bluuebunny/crossref_metadata_2025_split huggingface dataset:
Observations on the ecology of hybridisation in the clubmosses (Lycopodiaceae)
Authors: Øllgaard Benjamin 
Published: March 2014

SynopsisEcological conditions for intergametophytic mating and interspecific hybridisation in the clubmosses are discussed. Several features, including the number of recorded hybrids, records of gametophyte population densities, and conditions for movement of the male gamete in the soil, indicate that intergametophytic mating in Lycopodium is not especially impeded by the subterranean habitat, as has been commonly assumed. The evidence from one site indicates highly effective spore dispersal, and a greater ecological tolerance than expected for the species involved. Two cases are discussed in which hybrids have been formed between ecologically and/or taxonomically very different parent species, in the absence of one parent sporophyte, or with one of the parent species sporophyte poorly adapted to the hybrid habitat. The protected, relatively uniform, subterranean gametophyte habitat is thought to account for successful gametophyte growth and hybridisation between species of widely different sporophyte ecology.
The surface fauna of Xenopus skin
Authors: Tinsley R. C. , Whitear M. 
Published: March 2014

SynopsisRegular moulting can prevent colonisation of the skin surface by epibionts, although some invading organisms are sufficiently mobile to overcome this protective device. Bacteria and sessile protozoans settle on the surface of the claws of Xenopus, where the keratinised cells are not shed as regularly as on the skin. Alternatively, parasites may inhabit the orifices, which also are not affected by moulting.
Interactions between micro-organisms on skin
Authors: Noble W. C. 
Published: March 2014

SynopsisThe mechanisms of interaction are discussed in general terms; this is followed by a review of interaction which may occur in tinea paedis.The production of penicillin-like and other antibiotics by dermatophyte fungi in lesions of athletes foot may result in the selection of an antibiotic-resistant bacterial flora which, perhaps by production of antibiotic or other secondary metabolites, can reduce the viability of the fungi. The effect on the host is to bring about a change from a fungal skin lesion which is dry and scaly to a bacterial lesion which is macerated and malodorous.
BAT3 modulates p300-dependent acetylation of p53 and autophagy-related protein 7 (ATG7) during autophagy
Authors: Sebti Salwa , Prébois Christine , Pérez-Gracia Esther , Bauvy Chantal , Desmots Fabienne , Pirot Nelly , Gongora Céline , Bach Anne-Sophie , Hubberstey Andrew V. , Palissot Valérie , Berchem Guy , Codogno Patrice , Linares Laetitia K. , Liaudet-Coopman Emmanuelle , Pattingre Sophie 
Published: March 2014

Significance
Autophagy allows the lysosomal degradation of intracellular material. It is a tightly regulated process controlled by the tumor-suppressor gene p53, among others. Here we report a unique regulator of autophagy, BAT3, which modulates the intracellular localization of the enzyme p300, an enzyme that adds some acetyl residues on targets proteins (acetylation) to modulate their activity. To stimulate autophagy, BAT3 allows the acetylation of p53 by p300 in the nucleus, but limits the p300-dependent acetylation of ATG7, a protein specific for autophagy, in the cytosol. Thus, BAT3 acts on both the cytosol and the nucleus to tightly modulate autophagy.
Understanding the antagonism of retinoblastoma protein dephosphorylation by PNUTS provides insights into the PP1 regulatory code
Authors: Choy Meng S. , Hieke Martina , Kumar Ganesan Senthil , Lewis Greyson R. , Gonzalez-DeWhitt Kristofer R. , Kessler Rene P. , Stein Benjamin J. , Hessenberger Manuel , Nairn Angus C. , Peti Wolfgang , Page Rebecca 
Published: March 2014

Significance
Dephosphorylation of the tumor-suppressor retinoblastoma protein (Rb) leads to its activation. Our structure of the protein phosphatase 1 (PP1) nuclear targeting subunit (PNUTS):PP1 holoenzyme reveals how this reaction is regulated: PNUTS and Rb compete for an identical binding site on PP1. Because PP1 binds PNUTS 400-fold more strongly than Rb, when PNUTS is present, Rb is not dephosphorylated. However, when PNUTS levels are reduced, PP1 binds and dephosphorylates Rb, leading to its activation. This structure also led to the identification of additional common PP1 binding motifs, allowing us to predict how a quarter of the known PP1 regulators bind to PP1. This result is a key advance for understanding the regulation of PP1, which controls >50% of all dephosphorylation reactions.
Graph-based sampling for approximating global helical topologies of RNA
Authors: Kim Namhee , Laing Christian , Elmetwaly Shereef , Jung Segun , Curuksu Jeremy , Schlick Tamar 
Published: March 2014

