bluuebunny/crossref_metadata_2025 huggingface dataset:
DEPOSITIONAL FACIES, PORE TYPES AND ELASTIC PROPERTIES OF DEEP‐WATER GRAVITY FLOW CARBONATES
Authors: Hairabian A. , Fournier F. , Borgomano J. , Nardon S.
Published: June 2014

Quantitative petrographic analyses of deep‐water resedimented carbonates from the Gargano Peninsula (SE Italy) were integrated with petrophysical laboratory measurements (porosity, P‐and S‐wave velocities) to assess the impact of sedimentary fabrics and pore space architecture on velocity‐porosity transforms. Samples of Upper Cretaceous carbonate came from the Monte Sant'Angelo, Nevarra and Caramanica Formations and can be classified into four depositional facies associations: F1, lithoclastic breccias; F2, bioclastic packtones to grainstones; F3, interbedded grainstones‐packstones and wackestones; and F4, (hemi‐) pelagic mudstones. Five pore type classes were distinguished: I and II, dominant intercrystalline microporosity; IIIa, dominant intergranular macroporosity; IIIb, dominant mouldic macroporosity; and IIIc, mixed intergranular and mouldic macroporosity. Pore type was found to strongly control velocity‐porosity transforms, unlike depositional facies associations.

The equivalent pore aspect ratio (EPAR), derived from differential effective medium models, is proposed to identify pore types from elastic properties. The EPAR originates from the bulk modulus or shear modulus of the samples (K‐ and μ‐EPAR, respectively). Regardless of porosity values and depositional facies, microporous samples (type I) and samples with dominant intergranular porosity (type IIIa) are characterized by low values of K‐ and μ‐EPAR (<0.22) and by K‐EPAR > μ‐EPAR By contrast, samples with dominant mouldic porosity (type IIIb) display high values of K‐ and μ‐EPAR (>0.25 and 0.4 respectively) and K‐EPAR < μ‐EPAR.

High permeability limestones with dominant intergranular porosity cannot be discriminated from low permeability microporous carbonates. The petrophysical classes derived from elastic properties are shown to be distinct from reservoir property‐driven rock types. In the present case, a seismic‐based poro‐elastic model does not match the reservoir property model. Hence, a sedimentary facies model for the studied carbonates cannot accurately represent the petrophysical properties, which are determined by pores types and pore network architecture.
POROSITY PRESERVATION DUE TO AUTHIGENIC CHLORITE COATINGS IN DEEPLY BURIED UPPER TRIASSIC XUJIAHE FORMATION SANDSTONES, SICHUAN BASIN, WESTERN CHINA
Authors: Sun Zhi‐Xue , Sun Zhi‐Lei , Yao Jun , Wu Ming‐Lu , Liu Jun‐Rong , Dou Zhenya , Pei Chang‐rong
Published: June 2014

Non‐marine sandstones in the Upper Triassic Xujiahe Formation form an important reservoir unit in the Sichuan Basin, western China. Widespread authigenic chlorite cement is present in the second and fourth members of the formation, referred to as the Xu II and IV members. This study, based on data from 12 wells from three gasfields, focusses on chlorite development and evolution and attempts to evaluate its influence on reservoir quality. Data included results of X‐ray diffraction (XRD) and electron microprobe analyses (EMPA), scanning electron microscopy (SEM), and stable carbon and oxygen isotope analyses. The results showed that chlorite coatings preserve primary pore spaces in the sandstones by inhibiting the nucleation of quartz cements on grain surfaces. Iron for chlorite growth came from the dissolution of Fe‐rich magmatic rocks derived from the palaeo‐Longmenshan fold‐belt, from dissolved and colloidal iron which had been precipitated in the Xujiahe Formation in a fluvio‐deltaic environment, and from compacting mudstones in other pars of the formation.

The chlorite initially precipitated from pore waters during eodiagenesis (< 70 °C; < 2 km burial depth). During mesodiagenesis (>70 °C, > 2 km), the chlorite was modified due to exposure to Mg‐rich fluids derived from the underlying carbonate‐dominated Leikoupo Formation. Thus the Mg content of chlorite in the Xu II member increases with depth. However this phenomenon was not observed in the Xu IV member.

The effects of authigenic chlorite on the sandstones' petrophysical properties were evaluated from correlations between chlorite content and porosity. Optimum thicknesses for chlorite coatings range from 5 to 10 microns. Thicker or thinner coatings appear to be less capable of preserving primary porosity and permeability.
IN‐RESERVOIR FRACTIONATION AND THE ACCUMULATION OF OIL AND CONDENSATES IN THE SURMA BASIN, NE BANGLADESH
Authors: Hossain Md. A. , Suzuki N. , Matsumoto K. , Sakamoto R. , Takeda N.
Published: June 2014

