bluuebunny/crossref_metadata_2025 huggingface dataset:
Roles of benthic algae in the structure, function, and assessment of stream ecosystems affected by acid mine drainage
Authors: Smucker Nathan J. , Drerup Samuel A. , Vis Morgan L.
Published: March 2014

Tens of thousands of stream kilometers worldwide are degraded by a legacy of acid loads, high metal concentrations, and altered habitat caused by acid mine drainage (AMD) from abandoned underground and surface mines. As the primary production base in streams, the condition of algal‐dominated periphyton communities is particularly important to nutrient cycling, energy flow, and higher trophic levels. Here, we synthesize current knowledge regarding how AMD‐associated stressors affect (i) algal communities and their use as ecological indicators, (ii) their functional roles in stream ecosystems, and (iii) how these findings inform management decisions and evaluation of restoration effectiveness. A growing body of research has found ecosystem simplification caused by AMD stressors. Species diversity declines, productivity decreases, and less efficient nutrient uptake and retention occur as AMD severity increases. New monitoring approaches, indices of biological condition, and attributes of algal community structure and function effectively assess AMD severity and effectiveness of management practices. Measures of ecosystem processes, such as nutrient uptake rates, extracellular enzyme activities, and metabolism, are increasingly being used as assessment tools, but remain in their infancy relative to traditional community structure‐based approaches. The continued development, testing, and implementation of functional measures and their use alongside community structure metrics will further advance assessments, inform management decisions, and foster progress toward restoration goals. Algal assessments will have important roles in making progress toward improving and sustaining the water quality, ecological condition, and ecosystem services of streams in regions affected by the legacy of unregulated coal mining.
Symbiodinium (Dinophyceae) diversity in reef‐invertebrates along an offshore to inshore reef gradient near Lizard Island, Great Barrier Reef
Authors: Tonk Linda , Sampayo Eugenia M. , LaJeunesse Todd C. , Schrameyer Verena , Hoegh‐Guldberg Ove
Published: March 2014

Despite extensive work on the genetic diversity of reef invertebrate‐dinoflagellate symbioses on the Great Barrier Reef (GBR; Australia), large information gaps exist from northern and inshore regions. Therefore, a broad survey was done comparing the community of inshore, mid‐shelf and outer reefs at the latitude of Lizard Island. Symbiodinium (Freudenthal) diversity was characterized using denaturing gradient gel electrophoresis fingerprinting and sequencing of the ITS2 region of the ribosomal DNA. Thirty‐nine distinct Symbiodinium types were identified from four subgeneric clades (B, C, D, and G). Several Symbiodinium types originally characterized from the Indian Ocean were discovered as well as eight novel types (C1kk, C1LL, C3nn, C26b, C161a, C162, C165, C166). Multivariate analyses on the Symbiodinium species diversity data showed a strong link with host identity, consistent with previous findings. Of the four environmental variables tested, mean austral winter sea surface temperature (SST) influenced Symbiodinium distribution across shelves most significantly. A similar result was found when the analysis was performed on Symbiodinium diversity data of genera with an open symbiont transmission mode separately with chl a and PAR explaining additional variation. This study underscores the importance of SST and water quality related variables as factors driving Symbiodinium distribution on cross‐shelf scales. Furthermore, this study expands our knowledge on Symbiodinium species diversity, ecological partitioning (including host‐specificity) and geographic ranges across the GBR. The accelerating rate of environmental change experienced by coral reef ecosystems emphasizes the need to comprehend the full complexity of cnidarian symbioses, including the biotic and abiotic factors that shape their current distributions.
Developing an information leaflet on 22q11.2 deletion syndrome for parents to use with professionals during healthcare encounters
Authors: Nicholl Honor , Doyle Carmel , Begley Thelma , Murphy Maryanne , Lawlor Anne , Malone Helen
Published: March 2014

Purpose

The purpose of this project was to gather parents' expertise to inform an educational leaflet for parents to share with professionals caring for children with 22q11.2 deletion syndrome (22q11.2 DS).

Design and Methods

A mixed‐method design was adopted. Data were collected by one focus group interview (n = 8) and questionnaires with 92 other parents of children with 22q11.2 DS.

Results

Quantitative and qualitative responses informed the development of an information leaflet.

Practice Implications

Parents are well positioned to assist in development of information leaflets that can minimize “repeated storytelling” during professional encounters.
An updated description of the Australian dingo (Canis dingo Meyer, 1793)
Authors: Crowther M. S. , Fillios M. , Colman N. , Letnic M.
Published: March 2014

A sound understanding of the taxonomy of threatened species is essential for setting conservation priorities and the development of management strategies. Hybridization is a threat to species conservation because it compromises the integrity of unique evolutionary lineages and can impair the ability of conservation managers to identify threatened taxa and achieve conservation targets. Australia's largest land predator, the dingo Canis dingo, is a controversial taxon that is threatened by hybridization. Since their arrival <5000 yBP (years Before Present) dingoes have been subject to isolation, leading to them becoming a unique canid. However, the dingo's taxonomic status is clouded by hybridization with modern domesticated dogs and confusion about how to distinguish ‘pure’ dingoes from dingo‐dog hybrids. Confusion exists because there is no description or series of original specimens against which the identities of putative hybrid and ‘pure’ dingoes can be assessed. Current methods to classify dingoes have poor discriminatory abilities because natural variation within dingoes is poorly understood, and it is unknown if hybridization may have altered the genome of post‐19th century reference specimens. Here we provide a description of the dingo based on pre‐20th century specimens that are unlikely to have been influenced by hybridization. The dingo differs from the domestic dog by relatively larger palatal width, relatively longer rostrum, relatively shorter skull height and relatively wider top ridge of skull. A sample of 19th century dingo skins we examined suggests that there was considerable variability in the colour of dingoes and included various combinations of yellow, white, ginger and darker variations from tan to black. Although it remains difficult to provide consistent and clear diagnostic features, our study places morphological limits on what can be considered a dingo.
Endothelial Ephrin‐B2 is Essential for Arterial Vasodilation in Mice
Authors: Lin Yuankai , Jiang Weiya , Ng Jennifer , Jina Asmita , Wang Rong A.
Published: March 2014

