bluuebunny/crossref_metadata_2025 huggingface dataset:
Transmission Clusters of Methicillin-Resistant Staphylococcus Aureus in Long-Term Care Facilities Based on Whole-Genome Sequencing
Authors: Stine O. Colin , Burrowes Shana , David Sophia , Johnson J. Kristie , Roghmann Mary-Claire
Published: March 2016

OBJECTIVE

To define how often methicillin-resistant Staphylococcus aureus (MRSA) is spread from resident to resident in long-term care facilities using whole-genome sequencing

DESIGN

Prospective cohort study

SETTING

A long-term care facility

PARTICIPANTS

Elderly residents in a long-term care facility

METHODS

Cultures for MRSA were obtained weekly from multiple body sites from residents with known MRSA colonization over 12-week study periods. Simultaneously, cultures to detect MRSA acquisition were obtained weekly from 2 body sites in residents without known MRSA colonization. During the first 12-week cycle on a single unit, we sequenced 8 MRSA isolates per swab for 2 body sites from each of 6 residents. During the second 12-week cycle, we sequenced 30 MRSA isolates from 13 residents with known MRSA colonization and 3 residents who had acquired MRSA colonization.

RESULTS

MRSA isolates from the same swab showed little genetic variation between isolates with the exception of isolates from wounds. The genetic variation of isolates between body sites on an individual was greater than that within a single body site with the exception of 1 sample, which had 2 unrelated strains among the 8 isolates. In the second cycle, 10 of 16 residents colonized with MRSA (63%) shared 1 of 3 closely related strains. Of the 3 residents with newly acquired MRSA, 2 residents harbored isolates that were members of these clusters.

CONCLUSIONS

Point prevalence surveys with whole-genome sequencing of MRSA isolates may detect resident-to-resident transmission more accurately than routine surveillance cultures for MRSA in long-term care facilities.

Infect Control Hosp Epidemiol 2016;37:685–691
Spectral proper orthogonal decomposition
Authors: Sieber Moritz , Paschereit C. Oliver , Oberleithner Kilian
Published: March 2016

The identification of coherent structures from experimental or numerical data is an essential task when conducting research in fluid dynamics. This typically involves the construction of an empirical mode base that appropriately captures the dominant flow structures. The most prominent candidates are the energy-ranked proper orthogonal decomposition (POD) and the frequency-ranked Fourier decomposition and dynamic mode decomposition (DMD). However, these methods are not suitable when the relevant coherent structures occur at low energies or at multiple frequencies, which is often the case. To overcome the deficit of these ‘rigid’ approaches, we propose a new method termed spectral proper orthogonal decomposition (SPOD). It is based on classical POD and it can be applied to spatially and temporally resolved data. The new method involves an additional temporal constraint that enables a clear separation of phenomena that occur at multiple frequencies and energies. SPOD allows for a continuous shifting from the energetically optimal POD to the spectrally pure Fourier decomposition by changing a single parameter. In this article, SPOD is motivated from phenomenological considerations of the POD autocorrelation matrix and justified from dynamical systems theory. The new method is further applied to three sets of PIV measurements of flows from very different engineering problems. We consider the flow of a swirl-stabilized combustor, the wake of an airfoil with a Gurney flap and the flow field of the sweeping jet behind a fluidic oscillator. For these examples, the commonly used methods fail to assign the relevant coherent structures to single modes. The SPOD, however, achieves a proper separation of spatially and temporally coherent structures, which are either hidden in stochastic turbulent fluctuations or spread over a wide frequency range. The SPOD requires only one additional parameter, which can be estimated from the basic time scales of the flow. In spite of all these benefits, the algorithmic complexity and computational cost of the SPOD are only marginally greater than those of the snapshot POD.
Note de recherche. L’effet Westminster : les cibles et les stratégies de lobbying dans le système parlementaire canadien
Authors: Boucher Maxime
Published: March 2016

Cette note de recherche examine l'hypothèse selon laquelle les lobbies canadiens s'adressent principalement aux membres des institutions exécutives en raison des particularités du système parlementaire. Elle propose un examen du registre des lobbyistes qui mesure la fréquence des entretiens entre les lobbies et les fonctionnaires et politiciens canadiens entre l'été 2008 et l'été 2013. Cet exercice d'analyse systématique apporte une connaissance plus précise des cibles de lobbying au Canada. Les résultats indiquent que la majorité des activités de lobbying sont dirigées vers l'administration publique, mais que la Chambre des communes demeure tout de même l'une des institutions les plus sollicitées par les lobbyistes. En conclusion, il apparaît que les approches qui insistent trop fortement sur le rôle structurant des institutions parlementaires traduisent mal la réalité du lobbying. Les preuves empiriques montrent que de nombreux lobbies canadiens optent pour des stratégies intégrées axées sur l'intervention auprès des membres des branches exécutive et législative.
THE LIMITATIONS OF A HUMAN RIGHTS APPROACH TO CORRUPTION
Authors: Rose Cecily
Published: March 2016

