bluuebunny/crossref_metadata_2025 huggingface dataset:
Conflation of OpenStreetMap and Mobile Sports Tracking Data for Automatic Bicycle Routing
Authors: Bergman Cecilia , Oksanen Juha
Published: March 2016

This article investigates how workout trajectories from a mobile sports tracking application can be used to provide automatic route suggestions for bicyclists. We apply a Hidden Markov Model (HMM)‐based method for matching cycling tracks to a “bicycle network” extracted from crowdsourced OpenStreetMap (OSM) data, and evaluate its effective differences in terms of optimal routing compared with a simple geometric point‐to‐curve method. OSM has quickly established itself as a popular resource for bicycle routing; however, its high‐level of detail presents challenges for its applicability to popularity‐based routing. We propose a solution where bikeways are prioritized in map‐matching, achieving good performance; the HMM‐based method matched correctly on average 94% of the route length. In addition, we show that the extremely biased nature of the trajectory dataset, which is typical of volunteered user‐generated data, can be of high importance in terms of popularity‐based routing. Most computed routes diverged depending on whether the number of users or number of tracks was used as an indicator of popularity, which may imply varying preferences among different types of cyclists. Revising the number of tracks by diversity of users to surmount local biases in the data had a more limited effect on routing.
On the Emergence of Syntactic Structures: Quantifying and Modeling Duality of Patterning
Authors: Loreto Vittorio , Gravino Pietro , Servedio Vito D. P. , Tria Francesca
Published: March 2016

The complex organization of syntax in hierarchical structures is one of the core design features of human language. Duality of patterning refers, for instance, to the organization of the meaningful elements in a language at two distinct levels: a combinatorial level, where meaningless forms are combined into meaningful forms; and a compositional level, where meaningful forms are composed into larger lexical units. The question remains wide open regarding how such structures could have emerged. The aim of this paper is to address these two aspects in a self‐consistent way. First, we introduce suitable measures to quantify the level of combinatoriality and compositionality in a language, and we present a framework to estimate these observables in human natural languages. Second, we show that a recently introduced multi‐agent modeling scheme, namely the Blending Game, provides a mathematical framework to address the problem of how a population of individuals can bootstrap combinatoriality and compositionality. Theoretical predictions based on this model turn out to be in good agreement with empirical data. It is remarkable that the two sides of duality of patterning emerge simultaneously as a consequence of a pure cultural dynamics in a simulated environment that contains meaningful relations, provided a simple constraint on message transmission fidelity is also considered.
Language Evolution: Constraints and Opportunities From Modern Genetics
Authors: Dediu Dan , Christiansen Morten H.
Published: March 2016

Our understanding of language, its origins and subsequent evolution (including language change), is shaped not only by data and theories from the language sciences, but also fundamentally by the biological sciences. Recent developments in genetics and evolutionary theory offer both very strong constraints on what scenarios of language evolution are possible and probable, but also offer exciting opportunities for understanding otherwise puzzling phenomena. Due to the intrinsic breathtaking rate of advancement in these fields, and the complexity, subtlety, and sometimes apparent non‐intuitiveness of the phenomena discovered, some of these recent developments have either being completely missed by language scientists or misperceived and misrepresented. In this short paper, we offer an update on some of these findings and theoretical developments through a selection of illustrative examples and discussions that cast new light on current debates in the language sciences. The main message of our paper is that life is much more complex and nuanced than anybody could have predicted even a few decades ago, and that we need to be flexible in our theorizing instead of embracing a priori dogmas and trying to patch paradigms that are no longer satisfactory.
How Evolution May Work Through Curiosity‐Driven Developmental Process
Authors: Oudeyer Pierre‐Yves , Smith Linda B.
Published: March 2016

Infants' own activities create and actively select their learning experiences. Here we review recent models of embodied information seeking and curiosity‐driven learning and show that these mechanisms have deep implications for development and evolution. We discuss how these mechanisms yield self‐organized epigenesis with emergent ordered behavioral and cognitive developmental stages. We describe a robotic experiment that explored the hypothesis that progress in learning, in and for itself, generates intrinsic rewards: The robot learners probabilistically selected experiences according to their potential for reducing uncertainty. In these experiments, curiosity‐driven learning led the robot learner to successively discover object affordances and vocal interaction with its peers. We explain how a learning curriculum adapted to the current constraints of the learning system automatically formed, constraining learning and shaping the developmental trajectory. The observed trajectories in the robot experiment share many properties with those in infant development, including a mixture of regularities and diversities in the developmental patterns. Finally, we argue that such emergent developmental structures can guide and constrain evolution, in particular with regard to the origins of language.
Bartonella henselaetransmission by blood transfusion in mice
Authors: Silva Marilene Neves , Vieira‐Damiani Gislaine , Ericson Marna Elise , Gupta Kalpna , Gilioli Rovilson , de Almeida Amanda Roberta , Drummond Marina Rovani , Lania Bruno Grosselli , de Almeida Lins Karina , Soares Tânia Cristina Benetti , Velho Paulo Eduardo Neves Ferreira
Published: March 2016

BACKGROUND

Bartonellaspp. are neglected fastidious Gram‐negative bacilli. We isolatedBartonella henselaefrom 1.2% of 500 studied blood donors and demonstrated that the bacteria remain viable in red blood cell units after 35 days of experimental infection. Now, we aim to evaluate the possibility ofB. henselaetransmission by blood transfusion in a mouse model.

