Gobbi Massimiliano , Mastinu Gianpiero , Previati Giorgio
Published: January 2016

For the lightweight design of the wheel rim of motorcycles, the knowledge of the way in which contact forces are transmitted by the tire is of crucial importance. In this paper, an analytical model of the tire is developed and explicit formulae giving the distribution of the radial and axial forces acting on the wheel rim for a given vertical load are derived. The analytical model is validated by means of a finite element method (FEM) model and experimental tests. The proposed analytical model is able to predict the radial deflection of both a front and a rear tire for a racing motorbike with very good accuracy over a wide range of inflating pressures and vertical loads. The force distributions are in very good agreement with the results of the FEM model. Experimental tests show that the force distribution at the interface between the tire and rim can be used to predict the stress distribution in the rim with a good accuracy.
Nonlinear Parameters and State Estimation for Adaptive Nonlinear Model Predictive Control Design
Authors: Salhi Hichem , Bouani Faouzi
Published: January 2016

This paper deals with an adaptive nonlinear model predictive control (NMPC) based estimator in cases of mismatch modeling, presence of perturbations and/or parameter variations. Thus, we propose an adaptive nonlinear predictive controller based on the second-order divided difference filter (DDF) for multivariable systems. The controller uses a nonlinear state-space model for parameters and state estimation and for the control law synthesis. Two nonlinear optimization layers are included in the proposed algorithm. The first optimization problem is based on the output error (OE) model with a tuning factor, and it is dedicated to minimize the error between the model and the system at each sample time by estimating unknown parameters when assuming that all system states are available. The second optimization layer is used by the centralized nonlinear predictive controller to generate the control law which minimizes the error between future setpoints and future outputs along the prediction horizon. The proposed algorithm leads to a good tracking performance with an offset-free output and an effectiveness in perturbation attenuation. Practical results on a real setup show the reliability of the proposed approach.
Investigation of dilute-nitride alloys of GaAsNx (0.01 < x < 0.04) grown by MBE on GaAs (001) substrates for photovoltaic solar cell devices
Authors: Tang Dinghao , Vijaya Gopi Krishna , Mehrotra Akhil , Freundlich Alex , Smith David J.
Published: January 2016

Dilute-nitride GaAsNx epilayers were grown on GaAs (001) substrates at temperatures of ∼450 °C using a radio-frequency plasma-assisted molecular/chemical beam exitaxy system. The concentration of nitrogen incorporated into the films was varied in the range between 0.01 and 0.04. High-resolution electron microscopy was used to determine the cross-sectional morphology of the epilayers, and Z-contrast imaging showed that the incorporated nitrogen was primarily interstitial. {110}-oriented microcracks, which resulted in strain relaxation, were observed in the sample with the highest N concentration ([N] ∼ 3.7%). Additionally, Z-contrast imaging indicated the formation of a thin, high-N quantum-well-like layer associated with initial ignition of the N-plasma. Significant N contamination of the GaAs barrier layers was observed in all samples, and could severely affect the carrier extraction and transport properties in future targeted devices. Dilute-nitride quantum-well-based photovoltaic solar cells were fabricated having a band-gap energy of 1.19 eV, which was attributed to the dilute-nitride layer.
4D ML reconstruction as a tool for volumetric PET‐based treatment verification in ion beam radiotherapy
Authors: De Bernardi E. , Ricotti R. , Riboldi M. , Baroni G. , Parodi K. , Gianoli C.
Published: January 2016

Purpose:

An innovative strategy to improve the sensitivity of positron emission tomography (PET)‐based treatment verification in ion beam radiotherapy is proposed.

Methods:

Low counting statistics PET images acquired during or shortly after the treatment (Measured PET) and a Monte Carlo estimate of the same PET images derived from the treatment plan (Expected PET) are considered as two frames of a 4D dataset. A 4D maximum likelihood reconstruction strategy was adapted to iteratively estimate the annihilation events distribution in a reference frame and the deformation motion fields that map it in the Expected PET and Measured PET frames. The outputs generated by the proposed strategy are as follows: (1) an estimate of the Measured PET with an image quality comparable to the Expected PET and (2) an estimate of the motion field mapping Expected PET to Measured PET. The details of the algorithm are presented and the strategy is preliminarily tested on analytically simulated datasets.

