Controlling a virtual forehand prosthesis using an adaptive and affective Human-Machine Interface

This paper presents the design of an adaptable Human-Machine Interface (HMI) for controlling virtual forearm prosthesis. Direct physical performance measures (obtained score and completion time) for the requested tasks were calculated. Furthermore, bioelectric signals from the forehead were recorded using one pair of electrodes placed on the frontal region of the subject head to extract the mental (affective) measures while performing the tasks. By employing the proposed algorithm and above measures, the proposed HMI can adapt itself to the subject's mental states, thus improving the usability of the interface. The quantitative results from 15 subjects show that the proposed HMI achieved better physical performance measures in comparison to a conventional non-adaptive myoelectric controller (p < 0.001).

Optimization of a bacterial consortium for nitrobenzene degradation

Three bacterial strains, Arthrobacter sp. NB1, Serratia sp. NB2 and Stenotrophomonas sp. NB3, were isolated from contaminated sludge by using nitrobenzene as a sole source of carbon and nitrogen. It was observed that all three strains could degrade nitrobenzene at 400 mg/L initial concentration and mixed-cultivation of these strains could enhance the degradation of nitrobenzene compared with mono-cultivation. Mixture design was used for adjusting the proportions of each strain and the optimal ratio of inoculation size was NB1:NB2:NB3 = 4:4:5, where the nitrobenzene degradation percentage was two times higher than for by the single strain. The results of Plackett-Burman design indicated that Mg(2+), Ca(2+), Fe(2+), Zn(2+) and Mn(2+) had a positive effect on the degradation of nitrobenzene, while Cu(2+) and Co(2+) had a negative effect on it.

MS3-2: HIF-1, Metabolism, and Breast Cancer Metastasis

Increased glucose uptake and metabolism is a universal characteristic of advanced solid cancers. There are two well-established mechanisms underlying the reprogramming of tumor metabolism. First, intratumoral hypoxia induces the activity of the transcriptional activator hypoxia-inducible factor 1 (HIF-1) by inhibiting the O2-dependent prolyl and asparaginyl hydroxylases that inhibit HIF-1α stability and transactivation, respectively. Second, genetic alterations increase the activity of HIF-1, thereby increasing the expression of glucose transporters (GLUT1, GLUT3), glycolytic enzymes (ALDOA, ENO1, HK2, LDHA, PKM2), pH regulators (CAR9, NHE1, MCT4), and proteins that inhibit mitochondrial metabolism (BNIP3, PDK1). Metabolites, such as the glycolytic end-product lactate, also induce HIF-1 activity, thereby providing a signal to further increase glycolytic metabolism. Recently, we have identified a novel feed-forward mechanism by which glycolytic enzyme expression leads to increased HIF-1 transcriptional activity. Pyruvate kinase isoforms PKM1 and PKM2 are alternatively spliced products of the PKM2 gene. PKM2, but not PKM1, alters glucose metabolism in cancer cells and contributes to tumorigenesis by mechanisms that are not explained by its known biochemical activity. We show that PKM2 gene transcription is activated by HIF-1. PKM2 interacts directly with the HIF-1α subunit and promotes transactivation of HIF-1 target genes by enhancing HIF-1 binding and p300 recruitment to hypoxia response elements, whereas PKM1 fails to regulate HIF-1 activity. Interaction of PKM2 with prolyl hydroxylase 3 (PHD3) enhances PKM2 binding to HIF-1α and PKM2 coactivator function. Mass spectrometry and anti-hydroxyproline antibody assays demonstrate PKM2 hydroxylation on proline-403/408. PHD3 knockdown inhibits PKM2 coactivator function, reduces glucose uptake and lactate production, and increases O2 consumption in cancer cells. Thus, PKM2 participates in a positive feedback loop that promotes HIF-1 transactivation and reprograms glucose metabolism in cancer cells (1). HIF-1 also plays critical roles in breast cancer metastasis. HIF-1 controls metastatic niche formation by activating transcription of genes encoding lysyl oxidase (LOX) and LOX-like proteins 2 and 4, which remodel collagen in the lungs, thereby recruiting bone marrow-derived cells that establish a microenvironment suitable for colonization by breast cancer cells (2). HIF-1 also promotes the extravasation of circulating breast cancer cells in the lungs by activating transcription of the genes encoding L1CAM, which encodes a cell adhesion molecule that promotes the interaction of breast cancer cells with vascular endothelial cells (ECs), and angiopoietin-like 4, which encodes a secreted factor that inhibits EC-EC interaction (3). Inhibition of HIF-1 activity by genetic or pharmacologic strategies dramatically inhibits the metastasis of breast cancer cells to the lungs in orthotopic mouse models (2, 3).