Petroleum in the Surma basin, NE Bangladesh (part of the Bengal Basin) ranges from waxy crude oils to condensates. The origin and source rocks of these hydrocarbons were investigated based on the distributions of saturated and aromatic hydrocarbons in 20 oil samples from seven oil and gas fields. The relative compositions of pristane, phytane and adjacent n‐alkanes suggest that the source rock was deposited in a non‐marine setting. The abundance and similar distribution of biphenyls, cadalene and bicadinanes in most of the crude oils and condensates indicates a significant supply of higher‐plant derived organic matter to the source rocks. Maturity levels of the crude oils and condensates from the Surma basin correspond to calculated vitrinite reflectance (Rc) values of 1.0–1.3%, indicating hydrocarbon expulsion from the source rock at a comparatively high maturity level. The Rc values of oils from the Titas field in the southern margin of the Surma basin are relatively low (0.8–1.0%). Some oils were severely biodegraded. The similar distribution of diamondoid hydrocarbons in both biodegraded and non‐biodegraded oils indicated similar types of source rocks and similar maturity levels to those of oils from the Surma basin. The Oligocene Jenam Shale and/or underlying non‐marine deposits located at greater depths may be potential source rocks. The diversity of the petroleum in the Surma basin was likely due to evaporative fractionation, resulting in residual waxy oils and lighter condensates which subsequently underwent tertiary migration and re‐accumulation. Evaporative fractionation due to modification of the reservoir structure occurred during and after the Pliocene, when large‐scale tectonic deformation occurred in and around the Bengal Basin.
SEQUENCE STRATIGRAPHIC ANALYSIS OF THE MID‐CRETACEOUS MISHRIF FORMATION, SOUTHERN MESOPOTAMIAN BASIN, IRAQ
Authors: Mahdi T. A. , Aqrawi A. A. M.
Published: June 2014

The middle Cenomanian – early Turonian Mishrif Formation, a major carbonate reservoir unit in southern Iraq, was studied using cuttings and core samples and wireline logs (gamma‐ray, density and sonic) from 66 wells at 15 oilfields. Depositional facies ranging from deep marine to tidal flat were recorded. Microfacies interpretations together with wireline log interpretations show that the formation is composed of transgressive and regressive hemicycles. The regressive hemicycles are interpreted to indicate the progradation of rudist lithosomes (highstand systems tract deposits) towards distal basinal locations such as the Kumait, Luhais and Abu Amood oilfield areas. Transgressive hemicycles (transgressive systems tract deposits) represent flooding of the shallow carbonate platform and are recorded in oilfields such as Amara, Halfaya and Zubair.

A sequence stratigraphic framework has been constructed for the Mishrif Formation based on correlation of the transgressive and regressive hemicycles which are separated by maximum flooding surfaces. Three third‐order sequences are identified which show lateral and vertical facies variations depending on relative sea‐level changes. Sequence boundaries are characterized by karstic, exposure and drowning features. Middle Cenomanian – Turonian eustatic sea‐level changes together with regional‐scale tectonic deformation of the Arabian Plate controlled the availability of accommodation space and therefore the depositional profile during development of each sequence. Both of these factors controlled the maximum flooding surfaces and sequence boundaries which have been identified.

The sequence stratigraphic key surfaces presented in this study represent typical candidate horizons or datum surfaces for future seismic or resevoir modelling studies. Also, lateral facies variations in each transgressive‐regressive sequence and associated carbonate bodies (i.e. prograding shelf margin, forced regressive wedge) may form important stratigraphic traps in the Mesopotamian Basin.
Oral health status and academic performance among Ohio third‐graders, 2009‐2010
Authors: Detty Amber M.R. , Oza‐Frank Reena
Published: June 2014

Objective

Although recent literature indicated an association between dental caries and poor academic performance, previous work relied on self‐reported measures. This analysis sought to determine the association between academic performance and untreated dental caries (tooth decay) using objective measures, controlling for school‐level characteristics.

Methods

School‐level untreated caries prevalence was estimated from a 2009‐2010 oral health survey of Ohio third‐graders. Prevalence estimates were combined with school‐level academic performance and other school characteristics obtained from the Ohio Department of Education. Linear regression models were developed as a result of bivariate testing, and final models were stratified based upon the presence of a school‐based dental sealant program (SBSP).

Results

Preliminary bivariate analysis indicated a significant relationship between untreated caries and academic performance, which was more pronounced at schools with an SBSP. After controlling for other school characteristics, the prevalence of untreated caries was found to be a significant predictor of academic performance at schools without an SBSP (P = 0.001) but not at schools with an SBSP (P = 0.833).

Conclusions

The results suggest the association between untreated caries and academic performance may be affected by the presence of a school‐based oral health program. Further research focused on oral health and academic performance should consider the presence and/or availability of these programs.
Grammatically Conditioned Sound Change
Authors: W. Hill Nathan
Published: June 2014

In the first half of the 20th century following the Neogrammarian tradition, most researchers believed that sound change was always conditioned by phonetic phenomena and never by grammar. Beginning in the 1960s, proponents of the generative school put forward cases of grammatically conditioned sound change. From then until now, new cases have continued to come to light. A close look at the development of intervocalic ‐s‐ in Greek, reveals the divergent approach of the two schools of thought. All examples of grammatical conditioning are amenable to explanation as some combination of regular sound change, analogy, or borrowing. Neither the Neogrammarian belief in exceptionless phonetically conditioned sound change nor the generative inspired belief in grammatical conditioning is a falsifiable hypothesis. Because of its assumptions are more parsimonious and its descriptive power more subtle, the Neogrammarian position is the more appealing of these two equally unprovable doctrines.
New Deterrence Scripts in Australia's Rejuvenated Offshore Detention Regime for Asylum Seekers
Authors: Pickering Sharon , Weber Leanne
Published: June 2014