Results:

The algorithm demonstrates (1) robustness against noise, even in the worst conditions where 1.5 × 104 true coincidences and a random fraction of 73% are simulated; (2) a proper sensitivity to different kind and grade of mismatches ranging between 1 and 10 mm; (3) robustness against bias due to incorrect washout modeling in the Monte Carlo simulation up to 1/3 of the original signal amplitude; and (4) an ability to describe the mismatch even in presence of complex annihilation distributions such as those induced by two perpendicular superimposed ion fields.

Conclusions:

The promising results obtained in this work suggest the applicability of the method as a quantification tool for PET‐based treatment verification in ion beam radiotherapy. An extensive assessment of the proposed strategy on real treatment verification data is planned.
A validated tumor control probability model based on a meta‐analysis of low, intermediate, and high‐risk prostate cancer patients treated by photon, proton, or carbon‐ion radiotherapy
Authors: Walsh Seán , Roelofs Erik , Kuess Peter , Lambin Philippe , Jones Bleddyn , Georg Dietmar , Verhaegen Frank
Published: January 2016

Purpose:

A fully heterogeneous population averaged mechanistic tumor control probability (TCP) model is appropriate for the analysis of external beam radiotherapy (EBRT). This has been accomplished for EBRT photon treatment of intermediate‐risk prostate cancer. Extending the TCP model for low and high‐risk patients would be beneficial in terms of overall decision making. Furthermore, different radiation treatment modalities such as protons and carbon‐ions are becoming increasingly available. Consequently, there is a need for a complete TCP model.

Methods:

A TCP model was fitted and validated to a primary endpoint of 5‐year biological no evidence of disease clinical outcome data obtained from a review of the literature for low, intermediate, and high‐risk prostate cancer patients (5218 patients fitted, 1088 patients validated), treated by photons, protons, or carbon‐ions. The review followed the preferred reporting item for systematic reviews and meta‐analyses statement. Treatment regimens include standard fractionation and hypofractionation treatments. Residual analysis and goodness of fit statistics were applied.

Results:

The TCP model achieves a good level of fit overall, linear regression results in a p‐value of <0.000 01 with an adjusted‐weighted‐R2 value of 0.77 and a weighted root mean squared error (wRMSE) of 1.2%, to the fitted clinical outcome data. Validation of the model utilizing three independent datasets obtained from the literature resulted in an adjusted‐weighted‐R2 value of 0.78 and a wRMSE of less than 1.8%, to the validation clinical outcome data. The weighted mean absolute residual across the entire dataset is found to be 5.4%.

Conclusions:

This TCP model fitted and validated to clinical outcome data, appears to be an appropriate model for the inclusion of all clinical prostate cancer risk categories, and allows evaluation of current EBRT modalities with regard to tumor control prediction.
Astronomers see ashes of the first stars
Authors: Clery Daniel
Published: January 2016

Primordial clouds show how giant stars forged the heavy elements that fill today's universe.
Incandescent lights go green
Authors: Service Robert F.
Published: January 2016

Photonic technology boosts efficiency of warm, wasteful bulbs.
AMP-activated protein kinase mediates mitochondrial fission in response to energy stress
Authors: Toyama Erin Quan , Herzig Sébastien , Courchet Julien , Lewis Tommy L. , Losón Oliver C. , Hellberg Kristina , Young Nathan P. , Chen Hsiuchen , Polleux Franck , Chan David C. , Shaw Reuben J.
Published: January 2016

How to shape mitochondrial networks

Mitochondria undergo fragmentation or fusion in response to changes in cellular metabolism. Toyama
et al.
report that adenosine monophosphate-activated protein kinase (AMPK) is both necessary and sufficient to control mitochondrial fragmentation. AMPK functions as a sensor to monitor the energy status of the cell by phosphorylating mitochondrial fission factor (MFF), a protein of the mitochondrial outer membrane. MFF then acts to recruit a cytoplasmic guanosine triphosphatase that promotes mitochondrial fission.

