bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Study of Navigated versus Freehand Osteochondral Graft Transplantation of the Knee
Authors: Koulalis Dimitrios , Di Benedetto Paolo , Citak Mustafa , O'Loughlin Padhraig , Pearle Andrew D. , Kendoff Daniel O. 
Published: February 2009

Background Osteochondral lesions are a common sports-related injury for which osteochondral grafting, including mosaicplasty, is an established treatment. Computer navigation has been gaining popularity in orthopaedic surgery to improve accuracy and precision. Hypothesis Navigation improves angle and depth matching during harvest and placement of osteochondral grafts compared with conventional freehand open technique. Study Design Controlled laboratory study. Methods Three cadaveric knees were used. Reference markers were attached to the femur, tibia, and donor/recipient site guides. Fifteen osteochondral grafts were harvested and inserted into recipient sites with computer navigation, and 15 similar grafts were inserted freehand. The angles of graft removal and placement as well as surface congruity (graft depth) were calculated for each surgical group. Results The mean harvesting angle at the donor site using navigation was 4° (standard deviation, 2.3°; range, 1°-9°) versus 12° (standard deviation, 5.5°; range, 5°-24°) using freehand technique ( P < .0001). The recipient plug removal angle using the navigated technique was 3.3° (standard deviation, 2.1°; range, 0°-9°) versus 10.7° (standard deviation, 4.9°; range, 2°-17°) in freehand ( P < .0001). The mean navigated recipient plug placement angle was 3.6° (standard deviation, 2.0°; range, 1°-9°) versus 10.6° (standard deviation, 4.4°; range, 3°-17°) with freehand technique ( P = .0001). The mean height of plug protrusion under navigation was 0.3 mm (standard deviation, 0.2 mm; range, 0-0.6 mm) versus 0.5 mm (standard deviation, 0.3 mm; range, 0.2-1.1 mm) using a freehand technique ( P = .0034). Conclusion Significantly greater accuracy and precision were observed in harvesting and placement of the osteochondral grafts in the navigated procedures. Clinical studies are needed to establish a benefit in vivo. Clinical Relevance Improvement in the osteochondral harvest and placement is desirable to optimize clinical outcomes. Navigation shows great potential to improve both harvest and placement precision and accuracy, thus optimizing ultimate surface congruity.
Regulation of mir-196b by MLL and its overexpression by MLL fusions contributes to immortalization
Authors: Popovic Relja , Riesbeck Laurie E. , Velu Chinavenmeni S. , Chaubey Aditya , Zhang Jiwang , Achille Nicholas J. , Erfurth Frank E. , Eaton Katherine , Lu Jun , Grimes H. Leighton , Chen Jianjun , Rowley Janet D. , Zeleznik-Le Nancy J. 
Published: February 2009

AbstractChromosomal translocations involving the Mixed Lineage Leukemia (MLL) gene produce chimeric proteins that cause abnormal expression of a subset of HOX genes and leukemia development. Here, we show that MLL normally regulates expression of mir-196b, a hematopoietic microRNA located within the HoxA cluster, in a pattern similar to that of the surrounding 5′ Hox genes, Hoxa9 and Hoxa10, during embryonic stem (ES) cell differentiation. Within the hematopoietic lineage, mir-196b is most abundant in short-term hematopoietic stem cells and is down-regulated in more differentiated hematopoietic cells. Leukemogenic MLL fusion proteins cause overexpression of mir-196b, while treatment of MLL-AF9 transformed bone marrow cells with mir-196–specific antagomir abrogates their replating potential in methylcellulose. This demonstrates that mir-196b function is necessary for MLL fusion-mediated immortalization. Furthermore, overexpression of mir-196b was found specifically in patients with MLL associated leukemias as determined from analysis of 55 primary leukemia samples. Overexpression of mir-196b in bone marrow progenitor cells leads to increased proliferative capacity and survival, as well as a partial block in differentiation. Our results suggest a mechanism whereby increased expression of mir-196b by MLL fusion proteins significantly contributes to leukemia development.
Forward RNAi screens in primary human hematopoietic stem/progenitor cells
Authors: Ali Nicole , Karlsson Christine , Aspling Marie , Hu Guang , Hacohen Nir , Scadden David T. , Larsson Jonas 
Published: February 2009

