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13-lined ground squirrels (Ictidomys tridecemlineatus) enter hibernation as a survival strategy during extreme environmental conditions. Typical ground squirrel hibernation is characterized by prolonged periods of torpor with significantly reduced heart rate, blood pressure, and blood flow, interrupted every few weeks by brief interbout arousals (IBA) during which blood flow fluctuates dramatically. These physiological conditions should increase the risk of stasis-induced blood clots and myocardial ischemia. However, ground squirrels have adapted to survive repeated bouts of torpor and IBA without forming lethal blood clots or sustaining lethal ischemic myocardial damage. The purpose of this study was to determine if ground squirrels are resistant to thrombosis and myocardial ischemia during hibernation. Blood markers of coagulation, fibrinolysis, thrombosis, and ischemia, as well as histological markers of myocardial ischemia were measured throughout the annual hibernation cycle. Hibernating ground squirrels were also treated with isoprenaline to induce myocardial ischemia. Thrombin-antithrombin complex levels were significantly reduced (p < 0.05) during hibernation, while D-dimer level remained unchanged throughout the annual cycle, both consistent with an antithrombotic state. During torpor, the ground squirrels were in a hyperfibrinolytic state with an elevated ratio of tissue plasminogen activator complexed with plasminogen activator inhibitor to total plasminogen activator inhibitor (p < 0.05). Histological markers of myocardial ischemia were reversibly elevated during hibernation with no increase in markers of myocardial cell death in the blood. These data suggest that ground squirrels do not form major blood clots during hibernation through suppression of coagulation and a hyperfibrinolytic state. These animals also demonstrate myocardial resistance to ischemia.

Background: Branch-length parameters are a central component of phylogenetic models and of intrinsic biological interest. Default branch-length priors in some Bayesian phylogenetic software can be unintentionally informative and lead to branch- and tree-length estimates that are unreasonable. Alternatively, priors may be uninformative, but lead to diffuse posterior estimates. Despite the widespread availability of relevant datasets from other groups, biologists rarely leverage outside information to specify branch-length priors that are specific to the analysis they are conducting., Results: We developed the software package EmpPrior to facilitate the collection and incorporation of relevant, outside information when setting branch-length priors for phylogenetics. EmpPrior efficiently queries TreeBASE to find data that are similar to focal data, in terms of taxonomic and genetic sampling, and uses them to inform branch-length priors for the focal analysis. EmpPrior consists of two components: EmpPrior-search, written in Java to query TreeBASE, and EmpPrior-fit, written in R to parameterize branch-length distributions. In an example analysis, we show how the use of relevant, outside data is made possible by EmpPrior and improves tree-length estimates from a focal dataset., Conclusion: EmpPrior is easy to use, fast, and improves both the accuracy and precision of branch-length estimates in many circumstances. While EmpPrior's focus is on branch lengths, the strategy it employs could easily be extended to address other prior parameterization problems in phylogenetics.

Background: Papillary renal-cell carcinoma, which accounts for 15 to 20% of renal-cell carcinomas, is a heterogeneous disease that consists of various types of renal cancer, including tumors with indolent, multifocal presentation and solitary tumors with an aggressive, highly lethal phenotype. Little is known about the genetic basis of sporadic papillary renal-cell carcinoma, and no effective forms of therapy for advanced disease exist., Methods: We performed comprehensive molecular characterization of 161 primary papillary renal-cell carcinomas, using whole-exome sequencing, copy-number analysis, messenger RNA and microRNA sequencing, DNA-methylation analysis, and proteomic analysis., Results: Type 1 and type 2 papillary renal-cell carcinomas were shown to be different types of renal cancer characterized by specific genetic alterations, with type 2 further classified into three individual subgroups on the basis of molecular differences associated with patient survival. Type 1 tumors were associated with MET alterations, whereas type 2 tumors were characterized by CDKN2A silencing, SETD2 mutations, TFE3 fusions, and increased expression of the NRF2-antioxidant response element (ARE) pathway. A CpG island methylator phenotype (CIMP) was observed in a distinct subgroup of type 2 papillary renal-cell carcinomas that was characterized by poor survival and mutation of the gene encoding fumarate hydratase (FH)., Conclusions: Type 1 and type 2 papillary renal-cell carcinomas were shown to be clinically and biologically distinct. Alterations in the MET pathway were associated with type 1, and activation of the NRF2-ARE pathway was associated with type 2; CDKN2A loss and CIMP in type 2 conveyed a poor prognosis. Furthermore, type 2 papillary renal-cell carcinoma consisted of at least three subtypes based on molecular and phenotypic features. (Funded by the National Institutes of Health.).

