Abstract: Methods and apparatus for assessing tissue pathology involve computing an index having a value based upon measures of a plurality of morphological features of cell nuclei in the tissue. The methods may be performed completely automatically or semi-automatically. The index value can be predictive of outcome. The index value may be determined by computing discriminant scores for the cell nuclei based upon values of the measures of morphological features and classifying the nuclei into bins based upon the discriminant score values. The index may be based upon proportions of the nuclei classified in different ones of the bins.

Abstract: Disclosed herein are methods and materials for prognosing survival of lung cancer patients, the methods comprising the detection of gains and losses of minimal common regions and/or genes associated with prognosis and benefit of chemotherapy.

Abstract: Radiation treatment methods comprise: obtaining initial image data of a region of interest; initially optimizing one or more radiation delivery variables of a radiation treatment plan based on the initial image data; and dividing the plan into one or more fractional treatments. Each fractional treatment comprises: delivering an initial portion of a fraction based on the one or more initially optimized radiation delivery variables; obtaining fractional image data pertaining to the region of interest; fractionally optimizing the one or more radiation delivery variables based at least in part on the fractional image data; and delivering a subsequent portion of the fraction based on the one or more fractionally optimized radiation delivery variables. At least part of delivering the initial portion of the fraction overlaps temporally with at least one of: obtaining the fractional image data and fractionally optimizing the one or more radiation delivery variables.

Abstract: A method and system for characterizing tissue includes a probe connected to a red LASER source and a Raman spectroscope. The probe includes at least excitation fiber and one or more emission fibers that connect the probe with the LASER source and the Raman spectroscope. The excitation fiber is connected to the red LASER source and terminates in the first end of the probe adjacent the tip of the probe. The emission fibers are connected to the Raman spectroscope and terminate in the first end of the probe adjacent the tip of the probe. In one embodiment, the excitation fiber extends through the central portion of the probe and one or more emission fibers are arranged around the excitation fiber. The tip of the probe is intended to come in contact with the tissue to be examined. The tip includes a central opening to allow red LASER radiation to project out of the end of the red excitation fiber on to the tissue and to permit Raman spectra to enter the emission fiber(s) and travel to the Raman spectroscope.

Abstract: Imaging methods and apparatus may be applied to image tissues as well as other areas. A computer-controlled color-selectable light source is controlled to emit light having a desired spectral profile and to illuminate an area. An imaging detector images the illuminated area. The spectral profile may be selected to yield images in which contrast between features of interest and other features is enhanced. The images may be combined into a composite image. In some embodiments the spectral profile is based on a principal components analysis such that the images each correspond to one principal component.

Abstract: Systems and devices are provided to facilitate safe handling and injection of medicaments contained in vials. A vial handling system has at least one vial gripping member to hold a vial, and a filler pin movable relative to the vial gripping member for piercing a membrane seal on the vial. At least one window is provided in the vial handling system to permit access to remove a cap on the vial, while preventing needle access to the membrane seal through the window. In some embodiments, the vial contents are removed through a male end connector portion of a unique connector pair. A female end connector portion has a female socket with an inner fluid tube in fluid communication with a body of a syringe, while the male end connector portion has an engaging end dimensioned to fit within the female socket and securely overlap the inner fluid tube.

Abstract: Gene expression data provides a basis for more accurate identification and diagnosis of lymphoproliferative disorders. In addition, gene expression data can be used to develop more accurate predictors of survival. The present invention discloses methods for identifying, diagnosing, and predicting survival in a lymphoma or lymphoproliferative disorder on the basis of gene expression patterns. The invention discloses a novel microarray, the Lymph Dx microarray, for obtaining gene expression data from a lymphoma sample. The invention also discloses a variety of methods for utilizing lymphoma gene expression data to determine the identity of a particular lymphoma and to predict survival in a subject diagnosed with a particular lymphoma. This information will be useful in developing the therapeutic approach to be used with a particular subject.