Objective

The cell surface protein ephrin‐B2 is expressed in arterial and not venous ECs throughout development and adulthood. Endothelial ephrin‐B2 is required for vascular development and angiogenesis, but its role in established arteries is currently unknown. We investigated the physiological role of ephrin‐B2 signaling in adult endothelium.

Methods

We generated adult conditional knockout mice lacking the Efnb2 gene specifically in ECs and evaluated the vasodilation responses to blood flow increase and ACh in the cremaster muscle preparation by intravital microscope and in carotid artery by in vivo ultrasound.

Results

We found that the Efnb2 conditional knockout mice were defective in acute arterial dilation. Vasodilation was impaired in cremaster arterioles in response to either increased flow or ACh, and in the carotid arteries in response to increased flow. Levels of cGMP, an effector of NO, were diminished in mutant arteries following ACh stimulation. GSNO, a donor for the vasodilator NO, alleviated the vasodilatory defects in the mutants. Immunostaining showed that a subset of ephrin‐B2 proteins colocalized with caveolin‐1, a negative regulator of eNOS.

Conclusions

Our data suggest that endothelial ephrin‐B2 is required for endothelial‐dependent arterial dilation and NO signaling in adult endothelium.
NPHS2 mutation analysis and primary nephrotic syndrome in southern Indians
Authors: Jaffer Asra , Unnisa Wali , Raju DSB , Jahan Parveen
Published: March 2014

Aim

Nephrotic syndrome is one of the most commonly diagnosed primary kidney diseases and its progressive forms can lead to chronic kidney disease and or end‐stage renal disease. Steroid‐resistant nephrotic syndrome is defined by resistance to standard steroid therapy and it remains one of the most intractable causes of kidney failure. Mutations in NPHS2, which encodes for podocin, an integral membrane protein of the glomerular epithelial cells (podocytes), represent a frequent cause of steroid‐resistant nephrotic syndrome worldwide. This study was aimed at screening for known NPHS2 mutations in Indians with nephrotic syndrome.

Methods

We screened a cohort of 484 subjects from the southern Indian population for the presence of four missense mutations G92C, P118L, R138Q and D160G within the NPHS2 gene using tetra primer ARMS PCR.

Results

Our results revealed that these mutations were seen only among the patients (14.02%) and were absent in the controls, suggesting their disease‐causing nature. Further categorization revealed that these mutations were together responsible for 18.5% of steroid‐resistant cases in our study group. Conversely, the studied mutations were not found in the controls as well as in the patients with steroid‐sensitive nephrotic syndrome.

Conclusion

This is the first such report from India. More studies are warranted to establish the frequency of NPHS2 mutations in the Asian–Indian population and such analysis may help in developing mutation(s)‐specific therapeutic interventions in the future.
Mucinous adenocarcinoma arising from supratentorial intramedullary neuroenteric cyst with broncho‐pulmonary differentiation
Authors: Okabe Hidetoshi , Katsura Kanade , Yamano Tsuyoshi , Tenjin Hiroshi , Nakahara Yoshikazu , Ishida Mitsuaki , Kato Toshikazu
Published: March 2014

Neuroenteric cysts are benign intradural endoderm cysts lined by gastrointestinal (GI) or tracheobronchial epithelial cells. Their malignant transformation is extremely rare and only six cases have been reported. In these cases, tissue lineage of the cystic endoderm cells giving rise to carcinoma was not clearly identified either as respiratory or as GI type. Herein, we report a case of mucinous adenocarcinoma arising from the neuroenteric cyst with broncho‐pulmonary differentiation in the right cerebral hemisphere of a Japanese woman in her late 50s. The cyst wall was entirely lined by the following respiratory epithelial components: stratified bronchial ciliated columnar epithelium with basal cells positive for CK5 and p63, terminal bronchiolar Clara cells positive for thyroid transcription factor (TTF)‐1, surfactant B and negative for surfactant C, type I pneumocytes positive for TTF‐1, negative for surfactant B and C, and type II pneumocytes positive for TTF‐1 and surfactant B and C. In addition, nests of hyperplastic single layered mucinous epithelial cells with bronchial goblet cell phenotype were also demonstrated, and histologic features were almost the same as the pulmonary type I congenital adenomatoid malformation (CCAM) with mucinous epithelial proliferation. The mucinous epithelial nests of type I CCAM are liable to develop mucinous adenocarcinoma and frequently accompany K‐ras mutation and expression of p16. However, K‐ras mutation and p‐16 expression were not detected in this case.
Basophilic inclusions and neuronal intermediate filament inclusions in amyotrophic lateral sclerosis and frontotemporal lobar degeneration
Authors: Ito Hidefumi
Published: March 2014

