bluuebunny/crossref_metadata_2025 huggingface dataset:
Transient Thermal Performance of Rear Door Heat Exchanger in Local Contained Environment During Water Side Failure
Authors: Nemati Kourosh , Alissa Husam A. , Tradat Mohammad I. , Sammakia Bahgat
Published: October 2017

The constant increase in data center computational and processing requirements has led to increases in the IT equipment power demand and cooling challenges of high-density (HD) data centers. As a solution to this, the hybrid and liquid systems are widely used as part of HD data centers thermal management solutions.

This study presents an experimental based investigation and analysis of the transient thermal performance of a stand-alone server cabinet. The total heat load of the cabinet is controllable remotely and a rear door heat exchanger is attached with controllable water flow rate. The cooling performances of two different failure scenarios are investigated. One is in the water chiller and another is in the water pump for the Rear Door Heat eXchanger (RDHX). In addition, the study reports the impact of each scenario on the IT equipment thermal response and on the cabinet outlet temperature using a mobile temperature and velocity mesh (MTVM) experimental tool. Furthermore, this study also addresses and characterizes the heat exchanger cooling performance during both scenarios.
Effect of Bonding Structure and Heater Design on Performance Enhancement of FEEDS Embedded Manifold-Microchannel Cooling
Authors: Bae Daniel , Mandel Raphael , Ohadi Michael
Published: October 2017

This work presents the design and characterization of a two-phase, embedded manifold-microchannel (MMC) system for cooling of high heat flux electronics. The study uses a thin-Film Evaporation and Enhanced fluid Delivery System (FEEDS) MMC cooler for high heat flux cooling of electronics. The work builds upon our group’s earlier work in this area with a particular focus on the use of an improved bonding structure and implementation of uniform heat flux heaters that collectively contribute to enhanced performance of the system. In many MMC systems targeted for high heat flux applications microchannels and manifolds are fabricated separately due to different dimensions and tolerances required for each. However, assembly of the system often leaves a gap between the channels and the manifold, thus causing the working fluid to leak through the top of the microfins leading to decreased cooler performance. The effect of this gap is parametrized and analyzed with ANSYS Fluent CFD simulations and discussed in this paper. The findings show that even a few microns wide gap can cause a noticeable degradation of the MMC system performance. Imperfect assembly and the deformation of a microchannel chip due to working fluid pressure can cause gaps, indicating the necessity of uniform and hermetic bonding between the manifold and the tips of the microfins. Furthermore, this work presents the need for better heater designs to enable uniform and high heat flux to the heat transfer surface. Serpentine heaters are often used to mimic electronics in a laboratory environment, but there is a lack of study on the performance characterization of the heaters themselves. In the current work, the performance of a conventional serpentine heater is characterized using ANSYS thermo-electric modeling software. The results show that conventional serpentine heaters are insufficient at providing uniform heat flux in applications where there is a lack of heat spreading-such as in the current embedded cooler — showing deviations ranging over 200 % of the nominal value. The deviations are caused by the many bends present in a serpentine pattern where current density concentrations vary significantly. Two alternate designs are proposed, and numerical simulations show that these new heater designs are capable of providing uniform heat flux, not deviating more than 20% from the nominal heat flux value. The conventional and newly proposed heaters are fabricated, tested, and analyzed with a working FEEDS system.
In-Situ Monitoring via Synchrotron Radiation Laminography of Thermal Fatigue Cracks at Die-Attached Joints Under Cyclic Energization Loading
Authors: Tsuritani Hiroyuki , Sayama Toshihiko , Okamoto Yoshiyuki , Takayanagi Takeshi , Hoshino Masato , Uesugi Kentaro , Ooi Junya , Mori Takao
Published: October 2017

Recently, due to the increasing heat density of printed circuit boards (PCBs), thermal fatigue damage in the joints has exerted a more significant influence on the reliability of electronic components. Accordingly, the development of a new nondestructive inspection technology is strongly desired by related industries. The authors have applied a synchrotron radiation X-ray micro-tomography system to the nondestructive observation of micro-cracks. However, the reconstruction of CT images is difficult for planar objects such as PCB substrates, due to insufficient X-ray transmission in the direction parallel to the substrates. In order to solve this problem, a synchrotron radiation laminography system was developed to relax size restrictions on the observation samples, and was applied to the three-dimensional nondestructive evaluation of several kinds of solder joints, which were loaded under accelerated thermal cyclic conditions via thermal shock tests. Moreover, the thermal fatigue crack propagation process that occurs under actual PCB energization loading conditions will differ from that under the usual acceleration test conditions. In this work, the possibility of in-situ monitoring of the thermal fatigue crack propagation process using the laminography system was investigated at die-attached joints subjected to cyclic energization loading, which is close to the actual usage conditions of PCBs. The optical system developed for use in the laminography system was constructed to provide a rotation stage with a tilt from the horizontally incident X-ray beam, and to obtain X-ray projection images via a beam monitor. In this manner, the X-ray beam is sufficiently transmitted through the planar specimen in all projections. The observed specimens included several die-attached joints, in which 3 mm square ceramic dies had been mounted on a 40 mm square FR-4 substrate using Sn-3.0wt%Ag-0.5wt%Cu solder. Consequently, the laminography system was successfully applied to the in-situ monitoring of thermal fatigue cracks that appeared in the solder layer under cyclic energization. This was possible because the laminography images obtained in the energization state have a quality that is equivalent to those obtained in a non-energized state, provided that the temperature distribution of the specimen is stable. In addition, the fatigue crack propagation process can be quantitatively evaluated by measuring the crack surface area and calculating the average crack propagation rate. However, in some cases, the appearance of thermal fatigue cracks was not observed in a solder layer that had been loaded by the accelerated thermal cycle test. This result strongly suggests that delamination occurred at the interface, which indicates that the corresponding fracture mode was significantly influenced by the type of thermal loading.
Thermo-Mechanical Study of AlN Thin-Films As Heat Spreaders in III-V Photonic Devices
Authors: Lei Shenghui , Kardemir Ertugrul , McCloskey David , Donegan John F. , Enright Ryan
Published: October 2017

