bluuebunny/crossref_metadata_2025 huggingface dataset:
The cytoskeletal mechanisms of cell–cell junction formation in endothelial cells
Authors: Hoelzle Matthew K. , Svitkina Tatyana
Published: November 2011

The actin cytoskeleton and associated proteins play a vital role in cell–cell adhesion. However, the procedure by which cells establish adherens junctions remains unclear. We investigated the dynamics of cell–cell junction formation and the corresponding architecture of the underlying cytoskeleton in cultured human umbilical vein endothelial cells. We show that the initial interaction between cells is mediated by protruding lamellipodia. On their retraction, cells maintain contact through thin bridges formed by filopodia-like protrusions connected by VE-cadherin–rich junctions. Bridges share multiple features with conventional filopodia, such as an internal actin bundle associated with fascin along the length and vasodilator-stimulated phosphoprotein at the tip. It is striking that, unlike conventional filopodia, transformation of actin organization from the lamellipodial network to filopodial bundle during bridge formation occurs in a proximal-to-distal direction and is accompanied by recruitment of fascin in the same direction. Subsequently, bridge bundles recruit nonmuscle myosin II and mature into stress fibers. Myosin II activity is important for bridge formation and accumulation of VE-cadherin in nascent adherens junctions. Our data reveal a mechanism of cell–cell junction formation in endothelial cells using lamellipodia as the initial protrusive contact, subsequently transforming into filopodia-like bridges connected through adherens junctions. Moreover, a novel lamellipodia-to-filopodia transition is used in this context.
Time-course network analysis reveals TNF-α can promote G1/S transition of cell cycle in vascular endothelial cells
Authors: Chen Yang , Gu Jin , Li Dan , Li Shao
Published: November 2011

Motivation: Tumor necrosis factor-alpha (TNF-α), a major inflammatory cytokine, is closely related to several cardiovascular pathological processes. However, its effects on the cell cycle of vascular endothelial cells (VECs) have been the subject of some controversy. To investigate the molecular mechanism underlying this process, we constructed time-course protein–protein interaction (PPI) networks of TNF-α induced regulation of cell cycle in VECs using microarray datasets and genome-wide PPI datasets. Then, we analyzed the topological properties of the responsive PPI networks and calculated the node degree and node betweenness centralization of each gene in the networks. We found that p21, p27 and cyclinD1, key genes of the G1/S checkpoint, are in the center of responsive PPI networks and their roles in PPI networks are significantly altered with induction of TNF-α. According to the following biological experiments, we proved that TNF-α can promote G1/S transition of cell cycle in VECs and facilitate the cell cycle activation induced by vascular endothelial growth factor.

Contact:  shaoli@mail.tsinghua.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
Susceptibility of the male fitness phenotype to spontaneous mutation
Authors: Mallet Martin A. , Kimber Christopher M. , Chippindale Adam K.
Published: November 2011

Adult reproductive success can account for a large fraction of male fitness, however, we know relatively little about the susceptibility of reproductive traits to mutation-accumulation (MA). Estimates of the mutational rate of decline for adult fitness and its components are controversial in
Drosophila melanogaster
, and post-copulatory performance has not been examined. We therefore separately measured the consequences of MA for total male reproductive success and its major pre-copulatory and post-copulatory components: mating success and sperm competitive success. We also measured juvenile viability, an important fitness component that has been well studied in MA experiments. MA had strongly deleterious effects on both male viability and adult fitness, but the latter declined at a much greater rate. Mutational pressure on total fitness is thus much greater than would be predicted by viability alone. We also noted a significant and positive correlation between all adult traits and viability in the MA lines, suggesting pleiotropy of mutational effect as required by ‘good genes’ models of sexual selection.
A biomaterials approach to peripheral nerve regeneration: bridging the peripheral nerve gap and enhancing functional recovery
Authors: Daly W. , Yao L. , Zeugolis D. , Windebank A. , Pandit A.
Published: November 2011

Microsurgical techniques for the treatment of large peripheral nerve injuries (such as the gold standard autograft) and its main clinically approved alternative—hollow nerve guidance conduits (NGCs)—have a number of limitations that need to be addressed. NGCs, in particular, are limited to treating a relatively short nerve gap (4 cm in length) and are often associated with poor functional recovery. Recent advances in biomaterials and tissue engineering approaches are seeking to overcome the limitations associated with these treatment methods. This review critically discusses the advances in biomaterial-based NGCs, their limitations and where future improvements may be required. Recent developments include the incorporation of topographical guidance features and/or intraluminal structures, which attempt to guide Schwann cell (SC) migration and axonal regrowth towards their distal targets. The use of such strategies requires consideration of the size and distribution of these topographical features, as well as a suitable surface for cell–material interactions. Likewise, cellular and molecular-based therapies are being considered for the creation of a more conductive nerve microenvironment. For example, hurdles associated with the short half-lives and low stability of molecular therapies are being surmounted through the use of controlled delivery systems. Similarly, cells (SCs, stem cells and genetically modified cells) are being delivered with biomaterial matrices in attempts to control their dispersion and to facilitate their incorporation within the host regeneration process. Despite recent advances in peripheral nerve repair, there are a number of key factors that need to be considered in order for these new technologies to reach the clinic.
The awarding of the Copley Medal and the ‘discovery’ of the law of conservation of energy: Joule, Mayer and Helmholtz revisited
Authors: Cahan David
Published: November 2011

