bluuebunny/crossref_metadata_2025 huggingface dataset:
Helminth secretome database (HSD): a collection of helminth excretory/secretory proteins predicted from expressed sequence tags (ESTs)
Authors: Garg Gagan , Ranganathan Shoba
Published: December 2012

Background

Helminths are important socio-economic organisms, responsible for causing major parasitic infections in humans, other animals and plants. These infections impose a significant public health and economic burden globally. Exceptionally, some helminth organisms like Caenorhabditis elegans are free-living in nature and serve as model organisms for studying parasitic infections. Excretory/secretory proteins play an important role in parasitic helminth infections which make these proteins attractive targets for therapeutic use. In the case of helminths, large volume of expressed sequence tags (ESTs) has been generated to understand parasitism at molecular level and for predicting excretory/secretory proteins for developing novel strategies to tackle parasitic infections. However, mostly predicted ES proteins are not available for further analysis and there is no repository available for such predicted ES proteins. Furthermore, predictions have, in the main, focussed on classical secretory pathways while it is well established that helminth parasites also utilise non-classical secretory pathways.

Results

We developed a free Helminth Secretome Database (HSD), which serves as a repository for ES proteins predicted using classical and non-classical secretory pathways, from EST data for 78 helminth species (64 nematodes, 7 trematodes and 7 cestodes) ranging from parasitic to free-living organisms. Approximately 0.9 million ESTs compiled from the largest EST database, dbEST were cleaned, assembled and analysed by different computational tools in our bioinformatics pipeline and predicted ES proteins were submitted to HSD.

Conclusion

We report the large-scale prediction and analysis of classically and non-classically secreted ES proteins from diverse helminth organisms. All the Unigenes (contigs and singletons) and excretory/secretory protein datasets generated from this analysis are freely available. A BLAST server is available at http://estexplorer.biolinfo.org/hsd, for checking the sequence similarity of new protein sequences against predicted helminth ES proteins.
Novel missense mutation in the RSPO4 gene in congenital hyponychia and evidence for a polymorphic initiation codon (p.M1I)
Authors: Khan Tahir Naeem , Klar Joakim , Nawaz Sadia , Jameel Muhammad , Tariq Muhammad , Malik Naveed Altaf , Baig Shahid M , Dahl Niklas
Published: December 2012

Background

Anonychia/hyponychia congenita is a rare autosomal recessive developmental disorder characterized by the absence (anonychia) or hypoplasia (hyponuchia) of finger- and/or toenails frequently caused by mutations in the R-spondin 4 (RSPO4) gene.

Methods

Three hypo/anonychia consanguineous Pakistani families were ascertained and genotyped using microsatellite markers spanning the RSPO4 locus on chromosome 20p13. Mutation screening of the RSPO4 gene was carried out by direct sequencing of the entire coding region and all intron-exon boundaries.

Results

Mutations in the RSPO4 gene were identified in all families including a novel missense mutation c.178C>T (p.R60W) and two recurrent variants c.353G>A (p.C118Y) and c.3G>A (p.M1I). The c.3G>A variant was identified in unaffected family members and a control sample in a homozygous state.

Conclusions

This study raises to 17 the number of known RSPO4 mutations and further expands the molecular repertoire causing hypo/anonychia. The c.353G>A emerges as a recurrent change with a possible founder effect in the Pakistani population. Our findings suggest that c.3G>A is not sufficient to cause the disorder and could be considered a polymorphism.
Statins and the risk of gastric cancer in diabetes patients
Authors: Lee Jeeyun , Lee Soo Hyeon , Hur Kyu Yeon , Woo Sook Young , Kim Sun Woo , Kang Won Ki
Published: December 2012

Background

Several studies have suggested a cancer risk reduction in statin users although the evidence remains weak for stomach cancer. The purpose of this study was to use an exact-matching case–control design to examine the risk of gastric cancer associated with the use of statins in a cohort of patients with diabetes.

Methods

Cases were defined as patients with incident gastric cancer identified by International Classification of Diseases 16.0 ~ 16.9 recorded at Samsung Medical Center database during the period of 1999 to 2008, at least 6 months after the entry date of diabetes code. Each gastric cancer case patient was matched with one control patient from the diabetes patient registry in a 1:1 fashion, blinded to patient outcomes.

Results

A total of 983 cases with gastric cancer and 983 controls without gastric cancer, matched by age and sex, were included in the analysis. The presence of prescription for any statin was inversely associated with gastric cancer risk in the unadjusted conditional logistic regression model (OR: 0.18; 95% CI: 0.14 – 0.24; P < .0001). Multivariate analysis using conditional logistic regression with Bonferroni’s correction against aspirin indicated a significant reduction in the risk of gastric cancer in diabetes patients with statin prescriptions (OR: 0.21; 95% CI: 0.16 – 0.28; P < .0001). After adjustment for aspirin use, a longer duration of statin use was associated with reduced risk of gastric cancer, with statistical significance (P<.0001).

Conclusions

A strong inverse association was found between the risk of gastric adenocarcinoma and statin use in diabetic patients.
The allogeneic umbilical cord mesenchymal stem cells regulate the function of T helper 17 cells from patients with rheumatoid arthritis in an in vitro co-culture system
Authors: Wang Qin , Li Xiaofeng , Luo Jing , Zhang Li , Ma Lihui , Lv Zhiqin , Xue Lijin
Published: December 2012

Background

Previous in vivo studies have shown that mesenchymal stem cell (MSC) transplantation significantly improves the condition of a number of autoimmune diseases including autoimmune cerebrospinal meningitis, multiple sclerosis, glomerulonephritis and systemic lupus erythematosus.