As the Global North experiences a real or manufactured crisis in asylum, deterrence has become the central plank in border control policies. Following a resurgence of boat arrivals and faced with serious overcrowding in detention centers and a spate of drownings, the Australian government returned to the use of offshore detention for asylum seekers. In this article, the official media releases of the major political parties from the period surrounding the reopening of detention facilities on Nauru and Papua New Guinea are subject to systematic discourse analysis. This reveals a range of deterrence scripts that we have labeled “neoliberal deterrence,” “classical deterrence,” and an “ethic of care.” The resuscitation of the deterrence script in this second incarnation of Australian offshore processing arguably reveals increasingly nuanced and combative elements. The article details how these scripts make an important contribution to global immigration governance, which is presently incapable of thinking beyond deterrence in its various forms.
Strong inhibition of fimbrial 3 subunit gene transcription by a novel downstream repressive element in Bordetella pertussis
Authors: Chen Qing , Boulanger Alice , Hinton Deborah M. , Stibitz Scott
Published: June 2014

The Bvg‐regulated promoters for the fimbrial subunit genes fim2 and fim3 of Bordetella pertussis behave differently from each other both in vivo and in vitro. In vivo Pfim2 is significantly stronger than Pfim3, even though predictions based on the DNA sequences of BvgA‐binding motifs and core promoter elements would indicate the opposite. In vitro Pfim3 demonstrated robust BvgA∼P‐dependent transcriptional activation, while none was seen with Pfim2. This apparent contradiction was investigated further. By swapping sequence elements we created a number of hybrid promoters and assayed their strength in vivo. We found that, while Pfim3 promoter elements upstream of the +1 transcriptional start site do indeed direct Bvg‐activated transcription more efficiently than those of Pfim2, the overall promoter strength of Pfim3 in vivo is reduced due to sequences downstream of +1 that inhibit transcription more than 250‐fold. This element, the DRE (downstream repressive element), was mapped to the 15 bp immediately downstream of the Pfim3 +1. Placing the DRE in different promoter contexts indicated that its activity was not specific to fim promoters, or even to Bvg‐regulated promoters. However it does appear to be specific to Bordetella species in that it did not function in Escherichia coli.
Pin1 promotes degradation of Smad proteins and their interaction with phosphorylated tau in Alzheimer's disease
Authors: Ueberham Uwe , Rohn Susanne , Ueberham Elke , Wodischeck Susanne , Hilbrich Isabel , Holzer Max , Brückner Martina K. , Gruschka Hildegard , Arendt Thomas
Published: June 2014

Aims

Neurodegeneration in Alzheimer's disease (AD) is characterized by pathological protein aggregates and inadequate activation of cell cycle regulating proteins. Recently, Smad proteins were identified to control the expression of AD relevant proteins such as APP, CDK4 and CDK inhibitors, both critical regulators of cell cycle activation. This might indicate a central role for Smads in AD pathology where they show a substantial deficiency and disturbed subcellular distribution in neurones. Still, the mechanisms driving relocation and decrease of neuronal Smad in AD are not well understood. However, Pin1, a peptidyl‐prolyl‐cis/trans‐isomerase, which allows isomerization of tau protein, was recently identified also controlling the fate of Smads. Here we analyse a possible role of Pin1 for Smad disturbances in AD.

Methods

Multiple immunofluorescence labelling and confocal laser‐scanning microscopy were performed to examine the localization of Smad and Pin1 in human control and AD hippocampi. Ectopic Pin1 expression in neuronal cell cultures combined with Western blot analysis and immunoprecipitation allowed studying Smad level and subcellular distribution. Luciferase reporter assays, electromobility shift, RNAi‐technique and qRT‐PCR revealed a potential transcriptional impact of Smad on Pin1 promoter.

Results

We report on a colocalization of phosphorylated Smad in AD with Pin1. Pin1 does not only affect Smad phosphorylation and stability but also regulates subcellular localization of Smad2 and supports its binding to phosphorylated tau protein. Smads, in turn, exert a negative feed‐back regulation on Pin1.

Conclusion

Our data suggest both Smad proteins and Pin1 to be elements of a vicious circle with potential pathogenetic significance in AD.
INTERNATIONAL ENVIRONMENTAL AGREEMENTS WITH DEVELOPED AND DEVELOPING COUNTRIES IN A DYNAMIC APPROACH
Authors: BIANCARDI MARTA , VILLANI GIOVANNI
Published: June 2014

This paper is devoted to study the stability of international environmental agreements (IEAs) in a pollution abatement model. We focus our attention on two asymmetric agents: developed countries characterized by a strong measure of environmental awareness and developing ones characterized by less attention to environmental preservation. We model a differential game in order to determine both the optimal path of the abatement levels and stock pollutant as results of open‐loop and feedback Nash equilibria. By means of the concepts of internal and external stability, we explain how the environmental awareness of two types of countries and the number of cooperators and defectors influence the size of stable coalitions. The results establish that the asymmetry assumption does not have consequences for the stability of the grand coalition, which can be obtained only with transfers.
Different brain activity in response to emotional faces alone and augmented by contextual information
Authors: Lee Kyung Hwa , Siegle Greg J.
Published: June 2014

