bluuebunny/crossref_metadata_2025 huggingface dataset:
Segmental and Prosodic Effects on Intervocalic Voiced Stop Reduction in Connected Speech
Authors: Bouavichith Dominique , Davidson Lisa
Published: November 2013

De scriptions of lenition have often assumed that connected speech reductions are the phonetic precursors of phonological lenition processes. In this article, production of intervocalic voiced stops during reading in American English is examined to determine whether connected speech reduction processes mirror the stages of lenition that have been posited in the phonological literature. The first result shows that American English speakers never lenite to fricatives or debuccalize to [h] or glottal stop, but rather produce approximants whenever reduction occurs. Second, stress plays an essential role: 51% of stops are produced as approximants when stress is on the preceding syllable (e.g. ‘yoga'), but only 7% of stops weaken when stress is on the following syllable (e.g. ‘lagoon'). Approximant productions are longer and higher in intensity than stop productions when stress precedes the target consonant, but when stress follows the target consonant, the stop cues are enhanced. These acoustic findings suggest that English speakers prioritize the realization of acoustic cues to stress, including the robust production of stop consonants, over pressures to reduce or weaken consonants in intervocalic position.
Sonorant Onset Pitch as a Perceptual Cue of Lexical Tones in Mandarin
Authors: Chen Tsung-Ying , Tucker Benjamin V.
Published: November 2013

Lexical tone identification requires a number of secondary cues, when main tonal contours are unavailable. In this article, we examine Mandarin native speakers' ability to identify lexical tones by extracting tonal information from sonorant onset pitch (onset contours) on syllable-initial nasals ranging from 50to 70 ms in duration. In experiments I and II we test speakers' ability to identify lexical tones in a second syllable with and without onset contours in isolation (experiment I) and in a sentential context (experiment II). The results indicate that speakers can identify lexical tones with short distinctive onset contour patterns,they also indicate that misperception of tones 213 and 24 are common. Furthermore, in experiment III, we test whether onset contours in a following syllable can be utilized by listeners in tone identification. We find that onset contours in the following syllable also contribute to the identification of the target lexical tones. The conclusions are twofold: (1) Mandarin lexical tones can be identified with onset contours; (2) tonal domain must be extended to include not just typical cues of tones but also coarticulated tonal patterns.
Effects of a Facial Cream Containing the Minor Alkaloid Anatabine on Improving the Appearance of the Skin in Mild to Moderate Rosacea: An Open-Label Case Series Study
Authors: Lanier Ryan K. , Cohen Amy E. , Weinkle Susan H.
Published: November 2013

Background: Current medical and scientific research indicates that rosacea, a chronic and often debilitating skin condition that primarily affects the central face, may be caused by an overactive or excessive inflammatory immune response. Regardless of etiology, the accompanying redness and inflammation is unsightly and difficult for the patient. Anatabine is an alkaloid from the plant family Solanaceae that has been shown in several preclinical studies to modulate proinflammatory signaling pathways. Objective: A cream containing anatabine was developed and evaluated in an open-label case series study for safety and effects on the appearance of the skin in 10 patients with mild to moderate rosacea. Methods: Patients applied the cream to the face twice daily for a period of 30 days. Patients and the study physician completed safety and efficacy assessments at study end. Results: Results showed that 50% of the patients self-reported improvement in the appearance of their skin, and the physician noted improvement in 70% of the patients. Photographs taken before and after 30 days of cream use provide visual evidence of the improvement in several patients. There were no complications or adverse events reported by any of the patients in the study, indicating that the anatabine cream was safe and very well tolerated. Conclusion: The results of this open-label case series show that a facial cream containing anatabine can improve the appearance of the skin in patients with mild to moderate rosacea and suggest that a double-blind, vehicle-controlled trial in a larger number of subjects is warranted.
Hyperpigmentation following Treatment of Frontal Fibrosing Alopecia
Authors: Pérez-Rodríguez Irma Margarita , García-Melendez Martha Elena , Eichelmann Kristian , Vázquez-Martínez Osvaldo , Ocampo-Candiani Jorge
Published: November 2013

Introduction: Frontal fibrosing alopecia (FFA) is a scarring alopecia characterized by progressive recession of the frontotemporal hairline. Current treatment is aimed at stopping progression, and the combination of dutasteride and pimecrolimus is the most effective therapy. Side effects associated with dutasteride are erectile dysfunction as well as breast tenderness and enlargement, while pimecrolimus produces a burning sensation. Case Report: We present a 57-year-old postmenopausal female with a 3-year history of a scarring alopecic plaque in her frontotemporal region. Biopsy confirmed the diagnosis of FFA, and she was started on dutasteride 0.5 mg p.o. q.d., and later, topical pimecrolimus 1% b.i.d. was added. Eight months after initiating treatment, she showed hyperpigmentation on her metacarpophalangeal and interphalangeal joints, as well as on the cheeks and on the chin; dutasteride and pimecrolimus were discontinued. After 5 months of follow-up, her hyperpigmentation improved by 80% only by using photoprotection. Conclusion: Because of the variable clinical course of FFA, treatment is focused on halting its progression. Several therapeutic agents have been evaluated and the combination of dutasteride and pimecrolimus has shown a high response rate. There is no reported evidence of hyperpigmentation associated with this combination.
Two new Atlantic Forest Myrtaceae from Brazil
Authors: Bunger Mariana De Oliveira , Stehmann João Renato , Sobral Marcos
Published: November 2013