Science
, this issue p.
275
Transcriptome-wide distribution and function of RNA hydroxymethylcytosine
Authors: Delatte Benjamin , Wang Fei , Ngoc Long Vo , Collignon Evelyne , Bonvin Elise , Deplus Rachel , Calonne Emilie , Hassabi Bouchra , Putmans Pascale , Awe Stephan , Wetzel Collin , Kreher Judith , Soin Romuald , Creppe Catherine , Limbach Patrick A. , Gueydan Cyril , Kruys Véronique , Brehm Alexander , Minakhina Svetlana , Defrance Matthieu , Steward Ruth , Fuks François
Published: January 2016

Chemical modification of RNA for function

Chemical modifications play an important role in modifying and regulating the function of DNA and RNA. Delatte
et al.
show that, in the fruit fly, many messenger RNAs (mRNAs) contain the modified base 5-hydroxymethylcytosine (5hmC). The chemical mark is added by the same enzyme that adds 5hmC to DNA. Because many mRNAs involved in neuronal development contain 5hmC, blocking the enzyme causes brain defects and is lethal. In vivo, RNA hydroxymethylation promotes mRNA translation.

Science
, this issue p.
282
Inhibition protects acquired song segments during vocal learning in zebra finches
Authors: Vallentin Daniela , Kosche Georg , Lipkind Dina , Long Michael A.
Published: January 2016

Fixation on learned syllables

Zebra finches learn their beautiful songs by listening to other zebra finches. Vallentin
et al.
observed zebra finch brains as learning proceeded, only to find that inhibition of the neuronal circuits was critical to fixating on learned sequences. For song syllables that have been adequately learned, the inhibitory neurons fired coherently. Song syllables not yet learned failed to produce this flag. Thus, it is the learning process that alters the neuronal circuits. The inhibitory neuronal firing, not the age of the bird, locks in the learning.

Science
, this issue p.
267
Transkingdom control of viral infection and immunity in the mammalian intestine
Authors: Pfeiffer Julie K. , Virgin Herbert W.
Published: January 2016

Microbial villages shape viral infections

Viruses infecting the intestinal tract, such as noroviruses and rotaviruses, are major human pathogens. Despite facing an extreme environment within their hosts, which includes pH gradients, digestive enzymes, and the billions of microbes that inhabit human guts, these viruses somehow manage to survive and often thrive. Pfeiffer and Virgin review the complex microbial encounters that occur between enteric viruses and gut microbiota. Trans-kingdom interactions (that is, between viruses, bacteria, archaea, helminthes, fungi, and phage) are particularly important in shaping the course of a viral infection and the ensuing host immune response.

Science
, this issue p.
10.1126/science.aad5872
Allele-specific inhibitors inactivate mutant KRAS G12C by a trapping mechanism
Authors: Lito Piro , Solomon Martha , Li Lian-Sheng , Hansen Rasmus , Rosen Neal
Published: January 2016

Cancer therapy by entrapment

Mutations in the
KRAS
oncogene occur at high frequency in several of the most lethal human cancers, including lung and pancreatic cancer. Substantial effort has thus been directed toward developing KRAS inhibitors.
KRAS
encodes an enzyme that binds the nucleotide GTP and hydrolyzes it to GDP. It had been thought that oncogenic mutations disable this hydrolytic activity, locking KRAS in the GTP-bound, active state. Surprisingly, Lito
et al.
found that a certain KRAS mutant (G12C) retains hydrolytic activity and continues to cycle between its active and inactive states. They describe a compound that inhibits KRAS(G12C) signaling and tumor cell growth by binding to the GDPbound form of KRAS, trapping it in its inactive state.