(1) Luo W. et al. Cell 2011;145:732.

(2) Wong CC et al. Proc Natl Acad Sci USA 2011 Sept 12. doi:10.1073/pnas.1113483108.

(3) Zhang H. et al. Oncogene 2011 Aug 22. doi: 10.1038/onc.2011.365.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr MS3-2.

P5-14-12: Bayesian Belief Network Mortality Analysis of a Breast Cancer Registry Data Set

Introduction: Bayesian Belief Networks have been used in medicine to evaluate clinical data and develop predictive and prognostic models. As classification models, they allow us to represent pattern complexity beyond what can be accomplished with traditional Kaplan-Meier or regression models. We sought to evaluate the use of machine-learned Bayesian Belief Networks (ml-BBNs) to develop mortality models in breast cancer and to evaluate classification performance for this method.

Methods: A set of 2,300 breast bancer cases from a tumor registry at Thomas Jefferson University were used to train ml-BBNs. The registry set was broken into cohorts for modeling by follow-up times of 1 (n=2,202), 2 (n=2,183), 3 (n=2,157), and 5 (n=2,027) years. Each cohort was then used to train a ***m1-BBN and each model was evaluated for structure. Variables were recoded into categories: biomarkers (ER, PR, Ki67, HER2, p53) as positive or negative; grading, staging, and size were broken in categories; while race was recoded into Caucasian or African-American. Income and poverty level by census tract were also included. Models were evaluated for ability to classify mortality (yes/no) within the follow-up period using 10-fold cross-validation and Receiver Operating Characteristic curves.

Results: Area Under the Curve (AUC), Positive Predictive Value (PPV), and Negative Predictive Value (NPV) were calculated for each set of cohort training models and mean values and 95% confidence intervals were calculated for mortality (yes/no) within the follow-up period. AUCs (and CIs) for 1, 2, 3, and 5 years were: 0.81 (0.70 — 0.91), 0.74 (0.69 — 0.79), 0.81 (0.77 — 0.86), 0.77 (0.74 — 0.80). PPVs for 1, 2, 3, and 5 years were: 12.3% (7.5% — 17.1%), 18.8% (15.4% — 22.1%), 18.0% (15.1% — 20.9%), 28.2% (24.7% — 31.7%). NPVs for 1, 2, 3, and 5 years were: 99.2% (98.8% — 99.7%), 97.4% (96.9% — 97.8%), 96.4% (95.1% — 97.7%), 91.7% (89.1% — 94.3%). Predictors of mortality at 1 year were Tumor Stage, at 2 years were Estrogen Receptor and Tumor Stage, and at 3 and 5 years were Diagnosis Age, Tumor Stage, Estrogen Receptor status, and Ki-67 receptor status. Discussion / Conclusion: We were able to successfully train ***m1-BBNs to estimate mortality using breast cancer registry cohorts. Cross-validation showed the models to be robust. The structure of the models can inform us how different data elements contribute to the estimate of mortality. These models can be used to calculate individual probabilities for prognostic guidance given age, staging criteria, and biomarkers. Overall 5-year mortality in the study set is 15.2%, however we can derive subject-specific mortality estimates. For example, a 43-year old Stage 3, ER-Negative, Ki-67 Negative subject has a 19.9% probability of 5-year mortality, while the same subject with positive Ki-67 has a 37.8% probability of mortality. Meanwhile, the same probabilities for a 70 year old woman are 67.0% and 59.0%, respectively.