Two new Brazilian species of Eugenia are described and illustrated, Eugenia regia and  E. espinhacensis. Eugenia regia, collected in coastal Atlantic rainforests in the southeastern states of São Paulo and Rio de Janeiro, is related to E. bunchosiifolia, from which it differs by its larger leaves, flowers and trichomes. Eugenia espinhacensis was collected in seasonal Atlantic forests of the state of Minas Gerais; it is similar to E. bocainensis, from wich can be distinguished by its obtuse sepals and pilose branches, pedicels and flowers. São descritas e ilustradas duas novas espécies de Eugenia: Eugenia regia e E. espinhacensis. A primeira encontrada nas matas ombrófilas costeiras do litoral norte de São Paulo e sul do Rio de Janeiro tem sido frequentemente e erroneamente nomeada sob E. bunchosiifolia, da qual difere-se pelo discrepante tamanho das folhas, flores e pilosidade. E. espinhacensis é uma espécie ocorrente nas matas semidecíduas do Quadrilátero Ferrífero, em Minas Gerais, numa região altamente explorada pela extração de minério de ferro.  Esta assemelha-se a E. bocainensis, porém difere-se pelas sépalas obtusas e pilosidade dos pedicelos, sépalas e ramos.
Phamartes coronatus gen. nov. sp. nov. a new genus and species of stick insect from Bach Ma National Park, central Vietnam (Phasmida, Diapheromeridae, Necrosciinae)
Authors: BRESSEEL JOACHIM , CONSTANT JEROME
Published: November 2013

A new genus and species of stick insect Phamartes coronatus gen. nov. sp. nov. from Bach Ma National Park, central Vietnam is described and illustrated from both sexes and the egg. The genus is most closely related to Oxyartes Stål, 1875, but easily distinguishable by the presence of fully developed alae, the head armature and the split and asymmetrical anal segment, a character previously unknown in Necrosciinae.
Discovery of four new species of the genus Planaeschna from Southwestern China (Odonata: Anisoptera: Aeshnidae)
Authors: ZHANG HAO-MIAO , CAI QING-HUA
Published: November 2013

Four new species of the genus Planaeschna, P. robusta sp. nov. (holotype male; Mt. Emeishan, Emeishan City, Sichuan Province, China, 16. VIII. 2007), P. maculifrons sp. nov. (holotype male; Mt. Emeishan, Emeishan City, Sichuan Province, China, 20. VIII. 2007), P. caudispina sp. nov. (holotype male; Mt. Qingchengshan, Dujiangyan City, Sichuan Province, China, 30. VIII. 2007) and P. monticola sp. nov. (holotype male; Sanjiacun Stream, Fengyi Town, Dali City, Yunnan Province, China, 19. XI. 2012) are described and illustrated and diagnosed from their congeners. All the holotypes have been deposited in the Collection of Aquatic Animals, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan City, Hubei Province, China. Brief notes on the biology of each species are also provided.
Description of larva, redescription of adults and biology of Mortogenesia mesopotamica (Morton, 1921) (Ephemeroptera: Palingeniidae)
Authors: SOLDÁN TOMÁŠ , GODUNKO ROMAN J.
Published: November 2013

All life stages of Mortogenesia mesopotamica (Morton, 1921) are described, on the basis of material collected in the lower Euphrates–Tigris River basin. Adults are redescribed, and larvae are described for the first time, based on sets of larval exuviae. The monotypic genus Mortogenesia Lestage, 1923 is redefined using both adult and larval characteristics: eyes not contiguous, distinctly separated by a wide gap; vestigial mandibular tusks present, with 3–4 rounded lateral projections; forewing veins MP1 and iMP not brought together; CuA furcation absent on forewing; both claws similarly shaped in males; hind tarsi five-segmented; penes with roughly triangular, apically rounded and divergent lobes (in adults); seven conspicuous stout teeth on outer margin of mandibular tusk, with no apical spine-like setae; maxillary palps two-segmented; distal segment of labial palps asymmetric and bulbous; basal segment of labial palps densely pilose; forelegs with relatively short, triangular claws that are basally wider than tarsi; foretibiae with stout spines only; and a simple, leaf-like gill 1 (in larvae). The burrowing larvae of M. mesopotamica occur solely in large permanent lowland rivers, in clayey or muddy sediments, with particles exceeding 0.025–0.075 mm. Based on observations of their burrows, larval density is approximately 100–200 individuals per square meter. Various evidence suggests a unique phenomenon of male neoteny in Mortogenesia. Preliminary results of male dissections suggests a missing teneral adult cuticle, and male “subimagoes” and females occur simultaneously after oviposition. Mortogenesia mesopotamica is known currently from the Euphrates–Tigris basin in Iraq and from the Karkheh River in Iran.
New Pseudophyllinae from the Lesser Antilles (Orthoptera: Ensifera: Tettigoniidae)
Authors: HUGEL SYLVAIN , DESUTTER-GRANDCOLAS LAURE
Published: November 2013

Two new Cocconitini Brunner von Wattenwyl, 1895 species belonging to Nesonotus Beier, 1960 are described from the Lesser Antilles: Nesonotus caeruloglobus Hugel, n. sp. from Dominica, and Nesonotus vulneratus Hugel, n. sp. from Martinique. The songs of both species are described and elements of biology are given. The taxonomic status of species close to Nesonotus tricornis (Thunberg, 1815) is discussed.
Steep Shelf Stabilization of the Coastal Bransfield Current: Linear Stability Analysis
Authors: Poulin F. J. , Stegner A. , Hernández-Arencibia M. , Marrero-Díaz A. , Sangrà P.
Published: November 2013

