bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple replication origins with diverse control mechanisms in Haloarcula hispanica
Authors: Wu Zhenfang , Liu Jingfang , Yang Haibo , Liu Hailong , Xiang Hua 
Published: November 2013

Abstract
The use of multiple replication origins in archaea is not well understood. In particular, little is known about their specific control mechanisms. Here, we investigated the active replication origins in the three replicons of a halophilic archaeon, Haloarcula hispanica, by extensive gene deletion, DNA mutation and genome-wide marker frequency analyses. We revealed that individual origins are specifically dependent on their co-located cdc6 genes, and a single active origin/cdc6 pairing is essential and sufficient for each replicon. Notably, we demonstrated that the activities of oriC1 and oriC2, the two origins on the main chromosome, are differently controlled. A G-rich inverted repeat located in the internal region between the two inverted origin recognition boxes (ORBs) plays as an enhancer for oriC1, whereas the replication initiation at oriC2 is negatively regulated by an ORB-rich region located downstream of oriC2-cdc6E, likely via Cdc6E-titrating. The oriC2 placed on a plasmid is incompatible with the wild-type (but not the ΔoriC2) host strain, further indicating that strict control of the oriC2 activity is important for the cell. This is the first report revealing diverse control mechanisms of origins in haloarchaea, which has provided novel insights into the use and coordination of multiple replication origins in the domain of Archaea.
Context‐dependent costs and constraints of begging and non‐begging activity by common grackle nestlings at the scale of the nanoclimate
Authors: Glassey Barb , Gunson Melanie , Muir Robert 
Published: November 2013

SummaryEnvironmental factors such as heat and solar radiation directly affect the open‐cup nest environment and can impact nestling body temperature.The aim of our research was to understand how open‐cup passerine nestlings use behavioural thermoregulation to mitigate solar heat gain and to measure the metabolic cost of begging and non‐begging activity under three light treatments: room light (<2 Wm−2), simulated shade (500 Wm−2) and simulated sun (1000 Wm−2). Our study coupled behavioural (field) and physiological (laboratory) experiments to explore the adaptive behavioural response of passerine nestlings to nest cup nanoclimates (sun and shade), using the common grackle (Quiscalus quiscula) as a model species.Non‐begging behaviour was evaluated in the field by randomly assigning nestlings to a homogeneous (all sun) or heterogeneous (sun and shade) nest environment; measuring body temperature (Tb); and identifying behaviours from videotaped footage. TheTbof nestlings without access to shade was significantly higher, and nestlings spent more time moving and panting, suggesting an increased metabolic expenditure. To test this, we duplicated the insolation nanoclimate under laboratory conditions using a 1·0KWSciencetech Illumination System and measured the energetic cost of begging and non‐begging activity using open‐system respirometry on non‐irradiated and irradiated nestlings. Our results suggest that, in grackle nestlings, the relationship between activity (begging and non‐begging) and energy expenditure is context‐dependent.Our results identified: (i) a reduction in energy expenditure associated with accessing the shade; (ii) expenditure on non‐begging activity equalled or exceeded expenditure on begging activity; and (iii) a potential behavioural constraint on begging imposed by exposure to a homogeneous sun environment (sun without access to shade). The combination of context‐dependent costs and constraints suggests the potential for strategic costs associated with the heterogeneous nest environment.
Millennial stocks and fluxes of large woody debris in lakes of the North American taiga
Authors: Gennaretti Fabio , Arseneault Dominique , Bégin Yves 
Published: November 2013

Summary

Large woody debris (LWD) is an important cross‐boundary subsidy that enhances the productivity of lake ecosystems and the stability of aquatic food webs. LWD may also be an important carbon sink because LWD pieces are preserved for centuries in the littoral zone of lakes and rivers. However, a long‐term analysis of LWD stocks and fluxes in lakes, coupled with the reconstruction of past disturbances at the site level, has never been attempted.

Large woody debris was sampled in five lakes of the Quebec taiga. Actual LWD stocks were described and residence time of the LWD pieces was established using tree‐ring and radiocarbon dating. LWD losses by decomposition and burial and other factors influencing LWD residence time were investigated using linear regressions.

Impacts of wildfires on LWD fluxes during the last 1400 years were reconstructed separately for the five lakes using piecewise regression models. Fire years at each site were identified from the recruitment dates of charred LWD pieces.

