bluuebunny/crossref_metadata_2025 huggingface dataset:
Tephrochronology and the late Holocene volcanic and flood history of Eyjafjallajökull, Iceland
Authors: DUGMORE ANDREW J. , NEWTON ANTHONY J. , SMITH KATE T. , MAIRS KERRY‐ANN
Published: February 2013

The hugely disruptive Eyjafjallajökull eruptions of 2010 AD are well known, but the recent history of the volcano is not, which compromises both Icelandic and international hazard assessments and risk planning. This paper identifies and dates the floods caused by two flank eruptions (the c. 920 AD eruption of the Skerin ridge and 6–7th century AD activity around Miðtungugil) and clarifies understanding of c. 6th century AD central vent eruption. These specific contributions to volcanic history are used to illustrate applications of tephrochronology with widespread relevance: how to date eruptions that generate little tephra, better understand the flood hazards presented by glaciated, mountainous volcanoes and the relationship between long‐term patterns of activity in neighbouring volcanoes, in this case Eyjafjallajökull and its close (and much larger) neighbour, the volcano Katla. Copyright © 2013 John Wiley & Sons, Ltd.
A Facile Method for the Preparation of Monodisperse Beads with Uniform Pore Sizes for Cell Culture
Authors: Moon Seung‐Kwan , Oh Myeong‐Jin , Paik Dong‐Hyun , Ryu Tae‐Kyung , Park Kyeongsoon , Kim Sung‐Eun , Park Jong‐Hoon , Kim Jung‐Hyun , Choi Sung‐Wook
Published: February 2013

This paper describes a facile method for the preparation of porous gelatin beads with uniform pore sizes using a simple fluidic device and their application as supporting materials for cell culture. An aqueous gelatin droplet containing many uniform toluene droplets, produced in the fluidic device, is dropped into liquid nitrogen for instant freezing and the small toluene droplets evolve into pores in the gelatin beads after removal of toluene and then freeze‐drying. The porous gelatin beads exhibit a uniform pore size and monodisperse diameter as well as large open pores at the surface. Fluorescence microscopy images of fibroblast‐loaded gelatin beads confirm the attachment and proliferation of the cells throughout the porous gelatin beads.
Multifocal radiculoneuropathy during ipilimumab treatment of melanoma
Authors: Manousakis Georgios , Koch James , Sommerville R. Brian , El‐Dokla Ahmed , Harms Matthew B. , Al‐Lozi Muhammad T. , Schmidt Robert E. , Pestronk Alan
Published: February 2013

Introduction: Ipilimumab, a monoclonal anti–CTLA‐4 antibody, is used to treat melanoma. Neuromuscular side effects, possibly autoimmune, may occur. Methods: In this investigation we undertook a retrospective review of patient records. Results: After 3 doses of ipilimumab, a 31‐year‐old man developed asymmetric, severe weakness involving all limbs, respiration, and cranial nerves, which was progressive over 2 weeks. EMG/NCS showed an axonal polyradiculoneuropathy with multifocal motor conduction blocks. CSF protein was 749 mg/dl. Nerve pathology showed inflammation around the endoneurial microvessels and subperineurial edema and inflammation. Spine MRI showed leptomeningeal and anterior and posterior root enhancement. Strength improved slowly over months after ipilimumab discontinuation and immunomodulating treatment. Conclusions: Ipilimumab toxicity presented as a monophasic, multifocal, asymmetric polyradiculoneuropathy involving roots and peripheral and cranial nerves. Ipilimumab may produce a polyradiculoneuropathy with disruption of the blood–nerve barrier due to a microvasculopathy. Muscle Nerve 48: 440–444, 2013
Simulation of long‐term consolidation behavior of soft sensitive clay using an elasto‐viscoplastic constitutive model
Authors: Karim M.R. , Oka F. , Krabbenhoft K. , Leroueil S. , Kimoto S.
Published: February 2013

The phenomenon of excess pore water pressure increase or stagnation and continuing large ground deformation in soft sensitive clay following the completion of construction of embankment is simulated for a case study at Saint Alban, Quebec, Canada. The present model employs an updated Lagrangian finite element framework and is combined with an automatic time increment selection scheme. The simulation based on an elasto‐viscoplastic constitutive model considers soil‐structure degradation effect. It is shown that without consideration for the microstructural degradation effect, it is not possible to reproduce the field responses of soft sensitive clay even during the construction of the embankment. When the soil‐structure degradation effect is considered, the present model can offer reasonably accurate prediction for the consolidation behavior of soft sensitive clay, including the so‐called anomalous pore water pressure generation and continuing large deformation even after the end of construction, which has been posing numerous uncertainties on the long‐term performance of earth structures. Copyright © 2013 John Wiley & Sons, Ltd.
Cooked Bones? Method and Practice for Identifying Bones Treated at Low Temperature
Authors: Solari A. , Olivera D. , Gordillo I. , Bosch P. , Fetter G. , Lara V. H. , Novelo O.
Published: February 2013

Is it possible to determine low‐temperature cooking in archaeological bones? The indirect exposure of bones to fire at low temperature (≤ 100 °C), linked to cooking, produces macroscopic modifications on these bones. These modifications have not been clearly or systematically described previously. Instead, physicochemical changes at nanometric level are only now beginning to be understood. In this paper, our principle aim is to explore new methods and techniques that correlate macroscopic features such as smoothness or light transparency with physicochemical characterization results that could aid towards detecting cooked bones in the archaeological record.