Ridge-type hybrid III-V active waveguides on silicon-on-insulator (SOI) substrates demonstrate poor thermal performance due to several factors. One aspect of their typical design that leads to large thermal resistance is the use of polymer-based optical cladding around the waveguide. To address this issue, we have been exploring the use of deposited aluminium nitride (AlN) as an alternative optical cladding material. AlN is an excellent dielectric with optical properties making it suitable as a cladding around III-V waveguides. Crucially, this material can demonstrate thermal conductivities ∼100 times larger than current polymer cladding materials such as benzocyclobutene (BCB). Electro-thermo simulation results suggest that replacing BCB with AlN could reduce device thermal resistance by ∼2 times. However, our previous linear elastic mechanical modelling indicates that mismatched thermal expansion has the potential to cause mechanical tensile failure in the III-V waveguide when cooled from the processing temperature to room temperature if AlN is deposited in a neutral residual stress state.

Here, to facilitate the design of encapsulated reliable hybrid semiconductor lasers, we extend our finite element, electro-thermo-mechanical model to include a residual stress in the deposited AlN. Using the Christensen criterion to define the maximum allowable stress in the device, our simulations indicate that there is a window of residual compressive stress in the AlN where mechanical failure may be avoided. To assess the feasibility of accessing this region of compressive residual stress while maintaining suitable thermal properties in the deposited AlN, we measure the thermal conductivity of AlN thin films (∼1.6 μm thick) deposited on silicon using a time-domain thermo reflectance (TDTR) setup. Stress measurements demonstrate compressive residual stresses ranging from ∼0 to −0.5 GPa. The TDTR measurement results reveal a similar thermal conductivity of ∼155 Wm−1K−1 over the entire range of compressive residual stress. These results strengthen the promise of encapsulating III-V active waveguides with AlN that simultaneously satisfy both thermal and mechanical requirements.
Monitoring Fugitive Methane Gas Emission From Natural Gas Pads
Authors: Klein Levente J. , van Kessel Ted , Nair Dhruv , Muralidhar Ramachandran , Hamann Hendrik , Sosa Norma
Published: October 2017

Identifying fugitive methane leaks can improve predictive maintenance of the extraction process, can extend gas extraction equipment lifetime, and eliminate hazardous work conditions. We demonstrate a wireless sensor network based on cost effective and robust chemi-resistive methane sensors combined with real time analytics to identify leaks from 2 scfh to 1000 scfh. The chemi-resistive sensors were validated to have a sensitivity better than 1 ppm in methane plume detection. The real time chemical sensor and wind data is integrated into an inversion models to identify the location and the magnitude of the methane leak. This integrated sensing and analytics solution can be deployed in outdoor environment for long term monitoring of accidental methane plume emissions, generate recommendations about fixing them, and ensure compliance with local government regulations.
Color Uniformity Enhancement of White Light-Emitting Diodes With Novel Bell Shape Phosphor Layer
Authors: Yu Xingjian , Shu Weicheng , Shang Bofeng , Xie Bin , Cheng Yanhua , Luo Xiaobing
Published: October 2017

In this study, we proposed a bell shape phosphor layer geometry and the corresponding dual-step phosphor coating method for enhancing the angular color uniformity (ACU) of phosphor-converted white light-emitting diodes (pcLEDs). Numerical simulation based on Volume of Fluid (VOF) model was applied to predict phosphor geometries. Based on the simulated results, experiments were conducted to realize the phosphor geometries. The simulated results show that the VOF model can predict the phosphor geometries with an acceptable geometric deviation within 5%. The experimental results show that compared with the spherical cap phosphor layer geometry, the bell shape geometry can achieve better ACU performance, an optimal bell phosphor layer geometry with equal coating volume above and around the LED chip was achieved, for the corrected color temperature (CCT) of 4000 K, the angular CCT deviation of the optimal geometry is 62 K, while it is 382 K for the spherical cap geometry.
Optimization of Filling Mass Fraction for Composite PCMs Based Thermal Management System
Authors: Shang Bofeng , Hu Jinyan , Yu Xingjian , Xie Bin , Wu Ruikang , Luo Xiaobing
Published: October 2017

