bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization and gene expression analysis of the cir multi-gene family of plasmodium chabaudi chabaudi (AS)
Authors: Lawton Jennifer , Brugat Thibaut , Yan Yam Xue , Reid Adam James , Böhme Ulrike , Otto Thomas Dan , Pain Arnab , Jackson Andrew , Berriman Matthew , Cunningham Deirdre , Preiser Peter , Langhorne Jean 
Published: March 2012

AbstractBackgroundThepirgenes comprise the largest multi-gene family inPlasmodium, with members found inP. vivax, P. knowlesiand the rodent malaria species. Despite comprising up to 5% of the genome, little is known about the functions of the proteins encoded bypirgenes.P. chabaudicauses chronic infection in mice, which may be due to antigenic variation. In this model,pirgenes are calledcirs and may be involved in this mechanism, allowing evasion of host immune responses. In order to fully understand the role(s) of CIR proteins duringP. chabaudiinfection, a detailed characterization of thecirgene family was required.ResultsThecirrepertoire was annotated and a detailed bioinformatic characterization of the encoded CIR proteins was performed. Two major sub-families were identified, which have been named A and B. Members of each sub-family displayed different amino acid motifs, and were thus predicted to have undergone functional divergence. In addition, the expression of the entirecirrepertoire was analyzed via RNA sequencing and microarray. Up to 40% of thecirgene repertoire was expressed in the parasite population during infection, and dominantcirtranscripts could be identified. In addition, some differences were observed in the pattern of expression between thecirsubgroups at the peak ofP. chabaudiinfection. Finally, specificcirgenes were expressed at different time points during asexual blood stages.ConclusionsIn conclusion, the large number ofcirgenes and their expression throughout the intraerythrocytic cycle of development indicates that CIR proteins are likely to be important for parasite survival. In particular, the detection of dominantcirtranscripts at the peak ofP. chabaudiinfection supports the idea that CIR proteins are expressed, and could perform important functions in the biology of this parasite. Further application of the methodologies described here may allow the elucidation of CIR sub-family A and B protein functions, including their contribution to antigenic variation and immune evasion.
Breast cancer stage at diagnosis and area-based socioeconomic status: a multicenter 10-year retrospective clinical epidemiological study in China
Authors: Wang Qiong , Li Jing , Zheng Shan , Li Jia-Yuan , Pang Yi , Huang Rong , Zhang Bao-Ning , Zhang Bin , Yang Hong-Jian , Xie Xiao-Ming , Tang Zhong-Hua , Li Hui , He Jian-Jun , Fan Jin-Hu , Qiao You-Lin 
Published: March 2012

Abstract

Background
Although socioeconomic status (SES) has been focused on as a key determinant of cancer stage at diagosis in western countries, there has been no systemic study on the relationship of SES and breast cancer stage at diagnosis in China.

Methods
The medical charts of 4,211 eligible breast cancer patients from 7 areas across China who were diagnosed between 1999 and 2008 were reviewed. Four area-based socioeconomic indicators were used to calculate area-based SES by cluster analysis. The associations between area-based SES and stage at diagnosis were analyzed by trend chi-square tests. Binary logistic regression was performed to estimate odds ratios for individual demographic characteristics' effects on cancer stages, stratified by area-based SES.

Results
The individual demographic and pathologic characteristics of breast cancer cases were significantly different among the seven areas studied. More breast cancer cases in low SES areas (25.5%) were diagnosed later (stages III & IV) than those in high (20.4%) or highest (14.8%) SES areas (χ
2 for trend = 80.79, P < 0.001). When area-based SES is controlled for, in high SES areas, cases with less education were more likely to be diagnosed at later stages compared with more educated cases. In low SES areas, working women appeared to be diagnosed at earlier breast cancer stages than were homemakers (OR: 0.18-0.26).

