bluuebunny/crossref_metadata_2025_split huggingface dataset:
Studies on synthesis and characterization of hydroxyl-terminated polydimethylsiloxane-modified epoxy bismaleimide matrices
Authors: Selvaganapathi A. , Alagar M. , Gnanasundaram P. 
Published: February 2013

This work reports the development of hydroxyl-terminated polydimethylsiloxane (HTPDMS)-toughened tetraglycidyl diaminodiphenyl methane (TGDDM) epoxy matrix systems. The siliconized epoxy systems were further modified with various percentages of (5, 10 and 15 wt%) 10-phenyl-phenonoxaphosphine-3,8-di(2-hydroxy-3-( p-male-imidobenzoyloxy)propyl) ester-10-oxide (EPBMI) and cured by diaminodiphenyl sulfone. Thermal, mechanical and morphological properties of the prepared samples were studied by standard methods. In comparison with the unmodified epoxy resin, HTPDMS-incorporated TGDDM resin showed increased impact strength with a reduction in tensile strength, flexural strength and glass transition temperature ( Tg). But in the case of bismaleimide (BMI; EPBMI)-incorporated epoxy resin, tensile strength, flexural strength and Tg showed an increasing trend. However, the introduction of both siloxane and BMI into epoxy influences the mechanical and thermal properties according to their percentage content. The morphology of the silconized and the BMI-modified epoxy systems was also studied by scanning electron microscopy.
Fatigue heralding multiple sclerosis
Authors: Berger Joseph R , Pocoski Jennifer , Preblick Ronald , Boklage Susan 
Published: February 2013

Background: Fatigue is a common symptom in multiple sclerosis (MS) and is an important determinant of overall well-being and disability. Objective: To assess the frequency with which fatigue precedes the diagnosis of MS using a retrospective database analysis. Methods: Between January 1, 2003 and September 30, 2008, patients diagnosed with fatigue with and without fatigue-related medications within a 3-year period prior to newly diagnosed MS were identified from the MarketScan Databases. All statistical analysis was performed using SAS. Results: Of the 16,976 patients with MS in the overall population, 5305 (31.3%) were newly diagnosed with MS and had three years of continuous healthcare coverage prior to MS diagnosis. Of these patients, 1534 (28.9%) were labeled with chronic fatigue syndrome (ICD9-780.71) or malaise or fatigue (ICD9-780.79) prior to the diagnosis of MS. One-third of these patients were labeled with fatigue one to two years before the diagnosis; 30.8% were diagnosed only with fatigue and had no other MS symptoms prior to their MS diagnosis. Among the patients diagnosed with fatigue, 10.4% were also prescribed medication for fatigue. Conclusion: This study demonstrates that fatigue may herald MS, often by years. A careful history for transient neurological symptoms and a physical examination is warranted in any patient presenting with fatigue.
Naturally occurring oncogenic GATA1 mutants with internal deletions in transient abnormal myelopoiesis in Down syndrome
Authors: Toki Tsutomu , Kanezaki Rika , Kobayashi Eri , Kaneko Hiroshi , Suzuki Mikiko , Wang RuNan , Terui Kiminori , Kanegane Hirokazu , Maeda Miho , Endo Mikiya , Mizuochi Tatsuki , Adachi Souichi , Hayashi Yasuhide , Yamamoto Masayuki , Shimizu Ritsuko , Ito Etsuro 
Published: February 2013

Key Points
Naturally occurring oncogenic GATA1 mutants with internal deletions contribute to transient abnormal myelopoiesis in Down syndrome.
A dual role for Hdac1: oncosuppressor in tumorigenesis, oncogene in tumor maintenance
Authors: Santoro Fabio , Botrugno Oronza A. , Dal Zuffo Roberto , Pallavicini Isabella , Matthews Geoffrey M. , Cluse Leonie , Barozzi Iros , Senese Silvia , Fornasari Lorenzo , Moretti Simona , Altucci Lucia , Pelicci Pier Giuseppe , Chiocca Susanna , Johnstone Ricky W. , Minucci Saverio 
Published: February 2013

Key Points
Hdac1 and, to a lesser extent, Hdac2 behave as oncosuppressors during tumor initiation, but they work as oncogenes in tumor maintenance. Class I HDAC inhibitors (VPA) accelerate tumorigenesis in murine models of leukemia, which suggests caution in their clinical use.
Probabilistic models for CRISPR spacer content evolution
Authors: Kupczok Anne , Bollback Jonathan P 
Published: February 2013

