bluuebunny/crossref_metadata_2025 huggingface dataset:
Surviving cochlear function in the presence of auditory nerve agenesis
Authors: O'Leary S. J. , Gibson W. P.
Published: November 2007

This case reports electrophysiological evidence for cochlear function in a child with radiological evidence of bilateral auditory nerve agenesis or severe hypoplasia. The diagnosis of auditory nerve agenesis was supported by a bilateral atresia of internal auditory canals on computed tomography (CT) scan and magnetic resonance imaging (MRI) absent auditory brainstem responses and absent behavioural responses to sound. Despite the apparent absence of an auditory nerve or spiral ganglion, electrocochleography revealed surviving cochlear function at 70–80 db HL and an abnormal electrocochleographic waveform. This case demonstrates that cochlear function may develop without afferent, or efferent innervation. It also emphasizes that cochlear function may occur in the presence of profound deafness.
Radiological appearance of primary branchial cleft cyst carcinoma
Authors: Hong Ki Hwan , Moon Woo Sung , Chung Gyung Ho
Published: November 2007

The hypothesis that primary branchiogenic carcinoma originates from a branchial cleft cyst is controversial. Many reports regarding primary branchiogenic carcinoma failed to provide sufficient evidence to distinguish it from metastatic cervical lymph nodes arising from previously unrecognized primary tumours. The radiological appearance of malignant transformation from a branchial cleft cyst has not been reported previously in the English literature. A radiological study is presented that confirms the primary branchiogenic carcinoma. The management in suspected cases would be wide surgical excision of the tumour including ipsilateral radical neck dissection followed by radiation therapy.
Outcomes from adult implantation, the first 100 patients
Authors: Proops D. W. , Donaldson I. , Cooper H. R. , Thomas J. , Burrell S. P. , Stoddart R. L. , Moore A. , Cheshire I. M.
Published: November 2007

We present the outcome of implantation in the first 100 adult patients treated under the Midland Cochlear Implant Programme. All patients were post-lingually deaf with profound or total hearing loss. Performance was tested in lip-reading, implant only and combined lip-reading and implant modes using BKB sentences, connected discourse tracking (CDT) and environmental sound recognition. Assessments were made at nine and 18 months post-implant.

The dominant aetiologies were idiopathic and meningitis. Meningitis was associated with the greatest numbers of ossified cochleas. Forty-three per cent of cases of partial ossification were identified only at surgery. Four per cent of patients became non-users of their devices, however the majority used their implants for more than 12 hours each day. The mean scores at nine months post-implant, in the implant only mode, were for environmental sound recognition 56.7 per cent, for BKB sentences 46.6 per cent (80 per cent of patients scored above 0 per cent) and for CDT 31.2 words per minute (w.p.m.) (62 per cent scored above zero per cent). In the combined lip reading and implant mode the mean scores, at nine months, were for BKB sentences 81.5 per cent and for CDT 65.8 w.p.m. All results were sustained at 18 months.

Patients reported that implantation significantly reduced their hearing handicap. Pre-operative measures of depression were also significantly reduced at nine months post-implant. Results were sustained at 18 months.

Post-operative audiological outcomes in the electrical stimulation only mode correlated significantly with length of profound deafness. Results suggest that performance outcome is also related to the number of active electrodes.
The unsafeness of ‘safe’ ears
Authors: Browning G. G.
Published: November 2007

Active chronic otitis media affects 0.5 per cent of adults and has two main variants. The first is when there is a squamous epithelial retraction pocket or cholesteatoma. The second variant is when the disease is primarily of the mucosa of the middle ear and mastoid air-cell system. Classically a cholesteatoma is considered ‘unsafe’ because of the risk of complications, particularly intracranial infectioa Mucosal disease, on the other hand, is considered ‘safe’ because complications are thought to be rare. Surgery in the form of a modified radical mastoidectomy is considered to make active chronic otitis media ‘safe’.

A retrospective review of 26 consecutive brain abscesses considered secondary to active chronic otitis media revealed that a cholesteatoma was present in 12 (46 per cent), mucosal disease in 10 (38 per cent) and a modified radical mastoidectomy had been performed in four (15 per cent). Mucosal disease and a modified radical mastoidectomy should no longer be considered ‘safe’. However, the risk of developing an intracranial abscess from any type of active chronic otitis media is low, in the region of one in 3,500.
Clinical assessment of the irradiated larynx
Authors: Flood L. M. , Brightwell A. P.
Published: November 2007

Following radiotherapy for squamous carcinoma of the larynx, it may be impossible to differentiate occult persisting tumour from irradiation effects, possibly with chondroradionecrosis, even after repeated biopsy. In seven of the cases presented, post-treatment laryngectomy failed to provide histological evidence of residual or recurrent carcinoma, which clinical examination has indicated. None-theless, total laryngectomy was performed, subsequently revealing tumour in five of the seven excised larynges. The two tumour-free larynges were associated with cervical metastases. The clinical indications of persisting tumour, the factors compromising post-irradiation evaluation and the role of diagnostic aids are discussed.
Topographic anatomy of the external branch of the superior laryngeal nerve
Authors: Kambič V. , Žargi M. , Radšel Zora
Published: November 2007

