Raman spectra of graphene ribbons

Raman spectra of graphene nanoribbons with zigzag and armchair edges are calculated within non-resonant Raman theory. Depending on the edge structure and polarization direction of the incident and scattered photon beam relative to the edge direction, a symmetry selection rule for the phonon type appears. These Raman selection rules will be useful for the identification of the edge structure of graphene nanoribbons.

Clinicopathological and therapeutic significance of CXCL12 expression in lung cancer

Interactions between CXCL12 and its receptors CXCR4 or CXCR7 are involved in tumor growth and metastasis in various types of human cancer. However, CXCL12 expression and its role in lung cancer are not fully elucidated. Here we examined the expression of CXCL12 in 54 lung cancer cell lines consisting of 23 small cell lung cancers (SCLCs) and 31 non-small cell lung cancers (NSCLCs). CXCL12 was overexpressed in lung cancer cell lines compared to non-malignant human bronchial epithelial cell lines (N = 6). CXCL12 expression was positively but weakly correlated with the expression of CXCR4 or CXCR7. We also examined CXCL12 expression in 89 NSCLC specimens and found that CXCL12 expression was significantly higher in tumor specimens from female patients, non-smokers and adenocarcinoma patients. Small interfering RNAs targeting CXCL12 inhibited cellular proliferation, colony formation and migration of CXCL12-overexpressing lung cancer cells; however, this inhibition did not occur in lung cancer cells that lacked CXCL12. Furthermore, the anti-CXCL12 neutralizing antibody mediated inhibitory effects in three lung cancer cell lines that overexpressed CXCL12, but not in two CXCL12 non-expressing lung cancer cell lines nor two non-malignant bronchial epithelial cell lines. The present study demonstrates that: CXCL12 is concomitantly overexpressed with CXCR4 or CXCR7 in lung cancers; CXCL12 is highly expressed in NSCLCs from females, non-smokers and adenocarcinoma patients; and disruption of CXCL12 inhibits the growth and migration of lung cancer cells. Our findings indicate that CXCL12 is required for tumor growth and provide a rationale for the anti-CXCL12 treatment strategy in lung cancer.

Diameter dependence of the dielectric constant for the excitonic transition energy of single-wall carbon nanotubes

The measured optical transition energies Eii of single-wall carbon nanotubes are compared with bright exciton energy calculations. The Eii differences between experiment and theory are minimized by considering a diameter-dependent dielectric constant kappa, which comprises the screening from the tube and from the environment. Different kappa dependencies are obtained for (E11(S), E22(S), E11(M)) relative to (E33(S), E44(S)). A changing environment changes the kappa diameter dependence for (E11(S), E22(S), E11(M)), but for (E33(S), E44(S)) the environmental effects are minimal. The resulting calculated exciton energies reproduce experimental E_{ii} values within +/-70 meV for a diameter range (0.7<d(t)<3.8 nm) and 1.2<Eii<2.7 eV, thus providing a theoretical justification for Eii, environmental effects and important insights on the dielectric screening in one-dimensional structures.

Softening of the radial breathing mode in metallic carbon nanotubes

The softening of the radial breathing mode (RBM) of metallic single walled carbon nanotubes (m-SWNTs) due to electron-phonon coupling has been studied by observing the Fermi level [see text] dependence of the RBM Raman peak. In situ Raman spectra were obtained from several individual m-SWNTs while varying [see text] electrochemically. The RBM frequency of an intrinsic m-SWNT is shown to be down-shifted relative to highly doped tubes by approximately 2 cm(1). The down-shift is greatest for small diameter and small chiral angle SWNTs. Most tubes show no change in RBM linewidth. A comparison is drawn between the RBM and the G band (A(LO) phonon) with respect to the [see text] dependence of their frequencies and linewidths.

Influenza virus infections in Lebanese children in the 2007-2008 season

We conducted the first epidemiological study of influenza in Lebanon, a temperate country in the Middle East. Between January to May 2008, 39 patients with influenza-like illness were tested. Of these, 51% contracted influenza in January alone, while no influenza cases were detected in May. Among the 39 patients, 11 influenza A and 4 influenza B cases were detected by rapid kit in addition to 10 respiratory syncytial virus cases by real-time PCR. The influenza viruses were genetically divergent from the 2007/2008 season's vaccine strains, but resembled strains circulating in other countries during the same season.

