bluuebunny/crossref_metadata_2025 huggingface dataset:
Distinctiveness of the cagA Genotype in Children and Adults with Peptic Symptoms in South China
Authors: Li Juan , Ou Zhiying , Wang Fangjin , Guo Yu , Zhang Ren , Zhang Jun , Li Peiqiong , Xu Weijie , He Yunshao
Published: July 2009

Background:  Helicobacter pylori infection is different between children and adults, not only in infection rate but also in virulence genotypes. However, the 3′ region of CagA, important in stomach carcinogenesis, still remains unclear in children. The present study aims to compare the frequency of cagA and the distribution of its subtypes between children and adults in South China.

Materials and Methods:  One hundred and twenty‐eight children and 99 adults with peptic symptoms were enrolled in our research. Histology, rapid urease test, and real‐time polymerase chain reaction (PCR) assay were used to diagnose H. pylori infection. vacA s1 was detected by real‐time PCR, and EPIYA motifs in the 3′ region of CagA by conventional PCR and DNA sequencing.

Results:  H. pylori infection was diagnosed in 53 children and 62 adults. vacA s1 was identified in 90.6% and 91.9% of infected children and adults, respectively. Furthermore, cagA was identified in 73.6% and 82.3% of infected children and adults, respectively. No patient with multiple cagA subtypes was observed. A higher prevalence of more virulent cagA genotype was found in children compared to adults (p < .05). Thirty‐eight of 39 (97.4%) cagA‐positive children were found to have EPIYA‐ABD and only one (2.6%) with EPIYA‐ABC. In adults, four types of EPIYA motifs – ABC (29.4%), ABD (64.7%), ABAB (2%), and AAD (3.9%) – were identified, and the ABD type was found more commonly in severe diseases, such as atrophic gastritis (53.3%) and gastric cancer (71.4%).

Conclusion:  cagA genotypes in children and in adults are different, and EPIYA‐ABD may have potential clinical implication in the development of gastric cancer in South China.
Presence of High Numbers of Transcriptionally Active Helicobacter pylori in Vomitus from Bangladeshi Patients Suffering from Acute Gastroenteritis
Authors: Janzon Anders , Bhuiyan Taufiq , Lundgren Anna , Qadri Firdausi , Svennerholm Ann‐Mari , Sjöling Åsa
Published: July 2009

Background:  Helicobacter pylori is one of the most prevalent human bacterial pathogens; however, its transmission pathways remain unknown. New infections of H. pylori during outbreaks of gastroenteritis have been suggested previously, and to explore this transmission route further H. pylori was quantified in vomitus and diarrheal stool of patients suffering from acute gastroenteritis in Dhaka, Bangladesh.

Materials and Methods:  Vomitus and stool samples from 28 patients seeking care at the International Centre for Diarrhoeal Disease Research hospital were analyzed for presence of H. pylori and other pathogens using quantitative culturing, real‐time polymerase chain reaction (PCR), and H. pylori stool antigen test. Bacterial gene expression was analyzed using reverse transcriptase real‐time PCR.

Results:  The results of real‐time PCR show that 23 (88%) of the 26 vomitus samples and 17 (74%) of the 23 stool samples were H. pylori positive, while stool antigen test show that 14 (67%) of the 21 stool samples were H. pylori positive. H. pylori could not be isolated by culture. Analysis using quantitative culture and real‐time PCR to detect Vibrio cholerae showed strong correlation between these methods, and validating real‐time PCR. Analysis of H. pylori virulence gene transcription in vomitus, diarrheal stool, antral and duodenal biopsy specimens, and in vitro cultures showed that cagA, flaA, and ureA were highly transcribed in vomitus, biopsy specimens, and cultures, whereas hpaA and vacA were expressed at lower levels. No H. pylori gene expression was detected in diarrheal stool.

Conclusions:  We conclude that high numbers of transcriptionally active H. pylori are shed in vomitus, which indicates that new infections may be disseminated through vomiting.
Decrepitated UHP fluid inclusions: about diverse phase assemblages and extreme decompression rates (Erzgebirge, Germany)
Authors: STÖCKHERT B. , TREPMANN C. A. , MASSONNE H.‐J.
Published: July 2009

Minute polyphase inclusions in garnet of quartzofeldspathic rocks (saidenbachite) from the Saxonian Erzgebirge, Germany, contain microdiamond or graphite, phlogopite, quartz, paragonite, phengite and other minerals in minor amounts. These inclusions are interpreted to represent an original dense COH + silicate fluid, trapped in crystallizing garnet at depths of >150 km. Inspection of the inclusion population in a single garnet by SEM reveals two characteristic features: (i) The shape of most inclusions indicates healed radial cracks in the host garnet, and, thus, the buildup of a significant differential pressure ΔP, i.e. a contrast in pressure between the inclusion (Pi) and the host mineral (Pe). The mineral assemblages sealing the cracks and showing an equilibrated microstructure indicate temperatures of ∼750 ± 50 °C and pressures below 2.5 GPa. (ii) The diverse types of inclusions appear to be randomly distributed in the garnet host. Thus, the variable phase assemblages do not reflect a compositional evolution of the fluid trapped in the garnet. Combining observations (i) and (ii), we propose that the diversity of the phase assemblage in the inclusions is the result of decrepitation at different times, and thus, of distinct histories of Pi, as ΔP at decrepitation is primarily controlled by inclusion size and shape. Applying a flow law for dislocation creep of garnet, a low strength of garnet at 750 ± 50 °C for low geological strain rates is predicted. Thus, differential pressure should have been kept low (i.e. Pi≈ Pe) by continuous stretching of the inclusion for typical exhumation rates of metamorphic rocks. To attain the differential pressure (Pi >> Pe) required for catastrophic brittle failure of the garnet host, the decompression rate must have been extremely high. As a robust lower bound, a minimum exhumation rate on the order of 100 m year−1 is suggested, which corresponds to ascent rates of magma.
Specialization and Success: Evidence from Venture Capital
Authors: Gompers Paul , Kovner Anna , Lerner Josh
Published: July 2009

