A two-step drug repositioning method based on a protein-protein interaction network of genes shared by two diseases and the similarity of drugs

The present study proposed a two-step drug repositioning method based on a protein-protein interaction (PPI) network of two diseases and the similarity of the drugs prescribed for one of the two. In the proposed method, first, lists of disease related genes were obtained from a meta-database called Genotator. Then genes shared by a pair of diseases were sought. At the first step of the method, if a drug having its target(s) in the PPI network, the drug was deemed a repositioning candidate. Because targets of many drugs are still unknown, the similarities between the prescribed drugs for a specific disease were used to infer repositioning candidates at the second step. As a first attempt, we applied the proposed method to four different types of diseases: hypertension, diabetes mellitus, Crohn disease, and autism. Some repositioning candidates were found both at the first and second steps.

Systemes analysis of interactions between microRNAs and genes in hepatocellular carcinoma

MicroRNAs (miRNAs) are short noncoding RNAs and can regulate gene expression at the transcriptional and/or translational levels. There is mounting evidence that miRNAs play an important role in the control of the dynamics of localized gene expression. Expression profiling of miRNA in various cancers revealed that miRNA profiles could discriminate malignancies from their counter parts. In this study, to investigate the localized effect of miRNA in cancer, we analyzed gene and miRNA expressions in hepatocellular carcinoma (HCC) and surrounding nontumor tissues. Based on gene expression levels around miRNAs, we investigated how many miRNAs correlated positively/negatively in expression with genes in the vicinity. Next, the Pearson correlation coefficients were compared between the HCC and nontumor tissues. The results imply that the relationship between the intronic miRNAs and their host genes was altered in HCC, and that feedback loops including the host gene, intronic miRNA, target genes might be formed in HCC.

Loss of NKX3-1 as a potential marker for an increased risk of occult lymph node metastasis and poor prognosis in oral squamous cell carcinoma

The prognosis of oral squamous cell carcinoma (OSCC) is significantly dependent on the existence of cervical lymph node metastasis (LNM), with the overall survival rate being much lower in patients with LNM. Primary causes and molecular mechanisms of LNM are still largely unclear. We hypothesized that factors related with cancer progress and/or prognosis in OSCC are revealed by genome-wide investigation of DNA copy number aberrations (CNAs). In order to find biomarkers for occult LNM of OSCC, we comprehensively investigated genomic DNAs from 60 OSCC patients using Affymetrix mapping arrays and statistically analyzed correlations between CNAs of genes and the presence of occult LNM in the patients. The genome-wide CNA study indicated significant correlations between the presence of occult LNM and CNAs of certain genes. Through a literature survey, we narrowed down the candidates and focused on loss of NKX3-1, which is a homeodomain-containing transcription factor. NKX3-1 is known as a tumor suppressor gene in prostate cancer but has never been reported in OSCC. Quantitative RT-PCR and immunohistochemistry (IHC) analyses also showed significantly lower expression of NKX3-1 in the cases with occult LNM, which was further validated by IHC analysis in independent cases. The survival analyses indicated that NKX3-1 loss is a significant risk factor to decrease the disease-free survival (DFS) and the overall survival (OS) rates. This is the first time that the significant association of NKX3-1 loss and occult LNM was indicated in OSCC. The present results suggest that loss of NKX3-1 may be a potential biomarker for occult LNM of OSCC.

Genome-wide integrative analysis revealed a correlation between lengths of copy number segments and corresponding gene expression profile

Microarray analysis has been applied to comprehensively reveal the abnormalities of DNA copy number (CN) and gene expression in human cancer research during the last decade. These analyses have individually contributed to identify the genes associated with carcinogenesis, progression, metastasis of tumor cells and poor prognosis of cancer patients. However, it is known that the correlation between profiles of CN and gene expression does not highly correlate. Factors which determine the degree of correlation remain largely unexplained. To investigate one such factor, we performed trend analyses between the lengths of CN segments and corresponding gene expression profiles from microarray data in hepatocellular carcinoma (HCC) and colorectal carcinoma (CRC). Significant correlations were observed in CN gain of HCC and CRC (p<0.05). The trend of the CN loss showed a significant correlation in HCC although there was no correlation between the length of CN loss segments and gene expression in CRC. Our findings suggest that the influence of CN on gene expression highly depends on the length of CN region, especially in the case of CN gain. To the best of our knowledge, this is the first study describing the correlation between lengths of CNA segments and expression profiles of corresponding genes.

