bluuebunny/crossref_metadata_2025 huggingface dataset:
Discussion on STR and PFD Analysis of I&C System
Authors: Chao Zhang , Yanqin Su , Wei Li , Wanqing Chen , Qiang Chen
Published: October 2017

As the central part of the nuclear power plant (NPP), the Instrumentation &Control (I&C) system with high performance level has a significant impact on nuclear power plant safety. Probability theory, especially the reliability analysis is one of the best ways to support this. High reliability and availability requirements of I&C system could be satisfied by appropriate methods. This paper states the discussion on two of the most important reliability data (STR & PFD) analysis of one certain I&C system and describes how this process helps to improve the design and reliability from the perspective of nuclear I&C industry.
A New Reliability Optimization Allocation Method for Nuclear Power Systems Based on Goal Oriented Methodology
Authors: Xiao-jian Yi , Yong-cheng Xie , Jian Shi , Hui-na Mu , Peng Hou
Published: October 2017

This paper presents a new reliability optimization allocation method for complex nuclear power systems based on Goal Oriented (GO) method, whose goal is to minimize the system cost. First, the new reliability optimization allocation method is expounded in detail. And its process is formulated. Then, the hoisting mechanism in nuclear power plant is taken as an example to allocate its system reliability index to design unit by the new method. The reliability optimization allocation processes are mainly as follows: (i) Conducting system analysis, (ii) Developing GO model, (iii) Establishing reliability optimization allocation mathematic model, (iv) Solving the reliability optimization allocation mathematic model, (v) Determining the allocation results. The results analysis shows that the system costs for different solving times turn to a relatively stable value, and the allocated reliability indexes of unit are satisfied with engineering requirements. All in all, this new reliability optimization allocation method can not only obtain the reasonable allocation results quickly and effectively, but it also can overcome the disadvantages of existing reliability optimization allocation methods for complex nuclear power systems efficiently. Moreover, this paper provides a new approach for the reliability optimization allocation of complex nuclear power systems.
Incident Investigation and Root Cause Analysis Method and Technology Review
Authors: Jianjun Guan , Yinhui Che , Lei Ma
Published: October 2017

Incident investigation and root cause analysis (RCA) are widely used in nuclear power plant incident investigation and root cause confirmation. In this paper, based on the analysis literature reviews of root cause investigation of related incidents in IAEA (International Atomic Energy Agency), Europe and the United States, the analysis methods and techniques or tools of root causes in the world are studied, the incident investigation and analysis methods and techniques for root causes are analyzed and summarized. Through a comparison of various analysis methods and relevant application techniques and tools, differences between these root cause analysis techniques and tools are elaborated in terms of both concept and applicable application. In addition, application of RCA analysis methods and techniques is also briefed based on domestic RCA application practices.
Development of Instrumentation and Control Systems for UK ABWR
Authors: Naito Itsuki , Koyamada Taisuke , Yamamoto Keisuke , Igarashi Kingo , Harada Hideo , Suzuki Hirotsugu
Published: October 2017

This paper introduces the Instrumentation and Control (I&C) system for the proposed UK Advanced Boiling Water Reactor (UK ABWR) offered by Hitachi-GE Nuclear Energy, Ltd (Hitachi-GE). Hitachi-GE has been progressing the UK Generic Design Assessment (GDA) licensing process over the last 3 years. This is the process through which the Office for Nuclear Regulations (ONR) assesses the UK ABWR for suitability from a nuclear safety, security, environmental protection and waste management perspective and it is the first step towards proceeding with the construction phase in the UK.

ONR’s regulatory expectations setting out relevant good practice are described in the Safety Assessment principles (SAPs), which are considered into the I&C design for UK ABWR. In addition, it has also been designed to take into account relevant good practices and regulations.

In accordance with expectations derived from SAPs, the UK ABWR I&C systems are categorized and classified as required by IEC 61513 and IEC 61226. In addition, the overall I&C architecture, including all associated Human-Machine Interfaces (HMIs), abides by the principles independence and diversity of safety measures, segregation and separation of the protection and control systems.

As a result, the UK ABWR I&C architecture is composed of major eight sub-systems. The eight sub-systems are:

-Safety System Logic and Control system (SSLC)

-Hardwired Backup System (HWBS)

-Safety Auxiliary Control System (SACS)

-Plant Control System (PCntlS)

-Reactor/Turbine Auxiliary Control System (RTACS)

-Plant Computer System (PCS)

-Severe Accident Control and Instrumentation system (SA C&I)

-Other dedicated C&I systems.

The features for each sub-system such as redundancy of safety train or segregation among divisions are specified so that each sub-system will achieve its reliability as well as increase availability.

While in the Japanese ABWR safety I&C system, the main protection system (SSLC), is microprocessor-based from the decades of successful operating experience in the past BWR, to meet the UK regulatory regime expectation on diversity between Class 1 platform and non-Class 1 platform, the SSLC (Class 1) for the UK ABWR is by Field Programmable Gate Array (FPGA). This system is currently under development and complies with IEC 62556. Its safety integrity level is planned to be SIL 3 (as a single division) and SIL 4 (as a four division system) as defined in IEC 61508.