AbstractBackgroundThe CRISPR/Cas system is known to act as an adaptive and heritable immune system in Eubacteria and Archaea. Immunity is encoded in an array of spacer sequences. Each spacer can provide specific immunity to invasive elements that carry the same or a similar sequence. Even in closely related strains, spacer content is very dynamic and evolves quickly. Standard models of nucleotide evolution cannot be applied to quantify its rate of change since processes other than single nucleotide changes determine its evolution.MethodsWe present probabilistic models that are specific for spacer content evolution. They account for the different processes of insertion and deletion. Insertions can be constrained to occur on one end only or are allowed to occur throughout the array. One deletion event can affect one spacer or a whole fragment of adjacent spacers. Parameters of the underlying models are estimated for a pair of arrays by maximum likelihood using explicit ancestor enumeration.ResultsSimulations show that parameters are well estimated on average under the models presented here. There is a bias in the rate estimation when including fragment deletions. The models also estimate times between pairs of strains. But with increasing time, spacer overlap goes to zero, and thus there is an upper bound on the distance that can be estimated. Spacer content similarities are displayed in a distance based phylogeny using the estimated times.We use the presented models to analyze differentYersinia pestisdata sets and find that the results among them are largely congruent. The models also capture the variation in diversity of spacers among the data sets. A comparison of spacer-based phylogenies and Cas gene phylogenies shows that they resolve very different time scales for this data set.ConclusionsThe simulations and data analyses show that the presented models are useful for quantifying spacer content evolution and for displaying spacer content similarities of closely related strains in a phylogeny. This allows for comparisons of different CRISPR arrays or for comparisons between CRISPR arrays and nucleotide substitution rates.
Evolution of bone compactness in extant and extinct moles (Talpidae): exploring humeral microstructure in small fossorial mammals
Authors: Meier Patricia S , Bickelmann Constanze , Scheyer Torsten M , Koyabu Daisuke , Sánchez-Villagra Marcelo R 
Published: February 2013

Abstract

Background
Talpids include forms with different degree of fossoriality, with major specializations in the humerus in the case of the fully fossorial moles. We studied the humeral microanatomy of eleven extant and eight extinct talpid taxa of different lifestyles and of two non-fossorial outgroups and examined the effects of size and phylogeny. We tested the hypothesis that bone microanatomy is different in highly derived humeri of fossorial taxa than in terrestrial and semi-aquatic ones, likely due to special mechanical strains to which they are exposed to during digging. This study is the first comprehensive examination of histological parameters in an ecologically diverse and small-sized mammalian clade.

Results
No pattern of global bone compactness was found in the humeri of talpids that could be related to biomechanical specialization, phylogeny or size. The transition zone from the medullary cavity to the cortical compacta was larger and the ellipse ratio smaller in fossorial talpids than in non-fossorial talpids. No differences were detected between the two distantly related fossorial clades, Talpini and Scalopini.

Conclusions
At this small size, the overall morphology of the humerus plays a predominant role in absorbing the load, and microanatomical features such as an increase in bone compactness are less important, perhaps due to insufficient gravitational effects. The ellipse ratio of bone compactness shows relatively high intraspecific variation, and therefore predictions from this ratio based on single specimens are invalid.
qDTY12.1: a locus with a consistent effect on grain yield under drought in rice
Authors: Mishra Krishna Kumar , Vikram Prashant , Yadaw Ram Baran , Swamy BP Mallikarjuna , Dixit Shalabh , Cruz Ma Teresa Sta , Maturan Paul , Marker Shailesh , Kumar Arvind 
Published: February 2013

Abstract

Background
Selection for grain yield under drought is an efficient criterion for improving the drought tolerance of rice. Recently, some drought-tolerant rice varieties have been developed using this selection criterion and successfully released for cultivation in drought-prone target environments. The process can be made more efficient and rapid through marker-assisted breeding, a well-known fast-track approach in crop improvement. QTLs have been identified for grain yield under drought with large effects against drought-susceptible varieties. Most of the identified QTLs show large QTL × environment or QTL × genetic background interactions. The development of mapping populations in the background of popular high-yielding varieties, screening across environments, including the target environments, and the identification of QTLs with a consistent effect across environments can be a suitable alternative marker-assisted breeding strategy. An IR74371-46-1-1 × Sabitri backcross inbred line population was screened for reproductive-stage drought stress at the International Rice Research Institute, Philippines, and Regional Agricultural Research Station, Nepalgunj, Nepal, in the dry and wet seasons of 2011, respectively. A bulk segregant analysis approach was used to identify markers associated with high grain yield under drought.