Time course of the recovery of three-dimensional eye position in patients with acute cerebellitis

Listing's plane is a construction derived from eye position and reflects gravitational orientation. The cerebellum plays a key role in orienting and integrating sensory input concerning gravity from visual, vestibular and proprioceptive apparatuses. This suggests that the thickness of Listing's plane could serve as a novel parameter for evaluating the accuracy of the constructed gravity-oriented internal model. We report a case with acute cerebellitis along with data on Listing's plane, calculated from consecutive infrared video-oculogram recordings. We found thickening of Listing's plane at the early stage of the disease, and a gradual reduction of the thickness into normal range in parallel with the recovery of the patient's posture and gate. Notably, clinical improvement of the patient's posture was delayed relative to the normalization of the thickness of Listing's plane. The thickness of Listing's plane reflects the stability of the cerebellar-mediated cognitive gravitational reference frame. This thickness value could serve as a parameter to quantitatively evaluate the function of the constructed internal model. Recovery from cerebellar ataxia (manifested as normalization of the thickness of Listing's plane) was followed by recovery of muscular strength lost during the period the patient was by his disease forced to assume a lying position.

Adaptive thresholds to detect differentially expressed genes in microarray data

To detect changes in gene expression data from microarrays, a fixed threshold for fold difference is used widely. However, it is not always guaranteed that a threshold value which is appropriate for highly expressed genes is suitable for lowly expressed genes. In this study, aiming at detecting truly differentially expressed genes from a wide expression range, we proposed an adaptive threshold method (AT). The adaptive thresholds, which have different values for different expression levels, are calculated based on two measurements under the same condition. The sensitivity, specificity and false discovery rate (FDR) of AT were investigated by simulations. The sensitivity and specificity under various noise conditions were greater than 89.7% and 99.32%, respectively. The FDR was smaller than 0.27. These results demonstrated the reliability of the method.

Postural stability during visual stimulation and the contribution from the vestibular apparatus

CONCLUSION

When combined with vestibular dysfunction, visual flow can exacerbate reductions in postural stability. This effect may be one of the mechanisms underlying visual vertigo, which can be evaluated using frequency analysis of body sway elicited by optokinetic stimulation (OKS).

OBJECTIVE

To clarify the interaction between the postural responses to visual flow and to input from the vestibular apparatus as a mediator of visual vertigo.

METHODS

Horizontal and vertical OKS with a stable fixation target were presented to 14 healthy subjects and 38 peripheral vestibular patients standing in a Romberg's posture, and the center of standing pressure was monitored using a force platform. The direction and amplitude of induced body sway were analyzed, along with the power spectra of the body mass fluctuations.

RESULTS

Each directional optokinetic stimulus induced body sway that would compensate for the virtual inclination of the subject's gravitational reference frame. However, the amplitude of this body sway was not increased by vestibular dysfunction. Healthy subjects showed increased stability in response to downward OKS and decreased stability in response to upward OKS, whereas no specific changes were seen in response to horizontal OKS. This stability was greatly diminished in patients with vestibular dysfunction subjected to the same directional OKS.

Adaptive threshold for detecting differentially expressed genes in microarray data - a simulation study to investigate its performance

To detect changes in gene expression data from DNA microarrays, a fixed threshold value is used in various studies. However, it is not always guaranteed that a threshold value which is appropriate for highly expressed genes is suitable for genes with low expression. To address this issue, we have proposed adaptive threshold, which has different values for different expression levels. In this study, the performance of the adaptive threshold method was investigated through simulations. The sensitivity in various noise conditions was in a range between 72.7 and 100% while the specificity was better than 99% for all noise conditions. These results demonstrated the good performance of the proposed method.