This paper examines how organizational structure affects behavior and outcomes, studying the performance of different types of venture capital organizations. We find a strong positive relationship between the degree of specialization by individual venture capitalists at a firm and its success. When the individual investment professionals are highly specialized themselves, the marginal effect of increasing overall firm specialization is much weaker. The poorer performance by generalists appears to be due to both an inefficient allocation of funding across industries and poor selection of investments within industries. Venture capital organizations with more experience tend to outperform those with less experience.
Hidden Talents: Entrepreneurship and Pareto‐Improving Private Information
Authors: Daughety Andrew F. , Reinganum Jennifer F.
Published: July 2009

Two entrepreneurs, each privately informed about her own talent, simultaneously and noncooperatively choose their efforts in producing a new product. Product quality depends on both entrepreneurs’ talents and efforts, but is unobservable by potential buyers prior to purchase; however, buyers can observe the entrepreneurs’ individual efforts. Because the entrepreneurs share the payoff, each is tempted to shirk. However, the need to signal quality to potential buyers serves as a credible commitment to provide greater effort. Thus, the “problem” of adverse selection mitigates the problem of moral hazard, so that a new venture can perform better than the corresponding mature market.
Ethics and Animal Consciousness: How Rubber the Ethical Ruler?
Authors: Burghardt Gordon M.
Published: July 2009

The treatment of nonhuman animals has been marked by extremes of beneficence and cruelty. The ethical guidelines explicitly or informally underlying how we regard other species have been marked by inconsistency and an elastic ethics. One of the major controversies involved in nonhuman animal rights and welfare discussions involves the level of their awareness or consciousness of ill treatment. The varying ways in which this issue has been conceptualized, studied, and applied to the lives of other species throughout history are reviewed, and the difficulties of setting thresholds for differential ethical and moral concern for various taxa are discussed. A more holistic and ecological moral vision for valuing other animals is proposed.
Regression Calibration in Semiparametric Accelerated Failure Time Models
Authors: Yu Menggang , Nan Bin
Published: July 2009

Summary In large cohort studies, it often happens that some covariates are expensive to measure and hence only measured on a validation set. On the other hand, relatively cheap but error‐prone measurements of the covariates are available for all subjects. Regression calibration (RC) estimation method (Prentice, 1982, Biometrika 69, 331–342) is a popular method for analyzing such data and has been applied to the Cox model by Wang et al. (1997, Biometrics 53, 131–145) under normal measurement error and rare disease assumptions. In this article, we consider the RC estimation method for the semiparametric accelerated failure time model with covariates subject to measurement error. Asymptotic properties of the proposed method are investigated under a two‐phase sampling scheme for validation data that are selected via stratified random sampling, resulting in neither independent nor identically distributed observations. We show that the estimates converge to some well‐defined parameters. In particular, unbiased estimation is feasible under additive normal measurement error models for normal covariates and under Berkson error models. The proposed method performs well in finite‐sample simulation studies. We also apply the proposed method to a depression mortality study.
Expression of α‐methylacyl‐CoA racemase (P504S) in sebaceous neoplasms
Authors: Halsey Mark A. , Calder Kenneth B. , Mathew Rahel , Schlauder Scott , Morgan Michael B.
Published: July 2009

Background:α‐Methylacyl‐CoA racemase (AMACR), also known as P504S, is a protein that plays an important role in mitochondrial and peroxisomal β‐oxidation of branched‐chain fatty acid and bile acid intermediates. AMACR has been established as a valuable diagnostic marker for prostate cancer and has recently been shown to be useful in the diagnosis of colorectal carcinoma. Despite the importance of lipid metabolism in sebum production by sebaceous glands of the skin, there are no studies evaluating the expression of AMACR in sebaceous neoplasms.

Methods: Five samples of normal sebaceous glands as well as five cases each of sebaceous hyperplasia (SH), sebaceous adenoma (SA), basal cell carcinoma (BCC) with sebaceous differentiation and extraocular sebaceous carcinoma (SC) were evaluated for immunohistochemical (IHC) expression of AMACR. Each case was reviewed by a single dermatopathologist and graded using a semi‐objective grading schema.

Results: Normal sebaceous glands showed strong (4+) expression of AMACR. Among sebaceous neoplasms, SH showed the highest expression (4+), SA and BCC with sebaceous differentiation showed varied expression (2+ and 1+, respectively), and extraocular SC showed no expression of AMACR.

Conclusions: The expression of AMACR is increased in benign sebaceous glands and SH; with decreasing AMACR expression in tumors with less sebaceous differentiation (i.e. SA and SC). These findings provide insight into the potential pathogenesis of sebaceous neoplasms while assisting in the microscopic distinction of SA from SC.