STUDY DESIGN AND METHODS

Eight BALB/c mice were intraperitoneal inoculated with a 30 µL of suspension with 104CFU/mL ofB. henselaeand a second group of eight mice were inoculated with saline solution and used as control. After 96 hours of inoculation, the animals were euthanized. We collected blood and tissue samples from skin, liver, and spleen. Thirty microliters of blood from fourBartonella‐inoculated animals were transfused into a new group (n = 4). Another group received blood from the control animals.B. henselaeinfection was investigated by conventional and nested polymerase chain reaction (PCR).

RESULTS

Blood samples from all 24 mice were negative by molecular tests though half of the tissue samples were positive by nested PCR in the intraperitonealBartonella‐investigated animals. Tissues from two of the four mice that received blood transfusions fromBartonella‐inoculated animals were also nested PCR positives.

CONCLUSIONS

Transmission ofB. henselaeby transfusion is possible in mice even when donor animals have undetectable bloodstream infection. The impact of humanBartonellasp. transmission through blood transfusion recipients must be evaluated.
Hemoglobin assessment: precision and practicability evaluated in the Netherlands—the HAPPEN study
Authors: Baart A. Mireille , de Kort Wim L.A.M. , van den Hurk Katja , Pasker‐de Jong Pieternel C.M.
Published: March 2016

BACKGROUND

Most donors do not like the invasive hemoglobin (Hb) measurement in fingerstick capillary samples. Alternative noninvasive devices have recently become available. In this study we assessed the precision and practicability of noninvasive devices and compared them with measurements in capillary and venous samples.

STUDY DESIGN AND METHODS

A total of 2589 blood donors were included in the study. Hb levels were measured with the noninvasive devices NBM 200 or Haemospect and compared with values obtained with the invasive devices HemoCue 201 and HemoCue 301 and with venous values. Precision was evaluated in terms of sensitivity and specificity for detection of Hb levels below the cutoff level for donation, taking venous values as “reference values.”

RESULTS

Hb levels measured with both invasive and noninvasive devices differed significantly from venous measurements. Measurements with invasive devices correlated stronger with venous values and were more precise. Sensitivity ranged from 30.1% (HemoCue 201) to 3.5% (Haemospect) in men and from 36.6% (HemoCue 201) to 10.8% (Haemospect) in women. Specificity ranged from 99.8% (HemoCue 201) to 95.5% (Haemospect) in men and from 98.9% (HemoCue 201) to 94.6% (NBM 200) in women. Most donors preferred the noninvasive measurement.

CONCLUSION

Measurements with invasive devices showed stronger correlation and better agreement with venous values than noninvasive devices. Sensitivity was low for all measurement devices, particularly the noninvasive ones. In terms of precision invasive measurement would be preferred for donor screening, although a majority of donors preferred the noninvasive measurement.
Sequence analysis of two variable cytomegalovirus genes for distinction between transfusion‐ and breast milk–transmitted infections in a very‐low‐birthweight infant
Authors: Yamagishi Naoji , Furui Yasumi , Koshinami Syota , Ichijo Koichi , Shimizu Yoshito , Hoshi Yuji , Gotanda Yuko , Miyakawa Keiko , Uchida Shigeharu , Tadokoro Kenji , Nagai Tadashi , Satake Masahiro
Published: March 2016

BACKGROUND

Cytomegalovirus (CMV) infections in very‐low‐birthweight infants can lead to serious clinical consequences. When CMV‐related symptoms occur after transfusion, CMV transmission is often attributed to the transfusion products rather than to breast milk. However, it is sometimes difficult to distinguish between transfusion‐transmitted and breast milk–transmitted CMV infections.

PATIENT AND METHODS

A patient was born at 27 gestational weeks with a weight of 689 g. He was transfused with leukoreduced red blood cells (LR‐RBCs), which were later found to be CMV seropositive and CMV DNA positive. He was also fed with CMV DNA–positive breast milk. Thereafter, he developed CMV disease with thrombocytopenia and jaundice. To determine the route of transmission, we analyzed the sequences of two variable CMV genes, UL139 and UL146, by direct sequence analysis. We also performed deep sequence analysis to determine whether there were polyclonal CMV strains in the LR‐RBCs transfused.

RESULTS

CMV DNA sequence‐matching rates for the LR‐RBCs and the patient's blood were 64.6% for the UL139 gene and 68.6% for the UL146 gene. In contrast, the sequences of these genes in the patient's blood were 100% matched with those in the breast milk. Furthermore, by deep sequence analysis, the CMV strain found in the patient's blood was not detected in the LR‐RBCs transfused.

CONCLUSION

The results indicate that the pathogenic CMV strain was transmitted through breast milk, which is consistent with the claims that transfusion‐transmitted CMV infection due to leukoreduced blood products is uncommon.
Evaluation of a virtual pet visit system with live video streaming of patient images over the Internet in a companion animal intensive care unit in the Netherlands
Authors: Robben Joris H. , Melsen Diede N. , Almalik Osama , Roomer Wendy , Endenburg Nienke
Published: March 2016

Objective

To evaluate the impact of a virtual pet visit system (“TelePet” System, TPS) on owners and staff of a companion animal ICU.