The authors have studied the anatomy of the external branch of the superior laryngeal nerve in its entirety on 40 fresh cadavers, and they have drawn the following conclusions: the nerve ramifies from the vagus immediately below the nodose ganglion or in the ganglion itself. The nerve splits into two branches approximately 1.5 cm below the ganglion nodosum. In four cases, both branches originated from the vagus itself. In one case, anastomosis of the external branch of the superior laryngeal nerve with the recurrent nerve was found. The external branch of the superior laryngeal nerve is not usually severed at supraglottic laryngectomy but the nerve is at risk during neck dissections, resection of Zenker's diverticula and thyroidectomy. An accurate knowledge of its course should reduce the incidence of injury to the branches of the superior laryngeal nerve during surgery.
Malignant melanoma of the larynx
Authors: Hussain S. S. M. , Whitehead E.
Published: November 2007

Malignant melanoma of the larynx is a rare tumour. Only 31 cases of primary laryngeal melanoma have been reported in the literature. Cadyet al., (1968) found only four cases in a group of 2,500 cases of laryngeal cancer seen over a 25-year period.

A case of primary malignant melanoma of the larynx is presented along with a review of the literature. Problems associated with histological diagnosis are discussed. This patient was regarded as a poor risk for laryngectomy and appears to have control of local disease following application of Carbon dioxide laser.
Intrahyoid thyroglossal cyst
Authors: Podoshin L. , Fradis M. , Goldstein J. , Misselevitch I. , Boss J. H.
Published: November 2007

A rare case of an intrahyoid thyroglossal duct cyst in a 63-year-old woman is reported. The pertinent literature is discussed.
Alar haematoma
Authors: Green K. M. J. , Board T. , Mason J. D. T.
Published: November 2007

We present two cases of alar haematoma. This is a very rare complication of nasal trauma, and only two cases have been described previously. One case presented late and did not undergo surgical drainage and has a persistent cosmetic deformity. We recommend early surgical drainage when possible.
Tracheal ring herniation following percutaneous dilatational tracheostomy and its resection under endoscopic control
Authors: Osborne J. E. , Osman E. Z. , Cuddihy P. , Ranta M.
Published: November 2007

A 76-year-old patient had an elective percutaneous dilatational tracheostomy (PDT) under endoscopic control in the intensive care unit. Twelve days later when her general condition improved, two attempts at decannulation failed due to upper airway obstruction above the tracheostomy site.

Bronchoscopy showed herniation of the anterior tracheal wall above the tracheostomy tube occluding 80 per cent of the lumen. The herniated anterior segment was elevated and partially resected under endoscopic guidance. The patient made a full recovery and was decannulated on the first post-operative day. Pitfalls and possible complications of PDT are discussed.
Non-cardiogenic pulmonary oedema due to foreign body aspiration
Authors: Pahade A. , Green K. M. J. , de Carpentier J. P.
Published: November 2007

A patient who developed non-cardiogenic pulmonary oedema secondary to acute airway obstruction caused by an aspirated foreign body is presented. The literature is reviewed, discussing the theories regarding the formation of non-cardiogenic pulmonary oedema. The case highlights the importance of this rare complication of foreign body aspiration and surgeons and anaesthetists should be alert to continued respiratory symptoms following relief of acute airway obstruction.
Angiomyoma of the retropharyngeal space
Authors: Fuse Takeo , Yoshida Shin , Sakakibara Akira , Motoyama Teiichi
Published: November 2007

We encountered a 59-year-old man with angiomyoma of the retropharyngeal space. He had been referred to our hospital because of a six-month history of a sensation of a narrowed pharynx. A smooth-surfaced tumour arising from the posterior wall in the hypopharynx was observed by indirect laryngoscopy. Radiographical imaging revealed a solitary tumour with homogenous contents in the retropharyngeal space. The tumour was successfully removed via a lateral pharyngotomy approach under general anaesthesia. Histopathologically, the tumour was composed of numerous veins with thick muscular walls. To the best of our knowledge, this is the first report of an angiomyoma arising in the retropharyngeal space.
Cervical necrotizing fasciitis and radiotherapy: a report of two cases
Authors: Mortimore S. , Thorp M.
Published: November 2007

Two cases of cervical necrotizing fasciitis are presented. Both are unusual in that they had had radiotherapy for head and neck malignancy six and 14 years previously with no evidence of tumour recurrence. One case of necrotizing fasciitis has previously been cited in the literature associated with radiotherapy (Krespiet al., 1981). The two cases are discussed along with a review of the literature.
Pulsatile tinnitus: three cases of arteriovenous fistula treated by ligation of the occipital artery
Authors: Courteney-Harris R. G. , Ford G. R. , Innes A. J. , Colin J. F.
Published: November 2007

Pulsatile tinnitus resulting from an abnormal communication between the occipital artery and the transverse or lateral sinus is a rare clinical entity. We report three cases which presented over a period of three years who had such abnormalities demonstrated angiographically and were cured of their symptoms by exploration and ligation of the occipital artery.
Atypical supraglottitis caused by Streptococcus sanguis
Authors: Irvine M. C. G. , Solomons N. B.
Published: November 2007

A case of atypical supraglottitis in an 11-year-old boy is presented. The epiglottis was only mildly inflamed. The organism isolated from blood culture was Streptococcus sanguis. This organism is a normal commensal of the oral cavity and has not previously been reported as a cause of supraglottitis.
Use of a metal detector in the location of a swallowed razor blade in the oesophagus
Authors: Kessler Alexander , Yellin Alon , Kessler A. , Kronenberg Jona
Published: November 2007

A case describing the use of a metal detector to locate a metallic foreign body swallowed by a prisoner. Initial work up included plain thoracic X-rays and a gastrografin swallow which were negative. A metal detector was used to confirm the presence of a metal body in the oesophagus which was verified by a barium swallow.
Malignant mesenchymoma of the larynx
Authors: Kawashima Osamu , Kamei Tamio , Shimizu Yuji , Shizuka Takao , Nakayama Morito
Published: November 2007

A Case report of a laryngeal malignant mesenchymoma, a very rare head and neck and even rarer laryngeal leison, is reported.