This study examined the extent to which emotional face stimuli differ from the neural reactivity associated with more ecological contextually augmented stimuli. Participants were scanned when they viewed contextually rich pictures depicting both emotional faces and context, and pictures of emotional faces presented alone. Emotional faces alone were more strongly associated with brain activity in paralimbic and social information processing regions, whereas emotional faces augmented by context were associated with increased and sustained activity in regions potentially representing increased complexity and subjective emotional experience. Furthermore, context effects were modulated by emotional intensity and valence. These findings suggest that cortical elaboration that is apparent in contextually augmented stimuli may be missed in studies of emotional faces alone, whereas emotional faces may more selectively recruit limbic reactivity.
Using lung function measurements to greater advantage in patients with lung disease: Which test and when?
Authors: Hall Graham L. , Irvin Charles G.
Published: June 2014

Watch the Video introducing the Review Series on lung function testing
Normal crossing properties of complex hypersurfaces via logarithmic residues
Authors: Granger Michel , Schulze Mathias
Published: June 2014

We introduce a dual logarithmic residue map for hypersurface singularities and use it to answer a question of Kyoji Saito. Our result extends a theorem of Lê and Saito by an algebraic characterization of hypersurfaces that are normal crossing in codimension one. For free divisors, we relate the latter condition to other natural conditions involving the Jacobian ideal and the normalization. This leads to an algebraic characterization of normal crossing divisors. As a side result, we describe all free divisors with Gorenstein singular locus.
Development of cap-free sputtered GeTe films for inline phase change switch based RF circuits
Authors: King Matthew R. , Wagner Brian P. , Jones Evan B. , El-Hinnawy Nabil , Borodulin Pavel , McLaughlin Sean R. , Mason John S. , Howell Robert S. , Lee Michael J. , Young Robert M.
Published: June 2014

Germanium telluride (GeTe) films have been recently demonstrated as the active element in low-loss RF switches where a 7.3 THz cut-off frequency (Fco) was achieved. In order to simultaneously realize the low ON-state transmission loss and large OFF-state isolation required for this application, significant optimization of the GeTe films was required. In particular, minimizing contact resistance (Rc) and sheet resistivity (Rsheet) without the use of a capping layer is a necessity. Varying the GeTe deposition conditions led to a wide range of structural, chemical, and electrical properties, which ultimately enabled the demonstration of a capless GeTe inline phase change switch (IPCS) structure. Conversely, improper deposition conditions led to extensive oxidation which would push Rc and Rsheet to unacceptable levels. In addition to its relevance for IPCS devices, this work has implications for the environmental stability of GeTe as a function of its physical morphology.
Novel strategy for low-temperature, high-rate growth of dense, hard, and stress-free refractory ceramic thin films
Authors: Greczynski Grzegorz , Lu Jun , Bolz Stephan , Kölker Werner , Schiffers Christoph , Lemmer Oliver , Petrov Ivan , Greene Joseph E. , Hultman Lars
Published: June 2014

Growth of fully dense refractory thin films by means of physical vapor deposition (PVD) requires elevated temperatures Ts to ensure sufficient adatom mobilities. Films grown with no external heating are underdense, as demonstrated by the open voids visible in cross-sectional transmission electron microscopy images and by x-ray reflectivity results; thus, the layers exhibit low nanoindentation hardness and elastic modulus values. Ion bombardment of the growing film surface is often used to enhance densification; however, the required ion energies typically extract a steep price in the form of residual rare-gas-ion-induced compressive stress. Here, the authors propose a PVD strategy for the growth of dense, hard, and stress-free refractory thin films at low temperatures; that is, with no external heating. The authors use TiN as a model ceramic materials system and employ hybrid high-power pulsed and dc magnetron co-sputtering (HIPIMS and DCMS) in Ar/N2 mixtures to grow dilute Ti1−xTaxN alloys on Si(001) substrates. The Ta target driven by HIPIMS serves as a pulsed source of energetic Ta+/Ta2+ metal–ions, characterized by in-situ mass and energy spectroscopy, while the Ti target operates in DCMS mode (Ta-HIPIMS/Ti-DCMS) providing a continuous flux of metal atoms to sustain a high deposition rate. Substrate bias Vs is applied in synchronous with the Ta-ion portion of each HIPIMS pulse in order to provide film densification by heavy-ion irradiation (mTa = 180.95 amu versus mTi = 47.88 amu) while minimizing Ar+ bombardment and subsequent trapping in interstitial sites. Since Ta is a film constituent, primarily residing on cation sublattice sites, film stress remains low. Dense Ti0.92Ta0.08N alloy films, 1.8 μm thick, grown with Ts ≤ 120 °C (due to plasma heating) and synchronized bias, Vs = 160 V, exhibit nanoindentation hardness H = 25.9 GPa and elastic modulus E = 497 GPa compared to 13.8 and 318 GPa for underdense Ti-HIPIMS/Ti-DCMS TiN reference layers (Ts < 120 °C) grown with the same Vs, and 7.8 and 248 GPa for DCMS TiN films grown with no applied bias (Ts < 120 °C). Ti0.92Ta0.08N residual stress is low, σ = −0.7 GPa, and essentially equal to that of Ti-HIPIMS/Ti-DCMS TiN films grown with the same substrate bias.
Treatment Guidance from the Blood
Authors: Gerber David E.
Published: June 2014

Circulating tumor cells from small-cell lung cancer yield genomic information and animal models.
CD147 Hooks Meningococcus
Authors: Serezani Henrique
Published: June 2014

CD147 is a critical host receptor for the meningococcal pilus components PilE and PilV in human endothelial cells.
Partnerships: Beyond the Buzzword
Authors: Freire Maria C.
Published: June 2014

