Visual Interaction with Dimensionality Reduction: A Structured Literature Analysis

Dimensionality Reduction (DR) is a core building block in visualizing multidimensional data. For DR techniques to be useful in exploratory data analysis, they need to be adapted to human needs and domain-specific problems, ideally, interactively, and on-the-fly. Many visual analytics systems have already demonstrated the benefits of tightly integrating DR with interactive visualizations. Nevertheless, a general, structured understanding of this integration is missing. To address this, we systematically studied the visual analytics and visualization literature to investigate how analysts interact with automatic DR techniques. The results reveal seven common interaction scenarios that are amenable to interactive control such as specifying algorithmic constraints, selecting relevant features, or choosing among several DR algorithms. We investigate specific implementations of visual analysis systems integrating DR, and analyze ways that other machine learning methods have been combined with DR. Summarizing the results in a "human in the loop" process model provides a general lens for the evaluation of visual interactive DR systems. We apply the proposed model to study and classify several systems previously described in the literature, and to derive future research opportunities.

Sub-ppm electrical detection of hydrogen sulfide gas at room temperature based on printed copper acetate–gold nanoparticle composite films

This paper presents the sub-ppm level electrical detection of H₂S gas at room temperature using printed copper acetate–gold nanoparticle composite films either on (A) silver or (B) gold/AuNP electrodes.

Synthesis and in vitro phantom NMR and MRI studies of fully organic free radicals, TEEPO-glucose and TEMPO-glucose, potential contrast agents for MRI

Two organic radical contrast agents, TEMPO-Glc and TEEPO-Glc, were synthesized and their stabilities and contrast enhancing properties were tested with in vitro NMR and MRI experiments.

Toward computational cumulative biology by combining models of biological datasets

A main challenge of data-driven sciences is how to make maximal use of the progressively expanding databases of experimental datasets in order to keep research cumulative. We introduce the idea of a modeling-based dataset retrieval engine designed for relating a researcher's experimental dataset to earlier work in the field. The search is (i) data-driven to enable new findings, going beyond the state of the art of keyword searches in annotations, (ii) modeling-driven, to include both biological knowledge and insights learned from data, and (iii) scalable, as it is accomplished without building one unified grand model of all data. Assuming each dataset has been modeled beforehand, by the researchers or automatically by database managers, we apply a rapidly computable and optimizable combination model to decompose a new dataset into contributions from earlier relevant models. By using the data-driven decomposition, we identify a network of interrelated datasets from a large annotated human gene expression atlas. While tissue type and disease were major driving forces for determining relevant datasets, the found relationships were richer, and the model-based search was more accurate than the keyword search; moreover, it recovered biologically meaningful relationships that are not straightforwardly visible from annotations—for instance, between cells in different developmental stages such as thymocytes and T-cells. Data-driven links and citations matched to a large extent; the data-driven links even uncovered corrections to the publication data, as two of the most linked datasets were not highly cited and turned out to have wrong publication entries in the database.

PKCalpha/beta I inhibitor Go6976 induces dephosphorylation of constitutively hyperphosphorylated Rb and G1 arrest in T24 cells

BACKGROUND

Rb functions as a key controller of the G(1)-S transition of the cell cycle, and its inactivation leads to a defective G(1) checkpoint. Bladder cancer frequently displays alterations in Rb such as constitutive hyperphosphorylation which results in inactive Rb and progression of cells to the S-phase. Several protein kinase C (PKC) inhibitors are currently undergoing clinical trials as anticancer drugs.

MATERIALS AND METHODS

T24 urinary bladder carcinoma cells, known to express hyperphosphorylated Rb, were treated with PKCα/βI inhibitor Go6976. The treated cells were subjected to cell cycle analysis, cell growth assay and Western blots for Rb and cdc2 phosphorylation.

RESULTS

The treatment resulted in Rb dephosphorylation at Ser 795 and Ser 807/811, and cdc2 dephosphorylation at Tyr15. Subsequent G(0/1) arrest and reduced proliferation rates were observed.

CONCLUSION

The results show that Go6976 can be used to restore constantly hyperphosphorylated and therefore constantly inactive Rb function in cancer cells.

The function of the hand after operations for obstetric injuries to the brachial plexus

Hand function was evaluated in 105 patients who had been operated on in early infancy for brachial plexus birth palsy. The mean follow-up after surgery was for 13.4 years (5.0 to 31.5). Fine sensation, stereognosis, grip and pinch strength and the Raimondi scale were recorded.