Basophilic inclusions (BIs) and neuronal intermediate filament inclusions (NIFIs) are key structures of basophilic inclusion body disease and neuronal intermediate filament inclusion disease (NIFID), respectively. BIs are sharply‐defined, oval or crescent neuronal intracytoplasmic inclusions that appear pale blue‐gray in color with HE staining and purple in color with Nissl but are stained poorly with silver impregnation techniques. Immunohistochemically BIs are negative for tau, trans‐activation response DNA 43 (TDP‐43), α‐synuclein, neurofilament (NF) and α‐internexin, positive for p62, and variably ubiquitinated. Noticeably, BIs are consistently fused in sarcoma (FUS) positive. NIFIs are by definition immuno‐positive for class IV IFs including three NF triplet subunit proteins and α‐internexin but negative for tau, TDP‐43, and α‐synuclein. In NIFID cases several types of inclusions have been identified. Among them, hyaline conglomerate‐like inclusions are the only type that meets the above immunohistochemical features of NIFIs. This type of inclusion appears upon HE staining as multilobulated, faintly eosinophilic or pale amphophilic spherical masses with a glassy appearance. These hyaline conglomerates appear strongly argyrophilic, and robustly and consistently immuno‐positive for IFs. In contrast, this type of inclusion shows no or only occasional dot‐like FUS immunoreactivity. Therefore, BIs and NIFIs are distinct from each other in terms of morphological, tinctorial and immunohistochemical features. However, basophilic inclusion body disease (BIBD) and NIFID are difficult to differentiate clinically. Moreover, Pick body‐like inclusions, the predominant type of inclusions seen in NIFID, are considerably similar to the BIs of BIBD in that this type of inclusion is basophilic, poorly argyrophilic, negative for IFs and intensely immuno‐positive for FUS. As BIBD and NIFID share FUS accumulation as the most prominent molecular pathology, whether these two diseases are discrete entities or represent a pathological continuum remains a question to be answered.
Task motivation influences alpha suppression following errors
Authors: Compton Rebecca J. , Bissey Bryn , Worby‐Selim Sharoda
Published: March 2014

The goal of the present research is to examine the influence of motivation on a novel error‐related neural marker, error‐related alpha suppression (ERAS). Participants completed an attentionally demanding flanker task under conditions that emphasized either speed or accuracy or under conditions that manipulated the monetary value of errors. Conditions in which errors had greater motivational value produced greater ERAS, that is, greater alpha suppression following errors compared to correct trials. A second study found that a manipulation of task difficulty did not affect ERAS. Together, the results confirm that ERAS is both a robust phenomenon and one that is sensitive to motivational factors.
Local Spatial and Temporal Factors Influencing Population and Societal Vulnerability to Natural Disasters
Authors: Zhou Yang , Li Ning , Wu Wenxiang , Wu Jidong , Shi Peijun
Published: March 2014

The identification of societal vulnerable counties and regions and the factors contributing to social vulnerability are crucial for effective disaster risk management. Significant advances have been made in the study of social vulnerability over the past two decades, but we still know little regarding China's societal vulnerability profiles, especially at the county level. This study investigates the county‐level spatial and temporal patterns in social vulnerability in China from 1980 to 2010. Based on China's four most recent population censuses of 2,361 counties and their corresponding socioeconomic data, a social vulnerability index for each county was created using factor analysis. Exploratory spatial data analysis, including global and local autocorrelations, was applied to reveal the spatial patterns of county‐level social vulnerability. The results demonstrate that the dynamic characteristics of China's county‐level social vulnerability are notably distinct, and the dominant contributors to societal vulnerability for all of the years studied were rural character, development (urbanization), and economic status. The spatial clustering patterns of social vulnerability to natural disasters in China exhibited a gathering–scattering–gathering pattern over time. Further investigations indicate that many counties in the eastern coastal area of China are experiencing a detectable increase in social vulnerability, whereas the societal vulnerability of many counties in the western and northern areas of China has significantly decreased over the past three decades. These findings will provide policymakers with a sound scientific basis for disaster prevention and mitigation decisions.
Design and cost optimization for hierarchical data
Authors: Tokola Kari , Lundell Andreas , Nevalainen Jaakko , Oja Hannu
Published: March 2014

In this paper, we consider balanced hierarchical data designs for both one‐sample and two‐sample (two‐treatment) location problems. The variances of the relevant estimates and the powers of the tests strongly depend on the data structure through the variance components at each hierarchical level. Also, the costs of a design may depend on the number of units at different hierarchy levels, and these costs may be different for the two treatments. Finally, the number of units at different levels may be restricted by several constraints. Knowledge of the variance components, the costs at each level, and the constraints allow us to find the optimal design. Solving such problems often requires advanced optimization tools and techniques, which we briefly explain in the paper. We develop new analytical tools for sample size calculations and cost optimization and apply our method to a data set on Baltic herring.
Genomic full‐length sequence of two HLA‐A alleles, A*01:01:01:01 and A*01:03, identified by cloning and sequencing
Authors: Lu L. , Xu Y. P.
Published: March 2014

Genomic full‐length sequences of HLA‐A*01:01:01:01 and A*01:03, were identified by cloning and sequencing from two Chinese donors.
Schirmer tear test I and rebound tonometry findings in healthy calves
Authors: Tofflemire Kyle L. , Whitley Elizabeth M. , Gould Stacie A. , Dewell Renee D. , Allbaugh Rachel A. , Ben‐Shlomo Gil , O'Connor Annette M. , David Whitley R.
Published: March 2014

Objective

To describe Schirmer tear test I and rebound tonometry findings in healthy bovine calves.