Influence of work rate on dynamics of O2 uptake under hypoxic conditions in humans

AIM

It was the purpose of the investigation to determine whether an altered work rate could influence the oxygen uptake (V.O(2)) and heart rate (HR) dynamics at hypoxia and normoxia.

METHODS

Ten males performed a cycle exercise with 2 repetitions of 6 min each at a constant work load while breathing one of two inspiratory O(2) fractions (FIO(2)): 0.12 (moderate hypoxia) and 0.21 (normoxia). Each test began with unloaded pedaling. This was followed by three constant loads, which were 40%, 60%, and 80% of the subject's gas exchange threshold (GET) in hypoxia (F(I)O(2) = 0.12), with the 80% GET load repeated under normoxia (room air). V.O(2) was measured on a breath-by-breath basis and beat-by-beat HR via ECG, and the half time (t1/2) of each parameter was established, following interpolation data.

RESULTS

There were no remarkable differences in t1/2 V.O(2) dynamics among the 40%, 60% and 80% GET; however, the differences became significant at hypoxia compared with normoxia. The HR dynamics were significantly faster in normoxia compared with hypoxia, independent of work rates. During steady-state exercise, the alterations in HR and cardiac output (Q) using the acetylene rebreathing method depended on increases in the work rate, and a significantly increase in at 80% GET was observed when compared with normoxia. Increases of stroke volume (SV) were unaffected by altered work rates and inspired O(2) concentrations. The arteriovenous oxygen difference (Ca-vO(2)) at a steady-state of exercise increased proportionally with the work rate under hypoxia, and a much greater Ca-vO(2) was observed during normoxic exercise than under hypoxia.

CONCLUSION

These results seem to suggest that in humans, O(2) uptake dynamics are affected by lower O(2), not by changing work rates at hypoxia, to which the interaction between lower O(2) utilization in exercising muscles and hypoxic-induced greater blood flow can be attributed.

Clock gene dysfunction in patients with obstructive sleep apnoea syndrome

Clock genes regulate mammalian circadian rhythms, and dysfunction of clock genes can contribute to various disorders. To investigate whether obstructive sleep apnoea syndrome (OSAS) influences clock gene function, the present authors examined Period1 (Per1) mRNA expression in vitro and in vivo. In eight healthy subjects and eight OSAS patients, plasma noradrenaline, serum interleukin (IL)-6, high-sensitivity C-reactive protein (hsCRP) and Per1 mRNA expression in peripheral whole blood were measured. Expression of Per1 mRNA in cultured cells was examined under IL-6 or noradrenaline stimulation in vitro. After noradrenaline was administered to mice in vivo, Per1 mRNA expression in the brain was examined. The concentrations of serum IL-6, hsCRP and plasma noradrenaline were elevated in OSAS patients, but improved by continuous positive airway pressure (CPAP) therapy. Per1 mRNA expression in the peripheral blood significantly decreased at 02:00 h by CPAP in OSAS patients. Stimulation with IL-6 did not directly induce Per1 mRNA in vitro. Administration of noradrenaline induced Per1 mRNA in the cerebral cortex of mice in vivo. The current study revealed that obstructive sleep apnoea syndrome caused clock gene dysfunction, and continuous positive airway pressure helped to improve it. Sympathetic activation and elevation of the plasma noradrenaline concentration in obstructive sleep apnoea syndrome may be one of the factors involved in disorders of Period1 mRNA expression.

Adaptive threshold to detect biologically meaningful changes in microarray data

To detect changes in gene expression data from DNA microarrays, a fixed threshold value is widely used. However, it is not always guaranteed that a threshold value which is appropriate for highly expressed genes is suitable for genes with low expression. In this study, aiming at detecting biologically meaningful changes from a wide range of expression levels, we proposed an adaptive threshold method. The performance of the proposed method was investigated using publicly available expression data.