International human rights law may serve as a language through which lawyers and others describe the harms resulting from corruption, but this approach has significant limitations as a legal framework. Despite a growing emphasis among scholars and practitioners on a human rights approach to the problem of corruption, this body of law does not provide a strong basis for addressing such conduct. International human rights treaties make no mention of corruption, and human rights treaty bodies have not brought conceptual clarity to the question of how corruption violates or undermines human rights. Given that human rights law binds States alone, it is also ill-suited to a phenomenon that typically occurs at the intersection of the public and private sectors. Even as a language for describing how corruption harms social and economic rights, human rights law has its limitations, some of which come into relief when compared with the field of development economics.
TREATY SUCCESSION IN ANNEXED TERRITORY
Authors: Costelloe Daniel
Published: March 2016

This article explores the question whether the territorial application of a treaty extends to unlawfully annexed territory. In this context, it examines State succession and the territorial application of treaties under general international law, as well as the moving treaty-frontiers rule and the extraterritorial application of certain treaties, specifically with respect to annexed territory. The article concludes that, while in some cases there is scope to find that a treaty applies extraterritorially in annexed territory, notably as a result of its object and purpose or its provisions, there may also be room, subject to the provisions of the treaty, for a limited form of treaty succession in such territory. Limitations to the obligation of collective non-recognition offer theoretical and practical support for this position.
African Ephemeral Material
Authors: Wallerstein Immanuel
Published: March 2016

All of us when we go to Africa acquire, sometimes systematically, more often haphazardly, mimeographed and printed documents which we store, often unused, hopefully to be used in the future. Scattered issues of journals, when added together, can make nearly complete collections.
Bibliography of Materials on African Political Symbols
Authors: Smith Whitney
Published: March 2016

The Flag Research Center was established in February 1962 for the purposes of collecting all types of materials relating to political symbols, and especially the history of flags, and of making this information available to interested persons. In addition to a large number of actual flags, the Center Library (181 Commonwealth Avenue, Boston 16, Massachusetts) has voluminous files of notes and correspondence. There is also a collection of over 800 books and pamphlets on the subject of flags, heraldry, and related subjects. The New York headquarters of the Flag Research Center (at 1452 Leland Avenue, New York 60) contain the editorial offices for The Flag Bulletin, a quarterly journal of vexillology, the history of flags.
Utility of algorithms for the analysis of integratedSalmonellasurveillance data
Authors: VRBOVA L. , PATRICK D. M. , STEPHEN C. , ROBERTSON C. , KOEHOORN M. , PARMLEY E. J. , DE WITH N. I. , GALANIS E.
Published: March 2016

The objective of this study was to assess the use of statistical algorithms in identifying significant clusters ofSalmonellaspp. across different sectors of the food chain within an integrated surveillance programme. Three years of weeklySalmonellaserotype data from farm animals, meat, and humans were used to create baseline models (first two years) and identify weeks with counts higher than expected using surveillance algorithms in the third (test) year. During the test year, an expert working group identified events of interest reviewing descriptive analyses of same data. The algorithms did not identifySalmonellaevents presenting as gradual increases or seasonal patterns as identified by the working group. However, the algorithms did identify clusters for further investigation, suggesting they could be a valuable complementary tool within an integrated surveillance system.
A focus group consultation round exploring patient experiences of comfort during radiotherapy for head and neck cancer
Authors: Goldsworthy Simon D. , Tuke Kelly , Latour Jos M.
Published: March 2016

Purpose

The aim of this study was to consult patients about their experiences of comfort while wearing a thermoplastic mask during head and neck radiotherapy before designing a study to develop a comfort scale for radiotherapy.

Methods

A qualitative method using a focus group of patients receiving radiotherapy for head and neck cancer was deployed. Five patients were invited and agreed to participate. Semi-structured questions guided the focus group interview. Thematic analysis was used to identify themes.

Findings

Three patients participated in the focus group. Three main themes were identified: Physical comfort, Mental perception, Passivity. Physical comfort derived from feelings of pressure, unpleasantness, and generally being uncomfortable. Mental perception derived from how the physical comfort was perceived and derived from feelings of shock, anxiety, indifference and sensory systems. Passivity arose from feelings such as the ‘doctor knows best’, ‘putting up with it’, and ‘being taken for a ride’.

Conclusion

The insight of patient’s comfort and experiences are valuable for clinicians to provide patient-centred care. Findings of this study implicate further investigation of how the themes of patient comfort can be measured in radiotherapy to improve the patient experience.
Capturing the most wanted taxa through cross-sample correlations
Authors: Almeida Mathieu , Pop Mihai , Le Chatelier Emmanuelle , Prifti Edi , Pons Nicolas , Ghozlane Amine , Ehrlich S Dusko
Published: March 2016

The Human Microbiome Project (HMP) identified the 16S rRNA gene sequences of ‘most wanted’ taxa—prevalent in the healthy human microbiota but distant from previously known sequences. Since 2012, few of the corresponding genomes have been isolated and sequenced, and only through advanced isolation techniques. We demonstrate that the genomes of the most wanted taxa can be identified computationally through their correlation in abundance across multiple public metagenomic data sets. We link over 200 most wanted sequences with nearly complete genome sequences, including half of the taxa identified as high-priority targets by the HMP. The genomes we identify have strong similarity to genomes reconstructed through expensive isolation techniques, and provide a more complete functional characterization of these organisms than can be extrapolated from their 16S rRNA gene. We also provide insights into the function of organisms for which 16S rRNA gene signatures were recently reported to be associated with health and host genetic factors.
Commensurate antiferromagnetic excitations as a signature of the pseudogap in the tetragonal high-Tc cuprate HgBa2CuO4+δ
Authors: Chan M. K. , Dorow C. J. , Mangin-Thro L. , Tang Y. , Ge Y. , Veit M. J. , Yu G. , Zhao X. , Christianson A. D. , Park J. T. , Sidis Y. , Steffens P. , Abernathy D. L. , Bourges P. , Greven M.
Published: March 2016

