Nondispersive and dispersive collective electronic modes in carbon nanotubes

We propose a new theoretical interpretation of the electron energy-loss spectroscopy results of Pichler {\it et al.} on bulk carbon nanotube samples. The experimentally found nondispersive modes have been attributed by Pichler {\it et al.} to interband excitations between localized states polarized perpendicular to the nanotube axis. This interpretation has been challenged by a theorist who attributed the modes to optical plasmons carrying nonzero angular momenta. We point out that both interpretations suffer from difficulties. From our theoretical results of the loss functions for individual carbon nanotubes based on a tight-binding model, we find that the nondispersive modes could be due to collective electronic modes in chiral carbon nanotubes, while the observed dispersive mode should be due to collective electronic modes in armchair and zigzag carbon nanotubes. Momentum-dependent electron energy-loss experiments on individual carbon nanotubes should be able to confirm or disprove this interpretation decisively.Comment: 4 pages, 3 figure

Luttinger Parameter g for Metallic Carbon Nanotubes and Related Systems

The random phase approximation (RPA) theory is used to derive the Luttinger parameter g for metallic carbon nanotubes. The results are consistent with the Tomonaga-Luttinger models. All metallic carbon nanotubes, regardless if they are armchair tubes, zigzag tubes, or chiral tubes, should have the same Luttinger parameter g. However, a (10,10) carbon peapod should have a smaller g value than a (10,10) carbon nanotube. Changing the Fermi level by applying a gate voltage has only a second order effect on the g value. RPA theory is a valid approach to calculate plasmon energy in carbon nanotube systems, regardless if the ground state is a Luttinger liquid or Fermi liquid. (This paper was published in PRB 66, 193405 (2002). However, Eqs. (6), (9), and (19) were misprinted there.)Comment: 2 figure

High-spin and low-spin iron(II) complexes with facially-coordinated borohydride ligands

Rare examples of monometallic high-spin and low-spin L_3Fe(H_3BH) complexes have been characterized, where the two L_3 ligands are [Tp^(Ph2)] and [PhBP3] ([Tp^(Ph2)] = [HB(3,5-Ph_2pz)_3]− and [PhBP_3] = [PhB(CH_2PPh_2)_3]−). The structures are reported wherein the borohydride ligand is facially coordinated to the iron center in each complex. Density functional methods have been employed to explain the bonding in these unusual iron(II) centers. Despite the differences in spin states, short Fe–B distances are observed in both complexes and there is significant theoretical evidence to support a substantial bonding interaction between the iron and boron nuclei. In light of this interaction, we suggest that these complexes can be described as (L_3)Fe(η^4-H_3BH) complexes

Methicillin sensitive Staphylococcus aureus producing Panton-Valentine leukocidin toxin in Trinidad & Tobago: a case report

<p>Abstract</p> <p>Introduction</p> <p>Certain <it>Staphylococcus aureus </it>strains produce Panton-Valentine leukocidin, a toxin that lyses white blood cells causing extensive tissue necrosis and chronic, recurrent or severe infection. This report documents a confirmed case of methicillin-sensitive <it>Staphylococcus aureus </it>strain harboring Panton-Valentine leukocidin genes from Trinidad and Tobago. To the best of our knowledge, this is the first time that such a case has been identified and reported from this country.</p> <p>Case presentation</p> <p>A 13-year-old Trinidadian boy of African descent presented with upper respiratory symptoms and gastroenteritis-like syptoms. About two weeks later he was re-admitted to our hospital complaining of pain and weakness affecting his left leg, where he had received an intramuscular injection of an anti-emetic drug. He deteriorated and developed septic arthritis, necrotizing fasciitis and septic shock with acute respiratory distress syndrome, leading to death within 48 hours of admission despite intensive care treatment. The infection was caused by <it>S. aureus</it>. Bacterial isolates from specimens recovered from our patient before and after his death were analyzed using microarray DNA analysis and <it>spa </it>typing, and the results revealed that the <it>S. aureus </it>isolates belonged to clonal complex 8, were methicillin-susceptible and positive for Panton-Valentine leukocidin. An autopsy revealed multi-organ failure and histological tissue stains of several organs were also performed and showed involvement of his lungs, liver, kidneys and thymus, which showed Hassal's corpuscles.</p> <p>Conclusion</p> <p>Rapid identification of Panton-Valentine leukocidin in methicillin-sensitive <it>S. aureus </it>isolates causing severe infections is necessary so as not to miss their potentially devastating consequences. Early feedback from the clinical laboratories is crucial.</p

Methicillin sensitive Staphylococcus aureus producing Panton-Valentine leukocidin toxin in Trinidad & Tobago: a case report

<p>Abstract</p> <p>Introduction</p> <p>Certain <it>Staphylococcus aureus </it>strains produce Panton-Valentine leukocidin, a toxin that lyses white blood cells causing extensive tissue necrosis and chronic, recurrent or severe infection. This report documents a confirmed case of methicillin-sensitive <it>Staphylococcus aureus </it>strain harboring Panton-Valentine leukocidin genes from Trinidad and Tobago. To the best of our knowledge, this is the first time that such a case has been identified and reported from this country.</p> <p>Case presentation</p> <p>A 13-year-old Trinidadian boy of African descent presented with upper respiratory symptoms and gastroenteritis-like syptoms. About two weeks later he was re-admitted to our hospital complaining of pain and weakness affecting his left leg, where he had received an intramuscular injection of an anti-emetic drug. He deteriorated and developed septic arthritis, necrotizing fasciitis and septic shock with acute respiratory distress syndrome, leading to death within 48 hours of admission despite intensive care treatment. The infection was caused by <it>S. aureus</it>. Bacterial isolates from specimens recovered from our patient before and after his death were analyzed using microarray DNA analysis and <it>spa </it>typing, and the results revealed that the <it>S. aureus </it>isolates belonged to clonal complex 8, were methicillin-susceptible and positive for Panton-Valentine leukocidin. An autopsy revealed multi-organ failure and histological tissue stains of several organs were also performed and showed involvement of his lungs, liver, kidneys and thymus, which showed Hassal's corpuscles.</p> <p>Conclusion</p> <p>Rapid identification of Panton-Valentine leukocidin in methicillin-sensitive <it>S. aureus </it>isolates causing severe infections is necessary so as not to miss their potentially devastating consequences. Early feedback from the clinical laboratories is crucial.</p

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

RENEB intercomparisons applying the conventional Dicentric Chromosome Assay (DCA)

Purpose: Two quality controlled inter-laboratory exercises were organized within the EU project ‘Realizing the European Network of Biodosimetry (RENEB)’ to further optimize the dicentric chromosome assay (DCA) and to identify needs for training and harmonization activities within the RENEB network. Materials and methods: The general study design included blood shipment, sample processing, analysis of chromosome aberrations and radiation dose assessment. After manual scoring of dicentric chromosomes in different cell numbers dose estimations and corresponding 95% confidence intervals were submitted by the participants. Results: The shipment of blood samples to the partners in the European Community (EU) were performed successfully. Outside the EU unacceptable delays occurred. The results of the dose estimation demonstrate a very successful classification of the blood samples in medically relevant groups. In comparison to the 1st exercise the 2nd intercomparison showed an improvement in the accuracy of dose estimations especially for the high dose point. Conclusions: In case of a large-scale radiological incident, the pooling of ressources by networks can enhance the rapid classification of individuals in medically relevant treatment groups based on the DCA. The performance of the RENEB network as a whole has clearly benefited from harmonization processes and specific training activities for the network partners