Observations of the Vertical Structure of Tidal Currents in Two Inlets

Observations of the vertical structure of broad band tidal currents were obtained at two energetic inlets. Each experiment took place over a 4 week period, the first at Hampton Inlet in southeastern New Hampshire, USA, in the Fall of 2011, and the second at New River Inlet in southern North Carolina, USA, in the spring of 2012. The temporal variation and vertical structure of the currents were observed at each site with 600 kHz and 1200 kHz RDI Acoustic Doppler Current Profilers (ADCP) deployed on low-profile bottom tripods in 7.5 and 12.5 m water depths near the entrance to Hampton Inlet, and in 8 and 9 m water depth within and outside New River Inlet, respectively. In addition, a Nortek Aquapro ADCP was mounted on a jetted pipe in about 2.5 m water depth on the flank of the each inlet channel. Flows within the Hampton/Seabrook Inlet were dominated by semi-diurnal tides ranging 2.5 - 4 m in elevation, with velocities exceeding 2.5 m/s. Flows within New River inlet were also semi-diurnal with tides ranging about 1 – 1.5 m in elevation and with velocities exceeding 1.5 m/s. Vertical variation in the flow structure at the dominant tidal frequency are examined as a function of location within and near the inlet. Outside the inlet, velocities vary strongly over the vertical, with a nearly linear decay from the surface to near the bottom. The coherence between the upper most velocity bin and the successively vertically separated bins drops off quickly with depth, with as much as 50% coherence decay over the water column. The phase relative to the uppermost velocity bin shifts over depth, with as much as 40 deg phase lag over the vertical, with bottom velocities leading the surface. Offshore, rotary coefficients indicate a stable ellipse orientation with rotational directions consistent over the vertical. At Hampton, the shallower ADCP, but still outside the inlet, shows a rotational structure that changes sign in the vertical indicating a sense of rotation at the bottom that is opposite to that at the surface. Within the inlet, the flow is more aligned with the channel, the decay in amplitude over the vertical is diminished, the coherence and phase structure is nearly uniform, and the rotary coefficients indicate no sense of rotation in the flow. The observations are qualitatively consistent with behavior described by Prandle (1982) for shallow water tidal flows