The HMIs which constitute an integral part of the I&C systems are also designed to comply with the I&C architecture regarding their categorization and classification with consideration of Human Factors (HF) modern methods taken into accounts.
Application Research of Safety Control and Information Device Based on FirmSys Platform in ACPR1000 Nuclear Power Plant
Authors: Zhu Li-Ling , Wu Bin , Li Gang , Xie Yi-Qin , Sun Yong-Bin
Published: October 2017

Because of the rapid changes that are taking place in the digital computer and the graphic display technology employed in a modern human system interface, the use of integrated digital display devices to replace traditional instruments has become a new application tendency in nuclear power plant. The safety control and display device (refer as to SCID hereafter) is a safety class digital Human System Interface (HSI) device of FirmSys platform. It provides display and control function of the safety system in ACPR1000 nuclear power plant. This paper mainly introduces the typical application architecture of SCID in ACPR1000 NPP, the main functions (including control and display function, application mode management function, data processing function and data communication function) of SICD and the innovation and improvement of SCID. The application of SCID has improved the integration of the HMI system and reduced the workload of the operating staff. It has been successfully applied in several ACPR1000 nuclear power plants.
Optimization Design Based on Human Factors V&V of Human System Interfaces in Nuclear Power Plant
Authors: Xiaoyang Ming , Shiguang Deng , Xingwei Jiang
Published: October 2017

The main control room, the monitor and control center of nuclear plant, integrates quantities of Human System Interfaces (HSIs), with which, the operators maintain the plant running safely and effectively under different working conditions[1]. Human Factors Verification and Validation (HF V&V) is one of the twelve elements of a Human Factor Engineering (HFE) program according to NUREG-0711. Research on V&V methods has been carried out for years, however, the V&V implementation in domestic nuclear power plants looks forward to being consummated.

For HPR1000, the third generation of nuclear power technology with China’s self-owned independent intellectual property right[2], HF V&V activities include HSI HFE Design Verification (DV), HSI Task Support Verification (TSV), Partial Validation (PV), Integrated System Validation (ISV) and Human Engineering Discrepancy (HED) management. The V&V methods introduced in this paper gives an executable and effective way to evaluate whether the design conforms to HFE design principles and that the adequacy of the HSIs enable plant personnel to successfully perform their tasks and other operational goals, assuring plant safety. With these methods, plenty of suggestions based on the HEDs generated from different V&V activities are applied into the design of HSIs, and afterwards, an optimization for the main control room of HPR1000 will be achieved.
Probabilistic Approach for Assessing the Weather and External Forces Hazard Using Bayesian Belief Networks
Authors: Chaves Agudelo Julián , Aristizábal Ceballos Jaime Hernán , Alvarado Franco Juan Pablo , Buriticá Cortés Jessica
Published: October 2017

This paper presents a probabilistic approach for the assessment of the Weather and External Forces hazard in pipelines using a Bayesian Belief Network. Such model was constructed through structured expert judgment methods for those factors whose deterministic modelling is complex or unknown and existent models for those known factors or previously studied phenomena. For the hazard modelling, three fundamental groups of variables were considered: susceptibility, triggering events and vulnerability. Through this proposal, the hazard is described from a probabilistic perspective, including the uncertainty associated with instability processes, information gathering and analysis and risk perception, among others. A transportation system characterized by its high geotechnical complexity is used as a case study, and results were compared with the current assessment model. The results show that the new model has greater sensitivity to the hazard level while being consistent with both the condition of the Right of Way (ROW) and the hydrocarbon transportation infrastructure.
Safety Enhancement Study of CAP1400 Spent Fuel Storage Racks
Authors: He Xiaoming , Zhu Ziqiang , Shao Changlei , Huang Ran
Published: October 2017

Safety enhancement is essential to spent fuel storage racks of nuclear power plant after Fukushima accident. Criticality safety, cooling safety and structural safety enhancement for CAP1400 (a larger advanced pressurized water reactor developed by China) spent fuel storage racks of are proposed and prominent results have been obtained. The criticality analysis results indicate that neutron absorber insert is efficient to increase criticality safety of storage rack. The CFD simulation and seismic analysis reveal that these storage racks can meet the cooling safety and structural integrity requirements. Both neutron absorber inserts and passive spent fuel pool cooling technology have good application prospect.
Investigation of Transient Flow and Heat Transfer for Passive Nuclear Reactor Direct Safety Injection
Authors: Weng Yu , Liu Lang , Jiang Yang , Gu Hongfang , Wang Haijun
Published: October 2017

This paper describes a transient flow and heat transfer characteristics for a 1400MW passive pressurized-water reactor (PWR) direct vessel injection (DVI) system in different accident transient processes. The study components include reactor pressure vessel and a series reactor internal such as core barrel and radiation surveillance capsules, the flow channel include downcomer and lower plenum. Furthermore, the inject device is designed with special structures: first, a venturi type tube nozzle is connected to pressure vessel, second, a flow deflector is arranged in the downcomer which is facing the nozzle. This special structures will make the flow mixing and heat transfer very complicate and hard to predict. This study considers characteristics of the loops temperature and flow rate for both injection loop and reactor cold leg loop which are continuous change and long duration.

Computational fluid dynamics (CFD) method is used in this study. Before this study, the physical model and numerical method are verified by an independent scaled model experiment. In this real reactor scale study, two typical accident transient processes are analyzed in this study, and temperature distribution on both reactor vessel and reactor internals are obtained. According to results analysis, the characteristics of heat distribution in downcomer were obtained: The injection fluid which is supposed to flow to core barrel is driven to the side of reactor vessel by the reflector. With the injection fluid flows in downcomer, the injection flow shape comes to a triangle. In addition, the transient results show that correlation degree of temperature distribution and injection flow character is gradually decreased with the increase of time history for passive injection.

