bluuebunny/crossref_metadata_2025 huggingface dataset:
Delayed liver regeneration in C3H/HeJ mice: possible involvement of haemodynamic and structural changes in the hepatic microcirculation
Authors: Marlini Muhamad , Mabuchi Ayako , Mallard Beth L. , Hairulhisyam Ngatiman , Akashi‐Takamura Sachiko , Harper Jacquie L. , Wheatley Antony M.
Published: September 2016

New Findings

What is the central question of this study?

The liver regenerative process is complex and involves a sequence of signalling events, but the possible involvement of structural and haemodynamic changes in vivo during this process has never been explored.

What is the main finding and its importance?

Normal sinusoidal blood flow and velocity are crucial for a normal regenerative response, and delays in these haemodynamic events resulted in impaired liver regeneration in lipopolysaccharide‐insensitive, C3H/HeJ mice. Toll‐like receptor 4 signalling is required for restoration of normal liver architecture during the liver regenerative process.

Liver regeneration is delayed in mice with a defective Toll‐like receptor 4 (TLR4; C3H/HeJ mice) but is normal in TLR4 knockouts (TLR4−/−). Here, we investigated the possible involvement of structural and haemodynamic changes in vivo in the underlying mechanism. In lipopolysaccharide‐sensitive (C3H/HeN and C57BL/6) and lipopolysaccharide‐insensitive (C3H/HeJ and TLR4−/−) mice, a 70% partial hepatectomy (PH) was performed under inhalational anaesthesia. At days 3 and 7 after PH, the hepatic microcirculation was interrogated using intravital microscopy. Delayed liver regeneration was confirmed in C3H/HeJ, but not in C3H/HeN, C57BL/6 (WT) or TLR4−/− mice by liver weight‐to‐body‐weight ratio, the percentage of proliferating cell nuclear antigen (PCNA)‐positive cells and mitotic index data. At day 3 after PH, sinusoidal red blood cell velocity increased by 100% in C3H/HeN mice, but by only 40% in C3H/HeJ mice. Estimated sinusoidal blood flow was significantly higher at day 7 after PH in C3H/HeN than in C3H/HeJ mice. The hepatic cord width was significantly larger in C3H/HeN than in C3H/HeJ mice at day 3 and it was significantly larger in TLR4−/− than in C57BL/6 WT mice at day 7 after PH. Hepatocyte nucleus density and functional sinusoidal density was significantly reduced at days 3 and 7 after PH in all mouse strains compared with their zero‐time controls. Functional sinusoidal density was significantly lower in C3H/HeJ compared with C3H/HeN mice at day 7 after PH. The present study indicates that altered sinusoidal blood flow and velocity in C3H/HeJ mice may contribute to the observed delay in the regenerative response in these mice. In addition, restoration of normal liver architecture may be delayed in TLR4−/− mice.
Accumulation of K+ in the synaptic cleft modulates activity by influencing both vestibular hair cell and calyx afferent in the turtle
Authors: Contini Donatella , Price Steven D. , Art Jonathan J.
Published: September 2016

Key points

In the synaptic cleft between type I hair cells and calyceal afferents, K+ ions accumulate as a function of activity, dynamically altering the driving force and permeation through ion channels facing the synaptic cleft.

High‐fidelity synaptic transmission is possible due to large conductances that minimize hair cell and afferent time constants in the presence of significant membrane capacitance.

Elevated potassium maintains hair cells near a potential where transduction currents are sufficient to depolarize them to voltages necessary for calcium influx and synaptic vesicle fusion.

Elevated potassium depolarizes the postsynaptic afferent by altering ion permeation through hyperpolarization‐activated cyclic nucleotide‐gated (HCN) channels, and contributes to depolarizing the afferent to potentials where a single EPSP (quantum) can generate an action potential.

With increased stimulation, hair cell depolarization increases the frequency of quanta released, elevates [K+]cleft and depolarizes the afferent to potentials at which smaller and smaller EPSPs would be sufficient to trigger APs.

Fast neurotransmitters act in conjunction with slower modulatory effectors that accumulate in restricted synaptic spaces found at giant synapses such as the calyceal endings in the auditory and vestibular systems. Here, we used dual patch‐clamp recordings from turtle vestibular hair cells and their afferent neurons to show that potassium ions accumulating in the synaptic cleft modulated membrane potentials and extended the range of information transfer. High‐fidelity synaptic transmission was possible due to large conductances that minimized hair cell and afferent time constants in the presence of significant membrane capacitance. Increased potassium concentration in the cleft maintained the hair cell near potentials that promoted the influx of calcium necessary for synaptic vesicle fusion. The elevated potassium concentration also depolarized the postsynaptic neuron by altering ion permeation through hyperpolarization‐activated cyclic nucleotide‐gated (HCN) channels. This depolarization enabled the afferent to reliably generate action potentials evoked by single AMPA‐dependent EPSPs. Depolarization of the postsynaptic afferent could also elevate potassium in the synaptic cleft, and would depolarize other hair cells enveloped by the same neuritic process increasing the fidelity of neurotransmission at those synapses as well. Collectively, these data demonstrate that neuronal activity gives rise to potassium accumulation, and suggest that potassium ion action on HCN channels can modulate neurotransmission, preserving the fidelity of high‐speed synaptic transmission by dynamically shifting the resting potentials of both presynaptic and postsynaptic cells.
In-Process Monitoring of Selective Laser Melting: Spatial Detection of Defects Via Image Data Analysis
Authors: Grasso Marco , Laguzza Vittorio , Semeraro Quirico , Colosimo Bianca Maria
Published: September 2016

