bluuebunny/crossref_metadata_2025_split huggingface dataset:
Erosion of Biogenically Weathered Clarens Sandstone by Lichenophagous Bagworm Larvae (Lepidoptera; Pyschidae)
Authors: Wessels D. C. J. , Wessels L.-A. 
Published: June 2014

AbstractLichenophagous larvae of a bagworm moth species, associated with endolithic lichens occur in the Golden Gate Highlands National Park, South Africa. Endolithic lichens weather Clarens sandstone in the park by dissolving the cementing material of the sandstone. Bagworm larvae use such loosened quartz crystals to construct the bags in which they live. By erosion of the weathered sandstone, the bagworm larvae contribute to pedogenesis in the park at an estimated rate of 4.4 kilograms per hectare per year. In addition, bagworm larvae utilize endolithic lichens as a food source and contribute to dispersal of the lichens. The larvae further contribute an estimated 200 g of organic matter per hectare per year to the park and partake in the cycling of elements in the micro-ecosystem.
Mineral Cycling and Lichens: The Physiological Basis
Authors: Brown Dennis H. , Brown Rosalie M. 
Published: June 2014

AbstractA number of physiological processes relevant to the role of lichens in mineral cycling are discussed. Consideration is given to the cellular location of positively-charged cations, showing (a) the benefits of quantifying intracellular elements for the interpretation of toxic metal stress, and (b) how distribution patterns of physiologically essential elements may be altered by desiccation and rehydration under field and laboratory conditions. The quantitative significance of these dynamic processes associated with metal uptake and loss requires verification under field conditions. A modified sequential elution procedure is proposed that enables quantification of insoluble paniculate mineral matter (acquired by wet and dry deposition) in addition to soluble elements in intercellular, extracellular-exchangeable and intracellular sites.
Ecological Significance of Necromass Production In Mat-Forming Lichens
Authors: Crittenden P. D. 
Published: June 2014

AbstractAvailable evidence indicates that basal regions of well-developed lichen mats are composed largely of dead or senescent thallus material. Marked vertical gradients in concentrations of N, P and K in thalli of mat lichens, together with results of N budget studies in Cladonia stellaris and Stereocaulon paschale, suggest that these key elements may be recycled internally to fund new growth at the apices. It is argued that nutrient recycling will increase rates of both apical growth and basal necromass production and that under steady-state conditions this will result in deeper mats and facilitate dominance sensu Grime; thus accumulation of necromass may be an ecological advantage in mat-forming lichens. Basal necromass of the N2-fixing S. paschale contains more N than necromass of the non-N2-fixing C. stellaris; this may be due in part to a greater allocation of N to irrecoverable fungal cell wall components in S. paschale and may underlie a greater requirement for N in this mycobiont.
Loss of function of the ALS protein SigR1 leads to ER pathology associated with defective autophagy and lipid raft disturbances
Authors: Vollrath J T , Sechi A , Dreser A , Katona I , Wiemuth D , Vervoorts J , Dohmen M , Chandrasekar A , Prause J , Brauers E , Jesse C M , Weis J , Goswami A 
Published: June 2014

AbstractIntracellular accumulations of altered, misfolded proteins in neuronal and other cells are pathological hallmarks shared by many neurodegenerative diseases including amyotrophic lateral sclerosis (ALS). Mutations in several genes give rise to familial forms of ALS. Mutations in Sigma receptor 1 have been found to cause a juvenile form of ALS and frontotemporal lobar degeneration (FTLD). We recently described altered localization, abnormal modification and loss of function of SigR1 in sporadic ALS. In order to further elucidate the molecular mechanisms underlying SigR1-mediated alterations in sporadic and familial ALS, we extended our previous studies using neuronal SigR1 knockdown cell lines. We found that loss of SigR1 leads to abnormal ER morphology, mitochondrial abnormalities and impaired autophagic degradation. Consistent with these results, we found that endosomal trafficking of EGFR is impaired upon SigR1 knockdown. Furthermore, in SigR1-deficient cells the transport of vesicular stomatitis virus glycoprotein is inhibited, leading to the accumulation of this cargo protein in the Golgi apparatus. Moreover, depletion of SigR1 destabilized lipid rafts and associated calcium mobilization, confirming the crucial role of SigR1 in lipid raft and intracellular calcium homeostasis. Taken together, our results support the notion that loss of SigR1 function contributes to ALS pathology by causing abnormal ER morphology, lipid raft destabilization and defective endolysosomal pathways.
On the sustainability of an activity
Authors: Zachary Daniel S. 
Published: June 2014

