bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of diverse full-length endogenous betaretroviruses in megabats and microbats
Authors: Hayward Joshua A , Tachedjian Mary , Cui Jie , Field Hume , Holmes Edward C , Wang Lin-Fa , Tachedjian Gilda 
Published: March 2013

Abstract

Background
Betaretroviruses infect a wide range of species including primates, rodents, ruminants, and marsupials. They exist in both endogenous and exogenous forms and are implicated in animal diseases such as lung cancer in sheep, and in human disease, with members of the human endogenous retrovirus-K (HERV-K) group of endogenous betaretroviruses (βERVs) associated with human cancers and autoimmune diseases. To improve our understanding of betaretroviruses in an evolutionarily distinct host species, we characterized βERVs present in the genomes and transcriptomes of mega- and microbats, which are an important reservoir of emerging viruses.

Results
A diverse range of full-length βERVs were discovered in mega- and microbat genomes and transcriptomes including the first identified intact endogenous retrovirus in a bat. Our analysis revealed that the genus Betaretrovirus can be divided into eight distinct sub-groups with evidence of cross-species transmission. Betaretroviruses are revealed to be a complex retrovirus group, within which one sub-group has evolved from complex to simple genomic organization through the acquisition of an env gene from the genus Gammaretrovirus. Molecular dating suggests that bats have contended with betaretroviral infections for over 30 million years.

Conclusions
Our study reveals that a diverse range of betaretroviruses have circulated in bats for most of their evolutionary history, and cluster with extant betaretroviruses of divergent mammalian lineages suggesting that their distribution may be largely unrestricted by host species barriers. The presence of βERVs with the ability to transcribe active viral elements in a major animal reservoir for viral pathogens has potential implications for public health.
Bilateral central pain sensitization in rats following a unilateral thalamic lesion may be treated with high doses of ketamine
Authors: Castel Aude , Hélie Pierre , Beaudry Francis , Vachon Pascal 
Published: March 2013

Abstract

Background
Central post-stroke pain is a neuropathic pain condition caused by a vascular lesion, of either ischemic or hemorrhagic origin, in the central nervous system and more precisely involving the spinothalamocortical pathway responsible for the transmission of painful sensations. Few animal models have been developed to study this problem. The objectives of this study were to evaluate different modalities of pain in a central neuropathic pain rat model and to assess the effects of ketamine administered at different doses. Animals were evaluated on the rotarod, Hargreaves, Von Frey and acetone tests. A very small hemorrhage was created by injecting a collagenase solution in the right ventral posterolateral thalamic nucleus. Following the establishment of the neuropathy, ketamine was evaluated as a therapeutic drug for this condition.

Results
Histopathological observations showed a well localized lesion with neuronal necrosis and astrocytosis following the collagenase injection that was localized within the VPL. No significant change in motor coordination was observed following surgery in either the saline or collagensae groups. In the collagenase group, a significant decrease in mechanical allodynia threshold was observed. A sporadic and transient cold allodynia was also noted. No thermal hyperalgesia was seen following the collagenase injection. Ketamine was then tested as a potential therapeutic drug. A significant decrease in motor coordination was seen only following the administration of 25 mg/kg of ketamine in both groups. An alleviation of mechanical allodynia was achieved only with the high ketamine dose. The minimal effective ketamine serum concentration (150 ng/mL) was only achieved in animals that received 25 mg/kg.

Conclusions
An intrathalamic hemorrhage induced a bilateral mechanical allodynia in rats. Cold hyperalgesia was observed in 60% of these animals. Mechanical allodynia was alleviated with high doses of ketamine which corresponded with therapeutic plasmatic concentrations.
Developmental time rather than local environment regulates the schedule of epithelial polarization in the zebrafish neural rod
Authors: Girdler Gemma C , Araya Claudio , Ren Xiaoyun , Clarke Jonathan DW 
Published: March 2013

Abstract

Background
Morphogenesis requires developmental processes to occur both at the right time and in the right place. During neural tube formation in the zebrafish embryo, the generation of the apical specializations of the lumen must occur in the center of the neural rod after the neural cells have undergone convergence, invagination and interdigitation across the midline. How this coordination is achieved is uncertain. One possibility is that environmental signaling at the midline of the neural rod controls the schedule of apical polarization. Alternatively, polarization could be regulated by a timing mechanism and then independent morphogenetic processes ensure the cells are in the correct spatial location.