Results
A QTL, qDTY

12.1
, significantly associated with grain yield under reproductive-stage drought stress was identified on chromosome 12 with a consistent effect in two environments: IRRI, Philippines, and RARS, Nepalgunj, Nepal. This QTL explained phenotypic variance of 23.8% and contributed an additive effect of 45.3% for grain yield under drought. The positive QTL allele for qDTY

12.1
was contributed by tolerant parent IR74371-46-1-1.

Conclusions
In this study, qDTY

12.1
showed a consistent effect across environments for high grain yield under lowland reproductive-stage drought stress in the background of popular high-yielding but drought-susceptible recipient variety Sabitri. qDTY

12.1
was also reported previously [Crop Sci 47:507–516, 2007] to increase grain yield under upland reproductive-stage drought stress situations. qDTY

12.1
is the only QTL reported so far in rice to have shown a large effect against multiple recipient genetic backgrounds as well as under highly diverse upland and lowland rice ecosystems. qDTY

12.1
can be successfully introgressed to improve grain yield under drought of popular high-yielding but drought-susceptible lowland as well as upland adapted varieties following marker-assisted breeding.
Copynumber: Efficient algorithms for single- and multi-track copy number segmentation
Authors: Nilsen Gro , Liestøl Knut , Van Loo Peter , Moen Vollan Hans Kristian , Eide Marianne B , Rueda Oscar M , Chin Suet-Feung , Russell Roslin , Baumbusch Lars O , Caldas Carlos , Børresen-Dale Anne-Lise , Lingjærde Ole Christian 
Published: February 2013

Abstract

Background
Cancer progression is associated with genomic instability and an accumulation of gains and losses of DNA. The growing variety of tools for measuring genomic copy numbers, including various types of array-CGH, SNP arrays and high-throughput sequencing, calls for a coherent framework offering unified and consistent handling of single- and multi-track segmentation problems. In addition, there is a demand for highly computationally efficient segmentation algorithms, due to the emergence of very high density scans of copy number.

Results
A comprehensive Bioconductor package for copy number analysis is presented. The package offers a unified framework for single sample, multi-sample and multi-track segmentation and is based on statistically sound penalized least squares principles. Conditional on the number of breakpoints, the estimates are optimal in the least squares sense. A novel and computationally highly efficient algorithm is proposed that utilizes vector-based operations in R. Three case studies are presented.

Conclusions
The R package is a software suite for segmentation of single- and multi-track copy number data using algorithms based on coherent least squares principles.
Genetic analysis of the Trichuris muris-induced model of colitis reveals QTL overlap and a novel gene cluster for establishing colonic inflammation
Authors: Levison Scott E , Fisher Paul , Hankinson Jenny , Zeef Leo , Eyre Steve , Ollier William E , McLaughlin John T , Brass Andy , Grencis Richard K , Pennock Joanne L 
Published: February 2013

AbstractBackgroundGenetic susceptibility to colonic inflammation is poorly defined at the gene level. Although Genome Wide Association studies (GWAS) have identified loci in the human genome which confer susceptibility to Inflammatory Bowel Disease (Crohn’s and Ulcerative Colitis), it is not clear if precise loci exist which confer susceptibility to inflammation at specific locations within the gut e.g. small versus large intestine. Susceptibility loci for colitis in particular have been defined in the mouse, although specific candidate genes have not been identified to date. We have previously shown that infection withTrichuris muris(T. muris) induces chronic colitis in susceptible mouse strains with clinical, histological, and immunological homology to human colonic Crohn’s disease. We performed an integrative analysis of colitis susceptibility, using an F2 inter-cross of resistant (BALB/c) and susceptible (AKR) mice followingT. murisinfection. Quantitative Trait Loci (QTL), polymorphic and expression data were analysed alongsidein silicoworkflow analyses to discover novel candidate genes central to the development and biology of chronic colitis.Results7 autosomal QTL regions were associated with the establishment of chronic colitis following infection. 144 QTL genes had parental strain SNPs and significant gene expression changes in chronic colitis (expression fold-change ≥ +/-1.4). TheT. murisQTL on chromosome 3 (Tm3) mapped to published QTL in 3 unrelated experimental models of colitis and contained 33 significantly transcribed polymorphic genes. Phenotypic pathway analysis, text mining and time-course qPCR replication highlighted several potentialcis-QTL candidate genes in colitis susceptibility, includingFcgR1,Ptpn22,RORc,andVav3.ConclusionGenetic susceptibility to induced colonic mucosal inflammation in the mouse is conserved atTm3and overlaysCdcs1.1. Genes central to the maintenance of intestinal homeostasis reside within this locus, implicating several candidates in susceptibility to colonic inflammation. Combined methodology incorporating genetic, transcriptional and pathway data allowed identification of biologically relevant candidate genes, withVav3newly implicated as a colitis susceptibility gene of functional relevance.
Effect of emergency major abdominal surgery on CD4 cell count among HIV positive patients in a sub Saharan Africa tertiary hospital - a prospective study
Authors: Okumu Gabriel , Makobore Patson , Kaggwa Sam , Kambugu Andrew , Galukande Moses 
Published: February 2013