AbstractThis paper develops a framework to determine the sustainability of a general activity. We define an activity as an action or process that uses one or more resources and that responds either wholly or partially to a demand. A definition for sustainability is developed and is contingent on whether or not an activity can be sustained according to the available resources, the duration of an activity, the cost of its execution, or whether substitution is possible. A sustainability condition is met when the duration, cost and the chain of dependent activities satisfies the demand. Two conditions for sustainability are developed: a strong condition when the demand is met with no substitution and a weak condition when the demand is met via substitution. In the latter case, we show that the set of all sustainable activities is a subset of a N-level union of sustainable activities and forms a topological cover.
Failure Processes in Embedded Monolayer Graphene under Axial Compression
Authors: Androulidakis Charalampos , Koukaras Emmanuel N. , Frank Otakar , Tsoukleri Georgia , Sfyris Dimitris , Parthenios John , Pugno Nicola , Papagelis Konstantinos , Novoselov Kostya S. , Galiotis Costas 
Published: June 2014

AbstractExfoliated monolayer graphene flakes were embedded in a polymer matrix and loaded under axial compression. By monitoring the shifts of the 2D Raman phonons of rectangular flakes of various sizes under load, the critical strain to failure was determined. Prior to loading care was taken for the examined area of the flake to be free of residual stresses. The critical strain values for first failure were found to be independent of flake size at a mean value of –0.60% corresponding to a yield stress up to -6 GPa. By combining Euler mechanics with a Winkler approach, we show that unlike buckling in air, the presence of the polymer constraint results in graphene buckling at a fixed value of strain with an estimated wrinkle wavelength of the order of 1–2 nm. These results were compared with DFT computations performed on analogue coronene/PMMA oligomers and a reasonable agreement was obtained.
Ca2+ switches the effect of PS-containing membranes on Factor Xa from activating to inhibiting: implications for initiation of blood coagulation
Authors: Koklic Tilen , Majumder Rinku , Lentz Barry R. 
Published: June 2014

Calcium (Ca2+) plays a pivotal role in cellular and organismal physiology. The Ca2+ ion has an intermediate protein-binding affinity and thus it can serve as an on/off switch in the regulation of different biochemical processes. The serum level of ionized Ca2+ is regulated with normal ionized Ca2+ being in the range 1.10–1.3 mM. Hypocalcaemia (free Ca2+&lt;1.1 mM) in critically ill patients is commonly accompanied by haemostatic abnormalities, ranging from isolated thrombocytopenia to complex defects such as disseminated intravascular coagulation, commonly thought to be due to insufficient functioning of anticoagulation pathways. A small amount of fXa (Factor Xa) produced by Factor VIIa and exposed tissue factor is key to initiating blood coagulation by producing enough thrombin to induce the later stages of coagulation. fXa must bind to PS (phosphatidylserine)-containing membranes to produce thrombin at a physiologically significant rate. In the present study, we show that overall fXa activity on PS-containing membranes is sharply regulated by a ‘Ca2+ switch’ centred at 1.16 mM, below which fXa is active and above which fXa forms inactive dimers on PS-exposing membranes. Our data lead to a mathematical model that predicts the variation of fXa activity as a function of both Ca2+ and membrane concentrations. Because the critical Ca2+ concentration is at the lower end of the normal plasma ionized Ca2+ concentration range, we propose a new regulatory mechanism by which local Ca2+ concentration switches fXa from an intrinsically active form to a form requiring its cofactor [fVa (Factor Va)] to achieve significant activity.
Polyproline promotes tetramerization of recombinant human butyrylcholinesterase
Authors: Larson Marilynn A. , Lockridge Oksana , Hinrichs Steven H. 
Published: June 2014

