bluuebunny/crossref_metadata_2025 huggingface dataset:
Draft Genome Sequences of Four Propionibacterium acnes Strains Isolated from Implant-Related Infections
Authors: Aubin Guillaume Ghislain , Kambarev Stanimir , Guillouzouic Aurélie , Lepelletier Didier , Bémer Pascale , Corvec Stéphane
Published: January 2017

Propionibacterium acnes
was previously described as a potential implant-related pathogen. Here, we report the draft genome sequence of four
P. acnes
strains, isolated from spine material, hip arthroplasty, and knee arthroplasty infections in France belonging to different sequence types (ST18, ST27, and ST36).
Draft Genome Sequence of Cloacibacterium normanense NRS-1 Isolated from Municipal Wastewater
Authors: Gay Nicole R. , Fleming Elizabeth , Oh Julia
Published: January 2017

Cloacibacterium normanense
is a Gram-negative bacterium recovered from untreated human wastewater. Given its high abundance in wastewater and its apparent absence in human stool, it may contribute to biological phosphate removal. Here, we perform a whole-genome sequence of
C. normanense
NRS-1(T) and examine particular features of this draft genome.
Draft Genome Sequence of Streptococcus anginosus BVI, a New Vaginal Pathogen Candidate
Authors: Zuñiga-Bahamon Andres , Tobar-Tosse Fabian , Guillermo-Ortega Jose , Wibberg Daniel , Tauch Andreas
Published: January 2017

Streptococcus anginosus
is a pathogen implicated in urogenital and gastroinstestinal tract infections. Here, we report the draft genome sequence of
S. anginosus
BVI, isolated from a bacterial vaginosis patient attending a prenatal care unit in Cali, Colombia. The genome sequence of BVI consists of 2,014,025 bp, encoding 2,008 predicted proteins.
Complete Genome Sequence of Trueperella pyogenes, Isolated from Infected Farmland Goats
Authors: Zhang Su-hui , Qiu Jin-jie , Yang Rui , Shen Ke-fei , Xu Guo-yang , Fu Li-zhi
Published: January 2017

Trueperella pyogenes
is a significant pathogen of livestock, causing diverse diseases, such as mastitis, liver abscessation, and pneumonia. In this study, we have reported the genome sequence of
Trueperella pyogenes
2012CQ-ZSH. Moreover, several genes coding for virulence factors were found, such as pyolysin (PYO),
nanH
,
nanP
,
cbpA
,
fimC
, and
fimE
.
The Aspergillus fumigatus Damage Resistance Protein Family Coordinately Regulates Ergosterol Biosynthesis and Azole Susceptibility
Authors: Song Jinxing , Zhai Pengfei , Zhang Yuanwei , Zhang Caiyun , Sang Hong , Han Guanzhu , Keller Nancy P. , Lu Ling
Published: January 2017

Ergosterol is a major and specific component of the fungal plasma membrane, and thus, the cytochrome P450 enzymes (Erg proteins) that catalyze ergosterol synthesis have been selected as valuable targets of azole antifungals. However, the opportunistic pathogen
Aspergillus fumigatus
has developed worldwide resistance to azoles largely through mutations in the cytochrome P450 enzyme Cyp51 (Erg11). In this study, we demonstrate that a cytochrome
b
5
-like heme-binding damage resistance protein (Dap) family, comprised of DapA, DapB, and DapC, coordinately regulates the functionality of cytochrome P450 enzymes Erg5 and Erg11 and oppositely affects susceptibility to azoles. The expression of all three genes is induced in an azole concentration-dependent way, and the decreased susceptibility to azoles requires DapA stabilization of cytochrome P450 protein activity. In contrast, overexpression of DapB and DapC causes dysfunction of Erg5 and Erg11, resulting in abnormal accumulation of sterol intermediates and further accentuating the sensitivity of Δ
dapA
strains to azoles. The results of exogenous-hemin rescue and heme-binding-site mutagenesis experiments demonstrate that the heme binding of DapA contributes the decreased azole susceptibility, while DapB and -C are capable of reducing the activities of Erg5 and Erg11 through depletion of heme.
In vivo
data demonstrate that inactivated DapA combined with activated DapB yields an
A. fumigatus
mutant that is easily treatable with azoles in an immunocompromised mouse model of invasive pulmonary aspergillosis. Compared to the single Dap proteins found in
Saccharomyces cerevisiae
and
Schizosaccharomyces pombe
, we suggest that this complex Dap family regulatory system emerged during the evolution of fungi as an adaptive means to regulate ergosterol synthesis in response to environmental stimuli.