Phase Change Materials (PCMs) have been widely investigated as a cooling solution due to their significant latent heat capacity. However, the current PCMs generally suffer a low thermal conductivity, thus hindering the application of PCMs. Composite Phase Change Materials (CPCMs) filling with high thermal conductivity materials have been proposed to solve this issue. Nevertheless, the latent heat of the CPCMs decreases with the mass fraction of fillings, thus leading to a lower allowable working time under safe operating temperature. Therefore, an optimal filling mass fraction of CPCMs is in urgent needed to improve the application of CPCMs. In this study, we developed a one-dimensional conduction heat transfer model of CPCMs to predict the optimal filling mass fraction of CPCMs to realize the maximum allowable working time. The filling mass fraction was introduced into the model and the relationship between the thermal conductivity and latent heat was built. We adopted paraffin as the matrix material and Expanded Graphite (EG) as the thermal conductivity enhancer. The allowable working time of the CPCMs as the function of filling mass fraction was obtained. Based on the principle of the maximum allowable working time, the optimal filling mass fraction was calculated. Comparative experiments were also conducted to validate the accuracy of the prediction model. The parameters which affect the maximum allowable working temperature were also investigated, including input heat flux, safe temperature, and height of CPCMs. The results show that a higher heat flux and height requires a larger filling mass fraction, and it’s opposite for the safe temperature.
Meshed Photonic Crystals for Manipulating Near-Field Thermal Radiation Across Variable Nano/Micro Gap
Authors: Elzouka Mahmoud , Ndao Sidy
Published: October 2017

The ability to manipulate heat flow can result in wonderful applications such as thermal logic and memory devices. Thermal logic and memory devices are similar to their electronic counterparts, however, they are powered solely by heat. In addition, thermal logic and memory devices can operate in harsh environments where electronics typically fail. Despite our understanding of various mechanisms of heat transfer, controlling heat (in a sense of switching heat flow on or off) is more challenging than controlling electricity due to the lack of perfect thermal insulators. One possible solution is to control the near-field thermal radiation heat transfer between hot and cold terminals by manipulating the size of the vacuum gap separating the two. Unlike far-field thermal radiation, near-field thermal radiation intensity increases exponentially with decreasing the gap size. There are however challenges in manipulating the nano/micro vacuum gaps to achieve enough contrast in heat transfer between the high and low heat transfer cases. In this paper, we present a prototype of a microdevice with a controllable micro gap of size 3 μm (initial gap size) between the hot and cold terminals; this configuration achieves a contrast in near-field radiative heat transfer at temperatures as high as 600 K. Furthermore, we present numerical analysis for meshed photonic crystals to achieve even higher contrast in radiative heat transfer with enhancement in heat transfer as high as 26 times in comparison to far-field.
3D Wire Bondless Integration: The Future of Silicon Carbide (SiC) Packaging
Authors: Seal Sayan , Wallace Andrea K. , Zumbro John E. , Mantooth H. Alan
Published: October 2017

Wide bandgap (WBG) semiconductors are revolutionizing the world of power electronics. They have the potential to bring about an unprecedented increase in power density. The ability to switch at ultrafast rates, coupled with the promise of high temperature operation, make these devices extremely desirable. However, having superior semiconductor devices will not automatically translate to superior package characteristics. In real applications, the performance of a power device is only as good as the package allows. One of the major drawbacks plaguing contemporary power modules is the wire-bonded interconnection. Wire bonds offer a high parasitic inductance. This paper presents a novel wire bondless SiC power MOSFET packaging technique. A commercially available bare die was reconfigured into a chip-scale package. The new form factor enabled the MOSFET to be bonded to a patterned FR4 substrate using flip-chip bonding. The electrical interconnection between the package and the substrate was established using solder balls — thus eliminating the requirement for wire bonds. The motivation for using a wire bondless method was a reduction in stray parasitic inductances and an increase in the thermo-mechanical reliability. Lower parasitic inductances will facilitate high switching frequencies which will promote miniaturization, a reduction in electromagnetic interference (EMI), and lead to lower switching losses. The proposed approach was demonstrated to reduce the parasitic loop inductance by a fctor of > 3× as compared with wire bonded modules.
CFD Optimization of the Cooling of Yosemite Open Compute Server
Authors: Gupta Aditya , Sridhar Ananthavijayan , Agonafer Dereje
Published: October 2017

Over the past few years, there has been an ever increasing rise in energy consumption by IT equipment in Data Centers. Thus, the need to minimize the environmental impact of Data Centers by optimizing energy consumption and material use is increasing. In 2011, the Open Compute Project was started which was aimed at sharing specifications and best practices with the community for highly energy efficient and economical data centers. The first Open Compute Server was the ‘ Freedom’ Server. It was a vanity free design and was completely custom designed using minimum number of components and was deployed in a data center in Prineville, Oregon. Within the first few months of operation, considerable amount of energy and cost savings were observed. Since then, progressive generations of Open Compute servers have been introduced. Initially, the servers used for compute purposes mainly had a 2 socket architecture. In 2015, the Yosemite Open Compute Server was introduced which was suited for higher compute capacity. Yosemite has a system on a chip architecture having four CPUs per sled providing a significant improvement in performance per watt over the previous generations. This study mainly focuses on air flow optimization in Yosemite platform to improve its overall cooling performance. Commercially available CFD tools have made it possible to do the thermal modeling of these servers and predict their efficiency. A detailed server model is generated using a CFD tool and its optimization has been done to improve the air flow characteristics in the server. Thermal model of the improved design is compared to the existing design to show the impact of air flow optimization on flow rates and flow speeds which in turn affects CPU die temperatures and cooling power consumption and thus, impacting the overall cooling performance of the Yosemite platform. Emphasis is given on effective utilization of fans in the server as compared to the original design and improving air flow characteristics inside the server via improved ducting.
The Dependence of Moisture Induced Die Stresses Upon Moisture Properties of Polymer Materials in Electronic Packages
Authors: Nguyen Quang , Suhling Jeffrey C. , Jaeger Richard C. , Lall Pradeep
Published: October 2017

