bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogeography of red deer (Cervus elaphus) in Europe
Authors: Skog A. , Zachos F. E. , Rueness E. K. , Feulner P. G. D. , Mysterud A. , Langvatn R. , Lorenzini R. , Hmwe S. S. , Lehoczky I. , Hartl G. B. , Stenseth N. C. , Jakobsen K. S. 
Published: September 2008

AbstractAim  To investigate the phylogeographical patterns of red deer (Cervus elaphus) in Europe, and to disentangle the influence of ancient (e.g. Pleistocene ice ages) from more recent processes (e.g. human translocations).Location  Europe.Methods  In this study we provide by far the most extensive analysis of genetic structure in European red deer, based on analyses of variation at two mitochondrial markers (cyt b and D‐loop) in a large number of individuals from 39 locations. Relationships of mitochondrial DNA haplotypes were determined using minimum spanning networks and phylogenetic analyses. Population structure was examined by analyses of molecular variance. Historical processes shaping the present patterns were inferred from nested clade analysis and nucleotide diversity statistics.Results  Within Europe, we detected three deeply divergent mitochondrial DNA lineages. The three lineages displayed a phylogeographical pattern dividing individuals into western European, eastern European and Mediterranean (Sardinia, Spain and Africa) groups, suggesting contraction into three separate refugia during the last glaciation. Few haplotypes were shared among these three groups, a finding also confirmed by FST values. Calculations of divergence times suggest that the groups probably split during the Pleistocene.Main conclusions  The observed pattern is interpreted to result from isolation in different refugia during the last glaciation. The western and eastern European lineages could be linked to an Iberian and Balkan refugium, respectively. The third lineage might originate from a Sardinian or African refugium. We link local phylogeographical patterns observed in Europe to the post‐glacial recolonization process, shaped by the geographical localization of refugia and barriers to gene flow. Regardless of the importance of red deer as a game species and the tradition of translocating red deer in Europe, we detected few individuals that did not match the trichotomous pattern, suggesting that translocations have occurred mainly at smaller spatial scales.
The application of Bayesian spectral analysis to optical sectioning using structured light imaging
Authors: Ó RUANAIDH J.J.K. , MCKAY R.R. , ZHANG Y. , BRIGGS M. , GEORGE J. , MASOUMI Z. 
Published: September 2008

SummaryWe describe significant improvements to a well‐established method of obtaining optical sectioning in a conventional wide‐field microscope. This method relies on the projection of a single‐frequency grid pattern onto an object followed by mathematical manipulation of three images taken with the grid in different phases. Here, we present the use of Bayesian Spectral Analysis to determine accurate estimates of the phase of the grid pattern, permitting rapid and precise calibration of grid location. In common with previous algorithms, multiple images are combined to produce both an optical section and a wide‐field image. We describe innovations such as the use of non‐uniform phase or least‐squares solutions involving more than three images, in conjunction with direct phase estimates obtained using Bayesian Spectral Analysis, to yield images substantially free of artefacts. Auxiliary results, such as a method for determining the tilt of the grid, are also presented.
The fractional Talbot effect in differential x‐ray phase‐contrast imaging for extended and polychromatic x‐ray sources
Authors: ENGELHARDT M. , KOTTLER C. , BUNK O. , DAVID C. , SCHROER C. , BAUMANN J. , SCHUSTER M. , PFEIFFER F. 
Published: September 2008

SummaryThe influence of different physical parameters, such as the source size and the energy spectrum, on the functional capability of a grating interferometer applied for phase‐contrast imaging is discussed using numerical simulations based on Fresnel diffraction theory. The presented simulation results explain why the interferometer could be well combined with polychromatic laboratory x‐ray sources in recent experiments. Furthermore, it is shown that the distance between the two gratings of the interferometer is not in general limited by the width of the photon energy spectrum. This implies that interferometers that give a further improved image quality for phase measurements can be designed, because the primary measurement signal for phase measurements can be increased by enlargement of this distance. Finally, the mathematical background and practical instructions for the quantitative evaluation of measurement data acquired with a polychromatic x‐ray source are given.
Differentiation of live‐viable versus dead bacterial endospores by calibrated hyperspectral reflectance microscopy
Authors: ANDERSON J. , REYNOLDS C. , RINGELBERG D. , EDWARDS J. , FOLEY K. 
Published: September 2008