Halsey MA, Calder KB, Mathew R, Schlauder S, Morgan MB. Expression of α‐methylacyl‐CoA racemase (P504S) in sebaceous neoplasms.
Epidermotropic lesions: a review
Authors: Abbas Ossama , Bhawan Jag
Published: July 2009

Epidermotropism describes the spread of cells of lymphocytic, epithelial melanocytic, neuroendocrine, histiocytic or muscular origin into the epidermis from an underlying dermal or subcutaneous pathology, that may be primary cutaneous or metastatic. In this review, we aim to discuss the differential diagnosis of epidermotropic lesions and highlight the histological and immunohistochemical characteristics that can help in their differentiation.
WT 1 expression in nevi and melanomas: a marker of melanocytic invasion into the dermis
Authors: Garrido‐Ruiz M. C. , Rodriguez‐Pinilla S. M. , Pérez‐Gómez B. , Rodriguez‐Peralto J. L.
Published: July 2009

Background: WT1, first recognized as a tumor suppressor gene involved in the development of Wilms' tumor, may have apparently contradictory findings and functions. As WT1 has been identified as a molecular target for cancer immunotherapy, immunodetection of WT1 in tumor cells has become an essential step in cancer studies.

Methods: We compare the expression of this protein among different types of melanocytic nevi and among stages in primary melanoma progression. Tissue microarrays containing normal tissues and 271 primary melanocytic lesion samples (163 primary melanomas and 108 nevi) were studied by immunohistochemistry using monoclonal antibody against WT1.

Results and Discussion: The present study shows these: 1. WT1 protein is predominantly expressed in the cytoplasm of the neoplastic cells. 2. A higher rate of WT1 staining in melanocytic nevi against melanomas has been observed. 3. WT1 expression is increased in advanced stages of melanoma progression: a significant (p < 0.05) increase of expression of WT1 was detected in vertical cases 46.5% vs. radial cases 16.0%, in high levels of Clark (IV, V) 57.4% vs. low levels (I, II, III) 33.0% and when comparing depth of invasion within thickness subgroups. 4. Finally, this study establishes an association of WT1 protein expression with shorter overall survival in melanoma.

Garrido‐Ruiz MC, Rodriguez‐Pinilla SM, Pérez‐Gómez B, Rodriguez‐Peralto JL. WT 1 expression in nevi and melanomas: a marker of melanocytic invasion into the dermis.
Regression of established subcutaneous B16‐F10 murine melanoma tumors after gef gene therapy associated with the mitochondrial apoptotic pathway
Authors: Prados Jose , Melguizo Consolación , Ortiz Raúl , Boulaiz Houria , Carrillo Esmeralda , Segura Ana , Rodríguez‐Herva Jose Juan , Ramos Juan Luis , Aránega Antonia
Published: July 2009

Please cite this paper as: Regression of established subcutaneous B16‐F10 murine melanoma tumors after gef gene therapy associated with the mitochondrial apoptotic pathway. Experimental Dermatology 2009.

Abstract:  Novel treatment modalities, including gene therapy, are needed for patients with advanced melanoma. We evaluated whether the gef gene, a suicide gene from Escherichia coli, had a significant cytotoxic impact on melanoma in vivo. First, we used a non‐viral gene delivery approach (pcDNA3.1/gef) to study the inhibition of melanoma cells (B16‐F10) proliferation in vitro. Secondly, we used direct intra‐tumoral injection of pcDNA3.1/gef complexed with jetPEI to deliver gef cDNA to rapidly growing murine melanomas. We demonstrated that gef gene not only has an antiproliferative effect on B16‐F10 cells in vitro, but also induces an important decrease in melanoma tumor volume (77.7% in 8 days) in vivo. Interestingly, after gef gene treatment, melanoma showed apoptosis activation associated with the mitochondrial pathway, suggesting that the induction of this death mechanism may be an effective strategy for its treatment. Our in vivo results indicate that gef gene might become a suitable therapeutic strategy for patients with advanced melanoma.
Liver X receptor expression in human melanocytes, does it have a role in the pathogenesis of vitiligo?
Authors: Kumar Ravinder , Parsad Davinder , Kaul Deepak , Kanwar Amrinderjit
Published: July 2009

Abstract:  Vitiligo is a common, non‐contagious disorder. The basic pathogenesis of vitiligo generally, or for any of the putative subsets of vitiligo, remains unknown. The liver X receptors (LXRs), LXR‐α and LXR‐β are members of the nuclear hormone receptor superfamily of ligand‐activated transcription factors. Important genes involved in regulation of melanocytes are target genes of LXRs; it can be speculated that LXRs might be playing an important role in pathogenesis of pigmentary disorders. We have demonstrated in this study that there is expression of LXR‐α/β by human melanocytes at both transcriptional and translational levels. Our present data also revealed that the expression of LXR‐α at both mRNA and protein level was significantly higher in perilesional skin as compared to the normal skin of vitiligo patient.
Current therapy of HIV
Authors: Potthoff Anja Verena , Brockmeyer Norbert H.
Published: July 2009

Antiretroviral therapy has improved continuously. Almost every year a new drug has been approved. Nucleoside analogs still build the backbone of antiretroviral therapy. They inhibit reverse transcriptase and thus the transcription of RNA to DNA. They are combined with non‐nucleoside reverse transcriptase inhibitors or protease inhibitors. New therapeutic approaches are attachment or entry inhibitors, integrase inhibitors and maturation inhibitors. Multiple prospective multicenter studies have proven the life prolonging effect of antiretroviral therapy. With the optimal therapy life expectancy of HIV patients is only slightly reduced, similar to that of those with chronic diseases such as diabetes mellitus. One result of the higher age of HIV patients is an increase in concomitant diseases and medications. Drug interactions have to be considered and avoided. There has been a long discussion about the best time point to start antiretroviral therapy. In the late 1990s, every infected patient was treated hoping to eliminate the virus, ignoring the CD4+ cell count and viral load. This caused multiple (long‐term) side effects and a rising resistance problem. The guidelines now recommend starting therapy at about 350/μl CD4 lymphocytes. Due to its complexity antiretroviral therapy should be initiated and monitored in specialized centers.
The interaction of the Escherichia coli protein SlyD with nickel ions illuminates the mechanism of regulation of its peptidyl‐prolyl isomerase activity
Authors: Martino Luigi , He Yangzi , Hands‐Taylor Katherine L. D. , Valentine Elizabeth R. , Kelly Geoff , Giancola Concetta , Conte Maria R.
Published: July 2009