IMPORTANCE
Knowledge of the ergosterol biosynthesis route in fungal pathogens is useful in the design of new antifungal drugs and could aid in the study of antifungal-drug resistance mechanisms. In this study, we demonstrate that three cytochrome
b
5
-like Dap proteins coordinately regulate the azole resistance and ergosterol biosynthesis catalyzed by cytochrome P450 proteins. Our new insights into the Dap regulatory system in fungal pathogens may have broad therapeutic ramifications beyond their usefulness for classic azole antifungals. Moreover, our elucidation of the molecular mechanism of Dap regulation of cytochrome P450 protein functionality through heme-binding activity may extend beyond the Kingdom Fungi with applicability toward Dap protein regulation of mammalian sterol synthesis.
Improving ward environments and developing skills for discharge with the implementation of self-catering on a low secure forensic unit.
Authors: O'Reilly Alison
Published: January 2017

The opportunities for service users to develop skills for more independent living and take control of their environments are limited in secure mental health units. This paper will outline a quality improvement project that changed how the catering services were delivered in a low secure unit in East London NHS Foundation Trust (ELFT). A Quality Improvement methodology was adopted incorporating the Plan, Do, Study, Act (PDSA) cycle which included the trial of service users preparing their own meals on a daily basis. The participation rates were measured and functional daily living skills were recorded. Following success of the trial, long-term implementation of self-catering was agreed, with service users being supported to prepare a shared evening meal every day on the ward with an average of 60% participation. Functional living skills indicated an improvement in the area of process skills. The project aligned with ELFT's aims of service users working in collaboration with staff to implement changes in service delivery.
Quality improvement: The delivery of true early mobilisation in an intensive care unit
Authors: van Willigen Zoe , Collings Nikki , Richardson Dominic , Cusack Rebecca
Published: January 2017

Early mobilisation initiatives within the critical care environment have been shown to improve outcomes for patients. Early mobilisation has been defined as occurring within the first two to five days of the intensive care stay, but in practice this can be difficult to deliver.

We conducted a quality improvement (QI) project to deliver early mobilisation in a large general intensive care unit. Mechanically ventilated medical patients received an integrated package of care involving two additional daily sessions of mobility therapy, in combination with minimal sedation where possible.

Prospective baseline data was collected from January to March 2012; the QI project commenced in April 2012. Improvement cycle 1 completed in March 2015 and improvement cycle 2 in March 2016. Results have suggested a reduction in time to first mobilisation for intensive care survivors from 16.3 days in 2012, to 4.3 days at the end of improvement cycle 2. This was associated with a decrease in mean intensive care length of stay from 20.8 days in 2012, to 11.2 days at the end of improvement cycle 2.

This QI project enabled patients to mobilise out of bed within the first five days of their intensive care stay and to be discharged earlier from the ICU, on going analysis is required to verify these findings.
Improving timeliness for acute asthma care for paediatric ED patients using a nurse driven intervention: an interrupted time series analysis
Authors: Brown Kathleen , Iqbal Sabah , Sun Su-Lin , Fritzeen Jennifer , Chamberlain James , C. Mullan Paul
Published: January 2017

Asthma is the most common chronic paediatric disease treated in the emergency department (ED). Rapid corticosteroid administration is associated with improved outcomes, but our busy ED setting has made it challenging to achieve this goal. Our primary aim was to decrease the time to corticosteroid administration in a large, academic paediatric ED. We conducted an interrupted time series analysis for moderate to severe asthma exacerbations of one to 18 year old patients. A multidisciplinary team designed the intervention of a bedside nurse initiated administration of oral dexamethasone, to replace the prior system of a physician initiated order for oral prednisone. Our baseline and intervention periods were 12 month intervals. Our primary process measure was the time to corticosteroid administration. Other process measures included ED length of stay, admission rate, and rate of emesis. The balance measures included rate of return visits to the ED or clinic within five days, as well as the proportion of discharged patients who were admitted within five days. No special cause variation occurred in the baseline period. The mean time to corticosteroid administration decreased significantly, from 98 minutes in the baseline period to 59 minutes in the intervention period (p < 0.01), and showed special cause variation improvement within two months after the intervention using statistical process control methodology. We sustained the improvement and demonstrated a stable process. The intervention period had a significantly lower admission rate (p<0.01) and emesis rate (p<0.01), with no unforeseen harm to patients found with any of our balance measures. In summary, the introduction of a nurse initiated, standardized protocol for corticosteroid therapy for asthma exacerbations in a paediatric ED was associated with decreased time to corticosteroid administration, admission rates, and post-corticosteroid emesis.
Minority stress factors as mediators of sexual orientation disparities in mental health treatment: a longitudinal population-based study
Authors: Bränström Richard
Published: January 2017

Background

Substantial mental health disparities between lesbian, gay and bisexual (LGB) individuals compared with heterosexuals have been identified. The aim was to examine potential sexual orientation-based disparities in mental health treatment in a prospectively analysed population-based sample in Sweden and to explore potential moderators and mediators.

Method

30 730 individuals from the Stockholm Public Health Cohort were followed up with questionnaires and registry-based health record data on psychiatric healthcare visits and prescription drug use between 1 January 2011 and 31 December 2011.

Results

In adjusted analyses, gay and lesbian individuals were more likely to receive treatment for anxiety disorders (adjusted ORs (AOR)=3.80; 95% CI 2.54 to 5.69) and to use antidepressant medication (AOR=2.13; 95% CI 1.62 to 2.79); and bisexuals were more likely to receive treatment for mood disorders (AOR=1.58; 95% CI 1.00 to 2.48), anxiety disorders (AOR=3.23; 95% CI 2.22 to 4.72) and substance use disorders (AOR=1.91; 95% CI 1.12 to 3.25), and to use antidepressant medication (AOR=1.91; 95% CI 1.12 to 3.25) when compared with heterosexuals. The largest mental health treatment disparities based on sexual orientation were found among bisexual women, gay men and younger lesbian women. More frequent experiences of victimisation/threat of violence and lack of social support could partially explain these disparities.