Abstract

Background
Surgery plays a key role in HIV palliative care, specifically in the diagnosis and treatment of HIV related and non-related conditions. Yet major surgery depresses the immune system. Whereas the surgical consequences of HIV infection are well described, there is a paucity of published data, in resource-limited settings, on the effects of major surgery on the immune system. The purpose of this study was to determine the effect of major abdominal surgery on CD4 count in HIV positive and HIV negative patients after emergency major surgery.

Methods
A prospective cohort study was done for patients who underwent emergency major abdominal surgery. Their peri-operative CD4 counts were done for both HIV- and HIV + patients. Median CD4s were used in analysis.
Mann Whitney test of significance was used for continuous data and Fisher’ exact test used for categorical data. IRB approval was obtained.

Results
A total of 101 patients were recruited, 25 HIV positive and 76 HIV negative. The median CD4 cell reduction was higher in the HIV negative group (−68 cells) than HIV positive group (−29 cells) (p = 0.480).
There was a general increase in the median CD4 change by 72 cells for the HIV positives and 95 cells for the HIV negatives (p = 0.44). CD4 change rose in both the HIV positive and negative groups by 27 cells for the HIV positives and 28 cells for the HIV negatives (p = 0.94). Relative Risk was 0.96, {CI 0.60 – 1.53}.

Conclusion
Major emergency abdominal surgery had no significant effect on CD4 cell count among HIV positive patients.
Keratinocyte cytoskeletal roles in cell sheet engineering
Authors: Wei Qi , Reidler Daniel , Shen Min Ye , Huang Hayden 
Published: February 2013

Abstract

Background
There is an increasing need to understand cell-cell interactions for cell and tissue engineering purposes, such as optimizing cell sheet constructs, as well as for examining adhesion defect diseases. For cell-sheet engineering, one major obstacle to sheet function is that cell sheets in suspension are fragile and, over time, will contract. While the role of the cytoskeleton in maintaining the structure and adhesion of cells cultured on a rigid substrate is well-characterized, a systematic examination of the role played by different components of the cytoskeleton in regulating cell sheet contraction and cohesion in the absence of a substrate has been lacking.

Results
In this study, keratinocytes were cultured until confluent and cell sheets were generated using dispase to remove the influence of the substrate. The effects of disrupting actin, microtubules or intermediate filaments on cell-cell interactions were assessed by measuring cell sheet cohesion and contraction. Keratin intermediate filament disruption caused comparable effects on cell sheet cohesion and contraction, when compared to actin or microtubule disruption. Interfering with actomyosin contraction demonstrated that interfering with cell contraction can also diminish cell cohesion.

Conclusions
All components of the cytoskeleton are involved in maintaining cell sheet cohesion and contraction, although not to the same extent. These findings demonstrate that substrate-free cell sheet biomechanical properties are dependent on the integrity of the cytoskeleton network.
Heparanase induced by advanced glycation end products (AGEs) promotes macrophage migration involving RAGE and PI3K/AKT pathway
Authors: Qin Qiaojing , Niu Jianying , Wang Zhaoxia , Xu Wangjie , Qiao Zhongdong , Gu Yong 
Published: February 2013

Abstract

Background
Advanced glycation end products (AGEs), inflammatory-associated macrophage migration and accumulation are crucial for initiation and progression of diabetic vascular complication. Enzymatic activity of heparanase (HPA) is implicated strongly in dissemination of metastatic tumor cells and cells of the immune system. In addition, HPA enhances the phosphorylation of selected signaling molecules including AKT pathway independent of enzymatic activity. However, virtually nothing is presently known the role of HPA during macrophage migration exposed to AGEs involving signal pathway.