Large woody debris volume ranged between 0.92 and 1.57 m3 per 100 m of shoreline, and extrapolating these results to the landscape scale, it was concluded that LWD littoral carbon pools represent a minimal portion of boreal carbon storage.

Large woody debris residence time in boreal lakes was confirmed to be very long. Tree‐ring dates of 1571 LWD pieces, mainly black spruce (Picea mariana (Mill.) BSP.), spanned the last 1400 years, while LWD specimens of older floating chronologies were preserved from decomposition for up to five millennia. The most influential variables explaining the variation in LWD residence time were the degree of burial and the distance from the shore.

Large woody debris recruitment rates averaged 5.8 pieces per century per 100 m of shoreline. Fourteen wildfires were the primary cause for changes in the rates of tree establishment in the riparian forests and of LWD recruitment in the lakes.

Synthesis. Interactions between terrestrial and aquatic ecosystems in northern boreal regions are strongly influenced by wildfires whose effects can last for centuries due to the slow large woody debris decay rate. Actual LWD stocks and carbon pools are a legacy of the past fire history.
Using power sector reform as an opportunity to increase the uptake of renewable energy in the power sector: Responding to peak oil and climate change in Caribbean and Pacific small island developing States, between 1970‐2010
Authors: Niles Keron , Lloyd Bob 
Published: November 2013

AbstractSmall island developing States (SIDS) have narrow resource bases and are usually extremely reliant on fossil fuel based energy for transport and electricity generation. These island economies are thus particularly vulnerable to the impacts of peak oil and also to climate change, impacts which are likely to not only hamper economic development but also adversely affect the quality of life of local inhabitants. In order to reduce the vulnerability of SIDS to peak oil, an urgent transition to renewable sources of energy is necessary. This paper propounds that the reform of power sector that took place in Caribbean and Pacific SIDS (particularly between 1970 and 2000) should have been viewed as an opportunity to re‐orient power producers away from the proclivity to utilise conventional fossil fuel uses. Reasons why reform measures did not result in a substantive transition are put forward. Moreover, recommendations towards facilitating a transition to renewable energy in the power sector through future reforms are proposed.
CharacterizingDNApreservation in degraded specimens ofAmara alpina(Carabidae:Coleoptera)
Authors: Heintzman Peter D. , Elias Scott A. , Moore Karen , Paszkiewicz Konrad , Barnes Ian 
Published: November 2013

AbstractDNApreserved in degraded beetle (Coleoptera) specimens, including those derived from dry‐stored museum and ancient permafrost‐preserved environments, could provide a valuable resource for researchers interested in species and population histories over timescales from decades to millenia. However, the potential of these samples as genetic resources is currently unassessed. Here, using Sanger and Illumina shotgun sequence data, we exploredDNApreservation in specimens of the ground beetleAmara alpina, from both museum and ancient environments. Nearly all museum specimens had amplifiableDNA, with the maximum amplifiable fragment length decreasing with age. Amplification ofDNAwas only possible in 45% of ancient specimens. Preserved mitochondrialDNAfragments were significantly longer than those of nuclearDNAin both museum and ancient specimens. Metagenomic characterization of extractedDNAdemonstrated that parasite‐derived sequences, includingWolbachiaandSpiroplasma, are recoverable from museum beetle specimens. AncientDNAextracts contained beetleDNAin amounts comparable to museum specimens. Overall, our data demonstrate that there is great potential for both museum and ancient specimens of beetles in future genetic studies, and we see no reason why this would not be the case for other orders of insect.
Maternal and neonatal morbidity during off peak hours in a busy obstetric unit. Are deliveries after midnight more complicated?
Authors: Hehir Mark P. , Walsh Jennifer M. , Higgins Shane , Mahony Rhona 
Published: November 2013

