bluuebunny/crossref_metadata_2025 huggingface dataset:
Sway‐dependent changes in standing ankle stiffness caused by muscle thixotropy
Authors: Sakanaka Tania E. , Lakie Martin , Reynolds Raymond F.
Published: November 2015

Key points

The passive stiffness of the calf muscles contributes to standing balance, although the properties of muscle tissue are highly labile.

We investigated the effect of sway history upon intrinsic ankle stiffness and demonstrated reductions in stiffness of up to 43% during conditions of increased baseline sway.

This sway dependence was most apparent when using low amplitude stiffness‐measuring perturbations, and the short‐range stiffness component was smaller during periods of high sway.

These characteristics are consistent with the thixotropic properties of the calf muscles causing the observed changes in ankle stiffness.

Periods of increased sway impair the passive stabilization of standing, demanding more active neural control of balance.

Quiet standing is achieved through a combination of active and passive mechanisms, consisting of neural control and intrinsic mechanical stiffness of the ankle joint, respectively. The mechanical stiffness is partly determined by the calf muscles. However, the viscoelastic properties of muscle are highly labile, exhibiting a strong dependence on movement history. By measuring the effect of sway history upon ankle stiffness, the present study determines whether this lability has consequences for the passive stabilization of human standing. Ten subjects stood quietly on a rotating platform whose axis was collinear with the ankle joint. Ankle sway was increased by slowly tilting this platform in a random fashion, or decreased by fixing the body to a board. Ankle stiffness was measured by using the same platform to simultaneously apply small, brief perturbations (<0.6 deg; 140 ms) at the same time as the resulting torque response was recorded. The results show that increasing sway reduces ankle stiffness by up to 43% compared to the body‐fixed condition. Normal quiet stance was associated with intermediate values. The effect was most apparent when using smaller perturbation amplitudes to measure stiffness (0.1 vs. 0.6 deg). Furthermore, torque responses exhibited a biphasic pattern, consisting of an initial steep rise followed by a shallower increase. This transition occurred earlier during increased levels of ankle sway. These results are consistent with a movement‐dependent change in passive ankle stiffness caused by thixotropic properties of the calf muscle. The consequence is to place increased reliance upon active neural control during times when increased sway renders ankle stiffness low.
Relationship between retinal blood flow and arterial oxygen
Authors: Cheng Richard W. , Yusof Firdaus , Tsui Edmund , Jong Monica , Duffin James , Flanagan John G. , Fisher Joseph A. , Hudson Chris
Published: November 2015

Key points

Vascular reactivity, the response of the vessels to a vasoactive stimulus such as hypoxia and hyperoxia, can be used to assess the vascular range of adjustment in which the vessels are able to compensate for changes in .

Previous studies in the retina have not accurately quantified retinal vascular responses and precisely targeted multiple stimuli at the same time as controlling the level of carbon dioxide, thus precluding them from modelling the relationship between retinal blood flow and oxygen.

The present study modelled the relationship between retinal blood flow and , showing them to be a combined linear and hyperbolic function.

This model demonstrates that the resting tonus of the vessels is at the mid‐point and that they have great vascular range of adjustment, compensating for decreases in oxygen above a of 32–37 mmHg but being limited below this threshold.

Retinal blood flow (RBF) increases in response to a reduction in oxygen (hypoxia) but decreases in response to increased oxygen (hyperoxia). However, the relationship between blood flow and the arterial partial pressure of oxygen has not been quantified and modelled in the retina, particularly in the vascular reserve and resting tonus of the vessels. The present study aimed to determine the limitations of the retinal vasculature by modelling the relationship between RBF and oxygen. Retinal vascular responses were measured in 13 subjects for eight different blood gas conditions, with the end‐tidal partial pressure of oxygen () ranging from 40–500 mmHg. Retinal vascular response measurements were repeated twice; using the Canon laser blood flowmeter (Canon Inc., Tokyo, Japan) during the first visit and using Doppler spectral domain optical coherence tomography during the second visit. We determined that the relationship between RBF and can be modelled as a combination of hyperbolic and linear functions. We concluded that RBF compensated for decreases in arterial oxygen content for all stages of hypoxia used in the present study but can no longer compensate below a of 32–37 mmHg. These vessels have a great vascular range of adjustment, increasing diameter (8.5% arteriolar and 21% total venous area) with hypoxia (40 mmHg ; P < 0.001) and decreasing diameter (6.9% arteriolar and 23% total venous area) with hyperoxia (500 mmHg ; P < 0.001) to the same extent. This indicates that the resting tonus is near the mid‐point of the adjustment ranges at resting where sensitivity is maximum.
The consequences of fetal growth restriction on brain structure and neurodevelopmental outcome
Authors: Miller Suzanne L. , Huppi Petra S. , Mallard Carina
Published: November 2015

Fetal growth restriction (FGR) is a significant complication of pregnancy describing a fetus that does not grow to full potential due to pathological compromise. FGR affects 3–9% of pregnancies in high‐income countries, and is a leading cause of perinatal mortality and morbidity. Placental insufficiency is the principal cause of FGR, resulting in chronic fetal hypoxia. This hypoxia induces a fetal adaptive response of cardiac output redistribution to favour vital organs, including the brain, and is in consequence called brain sparing. Despite this, it is now apparent that brain sparing does not ensure normal brain development in growth‐restricted fetuses. In this review we have brought together available evidence from human and experimental animal studies to describe the complex changes in brain structure and function that occur as a consequence of FGR. In both humans and animals, neurodevelopmental outcomes are influenced by the timing of the onset of FGR, the severity of FGR, and gestational age at delivery. FGR is broadly associated with reduced total brain volume and altered cortical volume and structure, decreased total number of cells and myelination deficits. Brain connectivity is also impaired, evidenced by neuronal migration deficits, reduced dendritic processes, and less efficient networks with decreased long‐range connections. Subsequent to these structural alterations, short‐ and long‐term functional consequences have been described in school children who had FGR, most commonly including problems in motor skills, cognition, memory and neuropsychological dysfunctions.