Antiferromagnetic correlations have been argued to be the cause of the d-wave superconductivity and the pseudogap phenomena exhibited by the cuprates. Although the antiferromagnetic response in the pseudogap state has been reported for a number of compounds, there exists no information for structurally simple HgBa2CuO4+δ. Here we report neutron-scattering results for HgBa2CuO4+δ (superconducting transition temperature Tc≈71 K, pseudogap temperature T*≈305 K) that demonstrate the absence of the two most prominent features of the magnetic excitation spectrum of the cuprates: the X-shaped ‘hourglass’ response and the resonance mode in the superconducting state. Instead, the response is Y-shaped, gapped and significantly enhanced below T*, and hence a prominent signature of the pseudogap state.
An Evaluation of Active Learning Causal Discovery Methods for Reverse-Engineering Local Causal Pathways of Gene Regulation
Authors: Ma Sisi , Kemmeren Patrick , Aliferis Constantin F. , Statnikov Alexander
Published: March 2016

Reverse-engineering of causal pathways that implicate diseases and vital cellular functions is a fundamental problem in biomedicine. Discovery of the local causal pathway of a target variable (that consists of its direct causes and direct effects) is essential for effective intervention and can facilitate accurate diagnosis and prognosis. Recent research has provided several active learning methods that can leverage passively observed high-throughput data to draft causal pathways and then refine the inferred relations with a limited number of experiments. The current study provides a comprehensive evaluation of the performance of active learning methods for local causal pathway discovery in real biological data. Specifically, 54 active learning methods/variants from 3 families of algorithms were applied for local causal pathways reconstruction of gene regulation for 5 transcription factors inS. cerevisiae. Four aspects of the methods’ performance were assessed, including adjacency discovery quality, edge orientation accuracy, complete pathway discovery quality, and experimental cost. The results of this study show that some methods provide significant performance benefits over others and therefore should be routinely used for local causal pathway discovery tasks. This study also demonstrates the feasibility of local causal pathway reconstruction in real biological systems with significant quality and low experimental cost.
Self-Locking Optoelectronic Tweezers for Single-Cell and Microparticle Manipulation across a Large Area in High Conductivity Media
Authors: Yang Yajia , Mao Yufei , Shin Kyeong-Sik , Chui Chi On , Chiou Pei-Yu
Published: March 2016

Optoelectronic tweezers (OET) has advanced within the past decade to become a promising tool for cell and microparticle manipulation. Its incompatibility with high conductivity media and limited throughput remain two major technical challenges. Here a novel manipulation concept and corresponding platform called Self-Locking Optoelectronic Tweezers (SLOT) are proposed and demonstrated to tackle these challenges concurrently. The SLOT platform comprises a periodic array of optically tunable phototransistor traps above which randomly dispersed single cells and microparticles are self-aligned to and retained without light illumination. Light beam illumination on a phototransistor turns off the trap and releases the trapped cell, which is then transported downstream via a background flow. The cell trapping and releasing functions in SLOT are decoupled, which is a unique feature that enables SLOT’s stepper-mode function to overcome the small field-of-view issue that all prior OET technologies encountered in manipulation with single-cell resolution across a large area. Massively parallel trapping of more than 100,000 microparticles has been demonstrated in high conductivity media. Even larger scale trapping and manipulation can be achieved by linearly scaling up the number of phototransistors and device area. Cells after manipulation on the SLOT platform maintain high cell viability and normal multi-day divisibility.
Microwave dielectric characterisation of 3D-printed BaTiO3/ABS polymer composites
Authors: Castles F. , Isakov D. , Lui A. , Lei Q. , Dancer C. E. J. , Wang Y. , Janurudin J. M. , Speller S. C. , Grovenor C. R. M. , Grant P. S.
Published: March 2016

3D printing is used extensively in product prototyping and continues to emerge as a viable option for the direct manufacture of final parts. It is known that dielectric materials with relatively high real permittivity—which are required in important technology sectors such as electronics and communications—may be 3D printed using a variety of techniques. Among these, the fused deposition of polymer composites is particularly straightforward but the range of dielectric permittivities available through commercial feedstock materials is limited. Here we report on the fabrication of a series of composites composed of various loadings of BaTiO3microparticles in the polymer acrylonitrile butadiene styrene (ABS), which may be used with a commercial desktop 3D printer to produce printed parts containing user-defined regions with high permittivity. The microwave dielectric properties of printed parts with BaTiO3loadings up to 70 wt% were characterised using a 15 GHz split post dielectric resonator and had real relative permittivities in the range 2.6–8.7 and loss tangents in the range 0.005–0.027. Permittivities were reproducible over the entire process and matched those of bulk unprinted materials, to within ~1%, suggesting that the technique may be employed as a viable manufacturing process for dielectric composites.
MiR-630 Inhibits Endothelial-Mesenchymal Transition by Targeting Slug in Traumatic Heterotopic Ossification
Authors: Sun Yangbai , Cai Jiangyu , Yu Shiyang , Chen Shuai , Li Fengfeng , Fan Cunyi
Published: March 2016