Stability of the human upright stance depending on the frequency of external disturbances

During an upright stance of humans, it is usually assumed that a stiffer ankle joint contributes to stabilize the stance. To show that under certain conditions a stiffer ankle joint can reduce the stability, the frequency responses of the moment and the angle of the ankle joint against external disturbances caused by random horizontal translations of the support surface were evaluated in ten healthy adult subjects by varying the difficulty of the task at four levels. When it was difficult to keep the upright stance, the subject tended to make the ankle joint stiffer. The transfer function relating the external disturbance moment to the ankle joint moment showed a larger gain in the high frequency range (>0.3 Hz) compared with the gains obtained under easier conditions. A simulation analysis based on a simple inverted pendulum model also reproduced this tendency. These results indicate that the stiffer ankle joint and the resulting higher ankle moment for high frequency external disturbances enhance the possibility that the center of pressure exceeds the limit arising from the size of the feet and can make the upright stance unstable.

Range of motion measurement of an artificial hip joint using CT images

Total hip arthroplasty (THA) is one of the most effective treatments for osteoarthritis and rheumatoid arthritis. Dislocation of the femoral head from the acetabular socket is a major problem of THA. To prevent dislocation, it is important to know the range of motion (ROM) after THA. Although various studies on the ROM were carried out, there exist only a few reports on ROM evaluation in individual patients. This is because in clinical cases, bone-to-bone and bone-to-component contacts must be considered besides the impingement of components. In this study, a new method for evaluating ROM of internal/external rotation, which takes into account all combinations of contacts between the bones and components, was proposed. A computer simulation demonstrated that the RMS error of the proposed method was approximately 3 degrees . The method was applied to 33 THAs under various conditions of flexion and adduction angles. The method was able to detect any type of impingement. The evaluated ROM was in good agreement with that measured during the THA operation (correlation coefficient = 0.91).

Sensory stimulation triggers spindles during sleep stage 2

STUDY OBJECTIVES

Toward understanding the function of sleep spindle, we examined whether sensory stimulation triggers sleep spindles.

PARTICIPANTS

Eleven normal subjects participated in the experiments.

INTERVENTION

The subjects had a nap in the afternoon, and sensory stimulation was applied during sleep stage 2.

MEASUREMENTS

21-channel EEG was recorded during the 2-3 hour experiment carried out between 13:00 and 16:00. Somatosensory, auditory, or visual stimulation was performed over a 5-minute period during stage 2. The frequency and duration of spindles were compared in 2 different segments of 5 minutes, with and without sensory stimulation. The latency from the onset of a sensory stimulus to the succeeding spindle was also analyzed. To estimate the active brain regions during a spindle, the EEG recordings were modeled with a single equivalent moving dipole (SEMD) model.

RESULTS

In the period with stimulation, spindle frequency and duration increased compared with the period without stimulation. Statistical tests revealed that with stimulation, the interval between 2 consecutive spindles was significantly shorter (p < 0.05, regardless of the modality) and that the duration of the spindles was significantly longer with stimulation (p < 0.05, regardless of the modality). The latency was approximately 2 s. During a spindle after somatosensory stimulation brain activities were observed near the somatosensory area, while with auditory stimulation active regions were observed near the auditory cortex.

CONCLUSIONS

A sensory stimulus appeared to trigger a sleep spindle during sleep stage 2. SEMD trajectories suggest that active brain regions during spindle are different according to the modality of the preceding stimulus.

Evidence of spatially bound gene regulation in Mus musculus: decreased gene expression proximal to microRNA genomic location

The extent, spatially and in time, of the phenomenon of localized decreased expression in the chromosomal vicinity of microRNA (miRNA) previously described in Caenorhabditis elegans is reproduced in Mus musculus across a wide range of tissues in several independent experiments. Computationally predicted miRNA targets are enriched in the vicinity of miRNAs, and transcription factors are identified as the class of genes that systematically exhibit this localized decrease. Also, those mRNA with AT-rich UTRs, particularly those that are not in the vicinity of CpG islands, most often exhibit this localized decrease. This localization broadens with the shift from developing to mature/differentiated tissues and suggests a developmentally controlled and spatially bound regulation.

Cross-coupling in a body-translating reaction: interaural optokinetic stimulation reflects a gravitational cue

CONCLUSION

The velocity storage integrator does not play a dominant role in the postural response to vertical visual cues; more likely, retinal slip provides the main driving force. By contrast, sideways eye movement can drive the velocity storage integrator and preserve a gravitational cue, which would be observed as a cross-coupling effect on the postural response.