Results
Ectopic transplantation demonstrates the local environment of the neural midline is not required for neural cell polarization. Neural cells can self-organize into epithelial cysts in ectopic locations in the embryo and also in three-dimensional gel cultures. Heterochronic transplants demonstrate that the schedule of polarization and the specialized cell divisions characteristic of the neural rod are more strongly regulated by time than local environmental signals. The cells’ schedule for polarization is set prior to gastrulation, is stable through several rounds of cell division and appears independent of the morphogenetic movements of gastrulation and neurulation.

Conclusions
Time rather than local environment regulates the schedule of epithelial polarization in zebrafish neural rod.
Role of oxygen consumption in hypoxia protection by translation factor depletion
Authors: Scott Barbara , Sun Chun-Ling , Mao Xianrong , Yu Cong , Vohra Bhupinder P. S. , Milbrandt Jeffrey , Crowder C. Michael 
Published: March 2013

Summary
Reduction of protein synthesis has been associated with resistance to hypoxic cell death. Which components of the translation machinery control hypoxic sensitivity and the precise mechanism has not been systematically investigated although a reduction in oxygen consumption has been widely assumed to be the mechanism. Using genetic reagents in C. elegans, we examined the effect on organismal survival after hypoxia of knockdown of ten factors functioning at the three principal steps in translation. Reduction-of-function of all ten translation factors significantly increased hypoxic survival to varying degrees, not fully accounted for by the level of translational suppression. Measurement of oxygen consumption found that strong hypoxia resistance was possible without a significant decrease in oxygen consumption. Hypoxic sensitivity had no correlation with lifespan or reactive oxygen species sensitivity, two phenotypes associated with reduced translation. Resistance to tunicamycin, which produces misfolded protein toxicity, was the only phenotype that significantly correlated with hypoxic sensitivity. Translation factor knockdown was also hypoxia protective for mouse primary neurons. These data show that translation factor knockdown is hypoxia protective in both C. elegans and mouse neurons and that oxygen consumption does not necessarily determine survival; rather, mitigation of misfolded protein toxicity is more strongly associated with hypoxic protection.
Identification and characterisation of functional aquaporin water channel (Anomala cuprea DRIP) in a coleopteran insect
Authors: Nagae Tomone , Miyake Seiji , Kosaki Shiho , Azuma Masaaki 
Published: March 2013

Summary
Water transport across the plasma membrane depends on the presence of the water channel aquaporin (AQP), which mediates the bulk movement of water through osmotic and pressure gradients. In terrestrial insects, which are solid/plant feeders, the entrance and exit of water is primarily executed along the alimentary tract, where the hindgut, particularly the rectum, is the major site of water conservation. A cDNA encoding the homologue of the water-specific Drosophila AQP (Drosophila integral protein: DRIP) was identified through the RT-PCR of RNA isolated from the rectum of the cupreous chafer larvae, Anomala cuprea, a humus and plant root feeder. This gene (Anocu AQP1) has a predicted molecular mass of 26.471 kDa similar to the DRIP clade of insect AQPs characterised from caterpillars, flies and several liquid-feeding insects. When expressed in Xenopus laevis oocytes, Anocu AQP1 showed the hallmarks of aquaporin-mediated water transport but no glycerol nor urea permeability, and the reversible inhibition of elevated water transport through 1 mM HgCl2. This is the first experimental demonstration of the presence of a water-specific AQP, namely DRIP, in the Coleoptera. The genome of the model beetle, Tribolium castaneum, contains six putative AQP sequences, one of which (Trica-1a, XP_972862) showed the highest similarity to Anocu AQP1 (~60% amino acid identity). Anocu AQP1 is predominantly expressed in the rectum. Using a specific antibody raised against DRIP in the silkworm, Bombyx mori (AQP-Bom1), Anocu AQP1 was localised to the apical plasma membrane of rectal epithelial cells, and lacking in the midgut and gastric caecal epithelia. Based on the BeetleBase prediction, there are three putative AQPs (Trica-3a, 3b, 3c: XP_970728, 970912, 970791) that are homologous to B. mori aquaglyceroporin (AQP-Bom2 [GLP]). The immunocytochemical studies using the specific anti-peptide antibody against AQP-Bom2 revealed the presence of the GLP homologue at the apical plasma membrane of enterocytes in the midgut and gastric caeca. Thus, DRIP (Anocu AQP1) and the putative GLP share epithelial fluid-transporting roles along the alimentary tract in cupreous chafer larvae.
Intense pulsed light treatment of chronic mid-body Achilles tendinopathy
Authors: Hutchison A. M. , Pallister I. , Evans R. M. , Bodger O. , Topliss C. J. , Williams P. , Beard D. J. 
Published: March 2013