Heterotopic ossification (HO) is the abnormal formation of mature bone in extraskeletal soft tissues that occurs as a result of inflammation caused by traumatic injury or associated with genetic mutation. Despite extensive research to identify the source of osteogenic progenitors, the cellular origins of HO are controversial and the underlying mechanisms, which are important for the early detection of HO, remain unclear. Here, we used in vitro and in vivo models of BMP4 and TGF-β2-induced HO to identify the cellular origin and the mechanisms mediating the formation of ectopic bone in traumatic HO. Our results suggest an endothelial origin of ectopic bone in early phase of traumatic HO and indicate that the inhibition of endothelial-mesenchymal transition by miR-630 targeting Slug plays a role in the formation of ectopic bone in HO. A matched case-control study showed that miR-630 is specifically downregulated during the early stages of HO and can be used to distinguish HO from other processes leading to bone formation. Our findings suggest a potential mechanism of post-traumatic ectopic bone formation and identify miR-630 as a potential early indicator of HO.
Metal assisted cyclomerization of benzodipyrrins into expanded norroles, aza-heptalene and acyclic dimers
Authors: Gadekar Santosh C. , Reddy Baddigam K. , Panchal Santosh P. , Anand Venkataramanarao G.
Published: March 2016

In the presence of metal salt, N-confused monobenzo-dipyrrin cyclomerize to yield an unusual acyclic dimer and an expanded norrole, while doubly N-confused monobenzo and dibenzo-dipyrrins cyclodimerized into aza-heptalene and acyclic dimer respectively.
Inhibitor or promoter? The performance of polysaccharides from Ganoderma lucidum on human tumor cells with different p53 statuses
Authors: Zhang Jue , Chen Jun-ming , Wang Xiao-xia , Xia Yong-mei , Cui Steve W. , Li Jian , Ding Zhong-yang
Published: March 2016

GLPs inhibit cancer cell growth when the tumor suppressor protein p53 is functional but often stimulate cancer cells when p53 is absent.
Cloud point phenomena in aqueous solutions of an anionic gemini surfactant with a dibenzene spacer in the presence of tetra-n-propyl-ammonium bromide
Authors: Xie Danhua , Zhao Jianxi
Published: March 2016

The cloud point behaviour of a carboxylate gemini surfactant,O,O′-bis(sodium 2-dodecylcarboxylate)-p-dibenzenediol was observed in the presence of tetra-propyl-ammonium bromide.
Copper-catalyzed cascade annulation of unsaturated α-bromocarbonyls with enynals: a facile access to ketones from aldehydes
Authors: Che Chao , Huang Qianwen , Zheng Hanliang , Zhu Gangguo
Published: March 2016

A Cu-catalyzed cascade annulation of enynals with alkenyl or alkynyl α-bromocarbonyls for the synthesis of various cyclohexenone-fused polycyclic compounds is described.
Digital image colorimetry coupled with a multichannel membrane filtration-enrichment technique to detect low concentration dyes
Authors: Li Wei , Zhang Ruoqiu , Wang Haiting , Jiang Wei , Wang Lei , Li Hui , Wu Ting , Du Yiping
Published: March 2016

A sensitive and accessible digital image colorimetry method was developed based on the multichannel membrane filtration-enrichment technique utilizing a mobile phone as the analytical detector.
NO adsorption on Cu(110) and O(2 × 1)/Cu(110) surfaces from density functional theory calculations
Authors: Brión-Ríos Antón X. , Sánchez-Portal Daniel , Cabrera-Sanfelix Pepa
Published: March 2016

We have investigated NO adsorption on Cu(110) and O(2 × 1)/Cu(110) surfaces. On the clean Cu(110), consistently with experiments, dimer formation along [11̅0] is favoured due to the covalent NO–ON interaction. On the O(2 × 1)/Cu(110), NO attaches to two Cu atoms on adjacent Cu–O rows, distorting them.
Synthesis of indole-annulated sulfur heterocycles using copper-catalysed C–N coupling and palladium-catalysed direct arylation
Authors: Shelke Ganesh M. , Jha Mukund , Kumar Anil
Published: March 2016

A simple and efficient method for the synthesis of biologically relevant 5H-benzo[4,5][1,3]thiazino[3,2-a]indoles and 5,7-dihydroisothiochromeno[3,4-b]indoles has been developedviaintramolecular copper catalysed Ullmann-type C–N coupling and palladium catalysed direct arylation.
(Boratabenzene)(cyclooctatetraenyl) lanthanide complexes: a new type of organometallic single-ion magnet
Authors: Meng Yin-Shan , Wang Chun-Hong , Zhang Yi-Quan , Leng Xue-Bing , Wang Bing-Wu , Chen Yao-Feng , Gao Song
Published: March 2016