image
Spontaneous activity in the microvasculature of visceral organs: role of pericytes and voltage‐dependent Ca2+ channels
Authors: Hashitani Hikaru , Lang Richard J.
Published: November 2015

The microvasculature plays a primary role in the interchange of substances between tissues and the circulation. In visceral organs that undergo considerable distension upon filling, the microvasculature appears to display intrinsic contractile properties to maintain their flow. Submucosal venules in the bladder or gastrointestinal tract generate rhythmic spontaneous phasic constrictions and associated Ca2+ transients. These events are initiated within either venular pericytes or smooth muscle cells (SMCs) arising from spontaneous Ca2+ release from the sarcoplasmic reticulum (SR) and the opening of Ca2+‐activated chloride channels (CaCCs) that trigger Ca2+ influx through L‐type voltage‐dependent Ca2+ channels (VDCCs). L‐type VDCCs also play a critical role in maintaining synchrony within the contractile mural cells. In the stomach myenteric layer, spontaneous Ca2+ transients originating in capillary pericytes appear to spread to their neighbouring arteriolar SMCs. Capillary Ca2+ transients primarily rely on SR Ca2+ release, but also require Ca2+ influx through T‐type VDCCs for their synchrony. The opening of T‐type VDCCs also contribute to the propagation of Ca2+ transients into SMCs. In visceral microvasculature, pericytes act as either spontaneously active contractile machinery of the venules or as pacemaker cells generating synchronous Ca2+ transients that drive spontaneous contractions in upstream arterioles. Thus pericytes play different roles in different vascular beds in a manner that may well depend on the selective expression of T‐type and L‐type Ca2+ channels.

image
A Control Theoretic Approach for Solving Underdetermined Problems and Its Application to Control Allocation
Authors: Kumar Naskar Asim , Patra Sourav , Sen Siddhartha
Published: November 2015

In this paper, a new iterative algorithm is developed using control theoretic approach to find the minimum norm solution of underdetermined problems. The minimum norm solution is obtained by applying the H∞ optimization technique. The accuracy and convergence rate of the proposed algorithm are ensured using the framework of linear feedback control theory. The performances of the proposed method, the QR decomposition method, and the least square minimal residue (LSMR) method are compared numerically. The number of iterations in the proposed algorithm is comparable with the LSMR method. Finally, the developed algorithm is applied to the control allocation problem and its effectiveness is demonstrated through a detailed simulation study.
Vibration Reduction Using Near Time-Optimal Commands for Systems With Nonzero Initial Conditions
Authors: Dhanda Abhishek , Vaughan Joshua , Singhose William
Published: November 2015

The control of flexible systems has been an active area of research for many years because of its importance to a wide range of applications. The majority of previous research on time-optimal control has concentrated on the rest-to-rest problem. However, there are many cases when flexible systems are not at rest or are subjected to disturbances. This paper presents an approach to design optimal vibration-reducing commands for systems with nonzero initial conditions. The problem is first formulated as an optimal control problem, and the optimal solution is shown to be bang-bang. Once the structure of the optimal command is known, a parametric problem formulation is presented for the computation of the switching times. Solutions are experimentally verified using a portable bridge crane by moving the payload through a commanded motion while removing initial payload swing.
Global Finite Time Stabilization of a Class of Uncertain MIMO Nonlinear Systems
Authors: Abooee Ali , Moravej-Khorasani Masoud , Haeri Mohammad
Published: November 2015

It is aimed to obtain global finite time stabilization of a class of uncertain multi-input–multi-output (MIMO) nonlinear systems in the presence of bounded disturbances by applying nonsingular terminal sliding mode controllers. The considered nonlinear systems consist of double integrator subsystems which interact with each other. In the proposed methods, new terminal sliding surfaces are introduced along with design of proper control inputs. The terminal sliding surfaces are defined such that the global finite time stability of sliding mode dynamic is attained. The control inputs are designed to steer the states into sliding motion within finite time and retain them on the terminal sliding surfaces. The presented approaches guarantee the finite time convergence of states with low sensitivity to their initial values. The convergence rate could be adjusted by proper choice of existing arbitrary parameters in the suggested control schemes. Three numerical simulation examples including van de Pol system and two robotic manipulators are provided to confirm the applicability and effectiveness of the proposed control schemes.
More delays for ITER fusion project
Authors: Clery Daniel
Published: November 2015

Review notes progress but estimates “first plasma” will take 6 years longer than planned.
Gene drive turns mosquitoes into malaria fighters
Authors: Pennisi Elizabeth
Published: November 2015

Antiparasite genes made to spread among lab insects.
Clean revolution
Authors: Service Robert F.
Published: November 2015

Denmark is striving to become the world's first carbon-neutral nation.
Can India keep its promises?
Authors: Pulla Priyanka
Published: November 2015

India hopes that steps to limit climate change will also improve its citizens' lives. Critics say such “cobenefits” may be a pipe dream.
Fifty years after U.S. climate warning, scientists confront communication barriers
Authors: Stern Gavin
Published: November 2015

At the AAAS symposium, researchers searched for new avenues of public engagement to address the gap in climate change beliefs
AAAS Kavli Science Journalism Award winners named
Authors: Lane Earl
Published: November 2015

This year's winners included stories on the health impacts of urban violence, local signs of global climate change, and West Africa's Ebola epidemic
Near-unity photoluminescence quantum yield in MoS
2
Authors: Amani Matin , Lien Der-Hsien , Kiriya Daisuke , Xiao Jun , Azcatl Angelica , Noh Jiyoung , Madhvapathy Surabhi R. , Addou Rafik , KC Santosh , Dubey Madan , Cho Kyeongjae , Wallace Robert M. , Lee Si-Chen , He Jr-Hau , Ager Joel W. , Zhang Xiang , Yablonovitch Eli , Javey Ali
Published: November 2015

Brighter molybdenum layers

The confined layers of molybdenum disulphide (MoS
2
) exhibit photoluminescence that is attractive for optolectronic applications. In practice, efficiencies are low, presumably because defects trap excitons before they can recombine and radiate light. Amani
et al.
show that treatment of monolayer MoS
2
with a nonoxidizing organic superacid, bis(trifluoromethane) sulfonimide, increased luminescence efficiency in excess of 95%. The enhancement mechanism may be related to the shielding of defects, such as sulfur vacancies.

