bluuebunny/crossref_metadata_2025_split huggingface dataset:
Type of skin eruption is an independent prognostic indicator for adult T-cell leukemia/lymphoma
Authors: Sawada Yu , Hino Ryosuke , Hama Kayo , Ohmori Shun , Fueki Haruna , Yamada Shigenori , Fukamachi Shoko , Tajiri Makiko , Kubo Rieko , Yoshioka Manabu , Nakashima Daiki , Sugita Kazunari , Yoshiki Ryutaro , Shimauchi Takatoshi , Mori Tomoko , Izu Kunio , Kobayashi Miwa , Nakamura Motonobu , Tokura Yoshiki 
Published: February 2011

Abstract
Cutaneous involvement is seen in ∼ 50% of adult T-cell leukemia/lymphoma (ATLL) patients. We investigated the association between skin eruption type and prognosis in 119 ATLL patients. ATLL eruptions were categorized into patch (6.7%), plaque (26.9%), multipapular (19.3%), nodulotumoral (38.7%), erythrodermic (4.2%), and purpuric (4.2%) types. When the T stage of the tumor-node-metastasis-blood (TNMB) classification of mycosis fungoides/Sézary syndrome was applied to ATLL staging, 16.0% were T1, 17.7% T2, 38.7% T3, and 4.2% T4, and the remaining 23.5% were of the multipapular and purpuric types. For the patch type, the mean survival time (median survival time could not be estimated) was 188.4 months. The median survival times (in months) for the remaining types were as follows: plaque, 114.9; multipapular, 17.3; nodulotumoral, 17.3; erythrodermic, 3.0; and purpuric, 4.4. Kaplan-Meier curves of overall survival showed that the erythrodermic type had the poorest prognosis, followed by the nodulotumoral and multipapular types. The patch and plaque types were associated with better survival rates. Multivariate analysis demonstrated that the hazard ratios of the erythrodermic and nodulotumoral types were significantly higher than that of the patch type, and that the eruption type is an independent prognostic factor for ATLL. The overall survival was worse as the T stage became more advanced: the multipapular type and T2 were comparable, and the purpuric type had a significantly poorer prognosis than T1.
Serum amyloid A overrides Treg anergy via monocyte-dependent and Treg-intrinsic, SOCS3-associated pathways
Authors: Nguyen Khoa D. , Macaubas Claudia , Nadeau Kari C. , Truong Phi , Yoon Taejin , Lee Tzielan , Park Jane L. , Mellins Elizabeth D. 
Published: February 2011

Abstract
The acute phase protein serum amyloid A (SAA) has been well characterized as an indicator of inflammation. Nevertheless, its functions in pro versus anti-inflammatory processes remain obscure. Here we provide unexpected evidences that SAA induces the proliferation of the tolerogenic subset of regulatory T cells (Treg). Intriguingly, SAA reverses Treg anergy via its interaction with monocytes to activate distinct mitogenic pathways in Treg but not effector T cells. This selective responsiveness of Treg correlates with their diminished expression of SOCS3 and is antagonized by Treg–specific induction of this regulator of cytokine signaling. Collectively, these evidences suggest a novel anti-inflammatory role of SAA in the induction of a micro-environment that supports Treg expansion at sites of infection or tissue injury, likely to curb (auto)-inflammatory responses.
High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum
Authors: Samarakoon Upeka , Regier Allison , Tan Asako , Desany Brian A , Collins Brendan , Tan John C , Emrich Scott J , Ferdig Michael T 
Published: February 2011

Abstract

Background
Knowledge of the origins, distribution, and inheritance of variation in the malaria parasite (Plasmodium falciparum) genome is crucial for understanding its evolution; however the 81% (A+T) genome poses challenges to high-throughput sequencing technologies. We explore the viability of the Roche 454 Genome Sequencer FLX (GS FLX) high throughput sequencing technology for both whole genome sequencing and fine-resolution characterization of genetic exchange in malaria parasites.

Results
We present a scheme to survey recombination in the haploid stage genomes of two sibling parasite clones, using whole genome pyrosequencing that includes a sliding window approach to predict recombination breakpoints. Whole genome shotgun (WGS) sequencing generated approximately 2 million reads, with an average read length of approximately 300 bp. De novo assembly using a combination of WGS and 3 kb paired end libraries resulted in contigs ≤ 34 kb. More than 8,000 of the 24,599 SNP markers identified between parents were genotyped in the progeny, resulting in a marker density of approximately 1 marker/3.3 kb and allowing for the detection of previously unrecognized crossovers (COs) and many non crossover (NCO) gene conversions throughout the genome.