(Boratabenzene)(cyclooctatetraenyl) lanthanide complexes were synthesized, and the erbium ones showed single-ion magnet behaviours. One complex exhibited hysteresis up to 8 K, and another one featured energy barrier of 300 cm−1.
Molecular dynamics study on the mechanical response and failure behaviour of graphene: performance enhancement via 5–7–7–5 defects
Authors: Rajasekaran G. , Parashar Avinash
Published: March 2016

A one atom-thick sheet of carbon exhibits outstanding elastic moduli and tensile strength in its pristine form but structural defects which are inevitable in graphene due to its production techniques can alter its structural properties.
Ligand enhanced upconversion of near-infrared photons with nanocrystal light absorbers
Authors: Huang Zhiyuan , Simpson Duane E. , Mahboub Melika , Li Xin , Tang Ming L.
Published: March 2016

Tetracene derivatives enhance near-infrared photon upconversion by maximizing energy transfer from PbS and PbSe nanocrystal light absorbers.
(n, n(n‐1), n‐1) Permutation group codes
Authors: Peng Li
Published: March 2016

Two different subgroups Cn and Ln of symmetric group Sn are first designed and then to construct a family of permutation group codes Pn with code length n, minimum Hamming distance n − 1, cardinalityn(n − 1) and error‐correcting capability n − 2 is composited.
New virtualised AP for independent wireless network composition
Authors: Kim S.‐J.
Published: March 2016

Virtual access point (VAP) is one of the most useful wireless virtualisation technologies because of its concurrent operation to compose multiple wireless networks via generating service set identifier. A single physical wireless NIC could access multiple networks in a single channel and thus establish a variety of wireless access point without additional wireless network interface. However, as the number of VAP increases, available bandwidth is reduced due to the fact that the number of management frame is increased dramatically in a single channel. Since the management frames should be sent as a basic data rate, channel utilisation and overall network performance would be degraded. To address this problem, system virtualisation is employed to augment wireless NIC hardware. Augmented wireless NICs are exposed to the guest OS and thus can access different wireless channel physically. The results obtained mitigate the bandwidth utilisation of management frame composed to the legacy VAP scheme, increasing round‐trip time latency slightly.
High‐speed quantum cascade laser at room temperature
Authors: Zhou Yu Hong , Zhai Shen Qiang , Liu Junqi , Liu Fengqi , Zhang Jinchuan , Zhuo Ning , Wang Lijun , Wang Zhanguo
Published: March 2016

Room‐temperature, high‐speed quantum cascade lasers at 4.7 μm are presented. An output power of 115 mW and threshold current of 230 mA are obtained for the lasers working in continuous‐wave mode. Reliable single‐mode emission with a side‐mode suppression ratio more than 30 dB is observed. Using microwave rectification technology, a flat frequency response up to roughly 3 GHz for the laser operating at 10°C is demonstrated.
Inductance estimation method for linear switched reluctance machines considering iron losses
Authors: Wang Qianlong , Chen Hao , Xu Tong , Yuan Jinxia , Wang Jiewei , Abbas Saleem
Published: March 2016

The voltage pulse injection method is widely used at the starting and low‐speed sensorless operation of the rotary switched reluctance machine (SRM) and the linear SRM (LSRM). The conventional methods for the inductance estimation in voltage pulse injection, the current peak value method, and the current slope difference method have a limitation that the iron losses in the controlled SRMs/LSRMs should be negligible. In this study, a new inductance estimation method in the voltage pulse injection is proposed considering the iron losses. Assuming that the iron‐loss currents in the energising and de‐energising intervals are almost equal, the inductance estimations in the two intervals are conducted, respectively, and the actual inductance values without the influence of the iron losses can be obtained by a special operation of the two calculated inductance values. Take a designed LSRM as a test object, the results of the proposed method coincide well with the actual values as compared with the conventional methods. The novel inductance estimation can be utilised in the SRMs/LSRMs without the limitation of the iron losses, and then it can further improve the accuracy of the sensorless control in the voltage pulse injection method.
Multiconfigurational quantum propagation with trajectory-guided generalized coherent states
Authors: Grigolo Adriano , Viscondi Thiago F. , de Aguiar Marcus A. M.
Published: March 2016

A generalized version of the coupled coherent states method for coherent states of arbitrary Lie groups is developed. In contrast to the original formulation, which is restricted to frozen-Gaussian basis sets, the extended method is suitable for propagating quantum states of systems featuring diversified physical properties, such as spin degrees of freedom or particle indistinguishability. The approach is illustrated with simple models for interacting bosons trapped in double- and triple-well potentials, most adequately described in terms of SU(2) and SU(3) bosonic coherent states, respectively.
Giant magnetoresistance in the cluster glass regime of Co-Ga alloys
Authors: Mohammad Yasin Sk , Saha Ritwik , Srinivas V. , Kasiviswanathan S. , Nigam A. K.
Published: March 2016