Abstract
The mechanisms regulating key fate decisions such as self-renewal and differentiation in hematopoietic stem and progenitor cells (HSPC) remain poorly understood. We report here a screening strategy developed to assess modulators of human hematopoiesis using a lentiviral short hairpin RNA (shRNA) library transduced into cord blood-derived stem/progenitor cells. To screen for modifiers of self-renewal/differentiation, we used the limited persistence of HSPCs under ex vivo culture conditions as a baseline for functional selection of shRNAs conferring enhanced maintenance or expansion of the stem/progenitor potential. This approach enables complex, pooled screens in large numbers of cells. Functional selection identified novel specific gene targets (exostoses 1) or shRNA constructs capable of altering human hematopoietic progenitor differentiation or stem cell expansion, respectively, thereby demonstrating the potential of this forward screening approach in primary human stem cell populations.
A new regularized least squares support vector regression for gene selection
Authors: Chen Pei-Chun , Huang Su-Yun , Chen Wei J , Hsiao Chuhsing K 
Published: February 2009

Abstract

Background
Selection of influential genes with microarray data often faces the difficulties of a large number of genes and a relatively small group of subjects. In addition to the curse of dimensionality, many gene selection methods weight the contribution from each individual subject equally. This equal-contribution assumption cannot account for the possible dependence among subjects who associate similarly to the disease, and may restrict the selection of influential genes.

Results
A novel approach to gene selection is proposed based on kernel similarities and kernel weights. We do not assume uniformity for subject contribution. Weights are calculated via regularized least squares support vector regression (RLS-SVR) of class levels on kernel similarities and are used to weight subject contribution. The cumulative sum of weighted expression levels are next ranked to select responsible genes. These procedures also work for multiclass classification. We demonstrate this algorithm on acute leukemia, colon cancer, small, round blue cell tumors of childhood, breast cancer, and lung cancer studies, using kernel Fisher discriminant analysis and support vector machines as classifiers. Other procedures are compared as well.

Conclusion
This approach is easy to implement and fast in computation for both binary and multiclass problems. The gene set provided by the RLS-SVR weight-based approach contains a less number of genes, and achieves a higher accuracy than other procedures.
Convergent and divergent patterns of morphological differentiation provide more evidence for reproductive character displacement in a wood cricket Gryllus fultoni(Orthoptera: Gryllidae)
Authors: Jang Yikweon , Won Yong-Jin , Choe Jae Chun 
Published: February 2009

AbstractBackgroundIn ecological character displacement, traits involved in reproductive isolation may not evolve in arbitrary directions when changes in these traits are by-products of adaptation to an ecological niche. In reproductive character displacement, however, selection acts directly on reproductive characters to enhance the degree of reproductive isolation between sympatric populations. Thus, the direction of change in reproductive characters may be arbitrary in relation to changes in other morphological characters. We characterized both tegminal characters and characters indicative of body size in sympatric and allopatric populations ofGryllus fultoni, a species displaying character displacement in its calling song characters in areas of sympatry withG. vernalispopulations, to infer the nature and direction of selection acting on reproductive and morphological characters in sympatry.ResultsExcept for mirror area, the number of teeth in a file, and ovipositor length ofG. fultoni, all male and female morphological characters inG. fultoniandG. vernalisexhibited a uniform tendency to decrease in size with increasing latitude. There was no significant variation in female morphological characters between sympatric and allopatricG. fultonipopulations. However, males of sympatric and allopatricG. fultonipopulations significantly differed in head width, hind femur length, and mirror area even after controlling for clinal factors. Head width and hind femur length ofG. fultoniwere more similar to those ofG. vernalisin sympatric populations than in allopatric populations, resulting in morphological convergence ofG. fultoniandG. vernalisin sympatry. However, the mirror area ofG. fultonidisplayed the divergent pattern in relation to the sympatricG. vernalispopulations.ConclusionDivergence-enhancing selection may be acting on mirror area as well as calling song characters, whereas local adaptation or clinal effects may explain variation in other morphological characters in sympatric populations ofG. fultoni. This study also suggests that structures and behaviors that directly enhance reproductive isolation may evolve together, independently of other morphological traits.
Genetic diversity of canine olfactory receptors
Authors: Robin Stéphanie , Tacher Sandrine , Rimbault Maud , Vaysse Amaury , Dréano Stéphane , André Catherine , Hitte Christophe , Galibert Francis 
Published: February 2009