Design

Longitudinal interventional study (2010–2013).

Setting

Companion animal ICU at a university veterinary medical teaching hospital.

Study Populations

Pet owners, ICU technicians.

Interventions

The introduction of the TPS, with live video streaming of patient images over the Internet, in a companion animal ICU.

Measurements and Main Results

Pet owners experienced TPS as a valuable extra service. Most TPS users (72.4%) experienced less anxiety and felt less need (40.4% of TPS users) to visit their hospitalized pet in person. Most users (83.5%) shared TPS access with their family. The introduction of the TPS did not improve overall owner satisfaction, except for the score on “quality of medical treatment.” Seven of 26 indicators of owner satisfaction were awarded higher scores by TPS users than by TPS nonusers in the survey after the introduction of the system. However, the lack of randomization of owners might have influenced findings. The enthusiasm of the ICU technicians for the system was tempered by the negative feedback from a small number of owners. Nevertheless they recognized the value of the system for owners. The system was user friendly and ICU staff and TPS users experienced few technical problems.

Conclusions

As veterinary healthcare is moving toward a more client‐centered approach, a virtual pet visit system, such as TPS, is a relatively simple application that may improve the well‐being of most owners during the hospitalization of their pet.
Pericytes: A newly recognized player in wound healing
Authors: Bodnar Richard J. , Satish Latha , Yates Cecelia C. , Wells Alan
Published: March 2016

Pericytes have generally been considered in the context of stabilizing vessels, ensuring the blood barriers, and regulating the flow through capillaries. However, new reports suggest that pericytes may function at critical times to either drive healing with minimal scarring or, perversely, contribute to fibrosis and ongoing scar formation. Beneficially, pericytes probably drive much of the vascular involution that occurs during the transition from the regenerative to the resolution phases of healing. Pathologically, pericytes can assume a fibrotic phenotype and promote scarring. This perspective will discuss pericyte involvement in wound repair and the relationship pericytes form with the parenchymal cells of the skin. We will further evaluate the role pericytes may have in disease progression in relation to chronic wounds and fibrosis.
Educating Family Caregivers for Older Adults About Delirium: A Systematic Review
Authors: Bull Margaret J. , Boaz Lesley , Jermé Martha
Published: March 2016

Background

Delirium in older adults is considered a medical emergency; it contributes to a cascade of functional decline and to increased mortality. Early recognition of delirium symptoms is critical to prevent these negative consequences. Family caregivers who are educated about delirium could partner with nurses and other healthcare professionals in early recognition of delirium symptoms. Before implementing such partnership models, it is important to examine the effectiveness of educating family caregivers about delirium.

Aims

To examine whether providing education on delirium to family caregivers improved their knowledge, emotional state, or response in reducing the incidence of delirium in older adults.

Methods

For this systematic review, we conducted literature searches in CINAHL, Cochrane Library, Medline, PsycINFO, Web of Science, Social Sciences in ProQuest, Dissertations and Theses, and the Virginia Henderson Global Nursing eRepository for studies published in the English language between January 2000 and June 2015. Criteria for inclusion were: (a) primary focus on educating family caregivers for older adults about delirium; (b) use of experimental, quasi‐experimental, or comparative design; (c) measured family caregiver outcomes of delirium knowledge, emotional state, or response in reducing delirium incidence in older adults; and (d) published in the English language. Articles were appraised using Melnyk's rapid critical appraisal guides.

Results

Seven studies met the review criteria. Four studies found that family caregivers’ delirium knowledge increased; two noted that delirium incidence in older adults declined; and one study reported less distress following receipt of education.

Linking Evidence to Action

Providing family caregivers with information about delirium can be beneficial for both family caregivers and older adults. However, rigorous evaluation of education programs for family caregivers about delirium is needed.
Feral Swine Leptospira Seroprevalence Survey in Hawaii, USA, 2007–2009
Authors: Buchholz A. E. , Katz A. R. , Galloway R. , Stoddard R. A. , Goldstein S. M.
Published: March 2016

Leptospirosis is considered the most widespread of zoonotic diseases. It was a notifiable disease in the United States until 1995 and was reinstated to the list of nationally notifiable diseases in 2014. During the time of national surveillance, Hawaii consistently led the nation in reported annual incidence rates. Leptospirosis has remained a reportable disease in Hawaii. Significant changes have been documented since the early 1970s in the predominant serogroup infecting humans in Hawaii: infections due to Icterohaemorrhagiae have declined while infections due to Australis have increased. A recent study from Hawaii demonstrated that Australis was an uncommon infecting serogroup for small mammal hosts. Swine have not been previously studied in Hawaii but are well‐recognized maintenance hosts for leptospires belonging to the Australis serogroup. This study was undertaken to assess the prevalence of Leptospira antibody in feral swine in Hawaii. From January 2007 through December 2009, blood samples were collected opportunistically from feral swine. Using the microscopic agglutination test, we found antibody titres ≥1 : 100 to leptospires in 272 (33.8%) of 804 feral swine. The most frequently reacting serovars to the swine sera were Icterohaemorrhagiae (Icterohaemorrhagiae serogroup) (41.5%) and Bratislava (Australis serogroup) (33.8%). The high seroprevalence and presumptively infecting serovars suggest a link between swine and human infection.
Repeated ischaemic preconditioning: a novel therapeutic intervention and potential underlying mechanisms
Authors: Thijssen Dick H. J. , Maxwell Joseph , Green Daniel J. , Cable N. Timothy , Jones Helen
Published: March 2016

New Findings

What is the topic of this review?