Abstract: There is provided a composition for inducing an immune response to a Chlamydia species in a subject, the composition comprising one or more than one polypeptides selected from the group consisting of ribosomal peptide L/RplF, ribosomal protein L6 (RplF), PmpG protein, PmpG-1 peptide, PmpF protein, PmpE/F-2 family F2, glyceraldehyde 3-phosphate dehydrogenase and major outer membrane protein (MOMP), and the use of said composition to treat Chlamydia infections.

Abstract: Methods and systems are disclosed for radiation treatment of a subject involving one or more fractional treatments. A fractional treatment comprises: obtaining fractional image data pertaining to a region of interest of the subject; performing a fractional optimization of a radiation treatment plan to determine optimized values of one or more radiation delivery variables based at least in part on the fractional image data; and delivering a fraction of the radiation treatment plan to the region of interest using the optimized values of the one or more radiation delivery variables as one or more corresponding parameters of the radiation treatment plan. A portion of performing the fractional optimization overlaps temporally with a portion of at least one of: obtaining the fractional image data and delivering the fraction of the radiation treatment plan.

Abstract: The invention provides methods, uses, kits and compositions comprising a therapeutically effective amount of the microRNA miR-223 for treating myelogenous leukemia in a subject in need of such treatment. The invention further comprises methods encompassing the use of miR-223 for promoting the differentiation of a leukemia stem cell that is resistant to a differentiating agent, and a method of screening for candidate compounds capable of treating a myeloid leukemia by comparison of the therapeutic activity of the candidate compound with the therapeutic activity of miR-233.

Abstract: The application provides methods of prognosing, diagnosing, screening and classifying lung cancer patients into poor survival groups or good survival groups. A number of altered genomic regions have been identified that distinguish subtype of lung adenocarcinoma (ADC), specifically between bronchioloalveolar carcinoma (BAC) and invasive ADC with BAC features (AWBF), and genes and biomarkers whose expression are altered in individuals with pulmonary ADC according to different survival outcomes. The amplification and/or deletion of these genomic regions, and/or the biomarker expression profiles can be used to classify patients with ADC into a BAC group with excellent survival outcome, or an invasive ADC with BAC features group with higher risk of developing metastatic recurrence and poorer survival outcome. The application also includes kits for use in the methods of the application.

Abstract: The invention provides methods and materials related to a gene expression-based survival predictor for diffuse large B cell lymphoma (DLBCL) patients.

Abstract: A method of detecting a granulosa-cell tumor is described herein. The method involves detecting a mutation in a sample derived from a subject, indicative of substitution of tryptophan in place of cysteine at amino acid position 134 of FOXL2 protein. The mutation may be detected as a DNA mutation 402C>G in the FOXL2 gene. Methods for screening for a granulosa-cell tumor from a blood-based assay are provided, as well as methods for making a determination that an ovarian tumor is not a granulosa-cell tumor. Kits for granulosa-cell tumors are described, and a method of treating a granulosa-cell tumor are also described.

Abstract: The present invention provides pyrimidinyl compounds of formula (I) and pharmaceutically acceptable salts thereof. These compounds may be used for the inhibition of influenza. In particular, the compounds of the invention may be used for the treatment or prophylaxis of influenza A, most particularly H1N1 or H5N1 influenza. The compounds of the invention can also be used for the treatment or prophylaxis of a disease caused by Vibrio cholerae, Clostridium perfringens, Streptococcus pneumoniae, Arthrobacter sialophilus, an orthomyxovirus, a paramyxovirus, a parainfluenza virus, mumps virus, Newcastle disease virus, fowl plague virus or Sendai virus.

Abstract: There is provided a panel of biomarkers of tumour metastasis comprising any two of carbonic anhydrase-9 (CAIX), vascular endothelial growth factor C (VEGF-C), ephrin A5 (EFNA5), eph receptor B2 (EPHB2), transforming growth factor beta 3 (TGF-?3), pyruvate dehydrogenase kinase isoenzyme-3 (PDK3), carbonic anhydrase-12 (CAXII), keratin 14 (KRT14), hypoxia inducible factor 1 alpha subunit (HIF-1?), or tenascin C (TNC). CAIX, VEGF-C, EFNA5, EPHB2, TGF-?3 or PDK3 may be indicators of moderate metastatic potential, while CAXII, KRT14, HIF-1?, or TNC may be indicators of high metastatic potential. There is also provided a method of determining risk of tumour metastasis using the aforementioned biomarkers is also provided. The biomarkers may be used in diagnosis, prognosis, treatment selection, or to test putative therapeutics. The biomarkers may be used to assess malignancies or cancers having hypoxic regions, such as breast cancer.