IL23 differentially regulates the Th1/Th17 balance in ulcerative colitis and Crohn's disease

BACKGROUND

A novel T helper (Th) cell lineage, Th17, that exclusively produces the proinflammatory cytokine interleukin 17 (IL17) has been reported to play important roles in various inflammatory diseases. IL23 is also focused upon for its potential to promote Th17. Here, the roles of the IL23/IL17 axis in inflammatory bowel diseases such as ulcerative colitis (UC) and Crohn's disease (CD) were investigated.

METHODS

Mucosal samples were obtained from surgically resected specimens (controls, n = 12; UC, n = 17; CD, n = 22). IL17 production by isolated peripheral blood (PB) and lamina propria (LP) CD4(+) cells was examined. Quantitative PCR amplification was performed to determine the mRNA expression levels of IL17, interferon gamma (IFNgamma), IL23 receptor (IL23R) and retinoic acid-related orphan receptor gamma (RORC) in LP CD4(+) cells, and IL12 family members, such as IL12p40, IL12p35 and IL23p19, in whole mucosal specimens. The effects of exogenous IL23 on IL17 production by LP CD4(+) cells were also examined.

RESULTS

IL17 production was higher in LP CD4(+) cells than in PB. Significant IL17 mRNA upregulation in LP CD4(+) cells was found in UC, while IFNgamma was increased in CD. IL23R and RORC were upregulated in LP CD4(+) cells isolated from both UC and CD. IL17 production was significantly increased by IL23 in LP CD4(+) cells from UC but not CD. Upregulated IL23p19 mRNA expression was correlated with IL17 in UC and IFNgamma in CD.

CONCLUSIONS

IL23 may play important roles in controlling the differential Th1/Th17 balance in both UC and CD, although Th17 cells may exist in both diseases.

Resonant Raman scattering of the smallest single-walled carbon nanotubes

We report optical properties of the smallest single-walled carbon nanotubes (SWNTs) with a diameter of only 3 A. These ultrasmall SWNTs are fabricated in the elliptical nanochannels of an AlPO-11 (AEL) single crystal. Polarized and resonant Raman scattering unambiguously revealed that these 0.3 nm SWNTs are of (2,2) armchair symmetry. Interestingly, the (2,2) armchair tube has two metastable ground states corresponding to two slightly different lattice constants in the axial direction: one state is metallic and the other is semiconducting.

Histopathological evidence of small-vessel vasculitis within the skin and lungs associated with interstitial pneumonia in an adult patient with dermatomyositis

Dermatomyositis (DM) often has a poor prognosis, due to complications associated with malignancy or interstitial pneumonia (IP). It is uncommon to find histopathological small-vessel vasculitis within cutaneous lesions and pulmonary capillaritis in patients with DM. A 64-year-old woman was diagnosed with DM based on the presence of quadriparesis, typical heliotropic rash, Gottron's papules, increased serum levels of muscle enzymes and typical muscle biopsy findings. She also had associated IP, which subsequently developed into a rapidly progressive condition. We found a high titre of Krebs von den Lunge (KL)-6 in her serum. Measurement of serum KL-6 level is widely accepted as a diagnostic test to monitor the activity of interstitial lung diseases. Histopathological examinations of the cutaneous and lung-associated features showed small-vessel vasculitis. We suggest that investigation of KL-6 levels in patients with DM and associated conditions should be carried out to determine if raised KL-6 levels are useful at predicting outcome or severity of various features.

Clinical epidemiology of ciprofloxacin-resistant Proteus mirabilis isolated from urine samples of hospitalised patients

This study investigated the clinical characteristics of ciprofloxacin-resistant Proteus mirabilis isolates from urine samples associated with nosocomial infection or colonisation, and identified the risk-factors for ciprofloxacin resistance. Data for patients with ciprofloxacin-resistant P. mirabilis isolates (n=13) were compared with those for randomly selected patients with ciprofloxacin-susceptible P. mirabilis isolates (n=40) who were matched by temporal occurrence as control patients. The majority of ciprofloxacin-resistant P. mirabilis isolates were multiresistant, and ciprofloxacin resistance was associated significantly with previous use of fluoroquinolones and production of extended-spectrum beta-lactamases.