We conducted a randomised controlled trial to determine whether active intense pulsed light (IPL) is an effective treatment for patients with chronic mid-body Achilles tendinopathy. A total of 47 patients were randomly assigned to three weekly therapeutic or placebo IPL treatments. The primary outcome measure was the Victorian Institute of Sport Assessment – Achilles (VISA-A) score. Secondary outcomes were a visual analogue scale for pain (VAS) and the Lower Extremity Functional Scale (LEFS). Outcomes were recorded at baseline, six weeks and 12 weeks following treatment. Ultrasound assessment of the thickness of the tendon and neovascularisation were also recorded before and after treatment. There was no significant difference between the groups for any of the outcome scores or ultrasound measurements by 12 weeks, showing no measurable benefit from treatment with IPL in patients with Achilles tendinopathy. Cite this article: Bone Joint J 2013;95-B:504–9.
Diagnosis of 5α-Reductase 2 Deficiency: Is Measurement of Dihydrotestosterone Essential?
Authors: Chan Angel On Kei , But Betty Wai Man , Lee Ching Yin , Lam Yuen Yu , Ng Kwok Leung , Tung Joanna Yuet Ling , Kwan Elaine Yin Wah , Chan Yuk Kit , Tsui Teresa Kam Chi , Lam Almen Lai Na , Tse Wing Yee , Cheung Pik To , Shek Chi Chung 
Published: March 2013

BACKGROUND
5α-Reductase 2 deficiency (5ARD) is a known cause of 46,XY disorders of sex development (DSD). Traditionally, the diagnosis relies on dihydrotestosterone (DHT) measurement, but the results are often equivocal, potentially leading to misdiagnosis. We reviewed alternative approaches for diagnosis of 5ARD.

METHODS
We conducted a retrospective review of the results of urinary steroid profiling (USP) by GC-MS and mutational analysis of SRD5A2 [steroid-5-alpha-reductase, alpha polypeptide 2 (3-oxo-5 alpha-steroid delta 4-dehydrogenase alpha 2)] by PCR and direct DNA sequencing of all 46,XY DSD patients referred to our laboratory with biochemical and/or genetic findings compatible with 5ARD. We also performed a literature review on the laboratory findings of all 5ARD cases reported in the past 10 years.

RESULTS
Of 16 patients diagnosed with 5ARD between January 2003 and July 2012, 15 underwent USP, and all showed characteristically low 5α- to 5β-reduced steroid metabolite ratios. Four patients had DHT measured, but 2 did not reach the diagnostic cutoff. In all 12 patients who underwent genetic analysis, 2 mutations of the SRD5A2 gene were detected to confirm the diagnosis. Twenty-four publications involving 149 patients with 5ARD were published in the review period. Fewer than half of these patients had DHT tested. Nearly 95% of them had the diagnosis confirmed genetically.

CONCLUSIONS
5ARD can be confidently diagnosed by USP at 3 months postnatally and confirmed by mutational analysis of SRD5A2. Interpretation of DHT results may be problematic and is not essential in the diagnosis of 5ARD. We propose new diagnostic algorithms for 46,XY DSD.
Donor DNA Utilization During Gene Targeting with Zinc-Finger Nucleases
Authors: Beumer Kelly J , Trautman Jonathan K , Mukherjee Kusumika , Carroll Dana 
Published: March 2013

Abstract
Gene targeting is the term commonly applied to experimental gene replacement by homologous recombination (HR). This process is substantially stimulated by a double-strand break (DSB) in the genomic target. Zinc-finger nucleases (ZFNs) are targetable cleavage reagents that provide an effective means of introducing such a break in conjunction with delivery of a homologous donor DNA. In this study we explored several parameters of donor DNA structure during ZFN-mediated gene targeting in Drosophila melanogaster embryos, as follows. 1) We confirmed that HR outcomes are enhanced relative to the alternative nonhomologous end joining (NHEJ) repair pathway in flies lacking DNA ligase IV. 2) The minimum amount of homology needed to support efficient HR in fly embryos is between 200 and 500 bp. 3) Conversion tracts are very broad in this system: donor sequences more than 3 kb from the ZFN-induced break are found in the HR products at approximately 50% of the frequency of a marker at the break. 4) Deletions carried by the donor DNA are readily incorporated at the target. 5) While linear double-stranded DNAs are not effective as donors, single-stranded oligonucleotides are. These observations should enable better experimental design for gene targeting in Drosophila and help guide similar efforts in other systems.
Genome-Wide Association Analysis of Avian Resistance to Campylobacter jejuni Colonization Identifies Risk Locus Spanning the CDH13 Gene
Authors: Connell Sarah , Meade Kieran G , Allan Brenda , Lloyd Andrew T , Downing Tim , O’Farrelly Cliona , Bradley Daniel G 
Published: March 2013

