Knowledge-assisted recognition of cluster boundaries in gene expression data

BACKGROUND AND MOTIVATION: DNA microarray technology has made it possible to determine the expression levels of thousands of genes in parallel under multiple experimental conditions. Genome-wide analyses using DNA microarrays make a great contribution to the exploration of the dynamic state of genetic networks, and further lead to the development of new disease diagnosis technologies. An important step in the analysis of gene expression data is to classify genes with similar expression patterns into the same groups. To this end, hierarchical clustering algorithms have been widely used. Major advantages of hierarchical clustering algorithms are that investigators do not need to specify the number of clusters in advance and results are presented visually in the form of a dendrogram. However, since traditional hierarchical clustering methods simply provide results on the statistical characteristics of expression data, biological interpretations of the resulting clusters are not easy, and it requires laborious tasks to unveil hidden biological processes regulated by members in the clusters. Therefore, it has been a very difficult routine for experts. OBJECTIVE: Here, we propose a novel algorithm in which cluster boundaries are determined by referring to functional annotations stored in genome databases. MATERIALS AND METHODS: The algorithm first performs hierarchical clustering of gene expression profiles. Then, the cluster boundaries are determined by the Variance Inflation Factor among the Gene Function Vectors, which represents distributions of gene functions in each cluster. Our algorithm automatically specifies a cutoff that leads to functionally independent agglomerations of genes on the dendrogram derived from similarities among gene expression patterns. Finally, each cluster is annotated according to dominant gene functions within the respective cluster. RESULTS AND CONCLUSIONS: In this paper, we apply our algorithm to two gene expression datasets related to cell cycle and cold stress response in budding yeast Saccharomyces cerevisiae. As a result, we show that the algorithm enables us to recognize cluster boundaries characterizing fundamental biological processes such as the Early G1, Late G1, S, G2 and M phases in cell cycles, and also provides novel annotation information that has not been obtained by traditional hierarchical clustering methods. In addition, using formal cluster validity indices, high validity of our algorithm is verified by the comparison through other popular clustering algorithms, K-means, self-organizing map and AutoClass.     

Pacemaker frequency is increased by sodium nitroprusside in the guinea pig gastric antrum

The basis of rhythmic activity observed at the dorsal column nuclei (DCN) is still open to debate. This study has investigated the electrophysiological properties of isolated DCN neurones deprived of any synaptic influence, using the perforated-patch technique. About half of the DCN neurones (64/130) were spontaneously active. More than half of the spontaneous neurones (36/64) showed a low threshold membrane oscillation (LTO) with a mean frequency of 11.4 Hz (range: 4.3–22.1 Hz, n = 20; I = 0). Cells showing LTOs also invariably showed a rhythmic 1.2 Hz clustering activity (groups of 2–5 action potentials separated by silent LTO periods). Also, more than one-third of the silent neurones presented clustering activity, always accompanied by LTOs, when slightly depolarised. The frequency of LTOs was voltage dependent and could be abolished by TTX (0.5 μM) and riluzole (30 μM), suggesting the participation of a sodium current. LTOs were also abolished by TEA (15 mM), which transformed clustering into tonic activity. In voltage clamp, most DCN neurones (85 %) showed a TTX-/riluzole-sensitive persistent sodium current ( I _Na,p), which activated at about -60 mV and had a half-maximum activation at −49.8 mV. An M-like, non-inactivating outward current was present in 95 % of DCN neurones, and TEA (15 mM) inhibited this current by 73.7 %. The non-inactivating outward current was also inhibited by barium (1 mM) and linopirdine (10 μM), which suggests its M-like nature; both drugs failed to block the LTOs, but induced a reduction in their frequency by 56 and 20 %, respectively. These results demonstrate for the first time that DCN neurones have a complex and intrinsically driven clustering discharge pattern, accompanied by subthreshold membrane oscillations. Subthreshold oscillations rely on the interplay of a persistent sodium current and a non-inactivating TEA-sensitive outward current.     