This review discusses the effects of repeated exposure of tissue to ischaemic preconditioning on cardiovascular function, the attendant adaptations and their potential clinical relevance.

What advances does it highlight?

We discuss the effects of episodic exposure to ischaemic preconditioning to prevent and/or attenuate ischaemic injury and summarize evidence pertaining to improvements in cardiovascular function and structure. Discussion is provided regarding the potential mechanisms that contribute to both local and systemic adaptation. Findings suggest that clinical benefits result from both the prevention of ischaemic events and the attenuation of their consequences.

Ischaemic preconditioning (IPC) refers to the phenomenon whereby short periods of cyclical tissue ischaemia confer subsequent protection against ischaemia‐induced injury. As a consequence, IPC can ameliorate the myocardial damage following infarction and can reduce infarct size. The ability of IPC to confer remote protection makes IPC a potentially feasible cardioprotective strategy. In this review, we discuss the concept that repeated exposure of tissue to IPC may increase the ‘dose’ of protection and subsequently lead to enhanced protection against ischaemia‐induced myocardial injury. This may be relevant for clinical populations, who demonstrate attenuated efficacy of IPC to prevent or attenuate ischaemic injury (and therefore myocardial infarct size). Furthermore, episodic IPC facilitates repeated exposure to local (e.g. shear stress) and systemic stimuli (e.g. hormones, cytokines, blood‐borne substances), which may induce improvement in vascular function and health. Such adaptation may contribute to prevention of cardio‐ and cerebrovascular events. The clinical benefits of repeated IPC may, therefore, result from both the prevention of ischaemic events and the attenuation of their consequences. We provide an overview of the literature pertaining to the impact of repeated IPC on cardiovascular function, related to both local and remote adaptation, as well as potential clinical implications.
Framing the grid: effect of boundaries on grid cells and navigation
Authors: Krupic Julija , Bauza Marius , Burton Stephen , O'Keefe John
Published: March 2016

Cells in the mammalian hippocampal formation subserve neuronal representations of environmental location and support navigation in familiar environments. Grid cells constitute one of the main cell types in the hippocampal formation and are widely believed to represent a universal metric of space independent of external stimuli. Recent evidence showing that grid symmetry is distorted in non‐symmetrical environments suggests that a re‐examination of this hypothesis is warranted. In this review we will discuss behavioural and physiological evidence for how environmental shape and in particular enclosure boundaries influence grid cell firing properties. We propose that grid cells encode the geometric layout of enclosures.

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Presynaptic BK channels control transmitter release: physiological relevance and potential therapeutic implications
Authors: Griguoli Marilena , Sgritta Martina , Cherubini Enrico
Published: March 2016

BK channels are large conductance potassium channels characterized by four pore‐forming α subunits, often co‐assembled with auxiliary β and γ subunits to regulate Ca2+ sensitivity, voltage dependence and gating properties. Abundantly expressed in the CNS, they have the peculiar characteristic of being activated by both voltage and intracellular calcium rise. The increase in intracellular calcium via voltage‐dependent calcium channels (Cav) during spiking triggers conformational changes and BK channel opening. This narrows the action potential and induces a fast after‐hyperpolarization that shuts calcium channels. The tight coupling between BK and Cav channels at presynaptic active zones makes them particularly suitable for regulating calcium entry and neurotransmitter release. While in most synapses, BK channels exert a negative control on transmitter release under basal conditions, in others they do so only under pathological conditions, serving as an emergency brake to protect against hyperactivity. In particular cases, by interacting with other channels (i.e. limiting the activation of the delayed rectifier and the inactivation of Na+ channels), BK channels induce spike shortening, increase in firing rate and transmitter release. Changes in transmitter release following BK channel dysfunction have been implicated in several neurological disorders including epilepsy, schizophrenia, fragile X syndrome, mental retardation and autism. In particular, two mutations, one in the α and one in the β3 subunit, resulting in a gain of function have been associated with epilepsy. Hence, these discoveries have allowed identification of BK channels as new drug targets for therapeutic intervention.

image
Design and Validation of a High-Temperature Thermal Interface Resistance Measurement System
Authors: Hao Menglong , Saviers Kimberly R. , Fisher Timothy S.
Published: March 2016

In order to measure thermal interface resistance (TIR) at temperatures up to 700 °C, a test apparatus based on two copper 1D reference bars has been developed. Design details are presented with an emphasis on how the system minimizes the adverse effects of heat losses by convection and radiation on measurement accuracy. Profilometer measurements of the contacting surface are presented to characterize surface roughness and flatness. A Monte Carlo method is applied to quantify experimental uncertainties, resulting in a standard deviation of thermal resistance as low as 2.5 mm2 K/W at 700 °C. In addition, cyclic measurements of a standard thermal interface material (TIM) sample (graphite foil) are presented up to an interface temperature of 400 °C. The interface resistance results range between approximately 40 and 100 mm2 K/W. Further, a bare Cu–Cu interface is evaluated at several interface temperatures up to 700 °C.
Choroidal vasculature characteristics based choroid segmentation for enhanced depth imaging optical coherence tomography images
Authors: Chen Qiang , Niu Sijie , Yuan Songtao , Fan Wen , Liu Qinghuai
Published: March 2016

Purpose:

In clinical research, it is important to measure choroidal thickness when eyes are affected by various diseases. The main purpose is to automatically segment choroid for enhanced depth imaging optical coherence tomography (EDI‐OCT) images with five B‐scans averaging.