Animals studied

Thirty‐three clinically normal dairy breed calves of mean (SD) 11 (1.1) weeks (range, 9.3–13.3 weeks) of age were evaluated.

Procedures

A Schirmer tear test I was performed on each eye followed by tonometry, using a TonoVet®without topical anesthesia. We report means (SD) and statistical analysis of data for each assay.

Results

For both Schirmer tear test (STT) I and tonometry, significant differences were not found between fellow eyes (P = 0.1536 andP = 0.83, respectively). The mean (SD)STTI value of all eyes was 20.4 (5.0) mm/min (range, 9–34 mm/min) while the mean (SD) intraocular pressure (IOP) value of all eyes was 15.2 (5.2) mmHg (range, 7–25 mmHg).

Conclusions

This study reports normal data for theSTTI and rebound tonometry in calves. This data may be useful in complete ophthalmic examinations of cattle, guiding diagnosis of glaucoma, uveitis, and keratoconjunctivitis sicca. However, results of these diagnostic modalities must be interpreted in light of clinical signs, given the wide range of normal values obtained in this study.
Deformations of the Lie–Poisson sphere of a compact semisimple Lie algebra
Authors: Mărcuț Ioan
Published: March 2014

A compact semisimple Lie algebra $\mathfrak{g}$ induces a Poisson structure $\pi _{\mathbb{S}}$ on the unit sphere $\mathbb{S}(\mathfrak{g}^*)$ in $\mathfrak{g}^*$. We compute the moduli space of Poisson structures on $\mathbb{S}(\mathfrak{g}^*)$ around $\pi _{\mathbb{S}}$. This is the first explicit computation of a Poisson moduli space in dimension greater or equal than three around a degenerate (i.e. not symplectic) Poisson structure.
Hybrid CO2 Laser/Waterjet Machining of Polycrystalline Diamond Substrate: Material Separation Through Transformation Induced Controlled Fracture
Authors: Kalyanasundaram Dinesh , Schmidt Andrea , Molian Pal , Shrotriya Pranav
Published: March 2014

This paper presents a combined experimental and computational investigation of a novel material separation mechanism in polycrystalline diamond (PCD) substrates. A hybrid CO2 laser/waterjet (CO2-LWJ) machining system that combines a CO2 laser for localized heating and an abrasive-free waterjet to rapidly quench the heated area is utilized for cutting experiments on PCD substrates. Scanning electron microscopy (SEM) and micro-Raman spectrometry characterization performed on the cut surfaces show that cut surfaces were divided into two zones—a thin transformed zone near the top where the PCD grains have transformed to graphite and diamond-like carbon; and a fracture zone with the same composition as-received substrate. The experimental results indicate that the PCD substrates were cut through a “score and snap” mechanism—laser heating leads to localized damage and phase transformation of surface layers; and subsequently, stress fields developed due to constrained expansion of transformed material and waterjet quenching act on the laser made “score” to propagate crack through the thickness. Analytical solutions for thermal diffusion and force equilibrium are used to determine the temperature and stress fields in the PCD substrate during CO2-LWJ cutting. Fracture mechanics analysis of crack propagation is performed to demonstrate the feasibility of the “score and snap” mechanism for cutting of PCD substrates.
Protection Against Local Failure for Impulsively Loaded Vessels
Authors: Clayton Alan M. , Duffey Thomas A.
Published: March 2014

Significant changes have been incorporated in design limits for pressurized vessels in Section VIII, Division 3 of the ASME Code, starting in 2007. There is now a local damage-mechanics based strain-exhaustion limit as well as a separate global plastic collapse limit. In addition, Code Case 2564 (Sec. VIII, Div 3) has recently been approved to address impulsively loaded vessels. Recent studies (Nakamura, T., Kaguchi, H., and Kubo, S., 2000, “Failure Strain of Thin Cylindrical Vessel Subjected to Dynamic Internal Pressure,” Design and Analysis of Pressure Vessels and Piping, Vol. 399, R. Baliga, ed., pp. 47–54 and Duffey, T. A., 2011, “Plastic Instabilities in Spherical Vessels for Static and Dynamic Loading,” ASME J. Pressure Vessel Technol., 133(5), p. 051210) have shown that local strain limits play a particularly important role for these impulsively loaded vessels. In this paper, the new local strain-exhaustion procedure, originally intended for static-pressure-loaded vessels, is evaluated for adequacy in conservatively predicting failure for impulsively loaded vessels. Based upon symmetrically loaded cylindrical shell geometry, it is found that direct extension of the new local failure rules in the ASME Code to impulsively loaded vessels is unconservative. However, a hoop-strain local failure criterion predicts failures reasonably well.
Extrinsic origins of electronic disorder in 2D organic crystals
Authors: Wang Jiuyang , Dougherty Daniel B.
Published: March 2014