SummaryThis paper describes the use of hyperspectral imaging microscopy (HIM) for the characterization and differentiation of live viable versus dead/non‐viable bacterial endospores for two species of Bacillus. To accomplish this, endospore‐forming Bacillus were cultured and differentiated into endospores. Non‐viable endospores were produced using sporicidal methods representing standard decontamination procedures incorporating chlorine and peroxide. Finally, endospore samples were lyophilized to prepare them for spectral analysis. Prior to HIM, baseline spectral reflectance characterizing the endospores was measured using an ASD (400–900 nm) reflectance spectrometer. These data were used to calibrate the resulting spectral image data. HIM data comprising 32 images ranging from 400 to 720 nm (visible to near infrared) were recorded using a C‐mounted VariSpec hyperspectral camera attached to an epifluorescent microscope. The images produced by the system record the reflectance and absorption features of endospores based on the structure of the outer coat. Analysis of the HIM data was performed using accepted image and spectral processing routines. Where peroxide was the sporicide, changes in the outer endospore coat contributed to structurally significant visible and near infrared signature differences between live‐viable versus dead, non‐viable endospores. A statistical test for divergence, a method for scoring spectral structural diversity, also showed the difference between viable and non‐viable peroxide killed endospores to be statistically significant. These findings may lead to an improved optical procedure to rapidly identify viable and non‐viable endospores in situations of decontamination.
Contribution of electron precession to the study of perovskites displaying small symmetry departures from the ideal cubic ABO3 perovskite: applications to the LaGaO3 and LSGM perovskites
Authors: MORNIROLI J.‐P. , AUCHTERLONIE G. J. , DRENNAN J. , ZOU J. 
Published: September 2008

SummaryElectron microscopy and electron diffraction are well adapted to the study of the fine‐grained, faulted pure and doped LaGaO3 and LSGM perovskites in which the latter is useful for fuel cell components. Because these perovskites display small symmetry departures from an ideal cubic ABO3 perovskite, many conventional electron diffraction patterns look similar and cannot be indexed without ambiguity. Electron precession can easily overcome this difficulty mainly because the intensity of the diffracted beams on the precession patterns is integrated over a large deviation domain around the exact Bragg condition. This integrated intensity can be trusted and taken into account to identify the ‘ideal’ symmetry of the precession patterns (the symmetry which takes into account both the position and the intensity of the diffracted beams). In the present case of the LaGaO3 and LSGM perovskites, the determination of the ‘ideal’ symmetry of the precession patterns is based on the observation of weak ‘superlattice’ reflections typical of the symmetry departures. It allows an easy and sure identification of any zone axes as well as the correct attribution of hkl indices to each of the diffracted beams. Examples of applications of this analysis to the characterizations of twins and to the identification of the space groups are given. This contribution of electron precession can be easily extended to any other perovskites or to any crystals displaying small symmetry departures.
Characterization of precipitates size distribution: validation of low‐voltage STEM
Authors: ACEVEDO‐REYES D. , PEREZ M. , VERDU C. , BOGNER A. , EPICIER T. 
Published: September 2008

SummaryThe size distribution of second phase precipitates is frequently determined using conventional transmission electron microscopy (CTEM). However, other techniques, which present different advantages, can also be used for this purpose. In this paper, we focus on high angle annular dark field (HAADF) in TEM and scanning TEM (STEM) in scanning electron microscopy (SEM) imaging modes. The mentioned techniques will be first described, then compared to more conventional ones for the measurement of carbides size distribution in two FeCV and FeCVNb model alloys. This comparative study shows that STEM in SEM, a technique much easier to undertake compared to TEM, is perfectly adapted for size distribution measurements of second phase particles, with sizes ranging between 5 and 200 nm in these systems.
Electron tomography of regularly shaped nanostructures under non‐linear image acquisition
Authors: SAGHI Z. , XU X. , MÖBUS G. 
Published: September 2008

