bluuebunny/crossref_metadata_2025 huggingface dataset:
Loneliness and acute stress reactivity: A systematic review of psychophysiological studies
Authors: Brown Eoin G. , Gallagher Stephen , Creaven Ann‐Marie
Published: November 2017

Physiological reactivity to acute stress has been proposed as a potential biological mechanism by which loneliness may lead to negative health outcomes such as cardiovascular disease. This review was conducted to investigate the association between loneliness and physiological responses to acute stress. A series of electronic databases were systematically searched (PsycARTICLES, PsycINFO, Medline, CINAHL Plus, EBSCOhost, PubMed, SCOPUS, Web of Science, Science Direct) for relevant studies, published up to October 2016. Eleven studies were included in the review. Overall, the majority of studies reported positive associations between loneliness and acute stress responses, such that higher levels of loneliness were predictive of exaggerated physiological reactions. However, in a few studies, loneliness was also linked with decreased stress responses for particular physiological outcomes, indicating the possible existence of blunted relationships. There was no clear pattern suggesting any sex‐ or stressor‐based differences in these associations. The available evidence supports a link between loneliness and atypical physiological reactivity to acute stress. A key finding of this review was that greater levels of loneliness are associated with exaggerated blood pressure and inflammatory reactivity to acute stress. However, there was some indication that loneliness may also be related to blunted cardiac, cortisol, and immune responses. Overall, this suggests that stress reactivity could be one of the biological mechanisms through which loneliness impacts upon health.
Does the Motivation for Market‐Based Reform Matter? The Case of Responsibility‐Centered Management
Authors: Rutherford Amanda , Rabovsky Thomas
Published: November 2017

Organizational theorists have long examined the implications of market‐oriented policies for public agencies. Current research often aims to understand the effects of policies imposed on organizations by external stakeholder groups, but few studies have attempted to gain a better understanding of what mechanisms cause agencies to select into these strategies. The purpose of this article is to understand, first, which factors make an organization more likely to adopt a decentralized, market‐based budgeting system—termed “responsibility‐centered management (RCM)—and, second, whether this type of system has implications for organizational performance. Using data on doctorate‐granting public and private nonprofit four‐year universities in the United States, the authors find that mission, resource dependence, and state party control influence the take‐up of RCM. In terms of effects, RCM creates winners for graduation rates (white students) and degree production (science, technology, engineering, and math departments), which raises questions of equity across groups.
Energy dissipation differs between females with and without chronic ankle instability
Authors: McCann R. S. , Terada M. , Kosik K. B. , Gribble P. A.
Published: November 2017

Chronic ankle instability (CAI) is associated with altered energy dissipation patterns, but comparisons to lateral ankle sprain (LAS) copers have not been explored. The purpose of this study was to examine differences in relative sagittal plane energy dissipation during a single‐leg landing between female CAI and LAS coper participants. We separated 33 females (23.6 ± 4.6 years, 164.3 ± 6.2 cm, 69.4 ± 13.7 kg) into CAI (n = 17) and LAS coper (n = 16) groups. Participants completed 5 single‐leg landings followed by a 5‐second stabilization. We collected sagittal plane kinematics and joint moments at the ankle, knee, hip, and proximal joints (knee and hip) combined then calculated each joint's energy dissipation at 50, 100, 150, and 200 ms post‐landing. We compared the percentage of total energy dissipated by the ankle, knee, hip, and proximal joints during each interval utilizing independent t tests and Cohen's d effect sizes. Statistical significance was set a priori at P < .05. The CAI group had lower relative energy dissipation from the ankle at 50 (24.7 ± 11.5% vs 39.2 ± 11.8%, P < .01, d = 1.25 [0.47, 1.95]), 100 (66.9 ± 19.4% vs 77.7 ± 6.5%, P = .04, d = 0.74 [0.01, 1.42]), and 150 ms (70.7 ± 17.8% vs 81.0 ± 5.7%, P = .03, d = 0.77 [0.04, 1.46]) compared to LAS copers. The CAI group had a greater hip contribution through 150 ms (17.9 ± 10.7% vs 11.7 ± 4.4%, P = .04, d =‐0.75 [‐1.44, ‐0.03]) and the proximal joints at 50 (75.3 ± 11.5% vs 60.8 ± 11.8%, P < .01, d = ‐1.25 [‐1.96, ‐0.47]), 100 (33.1 ± 19.4% vs 22.3 ± 6.5%, P = .04, d = ‐0.74 [‐1.42, ‐0.01]), and 150 ms (29.3 ± 17.8 vs 19.0 ± 5.7%, P = .03, d =‐0.77 [‐1.46, ‐0.04]) compared to LAS copers. Females with CAI may benefit from therapeutic exercises designed to correct a single‐leg energy dissipation strategy that relies less on the ankle joint.
Handicapping in squash
Authors: Wagaman John , Fletcher Michael
Published: November 2017

This article considers how a handicapping system should be devised for squash. It looks at the American scoring system, and whether it is possible to have a fair system of handicapping. We consider ‘fair’ from a perspective of expected number of rallies won and probability of winning.
Epidemiology of donors and recipients: lessons from the SCANDAT database
Authors: Edgren G. , Hjalgrim H.
Published: November 2017