This article analyses the awarding of the Royal Society's Copley Medal to James Prescott Joule (1870), Julius Robert Mayer (1871) and Hermann Helmholtz (1873) in the wake of the establishment of the law of conservation of energy during the 1850s and 1860s. It seeks to reconstruct the context in which the awards occurred, emphasizing at once a combination of individual scientific achievement, advocacy on behalf of Joule's supporters, nationalism, and the special role that Helmholtz played thanks to the strong social relationship that he had developed with the British scientific elite in the two decades before receiving his award, the last of the three. The award in turn strengthened that relationship, as the great subject of discussion in physics now gradually turned from thermodynamics to electromagnetism and to reaching practical agreements in electrical metrology between the British, the Germans and others.
Recovery of inclusion separations in strongly heterogeneous composites from effective property measurements
Authors: Orum Chris , Cherkaev Elena , Golden Kenneth M.
Published: November 2011

An effective property of a composite material consisting of inclusions within a host matrix depends on the geometry and connectedness of the inclusions. This dependence may be quite strong if the constituents have highly contrasting properties. Here, we consider the inverse problem of using effective property data to obtain information on the geometry of the microstructure. While previous work has been devoted to recovering the volume fractions of the constituents, our focus is on their connectedness—a key feature in critical behaviour and phase transitions. We solve exactly a reduced inverse spectral problem by bounding the volume fraction of the constituents, an inclusion separation parameter and the spectral gap of a self-adjoint operator that depends on the geometry of the composite. We present a new algorithm based on the Möbius transformation structure of the forward bounds whose output is a set of algebraic curves in parameter space bounding regions of admissible parameter values. These results advance the development of techniques for characterizing the microstructure of composite materials. As an example, we obtain inverse bounds on the volume fraction and separation of the brine inclusions in sea ice from measurements of its effective complex permittivity.
Diversification of acorn worms (Hemichordata, Enteropneusta) revealed in the deep sea
Authors: Osborn Karen J. , Kuhnz Linda A. , Priede Imants G. , Urata Makoto , Gebruk Andrey V. , Holland Nicholas D.
Published: November 2011

Enteropneusts (phylum Hemichordata), although studied extensively because of their close relationship to chordates, have long been considered shallow-water, burrowing animals. The present paper more than doubles the number of enteropneust species recorded in the deep sea based on high-resolution imaging and sampling with remotely operated vehicles. We provide direct evidence that some enteropneusts are highly mobile—using changes in posture and currents to drift between feeding sites—and are prominent members of deep, epibenthic communities. In addition, we provide ecological information for each species. We also show that despite their great morphological diversity, most deep-living enteropneusts form a single clade (the rediagnosed family Torquaratoridae) on the basis of rDNA sequences and morphology of the proboscis skeleton and stomochord. The phylogenetic position of the torquaratorids indicates that the group, after evolving from near-shore ancestors, radiated extensively in the deep sea.
Non-breeding feather concentrations of testosterone, corticosterone and cortisol are associated with subsequent survival in wild house sparrows
Authors: Koren Lee , Nakagawa Shinichi , Burke Terry , Soma Kiran K. , Wynne-Edwards Katherine E. , Geffen Eli
Published: November 2011

Potential mechanistic mediators of Darwinian fitness, such as stress hormones or sex hormones, have been the focus of many studies. An inverse relationship between fitness and stress or sex hormone concentrations has been widely assumed, although empirical evidence is scarce. Feathers gradually accumulate hormones during their growth and provide a novel way to measure hormone concentrations integrated over time. Using liquid chromatography–tandem mass spectrometry, we measured testosterone, corticosterone and cortisol in the feathers of house sparrows (
Passer domesticus
) in a wild population which is the subject of a long-term study. Although corticosterone is considered the dominant avian glucocorticoid, we unambiguously identified cortisol in feathers. In addition, we found that feathers grown during the post-nuptial moult in autumn contained testosterone, corticosterone and cortisol levels that were significantly higher in birds that subsequently died over the following winter than in birds that survived. Thus, feather steroids are candidate prospective biomarkers to predict the future survival of individuals in the wild.
Infectious personalities: behavioural syndromes and disease risk in larval amphibians
Authors: Koprivnikar Janet , Gibson Chris H. , Redfern Julia C.
Published: November 2011

Behavioural consistency or predictability through time and/or different contexts (‘syndromes’ or ‘personality types’) is likely to have substantial influence on animal life histories and fitness. Consequently, there is much interest in the forces driving and maintaining various syndromes. Individual host behaviours have been associated with susceptibility to parasitism, yet the role of pre-existing personality types in acquiring infections has not been investigated experimentally. Using a larval amphibian–trematode parasite model system, we report that tadpoles generally showed consistency in their activity level in response to both novel food and parasite exposure. Not only were individual activity level and exploration in the novel food context correlated with each other and with anti-parasite behaviour, all three were significant predictors of host parasite load. This is the first empirical demonstration that host behaviours in other contexts are related to behaviours mitigating infection risk and, ultimately, host parasite load. We suggest that this system illustrates how reliably high levels of activity and exploratory behaviour in different contexts might maximize both energy acquisition and resistance to trematode parasites. Such benefits could drive selection for the behavioural syndrome seen here owing to the life histories and ecological circumstances typical of wood frog (Lithobates sylvaticus) larvae.
Infection of human alveolar macrophages by human coronavirus strain 229E
Authors: Funk C. Joel , Wang Jieru , Ito Yoko , Travanty Emily A. , Voelker Dennis R. , Holmes Kathryn V. , Mason Robert J.
Published: November 2011