AbstractObjectiveWe sought to compare maternal and neonatal outcomes in deliveries occurring overnight with those in daylight hours.DesignProspective observational study.SettingLarge national tertiary referral center.PopulationAll singleton laboring nulliparous parturients delivering infants >500 g over a 2‐year period, 1 January 2008 to 31 December 2009.MethodsDetails of intrapartum characteristics and neonatal outcomes of deliveries occurring between midnight and 08.00 h were compared with deliveries occurring outside of these hours.Main outcome measuresMaternal and neonatal morbidity.ResultsDuring the study period there were 8450 nulliparous deliveries. 2668 (31.6%) delivered between midnight and 08.00 h, and 5782 (68.4%) outside of these hours. There was a significant difference between the time periods in the number of babies born with a cord pH <7.1: 10.8% (44/406) of babies were born between midnight and 08.00 h, and 6.3% (63/1007) of babies were born outside these hours (p = 0.003). There was no significant difference in terms of Apgar score <7 at 5 min (p = 0.17). There was a trend toward a larger number of anal sphincter injuries occurring between midnight and 08.00 h (3% vs. 2.3%; p = 0.05).ConclusionOur findings suggest that infants are more likely to be born with a pH <7.1 and there was a trend toward an increased rate of anal sphincter injury during time periods when staffing levels are low and clinician fatigue may play a role in decision‐making and patient management. This may play a role in service provision planning and staff recruitment.
Individual Differences in Children's and Parents' Generic Language
Authors: Gelman Susan A. , Ware Elizabeth A. , Kleinberg Felicia , Manczak Erika M. , Stilwell Sarah M. 
Published: November 2013

Generics (“Dogsbark”) convey important information about categories and facilitate children's learning. Two studies with parents and their 2‐ or 4‐year‐old children (N = 104 dyads) examined whether individual differences in generic language use are as follows: (a) stable over time, contexts, and domains, and (b) linked to conceptual factors. For both children and parents, individual differences in rate of generic production were stable across time, contexts, and domains, and parents' generic usage significantly correlated with that of their own children. Furthermore, parents' essentialist beliefs correlated with their own and their children's rates of generic frequency. These results indicate that generic language use exhibits substantial stability and may reflect individual differences in speakers' conceptual attitudes toward categories.
C3 dysregulation due to factor H deficiency is mannan-binding lectin-associated serine proteases (MASP)-1 and MASP-3 independentin vivo
Authors: Ruseva M M , Takahashi M , Fujita T , Pickering M C 
Published: November 2013

SummaryUncontrolled activation of the complement alternative pathway is associated with complement-mediated renal disease. Factor B and factor D are essential components of this pathway, while factor H (FH) is its major regulator. In complete FH deficiency, uncontrolled C3 activation through the alternative pathway results in plasma C3 depletion and complement-mediated renal disease. These are dependent on factor B. Mannan-binding lectin-associated serine proteases 1 and 3 (MASP-1, MASP-3) have been shown recently to contribute to alternative pathway activation by cleaving pro-factor D to its active form, factor D. We studied the contribution of MASP-1 and MASP-3 to uncontrolled alternative pathway activation in experimental complete FH deficiency. Co-deficiency of FH and MASP-1/MASP-3 did not ameliorate either the plasma C3 activation or glomerular C3 accumulation in FH-deficient mice. Our data indicate that MASP-1 and MASP-3 are not essential for alternative pathway activation in complete FH deficiency.
Expression of transforming growth factor β and fibroblast growth factor 2 in the lens epithelium of Morioka cataract mice
Authors: Kondo Tomohiro , Ishiga‐Hashimoto Naoko , Nagai Hiroaki , Takeshita Ai , Mino Masaki , Morioka Hiroshi , Kusakabe Ken Takeshi , Okada Toshiya 
Published: November 2013

AbstractIn the Morioka cataract (MCT) mice, lens opacity appears at 6 to 8 weeks of age, and swollen lens fiber is electron‐microscopically observed at 3 weeks after birth. The present study was designed to characterize the expression of transforming growth factor β (TGFβ) and fibroblast growth factor 2 (FGF2) in the lens epithelium of the MCT mice. Immunohistochemical analysis showed that the expression of TGFβ in the lens epithelium of the MCT mice was stronger than that of the wild‐type ddY mice at 2 and 4 weeks after birth. The expression of TGFβ receptors (TGFβRI and TGFβRII) and FGF2 in the lens epithelium of the MCT mice was stronger than that of the wild‐type ddY mice at 4 weeks and weaker than that of the wild‐type ddY mice at 15 weeks after birth. Using real time polymerase chain reaction (PCR), quantitative RT‐PCR analysis showed that expression of TGFβ1 and TGFβ2 mRNA in the lens of 2‐week‐old MCT mice was significantly higher compared to age‐matched wild‐type ddY mice. These findings indicate that the lens epithelium of MCT mice has increased expression of TGFβ before cataract affection and that changes in the expression of FGF2 as well as TGFβ may contribute to the progression of the cataract in the mice.
Prognostic Value of a Nine‐Gene Signature in Glioma Patients Based on mRNA Expression Profiling
Authors: Bao Zhao‐Shi , Li Ming‐Yang , Wang Jia‐Yin , Zhang Chuan‐Bao , Wang Hong‐Jun , Yan Wei , Liu Yan‐Wei , Zhang Wei , Chen Ling , Jiang Tao 
Published: November 2013