Whsc1l1 Regulates Estrogen Receptor Activity In Sum44 Breast Cancer Cells

Breast cancer is the most common cancer and the second leading cause of cancer death in women. While ER-positive breast cancer subtypes are initially well-managed by targeted therapies targeting estrogen signaling, many women are suffering from recurrence of a more aggressive, hormone insensitive cancer 5 or more years after initial remission. Late recurrence of hormone resistant breast cancer in patients who were previously successfully treated with anti-estrogen therapies worsens overall long-term outcomes, and specific oncogenic mutations may be driving late recurring aggressive disease in these patients. More complete characterization of the oncogenome of a tumor may allow for the possibility of customized therapy targeting each patient\u27s specific oncogene-activating mutations, and in doing so increase the probability of durable remission over the long term. Basic research on cell lines modeling different breast cancer subtypes makes possible discovery and characterization of novel driving oncogenes and their context in a breast cancer subtype model. The Wolf Hirschhorn Syndrome Candidate 1-Like 1 gene (WHSC1L1) is one of approximately 50 genes in the chromosome 8p11-p12 amplicon, an amplified region of the short arm of chromosome 8 found in 12-15% of human breast cancers, as well as other cancer types such as lung. Amplification of the 8p11-p12 region is most often found in breast cancers of the luminal B subtype. WHSC1L1 is a member of the NSD family of histone lysine methyltransferases, SET domain-containing proteins which catalyze the addition of a methyl group to lysines on the amino-terminal tail of histone H3 subunits. The WHSC1L1 gene expresses two known isoforms which code for two distinct proteins, WHSC1L1-long and WHSC1L1-short. The short isoform of WHSC1L1 codes for the first 647 of the 1437 amino acids present in the long isoform, and lacks the catalytic SET domain and several PHD and PWWP chromatin interacting domains, containing a single PWWP domain and a recently characterized acidic transactivation domain. In both normal and tumor breast tissue, WHSC1L1-short is expressed at greater levels than WHSC1L1-long. Several breast cancer cell lines established in the Ethier lab harbor WHSC1L1 amplifications and also overexpress both isoforms of WHSC1L1. The SUM44 cell line is a highly ER-positive cell line model of luminal B breast cancer isolated from a pleural effusion metastasis of a patient with aggressive disease. It is known that the short isoform of WHSC1L1, WHSC1L1-short, is a potent driving oncogene in SUM44 cells, however the specific mechanism of WHSC1L1-short as an oncomodifier is not known. To investigate WHSC1L1-short function as an oncogene in SUM44 cells, we developed an shRNA knockdown model that specifically knocked down expression of WHSC1L1-short through its unique 3\u27 UTR sequence (shWHSC1L1-short), and a model that knocked down both WHSC1L1 isoforms (shWHSC1L1-total). We found that knockdown of both total WHSC1L1 and WHSC1L1-short alone negatively affected SUM44 proliferation, and that WHSC1L1-short knockdown had a larger effect than knockdown of both isoforms. After finding that WHSC1L1 expression was required for typical proliferation rates of SUM44 cells, we performed genome-wide expression profiling of SUM44 WHSC1L1-short and total WHSC1L1 knockdown cell lines relative to a control SUM44 line transduced with shRNA against lacZ. Again we found that knockdown of the WHSC1L1-short alone had a greater affect than total WHSC1L1 knockdown, this time on the number of significantly differentially expressed genes; 1131 genes were found to be differentially expressed in the WHSC1L1-short knockdown cells relative to shLacZ control, while 238 genes were differentially expressed in the total WHSC1L1 knockdown SUM44 cells relative to shLacZ control. Interestingly, the ESR1 gene, which codes for the estrogen receptor alpha protein, was significantly downregulated by WHSC1L1-short knockdown. This was confirmed by immunoblotting with ERa antibody. While total WHSC1L1 knockdown also had a negative effect on ERa protein levels in SUM44, knockdown of WHSC1L1-short alone almost completely abrogated ERa in SUM44 as measured by western blot. We subsequently found that SUM44 cells were extremely sensitive to treatment with beta-estradiol, and that proliferation actually decreased upon as little as 100 picomolar beta-estradiol treatment, with dose-dependent decreases in proliferation as estrogen concentrations increased. We also found SUM44 cells to be relatively insensitive to Tamoxifen. Knockdown of WHSC1L1-short reduced proliferation of SUM44 cells in estrogen-free conditions, and treatment of SUM44 shWHSC1L1-short cells with increasing concentrations of beta-estradiol resulted in a marginal increase in proliferation up to 100pM beta-estradiol, then proliferation decreased with increasing beta-estradiol concentrations similar to results seen in SUM44 shLacZ control cells. After observing that WHSC1L1-short overexpression was required for expression of ERa in SUM44 cells, we asked whether knockdown of WHSC1L1-short affected genome-wide binding patterns of the estrogen receptor in SUM44 cells. Interestingly we found that ERa was binding to thousands of genomic loci in the absence of exogenous estrogen. Treatment with high doses (10nM) of beta-estradiol for 45 minutes resulted in an approximately even increase in ERa binding across sites already bound in the absence of estrogen, with some additional weak binding sites, but no significant changes in the pattern of ERa binding. No ERa binding sites were detected in SUM44 shWHSC1L1-short cells under estrogen-free conditions, and weak ERa binding was detected in SUM44 shWHSC1L1-short cells treated with 10nM beta-estradiol at loci where strong ERa binding was observed in control SUM44 cells, suggesting that WHSC1L1-short knockdown was reducing ERa expression levels, which made less ERa available to bind to chromatin in SUM44 shWHSC1L1-short cells. Our investigation of WHSC1L1 oncogenic activity in SUM44 cells resulted in the interesting observation that the short isoform of WHSC1L1 is required for expression of the estrogen receptor alpha in these cells, and that ERa is bound extensively to chromatin without activation of ERa by estrogen. SUM44 is a model for luminal B breast cancer, and is highly ER-positive, and expresses little to no progesterone receptor (PR). While the implications of ERa expression dependence on WHSC1L1-short overexpression in SUM44 cells are not yet clear, the extensive binding of ERa to estrogen response elements (ERE\u27s) in the absence of exogenous estrogen and the negative proliferative response of SUM44 to estrogen indicate that WHSC1L1 amplification and overexpression may alter the biology of the estrogen receptor in breast cancers harboring WHSC1L1 amplification and overexpression. Additionally, the differences seen in ERa binding to chromatin and the negative response of SUM44 cells to ERa agonists illustrate the importance of researching ER-positive breast cancer using additional cell line models rather than consistently using MCF7 cells to represent ER-positive disease. The dominant role of the catalytically-inactive short isoform of WHSC1L1 in regulating ERa expression and maintaining the proliferation rate of SUM44 cells suggests that catalytically inactive isoforms of chromatin modifying enzymes can be important regulators of gene expression. Interestingly, recent work has shown that WHSC1L1-short is likely not regulating target gene expression through histone methylation, but instead is acting as a co-factor for a different chromatin-binding complex, the BRD4-CHD8 complex, which has been shown to be recruited to superenhancer regions (marked by histone acetylation) by WHSC1L1-short, which results in activation of pTEFb through BRD4 and directly activates target gene transcription. It will be important to avoid assumptions about binding substrate identities of catalytically inactive isoforms of future chromatin modifiers of interest, as the catalytically inactive isoforms of these genes may also bind to chromatin substrates unrelated to the substrate of the catalytically active isoform