Abstract

Background
Evolution has resulted in large repertoires of olfactory receptor (OR) genes, forming the largest gene families in mammalian genomes. Knowledge of the genetic diversity of olfactory receptors is essential if we are to understand the differences in olfactory sensory capability between individuals. Canine breeds constitute an attractive model system for such investigations.

Results
We sequenced 109 OR genes considered representative of the whole OR canine repertoire, which consists of more than 800 genes, in a cohort of 48 dogs of six different breeds. SNP frequency showed the overall level of polymorphism to be high. However, the distribution of SNP was highly heterogeneous among OR genes. More than 50% of OR genes were found to harbour a large number of SNP, whereas the rest were devoid of SNP or only slightly polymorphic. Heterogeneity was also observed across breeds, with 25% of the SNP breed-specific. Linkage disequilibrium within OR genes and OR clusters suggested a gene conversion process, consistent with a mean level of polymorphism higher than that observed for introns and intergenic sequences. A large proportion (47%) of SNP induced amino-acid changes and the Ka/Ks ratio calculated for all alleles with a complete ORF indicated a low selective constraint with respect to the high level of redundancy of the olfactory combinatory code and an ongoing pseudogenisation process, which affects dog breeds differently.

Conclusion
Our demonstration of a high overall level of polymorphism, likely to modify the ligand-binding capacity of receptors distributed differently within the six breeds tested, is the first step towards understanding why Labrador Retrievers and German Shepherd Dogs have a much greater potential for use as sniffer dogs than Pekingese dogs or Greyhounds. Furthermore, the heterogeneity in OR polymorphism observed raises questions as to why, in a context in which most OR genes are highly polymorphic, a subset of these genes is not? This phenomenon may be related to the nature of their ligands and their importance in everyday life.
Comparative genomic analysis of light-regulated transcripts in the Solanaceae
Authors: Rutitzky Mariana , Ghiglione Hernan O , Curá José A , Casal Jorge J , Yanovsky Marcelo J 
Published: February 2009

Abstract

Background
Plants use different light signals to adjust their growth and development to the prevailing environmental conditions. Studies in the model species Arabidopsis thaliana and rice indicate that these adjustments are mediated by large changes in the transcriptome. Here we compared transcriptional responses to light in different species of the Solanaceae to investigate common as well as species-specific changes in gene expression.

Results
cDNA microarrays were used to identify genes regulated by a transition from long days (LD) to short days (SD) in the leaves of potato and tobacco plants, and by phytochrome B (phyB), the photoreceptor that represses tuberization under LD in potato. We also compared transcriptional responses to photoperiod in Nicotiana tabacum Maryland Mammoth (MM), which flowers only under SD, with those of Nicotiana sylvestris, which flowers only under LD conditions. Finally, we identified genes regulated by red compared to far-red light treatments that promote germination in tomato.

Conclusion
Most of the genes up-regulated in LD were associated with photosynthesis, the synthesis of protective pigments and the maintenance of redox homeostasis, probably contributing to the acclimatization to seasonal changes in irradiance. Some of the photoperiodically regulated genes were the same in potato and tobacco. Others were different but belonged to similar functional categories, suggesting that conserved as well as convergent evolutionary processes are responsible for physiological adjustments to seasonal changes in the Solanaceae. A β-ZIP transcription factor whose expression correlated with the floral transition in Nicotiana species with contrasting photoperiodic responses was also regulated by photoperiod and phyB in potato, and is a candidate gene to act as a general regulator of photoperiodic responses. Finally, GIGANTEA, a gene that controls flowering time in Arabidopsis thaliana and rice, was regulated by photoperiod in the leaves of potato and tobacco and by red compared to far-light treatments that promote germination in tomato seeds, suggesting that a conserved light signaling cascade acts across developmental contexts and species.
A Candida albicans early stage biofilm detachment event in rich medium
Authors: Sellam Adnane , Al-Niemi Thamir , McInnerney Kathleen , Brumfield Susan , Nantel Andre , Suci Peter A 
Published: February 2009