Science
, this issue p.
1065
Malaria parasites target the hepatocyte receptor EphA2 for successful host infection
Authors: Kaushansky Alexis , Douglass Alyse N. , Arang Nadia , Vigdorovich Vladimir , Dambrauskas Nicholas , Kain Heather S. , Austin Laura S. , Sather D. Noah , Kappe Stefan H.I.
Published: November 2015

How malaria parasites infect the liver

Early in infection, malaria parasites establish themselves within hepatocytes in the liver. Inside these cells, the parasites occupy a so-called parasitophorous vacuole. Kaushansky
et al.
show that malaria parasites prefer to create vacuoles within hepatocytes that express the EphA2 receptor. Hepatocytes with low levels of this receptor were less conducive to malaria infection.

Science
, this issue p.
1089
Semiconductor interfacial carrier dynamics via photoinduced electric fields
Authors: Yang Ye , Gu Jing , Young James L. , Miller Elisa M. , Turner John A. , Neale Nathan R. , Beard Matthew C.
Published: November 2015

Charge separation viewed in reflection

When light strikes a semiconductor, excited electrons travel across the interface. Y. Yang
et al.
applied ultrafast reflection spectroscopy to probe this process in a gallium indium phosphide system used for hydrogen generation from water (see the Perspective by Hansen
et al.
). Platinum and titanium dioxide (TiO
2
) coatings enhanced charge separation of the excited electrons from the positive holes they left behind. TiO
2
, however, was more effective at suppressing the reverse process of unproductive recombination.

Science
, this issue p.
1061
; see also p.
1030
Optical meta-atoms: Going nonlinear
Authors: Litchinitser Natalia M. , Sun Jingbo
Published: November 2015

Metamaterials are poised to transform nonlinear optics
Could microbial therapy boost cancer immunotherapy?
Authors: Snyder Alexandra , Pamer Eric , Wolchok Jedd
Published: November 2015

Intestinal microbes affect immunotherapy responses in mouse models of cancer

[Also see Reports by

Vétizou
et al.

and

Sivan
et al.

]
Christopher Marshall (1949–2015)
Authors: Marais Richard
Published: November 2015

A cell biologist's meticulous work drove the discovery of new cancer treatments
Turning the focus to solutions
Authors: Lee Hoesung
Published: November 2015

Next week, the United Nations Climate Change Conference, COP21, will be held in Paris. The goal is to achieve an international agreement to stem climate change—in particular, an agreement on how to keep global warming below a 2°C rise, or less, over preindustrial levels. As the newly elected chair of the Intergovernmental Panel on Climate Change (IPCC), I am hopeful that an agreement will be reached that builds a more sustainable, prosperous world.
Unprecedented Melioidosis Cases in Northern Australia Caused by an Asian Burkholderia pseudomallei Strain Identified by Using Large-Scale Comparative Genomics
Authors: Price Erin P. , Sarovich Derek S. , Smith Emma J. , MacHunter Barbara , Harrington Glenda , Theobald Vanessa , Hall Carina M. , Hornstra Heidie M. , McRobb Evan , Podin Yuwana , Mayo Mark , Sahl Jason W. , Wagner David M. , Keim Paul , Kaestli Mirjam , Currie Bart J.
Published: November 2015

Melioidosis is a disease of humans and animals that is caused by the saprophytic bacteriumBurkholderia pseudomallei. Once thought to be confined to certain locations, the known presence ofB. pseudomalleiis expanding as more regions of endemicity are uncovered. There is no vaccine for melioidosis, and even with antibiotic administration, the mortality rate is as high as 40% in some regions that are endemic for the infection. Despite high levels of recombination, phylogenetic reconstruction ofB. pseudomalleipopulations using whole-genome sequencing (WGS) has revealed surprisingly robust biogeographic separation between isolates from Australia and Asia. To date, there have been no confirmed autochthonous melioidosis cases in Australia caused by an Asian isolate; likewise, no autochthonous cases in Asia have been identified as Australian in origin. Here, we used comparative genomic analysis of 455B. pseudomalleigenomes to confirm the unprecedented presence of an Asian clone, sequence type 562 (ST-562), in Darwin, northern Australia. First observed in Darwin in 2005, the incidence of melioidosis cases attributable to ST-562 infection has steadily risen, and it is now a common strain in Darwin. Intriguingly, the Australian ST-562 appears to be geographically restricted to a single locale and is genetically less diverse than other common STs from this region, indicating a recent introduction of this clone into northern Australia. Detailed genomic and epidemiological investigations of new clinical and environmentalB. pseudomalleiisolates in the Darwin region and ST-562 isolates from Asia will be critical for understanding the origin, distribution, and dissemination of this emerging clone in northern Australia.
Draft Genome Sequence of Porphyrobacter mercurialis (sp. nov.) Strain Coronado
Authors: Coil David A. , Eisen Jonathan A.
Published: November 2015

Here, we present the draft genome of
Porphyrobacter mercurialis
strain Coronado, the proposed type strain for this species. The assembly contains 3,482,341 bp in 10 contigs.
Draft Genome Sequence of a European Isolate of the Apple Canker Pathogen
Neonectria ditissima
Authors: Gómez-Cortecero Antonio , Harrison Richard J. , Armitage Andrew D.
Published: November 2015