Selective laser melting (SLM) has been attracting a growing interest in different industrial sectors as it is one of the key technologies for metal additive manufacturing (AM). Despite the relevant improvements made by the SLM technology in the recent years, process capability is still a major issue for its industrial breakthrough. As a matter of fact, different kinds of defect may originate during the layerwise process. In some cases, they propagate from one layer to the following ones leading to a job failure. In other cases, they are hardly visible and detectable by inspecting the final part, as they can affect the internal structure or structural features that are difficult to measure. This implies the need for in-process monitoring methods able to rapidly detect and locate defect onsets during the process itself. Different authors have been investigating machine sensorization architectures, but the development of statistical monitoring techniques is still in a very preliminary phase. This paper proposes a method for the detection and spatial identification of defects during the layerwise process by using a machine vision system in the visible range. A statistical descriptor based on principal component analysis (PCA) applied to image data is presented, which is suitable to identify defective areas of a layer. The use of image k-means clustering analysis is then proposed for automated defect detection. A real case study in SLM including both simple and complicated geometries is discussed to demonstrate the performances of the method.
Process Development for Vacuum Brazed Niobium–316L Stainless Steel Transition Joints for Superconducting Cavities
Authors: Kumar Abhay , Ganesh P. , Kaul R. , Chinna Rao P. , Yadav D. P. , Sindal B. K. , Gupta R. K. , Sridhar R. , Joshi S. C. , Singh B.
Published: September 2016

The paper describes process development for producing sound, strong, and ductile Nb pipe–316L stainless steel (SS) flange brazed joint suitable for application in superconducting radiofrequency (SRF) cavities. The developed transition joints, made with BVAg-8 braze filler metal (BFM), were free of brittle intermetallic compounds, in contrast to the existing global brazing practice of using oxygen-free electronic copper as BFM which results in the formation of a continuous layer of Fe–Nb brittle intermetallic compound at Nb–braze interface. In view of the large difference in the mean thermal expansion coefficients between niobium and 316L stainless steel, a new design for manufacturing and assembly (DFMA) has been developed to ensure achievement of desired joint thickness with uniformity in circumferential and longitudinal directions. An environment-friendly prebraze cleaning procedure has been qualified and implemented. DFMA has resulted in (i) significant reduction of the out-of-roundness errors (≤10 μm) while machining of the niobium pipe, (ii) simplified clearance fit prebraze assembly at room temperature (RT), and (iii) uniformity of joint thickness. A process flow chart has been developed to ensure repeatability of joint characteristics. The brazed joint, of niobium pipe and 100CF knife edge 316L SS flange made by standardized practice, displayed helium leak tightness better than 5 × 10−10 mbar l/s at RT and at liquid helium temperature (LHT). The braze-joint sustained 873 K/10 h postbraze hydrogen degassing treatment and thermal cycling between RT and LHT without any loss in hermeticity.
Shallow Angle Drilling of Inconel 718 Using a Helical Laser Drilling Technique
Authors: Shin Joonghan , Mazumder Jyotirmoy
Published: September 2016

This study reports an experimental investigation for the shallow angle laser drilling of Inconel 718. In this study, a helical laser drilling technique was used to effectively produce holes with a diameter of several hundred microns. The design of experiment (DOE) using the Taguchi method was employed to examine the influence of various process parameters on the geometrical and metallurgical features of drilled holes. A higher laser power, lower speed, and closer focal position to the workpiece surface contributed to the further removal of material by the absorption of more laser energy and larger beam intensity. This resulted in a larger exit hole diameter and less hole taper. The increase in laser power reduced a thickness of the recast layer due to material removal by vaporization. From the DOE result, a regression model to estimate a correlation between experimental factors and hole quality was also suggested. In the second stage of this study, trials to improve drilling performance were made. Using the O2 assist gas of 50 kPa significantly enhanced the drilling performance owing to the delivery of more energy to the workpiece by an exothermic reaction. However, the further increase of O2 gas caused rapid cooling of the workpiece, which lowered the drilling performance. The drilling performance was greatly improved as well using the high laser duty cycle to provide more laser energy. The moving focal position was only beneficial to the drilling performance when a focusing of the beam was moderately maintained on the interaction region of the laser–workpiece.
Externally Fired Micro-Gas Turbine and Organic Rankine Cycle Bottoming Cycle: Optimal Biomass/Natural Gas Combined Heat and Power Generation Configuration for Residential Energy Demand
Authors: Camporeale Sergio Mario , Ciliberti Patrizia Domenica , Fortunato Bernardo , Torresi Marco , Pantaleo Antonio Marco
Published: September 2016