The sensitive to lysis D (SlyD) protein from Escherichia coli is related to the FK506‐binding protein family, and it harbours both peptidyl‐prolyl cis–trans isomerase (PPIase) and chaperone‐like activity, preventing aggregation and promoting the correct folding of other proteins. Whereas a functional role of SlyD as a protein‐folding catalyst in vivo remains unclear, SlyD has been shown to be an essential component for [Ni–Fe]‐hydrogenase metallocentre assembly in bacteria. Interestingly, the isomerase activity of SlyD is uniquely modulated by nickel ions, which possibly regulate its functions in response to external stimuli. In this work, we investigated the solution structure of SlyD and its interaction with nickel ions, enabling us to gain insights into the molecular mechanism of this regulation. We have revealed that the PPIase module of SlyD contains an additional C‐terminal α‐helix packed against the catalytic site of the domain; unexpectedly, our results show that the interaction of SlyD with nickel ions entails participation of the novel structural features of the PPIase domain, eliciting structural alterations of the catalytic pocket. We suggest that such conformational rearrangements upon metal binding underlie the ability of nickel ions to regulate the isomerase activity of SlyD.
Mutagenic probes of the role of Ser209 on the cavity shaping loop of human monoamine oxidase A
Authors: Wang Jin , Harris Johnny , Mousseau Darrell D. , Edmondson Dale E.
Published: July 2009

The available literature implicating human monoamine oxidase A (MAO A) in apoptotic processes reports levels of MAO A protein that do not correlate with activity, suggesting that unknown mechanisms may be involved in the regulation of catalytic function. Bioinformatic analysis suggests Ser209 as a possible phosphorylation site that may be relevant to catalytic function because it is adjacent to a six‐residue loop termed the ‘cavity shaping loop’ from structural data. To probe the functional role of this site, MAO A Ser209Ala and Ser209Glu mutants were created and investigated. In its membrane‐bound form, the MAO A Ser209Glu phosphorylation mimic exhibits catalytic and inhibitor binding properties similar to those of wild‐type MAO A. Solubilization in detergent solution and purification of the Ser209Glu mutant results in considerable decreases in these functional parameters. By contrast, the MAO A Ser209Ala mutant exhibits similar catalytic properties to those of wild‐type enzyme when purified. Compared to purified wild‐type and Ser209Ala MAO A proteins, the Ser209Glu MAO A mutant shows significant differences in covalent flavin fluorescence yield, CD spectra and thermal stability. These structural differences in the purified MAO A Ser209Glu mutant are not exhibited in quantitative structure–activity relationship patterns using a series of para‐substituted benzylamine analogs similar to the wild‐type enzyme. These data suggest that Ser209 in MAO A does not appear to be the putative phosphorylation site for regulation of MAO A activity and demonstrate that the membrane environment plays a significant role in stabilizing the structure of MAO A and its mutant forms.
Reactive oxygen species in rostral ventrolateral medulla modulate cardiac sympathetic afferent reflex in rats
Authors: Zhong M.‐K. , Gao J. , Zhang F. , Xu B. , Fan Z.‐D. , Wang W. , Zhu G.‐Q.
Published: July 2009

Aim:  The aim of the present study was to investigate whether reactive oxygen species (ROS) in rostral ventrolateral medulla (RVLM) modulate cardiac sympathetic afferent reflex (CSAR) and the enhanced CSAR response caused by microinjection of angiotensin II (Ang II) into the paraventricular nucleus (PVN).

Methods:  Under urethane and α‐chloralose anaesthesia, renal sympathetic nerve activity (RSNA) and mean arterial pressure (MAP) were recorded in sinoaortic‐denervated and cervical‐vagotomized rats. The CSAR was evaluated by the RSNA response to epicardial application of capsaicin (1.0 nmol).

Results:  Bilateral RVLM microinjection of tempol (a superoxide anion scavenger) or polyethylene glycol‐superoxide dismutase (PEG‐SOD, an analogue of endogenous superoxide dismutase) attenuated the CSAR, but did not cause significant change in baseline RSNA and MAP. NAD(P)H oxidase inhibitors apocynin or phenylarsine oxide (PAO) also showed similar effects, but SOD inhibitor diethyldithio‐carbamic acid (DETC) enhanced the CSAR and baseline RSNA, and increased the baseline MAP. Bilateral PVN microinjection of Ang II (0.3 nmol) enhanced the CSAR and increased RSNA and MAP, which was inhibited by the pre‐treatment with RVLM administration of tempol, PEG‐SOD, apocynin or PAO. The pre‐treatment with DETC in the RVLM only showed a tendency in potentiating the CSAR response of Ang II in the PVN, but significantly potentiated the RSNA and MAP responses of Ang II.

Conclusion:  These results suggest that the NAD(P)H oxidase‐derived ROS in the RVLM modulate the CSAR. The ROS in the RVLM is necessary for the enhanced CSAR response caused by Ang II in the PVN.
Psychometric properties of the Chinese (Cantonese) Tinnitus Handicap Inventory
Authors: Kam A.C.S. , Cheung A.P.P. , Chan P.Y.B. , Leung E.K.S. , Wong T.K.C. , Van Hasselt C.A. , Tong M.C.F.
Published: July 2009

Objectives:  To establish the reliablity and validity of the Chinese (Cantonese) version of the Tinnitus Handicap Inventory to measure the self‐perceived handicapping effect and severity of the condition in patients with chronic tinnitus.