Methods:

The authors present an automated choroid segmentation method based on choroidal vasculature characteristics for EDI‐OCT images with five B‐scans averaging. By considering the large vascular of the Haller's layer neighbor with the choroid‐sclera junction (CSJ), the authors measured the intensity ascending distance and a maximum intensity image in the axial direction from a smoothed and normalized EDI‐OCT image. Then, based on generated choroidal vessel image, the authors constructed the CSJ cost and constrain the CSJ search neighborhood. Finally, graph search with smooth constraints was utilized to obtain the CSJ boundary.

Results:

Experimental results with 49 images from 10 eyes in 8 normal persons and 270 images from 57 eyes in 44 patients with several stages of diabetic retinopathy and age‐related macular degeneration demonstrate that the proposed method can accurately segment the choroid of EDI‐OCT images with five B‐scans averaging. The mean choroid thickness difference and overlap ratio between the authors’ proposed method and manual segmentation drawn by experts were −11.43 μm and 86.29%, respectively.

Conclusions:

Good performance was achieved for normal and pathologic eyes, which proves that the authors’ method is effective for the automated choroid segmentation of the EDI‐OCT images with five B‐scans averaging.
Global examination of the wind-dependence of very low frequency underwater ambient noise
Authors: Nichols Stephen M. , Bradley David L.
Published: March 2016

Ocean surface winds play a key role in underwater ambient noise generation. One particular frequency band of interest is the infrasonic or very low frequency (VLF) band from 1 to 20 Hz. In this spectral band, wind generated ocean surface waves interact non-linearly to produce acoustic waves, which couple into the seafloor to generate microseisms, as explained by the theory developed by Longuet-Higgins. This study examines long term data sets in the VLF portion of the ambient noise spectrum, collected by the hydroacoustic systems of the Comprehensive Nuclear-Test Ban Treaty Organization in the Atlantic, Pacific, and Indian Oceans. Three properties of the noise field were examined: (a) the behavior of the acoustic spectrum slope from 1 to 5 Hz, (b) correlation of noise levels and wind speeds, and (c) the autocorrelation behavior of both the noise field and the wind. Analysis results indicate the spectrum slope is site dependent, and for both correlation methods, a high correlation between wind and the noise field in the 1–5 Hz band.
Temporal alignment of pupillary response with stimulus events via deconvolution
Authors: McCloy Daniel R. , Larson Eric D. , Lau Bonnie , Lee Adrian K. C.
Published: March 2016

Analysis of pupil dilation has been used as an index of attentional effort in the auditory domain. Previous work has modeled the pupillary response to attentional effort as a linear time-invariant system with a characteristic impulse response, and used deconvolution to estimate the attentional effort that gives rise to changes in pupil size. Here it is argued that one parameter of the impulse response (the latency of response maximum, tmax) has been mis-estimated in the literature; a different estimate is presented, and it is shown how deconvolution with this value of tmax yields more intuitively plausible and informative results.
Interpersonal Emotion Regulation Among Adolescent Athletes: A Bayesian Multilevel Model Predicting Sport Enjoyment and Commitment
Authors: Tamminen Katherine A. , Gaudreau Patrick , McEwen Carolyn E. , Crocker Peter R.E.
Published: March 2016

Efforts to regulate emotions can influence others, and interpersonal emotion regulation within teams may affect athletes’ own affective and motivational outcomes. We examined adolescent athletes’ (N = 451, N teams = 38) self- and interpersonal emotion regulation, as well as associations with peer climate, sport enjoyment, and sport commitment within a multilevel model of emotion regulation in teams. Results of multilevel Bayesian structural equation modeling showed that athletes’ self-worsening emotion regulation strategies were negatively associated with enjoyment while other-improving emotion regulation strategies were positively associated enjoyment and commitment. The team-level interpersonal emotion regulation climate and peer motivational climates were also associated with enjoyment and commitment. Team-level factors moderated some of the relationships between athletes’ emotion regulation with enjoyment and commitment. These findings extend previous research by examining interpersonal emotion regulation within teams using a multilevel approach, and they demonstrate the importance of person- and team-level factors for athletes’ enjoyment and commitment.
Rapid assessment of disaster damage using social media activity
Authors: Kryvasheyeu Yury , Chen Haohui , Obradovich Nick , Moro Esteban , Van Hentenryck Pascal , Fowler James , Cebrian Manuel
Published: March 2016

Researchers show a correlation between per-capita social media activity and disaster damage, facilitating its rapid assessment.
Resolving enantiomers using the optical angular momentum of twisted light
Authors: Brullot Ward , Vanbel Maarten K. , Swusten Tom , Verbiest Thierry
Published: March 2016

Helical dichroism to resolve enantiomers using twisted light carrying only optical orbital angular momentum.
Accurate and predictive antibody repertoire profiling by molecular amplification fingerprinting
Authors: Khan Tarik A. , Friedensohn Simon , Gorter de Vries Arthur R. , Straszewski Jakub , Ruscheweyh Hans-Joachim , Reddy Sai T.
Published: March 2016