Prior distributions can have a strong effect on the results of Bayesian analyses. However, no general consensus exists for how priors should be set in all circumstances. Branch-length priors are of particular interest for phylogenetics, because they affect many parameters and biologically relevant inferences have been shown to be sensitive to the chosen prior distribution. Here, we explore the use of outside information to set informed branch-length priors and compare inferences from these informed analyses to those using default settings. For both the commonly used exponential and the newly proposed compound Dirichlet prior distributions, the incorporation of relevant outside information improves inferences for data sets that have produced problematic branch- and tree-length estimates under default settings. We suggest that informed priors are worthy of further exploration for phylogenetics., (© The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Dimeric peptide-based inhibitors of postsynaptic density-95 (PSD-95) can reduce ischemic brain damage and inflammatory pain in rodents. To modify the pharmacokinetic profile, we designed a series of fatty acid linked dimeric ligands, which potently inhibits PSD-95 and shows improved in vitro blood plasma stability. Subcutaneous administration in rats showed extended stability and sustained release of these ligands. This can facilitate new pharmacological uses of PSD-95 inhibitors and further exploration of PSD-95 as a drug target.

Background: Variations exist in compliance with NCCN Guidelines. Prior reports of adherence to NCCN Guidelines contain limitations because of lack of contemporary review and incomplete listing of reasons for noncompliance., Purpose: To assess institutional compliance and assist national quality improvement strategies through identifying valid reasons for noncompliance., Methods: Compliance with NCCN Guidelines was recorded prospectively using electronic synoptic templates for patients with newly diagnosed breast cancer treated at a single institution between January 2010 and December 2011. Compliance with NCCN Guidelines was recorded. The accuracy of real-time synoptic auditing methods compared with retrospective chart review and reasons for noncompliance was assessed. SAS 9.3 software was used for data analysis., Results: Compliance with NCCN Guidelines among 395 patients was 94% for initial staging evaluation, 97% for surgery, 91% for chemotherapy, 89% for hormone therapy, 91% for radiation therapy, 85% for follow-up, and 100% for determination of estrogen receptor/progesterone receptor and HER2 status. Age, comorbidities, and stage influenced guideline compliance. The most common reasons for noncompliance were patient refusal, patient choice after shared decision-making, and overuse of testing. Synoptic templated reporting was accurate in 97% patients., Conclusions: High compliance with NCCN Guidelines was demonstrated. Reasons for noncompliance were identifiable. Compliance and nonadherence can be evaluated quickly with electronic synoptic reporting. This allows real-time action plans to address quality concerns and aids national risk adjustment for comparison and benchmarking., (Copyright © 2015 by the National Comprehensive Cancer Network.)

We report 17 novel microsatellite loci in the parasitic chewing louse Geomydoecus ewingi, a common parasite of the pocket gopher, Geomys breviceps . Thirty-three G. ewingi individuals from 1 geographic locality and 3 pocket gopher hosts (populations) were genotyped at each locus. The number of alleles per locus ranged from 3 to 13. Observed heterozygosity ranged from 0.182 to 0.788. Four to 6 loci per louse population fell outside of Hardy-Weinberg expectations (HWE) and examination of population structure also revealed substantial homozygote excess as well as significant structure among louse populations. These findings are likely the consequence of biological characteristics of the lice (low dispersal abilities, population bottlenecks, etc.), which can result in inbreeding. Notably, when all louse individuals were analyzed together as 1 population, a Wahlund effect was detected, supporting that louse populations are restricted to 1 host individual. The microsatellite markers characterized in this study will be useful in future studies exploring the population dynamics in host-parasite systems, potentially yielding a better understanding of the processes underlying symbiotic associations.