Conclusions
In China, women in low SES areas are more likely to be diagnosed at later breast cancer stages than those in high SES areas.
Methylation profiling of Epstein-Barr virus immediate-early gene promoters, BZLF1 and BRLF1in tumors of epithelial, NK- and B-cell origins
Authors: Li Lili , Su Xianwei , Choi Gigi Ching Gee , Cao Ya , Ambinder Richard F , Tao Qian 
Published: March 2012

Abstract

Background
Epstein-Barr virus (EBV) establishes its latency in EBV-associated malignancies, accompanied by occasionally reactivated lytic cycle. Promoter CpG methylation of EBV genome plays an essential role in maintaining viral latency. Two immediate-early (IE) genes, BZLF1 and BRLF1, induce the switch from latent to lytic infection. Studies of methylation-dependent binding of BZLF1 and BRLF1 to EBV promoters have been well reported, but little is known about the methylation status of BZLF1 and BRLF1 promoters (Zp and Rp) in tumor samples.

Methods
We evaluated the methylation profiles of Zp and Rp by methylation-specific PCR (MSP) and bisulfite genomic sequencing (BGS), as well as BZLF1 and BRLF1 expression by semiquantitative reverse transcription (RT)-PCR in tumors of epithelial, NK- and B-cell origins.

Results
We found that both Zp and Rp were hypermethylated in all studied EBV-positive cell lines and tumors of lymphoid (B- or NK cell) or epithelial origin, while unmethylated Zp and Rp alleles were detected in cell lines expressing BZLF1 and BRLF1. Following azacytidine treatment or combined with trichostatin A (TSA), the expression of BZLF1 and BRLF1 was restored along with concomitant promoter demethylation, which subsequently induced the reactivation of early lytic gene BHRF1 and late lytic gene BLLF1.

Conclusions
Hypermethylation of Zp and Rp mediates the frequent silencing of BZLF1 and BRLF1 in EBV-associated tumors, which could be reactivated by demethylation agent and ultimately initiated the EBV lytic cascade.
Genetically divergent methicillin-resistant Staphylococcus aureus and sec-dependent mastitis of dairy goats in Taiwan
Authors: Chu Chishih , Yu Changyou , Lee Yanhaui , Su Yaochi 
Published: March 2012

Abstract

Background
Widespread in the environment, Staphylococcus spp. infect animals and humans as normal flora or pathogens. By extending our recent report of multi-drug resistant (MDR) S. aureus in dairy goats, this study investigated the staphylococcal infection and characterized the MDR-S. aureus and methicillin-resistant S. aureus (MRSA) isolates collected from goats in 2008 to elucidate the appearance of MRSA in goats and the mastitis associated staphylococcus enterotoxin (SE) types. A total of 555 samples were collected from six goat parts and three environmental sources among four dairy goat farms in southern Taiwan. Coagulase-positive and negative Staphylococcus spp. (CPS and CNS, respectively) were also identified. Furthermore, predominant SE genes of nine enterotoxin genes sea through sej along with antimicrobial resistance and genetic variations were determined.

Results
In total, 137 staphylococcal strains were identified and found predominantly in milk, and in the vagina, anus, and nasal cavity. The most prevalent species was S. lentus, followed by S. aureus, S. epidermidis, and S. xylosus. Enterotoxin genes were not identified in any CNS isolates, however sec and see were identified only in S. aureus associated with mastitis in goat. In compared to the isolates from 2006 to 2007, 27 S. aureus isolates from 2008 were found to be more resistant to ampicillin, cephalothin, oxacillin, oxytetracycline, penicillin G, and tetracycline. Eleven MRSA isolates were identified and belonged to SCCmec type III (nine isolates) as the major type and SCCmec type II (two isolates). These MRSA isolates revealed pulse-field gel electrophoresis (PFGE) pattern A (five isolates), C (one isolate), and D (one isolate) of human isolates. The other two isolates without pulsotypes belonged to ST59.