P1-03-06: Fibroadenomatoid Changes Have a Higher Occurrence Rate in Middle-Aged Benign Breast Disease Patients with the Trend Retained in Cancer Patients

Background: Fibroadenoma (FA) is a common benign breast lesion known to have a high incidence rate in younger women. There are controversial reports whether FA elevates the risk of developing breast cancers. In clinical practice, FA may be surgically removed due to multiple reasons making it complicated to study its impact on the development of breast cancers that have a higher incidence rate in older women. Fibroadenomatoid change (FAC), also known as fibroadenomatous hyperplasia, is an uncommon lesion with histologic features similar to that of FA but lacking well-defined borders and usually discovered incidentally on breast biopsy specimens. FAC is not surgically targeted. The Walter Reed Army Medical Center, through the Clinical Breast Care Project, has enrolled over 2000 subjects undergoing a biopsy; all the pathology was reviewed by a single pathologist. These subjects provide an opportunity to study the age-dependent pattern of FAC in different patient populations.

Methods: Subjects were enrolled following IRB-approved protocols with data collected through two comprehensive questionnaires, a Core Questionnaire and a Pathology Checklist. A total of 1964 female subjects were identified for this study, including 1135 benign/atypical, 192 in situ, and 637 invasive cancer patients. Patients were divided into three age groups: &lt;=45 years, 46–65 years, and &gt;=66 years. Chi-Square test in the SAS was used for statistical analysis.

Results: As shown in the table, FA occurrence rate decreases significantly with increasing age in benign disease patients. FAC, on the other hand, shows a significantly higher occurrence rate in middle-aged patients with benign findings, and this trend is retained in the invasive or in situ cancer populations. FAC rate is also significantly higher in patients with cancer (invasive, or invasive and in situ combined) compared to benign patients in each age group with p-values ranging from 0.0001 to 0.019 (not shown).

P3-06-06: Comparison of Gene Expression Profiles of Lymph Node Positive and Lymph Node Negative ER Positive Breast Tumors in Pre- and Postmenopausal Women

Background

Breast cancer is the most common female cancer in US and is the second leading cause of cancer related death in women. Metastases are the primary cause of cancer morbidity and mortality. Axillary lymph node (LN) status has long been used as a prognostic factor for breast cancer. The molecular mechanisms that control LN metastasis remains poorly understood. To better understand the various genes and regulatory pathways that drive breast cancer LN metastasis, we compared the gene expression profiles between breast tumors that have metastasized to the LNs and those which have not in pre- and postmenopausal women.

Material and Methods: Tumor cells were isolated from the primary tumors (ER+) of postmenopausal node positive (PMNP; N=20), postmenopausal node negative (PMNN; N=19), premenopausal node positive (PRNP; N=18) and premenopausal node negative (PRNN; N=16) women using laser capture microdissection. RNA was isolated using the RNAqueous®-micro kit (Ambion, Austin, TX). Total RNA was converted to Biotin-labelled aRNA using two rounds of amplification with MessageAmp II aRNA amplification kit (Applied Biosystems, Foster City, CA). The aRNA concentration was determined by Nanodrop 1000 and the quality was assessed with a Bioanalyzer. The aRNA was fragmented and hybridized to Human Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA). Microarray raw data were analyzed using a variety of R programming packages for probe density processing, background correction, normalization, quality control/quality assessment, and calculation of gene expression value, etc. To identify differentially expressed genes, Wilcoxon rank sum test with FDR (false discovery rate) control was performed for pair-wise comparison between different groups. Functional analyses were performed on the identified statistically significant differentially expressed genes to search for the functional categories and pathways in which they are involved and further understand their potential roles in breast cancer metastatic process.