Fine sensation was normal in 34 of 49 patients (69%) with C5–6 injury, 15 of 31 (48%) with C5–7 and in 8 of 25 (32%) with total injury. Loss of protective sensation or absent sensation was noted in some palmar areas of the hand in 12 of 105 patients (11%). Normal stereognosis was recorded in 88 of the 105 patients (84%), whereas only 9 of the 105 (9%) had normal grip strength. The mean Raimondi scale scores were 4.57 (3 to 5) (C5–6), 4.26 (1 to 5) (C5–7) and 2.16 (0 to 5) in patients with total injury.

The location of impaired sensation was related to the distribution of the root injury. Avulsion type of injury correlated with poor recovery of hand function.

Tight junction components occludin, ZO-1, and claudin-1, -4 and -5 in active and healing psoriasis

BACKGROUND

Cells of the granular layer are interconnected by tight junctions (TJs) in normal epidermis. The structural proteins of epidermal TJs include occludin, ZO-1, and claudin-1 and -4.

OBJECTIVES

Our aim was to correlate the expression of TJ components with keratinocyte differentiation using psoriasis as a model of premature keratinization.

METHODS

The distribution of TJ proteins was evaluated in the skin of nine patients with psoriasis. Punch biopsies were taken from perilesional skin, from active psoriasis plaques, and from healed, previously lesional locations. The punch biopsies were analysed using indirect immunolabelling for ZO-1, occludin and claudin-1, -4 and -5. In addition, epidermal samples were analysed by reverse transcription-polymerase chain reaction for claudin-1, -4 and -5 mRNAs.

RESULTS

Claudin-5 was localized to the granular cell layers of normal control skin as well as perilesional and lesional psoriatic epidermis. This was unexpected, as previous studies have not detected claudin-5 in the epidermis. Occludin and ZO-1 were expressed in the granular cell layer in psoriatic perilesional epidermis. In the psoriasis plaques, ZO-1 and occludin were detected in a wider zone extending from the granular layer to the middle spinous cell layers. In healed psoriasis plaques, the expression of occludin and ZO-1 resumed a normal-looking profile, being restricted to the upper epidermis only. Claudin-1 and -4 did not show marked changes in psoriasis compared with normal skin.

CONCLUSIONS

The results demonstrate claudin-5 in normal epidermis and psoriatic skin, and abnormal distribution of occludin and ZO-1 in psoriasis plaques. Clinical healing of aberrant keratinization is associated with restoration of the normal distribution of occludin, ZO-1 and also involucrin.

Methods for estimating human endogenous retrovirus activities from EST databases

Background

Human endogenous retroviruses (HERVs) are surviving traces of ancient retrovirus infections and now reside within the human DNA. Recently HERV expression has been detected in both normal tissues and diseased patients. However, the activities (expression levels) of individual HERV sequences are mostly unknown.

Results

We introduce a generative mixture model, based on Hidden Markov Models, for estimating the activities of the individual HERV sequences from EST (expressed sequence tag) databases. We use the model to estimate the relative activities of 181 HERVs. We also empirically justify a faster heuristic method for HERV activity estimation and use it to estimate the activities of 2450 HERVs. The majority of the HERV activities were previously unknown.

Conclusion

(i) Our methods estimate activity accurately based on experiments on simulated data. (ii) Our estimate on real data shows that 7% of the HERVs are active. The active ones are spread unevenly into HERV groups and relatively uniformly in terms of estimated age. HERVs with the retroviral env gene are more often active than HERVs without env. Few of the active HERVs have open reading frames for retroviral proteins.

Is there a role for PCR-SSCP among the methods for missense mutation detection of TP53 gene?

Mutation analysis methods have increased in variety during the past years. High-throughput microarray methods have especially increased in popularity. However, new methods require reference points, and not all of the methods are equal in sensitivity and specificity. Furthermore, the detection of unknown missense mutations, such as unknown TP53 mutations in human tumors, for clinical purposes requires great accuracy, which may be difficult to acquire with the current high-throughput methods. For these reasons, the classical methods, such as PCR-manual sequencing and PCR-SSCP, are still valuable and necessary.

p38α and p38δ mitogen-activated protein kinase isoforms regulate invasion and growth of head and neck squamous carcinoma cells