The
Sordariomycetes
fungus
Neonectria ditissima
is a major pathogen of apples, causing canker on trees and fruit spoilage. We report here the draft genome sequence of a European strain isolated from cankerous tissue.
Draft Genome Sequence of
Pseudomonas
sp. Strain In5 Isolated from a Greenlandic Disease Suppressive Soil with Potent Antimicrobial Activity
Authors: Hennessy Rosanna C. , Glaring Mikkel A. , Michelsen Charlotte F. , Olsson Stefan , Stougaard Peter
Published: November 2015

Pseudomonas
sp. In5 is an isolate of disease suppressive soil with potent activity against pathogens. Its antifungal activity has been linked to a gene cluster encoding nonribosomal peptide synthetases producing the peptides nunamycin and nunapeptin. The genome sequence will provide insight into the genetics behind the antimicrobial activity of this strain.
Draft Genome Sequences of Facultative Methylotrophs,
Gemmobacter
sp. Strain LW1 and
Mesorhizobium
sp. Strain 1M-11, Isolated from Movile Cave, Romania
Authors: Kumaresan Deepak , Wischer Daniela , Hillebrand-Voiculescu Alexandra M. , Murrell J. Colin
Published: November 2015

Facultative methylotrophs belonging to the genera
Gemmobacter
and
Mesorhizobium
were isolated from microbial mat and cave water samples obtained from the Movile Cave ecosystem. Both bacteria can utilize methylated amines as their sole carbon and nitrogen source. Here, we report the draft genome sequences of
Gemmobacter
sp. strain LW1 and
Mesorhizobium
sp. strain IM1.
Draft Genome Sequence of the FungusTrametes hirsuta072
Authors: Pavlov Andrey R. , Tyazhelova Tatiana V. , Moiseenko Konstantin V. , Vasina Daria V. , Mosunova Olga V. , Fedorova Tatiana V. , Maloshenok Lilya G. , Landesman Elena O. , Bruskin Sergei A. , Psurtseva Nadezhda V. , Slesarev Alexei I. , Kozyavkin Sergei A. , Koroleva Olga V.
Published: November 2015

A standard draft genome sequence of the white rot saprotrophic fungusTrametes hirsuta072 (Basidiomycota,Polyporales) is presented. The genome sequence contains about 33.6 Mb assembled in 141 scaffolds with a G+C content of ~57.6%. The draft genome annotation predicts 14,598 putative protein-coding open reading frames (ORFs).
Complete Genome Sequence of
Enterococcus
Bacteriophage EFLK1
Authors: Khalifa Leron , Coppenhagen-Glazer Shunit , Shlezinger Mor , Kott-Gutkowski Miriam , Adini Omri , Beyth Nurit , Hazan Ronen
Published: November 2015

We previously isolated EFDG1, a lytic phage against enterococci for therapeutic use. Nevertheless, EFDG1-resistant bacterial strains (EFDG1
r
) have evolved. EFLK1, a new highly effective phage against EFDG1
r
strains, was isolated in this study. The genome of EFLK1 was fully sequenced, analyzed, and deposited in GenBank.
Draft Genome Sequence of Amantichitinum ursilacus IGB-41, a New Chitin-Degrading Bacterium
Authors: Kirstahler Philipp , Günther Michael , Grumaz Christian , Lindemann Elena , Rupp Steffen , Zibek Susanne , Sohn Kai
Published: November 2015

Amantichitinum ursilacus
IGB-41 is a new species of chitin-degrading bacterium isolated from soil, which secretes potential industrial enzymes. The genome of
A. ursilacus
was sequenced, and the gene set encoding chitinases was identified. Here, we present the draft genome of 4.9 Mb, comprising 38 contigs, and the corresponding annotation.
Draft Genome Sequences from Cyclospora cayetanensis Oocysts Purified from a Human Stool Sample
Authors: Qvarnstrom Yvonne , Wei-Pridgeon Yuping , Li Wen , Nascimento Fernanda S. , Bishop Henry S. , Herwaldt Barbara L. , Moss Delynn M. , Nayak Vishal , Srinivasamoorthy Ganesh , Sheth Mili , Arrowood Michael J.
Published: November 2015

The parasite
Cyclospora cayetanensis
causes foodborne diarrheal illness. Here, we report draft genome sequences obtained from
C. cayetanensis
oocysts purified from a human stool sample. The genome assembly consists of 865 contigs with a total length of 44,563,857 bases. These sequences can facilitate the development of subtyping tools to aid outbreak investigations.
High-Quality Draft Genome Sequence of Bacillus amyloliquefaciens Strain 629, an Endophyte from Theobroma cacao
Authors: SantAnna Brena M. M. , Marbach Phellippe P. A. , Rojas-Herrera Marcelo , De Souza Jorge T. , Roque Milton R. A. , Queiroz Artur T. L.
Published: November 2015

Bacillus amyloliquefaciens
strain 629 is an endophyte isolated from
Theobroma cacao
L. Here, we report the draft genome sequence (3.9 Mb) of
B. amyloliquefaciens
strain 629 containing 16 contigs (3,903,367 bp), 3,912 coding sequences, and an average 46.5% G+C content.
Genome Sequences of Three Turkey Orthoreovirus Strains Isolated in Hungary
Authors: Dandár Eszter , Fehér Enikő , Bálint Ádám , Kisfali Péter , Melegh Béla , Mató Tamás , Kecskeméti Sándor , Palya Vilmos , Bányai Krisztián , Farkas Szilvia L.
Published: November 2015