Design:  Cross‐sectional psychometric validation study.

Setting:  Audiology clinics in a hospital setting.

Participants:  Subjects were 114 adult Chinese who attended the audiology clinics with a complaint of tinnitus.

Main outcome measures:  Test‐retest and internal consistency reliability; construct validity.

Results:  The Chinese version of the Tinnitus Handicap Inventory and its subscales showed good internal consistency reliabilities (α = 0.72–0.94) that are comparable to those of the original version. High correlations were observed between the Tinnitus Handicap Inventory and psychological distress, tinnitus‐related problem ratings and severity ratings. Factor analysis showed that the Chinese version of the Tinnitus Handicap Inventory has a unifactorial structure. A high degree of test‐retest reliablity was observed (intraclass correlation coefficient = 0.88).

Conclusions:  The results suggest that the Chinese (Cantonese) version of the Tinnitus Handicap Inventory is a reliable and valid measure of general tinnitus‐related distress that can be used in clinical settings to quantify the impact of tinnitus on daily life.
Effect of parthenolide on proliferation and apoptosis in gastric cancer cell line SGC7901
Authors: ZHAO Li Jie , XU Yong Hong , LI Yan
Published: July 2009

OBJECTIVE:  To investigate the effect of parthenolide (PAR) on proliferation and apoptosis in gastric cancer cell line SGC7901.

METHODS:  Human gastric cancer cell line SGC7901 cells were incubated with various concentration of PAR. After various periods of incubation, the proliferation of SGC7901 cells was assessed by 3‐(4,5‐Dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide methyl thiazolyl tetrazolium (MTT) assay. Apoptosis was measured by the annexin V‐fluorescein isothiocyanate fluoresceine isothiocyanate (FITC)/propidium iodide (PI) double labeled staining method and the morphology of the cell was observed under a fluorescent microscope. Mitochondrial potential was measured by flow cytometry after Rhodamine 123 staining. The expressions of cytochrome C and the Bcl‐2 family of proteins, including Bcl‐2, Bax, Bid and tBid were measured by Western blot. Caspase 3 and 8 activities were measured by enzyme‐linked immunosorbent assay.

RESULTS:  Treatment with PAR induced apoptosis as confirmed by annexin V‐FITC/PI assay. PAR‐induced apoptosis was associated with intracellular events including the decline of mitochondrial potential, increased release of cytochrome C from the mitochondria, decreased expression of Bcl‐2, increased expression of Bax, Bid and tBid and activation of caspase 3 and 8.

CONCLUSION:  These results suggest that possibly via activation of the mitochondrial pathway, PAR causes mitochondrial damage leading to the release of cytochrome C and by regulating the expression of the Bcl‐2 family of proteins and activating caspases which leads to results in apoptotic cell death in SGC7901 cells. Our results might be helpful in formulating new therapeutic approaches using Chinese herbal medicine.
Rapid assessments of tropical dung beetle and butterfly assemblages: contrasting trends along a forest disturbance gradient
Authors: HAYES LUCY , MANN DARREN J. , MONASTYRSKII ALEXANDER L. , LEWIS OWEN T.
Published: July 2009

Abstract.  1. We carried out rapid assessments of the richness and diversity of fruit‐feeding butterflies (sampled with baited traps) and dung beetles (sampled with buffalo dung‐baited pitfall traps) at 20 sites across an anthropogenic forest disturbance gradient in Ba Be National Park, Vietnam.

2. We investigated measures of diversity, richness, and functional composition for individual taxa in relation to the degree of disturbance, and verified whether dung beetles and butterflies showed congruent trends.

3. For butterflies, overall species richness increased with forest disturbance, but the richness of rare species decreased. Species diversity was uncorrelated with disturbance.

4. In dung beetles, species richness was unrelated to forest disturbance, but species diversity increased with forest disturbance. The richness of dung beetles in the telecoprid (roller) guild declined with forest disturbance.

5. There was no significant correlation between dung beetles and butterflies across sites for either species richness or species diversity.

6. Apparent effects of disturbance were thus sensitive to the particular metric used (species richness or diversity), the taxonomic group studied (butterflies or dung beetles), and the functional group investigated (different guilds of dung beetle).
Cytologic, histologic, and immunohistochemical features of maxillofacial alveolar rhabdomyosarcoma in a juvenile dog
Authors: Murakami Mami , Sakai Hiroki , Iwatani Nao , Asakura Aki , Hoshino Yuki , Mori Takashi , Yanai Tokuma , Maruo Kohji , Masegi Toshiaki
Published: July 2009

Abstract: A 15‐month‐old castrated male dog with a history of intermittent epistaxis and sneezing was admitted for the examination of a maxillofacial mass. An impression smear of a biopsy sample from the cauliflower‐shaped gingival mass contained numerous round cells, 5–25 μm in diameter, which contained a moderate amount of clear to pale blue cytoplasm and resembled lymphoid cells. Mitotic figures were frequently observed. The mass was diagnosed as malignant round cell neoplasia. On histologic examination the tumor was composed of diffusely arranged, small, atypical round cells with a small amount of fibrovascular stroma. Immunohistochemically, the cells were negative for CD3, CD18, CD20, CD79α, cytokeratin, melan‐A, chromogranin A, α‐smooth muscle actin, and myoglobin but positive for vimentin and desmin. The cells also had strong positive nuclear staining for myogenin and MyoD1. A diagnosis of solid‐pattern alveolar rhabdomyosarcoma was made on the basis of morphologic and immunohistochemical results. Alveolar rhabdomyosarcoma should be considered in the differential diagnosis of tumors in juvenile dogs, especially when cytologic findings reveal round, undifferentiated cells.
Tumbling for Stealth?
Authors: Stocker Roman , Durham William M.
Published: July 2009