With the development of several ‘vein‐to‐vein’ databases, which capture data on the entire donor–recipient continuum and link this data to health outcomes, there has been an increasing number of studies investigating the health effects of all aspects of the practice of transfusion medicine. The Scandinavian Donations and Transfusions (SCANDAT) database is one of several such databases, which includes all electronically available data on blood donors, donations and transfusions since the late 1960s in Sweden and the early 1980s in Denmark. The SCANDAT database has been used to characterise disease occurrence among blood donors and transfused patients, as well as to investigate possible health effects of blood donations, aspects of transfusion care and possible transfusion transmission of disease. Recent publications include studies on recipient mortality associated with the storage lesion, studies on the effects of donor demographics on patient mortality and health effects of frequent blood donation. Although this research approach is clearly very powerful, the appropriate analysis of such real‐world data is complex and requires close methodological attention. The purpose of this review is to present some of the research conducted within the SCANDAT collaboration. We hope more international collaboration may help improve our understanding of the important remaining questions about donor and recipient health.
A Contrast‐Based Computational Model of Surprise and Its Applications
Authors: Macedo Luis , Cardoso Amílcar
Published: November 2017

We review our work on a contrast‐based computational model of surprise and its applications. The review is contextualized within related research from psychology, philosophy, and particularly artificial intelligence. Influenced by psychological theories of surprise, the model assumes that surprise‐eliciting events initiate a series of cognitive processes that begin with the appraisal of the event as unexpected, continue with the interruption of ongoing activity and the focusing of attention on the unexpected event, and culminate in the analysis and evaluation of the event and the revision of beliefs. It is assumed that the intensity of surprise elicited by an event is a nonlinear function of the difference or contrast between the subjective probability of the event and that of the most probable alternative event (which is usually the expected event); and that the agent's behavior is partly controlled by actual and anticipated surprise. We describe applications of artificial agents that incorporate the proposed surprise model in three domains: the exploration of unknown environments, creativity, and intelligent transportation systems. These applications demonstrate the importance of surprise for decision making, active learning, creative reasoning, and selective attention.
For speaking against silence: Spivak's subaltern ethics in the field
Authors: Griffiths Mark
Published: November 2017

This paper addresses the gap between accounts of subalternity in the field and theoretical positions on ethics we find in the work of Gayatri Spivak. I provide a reading of Spivak's writing on subalternity and the ethics of representation to explicate three ethical injunctions connected to: (1) an antifoundationalist approach to subalternity; (2) “hyper‐self‐reflexivity” of an investigating subject; and (3) the imperative to name subalternity. Setting these ethical injunctions in the field, I draw on data from fieldwork with development workers on a gender education project in rural Madhya Pradesh, India, to discuss gender‐based discrimination, violence and intervention. The discussion draws out the ways that proximity to what Spivak terms the “radical alterity” of Otherness can contribute to a more ethical framework for engagement with subalternity. The paper argues that Spivak's work is not intended to implore us to further silencing, rather we must apply her work on the ground towards an ethical engagement with subalternity that rests on a mode of speaking for and about in an antifoundationalist and hyper‐self‐reflexive manner.
Faecal microbiota in dogs with multicentric lymphoma
Authors: Gavazza A. , Rossi G. , Lubas G. , Cerquetella M. , Minamoto Y. , Suchodolski J. S.
Published: November 2017

Malignant lymphoma B‐cell type is the most common canine haematopoietic malignancy. Changes in intestinal microbiota have been implicated in few types of cancer in humans. The aim of this prospective and case‐control study was to determine differences in faecal microbiota between healthy control dogs and dogs with multicentric lymphoma. Twelve dogs affected by multicentric, B‐cell, stage III‐IV lymphoma, and 21 healthy dogs were enrolled in the study. For each dog, faecal samples were analysed by Illumina sequencing of 16S rRNA genes and quantitative PCR (qPCR) for selected bacterial groups. Alpha diversity was significant lower in lymphoma dogs. Principal coordinate analysis plots showed different microbial clustering (P = .001) and linear discriminant analysis effect size revealed 28 differentially abundant bacterial groups in lymphoma and control dogs. The qPCR analysis showed significant lower abundance of Faecalibacterium spp. (q < .001), Fusobacterium spp. (q = .032), and Turicibacter spp. (q = .043) in dogs with lymphoma compared with control dogs. On the contrary, Streptococcus spp. was significantly higher in dogs with lymphoma (q = .041). The dysbiosis index was significantly higher (P < .0001) in dogs with lymphoma. In conclusion, both sequencing and qPCR analyses provided a global overview of faecal microbial communities and showed significant differences in the microbial communities of dogs presenting with multicentric lymphoma compared with healthy control dogs.
Effects of the Global Financial Crisis on the Agency Cost of Islamic Banks and Conventional Banks
Authors: Aldeehani Talla M
Published: November 2017

In this paper, we investigate the effect of the 2008 global financial crisis on the agency cost (AC) of Islamic banks (IBs) and conventional banks (CBs). Many pioneering scholars (see, for example, Archer et al., 1998) have recognized fundamental differences in the capital structures and risks of IBs compared to CBs and called for more empirical testing of these issues. This effort is in response to those calls. Focusing on AC, we collected data for all Gulf Cooperation Council (GCC) banks satisfying the period from 2001-2014. The data was split into “before” and “after” the 2008 crisis. Although statistically insignificant, the analysis shows higher AC for IB compared to CBs before and after the crisis. However, we provide evidence of significant differences in AC causal models for the two types of banks. For conventional banks, only profitability factors explain variability in AC before and after the crisis. For Islamic banks, however, in addition to profitability, liquidity, deposits and financing facilities matter depending on the status of the economy. We provide further discussions, implications, and recommendations.
An Adaptive Economic Model Predictive Control Approach for Wind Turbines
Authors: Shaltout Mohamed L. , Ma Zheren , Chen Dongmei
Published: November 2017