Small-scale combined heat and power (CHP) plants present lower electric efficiency in comparison to large scale ones, and this is particularly true when biomass fuels are used. In most cases, the use of both heat and electricity to serve on-site energy demand is a key issue to achieve acceptable global energy efficiency and investment profitability. However, the heat demand follows a typical daily and seasonal pattern and is influenced by climatic conditions, in particular in the case of residential and tertiary end users. During low heat demand periods, a lot of heat produced by the CHP plant is discharged. In order to increase the electric conversion efficiency of small-scale micro-gas turbine for heat and power cogeneration, a bottoming organic Rankine cycle (ORC) system can be coupled to the cycle, however, this option reduces the temperature and the amount of cogenerated heat available to the thermal load. In this perspective, the paper presents the results of a thermo-economic analysis of small-scale CHP plants composed of a micro-gas turbine (MGT) and a bottoming ORC, serving a typical residential energy demand. For the topping cycle, three different configurations are examined: (1) a simple recuperative micro-gas turbine fueled by natural gas (NG); (2) a dual fuel externally fired gas turbine (EFGT) cycle, fueled by biomass and natural gas (50% share of energy input) (DF); and (3) an externally fired gas turbine (EFGT) with direct combustion of biomass (B). The bottoming ORC is a simple saturated cycle with regeneration and no superheating. The ORC cycle and the fluid selection are optimized on the basis of the available exhaust gas temperature at the turbine exit. The research assesses the influence of the thermal energy demand typology (residential demand with cold, mild, and hot climate conditions) and CHP plant operational strategies (baseload versus heat-driven versus electricity-driven operation mode) on the global energy efficiency and profitability of the following three configurations: (A) MGT with cogeneration; (B) MGT+ ORC without cogeneration; and (C) MGT+ORC with cogeneration. In all cases, a back-up boiler is assumed to match the heat demand of the load (fed by natural gas or biomass). The research explores the profitability of bottoming ORC in view of the following trade-offs: (i) lower energy conversion efficiency and higher investment cost of biomass input with respect to natural gas; (ii) higher efficiency but higher costs and reduced heat available for cogeneration with the bottoming ORC; and (iii) higher primary energy savings and revenues from feed-in tariff available for biomass electricity fed into the grid.
On the Predicted Effect of Angular Misalignment on the Performance of Oil Lubricated Thrust Collars in Integrally Geared Compressors
Authors: Cable Travis A. , San Andrés Luis , Wygant Karl
Published: September 2016

Multiple-stage integrally geared compressors (IGCs) offer improved thermal efficiency and easier access for maintenance and overhaul than single-shaft centrifugal compressors. In an IGC, a main bull shaft drives pinion shafts, each having an impeller at its ends. The compression of process gas in the compressor stages induces axial loads along the pinion shafts that are transmitted via thrust collars (TCs) to the main bull gear (BG) shaft and balanced by a single thrust bearing. Manufacturing inaccuracies and a poor assembly process can lead to static angular misalignments of the TC and BG surfaces that affect the operating film thickness as well as the force and reaction moments of the lubricated mechanical element. In a follow-up to San Andrés et al. (2015, “On the Predicted Performance of Oil Lubricated Thrust Collars in Integrally Geared Compressors,” ASME J. Eng. Gas Turbines Power, 137(5), pp. 1–9), this paper presents an investigation of the performance of a single thrust collar configuration operating with increasing static angular misalignment of either the TC or BG. The flow model solves the Reynolds equation of hydrodynamic lubrication coupled to a thermal energy transport equation to determine the film pressure and bulk temperature fields, respectively. The model predicts performance parameters such as power loss and lubricant flow rate, and force and moment stiffness and damping coefficients. Predictions show that misaligning of either the thrust collar or bull gear alters the load-carrying area in the lubricated zone, shifts the pressure field with peak magnitudes doubling or more depending on the degree and direction of TC or BG misalignment. Static angular misalignment does not significantly affect the power loss, temperature rise, etc., but does have an effect on the dynamic coefficients (both axial and angular). Finally, a reduced complex dynamic stiffness matrix for the lubricated TC shows that some cross-coupled stiffness and moment coefficients are nonzero, indicating hydrodynamic coupling between axial and angular motions for the pinion and bull gear shafts. The coupling could affect the placement of the system natural frequencies and associated mode shapes as well as the system stability.
Heading Autopilot of Autonomous Underwater Vehicles With Internal Moving Mass
Authors: Li Bo , Su Tsung-Chow
Published: September 2016

Inspired by the designs of underwater gliders, hybrid autonomous underwater vehicles (AUVs) have emerged recently, which use internal actuators instead of control surfaces to control the heading angle and depth of the vehicles. In this paper, we focus on controlling the heading angle of a REMUS AUV by using an internal moving mass. We derive a nonlinear dynamical model of the vehicle with hydrodynamic forces and coupling between the vehicle and the internal moving mass. The model is used to study the stability of the horizontal-plane motion of the vehicle and to design a linear feedback law to stabilize its heading angle around a desired direction. Simulation results demonstrate that a controlled internal moving mass is able to fulfill the purpose of heading control.
Coordinate Mappings for Rigid Body Motions
Authors: Müller Andreas
Published: September 2016

Geometric methods have become increasingly accepted in computational multibody system (MBS) dynamics. This includes the kinematic and dynamic modeling as well as the time integration of the equations of motion. In particular, the observation that rigid body motions form a Lie group motivated the application of Lie group integration schemes, such as the Munthe-Kaas method. Also established vector space integration schemes tailored for structural and MBS dynamics were adopted to the Lie group setting, such as the generalized α integration method. Common to all is the use of coordinate mappings on the Lie group SE(3) of Euclidean motions. In terms of canonical coordinates (screw coordinates), this is the exponential mapping. Rigid body velocities (twists) are determined by its right-trivialized differential, denoted dexp. These concepts have, however, not yet been discussed in compact and concise form, which is the contribution of this paper with particular focus on the computational aspects. Rigid body motions can also be represented by dual quaternions, that form the Lie group Sp̂(1), and the corresponding dynamics formulations have recently found a renewed attention. The relevant coordinate mappings for dual quaternions are presented and related to the SE(3) representation. This relation gives rise to a novel closed form of the dexp mapping on SE(3). In addition to the canonical parameterization via the exponential mapping, the noncanonical parameterization via the Cayley mapping is presented.
Reinjection Probability Density for Type-III Intermittency With Noise and Lower Boundary of Reinjection
Authors: Elaskar Sergio , del Rio Ezequiel , Costa Andrea
Published: September 2016