A detailed study of low temperature electrical transport properties of CoxGa100−x (x = 54, 55.5, 57) alloy has been carried out. The origin of the resistivity anomalies and correlation between magnetic and electrical transport properties are identified through an elaborate analysis. The weak localization and enhanced electron-electron interaction effects partially support the electrical transport properties of the system. Further, the observed magnetoresistance can be well represented by localized model along with quantum corrections. The low temperature magnetoresistance value near critical composition is comparable to that reported in giant magnetoresistance materials.
Effect of different agricultural practices on carbon emission and carbon stock in organic and conventional olive systems
Authors: Mohamad Ramez Saeid , Verrastro Vincenzo , Al Bitar Lina , Roma Rocco , Moretti Michele , Al Chami Ziad
Published: March 2016

Agricultural practices, particularly land use, inputs and soil management, have a significant impact on the carbon cycle. Good management of agricultural practices may reduce carbon emissions and increase soil carbon sequestration. In this context, organic agricultural practices may have a positive role in mitigating environmental burden. Organic olive cultivation is increasing globally, particularly in Italy, which is ranked first worldwide for both organic olive production and cultivated area. The aim of the present study was to assess the effects of agricultural practices in organic and conventional olive systems on global warming potential (GWP) from a life cycle perspective and to identify the hot spots in each system. The impacts assessed were associated with the efficiency of both systems at sequestering soil in order to calculate the net carbon flux. There was a higher environmental impact on GWP in the organic system because of higher global greenhouse gas (GHG) emissions resulting from manure fertilisation rather than the synthetic foliar fertilisers used in the conventional system. However, manure was the main reason behind the higher soil organic carbon (SOC) content and soil carbon sequestration in the organic system. Fertilisation activity was the main contributor to carbon emissions, accounting for approximately 80% of total emissions in the organic system and 45% in the conventional system. Conversely, given the similarity of other factors (land use, residues management, soil cover) that may affect soil carbon content, manure was the primary contributor to increased SOC in the organic system, resulting in a higher efficiency of carbon sequestration in the soil following the addition of soil organic matter. The contribution of the manure to increased SOC compensated for the higher carbon emission from the organic system, resulting in higher negative net carbon flux in the organic versus the conventional system (–1.7 vs –0.52 t C ha–1 year–1, respectively) and higher efficiency of CO2 mitigation in the organic system.
Proteome analysis of Pueraria mirifica tubers collected in different seasons
Authors: Jungsukcharoen Jutarmas , Chokchaichamnankit Daranee , Srisomsap Chantragan , Cherdshewasart Wichai , Sangvanich Polkit
Published: March 2016

Pueraria mirifica-derived tuberous powder has been long-term consumed in Thailand as female hormone-replacement traditional remedies. The protein profiles of tubers collected in different seasons were evaluated. Phenol extraction, 2D-PAGE, and mass spectrometry were employed for tuberous proteome analysis. Out of the 322 proteins detected, over 59% were functionally classified as being involved in metabolism. The rest proteins were involved in defense, protein synthesis, cell structure, transportation, stress, storage, and also unidentified function. The proteins were found to be differentially expressed with respect to harvest season. Importantly, chalcone isomerase, isoflavone synthase, cytochrome p450, UDP-glycosyltransferase, and isoflavone reductase, which are all involved in the biosynthesis pathway of bioactive isoflavonoids, were most abundantly expressed in the summer-collected tubers. This is the first report on the proteomic patterns in P. mirifica tubers in relevant with seasonal variation. The study enlights the understanding of variance isoflavonoid production in P. mirifica tubers.
Efficient privacy-preserving string search and an application in genomics
Authors: Shimizu Kana , Nuida Koji , Rätsch Gunnar
Published: March 2016

Motivation: Personal genomes carry inherent privacy risks and protecting privacy poses major social and technological challenges. We consider the case where a user searches for genetic information (e.g. an allele) on a server that stores a large genomic database and aims to receive allele-associated information. The user would like to keep the query and result private and the server the database.

Approach: We propose a novel approach that combines efficient string data structures such as the Burrows–Wheeler transform with cryptographic techniques based on additive homomorphic encryption. We assume that the sequence data is searchable in efficient iterative query operations over a large indexed dictionary, for instance, from large genome collections and employing the (positional) Burrows–Wheeler transform. We use a technique called oblivious transfer that is based on additive homomorphic encryption to conceal the sequence query and the genomic region of interest in positional queries.

Results: We designed and implemented an efficient algorithm for searching sequences of SNPs in large genome databases. During search, the user can only identify the longest match while the server does not learn which sequence of SNPs the user queried. In an experiment based on 2184 aligned haploid genomes from the 1000 Genomes Project, our algorithm was able to perform typical queries within ≈ 4.6 s and ≈ 10.8 s for client and server side, respectively, on laptop computers. The presented algorithm is at least one order of magnitude faster than an exhaustive baseline algorithm.

Availability and implementation:  https://github.com/iskana/PBWT-sec and https://github.com/ratschlab/PBWT-sec.