Methods

To investigate the immunoregulatory effect of stem cell transplantation, human umbilical cord MSCs were co-cultured with peripheral blood mononuclear cells (PBMCs) from patients with rheumatoid arthritis (RA). Orphan nuclear receptor gamma (ROR-γ) mRNA and protein expression was detected with real-time PCR and Western blotting. Interleukin (IL)-17, IL-6 and tumor necrosis factor (TNF-α) in the cell culture supernatant were measured using a flow cytometric bead capture method.

Results

After 72 hours of co-culture, the mRNA and protein expression levels of ROR-γ in co-cultured PBMCs were decreased compared with that in PBMC of RA patients cultured alone (p < 0.05). Moreover, the decrement was positively related to the disease activity of RA (p < 0.05). Decreased secretion of IL-17, TNF-α and IL-6 were also found in co-culture supernatants of PBMCs from patients with severe and moderate disease activity, but not in supernatant from PBMCs cultured alone. The decreased cytokine expression levels were positively correlated to the concentrations of MSCs. In contrast, PBMCs from healthy controls or patients with mild RA did not show significant differences in ROR-γ expression or cytokine secretion following co-culture with MSCs as compared with those cultured alone.

Conclusions

In vitro co-culture with MSCs down-regulated the inflammatory response of PBMCs from RA patients with severe disease activity, but had no significant effect on PBMCs from healthy controls or patients with mild disease activity, suggesting that the immunoregulatory role of MSCs may associate with the occurrence of inflammatory mediators.
Glyceraldehyde 3-phosphate dehydrogenase negatively regulates human immunodeficiency virus type 1 infection
Authors: Kishimoto Naoki , Onitsuka Ayano , Kido Keishi , Takamune Nobutoki , Shoji Shozo , Misumi Shogo
Published: December 2012

Background

Host proteins are incorporated inside human immunodeficiency virus type 1 (HIV-1) virions during assembly and can either positively or negatively regulate HIV-1 infection. Although the identification efficiency of host proteins is improved by mass spectrometry, how those host proteins affect HIV-1 replication has not yet been fully clarified.

Results

In this study, we show that virion-associated glyceraldehyde 3-phosphate dehydrogenase (GAPDH) does not allosterically inactivate HIV-1 reverse transcriptase (RT) but decreases the efficiency of reverse transcription reactions by decreasing the packaging efficiency of lysyl-tRNA synthetase (LysRS) and tRNALys3 into HIV-1 virions. Two-dimensional (2D) gel electrophoresis demonstrated that some isozymes of GAPDH with different isoelectric points were expressed in HIV-1-producing CEM/LAV-1 cells, and a proportion of GAPDH was selectively incorporated into the virions. Suppression of GAPDH expression by RNA interference in CEM/LAV-1 cells resulted in decreased GAPDH packaging inside the virions, and the GAPDH-packaging-defective virus maintained at least control levels of viral production but increased the infectivity. Quantitative analysis of reverse transcription products indicated that the levels of early cDNA products of the GAPDH-packaging-defective virus were higher than those of the control virus owing to the higher packaging efficiencies of LysRS and tRNALys3 into the virions rather than the GAPDH-dependent negative allosteric modulation for RT. Furthermore, immunoprecipitation assay using an anti-GAPDH antibody showed that GAPDH directly interacted with Pr55
gag
and p160
gag-pol
and the overexpression of LysRS in HIV-1-producing cells resulted in a decrease in the efficiency of GAPDH packaging in HIV particles. In contrast, the viruses produced from cells expressing a high level of GAPDH showed decreased infectivity in TZM-bl cells and reverse transcription efficiency in TZM-bl cells and peripheral blood mononuclear cells (PBMCs).

Conclusions

These findings indicate that GAPDH negatively regulates HIV-1 infection and provide insights into a novel function of GAPDH in the HIV-1 life cycle and a new host defense mechanism against HIV-1 infection.
In vitro characterization of the antiviral activity of fucoidan from Cladosiphon okamuranus against Newcastle Disease Virus
Authors: Elizondo-Gonzalez Regina , Cruz-Suarez L Elizabeth , Ricque-Marie Denis , Mendoza-Gamboa Edgar , Rodriguez-Padilla Cristina , Trejo-Avila Laura M
Published: December 2012

Background

Newcastle Disease Virus (NDV) causes a serious infectious disease in birds that results in severe losses in the worldwide poultry industry. Despite vaccination, NDV outbreaks have increased the necessity of alternative prevention and control measures. Several recent studies focused on antiviral compounds obtained from natural resources. Many extracts from marine organisms have been isolated and tested for pharmacological purposes, and their antiviral activity has been demonstrated in vitro and in vivo. Fucoidan is a sulfated polysaccharide present in the cell wall matrix of brown algae that has been demonstrated to inhibit certain enveloped viruses with low toxicity. This study evaluated the potential antiviral activity and the mechanism of action of fucoidan from Cladosiphon okamuranus against NDV in the Vero cell line.