We have investigated the genomic properties of three turkey reovirus strains—19831M09, D1246, and D1104—isolated in Hungary in 2009. Sequence identity values and phylogenetic calculations indicated genetic conservativeness among the studied Hungarian strains and a close relationship with strains isolated in the United States.
Draft Genome Sequence of
Pseudoalteromonas
sp. Strain R3, a Red-Pigmented
l
-Amino Acid Oxidase-Producing Bacterium
Authors: Yu Zhiliang , Zhao Minyan , Qiu Juanping
Published: November 2015

Here, we report a draft 5.58-Mb genome sequence of
Pseudoalteromonas
sp. strain R3, isolated from an intertidal-zone sludge sample, which has
l
-amino acid oxidase activity. The genomics information of this strain will facilitate the study of
l
-amino acid oxidase, quorum sensing, and the relationship of the two.
Complete Genome Sequence of Mayaro Virus Imported from the Amazon Basin to São Paulo State, Brazil
Authors: Mota Mânlio Tasso Oliveira , Vedovello Danila , Estofolete Cassia , Malossi Camila Dantas , Araújo João Pessoa , Nogueira Maurício Lacerda
Published: November 2015

Mayaro (MAYV) is a neglected arbovirus from the tropical Americas. Here, we report the complete genome of an MAYV isolate from a patient returning from the Amazon basin and complaining of arthralgia, high fever, and headache, who was attended at an emergency service of São José do Rio Preto, São Paulo state, Brazil.
Draft Genome Sequence of Ardenticatena maritima 110S, a Thermophilic Nitrate- and Iron-Reducing Member of the
Chloroflexi
Class
Ardenticatenia
Authors: Hemp James , Ward Lewis M. , Pace Laura A. , Fischer Woodward W.
Published: November 2015

We report here the draft genome sequence of
Ardenticatena maritima
110S, the first sequenced member of class
Ardenticatenia
of the phylum
Chloroflexi
. This thermophilic organism is capable of a range of physiologies, including aerobic respiration and iron reduction. It also encodes a complete denitrification pathway with a novel nitric oxide reductase.
Draft Genome of
Thermanaerothrix daxensis
GNS-1, a Thermophilic Facultative Anaerobe from the
Chloroflexi
Class
Anaerolineae
Authors: Pace Laura A. , Hemp James , Ward Lewis M. , Fischer Woodward W.
Published: November 2015

We present the draft genome of
Thermanaerothrix daxensis
GNS-1, a thermophilic member of the
Chloroflexi
phylum. This organism was initially characterized as a nonmotile, strictly anaerobic fermenter; however, genome analysis demonstrates that it encodes genes for a flagellum and multiple pathways for aerobic and anaerobic respiration.
Draft Genome Sequence of Prosthecomicrobium hirschii ATCC 27832
T
Authors: Daniel Jeremy J. , Givan Scott A. , Brun Yves V. , Brown Pamela J. B.
Published: November 2015

We report the draft genome sequence of
Prosthecomicrobium hirschii
ATCC 27832
T
, an alphaproteobacterium with remarkable cellular morphologies. The chromosome comprises 6,484,983 bp in six scaffolds with a G+C content of 69%, and 6,066 potential coding sequences.
Complete Genome Sequence of Campylobacter jejuni RM1285, a Rod-Shaped Morphological Variant
Authors: Gunther Nereus W. , Bono James L. , Needleman David S.
Published: November 2015

Campylobacter jejuni
is a spiral shaped Gram-negative food-borne bacterial pathogen of humans found on poultry products. Strain RM1285 is a rod-shaped variant of this species. The genome of RM1285 was determined to be 1,635,803 bp, with a G+C content of 30.5%.
Complete Genome Sequences of Two Outbreak Strains of Salmonella enterica subsp.
enterica
Serovar Thompson Associated with Cilantro
Authors: Parker Craig T. , Huynh Steven , Gorski Lisa , Cooper Kerry K. , Miller William G.
Published: November 2015

Salmonella enterica
subsp.
enterica
serovar Thompson strains RM1984 (CADPH-99A2334) and RM1986 (CADPH-99A2345) are associated with a 1999 outbreak in contaminated cilantro. We report here the complete genome sequences and annotation of these two
S
. Thompson strains. These genomes are distinct and provide additional data for our understanding of
S. enterica
.
Complete Genome Sequence of Caulobacter crescentus Podophage Percy
Authors: Lerma Roxann A. , Tidwell T. J. , Cahill Jesse L. , Rasche Eric S. , Kuty Everett Gabriel F.
Published: November 2015

Podophage Percy infects
Caulobacter crescentus
, a Gram-negative bacterium that divides asymmetrically and is a commonly used model organism to study the cell cycle, asymmetric cell division, and cell differentiation. Here, we announce the sequence and annotated complete genome of the phiKMV-like podophage Percy and note its prominent features.
Draft Genome Sequences of Eight Nontypeable Haemophilus influenzae Strains Previously Characterized Using an Electrophoretic Typing Scheme
Authors: Mussa Huda J. , VanWagoner Timothy M. , Morton Daniel J. , Seale Thomas W. , Whitby Paul W. , Stull Terrence L.
Published: November 2015

Nontypeable
Haemophilus influenzae
is an important cause of human disease. Strains were selected for genome sequencing to represent the breadth of nontypeable strains within the species, as previously defined by the electrophoretic mobility of 16 metabolic enzymes.
Draft Genome Sequence of Bacillus vietnamensis Strain UCD-SED5 (Phylum
Firmicutes
)
Authors: Lee Ruth D. , Jospin Guillaume , Lang Jenna M. , Eisen Jonathan A. , Coil David A.
Published: November 2015