Fibroepithelial lesions (FELs) are a common histologic finding on core needle biopsy (CNB) of the breast. Fibroepithelial lesions include fibroadenoma and phyllodes tumor, which can be difficult to distinguish with an initial CNB. An institutional experience was reviewed from February 12, 2001, to January 4, 2007, to determine the safety of selective rather than routine excision of FELs and to determine the factors associated with upgrading diagnosis of FELs to phyllodes tumors without definitive phyllodes tumor diagnosis by CNB. Of 313 patients, 261 (83%) with FELs diagnosed by CNB received observation with long-term follow-up (mean, 8 years). Of the observed patients, 3 (1%) were diagnosed with phyllodes tumor on follow-up. Eighteen of 52 patients (35%) who received excision had an upgrade of diagnosis to phyllodes tumor. Sensitivity and specificity of the pathologist's comment of concern for phyllodes tumor on a CNB demonstrating FELs without definitive phyllodes tumor diagnosis were 82% and 93%, respectively. Our policy of selective excision of FELs without definitive phyllodes tumor diagnosis resulted in safe avoidance of many surgical procedures.

Stochastic models of sequence evolution have been developed to reflect many biologically important processes, allowing for accurate phylogenetic reconstruction when an appropriate model is selected. However, commonly used models do not incorporate several potentially important biological processes. Spurious phylogenetic inference may result if these processes play an important role in the evolution of a dataset yet are not incorporated into assumed models. Few studies have attempted to assess the relative importance of multiple processes in producing spurious inferences. The application of phylogenetic methods to infer the source of HIV-1 transmission clusters depends upon accurate phylogenetic results, yet there are several relevant unmodeled biological processes (e.g., recombination and convergence) that may cause complications. Here, through analyses of HIV-1 env sequences from a small, forensically important transmission cluster, we tease apart the impact of these processes and present evidence suggesting that convergent evolution and high rates of insertions and deletions (causing alignment uncertainty) led to spurious phylogenetic signal with forensic relevance. Previous analyses show paraphyly of HIV-1 lineages sampled from an individual who, based on non-phylogenetic evidence, had never acted as a source of infection for others in this transmission cluster. If true, this pattern calls into question assumptions underlying phylogenetic approaches to source and recipient identification. By systematically assessing the contribution of different unmodeled processes, we demonstrate that removal of sites likely influenced by strong positive selection both reduces the alignment-wide signal supporting paraphyly of viruses sampled from this individual and eliminates support for the effects of recombination. Additionally, the removal of ambiguously aligned sites alters strongly supported relationships among viruses sampled from different individuals. These observations highlight the need to jointly consider multiple unmodeled evolutionary processes and motivate a phylogenomic perspective when inferring viral transmission histories., (Copyright © 2014 Elsevier Inc. All rights reserved.)

Background: Sialophorin is a transmembrane sialoglycoprotein. Normally, the molecule is only produced by white blood cells where it regulates functions such as intercellular adhesion, intracellular signalling, apoptosis, migration and proliferation., Methods: Normal breast tissue and primary breast tumours were analysed by immunohistochemistry for sialophorin expression. The sialophorin-positive breast cancer cell line MCF7 was engineered to stably express either non-targeted or sialophorin-targeted small interfering RNA (siRNA). Assays were then performed in vitro to assess apoptosis, intracellular adhesion, transendothelial migration and cytotoxicity. An orthotopic mouse model assayed ability to produce tumours in vivo., Results: Normal breast epithelial cells exhibit expression of the N-terminal domain of sialophorin in the cytoplasm but not the nucleus. The majority of these normal cells are also negative for expression of the C-terminal domain. In contrast, malignant breast epithelial cells exhibit N-terminal expression both in the cytoplasm and nucleus and the majority express the C-terminus in the nucleus. Using differential patterns of intracellular expression of the N and C termini of sialophorin, we define six subtypes of breast cancer that are independent of histological and receptor status classification. Targeting sialophorin with siRNA resulted in the MCF7 breast cancer cell line exhibiting increased homotypic adhesion, decreased transendothelial migration, increased susceptibility to apoptosis, increased vulnerability to lysis by natural killer cells and decreased ability to produce tumours in mice., Conclusion: Our results indicate that intracellular patterns of sialophorin expression define a new molecular classification of breast cancer and that sialophorin represents a novel therapeutic target.