Methods

The cytotoxicity of fucoidan was determined by the MTT assay. To study its antiviral activity, fusion and plaque-forming unit (PFU) inhibition assays were conducted. The mechanism of action was determined by time of addition, fusion inhibition, and penetration assays. The NDV vaccine strain (La Sota) was used in the fusion inhibition assays. PFU and Western blot experiments were performed using a wild-type lentogenic NDV strain.

Results

Fucoidan exhibited antiviral activity against NDV La Sota, with an obtained IS50 >2000. In time of addition studies, we observed viral inhibition in the early stages of infection (0–60 min post-infection). The inhibition of viral penetration experiments with a wild-type NDV strain supported this result, as these experiments demonstrated a 48% decrease in viral infection as well as reduced HN protein expression. Ribavirin, which was used as an antiviral control, exhibited lower antiviral activity than fucoidan and high toxicity at active doses. In the fusion assays, the number of syncytia was significantly reduced (70% inhibition) when fucoidan was added before cleavage of the fusion protein, perhaps indicating a specific interaction between fucoidan and the F0 protein.

Conclusion

The results of this study suggest that fucoidan from C. okamuranus represents a potential low-toxicity antiviral compound for the poultry industry, and our findings provide a better understanding of the mode of action of sulfated polysaccharides.
Comparative study between bone marrow mononuclear fraction and mesenchymal stem cells treatment in sensorimotor recovery after focal cortical ablation in rats
Authors: de Freitas Helder Teixeira , da Silva Viviane Gomes , Giraldi-Guimarães Arthur
Published: December 2012

Background

Different models of cortical lesion lead to different effects on plasticity of connections and loss of function. In opposition to ischemia, cortical lesion made by ablation does not induce significant adaptive plasticity of corticocortical and corticostriatal projections and leads to functional alterations other than those observed after ischemia. We have demonstrated sensorimotor recovery after treatment with bone marrow-derived mesenchymal stem cells (MSCs) or bone marrow mononuclear cells (BMMCs) in a model of focal cortical ischemia. Here, we extended this analysis evaluating the effect of these cells on sensorimotor recovery after focal cortical ablation, reproducing the same size and location of previous ischemic lesion.

Findings

Focal cerebral aspiration of the six cortical layers in left frontoparietal cortex was performed in male Wistar rats. One day later, MSCs or BMMCs were administrated (i.v.) in the ablated animals. Vehicle was administrated in the control group. Sensorimotor tests were performed before and after injury followed by i.v. injection. The monitoring of functional recovery was performed weekly during three post-ablation months. The results showed significant sensorimotor recovery with both treatments, whereas control groups had no recovery. Moreover, both cell types induced the same level of recovery.

Conclusions

Bone marrow cells showed therapeutic efficacy in a model of brain injury known to promote low structural plasticity. Thus, the results support the idea of BMMCs as better candidates to treat acute CNS injuries than MSCs, since they have the same therapeutic potential, but its obtainment for autologous transplantation has been shown to be faster and easier.
Development of a teledermatopathology consultation system using virtual slides
Authors: Nakayama Ikunori , Matsumura Tsubasa , Kamataki Akihisa , Uzuki Miwa , Saito Kenji , Hobbs James , Akasaka Toshihide , Sawai Takashi
Published: December 2012

Background

An online consultation system using virtual slides (whole slide images; WSI) has been developed for pathological diagnosis, and could help compensate for the shortage of pathologists, especially in the field of dermatopathology and in other fields dealing with difficult cases. This study focused on the performance and future potential of the system.

Method

In our system, histological specimens on slide glasses are digitalized by a virtual slide instrument, converted into web data, and up-loaded to an open server. Using our own purpose-built online system, we then input patient details such as age, gender, affected region, clinical data, past history and other related items. We next select up to ten consultants. Finally we send an e-mail to all consultants simultaneously through a single command. The consultant receives an e-mail containing an ID and password which is used to access the open server and inspect the images and other data associated with the case. The consultant makes a diagnosis, which is sent to us along with comments.

Because this was a pilot study, we also conducted several questionnaires with consultants concerning the quality of images, operability, usability, and other issues.

Results

We solicited consultations for 36 cases, including cases of tumor, and involving one to eight consultants in the field of dermatopathology. No problems were noted concerning the images or the functioning of the system on the sender or receiver sides. The quickest diagnosis was received only 18 minutes after sending our data. This is much faster than in conventional consultation using glass slides. There were no major problems relating to the diagnosis, although there were some minor differences of opinion between consultants. The results of questionnaires answered by many consultants confirmed the usability of this system for pathological consultation. (16 out of 23 consultants.)

Conclusion

We have developed a novel teledermatopathological consultation system using virtual slides, and investigated the usefulness of the system. The results demonstrate that our system can be a useful tool for international medical work, and we anticipate its wider application in the future.