In situ measurements obtained during the 2010 COUPLING cruise were analyzed in order to fully characterize the velocity structure of the coastal Bransfield Current. An idealized two-layer shallow-water model was used to investigate the various instability processes of the realistic current along the coastal shelf. Particularly studied is how the topographic parameter To (ratio between the shelf slope and the isopycnal slope of the surface current) impacts the growth and the wavelength of the unstable perturbations. For small bottom slopes, when the evolution of the coastal current is controlled by the baroclinic instability, the increase of the topographic parameter To yields a selection of smaller unstable wavelengths. The growth rates increase with small values of To. For larger values of To (To ≳ 10, which is relevant for the coastal Bransfield Current), the baroclinic instability is strongly dampened and the horizontal shear instability becomes the dominant one. In this steep shelf regime, the unstable growth rate and the wavelength selection of the baroclinic coastal current remains almost constant and weakly affected by the amplitude of the bottom velocity or the exact value of the shelf slope. Hence, the linear stability analysis of an idealized Bransfield Current predicts a typical growth time of 7.7 days and an alongshore scale of 47 km all along the South Shetland Island shelf. The fact that these large growth times are identical to the typical transit time of water parcels along the shelf may explain why the current does not exhibit any unstable meanders.
Kinematic and Precipitation Characteristics of Convective Systems Observed by Airborne Doppler Radar during the Life Cycle of a Madden–Julian Oscillation in the Indian Ocean
Authors: Guy Nick , Jorgensen David P.
Published: November 2013

This study presents characteristics of convective systems observed during the Dynamics of the Madden–Julian oscillation (DYNAMO) experiment by the instrumented NOAA WP-3D aircraft. Nine separate missions, with a focus on observing mesoscale convective systems (MCSs), were executed to obtain data in the active and inactive phase of a Madden–Julian oscillation (MJO) in the Indian Ocean. Doppler radar and in situ thermodynamic data are used to contrast the convective system characteristics during the evolution of the MJO. Isolated convection was prominent during the inactive phases of the MJO, with deepening convection during the onset of the MJO. During the MJO peak, convection and stratiform precipitation became more widespread. A larger population of deep convective elements led to a larger area of stratiform precipitation. As the MJO decayed, convective system top heights increased, though the number of convective systems decreased, eventually transitioning back to isolated convection. A distinct shift of echo top heights and contoured frequency-by-altitude diagram distributions of radar reflectivity and vertical wind speed indicated that some mesoscale characteristics were coupled to the MJO phase. Convective characteristics in the climatological initiation region (Indian Ocean) were also apparent. Comparison to results from the Tropical Ocean and Global Atmosphere Coupled Ocean–Atmosphere Response Experiment (TOGA COARE) in the western Pacific indicated that DYNAMO MCSs were linearly organized more parallel to the low-level shear and without strong cold pools than in TOGA COARE. Three-dimensional MCS airflow also showed a different dynamical structure, with a lack of the descending rear inflow present in shear perpendicularly organized TOGA COARE MCSs. Weaker, but deeper updrafts were observed in DYNAMO.
What does the Independent Visitor role offer looked after children?
Authors: Hurst Claire , Peel Mark
Published: November 2013

The Children Act 1989 introduced the role of Independent Visitors (IVs) for looked after children; their task is ‘visiting, advising and befriending the child’ (section 7(2)(a)). However, research has found that IVs are not being made available for all children in care who qualify for this support (Knight, 1998; Oakley and Masson, 2000). Knight (1998) estimated that there were fewer than 40 schemes running for around 120 English local authorities, a situation which is at the very least questionable given the established legal right of young people to access such a service. This article examines existing research studies of IV schemes and considers what Visitors can offer young people. Additionally, it shows that looked after children tend to view their IVs as friends and sources of emotional support, encouragement and practical advice, offering a consistent adult presence in their life, clearly demonstrating their significance for separated children.
‘Remember when…’: exploring the experiences of looked after children and their carers in engaging in collaborative reminiscence
Authors: Shotton Gillian
Published: November 2013

The background literature outlines the positive impact that life story work can have for children in care, but there is scant published research to support these claims and, to date, none exploring both carers’ and children’s experiences of engaging in collaborative memory work, which can form an important component of a child’s life story. This article explores the experiences of foster carers and looked after children in carrying out such work using the memory store approach, focusing on what their talk could tell us about how using this approach had affected the carer–child relationship, the child’s self-perception, aspects of the child’s thinking and learning, and their emotions. The participants were five foster carers and the four children in their care. Two to three months after a one-day training course for carers in using the memory store approach, semi-structured interviews were carried out with the carers and a board game session took place with each of the children to explore their views. Interpretative Phenomenological Analysis (IPA) was used to guide both the data generation and its subsequent analysis. Carers’ and children’s talk suggested that using the memory store approach has a number of perceived benefits, emotionally, relationally and in terms of the child’s self-perception and learning. A memory store approach model was postulated on the basis of these findings. One of the conclusions of this research is that using the memory store approach (or similar) should be a statutory requirement of foster carers, not only because of the potential benefits highlighted through this research but also because of the ethical necessity to safeguard the memories of a child’s time in care.
The Imperfect Substitutes Model in South Asia
Authors: Gopalan Sasidaran , Malik Ammar A. , Reinert Kenneth A.
Published: November 2013