A new experimental-bioinformatic method was developed for error and bias correction in high-throughput antibody sequencing.
Electromagnetic stress at the boundary: Photon pressure or tension?
Authors: Wang Shubo , Ng Jack , Xiao Meng , Chan Che Ting
Published: March 2016

Whether light pulls or pushes a material boundary depends on the underlying microscopic structure.
Designing durable icephobic surfaces
Authors: Golovin Kevin , Kobaku Sai P. R. , Lee Duck Hyun , DiLoreto Edward T. , Mabry Joseph M. , Tuteja Anish
Published: March 2016

Researchers successfully design materials with extremely low ice adhesion.
Isolation and Complete Genome Sequence of Algibacter alginolytica sp. nov., a Novel Seaweed-Degrading Bacteroidetes Bacterium with Diverse Putative Polysaccharide Utilization Loci
Authors: Sun Cong , Fu Ge-yi , Zhang Chong-ya , Hu Jing , Xu Lin , Wang Rui-jun , Su Yue , Han Shuai-bo , Yu Xiao-yun , Cheng Hong , Zhang Xin-qi , Huo Ying-yi , Xu Xue-wei , Wu Min
Published: March 2016

The members of the phylum
Bacteroidetes
are recognized as some of the most important specialists for the degradation of polysaccharides. However, in contrast to research on
Bacteroidetes
in the human gut, research on polysaccharide degradation by marine
Bacteroidetes
is still rare. The genus
Algibacter
belongs to the
Flavobacteriaceae
family of the
Bacteroidetes
, and most species in this genus are isolated from or near the habitat of algae, indicating a preference for the complex polysaccharides of algae. In this work, a novel brown-seaweed-degrading strain designated HZ22 was isolated from the surface of a brown seaweed (
Laminaria japonica
). On the basis of its physiological, chemotaxonomic, and genotypic characteristics, it is proposed that strain HZ22 represents a novel species in the genus
Algibacter
with the proposed name
Algibacter alginolytica
sp. nov. The genome of strain HZ22, the type strain of this species, harbors 3,371 coding sequences (CDSs) and 255 carbohydrate-active enzymes (CAZymes), including 104 glycoside hydrolases (GHs) and 18 polysaccharide lyases (PLs); this appears to be the highest proportion of CAZymes (∼7.5%) among the reported strains in the class
Flavobacteria
. Seventeen polysaccharide utilization loci (PUL) are predicted to be specific for marine polysaccharides, especially algal polysaccharides from red, green, and brown seaweeds. In particular, PUL N is predicted to be specific for alginate. Taking these findings together with the results of assays of crude alginate lyases, we prove that strain HZ22
T
can completely degrade alginate. This work reveals that strain HZ22
T
has good potential for the degradation of algal polysaccharides and that the structure and related mechanism of PUL in strain HZ22
T
are worth further research.
Detection and Diversity of Fungal Nitric Oxide Reductase Genes (
p450nor
) in Agricultural Soils
Authors: Higgins Steven A. , Welsh Allana , Orellana Luis H. , Konstantinidis Konstantinos T. , Chee-Sanford Joanne C. , Sanford Robert A. , Schadt Christopher W. , Löffler Frank E.
Published: March 2016

Members of the Fungi convert nitrate (NO
3
−
) and nitrite (NO
2
−
) to gaseous nitrous oxide (N
2
O) (denitrification), but the fungal contributions to N loss from soil remain uncertain. Cultivation-based methodologies that include antibiotics to selectively assess fungal activities have limitations, and complementary molecular approaches to assign denitrification potential to fungi are desirable. Microcosms established with soils from two representative U.S. Midwest agricultural regions produced N
2
O from added NO
3
−
or NO
2
−
in the presence of antibiotics to inhibit bacteria. Cultivation efforts yielded 214 fungal isolates belonging to at least 15 distinct morphological groups, 151 of which produced N
2
O from NO
2
−
. Novel PCR primers targeting the
p450nor
gene, which encodes the nitric oxide (NO) reductase responsible for N
2
O production in fungi, yielded 26 novel
p450nor
amplicons from DNA of 37 isolates and 23 amplicons from environmental DNA obtained from two agricultural soils. The sequences shared 54 to 98% amino acid identity with reference P450nor sequences within the phylum
Ascomycota
and expand the known fungal P450nor sequence diversity.
p450nor
was detected in all fungal isolates that produced N
2
O from NO
2
−
, whereas
nirK
(encoding the NO-forming NO
2
−
reductase) was amplified in only 13 to 74% of the N
2
O-forming isolates using two separate
nirK
primer sets. Collectively, our findings demonstrate the value of
p450nor
-targeted PCR to complement existing approaches to assess the fungal contributions to denitrification and N
2
O formation.