Estimation of pulmonary oxygen consumption in the early postoperative period after thoracic surgery

Lung injury, including pneumonia, can occur in the early postoperative period following thoracic surgery. Pulmonary oxygen consumption is thought to increase in patients with pulmonary infection. This study measured oxygen consumption in relationship to lung injury in the early postoperative period after thoracic surgery. Thirty-five patients who underwent thoraco-abdominal oesophagectomy for oesophageal cancer were studied. Measured oxygen-consumption was obtained by indirect calorimetry and calculated oxygen-consumption was simultaneously determined by the reverse Fick method. The difference in oxygen consumption was attributed to pulmonary oxygen consumption. The difference in oxygen consumption increased to 23.1 ml.min(-1).m(-2) on postoperative day 2. In patients with pneumonia the difference in oxygen consumption increased significantly to 39.0 ml.min(-1).m(-2) the day before clinical onset of pneumonia, and it increased further to 65.7 ml.min(-1).m(-2) on the day that pneumonia became clinically apparent. These findings suggest that the difference in oxygen consumption may be useful for estimating the extent of lung injury and for predicting pulmonary complications in the postoperative period.

Pitavastatin ameliorates albuminuria and renal mesangial expansion by downregulating NOX4 in db/db mice

Recent studies have uncovered various pleiotrophic effects of 3-hydroxy-3-methylglutaryl coenzyme A reductase-inhibiting drugs (statins). Several studies have identified a beneficial effect of statins on diabetic nephropathy; however, the molecular mechanisms are unclear. In this study, we show that statin ameliorates nephropathy in db/db mice, a rodent model of type 2 diabetes, via downregulation of NAD(P)H oxidase NOX4, which is a major source of oxidative stress in the kidney. Pitavastatin treatment for 2 weeks starting at 12 weeks of age significantly reduced albuminuria in the db/db mice concomitant with a reduction of urinary 8-hydroxy-2'-deoxyguanosine and 8-epi-prostaglandin F(2alpha). Immunohistochemical analysis found increased amounts of 8-hydroxy-2'-deoxyguanosine and NOX4 protein in the kidney of db/db mice. Quantitative reverse transcription-polymerase chain reaction also showed increased levels of NOX4 mRNA. Pitavastatin normalized all of these changes in the kidneys of diabetic animals. Additionally, 12-week treatment with the statin completely normalized the levels of transforming growth factor-beta1 and fibronectin mRNA as well as the mesangial expansion characteristic of diabetic nephropathy. Our study demonstrates that pitavastatin ameliorates diabetic nephropathy in db/db mice by minimizing oxidative stress by downregulating NOX4 expression. These findings may provide insight into the mechanisms of statin therapy in early stages of diabetic nephropathy.

Sound spectrogram analysis in patients receiving Kawahara's surgical voice restoration for advanced carcinoma of the hypopharynx and cervical esophagus

Loss of voice after total laryngectomy is a major concern that has prompted much effort to develop methods of surgical voice restoration. In 1992, Kawahara described a tracheocolic shunt for voice restoration using a revascularized ileocolic graft. With this method, aspiration through the phonatory shunt is prevented by the ileocolic valve (Bauhin's valve), while vocalization is allowed. The purpose of this study was to use sound spectrogram analysis to evaluate voices surgically restored in that way. Between 2002 and 2005, 10 consecutive patients underwent laryngopharyngoesophagectomy with Kawahara's surgical voice restoration for advanced carcinoma of the hypopharynx and/or cervical esophagus at Akita University Hospital, Japan. We then used sound spectrography to analyze and compare the voices of patients receiving Kawahara's voice restoration, against healthy volunteers and patients who underwent the same surgery without voice restoration and spoke using an electronic larynx. We also evaluated the intelligibility of conversation and performed a listening test. The sound spectrograms showed that when produced by the electronic larynx, consonant sounds and voice frequencies below 300 Hz were not clearly recognized. By contrast, in patients who received Kawahara's surgical voice restoration, consonant and vowel sounds at frequencies above and below 300 Hz were clearly recognized. Although conversation was intelligible with both Kawahara's surgical voice restoration and the electronic device, listeners judged the voice produced by the former to be superior. Thus, the voice produced by Kawahara's surgical voice restoration is superior to that produced by the electronic larynx.