Virtual slides

The virtual slides for this article can be found here:http://www.diagnosticpathology.diagnomx.eu/vs/1902376044831574
LMP1 and LMP2A are potential prognostic markers of extranodal NK/T-cell lymphoma, nasal type (ENKTL)
Authors: Mao Yuan , Zhang Da-Wei , Zhu Huijun , Lin Hong , Xiong Lin , Cao Qing , Liu Ying , Li Qing-Dong , Xu Jia-Ren , Xu Lin-Feng , Chen Ren-Jie
Published: December 2012

Background

Latent membrane protein (LMP) 1 and LMP2A encoded by Epstein-Barr virus (EBV) are associated with the development of malignancies, but their expression in extranodal NK/T-cell lymphoma, nasal type (ENKTL) and the relationship with clinical characteristics of this disease remain poorly understood. In the present study, we examined the expression of LMP1 and LMP2A in ENKTL, and investigated the correlations between LMP1 and LMP2A expression with clinicopathological characteristics of ENKTL patients.

Methods

Paraffin sections of surgically removed samples from 16 ENKTL patients were analyzed by immunohistochemistry and the related clinicopathological data were collected and analyzed.

Results

Elevated expression (immunohistochemistry score ≥ 4) of LMP1 and LMP2A was detected in the tumor cells of ENKTL. High LMP1 expression was associated with positive B symptoms (p = 0.012), while high LMP2A expression was related to gender (p = 0.029). The expression of both LMP1 and LMP2A showed significant correlations with patients’ overall survival (p = 0.049, p = 0.036).

Conclusion

LMP1 and LMP2A may be prognostic indicators of survival in patients with ENKTL.

Virtual slides

http://www.diagnosticpathology.diagnomx.eu/vs/2443352538545899
Adenoid cystic carcinoma of the esophagus: report of two cases and review of the Chinese literature
Authors: Guo Xu-feng , Mao Ten , Gu Zhi-tao , Fang Wen-tao , Chen Wen-hu , Shao Jin-chen
Published: December 2012

Squamous cell carcinoma is the major pathology type of esophageal cancer in China, where adenocarcinoma is rare and adenoid cystic carcinoma (ACC) is more rare comparing to the western countries. We report the surgical and pathologic findings of two cases of primary ACC of the esophagus, and review of the Chinese literature of this tumor.

Virtual slides

The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1507582238843246
Herpes virus infection associated with interstitial nephritis in a beaked whale (Mesoplodon densirostris)
Authors: Arbelo Manuel , Bellière Edwige N , Sierra Eva , Sacchinni Simona , Esperón Fernando , Andrada Marisa , Rivero Miguel , Diaz-Delgado Josue , Fernández Antonio
Published: December 2012

Background

The capacity for herpesvirus to cause disease in cetaceans is unclear and may be varied depending on the different conditions of individuals and between different species. Kidney pathology and intralesional virus-associated infection have been rarely reported in cetaceans.

Result

On April 2004, an old adult male Blainville’s beaked whale (Mesoplodon densirostris) 420 cm long with a poor body condition was stranded on Tenerife Island. During necropsy, no gross lesions were observed in the kidneys. However, membranous glomerulonephritis, multifocal interstitial lymphoplasmacytic nephritis and acute multifocal necrotizing tubulointerstitial nephritis with intranuclear inclusion bodies was diagnosed by histological analysis. Tissue samples were submitted for bacteriological analysis and molecular viral screening.

Conclusion

A novel alpha herpesvirus associated with interstitial nephritis was identified in an old adult male Blainville's beaked whale (M. densirostris) with a poor body condition stranded in the Canary Islands. This report suggests that identification of herpesvirus infection could be used as a differential diagnosis for interstitial nephritis in cetaceans.
Screening for primary creatine deficiencies in French patients with unexplained neurological symptoms
Authors: Cheillan David , Curt Marie Joncquel-Chevalier , Briand Gilbert , Salomons Gajja S , Mention-Mulliez Karine , Dobbelaere Dries , Cuisset Jean-Marie , Lion-François Laurence , Portes Vincent Des , Chabli Allel , Valayannopoulos Vassili , Benoist Jean-François , Pinard Jean-Marc , Simard Gilles , Douay Olivier , Deiva Kumaran , Afenjar Alexandra , Héron Delphine , Rivier François , Chabrol Brigitte , Prieur Fabienne , Cartault François , Pitelet Gaëlle , Goldenberg Alice , Bekri Soumeya , Gerard Marion , Delorme Richard , Tardieu Marc , Porchet Nicole , Vianey-Saban Christine , Vamecq Joseph
Published: December 2012

A population of patients with unexplained neurological symptoms from six major French university hospitals was screened over a 28-month period for primary creatine disorder (PCD). Urine guanidinoacetate (GAA) and creatine:creatinine ratios were measured in a cohort of 6,353 subjects to identify PCD patients and compile their clinical, 1H-MRS, biochemical and molecular data. Six GAMT [N-guanidinoacetatemethyltransferase (EC 2.1.1.2)] and 10 X-linked creatine transporter (SLC6A8) but no AGAT (GATM) [L-arginine/glycine amidinotransferase (EC 2.1.4.1)] deficient patients were identified in this manner. Three additional affected sibs were further identified after familial inquiry (1 brother with GAMT deficiency and 2 brothers with SLC6A8 deficiency in two different families). The prevalence of PCD in this population was 0.25% (0.09% and 0.16% for GAMT and SLC6A8 deficiencies, respectively). Seven new PCD-causing mutations were discovered (2 nonsense [c.577C > T and c.289C > T] and 1 splicing [c.391 + 15G > T] mutations for the GAMT gene and, 2 missense [c.1208C > A and c.926C > A], 1 frameshift [c.930delG] and 1 splicing [c.1393-1G > A] mutations for the SLC6A8 gene). No hot spot mutations were observed in these genes, as all the mutations were distributed throughout the entire gene sequences and were essentially patient/family specific. Approximately one fifth of the mutations of SLC6A8, but not GAMT, were attributed to neo-mutation, germinal or somatic mosaicism events. The only SLC6A8-deficient female patient in our series presented with the severe phenotype usually characterizing affected male patients, an observation in agreement with recent evidence that is in support of the fact that this X-linked disorder might be more frequent than expected in the female population with intellectual disability.
Mucosa-associated but not luminal Escherichia coli is augmented in Crohn’s disease and ulcerative colitis
Authors: de Souza Helton Luis , de Carvalho Vanessa R , Romeiro Fernando Gomes , Sassaki Ligia Yukie , Keller Rogeria , Rodrigues Josias
Published: December 2012