OBJECTIVES

To investigate the mechanism by which optokinetic stimulation causes the body to translate and to determine whether the optokinetic information is accompanied by a gravitational cue, which would appear as a cross-coupling effect.

MATERIALS AND METHODS

Directionally diverse optokinetic stimuli were presented to seven healthy subjects, with and without a fixation target, and the body-translation of the subjects was recorded.

RESULTS

Horizontal optokinetic stimulation with a fixation target caused the body to translate in the same direction as the optic flow. Upward or downward vertical optokinetic stimulation caused the body to translate backward or forward, respectively, only when a fixation target was present. When the subject's interaural axis was parallel to the optokinetic flow, diagonal optokinetic stimulation in the absence of a fixation target elicited responses in the pitch plane similar to those elicited by vertical stimulation in the presence of a fixation target.

Applicability of the Single Equivalent Moving Dipole Model in an Infinite Homogeneous Medium to Identify Cardiac Electrical Sources: A Computer Simulation Study in a Realistic Anatomic Geometry Torso Model

We have previously proposed an inverse algorithm for fitting potentials due to an arbitrary bio-electrical source to a single equivalent moving dipole (SEMD) model. The algorithm achieves fast identification of the SEMD parameters by employing a SEMD model embedded in an infinite homogeneous volume conductor. However, this may lead to systematic error in the identification of the SEMD parameters. In this paper, we investigate the accuracy of the algorithm in a realistic anatomic geometry torso model (forward problem). Specifically, we investigate the effect of measurement noise, dipole position and electrode configuration in the accuracy of the algorithm. The boundary element method was used to calculate the forward potential distribution at multiple electrode positions on the body surface due to a point dipole in the heart. We have found that the position and not the number of electrodes as well as the site of the origin of the arrhythmia in the heart have a significant effect on the accuracy of the inverse algorithm, while the measurement noise does not. Finally, we have shown that the inverse algorithm preserves the topology of the source distribution in the heart, thus potentially allowing the cardiac electrophysiologist to efficiently and accurately guide the tip of the catheter to the ablation site.

Lower expression of genes near microRNA in C. elegans germline

Background

MicroRNAs (miRNAs) are recently discovered short non-protein-coding RNA molecules. miRNAs are increasingly implicated in tissue-specific transcriptional control and particularly in development. Because there is mounting evidence for the localized component of transcriptional control, we investigated if there is a distance-dependent effect of miRNA.

Results

We analyzed gene expression levels around the 84 of 113 know miRNAs for which there are nearby gene that were measured in the data in two independent C. elegans expression data sets. The expression levels are lower for genes in the vicinity of 59 of 84 (71%) miRNAs as compared to genes far from such miRNAs. Analysis of the genes with lower expression in proximity to the miRNAs reveals increased frequency matching of the 7 nucleotide "seed"s of these miRNAs.

Conclusion

We found decreased messenger RNA (mRNA) abundance, localized within a 10 kb of chromosomal distance of some miRNAs, in C. elegans germline. The increased frequency of seed matching near miRNA can explain, in part, the localized effects.

Time course analysis of angular control of the body and head while rising from a chair

OBJECTIVE

To use time course information to improve understanding of the vestibular contribution to postural control as one rises from a chair.

MATERIAL AND METHODS

A total of 24 healthy controls and 42 patients with varying degrees of vestibular dysfunction were studied. The time course of the angular motion of the body and head when rising from a chair with eyes open and closed was evaluated. The delay between the onset of the motions of the body and head was compared between subject groups. We also investigated transition points from forward lean of the body to backward reversion and from backward tilt of the head to forward reversion.

RESULTS

With regard to the onset of chair rise, we found a significant difference in the delay between head and body motion between healthy controls and subjects with bilaterally impaired vestibular deficiency only when the eyes were closed. The time between the transition points of the head and body was stable between these groups.

CONCLUSION

The mechanisms controlling the onset of head and body movements differ between normal subjects and those with bilateral vestibular deficits. In the latter, the loss of a reference of gravity causes a decrease in feed-forward postural control, which is compensated for by a somato-sensory feedback mechanism. Visual input seems to provide an alternative reference of gravity.