Contacts:  shimizu-kana@aist.go.jp or Gunnar.Ratsch@ratschlab.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
Genotyping Allelic and Copy Number Variation in the Immunoglobulin Heavy Chain Locus
Authors: Luo Shishi , Yu Jane A. , Song Yun S.
Published: March 2016

The study of genomic regions that contain gene copies and structural variation is a major challenge in modern genomics. Unlike variation involving single nucleotide changes, data on the variation of copy number is difficult to collect and few tools exist for analyzing the variation between individuals. The immunoglobulin heavy variable (IGHV) locus, which plays an integral role in the adaptive immune response, is an example of a genomic region that is known to vary in gene copy number. Lack of standard methods to genotype this region prevents it from being included in association studies and is holding back the growing field of antibody repertoire analysis. Here, we establish a convention of representing the locus in terms of a reference panel of operationally distinguishable segments defined by hierarchical clustering. Using this reference set, we develop a pipeline that identifies copy number and allelic variation in the IGHV locus from whole-genome sequencing reads. Tests on simulated reads demonstrate that our approach is feasible and accurate for detecting the presence and absence of gene segments using reads as short as 70 bp. With reads 100 bp and longer, coverage depth can also be used to determine copy number. When applied to a family of European ancestry, our method finds new copy number variants and confirms existing variants. This study paves the way for analyzing population-level patterns of variation in the IGHV locus in larger diverse datasets and for quantitatively handling regions of copy number variation in other structurally varying and complex loci.
Visualizing allele-specific expression in single cells reveals epigenetic mosaicism in an H19 loss-of-imprinting mutant
Authors: Ginart Paul , Kalish Jennifer M. , Jiang Connie L. , Yu Alice C. , Bartolomei Marisa S. , Raj Arjun
Published: March 2016

Imprinting is a classic mammalian epigenetic phenomenon that results in expression from a single parental allele. Imprinting defects can lead to inappropriate expression from the normally silenced allele, but it remains unclear whether every cell in a mutant organism follows the population average, which would have profound implications for human imprinting disorders. Here, we apply a new fluorescence in situ hybridization method that measures allele-specific expression in single cells to address this question in mutants exhibiting aberrant H19/Igf2 (insulin-like growth factor 2) imprinting. We show that mutant primary embryonic mouse fibroblasts are comprised of two subpopulations: one expressing both H19 alleles and another expressing only the maternal copy. Only in the latter cell population is Igf2 expression detected. Furthermore, the two subpopulations are stable in that cells do not interconvert between the two expression patterns. Combined small input methylation analysis and transcriptional imaging revealed that these two mutant subpopulations exhibit distinct methylation patterns at their imprinting control regions. Consistently, pharmacological inhibition of DNA methylation reduced the proportion of monoallelic cells. Importantly, we observed that the same two subpopulations are also present in vivo within murine cardiac tissue. Our results establish that imprinting disorders can display striking single-cell heterogeneity in their molecular phenotypes and suggest that such heterogeneity may underlie epigenetic mosaicism in human imprinting disorders.
Coupling pre-mRNA splicing and 3′ end formation to mRNA export: alternative ways to punch the nuclear export clock
Authors: Elbarbary Reyad A. , Maquat Lynne E.
Published: March 2016

How does a mammalian cell determine when newly synthesized mRNAs are fully processed and appropriate for nuclear export? Müller-McNicoll and colleagues (pp. 553–566) expand on mechanisms known to be mediated by nuclear export factor 1 (NXF1) by describing SR proteins as NXF1 adaptors that flag alternatively spliced and polyadenylated mRNA isoforms as cargo ready for the cytoplasm.
Simple and easy-operated method for filtering eco-friendly corrosion inhibitors
Authors: Yang Na , Liao Qin , Li Qing , Zhang Peng , Li Longqin
Published: March 2016

Purpose

– The purpose of this paper was to find a simple and easy-operated method for filtering eco-friendly corrosion inhibitors.

Design/methodology/approach

– The molecular structures and atomic electronegativities of the four kinds of natural reagents, iota-Carrageenan, sodium alginate, sodium dodecanesulphonate (SDS) and sodium dodecylbenzene sulfonate were calculated by Gaussian and Natural Bond Orbital, and the corrosion inhibition rates were forecasted by the calculated results. Then, the realistic corrosion inhibition efficiency were confirmed by electrochemical impedance spectroscopy and potentiodynamic polarization tests in 3.5 Wt.% sodium chloride corrosive solutions. At the same time, the function of pefloxacin mesylate (PM) was explored in this paper polarization tests in 3.5 Wt.% sodium chloride corrosive solutions.

Findings

– Results showed that the order calculated by the chemical software was correct, and the corrosion inhibition of SDS was the best. Optimum addition of PM not only can reduce microbial corrosion but also can improve the corrosion inhibition by spatial cooperation.

Practical implications

– This method can be used to filter eco-friendly corrosion inhibitors quickly. PM can be also used to improve the corrosion inhibition rate of corrosion inhibitors.

Originality/value

– The present method to filter corrosion inhibitors was time-consuming, which needed lots of experiments to verify the corrosion inhibitive efficiency. The calculated method was simpler than others, which need complicated calculation process.
The concept of Datenherrschaft of patient information from a Lockean perspective
Authors: Koskinen Jani Simo Sakari , Kainu Ville Matti Antero , Kimppa Kai Kristian
Published: March 2016

Purpose

– The purpose of this paper is to analyse the current status of ownership of patient information from a Lockean perspective and then present Datenherrschaft (German for “mastery over information”) as a new model for patient ownership of patient information.

Design/methodology/approach

– This paper is theoretical in approach. It is based on arguments derived from Locke’s Two Treatises of Government. Legal examples of the current situation are derived from Finnish, UK and Swedish legislation.