Polymer materials have been widely used in electronic packaging with many advantages such as: lower cost, light weight and good performance. They however suffer a major drawback that results in a number of challenges for reliability engineers and researchers, in which polymer materials are quite sensitive to moisture absorption when exposed to humid environment, causing many failure modes in electronic packages such as: popcorn cracking, delamination or corrosion. It is well-known that finite element simulation is a powerful tool to evaluate the effects of moisture on electronic package reliability. In this study, three moisture properties (diffusivity, saturated concentration, and coefficient of moisture expansion) were experimentally characterized. The obtained results were then used to perform moisture diffusion simulations on various types of electronic package. Finally, a numerical study was conducted on the dependence of the moisture effects (weight gains, die stresses) upon each moisture property of polymeric components of three kinds of electronic packages (Quad Flat Package, Plastic Ball Grid Array, and Flip Chip on Laminate). The results of the study provided valuable insights into how moisture induced die stresses vary with each moisture property of polymeric components in the packages.
A Computational Approach to Study the Impact of PCB Thickness on QFN Assembly Under Drop Testing With Package Power Supply
Authors: Rahangdale Unique , Rajmane Pavan , Misrak Abel , Agonafer Dereje
Published: October 2017

Most of the electronic devices manufactured are used in daily life and with the miniaturization process of these devices, in the day to day life there is a risk of drop impact failure. It has been important to analyze and ensure the reliability of any electronic devices under every type of loading. Drop impact is not only loading that can affect reliability, but the simultaneous thermal load, moisture, convection is also acting. Smaller devices like cell phones, laptops, tablets are more prone to accidental impact loads which create board interconnects failure by frequent drop occurrence. Therefore, a multi-dimensional approach is taking place in research to study product reliability. In this paper, comprehensive study of drop and shock test is done on Quad Flat No-lead (QFN) package board of two different thickness. The computation setup is done with thermal analysis by providing power to die of the package which creates non-uniform temperature distribution during the drop testing analysis. This way drop test is coupled with a thermal load which is more realistic analysis. Our study depends on young’s modulus, density, CTE, thermal conductivity, specific heat and Poisson’s ratio of the material. Therefore, Experimental work includes material properties characterization of two boards to get temperature dependent Coefficient of thermal expansion, poison’s ratio and young’s modulus values using Thermal mechanical analyzer (TMA), the Dynamic mechanical analyzer (DMA) and Universal testing machine. Finite element analysis (FEA) method is used for computational analysis. Effect of impact loading for two boards has been done to investigate board and solder joint reliability due thickness and layer stack-ups in PCBs in environmental condition and at elevated temperature. For computational analysis, the assembly is subjected to the drop test per JEDEC standards. [12] The main purpose of this work is to study the impact of drop test with the powered package and how the reliability of any assembly changes with changing the stiffness of printed circuit board. The comparison of the boards has been made to understand the effect of PCB layer stack-ups, thickness, and temperature effect on the reliability of solder interconnects by considering the stress-strain generation that is induced in the PCBs during the drop test.
Measurement of Ion-Mobility in Copper-Aluminum Wirebond Electronics Under Operation at High Voltage and High Temperature
Authors: Lall Pradeep , Luo Yihua , Deshpande Shantanu , Nguyen Luu
Published: October 2017

Transition of ground vehicles to HEV and FEV has necessitated the operation of electronics in automotive underhood at high voltage bias and high temperature for extended period-of-time. Examples include gate drivers and IGBT modules. A typical automotive benchmark is operation for 10 years and 100,000 miles. Simultaneously, the first-level interconnects are migrating to use copper-wire interconnects in place of the previously used gold wire. Copper wire has higher propensity for corrosion and a narrower process-bonding window in comparison with gold wire based systems. Exposure to high temperature, humidity and bias influences the mobility of ions in the EMC and thus the contaminant transport to the WB interfaces. Measurements of diffusion behavior of EMCs at high temperature and high voltage bias are not available for readily being used in models. Prior studies have focused on biased humidity tests on wire bonds with the amplitude of the bias being limited up to 3.5Volts. In this paper, a PWM-controlled-gate drive-based test setup is established to study the effect of high voltage (up to 20Volts) on Cu-Al wire bond interconnects. A migration-diffusion cell experiment is designed to quantify the effect of voltage bias on transport of chlorine in EMCs. Diffusion coefficient and ionic mobility of chlorine at different temperatures are obtained. Resistance spectroscopy measurements show the progression of corrosion induced by voltage bias. A corrosion simulation is used to quantify the effect of voltage bias on corrosion rate of Cu-Al wire bond.
Formation of hydroxyapatite on titanium implants in vivo precedes bone-formation during healing
Authors: Malmberg Per , Bigdeli Narmin , Jensen Jens , Nygren Håkan
Published: October 2017