Background

Escherichia coli is believed to participate in the etiology of Crohn’s disease (CD) and possibly of ulcerative colitis (UC), due at least in part to the observed rise in the number of these bacteria in the gut microbiota of CD and UC patients. Nevertheless, it is not fully understood whether this quantitative variation occurs equally throughout the mucosal and luminal spaces of the gut. To assess this question, stools and mucosa biopsies from distinct intestinal sites were cultured aiming at determining their E. coli concentration. The cultures were additionally screened for the presence of some virulence genes of pathogenic E. coli.

Results

Analyses of clinical materials from 14 controls (38 biopsies and 14 stools samples), 11 CD (25 biopsies and 11 stools samples) and 7 UC patients (18 biopsies and 7 stools samples) indicated no significant variation in the number of E. coli present in stools, but a rise of at least one log10 CFU/mg in biopsies from the ileum of CD patients and the sigmoid and rectum of CD and UC patients. The cultures were screened for the presence of E. coli attaching and effacing (eae), invasion plasmid antigen H (ipaH), aggregative adherence transcriptional activator (aggR), Shiga cytotoxins (stx), and heat labile enterotoxin (elt) and the following serine proteases autotransporters of Enterobacteriaceae (SPATE) genes: plasmid encoded toxin (pet), secreted autotransporter toxin (sat), Shigella extracellular protein (sepA), protein involved in intestinal colonization (pic) and Shigella IgA-like protease homolog (sigA). Six of the 10 genes screened were detected in the total of samples investigated: aggR, eae, pet, sat, sepA and sigA. No difference in the prevalence of any of these markers was observed in cultures from different clinical materials or groups of patients.

Methods

Bacterial quantitation was carried out following cultures of diluted samples suspensions in MacConkey agar, Wilkins Chalgren agar for anaerobes, E. coli/ coliform chromocult agar, and blood agar. Screening for E. coli virulence genes was performed by multiplex PCR of DNA purified from total MacConkey undiluted broth cultures.

Conclusion

In CD and UC patients only the mucosa associated population of E. coli is augmented and the proliferation is prominent in the ileum of CD and rectum and sigmoid of both UC and CD patients which are sites where the lesions usually are observed. The augmented E. coli population in these sites presented a low number of the virulence markers, possibly meaning that they are not relevant for the disease process.
Inhibition of cancer cell proliferation by 5-fluoro-2'-deoxycytidine, a DNA methylation inhibitor, through activation of DNA damage response pathway
Authors: Zhao Quanyi , Fan Jiadong , Hong Wei , Li Lianyun , Wu Min
Published: December 2012

Multiple epigenetic changes, including alterations in DNA methylation occur during tumorigenesis. Various inhibitors of DNA methylation have been developed to prevent proliferation of cancer cells. 5-fluoro-2′-deoxycytidine (FCdR) is one such DNA methylation inhibitor, which is currently in phase II clinical trial. To investigate the molecular mechanism/s by which FCdR might mediate repression of tumor cell proliferation, we analyzed the toxicity of FCdR in various cell lines established from different sarcomas. We found HCT116, a colon cancer cell line, is much more sensitive to FCdR compared to others. FCdR treatment inhibited HCT116 cells at G2/M check point and up-regulated expression of multiple cancer-related genes, which could be due to its inhibitory activity towards DNA methylation. Furthermore, we found that FCdR activates DNA damage response pathway. Using an inhibitor for ATM and ATR kinases activity, which are required for amplifying the DNA damage repair signal, we show that FCdR induced inhibition of HCT116 cells at G2/M is mediated through activation of DNA damage response pathway.
Widespread promoter-mediated coordination of transcription and mRNA degradation
Authors: Dori-Bachash Mally , Shalem Ophir , Manor Yair S , Pilpel Yitzhak , Tirosh Itay
Published: December 2012

Background

Previous work showed that mRNA degradation is coordinated with transcription in yeast, and in several genes the control of mRNA degradation was linked to promoter elements through two different mechanisms. Here we show at the genomic scale that the coordination of transcription and mRNA degradation is promoter-dependent in yeast and is also observed in humans.

Results

We first demonstrate that swapping upstream cis-regulatory sequences between two yeast species affects both transcription and mRNA degradation and suggest that while some cis-regulatory elements control either transcription or degradation, multiple other elements enhance both processes. Second, we show that adjacent yeast genes that share a promoter (through divergent orientation) have increased similarity in their patterns of mRNA degradation, providing independent evidence for the promoter-mediated coupling of transcription to mRNA degradation. Finally, analysis of the differences in mRNA degradation rates between mammalian cell types or mammalian species suggests a similar coordination between transcription and mRNA degradation in humans.