Overall, the exercise complements the activities in reactor safety analysis areas in understanding the origins of thermal load in reactor vessel, and being able to quantify them. Results of this study can be directly used by analyzing of reactor fatigue mechanics. (CSPE)
Investigation on Creep Mechanisms of Alloy 709
Authors: Alomari Abdullah S. , Kumar Nilesh , Murty Korukonda L.
Published: October 2017

To improve efficiency, safety, and reliability of nuclear reactors, structural materials for Gen-IV reactors are being designed and developed. Alloy 709, a 20Cr-25Ni austenitic stainless steel, has superior mechanical properties to be a preferred candidate material for Sodium Fast Reactor structural application. Creep tensile tests were performed at temperatures of 700 °C, 725 °C and 750 °C and range of stresses from 100 MPa to 250 MPa. The apparent stress exponent and activation energy were found to be 10.3±0.4 and 368.6±14.7 kJ/mol. Linear extrapolation method was used to rationalize the higher stress exponent and activation energy relative to the mechanism in power law creep yielding to a true stress exponent of 7.1 ± 0.3 and a true activation energy of 277 ± 12.8 kJ/mol which is close to the lattice diffusion of iron in Fe-20Cr-25Ni. Hence, the lattice diffusion controlled dislocation climb process is believed to be the rate controlling creep deformation mechanism in this range of stresses and temperatures. The appropriate constitutive equation was developed based on the results; however, microstructural evaluations are under investigation to confirm the rate controlling mechanism. In addition, creep tests at higher temperatures and lower stresses are being conducted to extend the stress and strain-rate ranges to observe possible transition in creep mechanism.
Study of CO2 ashing for porous SiOCH film using 100 MHz/13.56 MHz dual frequency superimposed capacitive coupled plasma
Authors: Imamura Tsubasa , Yamamoto Katsumi , Kurihara Kazuaki , Hayashi Hisataka
Published: October 2017

CO2 plasma has advantages over O2 and N2/H2 plasma in low damage resist ashing processes for porous SiOCH films. To understand why CO2 plasma has advantages, the authors investigated the damage mechanisms in O2, N2/H2, and CO2 plasma using 100 MHz/13.56 MHz dual frequency superimposed capacitive coupled plasma. According to the results of pallet for plasma evaluation tests, O radical, vacuum ultraviolet light, and ions were the main cause of damage to the porous SiOCH films in the O2 plasma, the N2/H2 plasma, and the CO2 plasma, respectively. The authors believe that CO2 plasma has fewer O radicals in it than O2 plasma and is less intense than the light produced by a N2/H2 plasma. To suppress damage further, the authors propose controlling the O radicals by using pulse-modulated 100 MHz CO2 plasma.
Low reflection Fresnel lenses via double imprint combined with vacuum-UV surface hardening
Authors: Steinberg Christian , Al-Hussainawi Nour , Papenheim Marc , Mayer Andre , Scheer Hella-Christin , Matschuk Maria , Pranov Henrik
Published: October 2017

To improve the optical performance of Fresnel lenses, a technique for preparing them with antireflective structures of the moth-eye type is developed. Masters featuring such hierarchical structures are prepared in SU-8, a negative tone photoresist, by two consecutive thermal imprint steps. The moth-eye structures imprinted first are vacuum ultraviolet-treated at 172 nm to provide a surface-near the cross-linked layer that remains stable during the second imprint of the 100 μm sized Fresnel structures. A successful combination of both structure types is possible at an imprint temperature as low as 45 °C. This can be understood on the basis of the typical exposure and the crosslinking behavior of a chemically amplified negative tone resist like SU-8. The masters prepared in this way will be subjected to extrusion coating, the process of choice for future large area preparation of such structures in a single step.
Bias error analysis for phase and amplitude gradient estimation of acoustic intensity and specific acoustic impedance
Authors: Whiting Eric B. , Lawrence Joseph S. , Gee Kent L. , Neilsen Tracianne B. , Sommerfeldt Scott D.
Published: October 2017

Sound intensity measurements using two microphones have traditionally been processed using a cross-spectral method with inherent error in the finite-sum and finite-difference formulas. The phase and amplitude gradient estimator method (PAGE) has been seen experimentally to extend the bandwidth of broadband active intensity estimates by an order of magnitude. To provide an analytical foundation for the method, bias errors in active intensity and specific acoustic impedance are presented and compared to those of the traditional method. Bias errors are reported for a plane-wave field and sound radiated from a monopole and a dipole. Additionally, bias errors are reported for reactive intensity, the estimation of which is unchanged by the PAGE method for the two-microphone case.
Bioinspired phase-separated disordered nanostructures for thin photovoltaic absorbers
Authors: Siddique Radwanul H. , Donie Yidenekachew J. , Gomard Guillaume , Yalamanchili Sisir , Merdzhanova Tsvetelina , Lemmer Uli , Hölscher Hendrik
Published: October 2017

Inspired by black butterfly scales, self-assembled phase-separated nanostructures form efficient photovoltaic absorbers.
The Enigmatic Genome of an Obligate Ancient Spiroplasma Symbiont in a Hadal Holothurian
Authors: He Li-Sheng , Zhang Pei-Wei , Huang Jiao-Mei , Zhu Fang-Chao , Danchin Antoine , Wang Yong
Published: October 2017