The dominant impact of extrinsic electronic disorder was observed in α-sexithiophene (α-6T) films grown on C60/Au(111) substrates by scanning tunneling microscopy and spectroscopy measurements. Sexithiophene molecules adopt an upright orientation with a structure that reflects both bulklike α-6T packing and C60 substrate templating effects. Apparent height variations in these films are assigned as molecular sliding defects but are observed to have negligible impact on the energy of the highest occupied molecular orbital. This orbital energy varies more significantly in response to random changes in probe tip, implying that the dominant origin of electronic disorder in two-dimensional organic crystals can be extrinsic to the film.
A Spectacular Experiment Exhibiting Atmospheric Pressure
Authors: Le Noxaïc Armand
Published: March 2014

The experiment described here is fairly easy to reproduce and dramatically shows the magnitude of ambient air pressure. Two circular plates of aluminum are applied one against the other. How do you make their separation very difficult? With only the help of an elastic band! You don't have to use a vacuum pump for this experiment.
Measuring Earth's Local Magnetic Field Using a Helmholtz Coil
Authors: Williams Jonathan E.
Published: March 2014

In this paper, I present a low-cost interactive experiment for measuring the strength of Earth's local magnetic field. This activity can be done in most high schools or two-year physics laboratories with limited resources, yet will have a tremendous learning impact. This experiment solidifies the three-dimensional nature of Earth's magnetic field vector and helps reinforce the aspect of the vertical component of Earth's magnetic field. Students should realize that Earth's magnetic field is not fully horizontal (except at the magnetic equator) and that a compass simply indicates the direction of the horizontal component of Earth's magnetic field. A magnetic dip needle compass can be used to determine the angle (known as the “dip angle” or “inclination angle”) measured from the direction in which Earth's magnetic field vector points to the horizontal. In this activity, students will be able to determine the horizontal component of the field using a Helmholtz coil and, knowing the dip angle, the Earth's magnetic field strength can be determined.
Squeeze flow behaviors of magnetorheological plastomers under constant volume
Authors: Xu Yangguang , Gong Xinglong , Liu Taixiang , Xuan Shouhu
Published: March 2014

The squeeze flow behaviors (including compressive, tensile, and oscillatory squeeze behaviors) of magnetorheological plastomers (MRPs, a kind of solidlike magnetic gels) under different experimental conditions are systematically investigated. Both compression and tension processes can be classified as elastic deformation region, stress relaxation region, and plastic flow region. A squeeze flow equation is used to describe the compressive behaviors of MRP in plastic flow region from which the compressive yield stress can be obtained and compared. The results demonstrate that both compressive yield stress and tensile yield stress are sensitive to magnetic field, particle distribution, and particle concentration. The yield stress of MRP under squeeze flow is larger than that of MR fluids due to the existence of polymer matrix. Asymmetry of hysteresis loop is found under oscillatory squeeze mode. The oscillatory squeeze behaviors of MRP are also influenced by magnetic field and particle concentration, but the influence of particle distribution is not so obvious. The related results under three operational modes are compared and qualitatively analyzed, which are helpful for further understanding the MR mechanism in the solidlike magnetic gels.
Structure of the Yeast Mitochondrial Large Ribosomal Subunit
Authors: Amunts Alexey , Brown Alan , Bai Xiao-chen , Llácer Jose L. , Hussain Tanweer , Emsley Paul , Long Fei , Murshudov Garib , Scheres Sjors H. W. , Ramakrishnan V.
Published: March 2014

Mitoribosomes

Mitochondria—found in all eukaryotic cells—have transferred most of their genes to the nuclear genome. The nuclear-localized mitochondrial genes are expressed and translated in the cytoplasm and the resulting mitochondrial proteins are imported into the mitochondria. Nevertheless, a few genes remain within mitochondria in the mitochondrial genome, and these genes are translated by mitochondrial ribosomes (mitoribosomes).

Amunts
et al.

(p.
1485
; see the Perspective by

Kühlbrandt

) determined the structure of mitoribosomes from yeast using single-particle cryo–electron microscopy. The mitoribosome is highly diverged from the bacterial and eukaryotic ribosomes with, for example, a distinctive exit tunnel for the newly synthesized peptide, and a membrane facing protuberance that might help to anchor the mitoribosome to the mitochondrial membrane.
The
Drosophila
Circadian Clock Is a Variably Coupled Network of Multiple Peptidergic Units
Authors: Yao Z. , Shafer O. T.
Published: March 2014

Circadian Rhythms

Circadian rhythms in the fruit fly
Drosophila
are driven by neurons in the brain.
Yao and Shafer
(p.
1516
) analyzed different sets of neurons that can drive circadian rhythms. Manipulating the period of each set of neurons separately revealed that when the various clock signals were fairly consistent, the fly showed a robust circadian rhythm. But when the various clock signals were seriously out of sync with one another, the fly was oblivious to the day-night cycle.
Two Decades After
BRCA:
Setting Paradigms in Personalized Cancer Care and Prevention
Authors: Couch Fergus J. , Nathanson Katherine L. , Offit Kenneth
Published: March 2014

The cloning of the breast cancer susceptibility genes
BRCA1
and
BRCA2
nearly two decades ago helped set in motion an avalanche of research exploring how genomic information can be optimally applied to identify and clinically care for individuals with a high risk of developing cancer. Genetic testing for mutations in
BRCA1
,
BRCA2
, and other breast cancer susceptibility genes has since proved to be a valuable tool for determining eligibility for enhanced screening and prevention strategies, as well as for identifying patients most likely to benefit from a targeted therapy. Here, we discuss the landscape of inherited mutations and sequence variants in
BRCA1
and
BRCA2
, the complexities of determining disease risk when the pathogenicity of sequence variants is uncertain, and current strategies for clinical management of women who carry
BRCA1/2
mutations.
Molecular Tuning of Quantum Plasmon Resonances
Authors: Nordlander Peter
Published: March 2014

The tuning of nanostructure plasmon resonances with bridging molecules offers opportunities for both plasmonics and molecular electronics.