Motivated by the reduction of overall wind power cost, considerable research effort has been focused on enhancing both efficiency and reliability of wind turbines. Maximizing wind energy capture while mitigating fatigue loads has been one of the main goals for control design. Recent developments in remote wind speed measurement systems (e.g., light detection and ranging (LIDAR)) have paved the way for implementing advanced control algorithms in the wind energy industry. In this paper, an LIDAR-assisted economic model predictive control (MPC) framework with a real-time adaptive approach is presented to achieve the aforementioned goal. First, the formulation of a convex optimal control problem is introduced, with linear dynamics and convex constraints that can be solved globally. Then, an adaptive approach is proposed to reject the effects of model-plant mismatches. The performance of the developed control algorithm is compared to that of a standard wind turbine controller, which is widely used as a benchmark for evaluating new control designs. Simulation results show that the developed controller can reduce the tower fatigue load with minimal impact on energy capture. For model-plant mismatches, the adaptive controller can drive the wind turbine to its optimal operating conditions while satisfying the optimal control objectives.
Robust Tracking Control of a Class of Switched Nonlinear Systems With Input Delay Under Asynchronous Switching
Authors: Pezeshki Saeed , Badamchizadeh Mohammad Ali , Ghiasi Amir Rikhtehgar , Ghaemi Sehraneh
Published: November 2017

This paper concerns the problems of stability and robust model reference tracking control for a class of switched nonlinear systems with input delay under asynchronous switching. By proposing a new Lyapunov–Krasovskii functional, and using free-weighting matrices and average dwell-time (ADT) technique, new input-to-state stability (ISS) conditions are derived in terms of linear matrix inequalities (LMIs) under a certain delay bound. Then, robust model reference tracking control problem is studied based on the proposed Lyapunov–Krasovskii functional; Finally a kind of state feedback control law which guarantees robust model reference tracking performance is proposed. Illustrative examples are presented to demonstrate the efficacy and feasibility of results.
A Phase-Field Damage Model for Orthotropic Materials and Delamination in Composites
Authors: Dhas Bensingh , Masiur Rahaman Md. , Akella Kiran , Roy Debasish , Reddy J. N.
Published: November 2017

A phase-field damage model for orthotropic materials is proposed and used to simulate delamination of orthotropic laminated composites. Using the deviatoric and hydrostatic tensile components of the stress tensor for elastic orthotropic materials, a degraded elastic free energy that can accommodate damage is derived. The governing equations follow from the principle of virtual power and the resulting damage model, by its construction, conforms with the physical relevant condition of no matter interpenetration along the crack faces. The model also dispenses with the traction separation law, an extraneous hypothesis conventionally brought in to model the interlaminar zones. The model is assessed through numerical simulations on delaminations in mode I, mode II, and another such problem with multiple initial notches. The present method is able to reproduce nearly all the features of the experimental load displacement curves, allowing only for small deviations in the softening regime. Numerical results also show forth a superior performance of the proposed method over existing approaches based on a cohesive law.
Surrogate Model-Based Control Considering Uncertainties for Composite Fuselage Assembly
Authors: Yue Xiaowei , Wen Yuchen , Hunt Jeffrey H. , Shi Jianjun
Published: November 2017

Shape control of composite parts is vital for large-scale production and integration of composite materials in the aerospace industry. The current industry practice of shape control uses passive manual metrology. This has three major limitations: (i) low efficiency: it requires multiple trials and a longer time to achieve the desired shape during the assembly process; (ii) nonoptimal: it is challenging to reach optimal deviation reduction; and (iii) experience-dependent: highly skilled engineers are required during the assembly process. This paper describes an automated shape control system that can adjust composite parts to an optimal configuration in a manner that is highly effective and efficient. The objective is accomplished by (i) building a finite element analysis (FEA) platform, validated by experimental data; (ii) developing a surrogate model with consideration of actuator uncertainty, part uncertainty, modeling uncertainty, and unquantified uncertainty to achieve predictive performance and embedding the model into a feed-forward control algorithm; and (iii) conducting multivariable optimization to determine the optimal actions of actuators. We show that the surrogate model considering uncertainties (SMU) achieves satisfactory prediction performance and that the automated optimal shape control system can significantly reduce the assembly time with improved dimensional quality.
Comparison on atomic/molecular layer deposition grown aluminum alkoxide polymer films using alkane and alkyne organic precursors
Authors: Choudhury Devika , Rajaraman Gopalan , Sarkar Shaibal K.
Published: November 2017