Abstract

Background
Dispersal from Candida albicans biofilms that colonize catheters is implicated as a primary factor in the link between contaminated catheters and life threatening blood stream infections (BSI). Appropriate in vitro C. albicans biofilm models are needed to probe factors that induce detachment events.

Results
Using a flow through system to culture C. albicans biofilms we characterized a detachment process which culminates in dissociation of an entire early stage biofilm from a silicone elastomer surface. We analyzed the transcriptome response at time points that bracketed an abrupt transition in which a strong adhesive association with the surface is weakened in the initial stages of the process, and also compared batch and biofilm cultures at relevant time points. K means analysis of the time course array data revealed categories of genes with similar patterns of expression that were associated with adhesion, biofilm formation and glycoprotein biosynthesis. Compared to batch cultures the biofilm showed a pattern of expression of metabolic genes that was similar to the C. albicans response to hypoxia. However, the loss of strong adhesion was not obviously influenced by either the availability of oxygen in the medium or at the silicone elastomer surface. The detachment phenotype of mutant strains in which selected genes were either deleted or overexpressed was characterized. The microarray data indicated that changes associated with the detachment process were complex and, consistent with this assessment, we were unable to demonstrate that transcriptional regulation of any single gene was essential for loss of the strong adhesive association.

Conclusion
The massive dispersal of the early stage biofilm from a biomaterial surface that we observed is not orchestrated at the level of transcriptional regulation in an obvious manner, or is only regulated at this level by a small subpopulation of cells that mediate adhesion to the surface.
FIP1L1-PDGFRA molecular analysis in the differential diagnosis of eosinophilia
Authors: Loules Gedeon , Kalala Fani , Giannakoulas Nikolaos , Papadakis Emmanouil , Matsouka Panagiota , Speletas Matthaios 
Published: February 2009

Abstract

Background
Primary eosinophlia associated with the FIP1L1-PDGFRA rearrangement represents a subset of chronic eosinophilic leukaemia (CEL) and affected patients are very sensitive to imatinib treatment. This study was undertaken in order to examine the prevalence and the associated clinicopathologic and genetic features of FIP1L1-PDGFRA rearrangement in a cohort of 15 adult patients presenting with profound eosinophilia (> 1.5 × 109/L).

Methods
Reverse transcriptase-polymerase chain reaction (RT-PCR) was used for the detection of FIP1L1-PDGFRA rearrangement and the results confirmed by direct sequencing. C-KIT-D816V mutation was analysed retrospectively by PCR and restriction-fragment-length-polymorphism (PCR-RFLP), in all cases with primary eosinophilia.

Results
Two male patients with splenomegaly carried the FIP1L1-PDGFRA rearrangement, whilst 2 others were ultimately classified as suffering from idiopathic hypereosinophlic syndrome (HES) and one from systemic mastocytosis. These patients were negative for the C-KIT-D816V mutation and received imatinib (100–400 mg daily). Patients with CEL and HES responded to imatinib and remained in complete haematological, clinical and molecular (for carriers of FIP1L1-PDGFRA rearrangement) remission for a median of 28.2 months (range: 11–54), whilst the patient with systemic mastocytosis did not respond. Interestingly, in both patients with FIP1L1-PDGFRA rearrangement, the breakpoints into PDGFRA were located within exon 12 and fused with exons 8 and 8a of FIP1L1, respectively.