Science
, this issue p.
604
Complete Genome Sequence of Helicobacter pylori Strain 29CaP Isolated from a Mexican Patient with Gastric Cancer
Authors: Mucito-Varela Eduardo , Castillo-Rojas Gonzalo , Cevallos Miguel A. , Lozano Luis , Merino Enrique , López-Leal Gamaliel , López-Vidal Yolanda
Published: January 2016

Helicobacter pylori
infection is a risk factor for the development of gastric cancer and other gastroduodenal diseases. We report here the complete genome sequence of
H. pylori
strain 29CaP, isolated from a Mexican patient with gastric cancer. The genomic data analysis revealed a
cag
-negative
H. pylori
strain that contains a prophage sequence.
Draft Genome Sequences of Achromobacter piechaudii GCS2,
Agrobacterium
sp. Strain SUL3,
Microbacterium
sp. Strain GCS4,
Shinella
sp. Strain GWS1, and
Shinella
sp. Strain SUS2 Isolated from Consortium with the Hydrocarbon-Producing Alga
Botryococcus braunii
Authors: Jones Katy J. , Moore Karen , Sambles Christine , Love John , Studholme David J. , Aves Stephen J.
Published: January 2016

A variety of bacteria associate with the hydrocarbon-producing microalga
Botryococcus braunii
, some of which may influence its growth. We report here the genome sequences for
Achromobacter piechaudii
GCS2,
Agrobacterium
sp. strain SUL3,
Microbacterium
sp. strain GCS4, and
Shinella
sp. strains GWS1 and SUS2, isolated from a laboratory culture of
B. braunii
, race B, strain Guadeloupe.
Complete Genome Sequence of Enterococcus faecalis Strain P8-1 Isolated from Wild Magellanic Penguin (Spheniscus magellanicus) Feces on the South Coast of Brazil
Authors: Prichula Janira , Campos Fabricio Souza , Pereira Rebeca Inhoque , Cardoso Leonardo Almansa , Wachholz Guilherme Raffo , Pieta Luiza , Mariot Roberta Fogliatto , de Moura Tiane Martin , Tavares Maurício , d'Azevedo Pedro Alves , Frazzon Jeverson , Frazzon Ana Paula Guedes
Published: January 2016

Enterococcus faecalisstrains have a ubiquitous nature that allows them to survive in different niches. Studies involving enterococci isolated from marine animals are scarce. Therefore, in this study, we report the complete genome sequence ofE. faecalisstrain P8-1 isolated from feces of a Magellanic penguin on the south coast of Brazil.
Complete Genome Sequence of the Hyperthermophilic and Piezophilic Archaeon Thermococcus barophilus Ch5, Capable of Growth at the Expense of Hydrogenogenesis from Carbon Monoxide and Formate
Authors: Oger Philippe , Sokolova Tatyana G. , Kozhevnikova Darya A. , Taranov Evgeny A. , Vannier Pauline , Lee Hyun Sook , Kwon Kae Kyoung , Kang Sung Gyun , Lee Jung-Hyun , Bonch-Osmolovskaya Elizaveta A. , Lebedinsky Alexander V.
Published: January 2016

We report here the complete sequence and fully manually curated annotation of the genome of strain Ch5, a new member of the piezophilic hyperthermophilic species
Thermococcus barophilus
.
Draft Genome Sequence of a Novel
Desulfobacteraceae
Member from a Sulfate-Reducing Bioreactor Metagenome
Authors: Almstrand Robert , Pinto Ameet J. , Figueroa Linda A. , Sharp Jonathan O.
Published: January 2016

Sulfate-reducing bacteria are important players in the global sulfur cycle and of considerable commercial interest. The draft genome sequence of a sulfate-reducing bacterium of the family
Desulfobacteraceae
, assembled from a sulfate-reducing bioreactor metagenome, indicates that heavy-metal– and acid-resistance traits of this organism may be of importance for its application in acid mine drainage mitigation.
Genome Sequence of Nitrosomonas communis Strain Nm2, a Mesophilic Ammonia-Oxidizing Bacterium Isolated from Mediterranean Soil
Authors: Kozlowski Jessica A. , Kits K. Dimitri , Stein Lisa Y.
Published: January 2016

The complete genome sequence ofNitrosomonas communisstrain Nm2, a mesophilic betaproteobacterial ammonia oxidizer isolated from Mediterranean soils in Corfu, Greece, is reported here. This is the first genome to describe a cluster 8Nitrosomonasspecies and represents an ammonia-oxidizing bacterium commonly found in terrestrial ecosystems.
Draft Genome Sequence of the Oral Commensal Streptococcus oralis 89a with Interference Activity against Respiratory Pathogens
Authors: Sidjabat Hanna E. , Grahn Håkansson Eva , Cervin Anders
Published: January 2016

