bluuebunny/crossref_metadata_2025_split huggingface dataset:
Feeding habits of extant and fossil canids as determined by their skull geometry
Authors: Meloro C. , Hudson A. , Rook L. 
Published: December 2014

AbstractThe canids belong to one of the most prominent families of mammalian carnivores. Feeding adaptations of extant species is well documented by field observations; however, we are still missing palaeoecological insights for many enigmatic fossil specimens. We employ geometric morphometrics to quantify skull size and shape in extant and fossil members of the Canini tribe, inclusive of jackals and wolf‐like taxa. Skull data are tested to identify correlates of dietary adaptations in extant species for predicting adaptations in fossils. Main vectors of shape variation correlate with the relative skull‐palatal length, the position of the upper carnassial tooth and the anterior tip of the secondary palate. Allometry occurs in the palatal shape but size explains only a small fraction (about 4%) of shape variance. Although we quantified only palatal and tooth shape for the inclusion of fragmentary fossils, discriminant function analysis successfully classify extant Canini in dietary groups (small, medium and large prey specialist) with 89% of accuracy. The discriminant functions provide insights into many enigmatic specimens such as Eucyon adoxus (=small prey), fossil jackal‐like from Koobi Fora formation (=small prey) and the Plio‐Pleistocene Old World canid guild (Canis etruscus, C. arnensis and Lycaon falconeri). Clearly, both skull size and shape are excellent predictors of feeding habits in Canini thus also provide information about fossil taxonomic affinities.
Fluorescent protein‐mediated colour polymorphism in reef corals: multicopy genes extend the adaptation/acclimatization potential to variable light environments
Authors: Gittins John R. , D'Angelo Cecilia , Oswald Franz , Edwards Richard J. , Wiedenmann Jörg 
Published: December 2014

AbstractThe genomic framework that enables corals to adjust to unfavourable conditions is crucial for coral reef survival in a rapidly changing climate. We have explored the striking intraspecific variability in the expression of coral pigments from the green fluorescent protein (GFP) family to elucidate the genomic basis for the plasticity of stress responses among reef corals. We show that multicopy genes can greatly increase the dynamic range over which corals can modulate transcript levels in response to the light environment. Using the red fluorescent protein amilFP597 in the coral Acropora millepora as a model, we demonstrate that its expression increases with light intensity, but both the minimal and maximal gene transcript levels vary markedly among colour morphs. The pigment concentration in the tissue of different morphs is strongly correlated with the number of gene copies with a particular promoter type. These findings indicate that colour polymorphism in reef corals can be caused by the environmentally regulated expression of multicopy genes. High‐level expression of amilFP597 is correlated with reduced photodamage of zooxanthellae under acute light stress, supporting a photoprotective function of this pigment. The cluster of light‐regulated pigment genes can enable corals to invest either in expensive high‐level pigmentation, offering benefits under light stress, or to rely on low tissue pigment concentrations and use the conserved resources for other purposes, which is preferable in less light‐exposed environments. The genomic framework described here allows corals to pursue different strategies to succeed in habitats with highly variable light stress levels. In summary, our results suggest that the intraspecific plasticity of reef corals’ stress responses is larger than previously thought.
Mediation analysis of health‐related quality of life among people living with HIV infection in China
Authors: Li Xianhong , Li Ling , Wang Honghong , Fennie Kristopher P , Chen Jia , Williams Ann Bartley 
Published: December 2014

AbstractThe effects of stigma, social support, and depressive symptoms on health‐related quality of life are well documented in the literature, but how these psychological factors interact with each other, and the combined effects when taken together on the health‐related quality of life for people living with HIV, remain unclear. This cross‐sectional study investigated 114 people living with HIV who were taking antiretroviral medication using the HIV/AIDS‐related Stigma Scale (Chinese version), the Social Support Rating Scale, the Center for Epidemiological Studies Depression Scale, and the Medical Outcomes Study–HIV health survey. Multiple linear regression analyses were used to examine the mediation effect of the psychosocial factors on health‐related quality of life. Results showed that stigma and social support did not have direct effects, but indirect effects on health‐related quality of life through a full mediation effect of depressive symptoms. The results indicate that interventions targeting depression might be the most effective approach to improving health‐related quality of life among people living with HIV who are taking antiretroviral medication in China.
THE ROLE OF ISSUE LINKAGE IN MANAGING NONCOOPERATING BASINS: THE CASE OF THE MEKONG
Authors: DO KIM HANG PHAM , DINAR ARIEL 
Published: December 2014