This study then selected 11 archaeological samples, both human and non‐human. Bones were considered to be thermally treated or not, on the basis of macroscopic criteria. Complementary characterization techniques were used to study morphology (scanning electron microscopy and small angle X‐ray scattering), structure (X‐ray diffraction and transmission electron microscopy), local composition (energy‐dispersive X‐ray spectroscopy) and texture (gas adsorption). Indeed, fractal dimension, particle size, crystalline percentage or specific surface area may well explain some of the macroscopically observed modifications on these samples. The possibility that such apparent modifications may also be due to diagenesis is also considered.

From an archaeological point of view, the results are promising. Our characterization of human and non‐human bones demonstrates that physicochemical techniques are complementary and provide good criteria against which to distinguish boiled from un‐boiled archaeological samples. Copyright © 2013 John Wiley & Sons, Ltd.
Deep nuclear resonant tunneling thermal rate constant calculations
Authors: Mandrà Salvatore , Valleau Stéphanie , Ceotto Michele
Published: February 2013

A fast and robust time‐independent method to calculate thermal rate constants in the deep resonant tunneling regime for scattering reactions is presented. The method is based on the calculation of the cumulative reaction probability which, once integrated, gives the thermal rate constant. We tested our method with both continuous (single and double Eckart barriers) and discontinuous first derivative potentials (single and double rectangular barriers). Our results show that the presented method is robust enough to deal with extreme resonating conditions such as multiple barrier potentials. Finally, the calculation of the thermal rate constant for double Eckart potentials with several quasi‐bound states and the comparison with the time‐independent log‐derivative method are reported. An implementation of the method using the Mathematica Suite is included in the Supporting Information. © 2013 Wiley Periodicals, Inc.
The investigation of NbO2 and Nb2O5 electronic structure by XPS, UPS and first principles methods
Authors: Weibin Zhang , Weidong Wu , Xueming Wang , Xinlu Cheng , Dawei Yan , Changle Shen , Liping Peng , Yuying Wang , Li Bai
Published: February 2013

In this paper, the electronic structures of NbO2 and Nb2O5 are theoretically and experimentally analyzed. The oxides in the samples are mainly consisted of NbO2 and NbO, whereas the outmost layer of the samples is NbO2. After exposure to air, the outermost layer on all niobium samples is Nb2O5. The photoelectrons from the first 2–4 Å contribute to the spectra, so the valence band structure of NbO2 and Nb2O5 can be confirmed from ultraviolet photoelectron spectroscopy (UPS). By comparing the UPS with density of state results, the electronic structure of NbO2 and Nb2O5 can be distinguished from each other, and then the electronic structure was deconvoluted into several electronic states. The agreement between experimental result and theory is, in the best case, satisfactory. Copyright © 2013 John Wiley & Sons, Ltd.
Transoral robotic surgery for large mixed laryngocoele
Authors: Ciabatti P G , Burali G , D'Ascanio L
Published: February 2013

Background:

A laryngocoele is an abnormal dilatation of Morgagni's ventricle in direct communication with the laryngeal lumen. Surgical excision through a cervical approach is traditionally considered the treatment of choice for large (external and mixed) laryngocoeles. This paper describes the first reported case of a large mixed laryngocoele treated with transoral robotic surgery without cervical incisions.

Method:

A 69-year-old female underwent transoral robotic surgery for the excision of a large mixed left laryngocoele. The surgery was performed using the da Vinci S surgical robotic system (Intuitive Surgical, Sunnyvale, California, USA).

Results:

No complications were observed and the patient was discharged 2 days post-operation.

Conclusion:

Transoral robotic surgery enabled accurate dissection with complete removal of the large mixed laryngocoele via a minimally invasive approach. The advantages of transoral robotic surgery over other techniques for laryngocoele excision are discussed.
Endolymphatic sac tumour: case report and literature review
Authors: Virk J S , Randhawa P S , Saeed S R
Published: February 2013

Objective:

To increase awareness of the presentation, diagnostic difficulties and management of endolymphatic sac tumours.

Case reports:

A 79-year-old man with a 6-month history of unilateral hearing loss, tinnitus and vertigo, who was suspected to have an endolymphatic sac tumour on imaging, underwent successful transmastoid-translabyrinthine resection. A 53-year-old man with unilateral hearing loss and pulsatile tinnitus underwent subtotal resection of a suspected paraganglioma, which was identified histologically. Due to interval growth, gamma knife radiosurgery was performed followed by subtotal petrosectomy, at which juncture an endolymphatic sac tumour was reported.

Methods:

A review of the world literature was carried out using Medline, which identified less than 150 reported cases of endolymphatic sac tumour.