Conclusions
By sequencing the 23 Mb genomes of two haploid progeny clones derived from a genetic cross at more than 30× coverage, we captured high resolution information on COs, NCOs and genetic variation within the progeny genomes. This study is the first to resequence progeny clones to examine fine structure of COs and NCOs in malaria parasites.
Characterization of the Conus bullatus genome and its venom-duct transcriptome
Authors: Hu Hao , Bandyopadhyay Pradip K , Olivera Baldomero M , Yandell Mark 
Published: February 2011

Abstract

Background
The venomous marine gastropods, cone snails (genus Conus), inject prey with a lethal cocktail of conopeptides, small cysteine-rich peptides, each with a high affinity for its molecular target, generally an ion channel, receptor or transporter. Over the last decade, conopeptides have proven indispensable reagents for the study of vertebrate neurotransmission. Conus bullatus belongs to a clade of Conus species called Textilia, whose pharmacology is still poorly characterized. Thus the genomics analyses presented here provide the first step toward a better understanding the enigmatic Textilia clade.

Results
We have carried out a sequencing survey of the Conus bullatus genome and venom-duct transcriptome. We find that conopeptides are highly expressed within the venom-duct, and describe an in silico pipeline for their discovery and characterization using RNA-seq data. We have also carried out low-coverage shotgun sequencing of the genome, and have used these data to determine its size, genome-wide base composition, simple repeat, and mobile element densities.

Conclusions
Our results provide the first global view of venom-duct transcription in any cone snail. A notable feature of Conus bullatus venoms is the breadth of A-superfamily peptides expressed in the venom duct, which are unprecedented in their structural diversity. We also find SNP rates within conopeptides are higher compared to the remainder of C. bullatus transcriptome, consistent with the hypothesis that conopeptides are under diversifying selection.
Selection of reference genes for gene expression studies in ultraviolet B-irradiated human skin fibroblasts using quantitative real-time PCR
Authors: Li Li , Yan Yan , Xu Haoxiang , Qu Tao , Wang Baoxi 
Published: February 2011

Abstract

Background
Reference genes are frequently used to normalise mRNA levels between different samples. The expression level of these genes, however, may vary between tissues or cells and may change under certain circumstances. Cytoskeleton genes have served as multifunctional tools for experimental studies as reference genes. Our previous studies have demonstrated that the expression of vimentin, one cytoskeletal protein, was increased in ultraviolet B (UVB)-irradiated fibroblasts. Thus, we examined the expression of other cytoskeleton protein genes, ACTB (actin, beta), TUBA1A (tubulin, alpha 1a), and TUBB1 (tubulin, beta 1), in human dermal fibroblasts irradiated by UVB to determine which of these candidates were the most appropriate reference genes.

Results
Quantitative real-time PCR followed by analysis with the NormFinder and geNorm software programmes was performed. The initial screening of the expression patterns demonstrated that the expression of VIM was suppressed after UVB irradiation at doses ≥25 mJ/cm2 and that the expression of TUBA1A was significantly reduced by UVB doses ≥75 mJ/cm2 in cultured human dermal fibroblasts. The analysis of the experimental data revealed ACTB to be the most stably expressed gene, followed by GAPDH (aglyceraldehyde-3-phosphate dehydrogenase), under these experimental conditions. By contrast, VIM was found to be the least stable gene. The combination of ACTB and TUBB1 was revealed to be the gene pair that introduced the least systematic error into the data normalisation.

Conclusion
The data herein provide evidence that ACTB and TUBB1 are suitable reference genes in human skin fibroblasts irradiated by UVB, whereas VIM and TUBA1A are not and should therefore be excluded as reference genes in any gene expression studies involving UVB-irradiated human skin fibroblasts.
Clinical and Molecular Characterization of Ataxia with Oculomotor Apraxia Patients In Saudi Arabia
Authors: Bohlega Saeed A , Shinwari Jameela M , Al Sharif Latifa J , Khalil Dania S , Alkhairallah Thamer S , Al Tassan Nada A 
Published: February 2011

Abstract

Background
Autosomal recessive ataxias represent a group of clinically overlapping disorders. These include ataxia with oculomotor apraxia type1 (AOA1), ataxia with oculomotor apraxia type 2 (AOA2) and ataxia-telangiectasia-like disease (ATLD). Patients are mainly characterized by cerebellar ataxia and oculomotor apraxia. Although these forms are not quite distinctive phenotypically, different genes have been linked to these disorders. Mutations in the APTX gene were reported in AOA1 patients, mutations in SETX gene were reported in patients with AOA2 and mutations in MRE11 were identified in ATLD patients. In the present study we describe in detail the clinical features and results of genetic analysis of 9 patients from 4 Saudi families with ataxia and oculomotor apraxia.