Peptide YY (PYY) is a gut hormone that activates the G protein-coupled neuropeptide Y (NPY) receptors, and because of its appetite reducing actions, it is evaluated as an antiobesity drug candidate. The C-terminal tail of PYY is crucial for activation of the NPY receptors. Here, we describe the design and preparation of a series of PYY(3-36) depsipeptide analogues, in which backbone amide-to-ester modifications were systematically introduced in the C-terminal. Functional NPY receptor assays and circular dichroism revealed that the ψ(CONH) bonds at positions 30-31 and 33-34 are particularly important for receptor interaction and that the latter is implicated in Y2 receptor selectivity.

The Great Basin Desert of western North America has experienced frequent habitat alterations due to a complex biogeographic history and recent anthropogenic impacts, with the more recent alterations likely resulting in the decline of native fauna and flora. Dark (Microdipodops megacephalus) and pallid (M. pallidus) kangaroo mice are ecological specialists found within the Great Basin Desert and are potentially ideal organisms for assessing ecosystem health and inferring the biogeographic history of this vulnerable region. Herein, newly acquired nuclear-encoded microsatellite loci were utilized to assess patterns of variation within and among spatially discrete groups of kangaroo mice and to evaluate gene flow, demographic trends, and genetic integrity. Results confirm that there are at least three genetically distinct units within M. megacephalus and two such units within M. pallidus. The three units of M. megacephalus appear to have different demographic histories, with effectively no gene flow among them since their divergence. Similarly, the two units of M. pallidus also appear to have experienced different demographic histories, with effectively no gene exchange. Contemporary effective population sizes of all groups within Microdipodops appear to be low (<500), suggesting that each genetic lineage may have difficulty coping with changing environmental pressures and hence may be at risk of extirpation. Results of this study indicate that each Microdipodops group should be recognized, and therefore managed, as a separate unit in an effort to conserve these highly specialized taxa that contribute to the diversity of the Great Basin Desert ecosystem. The Great Basin Desert of western North America has experienced frequent habitat alterations due to a complex biogeographic history and recent anthropogenic impacts, with the more recent alterations likely resulting in the decline of native fauna and flora. Herein, newly acquired nuclear-encoded microsatellite loci were utilized to assess patterns of variation within and among spatially discrete groups of the dark (Microdipodops megacephalus) and pallid (M. pallidus) kangaroo mouse, and to evaluate gene flow, demographic trends, and genetic integrity. Results of this study indicate that each Microdipodops group should be recognized, and therefore managed, as a separate unit in an effort to conserve these highly specialized taxa that contribute to the diversity of the Great Basin Desert ecosystem (photo credit J. C. Hafner).

CD43 is a transmembrane sialoglycoprotein. Normally the molecule is only produced by white blood cells where it regulates functions such as intercellular adhesion, intracellular signaling, apoptosis, migration and proliferation. Two CD43 antibodies were used to interrogate 66 cases of non-small cell lung cancer (NSCLC) and 24 cases of small cell lung cancer (SCLC). In addition, we engineered the CD43-positive lung cancer cell line A549 to stably express either non-targeted or CD43-targeted small-interfering RNA (siRNA). These lines were then subjected to in vitro assays of apoptosis, natural killer (NK) cell cytotoxicity, intercellular adhesion and transendothelial migration. A xenograft mouse model evaluated the ability of the lines to grow primary tumors in vivo. CD43 was found to be expressed in the majority of both SCLC and NSCLC. Inclusive of CD43-negative tumors, differential patterns of nuclear and cytoplasmic expression of CD43 define four molecular subcategories of lung cancer. Targeting CD43 in A549 lung cancer cells, increased homotypic adhesion, decreased heterotypic adhesion and transendothelial migration, increased susceptibility to apoptosis and increased vulnerability to lysis by NK cells. Furthermore, targeting inhibited the growth of primary tumors in nude mice., (Copyright © 2012 UICC.)