SummaryElectron tomography allows the 3D quantitative characterization of nanostructures, provided a monotonic relationship is fulfilled between the projected signal and the atomic number and thickness of the specimen. This requirement is not satisfied if the micrographs are affected by (i) diffraction contrast, (ii) detector saturation or (iii) contrast inversion due to absorption (high‐angle scattering) at high thickness. Artefacts related to the non‐monotonic tomography acquisition are examined using computer simulations and experimental tilt series of tungsten tips and CeO2 nanoparticles. Conditions are derived under which in spite of the non‐linear artefacts the information is sufficient for reconstructing the 3D morphology of convex objects by geometric tomography.
A shifty stop for a hairy tail
Authors: Olia Adam S. , Cingolani Gino 
Published: September 2008

SummaryThe tail apparatus of the bacteriophage SPP1 is an extraordinary ∼1600‐Å‐long molecular machine. The tail mediates attachment of the virus to the host surface receptor, as well‐as ejection of the viral genome into the host. The distal tip of the tail binds the extracellular ectodomain of the Bacillus subtilis receptor YueB, while the tail tube provides a conduit to funnel the viral genome into the host. This process, which culminates with the ejection of the ∼44 kb of viral DNA across the thick, cell envelope of the Gram‐positive bacterial cell, takes place in a time scale of seconds to minutes and represents a remarkable example of biotransformation. In this issue of Molecular Microbiology, Auzat et al. provide compelling evidence that the two major structural proteins of the SPP1 tail, gp17.1 (∼19.1 kDa) and gp17.1* (∼28 kDa), share a common N‐terminal sequence, and that gp17.1* is generated by a translational frameshift in the gene 17.1. The extra domain fused to gp17.1* is synthesized by a +1 programmed translational frameshift at the end of gene 17.1, which leads to the synthesis of approximately one gp17.1* for every three equivalents of gp17.1. This finding extends our current knowledge of translational frameshifts and provides a framework to understand how Siphoviridae phages like SPP1 have developed long‐tail machines using only two major structural proteins.
Intrinsic properties of the two replicative DNA polymerases of Pyrococcus abyssi in replicating abasic sites: possible role in DNA damage tolerance?
Authors: Palud Adeline , Villani Giuseppe , L'Haridon Stéphane , Querellou Joël , Raffin Jean‐Paul , Henneke Ghislaine 
Published: September 2008

SummarySpontaneous and induced abasic sites in hyperthermophiles DNA have long been suspected to occur at high frequency. Here, Pyrococcus abyssi was used as an attractive model to analyse the impact of such lesions onto the maintenance of genome integrity. We demonstrated that endogenous AP sites persist at a slightly higher level in P. abyssi genome compared with Escherichia coli. Then, the two replicative DNA polymerases, PabpolB and PabpolD, were characterized in presence of DNA containing abasic sites. Both Pabpols had abortive DNA synthesis upon encountering AP sites. Under running start conditions, PabpolB could incorporate in front of the damage and even replicate to the full‐length oligonucleotides containing a specific AP site, but only when present at a molar excess. Conversely, bypassing activity of PabpolD was strictly inhibited. The tight regulation of nucleotide incorporation opposite the AP site was assigned to the efficiency of the proof‐reading function, because exonuclease‐deficient enzymes exhibited effective TLS. Steady‐state kinetics reinforced that Pabpols are high‐fidelity DNA polymerases onto undamaged DNA. Moreover, Pabpols preferentially inserted dAMP opposite an AP site, albeit inefficiently. While the template sequence of the oligonucleotides did not influence the nucleotide insertion, the DNA topology could impact on the progression of Pabpols. Our results are interpreted in terms of DNA damage tolerance.
A case of simultaneously occurring lichen sclerosus and segmental vitiligo: connecting the underlying autoimmune pathogenesis
Authors: Weisberg Eric L. , Le Lu Q. , Cohen Jack B. 
Published: September 2008