Significance
RNA molecules are important components of the cellular machinery and perform many essential roles, including catalysis, transcription, and regulation. Because the structural features are intimately connected to their biological functions, there is great interest in predicting RNA structure from sequence. Present RNA 3D folding algorithms are limited to small RNA structures due to inefficient sampling of RNA structure space. We report a computational approach to predict RNA 3D topologies based on hierarchical sampling of RNA 3D candidate topologies represented as 3D graphs guided by geometrical measures based on known structures. The combination of tools shows great promise for assembling global features of RNA architecture. Applications to RNA design can be envisioned.
Dendritic cell fate is determined by BCL11A
Authors: Ippolito Gregory C. , Dekker Joseph D. , Wang Yui-Hsi , Lee Bum-Kyu , Shaffer Arthur L. , Lin Jian , Wall Jason K. , Lee Baeck-Seung , Staudt Louis M. , Liu Yong-Jun , Iyer Vishwanath R. , Tucker Haley O. 
Published: March 2014

Significance
This work demonstrates a key role of the B lymphocyte transcription factor BCL11A in dendritic cell (DC) development. Two major DC subsets—the plasmacytoid DC (pDC) and the conventional DC (cDC)—are believed to arise from a shared precursor called the common DC progenitor (CDP). Potential precursor differences between cDC and pDC generation might nevertheless remain to be elucidated. Here, we show that mutant mice can generate CDPs and cDCs in the absence of BCL11A, whereas pDCs (and also B cells) are abolished. This study also identifies and validates BCL11A target genes using a variety of techniques, and provides a molecular model for BCL11A activity in the B lymphocyte and pDC lineages.
Blood–spinal cord barrier disruption contributes to early motor-neuron degeneration in ALS-model mice
Authors: Winkler Ethan A. , Sengillo Jesse D. , Sagare Abhay P. , Zhao Zhen , Ma Qingyi , Zuniga Edward , Wang Yaoming , Zhong Zhihui , Sullivan John S. , Griffin John H. , Cleveland Don W. , Zlokovic Berislav V. 
Published: March 2014

Significance
The blood–spinal cord barrier (BSCB) is damaged in human ALS and rodents expressing ALS-associated superoxide dismutase mutations. The role of BSCB breakdown in disease pathogenesis remains, however, unclear. Early motor-neuron dysfunction and injury are now shown to be proportional to the degree of BSCB disruption, and early protection of the BSCB integrity with an activated protein C analog is found to delay onset of motor-neuron impairment and degeneration. Altogether, these findings in mice show that BSCB breakdown plays a role in early-stage disease pathogenesis and that restoring BSCB integrity retards the disease process. These findings are relevant to the corresponding disease mechanism in human ALS in which ALS-associated vascular pathology is associated.
Challenges in RNA virus bioinformatics
Authors: Marz Manja , Beerenwinkel Niko , Drosten Christian , Fricke Markus , Frishman Dmitrij , Hofacker Ivo L. , Hoffmann Dieter , Middendorf Martin , Rattei Thomas , Stadler Peter F. , Töpfer Armin 
Published: March 2014

Abstract
Motivation: Computer-assisted studies of structure, function and evolution of viruses remains a neglected area of research. The attention of bioinformaticians to this interesting and challenging field is far from commensurate with its medical and biotechnological importance. It is telling that out of &gt;200 talks held at ISMB 2013, the largest international bioinformatics conference, only one presentation explicitly dealt with viruses. In contrast to many broad, established and well-organized bioinformatics communities (e.g. structural genomics, ontologies, next-generation sequencing, expression analysis), research groups focusing on viruses can probably be counted on the fingers of two hands.
Results: The purpose of this review is to increase awareness among bioinformatics researchers about the pressing needs and unsolved problems of computational virology. We focus primarily on RNA viruses that pose problems to many standard bioinformatics analyses owing to their compact genome organization, fast mutation rate and low evolutionary conservation. We provide an overview of tools and algorithms for handling viral sequencing data, detecting functionally important RNA structures, classifying viral proteins into families and investigating the origin and evolution of viruses.
Contact: manja@uni-jena.de
Supplementary information: Supplementary data are available at Bioinformatics online. The references for this article can be found in the Supplementary Material.
Accessibility of Apple iPad for partially sighted users: pilot study
Authors: Hewett Rachel , Torgerson Carole , Douglas Graeme 
Published: March 2014