In this paper, we extend a methodology developed recently to study type-III intermittency considering different values of the noise intensity and the lower boundary of reinjection (LBR). We obtain accurate analytic expressions for the reinjection probability density (RPD). The proposed RPD has a piecewise definition depending on the nonlinear behavior, the LBR value, and the noise intensity. The new RPD is a sum of exponential functions with exponent α + 2, where α is the exponent of the noiseless RPD. The theoretical results are verified with the numerical simulations.
Nonlinear Dynamic Response of Carbon Nanotube Nanocomposite Microbeams
Authors: Cetraro Marek , Lacarbonara Walter , Formica Giovanni
Published: September 2016

The nonlinear dynamic response of nanocomposite microcantilevers is investigated. The microbeams are made of a polymeric hosting matrix (e.g., epoxy, polyether ether ketone (PEEK), and polycarbonate) reinforced by longitudinally aligned carbon nanotubes (CNTs). The 3D transversely isotropic elastic constitutive equations for the nanocomposite material are based on the equivalent inclusion theory of Eshelby and the Mori–Tanaka homogenization approach. The beam-generalized stress resultants, obtained in accordance with the Saint-Venant principle, are expressed in terms of the generalized strains making use of the equivalent constitutive laws. These equations depend on both the hosting matrix and CNTs elastic properties as well as on the CNTs volume fraction, geometry, and orientation. The description of the geometry of deformation and the balance equations for the microbeams are based on the geometrically exact Euler–Bernoulli beam theory specialized to incorporate the additional inextensibility constraint due to the relevant boundary conditions of microcantilevers. The obtained equations of motion are discretized via the Galerkin method retaining an arbitrary number of eigenfunctions. A path following algorithm is then employed to obtain the nonlinear frequency response for different excitation levels and for increasing volume fractions of carbon nanotubes. The fold lines delimiting the multistability regions of the frequency responses are also discussed. The volume fraction is shown to play a key role in shifting the linear frequencies of the beam flexural modes to higher values. The CNT volume fraction further shifts the fold lines to higher excitation amplitudes, while it does not affect the backbones of the modes (i.e., oscillation frequency–amplitude curves).
Consumers’ Perceived Value of Sport Team Games—A Multidimensional Approach
Authors: Kunkel Thilo , Doyle Jason Patrick , Berlin Alexander
Published: September 2016

Consumers’ evaluations of their favorite sport team’s contests are influenced by the value that the team provides to them. The current research contributes to the sport management literature through conceptualizing and measuring the dimensions that influence the perceived value consumers link with their favorite sport team’s games and testing the explanatory ability of this perceived value on their satisfaction with, and commitment toward, the team. Five semistructured expert interviews were conducted to conceptualize perceived value dimensions and measurement items. Next, a multidimensional Consumers’ Perceived Value of Sport Games scale (CPVSG) was developed and tested across two studies with football (soccer) consumers (N1 = 225; N2 = 382) in Germany. Results from confirmatory factor and structural equation modeling analyses indicate that five dimensions—functional, social, emotional, epistemic, and economic value—reflect perceived value dimensions that consumers associate with sport team games. Results also indicated these perceived value dimensions were predictive of consumers’ satisfaction with, and commitment toward, their favorite team. Thus, this research adds to the literature by providing the multidimensional CPVSG scale and demonstrating its value in explaining variance in attitudinal outcome variables.
Prioritizing Sponsorship Resources in Formula One Racing: A Longitudinal Analysis
Authors: Cobbs Joe , Tyler B. David , Jensen Jonathan A. , Chan Kwong
Published: September 2016

Accessing and exploiting organizational resources are essential capabilities for competitive sport organizations, particularly those engaged in motorsports, where teams lacking resources frequently dissolve. Corporate sponsorship represents a common method for resource acquisition, yet not all sponsorships equally benefit the sponsored organization. Sponsorship utility can be dependent on institutional dynamics such as league governance that produces competitive disparities. Through this study we extend the resource-based view to assert that sponsorships vary in their propensity to contribute to team survival, warranting prioritization in sponsorship strategy based on access to different sponsor resources. To empirically investigate the influence of a variety of sponsorships, survival analysis modeling was used to examine 40 years of corporate sponsorship of Formula One racing teams. One finding from the longitudinal analysis was that sponsorships offering financial or performance-based resources enhance team survival to a greater degree than operational sponsorships. However, such prioritization is subject to team experience, changes in institutional monetary allocation, and diminishing returns.
The Validity of the Quick-FAAM in Patients Seeking Treatment for an Acute or Subacute Foot or Ankle Condition
Authors: Hoch Johanna M. , Legner Jamie L. , Lorete Christina , Hoch Matthew C.
Published: September 2016