[Also see Research Article by

Tan
et al.

]
25 Years After the
Exxon Valdez
, Where Are the Herring?
Authors: Malakoff David
Published: March 2014

Twenty-five years after the
Exxon Valdez
oil spill, researchers are still puzzling out the disaster's ecological impacts.
The Camel Connection
Authors: Kupferschmidt Kai
Published: March 2014

Two years after the first recorded deaths from MERS, most scientists agree that camels are key to the spread of the deadly disease. But containing it won't be easy.
Student Assembly Drives Yeast Project
Authors: Pennisi Elizabeth
Published: March 2014

For two undergraduates, helping build a synthetic yeast genome proved much more than just another lab course.
Dare to Do Less
Authors: Marshall Eliot
Published: March 2014

Scientists are looking for ways to spare women from aggressive treatment of ductal carcinoma in situ, a diagnosis that only sometimes leads to invasive breast cancer.
The Advocate
Authors: Kaiser Jocelyn
Published: March 2014

For more than 2 decades, Fran Visco, president of the National Breast Cancer Coalition, has been a force behind the second biggest U.S. breast cancer research program.
A New Breed of Cancer Researcher
Authors: Sinha Gunjan
Published: March 2014

As our understanding of cancer has gone from simplistic to complex, so too has research on treatment and detection. In a field once dominated by scientists with biomedical backgrounds, cancer research today includes engineers, chemists, and physicists. To land a job in any emerging area of cancer research, interdisciplinary training is becoming increasingly important. Luckily for job seekers, educational institutions are rising to meet the need.
Varicella and Varicella Vaccination in South Korea
Authors: Oh Sung Hee , Choi Eun Hwa , Shin Seon Hee , Kim Yun-Kyung , Chang Jin Keun , Choi Kyong Min , Hur Jae Kyun , Kim Kyung-Hyo , Kim Jae Youn , Chung Eun Hee , Lee Soo Young , Park Su Eun , Cha Sungho , Kim Kwang-Nam , Ma Sang Hyuk , Eun Byung Wook , Kim Nam Hee , Jo Dae Sun , Choi Bo Youl , Kim Shin Ah
Published: March 2014

With continuing occurrence of varicella despite increasing vaccine coverage for the past 20 years, a case-based study, a case-control study, and an immunogenicity and safety study were conducted to address the impact of varicella vaccination in South Korea. Varicella patients under the age of 16 years were enrolled for the case-based study. For the case-control study, varicella patients between 12 months and 15 years of age were enrolled with one control matched for each patient. For the immunogenicity and safety study, otherwise healthy children from 12 to 24 months old were immunized with Suduvax (Green Cross, South Korea). Fluorescent antibody to membrane antigen (FAMA) varicella-zoster virus (VZV) antibody was measured before and 6 weeks after immunization. In the case-based study, the median age of the patients was 4 years. Among 152 patients between 1 and 15 years of age, 139 children received varicella vaccine and all had breakthrough infections. Clinical courses were not ameliorated in vaccinated patients, but more vaccinated patients received outpatient rather than inpatient care. In the case-control study, the adjusted overall effectiveness of varicella vaccination was 54%. In the immunogenicity and safety study, the seroconversion rate and geometric mean titer for FAMA antibody were 76.67% and 5.31. Even with increasing varicella vaccine uptake, we illustrate no upward age shift in the peak incidence, a high proportion of breakthrough disease, almost no amelioration in disease presentation by vaccination, and insufficient immunogenicity of domestic varicella vaccine. There is need to improve the varicella vaccine used in South Korea.
Development and Use of a Serum Bactericidal Assay Using Pooled Human Complement To Assess Responses to a Meningococcal Group A Conjugate Vaccine in African Toddlers
Authors: Bash Margaret C. , Lynn Freyja , Mocca Brian , Borrow Ray , Findlow Helen , Hassan-King Musa , Preziosi Marie-Pierre , Idoko Olubukola , Sow Samba , Kulkarni Prasad , LaForce F. Marc
Published: March 2014

A meningococcal group A polysaccharide (PS) conjugate vaccine (PsA-TT) has been developed for African countries affected by epidemic meningitis caused byNeisseria meningitidis. Complement-mediated serum bactericidal antibody (SBA) assays are used to assess protective immune responses to meningococcal vaccination. Human complement (hC′) was used in early studies demonstrating antibody-mediated protection against disease, but it is difficult to obtain and standardize. We developed and evaluated a method for sourcing hC′ and then used the SBA assay with hC′ (hSBA) to measure bactericidal responses to PsA-TT vaccination in 12- to 23-month-old African children. Sera with active complement from 100 unvaccinated blood donors were tested for intrinsic bactericidal activity, SBA titer using rabbit complement (rSBA), and anti-group A PS antibody concentration. Performance criteria and pooling strategies were examined and then verified by comparisons of three independently prepared hC′ lots in two laboratories. hSBA titers of clinical trial sera were then determined using this complement sourcing method. Two different functional antibody tests were necessary for screening hC′. hSBA titers determined using three independent lots of pooled hC′ were within expected assay variation among lots and between laboratories. In African toddlers, PsA-TT elicited higher hSBA titers than meningococcal polysaccharide or Hib vaccines. PsA-TT immunization or PS challenge of PsA-TT-primed subjects resulted in vigorous hSBA memory responses, and titers persisted in boosted groups for over a year. Quantifying SBA using pooled hC′ is feasible and showed that PsA-TT was highly immunogenic in African toddlers.
Catheter-Related Bloodstream Infection by Tsukamurella inchonensis in an Immunocompromised Patient
Authors: Takebe Isao , Sawabe Etsuko , Ohkusu Kiyofumi , Tojo Naoko , Tohda Shuji
Published: March 2014