Studying disorder in graphite-based systems by Raman spectroscopy

Raman spectroscopy has historically played an important role in the structural characterization of graphitic materials, in particular providing valuable information about defects, stacking of the graphene layers and the finite sizes of the crystallites parallel and perpendicular to the hexagonal axis. Here we review the defect-induced Raman spectra of graphitic materials from both experimental and theoretical standpoints and we present recent Raman results on nanographites and graphenes. The disorder-induced D and D' Raman features, as well as the G'-band (the overtone of the D-band which is always observed in defect-free samples), are discussed in terms of the double-resonance (DR) Raman process, involving phonons within the interior of the 1st Brillouin zone of graphite and defects. In this review, experimental results for the D, D' and G' bands obtained with different laser lines, and in samples with different crystallite sizes and different types of defects are presented and discussed. We also present recent advances that made possible the development of Raman scattering as a tool for very accurate structural analysis of nano-graphite, with the establishment of an empirical formula for the in- and out-of-plane crystalline size and even fancier Raman-based information, such as for the atomic structure at graphite edges, and the identification of single versus multi-graphene layers. Once established, this knowledge provides a powerful machinery to understand newer forms of sp(2) carbon materials, such as the recently developed pitch-based graphitic foams. Results for the calculated Raman intensity of the disorder-induced D-band in graphitic materials as a function of both the excitation laser energy (E(laser)) and the in-plane size (L(a)) of nano-graphites are presented and compared with experimental results. The status of this research area is assessed, and opportunities for future work are identified.

Strain-induced interference effects on the resonance Raman cross section of carbon nanotubes

In this Letter, we report the effects of strain on the electronic properties of single-wall carbon nanotubes. When we normalize the electronic transition energies to the corresponding values obtained for unstrained tubes, we obtain that, regardless of the tube diameter, all the data collapse onto universal curves following an n - m = constant family pattern. In the case of metallic tubes, quantum interference effects on the Raman cross section are predicted for strained tubes when the energies of the lower and the upper components have nearly the same values. Experimental evidence for the strain-induced Raman cross section changes is observed in single nanotube spectroscopy.

Infrared-active vibrational modes of single-walled carbon nanotubes

The IR-active vibrational modes of single-walled carbon nanotubes have been observed by optical transmission through thin films of bundled nanotubes. Because IR-active chemical functional groups, e.g., -COOH, -OH, might be attached to the tube walls and contribute additional spectral features, we have also studied the effects of chemical purification and long-term high-temperature vacuum annealing on the IR spectrum. Through comparison with theory, we are able to assign much of the sharp structure observed in our IR spectra.

Phonon-assisted excitonic recombination channels observed in DNA-wrapped carbon nanotubes using photoluminescence spectroscopy

By using a sample of DNA-wrapped single-wall carbon nanotubes strongly enriched in the (6,5) nanotube, photoluminescence emissions observed at special excitation energy values were identified with specific mechanisms of phonon-assisted excitonic absorption and recombination processes associated with (6,5) nanotubes, including one-phonon, two-phonon, and some continuous-luminescence processes. Such detailed processes are not separately identified in three-dimensional semiconducting materials. A general theoretical framework is presented to interpret the experimentally observed phonon-assisted processes in terms of excitonic states.

Allelic losses on chromosome 3p are accumulated in relation to morphological changes of lung adenocarcinoma

We performed allelotyping analysis at nine regions on chromosome 3p using 56 microdissected samples from 23 primary lung adenocarcinomas to examine the process of progression within individual lung adenocarcinoma with various grades of differentiation. Identical allelic patterns among various grades of differentiation were found in eight cases. Accumulation of allelic losses from high to lower differentiated portions was found in seven cases and accumulation of allelic losses from low to higher differentiated portions was found in five cases. Various allelic patterns among various grades of differentiation were found in three cases. These results suggested that allelic losses on 3p play an important role in morphological changes of lung adenocarcinomas. We also investigated the relationship between allelic losses on 3p and histological subtypes of lung adenocarcinoma. The frequencies of allelic losses at 3p14.2 and telomeric region of 3p21.3 were higher in papillary type tumour (nine out of 14, 64% and 11 out of 15, 73%) than in bronchioloalveolar carcinoma-type tumour (one out of 8, 13%; P=0.031 and four out of 12, 33%; P = 0.057). These results indicated that allelic losses at 3p14.2 and telomeric region of 3p21.3 are related to pattern of the proliferation of lung adenocarcinoma.