Conclusions

Our results extend previous studies and suggest a pervasive promoter-mediated coordination between transcription and mRNA degradation in yeast. The diverse genes and regulatory elements associated with this coordination suggest that it is generated by a global mechanism of gene regulation and modulated by gene-specific mechanisms. The observation of a similar coupling in mammals raises the possibility that coupling of transcription and mRNA degradation may reflect an evolutionarily conserved phenomenon in gene regulation.
Frequency-domain full waveform inversion with plane-wave data
Authors: Tao Yi , Sen Mrinal K.
Published: December 2012

We derived an efficient frequency-domain full waveform inversion (FWI) method using plane-wave encoded shot records. The forward modeling involved application of position dependent linear time shifts at all source locations. This was followed by propagation of wavefields into the medium from all shotpoints simultaneously. The gradient of the cost function needed in the FWI was calculated first by transforming the densely sampled seismic data into the frequency-ray parameter domain and then backpropagating the residual wavefield using an adjoint-state approach. We used a Gauss-Newton framework for model updating. The approximate Hessian matrix was formed with a plane-wave encoding strategy, which required a summation over source and receiver ray parameters of the Green’s functions. Plane-wave encoding considerably reduces the computational burden and crosstalk artifacts are effectively suppressed by stacking over different ray parameters. It also has the advantage of directional illumination of the selected targets. Numerical examples show the accuracy and efficiency of our method.
The potential for induced seismicity in energy technologies
Authors: Shemeta Julie E. , Eide Elizabeth A. , Hitzman Murray W. , Clarke Donald D. , Detournay Emmanuel , Dieterich James H. , Dillon David K. , Green Sidney J. , Habiger Robert M. , McGuire Robin K. , Mitchell James K. , Smith John L. (Bill) , Ortego Jason R. , Gibbs Courtney R.
Published: December 2012

The great majority of earthquakes that occur each year around the world have natural causes. A small number of lesser-magnitude seismic events have been related to human activities and are called “induced seismic events” or “induced earthquakes” (NRC, 2012). Of concern are induced events that are large enough to be noticed by the public, typically events larger than magnitude 3 (note the range earthquake sizes that are felt can widely vary depending on project location and site characteristics). Induced seismic activity has been described since at least the 1920s and attributed to various human activities including the impoundment of water reservoirs, controlled explosions related to mining and construction, underground nuclear tests, and energy technology developments that involve injection or withdrawal of fluids from the subsurface. Historically known induced seismicity has generally been small in both magnitude and intensity of ground shaking.
Source characteristics of seismicity associated with underground wastewater disposal: A case study from the 2008 Dallas-Fort Worth earthquake sequence
Authors: Reiter Delaine , Leidig Mark , Yoo Seung-Hoon , Mayeda Kevin
Published: December 2012

Oil and natural gas production from shale formations using hydraulic fracturing or “hydrofracking” techniques has grown rapidly since 2008 and represents a vital and growing domestic energy resource. The waste fluids from increased production (called “brine”) are typically injected into deep underground disposal wells to avoid discharge into streams and other sensitive drinking water supplies. The Environmental Protection Agency estimates that approximately 400 million gallons of brine are currently disposed of on a daily basis in more than 28,000 wells in the United States, and the volume of injection continues to grow dramatically. This process has recently been implicated as the source of some potentially induced seismicity in gas-producing states such as Oklahoma, Texas, Arkansas, and Ohio.
Measuring earthquakes
Authors: Monk David
Published: December 2012

Measuring the magnitude and intensity of earthquakes is subject to enormous misunderstanding; there are several basic methods and scales that can lead to confusion. What does it mean if someone says an earthquake had a magnitude of 7? Or a microseismic event generated by a hydraulic fracturing operation has a magnitude of −2? There are two fundamentally different types of scales commonly used by seismologists to describe earthquakes. A magnitude scale measures the force or energy of an earthquake, but an intensity scale measures the level of shaking which occurs at an observation point on the Earth's surface.
Combined microseismic and 4D to calibrate and confirm surface 3D azimuthal AVO/LMR predictions of completions performance and well production in the Horn River gas shales of NEBC
Authors: Goodway Bill , Monk Dave , Perez Marco , Purdue Greg , Anderson Paul , Iverson Andrew , Vera Virginia , Cho David
Published: December 2012

The ability to high-grade gas shales is essential to optimizing completions and maximizing stimulated rock volume (SRV) in the capital-intensive development of the Horn River resource play in northeast British Columbia (NEBC). To assist in optimizing stimulation efforts, seismic data are used to estimate and map four parameters that influence hydraulic fracture effectiveness: rock properties, in-situ stress, natural fractures, and reservoir geometry.
Supercarboranes: Achievements and perspectives
Authors: Zhang Jian , Xie Zuowei
Published: December 2012