Most hybrid films grown by atomic and molecular layer deposition (ALD and MLD) at relatively low temperatures commonly incorporate aliphatic organic bifunctional hydrocarbons as their organic counterparts. This often results in “double reactions” leading to lower growth rates, relatively poor film quality, and atmospherically unstable hybrid films. Although such a drawback has been overcome in the past using three-step ABC reactions, aromatic organic precursors, and heterobifunctional precursors, each has displayed one or the other limitations of growth. In this work, the possibility of overcoming double reactions during hybrid film growth by MLD at relatively low temperatures using an sp-hybridized carbon backbone organic precursor is explored. 1,4-butynediol (BDy) along with trimethylaluminum (TMA) is used to deposit “alucone” films at 80 °C. A comparison on growth and properties of the resultant film is drawn with another alucone film deposited using alkane based hydrocarbon, 1,4-butanediol (BD). In situ quartz crystal microbalance and fourier transform infrared (FTIR) spectroscopy studies are performed to determine and compare the growth and surface chemistry of the deposited films. Unfortunately, TMA-BDy films show similar growth characteristics to TMA-BD ones. A 2:1 stoichiometry of growth is observed not only for TMA-BD but also for TMA-BDy films. This shows the occurrence of double reactions irrespective of the carbon–carbon linkages for the linear homobifunctional organic precursors used. A detailed understanding of the stability issue of the deposited hybrid films is further obtained utilizing ex situ FTIR and x-ray reflectivity measurements in this work.
A common microstructure in behavioral hearing thresholds and stimulus-frequency otoacoustic emissions
Authors: Dewey James B. , Dhar Sumitrajit
Published: November 2017

Behavioral hearing thresholds and otoacoustic emission (OAE) spectra often exhibit quasiperiodic fluctuations with frequency. For behavioral and OAE responses to single tones—the latter referred to as stimulus-frequency otoacoustic emissions (SFOAEs)—this microstructure has been attributed to intracochlear reflections of SFOAE energy between its region of generation and the middle ear boundary. However, the relationship between behavioral and SFOAE microstructures, as well as their presumed dependence on the properties of the SFOAE-generation mechanism, have yet to be adequately examined. To address this, behavioral thresholds and SFOAEs evoked by near-threshold tones were compared in 12 normal-hearing female subjects. The microstructures observed in thresholds and both SFOAE amplitudes and delays were found to be strikingly similar. SFOAE phase accumulated an integer number of cycles between the frequencies of microstructure maxima, consistent with a dependence of microstructure periodicity on SFOAE propagation delays. Additionally, microstructure depth was correlated with SFOAE magnitude in a manner resembling that predicted by the intracochlear reflection framework, after assuming reasonable values of parameters related to middle ear transmission. Further exploration of this framework may yield more precise estimates of such parameters and provide insight into their frequency dependence.
A
cheZ
-Like Gene in Azorhizobium caulinodans Is a Key Gene in the Control of Chemotaxis and Colonization of the Host Plant
Authors: Liu Xiaolin , Liu Wei , Sun Yu , Xia Chunlei , Elmerich Claudine , Xie Zhihong
Published: November 2017

Chemotaxis can provide bacteria with competitive advantages for survival in complex environments. The CheZ chemotaxis protein is a phosphatase, affecting the flagellar motor in
Escherichia coli
by dephosphorylating the response regulator phosphorylated CheY protein (CheY∼P) responsible for clockwise rotation. A
cheZ
gene has been found in
Azorhizobium caulinodans
ORS571, in contrast to other rhizobial species studied so far. The CheZ protein in strain ORS571 has a conserved motif similar to that corresponding to the phosphatase active site in
E. coli
. The construction of a
cheZ
deletion mutant strain and of
cheZ
mutant strains carrying a mutation in residues of the putative phosphatase active site showed that strain ORS571 participates in chemotaxis and motility, causing a hyperreversal behavior. In addition, the properties of the
cheZ
deletion mutant revealed that ORS571 CheZ is involved in other physiological processes, since it displayed increased flocculation, biofilm formation, exopolysaccharide (EPS) production, and host root colonization. In particular, it was observed that the expression of several
exp
genes, involved in EPS synthesis, was upregulated in the
cheZ
mutant compared to that in the wild type, suggesting that CheZ negatively controls
exp
gene expression through an unknown mechanism. It is proposed that CheZ influences the
Azorhizobium
-plant association by negatively regulating early colonization via the regulation of EPS production. This report established that CheZ in
A. caulinodans
plays roles in chemotaxis and the symbiotic association with the host plant.

IMPORTANCE
Chemotaxis allows bacteria to swim toward plant roots and is beneficial to the establishment of various plant-microbe associations. The level of CheY phosphorylation (CheY∼P) is central to the chemotaxis signal transduction. The mechanism of the signal termination of CheY∼P remains poorly characterized among
Alphaproteobacteria
, except for
Sinorhizobium meliloti
, which does not contain CheZ but which controls CheY∼P dephosphorylation through a phosphate sink mechanism.
Azorhizobium caulinodans
ORS571, a microsymbiont of
Sesbania rostrata
, has an orphan
cheZ
gene besides two
cheY
genes similar to those in
S. meliloti
. In addition to controlling the chemotaxis response, the CheZ-like protein in strain ORS571 is playing a role by decreasing bacterial adhesion to the host plant, in contrast to the general situation where chemotaxis-associated proteins promote adhesion. In this study, we identified a CheZ-like protein among
Alphaproteobacteria
functioning in chemotaxis and the
A. caulinodans
-
S. rostrata
symbiosis.
The Tape Measure Protein Is Involved in the Heat Stability of Lactococcus lactis Phages
Authors: Geagea Hany , Labrie Simon J. , Subirade Muriel , Moineau Sylvain
Published: November 2017