Conclusion:

Endolymphatic sac tumours are rare lesions of the petrous temporal bone. Although benign, they can be locally destructive. At present, there is no consensus regarding the management and long-term follow up of these tumours. Surgical resection is usually favoured, although treatment with radiotherapy and gamma knife surgery has also been reported.
Behavioral characteristics of Chinese adolescents with dyslexia: The use of teachers’ behavior checklist in Hong Kong
Authors: CHING BOBY HO-HONG , HO CONNIE SUK-HAN , CHAN DAVID W. , CHUNG KEVIN K. H. , LO LAP-YAN
Published: February 2013

We developed the Hong Kong Specific Learning Difficulties Behavior Checklist for Junior Secondary School Students (BCL-JS) for teachers to rate the frequency of 52 reading-related behavioral characteristics of Chinese secondary school students. An item factor analysis based on ratings on 947 students yielded seven distinct dimensions. In a separate sample of 90 students, the seven constructs of the BCL-JS significantly correlated with students’ performances on most literacy and reading-related cognitive measures, and differentiated adolescents with or without dyslexia. Discriminant analysis showed that the BCL-JS had a high rate of correct classification (82.2%). These findings support that the BCL-JS is a reliable screening tool for Chinese junior secondary school students at risk for dyslexia.
Evaluating the clinical and economic burden of healthcare-associated infections during hospitalization for surgery in France
Authors: LAMARSALLE L. , HUNT B. , SCHAUF M. , SZWARCENSZTEIN K. , VALENTINE W. J.
Published: February 2013

Over 4 million patients suffer nosocomial infections annually in the European Union. This study aimed to estimate the healthcare burden associated with healthcare-associated infections (HAIs) following surgery in France, and explore the potential impact of infection control strategies and interventions on the clinical and economic burden of disease. Data on the frequency of HAIs were gathered from the 2010 Programme de Médicalisation des Systèmes d'Information (PMSI), and cost data were taken from the 2009 Echelle Nationale de Coûts à Méthodologie Commune (ENCC). It was estimated that 3% of surgical procedures performed in 2010 in France resulted in infection, resulting in an annual cost of €57 892 715. Patients experiencing a HAI had a significantly increased mortality risk (4·15-fold) and an increased length of hospital stay (threefold). Scenario analysis in which HAI incidence following surgery was reduced by 8% (based on a study of the effectiveness of triclosan-coated sutures), suggested that, annually, 20 205 hospital days and €4 588 519 could be saved. Analyses of 20% and 30% reductions in incidence (based on an estimate of the number of preventable nosocomial infections) suggested that annual savings of €11 548 057 and €17 334 696, respectively, could be made. New infection control interventions which reduce HAI incidence during hospitalization for surgery have the potential to provide valuable cost savings to healthcare providers.
Towards a Weighted Version of the Hajnal–Szemerédi Theorem
Authors: BALOGH JOZSEF , KEMKES GRAEME , LEE CHOONGBUM , YOUNG STEPHEN J.
Published: February 2013

For a positive integer r ≥ 2, a Kr-factor of a graph is a collection vertex-disjoint copies of Kr which covers all the vertices of the given graph. The celebrated theorem of Hajnal and Szemerédi asserts that every graph on n vertices with minimum degree at least $(1-\frac{1}{r})n contains a Kr-factor. In this note, we propose investigating the relation between minimum degree and existence of perfect Kr-packing for edge-weighted graphs. The main question we study is the following. Suppose that a positive integer r ≥ 2 and a real t ∈ [0, 1] is given. What is the minimum weighted degree of Kn that guarantees the existence of a Kr-factor such that every factor has total edge weight at least $$t\binom{r}{2}$?$ We provide some lower and upper bounds and make a conjecture on the asymptotics of the threshold as n goes to infinity.
Drei Sozialformeln zur Schätzung der (prämorbiden) Intelligenzquotienten nach Wechsler
Authors: Jahn Thomas , Beitlich Daniela , Hepp Sandra , Knecht Ruth , Köhler Karsten , Ortner Clarissa , Sperger Eva , Kerkhoff Georg
Published: February 2013

Im Rahmen neuropsychologischer Untersuchungen dient die Einschätzung der prämorbiden Leistungsfähigkeit der individuellen Defizitdiagnostik ebenso wie der realistischen Behandlungszielsetzung. Die dafür unverzichtbare biographische Anamnese kann durch Schätzmethoden ergänzt werden, deren Vor- und Nachteile skizziert werden. Insbesondere soziodemographische Formeln erlauben die Schätzung prämorbider Intelligenzniveaus unabhängig vom Krankheitsgeschehen, doch sind solche „Sozialformeln” hierzulande nicht verfügbar. Daher wurde eine nach Alter, Geschlecht und Schulbildung bevölkerungsrepräsentativ quotierte Stichprobe von 612 Gesunden zu zahlreichen soziodemographischen Merkmalen befragt. Zusätzlich wurden eine Intelligenztestbatterie (HAWIE-R), ein Wortschatztest (MWT-B) und ein Lesetest (LECTOR) durchgeführt. Mittels Regressionsanalysen wurden Vorhersagemodelle für den Gesamt-, Verbal- und Handlungs-IQ gewonnen und erfolgreich kreuzvalidiert. Trotz unvermeidlicher Regression zur Mitte ergab sich eine ausreichende Vorhersagegüte zumindest für den Gesamt- und Verbal-IQ. Die Schätzformeln sind anwendbar für Bewohner der Alten Bundesrepublik sowie nach 1985 geborene Ostdeutsche. Ein Fallbeispiel und das im Anhang enthaltene Berechnungsblatt erleichtern zusammen mit der Diskussion relevanter Indikations- und Interpretationsfragen die Formelanwendung.
Sexuell übertragbare Infektionen: Update 2013
Authors: Lautenschlager Stephan
Published: February 2013