Stereoregulating behaviour of organoalkali and organoalkaline earth compounds in polymerization of methyl methacrylate

Stereoregulating behaviour of organoalkali and organoalkaline earth metal compounds in methyl methacrylate (MMA) polymerization has been studied. Low temperature and polar solvents such as tetrahydrofuran (THF) favour formation of syndiotactic polymer when lithium and magnesium ketyls are used as catalysts. Whereas isotactic polymer is obtained with sodium ketyl even in THF at ?70°C. Lithium aluminum hydride (LiAlH₄) gave almost complete isotactic polymer in high conversion in diethyl ether or toluene even at low temperature, and lithium aluminum tetraethyl (LiAlEt₄), on the other hand, gave very highly syndiotactic polymer under the same conditions. The solvent, besides, showed very important role in stereoregulation, that is, LiAlH₄ could give syndiotactic polymer in a polar solvent at low temperature. Polymer structure was analyzed by NMR- and IR-spectroscopy. The electrical conductivities of these catalyst systems were measured and there was found a parallelism between those values and stereoregularities of polymers obtained by the respective catalyst systems.     

Copolymerization of N-carboxy-α-amino acid anhydrides by organometallic compounds

During thermal degradation of poly(vinyl chloride) in a nitrogen atmosphere polyene sequences of different lengths are formed by dehydrochlorination. The distribution of the sequence lengths in the polymer is approximated by analysis of the electron spectra, and the spectroscopically determined polyene content is compared with the amount of hydrogen chloride split off. With increasing temperature, as well as with increasing time of degradation, the distribution of the polyene sequence lengths shifts towards shorter sequences. In contrast to degraded poly(vinyl chloride) powder, degraded poly(vinyl chloride) foils exhibit a marked shift towards longer sequences. Vinylisobutyl ether as comonomer unit in the polymer chains effects a considerable shift of the sequence lengths distribution towards shorter polyene sequences. The spectroscopically determined polyene content agrees with the amount of liberated hydrogen chloride only a t very low conversions while with increasing dehydrochlorination a growing polyene deficit is found. Therefore, it is to be concluded that polyene sequences are consumed by consecutive reactions in which primarily the longer polyene sequences are involved. A further conclusion that may be drawn from these experiments is that the formation of long polyene sequences takes place very rapidly once the initial step of dehydrochlorination has occurred at a labile site. Apart from the above mentioned consecutive reactions, only the number, not the average length, of the polyene sequences changes substantially with increasing time of degradation.     

Efficacy and immunologic responses to influenza vaccine in HIV-1-infected patients

Influenza vaccine is recommended for HIV-1-infected patients. The present prospective study was conducted to evaluate the clinical efficacy and immunologic responses to the vaccine. From November 1 to December 27, 2002, 262 HIV-1-infected patients received a trivalent influenza subunit vaccine, whereas 66 did not. Influenza illness occurred in 16 vaccinated and 14 nonvaccinated patients (incidence = 6.1% [95% confidence interval (CI): 4%-10%] in vaccinated vs. 21.2% [CI: 13%-35%] in nonvaccinated persons, P < 0.001; relative risk = 0.29 [CI: 0.14-0.55]). Influenza vaccine provided clinically effective protection against influenza illness in HIV-1-infected patients. In baseline antibody-negative patients, anti-H1 and anti-H3 antibody responses to the vaccination were significant in those patients with a CD4 count >200 cells/muL compared with those with a CD4 count <200 cells/muL (P < 0.05). In contrast, in baseline antibody-positive patients, good antibody responses were observed irrespective of CD4 counts, like the healthy controls. Based on these results, annual vaccination is recommended. Specific CD4 responses correlated with HIV-1 viral load (VL), especially in patients treated with highly active antiretroviral therapy (HAART) compared with those without HAART (P < 0.01), although the clinical efficacy did not correlate with HIV-1 VL. HAART may enhance the immunologic efficacy of influenza vaccine.     

Characteristics affecting cervical sagittal alignment in patients with chronic low back pain