Results: Multivariate data mining (hierarchical clustering analysis and principal component analysis, etc) revealed that in postmenopausal women, the node positive and node negative women are well separated while this was not the case in premenopausal women. Further analysis of the PMNN and PMNP groups to identify differentially expressed genes (with at least a 1.5 fold difference) at FDR =0.1 showed that 232 genes were upregulated and 470 genes were downregulated in PMNP vs PMNN groups. Gene function analysis revealed that genes down regulated in the PMNP group compared to PMNN are related to extracellular matrix, cell adhesion, EGF-like pathway, cytoskeleton etc, while the over-expressed genes are related to cell cycle and cell division, chromosome condensation, etc.

Discussion: The ability to differentiate lymph node positive cases from lymph node negative cases in ER+ breast cancer based on transcriptional profiling may have an impact on the clinical management of ER+ breast cancer cases. Having transcriptional profiles that identify ER+ tumors likely to have poor outcomes would suggest more aggressive treatment for such patients.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P3-06-06.

P3-05-02: Subtype-Specific Co-Occurrence of Atypical Hyperplasia and In Situ Carcinoma with Invasive Breast Cancers

Background

Atypical ductal hyperplasia (ADH), lobular carcinoma in situ (LCIS), and ductal carcinoma in situ (DCIS) are considered risk factors for the development of invasive breast cancer (IBC). The co-occurrence of these lesions with IBC may provide insights into cancer initiation and development. IBC subtypes have distinct clinicopathological features. A clinically practical IHC-based subtyping classification has been developed based on the expression of ER, PR, HER2, and Ki67, defining Luminal A (LA), Luminal B (LB), HER2+, and Triple Negative (TN) subtypes. The Walter Reed Army Medical Center (WRAMC), through the Clinical Breast Care Project (CBCP), has enrolled over 500 IBC subjects with single pathologist review and central lab analysis. The co-occurrence of ADH, LCIS, and DCIS will be studied in relation to IBC subtypes.

Methods: Subjects were enrolled following IRB-approved protocols. IBC patients enrolled at WRAMC were selected and their clinical and pathology data were reviewed. ER and PR positivity is defined as &gt; 5% nuclear staining. The HER2 result is negative if the IHC=0 or 1+ and positive if IHC=3+. For IHC=2+, the FISH result determines the final HER2 status. Ki67 is considered positive if nuclear staining is &gt;= 15%. For IBC subtypes, LA is ER+/HER2−/Ki67-; LB is either ER+/HER2−/Ki67+, or ER+/HER2+; HER2+ is ER-/PR-/HER2+; TN is ER-/PR-/HER2−. Statistical analysis was performed using SAS, and the Chi-Square test was used for categorical data analysis supplemented by the Fisher's Exact test where appropriate. For age analysis, ANOVA was performed with Bonferroni adjustment for multi-pair t-test.

Results: A total of 459 IBC patients were identified and categorized into LA (41.6%), LB (27.7%), HER2+ (10.2%), and TN (20.5%). Many of the previously reported subtype-specific characteristics were confirmed. Age at diagnosis varied by subtype (p=0.0034) with LA being the oldest (Mean±SD=59.9+12.5 years) and TN the youngest (54±12.6 years, p=0.0048). Ethnicity distribution of African American (AA) relative to Caucasian American patients varied significantly in subtypes with AA=18% in LA, 31% in LB, 32% in Her2+, and 42% in TN (p=0.0008). The grade, the AJCC stage and its components T and N were all significantly different among the subtypes (p ranges from &lt;0.0001 to 0.0020). The grades and stages were consistently lowest for LA, highest for HER2+ and TN. We further found that the co-occurrence of ADH, DCIS, and LCIS with IBC were subtype-specific with the following distributions: ADH—LA (25.1%), LB (18.9%), HER2+ (0%), and TN (6.4%) (p&lt;0.0001, n=78); DCIS—LA (63.4%), LB (76.4%), HER2+ (80.9%), and TN (58.5%) (p=0.0039, n=311); LCIS—LA (36.7%), LB (19.7%), HER2+ (4.3%), and TN (6.4%) (p&lt;0.0001, n=103).