Human coronavirus strain 229E (HCoV-229E) commonly causes upper respiratory tract infections. However, lower respiratory tract infections can occur in some individuals, indicating that cells in the distal lung are susceptible to HCoV-229E. This study determined the virus susceptibility of primary cultures of human alveolar epithelial cells and alveolar macrophages (AMs). Fluorescent antibody staining indicated that HCoV-229E could readily infect AMs, but no evidence was found for infection in differentiated alveolar epithelial type II cells and only a very low level of infection in type II cells transitioning to the type I-like cell phenotype. However, a human bronchial epithelial cell line (16HBE) was readily infected. The innate immune response of AMs to HCoV-229E infection was evaluated for cytokine production and interferon (IFN) gene expression. AMs secreted significant amounts of tumour necrosis factor alpha (TNF-α), regulated on activation normal T-cell expressed and secreted (RANTES/CCL5) and macrophage inflammatory protein 1β (MIP-1β/CCL4) in response to HCoV-229E infection, but these cells exhibited no detectable increase in IFN-β or interleukin-29 in mRNA levels. AMs from smokers had reduced secretion of TNF-α compared with non-smokers in response to HCoV-229E infection. Surfactant protein A (SP-A) and SP-D are part of the innate immune system in the distal lung. Both surfactant proteins bound to HCoV-229E, and pre-treatment of HCoV-229E with SP-A or SP-D inhibited infection of 16HBE cells. In contrast, there was a modest reduction in infection in AMs by SP-A, but not by SP-D. In summary, AMs are an important target for HCoV-229E, and they can mount a pro-inflammatory innate immune response to infection.
Hazara virus infection is lethal for adult type I interferon receptor-knockout mice and may act as a surrogate for infection with the human-pathogenic Crimean–Congo hemorrhagic fever virus
Authors: Dowall Stuart D. , Findlay-Wilson Stephen , Rayner Emma , Pearson Geoff , Pickersgill Janice , Rule Antony , Merredew Natasha , Smith Hazel , Chamberlain John , Hewson Roger
Published: November 2011

Hazara virus (HAZV) is closely related to the Crimean–Congo hemorrhagic fever virus (CCHFV). HAZV has not been reported to cause human disease; work with infectious material can be carried out at containment level (CL)-2. By contrast, CCHFV causes a haemorrhagic fever in humans and requires CL-4 facilities. A disease model of HAZV infection in mice deficient in the type I interferon receptor is reported in this study. Dose–response effects were seen with higher doses, resulting in a shorter time to death and earlier detection of viral loads in organs. The lowest dose of 10 p.f.u. was still lethal in over 50 % of the mice. Histopathological findings were identified in the liver, spleen and lymph nodes, with changes similar to a recent mouse model of CCHFV infection. The findings demonstrate that inoculation of mice with HAZV may act as a useful surrogate model for the testing of antiviral agents against CCHFV.
A Brief Overview of Adolescent Developmental Problems in Hong Kong
Authors: Shek Daniel T. L. , Keung Ma Hing , Sun Rachel C. F.
Published: November 2011

Several adolescent developmental problems in Hong Kong are briefly reviewed in this paper. First, rising adolescent substance abuse trends are described. Second, Internet use problems and Internet addiction among young people are examined. Third, worrying trends in adolescent sexuality are identified. Fourth, phenomena on bullying among young people are reviewed. Finally, phenomena related to adolescent materialistic orientation are focused upon. With reference to these adolescent developmental problems, possible solutions are briefly discussed particularly with reference to the ecological perspective. It is argued that the related scientific literature provides useful pointers for designing the curriculum in the extension phase of the Project P.A.T.H.S. in Hong Kong.
Calling amplified haplotypes in next generation tumor sequence data
Authors: Dewal Ninad , Hu Yang , Freedman Matthew L. , LaFramboise Thomas , Pe'er Itsik
Published: November 2011

During tumor initiation and progression, cancer cells acquire a selective advantage, allowing them to outcompete their normal counterparts. Identification of the genetic changes that underlie these tumor acquired traits can provide deeper insights into the biology of tumorigenesis. Regions of copy number alterations and germline DNA variants are some of the elements subject to selection during tumor evolution. Integrated examination of inherited variation and somatic alterations holds the potential to reveal specific nucleotide alleles that a tumor “prefers” to have amplified. Next-generation sequencing of tumor and matched normal tissues provides a high-resolution platform to identify and analyze such somatic amplicons. Within an amplicon, examination of informative (e.g., heterozygous) sites deviating from a 1:1 ratio may suggest selection of that allele. A naive approach examines the reads for each heterozygous site in isolation; however, this ignores available valuable linkage information across sites. We, therefore, present a novel hidden Markov model-based method—Haplotype Amplification in Tumor Sequences (HATS)—that analyzes tumor and normal sequence data, along with training data for phasing purposes, to infer amplified alleles and haplotypes in regions of copy number gain. Our method is designed to handle rare variants and biases in read data. We assess the performance of HATS using simulated amplified regions generated from varying copy number and coverage levels, followed by amplicons in real data. We demonstrate that HATS infers the amplified alleles more accurately than does the naive approach, especially at low to intermediate coverage levels and in cases (including high coverage) possessing stromal contamination or allelic bias.
The not so simple cubic structure of PbZr1 − x
Ti
x
O3 (PZT): complex local structural effects in perovskites
Authors: Zhang Nan , Yokota Hiroko , Glazer A. M. , Thomas P. A.
Published: November 2011