Determination of nanotubes properties by Raman spectroscopy

The basic concepts and characteristics of Raman spectra from single-wall carbon nanotubes (SWNTs, both isolated and bundled) are presented. The physical properties of the SWNTs are introduced, followed by the conceptual framework and characteristics of their Raman spectra. Each Raman feature, namely the radial breathing mode, the tangential G band, combination modes and disorder-induced bands are discussed, addressing their physical origin, as well as their capability for characterizing SWNT properties.

One-dimensional character of combination modes in the resonance Raman scattering of carbon nanotubes

Resonance Raman spectroscopy with an energy tunable system is used to analyze the 600-1100 cm(-1) spectral region in single-wall carbon nanotubes. Sharp peaks are associated with the combination of zone folded optic and acoustic branches from 2D graphite. These combination modes exhibit a peculiar dependence on the excitation laser energy that is explained on the basis of a highly selective resonance process that considers phonons and electrons in low dimensional materials.

Anisotropy of the Raman spectra of nanographite ribbons

A polarized Raman study of nanographite ribbons on a highly oriented pyrolytic graphite substrate is reported. The Raman peak of the nanographite ribbons exhibits an intensity dependence on the light polarization direction relative to the nanographite ribbon axis. This result is due to the quantum confinement of the electrons in the 1D band structure of the nanographite ribbons, combined with the anisotropy of the light absorption in 2D graphite, in agreement with theoretical predictions.

[Microorganism "Montezuma" of the order Rickettsiales: the potential causative agent of tick-borne disease in the Far East of Russia]

A new microorganism, tentatively named "Montezuma" was detected in ticks and in specimens (blood, bioptic specimens of the primary affect) taken from patients with an acute fever disease, etiologically linked with the bites of Ixodes ticks in the Far East of the Russian Federation. After sequencing the products of the amplification of DNA isolated from ticks with wide-spectrum primers new primers were developed, highly specific to the unusual sequence thus obtained. The study revealed that ticks of the species Ixodes persulcatus (97%) and Haemophysalis concinnae (5%) contained DNA of this microorganism. The same DNA was detected in materials taken from the patients. The phylogenetic analysis of the gene showed that this organism formed an independent and well defined branch within the order Rickettsiales. The nearest homology (89%) was observed with recently detected endosymbiotes Acanthamoeba. The similarity with their relatives from the families Rickettsiaceae and Anaplasmataceae of the order Rickettsiales was within 81-86%, which made it possible to infer the existence of, probably, only a new genus, but also a family. The isolated DNA belonged, supposedly, to the new microoganism which caused a tick-borne disease in humans, transmitted through bites of Ixodes ticks, and was, supposedly, widely spread in the southern area of the Khabarovsk Territory.

The concept of cutting lines in carbon nanotube science

A review is presented of one-dimensional cutting lines that are utilized to obtain the physical properties of carbon nanotubes from the corresponding properties of graphite by the zone-folding scheme. Quantization effects in general low-dimensional systems are briefly discussed, followed by a more detailed consideration of one-dimensional single-wall carbon nanotubes. The geometrical structure of the nanotube is described, from which quantum confined states are constructed. These allowed states in the momentum space of graphite are known as cutting lines. Different representations of the cutting lines in momentum space are introduced. Electronic and phonon dispersion relations for nanotubes are derived by using cutting lines and the zone-folding scheme. The relation between cutting lines and singularities in the electronic density of states is considered. The selection rules for carbon nanotubes are shown to be directly connected with the cutting lines. Different experimental techniques are considered that confirm the validity of cutting lines and the zone-folding approach.