In large number of circumstances, trade policy modellers turn to partial equilibrium modelling in an imperfect substitutes framework. This article develops a formal representation of this imperfect substitutes model and applies it to trade liberalization within the negative list between Pakistan and India following Pakistan’s decision to grant most favoured nation (MFN) status to India. It provides estimates for ranges of output and welfare effects for a number of sectors of interest. It sets these results within the history of Pakistan–India trade and the political economy of the negative list.
Pruning the SAFTA Sensitive List of Bangladesh
Authors: Moazzem Khondaker Golam , Basak Kishore Kumer
Published: November 2013

A long list of products in sensitive list maintained by the member countries is one of the major weaknesses of SAFTA agreement for its effective operation. Present study analyzes the sensitive list of Bangladesh with a view to identify products for pruning. Pruning the sensitive list should follow justifiable method based on arguments and reasoning, particularly against the rationale behind keeping the products in the sensitive list. The study identified a set of sensitive products that could be pruned from the list taking into account their competitiveness, trade potentials and extent of revenue collected from those products. Analysis reveals that identified sensitive products, if pruned from the list, would have insignificant adverse effect on local industries since those are raw materials, intermediate products and capital machineries which have limited domestic production capacity. The method can be followed by other member countries of the SAFTA to prune their sensitive lists.
Remittances, Financial Development and Economic Growth in Bangladesh
Authors: Uddin Gazi Salah , Sjö Bo
Published: November 2013

In Bangladesh, remittances from migrant workers are an important component of national income and a source for financing consumption and investment. This article investigates the relationship between remittances, financial sector development and economic growth in Bangladesh over the period of 1976–2011. In the long run, the inflow of remittances and the expansion of the financial sector drive the growth in GDP, whereas in the short run, remittances act as a shock absorber to income changes.
Annealing behaviour of 6061 aluminium deposited by high pressure cold spray
Authors: Rokni M. R. , Widener C. A. , Ahrenkiel S. P. , Jasthi B. K. , Champagne V. R.
Published: November 2013

Aluminium 6061 deposited by high pressure cold spray was analysed using a transmission electron microscope (TEM) to characterise its microstructure and response to annealing to 450°C in the plane of the deposition and perpendicular to the deposited layers. The cold sprayed deposition was also analysed with scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDS) analysis and differential scanning calorimeter (DSC). Segregation of the solute atoms (Mg and Si) at the grain boundaries during cold spraying was seen to play a crucial role in stabilising the deformation substructure until specific temperatures, and was found to have a significant effect on the annealing behaviour of the microstructure in the two different directions.
Effects of M2CO3 (M = Li, Na, K) on electrolytic boronising of titanium in Na2B4O7 melts
Authors: Huang Y-G. , Chen J-R. , Zhang M-L. , Zhong X-X. , Li Q-Y. , Wang H-Q.
Published: November 2013

The effect of M2CO3 (M = Li, Na, K) on electrolytic boronising of titanium in Na2B4O7–20M2CO3 was investigated. The phase composition of boride was determined by X-ray diffraction. The morphology of boride was determined by scanning electron microscopy, and the composition of boride was measured by X-ray energy dispersive spectroscopy. The results show that the boride layer comprised TiB2 and TiB. TiB2 presented a dense phase, whereas TiB presented whiskers. TiB2 became thicker in the order of Li2CO3, Na2CO3 and K2CO3, in the melts. Simultaneously, TiB whiskers gradually changed from short and thick to long and thin. This change was due to the different polarisation abilities of alkali metal ions in M2CO3 (M = Li, Na, K).
Microporosity formation in Mg alloys and its effect on protective coatings
Authors: Liu B.-S. , Wei Y.-H. , Chen W.-Y. , Hou L.-F.
Published: November 2013

A notebook computer component with a complex geometry was manufactured with a die cast process (DCP), using an AZ91D alloy. Chemical conversion and organic coatings were sequentially applied to provide protection against physical and chemical damage. Air content in the component, which gives rise to microporosity, was determined with a DCP computer simulation using MAGMA software. The surface layer characteristics of the component were also investigated using scanning electron microscopy coupled with energy dispersive X-ray spectroscopy. The microporosity content was higher at the end of the filling process compared with the regions that filled first. Corrosion resistance was poorer for discontinuous conversion coatings that resulted from surface microporosity. Moreover, adhesion of an organic coating was degraded at areas with higher microporosity.
On strong law of large numbers and growth rate for a class of random variables
Authors: Shen Yan , Yang Jie , Hu Shuhe
Published: November 2013

In this paper, we study the strong law of large numbers for a class of random variables satisfying the maximal moment inequality with exponent 2. Our results embrace the Kolmogorov strong law of large numbers and the Marcinkiewicz strong law of large numbers for this class of random variables. In addition, strong growth rate for weighted sums of this class of random variables is presented.

MSC:60F15.
Autonomic dysfunction in reversible cerebral vasoconstriction syndromes
Authors: Chen Shih-Pin , Yang Albert C , Fuh Jong-Ling , Wang Shuu-Jiun
Published: November 2013

Background

Autonomic imbalance may play an important role in the pathogenesis of reversible cerebral vasoconstriction syndromes (RCVS). This study aimed to assess the autonomic function by analyzing heart rate variability (HRV) in patients with RCVS.