Findings

– Current legislation concerning patient information is not clearly formulated and so recognising a new right on the part of the patient, Datenherrschaft, would be an ethically justifiable way of remedying the issue.

Research limitations/implications

– The legal analysis was limited to Finland, the UK and Sweden, and so other legislation should be looked at in future research. Datenherrschaft is used as an example of an ethically justified way of regulating patient information ownership and should be analysed further.

Originality/value

– Patient information ownership is an issue that is not unambiguously solved in many countries, nor has it, in our view, been ethically justified. The potential solution presented in this paper is clear and has strong ethical justifications.
Making it clear and relevant: patients and carers add value to studies through research document reviews
Authors: Staley Kristina , Ashcroft Joanne , Doughty Lisa , Szmukler George
Published: March 2016

Purpose

– The National Institute of Health Research MHRN established the Feasibility and Support to Timely recruitment for Research (FAST-R) service in 2011, to provide rapid patient and carer feedback on research documents, prior to ethical review. The aims were to improve the feasibility of studies, to speed up regulatory processes and enhance study set up and completion. The purpose of this paper is to explore whether and how the FAST-R service benefits the review process.

Design/methodology/approach

– An independent evaluator analysed the comments made by FAST-R members on 85 studies over the past 3.5 years. The evaluation team reflected on the nature of these comments and the implications for future practice.

Findings

– The FAST-R members’ comments fell into seven categories relating to: the quality of the information, the informed consent process, care and protection of participants, practical arrangements for participants, data protection and confidentiality, recruitment and research design. Based on the evaluation team’s experience of research document review, some of these comments were similar to those made by ethics committees. In other cases, the FAST-R Panel provided a different kind of input by identifying concerns specific to service users and carers.

Practical implications

– Patient/carer involvement in reviewing research documents brings added benefits to existing processes because their views are informed by their knowledge and experience. They are able to question assumptions and highlight concerns that people lacking their perspective might otherwise miss. These findings suggest that patient/carer involvement should form an integral part of ethical review, and that the FAST-R model might be usefully applied to other areas of health and social care research.

Originality/value

– This original work adds value to the practice of patient and public involvement in research.
Genome Sequence of a
Mycoplasma meleagridis
Field Strain
Authors: Rocha Ticiana S. , Bertolotti Luigi , Catania Salvatore , Pourquier Philippe , Rosati Sergio
Published: March 2016

Mycoplasma meleagridis
is a major cause of disease and economic loss in turkeys. Here, we report the genome sequence of an
M. meleagridis
field strain, which enlarges the knowledge about this bacterium and helps the identification of possible coding sequences for drug resistance genes and specific antigens.
Complete Genome Sequence of
Pseudomonas syringae
pv. lapsa Strain ATCC 10859, Isolated from Infected Wheat
Authors: Kong Jun , Jiang Hongshan , Li Baiyun , Zhao Wenjun , Li Zhihong , Zhu Shuifang
Published: March 2016

Pseudomonas syringae
pv. lapsa is a pathovar of
Pseudomonas syringae
that can infect wheat. The complete genome of
P. syringae
pv. lapsa strain ATCC 10859 contains a 5,918,899-bp circular chromosome with 4,973 coding sequences, 16 rRNAs, 69 tRNAs, and an average GC content of 59.13%. The analysis of this genome revealed several gene clusters that are related to pathogenesis and virulence.
Draft Genome Sequence of a Strictly Anaerobic Dichloromethane-Degrading Bacterium
Authors: Kleindienst Sara , Higgins Steven A. , Tsementzi Despina , Konstantinidis Konstantinos T. , Mack E. Erin , Löffler Frank E.
Published: March 2016

An anaerobic, dichloromethane-degrading bacterium affiliated with novelPeptococcaceaewas maintained in a microbial consortium. The organism originated from pristine freshwater sediment collected from Rio Mameyes in Luquillo, Puerto Rico, in October 2009 (latitude 18°21′43.9″, longitude −65°46′8.4″). The draft genome sequence is 2.1 Mb and has a G+C content of 43.5%.
Complete Genome Sequence of Bovine Polyomavirus Type 1 from Aborted Cattle, Isolated in Belgium in 2014
Authors: Van Borm Steven , Rosseel Toon , Behaeghel Isabelle , Saulmont Marc , Delooz Laurent , Petitjean Thierry , Mathijs Elisabeth , Vandenbussche Frank
Published: March 2016

The complete and fully annotated genome sequence of a bovine polyomavirus type 1 (BPyV/BEL/1/2014) from aborted cattle was assembled from a metagenomics data set. The 4,697-bp circular dsDNA genome contains 6 protein-coding genes. Bovine polyomavirus is unlikely to be causally related to the abortion cases.
Corynebacterium striatumempyema and osteomyelitis in a patient with advanced rheumatoid arthritis
Authors: Verma Rajanshu , Kravitz Gary R
Published: March 2016

Corynebacterium striatum, which is a common coloniser of human skin and mucous membranes, is increasingly being recognised as an emerging pathogen. We present a case of a 69-year-old woman with empyema and osteomyelitis caused byC. striatum. To the best of our knowledge, this is the first case where these two infections from this bacterium were identified together in the same individual.