IMPORTANCE
A comprehensive understanding of the microbiota controlling soil N loss and greenhouse gas (N
2
O) emissions is crucial for sustainable agricultural practices and addressing climate change concerns. We report the design and application of a novel PCR primer set targeting fungal
p450nor
, a biomarker for fungal N
2
O production, and demonstrate the utility of the new approach to assess fungal denitrification potential in fungal isolates and agricultural soils. These new PCR primers may find application in a variety of biomes to assess the fungal contributions to N loss and N
2
O emissions.
Transcriptional Profile during Deoxycholate-Induced Sporulation in a Clostridium perfringens Isolate Causing Foodborne Illness
Authors: Yasugi Mayo , Okuzaki Daisuke , Kuwana Ritsuko , Takamatsu Hiromu , Fujita Masaya , Sarker Mahfuzur R. , Miyake Masami
Published: March 2016

Clostridium perfringens
type A is a common source of foodborne illness (FBI) in humans. Vegetative cells sporulate in the small intestinal tract and produce the major pathogenic factor
C. perfringens
enterotoxin. Although sporulation plays a critical role in the pathogenesis of FBI, the mechanisms inducing sporulation remain unclear. Bile salts were shown previously to induce sporulation, and we confirmed deoxycholate (DCA)-induced sporulation in
C. perfringens
strain NCTC8239 cocultured with human intestinal epithelial Caco-2 cells. In the present study, we performed transcriptome analyses of strain NCTC8239 in order to elucidate the mechanism underlying DCA-induced sporulation. Of the 2,761 genes analyzed, 333 were up- or downregulated during DCA-induced sporulation and included genes for cell division, nutrient metabolism, signal transduction, and defense mechanisms. In contrast, the virulence-associated transcriptional regulators (the VirR/VirS system, the
agr
system,
codY
, and
abrB
) were not activated by DCA. DCA markedly increased the expression of signaling molecules controlled by Spo0A, the master regulator of the sporulation process, whereas the expression of
spo0A
itself was not altered in the presence or absence of DCA. The phosphorylation of Spo0A was enhanced in the presence of DCA. Collectively, these results demonstrated that DCA induced sporulation, at least partially, by facilitating the phosphorylation of Spo0A and activating Spo0A-regulated genes in strain NCTC8239 while altering the expression of various genes.

IMPORTANCE
Disease caused by
Clostridium perfringens
type A consistently ranks among the most common bacterial foodborne illnesses in humans in developed countries. The sporulation of
C. perfringens
in the small intestinal tract is a key event for its pathogenesis, but the factors and underlying mechanisms by which
C. perfringens
sporulates
in vivo
currently remain unclear. Bile salts, major components of bile, which is secreted from the liver for the emulsification of lipids, were shown to induce sporulation. However, the mechanisms underlying bile salt-induced sporulation have not yet been clarified. In the present study, we demonstrate that deoxycholate (one of the bile salts) induces sporulation by facilitating the phosphorylation of Spo0A and activating Spo0A-regulated genes using a transcriptome analysis. Thus, this study enhances our understanding of the mechanisms underlying sporulation, particularly that of bile salt-induced sporulation, in
C. perfringens
.
Complementation of Arginine Auxotrophy for Genetic Transformation of Coxiella burnetii by Use of a Defined Axenic Medium
Authors: Sandoz Kelsi M. , Beare Paul A. , Cockrell Diane C. , Heinzen Robert A.
Published: March 2016

Host cell-free (axenic) culture of
Coxiella burnetii
in acidified citrate cysteine medium-2 (ACCM-2) has provided important opportunities for investigating the biology of this naturally obligate intracellular pathogen and enabled the development of tools for genetic manipulation. However, ACCM-2 has complex nutrient sources that preclude a detailed study of nutritional factors required for
C. burnetii
growth. Metabolic reconstruction of
C. burnetii
predicts that the bacterium cannot synthesize all amino acids and therefore must sequester some from the host. To examine
C. burnetii
amino acid auxotrophies, we developed a nutritionally defined medium with known amino acid concentrations, termed ACCM-D. Compared to ACCM-2, ACCM-D supported longer logarithmic growth, a more gradual transition to stationary phase, and approximately 5- to 10-fold greater overall replication. Small-cell-variant morphological forms generated in ACCM-D also showed increased viability relative to that generated in ACCM-2. Lack of growth in amino acid-deficient formulations of ACCM-D revealed
C. burnetii
auxotrophy for 11 amino acids, including arginine. Heterologous expression of
Legionella pneumophila
argGH
in
C. burnetii
permitted growth in ACCM-D missing arginine and supplemented with citrulline, thereby providing a nonantibiotic means of selection of
C. burnetii
genetic transformants. Consistent with bioinformatic predictions, the elimination of glucose did not impair
C. burnetii
replication. Together, these results highlight the advantages of a nutritionally defined medium in investigations of
C. burnetii
metabolism and the development of genetic tools.

IMPORTANCE
Host cell-free growth and genetic manipulation of
Coxiella burnetii
have revolutionized research of this intracellular bacterial pathogen. Nonetheless, undefined components of growth medium have made studies of
C. burnetii
physiology difficult and have precluded the development of selectable markers for genetic transformation based on nutritional deficiencies. Here, we describe a medium, containing only amino acids as the sole source of carbon and energy, which supports robust growth and improved viability of
C. burnetii
. Growth studies confirmed that
C. burnetii
cannot replicate in medium lacking arginine. However, genetic transformation of the bacterium with constructs containing the last two genes in the
L. pneumophila
arginine biosynthesis pathway (
argGH
) allowed growth on defined medium missing arginine but supplemented with the arginine precursor citrulline. Our results advance the field by facilitating studies of
C. burnetii
metabolism and allowing non-antibiotic-based selection of
C. burnetii
genetic transformants, an important achievement considering that selectable makers based on antibiotic resistance are limited.
Nanomechanical Characterization of Bacillus anthracis Spores by Atomic Force Microscopy
Authors: Li Alex G. , Burggraf Larry W. , Xing Yun
Published: March 2016