AbstractThe Mekong River (MR) is the major water source in Southeast Asia, sharedby six countries. There is a rush, by riparian states, to acquire sources of alternative energy and other benefits to meet growing demands for water and energy. China and Myanmar have refused to cooperate fully in the MR Forum, leading to increase risks within the region. Development of the water resources of the MR Basin is the subject of intense debate both within the Mekong region and internationally. This paper investigates the concept of issue linkage to resolve unidirectional externalities in the MR. Using linked games, the paper shows that the downstream nations can consider the use of linkage as a form of side payment in achieving a basin‐wide agreement. While this approach supports the Integrated Water Resource Management‐based Basin Development Strategy adopted by the Mekong River Commission in April 2011 for managing the region's sustainability development, facts on the ground suggest that traditional issues to be linked may not be sufficient. The paper addresses this observation and suggests a cadre of issues, including nontraditional ones, to be analyzed in a future work.
DEGREE OF ECONOMIC UNSUSTAINABILITY IN THE MANAGEMENT OF RENEWABLE RESOURCES
Authors: KITTI MITRI 
Published: December 2014

AbstractA criterion commonly used to determine economic sustainability posits that the discounted welfare should not decrease over time. Resource management problems involving fluctuating stocks may be exacerbated by a lack of sustainable policies unless some violations of this condition are accepted. Moreover, sustainable policies may lead to the minimal welfare levels. To alleviate these problems, a new notion of sustainability is suggested. In this new form of sustainability, violations of nondecreasing welfare are accepted to a certain degree. The policies that maximize the discounted welfare under the constraint for the largest accepted violation for sustainability satisfy a dynamic programming type of fixed‐point condition that can be effectively utilized for finding optimal policies. The new notion of sustainability can also be utilized in defining an index for measuring the degree of overall unsustainability of resource management problems and different harvesting policies.
Near‐infrared spectroscopy reveals link between chronic physical activity and anterior frontal oxygenated hemoglobin in healthy young women
Authors: Cameron Tracy A. , Lucas Samuel J. E. , Machado Liana 
Published: December 2014

AbstractCerebrovascular and cognitive functioning peak developmentally in young adults, yet recent evidence indicates they may benefit on these fronts from regular engagement in physical activity. In light of epidemiological trends for increasingly sedentary lifestyles and the importance of optimal cerebrovascular and cognitive functioning, here we investigated relationships between physical activity levels, anterior frontal hemodynamics, and cognitive performance in 52 healthy young women. Analyses positively linked chronic physical activity level (CPAL) with anterior frontal oxygenated hemoglobin and cognitive inhibitory control, indicating regular physical activity may lead to hemodynamic and cognitive benefits, even in a cohort at developmental peak. In addition, higher anterior frontal oxygenated hemoglobin was linked to better performance for the most difficult cognitive task. Given the importance of oxygen availability for cognitive functioning, the current discovery of a relationship with CPAL may provide important insight toward understanding exercise‐cognition links.
Comparison of the canine corneal epithelial cell sheets cultivated from limbal stem cells on canine amniotic membrane, atelocollagen gel, and temperature‐responsive culture dish
Authors: Nam Eunryel , Fujita Naoki , Morita Maresuke , Tsuzuki Keiko , Lin Hsing Yi , Chung Cheng Shu , Nakagawa Takayuki , Nishimura Ryohei 
Published: December 2014