Conclusions

This study shows a substantially elevated risk of poor mental health among LGB individuals as compared with heterosexuals. Findings support several factors outlined in the minority stress theory in explaining the mechanisms behind these disparities.
Vitamin D status is not related to insulin resistance in different phenotypes of moderate obesity
Authors: Al Masri Manal , Romain Ahmed Jerome , Boegner Catherine , Maimoun Laurent , Mariano-Goulart Denis , Attalin Vincent , Leprieur Elodie , Picandet Marion , Avignon Antoine , Sultan Ariane
Published: January 2017

Low plasma 25-hydroxy-vitamin D (25OHD) and high levels of parathyroid hormone (PTH) are associated with obesity and could play a role in the occurrence of complications such as insulin resistance. The objective of the study was to evaluate whether the relationship between 25OHD status and phosphocalcic parameters differs between metabolically healthy obese (MHO) and insulin-resistant obese (IRO). This cross-sectional study included 158 consecutive adults (121 females) with obesity (body mass index (BMI) 35.15 ± 2.8 kg/m2), aged 43.21 ± 13.6 years. Serum 25OHD, calcemia, phosphatemia, PTH, plasma lipids, fasting plasma glucose, insulin levels, and body composition were measured. Participants were classified as MHO (n = 65) or IRO (n = 93) based on homeostatic model assessment insulin-resistance value. IRO patients had a higher BMI (p = 0.001), waist circumference (p = 0.03), and trunk fat mass (p = 0.007) than MHO patients. Mean HbA1c (p = 0.03), triglycerides (p = 0.02), and hsCRP (p = 0.04) plasmatic levels were increased in the IRO group. No between-group difference was found on 25OHD, PTH, calcium, or phosphorus plasmatic levels. Only age-predicted 25OHD levels were identified among IRO participants, whereas no factors were identified in MHO. No predictive factors of PTH plasmatic level were identified in the IRO and MHO groups. Although MHO and IRO patients have different metabolic profiles, we did not detect any difference regarding either 25OHD or PTH. Insulin resistance was not a predictive factor of vitamin D status. Our results confirm the absence of link between vitamin D status and insulin resistance in moderate obesity.
Long-term effects of daily postprandial physical activity on blood glucose: a randomized controlled trial
Authors: Nygaard Håvard , Grindaker Eirik , Rønnestad Bent Ronny , Holmboe-Ottesen Gerd , Høstmark Arne Torbjørn
Published: January 2017

Previous studies have shown that a bout of moderate or light postprandial physical activity effectively blunts the postprandial increase in blood glucose. The objective of this study was to test whether regular light postprandial physical activity can improve glycemia in persons with hyperglycemia or with a high risk of hyperglycemia. We randomized 56 participants to an intervention or a control group. They were diagnosed as hyperglycemic, not using antidiabetics, or were categorized as high-risk individuals for type 2 diabetes. The intervention group was instructed to undertake a minimum 30 min of daily light physical activity, starting a maximum of 30 min after a meal in addition to their usual physical activity for 12 weeks. The control group maintained their usual lifestyle. Blood samples were taken pre- and post-test. Forty participants completed the study and are included in the results. The self-reported increase in daily physical activity from before to within the study period was higher in the intervention group compared with control (41 ± 25 vs. 2 ± 16 min, p < 0.001). Activity diaries and accelerometer recordings supported this observation. The activity in the intervention group started earlier after the last meal compared with control (30 ± 13 vs. 100 ± 57 min, p = 0.001). There were no within- or between-group differences in any glycemic variable from pre- to post-test. In conclusion, the present study does not seem to support the notion that regular light postprandial physical activity improves blood glucose in the long term in persons with hyperglycemia or with high risk of hyperglycemia.
Does avian gut passage favour seed germination of woody species of the Chaco Serrano Woodland in Argentina?
Authors: Díaz Vélez María Celeste , Ferreras Ana Elisa , Silva Wesley Rodrigues , Galetto Leonardo
Published: January 2017

Frugivorous birds are key dispersal agents of many plant species and also may facilitate seed germination after gut passage. However, the general effects of gut passage on seed germination are still not clear, with positive, negative, and neutral effects reported on seed germination. We evaluated seed germination of seven bird-dispersed plant species of the Chaco Serrano Woodland in Córdoba, Argentina: Celtis ehrenbergiana (Klotzsch) Liebm., Condalia spp. Cav., Lantana camara L., Lithraea molleoides (Vell.) Engl., Lycium cestroides Schltdl., Schinus fasciculatus (Griseb.) I.M. Johnst., and Zanthoxylum coco Gillies. We compared germination percentages and germination speed among seeds ingested by birds, manually extracted seeds, and seeds from intact fruits to understand which mechanisms are acting on bird gut-passed seeds. For six plant species, the action of frugivorous birds increased seed germination percentages and germination speed, through scarification, deinhibition, or combined mechanisms. Our results contribute to a better understanding of the mechanisms acting on seeds passed through bird gut. Also, we show the pivotal role that frugivorous birds exert on the seed germination of native woody plant species in the threatened ecosystem of the Chaco Serrano Woodland.
Different soil moisture control of net methane oxidation and production in organic upland and wet forest soils of the Pacific coastal rainforest in Canada
Authors: Christiansen Jesper Riis , Levy-Booth David , Prescott Cindy E. , Grayston Sue J.
Published: January 2017