Methods
This study was conducted in the period between 2005-2010 to clinically and molecularly characterize patients with AOA phenotype. Comprehensive sequencing of all coding exons of previously reported genes related to this disorder (APTX, SETX and MRE11).

Results
A novel nonsense truncating mutation c.6859 C > T, R2287X in SETX gene was identified in patients from one family with AOA2. The previously reported missense mutation W210C in MRE11 gene was identified in two families with autosomal recessive ataxia and oculomotor apraxia.

Conclusion
Mutations in APTX , SETX and MRE11 are common in patients with autosomal recessive ataxia and oculomotor apraxia. The results of the comprehensive screening of these genes in 4 Saudi families identified mutations in SETX and MRE11 genes but failed to identify mutations in APTX gene.
Design and implementation of the canadian kidney disease cohort study (CKDCS): A prospective observational study of incident hemodialysis patients
Authors: Bello Aminu K , Thadhani Ravi , Hemmelgarn Brenda , Klarenbach Scott , Gill John , Chan Christopher , Zimmerman Deborah , Holmes Daniel , Cembrowski George , Opgenorth Dawn , Sibrian Rafael , Karkhaneh Mohammad , Tiv Sophanny , Wiebe Natasha , Tonelli Marcello 
Published: February 2011

Abstract

Background
Many nephrology observational studies use renal registries, which have well known limitations. The Canadian Kidney Disease Cohort Study (CKDCS) is a large prospective observational study of patients commencing hemodialysis in five Canadian centers. This study focuses on delineating potentially reversible determinants of adverse outcomes that occur in patients receiving dialysis for end-stage renal disease (ESRD).

Methods/Design
The CKDCS collects information on risk factors and outcomes, and stores specimens (blood, dialysate, hair and fingernails) at baseline and in long-term follow-up. Such specimens will permit measurements of biochemical markers, proteomic and genetic parameters (proteins and DNA) not measured in routine care. To avoid selection bias, all consenting incident hemodialysis patients at participating centers are enrolled, the large sample size (target of 1500 patients), large number of exposures, and high event rates will permit the exploration of multiple potential research questions.

Preliminary Results
Data on the baseline characteristics from the first 1074 subjects showed that the average age of patients was 62 (range; 50-73) years. The leading cause of ESRD was diabetic nephropathy (41.9%), and the majority of the patients were white (80.0%). Only 18.7% of the subjects received dialysis in a satellite unit, and over 80% lived within a 50 km radius of the nearest nephrologist's practice.

Discussion
The prospective design, detailed clinical information, and stored biological specimens provide a wealth of information with potential to greatly enhance our understanding of risk factors for adverse outcomes in dialysis patients. The scientific value of the stored patient tissue will grow as new genetic and biochemical markers are discovered in the future.
Leiomyosarcoma with partial rhabdomyoblastic differentiation: First case report of primary cardiac origin
Authors: Okubo Yoichiro , Shibuya Kazutoshi , Namiki Atsushi , Takamura Kazuhisa , Kameda Noriaki , Nemoto Tetsuo , Mitsuda Aki , Wakayama Megumi , Shinozaki Minoru , Hiruta Nobuyuki , Kitahara Kanako , Ishiwatari Takao , Yamazaki Junichi 
Published: February 2011

Abstract

Background
Leiomyosarcoma occurring as a primary cardiac tumor has been known as an extremely rare condition. Previous studies of leiomyosarcoma with rhabdomyoblastic differentiation have conducted to those arisen from another site, and they indicated a poorer prognosis of this tumor.

Case presentation
A 69-year-old woman was referred to our hospital for an operation concerning umbilical hernia. Subsequent imaging examinations before an operation indicated the presence of primary cardiac malignant tumor due to its atypical shape. And then, it was surgically removed. Histopathologically, tumor cells consisted of two different types: spindle and polyhedral cells. Immunohistochemically, it is interesting to note that 2.1% of spindle cells and 23.1% of polyhedral cells showed positive reactivity for myogenin. Furthermore, we performed double-immunostaining for alpha-smooth muscle actin (SMA) and myogenin. The rates of alpha-SMA and myogenin double negative, alpha-SMA single positive, myogenin single positive, and alpha-SMA and myogenin double positive in spindle cells were estimated as 69.1%, 28.8%, 1.1% and 1.0%, respectively. In contrast, the rates in polyhedral cells were estimated as 76.9%, 0.0%, 23.1%, and 0.0%, respectively.