Context: Documented barriers to implementation of patient-reported outcome instruments (PROs) in practice include administration and scoring time. The Quick Foot and Ankle Ability Measure (Quick-FAAM) was developed to decrease these barriers; however, the clinometric properties in an acute population are unknown. Purpose: To determine the internal consistency, validity, and the floor and ceiling effects of the Quick-FAAM in patients seeking treatment for an acute or subacute ankle or foot health condition. Study Design: Cross-Sectional. Setting: Healthcare facilities.Patients: 50 patients (20.3 ± 2.2 y, 177.9 ± 10.7 cm, 80 ± 19.4 kg) seeking treatment for an acute or subacute ankle or foot condition. Main Outcome Measures: Each patient completed a demographic and health-history questionnaire followed by 5 PROs: the Quick-FAAM, the FAAM-Activities of Daily Living (ADL), FAAM-Sport, the modified Disablement in the Physically Active Scale (mDPA), the Short-Form 12 (SF-12) and the PROMISv1.2 Physical Function (PROMIS-PF). Cronbach alpha was used to determine internal consistency and Spearman’s rank correlations were performed to examine the relationship between the Quick-FAAM and all other outcomes. Results: The Quick-FAAM was very strongly correlated with the FAAM-Total (r = .91, r2 = .83, P < .001), FAAM-ADL (r = .83, r2 = .69, P < .001), FAAM-Sport (r = .89, r2 = .79, P < .001), SF12-Physical Component Score (PCS, r = .74, r2 = .55, P < .001), mDPA-PCS (r = -.83, r2 = .69, P < .001) and PROMIS PF (r = .85, r2 = .72, P < .001). There was a weak or no relationship with the SF12-Mental Component Score (MCS, r = .04, r2 = .00, P < .001) and the mDPA-MCS (r = -.35, r2 = .12, P < .001). A total of 8% (n = 4) of the patients scored a 0, and 2% (n = 1) patients scored a 48. Conclusion: The Quick-FAAM demonstrated good convergent and divergent validity along with good internal consistency. There was no evidence of a floor or ceiling effect. Therefore, the Quick-FAAM should be considered for use in practice when determining treatment effectiveness for patients with acute or subacute ankle or foot health conditions. Future research should determine the test-retest reliability and the minimal detectable change of this instrument.
MAVS-dependent host species range and pathogenicity of human hepatitis A virus
Authors: Hirai-Yuki Asuka , Hensley Lucinda , McGivern David R. , González-López Olga , Das Anshuman , Feng Hui , Sun Lu , Wilson Justin E. , Hu Fengyu , Feng Zongdi , Lovell William , Misumi Ichiro , Ting Jenny P.-Y. , Montgomery Stephanie , Cullen John , Whitmire Jason K. , Lemon Stanley M.
Published: September 2016

Hepatotropic viruses are important causes of human disease, but the intrahepatic immune response to hepatitis viruses is poorly understood because of a lack of tractable small- animal models. We describe a murine model of hepatitis A virus (HAV) infection that recapitulates critical features of type A hepatitis in humans. We demonstrate that the capacity of HAV to evade MAVS-mediated type I interferon responses defines its host species range. HAV-induced liver injury was associated with interferon-independent intrinsic hepatocellular apoptosis and hepatic inflammation that unexpectedly resulted from MAVS and IRF3/7 signaling. This murine model thus reveals a previously undefined link between innate immune responses to virus infection and acute liver injury, providing a new paradigm for viral pathogenesis in the liver.
First Draft Genome Sequence of a UK Strain (UK99) of
Fusarium culmorum
Authors: Urban Martin , King Robert , Andongabo Ambrose , Maheswari Uma , Pedro Helder , Kersey Paul , Hammond-Kosack Kim
Published: September 2016

Fusarium culmorum
is a soilborne fungal plant pathogen that causes foot and root rot and
Fusarium
head blight on small-grain cereals, in particular on wheat and barley. We report herein the draft genome sequence of a 1998 field strain called FcUK99 adapted to the temperate climate found in England.
Draft Genome Sequence of the
Bactrocera oleae
Symbiont “
Candidatus
Erwinia dacicola”
Authors: Blow Frances , Gioti Anastasia , Starns David , Ben-Yosef Michael , Pasternak Zohar , Jurkevitch Edouard , Vontas John , Darby Alistair C.
Published: September 2016

“
Candidatus
Erwinia dacicola” is a
Gammaproteobacterium
that forms a symbiotic association with the agricultural pest
Bactrocera oleae
. Here, we present a 2.1-Mb draft hybrid genome assembly for “
Ca.
Erwinia dacicola” generated from single-cell and metagenomic data.
Draft Genome Sequence of Two Monosporidial Lines of the Karnal Bunt Fungus
Tilletia indica
Mitra (PSWKBGH-1 and PSWKBGH-2)
Authors: Sharma Pradeep , Tiwari Ratan , Saharan M. S. , Sharma Indu , Kumar Jitender , Mishra Shefali , Muthusamy Senthilkumar K. , Gupta R. K. , Jaiswal Sarika , Iquebal M. A. , Angadi U. B. , Kumar Neeraj , Fatma Samar , Rai Anil , Kumar Dinesh
Published: September 2016

Karnal bunt disease caused by the fungus
Tilletia indica
Mitra is a serious concern due to strict quarantines affecting international trade of wheat. We announce here the first draft assembly of two monosporidial lines, PSWKBGH-1 and -2, of this fungus, having approximate sizes of 37.46 and 37.21 Mbp, respectively.
Complete Genome Sequences of 12 Species of Stable Defined Moderately Diverse Mouse Microbiota 2
Authors: Uchimura Yasuhiro , Wyss Madeleine , Brugiroux Sandrine , Limenitakis Julien P. , Stecher Bärbel , McCoy Kathy D. , Macpherson Andrew J.
Published: September 2016

We report here the complete genome sequences of 12 bacterial species of stable defined moderately diverse mouse microbiota 2 (sDMDMm2) used to colonize germ-free mice with defined microbes. Whole-genome sequencing of these species was performed using the PacBio sequencing platform yielding circularized genome sequences of all 12 species.
Genome Sequence of the Facultative Anaerobe Oerskovia enterophila DFA-19 (DSM 43852
T
)
Authors: Jag Vanessa , Poehlein Anja , Bengelsdorf Frank R. , Daniel Rolf , Dürre Peter
Published: September 2016