The bone material interface has been an area of intense study over many decades, where studies of the healing process ranging from simple mineral deposition in vitro to actual healing in vivo have given important clues to the importance of calcium minerals in the bone/implant interface. Here, the authors use a combination of in vitro cell culture methods and in vivo implantation to study how the role of the spontaneously formed hydroxyapatite layer on Ti-implants for the in vivo-healing into the bone tissue of rat tibia. Initial experiments were made in reduced systems by incubation of TiO2 in cell culture medium and analysis by time of flight secondary ion mass spectrometry (ToF-SIMS) and energy-dispersive x-ray spectroscopy followed by subsequent exposure of human embryological stem cells analyzed by von Kossa staining and environmental scanning electron microsopy. In vivo studies of the bone–material interface was analyzed by ToF-SIMS depth profiling using both C60+ ions as well as a gas cluster ion source beam, Ar1500+ as sputter source. The low ion yield of the Ar1500+ for inorganics allowed the inorganic/organic interface of the implant to be studied avoiding the erosion of the inorganic materials caused by the conventional C60+ beam.
Structural defects of GaN deposited on (111) Si with Gd2O3-related buffer layers
Authors: Lo Ko-Ying , Lin Pei-Hsin , Chen Hung-Jung , Gong Jyh-Rong , Hsu Hsun-Feng , Lee Yu-Wei , Chen Wei-Li
Published: October 2017

The structural defects of GaN deposited on (111) Si with Gd2O3-related rare earth oxide buffer layers were investigated using a double-crystal x-ray rocking curve (DCXRC), high resolution transmission electron microscopy (HRTEM). By comparing the DCXRC signals of (11¯02)GaN and (12¯12)GaN asymmetric planes and (0002)GaN symmetric plane, respectively, it was found that most of the threading dislocations (TDs) in GaN of the GaN on (111) Si using Gd2O3 or Er2O3/Gd2O3 buffer layer are type a TDs in nature. Based on the results of DCXRC studies, it is believed that the full-width at half maxima of the DCXRC signals of (11¯02)GaN and (12¯12)GaN asymmetric planes are primarily due to the contributions of the 1/3⟨12¯10⟩GaN components of the Burgers vectors of type a and type c + a TDs on the interplanar spacing distortions of (11¯02)GaN and (12¯12)GaN planes in GaN of the GaN/Er2O3/Gd2O3/(111) Si samples. HRTEM observations also revealed the presence of extrinsic stacking faults and Frankel partial dislocations in GaN of the GaN on the (111) Si sample with Gd2O3 or Er2O3/Gd2O3 buffer layer.
Continued search for better prediction of aided speech understanding in multi-talker environments
Authors: Xia Jing , Kalluri Sridhar , Micheyl Christophe , Hafter Ervin
Published: October 2017

To better understand issues of hearing-aid benefit during natural listening, this study examined the added demand placed by the goal of understanding speech over the more typically studied goal of simply recognizing speech sounds. The study compared hearing-aid benefit in two conditions, and examined factors that might account for the observed benefits. In the phonetic condition, listeners needed only identify the correct sound to make a correct response. In the semantic condition, listeners had to understand what they had heard to respond correctly, because the answer did not include any keywords from the spoken speech. Hearing aids provided significant benefit for listeners in the phonetic condition. In the semantic condition on the other hand, there were large inter-individual differences, with many listeners not experiencing any benefit of aiding. Neither a set of cognitive and linguistic tests, nor age, could explain this variability. Furthermore, analysis of psychometric functions showed that enhancement of the target speech fidelity through improvement of signal-to-noise ratio had a larger impact on listeners' performance in the phonetic condition than in the semantic condition. These results demonstrate the importance of incorporating naturalistic elements in the simulation of multi-talker listening for assessing the benefits of intervention in communication success.
Abundance and Multilocus Sequence Analysis of Vibrio Bacteria Associated with Diseased Elkhorn Coral (Acropora palmata) of the Florida Keys
Authors: Kemp Keri M. , Westrich Jason R. , Alabady Magdy S. , Edwards Martinique L. , Lipp Erin K.
Published: October 2017