The study of structures and properties of bacterial spores is important to understanding spore formation and biological responses to environmental stresses. While significant progress has been made over the years in elucidating the multilayer architecture of spores, the mechanical properties of the spore interior are not known. Here, we present a thermal atomic force microscopy (AFM) study of the nanomechanical properties of internal structures of
Bacillus anthracis
spores. We developed a nanosurgical sectioning method in which a stiff diamond AFM tip was used to cut an individual spore, exposing its internal structure, and a soft AFM tip was used to image and characterize the spore interior on the nanometer scale. We observed that the elastic modulus and adhesion force, including their thermal responses at elevated temperatures, varied significantly in different regions of the spore section. Our AFM images indicated that the peptidoglycan (PG) cortex of
Bacillus anthracis
spores consisted of rod-like nanometer-sized structures that are oriented in the direction perpendicular to the spore surface. Our findings may shed light on the spore architecture and properties.

IMPORTANCE
A nanosurgical AFM method was developed that can be used to probe the structure and properties of the spore interior. The previously unknown ultrastructure of the PG cortex of
Bacillus anthracis
spores was observed to consist of nanometer-sized rod-like structures that are oriented in the direction perpendicular to the spore surface. The variations in the nanomechanical properties of the spore section were largely correlated with its chemical composition. Different components of the spore materials showed different thermal responses at elevated temperatures.
Isolation of Endohyphal Bacteria from Foliar Ascomycota and
In Vitro
Establishment of Their Symbiotic Associations
Authors: Arendt Kayla R. , Hockett Kevin L. , Araldi-Brondolo Sarah J. , Baltrus David A. , Arnold A. Elizabeth
Published: March 2016

Endohyphal bacteria (EHB) can influence fungal phenotypes and shape the outcomes of plant-fungal interactions. Previous work has suggested that EHB form facultative associations with many foliar fungi in the Ascomycota. These bacteria can be isolated in culture, and fungi can be cured of EHB using antibiotics. Here, we present methods for successfully introducing EHB into axenic mycelia of strains representing two classes of Ascomycota. We first establish
in vitro
conditions favoring reintroduction of two strains of EHB (
Luteibacter
sp.) into axenic cultures of their original fungal hosts, focusing on fungi isolated from healthy plant tissue as endophytes:
Microdiplodia
sp. (Dothideomycetes) and
Pestalotiopsis
sp. (Sordariomycetes). We then demonstrate that these EHB can be introduced into a novel fungal host under the same conditions, successfully transferring EHB between fungi representing different classes. Finally, we manipulate conditions to optimize reintroduction in a focal EHB-fungal association. We show that EHB infections were initiated and maintained more often under low-nutrient culture conditions and when EHB and fungal hyphae were washed with MgCl
2
prior to reassociation. Our study provides new methods for experimental assessment of the effects of EHB on fungal phenotypes and shows how the identity of the fungal host and growth conditions can define the establishment of these widespread and important symbioses.
The
apt
/6-Methylpurine Counterselection System and Its Applications in Genetic Studies of the Hyperthermophilic Archaeon Sulfolobus islandicus
Authors: Zhang Changyi , She Qunxin , Bi Hongkai , Whitaker Rachel J.
Published: March 2016

Sulfolobus islandicus
serves as a model for studying archaeal biology as well as linking novel biology to evolutionary ecology using functional population genomics. In the present study, we developed a new counterselectable genetic marker in
S. islandicus
to expand the genetic toolbox for this species. We show that resistance to the purine analog 6-methylpurine (6-MP) in
S. islandicus
M.16.4 is due to the inactivation of a putative adenine phosphoribosyltransferase encoded by
M164_0158
(
apt
). The application of the
apt
gene as a novel counterselectable marker was first illustrated by constructing an unmarked α-amylase deletion mutant. Furthermore, the 6-MP counterselection feature was employed in a forward (loss-of-function) mutation assay to reveal the profile of spontaneous mutations in
S. islandicus
M.16.4 at the
apt
locus. Moreover, the general conservation of
apt
genes in the crenarchaea suggests that the same strategy can be broadly applied to other crenarchaeal model organisms. These results demonstrate that the
apt
locus represents a new tool for genetic manipulation and sequence analysis of the hyperthermophilic crenarchaeon
S. islandicus
.

IMPORTANCE
Currently, the
pyrEF
/5-fluoroorotic acid (5-FOA) counterselection system remains the sole counterselection marker in crenarchaeal genetics. Since most
Sulfolobus
mutants constructed by the research community were derived from genetic hosts lacking the
pyrEF
genes, the
pyrEF
/5-FOA system is no longer available for use in forward mutation assays. Demonstration of the
apt
/6-MP counterselection system for the
Sulfolobus
model renders it possible to again study the mutation profiles in mutants that have already been constructed by the use of strains with a
pyrEF
-deficient background. Furthermore, additional counterselectable markers will allow us to conduct more sophisticated genetic studies, i.e., investigate mechanisms of chromosomal DNA transfer and quantify recombination frequencies among
S. islandicus
strains.