In this case, an 85-years-old man, who had undergone several panendoscopies and biopsies that were non-diagnostic, subsequently succumbed to pulmonary metastases and died from respiratory failure. At autospy, tumour cells were demonstrated to constiute both bone and straited muscle cell types. As the tumour cells differentiated into two types of specialized cells from one type of embryonal tissue, the diagnosis of maligant mesenchymoma was established.
Co-morbid major depression and generalized anxiety disorders in the National Comorbidity Survey follow-up
Authors: Kessler R. C. , Gruber M. , Hettema J. M. , Hwang I. , Sampson N. , Yonkers K. A.
Published: November 2007

Background

Although generalized anxiety disorder (GAD) and major depressive episode (MDE) are known to be highly co-morbid, little prospective research has examined whether these two disorders predict the subsequent first onset or persistence of the other or the extent to which other predictors explain the time-lagged associations between GAD and MDE.

Method

Data were analyzed from the nationally representative two-wave panel sample of 5001 respondents who participated in the 1990–1992 National Comorbidity Survey (NCS) and the 2001–2003 NCS follow-up survey. Both surveys assessed GAD and MDE. The baseline NCS also assessed three sets of risk factors that are considered here: childhood adversities, parental history of mental-substance disorders, and respondent personality.

Results

Baseline MDE significantly predicted subsequent GAD onset but not persistence. Baseline GAD significantly predicted subsequent MDE onset and persistence. The associations of each disorder with the subsequent onset of the other attenuated with time since onset of the temporally primary disorder, but remained significant for over a decade after this onset. The risk factors predicted onset more than persistence. Meaningful variation was found in the strength and consistency of associations between risk factors and the two disorders. Controls for risk factors did not substantially reduce the net cross-lagged associations of the disorders with each other.

Conclusions

The existence of differences in risk factors for GAD and MDE argues against the view that the two disorders are merely different manifestations of a single underlying internalizing syndrome or that GAD is merely a prodrome, residual, or severity marker of MDE.
The European Social Dialogue in the Shadow of Hierarchy
Authors: SMISMANS STIJN
Published: November 2007

The European social dialogue provides for the signing of collective agreements between employers’ associations and trade unions organised at the European level. Effectiveness to a great extent depends on the shadow of hierarchy, which is cast by the threat of legislative action and by ensuring implementation of collective agreements through public intervention. The need for the shadow is illustrated by the initial priority given to statutory agreements and the problems of implementation of more recent non-statutory agreements. While the shadow of hierarchy is important to ensure the effectiveness of social dialogue, social dialogue procedures are not characterised by strong principal-agent relationships. In particular, non-statutory agreements stem from a bottom-up private sector-inspired tradition of industrial relations. Even in the case of statutory agreements, the European Commission, as principal, does not appoint the agent and the delegation is implicit rather than explicit. Moreover, successful delegation entirely depends on whether the agents reach agreement between themselves. While the Commission could revoke delegation if Community objectives are not realised and by setting statutory criteria for implementing an agreement, its room for manoeuvre is limited for reasons of political pragmatism.
An outbreak of epidemic keratoconjunctivitis in a regional ophthalmology clinic in New South Wales
Authors: VINEY K. A. , KEHOE P. J. , DOYLE B. , SHEPPEARD V. , ROBERTS-WITTEVEEN A. R. , SEMIRLI H. , McPHIE K. A. , DWYER D. E. , McANULTY J. M.
Published: November 2007

The objective of the study was to identify the extent and cause of an outbreak of epidemic keratoconjunctivitis (EKC). The study design was active case finding and a case-control study of clinic patients who developed symptoms of EKC between 31 December 2005 and 31 March 2006. The main outcome measures were clinical procedures carried out and clinicians seen during clinic visit. Significantly more cases than controls had tonometry with instillation of anaesthetic drops (OR 16·5, 95% CI 3·9–145·1, P<0·01), optical coherence tomography (OR 4·7, 95% CI 1·2–21·9, P=0·01), or instillation of dilating drops by an orthoptist (OR 2·3, 95% CI 1·1–4·7, P=0·01). Significantly more cases than controls were seen by one orthoptist (OR 21·8, 95% CI 8·2–60·0, P<0·01). Transmission of EKC within the clinic was probably due to contamination of either or both the anaesthetic drops and the tonometer head in the room used by an orthoptist. A comprehensive suite of strategies is required to prevent healthcare-associated EKC.
Meta-Analysis of Binary Data Based upon Dichotomized Criteria
Authors: Holling Heinz , Böhning Dankmar , Böhning Walailuck
Published: November 2007