The critically endangered elkhorn coral (
Acropora palmata
) is affected by white pox disease (WPX) throughout the Florida Reef Tract and wider Caribbean. The bacterium
Serratia marcescens
was previously identified as one etiologic agent of WPX but is no longer consistently detected in contemporary outbreaks. It is now believed that multiple etiologic agents cause WPX; however, to date, no other potential pathogens have been thoroughly investigated. This study examined the association of
Vibrio
bacteria with WPX occurrence from August 2012 to 2014 at Looe Key Reef in the Florida Keys, USA. The concentration of cultivable
Vibrio
was consistently greater in WPX samples than in healthy samples. The abundance of
Vibrio
bacteria relative to total bacteria was four times higher in samples from WPX lesions than in adjacent apparently healthy regions of diseased corals based on quantitative PCR (qPCR). Multilocus sequence analysis (MLSA) was used to assess the diversity of 69
Vibrio
isolates collected from diseased and apparently healthy
A. palmata
colonies and the surrounding seawater.
Vibrio
species with known pathogenicity to corals were detected in both apparently healthy and diseased samples. While the causative agent(s) of contemporary WPX outbreaks remains elusive, our results suggest that
Vibrio
spp. may be part of a nonspecific heterotrophic bacterial bloom rather than acting as primary pathogens. This study highlights the need for highly resolved temporal sampling
in situ
to further elucidate the role of
Vibrio
during WPX onset and progression.

IMPORTANCE
Coral diseases are increasing worldwide and are now considered a major contributor to coral reef decline. In particular, the Caribbean has been noted as a coral disease hot spot, owing to the dramatic loss of framework-building acroporid corals due to tissue loss diseases. The pathogenesis of contemporary white pox disease (WPX) outbreaks in
Acropora palmata
remains poorly understood. This study investigates the association of
Vibrio
bacteria with WPX.
Genomes of Novel Microbial Lineages Assembled from the Sub-Ice Waters of Lake Baikal
Authors: Cabello-Yeves Pedro J. , Zemskaya Tamara I. , Rosselli Riccardo , Coutinho Felipe H. , Zakharenko Alexandra S. , Blinov Vadim V. , Rodriguez-Valera Francisco
Published: October 2017

We present a metagenomic study of Lake Baikal (East Siberia). Two samples obtained from the water column under the ice cover (5 and 20 m deep) in March 2016 have been deep sequenced and the reads assembled to generate metagenome-assembled genomes (MAGs) that are representative of the microbes living in this special environment. Compared with freshwater bodies studied around the world, Lake Baikal had an unusually high fraction of
Verrucomicrobia
. Other groups, such as
Actinobacteria
and
Proteobacteria
, were in proportions similar to those found in other lakes. The genomes (and probably cells) tended to be small, presumably reflecting the extremely oligotrophic and cold prevalent conditions. Baikal microbes are novel lineages recruiting very little from other water bodies and are distantly related to other freshwater microbes. Despite their novelty, they showed the closest relationship to genomes discovered by similar approaches from other freshwater lakes and reservoirs. Some of them were particularly similar to MAGs from the Baltic Sea, which, although it is brackish, connected to the ocean, and much more eutrophic, has similar climatological conditions. Many of the microbes contained rhodopsin genes, indicating that, in spite of the decreased light penetration allowed by the thick ice/snow cover, photoheterotrophy could be widespread in the water column, either because enough light penetrates or because the microbes are already adapted to the summer ice-less conditions. We have found a freshwater SAR11 subtype I/II representative showing striking synteny with
Pelagibacter
ubique
strains, as well as a phage infecting the widespread freshwater bacterium
Polynucleobacter
.

IMPORTANCE
Despite the increasing number of metagenomic studies on different freshwater bodies, there is still a missing component in oligotrophic cold lakes suffering from long seasonal frozen cycles. Here, we describe microbial genomes from metagenomic assemblies that appear in the upper water column of Lake Baikal, the largest and deepest freshwater body on Earth. This lake is frozen from January to May, which generates conditions that include an inverted temperature gradient (colder up), decrease in light penetration due to ice, and, especially, snow cover, and oligotrophic conditions more similar to the open-ocean and high-altitude lakes than to other freshwater or brackish systems. As could be expected, most reconstructed genomes are novel lineages distantly related to others in cold environments, like the Baltic Sea and other freshwater lakes. Among them, there was a broad set of streamlined microbes with small genomes/intergenic spacers, including a new nonmarine
Pelagibacter
-like (subtype I/II) genome.
Complete Genome Sequence of West Nile Virus (WNV) from the First Human Case of Neuroinvasive WNV Infection in Cyprus
Authors: Richter Jan , Tryfonos Christina , Tourvas Aristomenis , Floridou Dora , Paphitou Niki I. , Christodoulou Christina
Published: October 2017

We report here the complete genome sequence of a West Nile virus (WNV) strain from the first laboratory-confirmed human case of neuroinvasive WNV infection in Cyprus. Phylogenetic analysis showed that this WNV strain grouped clearly into genetic lineage 1, clade 1a, cluster 2.
Genome Sequence of Kocuria polaris Strain CD08_4, an Isolate from the Duodenal Mucosa of a Celiac Disease Patient
Authors: Chander Atul Munish , Kumari Munesh , Kochhar Rakesh , Dhawan Devinder Kumar , Bhadada Sanjay Kumar , Mayilraj Shanmugam
Published: October 2017

We report here the 3.8-Mb genome sequence of
Kocuria polaris
strain CD08_4, an isolate from the duodenal mucosa of a celiac disease patient. The genome consists of specific virulence determinant genes, antibiotic resistance genes, genes for coping with oxidative stress, and genes responsible for iron acquisition and metabolism, suggestive of its pathogenic attributes.
Complete Genome Sequence of Eubacterium hallii Strain L2-7
Authors: Shetty Sudarshan A. , Ritari Jarmo , Paulin Lars , Smidt Hauke , De Vos Willem M.
Published: October 2017