A green alga changes its flagellar beating patterns to create a run-and-tumble motion that may help it escape predation.
NOAA Project to Measure Gravity Aims to Improve Coastal Monitoring
Authors: Johnson Brittany
Published: July 2009

How high is up? The U.S. government has launched a 10-year, $38 million research project to answer that question in hopes of improving its management of coastal regions and reducing the damage from severe storms and rising sea levels.
A Good Sign
Authors: Saini Angela
Published: July 2009

When existing notation for explaining a complex mathematical problem wasn't enough, Byron Cook teamed up with an artist to design his own.
Econophysics: Still Controversial After All These Years
Authors: Cho Adrian
Published: July 2009

Econophysics is the biggest branch of complex-systems research, and physicists have flocked into finance. But many economists view econophysicists as dilettantes.
New Real-Time PCR Detects Prolonged Norovirus Excretion in Highly Immunosuppressed Patients and Children
Authors: Henke-Gendo C. , Harste G. , Juergens-Saathoff B. , Mattner F. , Deppe H. , Heim A.
Published: July 2009

Noroviruses (NoV) are a major cause of epidemic nonbacterial gastroenteritis and affect all age groups worldwide. Three of five NoV genogroups, namely, genogroup I (GI), GII, and GIV, are associated with human disease. Unfortunately, these genogroups demonstrate a high degree of sequence diversity, complicating the design of pan-NoV diagnostic PCR tests. To decrease the risk of false-negative test results, we have developed a new one-step real-time TaqMan reverse transcription-PCR protocol. This protocol detects all human NoV genogroups in one reaction with a sensitivity of 400 virus genome equivalents/reaction for both GI and GII. The use of in vitro-transcribed NoV RNA as an external standard allows (semi)quantification of viral loads in samples. In a retrospective analysis of 206 stool samples from 77 patient episodes, the duration of NoV excretion and the amount of virus excreted were determined. Twenty (26.0%) of these episodes lasted longer than 10 days. Univariate risk factor analysis revealed the patient status after organ transplantation (odds ratio [OR], 7.49 [95% confidence interval, 2.06 to 28.32];
P
< 0.001), immunosuppression (OR, 9.19 [95% confidence interval, 2.50 to 35.39];
P
< 0.001), and age of less than 10 years (OR, 4.58 [95% confidence interval, 1.36 to 15.77];
P
= 0.004) as risk factors for a NoV excretion period of more than 10 days. These findings were confirmed by time-dependent Kaplan-Meier analyses, whereas multivariate Cox regression analyses identified immunosuppression as the sole risk factor. Surprisingly, in contrast to the excretion periods, the viral loads in stools did not increase in connection with age or immunosuppressive status. This fact may be one important piece in the pattern of high-level NoV transmissibility and may have an impact on the development of transmission prevention strategies.
Human Immunodeficiency Virus and Leprosy Coinfection in Pune, India
Authors: Vinay Kulkarni , Smita Joshi , Nikhil Gupte , Neeta Gokhale
Published: July 2009

We report eight cases and the incidence of leprosy in human immunodeficiency virus (HIV)-infected individuals after initiation of antiretroviral treatment (ART). The incidence of leprosy in patients on ART was 5.22 per 1,000 person-years (95% confidence interval, 2.25 to 10.28). This high incidence suggests that there should be regular examination of HIV-infected individuals for clinical signs of leprosy.
Detection of Low Levels of Human Immunodeficiency Virus (HIV) May Be Critical for Early Diagnosis of Pediatric HIV Infection by Use of Dried Blood Spots
Authors: Walter Jan , Kuhn Louise , Semrau Katherine , Decker Don W. , Sinkala Moses , Kankasa Chipepo , Thea Donald M. , Bulterys Marc , Ou Chin-Yih , Aldrovandi Grace M.
Published: July 2009

We compared a DNA-based assay with a total nucleic acid-based assay for early detection of infant human immunodeficiency virus (HIV) infection. The codetection of DNA and RNA did not result in an overall higher sensitivity compared to that of DNA alone. Discordant results were associated with low levels of HIV DNA, indicating that the sample amount may be critical.
Wild-Type p53 Enhances Efficiency of Simian Virus 40 Large-T-Antigen-Induced Cellular Transformation
Authors: Hermannstädter Andrea , Ziegler Christine , Kühl Marion , Deppert Wolfgang , Tolstonog Genrich V.
Published: July 2009