Protective symbiosis has been reported in many organisms, but the molecular mechanisms of the mutualistic interactions between the symbionts and their hosts are unclear. Here, we sequenced the 424-kbp genome of “
Candidatus
Spiroplasma holothuricola,” which dominated the hindgut microbiome of a sea cucumber, a major scavenger captured in the Mariana Trench (6,140 m depth). Phylogenetic relationships indicated that the dominant bacterium in the hindgut was derived from a basal group of
Spiroplasma
species. In this organism, the genes responsible for the biosynthesis of amino acids, glycolysis, and sugar transporters were lost, strongly suggesting endosymbiosis. The highly decayed genome consists of two chromosomes and harbors genes coding for proteolysis, microbial toxin, restriction-methylation systems, and clustered regularly interspaced short palindromic repeats (CRISPRs), composed of three
cas
genes and 76 CRISPR spacers. The holothurian host is probably protected against invading viruses from sediments by the CRISPRs/Cas and restriction systems of the endosymbiotic spiroplasma. The protective endosymbiosis indicates the important ecological role of the ancient
Spiroplasma
symbiont in the maintenance of hadal ecosystems.

IMPORTANCE
Sea cucumbers are major inhabitants in hadal trenches. They collect microbes in surface sediment and remain tolerant against potential pathogenic bacteria and viruses. This study presents the genome of endosymbiotic spiroplasmas in the gut of a sea cucumber captured in the Mariana Trench. The extreme reduction of the genome and loss of essential metabolic pathways strongly support its endosymbiotic lifestyle. Moreover, a considerable part of the genome was occupied by a CRISPR/Cas system to provide immunity against viruses and antimicrobial toxin-encoding genes for the degradation of microbes. This novel species of
Spiroplasma
is probably an important protective symbiont for the sea cucumbers in the hadal zone.
Transcriptional Activities of the Microbial Consortium Living with the Marine Nitrogen-Fixing Cyanobacterium Trichodesmium Reveal Potential Roles in Community-Level Nitrogen Cycling
Authors: Lee Michael D. , Webb Eric A. , Walworth Nathan G. , Fu Fei-Xue , Held Noelle A. , Saito Mak A. , Hutchins David A.
Published: October 2017

Trichodesmium
is a globally distributed cyanobacterium whose nitrogen-fixing capability fuels primary production in warm oligotrophic oceans. Like many photoautotrophs,
Trichodesmium
serves as a host to various other microorganisms, yet little is known about how this associated community modulates fluxes of environmentally relevant chemical species into and out of the supraorganismal structure. Here, we utilized metatranscriptomics to examine gene expression activities of microbial communities associated with
Trichodesmium erythraeum
(strain IMS101) using laboratory-maintained enrichment cultures that have previously been shown to harbor microbial communities similar to those of natural populations. In enrichments maintained under two distinct CO
2
concentrations for ∼8 years, the community transcriptional profiles were found to be specific to the treatment, demonstrating a restructuring of overall gene expression had occurred. Some of this restructuring involved significant increases in community respiration-related transcripts under elevated CO
2
, potentially facilitating the corresponding measured increases in host nitrogen fixation rates. Particularly of note, in both treatments, community transcripts involved in the reduction of nitrate, nitrite, and nitrous oxide were detected, suggesting the associated organisms may play a role in colony-level nitrogen cycling. Lastly, a taxon-specific analysis revealed distinct ecological niches of consistently cooccurring major taxa that may enable, or even encourage, the stable cohabitation of a diverse community within
Trichodesmium
consortia.

IMPORTANCE
Trichodesmium
is a genus of globally distributed, nitrogen-fixing marine cyanobacteria. As a source of new nitrogen in otherwise nitrogen-deficient systems, these organisms help fuel carbon fixation carried out by other more abundant photoautotrophs and thereby have significant roles in global nitrogen and carbon cycling. Members of the
Trichodesmium
genus tend to form large macroscopic colonies that appear to perpetually host an association of diverse interacting microbes distinct from the surrounding seawater, potentially making the entire assemblage a unique miniature ecosystem. Since its first successful cultivation in the early 1990s, there have been questions about the potential interdependencies between
Trichodesmium
and its associated microbial community and whether the host's seemingly enigmatic nitrogen fixation schema somehow involved or benefited from its epibionts. Here, we revisit these old questions with new technology and investigate gene expression activities of microbial communities living in association with
Trichodesmium
.
Complete Genome Sequence of Rathayibacter toxicus Phage NCPPB3778
Authors: Schneider William L. , Sechler Aaron J. , Rogers Elizabeth E.
Published: October 2017

The phage NCPPB3778 was isolated from
Rathayibacter toxicus
strain CS14, and the genomic DNA was sequenced. The genome is similar to siphoviruses, consisting of 44,520 bases including 77 predicted open reading frames. Portions of the genome are annotated as typical phage proteins, but much of the genome sequence is unique from other bacteriophages.
First Complete Genome Sequence of Methicillin-Resistant Staphylococcus aureus Strain SO-1977 Isolated from Khartoum, Sudan
Authors: Mohamed Sofia B. , Ali Mohamed S. , Alamir Faisal M. , Alyas Tahani B. , Ahmed Abdallah E. , Seed Almeen O. , Omer Rihab A.
Published: October 2017