BackgroundSagittal spino-pelvic malalignment in patients with chronic low back pain (CLBP) have been reported in the past, which may also affect cervical spine lesions. The purpose of this study is to investigate the cervical alignment in patients with CLBP.MethodOf the patients who visited an orthopedic specialist due to low back pain lasting more than three months, 121 cases (average 71.5-years-old, 46 male and 75 female) with whole standing spinal screening radiographs were reviewed (CLBP group). Cervical parameters included cervical lordosis (CL), C2–C7 sagittal vertical axis (C2-7 SVA), and the T1 slope minus CL (T1S-CL). Cervical spine deformity was defined as C2-7 SVA >4 cm, CL <0°, or T1S-CL ≧20°. We compared the cervical alignment of these patients with 121 age and gender matched volunteers (control group).ResultsThe prevalence of cervical spine deformity was significantly higher in the CLBP group than in the control group (20.7% vs. 10.7%, P = 0.034). The mean CL was smaller in the CLBP group than in the control group (16.1° vs. 21.4°, P = 0.002). The mean C2-7 SVA was 17.6 mm vs. 18.7 mm in the CLBP group and in the control group, respectively (P = 0.817). The mean T1S-CL was larger in the CLBP group than in the control group (9.1° vs. 3.5°, P < 0.001). Multivariate analysis showed that people with CLBP were more likely to have cervical deformities than people without CLBP (odds ratio 2.16, 95% confidence interval 1.006 to 4.637).ConclusionsThis study results suggest that people with CLBP present with worse cervical sagittal alignment and higher prevalence of cervical spine deformities than age and gender matched volunteers with no CLBP. This means CLBP impacts cervical spine lesions negatively.Level of evidenceⅣ     

Novel organosilicon-containing polymers for an oxygen permselective membrane

Synthesis and gas permeation measurements of several types of polymers from methylstyrene derivatives containing mono-and bis(trialkylsilyl) group(s) were carried out. Upon radical homo-and co-polymerization of silicon-containing monomers high-molecular-weight polymers were obtained. Results from gas permeation measurements showed that these types of silicon-containing polymers exhibit fairly high oxygen permselectivity (ratio of oxygen and nitrogen permeation coefficients P/P = 3,1 ? 4,6), keeping the oxygen permeation coefficients (P) in the range of between 1,4 · 10^?9 and 4,5·10^?9 cm³ (STP) · cm · cm^?2 · s^?1 · cmHg^?1. From time lag measurements, it was found that permeation coefficients are dependent on the solubility of gases in the membranes rather than on diffusivity. Actually, the oxygen solubility coefficients increase with increasing silicon content in the polymers. Permselectivity of oxygen against nitrogen is governed by polymer constitution rather than by silicon content.     

In vivo differences between Asian, Black and White in the stratum corneum barrier function

The stratum corneum barrier function of Blacks, Caucasians and Asians were compared in vivo. A noninvasive technic, laser doppler velocimetry (LDV), was used to evaluate the cutaneous penetration of nicotinates by the determination of the lag time before vasodilatation induced by the application of those local vasodilatator drugs. The study was performed on untreated skin and after removal of the stratum corneum by 12 strips. The influence of molecular weight and solubility of different nicotinates (methyl, ethyl, hexyl and vitamin E) were also studied on Japanese skin. Vasodilatation lag times assessed by LDV, with methyl nicotinate (MN), showed that skin permeability was more important in Asians (P < 0.01)=" and=" in=" caucasians=">P < 0.05)=" than=" in=" blacks.=" moreover=" asian=" skin=" was=" significantly=" more=" sensitive=" to=" stripping=">P < 0.05)=" than=" black=" skin.=" a=" significant=" shorter=" lag=" time=" was=" obtained=" with=" small=" and=" hydrophilic=" nicotinates=" (methyl=" and=" ethyl)=">P < 0.01)=" compared=" to=" a=" lipophilic=" one=" (hexyl).=" the=" alteration=" of=" the=" stratum=" corneum=" barrier=" function=" by=" stripping=" showed=" a=" more=" important=" modification=" with=" mn=">P < 0.05)=" than=" with=" hexyl=" nicotinate.=" consequently,=" this=" noninvasive=" method=" can=" evaluate=" the=" modifications=" of=" the=" stratum=" corneum=" barrier=" function=" and=" racial=" origin=" has=" to=" be=" taken=" into=" account=" in=" the=" determination=" of=" skin=">     

The development of a small bowel volvulus in the early postoperative period following a distal gastrectomy: Report of a case

A 51-year-old Japanese man who underwent a standard distal gastrectomy for cancer of the stomach developed abdominal pain when oral intake was commenced on the 6th postoperative day after an uneventful postoperative course. Complete obstruction of the jejunum led to a sudden deterioration in his general condition and a laparotomy was performed, revealing counterclockwise rotation of the mesenterium. The necrotic portion of the small intestine was removed, while 10 cm of the upper jejunum and 100 cm of the terminal ileum were preserved. His second postoperative course was uneventful apart from the development of intestinal hurry, which is now under medical control 9 months after his second laparotomy.