High-resolution neutron diffraction on the important piezoelectric lead zirconate titanate (PZT) has found that oxygen disorder exists well into the cubic phase. This unexpected result shows that within this phase there persists a remnant of the tilted oxygen octahedra present within the room-temperature ferroelectric phase. The result is that the cubic phase, far from having a simple crystal structure, exhibits a more complex local structure than had hitherto been thought.
Towards crystal structure prediction of complex organic compounds – a report on the fifth blind test
Authors: Bardwell David A. , Adjiman Claire S. , Arnautova Yelena A. , Bartashevich Ekaterina , Boerrigter Stephan X. M. , Braun Doris E. , Cruz-Cabeza Aurora J. , Day Graeme M. , Della Valle Raffaele G. , Desiraju Gautam R. , van Eijck Bouke P. , Facelli Julio C. , Ferraro Marta B. , Grillo Damian , Habgood Matthew , Hofmann Detlef W. M. , Hofmann Fridolin , Jose K. V. Jovan , Karamertzanis Panagiotis G. , Kazantsev Andrei V. , Kendrick John , Kuleshova Liudmila N. , Leusen Frank J. J. , Maleev Andrey V. , Misquitta Alston J. , Mohamed Sharmarke , Needs Richard J. , Neumann Marcus A. , Nikylov Denis , Orendt Anita M. , Pal Rumpa , Pantelides Constantinos C. , Pickard Chris J. , Price Louise S. , Price Sarah L. , Scheraga Harold A. , van de Streek Jacco , Thakur Tejender S. , Tiwari Siddharth , Venuti Elisabetta , Zhitkov Ilia K.
Published: November 2011

Following on from the success of the previous crystal structure prediction blind tests (CSP1999, CSP2001, CSP2004 and CSP2007), a fifth such collaborative project (CSP2010) was organized at the Cambridge Crystallographic Data Centre. A range of methodologies was used by the participating groups in order to evaluate the ability of the current computational methods to predict the crystal structures of the six organic molecules chosen as targets for this blind test. The first four targets, two rigid molecules, one semi-flexible molecule and a 1:1 salt, matched the criteria for the targets from CSP2007, while the last two targets belonged to two new challenging categories – a larger, much more flexible molecule and a hydrate with more than one polymorph. Each group submitted three predictions for each target it attempted. There was at least one successful prediction for each target, and two groups were able to successfully predict the structure of the large flexible molecule as their first place submission. The results show that while not as many groups successfully predicted the structures of the three smallest molecules as in CSP2007, there is now evidence that methodologies such as dispersion-corrected density functional theory (DFT-D) are able to reliably do so. The results also highlight the many challenges posed by more complex systems and show that there are still issues to be overcome.
The whole range of hydrogen bonds in one crystal structure: neutron diffraction and charge-density studies ofN,N-dimethylbiguanidinium bis(hydrogensquarate)
Authors: Şerb Mihaela-Diana , Wang Ruimin , Meven Martin , Englert Ulli
Published: November 2011

N,N-Dimethylbiguanidinium bis(hydrogensquarate) features an impressive range of hydrogen bonds within the same crystal structure: neighbouring anions aggregate to a dianionic pair through two strong O—H...O interactions; one of these can be classified among the shortest hydrogen bonds ever studied. Cations and anions in this organic salt further interactviaconventional N—H...O and nonclassical C—H...O contacts to an extended structure. As all these interactions occur in the same sample, the title compound is particularly suitable to monitor even subtle trends in hydrogen bonds. Neutron and high-resolution X-ray diffraction experiments have enabled us to determine the electron density precisely and to address its properties with an emphasis on the nature of theX—H...O interactions. Sensitive criteria such as the Laplacian of the electron density and energy densities in the bond-critical points reveal the incipient covalent character of the shortest O—H...O bond. These findings are in agreement with the precise geometry from neutron diffraction: the shortest hydrogen bond is also significantly more symmetric than the longer interactions.
Dynamic orientational disorder in crystals of fluoroelpasolites, structural refinement of (NH4)3AlF6, (NH4)3TiOF5 and Rb2KTiOF5
Authors: Udovenko Anatoly A. , Laptash Natalia M.
Published: November 2011

Room-temperature crystal structures of triammonium hexafluoroaluminate, (NH4)3AlF6 (I), and triammonium oxopentafluorotitanate, (NH4)3TiOF5 (II), were refined, and the crystal structures of dirubidium potassium oxopentaflourotitanate, Rb2KTiOF5, at 297 K (III) and 218 K (IV) were determined using single-crystal X-ray diffraction techniques. In ammonium fluoroelpasolites [(I) and (II)], the ligand (O, F) atoms are located in the mixed 24e + 96j position of the Fm3m unit cell. The 24e position is occupied by the ligand atoms predominantly in (III) and fully in (IV). `Ordered' N1 and Rb atoms are tetrahedrally displaced from the 8c position into the 32f site, and the H atoms of the disordered ammonium group N2 are statistically distributed in the 96k and 32f positions. The Ti atoms in (II) and (IV) are shifted from the 4a position to 24e thus allowing identification of the O and F atoms in the octahedron on a local scale. The disorder in the crystals is of a dynamic nature. Unique Raman spectra of Rb2KTiOF5 under the laser beam of 1064 nm indicate fast octahedral reorientations resulting in physical equalizations of the Ti—O and Ti—F distances as well as in the appearance of totally synchronous Ti—O and Ti—F stretching vibrations at 750 cm−1. This phenomenon is assumed to also take place under X-rays.
Greater prevalence of proposed DSM‐5 nicotine use disorder compared to DSM‐IV nicotine dependence in treated adolescents and young adults
Authors: Chung Tammy , Martin Christopher S. , Maisto Stephen A. , Cornelius Jack R. , Clark Duncan B.
Published: November 2011