Here, we report the draft genome sequence of
Oerskovia enterophila
DFA-19 (DSM 43852
T
), a facultative anaerobe soil bacterium, which was originally isolated from millipede feces and first described as
Promicromonospora enterophila
. The genome consists of a circular chromosome comprising approximately 4.65 Mb and 4,044 predicted protein-encoding genes.
Complete Genome Sequences of Bordetella pertussis Vaccine Reference Strains 134 and 10536
Authors: Weigand Michael R. , Peng Yanhui , Loparev Vladimir , Batra Dhwani , Burroughs Mark , Johnson Taccara , Juieng Phalasy , Rowe Lori , Tondella M. Lucia , Williams Margaret M.
Published: September 2016

Vaccine formulations and vaccination programs against whooping cough (pertussis) vary worldwide. Here, we report the complete genome sequences of two divergent
Bordetella pertussis
reference strains used in the production of pertussis vaccines.
Complete Mitochondrial Genome Sequence of Sunflower (
Helianthus annuus
L.)
Authors: Grassa Christopher J. , Ebert Daniel P. , Kane Nolan C. , Rieseberg Loren H.
Published: September 2016

This is the first complete mitochondrial genome sequence for sunflower and the first complete mitochondrial genome for any member of
Asteraceae
, the largest plant family, which includes over 23,000 named species. The master circle is 300,945-bp long and includes 27 protein-coding sequences, 18 tRNAs, and the 26S, 5S, and 18S rRNAs.
Complete Genome Sequence of the Filamentous Fungus Aspergillus westerdijkiae Reveals the Putative Biosynthetic Gene Cluster of Ochratoxin A
Authors: Chakrabortti Alolika , Li Jinming , Liang Zhao-Xun
Published: September 2016

Ochratoxin A (OTA) is a common mycotoxin that contaminates food and agricultural products. Sequencing of the complete genome of
Aspergillus westerdijkiae
, a major producer of OTA
,
reveals more than 50 biosynthetic gene clusters, including a putative OTA biosynthetic gene cluster that encodes a dozen of enzymes, transporters, and regulatory proteins.
Draft Genome Sequence of the Heavy-Metal-Tolerant Marine Yeast Debaryomyces hansenii J6
Authors: Berrocal Camille A. , Rivera-Vicens Ramon E. , Nadathur Govind S.
Published: September 2016

Debaryomyces hansenii
J6 is a heavy-metal-tolerant, flavinogenic yeast isolated from a Swedish estuary. We present here the 11.63-Mb genome of this organism containing 5,717 open reading frames. Comparison with available
Debaryomyces
genomes demonstrated that J6 is closer to
D. hansenii
MTCC234 than
D. fabry
CBS789 and
D. hansenii
CBS767.
Draft Genome Sequences of Microbacterium hominis LCDC-84-0209
T
Isolated from a Human Lung Aspirate and Microbacterium laevaniformans LCDC 91-0039 Isolated from a Human Blood Culture
Authors: Bernier Anne-Marie , Bernard Kathryn
Published: September 2016

Draft genomes for
Microbacterium hominis
84-0209
T
and
M. laevaniformans
91-0039 were studied. Genome sizes (bps, [G+C contents]) were 3,506,522 (70.96%) and 2,999,965 (69.51%), respectively. Annotation revealed: (
M. hominis
) three rRNA sequences, 45 tRNA genes, and 3,218 coding sequences; (
M. laevaniformans
) three rRNA sequences, 49 tRNA genes, and 2,874 coding sequences.
Complete Genome Sequences of 17 Canadian Isolates of Salmonella enterica subsp.
enterica
Serovar Heidelberg from Human, Animal, and Food Sources
Authors: Labbé Geneviève , Ziebell Kim , Bekal Sadjia , Macdonald Kimberley A. , Parmley E. Jane , Agunos Agnes , Desruisseau Andrea , Daignault Danielle , Slavic Durda , Hoang Linda , Ramsay Danielle , Pollari Frank , Robertson James , Nash John H. E. , Johnson Roger P.
Published: September 2016

Salmonella enterica
subsp.
enterica
serovar Heidelberg is a highly clonal serovar frequently associated with foodborne illness. To facilitate subtyping efforts, we report fully assembled genome sequences of 17 Canadian
S
. Heidelberg isolates including six pairs of epidemiologically related strains. The plasmid sequences of eight isolates contain several drug resistance genes.
Draft Genome Sequences of Histamine-Producing Morganella psychrotolerans Strains
Authors: Bjornsdottir-Butler Kristin , Leon Maria Sanchez , Benner Ronald A.
Published: September 2016

Histamine-producing bacteria are responsible for scombrotoxin (histamine) fish poisoning, a leading cause of fish poisoning in the United States. We report here the first draft genomes of three histamine-producing
Morganella psychrotolerans
strains, isolated from tuna and mahi-mahi.
Complete Genome Sequences of the Plasmid-Bearing Campylobacter coli Strains HC2-48, CF2-75, and CO2-160 Isolated from Retail Beef Liver
Authors: Marasini Daya , Fakhr Mohamed K.
Published: September 2016