Trotz beachtlicher Fortschritte in Diagnostik, Therapie und Aufklärung sind sexuell übertragbare Infektionen (STI) weltweit und speziell auch in der Schweiz weiterhin zunehmend. Die häufigsten sexuell übertragbaren Erreger umfassen humane Papillomviren, Chlamydien, Herpes-simplex-Viren (Typ 1 und 2), Neisseria gonorrhoeae, Treponema pallidum, Hepatitis-B-Viren und Trichomonaden. Infolge des häufig asymptomatischen oder oligosymptomatischen Verlaufs bedeuten diese Infektionen sowohl diagnostisch als auch therapeutisch weiterhin eine grosse Herausforderung für das Gesundheitswesen. Erfreulicherweise konnten aktuelle epidemiologische Studien zu Infektionen mit humanen Papillomviren zeigen, dass geimpfte Frauen kaum noch an Kondylomen erkranken und ebenfalls deutlich seltener Zervix-Dysplasien aufweisen. Auf der anderen Seite ist die Zunahme von Urethritisfällen durch unterschiedliche Erreger sowie der Syphilis ungebrochen. Alarmierend ist zusätzlich die aktuelle Resistenzlage der Gonokokken, die zunehmend auf die Cephalosporine – die letzte verbleibende wirksame Antibiotikagruppe – eine reduzierte Empfindlichkeit aufweist. In dieser Situation sollten die aktuellen Therapierichtlinien streng eingehalten werden. Weitere aktuelle Trends und deren Konsequenzen werden im Artikel diskutiert.
Selection, Optimization, Compensation, and Equilibrium Dynamics
Authors: Boker Steven M.
Published: February 2013

One of the major theoretic frameworks through which human development is studied is a process-oriented model involving selection, optimization, and compensation. These three processes each provide accounts for methods by which gains are maximized and losses minimized throughout the lifespan, in particular during later life. These processes can be cast within the framework of dynamical systems theory and then modeled using differential equations. The current article will review basic tenets of selection, optimization, and compensation while introducing language and concepts from dynamical systems. Four categories of interindividual differences and intraindividual variability in dynamics are then described and discussed in the context of selection, optimization, and compensation.
Archaeal and anaerobic methane oxidizer communities in the Sonora Margin cold seeps, Guaymas Basin (Gulf of California)
Authors: Vigneron Adrien , Cruaud Perrine , Pignet Patricia , Caprais Jean-Claude , Cambon-Bonavita Marie-Anne , Godfroy Anne , Toffin Laurent
Published: February 2013

Cold seeps, located along the Sonora Margin transform fault in the Guaymas Basin, were extensively explored during the ‘BIG’ cruise in June 2010. They present a seafloor mosaic pattern consisting of different faunal assemblages and microbial mats. To investigate this mostly unknown cold and hydrocarbon-rich environment, geochemical and microbiological surveys of the sediments underlying two microbial mats and a surrounding macrofaunal habitat were analyzed in detail. The geochemical measurements suggest biogenic methane production and local advective sulfate-rich fluxes in the sediments. The distributions of archaeal communities, particularly those involved in the methane cycle, were investigated at different depths (surface to 18 cm below the sea floor (cmbsf)) using complementary molecular approaches, such as Automated method of Ribosomal Intergenic Spacer Analysis (ARISA), 16S rRNA libraries, fluorescence in situ hybridization and quantitative polymerase chain reaction with new specific primer sets targeting methanogenic and anaerobic methanotrophic lineages. Molecular results indicate that metabolically active archaeal communities were dominated by known clades of anaerobic methane oxidizers (archaeal anaerobic methanotroph (ANME)-1, -2 and -3), including a novel ‘ANME-2c Sonora’ lineage. ANME-2c were found to be dominant, metabolically active and physically associated with syntrophic Bacteria in sulfate-rich shallow sediment layers. In contrast, ANME-1 were more prevalent in the deepest sediment samples and presented a versatile behavior in terms of syntrophic association, depending on the sulfate concentration. ANME-3 were concentrated in small aggregates without bacterial partners in a restricted sediment horizon below the first centimetres. These niche specificities and syntrophic behaviors, depending on biological surface assemblages and environmental availability of electron donors, acceptors and carbon substrates, suggest that ANME could support alternative metabolic pathways than syntrophic anaerobic oxidation of methane.
Short-term observations of marine bacterial and viral communities: patterns, connections and resilience
Authors: Needham David M , Chow Cheryl-Emiliane T , Cram Jacob A , Sachdeva Rohan , Parada Alma , Fuhrman Jed A
Published: February 2013

Observation of short-term temporal variation in bacterial and viral communities is important for understanding patterns of aquatic microbial diversity. We collected surface seawater once daily for 38 consecutive days with seven more samples interspersed over 40 more days at one location ∼2 km from Santa Catalina Island, California. Bacterial communities were analyzed by automated ribosomal intergenic spacer analysis (ARISA) and viral communities were analyzed by terminal restriction fragment length polymorphism (TRFLP) of the conserved T4-like myoviral gene encoding the major capsid protein (g23). Common bacterial and viral taxa were consistently dominant, and relatively few displayed dramatic increases/decreases or ‘boom/bust’ patterns that might be expected from dynamic predator-prey interactions. Association network analysis showed most significant covariations (associations) occurred among bacterial taxa or among viral taxa and there were several modular (highly-interconnected) associations (P⩽0.005). Associations observed between bacteria and viruses (P⩽0.005) occurred with a median time lag of 2 days. Regression of all pairwise Bray-Curtis similarities between samples indicated a rate of bacterial community change that slows from 2.1%–0.18% per day over a week to 2 months; the rate stays around 0.4% per day for viruses. Our interpretation is that, over the scale of days, individual bacterial and viral OTUs can be dynamic and patterned; resulting in statistical associations regarded as potential ecological interactions. However, over the scale of weeks, average bacterial community variation is slower, suggesting that there is strong community-level ecological resilience, that is, a tendency to converge towards a ‘mean’ microbial community set by longer-term controlling factors.
Enrichment of specific protozoan populations during in situ bioremediation of uranium-contaminated groundwater
Authors: Holmes Dawn E , Giloteaux Ludovic , Williams Kenneth H , Wrighton Kelly C , Wilkins Michael J , Thompson Courtney A , Roper Thomas J , Long Philip E , Lovley Derek R
Published: February 2013