Methicillin-resistant
Staphylococcus aureus
is increasingly becoming resistant to most antibiotics and consequently has become a challenging public health problem in Sudan. The present study documented the first complete genome sequence of strain SO-1977, isolated from a contaminated wound in Sudan.
Genome Sequences of Crimean-Congo Hemorrhagic Fever Virus Strains Isolated in South Africa, Namibia, and Turkey
Authors: Zivcec Marko , Albarino Cesar G. , Guerrero Lisa I. W. , Ksiazek Thomas G. , Nichol Stuart T. , Swanepoel Robert , Rollin Pierre E. , Spiropoulou Christina F.
Published: October 2017

We report here the full-length sequences of 16 historical isolates of Crimean-Congo hemorrhagic fever orthonairovirus (CCHFV) obtained in Turkey, Namibia, and South Africa. The strains may be useful for future work to develop molecular diagnostics or viral evolution studies.
Genome Sequence of an Endophytic Fungus, Fusarium solani JS-169, Which Has Antifungal Activity
Authors: Kim Jung A , Jeon Jongbum , Park Sook-Young , Kim Ki-Tae , Choi Gobong , Lee Hyun-jung , Kim Yangsun , Yang Hee-sun , Yeo Joo-Hong , Lee Yong-Hwan , Kim Soonok
Published: October 2017

An endophytic fungus,
Fusarium solani
strain JS-169, isolated from a mulberry twig, showed considerable antifungal activity. Here, we report the draft genome sequence of this strain. The assembly comprises 17 scaffolds, with an
N
50
value of 4.93 Mb. The assembled genome was 45,813,297 bp in length, with a G+C content of 49.91%.
Characterization of Two
Bovine viral diarrhea virus
Strains Originating from Cattle in Tibet, China
Authors: Luo Runbo , Wei Xiaoqin , Zhou Hongbo , Sizhu Suolang
Published: October 2017

Here, we report two strains of
Bovine viral diarrhea virus
(BVDV), named XZ01 and XZ02, that were isolated from cattle in Tibet, China. They belong to subgenotype 1b. This report will help in understanding the molecular characteristics of BVDV in Tibetan cattle.
Metagenomic Analysis of Microbial Diversity in Landfill Lysimeter Soil of Ghazipur Landfill Site, New Delhi, India
Authors: Gupta Juhi , Rathour Rashmi , Kumar Madan , Thakur Indu Shekhar
Published: October 2017

We report the soil microbial diversity and functional aspects related to degradation of recalcitrant compounds, determined using a metagenomic approach, in a landfill lysimeter prepared with soil from Ghazipur landfill site, New Delhi, India. Metagenomic analysis revealed the presence and functional diversity of complex microbial communities responsible for waste degradation.
Complete Genome Sequence of Serotype III Streptococcus agalactiae Sequence Type 17 Strain 874391
Authors: Sullivan Matthew J. , Forde Brian M. , Prince Darren W. , Ipe Deepak S. , Ben Zakour Nouri L. , Davies Mark R. , Dougan Gordon , Beatson Scott A. , Ulett Glen C.
Published: October 2017

Here we report the complete genome sequence of
Streptococcus agalactiae
strain 874391. This serotype III isolate is a member of the hypervirulent sequence type 17 (ST-17) lineage that causes a disproportionate number of cases of invasive disease in humans and mammals. A brief historical context of the strain is discussed.
Genome Sequences of Salmonella enterica subsp.
enterica
Serovar Kentucky Sequence Type 152 Isolated from Dairy Cows in the United States
Authors: Haley Bradd J. , Luo Yan , Wang Charles , Brown Eric , Allard Marc , Karns Jeffrey S. , Van Kessel Jo Ann S.
Published: October 2017

Salmonella enterica
subsp.
enterica
serovar Kentucky (
S.
Kentucky) is frequently isolated from dairy cows in the United States, but is an infrequent cause of human salmonellosis. To investigate the genomic features of
S
. Kentucky strains isolated from a single dairy farm, the genomes of eight isolates were sequenced and added to the public domain.
Draft Genome Sequence of Salmonella enterica subsp.
enterica
Serovar Typhimurium Q1
Authors: Eichhorn Inga , Tedin Karsten , Fulde Marcus
Published: October 2017

Here, we report the draft genome sequence of
Salmonella enterica
subsp.
enterica
serovar Typhimurium strain Q1. The draft genome contains 4,793,493 bp in 149 contigs.
Engineering Diagnostic and Therapeutic Gut Bacteria
Authors: Landry Brian P. , Tabor Jeffrey J.
Published: October 2017

Genetically engineered bacteria have the potential to diagnose and treat a wide range of diseases linked to the gastrointestinal tract, or gut. Such engineered microbes will be less expensive and invasive than current diagnostics and more effective and safe than current therapeutics. Recent advances in synthetic biology have dramatically improved the reliability with which bacteria can be engineered with the sensors, genetic circuits, and output (actuator) genes necessary for diagnostic and therapeutic functions. However, to deploy such bacteria
in vivo
, researchers must identify appropriate gut-adapted strains and consider performance metrics such as sensor detection thresholds, circuit computation speed, growth rate effects, and the evolutionary stability of engineered genetic systems. Other recent reviews have focused on engineering bacteria to target cancer or genetically modifying the endogenous gut microbiota
in situ
. Here, we develop a standard approach for engineering “smart probiotics,” which both diagnose and treat disease, as well as “diagnostic gut bacteria” and “drug factory probiotics,” which perform only the former and latter function, respectively. We focus on the use of cutting-edge synthetic biology tools, gut-specific design considerations, and current and future engineering challenges.
Strange case of dimorphic skin rash in a patient with cirrhosis: atypical herpes simplex and sweet’s syndrome
Authors: Philips Cyriac Abby , Paramaguru Rajaguru , Augustine Philip
Published: October 2017

