bluuebunny/crossref_metadata_2025_split huggingface dataset:
Warty dyskeratoma/focal acantholytic dyskeratosis – an update on a rare oral lesion
Authors: Allon Irit , Buchner Amos 
Published: September 2011

J Oral Pathol Med (2012) 41: 261–267Background:  Warty dyskeratoma (WD) is an uncommon lesion of the skin that is considered to be associated with the pilosebaceous apparatus. Histologically similar lesions have been described in the oral region mainly by case reports and under the terms ‘WD’ or ‘focal acantholytic dyskeratosis (FAD)’. Owing to the paucity of reports, many aspects of the oral lesions remain unclear. The purpose of this study is to report a new case in an extremely rare location, the buccal mucosa, and to present a comprehensive updated review and analysis of the literature.Methods:  We reviewed all cases of oral lesions that were diagnosed as WD and FAD and analyzed them according to their clinical and pathologic features.Results:  The search yielded only 41 cases. The lesions usually appeared as asymptomatic, solitary, white nodules, papules, or patches on bone‐bound mucosa. They occasionally had a rough surface and depressed center. The lesions were most common in the fifth to seventh decades. Use of tobacco appeared to be the most prevalent predisposing factor. The histopathological differential diagnosis of the lesion included acantholytic squamous cell carcinoma, keratoacanthoma, and Darier’s disease.Conclusion:  Warty dyskeratoma/FAD are uncommon oral lesions which are not encountered in the daily practice of oral pathologists. The absence of an association of oral lesions with the pilosebaceous apparatus suggests that they are probably distinctly different from cutaneous ones. As such, we suggest the histologic term isolated FAD for oral lesions, rather than WD.
The right relevé in the right vegetation unit: a new typicality index to reproduce expert judgement with an automatic classification programme
Authors: Gégout Jean‐Claude , Coudun Christophe 
Published: September 2011

AbstractQuestionHow to classify forest vegetation relevés automatically in the traditional phytosociological system and thus distinguish typical relevés – easier to classify – from relevés with non‐diagnostic species and intermediate relevés?MaterialA data set of 11 324 forest vegetation relevés, including 4880 relevés classified a priori by experts in phytosociology down to the association level (100 associations in 30 alliances and ten classes, covering all forest vegetation and environmental conditions encountered in France).MethodsA new typicality index was formalized to quantify the probability of automatically classifying a given relevé in the same vegetation unit as would do an expert in phytosociology. Computation of the typicality index is based on two parameters: a level of affinity linked to the number of diagnostic species of the vegetation unit present in the relevé, and a level of differentiation that is greater when the risk of confusion in classification of the relevé between different units is smaller.ResultsThe automatic classification was identical to expert judgement for 60% of the 4080 calibration relevés. The typicality index isolated atypical relevés that are more difficult to classify. The model was successfully transferred to classify an independent data set of 6444 relevés from the French National Forest Inventory performed in 2008 and to distinguish 1114 (17%) typical relevés of phytosociological associations.ConclusionsInterest in this new typicality index is manifold. It is: (1) operational for the current phytosociological system that forms the basis of the Natura 2000 system; (2) easy to implement from characteristics of species and communities; and (3) based on criteria of uncertainty used by phytosociological experts. This study establishes a clear bridge between recent works on collecting, storing and analysing vegetation relevés, on one hand, and the traditional phytosociological approach, on the other. It should trigger further studies on the spatial and temporal distribution of European habitats.
The Neuroprotective Effect of a Specific P2X7 Receptor Antagonist Derives from its Ability to Inhibit Assembly of the NLRP3 Inflammasome in Glial Cells
Authors: Murphy Niamh , Cowley Thelma R. , Richardson Jill C. , Virley David , Upton Neil , Walter Daryl , Lynch Marina A. 
Published: September 2011