Presentation by the University of Nevada, Las Vegas: College of Fine Arts

Program listing performers and works performe

Image-guided fluorescence tomography in head & neck surgical models

Clinical indications for fluorescence-guided surgery continue to expand, and are being spurred by the rapid development of new agents that improve biological targeting.1 There is a corresponding need to develop imaging systems that quantify fluorescence - not only at the tissue surface, but at depth. We have recently described an image-guided fluorescence tomography system that leverages geometric data from intraoperative cone-beam CT and surgical navigation,2 and builds on finite-element method software (NIRFAST) for diffuse optical tomography (DOT).3 DOT systems have most commonly been used for sub-surface inclusions buried within tissue (e.g., breast and neurological tumors). Here, we focus on inclusion models relevant to tumors infiltrating from the mucosal surface (an “iceberg” model), as is most often the case in head and neck cancer, where over 85% of tumors are squamous cell carcinoma.4 This work presents results from simulations, tissue-simulating anatomical phantoms, and animal studies involving infiltrative tumor models. The objective is to characterize system performance across a range of inclusion diameters, depths, and optical properties. For example, Fig. 1 shows a fluorescence reconstruction of a simulated tonsil tumor in an oral cavity phantom. Future clinical studies are necessary to assess in vivo performance and intraoperative workflow. Please click Additional Files below to see the full abstract

Joint Modeling and Registration of Cell Populations in Cohorts of High-Dimensional Flow Cytometric Data

In systems biomedicine, an experimenter encounters different potential sources of variation in data such as individual samples, multiple experimental conditions, and multi-variable network-level responses. In multiparametric cytometry, which is often used for analyzing patient samples, such issues are critical. While computational methods can identify cell populations in individual samples, without the ability to automatically match them across samples, it is difficult to compare and characterize the populations in typical experiments, such as those responding to various stimulations or distinctive of particular patients or time-points, especially when there are many samples. Joint Clustering and Matching (JCM) is a multi-level framework for simultaneous modeling and registration of populations across a cohort. JCM models every population with a robust multivariate probability distribution. Simultaneously, JCM fits a random-effects model to construct an overall batch template -- used for registering populations across samples, and classifying new samples. By tackling systems-level variation, JCM supports practical biomedical applications involving large cohorts

Response rates for mailout survey-driven studies in patients with head and neck cancer

Background: Mailout survey studies are becoming more prevalent in the head and neck literature. The objective of this paper is to summarize response rates in patients with head and neck cancer, and to provide recommendations surrounding methodology used to design and implement mailout survey questionnaires. Methods: The results of this paper are from a study assessing the measurement properties of the Disabilities of the Arm, Shoulder and Hand Questionnaire (DASH) in head and neck cancer patients. A modified Dillman tailored design approach was used. Results: The methods used yielded a response rate of 80% with this patient population. Conclusion: This is a considerably higher response rate than other reports in the oncology literature. © 2010 Wiley Periodicals, Inc. Head Neck, 2010Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/78489/1/21363_ftp.pd

Fatigue is not a necessary stimulus for strength gains during resistance training

BACKGROUND: High resistance training enhances muscular strength, and recent work has suggested an important role for metabolite accumulation in this process. OBJECTIVE: To investigate the role of fatigue and metabolite accumulation in strength gains by comparing highly fatiguing and non-fatiguing isotonic training protocols. METHODS: Twenty three healthy adults (18-29 years of age; eight women) were assigned to either a high fatigue protocol (HF: four sets of 10 repetitions with 30 seconds rest between sets) to maximise metabolic stress or a low fatigue protocol (LF: 40 repetitions with 30 seconds between each repetition) to minimise changes. Subjects lifted on average 73% of their 1 repetition maximum through the full range of knee extension with both legs, three times a week. Quadriceps isometric strength of each leg was measured at a knee joint angle of 1.57 rad (90 degrees ), and a Cybex 340 isokinetic dynamometer was used to measure the angle-torque and torque-velocity relations of the non-dominant leg. RESULTS: At the mid-point of the training, the HF group had 50% greater gains in isometric strength, although this was not significant (4.5 weeks: HF, 13.3 (4.4)%; LF, 8.9 (3.6)%). This rate of increase was not sustained by the HF group, and after nine weeks of training all the strength measurements showed similar improvements for both groups (isometric strength: HF, 18.2 (3.9)%; LF, 14.5 (4.0)%). The strength gains were limited to the longer muscle lengths despite training over the full range of movement. CONCLUSIONS: Fatigue and metabolite accumulation do not appear to be critical stimuli for strength gain, and resistance training can be effective without the severe discomfort and acute physical effort associated with fatiguing contractions

High-dimensional analysis reveals distinct endotypes in patients with idiopathic inflammatory myopathies