We report the draft genome sequence of the oral commensal
Streptococcus oralis
89a isolated from the throat of a healthy child during a streptococcal tonsillitis outbreak in Umeå, Sweden.
S. oralis
89a was known to have interference activity against respiratory pathogens in which the colicin V was the potential bacteriocin-encoding gene.
Complete Genome Sequence of Klebsiella pneumoniae subsp.
pneumoniae
KP617, Coproducing OXA-232 and NDM-1 Carbapenemases, Isolated in South Korea
Authors: Kwon Taesoo , Yang Ji Woo , Lee Sanghyun , Yun Mi-ran , Yoo Won Gi , Kim Hwa Su , Cha Jeong-Ok , Kim Dae-Won
Published: January 2016

The prevalence of
Klebsiella pneumoniae
coproducing carbapenemase metallo-β-lactamase 1 (NDM-1) and OXA-48 has been increasing globally since 2013. The complete genome of KP617 was sequenced and assembled into a circular chromosome and two plasmids. This sequence provides the genetic background for understanding the evolution of carbapenemase genes in
K. pneumoniae
KP617.
Draft Genome Sequence of Altererythrobacter troitsensis JCM 17037, Isolated from the Sea Urchin
Strongylocentrotus intermedius
Authors: Zhou Peng , Wu Yue-Hong , Cheng Hong , Wang Chun-Sheng , Xu Xue-Wei
Published: January 2016

The habitats of the genus
Altererythrobacter
are various, including marine sediment, seawater, rhizosphere of wild rice, desert sand, etc. The genome of the type strain of
Altererythrobacter troitsensis
JCM 17037, isolated from sea urchin, was sequenced. This study would not only facilitate the understanding of the physiology, adaptation, and evolution of the
Altererythrobacter
species, but also provide a good resource for the study of synthesis of astaxanthin, since several enzymes involved in the production of astaxanthin were predicted.
Draft Genome Sequences of Two Novel
Acidimicrobiaceae
Members from an Acid Mine Drainage Biofilm Metagenome
Authors: Pinto Ameet J. , Sharp Jonathan O. , Yoder Michael J. , Almstrand Robert
Published: January 2016

Bacteria belonging to the family
Acidimicrobiaceae
are frequently encountered in heavy metal-contaminated acidic environments. However, their phylogenetic and metabolic diversity is poorly resolved. We present draft genome sequences of two novel and phylogenetically distinct
Acidimicrobiaceae
members assembled from an acid mine drainage biofilm metagenome.
Genome Sequences of Rotavirus A Strains Ty-1 and Ty-3, Isolated from Turkeys in Ireland in 1979
Authors: Fujii Yuji , Mitake Hiromichi , Yamada Daigo , Nagai Makoto , Okadera Kota , Ito Naoto , Okada Kazuma , Nakagawa Kento , Mizutani Tetsuya , Sugiyama Makoto
Published: January 2016

To obtain complete genome sequences of turkey rotavirus A strains Ty-1 and Ty-3, we sequenced the gene segments that had not been decoded previously. The genotype constellations of the respective strains were determined to be G17-P[38]-I4-R4-C4-M4-A16-N4-T4-E4-H4 and G7-P[35]-I4-R4-C4-M4-A16-N4-T4-E11-H14. Notably, their VP4 and NSP5 genes were classified into novel genotypes.
Complete Genome Sequence of
Arthrobacter
sp. Strain LS16, Isolated from Agricultural Soils with Potential for Applications in Bioremediation and Bioproducts
Authors: Hassan Ikrema , Eastman Alexander W. , Weselowski Brian , Mohamedelhassan Eltayeb , Yanful Ernest K. , Yuan Ze-Chun
Published: January 2016

Here we report the complete genomic sequence of the bacterium
Arthrobacter
sp. strain LS16, consisting of a single circular chromosome of 3.85 Mb with no identified plasmid. Data contained within will facilitate future genetic modification and engineering of the
Arthrobacter
sp. LS16 metabolic network to enhance traits relevant to bioremediation and bioproducts.
Permanent Draft Genome Sequences for Two Variants of
Frankia
sp. Strain CpI1, the First
Frankia
Strain Isolated from Root Nodules of
Comptonia peregrina
Authors: Oshone Rediet , Hurst Sheldon G. , Abebe-Akele Feseha , Simpson Stephen , Morris Krystalynne , Thomas W. Kelley , Tisa Louis S.
Published: January 2016