AbstractRelease of interleukin (IL)‐1β from immunocompetent cells requires formation of the NACHT, LLR and PYD domains‐containing protein 3 (NLRP3) inflammasome and caspase 1 activation. Adenosine 5′‐triphosphate (ATP), acting on the P2X7 receptor, is one factor that stimulates inflammasome assembly. We show that a novel specific P2X7 receptor antagonist, GSK1370319A, inhibits ATP‐induced increase in IL‐1β release and caspase 1 activation in lipopolysaccharide (LPS)‐primed mixed glia by blocking assembly of the inflammasome in a pannexin 1‐dependent manner. GSK1370319A also inhibits ATP‐induced subregion‐specific neuronal loss in hippocampal organotypic slice cultures, which is dependent on its ability to prevent inflammasome assembly in glia. Significantly, GSK1370319A attenuates age‐related deficits in long‐term potentiation (LTP) and inhibits the accompanying age‐related caspase 1 activity. We conclude that inhibiting P2X7 receptor‐activated NLRP3 inflammasome formation and the consequent IL‐1β release from glia preserve neuronal viability and synaptic activity.
Efficacy and safety of methotrexate in articular and cutaneous manifestations of systemic lupus erythematosus
Authors: ISLAM Md. Nazrul , HOSSAIN Mohsin , HAQ Syed A. , ALAM Mohammad N. , TEN KLOOSTER Peter M. , RASKER Johannes J. 
Published: September 2011

Abstract
Aim:  A prospective open‐label study comparing the efficacy and safety of methotrexate (MTX) and chloroquine (CQ) in articular and cutaneous manifestations of systemic lupus erythematosus (SLE).
Methods:  Consecutive SLE patients were randomly assigned to either 10 mg MTX weekly or 150 mg CQ daily during 24 weeks. Outcome measures were: numbers of swollen and tender joints, duration of morning stiffness, visual analog scale (VAS) for articular pain, physician global assessment index, patient global assessment index, SLE Disease Activity Index (SLEDAI), disappearance of skin rash and erythrocyte sedimentation rate (ESR).
Results:  Forty‐one patients consented to participate, 15 were allocated in the MTX group and 26 in the CQ group. Two patients on MTX dropped out due to side‐effects and two in the CQ group, one due to side‐effects and one due to inefficacy. Baseline demographic, clinical and laboratory parameters of the two groups were nearly identical. In both groups the clinical and laboratory parameters improved significantly over 24 weeks, except the ESR in the MTX group. The results of the outcome measures at the end of the trial did not differ significantly between the two groups, except morning stiffness (P < 0.05 in favor of the MTX group) and ESR (P < 0.01 in favor of the CQ group). Rise of serum alanine aminotransferase was observed in two cases in the MTX group and in none in the CQ group.
Conclusion:  Low‐dose MTX appears to be as effective as CQ in patients with articular and cutaneous manifestations of SLE, having an acceptable toxicity profile. Results of this prospective study need to be confirmed in a larger study.
Next-Generation Sequencing Reveals HIV-1-Mediated Suppression of T Cell Activation and RNA Processing and Regulation of Noncoding RNA Expression in a CD4
+
T Cell Line
Authors: Chang Stewart T. , Sova Pavel , Peng Xinxia , Weiss Jeffrey , Law G. Lynn , Palermo Robert E. , Katze Michael G. 
Published: September 2011

ABSTRACT

Next-generation sequencing (NGS) enables the highly sensitive measurement of whole transcriptomes. We report the first application to our knowledge of this technology to the analysis of RNA from a CD4
+
T cell line infected with intact HIV. We sequenced the total mRNA from infected cells and detected differences in the expression of both host and viral mRNA. Viral reads represented a large portion of the total mapped sequencing reads: approximately 20% at 12 h postinfection (hpi) and 40% at 24 hpi. We also detected a small but significant suppression of T cell activation-related genes at 12 hpi. This suppression persisted and expanded by 24 hpi, providing new possible markers of virus-induced T cell cytopathology. By 24 hpi, the expression of over 50% of detectable host loci was also altered, indicating widespread alteration of host processes, including RNA processing, splicing, and transport to an extent not previously reported. In addition, next-generation sequencing provided insights into alternative viral RNA splice events and the expression of noncoding RNAs, including microRNA host genes.