Conclusion
The prevalence and infection sites of CNS differed from those of CPS. Genetic analyses indicated that genetic divergence, possible zoonotic transfer of MRSA, and the involvement of sec as important virulence factors for of S. aureus that lead to mastitis in goats.
Pannexin 1 regulates postnatal neural stem and progenitor cell proliferation
Authors: Wicki-Stordeur Leigh E , Dzugalo Adrian D , Swansburg Rose M , Suits Jocelyne M , Swayne Leigh Anne 
Published: March 2012

Abstract

Background
Pannexin 1 forms ion and metabolite permeable hexameric channels and is abundantly expressed in the brain. After discovering pannexin 1 expression in postnatal neural stem and progenitor cells we sought to elucidate its functional role in neuronal development.

Results
We detected pannexin 1 in neural stem and progenitor cells in vitro and in vivo. We manipulated pannexin 1 expression and activity in Neuro2a neuroblastoma cells and primary postnatal neurosphere cultures to demonstrate that pannexin 1 regulates neural stem and progenitor cell proliferation likely through the release of adenosine triphosphate (ATP).

Conclusions
Permeable to ATP, a potent autocrine/paracine signaling metabolite, pannexin 1 channels are ideally suited to influence the behavior of neural stem and progenitor cells. Here we demonstrate they play a robust role in the regulation of neural stem and progenitor cell proliferation. Endogenous postnatal neural stem and progenitor cells are crucial for normal brain health, and their numbers decline with age. Furthermore, these special cells are highly responsive to neurological injury and disease, and are gaining attention as putative targets for brain repair. Therefore, understanding the fundamental role of pannexin 1 channels in neural stem and progenitor cells is of critical importance for brain health and disease.
Relevant phosphoproteomic and mass spectrometry: approaches useful in clinical research
Authors: López Elena , Muñoz Sarbelio Rodríguez , Pascual Juan López , Madero Luis 
Published: March 2012