Methods

Patients with RCVS and age- and gender-matched controls were consecutively recruited. All patients (both ictal and remission stage) and controls underwent 24-hour ambulatory electrocardiographic (ECG) recordings. HRV measures covering time and frequency domains were used to assess autonomic functioning.

Results

Thirty-nine patients with RCVS and 39 controls completed the study. Compared to the controls, RCVS patients during the ictal stage showed reductions in parasympathetic-related indices, including the root mean square of difference of consecutive interbeat intervals (RMSSD) (22.1 ± 7.0 vs. 35.2 ± 14.2, p < 0.001), the percentage of adjacent intervals that varied by more than 50 ms (pNN50) (3.7 ± 3.4 vs. 10.6 ± 8.1, p < 0.001), and high-frequency power (HF) (5.82 ± 0.73 vs. 6.77 ± 0.74; p < 0.001), and increased low-frequency/high-frequency (LF/HF) ratio (index of sympathovagal balance) (3.38 ± 1.32 vs. 2.48 ± 1.07; p =0.001). These HRV indices improved partially but remained significantly different from controls during remission.

Conclusions

Decreased parasympathetic modulations and accentuated sympathetic activity might be a biological trait in patients with RCVS.
The genome-wide binding profile of the Sulfolobus solfataricustranscription factor Ss-LrpB shows binding events beyond direct transcription regulation
Authors: Nguyen-Duc Trong , van Oeffelen Liesbeth , Song Ningning , Hassanzadeh-Ghassabeh Gholamreza , Muyldermans Serge , Charlier Daniel , Peeters Eveline
Published: November 2013

Background

Gene regulatory processes are largely resulting from binding of transcription factors to specific genomic targets. Leucine-responsive Regulatory Protein (Lrp) is a prevalent transcription factor family in prokaryotes, however, little information is available on biological functions of these proteins in archaea. Here, we study genome-wide binding of the Lrp-like transcription factor Ss-LrpB from Sulfolobus solfataricus.

Results

Chromatin immunoprecipitation in combination with DNA microarray analysis (ChIP-chip) has revealed that Ss-LrpB interacts with 36 additional loci besides the four previously identified local targets. Only a subset of the newly identified binding targets, concentrated in a highly variable IS-dense genomic region, is also bound in vitro by pure Ss-LrpB. There is no clear relationship between the in vitro measured DNA-binding specificity of Ss-LrpB and the in vivo association suggesting a limited permissivity of the crenarchaeal chromatin for transcription factor binding. Of 37 identified binding regions, 29 are co-bound by LysM, another Lrp-like transcription factor in S. solfataricus. Comparative gene expression analysis in an Ss-lrpB mutant strain shows no significant Ss-LrpB-mediated regulation for most targeted genes, with exception of the CRISPR B cluster, which is activated by Ss-LrpB through binding to a specific motif in the leader region.

Conclusions

The genome-wide binding profile presented here implies that Ss-LrpB is associated at additional genomic binding sites besides the local gene targets, but acts as a specific transcription regulator in the tested growth conditions. Moreover, we have provided evidence that two Lrp-like transcription factors in S. solfataricus, Ss-LrpB and LysM, interact in vivo.
Draft genome sequence of Xanthomonas fragariaereveals reductive evolution and distinct virulence-related gene content
Authors: Vandroemme Joachim , Cottyn Bart , Baeyen Steve , De Vos Paul , Maes Martine
Published: November 2013

Background

Xanthomonas fragariae (Xf) is a bacterial strawberry pathogen and an A2 quarantine organism on strawberry planting stock in the EU. It is taxonomically and metabolically distinct within the genus Xanthomonas, and known for its host specificity. As part of a broader pathogenicity study, the genome of a Belgian, virulent Xf strain (LMG 25863) was assembled to draft status and examined for its pathogenicity related gene content.

Results

The Xf draft genome (4.2 Mb) was considerably smaller than most known Xanthomonas genomes (~5 Mb). Only half of the genes coding for TonB-dependent transporters and cell-wall degrading enzymes that are typically present in other Xanthomonas genomes, were found in Xf. Other missing genes/regions with a possible impact on its plant-host interaction were: i) the three loci for xylan degradation and metabolism, ii) a locus coding for a ß-ketoadipate phenolics catabolism pathway, iii) xcs, one of two Type II Secretion System coding regions in Xanthomonas, and iv) the genes coding for the glyoxylate shunt pathway. Conversely, the Xf genome revealed a high content of externally derived DNA and several uncommon, possibly virulence-related features: a Type VI Secretion System, a second Type IV Secretion System and a distinct Type III Secretion System effector repertoire comprised of multiple rare effectors and several putative new ones.

Conclusions

The draft genome sequence of LMG 25863 confirms the distinct phylogenetic position of Xf within the genus Xanthomonas and reveals a patchwork of both lost and newly acquired genomic features. These features may help explain the specific, mostly endophytic association of Xf with the strawberry plant.
Biochemical and functional characterization of SpdA, a 2′, 3′cyclic nucleotide phosphodiesterase from Sinorhizobium meliloti
Authors: Mathieu-Demazière Céline , Poinsot Véréna , Masson-Boivin Catherine , Garnerone Anne-Marie , Batut Jacques
Published: November 2013

Background

3′, 5′cAMP signaling in Sinorhizobium meliloti was recently shown to contribute to the autoregulation of legume infection. In planta, three adenylate cyclases CyaD1, CyaD2 and CyaK, synthesizing 3′, 5′cAMP, together with the Crp-like transcriptional regulator Clr and smc02178, a gene of unknown function, are involved in controlling plant infection.