Methods
These studies were carried out in Ana-1 macrophages. Macrophage viability was measured by MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assays. HPA and AKT protein expression in macrophages are analysed by Western blotting and HPA mRNA expression by real time quantitative RT-PCR. Release of HPA was determined by ELISA. Macrophage migration was assessed by Transwell assays.

Results
HPA protein and mRNA were found to be increased significantly in AGEs-treated macrophages. Pretreatment with anti-HPA antibody which recognizes the nonenzymatic terminal of HPA prevented AGEs-induced AKT phosphorylation and macrophage migration. LY294002 (PI3k/AKT inhibitor) inhibited AGEs-induced macrophage migration. Furthermore, pretreatment with anti-receptor for advanced glycation end products (RAGE) antibody attenuated AGEs-induced HPA expression, AKT phosphorylation and macrophage migration.

Conclusions
These data indicate that AGEs-induced macrophage migration is dependent on HPA involving RAGE-HPA-PI3K/AKT pathway. The nonenzymatic activity of HPA may play a key role in AGEs-induced macrophage migration associated with inflammation in diabetic vascular complication.
Establishment and characterization of clear cell renal cell carcinoma cell lines with different metastatic potential from Chinese patients
Authors: Tan Xiaojie , He Songqin , Han Yifang , Yu Yongwei , Xiao Jianru , Xu Danfeng , Wang Guoping , Du Yan , Chang Wenjun , Yin Jianhua , Su Tong , Hou Jianguo , Cao Guangwen 
Published: February 2013

Abstracts

Background
Clear cell renal cell carcinoma (ccRCC) cell lines with distinct metastatic potential are essential to study the mechanism of ccRCC metastasis. However, none of them originated from Chinese.

Methods
Primary cell cultures were performed using a primary tumor of a 49-year-old male ccRCC patient and a metastatic tumor of a 62-year-old male patient who had received nephrectomy to excise primary ccRCC 10 years ago. Cell growth, microstructure, cytogenetics, cytometry, expression of metastasis-associated molecules, tumorigenesis and metastasis were subsequently characterized.

Results
Two successive cell lines named NRCC from the primary ccRCC and MRCC from the metastatic ccRCC were established, respectively. Compared to NRCC, MRCC exhibited stronger anchorage-independent growth and invasion potentials and contained more glycogen granules in the cytoplasm. Gains of chromosomes and some translocations were the major chromosomal aberrations in both cell strains. CD24 expression was more frequent in MRCC than in NRCC and the same was true for CD56. The transcriptional levels of TNF α, IL-6, VEGF, HIF2 α, MMP2, and RhoC were significantly higher in MRCC than in NRCC. Cytosolic IκBα protein was more degraded in MRCC than in NRCC following TNFα treatment. Both cell lines had strong tumorigenicity in athymic nude mice. However, MRCC had strong potential in generating metastasis to lung and hemorrhagic ascites than NRCC following orthotopic transplantations.

Conclusions
Cancer cells isolated from metastatic ccRCC have more malignant and metastatic potential than those from the primary tumor from the patients who shared the similar race background. Establishment of MRCC and NRCC may provide suitable models with which to investigate molecular mechanisms of ccRCC metastasis.
Stagnation-point flow over a permeable stretching/shrinking sheet in a copper-water nanofluid
Authors: Bachok Norfifah , Ishak Anuar , Nazar Roslinda , Senu Norazak 
Published: February 2013

Abstract
An analysis is carried out to study the heat transfer characteristics of steady two-dimensional stagnation-point flow of a copper (Cu)-water nanofluid over a permeable stretching/shrinking sheet. The stretching/shrinking velocity and the ambient fluid velocity are assumed to vary linearly with the distance from the stagnation-point. Results for the skin friction coefficient, local Nusselt number, velocity as well as the temperature profiles are presented for different values of the governing parameters. It is found that dual solutions exist for the shrinking case, while for the stretching case, the solution is unique. The results indicate that the inclusion of nanoparticles into the base fluid produces an increase in the skin friction coefficient and the heat transfer rate at the surface. Moreover, suction increases the surface shear stress and in consequence increases the heat transfer rate at the fluid-solid interface.

MSC: 34B15, 76D10.