Virulent lactococcal phages are still a major risk for milk fermentation processes as they may lead to slowdowns and low-quality fermented dairy products, particularly cheeses. Some of the phage control strategies used by the industry rely on heat treatments. Recently, a few
Lactococcus lactis
phages were found to be highly thermo-resistant. To identify the genetic determinant(s) responsible for the thermal resistance of lactococcal phages, we used the virulent phage CB14 (of the
Lactococcus lactis
936 [now
Sk1virus
] phage group) to select for phage mutants with increased heat stability. By treating phage CB14 to successive low and high temperatures, we were able to select two CB14 derivatives with increased heat stability. Sequencing of their genome revealed the same nucleotide sequences as the wild-type phage CB14, except for a same-sized deletion (120 bp) in the gene coding for the tape measure protein (TMP) of each phage mutant, but at a different position. The TMP protein sequences of these mutant phages were compared with their homologues in other wild-type
L. lactis
phages with a wide diversity in heat stability. Comparative analysis showed that the same nucleotide deletion appears to have also occurred in the gene coding for the TMP of highly thermo-resistant lactococcal phages P1532 and P680. We propose that the TMP is, in part, responsible for the heat stability of the highly predominant lactococcal phages of the
Sk1virus
group.

IMPORTANCE
Virulent lactococcal phages still represent a major risk for milk fermentation as they may lead to slowdowns and low-quality fermented dairy products. Heat treatment is one of the most commonly used methods to control these virulent phages in cheese by-products. Recently, a few
Lactococcus lactis
phages, members of the
Sk1virus
group, have emerged with high thermal stability. To our knowledge, the genetic determinant(s) responsible for this thermal resistance in lactococcal phages is unknown. A better understanding of the thermal stability of these emerging virulent lactococcal phages is needed to improve industrial control strategies. In this work, we report the identification of a phage structural protein that is involved in the heat stability of a virulent
Sk1virus
phage. Identifying such a genetic determinant for heat stability is a first step in understanding the emergence of this group of thermostable phages.
Biological Containment of Genetically Modified Bacillus subtilis
Authors: Hosseini Siamand , Curilovs Alex , Cutting Simon M.
Published: November 2017

Genetic manipulation of bacterial spores of the genus
Bacillus
has shown potential for vaccination and for delivery of drugs or enzymes. Remarkably, proteins displayed on the spore surface retain activity and generally are not degraded. The heat stability of spores, coupled with their desiccation resistance, makes them suitable for delivery to humans or to animals by the oral route. Despite these attributes, one regulatory obstacle has remained regarding the fate of recombinant spores shed into the environment as viable spores. We have addressed the biological containment of GMO spores by utilizing the concept of a thymineless death, a phenomenon first reported 6 decades ago. Using
Bacillus subtilis
, we have inserted chimeric genes in the two thymidylate synthase genes,
thyA
and
thyB
, using a two-step process. Insertion is made first at
thyA
and then at
thyB
whereby resistance to trimethoprim enables selection of recombinants. Importantly, this method requires introduction of no new antibiotic resistance genes. Recombinant spores have a strict dependence on thymine (or thymidine), and in its absence cells lyse and die. Insertions are stable with no evidence for suppression or reversion. Using this system, we have successfully created a number of spore vaccines as well as spores displaying active enzymes.

IMPORTANCE
Genetic manipulation of bacterial spores offers a number of exciting possibilities for public and animal health, including their use as heat-stable vehicles for delivering vaccines or enzymes. Despite this, one remaining problem is the fate of recombinant spores released into the environment where they could survive in a dormant form indefinitely. We describe a solution whereby, following genetic manipulation, the bacterium is rendered dependent on thymine. As a consequence, spores if released would produce bacteria unable to survive, and they would exhibit a thymineless death due to rapid cessation of metabolism. The method we describe has been validated using a number of exemplars and solves a critical problem for containing spores of GMOs in the environment.
High-Quality Draft Genome Sequence of “
Candidatus
Methanoperedens sp.” Strain BLZ2, a Nitrate-Reducing Anaerobic Methane-Oxidizing Archaeon Enriched in an Anoxic Bioreactor
Authors: Berger Stefanie , Frank Jeroen , Dalcin Martins Paula , Jetten Mike S. M. , Welte Cornelia U.
Published: November 2017

The high-quality draft genome of “
Candidatus
Methanoperedens sp.” strain BLZ2, a nitrate-reducing archaeon anaerobically oxidizing methane, is presented. The genome was obtained from an enrichment culture and measures 3.74 Mb. It harbors two nitrate reductase gene clusters, an ammonium-forming nitrite reductase, and the complete reverse methanogenesis pathway. Methane that escapes to the atmosphere acts as a potent greenhouse gas. Global methane emissions are mitigated by methanotrophs, which oxidize methane to CO
2
. “
Candidatus
Methanoperedens spp.” are unique methanotrophic archaea that can perform nitrate-dependent anaerobic oxidation of methane. A high-quality draft genome sequence of only 85 contigs from this archaeon is presented here.
First Insight into the Genome Sequences of Two Linezolid-Resistant Nocardia farcinica Strains Isolated from Patients with Cystic Fibrosis
Authors: Valdezate Sylvia , Monzón Sara , Garrido Noelia , Zaballos Angel , Medina-Pascual María J. , Azcona-Gutiérrez José M. , Vilar Begoña , Cuesta Isabel
Published: November 2017