The importance of bacteria in the anaerobic bioremediation of groundwater polluted with organic and/or metal contaminants is well recognized and in some instances so well understood that modeling of the in situ metabolic activity of the relevant subsurface microorganisms in response to changes in subsurface geochemistry is feasible. However, a potentially significant factor influencing bacterial growth and activity in the subsurface that has not been adequately addressed is protozoan predation of the microorganisms responsible for bioremediation. In field experiments at a uranium-contaminated aquifer located in Rifle, CO, USA, acetate amendments initially promoted the growth of metal-reducing Geobacter species, followed by the growth of sulfate reducers, as observed previously. Analysis of 18S rRNA gene sequences revealed a broad diversity of sequences closely related to known bacteriovorous protozoa in the groundwater before the addition of acetate. The bloom of Geobacter species was accompanied by a specific enrichment of sequences most closely related to the ameboid flagellate, Breviata anathema, which at their peak accounted for over 80% of the sequences recovered. The abundance of Geobacter species declined following the rapid emergence of B. anathema. The subsequent growth of sulfate-reducing Peptococcaceae was accompanied by another specific enrichment of protozoa, but with sequences most similar to diplomonadid flagellates from the family Hexamitidae, which accounted for up to 100% of the sequences recovered during this phase of the bioremediation. These results suggest a prey–predator response with specific protozoa responding to increased availability of preferred prey bacteria. Thus, quantifying the influence of protozoan predation on the growth, activity and composition of the subsurface bacterial community is essential for predictive modeling of in situ uranium bioremediation strategies.
Diversification of endosymbiosis: replacements, co-speciation and promiscuity of bacteriocyte symbionts in weevils
Authors: Toju Hirokazu , Tanabe Akifumi S , Notsu Yutaka , Sota Teiji , Fukatsu Takema
Published: February 2013

The processes and mechanisms underlying the diversification of host–microbe endosymbiotic associations are of evolutionary interest. Here we investigated the bacteriocyte-associated primary symbionts of weevils wherein the ancient symbiont Nardonella has experienced two independent replacement events: once by Curculioniphilus symbiont in the lineage of Curculio and allied weevils of the tribe Curculionini, and once by Sodalis-allied symbiont in the lineage of grain weevils of the genus Sitophilus. The Curculioniphilus symbiont was detected from 27 of 36 Curculionini species examined, the symbiont phylogeny was congruent with the host weevil phylogeny, and the symbiont gene sequences exhibited AT-biased nucleotide compositions and accelerated molecular evolution. These results suggest that the Curculioniphilus symbiont was acquired by an ancestor of the tribe Curculionini, replaced the original symbiont Nardonella, and has co-speciated with the host weevils over evolutionary time, but has been occasionally lost in several host lineages. By contrast, the Sodalis-allied symbiont of Sitophilus weevils exhibited no host–symbiont co-speciation, no AT-biased nucleotide compositions and only moderately accelerated molecular evolution. These results suggest that the Sodalis-allied symbiont was certainly acquired by an ancestor of the Sitophilus weevils and replaced the original Nardonella symbiont, but the symbiotic association must have experienced occasional re-associations such as new acquisitions, horizontal transfers, replacements and/or losses. We detected Sodalis-allied facultative symbionts in populations of the Curculionini weevils, which might represent potential evolutionary sources of the Sodalis-allied primary symbionts. Comparison of these newcomer bacteriocyte-associated symbiont lineages highlights potential evolutionary trajectories and consequences of novel symbionts after independent replacements of the same ancient symbiont.
The biogeography of fungal communities in wetland sediments along the Changjiang River and other sites in China
Authors: Wu Bing , Tian Jianqing , Bai Chunming , Xiang Meichun , Sun Jingzu , Liu Xingzhong
Published: February 2013

Whether fungal community structure depends more on historical factors or on contemporary factors is controversial. This study used culture-dependent and -independent (polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE)) methods to assess the influence of historical and contemporary factors on the distributions of fungi in the wetland sediments at 10 locations along the Changjiang River and at 10 other locations in China. The culture-dependent approach detected greater species diversity (177 operational taxonomic units (OTUs)) than PCR-DGGE analysis (145 OTUs), and the species in the genera of Penicillium (relative frequency=16.8%), Fusarium (15.4%), Aspergillus (7.6%), Trichoderma (5.8%) and Talaromyces (4.2%) were dominant. On the basis of DGGE data, fungal diversity along the Changjiang River increased from upstream to downstream; altitude explained 44.8% of this variation in diversity. And based on the data from all 20 locations, the fungal communities were geographically clustered into three groups: Southern China, Northern China and the Qinghai-Tibetan Plateau. Multivariate regression tree analysis for data from the 20 locations indicated that the fungal community was influenced primarily by location (which explained 61.8% of the variation at a large scale), followed by total potassium (9.4%) and total nitrogen (3.5%) at a local scale. These results are consistent with the concept that geographic distance is the dominant factor driving variation in fungal diversity at a regional scale (1000–4000 km), whereas environmental factors (total potassium and total nitrogen) explain variation in fungal diversity at a local scale (<1000 km).
Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes
Authors: Wang Jianjun , Shen Ji , Wu Yucheng , Tu Chen , Soininen Janne , Stegen James C , He Jizheng , Liu Xingqi , Zhang Lu , Zhang Enlou
Published: February 2013