SummaryIntroductionGliomas are the most common primary brain tumors in adults and a significant cause of cancer‐related mortality. A 9‐gene signature was identified as a novel prognostic model reflecting survival situation obviously in gliomas.AimsTo identify an mRNA expression signature to improve outcome prediction for patients with different glioma grades.ResultsWe used whole‐genome mRNA expression microarray data of 220 glioma samples of all grades from the Chinese Glioma Genome Atlas (CGGA) database (http://www.cgga.org.cn) as a discovery set and data from Rembrandt and GSE16011 for validation sets. Data from every single grade were analyzed by the Kaplan–Meier method with a two‐sided log‐rank test. Univariate Cox regression and linear risk score formula were applied to derive a gene signature with better prognostic performance. We found that patients who had high risk score according to the signature had poor overall survival compared with patients who had low risk score. Highly expressed genes in the high‐risk group were analyzed by gene ontology (GO) and gene set variation analysis (GSVA). As a result, the reason for the divisibility of gliomas was likely due to cell life processes and adhesion.ConclusionThis 9‐gene‐signature prediction model provided a more accurate predictor of prognosis that denoted patients with high risk score have poor outcome. Moreover, these risk models based on defined molecular profiles showed the considerable prospect in personalized cancer management.
Activation of Muscarinic Receptors Protects against Retinal Neurons Damage and Optic Nerve Degeneration In Vitro and In Vivo Models
Authors: Tan Pan‐Pan , Yuan Hai‐Hong , Zhu Xu , Cui Yong‐Yao , Li Hui , Feng Xue‐Mei , Qiu Yu , Chen Hong‐Zhuan , Zhou Wei 
Published: November 2013

SummaryAimsMuscarinic acetylcholine receptor agonist pilocarpine reduces intraocular pressure (IOP) of glaucoma mainly by stimulating ciliary muscle contraction and then increasing aqueous outflow. It is of our great interest to know whether pilocarpine has the additional properties of retinal neuroprotection independent of IOP lowering in vitro and in vivo models.MethodsIn rat primary retinal cultures, cell viability was measured using an MTT assay and the trypan blue exclusion method, respectively. Retinal ganglion cells (RGCs) were identified by immunofluorescence and quantified by flow cytometry. For the in vivo study, the retinal damage after retinal ischemia/reperfusion injury in rats was evaluated by histopathological study using hematoxylin and eosin staining, transmission electron microscopy, and immunohistochemical study on cleaved caspase‐3, caspase‐3, and ChAT.ResultsPretreatment of pilocarpine attenuated glutamate‐induced neurotoxicity of primary retinal neurons in a dose‐dependent manner. Protection of pilocarpine in both retinal neurons and RGCs was largely abolished by the nonselective muscarinic receptor antagonist atropine and the M1‐selective muscarinic receptor antagonist pirenzepine. After ischemia/reperfusion injury in retina, the inner retinal degeneration occurred including ganglion cell layer thinning and neuron lost, and the optic nerve underwent vacuolar changes. These degenerative changes were significantly lessened by topical application of 2% pilocarpine. In addition, the protective effect of pilocarpine on the ischemic rat retina was favorably reflected by downregulating the expression of activated apoptosis marker cleaved caspase‐3 and caspase‐3 and upregulating the expression of cholinergic cell marker ChAT.ConclusionsTaken together, this highlights pilocarpine through the activation of muscarinic receptors appear to afford significant protection against retinal neurons damage and optic nerve degeneration at clinically relevant concentrations. These data also further support muscarinic receptors as potential therapeutic neuroprotective targets in glaucoma.
Interactions between Carbon Sequestration and Shade Tree Diversity in a Smallholder Coffee Cooperative in El Salvador
Authors: RICHARDS MERYL BRETON , MÉNDEZ V. ERNESTO 
Published: November 2013