Purpose– The purpose of this paper is to present the results of a pilot trial, investigating the accessibility provided by a tablet computer (Apple iPad) to individuals with visual impairment. The study was designed around an N-of-1 randomised controlled trial (RCT), which was replicated for 12 participants. It served as an opportunity to evaluate the use N-of-1 trials in studies involving people who are visually impaired.Design/methodology/approach– The study centred round an N-of-1 RCT, comparing the accessibility provided by control equipment (Windows computer) against the intervention equipment (Apple iPad). Twelve participants conducted six tests on the equipment as per randomisation, followed by a quantitative-based evaluation and short interviews.Findings– One-sided individual randomisation tests showed a significant result for overall satisfaction in favour of the tablet at the 0.05 significance level for seven of the participants. Participants identified several strengths of the iPad in helping a partially sighted user in accessing the internet: inbuilt zoom and magnification options; increased control as a result of the touch screen; and accessibility tools being built into the operating system. The main limitation suggested was the way the zoom function operates by enlarging the onscreen keyboard. This caused difficulties for those with more severe visual impairments using this function in inputting text.Originality/value– There has been limited research to substantiate positive reviews of the tablet computer for low-vision users. The results of this pilot study gives evidence in support of these potential benefits, and demonstrates the importance of a more thorough investigation.
Fabrication and characterisation of PCL and PCL/PLA scaffolds for tissue engineering
Authors: Patrício T. , Domingos M. , Gloria A. , D'Amora U. , Coelho J.F. , Bártolo P.J. 
Published: March 2014

Purpose
– The main purpose of this research work is to study the effect of poly lactic acid (PLA) addition into poly (e-caprolactone) (PCL) matrices, as well the influence of the mixing process on the morphological, thermal, chemical, mechanical and biological performance of the 3D constructs produced with a novel biomanufacturing device (BioCell Printing).

Design/methodology/approach
– Two mixing processes are used to prepare PCL/PLA blends, namely melt blending and solvent casting. PCL and PCL/PLA scaffolds are produced via BioCell Printing using a 300-μm nozzle, 0/90° lay down pattern and 350-μm pore size. Several techniques such as scanning electron microscopy (SEM), simultaneous thermal analyzer (STA), nuclear magnetic resonance (NMR), static compression analysis and Alamar BlueTM are used to evaluate scaffold's morphological, thermal, chemical, mechanical and biological properties.

Findings
– Results show that the addition of PLA to PCL scaffolds strongly improves the biomechanical performance of the constructs. Additionally, polymer blends obtained by solvent casting present better mechanical and biological properties, compared to blends prepared by melt blending.

Originality/value
– This paper undertakes a detailed study on the effect of the mixing process on the biomechanical properties of PCL/PLA scaffolds. Results will enable to prepare customized PCL/PLA scaffolds for tissue engineering applications with improved biological and mechanical properties, compared to PCL scaffolds alone. Additionally, the accuracy and reproducibility of by the BioCell Printing enables to modulate the micro/macro architecture of the scaffolds enhancing tissue regeneration.
A comparison of aphasia therapy outcomes before and after a Very Early Rehabilitation programme following stroke
Authors: Godecke Erin , Ciccone Natalie A. , Granger Andrew S. , Rai Tapan , West Deborah , Cream Angela , Cartwright Jade , Hankey Graeme J. 
Published: March 2014