The draft genome sequences of two
Nocardia farcinica
strains isolated from two patients with cystic fibrosis (CF), resistant to trimethoprim/sulfamethoxazole and linezolid, are reported here. The estimated genome sizes were 5.8 Mb with a 70.63% G+C content. Transposases from
Tn
916 were detected, but not 23S rRNA mutation (G2576T) related to linezolid resistance.
Genome Sequences of Four Subcluster L2
Mycobacterium
Phages, Finemlucis, Miley16, Wilder, and Zakai
Authors: Herren Christopher D. , Peister Alexandra , Breton Timothy S. , Hill Maggie S. , Anderson Marcy S. , Chang Adeline W. , Klein Sydney B. , Thornton Mackenzie M. , Vars Stacy J. , Wagner Kasey E. , Wiebe Paige L. , Williams Thomas G. , Yanez Coraima P. , Ackles Jasanta M. , Artis Darius , Brazier Ryan J. , Bryant Ronald J. , Callwood Kerel O. , Carter Isaiah H. , DeBose Cameron L. , Edwards Christian D. , Ezemba Isaiah C. , Joaquin Renshal R. , Meghoo-Peddie Zakai M. , Meghoo-Peddie Ziha G. , Moore Ryan W. , Smith Christopher E. , Turner Adam J. , Vorters Raymond L. , Wider Jeffrey J. , Krout Liesel L. , Comis Mia S. , Davick Madison J. , Michaud Eli E. , Shevenell Bailey E. , Stanley Sarah E. , Frank Chelsey I. , Montgomery Jacob R. , Blumer Lawrence S. , Doty Jean A. , Smith-Caldas Martha , Pope Welkin H. , Cresawn Steven G. , Russell Daniel A. , Garlena Rebecca A. , Jacobs-Sera Deborah , Hatfull Graham F.
Published: November 2017

Four subcluster L2 mycobacteriophages, Finemlucis, Miley16, Wilder, and Zakai, that infect
Mycobacterium smegmatis
mc
2
155 were isolated. The four phages are closely related to each other and code for 12 to 14 tRNAs and 130 to 132 putative protein-coding genes, including tyrosine integrases,
cro
, immunity repressors, and excise genes involved in the establishment of lysogeny.
Draft Genome Sequences of Eight Streptogramin-Resistant
Enterococcus
Species Isolated from Animal and Environmental Sources in the United States
Authors: Sharma Poonam , Gupta Sushim Kumar , Barrett John B. , Hiott Lari M. , House Sandra L. , Woodley Tiffanie A. , Frye Jonathan G. , Jackson Charlene R.
Published: November 2017

Here, we present the draft genome sequences of eight streptogramin-resistant
Enterococcus
species isolated from animals and an environmental source in the United States from 2001 to 2004. Antimicrobial resistance genes were identified conferring resistance to the macrolide-lincosamide-streptogramins, aminoglycosides, tetracyclines, beta-lactams, and glycopeptides.
Complete Genome Sequences of BK Polyomavirus Strains from Two Patients with Urinary Tract Infection, Sequenced Using the Ion Torrent Platform
Authors: Rose Graham , Ranellou Kyriaki , Misra Raju , Crump Colin , Wooldridge David , Parmar Surendra , Maddren Christopher , Gharbia Saheer , Jalal Hamid
Published: November 2017

BK polyomavirus is an important pathogen in kidney transplant patients. We report here two complete genome sequences, those of isolates CAMB-1035 and CAMB-1055, identified in two urine samples tested for urinary tract infection at a hospital in eastern England, United Kingdom. Variation and phylogenetic analyses indicate that both isolates belong to subtype Ib-1.
Draft Genome Sequence of
Myroides
sp. N17-2, a Multidrug-Resistant Bacterium Isolated from Radiation-Polluted Soils
Authors: Liu Tingting , Zhu Liying , Zhang Zhidong , Jiang Ling , Huang He
Published: November 2017

We report here the 4.29-Mb draft genome sequence of
Myroides
sp. N17-2, a new bacterium isolated from radiation-polluted soils in Xinjiang, Uyghur Autonomous Region, China. The acquisition of its genome will provide valuable information to reveal the relationship between radiation and multidrug resistance.
Novel Genes and Regulators That Influence Production of Cell Surface Exopolysaccharides in Sinorhizobium meliloti
Authors: Barnett Melanie J. , Long Sharon R.
Published: November 2017

Sinorhizobium meliloti
is a soil-dwelling alphaproteobacterium that engages in a nitrogen-fixing root nodule symbiosis with leguminous plants. Cell surface polysaccharides are important both for adapting to stresses in the soil and for the development of an effective symbiotic interaction. Among the polysaccharides characterized to date, the acidic exopolysaccharides I (EPS-I; succinoglycan) and II (EPS-II; galactoglucan) are particularly important for protection from abiotic stresses, biofilm formation, root colonization, and infection of plant roots. Previous genetic screens discovered mutants with impaired EPS production, allowing the delineation of EPS biosynthetic pathways. Here we report on a genetic screen to isolate mutants with mucoid colonial morphologies that suggest EPS overproduction. Screening with Tn
5
-110, which allows the recovery of both null and upregulation mutants, yielded 47 mucoid mutants, most of which overproduce EPS-I; among the 30 unique genes and intergenic regions identified, 14 have not been associated with EPS production previously. We identified a new protein-coding gene,
emmD
, which may be involved in the regulation of EPS-I production as part of the EmmABC three-component regulatory circuit. We also identified a mutant defective in EPS-I production, motility, and symbiosis, where Tn
5
-110 was not responsible for the mutant phenotypes; these phenotypes result from a missense mutation in
rpoA
corresponding to the domain of the RNA polymerase alpha subunit known to interact with transcription regulators.