Abstract
The enteropathogen Campylobacter jejuni is a major worldwide health and economic burden, being one of the leading causes of bacterial gastroenteritis and commonly linked to postinfectious onset of autoimmune disease. Chickens are a major vector for human infection and even though variation in avian colonization level is heritable, no previous studies have identified regions of the genome associated with colonization resistance. We performed a genome-wide association study of resistance to C. jejuni colonization in the avian intestine by controlling for population structure, which revealed a risk locus with genome-wide significance spanning the T-cadherin (CDH13) gene. A second possible risk locus was also identified close to calmodulin (CALM1), a calcium-activated modulator of cadherin function. In addition, gene expression analysis of mRNA sequencing profiles revealed that the relative expression of the two genes is significantly associated with colonization resistance. Functional studies have previously demonstrated involvement of cadherins and calmodulin in C. jejuni intracellular invasion and colonization of human intestinal epithelial cells in vitro. Consistent with this finding, our analysis reveals that variation surrounding these genes is associated with avian colonization resistance in vivo and highlights their potential as possible targets for control of the bacterium in avian and human populations.
Debromination of 2,4,6-tribromophenol coupled with biodegradation
Authors: Weidlich Tomáš , Prokeš Lubomír , Pospíšilová Dagmar 
Published: March 2013

Abstract
The application effect of aluminium and their alloys and mixtures with nickel was studied for the complete hydrodebromination of 2,4,6-tribromophenol (TBP) to phenol in aqueous NaOH solution at room temperature. It was found that the Raney Al-Ni alloy can rapidly transform TBP to phenol. Removal efficiency of 25 mM TBP solution in aqueous NaOH (15 g L−1) solution at the end of 1h reaction was 100% using 4 g L−1 Al-Ni. The hydrodebromination is accompanied by the dissolution of aluminium and formation of soluble Al(OH)4−1 anions under these reaction conditions. After completion of the hydrodebromination reaction removal of the dissolved metals was achieved by precipitation of appropriate hydroxides by adjustment of the pH value and filtration, the filtrate was treated with Pseudomonas or Rhodococcus bacterial strains to degrade dissolved phenol. The combined application of both (chemical-biological) treatments produced degradations of 100% of aromatic compounds.
Periodic solution to p-Laplacian neutral Liénard type equation with variable parameter
Authors: Du Bo 
Published: March 2013

Abstract
Using Mawhin’s continuation theorem we obtain some existence results of periodic solutions for a type of p-Laplacian neutral Liénard equation $$\left( {\phi _p \left( {\left( {x\left( t \right) - c\left( t \right)x\left( {t - \tau } \right)} \right)^\prime } \right)} \right)^\prime + f\left( {x\left( t \right)} \right)x'\left( t \right) + g\left( {x\left( {t - \gamma \left( t \right)} \right)} \right) = e\left( t \right).$$ It is worth noting that c(t) is no longer a constant which is different from the corresponding ones of past work.
Évolutions démographiques et retraites : quinze ans de débats
Authors: Blanchet Didier 
Published: March 2013

Alors que se précisent les modalités de modification par le gouvernement Ayrault de la réforme de 2010 des retraites, nous republions un article de synthèse de Didier Blanchet 1 , auteur du rapport Démographie et économie 2 du Conseil d’analyse économique. Les projections de population de 2006, confirmées par celles de 2010, ont légèrement infléchi le diagnostic formulé à l’époque 3 : sous l’effet d’une fécondité plus dynamique que les hypothèses retenues initialement, l’Insee ne prévoit plus une diminution de la population active de l’ampleur décrite mais sa quasi-stabilisation. Néanmoins, puisque la population des plus de 60 ans croît relativement rapidement sous l’effet de l’augmentation continue de l’espérance de vie, le ratio de dépendance ne peut qu’augmenter à un rythme soutenu.
Deriving ice thickness, glacier volume and bedrock morphology of Austre Lovénbreen (Svalbard) using GPR
Authors: Saintenoy A. , Friedt J.‐M. , Booth A. D. , Tolle F. , Bernard E. , Laffly D. , Marlin C. , Griselin M. 
Published: March 2013