A 41‐year‐old African‐American woman reported a 6‐month history of asymptomatic white macules and patches that started on her left foot, and then spread proximally up her leg to her thigh, and then to her buttocks. She also noted that several of her pubic hairs had turned white, but only on the left side of the midline. She also complained of concomitant severe burning and itching in the vaginal area and that her vaginal skin had turned whitish pink. The patient denied contact with industrial or hazardous chemicals, and her medical history included childhood iron deficiency anemia only. On examination, the patient had linear guttate hypo‐ and depigmented macules on the left dorsal foot, extending up the medial calf, the medial and posterior thigh, and coalescing into scalloped patches across her left medial buttock (Fig. 1). There was sharp midline demarcation in the suprapubic region. Her pubic hairs on the left side were predominantly depigmented. Examination of the genital area revealed areas of atrophy, together with slightly hyperkeratotic pink and hypopigmented plaques covering the entire perineal area, with a slightly irregular rim of gray–brown hyperpigmentation almost encircling the introitus. The lichen sclerosus of the labia minora extended directly into the perianal region (Fig. 2). The vulvar area was tender to the touch.Hypo‐ and depigmented macules and patches on the medial left calf, thigh, and pubic areaimageDepigmented pubic hair on the left side and pink–white sclerotic plaques in the perineal areaimage A punch biopsy specimen taken from the perineum adjacent to the introitus showed a lichenoid infiltrate and papillary dermal sclerosis that was compatible with lichen sclerosus (Fig. 3). A Fontana–Masson stain showed complete absence of melanin in the epidermis, but melanophages were found in the dermis and in the lichenoid inflammatory infiltrate (Fig. 4). Melanin was also absent from the follicular epithelium of a hair follicle, but was present in the hair shaft of that follicle. Based on the clinical presentation and histology, a diagnosis was made of segmental vitiligo of the left lower extremity with overlapping lichen sclerosus in the perineal region.Histology shows hyperkeratosis, epidermal atrophy, and a lichenoid infiltrate with papillary dermal sclerosis (hematoxylin and eosin stain, ×4)imageComplete absence of melanocytes demonstrated in the epidermis (Fontana–Masson stain, ×10)image On two follow‐up evaluations spanning 6 weeks after a treatment regimen of clobetasol ointment 0.05% twice daily to all affected areas had been initiated, some repigmentation of the left lower leg was observed. There was markedly less erythema and the symptoms in the genital area had resolved, although slight scale remained in the vulvar plaques.
Goeckerman's therapy for psoriasis with special reference to serum pentraxin 3 level
Authors: Ctirad Andrys , Lenka Borska , David Pohl , Zdenek Fiala , Kveta Hamakova , Karel Ettler , Jan Krejsek 
Published: September 2008

AbstractBackground  Goeckerman's therapy (GT) of psoriasis is based on daily application of pharmacy grade coal tar on affected skin with subsequent exposure to UV light. Pentraxin 3 (PTX3) is a newly identified acute phase reactant with non redundant functions in innate immunity. PTX3 has been shown to be a reliable prognostic marker in patients with various inflammatory disorders including rheumatoid arthritis, vasculitis, and psoriasis.Methods  The aim of this study was to evaluate the influence of Goeckerman's therapy of psoriasis on levels of two pentraxins: long pentraxin PTX3 and C reactive protein in 49 patients with chronic plaque psoriasis. CRP was assessed by immunonephelometry on IMMAGE 800 (Beckman, USA). PTX3 was detected using sandwich ELISA detection set (Alexis Biochemicals, Switzerland).Results  The serum levels of both parameters (expressed as average ± 1 SD) were significantly diminished after GT. The level of PTX3 dropped from 1.92 ± 0.72 ng/ml before GT to 1.66 ± 0.58 ng/ml after GT (P= 0.0396) and the level of CRP fell from 4.64 ± 3.93 mg/l to 1.66 ± 0.58 mg/l (P < 0.0001).Comparing to healthy controls, the serum levels of both parameters before GT were significantly higher than those found in healthy blood donors and remained significantly increased after GT.Conclusion  Increased serum concentrations of pentraxin 3 and CRP are alleviated by GT in patients with psoriasis.
Necrolytic acral erythema: successful treatment with topical tacrolimus ointment
Authors: Manzur Amir , Siddiqui Abdul Hameed 
Published: September 2008