Comparative study of translation termination sites and release factors (RF1 and RF2) in procaryotes

Translation termination is catalyzed by release factors that recognize stop codons. However, previous works have shown that in some bacteria, the termination process also involves bases around stop codons. Recently, Ito et al. analyzed release factors and identified the amino acids therein that recognize stop codons. However, the amino acids that recognize bases around stop codons remain unclear. To identify the candidate amino acids that recognize the bases around stop codons, we aligned the protein sequences of the release factors of various bacteria and searched for amino acids that were conserved specifically in the sequence of bacteria that seemed to regulate translation termination by bases around stop codons. As a result, species having several highly conserved residues in RF1 and RF2 showed positive correlations between their codon usage bias and conservation of the bases around the stop codons. In addition, some of the residues were located very close to the SPF motif, which deciphers stop codons. These results suggest that these conserved amino acids enable the release factors to recognize the bases around the stop codons.

Resonance Raman spectra of carbon nanotubes by cross-polarized light

Resonance Raman studies on single wall carbon nanotubes (SWNTs) show that resonance with cross polarized light, i.e., with the E(mu,mu+/-1) van Hove singularities in the joint density of states needs to be taken into account when analyzing the Raman and optical absorption spectra from isolated SWNTs. This study is performed by analyzing the polarization, laser energy, and diameter dependence of two Raman features, the tangential modes (G band) and a second-order mode (G' band), at the isolated SWNT level.

Science and applications of single-nanotube Raman spectroscopy

A review is presented of the resonance Raman spectra from individual isolated single-wall carbon nanotubes (SWNTs). A brief summary is given of how the measurements are made. Why the resonance Raman effect allows single-carbon nanotube spectra to be observed easily and under normal operating conditions is summarized. The important structural information that is provided by single-nanotube spectroscopy using one laser line is discussed, and what else can be learned from tunable laser experiments is reviewed. Particular attention is given to the determination of the nanotube diameter and of the energy of its van Hove singularities Eii. Applications of single-nanotube spectroscopy are emphasized, such as measurements of isolated SWNTs connected with circuit-based samples and of isolated SWNTs mounted on an atomic force microscope tip. A critical assessment of the opportunities and limitations of the resonance Raman method for structural (n, m) identification is presented. The trigonal warping effect, which is central to the (n, m) identification in resonance Raman spectroscopy, is discussed in simple terms, and the importance of this effect in nanotube science and applications is reviewed.

Phonon trigonal warping effect in graphite and carbon nanotubes

The one-dimensional structure of carbon nanotubes leads to quantum confinement of the wave vectors for the electronic states, thus making the double resonance Raman process selective, not only of the magnitude, but also of the direction of the phonon wave vectors. This additional selectivity allows us to reconstruct the phonon dispersion relations of 2D graphite, by probing individual single wall carbon nanotubes of different chiralities by resonance Raman spectroscopy, and using different laser excitation energies. In particular, we are able to measure the anisotropy, or the trigonal warping effect, in the phonon dispersion relations around the hexagonal corner of the Brillouin zone of graphite.

Endoscopic ventriculo-cystomy for non-communicating hydrocephalus secondary to quadrigeminal cistern arachnoid cyst

INTRODUCTION

Intracranial arachnoid cysts are developmental, anomalous collections of cerebrospinal fluid (CSF), and occasionally cause symptoms when large enough to obliterate the CSF outflow pathway and give rise to non-communicating hydrocephalus. The treatment of choice for symptomatic arachnoid cysts has been surgical excision or fenestration of the cyst, but less invasive endoscopic fenestration has been attempted with favorable preliminary results.

CASE REPORT

We report a case of non-communicating hydrocephalus caused by a quadrigeminal cistern arachnoid cyst in a 35-year-old woman who presented with worsening headaches. She was successfully treated by endoscopic third ventriculostomy and fenestration of the cyst (ventriculo-cistomy).

DISCUSSION

Endoscopic fenestration of symptomatic arachnoid cysts can be as effective as open surgery in terms of short-term efficacy, and it is certainly less invasive than open surgery. However, its long-term outcome remains unknown, and these rare cases require careful clinical and radiological follow-up.

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.

Single nanotube Raman spectroscopy

A review is presented on the observation of the resonant Raman spectra from one isolated single wall carbon nanotube, focusing on the important structural information that is provided by single nanotube spectroscopy including the (n, m) determination of the individual tubes. The special sensitivity of the radial breathing mode to the (n, m) determination is emphasized, and the corroboration of this (n, m) assignment by diameter- and chirality-dependent phenomena in other Raman modes, such as the G-band, D-band, and G'-band features is also discussed. The significance of single nanotube spectroscopy for future nanotube research in general is briefly reviewed.