A short daytime test using correlation dimension for respiratory movement in OSAHS

In order to examine the pathology in patients with obstructive sleep apnoea/hypopnoea syndrome (OSAHS), the nonlinear properties of respiratory movement and breath-to-breath variations during resting wakefulness with eyes closed was investigated. Recording of the respiratory movement using inductive plethysmography was performed on 14 patients with OSAHS and 13 control subjects for 2 h in the supine position during daytime. To calculate the correlation dimension (D2) for respiratory movement, an algorithm proposed by Grassberger and Procaccia was applied. The indices of breath-to-breath variations were estimated. To calculate D2 and breath-to-breath variations, two different segments were selected (200 s each). The value of D2 for respiratory movement in patients with OSAHS was significantly greater than that in control subjects. In the case of > or = 2.0 of D2 for respiratory movement, the sensitivity and specificity of detecting the presence of OSAHS was 85.7% and 76.9%, respectively. On the basis of breath-to-breath variations, only the coefficient of variation of expiratory time for respiratory movement in patients with OSAHS was significantly greater than that in the control subjects. In conclusion, the measurements of correlation dimensions for respiratory movement with a brief period during wakefulness may be a useful index for identifying patients with obstructive sleep apnoea/hypopnoea syndrome.

Inter-species differences of co-expression of neighboring genes in eukaryotic genomes

BACKGROUND

There is increasing evidence that gene order within the eukaryotic genome is not random. In yeast and worm, adjacent or neighboring genes tend to be co-expressed. Clustering of co-expressed genes has been found in humans, worm and fruit flies. However, in mice and rats, an effect of chromosomal distance (CD) on co-expression has not been investigated yet. Also, no cross-species comparison has been made so far. We analyzed the effect of CD as well as normalized distance (ND) using expression data in six eukaryotic species: yeast, fruit fly, worm, rat, mouse and human.

RESULTS

We analyzed 24 sets of expression data from the six species. Highly co-expressed pairs were sorted into bins of equal sized intervals of CD, and a co-expression rate (CoER) in each bin was calculated. In all datasets, a higher CoER was obtained in a short CD range than a long distance range. These results show that across all studied species, there was a consistent effect of CD on co-expression. However, the results using the ND show more diversity. Intra- and inter-species comparisons of CoER reveal that there are significant differences in the co-expression rates of neighboring genes among the species. A pair-wise BLAST analysis finds 8-30 % of the highly co-expressed pairs are duplicated genes.

CONCLUSION

We confirmed that in the six eukaryotic species, there was a consistent tendency that neighboring genes are likely to be co-expressed. Results of pair-wised BLAST indicate a significant effect of non-duplicated pairs on co-expression. A comparison of CD and ND suggests the dominant effect of CD.

Contribution of the vestibular apparatus to postural control when rising from a chair

OBJECTIVE

The everyday act of rising from a chair is known to require the combined angular control of a number of the body's joints, especially those within the pitch plane. Precisely how this control is exerted, however, remains controversial. The aim of this study was to obtain a better understanding of the contribution made by the vestibular apparatus to postural control of the body and head when an individual rises from a chair.

MATERIAL AND METHODS

A total of 24 healthy controls and 38 patients with varying degrees of vestibular dysfunction were examined. Electromagnetic motion sensors were used to analyze the angular control of the head and body as subjects rose from a chair with their eyes open or closed.

RESULTS

We found that unilateral vestibular dysfunction caused fixation of the head with respect to the body, resulting in a loss of spatial stability of the head which was not compensated for by visual input. Visual input did appear to compensate for bilateral vestibular loss, enabling patients with bilateral vestibular apparatus impairment or central disorders to fix the position of their head in space.

CONCLUSION

The act of rising from a chair is normally controlled by vestibular and proprioceptive input; the head is aligned according to the gravitational reference so as to obtain stable visual information. In patients with unilateral vestibular hypofunction, posture is still controlled by these two inputs, although the ability to align the head is diminished. In patients with bilateral vestibular hypofunction or a central disorder, head alignment is maintained using visual input, although it may not be the sole or predominant stabilizing force.