AbstractObjectiveThe current study compared canine corneal epithelial cell sheets cultivated from limbal stem cells on amniotic membrane, atelocollagen gel, and temperature‐responsive culture dish.ProceduresWe collected limbal epithelial cells from the intact eyes of beagles and cultivated the cells on denuded canine amniotic membranes, temperature‐responsive cell culture labware, and collagen gel with 3T3 feeder cells. Immunofluorescence staining for Ki‐67 was used to analyze the capacity of cell proliferation in the sheets. Immunofluorescence staining was also performed for the corneal epithelium‐specific marker cytokeratin 3 and putative stem cell markers ABCG2 and p63. Reverse‐transcription polymerase chain reaction (RT‐PCR) was performed to detect ABCG2 and p63.ResultsThe growth rates of the cultivated cells, or the times it took them to reach confluency, were different for the three scaffolds. The cultivated sheet on the temperature‐responsive dish consisted of 2–3 layers, while those on the collagen gel and on the amniotic membrane consisted of 5–8 layers. The basal layer cells grown on all three scaffolds expressed putative stem cell markers. In real‐time RT‐PCR analysis, the highest level of p63 was observed in the sheets grown on collagen gel.ConclusionsIn this study, the cells cultured on the collagen gel demonstrated a capacity for cell proliferation, and the expressions of stem cells in the sheets suggested that collagen gel is the most suitable carrier for clinical use.
Monitoring external beam radiotherapy using real‐time beam visualization
Authors: Jenkins Cesare H. , Naczynski Dominik J. , Yu Shu‐Jung S. , Xing Lei 
Published: December 2014

Purpose:To characterize the performance of a novel radiation therapy monitoring technique that utilizes a flexible scintillating film, common optical detectors, and image processing algorithms for real‐time beam visualization (RT‐BV).Methods:Scintillating films were formed by mixing Gd2O2S:Tb (GOS) with silicone and casting the mixture at room temperature. The films were placed in the path of therapeutic beams generated by medical linear accelerators (LINAC). The emitted light was subsequently captured using a CMOS digital camera. Image processing algorithms were used to extract the intensity, shape, and location of the radiation field at various beam energies, dose rates, and collimator locations. The measurement results were compared with known collimator settings to validate the performance of the imaging system.Results:The RT‐BV system achieved a sufficient contrast‐to‐noise ratio to enable real‐time monitoring of the LINAC beam at 20 fps with normal ambient lighting in the LINAC room. The RT‐BV system successfully identified collimator movements with sub‐millimeter resolution.Conclusions:The RT‐BV system is capable of localizing radiation therapy beams with sub‐millimeter precision and tracking beam movement at video‐rate exposure.
A Diagnostic HIV-1 Tropism System Based on Sequence Relatedness
Authors: Edwards Suzanne , Stucki Heinz , Bader Joëlle , Vidal Vincent , Kaiser Rolf , Battegay Manuel , Klimkait Thomas 
Published: December 2014

ABSTRACTKey clinical studies for HIV coreceptor antagonists have used the phenotyping-based Trofile test. Meanwhile various simpler-to-do genotypic tests have become available that are compatible with standard laboratory equipment and Web-based interpretation tools. However, these systems typically analyze only the most prominent virus sequence in a specimen. We present a new diagnostic HIV tropism test not needing DNA sequencing. The system, XTrack, uses physical properties of DNA duplexes after hybridization of single-stranded HIV-1envV3 loop probes to the clinical specimen. Resulting “heteroduplexes” possess unique properties driven by sequence relatedness to the reference and resulting in a discrete electrophoretic mobility. A detailed optimization process identified diagnostic probe candidates relating best to a large number of HIV-1 sequences with known tropism. From over 500 V3 sequences representing all main HIV-1 subtypes (Los Alamos database), we obtained a small set of probes to determine the tropism in clinical samples. We found a high concordance with the commercial TrofileES test (84.9%) and the Web-based tool Geno2Pheno (83.0%). Moreover, the new system reveals mixed virus populations, and it was successful on specimens with low virus loads or on provirus from leukocytes. A replicative phenotyping system was used for validation. Our data show that the XTrack test is favorably suitable for routine diagnostics. It detects and dissects mixed virus populations and viral minorities; samples with viral loads (VL) of <200 copies/ml are successfully analyzed. We further expect that the principles of the platform can be adapted also to other sequence-divergent pathogens, such as hepatitis B and C viruses.
Dengue Virus Induces and Requires Glycolysis for Optimal Replication
Authors: Fontaine Krystal A. , Sanchez Erica L. , Camarda Roman , Lagunoff Michael 
Published: December 2014