Abstract. This paper considers meta-analysis of binary data that use a dichotomized continuous score. Classification into two categories, e.g., qualified or not qualified, is often based upon a threshold or cut-off value. This threshold might vary between studies since intentionally different values are used. However, conventional meta-analysis methodology analyzing sensitivity and specificity separately might then be confounded by a potentially unknown variation of the cut-off value. In order to cope with varying thresholds, an overall estimate of the misclassification error is suggested instead, which is equivalent to the well-known Youden index. It is argued that this index is less prone to between-study variation of cut-off values. To adjust for potential study effects a Mantel-Haenszel estimator of the overall misclassification error is suggested. Arguments are illustrated using, as an example, the diagnosis of alcoholism using the Alcohol Use Disorders Identification Test (AUDIT).
Current Methods for Meta-Analysis
Authors: Schulze Ralf
Published: November 2007

Abstract. The bulk of conceptual and statistical developments as well as applications of meta-analysis have been published in the last 30 years. The methods for meta-analysis continue to be refined and new methods are applied to new types of research questions and data. Such current approaches, issues, and developments prevalent in the behavioral sciences are presented, reviewed, and discussed in this paper. The areas that are covered include: the fixed effects and random effects model of meta-analysis, new findings concerning effect sizes and their statistical properties, the comparison of different meta-analytic approaches, and multivariate procedures for meta-analysis. The latter also covers the stepwise combination of meta-analysis and structural equation modeling (MASEM).
Cretaceous‐Tertiary structural evolution of the north central Lhasa terrane, Tibet
Authors: Volkmer John E. , Kapp Paul , Guynn Jerome H. , Lai Qingzhou
Published: November 2007

In the north central Lhasa terrane of Tibet, two distinct structural levels of an east–west striking thrust system are exposed along the north trending late Cenozoic Xiagangjiang rift. Upper Paleozoic strata deformed by the south directed Langgadong La thrust, and Cretaceous strata involved in variably north and south directed thrusting characterize these lower and upper structural levels, respectively. These two structural levels are separated by the Tagua Ri passive roof thrust. Balanced cross section restoration suggests that the thrust system accommodated ∼103 km (∼53%) shortening. The40Ar/39Ar results, together with an interpretation of synthrust deposition of Upper Cretaceous strata, suggest that the majority of shortening occurred during the Late Cretaceous–Paleocene. Cretaceous strata lie unconformable on Permian rocks; volcanic tuffs directly above the unconformity yield U‐Pb zircon ages of ∼131 Ma. Upper Cretaceous strata record a change from shallow marine to nonmarine deposition, indicating uplift above sea level during this time. The overall south directed vergence of the thrust belt is consistent with substantial crustal thickening in central Tibet by large‐scale northward underthrusting of Lhasa terrane basement beneath the Qiantang terrane prior to the Indo‐Asian collision. The documented decoupling of contractional deformation at shallow crustal levels appears to be a regional characteristic of Tibet from at least the Bangong suture in the north to the Tethyan Himalaya to the south. This style of deformation explains the absence of basement exposures and major denudation in this region despite substantial crustal shortening.
Efficient extraction of networks from three‐dimensional porous media
Authors: Jiang Z. , Wu K. , Couples G. , van Dijke M. I. J. , Sorbie K. S. , Ma J.
Published: November 2007

Fluid flow through porous media, and the thermal, electrical, and acoustic properties of these materials, is largely controlled by the geometry and topology (GT) of the pore system, which can be considered as a network. Network extraction techniques have been applied in many research fields, including shape representation, pattern recognition, and artificial intelligence. However, the set of algorithms presented here significantly improves the efficiency of common thinning algorithms by introducing a sufficiency condition based on the idea of a simple set. This paper describes an efficient and accurate algorithm for extracting the geometrical/topological network that represents the pore structure of a porous medium, referred to as the GT network. The accurate medial axis and the specific GT description of the network are achieved by applying symmetrical and interval strategies during the erosion step in the image processing. The GT network extraction algorithm presented here involves a number of steps, including (1) calculation of the three‐dimensional Euclidean distance map; (2) clustering of voxels; (3) extraction of the network of the pore space; (4) partitioning of the pore space; and (5) computation of shape factors. The focus of this paper is mainly on the thinning method that underpins points 1–3. The paper is primarily a method description, but we illustrate the functionality of the technique by extracting a pore scale GT network from micro–computer tomography images of three sandstones.
Common turbulent signature in sea surface temperature and chlorophyll maps
Authors: Nieves V. , Llebot C. , Turiel A. , Solé J. , García‐Ladona E. , Estrada M. , Blasco D.
Published: November 2007

Oceans and 2D turbulence present similar characteristics, as for instance the dominant role played by eddies in energy and matter transport. However, providing a complete justification of this analogy is difficult, as it requires knowledge of the ocean's dynamic state at different instants and over large scales. Recently, new techniques coming from the Microcanonical Multifractal Formalism have made it possible to infer the streamlines from the analysis of satellite images of some scalar variables. In this paper, we will show that this information is enough to characterize the scaling properties of the energy cascade, which is manifested as a multifractal signature; further, the multifractal signature is obtained at each location in a local basis. Different scalars obtained from satellite measurements such as Sea Surface Temperature or Surface Chlorophyll Concentration present essentially the same multifractal structure, which is interpreted as a consequence of the pervading character of the turbulent advection at the scales of observation.
3D global multi‐species Hall‐MHD simulation of the Cassini T9 flyby
Authors: Ma Ying‐Juan , Nagy Andrew F. , Toth Gabor , Cravens Thomas E. , Russell Christopher T. , Gombosi Tamas I. , Wahlund Jan‐Erik , Crary Frank J. , Coates Andrew J. , Bertucci César L. , Neubauer Fritz M.
Published: November 2007