Objective: The purpose of this study is to evaluate the rate of minimally invasive biopsy for diagnosis of breast cancer at an interdisciplinary breast center., Background: Percutaneous core needle biopsy (CNB) is optimal for minimizing surgery for the diagnosis of benign and malignant lesions of the breast while preserving surgery for definitive resection. Core needle biopsy increases patient satisfaction and reduces the cost of diagnosis and treatment. Despite the endorsement of CNB by many professional organizations, the literature documents underutilization., Methods: Institutional review board approval was obtained. An audit of a single institution's prospectively maintained cancer databases was performed for all breast cancers diagnosed in 2007 and 2008. Methods of diagnosis included image-guided and freehand-guided CNB, image-guided vacuum assisted needle biopsy, image-guided fine needle aspiration, punch biopsy, and open surgical biopsy., Results: Three hundred sixty new breast cancers were diagnosed in 2007 and 2008. Malignancy was diagnosed by minimally invasive techniques in 350/360 (97%) cancers., Conclusion: A very high rate of accurate tissue diagnosis of breast cancer by minimally invasive techniques is achievable.

Background and Objectives: Patient-centered care is recommended by the Institute of Medicine to build a better healthcare system. The aim of this study was to audit patient-centered quality measures (QM) to create a breast center report card that could be provided to patients for education and informed consent., Methods: An IRB approved retrospective review of 695 patients undergoing sentinel lymph node biopsy for breast cancer was conducted to audit the components of one step surgery and other QM., Results: The intraoperative sensitivity to detect node positive patients was 25% (2/8), 27% (9/34), and 87% (68/78) for pN0(i+), pN1mi, pN1 patients, respectively. The re-excision lumpectomy rate was 15% (72/471) and the one step surgery success rate, which included lumpectomy and mastectomy patients, was 86% (598/695). Patient self-assessment of "very good to excellent" cosmesis and pain control were 77% (103/134) and 83% (60/72). Local recurrence rate was 2% (12/695) at a mean 3.1-year follow-up., Conclusions: The components of care that contribute to a patient-centered assessment of breast cancer surgery are measurable. "Bundling" of QM creates a perioperative report card that aids patients' informed consent and provides a framework for future comparative effectiveness studies., ((c) 2010 Wiley-Liss, Inc.)

Controversy exists over the optimal patient selection criteria for accelerated partial-breast irradiation (APBI), which has been introduced as an alternative to whole-breast irradiation. The goal is to select patients with the lowest risk for tumor spread outside of the original lumpectomy bed targeted by the local internal radiation dose. Therefore, patients with more aggressive types of breast cancer might not be ideal candidates for partial breast irradiation. We discuss the case of a 67-year-old woman who presented with local recurrence of invasive micropapillary breast cancer, a rare aggressive tumor type, 5 years after MammoSite brachytherapy. The patient's primary tumor possessed all favorable indicators except for the histology of invasive micropapillary carcinoma. This is the first report of invasive micropapillary carcinoma recurring after APBI. Although this is a single case, it supports the hypothesis that more aggressive types of breast cancer have a higher risk of local recurrence after APBI. We propose that invasive micropapillary carcinoma be considered a potential exclusion criterion until it can be validated in prospective clinical trials. More aggressive treatment approaches including whole-breast irradiation and/or chemotherapy might be needed to reduce the risk of local recurrence for invasive micropapillary breast cancer.