Abortive infection of BALB/c mouse embryo fibroblasts differing in
p53
gene status (p53
+/+
versus p53
−/
−
) with simian virus 40 (SV40) revealed a quantitatively and qualitatively decreased transformation efficiency in p53
−/−
cells compared to p53
+/+
cells, suggesting a supportive effect of wild-type (wt) p53 in the SV40 transformation process. SV40 transformation efficiency also was low in immortalized p53
−/−
BALB/c 10-1 cells but could be restored to approximately the level in immortalized p53
+/+
BALB/c 3T3 cells by reconstituting wt p53, but not mutant p53 (mutp53), expression. Stable expression of large T antigen (LT) in p53
+/+
3T3 cells resulted in full transformation, while LT expression in p53
−/−
10-1 cells could not promote growth in suspension or in soft agar to a significant extent. The helper effect of wt p53 is mediated by its cooperation with LT and resides in the p53 N terminus, as an N-terminally truncated p53 (ΔNp53) could not rescue the p53-null phenotype. The p53 N terminus serves as a scaffold for recruiting transcriptional regulators like p300/CBP and Mdm2 into the LT-p53 complex. Consequently, LT affected global and specific gene expression in p53
+/+
cells significantly more than in p53
−/−
cells. Our data suggest that recruitment of transcriptional regulators into the LT-p53 complex may help to modify cellular gene expression in response to the needs of cellular transformation.
Rho GTPases Modulate Entry of Ebola Virus and Vesicular Stomatitis Virus Pseudotyped Vectors
Authors: Quinn Kathrina , Brindley Melinda A. , Weller Melodie L. , Kaludov Nikola , Kondratowicz Andrew , Hunt Catherine L. , Sinn Patrick L. , McCray Paul B. , Stein Colleen S. , Davidson Beverly L. , Flick Ramon , Mandell Robert , Staplin William , Maury Wendy , Chiorini John A.
Published: July 2009

To explore mechanisms of entry for Ebola virus (EBOV) glycoprotein (GP) pseudotyped virions, we used comparative gene analysis to identify genes whose expression correlated with viral transduction. Candidate genes were identified by using EBOV GP pseudotyped virions to transduce human tumor cell lines that had previously been characterized by cDNA microarray. Transduction profiles for each of these cell lines were generated, and a significant positive correlation was observed between RhoC expression and permissivity for EBOV vector transduction. This correlation was not specific for EBOV vector alone as RhoC also correlated highly with transduction of vesicular stomatitis virus GP (VSVG) pseudotyped vector. Levels of RhoC protein in EBOV and VSV permissive and nonpermissive cells were consistent with the cDNA gene array findings. Additionally, vector transduction was elevated in cells that expressed high levels of endogenous RhoC but not RhoA. RhoB and RhoC overexpression significantly increased EBOV GP and VSVG pseudotyped vector transduction but had minimal effect on human immunodeficiency virus (HIV) GP pseudotyped HIV or adeno-associated virus 2 vector entry, indicating that not all virus uptake was enhanced by expression of these molecules. RhoB and RhoC overexpression also significantly enhanced VSV infection. Similarly, overexpression of RhoC led to a significant increase in fusion of EBOV virus-like particles. Finally, ectopic expression of RhoC resulted in increased nonspecific endocytosis of fluorescent dextran and in formation of increased actin stress fibers compared to RhoA-transfected cells, suggesting that RhoC is enhancing macropinocytosis. In total, our studies implicate RhoB and RhoC in enhanced productive entry of some pseudovirions and suggest the involvement of actin-mediated macropinocytosis as a mechanism of uptake of EBOV GP and VSVG pseudotyped viral particles.
Human Immunodeficiency Virus Type 1 V1-to-V5 Envelope Variants from the Chronic Phase of Infection Use CCR5 and Fuse More Efficiently than Those from Early after Infection
Authors: Etemad Behzad , Fellows Angela , Kwambana Brenda , Kamat Anupa , Feng Yang , Lee Sandra , Sagar Manish
Published: July 2009

Human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein modifications over the course of infection have been associated with coreceptor switching and antibody neutralization resistance, but the effect of the changes on replication and host cell receptor usage remains unclear. To examine this question, unique early- and chronic-stage infection envelope V1-toV5 (V1-V5) segments from eight HIV-1 subtype A-infected subjects were incorporated into an isogenic background to construct replication-competent recombinant viruses. In all subjects, viruses with chronic-infection V1-V5 segments showed greater replication capacity than those with early-infection V1-V5 domains in cell lines with high levels of both the CD4 and the CCR5 receptors. Viruses with chronic-infection V1-V5s demonstrated a significantly increased ability to replicate in cells with low CCR5 receptor levels and greater resistance to CCR5 receptor and fusion inhibitors compared to those with early-infection V1-V5 segments. These properties were associated with sequence changes in the envelope V1-V3 segments. Viruses with the envelope segments from the two infection time points showed no significant difference in their ability to infect cells with low CD4 receptor densities, in their sensitivity to soluble CD4, or in their replication capacity in monocyte-derived macrophages. Our results suggest that envelope changes, primarily in the V1-V3 domains, increase both the ability to use the CCR5 receptor and fusion kinetics. Thus, envelope modifications over time within a host potentially enhance replication capacity.
Interaction of the
Tobacco Mosaic Virus
Replicase Protein with a NAC Domain Transcription Factor Is Associated with the Suppression of Systemic Host Defenses
Authors: Wang Xiao , Goregaoker Sameer P. , Culver James N.
Published: July 2009

An interaction between the helicase domain of the
Tobacco mosaic virus
(TMV) 126-/183-kDa replicase protein(s) and the
Arabidopsis thaliana
NAC domain transcription factor ATAF2 was identified via yeast two-hybrid and in planta immunoprecipitation assays. ATAF2 is transcriptionally induced in response to TMV infection, and its overexpression significantly reduces virus accumulation. Proteasome inhibition studies suggest that ATAF2 is targeted for degradation during virus infection. The transcriptional activity of known defense-associated marker genes
PR1
,
PR2
, and
PDF1.2
significantly increase within transgenic plants overexpressing ATAF2. In contrast, these marker genes have reduced transcript levels in ATAF2 knockout or repressor plant lines. Thus, ATAF2 appears to function in the regulation of host basal defense responses. In response to TMV infections,
ATAF2
and
PR1
display increased transcript accumulations in inoculated tissues but not in systemically infected tissues.
ATAF2
and
PR1
transcript levels also increase in response to salicylic acid treatment. However, the salicylic acid treatment of systemically infected tissues did not produce a similar increase in either
ATAF2
or
PR1
transcripts, suggesting that host defense responses are attenuated during systemic virus invasion. Similarly, noninfected ATAF2 knockout or ATAF2 repressor lines display reduced levels of
PR1
transcripts when treated with salicylic acid. Taken together, these findings suggest that the replicase-ATAF2 interaction suppresses basal host defenses as a means to promote systemic virus accumulation.
QUANTITATIVE IDENTIFICATION OF ROTOR CRACKS BASED ON FINITE ELEMENT OF B-SPLINE WAVELET ON THE INTERVAL
Authors: CHEN XUEFENG , LI BING , XIANG JIAWEI , HE ZHENGJIA
Published: July 2009