The wake region of Titan is an important component of Titan's interaction with its surrounding plasma and therefore a thorough understanding of its formation and structure is of primary interest. The Cassini spacecraft passed through the distant downstream region of Titan on 18:59:30 UT Dec. 26, 2005, which is referred to as the T9 flyby and provided a great opportunity to test our understanding of the highly dynamic wake region. In this paper we compare the observational data (from the magnetometer, plasma analyzer and Langmuir probe) with numerical results using a 7‐species Hall MHD Titan model. There is a good agreement between the observed and modeled parameters, given the uncertainties in plasma measurements and the approximations inherent in the Hall MHD model. Our simulation results also show that Hall MHD model results fit the observations better than the non‐Hall MHD model for the flyby, consistent with the importance of kinetic effects in the Titan interaction. Based on the model results, we also identify various regions near Titan where Hall MHD models are applicable.
Systematic deviations from Gaussianity in models of quasigeostrophic turbulence
Authors: Timofeyev I.
Published: November 2007

Microcanonical simulations of spectral truncations of the barotropic quasigeostrophic model are utilized to demonstrate systematic departures from Gaussianity in these models. Truncated equations conserve both the energy and the enstrophy, and predictions of the equilibrium statistical theory are Gaussian for all values of geophysical parameters. Nevertheless, nonzero topographic modes induce significant departures from Gaussianity in corresponding Fourier wavenumbers of the stream function. In particular, the distribution becomes asymmetric, resulting in a significant increase of the third moment. This behavior is most noticeable for large-scale topographic components (with small wavenumbers) and intermediate truncation sizes.
Broadband magneto-optical absorption by a Rashba spintronic system
Authors: Xu W. , Yang C. H. , Zhang J.
Published: November 2007

We examine the selection rules for electron-photon interaction in a two-dimensional electron gas (2DEG) in the presence of the Rashba spin-orbit interaction and quantizing magnetic fields. In such a case, new channels open up for electronic transition accompanied by the absorption of photons. As a result, two absorption peaks and a broadband absorption spectrum can be observed for high-mobility samples at relatively high magnetic fields. We find that electronic transitions between the neighboring Landau levels within the same spin orientation are the main channels for magneto-optical absorption in a spin-split 2DEG.
Practical sensor for nitrogen in direct current glow discharges
Authors: Popović D. , Milosavljević V. , Daniels S.
Published: November 2007

This paper presents a method for precise measurement of atomic and molecular nitrogen in an oxygen-nitrogen dc plasma. This is achieved by monitoring the intensities of the atomic nitrogen spectral line at 821.6 nm and the molecular nitrogen bandhead at 337.1 nm, relative to the atomic oxygen spectral line at 844.7 nm. Oxygen is one of the most frequently used gases for surface chemical treatment, including deposition and etching, therefore the ability to measure and control the process and chemical composition of the process is essential. To validate this oxygen actimometry method for N2-xO2 (where x varies from 0 to 1) dc plasmas, threshold tests have been performed with Ar actinometry. The optical measurements have been performed using two methods. The first approach uses a USB2000 fiber optic spectrometer, calibrated with a Gigahertz–Optik BN-0102-1 reference standard source, to record the desired spectral lines. The second approach uses narrow bandwidth optical filters (∼0.7–0.07 nm) with central wavelengths of 821.6, 337.1, and 844.69 nm and photodiodes to detect the emission intensity, also calibrated with the same standard source. Optical data are collected for a range of experimental conditions in a flowing glow discharge of N2-xO2 mixture. The maximum dc voltage is 2.2 kV and maximum chamber pressure is 266 Pa. Data from both optical methods are compared and used to interpret the relative atomic and molecular nitrogen concentrations under various operating conditions.
A generalized model for probing frictional characteristics of pressure-driven liquid microflows
Authors: Chakraborty Suman , Das Tamal , Chattoraj Shubhasish
Published: November 2007

In this article, a fundamental model was postulated to capture the influences of microfabrication characteristics on the frictional behavior of pressure-driven liquid microflows through a detailed analysis of the underlined surface effects that effectively link up these two strongly correlated aspects. For theoretical analysis, a continuum-based generalized formalism was derived for critically assessing the competing aspects of the stick-slip influences of the surface roughness elements, the randomness related to the spontaneous production, size distribution and coverage of the nanobubble layers, and the consequent apparent slip mechanisms due to hydrophobic interactions. Uncertainties pertaining to surface texture were accounted for by employing a stochastic version of the Navier-Stokes equation. The theoretical formulation was simultaneously validated with the data obtained from indigenous experiments and other benchmark studies reported in the literature and excellent quantitative trends in this regard were obtained for all cases.
Effects of a thin Mg layer on the structural and magnetoresistance properties of CoFeB∕MgO∕CoFeB magnetic tunnel junctions
Authors: Lu Y. , Deranlot C. , Vaurès A. , Petroff F. , George J.-M. , Zheng Y. , Demailles D.
Published: November 2007

We have combined in situ reflection high energy electron diffraction, high-resolution transmission electron microscopy, and magnetotransport experiments to investigate the role of a thin inserted Mg layer on the crystalline texture of MgO barriers in magnetic tunnel junctions grown in a standard sputtering system. It was found that an ultrathin Mg layer of 2–6Å can efficiently promote a MgO (001) texture prior to any annealing. For thicker Mg layers, the MgO (001) texture was found to degrade due to the hexagonal structure of Mg. For tunneling magnetoresistance (TMR), the efficient role of the MgO crystallization induced by the Mg layer appears after a 400°C annealing. The optimum was found for a 4Å inserted Mg layer with a TMR of 120% at room temperature (210% at 3K) which could be considerably improved for fully (001) oriented magnetic tunnel junctions.
Characteristics of direct current microhollow cathode discharges combined with dielectric barrier discharges as preionizer
Authors: Watanabe Jun , Ogino Akihisa , Nagatsu Masaaki
Published: November 2007