Partnerships play a critical role in disrupting the status quo to drive biomedical innovation and contribute to the development of creative and powerful research paradigms.
Early MicroRNA Expression Profile as a Prognostic Biomarker for the Development of Pelvic Inflammatory Disease in a Mouse Model of Chlamydial Genital Infection
Authors: Yeruva Laxmi , Myers Garry S. A. , Spencer Nicole , Creasy Heather Huot , Adams Nancy E. , Maurelli Anthony T. , McChesney Grant R. , Cleves Mario A. , Ravel Jacques , Bowlin Anne , Rank Roger G.
Published: June 2014

It is not currently possible to predict the probability of whether a woman with a chlamydial genital infection will develop pelvic inflammatory disease (PID). To determine if specific biomarkers may be associated with distinct chlamydial pathotypes, we utilized two
Chlamydia muridarum
variants (
C. muridarum
Var001 [CmVar001] and CmVar004) that differ in their abilities to elicit upper genital tract pathology in a mouse model. CmVar004 has a lower growth rate
in vitro
and induces pathology in only 20% of C57BL/6 mouse oviducts versus 83.3% of oviducts in CmVar001-infected mice. To determine if chemokine and cytokine production within 24 h of infection is associated with the outcome of pathology, levels of 15 chemokines and cytokines were measured. CmVar004 infection induced significantly lower levels of CXCL1, CXCL2, tumor necrosis factor alpha (TNF-α), and CCL2 in comparison to CmVar001 infection with similar rRNA (
rs16
) levels for
Chlamydiae
. A combination of microRNA (miRNA) sequencing and quantitative real-time PCR (qRT-PCR) analysis of 134 inflammation-related miRNAs was performed 24 h postinfection to determine if the chemokine/cytokine responses would also be reflected in miRNA expression profiles. Interestingly, 12 miRNAs (miR-135a-5p, miR298-5p, miR142-3p, miR223-3p, miR299a-3p, miR147-3p, miR105, miR325-3p, miR132-3p, miR142-5p, miR155-5p, and miR-410-3p) were overexpressed during CmVar004 infection compared to CmVar001 infection, inversely correlating with the respective chemokine/cytokine responses. To our knowledge, this is the first report demonstrating that early biomarkers elicited in the host can differentiate between two pathological variants of chlamydiae and be predictive of upper tract disease.

IMPORTANCE
It is apparent that an infecting chlamydial population consists of multiple genetic variants with differing capabilities of eliciting a pathological response; thus, it may be possible to identify biomarkers specific for a given virulence pathotype. miRNAs are known to regulate genes that in turn regulate signaling pathways involved in disease pathogenesis. Importantly, miRNAs are stable and can reflect a tissue response and therefore have the potential to be biomarkers of disease severity. Currently, with respect to chlamydial infections, there is no way to predict whether an infected patient is more or less likely to develop PID. However, data presented in this study indicate that the expression of a specific miRNA profile associated with a virulent variant early in the infection course may be predictive of an increased risk of pelvic inflammatory disease, allowing more aggressive treatment before significant pathology develops.
Novel Components of the Flagellar System in Epsilonproteobacteria
Authors: Gao Beile , Lara-Tejero Maria , Lefebre Matthew , Goodman Andrew L. , Galán Jorge E.
Published: June 2014

Motility is essential for the pathogenesis of many bacterial species. Most bacteria move using flagella, which are multiprotein filaments that rotate propelled by a cell wall-anchored motor using chemical energy. Although some components of the flagellar apparatus are common to many bacterial species, recent studies have shown significant differences in the flagellar structures of different bacterial species. The molecular bases for these differences, however, are not understood. The flagella from epsilonproteobacteria, which include the bacterial pathogens
Campylobacter jejuni
and
Helicobacter pylori
, are among the most divergent. Using next-generation sequencing combined with transposon mutagenesis, we have conducted a comprehensive high-throughput genetic screen in
Campylobacter jejuni
, which identified several novel components of its flagellar system. Biochemical analyses detected interactions between the identified proteins and known components of the flagellar machinery, and
in vivo
imaging located them to the bacterial poles, where flagella assemble. Most of the identified new components are conserved within but restricted to epsilonproteobacteria. These studies provide insight into the divergent flagella of this group of bacteria and highlight the complexity of this remarkable structure, which has adapted to carry out its conserved functions in the context of widely diverse bacterial species.

IMPORTANCE
Motility is essential for the normal physiology and pathogenesis of many bacterial species. Most bacteria move using flagella, which are multiprotein filaments that rotate propelled by a motor that uses chemical energy as fuel. Although some components of the flagellar apparatus are common to many bacterial species, recent studies have shown significant divergence in the flagellar structures across bacterial species. However, the molecular bases for these differences are not understood. The flagella from epsilonproteobacteria, which include the bacterial pathogens
Campylobacter jejuni
and
Helicobacter pylori
, are among the most divergent. We conducted a comprehensive genetic screen in
Campylobacter jejuni
and identified several novel components of the flagellar system. These studies provide important information to understand how flagella have adapted to function in the context of widely diverse sets of bacterial species and bring unique insight into the evolution and function of this remarkable bacterial organelle.
Spinal cord infarction: a rare cause of paraplegia
Authors: Patel Sonali , Naidoo Khimara , Thomas Peter
Published: June 2014