Based on finite element of B-spline wavelet on the interval (BSWI), the quantitative identification method of transverse crack for rotor systems was studied. The new model of BSWI Rayleigh–Euler rotary beam element considering gyroscopic effect and rotational inertia was constructed to solve the first three natural frequencies of the cracked rotor with high precision, and the first three frequencies solution surfaces of normalized crack location and size were obtained by using surface-fitting technique. Then the first three metrical natural frequencies were employed as inputs of the solution curve surfaces. The intersection of the three frequencies contour lines predicted the normalized crack location and size. The numerical and experimental examples were given to verify the validity of the beam element for crack quantitative identification in rotor systems. The new method can be applied to prognosis and quantitative diagnosis of cracks in the rotor system.
ALIASING IN GENE FEATURE DETECTION BY PROJECTIVE METHODS
Authors: CAPOBIANCO ENRICO
Published: July 2009

Because of measurements obtained under limited experimental conditions or time points compared to the presence of many genes, also known as the "large dimension, small sample size" problem, dimensionality reduction techniques are a common practice in statistical bioinformatics involving microarray analysis. However, in order to improve the performance of reverse engineering and statistical inference procedures aimed to estimate gene–gene connectivity links, some kind of regularization is usually needed to reduce the overall data complexities, together with ad hoc feature selection to uncover biologically relevant gene associations. The paper deals with feature selection by projective methods; in particular, it addresses some issues: Can the impact of noise on the data be limited by shrinkage or de-noising? How can complexity from convoluted dynamics associated with microarray measurements be discounted? In modeling such data, how to deal with over-parametrization, and control it? The problem of aliasing is then discussed and classified into two categories according to the trade-off between biological relevance and noise, and finally reported in analytical form via subspace analysis.
INFERENCE OF LARGE-SCALE GENE REGULATORY NETWORKS USING REGRESSION-BASED NETWORK APPROACH
Authors: KIM HASEONG , LEE JAE K. , PARK TAESUNG
Published: July 2009

The gene regulatory network modeling plays a key role in search for relationships among genes. Many modeling approaches have been introduced to find the causal relationship between genes using time series microarray data. However, they have been suffering from high dimensionality, overfitting, and heavy computation time. Further, the selection of a best model among several possible competing models is not guaranteed that it is the best one. In this study, we propose a simple procedure for constructing large scale gene regulatory networks using a regression-based network approach. We determine the optimal out-degree of network structure by using the sum of squared coefficients which are obtained from all appropriate regression models. Through the simulated data, accuracy of estimation and robustness against noise are computed in order to compare with the vector autoregressive regression model. Our method shows high accuracy and robustness for inferring large-scale gene networks. Also it is applied to Caulobacter crecentus cell cycle data consisting of 1472 genes. It shows that many genes are regulated by two transcription factors, ctrA and gcrA, that are known for global regulators.
Adverse effects of high glucose and free fatty acid on cardiomyocytes are mediated by connective tissue growth factor
Authors: Wang Xiaoyu , McLennan Susan V. , Allen Terri J. , Tsoutsman Tatiana , Semsarian Christopher , Twigg Stephen M.
Published: July 2009

Diabetic cardiomyopathy is characterized by interstitial fibrosis and cardiomyocyte hypertrophy and apoptosis. Also known as CCN2, connective tissue growth factor (CTGF) is implicated in the fibrosis; however, whether it contributes to cardiomyocytes changes and adverse effects of high glucose and lipids on these cells remains unknown. Hearts from streptozotocin-induced diabetic rats had elevated CTGF and changes of pathological myocardial hypertrophy, fibrosis, and cardiomyocyte apoptosis. Rat H9c2 cardiomyocytes were then treated with recombinant human (rh)CTGF, high glucose, or the saturated free fatty acid palmitate. Each reagent induced cell hypertrophy, as indicated by the ratio of total protein to cell number, cell size, and gene expression of cardiac hypertrophy marker genes atrial natriuretic peptide (ANP), and α-skeletal actin. Each treatment also caused apoptosis measured by increased caspase3/7 activity, apoptotic cells by transferase-mediated dUTP nick end labeling (TUNEL) assay, and lower viable cell number. Further studies showed CTGF mRNA was rapidly induced by high glucose and palmitate in H9c2 cells and in mouse neonatal cardiomyocyte primary cultures. small interfering RNA against CTGF blocked the high glucose and palmitate induction of hypertrophy and apoptosis. In addition, these CTGF effects were through the tyrosine kinase A (TrkA) receptor with tyrosine kinase activity, which has previously been implicated in CTGF signaling: TrkA was phosphorylated by CTGF, and a specific TrkA blocker abrogated CTGF-induced effects on hypertrophy and apoptosis. For the first time in any system, fatty acid is newly identified as a regulator of CTGF, and this work implicates autocrine CTGF as a mediator of adverse effects of high glucose and fatty acids in cardiomyocytes.