Conclusion
Our immunohistochemical evaluation suggested that rhabdomyoblastic differentiation in leiomyosarcoma might be generated not only by de novo generation from mesenchymal cells. To the best of our knowledge, this is the first case of primary cardiac leiomyosarcoma with partial rhabdomyoblastic differentiation.
Predictors of consistent condom use based on the Information-Motivation-Behavioral Skills (IMB) model among female sex workers in Jinan, China
Authors: Zhang Hua , Liao Meizhen , Nie Xijuan , Pan Rongjian , Wang Chuangxin , Ruan Shiman , Zhang Changqing , Tao Xiaorun , Kang Dianmin , Jiang Baofa 
Published: February 2011

Abstract

Background
Female commercial sex workers (FSWs) are at high risk of human immunodeficiency virus (HIV) transmission in China. This study was designed to examine the predictors of condom use with clients during vaginal intercourse among FSWs based on the Information-Motivation-Behavioral Skills (IMB) model and to describe the relationships between IMB model constructs.

Methods
A cross-sectional study was conducted in Jinan of Shandong Province, from May to October, 2009. Participants (N = 432) were recruited using Respondent-Driven Sampling (RDS). A self-administered questionnaire was used to collect data. Structural equation modeling was used to assess the IMB model.

Results
A total of 427 (98.8%) participants completed their questionnaires. Condom use was significantly predicted by social referents support, experiences with and attitudes toward condoms, self-efficacy, and health behaviors and condom use skills. Significant indirect predictors of condom use mediated through behavioral skills included HIV knowledge, social referents support, and substance use.

Conclusions
These results suggest that the IMB model could be used to predict condom use among Chinese FSWs. Further research is warranted to develop preventive interventions on the basis of the IMB model to promote condom use among FSWs in China.
High cell density cultivation of Escherichia coli K4 in a microfiltration bioreactor: a step towards improvement of chondroitin precursor production
Authors: Restaino Odile Francesca , Cimini Donatella , De Rosa Mario , Catapano Angela , De Rosa Mario , Schiraldi Chiara 
Published: February 2011

Abstract

Background
The bacteria Escherichia coli K4 produces a capsular polysaccharide (K4 CPS) whose backbone is similar to the non sulphated chondroitin chain. The chondroitin sulphate is one of the major components of the extra-cellular matrix of the vertebrate connective tissues and a high value molecule, widely employed as active principle in the treatment of osteoarthritis. It is usually obtained by extraction from animal tissues, but the risk of virus contaminations, as well as the scarceness of raw material, makes this productive process unsafe and unable to satisfy the growing market demand. In previous studies a new biotechnological process to produce chondroitin from Escherichia coli K4 capsular polysaccharide was investigated and a 1.4 g·L-1 K4 CPS concentration was reached using fed-batch fermentation techniques. In this work, on the trail of these results, we exploited new fermentation strategies to further improve the capsular polysaccharide production.

Results
The inhibitory effect of acetate on the bacterial cells growth and K4 CPS production was studied in shake flask conditions, while a new approach, that combined the optimization of the feeding profiles, the improvement of aeration conditions and the use of a microfiltration bioreactor, was investigated in three different types of fermentation processes. High polysaccharide concentrations (4.73 ± 0.2 g·L-1), with corresponding average yields (0.13 ± 0.006 gK4 CPS·gcdw
-1), were obtained; the increase of K4 CPS titre, compared to batch and fed-batch results, was of 16-fold and 3.3-fold respectively, while average yield was almost 3.5 and 1.4 fold higher.

Conclusion
The increase of capsular polysaccharide titre confirmed the validity of the proposed fermentation strategy and opened the way to the use of the microfiltration bioreactor for the biotechnological production of chondroitin.
Purification and biochemical characterization of pancreatic phospholipase A2 from the common stingray Dasyatis pastinaca
Authors: Bacha Abir Ben , Karray Aida , Bouchaala Emna , Gargouri Youssef , Ali Yassine Ben 
Published: February 2011

Abstract

Background
Mammalian sPLA2-IB are well characterized. In contrast, much less is known about aquatic ones. The aquatic world contains a wide variety of living species and, hence represents a great potential for discovering new lipolytic enzymes.