Frankia
stains CpI1-S and CpI1-P are members of
Frankia
lineage Ia that are able to reinfect plants of the
Betulaceae
and
Myricaceae
families. Here, we report two 7.6-Mbp draft genome sequences with 6,396 and 6,373 candidate protein-coding genes for CpI1-S and CpI1-P, respectively.
Proliferation of gynaecological scientific societies and their financial transparency: an Italian survey
Authors: Vercellini Paolo , Viganò Paola , Frattaruolo Maria Pina , Somigliana Edgardo
Published: January 2016

Objectives

To determine the number of Italian obstetrical and gynaecological societies, and to ascertain their financial transparency.

Design

Internet-based national survey and website content analysis.

Participants

Currently active, not privately owned, non-religious, apolitical, obstetrical and gynaecological associations.

Methods

From October 2014 to June 2015, scientific societies were identified using combinations of search terms, and examining the website of the two main Italian obstetrical and gynaecological organisations. Individual societies’ websites were scrutinised by two independent investigators.

Primary and secondary outcome measures

Number of Italian obstetrical and gynaecological associations and its variation over time; 12 information categories defining the general characteristics of the societies and their websites, and the financial transparency of the associations.

Results

The initial web search yielded 56 professional obstetrical and gynaecological associations but nine were excluded for various reasons. Of the remaining 47 professional associations, 17 covered both obstetrics and gynaecology, four were specialised in obstetrics, 26 in gynaecology and 46 provided continuing medical education (CME) activities. The number of societies has quadrupled in the last 35 years, increasing at a mean rate of one additional society per year. The headquarters of the associations were located in the offices of a professional congress organiser in 15 instances, and advertisements or links to industry products were present in 12 societies’ websites. Bylaws were accessible in 32 websites. No information was publicly available regarding competing interests, financial statements and quantitative external funding.

Conclusions

The number of obstetrical and gynaecological societies is remarkably high in Italy, particularly in the gynaecological area. Despite CME activity provision, transparency of societies regarding financial issues and competing interests was almost non-existent. Policies addressing the interactions between medical associations and industry are available and should be implemented.
Association between toothbrushing and risk factors for cardiovascular disease: a large-scale, cross-sectional Japanese study
Authors: Kuwabara Masanari , Motoki Yoko , Ichiura Kayoko , Fujii Mizue , Inomata Chisato , Sato Hiroki , Morisawa Taichiro , Morita Yoshinori , Kuwabara Kazumichi , Nakamura Yosikazu
Published: January 2016

Objectives

To clarify the association between toothbrushing and risk factors for cardiovascular disease—namely, hypertension (HT), diabetes mellitus (DM), dyslipidaemia (DL), hyperuricaemia (HUA) and chronic kidney disease (CKD).

Design

A large-scale, single-centre, cross-sectional study.

Setting

St Luke's International Hospital, Center for Preventive Medicine, Tokyo, Japan, between January 2004 and June 2010.

Participants

This study examined the toothbrushing practices of 85 866 individuals according to the 3-category frequency criterion: ‘after every meal’, ‘at least once a day’ and ‘less than once a day’. The ORs by frequency were calculated for the prevalences of HT, DM, DL, HUA and CKD according to binominal logistic regression analyses adjusted for age, gender, body mass index and lifestyle habits—smoking, drinking, walk time and sleep time.

Results

The prevalences of the risk factors were as follows: HT (‘after every meal’: 13.3%, ‘at least once a day’: 17.9% and ‘less than once a day’: 31.0%), DM (3.1%, 5.3% and 17.4%, respectively), DL (29.0%, 42.1% and 60.3%, respectively), HUA (8.6%, 17.5% and 27.2%, respectively) and CKD (3.8%, 3.1% and 8.3%, respectively). The prevalences were significantly higher in the ‘less than once a day’ group than in the ‘after every meal’ group for DM (OR=2.03; 95% CI 1.29 to 3.21) and DL (OR=1.50; 95% CI 1.06 to 2.14), but not for HT, HUA and CKD.