This article highlights the achievements in the chemistry of supercarboranes (carboranes with more than 12 vertices) in the past decade and the future perspectives. The chemistry of boron clusters has been dominated by 12-vertex carboranes for several decades. Only in recent years has significant progress been made in the chemistry of supercarboranes. Such a breakthrough relies on the use of CAd (carbon-atoms-adjacent) 12-vertexnido-carborane anions as starting materials. A series of 13- and 14-vertex carboranes as well as their corresponding 14- and 15-vertex metallacarboranes have been prepared and structurally characterized. Reactions of supercarboranes with reducing agents, electrophiles, and nucleophiles are studied, which reveal a more diverse and richer reaction chemistry than their icosahedral cousins.
The emerging role of the mitochondrial-derived peptide humanin in stress resistance
Authors: Yen Kelvin , Lee Changhan , Mehta Hemal , Cohen Pinchas
Published: December 2012

The discovery of humanin, a novel, mitochondrial-derived peptide, has created a potentially new category of biologically active peptide. As more research unravels the endogenous role of humanin as well as its potential pharmacological use, its role in stress resistance has become clearer. Humanin protects cells from oxidative stress, serum starvation, hypoxia, and other insultsin vitroand also improves cardiovascular disease as well as Alzheimer's diseasein vivo. In this review, we discuss the emerging role of humanin in stress resistance and its proposed mechanism of action.
The theory of the Strategic Speaker – The psychological background of indirect speech
Authors: Jagodics Balázs , Németh Dezső
Published: December 2012

Az indirekt beszédaktusok a mindennapi nyelvhasználat szerves részét képezik. Nemcsak a megvesztegetési, csábítási, fenyegetési helyzetekben használjuk őket, hanem a hétköznapi udvariassági aktusoknál is. Az indirekt beszédaktusok annak ellenére elterjedtek, hogy kétértelműségüknél és homályosságuknál fogva megszegni látszanak az emberi kommunikáció megszokott normáit. Jelen tanulmány célja, hogy áttekintést nyújtson az indirekt beszédaktusok jelenségének mai empirikus és elméleti megközelítéseiről, elsősorban a Pinker és munkatársai által kidolgozott stratégiai beszélő elméletének bemutatásával. Ez egy olyan háromfaktoros modell, amely rámutat az indirekt beszédaktusok használatának előnyeire: 1. elfogadható tagadhatóságot nyújt, 2. segít tisztázni az emberek közötti kapcsolatokat, illetve 3. a beszélő szándéka szerint elkerülhetők a biztos állításként kezelt kijelentések, valamint az információ köztudomásúvá tétele. Összefoglaló tanulmányunk a jelenség pszicholingvisztikai hátterének áttekintésén, valamint a magyarázó elméletek ismertetésén túl kitekintést kíván nyújtani a téma további empirikus kutatási lehetőségei felé.
Word order and information structure in English and Swedish
Authors: Herriman Jennifer
Published: December 2012

Both English and Swedish follow the principles of information and end-weight when ordering the elements of the clause and both languages have translationally equivalent means of re-ordering clause elements to follow these principles, i.e., fronting, postponement by extraposition, existential constructions and cleft sentences. This paper compares these word order changes in English and Swedish and shows that Swedish follows the principles of information and end-weight more strictly than English. This is supported by empirical evidence from comparisons of original texts in English and Swedish and their translations, and comparisons of writing in English by Swedish advanced learners and native speaker students, where an overuse of certain re-ordering reflects the transfer of a different usage in Swedish.
Lying as metaphor in a bilingual phraseological corpus (German-Spanish)
Authors: Mansilla Ana
Published: December 2012

The aim of this paper is the exploration of the conceptual metaphors that are activated in a set of German and Spanish phraseologisms covering concepts to do with lying, deceit and falsehood. The exploration is based on a bilingual onomasiological corpus that is part of the current research project FRASESPAL (‘The idiomatic structure of German and Spanish. An onomasiological corpus-based cognitive study’. Code HUM2007-62198/FILO). Theoretically rooted in the experientialist approach (Lakoff and Johnson, 1980) and using the phraseologisms from our own corpus as an empirical basis, the paper examines different metaphorical expressions and cognitive models for the images that underlie the conceptual fields of ‘lying’, ‘deceit’ and ‘falsehood’. Metaphor analysis is an extremely useful tool for revealing the way in which each linguistic community construes extralinguistic reality and for describing both the particularities of each language and the features common to them both, which may be systematized in ‘supranational’ metaphorical models.
Late Maxillary Protraction in Patients with Unilateral Cleft Lip and Palate: A Retrospective Study
Authors: Borzabadi-Farahani Ali , Lane Christianne J. , Yen Stephen L.-K.
Published: December 2012

Objectives

This retrospective study assessed the dentoskeletal effect of late maxillary protraction (LMP; reverse-pull headgear, Class III elastics, and maxillary suturai loosening) in unilateral cleft lip and palate (UCLP) patients versus a control group of untreated UCLP patients.

Materials and Methods

Cephalograms taken at age 13 to 14 years (T1) and 17 to 18 years (T2) were used for this study. The study group comprised 18 patients (10 male and 8 female, mean age at start of LMP therapy = 13.4 [0.45] years). A control groups of 17 patients (8 male and 9 female, mean age = 13.5 [0.44] years) was used for comparison.