ABSTRACTViruses rely on host cellular metabolism to provide the energy and biosynthetic building blocks required for their replication. Dengue virus (DENV), a member of theFlaviviridaefamily, is one of the most important arthropod-borne human pathogens worldwide. We analyzed global intracellular metabolic changes associated with DENV infection of primary human cells. Our metabolic profiling data suggested that central carbon metabolism, particularly glycolysis, is strikingly altered during a time course of DENV infection. Glucose consumption is increased during DENV infection and depriving DENV-infected cells of exogenous glucose had a pronounced impact on viral replication. Furthermore, the expression of both glucose transporter 1 and hexokinase 2, the first enzyme of glycolysis, is upregulated in DENV-infected cells. Pharmacologically inhibiting the glycolytic pathway dramatically reduced DENV RNA synthesis and infectious virion production, revealing a requirement for glycolysis during DENV infection. Thus, these experiments suggest that DENV induces the glycolytic pathway to support efficient viral replication. This study raises the possibility that metabolic inhibitors, such as those that target glycolysis, could be used to treat DENV infection in the future.IMPORTANCEApproximately 400 million people are infected with dengue virus (DENV) annually, and more than one-third of the global population is at risk of infection. As there are currently no effective vaccines or specific antiviral therapies for DENV, we investigated the impact DENV has on the host cellular metabolome to identify metabolic pathways that are critical for the virus life cycle. We report an essential role for glycolysis during DENV infection. DENV activates the glycolytic pathway, and inhibition of glycolysis significantly blocks infectious DENV production. This study provides further evidence that viral metabolomic analyses can lead to the discovery of novel therapeutic targets to block the replication of medically important human pathogens.
Timing of Galectin-1 Exposure Differentially Modulates Nipah Virus Entry and Syncytium Formation in Endothelial Cells
Authors: Garner Omai B. , Yun Tatyana , Pernet Olivier , Aguilar Hector C. , Park Arnold , Bowden Thomas A. , Freiberg Alexander N. , Lee Benhur , Baum Linda G. 
Published: December 2014

ABSTRACTNipah virus (NiV) is a deadly emerging enveloped paramyxovirus that primarily targets human endothelial cells. Endothelial cells express the innate immune effector galectin-1 that we have previously shown can bind to specific N-glycans on the NiV envelope fusion glycoprotein (F). NiV-F mediates fusion of infected endothelial cells into syncytia, resulting in endothelial disruption and hemorrhage. Galectin-1 is an endogenous carbohydrate-binding protein that binds to specific glycans on NiV-F to reduce endothelial cell fusion, an effect that may reduce pathophysiologic sequelae of NiV infection. However, galectins play multiple roles in regulating host-pathogen interactions; for example, galectins can promote attachment of HIV to T cells and macrophages and attachment of HSV-1 to keratinocytes but can also inhibit influenza entry into airway epithelial cells. Using live Nipah virus, in the present study, we demonstrate that galectin-1 can enhance NiV attachment to and infection of primary human endothelial cells by bridging glycans on the viral envelope to host cell glycoproteins. In order to exhibit an enhancing effect, galectin-1 must be present during the initial phase of virus attachment; in contrast, addition of galectin-1 postinfection results in reduced production of progeny virus and syncytium formation. Thus, galectin-1 can have dual and opposing effects on NiV infection of human endothelial cells. While various roles for galectin family members in microbial-host interactions have been described, we report opposing effects of the same galectin family member on a specific virus, with the timing of exposure during the viral life cycle determining the outcome.IMPORTANCENipah virus is an emerging pathogen that targets endothelial cells lining blood vessels; the high mortality rate (up to 70%) in Nipah virus infections results from destruction of these cells and resulting catastrophic hemorrhage. Host factors that promote or prevent Nipah virus infection are not well understood. Endogenous human lectins, such as galectin-1, can function as pattern recognition receptors to reduce infection and initiate immune responses; however, lectins can also be exploited by microbes to enhance infection of host cells. We found that galectin-1, which is made by inflamed endothelial cells, can both promote Nipah virus infection of endothelial cells by “bridging” the virus to the cell, as well as reduce production of progeny virus and reduce endothelial cell fusion and damage, depending on timing of galectin-1 exposure. This is the first report of spatiotemporal opposing effects of a host lectin for a virus in one type of host cell.
Structural Analysis of a Rabbit Hemorrhagic Disease Virus Binding to Histo-Blood Group Antigens
Authors: Leuthold Mila M. , Dalton Kevin P. , Hansman Grant S. 
Published: December 2014