Aims  Compared to DSM‐IV nicotine dependence, proposed DSM‐5 nicotine use disorder (NUD) would lower the threshold from three to two symptoms, and increase the number of criteria used for diagnosis from seven to 11. The impact of the proposed changes on nicotine disorder prevalence and the concurrent validity of diagnostic criteria were examined.

Design  Cross‐sectional survey to compare DSM‐IV and proposed DSM‐5 algorithms.

Setting and participants  Adolescent (n = 179) and young adult (n = 292) past‐year cigarette users recruited from addictions treatment.

Measurements  Semi‐structured clinical interview to evaluate DSM‐IV nicotine dependence, and 10 of the 11 proposed DSM‐5 NUD criteria; 30‐day time‐line follow‐back; and the Fagerström Test for Nicotine Dependence (FTND).

Findings  Prevalence of proposed DSM‐5 NUD (two‐symptom threshold) was much higher (adolescents: 68.7%, young adults: 86.0%) than DSM‐IV nicotine dependence (33.0% and 59.6%, respectively), although prevalence of DSM‐5 severe NUD (four‐symptom threshold) was similar to DSM‐IV nicotine dependence. Concurrent validity analyses in both samples indicated consistent support for DSM‐5 severe NUD diagnosis (four symptoms) but not for the moderate NUD (two symptoms) diagnosis, which had modest relations with only FTND score. IRT analyses indicated strong support for the new craving item, but not for the proposed interpersonal problems and hazardous use items.

Conclusions  The proposed DSM‐5 nicotine use disorder criteria have substantial limitations when applied to adolescents and young adults, and appear to have low concurrent validity.
Impaired phagocytosis among patients infected by the human immunodeficiency virus: implication for a role of highly active anti-retroviral therapy
Authors: Michailidis C , Giannopoulos G , Vigklis V , Armenis K , Tsakris A , Gargalianos P
Published: November 2011

In patients with human immunodeficiency virus (HIV) infection, neutrophil and monocyte functions, including phagocytosis, are impaired. The purpose of this study was to investigate changes of phagocytic function and respiratory burst occurring over the course of patients infected by the HIV-1 virus. Treatment-naive patients (group B), patients receiving highly active anti-retroviral treatment (HAART) (group C) and patients in which HAART has failed (group D) were studied and compared with healthy volunteers (group A). Phagocytosis and oxidative burst were evaluated using commercially available kits. Results clearly denote a significant decrease of the phagocytic function of both cell types of groups B and C compared with group A. Among group C patients, those in the upper quartile of CD4 increase had higher oxidative burst compared with patients of the other quartiles. In addition, comparisons clearly showed a lower degree of phagocytic function and of oxidative burst of both monocytes and neutrophils of group D compared with group B. Finally, it was found that monocyte and neutrophil function was correlated inversely to the change in viral load, i.e. the greater the decrease of viral load, the better the phagocytic and oxidative activity. Innate immunity defects appear to be present in HIV-positive patients, regarding phagocytic activity and oxidative burst of monocytes and neutrophils. These defects are greatly influenced by the level of treatment efficacy, with emphasis on CD4 cell counts and viral load.
Focal active colitis: a prospective study of clinicopathological correlations in 90 patients
Authors: Shetty Sharan , Anjarwalla Salim M , Gupta Jyoti , Foy Chris J W , Shaw Ian S , Valori Roland M , Shepherd Neil A
Published: November 2011

Shetty S, Anjarwalla S M, Gupta J, Foy C J W, Shaw I S, Valori R M & Shepherd N A  (2011) Histopathology59, 850–856

Focal active colitis: a prospective study of clinicopathological correlations in 90 patients

Aims:  Considerable controversy exists about the clinical implication of a diagnosis of focal active colitis (FAC). The aim of this study was to assess clinicopathological correlations of FAC in 90 adults, representing the largest and only prospective series of FAC.

Methods and results:  Patients were assessed by comprehensive clinical follow‐up and questionnaires. Fifteen histopathological features were scored and correlated with clinical outcome. In 24% of patients drugs, especially NSAIDs, were implicated. Infection was a probable cause in 19%. In 14 patients (15.6%), predominantly women, a diagnosis of chronic inflammatory bowel disease was ultimately made. Most were Crohn’s disease, but this is the first study in which FAC has presaged an ultimate diagnosis of ulcerative colitis in adults (in two patients). A specific subtype of FAC, termed basal FAC, was significantly associated with drugs. These excepted, this study has found no histopathological parameters of FAC, such as amount, location and/or distribution, to correlate with clinical outcome or allowed selection of those patients more likely to show subsequent evidence of chronic inflammatory bowel disease.