Background: Survivin, which is a member of the inhibitor of apoptosis protein gene family, regulates both programmed cell death and mitosis. It has been shown that survivin expression and its subcellular localization both have prognostic value for patients with malignant disease. In this study, the authors investigated whether nuclear or cytoplasmic staining of survivin was a prognostic marker for patients with lung carcinoma., Methods: Paraffin-embedded tissue blocks from 144 patients with Stage I and II resected nonsmall cell lung carcinoma (NSCLC) were obtained for immunohistochemical staining. Three specimens from each patient were prepared and stained with a survivin-specific antibody. Nuclear and cytoplasmic staining was graded from 1 to 3 based on intensity., Results: Patients who had nuclear staining for survivin had a significantly increased risk of disease recurrence (hazard ratio, 2.95; P = 0.0046) and death (hazard ratio, 2.74; P = 0.0086)., Conclusions: The nuclear presence of survivin may be an independent biomarker for disease recurrence and overall survival in patients with resected Stage I and II NSCLC., ((c) 2005 American Cancer Society.)

Signaling through the phosphatidylinositol 3-kinase (PI3-kinase) pathway has been associated with lung tumorigenesis. We examined the association between gene copy number of the PI3-kinase catalytic subunit alpha (PIK3CA) and phosphorylated Akt expression in invasive and preinvasive lung cancers. We sought to determine at what stage of tumor development gene copy number increase or phosphorylated Akt overexpression might affect tumor development. We assessed PIK3CA gene copy number by fluorescence in situ hybridization and expression of phosphorylated Akt by immunohistochemistry in 242 invasive and 43 preinvasive lung cancers and correlated our findings with clinical outcome. The PIK3CA was amplified in 70% of squamous carcinomas, 38% of large cell carcinomas, 19% of adenocarcinomas, and 67% of small cell lung cancers. Phosphorylated Akt overexpression was frequently observed, and strongly so in 12 to 17% of lung cancers depending on nuclear or cytoplasmic localization. Neither PIK3CA gene copy number nor phosphorylated Akt protein expression had prognostic significance. In preinvasive lesions, amplification of the PIK3CA and overexpression of phosphorylated Akt were associated with severe dysplasia and each other. These observations suggest frequent and early involvement of the PI3-kinase pathway in lung cancer.

This study documents the initial reliability and validity of the Child Suicide Risk Assessment (CSRA) for children under the age of 13. The revised CSRA retained 18 of 20 original items based on item-specific psychometric data from 140 pre-adolescents in out-of-home treatment programs. The CSRA demonstrated adequate internal consistency (alpha=.69) for a multi-dimensional scale (3 factors: Worsening Depression, Lack of Support, and Death as Escape). CSRA scores correlated significantly with criterion measures of prior suicide attempts and ideations. A receiver operating characteristic (ROC) curve discriminated significantly between prior attempters and non-attempters and was used to select preliminary CSRA cut-off scores for identifying substantial suicide risk. The CSRA is the first screening measure of suicide risk in pre-adolescents validated by associations with suicide attempts as well as ideations.

Charleston Area Medical Center shows how the business office and medical records department can work together to improve accounts receivables.

A temperature-sensitive mutant of Bacillus subtilis is defective in deoxyribonucleic acid (DNA) synthesis, contains a lesion in the dnaC locus, and is not primarily an initiation mutant. The amount of DNA synthesized by this mutant at temperatures above 40 C decreases with increasing temperature. DNA synthesis resumes within 20 min after the temperature is lowered to 30 C. In the presence of chloramphenical, DNA synthesis begins at a reduced rate after the temperature is lowered to 30 C. Spores germinated at 46 C cannot initiate DNA replication. The capacity for residual DNA synthesis is stable at the restrictive temperature during inhibition of DNA synthesis. When the temperature is lowered to 30 C after a period of incubation at 43 C, DNA synthesis starts at the origin of the chromosome as well as at preexisting growing points. Similar DNA synthesis patterns are found in mutant cells in vivo and after toluene treatment.