In a changing climate, understanding how soil hydrology impacts greenhouse gas dynamics will be important for the future management of the soils in the forests on the Canadian Pacific west coast. In a laboratory study, the impact of soil hydrology on potential net methane (CH4) exchange rates and the abundance of methanotrophs (CH4oxidation) and methanogens (CH4production) in upland and water-saturated wet soils were investigated. CH4oxidation and production rates were highest in the wet soils, which corresponded to higher numbers of methanotrophs and methanogens, indicating a link between the microbial abundance and CH4exchange rates. Also, CH4production was induced in the upland soils, indicating the presence of methanogens. The optimum soil moisture content for CH4oxidation was highest in upland soils and the wet soils sustained higher CH4oxidation rates over a broader range of soil moisture. These results underline the importance of the soil hydrological controls of CH4oxidation in contrasting soils and forest types, which deserves further attention in field-based studies.
Design and Fabrication of Terahertz Detectors Based on 180-nm CMOS Process Technology
Authors: Wakita Kosuke , Sano Eiichi , Ikebe Masayuki , Arnold Stevanus , Otsuji Taiichi , Takida Yuma , Minamide Hiroaki
Published: January 2017

A CMOS cascode amplifier, biased near the threshold voltage of a MOSFET, for terahertz direct detection is proposed. A CMOS terahertz imaging circuit (size: 250 × 180 ìm) is designed and fabricated on the basis of low-cost 180-nm CMOS process technology. The imaging circuit consists of a microstrip patch antenna, an impedance-matching circuit, and a direct detector. It achieves a responsivity of 51.9 kV/W at 0.915 THz and a noise equivalent power (NEP) of 358 pW/Hz1/2 at a modulation frequency of 31 Hz. NEP is estimated to be reduced to 42 pW/Hz1/2 at 100 kHz. These results suggest that cost-efficient terahertz imaging is possible in the near future.
THz Spectroscopic Imaging of Chemicals Using IS-TPG
Authors: Murate Kosuke , Kato Mikiya , Kawase Kodo
Published: January 2017

In 2003, we demonstrated a non-destructive terahertz spectroscopic imaging of illicit drugs hidden in envelopes using a widely tunable THz-wave parametric source, though its dynamic range at that time was less than four orders. Recently, we have realized more than nine orders of dynamic range with an evolved injection seeded THz-wave spectrometer. Now we can detect drugs under much thicker obstacles than before. In this report, we introduce the result of THz spectroscopic imaging of chemicals under thick envelopes and related topics; Enhanced tuning range of is-TPG up to 5 THz and >90 dB dynamic range THz spectroscopic system.
Plasmonic Enhancement of Terahertz Devices Efficiency
Authors: Mitin Vladimir , Ryzhii Victor , Ryzhii Maxim , Satou Akira , Otsuji Taiichi , Shur Michael S.
Published: January 2017

This paper reviews the plasmonic effects in graphene THz photodetectors (PD) and light emitters (LE). It is demonstrated that the devices based on double graphene-layer (DGL) or multiple graphene-layer structures with the graphene layers separated by thin tunnel barrier layers have advantages over the single graphene-layer (SGL) devices. In DGLs, this advantage is due to the photon-assisted resonant tunneling when the band offset of the graphene layers is aligned to the THz photon energy. The resonant emission or absorption of the THz radiation is enhanced by the cooperative resonant excitation of the graphene plasmons leading to an extremely high gain and/or responsivity in the graphene THz device structures.
Improved Performance of Ultrahigh-Sensitive Charge-Sensitive Infrared Phototransistors (CSIP)
Authors: Kim Sunmi , Komiyama Susumu , Matsuda Shinpei , Patrashin Mikhail , Kajihara Yusuke
Published: January 2017

Charge-sensitive infrared phototransistor (CSIP) is a highly sensitive semiconductor terahertz (THz) detector with single-photon sensitivity. Due to the excitation mechanism via intersubband transition in a quantum well, the CSIP requires careful design of the photo-coupler and proper light illumination method to achieve high quantum efficiency. We have improved the quantum efficiency by introducing the radiation from the backside of the CSIP substrate, which leads to efficient surface plasmon excitation in the photo-coupler.
Intensive Terahertz Radiation from InXGa1-XAs due to Photo-Dember Effect
Authors: Ponomarev Dmitry S. , Khabibullin Rustam A. , Yachmenev Aleksandr E. , Maltsev Petr P. , Ilyakov Igor E. , Shiskin Boris V. , Akhmedzhanov Rinat A.
Published: January 2017