Spinal cord infarction is rare and represents a diagnostic challenge for many physicians. There are few reported cases worldwide with a prevalence of 1.2% of all strokes. Circulation to the spinal cord is supplied by a rich anastomosis. The anterior spinal artery supplies the anterior two thirds of the spinal cord and infarction to this area is marked by paralysis, spinothalamic sensory deficit and loss of sphincter control depending on where the lesion is. Treatment of spinal cord infarction focuses on rehabilitation with diverse outcomes. This report presents a case of acute spinal cord infarction with acquisition of MRI to aid diagnosis.
Management of a patient with autism following ingestion of a foreign body
Authors: McCain Stephen , Tan Samantha , Mark David
Published: June 2014

Patients with autism often find admission to hospital an anxious time. Awareness of the condition, a speedy diagnosis and flexibility in adapting treatment plans will facilitate early discharge and return to their familiar environment. We describe a patient with severe autism who presented with an acute abdomen secondary to ingestion of a foreign body which required laparotomy. Communication directly to medical staff was greatly limited due to severe autism and close liaison with family members was essential in interpreting scant clinical signs. At the time of surgery a rubber bottle teat was found causing transection of small bowel due to erosion of the foreign body. The postoperative course was fraught with challenges and ensuring side room nursing care with family members present throughout his admission minimised postoperative stress and confusion. We recommend awareness of management strategies for patients with autism to ensure rapid recovery and early discharge home.
Incidence of sudden cardiac death in athletes: a state-of-the-art review
Authors: Harmon Kimberly G , Drezner Jonathan A , Wilson Mathew G , Sharma Sanjay
Published: June 2014

Sudden cardiac death (SCD) is the leading medical cause of death in athletes; however, the precise incidence is unknown. The objectives of this review were to examine studies on the rate of SCD in athletes, assess the methodological strengths and weaknesses used to arrive at estimates, compare studies in athletes with estimates in similar populations and arrive at an approximation of the incidence of SCD based on the best available evidence. A comprehensive literature search was performed in PubMed using key terms related to SCD in athletes. Articles were reviewed for relevance and included if they contained information on the incidence of SCD in athletes or young persons up to the age of 40. The reference list from each manuscript was reviewed for additional relevant articles. The methods for case identification were examined, as well as the inclusion and exclusion criteria and the precision of the population denominator studied. Thirteen studies were found investigating the rate of SCD in athletes who ranged in age from 9 to 40. An additional 15 incidence studies were located examining the rate of SCD in other populations under the age of 40. Rates of SCD varied from 1:917 000 to 1:3000. Studies with higher methodological quality consistently yielded incidence rates in the range of 1:40 000 to 1:80 000. Some athlete subgroups, specifically men, African-American/black athletes and basketball players, appear to be at higher risk. The incidence of SCD in athletes is likely higher than traditional estimates which may impact the development of more effective prevention strategies.
The safety and efficacy of daptomycin versus other antibiotics for skin and soft-tissue infections: a meta-analysis of randomised controlled trials
Authors: Wang Shou Zhen , Hu Jun Tao , Zhang Chi , Zhou Wei , Chen Xian Feng , Jiang Liang Yan , Tang Zhan Hong
Published: June 2014

Objective

Daptomycin, a cyclic lipopeptide that exhibits rapid, concentration-dependent bactericidal activity in vitro against a broad spectrum of Gram-positive pathogens, has now, since 2003, been approved in more than 70 countries and regions to treat skin and soft-tissue infections (SSTIs). The purpose of this meta-analysis was to compare the safety and efficacy of daptomycin with other antibiotics, especially with vancomycin which has long been considered the standard therapy for complicated SSTIs.

Design

Meta-analysis of randomised controlled trials (RCTs).

Data sources

We thoroughly searched PubMed, EMBASE, Cochrane Central to identify relevant RCTs. Six RCTs with a total of 1710 patients were included in this meta-analysis.

Results

The results demonstrated that the efficacy of daptomycin was at par with or maybe better than other first-line antibiotics for treating SSTIs as shown by the OR for clinical success (OR=1.05, 95% CI 0.84 to 1.31, p=0.65, I2=0%); daptomycin versus vancomycin subgroup (OR=1.19, 95% CI 0.77 to 1.83, p=0.43, I2=0%); overall microbiological success (OR=1.05, 95% CI 0.61 to 1.79, p=0.86, I2=42%); microbiological success of daptomycin versus comparators forStaphylococcus aureus(SA, OR=1.05, 95% CI 0.61 to 2.60, p=0.53, I2=47%), for methicillin-resistantS. aureus(OR=0.90, 95% CI 0.77 to 1.06, p=0.20, I2=56%). However, daptomycin tended to have a similar treatment-related adverse events (AEs) incidence in comparison with other antibiotics (OR=1.06, 95% CI 0.71 to 1.59, p=0.76, I2=41%). The trend showed that daptomycin might cause less discontinuation due to AEs and death compared with other first-line antibiotics (OR=0.71, 95% CI 0.46 to 1.10, p=0.12, I2=11%). Significantly more patients in the daptomyicn group had creatine phosphokinase elevation than those in the control group; however, it could be reversed when the therapy ended (OR=1.95, 95% CI 1.04 to 3.65, p=0.04, I2=0).