Conclusion
An early diagnosis of FIPIL1-PDGFRA-positive CEL and imatinib treatment offer to the affected patients an excellent clinical therapeutic result, avoiding undesirable morbidity. Moreover, although the molecular mechanisms underlying disease pathogenesis remain to be determined, imatinib can be effective in patients with idiopathic HES.
Secretion of MCP-1 and other paracrine factors in a novel tumor-bone coculture model
Authors: Schiller Katherine R , Zillhardt Marion R , Alley Jeremy , Borjesson Dori L , Beitz Alvin J , Mauro Laura J 
Published: February 2009

Abstract

Background
The bone-tumor microenvironment encompasses unique interactions between the normal cells of the bone and marrow cavity and the malignant cells from a primary or metastasized cancer. A multitude of paracrine factors within this microenvironment such as the growth factor, TGF-β, and the chemokine, MCP-1, are secreted by many of these cell types. These factors can act in concert to modulate normal and malignant cell proliferation, malignant cell migration and invasion and, often, mediate bone cancer pain. Although many valuable in vitro and in vivo models exist, identifying the relevant paracrine factors and deciphering their interactions is still a challenge. The aim of our study is to test an ex vivo coculture model that will allow monitoring of the expression, release and regulation of paracrine factors during interactions of an intact femur explant and tumor cells.

Methods
Intact or marrow-depleted neonatal mouse femurs and select murine and human sarcoma or carcinoma cell lines were incubated singly or in coculture in specialized well plates. Viability of the bone and cells was determined by immunohistochemical stains, microscopy and marrow cytopreps. Secretion and mRNA expression of paracrine factors was quantitated by ELISA and real-time RT-PCR.

Results
Compartments of the bone were optimally viable for up to 48 h in culture and tumor cells for up to 4 days. Bone was the major contributor of TGF-β and MMP2 whereas both bone and sarcoma cells secreted the chemokine MCP-1 in cocultures. Synergistic interaction between the femur and sarcoma resulted in enhanced MCP-1 secretion and expression in cocultures and was dependent on the presence of the hematopoietic component of the bone as well as other bone cells. In contrast, coculturing with breast carcinoma cells resulted in reduction of TGF-β and MCP-1 secretion from the bone.

Conclusion
These studies illustrate the feasibility of this model to examine paracrine interactions between intact bone and tumor cells. Further study of unique regulation of MCP-1 secretion and signaling between these cell types in different types of cancer will be possible using this simulated microenvironment.
The effect of health and nutrition education intervention on women's postpartum beliefs and practices: a randomized controlled trial
Authors: Liu Nian , Mao Limei , Sun Xiufa , Liu Liegang , Yao Ping , Chen Banghua 
Published: February 2009

Abstract

Background
'Sitting month' is the Chinese tradition for postpartum customs. Available studies indicate that some of the traditional postpartum practices are potentially harmful for women's health. However, no intervention study aiming at postpartum practices has been performed. In this paper we evaluated the effect of a health and nutrition education intervention, which focused on improving postpartum dietary quality and optimal health behaviors.

Methods
The study design was a randomized controlled trial conducted in both urban and rural area of Hubei between August 2003 and June 2004. A total of 302 women who attended the antenatal clinic during the third trimester with an uncomplicated pregnancy were recruited. Women randomized to the education intervention group in both urban and rural area received two two-hour prenatal education sessions and four postpartum counseling visits. Control group women received usual health care during pregnancy and postpartum period. Women were followed up until 42 days postpartum. Outcome measures were nutrition and health knowledge, dietary behavior, health behavior and health problems during the postpartum period.

Results
Women in the intervention groups exhibited significantly greater improvement in overall dietary behaviors such as consumption of fruits, vegetables, soybean and soybean products as well as nutrition and health knowledge than those in the control groups. Significantly more women in the intervention groups give up the traditional behavior taboos. The incidence of constipation, leg cramp or joint pain and prolonged lochia rubra was significantly lower in the intervention groups as compared with the control groups.

Conclusion
The study shows that health and nutrition education intervention enable the women take away some of the unhealthy traditional postpartum practices and decrease the prevalence of postpartum health problems. The intervention has potential for adaptation and development to large-scale implementation.

Trial registration number
klACTRN12607000549426