Results
A marine stingray phospholipase A2 (SPLA2) was purified from delipidated pancreas. Purified SPLA2, which is not glycosylated protein, was found to be monomeric protein with a molecular mass of 14 kDa. A specific activity of 750 U/mg for purified SPLA2 was measured at optimal conditions (pH 8.5 and 40 °C) in the presence of 4 mM NaTDC and 8 mM CaCl2 using PC as substrate. The sequence of the first twenty first amino-acid residues at the N-terminal extremity of SPLA2 was determined and shows a close similarity with known mammal and bird pancreatic secreted phospholipases A2. SPLA2 stability in the presence of organic solvents, as well as in acidic and alkaline pH and at high temperature makes it a good candidate for its application in food industry.

Conclusions
SPLA2 has several advantageous features for industrial applications. Stability of SPLA2 in the presence of organic solvents, and its tolerance to high temperatures, basic and acidic pH, makes it a good candidate for application in food industry to treat phospholipid-rich industrial effluents, or to synthesize useful chemical compounds.
Characterization of silicon heterojunctions for solar cells
Authors: Kleider Jean-Paul , Alvarez Jose , Ankudinov Alexander Vitalievitch , Gudovskikh Alexander Sergeevitch , Gushchina Ekaterina Vladimirovna , Labrune Martin , Maslova Olga Alexandrovna , Favre Wilfried , Gueunier-Farret Marie-Estelle , Roca i Cabarrocas Pere , Terukov Eugene Ivanovitch 
Published: February 2011

AbstractConductive-probe atomic force microscopy (CP-AFM) measurements reveal the existence of a conductive channel at the interface between p-type hydrogenated amorphous silicon (a-Si:H) and n-type crystalline silicon (c-Si) as well as at the interface between n-type a-Si:H and p-type c-Si. This is in good agreement with planar conductance measurements that show a large interface conductance. It is demonstrated that these features are related to the existence of a strong inversion layer of holes at the c-Si surface of (p) a-Si:H/(n) c-Si structures, and to a strong inversion layer of electrons at the c-Si surface of (n) a-Si:H/(p) c-Si heterojunctions. These are intimately related to the band offsets, which allows us to determine these parameters with good precision.
Combined plasma gas-phase synthesis and colloidal processing of InP/ZnS core/shell nanocrystals
Authors: Gresback Ryan , Hue Ryan , Gladfelter Wayne L , Kortshagen Uwe R 
Published: February 2011

AbstractIndium phosphide nanocrystals (InP NCs) with diameters ranging from 2 to 5 nm were synthesized with a scalable, flow-through, nonthermal plasma process at a rate ranging from 10 to 40 mg/h. The NC size is controlled through the plasma operating parameters, with the residence time of the gas in the plasma region strongly influencing the NC size. The NC size distribution is narrow with the standard deviation being less than 20% of the mean NC size. Zinc sulfide (ZnS) shells were grown around the plasma-synthesized InP NCs in a liquid phase reaction. Photoluminescence with quantum yields as high as 15% were observed for the InP/ZnS core-shell NCs.
The encapsulation effect of UV molecular absorbers into biocompatible lipid nanoparticles
Authors: Lacatusu Ioana , Badea Nicoleta , Murariu Alina , Meghea Aurelia 
Published: February 2011

AbstractThe efficiency of a cosmetic product depends not only on the active ingredients, but also on the carrier system devoted to improve its bioavailability. This article aims to encapsulate two couples of UV molecular absorbers, with a blocking action on both UV-A and UV-B domains, into efficient lipid nanoparticles. The effect of encapsulation on the specific properties such as sun protection factor and photostability behaviour has been demonstrated. The lipid nanoparticles with size range 30-350 nm and a polydispersity index between 0.217 and 0.244 are obtained using a modified high shear homogenisation method. The nanoparticles had spherical shapes with a single crystallisation form of lipid matrices characteristic for the least ordered crystal structure (α-form). The in vitro determination of photoprotection has led to high SPF ratings, with values of about 20, which assure a good photoprotection and filtering about 95% of UV radiation. The photoprotection effect after irradiation stage was observed to be increased more than twice compared to initial samples as a result of isomerisation phenomena. All the results have shown that good photoprotection effect and improved photostability could be obtained using such sunscreen couples, thus demonstrating that UV absorbers-solid lipid nanoparticles are promising carriers for cosmetic formulations.