Results

Here we report on the characterization of a gene (smc02179, spdA) at the cyaD1 locus that we predicted to encode a class III cytoplasmic phosphodiesterase.

First, we have shown that spdA had a similar pattern of expression as smc02178 in planta but did not require clr nor 3′, 5′cAMP for expression.

Second, biochemical characterization of the purified SpdA protein showed that, contrary to expectation, it had no detectable activity against 3′, 5′cAMP and, instead, high activity against the positional isomers 2′, 3′cAMP and 2′, 3′cGMP.

Third, we provide direct experimental evidence that the purified Clr protein was able to bind both 2′, 3′cAMP and 3′, 5′cAMP in vitro at high concentration. We further showed that Clr is a 3′, 5′cAMP-dependent DNA-binding protein and identified a DNA-binding motif to which Clr binds. In contrast, 2′, 3′cAMP was unable to promote Clr specific-binding to DNA and activate smc02178 target gene expression ex planta.

Fourth, we have shown a negative impact of exogenous 2′, 3′cAMP on 3′, 5′cAMP-mediated signaling in vivo. A spdA null mutant was also partially affected in 3′, 5′cAMP signaling.

Conclusions

SpdA is a nodule-expressed 2′, 3′ specific phosphodiesterase whose biological function remains elusive. Circumstantial evidence suggests that SpdA may contribute insulating 3′, 5′cAMP-based signaling from 2′, 3′ cyclic nucleotides of metabolic origin.
Characterization and co-expression analysis of WRKY orthologs involved in responses to multiple abiotic stresses in Pak-choi (Brassica campestris ssp. chinensis)
Authors: Tang Jun , Wang Feng , Wang Zhen , Huang Zhinan , Xiong Aisheng , Hou Xilin
Published: November 2013

Background

The WRKY transcription factor is an important member of the stress-related transcription factors, which mediate diverse abiotic stresses in many plants. However, up until now, the number of WRKY members, and the regulatory mechanisms involved in abiotic stress responses in Pak-choi (Brassica campestris ssp. chinensis), remained unknown.

Results

We isolated and identified 56 full-length WRKY cDNAs from a Pak-choi stress-induced cDNA library. The 56 putative BcWRKY proteins were divided into three groups based on structural and phylogenetic analyses. A subcellular localization prediction indicated that the putative BcWRKY proteins were enriched in the nuclear region. Experiments involving BcWRKY25 and BcWRKY40 confirmed the prediction. A total of 22 BcWRKYs were differentially expressed in response to at least one stress condition (abscisic acid, cold, salinity, heat, or osmosis) tested on Pak-choi leaves, and a co-expression analysis indicated stress-inducible BcWRKYs co-regulated multiple abiotic stresses. BcWRKY33, BcWRKY40, BcWRKY53, and BcWRKY70 acted as key regulators and played dominant roles within co-regulatory networks of stress-inducible BcWRKYs.

Conclusions

We first isolated and characterized the 56 stress-inducible WRKY transcription factor family members. A total of 22 stress-inducible BcWRKYs found in leaves can co-regulate multiple environmental stresses by integrating the potential mutual interactions of WRKYs in Pak-choi. This information will be valuable when exploring the molecular mechanisms of WRKYs in response to abiotic stresses in plants.
Phenotypic, immunologic, and clinical characteristics of patients with nontuberculous mycobacterial lung disease in Korea
Authors: Lee Ae-Ra , Lee Jinwoo , Choi Sun-Mi , Seong Moon-Woo , Kim Sung A , Kim Myoungsil , Chae Kyung Ok , Lee Ji Sun , Yim Jae-Joon
Published: November 2013

Background

This study aimed to elucidate the phenotypic, immunologic, and clinical characteristics of Korean patients with nontuberculous mycobacterial (NTM) lung disease and compare them with non-NTM bronchiectasis (BE) patients.

Methods

We prospectively recruited patients between 20 and 80 years of age who had nodular BE type NTM lung disease. Phenotypic, immunologic, and clinical characteristics were evaluated through physical examination, laboratory tests, pulmonary function tests, and radiographic examinations. Questionnaires were also answered. The results of the evaluations were compared with the results of non-NTM BE patients.

Results

A total of 84 patients with NTM lung disease and 47 non-NTM BE patients participated in the study. Mycobacterium avium complex lung disease and M. abscessus lung disease were most common. Patients with NTM lung disease had lower body mass index than non-NTM BE patients. Scoliosis was observed more frequently in patients with NTM lung disease than in non-NTM BE patients.

Conclusions

Significant similarities were seen between Korean patients with NTM lung disease and patients from other countries. Differences in phenotypic and clinical characteristics between NTM lung disease and non-NTM BE patients suggest differences in the immunopathogenesis of NTM lung disease and non-NTM BE.

Trial registration information

ClinicalTrials.gov Registration number; NCT01616745
Pharmacoeconomic evaluation of voriconazole vs. liposomal amphotericin B in empiric treatment of invasive fungal infections in Turkey
Authors: Turner Stuart J , Senol Esin , Kara Ates , Al-Badriyeh Daoud , Dinleyici Ener C , Kong David CM
Published: November 2013

Background

Invasive fungal infections (IFI) are associated with considerable expense and mortality on healthcare systems. There is a need to provide evidence of both clinical efficacy and value for money with any health technology. The current pharmacoeconomic evaluation investigated the use of liposomal amphotericin B (LAmB) and voriconazole for the empiric treatment of IFI in the Turkish setting.