Results

The repeated-measures analysis of variance showed statistically significant changes across time between groups for the following variables (mean difference [T2–T1] in the study group, 95% confidence interval): SNA (°) (1.95, 0.75 to 3.15), A ┴ Na Perp (mm) (1.82, 0.86 to 2.77), CoA (mm) (2.92, 1.53 to 4.31), ANB (°) (3.13, 2.02 to 4.24), Wits (mm) (7.82, 5.01 to 10.54), Mx-Md Diff (mm) (0.62, −1.58 to 2.83), Occl P-SN (°) (-3.98, −5.99 to −1.98), overjet (mm) (8.82, 5.90 to 11.74), FMIA (°) (4.05, −0.05 to 8.15), and IMPA (°) (-5.77, −9.74 to −1.80). Late maxillary protraction created a slight open bite (0.66 mm). Trends for overeruption of mandibular incisors and an increase in lower face height ( P = .07 for both) were noted in the study group.

Conclusions

Late maxillary protraction produced a combination of skeletal changes (protraction of maxilla, improvement in the maxillo-mandibular skeletal relationship) and dental compensations (counterclockwise rotation of occlusal plane, retroclination of mandibular incisors) in patients with UCLP. Late maxillary protraction was also associated with some unwanted tooth movements (open bite tendency, mandibular incisors overeruption).
Dental Caries in the Primary Dentition of German Children with Cleft Lip, Alveolus, and Palate
Authors: Kirchberg Anja , Makuch Almut , Hemprich Alexander , Hirsch Christian
Published: December 2012

Objective

The purpose of this cross-sectional study was to assess the prevalence of dental caries in children with cleft lip, alveolus, and/or cleft palate living in central Germany between 1996 and 2010.

Participants

A total of 295 children 1 to 6 years of age from three birth cohorts (BC) with clefts from central Germany were included in the study. They were compared with 548 1- to 6-year-old cleft-free children from the same region.

Setting

Children with clefts underwent a dental examination in an outpatient dental clinic at the University of Leipzig. The first BC was examined between 1996 and 1998, the second between 2002 and 2004, and the third between 2008 and 2010. Controls were examined at day-care centers in Leipzig during the same periods.

Main Outcome Measure

The standard dental caries index for the primary dentition (dmf/t3-4) was used for clinical assessment.

Results

Over the entire study period, the mean prevalence of dental caries in deciduous teeth was significantly higher (1.32 dmf/t3-4) in children with clefts compared with cleft-free children. However, a decline in caries (approximately 1 dmf/t3-4) and an increase in the proportion of children with healthy primary dentition were observed in both groups. These results represent a caries decline of 61% in children with clefts.

Conclusions

Caries rates for children 1 to 6 years of age with clefts from central Germany showed a considerable decline over the last years. The caries rates for clefts patients in the third BC (2008 to 2010) was similar to that of cleft-free children in the first BC (1996 to 1998).
Root depth distribution and the diversity–productivity relationship in a long‐term grassland experiment
Authors: Mueller Kevin E. , Tilman David , Fornara Dario A. , Hobbie Sarah E.
Published: December 2012

The relationship between plant diversity and productivity in grasslands could depend, partly, on how diversity affects vertical distributions of root biomass in soil; yet, no prior study has evaluated the links among diversity, root depth distributions, and productivity in a long‐term experiment. We used data from a 12‐year experiment to ask how plant species richness and composition influenced both observed and expected root depth distributions of plant communities. Expected root depth distributions were based on the abundance of species in each community and two traits of species that were measured in monocultures: root depth distributions and root‐to‐shoot ratios. The observed proportion of deep‐root biomass increased more than expected with species richness and was positively correlated with aboveground productivity. Indeed, the proportion of deep‐root biomass explained variation in productivity even after accounting for legume presence/abundance and greater nitrogen availability in diverse plots. Diverse plots had root depth distributions that were twice as deep as expected from their species composition and corresponding monoculture traits, partly due to interactions between C4 grasses and legumes. These results suggest that the productivity of diverse plant communities was partly dependent on belowground plant interactions that caused roots to be distributed more deeply in soil.
High Salivary Estrogen and Risk of Developing Pregnancy Gingivitis
Authors: Gürsoy Mervi , Gürsoy Ulvi Kahraman , Sorsa Timo , Pajukanta Riitta , Könönen Eija
Published: December 2012

Background: Estrogen regulates the cellular functions of several tissues that may disturb the host response against bacteria. The present aim is to evaluate the contribution of estrogen to the severity of gingival inflammation during pregnancy.

Methods: Salivary estrogen levels from 30 pregnant and 24 non‐pregnant females were related to their periodontal health parameters, including visible plaque index (VPI) and bleeding on probing (BOP) from six sites per tooth. The pregnant group was examined three times during pregnancy and twice during postpartum, and the non‐pregnant group was examined three times, once per subsequent month.

Results: Salivary estrogen levels increased significantly during the second (P <0.01) and third (P <0.05) trimesters. In both participant groups, BOP scores correlated significantly with VPI scores (r = 0.498 to 0.870) but not with estrogen levels. In all trimesters and postpartum, the individuals with both high estrogen and high VPI levels had the highest frequency of pregnancy gingivitis. During the second and third trimesters, simultaneously enhanced estrogen levels and VPI scores brought an additional risk of developing gingivitis compared with a high VPI score alone.

Conclusion: The present findings suggest that, during pregnancy, the estrogen level determines the magnitude of gingival inflammation developed against microbial plaque at the gingival margin.