Here, we present the draft genome sequence of
Bacillus vietnamensis
UCD-SED5 (phylum
Firmicutes
). This strain was isolated from sediment surrounding
Zostera marina
roots near the UC Davis Bodega Marine Laboratory (Bodega, Bay, California) and represents the second genome of this species. The assembly consists of 4,325,707 bp, in 108 contigs.
Draft Genome Sequence of Streptococcus thermophilus C106, a Dairy Isolate from an Artisanal Cheese Produced in the Countryside of Ireland
Authors: Wels Michiel , Serrano L. Mariela , Eibrink Beerd-Jan , Backus Lennart , Bongers Roger S. , Vriesendorp Bastienne , Siezen Roland J. , van Hijum Sacha A. F. T. , Meijer Wilco C.
Published: November 2015

The lactic acid bacterium
Streptococcus thermophilus
is widely used for the fermentation of dairy products. Here, we present the draft genome sequence of
S. thermophilus
C106 isolated from an artisanal cheese produced in the countryside of Ireland.
Complete Genome Sequences of Three Clinical Isolates of Dengue Virus Serotype 1 from South Korean Travelers
Authors: Go Yun Young , Jung Eunhye , Jeong Young Eui , Balasuriya Udeni B. R.
Published: November 2015

In this study, we report the complete genome sequences of three clinical isolates of dengue virus serotype 1 isolated from South Korean travelers returning from different countries in Southeast Asia. The nucleotide sequence identities ranged from 91.5 to 92.2%, while the amino acid sequence identities ranged from 97.5 to 97.9% among the three clinical isolates.
Complete Genome Sequences of 11 Bordetella pertussis Strains Representing the Pandemic
ptxP3
Lineage
Authors: Bart Marieke J. , van der Heide Han G. J. , Zeddeman Anne , Heuvelman Kees , van Gent Marjolein , Mooi Frits R.
Published: November 2015

Pathogen adaptation has contributed to the resurgence of pertussis. To facilitate our understanding of this adaptation we report here 11 completely closed and annotated
Bordetella pertussis
genomes representing the pandemic
ptxP3
lineage. Our analyses included six strains which do not produce the vaccine components pertactin and/or filamentous hemagglutinin.
Draft Genome Sequence of a 16SrII-A Subgroup Phytoplasma Associated with Purple Coneflower (
Echinacea purpurea
) Witches’ Broom Disease in Taiwan
Authors: Chang Shu-Heng , Cho Shu-Ting , Chen Chung-Li , Yang Jun-Yi , Kuo Chih-Horng
Published: November 2015

The bacterial genus “
Candidatus
Phytoplasma” contains a group of insect-transmitted plant pathogens in the class
Mollicutes
. Here, we report a draft genome assembly and annotation of strain NCHU2014, which belongs to the 16SrII-A subgroup within this genus and is associated with purple coneflower witches’ broom disease in Taiwan.
Comparative Evaluation of Inoculation of Urine Samples with the Copan WASP and BD Kiestra InoqulA Instruments
Authors: Iversen Jesper , Stendal Gitta , Gerdes Cecilie M. , Meyer Christian H. , Andersen Christian Østergaard , Frimodt-Møller Niels
Published: November 2015

This study evaluated the quantitative results from and quality of the inoculation patterns of urine specimens produced by two automated instruments, the Copan WASP and the BD InoqulA. Five hundred twenty-six urine samples submitted in 10-ml canisters containing boric acid were processed within 30 min on an InoqulA instrument plating 10 μl of specimen, and on two WASP instruments, one plating 1 μl of specimen (WASP-1), and the second plating 10 μl of WASP (WASP-10). All samples were incubated, analyzed, and digitally imaged using the BD Kiestra total lab automation system. The results were evaluated using a quantitative protocol and assessed for the presence or absence of ≥5 distinct colonies. Separate studies were conducted using quality control (QC) organisms to determine the relative accuracy of WASP-1, WASP-10, and InoqulA instruments compared to the results obtained with a calibrated pipette. The results with QC organisms were calculated as the ratios of the counts of the automated instruments divided by the counts for the calibrated pipette (the gold standard method). The ratios for the InoqulA instrument were closest to 1.0, with the smallest standard deviations indicating that compared to a calibrated pipette, the InoqulA results were more accurate than those with the WASP instrument. For clinical samples, the WASP instruments produced higher colony counts and more commensals than the InoqulA instrument, with differences most notable for WASP-1. The InoqulA instrument was significantly better at dispersing organisms with counts of ≥105bacteria/ml of urine than were the WASP-1 and WASP-10 instruments (P< 0.05). Our results suggest that the InoqulA quantitative results are more accurate than the WASP results, and, moreover, the number of isolated colonies produced by the InoqulA instrument was significantly greater than that produced by the WASP instrument.
Detection of Carbapenemase Production in a Collection of Enterobacteriaceae with Characterized Resistance Mechanisms from Clinical and Environmental Origins by Use of Both Carba NP and Blue-Carba Tests
Authors: García-Fernández Sergio , Morosini María-Isabel , Gijón Desirèe , Beatobe Lorena , Ruiz-Garbajosa Patricia , Domínguez Lucas , Cantón Rafael , Valverde Aránzazu
Published: November 2015

Rapid-screening methods to confirm the presence of resistance mechanisms in multidrug-resistant bacteria are currently recommended. Carba NP and Blue-Carba tests were evaluated in carbapenemase-producing
Enterobacteriaceae
from hospital (
n
= 102) and environmental (
n
= 57) origins for detecting the different molecular classes among them. Both methods showed to be fast and cost-effective, with high sensitivity (98% to 100%) and specificity (100%), and may be easily introduced in the routine laboratory.
Evaluation of Oxacillin and Cefoxitin Disk and MIC Breakpoints for Prediction of Methicillin Resistance in Human and Veterinary Isolates of Staphylococcus intermedius Group
Authors: Wu M. T. , Burnham C.-A. D. , Westblade L. F. , Dien Bard J. , Lawhon S. D. , Wallace M. A. , Stanley T. , Burd E. , Hindler J. , Humphries R. M.
Published: November 2015