A middle-aged man with decompensated cirrhosis and a dimorphic multisite skin rash is diagnosed with rare atypical herpes simplex infection, manifesting Sweet’s syndrome (SS) in the absence of other described associations. SS, an acute febrile neutrophilic dermatosis, has three common forms—classical or idiopathic, malignancy associated and drug induced. Systemic autoimmune, connective tissue diseases and infections are also strong associations. The latter is commonly described in Gram-positive bacteria, salmonellosis andYersinia. Herpes infections are a rare cause of SS, reported only thrice in literature, one with concomitant lupus, the second with associated mycobacterial infection and third, in metastatic breast disease in contrast to our patient. Atypical rash, especially if dimorphic, warrants histopathological evaluation to confirm underlying disease.
Renal cell carcinoma metastases to the maxillary sinus
Authors: Wong Eugene Hung Chih , Tetter Nora , Glatz Katharina , Brand Yves
Published: October 2017

Metastasis of renal cell carcinoma (RCC) to the head and neck region is rare. We report the case of a 65-year-old man with history of RCC, presented 7 years after nephrectomy, adrenalectomy and lung metastasectomy for his primary tumour, with symptoms of nasal obstruction, postnasal drip, productive cough and pressure sensation in the left maxillary sinus. CT revealed a unilateral, irregular opacification in the left maxillary sinus with bony erosion of the infraorbital canal wall. A yellow cystic lesion was completely removed from the maxillary sinus during functional endoscopic sinus surgery and histopathological analysis confirmed the diagnosis of a metastatic RCC. Patient continued to be managed with his pre-existing treatment for advanced RCC.
Improving a process to obtain hepatitis B serology among patients treated with infliximab at a large urban children’s hospital
Authors: Jean M Raphaelle , Weaver Ann , Mastin-Diebold Teresa , Kissinger Krista , Smitherman Emily A , Favier Leslie , Danziger-Isakov Lara , Williams Elizabeth , Brady Rebecca C , Huggins Jennifer , Denson Lee A , Saeed Shehzad A , Morgan Pamela , Dykes Dana Michelle Hines
Published: October 2017

Background

Hepatitis B infection is a significant public health challenge despite improvements in vaccination efforts. Patients such as those on chronic immunosuppressive therapy for inflammatory bowel disease (IBD) or rheumatic disease may incur greater risk. The risk of reactivation of hepatitis B while on immunosuppressive therapy may have mortality rates up to 25%. These patients should be screened for acute or chronic infection and vaccinated if necessary. Our aim was to reliably complete hepatitis B screenings in patients receiving infliximab at Cincinnati Children’s Hospital Medical Center (CCHMC).

Methods

Eligible patients included all patients with gastroenterology (GI) IBD and rheumatology receiving infliximab between October 2015 and March 2016. Using quality improvement methodology and the ‘plan–do–study–act’ (PDSA) approach, interventions centred around education of clinical providers, previsit planning and the development of ‘talking points’ for patients.

Results

An initial screen of the IBD population revealed that 48% of the IBD patient population had been screened for anti-HBs alone, but no patients from GI or rheumatology divisions had a complete set of hepatitis B serology prior to the intervention including anti-Hep B Core and Hep B Surface Antigen. Seven PDSA cycles were performed during the 32-week intervention period, resulting in an increase in patients screened from 0% to ~85%. By March 2016, a total of 251 patients (201 GI, 50 rheumatology) had up-to-date hepatitis B serology screening. Automated ordering of the hepatitis B serology and ‘talking points’ for the provider had the greatest impact on successful screening.

Conclusions

We developed a method to obtain hepatitis B serology on at-risk patients on infliximab within two subspecialty divisions within a large children’s hospital. Next steps will be to develop a process to reliably provide vaccines for patients who are seronegative, expand this process to all patients who are identified as immunocompromised within GI and rheumatology and then expand this process to other divisions at the CCHMC.
Profile of pig farms combining high performance and low antimicrobial usage within four European countries
Authors: Collineau Lucie , Backhans Annette , Dewulf Jeroen , Emanuelson Ulf , grosse Beilage Elisabeth , Lehébel Anne , Loesken Svenja , Okholm Nielsen Elisabeth , Postma Merel , Sjölund Marie , Stärk Katharina D C , Belloc Catherine
Published: October 2017