AbstractBackground“It's not what we do, it's the way that we do it”. Never has this maxim been truer in proteomics than now. Mass Spectrometry‐based proteomics/phosphoproteomics tools are critical to understand the structure and dynamics (spatial and temporal) of signalling that engages and migrates through the entire proteome. Approaches such as affinity purification followed by Mass Spectrometry (MS) have been used to elucidate relevant biological questions disease vs. health. Thousands of proteins interact via physical and chemical association. Moreover, certain proteins can covalently modify other proteins post‐translationally. These post‐translational modifications (PTMs) ultimately give rise to the emergent functions of cells in sequence, space and time.FindingsUnderstanding the functions of phosphorylated proteins thus requires one to study proteomes as linked‐systems rather than collections of individual protein molecules. Indeed, the interacting proteome or protein‐network knowledge has recently received much attention, as network‐systems (signalling pathways) are effective snapshots in time, of the proteome as a whole. MS approaches are clearly essential, in spite of the difficulties of some low abundance proteins for future clinical advances.ConclusionClinical proteomics‐MS has come a long way in the past decade in terms of technology/platform development, protein chemistry, and together with bioinformatics and other OMICS tools to identify molecular signatures of diseases based on protein pathways and signalling cascades. Hence, there is great promise for disease diagnosis, prognosis, and prediction of therapeutic outcome on an individualized basis. However, and as a general rule, without correct study design, strategy and implementation of robust analytical methodologies, the efforts, efficiency and expectations to make biomarkers (especially phosphorylated kinases) a useful reality in the near future, can easily be hampered.
The Transcription Factor Encyclopedia
Authors: Yusuf Dimas , Butland Stefanie L , Swanson Magdalena I , Bolotin Eugene , Ticoll Amy , Cheung Warren A , Cindy Zhang Xiao Yu , Dickman Christopher TD , Fulton Debra L , Lim Jonathan S , Schnabl Jake M , Ramos Oscar HP , Vasseur-Cognet Mireille , de Leeuw Charles N , Simpson Elizabeth M , Ryffel Gerhart U , Lam Eric W-F , Kist Ralf , Wilson Miranda SC , Marco-Ferreres Raquel , Brosens Jan J , Beccari Leonardo L , Bovolenta Paola , Benayoun Bérénice A , Monteiro Lara J , Schwenen Helma DC , Grontved Lars , Wederell Elizabeth , Mandrup Susanne , Veitia Reiner A , Chakravarthy Harini , Hoodless Pamela A , Mancarelli M Michela , Torbett Bruce E , Banham Alison H , Reddy Sekhar P , Cullum Rebecca L , Liedtke Michaela , Tschan Mario P , Vaz Michelle , Rizzino Angie , Zannini Mariastella , Frietze Seth , Farnham Peggy J , Eijkelenboom Astrid , Brown Philip J , Laperrière David , Leprince Dominique , de Cristofaro Tiziana , Prince Kelly L , Putker Marrit , del Peso Luis , Camenisch Gieri , Wenger Roland H , Mikula Michal , Rozendaal Marieke , Mader Sylvie , Ostrowski Jerzy , Rhodes Simon J , Van Rechem Capucine , Boulay Gaylor , Olechnowicz Sam WZ , Breslin Mary B , Lan Michael S , Nanan Kyster K , Wegner Michael , Hou Juan , Mullen Rachel D , Colvin Stephanie C , Noy Peter John , Webb Carol F , Witek Matthew E , Ferrell Scott , Daniel Juliet M , Park Jason , Waldman Scott A , Peet Daniel J , Taggart Michael , Jayaraman Padma-Sheela , Karrich Julien J , Blom Bianca , Vesuna Farhad , O'Geen Henriette , Sun Yunfu , Gronostajski Richard M , Woodcroft Mark W , Hough Margaret R , Chen Edwin , Europe-Finner G Nicholas , Karolczak-Bayatti Magdalena , Bailey Jarrod , Hankinson Oliver , Raman Venu , LeBrun David P , Biswal Shyam , Harvey Christopher J , DeBruyne Jason P , Hogenesch John B , Hevner Robert F , Héligon Christophe , Luo Xin M , Blank Marissa Cathleen , Millen Kathleen Joyce , Sharlin David S , Forrest Douglas , Dahlman-Wright Karin , Zhao Chunyan , Mishima Yuriko , Sinha Satrajit , Chakrabarti Rumela , Portales-Casamar Elodie , Sladek Frances M , Bradley Philip H , Wasserman Wyeth W 
Published: March 2012

AbstractHere we present the Transcription Factor Encyclopedia (TFe), a new web-based compendium of mini review articles on transcription factors (TFs) that is founded on the principles of open access and collaboration. Our consortium of over 100 researchers has collectively contributed over 130 mini review articles on pertinent human, mouse and rat TFs. Notable features of the TFe website include a high-quality PDF generator and web API for programmatic data retrieval. TFe aims to rapidly educate scientists about the TFs they encounter through the delivery of succinct summaries written and vetted by experts in the field. TFe is available at http://www.cisreg.ca/tfe.
CX3CL1/fractalkine is a novel regulator of normal and malignant human B cell function
Authors: Corcione Anna , Ferretti Elisa , Pistoia Vito 
Published: March 2012