Human BChE (butyrylcholinesterase) protects against the toxicity of organophosphorus nerve agents and pesticides. BChE purified from human plasma is limited and pathogen carry-over is a concern. Unlike the native BChE tetrameric complex with a residence time of days, rBChE (recombinant BChE) is produced predominantly as dimers and monomers that are cleared from the circulation within minutes. Assembly into tetramers requires incorporation of proline-rich peptides, a process that was thought to occur intracellularly. Our goal was to determine whether polyproline added to rBChE under cell-free conditions would promote tetramerization. Secreted rBChE was purified by procainamide affinity chromatography, and synthetic polyprolines (8-mer to 300-mer) were tested to determine their effect on tetramer assembly. These studies demonstrated that 90–98% of purified rBChE (65 μM) could be assembled into tetramers when incubated with synthetic 17-mer or 50-mer polyproline peptides (100 μM) for 1.5 h at 25°C. However, rBChE tetramerization was inefficient with smaller 8-mer polyproline peptides and larger 300-mer polyproline proteins. Collectively, these studies demonstrated that the eukaryotic cellular machinery is not required for assembly of active BChE into tetramers and that this process can occur in vitro with purified rBChE in the presence of peptides containing 15–50 consecutive proline residues.
Network-guided regression for detecting associations between DNA methylation and gene expression
Authors: Wang Zi , Curry Edward , Montana Giovanni 
Published: June 2014

AbstractMotivation: High-throughput profiling in biological research has resulted in the availability of a wealth of data cataloguing the genetic, epigenetic and transcriptional states of cells. These data could yield discoveries that may lead to breakthroughs in the diagnosis and treatment of human disease, but require statistical methods designed to find the most relevant patterns from millions of potential interactions. Aberrant DNA methylation is often a feature of cancer, and has been proposed as a therapeutic target. However, the relationship between DNA methylation and gene expression remains poorly understood.Results: We propose Network-sparse Reduced-Rank Regression (NsRRR), a multivariate regression framework capable of using prior biological knowledge expressed as gene interaction networks to guide the search for associations between gene expression and DNA methylation signatures. We use simulations to show the advantage of our proposed model in terms of variable selection accuracy over alternative models that do not use prior network information. We discuss an application of NsRRR to The Cancer Genome Atlas datasets on primary ovarian tumours.Availability and implementation: R code implementing the NsRRR model is available at http://www2.imperial.ac.uk/∼gmontanaContact: giovanni.montana@kcl.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online.
Blue: correcting sequencing errors using consensus and context
Authors: Greenfield Paul , Duesing Konsta , Papanicolaou Alexie , Bauer Denis C. 
Published: June 2014