IMPORTANCE
The alphaproteobacterium
Sinorhizobium meliloti
converts dinitrogen to ammonium while inhabiting specialized plant organs termed root nodules. The transformation of
S. meliloti
from a free-living soil bacterium to a nitrogen-fixing plant symbiont is a complex developmental process requiring close interaction between the two partners. As the interface between the bacterium and its environment, the
S. meliloti
cell surface plays a critical role in adaptation to varied soil environments and in interaction with plant hosts. We isolated and characterized
S. meliloti
mutants with increased production of exopolysaccharides, key cell surface components. Our diverse set of mutants suggests roles for exopolysaccharide production in growth, metabolism, cell division, envelope homeostasis, biofilm formation, stress response, motility, and symbiosis.
Demonstrating Principles of Metabolism through Herbicide Treatment of Microalgae
Authors: Leverett Betsy
Published: November 2017

An undergraduate laboratory experiment is described which illustrates blockade of a metabolic pathway and the potential environmental impacts of some herbicides. Students use a spectrophotometric assay to examine branched chain amino acid (BCAA) depletion in microalgae cultures treated with sulfosulfuron, an herbicide and known inhibitor of BCAA biosynthesis. Students also compare the growth of microalgae with and without sulfosulfuron treatment. The experiment provides student training in basic cell culture, biochemical assay techniques, and the use of a microplate spectrophotometer.
Month of birth and risk of autism spectrum disorder: a retrospective cohort of male children born in Israel
Authors: Shalev Hila , Solt Ido , Chodick Gabriel
Published: November 2017

Background

Increased incidence and prevalence of autism spectrum disorder (ASD) over the last two decades have prompted considerable efforts to investigate its aetiological factors. We examined an association between month of birth and ASD incidence.

Methods

In a retrospective cohort of male children born from January 1999 to December 2008 in a large health organisation in Israel (Maccabi Healthcare Services), ASD was followed from birth through December 2015.

Results

Of 108 548 boys, 975 cases of ASD were identified. The highest rates (10.3 and 10.2 per 1000 male live births) were recorded for children born in May and August, respectively, and the lowest rates for February (7.6 per 1000 male live births). Among lower socioeconomic status households, boys born in August were more likely (OR=1.71; 95% CI 1.06 to 2.74) of being diagnosed with ASD than children born in January. Significantly higher rates were not observed for other months.

Conclusions

In line with several previous studies, we found a modestly higher likelihood of autism occurrence among male children of lower socioeconomic levels born in August.
Core Outcome Sets in Miscarriage Trials (COSMisT) study: a study protocol
Authors: Smith Paul , Cooper Natalie , Dhillon-Smith Rima , O’Toole Emily , Clark T Justin , Coomarasamy Arri
Published: November 2017

Introduction

‘Core outcome sets’ are an agreed, standardised set of outcomes based on what key stakeholders (clinicians, patients, their partners, researchers, service developers, funding organisations and so on) consider the important outcomes in the management or prevention of a condition. This paper describes the rationale and design for the development of Core Outcome Sets for Miscarriage Trials.

Methods and analysis

Systematic reviews, interviews and focus groups with patients and their partners will be conducted to identify potential core outcomes that will be introduced into a modified Delphi survey. To ensure all key stakeholders are included, patients, partners, clinicians, charities and researchers will be invited to take part in the modified Delphi survey. There will be three rounds of scoring and rescoring during the Delphi survey to reach consensus regarding outcomes to be included in the core set, which will be subsequently refined through face-to-face consensus discussions.

Ethics and dissemination

The use of core outcome sets allows results from different studies to be compared and combined, thereby reducing inconsistency and aiding interpretation of study findings. It also means research is more likely to report relevant outcomes and so can reduce reporting bias. Understanding which outcomes are important to patients has the potential to act as a driver to improve both the quality and cost-effectiveness of miscarriage services.
Mechanical thrombectomy performs similarly in real world practice: a 2016 nationwide study from the Czech Republic
Authors: Volny Ondrej , Krajina Antonin , Belaskova Silvie , Bar Michal , Cimflova Petra , Herzig Roman , Sanak Daniel , Tomek Ales , Köcher Martin , Rocek Miloslav , Padr Radek , Cihlar Filip , Nevsimalova Miroslava , Jurak Lubomir , Havlicek Roman , Kovar Martin , Sevcik Petr , Rohan Vladimir , Fiksa Jan , Menon Bijoy K , Mikulik Robert
Published: November 2017

Background

Randomized clinical trials have proven mechanical thrombectomy (MT) to be a highly effective and safe treatment in acute stroke. The purpose of this study was to compare neurothrombectomy data from the Czech Republic (CR) with data from the HERMES meta-analysis.