Abstract
Review of the role of the CX3CL1/CX3CR1 axis in the regulation of normal B cells and malignant B cell microenvironment.
CX3CL1, or fractalkine, the unique member of the CX3C chemokine family, exists as a transmembrane glycoprotein, as well as in soluble form, each mediating different biological activities, and is constitutively expressed in many hematopoietic and nonhematopoietic tissues. CX3CR1, the CX3CL1 exclusive receptor, is a classical GPCR, expressed on NK cells, CD14+ monocytes, and some subpopulation of T cells, B cells, and mast cells. A recent paper by our group has demonstrated for the first time that highly purified human B cells from tonsil and peripheral blood expressed CX3CR1 at mRNA and protein levels. In particular, tonsil naïve, GC, and memory B cells expressed CX3CR1, but only GC centrocytes were attracted by soluble CX3CL1, which with its receptor, are also involved in the pathogenesis of several inflammatory disorders, as well as of cancer. Previous studies have shown that CX3CR1 is up-regulated in different types of B cell lymphoma, as well as in B-CLL. Recently, we have demonstrated that the CX3CL1/CX3CR1 axis is involved in the interaction of B-CLL cells with their microenvironment. Taken together, our data delineate a novel role for the CX3CL1/CX3CR1 complex in the biology of normal B cells and B-CLL cells. These topics are the subject of this review article.
The Endemic Paraganglioma Syndrome Type 1: Origin, Spread, and Clinical Expression
Authors: Schiavi Francesca , Demattè Serena , Cecchini Maria Enrica , Taschin Elisa , Bobisse Sara , Del Piano Antonella , Donner Davide , Barbareschi Mattia , Manera Vittorio , Zovato Stefania , Erlic Zoran , Savvoukidis Theodoros , Barollo Susi , Grego Franco , Trabalzini Franco , Amistà Pietro , Grandi Cesare , Branz Fabio , Marroni Fabio , Neumann Hartmut P. H. , Opocher Giuseppe 
Published: March 2012

Context:
Anecdotal evidence suggests a high incidence in Trentino, Italy, of head and neck paragangliomas (HNPGL), a rare autosomal dominant disease called paraganglioma type 1 syndrome and caused by germ-line mutations of the SDHD gene.

Objective:
The aim of this study was to investigate the origin, spread, and clinical expression of the disease in this geographic region.

Design, Setting, and Participants:
Trentino natives with HNPGL were recruited for establishing clinical expression of the disease, presence of a founder effect, and age of common ancestor. A large sample of the local population was recruited for determination of mutation prevalence and spread.

Main Outcome Measures:
SDHD genetic testing was offered to first-degree relatives, and clinical surveillance was offered to at-risk carriers. The hypothesis of a founder effect was explored by haplotype analysis, and time to the most recent common ancestor was estimated by decay of haplotype sharing over time.

Results:
A total of 287 of the 540 recruited individuals from 95 kindreds carried the SDHD c.341A&gt;G p.Tyr114Cys mutation. The prevalent phenotype was bilateral or multiple HNPGL, with low prevalence of pheochromocytoma and malignant forms. Penetrance was high. A common ancestor was dated between the 14th and 15th century, with the mutation spreading from the Mocheni Valley, a geographic, cultural and, presumably, a genetic isolate to 1.5% of the region's population.

Conclusions:
A combination of particular demographic, geographical, and historical conditions has resulted in the oldest and largest SDHD founder effect so far characterized and has transformed a rare disease into an endemic disease with major public health implications.
Daptomycin Experience in Critical Care Patients: Results from a Registry
Authors: Brown Jack E , Fominaya Cory , Christensen Keith J , McConnell Scott A , Lamp Kenneth C 
Published: March 2012

Background: Vancomycin is often the drug of choice in critically ill patients with gram-positive infections, although circumstances often prevent its use. In these situations, clinicians are frequently left with limited data regarding alternative agents. Objective: To describe patients with reported sepsis receiving daptomycin in a critical care unit. Methods: This multicenter, noncomparative, noninterventional study identified patients in critical care units, using the Cubicin Outcomes Registry and Experience (CORE) 2005-2009 registry. A descriptive account of patient characteristics, infectious etiology, outcomes at the end of daptomycin therapy, and 30-day mortality is reported. Nonevaluable patients were excluded from the efficacy analysis but included in the safety analysis. Results: We identified 128 patients, 98 (77%) of whom were evaluable for efficacy. Patient characteristics for the efficacy population were 55 (56%) males, 30 (31%) aged 66 years or older, 38 (39%) had creatinine clearance less than 30 mL/min, and 27 (28%) were on dialysis. Common underlying diseases included acute or chronic renal failure 44 (45%), hypertension 40 (41%), and diabetes 27 (28%). Seventy-two (73%) patients were bacteremic The most common pathogens found were methicillin-resistant Staphylococcus aureus (32%), vancomycin-resistant Enterococcus faecium (21%), and coagulase-negative staphylococci (20%). Prior to daptomycin, antibiotics were used in 84 (86%) patients, most commonly vancomycin (65/84; 77%). The median (range) initial daptomycin dose was 6 mg/kg (3-10) and duration of 10 days (1-58). Overall success rate was 70% (31% cured; 39% improved). Twelve adverse events possibly related to daptomycin were reported in 9 of 128 (7%) patients in the safety population; 4 of these in 4 (3%) patients were serious. The mortality rate within 30 days of completing daptomycin was 42 of 128 (33%) patients. Conclusions: These data provide preliminary results on the use of daptomycin in critically ill patients with complicated conditions. Controlled studies are needed to best evaluate daptomycin use in these patients.
Optimal Alcohol Taxes for Australia
Authors: Fogarty James J. 
Published: March 2012