The complete genome sequence of
Eubacterium hallii
strain L2-7 is reported here. This intestinal strain produces butyrate from glucose as well as lactate when acetate is provided in the growth medium. In addition, strain L2-7 has been shown to improve insulin sensitivity in db/db mice, indicating its application potential.
Genomic Sequences of Epizootic Hemorrhagic Disease Viruses Isolated from Florida White-Tailed Deer
Authors: Subramaniam Kuttichantran , Lednicky John A. , Loeb Julia , Sayler Katherine A. , Wisely Samantha M. , Waltzek Thomas B.
Published: October 2017

Epizootic hemorrhagic disease virus
(EHDV) serotypes 1 and 2 were isolated from Florida white-tailed deer in 2015 and 2016, respectively, and their genomes were completely sequenced. To our knowledge, these are the first full genome sequences for EHDV-1 and -2 from Florida.
Genome Sequence of the Lager-Brewing Yeast
Saccharomyces
sp. Strain M14, Used in the High-Gravity Brewing Industry in China
Authors: Liu Chunfeng , Li Qi , Niu Chengtuo , Zheng Feiyun , Li Yongxian , Zhao Yun , Yin Xiangsheng
Published: October 2017

Lager-brewing yeasts are mainly used for the production of lager beers. Illumina and PacBio-based sequence analyses revealed an approximate genome size of 22.8 Mb, with a GC content of 38.98%, for the Chinese lager-brewing yeast
Saccharomyces
sp. strain M14. Based on
ab initio
prediction, 9,970 coding genes were annotated.
Complete Genome Sequence of Desulfovibrio desulfuricans Strain G11, a Model Sulfate-Reducing, Hydrogenotrophic, and Syntrophic Partner Organism
Authors: Sheik Cody S. , Sieber Jessica R. , Badalamenti Jonathan P. , Carden Kendall , Olson Adam
Published: October 2017

Here, we report the draft genome of the Gram-negative, sulfate-reducing bacterium
Desulfovibrio desulfuricans
strain G11. Isolated from a rumen fluid enrichment, this culture has been a model syntrophic partner due to its metabolic flexibility. The assembly yielded a single circular chromosome of 3,414,943 bp and a 57% G+C content.
Complete Genome Sequence of the Hippuricase-Positive Campylobacter avium Type Strain LMG 24591
Authors: Miller William G. , Chapman Mary H. , Yee Emma , Revez Joana , Bono James L. , Rossi Mirko
Published: October 2017

Campylobacter avium
is a thermotolerant
Campylobacter
species that has been isolated from poultry.
C. avium
was also the second hippuricase-positive species to be identified within
Campylobacter
. Here, we present the genome sequence of the
C. avium
type strain LMG 24591 (=CCUG 56292
T
), isolated in 2006 from a broiler chicken in Italy.
Mechanisms of liver disease in patients infected with HIV
Authors: Kaspar Matthew B , Sterling Richard K
Published: October 2017

Objective

To describe the various mechanisms of liver disease in patients with HIV infection, and to link these mechanisms to disease states which may utilise them.

Background

Non-AIDS causes of morbidity and mortality are becoming increasingly common in patients chronically infected with HIV. In particular, liver-related diseases have risen to become one of the leading causes of non-AIDS-related death. A thorough understanding of the mechanisms driving the development of liver disease in these patients is essential when evaluating and caring for these patients.

Methods

The literature regarding mechanisms of liver disease by which different disease entities may cause hepatic injury and fibrosis was reviewed and synthesised.

Results

A number of discrete mechanisms of injury were identified, to include: oxidative stress, mitochondrial injury, lipotoxicity, immune-mediated injury, cytotoxicity, toxic metabolite accumulation, gut microbial translocation, systemic inflammation, senescence and nodular regenerative hyperplasia. Disease states may use any number of these mechanisms to exert their effect on the liver.

Conclusions

The mechanisms by which liver injury may occur in patients with HIV infection are numerous. Most disease states use multiple mechanisms to cause hepatic injury and fibrosis.
Combination of obstructive sleep apnoea and insomnia treated by continuous positive airway pressure with the SensAwake pressure relief technology to assist sleep: a randomised cross-over trial protocol
Authors: Pepin Jean Louis , Gagnadoux Frédéric , Foote Alison , Vicars Rachel , Ogra Bhavi , Viot-Blanc Véronique , Benmerad Meriem , D’Ortho Marie-Pia , Tamisier Renaud
Published: October 2017

Introduction

Obstructive sleep apnoea (OSA) is a common sleep breathing disorder affecting up to 17% of the middle-aged population. Continuous positive airway pressure (CPAP) is the primary treatment for patients with OSA, but acceptance and adherence to therapy is suboptimal in specific subgroups particularly those with insomnia or poor sleep quality (40%–80% of patients with OSA). Pressure intolerance, particularly during periods of wakefulness, inhibiting sleep onset or return to sleep, is one reason for poor CPAP adherence. AutoCPAPs continually monitor airflow changes and only increase the pressure when the upper airway requires it. Reducing the pressure during wakefulness-sleep transition and wakefulness-after-sleep-onset (WASO) may improve therapy comfort and potentially adherence without compromising therapy efficacy. We hypothesise that SensAwake, a pressure relief function that reduces CPAP pressure on the transition from sleep to wakefulness and on WASO, may improve objective sleep quality.