Increasing evidence has emerged for non-random spatial distributions of microbes, but knowledge of the processes that cause variation in microbial assemblage among ecosystems is lacking. For instance, some studies showed that deterministic processes such as habitat specialization are important, while other studies hold that bacterial communities are assembled by stochastic forces. Here we examine the relative influence of deterministic and stochastic processes for bacterial communities from subsurface environments, stream biofilm, lake water, lake sediment and soil using pyrosequencing of the 16S ribosomal RNA gene. We show that there is a general pattern in phylogenetic signal in species ecological niches across recent evolutionary time for all studied habitats, enabling us to infer the influences of community assembly processes from patterns of phylogenetic turnover in community composition. The phylogenetic dissimilarities among-habitat types were significantly higher than within them, and the communities were clustered according to their original habitat types. For communities within-habitat types, the highest phylogenetic turnover rate through space was observed in subsurface environments, followed by stream biofilm on mountainsides, whereas the sediment assemblages across regional scales showed the lowest turnover rate. Quantifying phylogenetic turnover as the deviation from a null expectation suggested that measured environmental variables imposed strong selection on bacterial communities for nearly all sample groups. For three sample groups, spatial distance reflected unmeasured environmental variables that impose selection, as opposed to spatial isolation. Such characterization of spatial and environmental variables proved essential for proper interpretation of partial Mantel results based on observed beta diversity metrics. In summary, our results clearly indicate a dominant role of deterministic processes on bacterial assemblages and highlight that bacteria show strong habitat associations that have likely emerged through evolutionary adaptation.
RegulatING chromatin regulators: post-translational modification of the ING family of epigenetic regulators
Authors: Satpathy Shankha , Nabbi Arash , Riabowol Karl
Published: February 2013

The five human ING genes encode at least 15 splicing isoforms, most of which affect cell growth, differentiation and apoptosis through their ability to alter gene expression by epigenetic mechanisms. Since their discovery in 1996, ING proteins have been classified as type II tumour suppressors on the basis of reports describing their down-regulation and mislocalization in a variety of cancer types. In addition to their regulation by transcriptional mechanisms, understanding the range of PTMs (post-translational modifications) of INGs is important in understanding how ING functions are fine-tuned in the physiological setting and how they add to the repertoire of activities affected by the INGs. In the present paper we review the different PTMs that have been reported to occur on INGs. We discuss the PTMs that modulate ING function under normal conditions and in response to a variety of stresses. We also describe the ING PTMs that have been identified by several unbiased MS-based PTM enrichment techniques and subsequent proteomic analysis. Among the ING PTMs identified to date, a subset has been characterized for their biological significance and have been shown to affect processes including subcellular localization, interaction with enzymatic complexes and ING protein half-life. The present review aims to highlight the emerging role of PTMs in regulating ING function and to suggest additional pathways and functions where PTMs may effect ING function.
Rational engineering of plasticity residues of sesquiterpene synthases from Artemisia annua: product specificity and catalytic efficiency
Authors: Li Jian-Xu , Fang Xin , Zhao Qin , Ruan Ju-Xin , Yang Chang-Qing , Wang Ling-Jian , Miller David J. , Faraldos Juan A. , Allemann Rudolf K. , Chen Xiao-Ya , Zhang Peng
Published: February 2013

Most TPSs (terpene synthases) contain plasticity residues that are responsible for diversified terpene products and functional evolution, which provide a potential for improving catalytic efficiency. Artemisinin, a sesquiterpene lactone from Artemisia annua L., is widely used for malaria treatment and progress has been made in engineering the production of artemisinin or its precursors. In the present paper, we report a new sesquiterpene synthase from A. annua, AaBOS (A. annua α-bisabolol synthase), which has high sequence identity with AaADS (A. annua amorpha-4,11-diene synthase), a key enzyme in artemisinin biosynthesis. Comparative analysis of the two enzymes by domain-swapping and structure-based mutagenesis led to the identification of several plasticity residues, whose alteration changed the product profile of AaBOS to include γ-humulene as the major product. To elucidate the underlying mechanisms, we solved the crystal structures of AaBOS and a γ-humulene-producing AaBOS mutant (termed AaBOS-M2). Among the plasticity residues, position 399, located in the substrate-binding pocket, is crucial for both enzymes. In AaBOS, substitution of threonine for leucine (AaBOSL339T) is required for γ-humulene production; whereas in AaADS, replacing the threonine residue with serine (AaADST399S) resulted in a substantial increase in the activity of amorpha-4,11-diene production, probably as a result of accelerated product release. The present study demonstrates that substitution of plasticity residues has potential for improving catalytic efficiency of the enzyme.
Electrical resistivity of HTSC–normal metal interface
Authors: Sokolenko V. I. , Frolov V. A.
Published: February 2013