We report a case of catheter-related bloodstream infection byTsukamurella inchonensis, identified using 16S rRNA gene sequencing, in a patient with myelofibrosis who underwent a bone marrow transplant.Tsukamurellaspecies infections are rare. To our knowledge, this is the first case ofT. inchonensisbloodstream infection in an immunocompromised patient.
Multicenter Evaluation of the Quidel Lyra Direct C. difficile Nucleic Acid Amplification Assay
Authors: Beck Eric T. , Buchan Blake W. , Riebe Katherine M. , Alkins Brenda R. , Pancholi Preeti , Granato Paul A. , Ledeboer Nathan A.
Published: March 2014

Clostridium difficileis a Gram-positive bacterium commonly found in health care and long-term-care facilities and is the most common cause of antibiotic-associated diarrhea. Rapid detection of this bacterium can assist physicians in implementing contact precautions and appropriate antibiotic therapy in a timely manner. The purpose of this study was to compare the clinical performance of the Quidel Lyra Direct C. difficile assay (Lyra assay) (Quidel, San Diego, CA) to that of a direct cell culture cytotoxicity neutralization assay (CCNA) and enhanced toxigenic culture. This study was performed at three geographically diverse laboratories within the United States using residual stool specimens submitted for routineC. difficiletesting. Residual samples were tested using the Lyra assay on three real-time PCR platforms, and results were compared to those for direct CCNA and enhanced toxigenic culture. The test results for all platforms were consistent across all three test sites. The sensitivity and specificity of the Lyra assay on the SmartCycler II, ABI 7500 Fast DX, and ABI QuantStudio DX instruments compared to CCNA were 90.0% and 93.3%, 95.0% and 94.2%, and 93.8% and 95.0%, respectively. Compared to enhanced toxigenic culture, the sensitivity and specificity of the Lyra assay on the SmartCycler II, ABI 7500, and QuantStudio instruments were 82.1% and 96.9%, 89.3% and 98.8%, and 85.7% and 99.0%, respectively. Overall, the Lyra assay is easy to use and versatile and compares well toC. difficileculture methods.
Clonal Relationship and Differentiation among Mycobacterium abscessus Isolates as Determined Using the Semiautomated Repetitive Extragenic Palindromic Sequence PCR-Based DiversiLab System
Authors: Mougari Faiza , Raskine Laurent , Ferroni Agnes , Marcon Estelle , Sermet-Gaudelus Isabelle , Veziris Nicolas , Heym Beate , Gaillard Jean-Louis , Nassif Xavier , Cambau Emmanuelle
Published: March 2014

Mycobacterium abscessus
is a rapidly growing mycobacterium that causes respiratory tract infections in predisposed patients, such as those with cystic fibrosis and nosocomial skin and soft tissue infections. In order to investigate the clonal relationships between the strains causing epidemic episodes, we evaluated the discriminatory power of the semiautomated DiversiLab (DL) repetitive extragenic palindromic sequence PCR (REP-PCR) test for
M. abscessus
genotyping. Since
M. abscessus
was shown to be composed of subspecies (
M. abscessus
subsp.
massiliense
,
M. abscessus
subsp.
bolletii
, and
M. abscessus
subsp.
abscessus
), we also evaluated the ability of this technique to differentiate subspecies. The technique was applied to two collections of clinical isolates, (i) 83
M. abscessus
original isolates (43
M. abscessus
subsp.
abscessus
, 12
M. abscessus
subsp.
bolletii
, and 28
M. abscessus
subsp.
massiliense
) from infected patients and (ii) 35 repeated isolates obtained over 1 year from four cystic fibrosis patients. The DL REP-PCR test was standardized for DNA extraction, DNA amplification, and electrophoresis pattern comparisons. Among the isolates from distinct patients, 53/83 (62%) isolates showed a specific pattern, and 30 were distributed in 11 clusters and 6 patterns, with 2 to 4 isolates per pattern. The clusters and patterns did not fully correlate with multilocus sequence typing (MLST) analysis results. This revealed a high genomic diversity between patients, with a discriminatory power of 98% (Simpson's diversity index). However, since some isolates shared identical patterns, this raises the question of whether it is due to transmission between patients or a common reservoir. Multiple isolates from the same patient showed identical patterns, except for one patient infected by two strains. Between the
M. abscessus
subspecies, the indexes were <70%, indicating that the DL REP-PCR test is not an accurate tool for identifying organisms to the subspecies level. REP-PCR appears to be a rapid genotyping method that is useful for investigating epidemics of
M. abscessus
infections.
High Level of Vector Competence of Aedes aegypti and Aedes albopictus from Ten American Countries as a Crucial Factor in the Spread of Chikungunya Virus
Authors: Vega-Rúa Anubis , Zouache Karima , Girod Romain , Failloux Anna-Bella , Lourenço-de-Oliveira Ricardo
Published: March 2014