Comprehensive sequence analysis of translation termination sites in various eukaryotes

Recent investigations into the translation termination sites of various organisms have revealed that not only stop codons but also sequences around stop codons have an effect on translation termination. To investigate the relationship between these sequence patterns and translation as well as its termination efficiency, we analysed the correlation between strength of consensus and translation efficiency, as predicted according to Codon Adaptation Index (CAI) value. We used RIKEN full-length mouse cDNA sequences and ten other eukaryotic UniGene datasets from NCBI for the analyses. First, we conducted sequence profile analyses following translation termination sites. We found base G and A at position +1 as a strong consensus for mouse cDNA. A similar consensus was found for other mammals, such as Homo sapiens, Rattus norvegicus and Bos taurus. However, some plants had different consensus sequences. We then analysed the correlation between the strength of consensus at each position and the codon biases of whole coding regions, using information content and CAI value. The results showed that in mouse cDNA, CAI value had a positive correlation with information content at positions +1. We also found that, for positions with strong consensus, the strength of the consensus is likely to have a positive correlation with CAI value in some other eukaryotes. Along with these observations, biological insights into the relationship between gene expression level, codon biases and consensus sequence around stop codons will be discussed.

On biased distribution of introns in various eukaryotes

We conducted comprehensive analyses on intron positions in the Mus musculus genome by comparing genomic sequences in the GenBank database and cDNA sequences in the mouse cDNA library recently developed by Riken Genomic Sciences Center. Our results confirm that introns have a tendency to be located toward the 5' end of the gene. The same type of analysis was conducted in the coding region of seven eukaryotes (Saccharomyces cerevisiae, Plasmodium falciparum, Caenorhabditis elegans, Drosophila melanogaster, M. musculus, Homo sapiens, Arabidopsis thaliana). Introns in genes with a single intron have a locational bias toward the 5' end in all species except A. thaliana. We also measured the distance from the start codon to the position of the intron, and found that single introns prefer the location immediately after the start codon in S. cerevisiae and P. falciparum. We discuss three possible explanations for these findings: (1) they are the consequence of intron loss by reverse-transcriptase; (2) they are necessary to accommodate the function; and (3) they are concerned with the mechanism of pre-mRNA splicing.

Surgical treatment of a mixed pineocytoma/pineoblastoma in a 72-year-old patient

BACKGROUND

Although pineal parenchymal tumours are very rare in elderly patients, we recently successfully treated a 72-year-old male patient. Interestingly, the histology of his pineal parenchymal tumour was mixed pineocytoma/pineoblastoma, which is reported to be extremely rare in aged patients. We present his clinical manifestations, follow-up MRI, surgical treatment, pathological findings, and review the literature.

CLINICAL MATERIAL

This 72-year-old man had a mass in the pineal region detected 3 years previously on MRI in February 1996 following symptoms of headache and vertigo. Two years later, he experienced gait disturbance and disorientation. CT scans disclosed obstructive hydrocephalus, and ventriculo-peritoneal shunt placement was then performed. The tumour mass began to enlarge in July 1999 (at age 72). On October 13, 1999, total removal of the pineal region tumour was performed through an occipital transtentorial approach. The postoperative course was uneventful. The pathological diagnosis of the tumour was mixed pineocytoma/pineoblastoma.

CONCLUSION

Pineal parenchymal tumours are uncommon in elderly patients, and mixed pineocytoma/pineoblastomas are particularly rare. We followed this patient closely for more than 3.5 years and finally performed total surgical removal of the tumour, with excellent outcome. The present case suggests that a mixed pineocytoma/pineoblastoma tumour is controllable even in elderly patients through careful evaluation and management.

Probing phonon dispersion relations of graphite by double resonance Raman scattering

The phonon dispersion relations of graphite can be probed over a wide range of the Brillouin zone by double resonance Raman spectroscopy. The double resonance Raman process provides us with new assignments for the dispersive and nondispersive features observed in the Raman spectra of disordered graphite and carbon nanotubes, some features having been incorrectly assigned previously, or not assigned at all.