Conclusions

This meta-analysis demonstrated that the safety and efficacy of daptomycin was not inferior to that of other first-line drugs, and daptomycin tended to exhibit superior efficacy when compared with vancomycin or with comparators for SA infections; nevertheless, more high-quality RCTs are needed to draw a more credible conclusion.
Digitised audio questionnaire for assessment of informed consent comprehension in a low-literacy African research population: development and psychometric evaluation
Authors: Afolabi Muhammed O , Bojang Kalifa , D'Alessandro Umberto , Ota Martin O C , Imoukhuede Egeruan B , Ravinetto Raffaella , Larson Heidi J , McGrath Nuala , Chandramohan Daniel
Published: June 2014

Objective

To develop and psychometrically evaluate an audio digitised tool for assessment of comprehension of informed consent among low-literacy Gambian research participants.

Setting

We conducted this study in the Gambia where a high illiteracy rate and absence of standardised writing formats of local languages pose major challenges for research participants to comprehend consent information. We developed a 34-item questionnaire to assess participants’ comprehension of key elements of informed consent. The questionnaire was face validated and content validated by experienced researchers. To bypass the challenge of a lack of standardised writing formats, we audiorecorded the questionnaire in three major Gambian languages: Mandinka, Wolof and Fula. The questionnaire was further developed into an audio computer-assisted interview format.

Participants

The digitised questionnaire was administered to 250 participants enrolled in two clinical trials in the urban and rural areas of the Gambia. One week after first administration, the questionnaire was readministered to half of the participants who were randomly selected. Participants were eligible if enrolled in the parent trials and could speak any of the three major Gambian languages.

Outcome measure

The primary outcome measure was reliability and validity of the questionnaire.

Results

Item reduction by factor analysis showed that 21 of the question items have strong factor loadings. These were retained along with five other items which were fundamental components of informed consent. The 26-item questionnaire has high internal consistency with a Cronbach's α of 0.73–0.79 and an intraclass correlation coefficient of 0.94 (95% CI 0.923 to 0.954). Hypotheses testing also showed that the questionnaire has a positive correlation with a similar questionnaire and discriminates between participants with and without education.

Conclusions

We have developed a reliable and valid measure of comprehension of informed consent information for the Gambian context, which might be easily adapted to similar settings. This is a major step towards engendering comprehension of informed consent information among low-literacy participants.
Nutrient intake and brain biomarkers of Alzheimer's disease in at-risk cognitively normal individuals: a cross-sectional neuroimaging pilot study
Authors: Mosconi Lisa , Murray John , Davies Michelle , Williams Schantel , Pirraglia Elizabeth , Spector Nicole , Tsui Wai H , Li Yi , Butler Tracy , Osorio Ricardo S , Glodzik Lidia , Vallabhajosula Shankar , McHugh Pauline , Marmar Charles R , de Leon Mony J
Published: June 2014

Objective

There is increasing evidence to suggest that diet, one of the most important modifiable environmental factors, may play a role in preventing or delaying cognitive decline and Alzheimer's disease (AD). This study examines the relationship between dietary nutrients and brain biomarkers of AD in cognitively normal individuals (NL) with and without AD risk factors.

Design

As part of an ongoing brain imaging study, participants received clinical and laboratory examinations, a neurocognitive test battery, positron emission tomography (PET) with11C-Pittsburgh Compound-B (PiB; a measure of amyloid-β (Aβ) load) and18F-fluorodeoxyglucose (FDG; a proxy of neuronal activity), and completed semiquantitative food frequency questionnaires.

Setting

Research centre affiliated with the Alzheimer's disease Core Center at New York University School of Medicine.

Participants

49 NL individuals (age 25–72 years, 69% women) with dietary information,11C-PiB and18F-FDG PET scans were examined.

Results

Controlling for age and total caloric intake, higher intake of vitamin B12, vitamin D and ω-3 polyunsaturated fatty acid (PUFA) was associated with lower Aβ load in AD regions on PiB-PET, while higher intake of β-carotene and folate was associated with higher glucose metabolism on FDG-PET. β-carotene and folate were associated with reduced glucose metabolism for women, apolipoprotein E epsilon 4 (APOE4) carriers and participants with positive AD family history, but not for their risk-free counterparts. The associations of vitamin B12, vitamin D and ω-3 PUFA with PiB retention were independent of gender, APOE and family history. The identified nutrient combination was associated with higher intake of vegetables, fruit, whole grains, fish and legumes, and lower intake of high-fat dairies, meat and sweets.

Conclusions

Our data provide a potential pathophysiological mechanism for epidemiological findings showing that dietary interventions may play a role in the prevention of AD. Longitudinal studies are needed to determine whether there is a direct link between nutrient intake, brain biomarkers and risk of AD.
FluMum: a prospective cohort study of mother–infant pairs assessing the effectiveness of maternal influenza vaccination in prevention of influenza in early infancy
Authors: O'Grady Kerry-Ann F , McHugh Lisa , Nolan Terry , Richmond Peter , Wood Nicholas , Marshall Helen S , Lambert Stephen B , Chatfield Mark , Andrews Ross M
Published: June 2014

Introduction

Influenza vaccination in pregnancy is recommended for all women in Australia, particularly those who will be in their second or third trimester during the influenza season. However, there has been no systematic monitoring of influenza vaccine uptake among pregnant women in Australia. Evidence is emerging of benefit to the infant with respect to preventing influenza infection in the first 6 months of life. The FluMum study aims to systematically monitor influenza vaccine uptake during pregnancy in Australia and determine the effectiveness of maternal vaccination in preventing laboratory-confirmed influenza in their offspring up to 6 months of age.