Characteristics of direct current microhollow cathode discharges (MHCDs) combined with dielectric barrier discharge (DBD) electrodes as preionization source were studied experimentally and theoretically. The DBD preionization significantly reduced the sparking voltage (from 3.1–3.2to2.4–2.5kV) and improved the spatial uniformity of the multihole MHCDs. Theoretical calculations using the finite element method indicate that the electrons generated by DBDs in the negative phase of the applied voltage could be accelerated into the MHCD electrodes and serve as the seeding electrons for initiating MHCDs. It was experimentally demonstrated that pulselike MHCDs were synchronously triggered by the preionized DBD current pulses.
The Copernican myths
Authors: Singham Mano
Published: November 2007

The real story of how the scientific and religious establishments greeted the Copernican revolution is quite different from the folklore. And it’s a lot more interesting.
Human papillomaviruses activate caspases upon epithelial differentiation to induce viral genome amplification
Authors: Moody Cary A. , Fradet-Turcotte Amelie , Archambault Jacques , Laimins Laimonis A.
Published: November 2007

The life cycle of human papillomaviruses (HPVs) is linked to epithelial differentiation, with late viral events restricted to the uppermost stratified layers. Our studies indicated that HPV activates capases-3, -7, and -9 upon differentiation, whereas minimal activation was observed in differentiating normal keratinocytes. Activation occurred in the absence of significant levels of apoptosis, suggesting a potential role for caspases in the viral life cycle. In support of this, the addition of caspase inhibitors significantly impaired differentiation-dependent viral genome amplification. A conserved caspase cleavage motif was identified in the replication protein E1 (
46
DxxD
49
) that was targeted
in vitro
by both recombinant caspase-3 and caspase-7. Mutation of this site inhibited amplification of viral genomes, indicating that caspase cleavage is necessary for the productive viral life cycle. Our study demonstrates that HPV activates caspases upon differentiation to facilitate productive viral replication and represents a way by which HPV controls viral gene function in differentiating cells.
The
all-trans
-retinal dimer series of lipofuscin pigments in retinal pigment epithelial cells in a recessive Stargardt disease model
Authors: Kim So R. , Jang Young P. , Jockusch Steffen , Fishkin Nathan E. , Turro Nicholas J. , Sparrow Janet R.
Published: November 2007

The bis-retinoid pigments that accumulate in retinal pigment epithelial cells as lipofuscin are associated with inherited and age-related retinal disease. In addition to A2E and related
cis
isomers, we previously showed that condensation of two molecules of
all-trans
-retinal leads to the formation of a protonated Schiff base conjugate,
all-trans
-retinal dimer-phosphatidylethanolamine. Here we report the characterization of the related pigments,
all-trans
-retinal dimer-ethanolamine and unconjugated
all-trans
-retinal dimer, in human and mouse retinal pigment epithelium. In eyecups of
Abcr
−/−
mice, a model of recessive Stargardt macular degeneration,
all-trans
-retinal dimer-phosphatidylethanolamine was increased relative to wild type and was more abundant than A2E. Total pigment of the
all-trans
-retinal dimer series (sum of
all-trans
-retinal dimer-phosphatidylethanolamine,
all-trans
-retinal dimer-ethanolamine, and
all-trans
-retinal dimer) increased with age in
Abcr
−/−
mice and was modulated by amino acid variants in Rpe65. In
in vitro
assays, enzyme-mediated hydrolysis of
all-trans
-retinal dimer-phosphatidylethanolamine generated
all-trans
-retinal dimer-ethanolamine, and protonation/deprotonation of the Schiff base nitrogen of
all-trans
-retinal dimer-ethanolamine was pH-dependent. Unconjugated
all-trans
-retinal dimer was a more efficient generator of singlet oxygen than A2E, and the
all-trans
-retinal dimer series was more reactive with singlet oxygen than was A2E. By analyzing chromatographic properties and UV-visible spectra together with mass spectrometry, mono- and bis-oxygenated
all-trans
-retinal dimer photoproducts were detected in
Abcr
−/−
mice. The latter findings are significant to an understanding of the adverse effects of retinal pigment epithelial cell lipofuscin.
Parallel genomic evolution and metabolic interdependence in an ancient symbiosis
Authors: McCutcheon John P. , Moran Nancy A.
Published: November 2007

Obligate symbioses with nutrient-provisioning bacteria have originated often during animal evolution and have been key to the ecological diversification of many invertebrate groups. To date, genome sequences of insect nutritional symbionts have been restricted to a related cluster within Gammaproteobacteria and have revealed distinctive features, including extreme reduction, rapid evolution, and biased nucleotide composition. Using recently developed sequencing technologies, we show that
Sulcia muelleri
, a member of the Bacteroidetes, underwent similar genomic changes during coevolution with its sap-feeding insect host (sharpshooters) and the coresident symbiont
Baumannia cicadellinicola
(Gammaproteobacteria). At 245 kilobases,
Sulcia
's genome is approximately one tenth of the smallest known Bacteroidetes genome and among the smallest for any cellular organism. Analysis of the coding capacities of
Sulcia
and
Baumannia
reveals striking complementarity in metabolic capabilities.
Identification of retinoic acid as an inhibitor of transcription factor Nrf2 through activation of retinoic acid receptor alpha
Authors: Wang Xiu Jun , Hayes John D. , Henderson Colin J. , Wolf C. Roland
Published: November 2007