IMPORTANCE
Recent advances in sequencing technology now allow the measurement of effectively all the RNA in a cell. This approach is especially useful for studying models of virus infection, as it allows the simultaneous measurement of both host and viral RNA. Using next-generation sequencing (NGS), we measured changes in total mRNA from a HIV-infected T cell line. To our knowledge, this is the first application of this technology to the investigation of HIV-host interactions involving intact HIV. We directly measured the amount of viral mRNA in infected cells and detected novel viral RNA splice variants and changes in the host expression of noncoding RNA species. We also detected small changes in T cell activation and other host processes during the early stages of viral replication that increased near the peak of viral replication, providing new candidate biomarkers of T cell death.
Ovarian and cervical cancer awareness: development of two validated measurement tools
Authors: Simon Alice E , Wardle Jane , Grimmett Chloe , Power Emily , Corker Elizabeth , Menon Usha , Matheson Lauren , Waller Jo 
Published: September 2011

BackgroundThe aim of the study was to develop and validate measures of awareness of symptoms and risk factors for ovarian and cervical cancer (Ovarian and Cervical Cancer Awareness Measures).MethodsPotentially relevant items were extracted from the literature and generated by experts. Four validation studies were carried out to establish reliability and validity. Women aged 21–67 years (n=146) and ovarian and cervical cancer experts (n=32) were included in the studies. Internal reliability was assessed psychometrically. Test-retest reliability was assessed over a 1-week interval. To establish construct validity, Cancer Awareness Measure (CAM) scores of cancer experts were compared with equally well-educated comparison groups. Sensitivity to change was tested by randomly assigning participants to read either a leaflet giving information about ovarian/cervical cancer or a leaflet with control information, and then completing the ovarian/cervical CAM.ResultsInternal reliability (Cronbach's α=0.88 for the ovarian CAM and α=0.84 for the cervical CAM) and test-retest reliability (r=0.84 andr=0.77 for the ovarian and cervical CAMs, respectively) were both high. Validity was demonstrated with cancer experts achieving higher scores than controls [ovarian CAM:t(36)= –5.6,p<0.001; cervical CAM:t(38)= –3.7,p=0.001], and volunteers who were randomised to read a cancer leaflet scored higher than those who received a control leaflet [ovarian CAM:t(49)=7.5,p<0.001; cervical CAM:t(48)= –5.5,p<0.001].ConclusionsThis study demonstrates the psychometric properties of the ovarian and cervical CAMs and supports their utility in assessing ovarian and cervical cancer awareness in the general population.
Targeting Axl and Mer Kinases in Cancer
Authors: Verma Anupam , Warner Steven L. , Vankayalapati Hariprasad , Bearss David J. , Sharma Sunil 
Published: September 2011

Abstract
Receptor tyrosine kinases (RTK) are cell-surface transmembrane receptors that contain regulated kinase activity within their cytoplasmic domain and play an important role in signal transduction in both normal and malignant cells. The mammalian TAM RTK family includes 3 closely related members: Tyro-3, Axl, and Mer. Overexpression or ectopic expression of the TAM receptors has been detected in a wide array of human cancers. Growth arrest-specific gene 6 has been identified as the major ligand for these TAM RTKs, and its binding to the receptors has been shown to promote proliferation and survival of cancer cells in vitro. Abnormal expression and activation of Axl or Mer can provide a survival advantage for certain cancer cells. Inhibition of Axl and Mer may enhance the sensitivity of cancer cells to cytotoxic agents and would potentially be a therapeutic strategy to target cancer cells. This review elucidates the role of Axl and Mer in normal cellular function and their role in oncogenesis. In addition, we review the potential to inhibit these RTKs for the development of therapeutic targets in treatment of cancer. Mol Cancer Ther; 10(10); 1763–73. ©2011 AACR.
Momordica Charantia Lectin, a Type II Ribosome Inactivating Protein, Exhibits Antitumor Activity toward Human Nasopharyngeal Carcinoma Cells In Vitro and In Vivo
Authors: Fang Evandro Fei , Zhang Chris Zhi Yi , Ng Tzi Bun , Wong Jack Ho , Pan Wen Liang , Ye Xiu Juan , Chan Yau Sang , Fong Wing Ping 
Published: September 2011