We have proposed and investigated InyGa1-yAs photoconductor grown by molecular-beam epitaxy on low-temperature step-graded metamorphic buffer. It exhibits superior bandwidth up to 6 THz and provides optical-to-terahertz conversion efficiency up to ~ 10−5 for rather low optical fluence ~ 40 μJ/cm2. The intensity of THz generation for the given structure is two orders higher than for lowtemperature grown GaAs due substantial contribution of photo-Dember effect.
Numerical Characterization of Dyakonov-Shur Instability in Gated Two-Dimensional Electron Systems
Authors: Satou Akira , Narahara Koichi
Published: January 2017

We numerically analyze the system based on the essentially non-oscillatory shock capturing scheme in order to characterize the Dyakonov-Shur (DS) instability in a gated two-dimensional electron gas system (2DES). The predictions of the linearized model are examined for a 2DES sandwiched by the top and back metallic gates. By solving Poisson equation self-consistently, the dispersive properties of plasma wave are properly estimated. Special attention is paid to the impact of dispersion to nonlinear dynamics of plasma-wave oscillation. A single-gated 2DES is also investigated for demonstrating the DS instability in practical devices.
Global Optimization of Fixed-Priority Real-Time Systems by RTOS-Aware Control-Flow Analysis
Authors: Dietrich Christian , Hoffmann Martin , Lohmann Daniel
Published: January 2017

Cyber--physical systems typically target a dedicated purpose; their embedded real-time control system, such as an automotive control unit, is designed with a well-defined set of functionalities. On the software side, this results in a large amount of implicit and explicit static knowledge about the system and its behavior already at compile time. Compilers have become increasingly better at extracting and exploiting such static knowledge. For instance, many optimizations have been lifted up to the interprocedural or even to the whole-program level. However, whole-program optimizations generally stop at the application--kernel boundary: control-flow transitions between different threads are not yet analyzed.

In this article, we cross the application--kernel boundary by combining the semantics of a real-time operating system (RTOS) with deterministic fixed-priority scheduling (e.g., OSEK/AUTOSAR, ARINC 653, μITRON, POSIX.4) and the explicit application knowledge to enable system-wide, flow-sensitive compiler optimizations. We present two methods to extract a cross-kernel, control-flow--graph that provides a global view on all possible execution paths of a real-time system. Having this knowledge at hand, we tailor the operating system kernel more closely to the particular application scenario. For the example of a real-world safety-critical control system, we present three possible use cases. (1) Runtime optimizations, by means of specialized system calls for each call site, allow one speed up the kernel execution path by 28% in our benchmark scenario. Furthermore, we target transient hardware fault tolerance with two automated software-based countermeasures: (2) generation of OS state assertions on the expected system behavior, and (3) a system-wide dominator-region based control-flow error detection, both of which leverage significant robustness improvements.
Protecting Mobile Health Records in Cloud Computing
Authors: Liu Jianghua , Ma Jinhua , Wu Wei , Chen Xiaofeng , Huang Xinyi , Xu Li
Published: January 2017

Electronic healthcare (eHealth) systems have replaced traditional paper-based medical systems due to attractive features such as universal accessibility, high accuracy, and low cost. As a major constituent part of eHealth systems, mobile healthcare (mHealth) applies Mobile Internet Devices (MIDs) and Embedded Devices (EDs), such as tablets, smartphones, and other devices embedded in the bodies of individuals, to improve the quality of life and provide more convenient healthcare services for patients. Unfortunately, MIDs and EDs have only limited computational capacity, storage space, and power supply. By taking this into account, we present a new design to guarantee the integrity of eHealth records and the anonymity of the data owner in a more efficient and flexible way. The essence of our design is a general method which can convert any secure Attribute-Based Signature (ABS) scheme into a highly efficient and secure Online/Offline Attribute-Based Signature (OOABS) scheme. We prove the security and analyze the efficiency improvement of the new design. Additionally, we illustrate the proposed generic construction by applying it to a specific ABS scheme.
Improving Archaeologists’ Online Archive Experiences Through User-Centred Design
Authors: Power Christopher , Lewis Andrew , Petrie Helen , Green Katie , Richards Julian , Eramian Mark , Chan Brittany , Walia Ekta , Sijaranamual Isaac , Rijke Maarten De
Published: January 2017

Traditionally, the preservation of archaeological data has been limited by the cost of materials and the physical space required to store them, but for the last 20 years, increasing amounts of digital data have been generated and stored online. New techniques in digital photography and document scanning have dramatically increased the amount of data that can be retained in digital format, while at the same time reducing the physical cost of production and storage. Vast numbers of hand written notes, grey literature documents, images of assemblages, contexts, and artefacts have been made available online. However, accessing these repositories is not always straightforward. Superficial interaction design, sparsely populated metadata, and heterogeneous schemas may prevent users from working the data that they need within archaeological archives.

In this article, we present the work of the Digging into Archaeological Data and Image Search Metadata project (DADAISM), a multidisciplinary project that draws together the work of researchers from the fields of archaeology, interaction design, image processing and text mining to create an interactive system that supports archaeologists in their tasks in online archives. By adopting a user-centred approach with techniques grounded in contextual design, we identified the phases of archaeologists work in online archives, which are distinctive to this user group. The insights from this work drove the design and evaluation of an interactive system that successfully integrates content-based image based retrieval and improved metadata searching to deliver a positive user experience when working with online archives.
The Digital Music Lab
Authors: Abdallah Samer , Benetos Emmanouil , Gold Nicolas , Hargreaves Steven , Weyde Tillman , Wolff Daniel
Published: January 2017

In musicology and music research generally, the increasing availability of digital music, storage capacities, and computing power enable and require new and intelligent systems. In the transition from traditional to digital musicology, many techniques and tools have been developed for the analysis of individual pieces of music, but large-scale music data that are increasingly becoming available require research methods and systems that work on the collection-level and at scale. Although many relevant algorithms have been developed during the past 15 years of research in Music Information Retrieval, an integrated system that supports large-scale digital musicology research has so far been lacking.