Abstract: Systems and methods for the quantitative automated analysis of pathology samples identify groups of spatially-associated similar cells. Cells may be identified as belonging to a group on the basis of spatial location and biomarkers. In some embodiments the biomarkers are multicolour fluorescence in situ hybridization (FISH) signals. Characteristics of the cells in a group may be combined to provide quantitative FISH results that may compensate for variations and artefacts such as thin sectioning that can result in the loss of information due to damage. In heterogeneous tissue samples, grouping cells can permit quantitative results regarding pathological cells to be extracted despite the presences of infiltrating non pathological cells.

Abstract: A method is described for detecting lung cancer comprising detecting an elevated level of a CTAP III-related biomarker in a biological sample from a subject at risk for developing lung cancer. Further, a method is described for predicting risk of developing lung cancer in a subject comprising detecting an elevated level of a CTAP III-related biomarker in a biological sample from a subject. Additionally, a method of monitoring the success of lung cancer treatment with curative intent is described comprising detecting levels of a CTAP III-related biomarker in a biological sample from a subject undergoing treatment for lung cancer for comparison with the a previous level obtained from the subject. Multivariate analysis may be incorporated into these methods, evaluating such clinical, or demographic risk factors as age, sex, smoking history, smoking status, smoking family history, education level, COPD, socio-economic status, body mass index and lung function. Kits for conducting such methods are described.

Abstract: The present invention relates to an improved method that permits the differential isolation of mouse mammary stem cells and colony forming cells (CFCs). The method involves depletion of non-epithelial cells from freshly dissociated mouse mammary tissue by incubation with an antibody composition containing antibodies specific for CD45, Ter119, CD35 and optionally CD140a. After formation of conjugates between the non-epithelial mammary cells and the antibodies specific for CD45, Ter119, CD35 and optionally CD140a, the cell conjugates are removed and the remaining epithelial cells are then incubated with an antibody composition containing antibodies specific for CD24 and CD49f or CD24 and CD14. After formation of conjugates between the epithelial cells and the antibodies specific for CD24 and CD49f or CD24 and CD14, the mouse mammary stem and the luminal-restricted CFC cells can be differentially isolated.

Abstract: The present invention relates to an improved method that permits the differential isolation of mouse mammary stem cells and colony forming cells (CFCs). The method involves depletion of non-epithelial cells from freshly dissociated mouse mammary tissue by incubation with an antibody composition containing antibodies specific for CD45, Ter119, CD35 and optionally CD140a. After formation of conjugates between the non-epithelial mammary cells and the antibodies specific for CD45, Ter119, CD35 and optionally CD140a, the cell conjugates are removed and the remaining epithelial cells are then incubated with an antibody composition containing antibodies specific for CD24 and CD49f. After formation of conjugates between the epithelial cells and the antibodies specific for CD24 and CD49f, the mouse mammary stem and the luminal-restricted CFC cells can be differentially isolated. The invention also relates to kits for carrying out this method and to the cell preparations prepared by this method.

Abstract: A method is described for increasing the engraftment efficiency of S/G2/M phase stem cells, which involves treating a recipient with the stromal cell-derived factor-1 (SDF-1) antagonist SDF-1G2 prior to delivery of the cells to said recipient. Further, a method of transplanting proliferating or S/G2/M phase stem cells is described, comprising the steps of: (a) obtaining stem cells; (b) inducing stem cells ex vivo to proliferate or enter S/G2/M phase; (c) treating the recipient with the SDF-1 antagonist SDF-1G2; and (d) providing the stem cells to the recipient.