Isothiocyanates and phenolic antioxidants can prevent cancer through activation of Nrf2 (NF-E2 p45-related factor 2), a transcription factor that controls expression of cytoprotective genes through the antioxidant response element (ARE) enhancer. Using a human mammary MCF7-derived AREc32 reporter cell line, we now report that
all-trans
retinoic acid (ATRA), and other retinoic acid receptor alpha (RARα) agonists, markedly reduces the ability of Nrf2 to mediate induction of ARE-driven genes by cancer chemopreventive agents including the metabolite of butylated hydroxyanisole,
tert
-butylhydroquinone (tBHQ). The basal and tBHQ-inducible expression of aldo-keto reductase (
AKR
)
AKR1C1
and
AKR1C2
genes, which are regulated by Nrf2, was also repressed by ATRA in AREc32 cells. Antagonists of RARα augmented induction of ARE-driven gene expression by tBHQ, as did knockdown of RARα by using RNAi. The expression of the ARE-gene battery was increased in the small intestine of mice fed on a vitamin A-deficient diet, and this increase was repressed by administration of ATRA. By contrast, in the small intestine of Nrf2 null mice, the expression of ARE-driven genes was not affected by vitamin A status. In MCF7 cells, ATRA did not block the nuclear accumulation of Nrf2 but reduced the binding of Nrf2 to the ARE enhancer as a consequence of forming a complex with RARα. These data suggest that cross-talk between Nrf2 and RARα could markedly influence the sensitivity of cells to electrophiles and oxidative stressors and, as a consequence, to carcinogenesis.
A forest-based approach to identifying gene and gene–gene interactions
Authors: Chen Xiang , Liu Ching-Ti , Zhang Meizhuo , Zhang Heping
Published: November 2007

Multiple genes, gene-by-gene interactions, and gene-by-environment interactions are believed to underlie most complex diseases. However, such interactions are difficult to identify. Although there have been recent successes in identifying genetic variants for complex diseases, it still remains difficult to identify gene–gene and gene–environment interactions. To overcome this difficulty, we propose a forest-based approach and a concept of variable importance. The proposed approach is demonstrated by simulation study for its validity and illustrated by a real data analysis for its use. Analyses of both real data and simulated data based on published genetic models show the effectiveness of our approach. For example, our analysis of a published data set on age-related macular degeneration (AMD) not only confirmed a known genetic variant (
P
value = 2E-6) for AMD, but also revealed an unreported haplotype surrounding single-nucleotide polymorphism (SNP) rs10272438 on chromosome 7 that was significantly associated with AMD (
P
value = 0.0024). These significance levels are obtained after the consideration for a large number of SNPs. Thus, the importance of this work is twofold: it proposes a powerful and flexible method to identify high-risk haplotypes and their interactions and reveals a potentially protective variant for AMD.
RFCCtf18and the Swi1-Swi3 Complex Function in Separate and Redundant Pathways Required for the Stabilization of Replication Forks to Facilitate Sister Chromatid Cohesion inSchizosaccharomyces pombe
Authors: Ansbach Alison B. , Noguchi Chiaki , Klansek Ian W. , Heidlebaugh Mike , Nakamura Toru M. , Noguchi Eishi
Published: November 2007

Sister chromatid cohesion is established during S phase near the replication fork. However, how DNA replication is coordinated with chromosomal cohesion pathway is largely unknown. Here, we report studies of fission yeast Ctf18, a subunit of the RFCCtf18replication factor C complex, and Chl1, a putative DNA helicase. We show that RFCCtf18is essential in the absence of the Swi1–Swi3 replication fork protection complex required for the S phase stress response. Loss of Ctf18 leads to an increased sensitivity to S phase stressing agents, a decreased level of Cds1 kinase activity, and accumulation of DNA damage during S phase. Ctf18 associates with chromatin during S phase, and it is required for the proper resumption of replication after fork arrest. We also show that chl1Δ is synthetically lethal with ctf18Δ and that a dosage increase of chl1+rescues sensitivities of swi1Δ to S phase stressing agents, indicating that Chl1 is involved in the S phase stress response. Finally, we demonstrate that inactivation of Ctf18, Chl1, or Swi1-Swi3 leads to defective centromere cohesion, suggesting the role of these proteins in chromosome segregation. We propose that RFCCtf18and the Swi1–Swi3 complex function in separate and redundant pathways essential for replication fork stabilization to facilitate sister chromatid cohesion in fission yeast.
MutaGeneSys: estimating individual disease susceptibility based on genome-wide SNP array data
Authors: Stoyanovich Julia , Pe'er Itsik
Published: November 2007

Summary: We present MutaGeneSys: a system that uses genome-wide genotype data to estimate disease susceptibility. Our system integrates three data sources: the International HapMap project, whole-genome marker correlation data and the Online Mendelian Inheritance in Man (OMIM) database. It accepts SNP data of individuals as query input and delivers disease susceptibility hypotheses even if the original set of typed SNPs is incomplete. Our system is scalable and flexible: it produces population, technology and confidence-specific predictions in interactive time.