In the Digital Music Lab (DML) project, a collaboration among music librarians, musicologists, computer scientists, and human-computer interface specialists, the DML software system has been developed that fills this gap by providing intelligent large-scale music analysis with a user-friendly interactive interface supporting musicologists in their exploration and enquiry. The DML system empowers musicologists by addressing several challenges: distributed processing of audio and other music data, management of the data analysis process and results, remote analysis of data under copyright, logical inference on the extracted information and metadata, and visual web-based interfaces for exploring and querying the music collections. The DML system is scalable and based on Semantic Web technology and integrates into Linked Data with the vision of a distributed system that enables music research across archives, libraries, and other providers of music data. A first DML system prototype has been set up in collaboration with the British Library and I Like Music Ltd. This system has been used to analyse a diverse corpus of currently 250,000 music tracks. In this article, we describe the DML system requirements, design, architecture, components, and available data sources, explaining their interaction. We report use cases and applications with initial evaluations of the proposed system.
The European Holocaust Research Infrastructure Portal
Authors: Blanke Tobias , Bryant Michael , Frankl Michal , Kristel Conny , Speck Reto , Daelen Veerle Vanden , Horik René Van
Published: January 2017

Over the course of the past century, there have been significant changes in the practices of archives driven by the massive increase in the volume of records for archiving, a larger and more diverse user base, and the digital turn. This paper analyses work undertaken by the European Holocaust Research Infrastructure project (EHRI) to develop heritage archives into research infrastructures by connecting their knowledge and making it relevant for research. In the article, we focus on EHRI’s work on an integrated collection portal, acting as a central gateway to the rich information on Holocaust-related sources. At the time of writing, the portal contains over 150,000 descriptions of over 1,850 institutions that hold Holocaust-related archival material in 51 countries. In addition, it hosts concise reports that provide in-depth per-country information about the Holocaust history and archival situation in 47 countries, topic-focused research guides, and a range of other services. The article presents how the EHRI portal work connects to the state of the art of heritage portals and the novel solutions we had to develop to align the portal with the requirements of a research infrastructure.
Current Research and Open Problems in Attribute-Based Access Control
Authors: Servos Daniel , Osborn Sylvia L.
Published: January 2017

Attribute-based access control (ABAC) is a promising alternative to traditional models of access control (i.e., discretionary access control (DAC), mandatory access control (MAC), and role-based access control (RBAC)) that is drawing attention in both recent academic literature and industry application. However, formalization of a foundational model of ABAC and large scale adoption is still in its infancy. The relatively recent emergence of ABAC still leaves a number of problems unexplored. Issues like delegation, administration, auditability, scalability, hierarchical representations, and the like, have been largely ignored or left to future work.

This article provides a basic introduction to ABAC and a comprehensive review of recent research efforts toward developing formal models of ABAC. A taxonomy of ABAC research is presented and used to categorize and evaluate surveyed articles. Open problems are identified based on the shortcomings of the reviewed works and potential solutions discussed.
Multi-valued Simulation and Abstraction Using Lattice Operations
Authors: Vijzelaar Stefan , Fokkink Wan
Published: January 2017

Abstractions can cause spurious results, which need to be verified in the concrete system to gain conclusive results. Verification based on a multi-valued logic can distinguish between conclusive and inconclusive results, provides increased precision, and allows for encoding additional information into the model. To ensure a correct abstraction, one can use a mixed simulation [Meller et al. 2009]. We extend mixed simulation to include inconsistent values, thereby resolving an asymmetry and allowing for abstractions with increased precision when inconsistent values are available. In addition, we present a set of abstraction rules, compatible with the extended notion, for constructing abstract models.
The State-of-the-Art of Preconditioners for Sparse Linear Least-Squares Problems
Authors: Gould Nicholas , Scott Jennifer
Published: January 2017

In recent years, a variety of preconditioners have been proposed for use in solving large sparse linear least-squares problems. These include simple diagonal preconditioning, preconditioners based on incomplete factorizations, and stationary inner iterations used with Krylov subspace methods. In this study, we briefly review preconditioners for which software has been made available, then present a numerical evaluation of them using performance profiles and a large set of problems arising from practical applications. Comparisons are made with state-of-the-art sparse direct methods.
Certified Roundoff Error Bounds Using Semidefinite Programming
Authors: Magron Victor , Constantinides George , Donaldson Alastair
Published: January 2017

Roundoff errors cannot be avoided when implementing numerical programs with finite precision. The ability to reason about rounding is especially important if one wants to explore a range of potential representations, for instance, for FPGAs or custom hardware implementations. This problem becomes challenging when the program does not employ solely linear operations as non-linearities are inherent to many interesting computational problems in real-world applications.