Methods and analysis

This is a multicentre, randomised double-blind crossover clinical trial on patients with both OSA and insomnia. Insomnia is defined as Insomnia Severity Index >15 at screening. Baseline data, including actigraphy, are collected for 1 week before randomisation (1:1) to either conventional AutoCPAP or AutoCPAP with SensAwake for 4 weeks. After an evaluation visit, patients are switched to the other treatment arm for a further 4 weeks. Allowing for 20% dropout, 48 patients are required. If applicable, repeated measures analysis of variance will be used to assess differences in WASO measured by actigraphy (primary outcome), other actigraphy measures, AutoCPAP compliance, subjective questionnaire scores (Epworth Sleepiness Scale, Pittsburgh Sleep Quality Index, Short-Form 12 Health Survey) and 24 hours blood pressure (secondary outcomes).

Ethics and dissemination

The protocol was approved by the regional Ethics Committee (CPP Sud-Est–V, IRB N°6705) on 9 December 2015, is registered on ClincalTrials.gov (NCT02721329) and started in June 2016 with expected publication of primary outcome results in 2018.

Trial registration number

NCT0272132; Pre-results.
Cohort profile: a nationwide cohort of Finnish military recruits born in 1958 to study the impact of lifestyle factors in early adulthood on disease outcomes
Authors: Sormunen Jorma , Arnold Melina , Soerjomataram Isabelle , Pukkala Eero
Published: October 2017

Purpose

The cohort was set up to study the impact of lifestyle factors in early adulthood on disease outcomes, with a focus on assessing the influence of body composition and physical performance in early adulthood on subsequent cancer risk.

Participants

Men born in 1958 who performed their military service between the ages of 17 and 30 years were included in this study (n=31 158). They were eligible for military service if they were healthy or had only minor health problems diagnosed at the beginning of their service. Men with chronic illnesses requiring regular medication or treatment were not eligible for service. Comprehensive health data including diagnosed illnesses, anthropometric measures and health behaviour were collected at the beginning and at the end of military service, including data from medical check-ups.

Findings to date

During the follow-up, 1124 new cancer cases were diagnosed between baseline (ie, end of the military service for each individual) and end of the year 2014. In the end of the follow-up, 91% of the study participants were still alive. Overweight (body mass index (BMI) ≥25 kg/m2) and obesity (BMI ≥30 kg/m2) were associated with an overall increased risk of cancer. A good or excellent physical condition significantly reduced cancer risk.

Future plans

The dataset offers the possibility of linkage with other databases, such as the Finnish Cancer Registry (eg, primary site of the tumour, morphology, time of detection, spreading and primary treatment), vital statistics (date of emigration or deaths), censuses (socioeconomic indicators), hospital discharge data (comorbidity) and population surveys (life habits).
Prevalence and time trends in overweight and obesity among urban women: an analysis of demographic and health surveys data from 24 African countries, 1991–2014
Authors: Amugsi Dickson Abanimi , Dimbuene Zacharie T , Mberu Blessing , Muthuri Stella , Ezeh Alex C
Published: October 2017

Objective

To examine the prevalence and trends in overweight and obesity among non-pregnant urban women in Africa over the past two and a half decades.

Design

Cross-sectional surveys conducted between 1991 and 2014.

Settings

Demographic and Health Surveys (DHS), repeated cross-sectional data collected in 24 African countries.

Participants

Adult non-pregnant women aged 15–49 years. The earlier DHS collected anthropometric data on only those women who had children aged 0–5 years. The main analyses were limited to this subgroup. The participants were classified as overweight (25.0–29.9 kg/m2) and obese (≥30.0 kg/m2).

Results

The prevalence of overweight and obesity among women increased in all the 24 countries. Trends were statistically significant in 17 of the 24 countries in the case of obesity and 13 of the 24 for overweight. In Ghana, overweight almost doubled (p=0.001) while obesity tripled (p=0.001) between 1993 and 2014. Egypt has the highest levels of overweight and obesity at 44% (95% CI 42%, 46.5%) and 39% (95% CI 36.6%, 41.8%), respectively, in 2014 and the trend showed significant increase (p=0.005) from 1995 levels. Also, obesity doubled in Kenya, Benin, Niger, Rwanda, Ivory Coast and Uganda, while tripled in Zambia, Burkina Faso, Mali, Malawi and Tanzania. Ethiopia and Madagascar had the lowest prevalence of both obesity and overweight, with overweight ranging from 7% to 12% and obesity from 1% to 4%.

Conclusions

Overweight and obesity are increasing among women of reproductive age in urban Africa, with obesity among this age group having more than doubled or tripled in 12 of the 24 countries. There is an urgent need for deliberate policies and interventions to encourage active lifestyles and healthy eating behaviour to curb this trend in urban Africa.