Availability: Our system is available as an online resource at http://magnet.c2b2.columbia.edu/mutagenesys/. Our findings have also been incorporated into the HapMap Genome Browser as the OMIM_Disease_Associations track.

Contact:  jds1@cs.columbia.edu
Individual variation and the endocrine regulation of behaviour and physiology in birds: a cellular/molecular perspective
Authors: Ball Gregory F , Balthazart Jacques
Published: November 2007

Investigations of the cellular and molecular mechanisms of physiology and behaviour have generally avoided attempts to explain individual differences. The goal has rather been to discover general processes. However, understanding the causes of individual variation in many phenomena of interest to avian eco-physiologists will require a consideration of such mechanisms. For example, in birds, changes in plasma concentrations of steroid hormones are important in the activation of social behaviours related to reproduction and aggression. Attempts to explain individual variation in these behaviours as a function of variation in plasma hormone concentrations have generally failed. Cellular variables related to the effectiveness of steroid hormone have been useful in some cases. Steroid hormone target sensitivity can be affected by variables such as metabolizing enzyme activity, hormone receptor expression as well as receptor cofactor expression. At present, no general theory has emerged that might provide a clear guidance when trying to explain individual variability in birds or in any other group of vertebrates. One strategy is to learn from studies of large units of intraspecific variation such as population or sex differences to provide ideas about variables that might be important in explaining individual variation. This approach along with the use of newly developed molecular genetic tools represents a promising avenue for avian eco-physiologists to pursue.
Reclassification of Vibrio fischeri, Vibrio logei, Vibrio salmonicida and Vibrio wodanis as Aliivibrio fischeri gen. nov., comb. nov., Aliivibrio logei comb. nov., Aliivibrio salmonicida comb. nov. and Aliivibrio wodanis comb. nov.
Authors: Urbanczyk Henryk , Ast Jennifer C. , Higgins Melissa J. , Carson Jeremy , Dunlap Paul V.
Published: November 2007

Four closely related species,Vibrio fischeri,Vibrio logei,Vibrio salmonicidaandVibrio wodanis, form a clade within the familyVibrionaceae; the taxonomic status and phylogenetic position of this clade have remained ambiguous for many years. To resolve this ambiguity, we tested these species against other species of theVibrionaceaefor phylogenetic and phenotypic differences. Sequence identities for the 16S rRNA gene were ≥97.4 % among members of theV. fischerigroup, but were ≤95.5 % for members of this group in comparison with type species of other genera of theVibrionaceae(i.e.PhotobacteriumandVibrio, with which they overlap in G+C content, andEnterovibrio,GrimontiaandSalinivibrio, with which they do not overlap in G+C content). Combined analysis of therecA,rpoA,pyrH,gyrBand 16S rRNA gene sequences revealed that the species of theV. fischerigroup form a tightly clustered clade, distinct from these other genera. Furthermore, phenotypic traits differentiated theV. fischerigroup from other genera of theVibrionaceae, and a panel of 13 biochemical tests discriminated members of theV. fischerigroup from type strains ofPhotobacteriumandVibrio. These results indicate that the four species of theV. fischerigroup represent a lineage within theVibrionaceaethat is distinct from other genera. We therefore propose their reclassification in a new genus,Aliivibriogen. nov.Aliivibriois composed of four species:Aliivibrio fischericomb. nov. (the type species) (type strain ATCC 7744T=CAIM 329T=CCUG 13450T=CIP 103206T=DSM 507T=LMG 4414T=NCIMB 1281T),Aliivibrio logeicomb. nov. (type strain ATCC 29985T=CCUG 20283T=CIP 104991T=NCIMB 2252T),Aliivibrio salmonicidacomb. nov. (type strain ATCC 43839T=CIP 103166T=LMG 14010T=NCIMB 2262T) andAliivibrio wodaniscomb. nov. (type strain ATCC BAA-104T=NCIMB 13582T=LMG 24053T).
Micromonospora lupini sp. nov. and Micromonospora saelicesensis sp. nov., isolated from root nodules of Lupinus angustifolius
Authors: Trujillo Martha E. , Kroppenstedt Reiner M. , Fernández-Molinero Carmen , Schumann Peter , Martínez-Molina Eustoquio
Published: November 2007

A study was conducted to determine the taxonomic status of six actinomycete strains isolated from root nodules of Lupinus angustifolius. The strains were filamentous, Gram-positive and produced single spores at the tip of the hyphae. Phylogenetic, chemotaxonomic and morphological analyses demonstrated that all six strains belonged to the genus Micromonospora. According to the 16S rRNA gene sequence data, the strains were divided into two clusters that are moderately related to Micromonospora mirobrigensis, Micromonospora matsumotoense and Micromonospora purpureochromogenes. Fatty acid patterns also supported the division of the strains, and significant differences between the two groups were found in the amounts of iso-15 : 0, iso-16 : 0, iso-16 : 1 and iso-17 : 0. Furthermore, the two groups showed physiological differences which included utilization of arabinose, trehalose, alanine and sucrose and xylan hydrolysis. Finally, DNA–DNA hybridization and ribotyping studies confirmed that each group represents a novel species. Based on the genotypic and phenotypic data, the novel species Micromonospora lupini sp. nov. (type strain Lupac 14NT =DSM 44874T =LMG 24055T) and Micromonospora saelicesensis sp. nov. (type strain Lupac 09T =DSM 44871T =LMG 24056T) are proposed.