Methods

Available nationwide data for the CR from 2016 from the Safe Implementation of Treatments in Stroke–Thrombectomy (SITS-TBY) registry for patients with terminal internal carotid artery (ICA) and/or middle cerebral artery (MCA) occlusions were compared with data from HERMES. CR and HERMES patients were comparable in age, sex, and baseline National Institutes of Health Stroke Scale scores.

Results

From a total of 1053 MTs performed in the CR, 845 (80%) were reported in the SITS-TBY. From these, 604 (72%) were included in this study. Occlusion locations were as follows (CR vs HERMES): ICA 22% versus 21% (P=0.16), M1 MCA 62% versus 69% (P=0.004), and M2 MCA 16% versus 8% (P<0.0001). Intravenous thrombolysis was given to 76% versus 83% of patients, respectively (P=0.003). Median onset to reperfusion times were comparable: 232 versus 285 min, respectively (P=0.66). A modified Thrombolysis in Cerebral Infarction score of 2b/3 was achieved in 74% (433/584) versus 71% (390/549) of patients, respectively (OR 1.17, 95% CI 0.90–1.5, P=0.24). There was no statistically significant difference in the percentage of parenchymalhematoma type 2 (OR 1.12, 95% CI 0.66–1.90, P=0.68). A modified Rankin Scale score of 0–2 at 3 months was achieved in 48% (184/268) versus 46% (291/633) of patients, respectively (OR 0.92, 95% CI 0.71–1.18, P=0.48).

Conclusions

Data on efficacy, safety, and logistics of MT from the CR were similar to data from the HERMES collaboration.
Some observations considering undrained shear strength, liquidity index, and fluid/solid ratio of mono-mineralic clays with water–ethanol mixtures
Authors: Spagnoli Giovanni , Stanjek Helge , Sridharan Asuri
Published: November 2017

The mechanical properties of clays are influenced by the characteristics of the fluid in the pore space. The liquid limit reacts differently to the permittivity, ε, of the fluid: for smectites the slopes are positive, for kaolinite and illite they are negative and smaller. This dissimilarity can be explained by the structural differences between swelling smectites with solvated interlayer cations and nonswelling clay minerals such as kaolinite and illite. Undrained shear strengths, cu, of Ca–smectite, but not Na–smectite, correlate with the actual fluid ratio. Regressing cu against the liquidity index, IL, yields two different regression lines for Na–smectite and Ca–smectite. For the first time it is shown that normalizing cu to the ε of the pore fluid results in a single regression line for both smectitic clay types. As kaolinites and illites possess significantly less exchangeable cations than smectites, this yields significantly smaller ranges for Atterberg limits and reduces the impact of ε on almost pure particle–particle interactions. In addition, the much larger particle sizes of the kaolinite and illite may dominate the undrained shear strengths, as normalization of cu to ε did not change the relationship to either the actual water content or the liquidity index.
A differential capacity of arbuscular mycorrhizal fungal colonization under well-watered conditions and its relationship with drought stress mitigation in unimproved vs. improved soybean genotypes
Authors: Salloum María Soraya , Menduni María Florencia , Luna Celina Mercedes
Published: November 2017

Modern breeding programs may cause a reduction in plant responsiveness to arbuscular mycorrhizal (AM) fungi. In this study, we tested the hypothesis that responses such as higher arbuscule formation and mycorrhizal dependency (MD) in unimproved soybean genotypes than in improved genotypes is related to drought stress tolerance caused by enhanced growth parameters and oxidative stress regulation. Firstly, four unimproved and four improved soybean genotypes were compared under well-watered conditions. After 20 days, all of the unimproved soybean genotypes showed increased arbuscule formation, as well as a positive and higher MD index in foliar mineral nutrient and growth parameters compared with the four improved genotypes. Secondly, tolerance to drought stress was evaluated in the two improved soybean genotypes and the two unimproved genotypes selected for the most contrasting response to arbuscule formation under well-watered conditions. After 20 days of 30% of field capacity, arbuscule formation was higher in the unimproved than improved genotypes. Mycorrhizal dependency evaluated as leaf area as well as shoot and root dry mass were highest in the unimproved AM genotypes. Moreover, levels of malondiadehide were lower and proline was higher in the unimproved rather than the improved genotypes. The potential capacity of arbuscule formation is discussed as a selection criterion to identify improved soybean genotypes with increased efficiency under well-watered conditions and an enhanced capacity to relieve drought stress.
Competition improves quality-related external stem characteristics of Fagus sylvatica
Authors: Höwler Kirsten , Annighöfer Peter , Ammer Christian , Seidel Dominik
Published: November 2017

Accurate information on the timber quality of hardwoods is often lacking, in particular for standing trees. In situ measurements of timber quality have the potential to improve the economic yield of a stand and may contribute to the optimal timing of a harvest and, in general, to improving forest management. Here, we used terrestrial laser scanning (TLS) to assess external timber quality metrics nondestructively. We investigated how competition intensity affected the metrics of 118 European beech (Fagus sylvatica L.) trees. We found that two newly developed TLS-based measures of external stem characteristics (number of bark anomalies per metre and stem non-circularity) were affected by competition intensity, suggesting that regulating competition levels may improve timber quality. Our study confirms empirical findings indicating a positive relationship between competition intensity and timber quality of European beech and offers a new methodology to assess external timber quality measures in the field objectively and nondestructively.