Conclusion:  This study has provided powerful information on the implication of a diagnosis of FAC. In a small but not inconsiderable case number, the ultimate diagnosis will be chronic inflammatory bowel disease.
Aggressive colorectal carcinoma phenotypes of invasion can be assessed reproducibly and effectively predict poor survival: interobserver study and multivariate survival analysis of a prospectively collected series of 299 patients after potentially curative resections with long‐term follow‐up
Authors: Wöhlke Michael , Schiffmann Leif , Prall Friedrich
Published: November 2011

Wöhlke M, Schiffmann L & Prall F  (2011) Histopathology59, 857–866

Aggressive colorectal carcinoma phenotypes of invasion can be assessed reproducibly and effectively predict poor survival: interobserver study and multivariate survival analysis of a prospectively collected series of 299 patients after potentially curative resections with long‐term follow‐up

Aims:  To test whether assessment of colorectal carcinoma phenotypes of invasion can be taught successfully to pathologists not familiar with these features and to confirm their prognostic impact.

Methods and results:  A junior member of staff was supplied with written information and a generous set of images on how to type the invasive margin of colorectal carcinomas (expansive versus infiltrative) and how to assess tumour budding (counting on pan‐cytokeratin immunostains; cut‐off at the 66th percentile). An interobserver study yielded kappa values of 0.578 and 0.438 for typing the invasive margin and assessment of tumour budding, respectively. Margin typing improved significantly to κ = 0.939 after a training session. However, using a cut‐off, assessment of tumour budding improved only moderately to κ = 0.629 although, numerically, divergences were within ±10%. On univariate analysis, a high‐degree of tumour budding and the infiltrative type of invasive margin were strong negative prognostic factors. The Cox model included nodal status, tumour budding, serosal penetration and venous angioinvasion. Importantly, using the tumour budding counts as a numerical variable for the Cox model also yielded significant odds, allowing the constraints of a cut‐off to be relinquished.

Conclusions:  Assessment of colorectal carcinoma phenotypes of invasion can be learnt and performed with confidence, and their prognostic impact is confirmed in this independent series.
Human epidermal growth factor receptor 2 (HER2) immunoreactivity: specificity of three pharmacodiagnostic antibodies
Authors: Schrohl Anne‐Sofie , Pedersen Hans Christian , Jensen Sussie Steen , Nielsen Signe Lykke , Brünner Nils
Published: November 2011

Schrohl A‐S, Pedersen H C, Jensen S S, Nielsen S L & Brünner N  (2011) Histopathology59, 975–983

Human epidermal growth factor receptor 2 (HER2) immunoreactivity: specificity of three pharmacodiagnostic antibodies

Aims:  The availability of specific antibody‐based test systems is essential to testing of HER2 protein expression. Here, we mapped epitopes recognized by three pharmacodiagnostic HER2 antibodies and investigated their specificity towards peptides and fusion proteins homologous to the intracellular domains of HER1, HER2, HER3 and HER4. The investigated antibodies were PATHWAY® HER2 (clone 4B5; Ventana Medical Systems Inc., Tucson, AZ, USA), HercepTest™ (Dako Denmark A/S, Glostrup, Denmark), and Oracle® HER2 (clone CB11; Leica Microsystems GmbH, Wetzlar, Germany).

Methods and results:  Epitopes were mapped using the alanine scanning method. Specificity was investigated in immunohistochemical stainings, competitive enzyme‐linked immunosorbent assay (ELISA) and immunoblotting. All three antibodies reacted with HER2 proteins and peptides in immunohistochemical stainings, ELISA and immunoblotting. PATHWAY® HER2 also stained HER4‐expressing cells, reacted with HER4 peptide in ELISA and detected HER4 fusion protein in an immunoblot. Oracle® HER2 weakly detected HER4 in immunohistochemical stainings, whereas the HercepTest™ antibody showed no cross‐reactivity with other HER proteins.

Conclusion:  Our study shows that the PATHWAY® HER2 antibody can bind HER4 peptides and fusion proteins in three different experimental settings. This should be investigated further to determine whether binding of HER4 also occurs in tissue samples and if such binding would have implications for therapy decisions for breast cancer patients.
Dual‐colour chromogenic in‐situ hybridization is a potential alternative to fluorescence in‐situ hybridization in HER2 testing
Authors: Hwang Cheng‐Cheng , Pintye Mariann , Chang Liang‐Che , Chen Huang‐Yang , Yeh Kun‐Yan , Chein Hui‐Ping , Lee Nin , Chen Jim‐Ray
Published: November 2011

Hwang C‐C, Pintye M, Chang L‐C, Chen H‐Y, Yeh K‐Y, Chein H‐P, Lee N & Chen J‐R  (2011) Histopathology59, 984–992

Dual‐colour chromogenic in‐situ hybridization is a potential alternative to fluorescence in‐situ hybridization in HER2 testing

Aim:  Dual‐colour chromogenic in‐situ hybridization (dc‐CISH) is an emerging methodology for characterizing genomic alterations. This study was aimed at evaluating the performance of a dc‐CISH kit (ZytoVision) in determining human epidermal growth factor receptor 2 (HER2) status in breast cancer.

Methods and results:  Two hundred and twenty‐eight invasive breast carcinomas arranged in tissue microarrays were analysed in parallel with dc‐CISH, fluorescence in‐situ hybridization (FISH), and immunohistochemistry. Of 227 tumours with available FISH and dc‐CISH results, HER2 amplification and non‐amplification were detected in 49 (21.6%) and 178 (78.4%) tumours, respectively, by both assays. The concordance between dc‐CISH and FISH results showed 100% agreement (κ‐coefficient = 1.00). Immunohistochemically, 162 (71%), 25 (11.0%) and 41 (18%) tumours were scored 0/1+, 2+, and 3+, respectively. The corresponding results with both FISH and dc‐CISH demonstrated HER2 amplification in two (3.2%), nine (36%) and 38 (93%) tumours, respectively. Complete consensus among these three methods was observed in 197 cases, representing 98% of all 3+ and 0/1+ tumours (κ‐coefficient = 0.92). Confirmatory testing of 25 2+ tumours showed complete consensus between FISH and dc‐CISH.