Staphylococcuspseudintermediusis a coagulase-positive species that colonizes the nares and anal mucosa of healthy dogs and cats. Human infections withS. pseudintermediusrange in severity from bite wounds and rhinosinusitis to endocarditis; historically, these infections were thought to be uncommon, but new laboratory methods suggest that their true incidence is underreported. Oxacillin and cefoxitin disk and MIC tests were evaluated for the detection ofmecA- ormecC-mediated methicillin resistance in 115 human and animal isolates of theStaphylococcus intermediusgroup (SIG), including 111Staphylococcuspseudintermediusand 4Staphylococcusdelphiniisolates, 37 of which weremecApositive. The disk and MIC breakpoints evaluated included the Clinical and Laboratory Standards Institute (CLSI) M100-S25Staphylococcus aureus/Staphylococcuslugdunensisoxacillin MIC breakpoints and cefoxitin disk and MIC breakpoints, the CLSI M100-S25 coagulase-negativeStaphylococcus(CoNS) oxacillin MIC breakpoint and cefoxitin disk breakpoint, the CLSI VET01-S2S. pseudintermediusoxacillin MIC and disk breakpoints, and the European Committee on Antimicrobial Susceptibility Testing (EUCAST)S. pseudintermediuscefoxitin disk breakpoint. The oxacillin results interpreted by the VET01-S2 (disk and MIC) and M100-S25 CoNS (MIC) breakpoints agreed with the results ofmecA/mecCPCR for all isolates, with the exception of one false-resistant result (1.3% ofmecA/mecCPCR-negative isolates). In contrast, cefoxitin tests performed poorly, ranging from 3 to 89% false susceptibility (very major errors) and 0 to 48% false resistance (major errors). BD Phoenix, bioMérieux Vitek 2, and Beckman Coulter MicroScan commercial automated susceptibility test panel oxacillin MIC results were also evaluated and demonstrated >95% categorical agreement withmecA/mecCPCR results if interpreted by using the M100-S25 CoNS breakpoint. The Alere penicillin-binding protein 2a test accurately detected allmecA-positive isolates, although for four isolates, cefoxitin induction was required prior to testing. These data demonstrate that the cefoxitin surrogate test does not reliably detect the presence ofmecAinS. pseudintermediusisolates and that laboratories should perform oxacillin disk or MIC tests of these isolates when they are encountered.
Directed Molecular Evolution of an Engineered Gammaretroviral Envelope Protein with Dual Receptor Use Shows Stable Maintenance of Both Receptor Specificities
Authors: Friis Kristina Pagh , Iturrioz Xavier , Thomsen Jonas , Alvear-Perez Rodrigo , Bahrami Shervin , Llorens-Cortes Catherine , Pedersen Finn Skou
Published: November 2015

We have previously reported the construction of a murine leukemia virus-based replication-competent gammaretrovirus (SL3-AP) capable of utilizing the human G protein-coupled receptor APJ (hAPJ) as its entry receptor and its natural receptor, the murine Xpr1 receptor, with equal affinities. The apelin receptor has previously been shown to function as a coreceptor for HIV-1, and thus, adaptation of the viral vector to this receptor is of significant interest. Here, we report the molecular evolution of the SL3-AP envelope protein when the virus is cultured in cells harboring either the Xpr1 or the hAPJ receptor. Interestingly, the dual receptor affinity is maintained even after 10 passages in these cells. At the same time, the chimeric viral envelope protein evolves in a distinct pattern in the apelin cassette when passaged on D17 cells expressing hAPJ in three separate molecular evolution studies. This pattern reflects selection for reduced ligand-receptor interaction and is compatible with a model in which SL3-AP has evolved not to activate hAPJ receptor internalization.

IMPORTANCE
Few successful examples of engineered retargeting of a retroviral vector exist. The engineered SL3-AP envelope is capable of utilizing either the murine Xpr1 or the human APJ receptor for entry. In addition, SL3-AP is the first example of an engineered retrovirus retaining its dual tropism after several rounds of passaging on cells expressing only one of its receptors. We demonstrate that the virus evolves toward reduced ligand-receptor affinity, which sheds new light on virus adaptation. We provide indirect evidence that such reduced affinity leads to reduced receptor internalization and propose a novel model in which too rapid receptor internalization may decrease virus entry.
PACT- and RIG-I-Dependent Activation of Type I Interferon Production by a Defective Interfering RNA Derived from Measles Virus Vaccine
Authors: Ho Ting-Hin , Kew Chun , Lui Pak-Yin , Chan Chi-Ping , Satoh Takashi , Akira Shizuo , Jin Dong-Yan , Kok Kin-Hang
Published: November 2015

The live attenuated measles virus vaccine is highly immunostimulatory. Identification and characterization of its components that activate the innate immune response might provide new strategies and agents for the rational design and development of chemically defined adjuvants. In this study, we report on the activation of type I interferon (IFN) production by a defective interfering (DI) RNA isolated from the Hu-191 vaccine strain of measles virus. We found that the Hu-191 virus induced IFN-β much more potently than the Edmonston strain. In the search for IFN-inducing species in Hu-191, we identified a DI RNA specifically expressed by this strain. This DI RNA, which was of the copy-back type, was predicted to fold into a hairpin structure with a long double-stranded stem region of 206 bp, and it potently induced the expression of IFN-β. Its IFN-β-inducing activity was further enhanced when both cytoplasmic RNA sensor RIG-I and its partner, PACT, were overexpressed. On the contrary, this activity was abrogated in cells deficient in PACT or RIG-I. The DI RNA was found to be associated with PACT in infected cells. In addition, both the 5′-di/triphosphate end and the double-stranded stem region on the DI RNA were essential for its activation of PACT and RIG-I. Taken together, our findings support a model in which a viral DI RNA is sensed by PACT and RIG-I to initiate an innate antiviral response. Our work might also provide a foundation for identifying physiological PACT ligands and developing novel adjuvants or antivirals.