Chikungunya virus (CHIKV) causes a major public health problem. In 2004, CHIKV began an unprecedented global expansion and has been responsible for epidemics in Africa, Asia, islands in the Indian Ocean region, and surprisingly, in temperate regions, such as Europe. Intriguingly, no local transmission of chikungunya virus (CHIKV) had been reported in the Americas until recently, despite the presence of vectors and annually reported imported cases. Here, we assessed the vector competence of 35 American
Aedes aegypti
and
Aedes albopictus
mosquito populations for three CHIKV genotypes. We also compared the number of viral particles of different CHIKV strains in mosquito saliva at two different times postinfection. Primarily, viral dissemination rates were high for all mosquito populations irrespective of the tested CHIKV isolate. In contrast, differences in transmission efficiency (TE) were underlined in populations of both species through the Americas, suggesting the role of salivary glands in selecting CHIKV for highly efficient transmission. Nonetheless, both mosquito species were capable of transmitting all three CHIKV genotypes, and TE reached alarming rates as high as 83.3% and 96.7% in
A. aegypti
and
A. albopictus
populations, respectively.
A. albopictus
better transmitted the epidemic mutant strain CHIKV_0621 of the East-Central-South African (ECSA) genotype than did
A. aegypti
, whereas the latter species was more capable of transmitting the original ECSA CHIKV_115 strain and also the Asian genotype CHIKV_NC. Therefore, a high risk of establishment and spread of CHIKV throughout the tropical, subtropical, and even temperate regions of the Americas is more real than ever.

IMPORTANCE
Until recently, the Americas had never reported chikungunya (CHIK) autochthonous transmission despite its global expansion beginning in 2004. Large regions of the continent are highly infested with
Aedes aegypti
and
Aedes albopictus
mosquitoes, and millions of dengue (DEN) cases are annually recorded. Indeed, DEN virus and CHIK virus (CHIKV) share the same vectors. Due to a recent CHIK outbreak affecting Caribbean islands, the need for a Pan-American evaluation of vector competence was compelling as a key parameter in assessing the epidemic risk. We demonstrated for the first time that
A. aegypti
and
A. albopictus
populations throughout the continent are highly competent to transmit CHIK irrespective of the viral genotypes tested. The risk of CHIK spreading throughout the tropical, subtropical, and even temperate regions of the Americas is more than ever a reality. In light of our results, local authorities should immediately pursue and reinforce epidemiological and entomological surveillance to avoid a severe epidemic.
Substitution of Herpes Simplex Virus 1 Entry Glycoproteins with Those of Saimiriine Herpesvirus 1 Reveals a gD-gH/gL Functional Interaction and a Region within the gD Profusion Domain That Is Critical for Fusion
Authors: Fan Qing , Longnecker Richard , Connolly Sarah A.
Published: March 2014

To gain insight into the mechanism of herpesvirus entry into cells, the four glycoproteins that are necessary for herpes simplex virus (HSV) fusion were cloned from the saimiriine herpesvirus 1 (SaHV-1) genome, a primate member of the alphaherpesvirus family. Cell-cell fusion assays indicate that SaHV-1 entry glycoproteins function with the previously identified alphaherpesvirus entry receptors nectin-1 and CD155 but not with herpesvirus entry mediator (HVEM) or paired immunoglobulin-like type 2 receptor alpha (PILRα). Replacement of HSV-1 gD with the SaHV-1 gD homolog resulted in a complete loss of fusion function when coexpressed with HSV-1 gB and gH/gL. HSV-1 gD was also unable to substitute for SaHV-1 gD when coexpressed with SaHV-1 gB and gH/gL. Similarly, the gH/gL heterodimers from HSV-1 and SaHV-1 were not interchangeable. In contrast, both the HSV-1 and SaHV-1 gB homologs retained function in a heterotypic context. These results suggest that an essential interaction between homotypic gD and gH/gL occurs during both HSV-1 and SaHV-1 entry. To map the site of this homotypic interaction, we created a series of gD chimeras, focusing on the “profusion domain” (PFD) that consists of HSV-1 gD residues 261 to 305 or SaHV-1 gD residues 264 to 307. We identified a seven-amino-acid stretch (264 RTLPPPK 270) at the N terminus of the SaHV-1 gD PFD that contributes to homotypic fusion. Finally, we found that the gD receptor-binding region and PFD cannot function independently but that both can inhibit the function of wild-type gD.

IMPORTANCE
The herpesvirus entry machinery requires the concerted action of at least four glycoproteins; however, details of the interactions among these glycoproteins are not well understood. Like HSV-1, SaHV-1 belongs to the alphaherpesvirus subfamily. Using cell-cell fusion experiments, we found that SaHV-1 uses the entry receptors nectin-1 and CD155 but not HVEM or PILRα. By swapping the entry glycoproteins between HSV-1 and SaHV-1, we revealed a functional interaction between gD and gH/gL. To examine the homotypic interaction site on gD, we evaluated the function of a panel of HSV-1/SaHV-1 gD chimeras and identified a small region in the SaHV-1 gD profusion domain that is critical for SaHV-1 fusion. This study contributes to our understanding of the molecular mechanisms of herpesvirus entry and membrane fusion.