Conclusions:  dc‐CISH is a promising alternative to FISH in HER2 testing, and the single‐institute incidence of HER2 amplification in breast cancer in Taiwan is 21.2%.
The savanna‐grassland ‘treeline’: why don’t savanna trees occur in upland grasslands?
Authors: Wakeling Julia L. , Cramer Michael D. , Bond William J.
Published: November 2011

1. Treeless grasslands with climates that can support tree growth are common in upland regions around the world. In South Africa, the upland grasslands are adjacent to lowland savannas in many areas, with an abrupt boundary between them that could be termed a savanna‐grassland ‘treeline’. Both systems are dominated by C4 grasses and burn regularly, yet fire‐tolerant savanna trees do not survive in the grasslands. The upland grasslands experience lower temperatures throughout the year and frost in winter, compared with the warmer savannas.

2. We tested whether frost in the dormant season or slow growth in the growing season in conjunction with frequent fires may explain the tree‐less state of grasslands. We measured Acacia seedling growth for a year in a transplant experiment at ten sites across an altitudinal gradient (42–1704 m) from savannas to grasslands. The effect of frost on seedlings was scored during the following winter.

3. Across all species, height (t = −6.04, d.f. = 471, P < 0.001), biomass (t = −4.56, d.f. = 228, P < 0.001) and height increase (t = −3.40, d.f. = 471, P < 0.001) were significantly higher at savanna sites. As the plants were irrigated and initially supplied with nutrients, the main factor affecting growth was likely to be growing season temperature.

4. Saplings that experience slow growing conditions will take longer to reach a height above the flame zone and will therefore have a lower probability of reaching adult tree height and surviving fires. Day length may be the most important cue for the end of the growing season in savanna trees, as growth decreased with shortening day length in February–March while temperatures were still high and plants were not water limited.

5. Synthesis. Savanna trees grew more slowly in cooler upland grassland sites compared with lower elevation warm savanna sites and, under frequent fire regimes, would be prevented from reaching maturity. This may be true globally for similar grasslands where tree growth can occur and could partly explain the lack of trees in grasslands.
Transmission EBSD from 10 nm domains in a scanning electron microscope
Authors: KELLER R.R. , GEISS R.H.
Published: November 2011

The spatial resolution of electron diffraction within the scanning electron microscope (SEM) has progressed from channelling methods capable of measuring crystallographic characteristics from 10 μm regions to electron backscatter diffraction (EBSD) methods capable of measuring 120 nm particles. Here, we report a new form of low‐energy transmission Kikuchi diffraction, performed in the SEM. Transmission‐EBSD (t‐EBSD) makes use of an EBSD detector and software to capture and analyse the angular intensity variation in large‐angle forward scattering of electrons in transmission, without postspecimen coils. We collected t‐EBSD patterns from Fe–Co nanoparticles of diameter 10 nm and from 40 nm‐thick Ni films with in‐plane grain size 15 nm. The patterns exhibited contrast similar to that seen in EBSD, but are formed in transmission. Monte Carlo scattering simulations showed that in addition to the order of magnitude improvement in spatial resolution from isolated particles, the energy width of the scattered electrons in t‐EBSD is nearly two orders of magnitude narrower than that of conventional EBSD. This new low‐energy transmission diffraction approach builds upon recent progress in achieving unprecedented levels of imaging resolution for materials characterization in the SEM by adding high‐spatial‐resolution analytical capabilities.
Isolated cardiomyopathy caused by a DMD nonsense mutation in somatic mosaicism: genetic normalization in skeletal muscle
Authors: Juan‐Mateu J , Paradas C , Olivé M , Verdura E , Rivas E , González‐Quereda L , Rodríguez MJ , Baiget M , Gallano P
Published: November 2011

Juan‐Mateu J, Paradas C, Olivé M, Verdura E, Rivas E, González‐Quereda L, Rodríguez MJ, Baiget M, Gallano P. Isolated cardiomyopathy caused by a DMD nonsense mutation in somatic mosaicism: genetic normalization in skeletal muscle.

X‐linked dilated cardiomyopathy is a pure cardiac dystrophinopathy phenotype mainly caused by DMD mutations that present a specific transcription effect in cardiac tissue. We report a 26‐year‐old male who presented with severe dilated cardiomyopathy and high creatine kinase. The patient did not complain of skeletal muscle weakness. A muscle biopsy showed mild dystrophic changes and a low proportion of dystrophin‐negative fibres. A molecular study identified a nonsense DMD mutation (p.Arg2098X) in somatic mosaicism. The ratio of mutant versus normal allele in blood and skeletal muscle suggests selective pressure against mutant muscle cells, a process known as genetic normalization. We hypothesize that this process may have mitigated skeletal muscle symptoms in this patient. This is the second report of a DMD somatic mosaic with evidence of genetic normalization in muscle. Somatic DMD mutations should be considered in patients presenting with idiopathic dilated cardiomyopathy.
Evaluation of High‐resolution Melting Curve Analysis as a New Tool for Root‐knot Nematode Diagnostics
Authors: Holterman Martijn H. M. , Oggenfuss Markus , Frey Juerg Ernst , Kiewnick Sebastian
Published: November 2011