AbstractBackgroundVery early aphasia rehabilitation studies have shown mixed results. Differences in therapy intensity and therapy type contribute significantly to the equivocal results.AimsTo compare a standardized, prescribed very early aphasia therapy regimen with a historical usual care control group at therapy completion (4–5 weeks post‐stroke) and again at follow‐up (6 months).Methods & ProceduresThis study compared two cohorts from successive studies conducted in four Australian acute/sub‐acute hospitals. The studies had near identical recruitment, blinded assessment and data‐collection protocols. The Very Early Rehabilitation (VER) cohort (N = 20) had mild–severe aphasia and received up to 20 1‐h sessions of impairment‐based aphasia therapy, up to 5 weeks. The control cohort (n = 27) also had mild–severe aphasia and received usual care (UC) therapy for up to 4 weeks post‐stroke. The primary outcome measure was the Aphasia Quotient (AQ) and a measure of communicative efficiency (DA) at therapy completion. Outcomes were measured at baseline, therapy completion and 6 months post‐stroke and were compared using Generalised Estimating Equations (GEE) models.Outcomes & ResultsAfter controlling for initial aphasia and stroke disability, the GEE models demonstrated that at the primary end‐point participants receiving VER achieved 18% greater recovery on the AQ and 1.5% higher DA scores than those in the control cohort. At 6 months, the VER participants maintained a 16% advantage in recovery on the AQ and 0.6% more on DA scores over the control cohort participants.Conclusions & ImplicationsA prescribed, impairment‐based aphasia therapy regimen, provided daily in very early post‐stroke recovery, resulted in significantly greater communication gains in people with mild–severe aphasia at completion of therapy and at 6 months, when compared with a historical control cohort. Further research is required to demonstrate large‐scale and long‐term efficacy.
Uncoupling protein‐2 mediates the protective action of berberine against oxidative stress in rat insulinoma INS‐1E cells and in diabetic mouse islets
Authors: Liu Limei , Liu Jian , Gao Yuansheng , Yu Xiaoxing , Xu Gang , Huang Yu 
Published: March 2014

Background and PurposeUncoupling protein‐2 (UCP2) may regulate glucose‐stimulated insulin secretion. The current study investigated the effects of berberine, an alkaloid found in many medicinal plants, on oxidative stress and insulin secretion through restoration of UCP2 expression in high glucose (HG)‐treated INS‐1E cells and rat islets or in db/db mouse islets.Experimental ApproachMouse and rat pancreatic islets were isolated. Nitrotyrosine, superoxide dismutase (SOD)‐1 and UCP2 expression and AMPK phosphorylation were examined by Western blotting. Insulin secretion was measured by elisa. Mitochondrial reactive oxygen species (ROS) production was detected by confocal microscopy.Key ResultsIncubation of INS‐1E cells and rat islets with HG (30 mmol·L−1; 8 h) elevated nitrotyrosine level, reduced SOD‐1 and UCP2 expression and AMPK phosphorylation, and inhibited glucose‐stimulated insulin secretion. HG also increased mitochondrial ROS in INS‐1E cells. Co‐treatment with berberine inhibited such effects. The AMPK inhibitor compound C, the UCP2 inhibitor genipin and adenovirus ucp2 shRNA inhibited these protective effects of berberine. Furthermore, compound C normalized berberine‐stimulated UCP2 expression but genipin did not affect AMPK phosphorylation. Islets from db/db mice exhibited elevated nitrotyrosine levels, reduced expression of SOD‐1 and UCP2 and AMPK phosphorylation, and decreased insulin secretion compared with those from db/m+ mice. Berberine also improved these defects in diabetic islets and genipin blocked the effects of berberine.Conclusions and ImplicationsBerberine inhibited oxidative stress and restored insulin secretion in HG‐treated INS‐IE cells and diabetic mouse islets by activating AMPK and UCP2. UCP2 is an important signalling molecule in mediating anti‐diabetic effects of berberine.
KIBS and innovation: The geographic dynamics of innovation in Quebec
Authors: Plassart Mathilde , Shearmur Richard 
Published: March 2014