AbstractMotivation: Bioinformatics tools, such as assemblers and aligners, are expected to produce more accurate results when given better quality sequence data as their starting point. This expectation has led to the development of stand-alone tools whose sole purpose is to detect and remove sequencing errors. A good error-correcting tool would be a transparent component in a bioinformatics pipeline, simply taking sequence data in any of the standard formats and producing a higher quality version of the same data containing far fewer errors. It should not only be able to correct all of the types of errors found in real sequence data (substitutions, insertions, deletions and uncalled bases), but it has to be both fast enough and scalable enough to be usable on the large datasets being produced by current sequencing technologies, and work on data derived from both haploid and diploid organisms.Results: This article presents Blue, an error-correction algorithm based on k-mer consensus and context. Blue can correct substitution, deletion and insertion errors, as well as uncalled bases. It accepts both FASTQ and FASTA formats, and corrects quality scores for corrected bases. Blue also maintains the pairing of reads, both within a file and between pairs of files, making it compatible with downstream tools that depend on read pairing. Blue is memory efficient, scalable and faster than other published tools, and usable on large sequencing datasets. On the tests undertaken, Blue also proved to be generally more accurate than other published algorithms, resulting in more accurately aligned reads and the assembly of longer contigs containing fewer errors. One significant feature of Blue is that its k-mer consensus table does not have to be derived from the set of reads being corrected. This decoupling makes it possible to correct one dataset, such as small set of 454 mate-pair reads, with the consensus derived from another dataset, such as Illumina reads derived from the same DNA sample. Such cross-correction can greatly improve the quality of small (and expensive) sets of long reads, leading to even better assemblies and higher quality finished genomes.Availability and implementation: The code for Blue and its related tools are available from http://www.bioinformatics.csiro.au/Blue . These programs are written in C# and run natively under Windows and under Mono on Linux.Contact: paul.greenfield@csiro.auSupplementary information: Supplementary data are available at Bioinformatics online.
Outcome of Transplant-fallout Patients With Unresectable Cholangiocarcinoma
Authors: Sio Terence T. , Martenson James A. , Haddock Michael G. , Novotny Paul J. , Gores Gregory J. , Alberts Steven R. , Miller Robert C. , Heimbach Julie K. , Rosen Charles B. 
Published: June 2014

Objectives:
The aim of this was to determine survival after starting neoadjuvant therapy for patients who became ineligible for orthotopic liver transplantation (OLT).

Methods and Materials:
Since January 1993, 215 patients with unresectable cholangiocarcinoma began treatment with planned OLT. Treatment included external-beam radiation therapy (EBRT) with fluorouracil, bile duct brachytherapy, and postradiotherapy fluorouracil or capecitabine before OLT. Adverse findings at the staging operation, death, and other factors precluded OLT in 63 patients (29%), of whom 61 completed neoadjuvant chemoradiation.

Results:
By October 2012, 56 (89%) of the 63 patients unable to undergo OLT had died. Twenty-two patients (35%) became ineligible for OLT before the staging operation, 38 (60%) at the staging operation, and 3 (5%) after staging. From the date of diagnosis, median overall survival was 12.3 months. Survival was 17% at 18 months and 7% at 24 months. Median survival after fallout was 6.8 months. Median survival after the staging operation was 6 months. Two patients lived for 3.7 and 8.7 years before dying of cancer or liver failure caused by persistent biliary stricture at the site of the original cancer, respectively. Univariate analysis showed that time from diagnosis to fallout correlated with overall survival (P=0.04).

Conclusions:
In highly selected patients initially suitable for OLT, the mortality rate for cholangiocarcinoma was high in patients who became ineligible for OLT. Their survival, however, was comparable to expected survival for patients with locally advanced or metastatic disease treated with nontransplant therapies. The most common reason for patient fallout was adverse findings at the staging operation.
The rugged adaptive landscape of an emerging plant RNA virus
Authors: Lalić Jasna , Elena Santiago F. 
Published: June 2014

AbstractRNA viruses are the main source of emerging infectious diseases owed to the evolutionary potential bestowed by their fast replication, large population sizes and high mutation and recombination rates. However, an equally important parameter, which is usually neglected, is the topography of the fitness landscape, that is, how many fitness maxima exist and how well connected they are, which determines the number of accessible evolutionary pathways. To address this question, we have reconstructed the fitness landscape describing the adaptation ofTobacco etch potyvirusto its new host,Arabidopsis thaliana. Fitness was measured for most of the genotypes in the landscape, showing the existence of peaks and holes. We found prevailing epistatic effects between mutations, with cases of reciprocal sign epistasis being common at latter stages. Therefore, results suggest that the landscape was rugged and holey, with several local fitness peaks and a very limited number of potential neutral paths. The viral genotype fixed at the end of the evolutionary process was not on the global fitness optima but stuck into a suboptimal peak.
Polycomb-Group Proteins andFLOWERING LOCUS TMaintain Commitment to Flowering inArabidopsis thaliana
Authors: Müller-Xing Ralf , Clarenz Oliver , Pokorny Lena , Goodrich Justin , Schubert Daniel 
Published: June 2014