ABSTRACT

Rabbit hemorrhagic disease virus (RHDV) is a member of the
Caliciviridae
family (
Lagovirus
genus). RHDV is highly contagious and attaches to epithelial cells in the digestive or respiratory tract, leading to massive lesions with high mortality rates. A new variant of RHDV (termed RHDVb) recently has emerged, and previously vaccinated rabbits appear to have little protection against this new strain. Similar to human norovirus (
Caliciviridae
,
Norovirus
genus), RHDV binds histo-blood group antigens (HBGAs), and this is thought to be important for infection. Here, we report the HBGA binding site on the RHDVb capsid-protruding domain (P domain) using X-ray crystallography. The HBGA binding pocket was located in a negatively charged patch on the side of the P domain and at a dimeric interface. Residues from both monomers contributed to the HBGA binding and involved a network of direct hydrogen bonds and water-mediated interactions. An amino acid sequence alignment of different RHDV strains indicated that the residues directly interacting with the ABH-fucose of the HBGAs (Asp472, Asn474, and Ser479) were highly conserved. This result suggested that different RHDV strains also could bind HBGAs at the equivalent pocket. Moreover, several HBGA binding characteristics between RHDVb and human genogroup II norovirus were similar, which indicated a possible convergent evolution of HBGA binding interactions. Further structural studies with other RHDV strains are needed in order to better understand the HBGA binding mechanisms among the diverse RHDV strains.

IMPORTANCE
We identified, for the first time, the HBGA binding site on an RHDVb P domain using X-ray crystallography. Our results showed that RHDVb and human genogroup II noroviruses had similar HBGA binding interactions. Recently, it was discovered that synthetic HBGAs or HBGA-expressing enteric bacteria could enhance human genogroup II norovirus infection in B cells. Considering that RHDVb and genogroup II norovirus similarly interacted with HBGAs, it may be possible that a comparable cell culture system also could work with RHDVb. Taken together, these new findings will extend our understanding of calicivirus HBGA interactions and may help to elucidate the specific roles of HBGAs in calicivirus infections.
Functional Characterization of Nuclear Trafficking Signals in Pseudorabies Virus pUL31
Authors: Paßvogel Lars , Klupp Barbara G. , Granzow Harald , Fuchs Walter , Mettenleiter Thomas C. 
Published: December 2014

ABSTRACT
The herpesviral nuclear egress complex (NEC), consisting of pUL31 and pUL34 homologs, mediates efficient translocation of newly synthesized capsids from the nucleus to the cytosol. The tail-anchored membrane protein pUL34 is autonomously targeted to the nuclear envelope, while pUL31 is recruited to the inner nuclear membrane (INM) by interaction with pUL34. A nuclear localization signal (NLS) in several pUL31 homologs suggests importin-mediated translocation of the protein. Here we demonstrate that deletion or mutation of the NLS in pseudorabies virus (PrV) pUL31 resulted in exclusively cytosolic localization, indicating active nuclear export. Deletion or mutation of a predicted nuclear export signal (NES) in mutant constructs lacking a functional NLS resulted in diffuse nuclear and cytosolic localization, indicating that both signals are functional. pUL31 molecules lacking the complete NLS or NES were not recruited to the INM by pUL34, while site-specifically mutated proteins formed the NEC and partially complemented the defect of the UL31 deletion mutant. Our data demonstrate that the N terminus of pUL31, encompassing the NLS, is required for efficient nuclear targeting but not for pUL34 interaction, while the C terminus, containing the NES but not necessarily the NES itself, is required for complex formation and efficient budding of viral capsids at the INM. Moreover, pUL31-ΔNLS displayed a dominant negative effect on wild-type PrV replication, probably by diverting pUL34 to cytoplasmic membranes.

IMPORTANCE
The molecular details of nuclear egress of herpesvirus capsids are still enigmatic. Although the key players, homologs of herpes simplex virus pUL34 and pUL31, which interact and form the heterodimeric nuclear egress complex, are well known, the molecular basis of this interaction and the successive budding, vesicle formation, and scission from the INM, as well as capsid release into the cytoplasm, remain largely obscure. Here we show that classical cellular targeting signals for nuclear import and export are important for proper localization and function of the NEC, thus regulating herpesvirus nuclear egress.