AbstractThe question we address in this article concerns the possible existence of specifically geographic processes that influence the propensity of Québec City knowledge‐intensive business services (KIBS) firms to innovate. In other words, after controlling for factors of innovation that are internal to the firm, does their neighbourhood‐level environment within the Quebec census metropolitan area partly determine their propensity to innovate? More specifically, this study looks at whether proximity to certain types of economic activity —measured by their employment levels— is connected with innovation. We show that proximity effects do exist, but that these differ according to the type of innovation considered and according to the type of activity to which proximity is measured. Our results indicate that clusters including KIBS, manufacturing, and technical KIBS seem to benefit innovation. Service establishments are, however, more innovative when they are close to the centre of Quebec City, and remote from professional services and government. The nature of these results differs somewhat from those for Montreal—in particular there is no tendency for innovation to increase with the distance to the central business district (CBD). This suggests that the connection between intra‐metropolitan location and KIBS innovation is dependent on specific metropolitan context, and does not therefore reflect easily generalisable processes.
Collagen-induced arthritis: severity and immune response attenuation using multivalent N-acetyl glucosamine
Authors: Richter J , Čapková K , Hříbalová V , Vannucci L , Danyi I , Malý M , Fišerová A 
Published: March 2014

Summary
Rheumatoid arthritis is an autoimmunity leading to considerable impairment of quality of life. N-acetyl glucosamine (GlcNAc) has been described previously as a potent modulator of experimental arthritis in animal models and is used for osteoarthritis treatment in humans, praised for its lack of adverse effects. In this study we present a comprehensive immunological analysis of multivalent GlcNAc-terminated glycoconjugate (GC) application in the treatment of collagen-induced arthritis (CIA) and its clinical outcome. We used immunohistochemistry and FACS to describe conditions on the inflammation site. Systemic and clinical effects were evaluated by FACS, cytotoxicity assay, ELISA, cytometric bead array (CBA), RT–PCR and clinical scoring. We found reduced inflammatory infiltration, NKG2D expression on NK and suppression of T, B and antigen-presenting cells (APC) in the synovia. On the systemic level, GCs prevented the activation of monocyte- and B cell-derived APCs, the rise of TNF-α and IFN-γ levels, and subsequent type II collagen (CII)-specific IgG2a formation. Moreover, we detected an increase of anti-inflammatory IL-4 mRNA in the spleen. Similar to the synovia, the GCs caused a significant reduction of NKG2D-expressing NK cells in the spleen without influencing their lytic function. GCs effectively postponed the onset of arthritic symptoms, reduced their severity and in 18% (GN8P) and 31% (GN4C) of the cases completely prevented their appearance. Our data prove that GlcNAc glycoconjugates prevent the inflammatory response, involving proinflammatory cytokine rise, APC activation and NKG2D expression, leading to the attenuation of clinical symptoms. These results support the glycobiological approach to the treatment of collagen-induced arthritis/rheumatoid arthritis (CIA/RA) as a way of bringing new prospects for more effective therapeutic interventions.
Impact of the consideration of serrated polyps to the interval of colonoscopic surveillance in the NHS Bowel Cancer Screening Programme
Authors: Pullens B. , Dekker E. , Ellis A. J. , Guy R. , Madronal K. , Chetty R. , East J. E. 
Published: March 2014

AbstractAimMost international post polypectomy surveillance guidelines do not recommend surveillance for serrated polyps. In the present study the additional impact of serrated polyps on surveillance intervals from international adenoma surveillance guidelines was investigated.MethodEndoscopic and pathology records were audited of participants in the NHS Bowel Cancer Screening Programme (guaiac faecal occult blood test, gFOBT) in 2011. Surveillance intervals were calculated for current guidelines and also for serrated polyps based on previously described aggressive and conservative strategies.ResultsIn total, 389 patients were included of whom 141 (36.2%) were high risk (advanced adenoma: adenoma ≥ 10 mm, villous elements, high grade dysplasia, or adenoma ≥ 3 in number) needing surveillance at ≤ 3 years. Thirty‐three (8.5%) had significant serrated polyps, of whom 18 (4.6% of the total) had significant serrated lesions and simultaneous advanced adenoma or ≥ 3 adenomas. Adopting an aggressive surveillance strategy, the mean overall absolute additional proportion of all such patients in the surveillance group at 3 years or less was 4.0% (3.9% – 4.1%; 4.2% women; 3.8% men). These proportions varied according to endoscopist from 2.3% to 4.7%. For more conservative strategies the increase was only 1%.ConclusionThe impact of including serrated polyps in current guidelines would result in a small increase in surveillance intervals for FOBT based bowel cancer screening. About half of those who might need surveillance for serrated polyps would already receive surveillance for being in a high risk adenoma group.