Pig farmers are strongly encouraged to reduce their antimicrobial usage because of the rising threat from antimicrobial resistance. However, such efforts should not compromise the herd health status and performance. This study aimed to describe the profile of so‐called ‘top‐farms’ that managed to combine both high technical performance and low antimicrobial usage. A cross‐sectional study was conducted among 227 farrow‐to‐finish farms in Belgium, France, Germany and Sweden. Among them, 44 farms were allocated to the top‐farms group and were compared with the ’regular’ farms group in terms of farm characteristics, biosecurity and health status. Top‐farms had fewer gastrointestinal symptoms in suckling pigs and fewer respiratory symptoms in fatteners, which could partly explain their reduced need for antimicrobials and higher performance. They also had higher biosecurity and were located in sparsely populated pig areas. However, 14 farms of the top‐farms group were located in densely populated pig areas, but still managed to have low usage and high technical performance; they had higher internal biosecurity and more extensive vaccination against respiratory pathogens. These results illustrate that it is possible to control infectious diseases using other approaches than high antimicrobial usage, even in farms with challenging environmental and health conditions.
Quantitative analysis of antibiotic usage in British sheep flocks
Authors: Davies Peers , Remnant John G , Green Martin J , Gascoigne Emily , Gibbon Nick , Hyde Robert , Porteous Jack R , Schubert Kiera , Lovatt Fiona , Corbishley Alexander
Published: October 2017

The aim of this study was to examine the variation in antibiotic usage between 207 commercial sheep flocks using their veterinary practice prescribing records. Mean and median prescribed mass per population corrected unit (mg/PCU) was 11.38 and 5.95, respectively and closely correlated with animal defined daily dose (ADDD) 1.47 (mean), 0.74 (median) (R2=0.84, P<0.001). This is low in comparison with the suggested target (an average across all the UK livestock sectors) of 50 mg/PCU. In total, 80 per cent of all antibiotic usage occurred in the 39 per cent of flocks where per animal usage was greater than 9.0 mg/PCU. Parenteral antibiotics, principally oxytetracycline, represented 82 per cent of the total prescribed mass, 65.5 per cent of antibiotics (mg/PCU) were prescribed for the treatment of lameness. Oral antibiotics were prescribed to 49 per cent of flocks, 64 per cent of predicted lamb crop/farm. Lowland flocks were prescribed significantly more antibiotics than hill flocks. Variance partitioning apportioned 79 per cent of variation in total antibiotic usage (mg/PCU) to the farm level and 21 per cent to the veterinary practice indicating that veterinary practices have a substantial impact on overall antimicrobial usage. Reducing antibiotic usage in the sheep sector should be possible with better understanding of the drivers of high usage in individual flocks and of veterinary prescribing practices.
Static Characteristics of a New Three-Dimensional Linear Homeomorphic Saccade Model
Authors: Zhou Wei , Zhai Xiu , Ghahari Alireza , Korentis G. Alex , Kaputa David , Enderle John D.
Published: October 2017

A linear homeomorphic saccade model that produces 3D saccadic eye movements consistent with physiological and anatomical evidence is introduced. Central to the model is the implementation of a time-optimal controller with six linear muscles and pulleys that represent the saccade oculomotor plant. Each muscle is modeled as a parallel combination of viscosity [Formula: see text] and series elasticity [Formula: see text] connected to the parallel combination of active-state tension generator [Formula: see text], viscosity element [Formula: see text], and length tension elastic element [Formula: see text]. Additionally, passive tissues involving the eyeball include a viscosity element [Formula: see text], elastic element [Formula: see text], and moment of inertia [Formula: see text]. The neural input for each muscle is separately maintained, whereas the effective pulling direction is modulated by its respective mid-orbital constraint from the pulleys. Initial parameter values for the oculomotor plant are based on anatomical and physiological evidence. The oculomotor plant uses a time-optimal, 2D commutative neural controller, together with the pulley system that actively functions to implement Listing’s law during both static and dynamic conditions. In a companion paper, the dynamic characteristics of the saccade model is analyzed using a time domain system identification technique to estimate the final parameter values and neural inputs from saccade data. An excellent match between the model estimates and the data is observed, whereby a total of 20 horizontal, 5 vertical, and 64 oblique saccades are analyzed.
The evolution of pairing correlation in the anisotropic triangular lattice
Authors: Wang Jingyao , Zeng Yamei , Wang Peng , Liang Ying , Ma Tianxing
Published: October 2017

By using the determined quantum Monte Carlo method, we explore the evolution of the pairing correlation depending on doping and frustration in the two-dimensional Hubbard model on an anisotropic triangular lattice. In the full frustrated system where the nearest hoping term [Formula: see text] is equal to the next nearest hoping [Formula: see text], the [Formula: see text]-wave pairing dominates over [Formula: see text] as the electron filling [Formula: see text]. The [Formula: see text] superconducting pairing tends to be dominated as the frustration [Formula: see text] decreases, and the decreasing electron fillings also push the system into a possible [Formula: see text] superconducting state. Our intensive nonbiased numerical results reveal the competition between [Formula: see text] and [Formula: see text] superconducting pairing states, clarifying the different pairing symmetries in the [Formula: see text]-(BEDT-TTF)[Formula: see text] family of organic charge transfer salts.
Chiral tensor particles in the early Universe — Present status
Authors: Kirilova D. P. , Chizhov V. M.
Published: October 2017

In this work, an update of the cosmological role and place of the chiral tensor particles in the Universe history is provided. We discuss an extended model with chiral tensor particles. The influence of these particles on the early Universe evolution is studied. Namely, the increase of the Universe expansion rate caused by the additional particles in this extended model is calculated, their characteristic interactions with the particles of the hot Universe plasma are studied and the corresponding times of their creation, scattering, annihilation and decay are estimated for accepted values of their masses and couplings, based on the recent experimental constraints. The period of abundant presence of these particles in the Universe evolution is determined.
Holographic superconductors in Einstein-æther gravity
Authors: Lin Kai , Wu Yumei
Published: October 2017