AbstractNecrolytic acral erythema is a relatively recently described psoriasis‐like skin eruption seen in people infected with hepatitis C virus. Hepatitis C virus infection is endemic in many parts of the world with a steady increase of incidence in Pakistan. Recognition of this disorder is crucial to an early treatment of the underlying liver disease. Herein, we report the first case of necrolytic acral erythema from Asia and also describe good therapeutic response to topical tacrolimus ointment.
Pityriasis rubra pilaris exacerbation with topical use of imiquimod
Authors: Yang F. Clarissa , Jessup Chad , Dahiya Madhu , Reynolds Rachel 
Published: September 2008

AbstractThe role of immune response modifiers is increasing in the treatment of dermatologic diseases. Imiquimod, a toll‐like receptor agonist, results in up‐regulation of proinflammatory cytokines for improved immune surveillance. Although topical use is generally well‐tolerated, imiquimod can potentially result in systemic effects and exacerbate generalized inflammatory papulosquamous diseases of the skin. We report the case of a 67‐year‐old man who was treated with imiquimod for actinic keratosis and developed fever and a progressive erythematous papulosquamous eruption that was histologically consistent with pityriasis rubra pilaris.
Etiology and management of axillary bromidrosis: a brief review
Authors: Mao Guang‐Yu , Yang Song‐Lin , Zheng Jiang‐Hong 
Published: September 2008

AbstractBackground  Axillary bromidrosis is a distressing condition that poses significant social embarrassment in almost all the countries over the world. However, its definite etiology has not been generalized yet. There have been a lot of treatments for bromidrosis, which can be roughly divided into two types: conservative management and radical surgical therapy. In order to summarize the possible causes of axillary bromidrosis, a brief review of the literatures regarding bromidrosis was performed.Methods  An English literature search from 1975 to June 2007 was completed with references to treatments for bromidrosis. A total of 29 papers about the treatment were selected to review. After a close reading, all the extracted information was imported into Microsoft Excel.Results  Many therapies were carried out to treat bromidrosis, including nonoperative and operative ones. Almost all the authors thought that the nonoperative management, such as topical antiperspirants, systemic agents, and iontophoresis, did not have a permanent effect. Most surgeons (90%) chose surgical methods to remove axillary sweat glands for bromidrosis and 90.69% of the axillae had good results.Conclusion  Axillary sweat glands may play the most important role in the etiology of bromidrosis. In addition, axillary microorganism, hormone, and inherent also contribute to bromidrosis.
A comparison between BSA, PASI, PLASI and SAPASI as measures of disease severity and improvement by therapy in patients with psoriasis
Authors: Henseler Tilo , Schmitt‐Rau Karlheinz 
Published: September 2008

AbstractBackground  This study investigates four measures of disease severity in patients with psoriasis, both before and after therapy.Methods  Data records were analyzed from 33 patients with moderate‐to‐severe chronic plaque psoriasis who were treated with efalizumab, 1 mg/kg/week subcutaneously, for 12 weeks. Four measures of disease severity were used: body surface area (BSA), psoriasis area and severity index (PASI), psoriasis log‐based area and severity index (PLASI) and self‐administered PASI (SAPASI).Results  At the end of the 12‐week therapy, the mean percent improvement shown by each measure varied considerably, ranging from 48.6% (PASI) to 70.6% (SAPASI). PASI and PLASI were the most comparable (67.3% and 66.5%). These differences were smaller when a dermatologist's opinion about the improvement was taken into account, for example “very good improvement” ranged from mean percent improvement of 63.8% (BSA) to 83.8% (PASI). The correlation between all measures revealed a high level of significance (P≤ 10−5).Conclusions  Comparing the slopes and intercepts of the regression lines revealed PLASI as the most reliable measure for the severity and therapeutic improvement in patients with moderate‐to‐severe chronic plaque psoriasis. PLASI proved to be a marginally more accurate than PASI, and much more accurate than SAPASI and BSA. The superiority of PLASI may be a result of the logarithmic scale of the affected skin surface.