Methods and analysis

A prospective cohort study of 10 106 mother–infant pairs recruited between 38 weeks gestation and 55 days postdelivery in six Australian capital cities. Detailed maternal and infant information is collected at enrolment, including influenza illness and vaccination history with a follow-up data collection time point at infant age 6 months. The primary outcome is laboratory-confirmed influenza in the infant. Case ascertainment occurs through searches of Australian notifiable diseases data sets once the infant turns 6 months of age (with parental consent). The primary analysis involves calculating vaccine effectiveness against laboratory-confirmed influenza by comparing the incidence of influenza in infants of vaccinated mothers to the incidence in infants of unvaccinated mothers. Secondary analyses include annual and pooled estimates of the proportion of mothers vaccinated during pregnancy, the effectiveness of maternal vaccination in preventing hospitalisation for acute respiratory illness and modelling to assess the determinants of vaccination.

Ethics and dissemination

The study was approved by all institutional Human Research Ethics Committees responsible for participating sites. Study findings will be published in peer review journals and presented at national and international conferences.

Trial registration number

The study is registered with the Australia and New Zealand Clinical Trials Registry (ANZCTR) number: 12612000175875.
Next-generation sequencing reveals frequent consistent genomic alterations in small cell undifferentiated lung cancer
Authors: Ross J S , Wang K , Elkadi O R , Tarasen A , Foulke L , Sheehan C E , Otto G A , Palmer G , Yelensky R , Lipson D , Chmielecki J , Ali S M , Elvin J , Morosini D , Miller V A , Stephens P J
Published: June 2014

Aims

Small cell lung cancer (SCLC) carries a poor prognosis, and the systemic therapies currently used as treatments are only modestly effective, as demonstrated by a low 5-year survival at only ∼5%. In this retrospective collected from March 2013 to study, we performed comprehensive genomic profiling of 98 small cell undifferentiated lung cancer (SCLC) samples to identify potential targets of therapy not currently searched for in routine clinical practice.

Methods

DNA from 98 SCLC was sequenced to high, uniform coverage (Illumina HiSeq 2500) and analysed for all classes of genomic alterations.

Results

A total of 386 alterations were identified for an average of 3.9 alterations per tumour (range 1–10). Fifty-two (53%) of cases harboured at least 1 actionable alteration with the potential to personalise therapy including base substitutions, amplifications or homozygous deletions inRICTOR(10%),KIT(7%),PIK3CA(6%),EGFR(5%),PTEN(5%),KRAS(5%),MCL1(4%),FGFR1(4%),BRCA2,(4%),TSC1(3%), NF1(3%),EPHA3(3%)and CCND1.The most common non-actionable genomic alterations were alterations inTP53(86% of SCLC cases),RB1(54%) andMLL2(17%).

Conclusions

Greater than 50% of the SCLC cases harboured at least one actionable alteration. Given the limited treatment options and poor prognosis of patients with SCLC, comprehensive genomic profiling has the potential to identify new treatment paradigms and meet an unmet clinical need for this disease.
The use of expensive technologies instead of simple, sound and effective lifestyle interventions: a perpetual delusion
Authors: Carlos Silvia , de Irala Jokin , Hanley Matt , Martínez-González Miguel Ángel
Published: June 2014

A dangerous distortion of priorities seems to be currently apparent in the dominant approaches to major public health problems, including cardiovascular disease, diabetes, obesity, cancer and some infectious diseases. Relevant examples suggest an apparently inappropriate tendency to prioritise technocratic, partial solutions rather than confronting their true behavioural and structural determinants. Technically oriented preventive medicine often takes excessive precedence over simpler, more sensible approaches to modify lifestyles, the environment and the social structure. Structural factors (social, cultural, financial, familiar, educational, political or ideological factors) that act as determinants of individual behaviours should be effectively addressed to confront the essential causes of the most prevalent and important health problems. Some consumer-directed commercial forces seem to be increasingly driving many aspects of the current sociocultural environment, and may eventually compromise the main pursuits of public health. Population-wide strategies are needed to create a healthy sociocultural environment and to empower individuals and make themselves resistant to these adverse environmental and structural pressures. Otherwise most public health interventions will most likely end in failures.
Comparison of two detection systems to reveal AFLP markers in plants
Authors: Cara Nicolás , Marfil Carlos F. , García Lampasona Sandra C. , Masuelli Ricardo W.
Published: June 2014

Since their development, AFLP (amplified fragment length polymorphism) markers have been used for a wide variety of analyses and, up to this day, are considered highly informative, robust, and reproducible molecular markers. Originally, the visualization of the amplified fragments was done in polyacrylamide gels, followed by silver staining or by developing in an X-ray plate, when radioactivity is used. In the last 14 years, capillary electrophoresis of fluorescently labeled fragments has been gradually replacing gel-based systems. However, the latter continue to be better for isolating and cloning AFLP fragments. In this report, we compare the results obtained by capillary electrophoresis with those from silver staining. We found that if fluorescence-labeled amplification products are loaded in a polyacrylamide gel, duplicated bands (doublets) are seen. This phenomenon is probably due to a delay in the migration of the strand that carries the fluorophore. Therefore, we recommend a minimum separation of 4 bp from the nearest fragment to the target fragment for its unambiguous identification and isolation. If this requirement is not fulfilled, an alternative is to make new amplifications using the same primer combination, but with unlabeled primers.