The complete genome sequences of
Campylobacter coli
strains HC2-48, CF2-75, and CO2-160, isolated from retail beef liver, showed the presence of 1,663,782-, 1,711,393-, and 1,683,224-bp circular chromosomes and 44,064-, 44,233-, and 44,228-bp circular plasmids, respectively. This is the first reported
Campylobacter coli
genome sequence isolated from retail beef liver.
Draft Genome Sequence of Legionella jamestowniensis Isolated from a Patient with Chronic Respiratory Disease
Authors: Prochazka Birgit , Indra Alexander , Hasenberger Petra , Blaschitz Marion , Wagner Laura , Wewalka Günther , Sorschag Sieglinde , Schmid Daniela , Ruppitsch Werner
Published: September 2016

Legionella jamestowniensis
can be found in the environment in various water samples, in wet soil, and in compost facilities, but evidence of its human pathogenicity has not yet been demonstrated. Here, we report the first draft genome sequence of an
L. jamestowniensis
isolate, derived from a patient suffering from a chronic respiratory disease.
Proterozoic geology of the Baraboo Interval
Authors: Bjørnerud Marcia
Published: September 2016

The Proterozoic Baraboo Quartzite was laid down by braided rivers and in near-shore marine environments on the southern edge of Paleo–North America during a period of tectonic stability following a prolonged interval of orogenic activity. The exceptional chemical maturity of the Quartzite points to warm, wet, tropical climate conditions, and its distinctive maroon to pink and purple color marks it as one of the earliest “red beds” on Earth. Detrital zircons from the base of the Quartzite constrain its depositional age to be younger than ca. 1710 Ma. The Quartzite is overlain by two other units known only from subsurface exploration: the Seeley Slate, interpreted as a shallow marine deposit, and the Freedom Formation, which has the physical and mineralogical characteristics of classic Superior-type iron formations but is younger than any of these by at least 150 m.y. The folding event at Baraboo was previously thought to have occurred at ca. 1630 Ma, based on indirect regional arguments. However, a growing number of 40Ar/39Ar ages in the range of 1450–1480 Ma have been obtained from occurrences of muscovite in hydrothermal veins in the Quartzite and from tectonic cleavage surfaces in the Seeley Slate, and these suggest a possible connection with the Wolf River Batholith igneous interval. The remarkable topographic relief that existed in the Baraboo Range at the time of the late Cambrian marine transgression, one billion years after the folding event, is another aspect of the regional geologic history that remains incompletely understood.
Baraboo Quartzite
Authors: Davis Richard A.
Published: September 2016

The Baraboo Quartzite contains numerous well-preserved sedimentary structures that enable interpretation of environments of deposition. Included are various types of cross-stratification, reactivation surfaces, and tidal bedding. The bulk of the Baraboo was deposited under tidal influence. The remainder represents deposition in a braided stream system. The origin of the tremendous volume of quartz sand remains somewhat unknown.
Quaternary geology of the Baraboo area
Authors: Davis Richard A.
Published: September 2016

The surficial geology of the Baraboo area is very important because it includes the transition from a glaciated region to the Driftless Area. The eastern portion of this area was glaciated as part of the Green Bay lobe of the ice sheet in this area. The terminal moraine is present and is characterized by sandy till. No valid information that substantiates glacial activity exists west of the city of Baraboo. The Driftless Area includes a site of the earliest Wisconsin habitation.
Sublingual dermoid causing stertor in an infant
Authors: Naina P , Syed Kamran Asif , Koshy Lisa , Mathews Suma Susan
Published: September 2016

Sublingual dermoids are uncommon lesions in the floor of mouth. The most common age of presentation is early adulthood, but presentation in infancy has also been reported. This report highlights the clinical presentation and treatment challenges in infants. An 8-month-old infant presented with inability to close mouth, intermittent stertor and snoring. MRI suggested a sublingual dermoid which was confirmed on histopathology of the surgically enucleated specimen. Sublingual dermoids are uncommon lesions of the floor of mouth. The age of presentation of a sublingual dermoid depends on the initial size of the lesion. Large sublingual dermoids in neonates can present with respiratory embarrassment and need early surgical intervention. Surgical enucleation via an intraoral approach is the treatment of choice with external approach reserved for very large cysts below the mylohyoid. Large sublingual cysts can present with anaesthetic challenges and may need fibreoptic intubation.
Utility of clinical tests to diagnose MRI-confirmed gluteal tendinopathy in patients presenting with lateral hip pain
Authors: Grimaldi Alison , Mellor Rebecca , Nicolson Phillipa , Hodges Paul , Bennell Kim , Vicenzino Bill
Published: September 2016

Purpose

Gluteal tendinopathy (GT) is a source of lateral hip pain, yet common clinical diagnostic tests have limited validity. Patients with GT are often misdiagnosed, resulting in inappropriate management, including surgery. This study determined the diagnostic utility of clinical tests for GT, using MRI as the reference standard.

Methods

65 participants with lateral hip pain were examined to evaluate the ability of clinical tests to detect MRI-determined GT (an increase in intratendinous signal intensity on T2-weighted images). Palpation of the greater trochanter and several clinical pain provocation tests applying compressive and tensile loads on the gluteal tendons were investigated. MRI of the painful hip was examined by a radiologist, blind to clinical findings.

Results

Pain reported within 30 s of standing on the affected limb conclusively moves a (nominal) 50% pretest probability of GT presence on MRI to a post-test probability of 98% (specificity 100%, positive likelihood ratio ∼12), whereas no pain on palpation (80% sensitivity) would rule out its presence. 20 participants (31%) had GT on MRI but clinically negative (ie, not positive on palpation and another test).