Abstract
The 2010 Australian government tax review suggested Australia move to a uniform excise tax rate for all alcoholic beverages. Here, a model is presented and calibrated that shows the optimal per litre of pure alcohol (LAL) tax rates for beer, wine, spirits, and ready-to-drink spirits are substantially different to both current alcohol tax rates and the uniform tax rate recommended by the tax review. Specifically, given an individual consumer utility model, the best estimate values of the welfare maximising LAL tax rates are: $37 for beer, $11 for wine, $50 for spirits, and $77 for ready-to-drink spirits. The variation in the optimal tax rate across beverage types flows from differences in the externality costs associated with the consumption of each beverage type, and differences in the proportion of moderate consumption and abusive consumption associated with each beverage type. In addition, it is shown that the optimal tax rates are influenced by the range of costs that are considered to be externality costs, and the relative price responsiveness of abusers and moderate consumers.
Clinical, genetic, and immunohistochemical characterization of 70 Ukrainian adult cases with post-Chornobyl papillary thyroid carcinoma
Authors: Dinets Andrii , Hulchiy Mykola , Sofiadis Anastasios , Ghaderi Mehran , Höög Anders , Larsson Catharina , Zedenius Jan 
Published: March 2012

BackgroundIncreased incidence of papillary thyroid carcinoma (PTC) is observed as a consequence of radiation exposure in connection to the Chornobyl nuclear plant accident in 1986. In this study, we report a cohort of adult Ukrainian patients diagnosed with PTC from 2004 to 2008 following exposure at the age of 18 years or younger.MethodsIn total, 70 patients were identified and clinically characterized. The commonBRAF1799T>A mutation was assessed by pyrosequencing, theRET/PTC1andRET/PTC3(NCOA4) rearrangements by RT-PCR, and the expression of Ki-67 (MIB-1 index), BCL2, cyclin A, and cyclin D1 by immunohistochemistry.ResultsIn total, 46/70 (66%) cases carried aBRAFmutation and/or aRET/PTCrearrangement. ABRAFmutation was detected in 26 tumors,RET/PTC1in 20 cases, andRET/PTC3in four cases. In four of these cases,BRAFmutation andRET/PTCrearrangement were coexisting. TheBRAFmutation was underrepresented among PTCs with accompanying chronic lymphocytic thyroiditis (CLT) compared with PTCs without this feature (12 vs 44%). MIB-1 proliferation index determined by double staining with leukocyte common antigen was low (mean 0.8%; range 0.05–4.5%). Moreover, increased expression of cyclin A was observed in PTCs with a tumor size >2 cm compared with PTCs ≤2 cm (1.2 vs 0.6%). BCL2 and cyclin D1 showed frequent expression but without associations to clinical characteristics or amplification of theCCND1locus.ConclusionsOur results suggest that this cohort has frequentBRAFmutation,RET/PTC1rearrangement, and low proliferation index. Furthermore,BRAF1799T>A was underrepresented in PTCs with CLT, and cyclin A expression was associated with increased PTC tumor size.