AbstractAgroforestry systems have substantial potential to conserve native biodiversity and provide ecosystem services. In particular, agroforestry systems have the potential to conserve native tree diversity and sequester carbon for climate change mitigation. However, little research has been conducted on the temporal stability of species diversity and aboveground carbon stocks in these systems or the relation between species diversity and aboveground carbon sequestration. We measured changes in shade‐tree diversity and shade‐tree carbon stocks in 14 plots of a 35‐ha coffee cooperative over 9 years and analyzed relations between species diversity and carbon sequestration. Carbon sequestration was positively correlated with initial species richness of shade trees. Species diversity of shade trees did not change significantly over the study period, but carbon stocks increased due to tree growth. Our results show a potential for carbon sequestration and long‐term biodiversity conservation in smallholder coffee agroforestry systems and illustrate the opportunity for synergies between biodiversity conservation and climate change mitigation.Interacciones entre el Secuestro de Carbono y la Diversidad de Árboles de Sombra en una Cooperativa de Café de Pequeños Agricultores en El Salvador
Healing under pressure: hyperbaric oxygen and myocutaneous flap repair for extreme persistent perineal sinus after proctectomy for inflammatory bowel disease
Authors: Chan X. H. S. , Koh C. E. , Glover M. , Bryson P. , Travis S. P. L. , Mortensen N. J. 
Published: November 2013

AbstractAimPersistent perineal sinus (PPS) following proctectomy for inflammatory bowel disease affects about 50% of patients. Up to 33% of cases of PPS remain unhealed at 12 months and the most refractory cases are unhealed at 24 months despite optimal conventional therapy. Reports of hyperbaric oxygen therapy (HBOT) for chronic wounds and Crohn's perianal disease led us to explore perioperative HBOT with rectus abdominis myocutaneous (RAM) flap repair in a highly selected group of patients with extreme PPS who had failed all other interventions.MethodPatients with extreme PPS received preoperative HBOT (a 90‐min session at 2.2–2.4 atmospheres, five times per week for 5–6 weeks, for a total of up to 30 sessions), before abdominoperineal PPS excision and perineal reconstruction with vertical or transverse RAM flap repair within 2–4 weeks of completing HBOT. Postoperative HBOT (10 further 90‐min sessions) was administered within 2 weeks where practicable.ResultsBetween 2007 and 2011, four patients with extreme PPS underwent RAM flap repair with preoperative HBOT; two also received postoperative HBOT. The median (range) duration of PPS before HBOT was 88.5 (23–156) months. All patients had previously failed multiple (5 to > 35) surgical procedures. Complete healing occurred in all patients at a median (range) follow‐up of 2.5 (2–3) months. There were no further hospital admissions for PPS at a median (range) follow‐up of 35 (8–64) months.ConclusionHyperbaric oxygen therapy combined with PPS excision and perineal reconstruction with a RAM flap led to complete perineal healing in four patients with extreme PPS and appears a safe and effective extension to the therapeutic pathway for exceptionally treatment‐refractory PPS.
Effects of a Mangifera indica L. stem bark extract and mangiferin on radiation‐induced DNA damage in human lymphocytes and lymphoblastoid cells
Authors: Rodeiro I. , Delgado R. , Garrido G. 
Published: November 2013

AbstractObjectivesMangifera indica L. (mango) stem bark aqueous extract (MSBE) that has antioxidant, anti‐inflammatory and immunomodulatory properties, can be obtained in Cuba. It is rich in polyphenols, where mangiferin is the main component. In this study, we have tested DNA damage and protection effects of MSBE and mangiferin on primary human lymphocytes and lymphoblastoid cells.Material and methodsCell suspensions were incubated with the products (50–1000 μg/ml) for experiments on damage induction, and evaluation of any potential protective effects (5–100 μg/ml) for 60 min at 37 °C. Irradiation was performed using a γ‐ray source, absorbed dose 5 Gy. At the end of exposure, DNA damage, protection and repair processes were evaluated using the comet assay.ResultsMSBE (100–1000 μg/ml) induced DNA damage in a concentration dependent manner in both cell types tested, primary cells being more sensitive. Mangiferin (200 μg/ml) only induced light DNA damage at higher concentrations. DNA repair capacity was not affected after MSBE or mangiferin exposure. On the other hand, MSBE (25 and 50 μg/ml) and mangiferin (5–25 ug/ml) protected against gamma radiation‐induced DNA damage.ConclusionsThese results show MSBE has protector or harmful effects on DNA in vitro depending on the experimental conditions, which suggest that the extract could be acting as an antioxidant or pro‐oxidant product. Mangiferin was involved in protective effects of the extract.