ABSTRACTAustre Lovénbreen is a 4.6 km2 glacier on the Archipelago of Svalbard (79° N) that has been surveyed over the last 47 years in order to monitor in particular the glacier evolution and associated hydrological phenomena in the context of nowadays global warming. A three‐week field survey during April 2010 allowed for the acquisition of a dense mesh of ground‐penetrating radar (GPR) data with an average of 14 683 points per km2 (67 542 points total) on the glacier surface. The profiles were acquired using Mala equipment with 100 MHz antennas, towed slowly enough to record on average every 0.3 m, a trace long enough to sound down to 189 m of ice. One profile was repeated with a 50 MHz antenna set to improve electromagnetic wave propagation depth in scattering media observed in the cirques closest to the slopes. The GPR was coupled to a GPS system to position traces. Each profile was manually edited using standard GPR data processing including migration, to pick the reflection arrival time from the ice‐bedrock interface. Snow cover was evaluated through 42 snow drilling measurements regularly spaced to cover the entire glacier. These data were acquired at the time of the GPR survey and subsequently spatially interpolated using ordinary kriging. Using a snow velocity of 0.22 m/ns, the snow thickness was converted to electromagnetic wave traveltimes and subtracted from the picked traveltimes to the ice‐bedrock interface. The resulting traveltimes were converted to ice thickness using a velocity of 0.17 m/ns. The velocity uncertainty is discussed from a common midpoint profile analysis. A total of 67 542 geo‐referenced data points with GPR‐derived ice thicknesses, in addition to a glacier boundary line derived from satellite images taken during summer, were interpolated over the entire glacier surface using kriging with a 10 m grid size. Some uncertainty analyses were carried out and we calculated an averaged ice thickness of 76 m and a maximum depth of 164 m with a relative error of 11.9%. The volume of the glacier is derived as 0.3487 ± 0.041 km3. Finally a 10 m grid map of the bedrock topography was derived by subtracting the ice thicknesses from a dual‐frequency GPS‐derived digital elevation model of the surface. These two data sets are the first step for modelling thermal evolution of a glacier and its bedrock, as well as the main hydrological network.
Adaptation urbaine post-catastrophe : la recomposition territoriale de La Nouvelle Orléans
Authors: Zaninetti Jean-Marc 
Published: March 2013

La Nouvelle Orléans n’a pas encore fini de se relever de la dévastation provoquée par Katrina en 2005. Cependant, les recompositions territoriales du peuplement manifestent déjà une adaptation « du second ordre » à l’exposition récurrente de la région au risque cyclonique. Katrina a inversé la tendance antérieure à l’étalement urbain dans les marais. Le concept d’adaptation du second ordre désigne les ajustements résultant des décisions individuelles des acteurs privés plutôt que d’un aménagement décidé par les acteurs publics. Toutefois, La Nouvelle Orléans peine encore à admettre qu’elle gagnerait à regrouper sa population dans un périmètre plus restreint.
Mast Cell FcεRI-Induced Early Growth Response 2 Regulates CC Chemokine Ligand 1–Dependent CD4+ T Cell Migration
Authors: Wu Zhengli , MacNeil Adam J. , Junkins Robert , Li Bo , Berman Jason N. , Lin Tong-Jun 
Published: March 2013

Abstract
Mast cells are well positioned in host tissue for detecting environmental signals, including allergens, leading to activation of the high-affinity IgE receptor FcεRI, and initiating a signaling cascade that perpetuates the production of biologically potent mediators, including chemokines. We have identified a novel target of mast cell FcεRI activity in the transcription factor early growth response 2 (Egr2) and sought to characterize its function therein. Egr2 was transiently activated following FcεRI-mediated signaling, targeted the promoter of the chemokine CCL1, and was critical for allergen-induced mast cell CCL1 production. Egr2-deficient mast cells were incapable of directing CD4+ T cell migration via the CCL1–CCR8 axis. In a model of allergic asthma, reconstitution of mast cell–deficient mice with Egr2-deficient mast cells demonstrated that mast cell Egr2 was essential for migration of CD4+ T cells to the inflamed lung. These findings position Egr2 as a critical regulator of mast cell–directed CD4+ T cell migration.