Discussion: By including Ki67 in IHC-based IBC subtyping we confirmed many subtype-specific clinico-pathological characteristics in the CBCP WRAMC population. We further report subtype-specific co-occurrences of ADH, DCIS, and LCIS. These co-occurrence patterns may reveal distinct developmental mechanisms between the different subtypes of IBC.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P3-05-02.

Nonlinear properties of and nonlinear processing in hydrogenated amorphous silicon waveguides

We propose hydrogenated amorphous silicon nanowires as a platform for nonlinear optics in the telecommunication wavelength range. Extraction of the nonlinear parameter of these photonic nanowires reveals a figure of merit larger than 2. It is observed that the nonlinear optical properties of these waveguides degrade with time, but that this degradation can be reversed by annealing the samples. A four wave mixing conversion efficiency of + 12 dB is demonstrated in a 320 Gbit/s serial optical waveform data sampling experiment in a 4 mm long photonic nanowire.

Dural metastasis of atypical extraventricular neurocytoma with the codeletion of chromosomes 1p/19q

Extraventricular neurocytoma (EVN) is a rare neoplasm described in the 2007 World Health Organization classification of tumours of the nervous system. Due to the rarity of the tumour, there is limited literature available. The clinical characteristics, pathological features, biological behaviour and outcome of EVN remain unclear, and there are challenges regarding its diagnosis and management. The present case was a 75-year-old man who had been experiencing slow responses to stimuli for 1 month prior to hospital admission. A diagnosis of atypical EVN was made on the basis of pathology and immunohistochemistry results. Atypical pathological features included vascular proliferation, the presence of mitosis and a high MIB-1 (an antibody against Ki-67) labelling index. The disease recurred 7 months after the initial complete resection and radiation treatment, presenting with dural metastasis and codeletion of chromosomes 1p/19q. The present case history and treatment course are discussed with respect to the literature.

Metformin induces apoptosis of lung cancer cells through activating JNK/p38 MAPK pathway and GADD153

There are epidemiological and experimental evidences that metformin, an insulin-sensitizer agent widely used for diabetes treatment, has inhibitory effects on the growth of various human cancers. However, the underlying molecular mechanisms for its anti-neoplastic activity has not been yet clarified and the effect of metformin on human lung cancer remains unknown. In this study we revealed for the first time that metformin treatment led to increased apoptosis in human lung cancer cell lines A549 and NCI-H1299 and significantly inhibited the cells proliferation in a dose- and time-dependent manner, which was further demonstrated by the data obtained from A549 tumor xenografts in nude mice. We also found that metformin treatment can activate AMP-activated protein kinase, JNK/p38 MAPK signaling pathway and caspases, as well as upregulate the expression of growth arrest and DNA damage inducible gene 153 (GADD153). Either blockade of JNK/p38 MAPK pathway or knockdown of GADD153 gene abrogated the apoptosis-inducing effect of metformin. Taken together, our data suggest that metformin inhibits the growth of lung cancer cells and induces apoptosis through activating JNK/p38 MAPK pathway and GADD153.

Direct and reliable patterning of plasmonic nanostructures with sub-10-nm gaps

Nanoscale gaps in metal films enable strong field enhancements in plasmonic structures. However, the reliable fabrication of ultrasmall gaps (<10 nm) for real applications is still challenging. In this work, we report a method to directly and reliably fabricate sub-10-nm gaps in plasmonic structures without restrictions on pattern design. This method is based on a lift-off process using high-resolution electron-beam lithography with a negative-tone hydrogen silsesquioxane (HSQ) resist, where the resulting nanogap size is determined by the width of the patterned HSQ structure, which could be written at less than 10 nm. With this method, we fabricated densely packed gold nanostructures of varying geometries separated by ultrasmall gaps. By controlling structure sizes during lithography with nanometer precision, the plasmon resonances of the resulting patterns could be accurately tuned. Optical and surface-enhanced Raman scattering (SERS) measurements on the patterned structures show that this technique has promising applications in the fabrication of passively tunable plasmonic nanostructures with ultrasmall gaps.