It is analytically shown that the specific resistivity ρ of the contact layer in a hole-type HTSC abutting upon a metal Me with electronic conductivity is a non-monotonous function of the distance from the interface. The maximum value of ρ corresponds to ρAF of HTSC in the antiferromagnetic dielectric state at the distance x where the difference between the density of Fermi guest electrons and native holes nfe(x)−nfh(x)=0. In the case of nfe(x)=const, the value of contact resistivity rc of the HTSC/Me interface can serve as an indicator of changes in nfh(x), especially the temperature-related ones. The temperature dependences rc(T) in HTSC/Pb and HTSC/In interfaces were measured for optimally and lightly doped biphasic bismuth ceramics BiSrPbCaCuO. The anomalies observed in the measured temperature dependences agree with the concept of local pairs existing in the pseudogap phase up to the temperature of depairing, the idea of fluctuation superconductivity, and the transition into the superconducting state.
Oscillating modes of a massive single vortex line in an anisotropic superconductor: The role of temperature
Authors: Vasiliev S. V. , Chabanenko V. V. , Kuzovoi N. V. , Rusakov V. F.
Published: February 2013

The De Gennes and Matricon problem of the vibrations of a single vortex line was generalized by taking into account the pinning force, viscosity and vortex effective mass. The characteristic frequencies of vortex oscillations and their temperature dependences were calculated for YBaCuO anisotropic superconductor.
An effect of the curvature induced anisotropy on the spectrum of spin waves in a curved magnetic nanowire
Authors: Tkachenko V. S. , Kuchko A. N. , Kruglyak V. V.
Published: February 2013

Within the framework of the solid state theory, an expression for the spectrum of spin waves propagating in a thin magnetic nanowire curled into a helix (spiral) is obtained. Its modification under the effect of a periodic modulation of the helical pitch is analyzed. In particular, it is shown that the periodic modulation of the helix pitch leads to the appearance of band gaps in the spectrum of spin waves. The influence of the modulation depth of the helical pitch on a size of the first gap is considered.
Fire dependency of a rock-outcrop plant Calothamnus rupestris (Myrtaceae) and implications for managing fire in south-western Australian forests
Authors: Burrows Neil D.
Published: February 2013

Granite outcrops embedded in south-western Australian forests provide habitat for unique biotic assemblages and refugia for fire-sensitive taxa. Discontinuous vegetation and natural barriers to fire spread enable outcrops to function as fire refugia, provided fires in the surrounding forest are not of high intensity. In Summer 2003, lightning started a fire in jarrah forest that had not been burnt for almost 20 years. The high-intensity fire burned the vegetation on Mount Cooke, a large granite outcrop, providing an opportunity to study the response of Calothamnus rupestris Schauer, a fire-sensitive serotinous plant. The population was killed by the fire, but readily regenerated from seed stored in woody capsules. The post-fire population reached maturity after ~7.5 years, whereas the seed bank is unlikely to recover to the pre-fire level until ~14 years. The likelihood of intense forest wildfires affecting outcrop communities can be reduced by frequent low-intensity prescribed burning in the surrounding forests to reduce fuel hazard and quantity. Low-intensity forest fires are unlikely to be lethal to sensitive granite-outcrop communities.
Flammability is not selected for, it emerges
Authors: Midgley Jeremy J.
Published: February 2013

The present explanation for the evolution of flammability invokes the need for a flammable mutant parent plant (the torch) to be able to spread the negative effects of fire to less flammable, more fire-sensitive neighbouring plants (the damps). Thereafter, if the torch either produces more seedlings, or more competitive seedlings, in the post-fire environment, to take over the space vacated by both the dead damps and the torch, then torch genotypes could invade. Here, I argue that an individual flammable mutant genotype cannot invade the ‘group’ of non-flammable individuals because it implies unlikely patterns of seed dispersal and fitness advantages. The implication of this is that although flammability can evolve, it is an incidental or emergent property of species or ecosystems and that it confers no extra advantages to individual flammable plants. In contrast, anti-flammability could be both selected for, and evolve.
Dual function of the NDR-kinase Dbf2 in the regulation of the F-BAR protein Hof1 during cytokinesis
Authors: Meitinger Franz , Palani Saravanan , Hub Birgit , Pereira Gislene
Published: February 2013

The conserved NDR-kinase Dbf2 plays a critical role in cytokinesis in budding yeast. Among its cytokinesis-related substrates is the F-BAR protein Hof1. Hof1 colocalizes at the cell division site with the septin complex and, as mitotic exit progresses, moves to the actomyosin ring (AMR). Neither the function of Hof1 at the septin complex nor the mechanism by which Hof1 supports AMR constriction is understood. Here we establish that Dbf2 has a dual function in Hof1 regulation. First, we show that the coiled-coil region, which is adjacent to the conserved F-BAR domain, is required for the binding of Hof1 to septins. The Dbf2-dependent phosphorylation of Hof1 at a single serine residue (serine 313) in this region diminishes the recruitment of Hof1 to septins both in vitro and in vivo. Genetic and functional analysis indicates that the binding of Hof1 to septins is important for septin rearrangement and integrity during cytokinesis. Furthermore, Dbf2 phosphorylation of Hof1 at serines 533 and 563 promotes AMR constriction most likely by inhibiting the SH3-domain–dependent interactions of Hof1. Thus our data show that Dbf2 coordinates septin and AMR functions during cytokinesis through the regulation/control of Hof1.
Visualization of actin filaments and monomers in somatic cell nuclei
Authors: Belin Brittany J. , Cimini Beth A. , Blackburn Elizabeth H. , Mullins R. Dyche
Published: February 2013