Conclusions

Even taking into account lifestyle habits, a lower frequency of toothbrushing was associated with high prevalences of DM and DL. Toothbrushing practices may be beneficial for oral health improvement and also for prevention of certain systemic diseases.
Trends in incidence, prevalence and prescribing in type 2 diabetes mellitus between 2000 and 2013 in primary care: a retrospective cohort study
Authors: Sharma Manuj , Nazareth Irwin , Petersen Irene
Published: January 2016

Objective

To investigate trends in incident and prevalent diagnoses of type 2 diabetes mellitus (T2DM) and its pharmacological treatment between 2000 and 2013.

Design

Analysis of longitudinal electronic health records in The Health Improvement Network (THIN) primary care database.

Setting

UK primary care.

Participants

In total, we examined 8 838 031 individuals aged 0–99 years.

Outcome measures

The incidence and prevalence of T2DM between 2000 and 2013, and the effect of age, sex and social deprivation on these measures were examined. Changes in prescribing patterns of antidiabetic therapy between 2000 and 2013 were also investigated.

Results

Overall, 406 344 individuals had a diagnosis of T2DM, of which 203 639 were newly diagnosed between 2000 and 2013. The incidence of T2DM rose from 3.69 per 1000 person-years at risk (PYAR) (95% CI 3.58 to 3.81) in 2000 to 3.99 per 1000 PYAR (95% CI 3.90 to 4.08) in 2013 among men; and from 3.06 per 1000 PYAR (95% CI 2.95 to 3.17) to 3.73 per 1000 PYAR (95% CI 3.65 to 3.82) among women. Prevalence of T2DM more than doubled from 2.39% (95% CI 2.37 to 2.41) in 2000 to 5.32% (95% CI 5.30 to 5.34) in 2013. Being male, older, and from a more socially deprived area was strongly associated with having T2DM, (p<0.001). Prescribing changes over time reflected emerging clinical guidance and novel treatments. In 2013, metformin prescribing peaked at 83.6% (95% CI 83.4% to 83.8%), while sulfonylureas prescribing reached a low of 41.4% (95% CI 41.1% to 41.7%). Both remained, however, the most commonly used pharmacological treatments as first-line agents and add-on therapy. Thiazolidinediones and incretin based therapies (gliptins and GLP-1 analogues) were also prescribed as alternate add-on therapy options, however were rarely used for first-line treatment in T2DM.

Conclusions

Prevalent cases of T2DM more than doubled between 2000 and 2013, while the number of incident cases increased more steadily. Changes in prescribing patterns observed may reflect the impact of national policies and prescribing guidelines on UK primary care.
School education, physical performance in late midlife and allostatic load: a retrospective cohort study
Authors: Hansen Åse M , Andersen Lars L , Mendes de Leon Carlos F , Bruunsgaard Helle , Lund Rikke
Published: January 2016

Background

The mechanisms underlying the social gradient in physical functioning are not fully understood. Cumulative physiological stress may be a pathway. The present study aimed to investigate the association between highest attained school education and physical performance in late midlife, and to determine to what extent cumulative physiological stress mediated these associations.

Methods

The study is based on data from the Copenhagen Aging and Midlife Biobank (CAMB; n=5467 participants, aged 48–62 years, 31.5% women). School education was measured as highest examination passed in primary or secondary school (3 categories). Cumulative stress was operationalised as allostatic load (AL), and measured as the number of biological parameters (out of 14) in which participants scored in the poorest quartile. Physical performance included dynamic muscle performance (chair rise ability, postural balance, sagittal flexibility) and muscle strength (jump height, trunk extension and flexion, and handgrip strength).

Results

Among women, higher school education was associated with better performance in all physical performance tests. Among men, higher school education was associated with better performance only in chair rise and jump height. AL partially mediated the association between school education and physical performance, and accounted only for 2–30% of the total effect among women. Similar results were observed among men for chair rise and jump height.

Conclusions

These results might indicate that AL plays a minor role in the association between school education and late midlife dynamic muscle performance in both men and women, and in muscle strength among women.