Methods

Decision analytic modelling was used to create a pathway for patient treatment with a 5-point composite outcome measure. The data was obtained from a major non-inferiority multicentre randomised controlled study, with an expert panel of clinicians in Turkey providing transition probabilities and cost not available in the literature. Sensitivity analyses were performed on the inputs from the clinical trial and the expert panel.

Results

As per the base case analysis, voriconazole was preferred by Turkish Lira (TL) 2,523 per patient treated and TL2,520 per surviving patient. LAmB was the preferred alternative by TL5,362 per successfully treated patient. Removing fever resolution as part of the composite outcome measure resulted in voriconazole being the preferred alternative per successfully treated patient. Univariate sensitivity analysis highlighted that increasing the duration of voriconazole by >1.2 days or decreasing LAmB by >1.0 days changes the result. Monte Carlo Simulation resulted in 69.4% of simulations favouring voriconazole per patient treated.

Conclusion

There is a strong likelihood that voriconazole is economically more favourable than LAmB in the empiric treatment of IFI in Turkey.
Copy number variations in endoglin locus: mapping of large deletions in Spanish families with hereditary hemorrhagic telangiectasia type 1
Authors: Fontalba Ana , Fernández-Luna Jose L , Zarrabeitia Roberto , Recio-Poveda Lucia , Albiñana Virginia , Ojeda-Fernández Maria L , Bernabéu Carmelo , Alcaraz Luis A , Botella Luisa M
Published: November 2013

Background

The hereditary hemorrhagic telangiectasia syndrome (HHT), also known as the Rendu–Osler-Weber syndrome is a multiorganic vascular disorder inherited as an autosomal dominant trait. Diagnostic clinical criteria include: epistaxis, telangiectases in mucocutaneous and gastrointestinal sites, arteriovenous malformations (AVMs) most commonly found in pulmonary, hepatic and cerebral circulations, and familial inheritance. HHT is transmitted in 90% of the cases as an autosomal dominant condition due to mutations in either endoglin (ENG), or activin receptor-like kinase 1 (ACVRL1/ALK1) genes (HHT type 1 and 2, respectively).

Methods

We have carried out a genetic analysis of four independent Spanish families with HHT clinical criteria, which has permitted the identification of new large deletions in ENG. These mutations were first detected using the MLPA technique and subsequently, the deletion breakpoints were mapped using a customized copy number variation (CNV) microarray. The array was designed to cover the ENG gene and surrounding areas.

Results

All tested families carried large deletions ranging from 3-kb to 100-kb, involving the ENG gene promoter, several ENG exons, and the two downstream genes FGSH and CDK9. Interestingly, common breakpoints coincident with Alu repetitive sequences were found among these families.

Conclusions

The systematic hybridization of DNA from HHT families, with deletions or duplications, to custom designed microarrays, could allow the mapping of breakpoints, coincident with repetitive Alu sequences that might act as “hot spots” in the development of chromosomal anomalies.
Association study of gene polymorphisms and depression with abnormal humor in traditional Uighur medicine
Authors: Yusup Abdiryim , Upur Hanzohra , Abla Ayimgul , Upur Halmurat
Published: November 2013

Background

According to the humor theory of Traditional Uighur Medicine (TUM), a same disease is classified into different abnormal humor types and corresponding methods are applied to treat the diseases according to the type of abnormal humor characteristics. To date the biological foundation of classification of diseases by humor theory has been little studied and the mechanism of action is still unclear. In the present study, we aimed to investigate the association between some related gene polymorphisms and depression with abnormal humor in TUM.

Methods

201 cases of depression patients in a Uighur population were divided into two groups as: 107 cases of depression patients with abnormal black bile (ABB), 94 cases of depression patients with none abnormal black bile (nABB), and 50 healthy people were served as control group. Venous blood was used to isolate DNA samples, and the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique was used for genotyping of single nucleotide polymorphisms (SNPs). Polymorphisms in the serotonin 2A (5-HT2A) receptor gene, brain derived neurotrophic factor (BDNF), serotonin 1A (5-HT1A) receptor gene were investigated in each groups, respectively.

Results

The 5-HT2A A-1438G, 5-HT2A T102C, BDNF Val66Met, and 5-HT1A C-1019G gene polymorphisms showed significant association with ABB. However, no difference between nABB and controls was found for those genotype distribution and allele frequency. Moreover, the T102C and A1438G SNPs in the 5-HT2A receptor gene polymorphisms were in linkage disequilibrium. In addition, the OR associated with the combination of Val66Met-Val/Val genotype plus the presence of -1019C allele was 8.393 for ABB compared with controls (OR 8.393; 95% CI 1.807 ~ 38.991; P= 0.003). Moreover, the OR associated with the presence of -Met plus -1019C alleles was 12.194 for ABB compared with controls (OR 12.194; 95% CI 1.433 ~ 103.776; P= 0.005). The OR associated with the presence of -1438C/C plus Val/Val genotypes was 7.738 for ABB compared with controls (OR 7.738; 95% CI 1.566 ~ 38.241; P= 0.005).