Existing solutions to reasoning possibly lead to either inaccurate bounds or high analysis time in the presence of nonlinear correlations between variables. Furthermore, while it is easy to implement a straightforward method such as interval arithmetic, sophisticated techniques are less straightforward to implement in a formal setting. Thus there is a need for methods that output certificates that can be formally validated inside a proof assistant.

We present a framework to provide upper bounds on absolute roundoff errors of floating-point nonlinear programs. This framework is based on optimization techniques employing semidefinite programming and sums of squares certificates, which can be checked inside the Coq theorem prover to provide formal roundoff error bounds for polynomial programs. Our tool covers a wide range of nonlinear programs, including polynomials and transcendental operations as well as conditional statements. We illustrate the efficiency and precision of this tool on non-trivial programs coming from biology, optimization, and space control. Our tool produces more accurate error bounds for 23% of all programs and yields better performance in 66% of all programs.
Toward a Perceptually Uniform Parameter Space for Filter Transparency
Authors: Faul Franz
Published: January 2017

Filter models of perceptual transparency relate to regularities in the retinal projections caused by light transmitting objects like clear liquids or glass and have been found to predict the color conditions for perceptual transparency more accurately than alternative models. An important but unsolved problem is how exactly the model parameters are related to the properties of the perceived transparent layer. We previously proposed a parametrization in terms of hue, saturation, overall transmittance and clarity of the filter that seems to capture important dimensions of the phenomenal impressions. However, these parameters are not independent and the corresponding scales are not perceptually uniform. Here, an invertible transformation of this parameter space is proposed that strongly mitigates these problems. This results in a more intuitively interpretable parameter set that seems well suited for the analysis of existing stimuli and the generation of transparent overlays with predefined perceptual properties. The latter property makes it suitable for graphics and visualization applications.
Climate, Anchovy, and Sardine
Authors: Checkley David M. , Asch Rebecca G. , Rykaczewski Ryan R.
Published: January 2017

Anchovy and sardine populated productive ocean regions over hundreds of thousands of years under a naturally varying climate, and are now subject to climate change of equal or greater magnitude occurring over decades to centuries. We hypothesize that anchovy and sardine populations are limited in size by the supply of nitrogen from outside their habitats originating from upwelling, mixing, and rivers. Projections of the responses of anchovy and sardine to climate change rely on a range of model types and consideration of the effects of climate on lower trophic levels, the effects of fishing on higher trophic levels, and the traits of these two types of fish. Distribution, phenology, nutrient supply, plankton composition and production, habitat compression, fishing, and acclimation and adaptation may be affected by ocean warming, acidification, deoxygenation, and altered hydrology. Observations of populations and evaluation of model skill are essential to resolve the effects of climate change on these fish.
Regulation of the macrophage oxytocin receptor in response to inflammation
Authors: Szeto Angela , Sun-Suslow Ni , Mendez Armando J. , Hernandez Rosa I. , Wagner Klaus V. , McCabe Philip M.
Published: January 2017

It has been demonstrated that the neuropeptide oxytocin (OT) attenuates oxidative stress and inflammation in macrophages. In the current study, we examined the role of inflammation on the expression of the oxytocin receptor (OXTR). We hypothesized that OXTR expression is increased during the inflammation through a nuclear factor-κB (NF-κB)-mediated pathway, thus responding as an acute-phase protein. Inflammation was induced by treating macrophages (human primary, THP-1, and murine) with lipopolysaccharide (LPS) and monitored by expression of IL-6. Expression of OXTR and vasopressin receptors was assessed by qPCR, and OXTR expression was confirmed by immunoblotting. Inflammation upregulated OXTR transcription 10- to 250-fold relative to control in THP-1 and human primary macrophages and increased OXTR protein expression. In contrast, vasopressin receptor-2 mRNA expression was reduced following LPS treatment. Blocking NF-κB activation prevented the increase in OXTR transcription. OT treatment of control cells and LPS-treated cells increased ERK1/2 phosphorylation, demonstrating activation of the OXTR/Gαq/11 signaling pathway. OT activation of OXTR reduced secretion of IL-6 in LPS-activated macrophages. Collectively, these findings suggest that OXTR is an acute-phase protein and that its increased expression is regulated by NF-κB and functions to attenuate cellular inflammatory responses in macrophages.
Association of Toll-Like Receptor 3 Single-Nucleotide Polymorphisms and Hepatitis C Virus Infection
Authors: Al-Anazi Mashael R. , Matou-Nasri Sabine , Abdo Ayman A. , Sanai Faisal M. , Alkahtani Saad , Alarifi Saud , Alkahtane Abdullah A. , Al-Yahya Hamad , Ali Daoud , Alessia Mohammed S. , Alshahrani Bushra , Al-Ahdal Mohammed N. , Al-Qahtani Ahmed A.
Published: January 2017