IMPORTANCE
The live attenuated measles virus vaccine is one of the most successful human vaccines and has largely contained the devastating impact of a highly contagious virus. Identifying the components in this vaccine that stimulate the host immune response and understanding their mechanism of action might help to design and develop better adjuvants, vaccines, antivirals, and immunotherapeutic agents. We identified and characterized a defective interfering RNA from the Hu-191 vaccine strain of measles virus which has safely been used in millions of people for many years. We further demonstrated that this RNA potently induces an antiviral immune response through cellular sensors of viral RNA known as PACT and RIG-I. Similar types of viral RNA that bind with and activate PACT and RIG-I might retain the immunostimulatory property of measles virus vaccines but would not induce adaptive immunity. They are potentially useful as chemically defined vaccine adjuvants, antivirals, and immunostimulatory agents.
Persistent Simian Immunodeficiency Virus Infection Drives Differentiation, Aberrant Accumulation, and Latent Infection of Germinal Center Follicular T Helper Cells
Authors: Xu Huanbin , Wang Xiaolei , Malam Naomi , Aye Pyone P. , Alvarez Xavier , Lackner Andrew A. , Veazey Ronald S.
Published: November 2015

CD4
+
follicular T helper (Tfh) cells play a prominent role in humoral immune responses, but the mechanisms of their accumulation and infection in AIDS remain unclear. Here we found that germinal center (GC) Tfh cells, defined here as CXCR5
+
PD-1
HIGH
CD4
+
T cells, do not express the HIV coreceptor CCR5 yet serve as a latent reservoir in GCs. With disease progression, an expansion of GC Tfh cells is accompanied by increases in dysfunctional CD8
+
T cells. In contrast, Tfh precursor (CXCR5
−
CD4
+
T) cells in lymph nodes do express CCR5 and differentiate into GC Tfh cells following interleukin-6 (IL-6) and IL-21 stimulation, and viral DNA is detectable in fully differentiated GC Tfh cells
ex vivo
. This suggests that SIV-infected GC Tfh cells may be derived from Tfh precursor cell subsets that become infected in marginal zones and then migrate into GCs as fully mature GC Tfh cells that serve as persistent virus reservoirs. These findings suggest that viral persistence in lymph nodes drives compensatory differentiation, aberrant accumulation, and latent infection of GC Tfh cells, resulting in marked impairment of humoral immune responses.

IMPORTANCE
Generation of antibodies that can effectively eliminate viruses requires interactions of B cells with highly specialized T cells in GCs of lymphoid tissues called follicular T helper cells. Here we show that in simian immunodeficiency virus infection, these cells are initially infected in a precursor stage that leads to alterations in their homing, accumulation, and function that may be responsible for the inability of human immunodeficiency virus-infected patients to generate effective antibody responses.
Human T Cell Leukemia Virus Type 1 Infection of the Three Monocyte Subsets Contributes to Viral Burden in Humans
Authors: de Castro-Amarante Maria Fernanda , Pise-Masison Cynthia A. , McKinnon Katherine , Washington Parks Robyn , Galli Veronica , Omsland Maria , Andresen Vibeke , Massoud Raya , Brunetto Giovanna , Caruso Breanna , Venzon David , Jacobson Steven , Franchini Genoveffa
Published: November 2015

Because the viral DNA burden correlates with disease development, we investigated the contribution of monocyte subsets (classical, intermediate, and nonclassical monocytes) to the total viral burden in 22 human T cell leukemia virus type 1 (HTLV-1)-infected individuals by assessing their infectivity status, frequency, as well as chemotactic and phagocytic functions. All three monocyte subsets sorted from HTLV-1-infected individuals were positive for viral DNA, and the frequency of classical monocytes was lower in the blood of HTLV-1-infected individuals than in that of uninfected individuals, while the expression levels of the chemokine receptors CCR5, CXCR3, and CX3CR1 in classical monocytes were higher in HTLV-1-infected individuals than uninfected individuals; the percentage of intermediate monocytes and their levels of chemokine receptor expression did not differ between HTLV-1-infected and uninfected individuals. However, the capacity of intermediate monocytes to migrate to CCL5, the ligand for CCR5, was higher, and a higher proportion of nonclassical monocytes expressed CCR1, CXCR3, and CX3CR1. The level of viral DNA in the monocyte subsets correlated with the capacity to migrate to CCL2, CCL5, and CX3CL1 for classical monocytes, with lower levels of phagocytosis for intermediate monocytes, and with the level of viral DNA in CD8+and CD4+T cells for nonclassical monocytes. These data suggest a model whereby HTLV-1 infection augments the number of classical monocytes that migrate to tissues and become infected and the number of infected nonclassical monocytes that transmit virus to CD4+and CD8+T cells. These results, together with prior findings in a macaque model of HTLV-1 infection, support the notion that infection of monocytes by HTLV-1 is likely a requisite for viral persistence in humans.

IMPORTANCEMonocytes have been implicated in immune regulation and disease progression in patients with HTLV-1-associated inflammatory diseases. We detected HTLV-1 DNA in all three monocyte subsets and found that infection impacts surface receptor expression, migratory function, and subset frequency. The frequency of nonclassical patrolling monocytes is increased in HTLV-1-infected individuals, and they have increased expression of CCR1, CXCR3, and CX3CR1. The viral DNA level in nonclassical monocytes correlated with the viral DNA level in CD4+and CD8+T cells. Altogether, these data suggest an increased recruitment of classical monocytes to inflammation sites that may result in virus acquisition and, in turn, facilitate virus dissemination and viral persistence. Our findings thus provide new insight into the importance of monocyte infection in viral spread and suggest targeting of monocytes for therapeutic intervention.