The idiopathic inflammatory myopathies (IIM) are a rare clinically heterogeneous group of conditions affecting the skin, muscle, joint, and lung in various combinations. While myositis specific autoantibodies are well described, we postulate that broader immune endotypes exist in IIM spanning B cell, T cell, and monocyte compartments. This study aims to identify immune endotypes through detailed immunophenotyping of peripheral blood mononuclear cells (PBMCs) in IIM patients compared to healthy controls. We collected PBMCs from 17 patients with a clinical diagnosis of inflammatory myositis and characterized the B, T, and myeloid cell subsets using mass cytometry by time of flight (CyTOF). Data were analyzed using a combination of the dimensionality reduction algorithm t-distributed stochastic neighbor embedding (t-SNE), cluster identification, characterization, and regression (CITRUS), and marker enrichment modeling (MEM); supervised biaxial gating validated populations identified by these methods to be differentially abundant between groups. Using these approaches, we identified shared immunologic features across all IIM patients, despite different clinical features, as well as two distinct immune endotypes. All IIM patients had decreased surface expression of RP105/CD180 on B cells and a reduction in circulating CD3+CXCR3+ subsets relative to healthy controls. One IIM endotype featured CXCR4 upregulation across all cellular compartments. The second endotype was hallmarked by an increased frequency of CD19+CD21loCD11c+ and CD3+CD4+PD1+ subsets. The experimental and analytical methods we describe here are broadly applicable to studying other immune-mediated diseases (e.g., autoimmunity, immunodeficiency) or protective immune responses (e.g., infection, vaccination)

Assessment of the Disabilities of the Arm, Shoulder, and Hand (DASH) questionnaire for use in patients after neck dissection for head and neck cancer

BackgroundIn this cross‐sectional study, the sensibility, test‐retest reliability, and validity of the Disabilities of the Arm, Shoulder, and Hand (DASH) questionnaire were assessed in patients who underwent neck dissection.MethodsSensibility was assessed with a questionnaire. Test‐retest reliability was performed with completion of the DASH questionnaire 2 weeks after initial completion; validity, by evaluating differences in scores between patients undergoing different types of neck dissections and correlating DASH scores with Neck Dissection Impairment Index (NDII) scores.ResultsThe DASH questionnaire met sensibility criteria. For test‐retest reliability analysis, the intraclass coefficient was 0.91. The DASH questionnaire showed differences between patients who underwent accessory nerve‐sacrifice and nerve‐sparing neck dissection. DASH questionnaire scores strongly correlated with NDII scores (r = ‐0.86).ConclusionAlthough this study provides preliminary data on some psychometric properties of the DASH questionnaire in patients who have undergone a neck dissection, further assessment of responsiveness and other properties are required. © 2014 Wiley Periodicals, Inc. Head Neck 37: 234‐242, 2015Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/110617/1/hed23593.pd

mRNA transcript quantification in archival samples using multiplexed, color-coded probes

Background: A recently developed probe-based technology, the NanoString nCounter™ gene expression system, has been shown to allow accurate mRNA transcript quantification using low amounts of total RNA. We assessed the ability of this technology for mRNA expression quantification in archived formalin-fixed, paraffin-embedded (FFPE) oral carcinoma samples. Results: We measured the mRNA transcript abundance of 20 genes (COL3A1, COL4A1, COL5A1, COL5A2, CTHRC1, CXCL1, CXCL13, MMP1, P4HA2, PDPN, PLOD2, POSTN, SDHA, SERPINE1, SERPINE2, SERPINH1, THBS2, TNC, GAPDH, RPS18) in 38 samples (19 paired fresh-frozen and FFPE oral carcinoma tissues, archived from 1997-2008) by both NanoString and SYBR Green I fluorescent dye-based quantitative real-time PCR (RQ-PCR). We compared gene expression data obtained by NanoString vs. RQ-PCR in both fresh-frozen and FFPE samples. Fresh-frozen samples showed a good overall Pearson correlation of 0.78, and FFPE samples showed a lower overall correlation coefficient of 0.59, which is likely due to sample quality. We found a higher correlation coefficient between fresh-frozen and FFPE samples analyzed by NanoString (r = 0.90) compared to fresh-frozen and FFPE samples analyzed by RQ-PCR (r = 0.50). In addition, NanoString data showed a higher mean correlation (r = 0.94) between individual fresh-frozen and FFPE sample pairs compared to RQ-PCR (r = 0.53). Conclusions: Based on our results, we conclude that both technologies are useful for gene expression quantification in fresh-frozen or FFPE tissues; however, the probe-based NanoString method achieved superior gene expression quantification results when compared to RQ-PCR in archived FFPE samples. We believe that this newly developed technique is optimal for large-scale validation studies using total RNA isolated from archived, FFPE samples