Highly effective SERS substrates based on an atomic-layer-deposition-tailored nanorod array scaffold

When two metallic surfaces supporting plasmonic excitation are brought into close proximity of each other, a nanogap (of width on the subwavelength scale) will form, which boosts greatly the local optical field. Based on this idea, we fabricated two types of three-dimensional plasmonic substrates with such nanogaps, taking advantage of both atomic layer deposition (ALD) and the capillary effect. Owing to the counteraction of the gap-reducing and capillary, nanogaps with different widths and profiles have been formed on the scaffold of aligned ZnO nanorods and shown to induce large field enhancement with enhancement factor up to 2.64 × 10(6) for surface-enhanced Raman scattering (SERS).

Optical switching and detection of 640 Gbits/s optical time-division multiplexed data packets transmitted over 50 km of fiber

We demonstrate 1×4 optical-packet switching with error-free transmission of 640 Gbits/s single-wavelength optical time-division multiplexed data packets including clock distribution and short pulse generation for optical time demultiplexing based on a cavityless pulse source.

The brain-derived neurotrophic factor is associated with alcohol dependence-related depression and antidepressant response

Brain-derived neurotrophic factor (BDNF) plays an essential role in neuronal survival, proliferation, and synaptic remodeling and modulates the function of many other neurotransmitters. Additionally, it likely underlies neurodegenerative and psychiatric disorders, including alcohol dependence-related depression (AD-D). Here, we investigated the possible association between three single nucleotide polymorphisms (SNPs) of the BDNF gene (rs13306221, rs6265, rs16917204) and AD-D. Of 548 patients with alcohol dependence (AD), 166 had AD-D and 312 healthy controls. Response to 8-week sertraline treatment was also assessed. The frequency of the A allele of rs6265 (Val66Met) was significantly higher in AD-D patients than in the healthy controls (p=0.009 after Bonferroni correction). The analysis revealed a strong association between the rs6265 genotype distribution and AD-D (p=0.005 after Bonferroni correction), and the A allele of rs6265 was significantly overrepresented in AD-D patients compared to AD without depression (AD-nD) patients (p=0.001 after Bonferroni correction). Additionally, carriers of the A allele of rs6265 responded better to sertraline treatment (p=0.001). Our results suggested a novel association between BDNF rs6265 and AD-D. These findings might lead to earlier detection of AD-D, perhaps providing better tools for clinical care of these patients in the future.

Evolution of CDC42, a putative virulence factor triggering meristematic growth in black yeasts

The cell division cycle gene (CDC42) controlling cellular polarization was studied in members of Chaetothyriales. Based on ribosomal genes, ancestral members of the order exhibit meristematic growth in view of their colonization of inert surfaces such as rock, whereas in derived members of the order the gene is a putative virulence factor involved in expression of the muriform cell, the invasive phase in human chromoblastomycosis. Specific primers were developed to amplify a portion of the gene of 32 members of the order with known position according to ribosomal phylogeny. Phylogeny of CDC42 proved to be very different. In all members of Chaetohyriales the protein sequence is highly conserved. In most species, distributed all over the phylogenetic tree, introns and 3^rd codon positions are also invariant. However, a number of species had paralogues with considerable deviation in non-coding exon positions, and synchronous variation in introns, although non-synonomous variation had remained very limited. In some strains both orthologues and paralogues were present. It is concluded that CDC42 does not show any orthologous evolution, and that its paralogues haves the same function but are structurally relaxed. The variation or absence thereof could not be linked to ecological changes, from rock-inhabiting to pathogenic life style. It is concluded that eventual pathogenicity in Chaetothyriales is not expressed at the DNA level in CDC42 evolution.