Conclusions

Keeping in mind that the sample size was small (ie, possibly underpowered for indices of diagnostic utility with low precision), the results of this study indicate that a patient who reports lateral hip pain within 30 s of single-leg-standing is very likely to have GT. Patients with lateral hip pain who are not palpably tender over the greater trochanter are unlikely to have MRI-detected GT.
Can the UNAIDS 90-90-90 target be achieved? A systematic analysis of national HIV treatment cascades
Authors: Levi Jacob , Raymond Alice , Pozniak Anton , Vernazza Pietro , Kohler Philipp , Hill Andrew
Published: September 2016

Background

In 2014, the Joint United Nations Programme on HIV and AIDS (UNAIDS) and partners set the ‘90-90-90 targets’; aiming to diagnose 90% of all HIV positive people, provide antiretroviral therapy (ART) for 90% of those diagnosed and achieve viral suppression for 90% of those treated, by 2020. This results in 81% of all HIV positive people on treatment and 73% of all HIV positive people achieving viral suppression. We aimed to analyse how effective national HIV treatment programmes are at meeting these targets, using HIV care continuums or cascades.

Methods

We searched for HIV treatment cascades for 196 countries in published papers, conference presentations, UNAIDS databases and national reports. Cascades were constructed using reliable, generalisable, recent data from national, cross-sectional and longitudinal study cohorts. Data were collected for four stages; total HIV positive people, diagnosed, on treatment and virally suppressed. The cascades were categorised as complete (four stages) or partial (3 stages), and analysed for ‘break points’ defined as a drop >10% in coverage between consecutive 90-90-90 targets.

Results

69 country cascades were analysed (32 complete, 37 partial). Diagnosis (target one—90%) ranged from 87% (the Netherlands) to 11% (Yemen). Treatment coverage (target two—81% on ART) ranged from 71% (Switzerland) to 3% (Afghanistan). Viral suppression (target three—73% virally suppressed) was between 68% (Switzerland) and 7% (China).

Conclusions

No country analysed met the 90-90-90 targets. Diagnosis was the greatest break point globally, but the most frequent key break point for individual countries was providing ART to those diagnosed. Large disparities were identified between countries. Without commitment to standardised reporting methodologies, international comparisons are complex.
Small-for-gestational age and its association with maternal blood glucose, body mass index and stature: a perinatal cohort study among Chinese women
Authors: Leng Junhong , Hay John , Liu Gongshu , Zhang Jing , Wang Jing , Liu Huihuan , Yang Xilin , Liu Jian
Published: September 2016

Objective

To examine whether maternal low blood glucose (BG), low body mass index (BMI) and small stature have a joint effect on the risk of delivery of a small-for-gestational age (SGA) infant.

Design

Women from a perinatal cohort were followed up from receiving perinatal healthcare to giving birth.

Setting

Beichen District, Tianjin, China between June 2011 and October 2012.

Participants

1572 women aged 19–39 years with valid values of stature, BMI and BG level at gestational diabetes mellitus screening (gestational weeks 24–28), glucose challenge test <7.8 mmol/L and singleton birth (≥37 weeks’ gestation).

Main outcome measures

SGA was defined as birth weight <10th centile for gender separated gestational age of Tianjin singletons.

Results

164 neonates (10.4%) were identified as SGA. From multiple logistic regression models, the ORs (95% CI) of delivery of SGA were 0.84 (0.72 to 0.98), 0.61 (0.49 to 0.74) and 0.64 (0.54 to 0.76) for every 1 SD increase in maternal BG, BMI and stature, respectively. When dichotomises, maternal BG (<6.0 vs ≥6.0 mmol/L), BMI (<24 vs ≥24 kg/m2) and stature (<160.0 vs ≥160.0 cm), those with BG, BMI and stature all in the lower categories had ∼8 times higher odds of delivering an SGA neonate (OR (95% CI) 8.01 (3.78 to 16.96)) relative to the reference that had BG, BMI and stature all in the high categories. The odds for an SGA delivery among women who had any 2 variables in the lower categories were ∼2–4 times higher.

Conclusions

Low maternal BG is associated with an increased risk of having an SGA infant. The risk of SGA is significantly increased when the mother is also short and has a low BMI. This may be a useful clinical tool to identify women at higher risk for having an SGA infant at delivery.
Prognostic variables and scores identifying the last year of life in COPD: a systematic review protocol
Authors: Smith Laura-Jane E , Ali Ifrah , Stone Patrick , Smeeth Liam , Quint Jennifer K
Published: September 2016

Introduction

People living with advanced chronic obstructive pulmonary disease (COPD) suffer from significant morbidity, reduced quality of life and high mortality, and are likely to benefit from many aspects of a palliative care approach. Prognostic estimates are a meaningful part of decision-making and better evidence for such estimates would facilitate advance care planning. We aim to provide quality evidence on known prognostic variables and scores which predict a prognosis in COPD of <12 months for use in the community.

Methods and analysis

We will conduct a systematic review of randomised or quasi-randomised controlled trials, prospective and retrospective longitudinal cohort and case–control studies on prognostic variables, multivariate scores or models for COPD. The search will cover the period up to April 2016. Study selection will follow the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, with data extraction using fields from the Critical Appraisal and Data Extraction for Systematic Reviews of Prediction Modelling Studies (CHARMS) checklist for multivariate models, and study quality will be assessed using a modified version of the Quality In Prognosis Studies (QUIPS) tool.

Ethics and dissemination

The results will be disseminated through peer-reviewed publications and national and international conference presentations.

Systematic review registration number

CRD42016033866.