AbstractThe switch from vegetative to reproductive growth is extremely stable even if plants are only transiently exposed to environmental stimuli that trigger flowering. In the photoperiodic pathway, a mobile signal, florigen, encoded by FLOWERING LOCUS T (FT) in Arabidopsis thaliana, induces flowering. Because FT activity in leaves is not maintained after transient photoperiodic induction, the molecular basis for stable floral commitment is unclear. Here, we show that Polycomb-group (Pc-G) proteins, which mediate epigenetic gene regulation, maintain the identity of inflorescence and floral meristems after floral induction. Thus, plants with reduced Pc-G activity show a remarkable increase of cauline leaves under noninductive conditions and floral reversion when shifted from inductive to noninductive conditions. These phenotypes are almost completely suppressed by loss of FLOWERING LOCUS C (FLC) and SHORT VEGETATIVE PHASE, which both delay flowering and promote vegetative shoot identity. Upregulation of FLC in Pc-G mutants leads to a strong decrease of FT expression in inflorescences. We find that this activity of FT is needed to prevent floral reversion. Collectively, our results reveal that floral meristem identity is at least partially maintained by a daylength-independent role of FT whose expression is indirectly sustained by Pc-G activity.
Speech and language therapists’ approaches to communication intervention with children and adults with profound and multiple learning disability
Authors: Goldbart Juliet , Chadwick Darren , Buell Susan 
Published: June 2014

AbstractBackgroundPeople with profound intellectual and multiple disabilities (PMLD) have communication impairments as one defining characteristic.AimsTo explore speech and language therapists' (SLTs) decision making in communication interventions for people with PMLD, in terms of the intervention approaches used, the factors informing the decisions to use specific interventions and the extent to which the rationales underpinning these decisions related to the components of evidence based practice (EBP), namely empirical evidence, clinical experience and client/carer views and values.Methods & ProceduresA questionnaire on communication assessment and intervention for people with PMLD was sent to SLTs in the UK to elicit information on: the communication intervention approaches they used; their rationales for their intervention choices; their use of published evidence to inform decision making.Outcomes & ResultsIntensive interaction and objects of reference were the communication interventions most often used with people with PMLD, with some differences between children and adults evident. Rationales provided conformed somewhat to the EBP framework though extension of the existing framework and addition of practical and organizational considerations led to a revised typology of rationale for decision making. Rationales most frequently related to the empowerment, development and behavioural preferences of the person with PMLD.Conclusions & ImplicationsEmpirical research evidence was seldom mentioned by SLTs as informing intervention decision making leading to very diverse practice. There is a need for further research on the effectiveness of commonly used but under‐evaluated interventions. There is also a need to alert SLTs to the evidence base supporting other approaches, particularly switch‐based, cause and effect approaches.
Are we (mis)guided by current guidelines on intrapartum fetal heart rate monitoring? Case for a more physiological approach to interpretation
Authors: Ugwumadu A 
Published: June 2014

Original interpretations of fetal heart rate (FHR) patterns equated FHR decelerations with ‘fetal distress’, requiring expeditious delivery. This simplistic interpretation is still implied in our clinical guidelines despite 40 years of increasing understanding of the behaviour and regulation of the fetal cardiovascular system during labour. The physiological basis of FHR responses and adaptations to oxygen deprivation is de‐emphasised, whilst generations of obstetricians and midwives are trained to focus on, and classify, the morphological appearances of decelerations into descriptive categories, with no attempt to understand how the fetus defends itself and compensates for intrapartum hypoxic ischaemic insults, or the patterns that suggest progressive loss of compensation. Consequently, there is a lack of confidence, marked variation in FHR interpretation, defensive practices, unnecessary operative interventions, and a failure to recognise abnormal FHR patterns, resulting in adverse outcomes and expensive litigation.