Abstract
The incidence of nasopharyngeal carcinoma (NPC) remains high in endemic regions, including southern China, northern Africa, and North America. One of the promising therapeutic approaches on NPC is drug screening from natural products, such as components from traditional Chinese medicine. In this study, the antitumor activity of Momordica charantia lectin (MCL), a type II ribosome inactivating protein from bitter gourd, on NPC was investigated. MCL evinced potent cytotoxicity toward NPC CNE-1 (IC50 = 6.9) and CNE-2 (IC50 = 7.4) cells but minimally affected normal NP 69 cells. Further investigation disclosed that MCL induced apoptosis, DNA fragmentation, G1-phase arrest, and mitochondrial injury in both types of NPC cells. The reduction of cyclin D1 and phosphoretinoblastoma (Rb) protein expression contributed to arrest at G1-phase of the cell cycle. These events were associated with regulation of mitogen-activated protein kinases (MAPK; including p38 MAPK, JNK, and ERK) phosphorylation and promoted downstream nitric oxide (NO) production. Concurrent administration of the p38 MAPK inhibitor SB-203580 significantly diminished NO production and lethality of MCL toward NPC cells. Further studies revealed that MCL increased cytochrome c release into the cytosol, activated caspases-8, -9, and -3, and enhanced production of cleaved PARP, subsequently leading to DNA fragmentation and apoptosis. Finally, an intraperitoneal injection of MCL (1.0 mg/kg/d) led to an average of 45% remission of NPC xenograft tumors subcutaneously inoculated in nude mice. This is the first article that unveils the potential of a type II RIP, MCL, for prevention and therapy of NPC. Cancer Prev Res; 5(1); 109–21. ©2011 AACR.
Psychiatric comorbidities in women with Celiac Disease
Authors: Arigo Danielle , Anskis Alicia M , Smyth Joshua M 
Published: September 2011

Objective: Although the physical consequences of Celiac Disease are well studied, less is known about co-occurring psychiatric symptoms. This study examines psychiatric risk and comorbidities of women with Celiac Disease, who may be at increased risk for psychiatric symptoms (e.g. depression, and disordered eating behaviours). Methods: Women ( N = 177) with Celiac Disease responded to an extensive web-mediated survey assessing dietary compliance, illness symptoms, psychiatric functioning, and disordered eating. Results: Despite high reported dietary compliance, patients reported marked illness symptoms and impaired quality of life. A substantial minority endorsed symptoms that met criteria for the diagnosis of psychiatric disorders: 37% ( n = 65) met the threshold suggesting depression, and 22% ( n = 39) for disordered eating. Participants whose symptoms exceeded these clinical thresholds reported greater perceived stress and reduced overall mental health, relative to women below the clinical cutoffs. Conclusions: Despite largely adhering to a gluten-free diet, a substantial subset of women with Celiac Disease report clinically relevant symptoms of depression and disordered eating; such symptoms are associated with increased psychosocial distress in other domains. These results suggest potential to improve the patient well-being through attention to psychosocial care, in addition to existing dietary recommendations for individuals with Celiac Disease.
Hierarchical Parallelization of Gene Differential Association Analysis
Authors: Needham Mark , Hu Rui , Dwarkadas Sandhya , Qiu Xing 
Published: September 2011

Abstract

Background
Microarray gene differential expression analysis is a widely used technique that deals with high dimensional data and is computationally intensive for permutation-based procedures. Microarray gene differential association analysis is even more computationally demanding and must take advantage of multicore computing technology, which is the driving force behind increasing compute power in recent years. In this paper, we present a two-layer hierarchical parallel implementation of gene differential association analysis. It takes advantage of both fine- and coarse-grain (with granularity defined by the frequency of communication) parallelism in order to effectively leverage the non-uniform nature of parallel processing available in the cutting-edge systems of today.

Results
Our results show that this hierarchical strategy matches data sharing behavior to the properties of the underlying hardware, thereby reducing the memory and bandwidth needs of the application. The resulting improved efficiency reduces computation time and allows the gene differential association analysis code to scale its execution with the number of processors. The code and biological data used in this study are downloadable from http://www.urmc.rochester.edu/biostat/people/faculty/hu.cfm

Conclusions
The performance sweet spot occurs when using a number of threads per MPI process that allows the working sets of the corresponding MPI processes running on the multicore to fit within the machine cache. Hence, we suggest that practitioners follow this principle in selecting the appropriate number of MPI processes and threads within each MPI process for their cluster configurations. We believe that the principles of this hierarchical approach to parallelization can be utilized in the parallelization of other computationally demanding kernels.
Genomic insights into an obligate epibiotic bacterial predator: Micavibrio aeruginosavorus ARL-13
Authors: Wang Zhang , Kadouri Daniel E , Wu Martin 
Published: September 2011

Abstract

Background
Although bacterial predators play important roles in the dynamics of natural microbial communities, little is known about the molecular mechanism of bacterial predation and the evolution of diverse predatory lifestyles.