In the detection of plant pests, speed and accuracy are vital. High‐resolution melting curve (HRMC) analysis was therefore evaluated as a new tool for the identification of root‐knot nematodes (Meloidogyne spp.). On the basis of the second intergenic spacer (IGS2) region of the ribosomal DNA cistron, Meloidogyne chitwoodi, M. fallax and M. hapla were successfully distinguished from each other and the group of the three tropical species, M. incognita, M. arenaria and M. javanica. Conversely, it was shown that the IGS2 region is not suitable for the tropical species M. enterolobii (senior synonym of M. mayaguensis) as the amplification of multiple fragments of different lengths prevented a reliable HRMC analysis. However, the obtained results provide a proof of principle that HRMC analysis can be a suitable single‐tube assay for fast and accurate root‐knot nematode identification.
Impact of insulin pumps on glycaemic control in a pump‐naïve paediatric regional population
Authors: de Bock Martin , Gunn Alistair Jan , Holt Jean‐Ann , Derraik José G B , Reed Peter , Cutfield Wayne , Mouat Fran , Hofman Paul , Jefferies Craig
Published: November 2011

Aim:  To examine the clinical impact of insulin‐pump therapy for children with type 1 diabetes mellitus (T1DM) in a regional paediatric service, Auckland, New Zealand.

Methods:  Retrospective analysis of children with T1DM from the Starship paediatric diabetes database who started on insulin‐pump therapy from 2002 to 2008 compared with the whole T1DM population and with an equal number of non‐pump patients matched by age, sex, ethnicity and duration of diabetes.

Results:  From 621 subjects with 6680 clinic visits, 75 children were treated with insulin‐pump therapy for more than 12 months. Transitioning to insulin‐pump treatment was associated with an improvement in HbA1c compared with baseline (−0.3%/year, P < 0.001) for up to 3 years. In contrast, despite similar deprivation scores, non‐pump controls showed a continuing trend to higher HbA1C values (+0.2%/year, P < 0.01). The risk of severe hypoglycaemia fell after pump start (from 27 (0–223) to 5 (0–0.91) events/100 patient years) with no change in non‐pump controls; the rate of diabetic ketoacidosis remained low in both groups.

Conclusions:  In a pump‐naïve regional paediatric population, insulin‐pump therapy for T1DM was safe and effective, and associated with sustained improvements in HbA1c and lower risk of hypoglycaemia.
Excitatory amino acid transporter 2 and excitatory amino acid transporter 1 negatively regulate calcium‐dependent proliferation of hippocampal neural progenitor cells and are persistently upregulated after injury
Authors: Gilley Jennifer A. , Kernie Steven G.
Published: November 2011

Using a transgenic mouse (Mus musculus) in which nestin‐expressing progenitors are labeled with enhanced green fluorescent protein, we previously characterized the expression of excitatory amino acid transporter 2 (GltI) and excitatory amino acid transporter 1 (Glast) on early neural progenitors in vivo. To address their functional role in this cell population, we manipulated their expression in P7 neurospheres isolated from the dentate gyrus. We observed that knockdown of GltI or Glast was associated with decreased bromodeoxyuridine incorporation and neurosphere formation. Moreover, we determined that both glutamate transporters regulated progenitor proliferation in a calcium‐dependent and metabotropic glutamate receptor‐dependent manner. To address the relevance of this in vivo, we utilized models of acquired brain injury, which are known to induce hippocampal neurogenesis. We observed that GltI and Glast were specifically upregulated in progenitors following brain injury, and that this increased expression was maintained for many weeks. Additionally, we found that recurrently injured animals with increased expression of glutamate transporters within the progenitor population were resistant to subsequent injury‐induced proliferation. These findings demonstrate that GltI and Glast negatively regulate calcium‐dependent proliferation in vitro and that their upregulation after injury is associated with decreased proliferation after brain trauma.
Age‐related changes in the guinea pig auditory cortex: relationship with brainstem changes and comparison with tone‐induced hearing loss
Authors: Gourévitch Boris , Edeline Jean‐Marc
Published: November 2011

Elderly people often show degraded hearing performance and have difficulties in understanding speech, particularly in noisy environments. Although loss in peripheral hearing sensitivity is an important factor in explaining these low performances, central alterations also have an impact but their exact contributions remained unclear. In this study, we focus on the functional effects of aging on auditory cortex responses. Neuronal discharges and local field potentials were recorded in the auditory cortex of aged guinea pigs (> 3 years), and several parameters characterizing the processing of auditory information were quantified: the acoustic thresholds, response strength, latency and duration of the response, and breadth of tuning. Several of these parameters were also quantified from auditory brainstem responses collected from the same animals, and recordings obtained from a population of animals with trauma‐induced hearing loss were also included in this study. The results showed that aging and acoustic trauma reduced the response strength at both brainstem and cortical levels, and increased the response latencies more at the cortical level than at the brainstem level. In addition to the brainstem hearing loss, aging induced a ‘cortical hearing loss’ as judged by additive changes in the threshold and frequency response seen in the cortex. It also increased the duration of neural responses and reduced the receptive field bandwidth, effects that were not found in traumatized animals. These effects substantiate the notion that presbycusis involves both peripheral hearing loss and biological aging in the central auditory system.