Conclusion

It was concluded that there were significant relationship between the gene polymorphisms and classification of depression with abnormal humor in TUM. The 5-HT2A A-1438G, 5-HT2A T102C, BDNF Val66Met, and 5-HT1A C-1019G gene polymorphisms might predict the incidence of depression with ABB.
Obtaining subjects’ consent to publish identifying personal information: current practices and identifying potential issues
Authors: Yoshida Akiko , Dowa Yuri , Murakami Hiromi , Kosugi Shinji
Published: November 2013

Background

In studies publishing identifying personal information, obtaining consent is regarded as necessary, as it is impossible to ensure complete anonymity. However, current journal practices around specific points to consider when obtaining consent, the contents of consent forms and how consent forms are managed have not yet been fully examined. This study was conducted to identify potential issues surrounding consent to publish identifying personal information.

Methods

Content analysis was carried out on instructions for authors and consent forms developed by academic journals in four fields (as classified by Journal Citation Reports): medicine general and internal, genetics and heredity, pediatrics, and psychiatry. An online questionnaire survey of editors working for journals that require the submission of consent forms was also conducted.

Results

Instructions for authors were reviewed for 491 academic journals (132 for medicine general and internal, 147 for genetics and heredity, 100 for pediatrics, and 112 for psychiatry). Approximately 40% (203: 74 for medicine general and internal, 31 for genetics and heredity, 58 for pediatrics, and 40 for psychiatry) stated that subject consent was necessary. The submission of consent forms was required by 30% (154) of the journals studied, and 10% (50) provided their own consent forms for authors to use. Two journals mentioned that the possible effects of publication on subjects should be considered. Many journal consent forms mentioned the difficulties in ensuring complete anonymity of subjects, but few addressed the study objective, the subjects’ right to refuse consent and the withdrawal of consent. The main reason for requiring the submission of consent forms was to confirm that consent had been obtained.

Conclusion

Approximately 40% of journals required subject consent to be obtained. However, differences were observed depending on the fields. Specific considerations were not always documented. There is a need to address issues around the study objective, subjects’ right to refuse consent and the withdrawal of consent. Whether responsibility for ensuring that the consent form has been signed lies with publishers also needs to be discussed.
The effect of high fiber snacks on digestive function and diet quality in a sample of school-age children
Authors: Brauchla Mary , McCabe George P , Miller Kevin B , Kranz Sibylle
Published: November 2013

Background

Dietary fiber (DF) intake in American children is suboptimal, increasing the risk of GI distress and contributing to poor diet quality. The objective of this study was to determine the effect of introducing two high-fiber snacks per day on gastrointestinal function as well as nutrient and food group intake in healthy children ages 7–11 years old.

Methods

This study was a randomized controlled prospective intervention study of children 7–11 years of age (n = 81) attending a rural Midwestern elementary school. Children were randomized by classroom to consume two high-fiber snacks per day (total of 10-12 g DF) or their usual snacks for 8 weeks. Participants completed two 24-hour dietary recalls and a questionnaire about their GI health at baseline, mid-intervention (week 4), and post-intervention. Dietary data was entered into NDSR 2011 and t-tests utilized to assess changes. Analyses were completed in SAS 9.2.

Results

Children consumed at least half their snack 94% of the time when a snack was chosen (89% of time). Participants in both the intervention and control group had healthy scores on the GI health questionnaire at all time points. The intervention group increased DF (P = 0.0138) and whole grain (WG) intake (P = 0.0010) at mid-intervention but after the intervention returned to their baseline DF intake (P = 0.2205) and decreased their WG intake (P = 0.0420) compared to baseline. Eating high-fiber snacks increased DF intake by 2.5 g per day (21% increase), suggesting displacement of other fiber-rich foods.

Conclusions

Study results indicate that children accept high-fiber foods, thus making these high-fiber foods and snacks consistently available will increase DF intake.
Human tumor necrosis factor (TNF)-alpha-induced protein 8-like 2 suppresses hepatocellular carcinoma metastasis through inhibiting Rac1
Authors: Cao Xuelei , Zhang Li , Shi Yongyu , Sun Yue , Dai Shen , Guo Chun , Zhu Faliang , wang Qun , Wang Jianing , Wang Xiaoyan , Chen Youhai H , Zhang Lining
Published: November 2013

Background

Tumor invasion and metastasis are the major reasons for leading death of patients with hepatocellular carcinoma (HCC). Therefore, to identify molecules that can suppress invasion and metastasis of tumor will provide novel targets for HCC therapies. Tumor necrosis factor (TNF)-alpha-induced protein 8-like 2, TIPE2, is a novel immune negative molecule and an inhibitor of the oncogenic Ras in mice but its function in human is unclear. Our previous research has shown that TIPE2 is downregulated in human primary HCC compared with the paired adjacent non-tumor tissues.

Results

In present study, we provide evidence that TIPE2 inhibits effectively human hepatocellular carcinoma metastasis. The forced expression of TIPE2 in HCC-derived cell lines markedly inhibits tumor cell growth, migration and invasion in vitro and suppresses growth and metastasis of HCC in vivo. Clinical information from a cohort of 112 patients reveals that loss or reduced expression of TIPE2 in primary HCC tissues is significantly associated with tumor metastasis. Mechanically, TIPE2 inhibits the migration and invasion through targeting Rac1 and then reduces F-actin polymerization and expression of matrix metallopeptidase 9 (MMP9) and urokinase plasminogen activator (uPA).

Conclusion

Our results indicate that human TIPE2 is endogenous inhibitor of Rac1 in HCC by which it attenuates invasion and metastasis of HCC. The data suggest that TIPE2 will be a new target for HCC therapy.