Toll-like receptor 3 (TLR3) plays a key role in innate immunity by recognizing pathogenic, double-stranded RNAs. Thus, activation of TLR3 is a major factor in antiviral defense and tumor eradication. Although downregulation of TLR3 gene expression has been mainly reported in patients infected with hepatitis C virus (HCV), the influence of TLR3 genotype on the risk of HCV infection, HCV-related cirrhosis, and/or hepatocellular carcinoma (HCC) remains to be determined. Single-nucleotide polymorphisms (SNPs) within the TLR3 gene and their associations with HCV-related disease risk were investigated in a Saudi Arabian population in this study. Eight TLR3 SNPs were analyzed in 563 patients with HCV, which consisted of 437 patients with chronic HCV infections, 88 with HCV-induced liver cirrhosis, and 38 with HCC. A total of 599 healthy control subjects were recruited to the study. Among the eight TLR3 SNPs studied, the rs78726532 SNP was strongly associated with HCV infection when compared to that in healthy control subjects. The rs5743314 was also strongly associated with HCV-related liver disease progression (cirrhosis and HCC). In summary, these results indicate that distinct genetic variants of TLR3 SNPs are associated with HCV infection and HCV-mediated liver disease progression in the Saudi Arabian population.
Prediction of Time-Dependent Chloride Diffusion Coefficients for Slag-Blended Concrete
Authors: Park Ki-Bong , Lee Han-Seung , Wang Xiao-Yong
Published: January 2017

The chloride diffusion coefficient is considered to be a key factor for evaluating the service life of ground-granulated blast-furnace slag (GGBS) blended concrete. The chloride diffusion coefficient relates to both the concrete mixing proportions and curing ages. Due to the continuous hydration of the binders, the capillary porosity of the concrete decreases and the chloride diffusion coefficient also decreases over time. To date, the dependence of chloride diffusivity on the binder hydration and curing ages of slag-blended concrete has not been considered in detail. To fill this gap, this study presents a numerical procedure to predict time-dependent chloride diffusion coefficients for slag-blended concrete. First, by using a blended cement hydration model, the degree of the binder reaction for hardening concrete can be calculated. The effects of the water to binder ratios and slag replacement ratios on the degree of the binder reaction are considered. Second, by using the degree of the binder reaction, the capillary porosity of the binder paste at different curing ages can be determined. Third, by using the capillary porosity and aggregate volume, the chloride diffusion coefficients of concrete can be calculated. The proposed numerical procedure has been verified using the experimental results of concrete with different water to binder ratios, slag replacement ratios, and curing ages.
Different Characterizations of Large Submodules of QTAG-Modules
Authors: Sikander Fahad , Mehdi Alveera , Naji Sabah A. R. K.
Published: January 2017

A module M over an associative ring R with unity is a QTAG-module if every finitely generated submodule of any homomorphic image of M is a direct sum of uniserial modules. The study of large submodules and its fascinating properties makes the theory of QTAG-modules more interesting. A fully invariant submodule L of M is large in M if L+B=M, for every basic submodule B of M. The impetus of these efforts lies in the fact that the rings are almost restriction-free. This motivates us to find the necessary and sufficient conditions for a submodule of a QTAG-module to be large and characterize them. Also, we investigate some properties of large submodules shared by Σ-modules, summable modules, σ-summable modules, and so on.
Characterization and Expression Analysis of Common BeanHistone Deacetylase 6during Development and Cold Stress Response
Authors: Hayford Rita Kusi-Appiah , Ligaba-Osena Ayalew , Subramani Mayavan , Brown Adrianne , Melmaiee Kalpalatha , Hossain Khwaja , Kalavacharla Venu (Kal)
Published: January 2017

Histone deacetylases (HDACs) are important regulators of gene transcription thus controlling multiple cellular processes. Despite its essential role in plants,HDA6is yet to be validated in common bean. In this study, we show thatHDA6is involved in plant development and stress response. Differential expression ofHDA6was determined in various tissues and the expression was seen to be upregulated with plant age (seedling < flowering < maturity). Higher expression was observed in flowers and pods than in stem, leaf, and root. Upregulation ofHDA6gene during cold stress implies its prominent role in abiotic stress. Furthermore, theHDA6gene was isolated from three common bean genotypes and sequence analyses revealed homology with functionally characterized homologs in model species. The 53 kDa translated product was detected using anHDA6specific antibody and recombinant protein overexpressed inEscherichia colishowed HDAC activityin vitro. To our knowledge, this is the first report in the agriculturally important crop common bean describing the functional characterization and biological role ofHDA6.
Study on MPGA‐BP of Gravity Dam Deformation Prediction
Authors: Wang Xiaoyu , Yang Kan , Shen Changsong
Published: January 2017

Displacement is an important physical quantity of hydraulic structures deformation monitoring, and its prediction accuracy is the premise of ensuring the safe operation. Most existing metaheuristic methods have three problems: (1) falling into local minimum easily, (2) slowing convergence, and (3) the initial value’s sensitivity. Resolving these three problems and improving the prediction accuracy necessitate the application of genetic algorithm‐based backpropagation (GA‐BP) neural network and multiple population genetic algorithm (MPGA). A hybrid multiple population genetic algorithm backpropagation (MPGA‐BP) neural network algorithm is put forward to optimize deformation prediction from periodic monitoring surveys of hydraulic structures. This hybrid model is employed for analyzing the displacement of a gravity dam in China. The results show the proposed model is superior to an ordinary BP neural network and statistical regression model in the aspect of global search, convergence speed, and prediction accuracy.