In addition to its long-studied presence in the cytoplasm, actin is also found in the nuclei of eukaryotic cells. The function and form (monomer, filament, or noncanonical oligomer) of nuclear actin are hotly debated, and its localization and dynamics are largely unknown. To determine the distribution of nuclear actin in live somatic cells and evaluate its potential functions, we constructed and validated fluorescent nuclear actin probes. Monomeric actin probes concentrate in nuclear speckles, suggesting an interaction of monomers with RNA-processing factors. Filamentous actin probes recognize discrete structures with submicron lengths that are excluded from chromatin-rich regions. In time-lapse movies, these actin filament structures exhibit one of two types of mobility: 1) diffusive, with an average diffusion coefficient of 0.06–0.08 μm2/s, or (2) subdiffusive, with a mobility coefficient of 0.015 μm2/s. Individual filament trajectories exhibit features of particles moving within a viscoelastic mesh. The small size of nuclear actin filaments is inconsistent with a role in micron-scale intranuclear transport, and their localization suggests that they do not participate directly in chromatin-based processes. Our results instead suggest that actin filaments form part of a large, viscoelastic structure in the nucleoplasm and may act as scaffolds that help organize nuclear contents.
The BAR domain of amphiphysin is required for cleavage furrow tip–tubule formation during cellularization inDrosophilaembryos
Authors: Su Jing , Chow Brenda , Boulianne Gabrielle L. , Wilde Andrew
Published: February 2013

De novo formation of cells in the Drosophila embryo is achieved when each nucleus is surrounded by a furrow of plasma membrane. Remodeling of the plasma membrane during cleavage furrow ingression involves the exocytic and endocytic pathways, including endocytic tubules that form at cleavage furrow tips (CFT-tubules). The tubules are marked by amphiphysin but are otherwise poorly understood. Here we identify the septin family of GTPases as new tubule markers. Septins do not decorate CFT-tubules homogeneously: instead, novel septin complexes decorate different CFT-tubules or different domains of the same CFT-tubule. Using these new tubule markers, we determine that all CFT-tubule formation requires the BAR domain of amphiphysin. In contrast, dynamin activity is preferentially required for the formation of the subset of CFT-tubules containing the septin Peanut. The absence of tubules in amphiphysin-null embryos correlates with faster cleavage furrow ingression rates. In contrast, upon inhibition of dynamin, longer tubules formed, which correlated with slower cleavage furrow ingression rates. These data suggest that regulating the recycling of membrane within the embryo is important in supporting timely furrow ingression.
A translocation-defective telomerase with low levels of activity and processivity stabilizes short telomeres and confers immortalization
Authors: D'Souza Yasmin , Chu Tsz Wai , Autexier Chantal
Published: February 2013

Short, repetitive, G-rich telomeric sequences are synthesized by telomerase, a ribonucleoprotein consisting of telomerase reverse transcriptase (TERT) and an integrally associated RNA. Human TERT (hTERT) can repetitively reverse transcribe its RNA template, acting processively to add multiple telomeric repeats onto the same substrate. We investigated whether certain threshold levels of telomerase activity and processivity are required to maintain telomere function and immortalize human cells with limited lifespan. We assessed hTERT variants with mutations in motifs implicated in processivity and interaction with DNA, namely the insertion in fingers domain (V791Y), and the E primer grip motif (W930F). hTERT-W930F and hTERT-V791Y reconstitute reduced levels of DNA synthesis and processivity compared with wild-type telomerase. Of interest, hTERT-W930F is more defective in translocation than hTERT-V791Y. Nonetheless, hTERT-W930F, but not hTERT-V791Y, immortalizes limited-lifespan human cells. Both hTERT-W930F– and hTERT-V791Y–expressing cells harbor short telomeres, measured as signal free ends (SFEs), yet SFEs persist only in hTERT-V791Y cells, which undergo apoptosis, likely as a consequence of a defect in recruitment of hTERT-V791Y to telomeres. Our study is the first to demonstrate that low levels of DNA synthesis—on the order of 20% of wild-type telomerase levels—and extension of as few as three telomeric repeats are sufficient to maintain functional telomeres and immortalize limited-lifespan human cells.
Effectively addressing complex proteomic search spaces with peptide spectrum matching
Authors: Borges Diogo , Perez-Riverol Yasset , Nogueira Fabio C. S. , Domont Gilberto B. , Noda Jesus , da Veiga Leprevost Felipe , Besada Vladimir , França Felipe M. G. , Barbosa Valmir C. , Sánchez Aniel , Carvalho Paulo C.
Published: February 2013

Summary: Protein identification by mass spectrometry is commonly accomplished using a peptide sequence matching search algorithm, whose sensitivity varies inversely with the size of the sequence database and the number of post-translational modifications considered. We present the Spectrum Identification Machine, a peptide sequence matching tool that capitalizes on the high-intensity b1-fragment ion of tandem mass spectra of peptides coupled in solution with phenylisotiocyanate to confidently sequence the first amino acid and ultimately reduce the search space. We demonstrate that in complex search spaces, a gain of some 120% in sensitivity can be achieved.

Availability: All data generated and the software are freely available for academic use at http://proteomics.fiocruz.br/software/sim.

Contact:  paulo@pcarvalho.com

Supplementary information:  Supplementary data are available at Bioinformatics online.