Results
We determined the complete genome sequence of Micavibrio aeruginosavorus ARL-13, an obligate bacterial predator that feeds by "leeching" externally to its prey. Despite being an obligate predator depending on prey for replication, M. aeruginosavorus encodes almost all major metabolic pathways. However, our genome analysis suggests that there are multiple amino acids that it can neither make nor import directly from the environment, thus providing a simple explanation for its strict dependence on prey. Remarkably, despite apparent genome reduction, there is a massive expansion of genomic islands of foreign origin. At least nine genomic islands encode many genes that are likely important for Micavibrio-prey interaction such as hemolysin-related proteins. RNA-Seq analysis shows substantial transcriptome differences between the attack phase, when M. aeruginosavorus seeks its prey, and the attachment phase, when it feeds and multiplies. Housekeeping genes as well as genes involved in protein secretion were all dramatically up-regulated in the attachment phase. In contrast, genes involved in chemotaxis and flagellum biosynthesis were highly expressed in the attack phase but were shut down in the attachment phase. Our transcriptomic analysis identified additional genes likely important in Micavibrio predation, including porins, pilins and many hypothetical genes.

Conclusions
The findings from our phylogenomic and transcriptomic analyses shed new light on the biology and evolution of the epibiotic predatory lifestyle of M. aeruginosavorus. The analysis reported here and the availability of the complete genome sequence should catalyze future studies of this organism.
Cytoplasmic p21 is a potential predictor for cisplatin sensitivity in ovarian cancer
Authors: Xia Xi , Ma Quanfu , Li Xiao , Ji Teng , Chen Pingbo , Xu Hongbin , Li Kezhen , Fang Yong , Weng Danhui , Weng Yanjie , Liao Shujie , Han Zhiqiang , Liu Ronghua , Zhu Tao , Wang Shixuan , Xu Gang , Meng Li , Zhou Jianfeng , Ma Ding 
Published: September 2011

Abstract

Background
P21(WAF1/Cip1) binds to cyclin-dependent kinase complexes and inhibits their activities. It was originally described as an inhibitor of cancer cell proliferation. However, many recent studies have shown that p21 promotes tumor progression when accumulated in the cell cytoplasm. So far, little is known about the correlation between cytoplasmic p21 and drug resistance. This study was aimed to investigate the role of p21 in the cisplatin resistance of ovarian cancer.

Methods
RT-PCR, western blot and immunofluorescence were used to detect p21 expression and location in cisplatin-resistant ovarian cancer cell line C13* and its parental line OV2008. Regulation of cytoplasmic p21 was performed through transfection of p21 siRNA, Akt2 shRNA and Akt2 constitutively active vector in the two cell lines; their effects on cisplatin-induced apoptosis were evaluated by flow cytometry. Tumor tissue sections of clinical samples were analyzed by immunohistochemistry.

Results
p21 predominantly localizes to the cytoplasm in C13* compared to OV2008. Persistent exposure to low dose cisplatin in OV2008 leads to p21 translocation from nuclear to cytoplasm, while it had not impact on p21 localization in C13*. Knockdown of cytoplasmic p21 by p21 siRNA transfection in C13* notably increased cisplatin-induced apoptosis through activation of caspase 3. Inhibition of p21 translocation into the cytoplasm by transfection of Akt2 shRNA into C13* cells significantly increased cisplatin-induced apoptosis, while induction of p21 translocation into the cytoplasm by transfection of constitutively active Akt2 in OV2008 enhanced the resistance to cisplatin. Immunohistochemical analysis of clinical ovarian tumor tissues demonstrated that cytoplasmic p21 was negatively correlated with the response to cisplatin based treatment.

Conclusions
Cytoplasmic p21 is a novel biomarker of cisplatin resistance and it may represent a potential therapeutic target for ovarian tumors that are refractory to conventional treatment.