In this paper, we apply Anti-de Sitter (AdS) black hole solution of the Einstein-æther theory to the study of the holographic superconductor and show that the AdS black hole solution can be rewritten in some very simple forms, from which it is easy to identify the locations of various killing horizons. Then, we investigate the different effects of these horizons on the holographic superconductor.
Uniform regularity for the free surface compressible Navier–Stokes equations with or without surface tension
Authors: Mei Yu , Wang Yong , Xin Zhouping
Published: October 2017

In this paper, we investigate the uniform regularity of solutions to the three-dimensional isentropic compressible Navier–Stokes system with free surfaces and study the corresponding asymptotic limits of such solutions to that of the compressible Euler system for vanishing viscosity and surface tension. It is shown that there exists a unique strong solution to the free boundary problem for the compressible Navier–Stokes system in a finite time interval which is independent of the viscosity and the surface tension. The solution is uniformly bounded both in [Formula: see text] and a conormal Sobolev space. It is also shown that the boundary layer for the density is weaker than the one for the velocity field. Based on such uniform estimates, the asymptotic limits, to the free boundary problem for the ideal compressible Euler system with or without surface tension as both the viscosity and the surface tension tend to zero, are established by a strong convergence argument.
Structural properties of short glucagon-like peptide-1 in various solvents investigated by molecular dynamics simulations
Authors: Cao Hong-Yu , Guo Wei , Yu Ya-Xian , Wang Hong-Lei , Tang Qian , Li Shen-Min , Zheng Xue-Fang
Published: October 2017

It has been reported that short glucagon-like peptide-1 (sGLP-1), one of glucagon-like peptide 1 (GLP-1) analogues, has the same effect in treating type 2 diabetes mellitus (T2DM) as GLP-1 with increased half-life in human body. Although the high-resolution structure of complex of GLP-1 and its receptor has been achieved, the relationship between the structure of GLP-1 before recognition and its final function is still not clear. As for sGLP-1, few studies attempt to investigate the influences of different conditions on its structure. In present paper, molecular dynamics simulations were applied to explore molecular details of sGLP-1 under various environments. The results demonstrated that in low pH value solvent, the additional helical residue of Pro6 and the flexible N-terminal cannot keep [Formula: see text] helix biological conformation. At pH 3, the structure has undergone significant changes, resulting in the shortest helical length. Further studies showed that protonation states of Glu21 mainly determined the secondary structure of sGLP-1 when pH values increased from 3 to 7. Interestingly, with ions concentration varying from 0.18% to 0.72%, the fluctuating trend of backbone RMSDs is consistent with that of [Formula: see text] helix structure of sGLP-1. The structure of sGLP-1 had less helix content and became more flexible when temperatures increased in the range from 305[Formula: see text]K to 320[Formula: see text]K. Meanwhile, in mixtures of water and 2,2,2-trifluoroethanol (TFE) sGLP-1 showed a rigid structure with an additional helical residue (Pro6) at the N-terminal of original helix content.
Liquid Biopsies Using Plasma Exosomal Nucleic Acids and Plasma Cell-Free DNA Compared with Clinical Outcomes of Patients with Advanced Cancers
Authors: Möhrmann Lino , Huang Helen J. , Hong David S. , Tsimberidou Apostolia M. , Fu Siqing , Piha-Paul Sarina A. , Subbiah Vivek , Karp Daniel D. , Naing Aung , Krug Anne , Enderle Daniel , Priewasser Tina , Noerholm Mikkel , Eitan Erez , Coticchia Christine , Stoll Georg , Jordan Lisa-Marie , Eng Cathy , Kopetz E. Scott , Skog Johan , Meric-Bernstam Funda , Janku Filip
Published: October 2017

Purpose: Blood-based liquid biopsies offer easy access to genomic material for molecular diagnostics in cancer. Commonly used cell-free DNA (cfDNA) originates from dying cells. Exosomal nucleic acids (exoNAs) originate from living cells, which can better reflect underlying cancer biology.

Experimental Design: Next-generation sequencing (NGS) was used to test exoNA, and droplet digital PCR (ddPCR) and BEAMing PCR were used to test cfDNA for BRAFV600, KRASG12/G13, and EGFRexon19del/L858R mutations in 43 patients with progressing advanced cancers. Results were compared with clinical testing of archival tumor tissue and clinical outcomes.

Results: Forty-one patients had BRAF, KRAS, or EGFR mutations in tumor tissue. These mutations were detected by NGS in 95% of plasma exoNA samples, by ddPCR in 92% of cfDNA samples, and by BEAMing in 97% cfDNA samples. NGS of exoNA did not detect any mutations not present in tumor, whereas ddPCR and BEAMing detected one and two such mutations, respectively. Compared with patients with high exoNA mutation allelic frequency (MAF), patients with low MAF had longer median survival (11.8 vs. 5.9 months; P = 0.006) and time to treatment failure (7.4 vs. 2.3 months; P = 0.009). A low amount of exoNA was associated with partial response and stable disease ≥6 months (P = 0.006).

Conclusions: NGS of plasma exoNA for common BRAF, KRAS, and EGFR mutations has high sensitivity compared with clinical testing of archival tumor and testing of plasma cfDNA. Low exoNA MAF is an independent prognostic factor for longer survival. Clin Cancer Res; 24(1); 181–8. ©2017 AACR.