Recent studies indicate that the specificity of p38 mitogen-activated protein kinase (MAPK)-mediated cellular stress responses is determined by the expression pattern of the distinct p38 isoforms. Here, we have analysed the function of distinct p38 isoforms in the growth and invasion of head and neck squamous cell carcinomas (HNSCCs). Activation of p38 MAPK by arsenite resulted in inactivation of the ERK1,2 signaling pathway by dephosphorylation of MEK1,2 in primary human epidermal keratinocytes (HEKs), whereas in HNSCC cells this p38-mediated inhibition of the ERK1,2 pathway was absent. Quantitation of p38 pathway component mRNA expression in HNSCC cell lines (n=42) compared to HEKs (n=8) revealed that p38alpha and p38delta isoforms are predominantly expressed in both cell types and that MKK3 is the primary upstream activator expressed. Inhibition of endogenous p38alpha or p38delta activity by adenoviral delivery of corresponding dominant-negative p38 isoforms potently reduced MMP-13 and MMP-1 expressions, and suppressed the invasion of HNSCC cells through collagen. Dominant-negative p38alpha and p38delta inhibited squamous cell carcinoma (SCC) cell proliferation and inhibition of p38alpha activity also compromised survival of SCC cells. p38alpha and p38delta were predominantly expressed in HNSCCs (n=24) and nonneoplastic epithelium in vivo (n=6), with MKK3 being the primary upstream activator. Activation and expression of p38alpha and p38delta by tumor cells was detected in HNSCCs in vivo (n=16). Adenoviral expression of dominant-negative p38alpha or p38delta in cutaneous SCC cells potently inhibited their implantation in skin of severe combined immunodeficiency mice and growth of xenografts in vivo. Our results indicate that p38alpha and p38delta specifically promote the malignant phenotype of SCC cells by regulating cell survival, proliferation and invasion, suggesting these p38 MAPK isoforms as potential therapeutic targets in HNSCCs.

Activation of Smad signaling enhances collagenase-3 (MMP-13) expression and invasion of head and neck squamous carcinoma cells

Squamous cell carcinoma (SCC) cells of the head and neck specifically express collagenase-3 (matrix metalloproteinase-13 (MMP-13)), the expression of which correlates with their invasion capacity. Transforming growth factor-beta (TGF-beta) enhances MMP-13 and collagenase-1 (MMP-1) expression and invasion of SCC cells via p38 mitogen-activated protein kinase. Here, we have examined the role of Smad signaling in regulating MMP-13 expression and in invasion of head and neck SCC cells. Treatment with TGF-beta resulted in activation of Smad2 and Smad3 in SCC cells, but had no effect on their proliferation or viability. Basal activation of Smad3 and p38 was noted in SCC cells without exogenous TGF-beta stimulation, and adenoviral delivery of Smad7 and dominant-negative Smad3 inhibited p38 activation in these cells. Adenoviral overexpression of Smad3 augmented the upregulatory effect of TGF-beta on MMP-13 expression by SCC cells. Disruption of Smad signaling by adenoviral expression of kinase-defective TGF-beta type I receptor (activin-receptor-like kinase-5), Smad7, and dominant-negative Smad3 potently suppressed the basal and TGF-beta-induced expression of MMP-13 and MMP-1 in SCC cells, and inhibited their basal and TGF-beta-induced invasion through Matrigel and type I collagen. Adenoviral overexpression of Smad7 in cutaneous and oral SCC cells significantly inhibited their implantation in skin of SCID mice and growth of xenografts in vivo, as compared to LacZ adenovirus-transduced control cells. Together, these results show that Smad signaling plays an important role in promoting the invasive phenotype of human head and neck SCC cells by upregulating their collagenase expression.

Scoliosis after solid organ transplantation in children and adolescents

The occurrence of scoliosis in children after solid organ transplantation is not known. A total of 196 children, which is 93% of patients surviving kidney, liver and heart transplantation in our country, participated in a cross-sectional survey. All children were screened for rib hump, and those with clinically significant hump (over 6 degrees ) underwent radiographs of the spine. The occurrence of scoliosis was compared to data obtained from a previously published comparison group. Forty-three (21.9%) of the patients had scoliosis greater than 10 degrees , and 21 (10.7%) of them had curves greater than 20 degrees . The RR (95% CI) for scoliosis needing treatment (over 20 degrees ) was 17.0 (6.75-42.7) in the patients as compared with control population. The occurrence of scoliosis was 17.9% of the kidney, 13.6% of the liver and 51.7% of the heart transplant patients (p < 0.001). In a logistic regression model, heart transplantation (OR (95% CI) 7.27 (2.62-20.2)) and growth hormone treatment (3.98 (1.77-8.94)) were most significant risk factors for scoliosis. The risk of scoliosis is increased in patients with solid organ transplantation. Pediatricians treating these patients should be aware of this increased risk to diagnose early curves and to refer these patients to an orthopedic surgeon.