The generalized Robinson-Foulds metric

The Robinson-Foulds (RF) metric is arguably the most widely used measure of phylogenetic tree similarity, despite its well-known shortcomings: For example, moving a single taxon in a tree can result in a tree that has maximum distance to the original one; but the two trees are identical if we remove the single taxon. To this end, we propose a natural extension of the RF metric that does not simply count identical clades but instead, also takes similar clades into consideration. In contrast to previous approaches, our model requires the matching between clades to respect the structure of the two trees, a property that the classical RF metric exhibits, too. We show that computing this generalized RF metric is, unfortunately, NP-hard. We then present a simple Integer Linear Program for its computation, and evaluate it by an all-against-all comparison of 100 trees from a benchmark data set. We find that matchings that respect the tree structure differ significantly from those that do not, underlining the importance of this natural condition.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

HIF1A-Dependent Induction of Alveolar Epithelial PFKFB3 Dampens Acute Lung Injury

Acute lung injury (ALI) is a severe form of lung inflammation causing acute respiratory distress syndrome in patients. ALI pathogenesis is closely linked to uncontrolled alveolar inflammation. We hypothesize that specific enzymes of the glycolytic pathway could function as key regulators of alveolar inflammation. Therefore, we screened isolated alveolar epithelia from mice exposed to ALI induced by injurious ventilation to assess their metabolic responses. These studies pointed us toward a selective role for isoform 3 of the 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase (PFKFB3). Pharmacologic inhibition or genetic deletion of Pfkfb3 in alveolar epithelia (Pfkfb3loxP/loxP SPC-ER-Cre+ mice) was associated with profound increases in ALI during injurious mechanical ventilation or acid instillation. Studies in genetic models linked Pfkfb3 expression and function to Hif1a. Not only did intratracheal pyruvate instillation reconstitute Pfkfb3loxP/loxP or Hif1aloxP/loxP SPC-ER-Cre+ mice, but pyruvate was also effective in ALI treatment of wild-type mice. Finally, proof-of-principle studies in human lung biopsies demonstrated increased PFKFB3 staining in injured lungs and colocalized PFKFB3 to alveolar epithelia. These studies reveal a specific role for PFKFB3 in counterbalancing alveolar inflammation and lay the groundwork for novel metabolic therapeutic approaches during ALI

Ultrathin compound semiconductor on insulator layers for high performance nanoscale transistors

Over the past several years, the inherent scaling limitations of electron devices have fueled the exploration of high carrier mobility semiconductors as a Si replacement to further enhance the device performance. In particular, compound semiconductors heterogeneously integrated on Si substrates have been actively studied, combining the high mobility of III-V semiconductors and the well-established, low cost processing of Si technology. This integration, however, presents significant challenges. Conventionally, heteroepitaxial growth of complex multilayers on Si has been explored. Besides complexity, high defect densities and junction leakage currents present limitations in the approach. Motivated by this challenge, here we utilize an epitaxial transfer method for the integration of ultrathin layers of single-crystalline InAs on Si/SiO2 substrates. As a parallel to silicon-on-insulator (SOI) technology14,we use the abbreviation "XOI" to represent our compound semiconductor-on-insulator platform. Through experiments and simulation, the electrical properties of InAs XOI transistors are explored, elucidating the critical role of quantum confinement in the transport properties of ultrathin XOI layers. Importantly, a high quality InAs/dielectric interface is obtained by the use of a novel thermally grown interfacial InAsOx layer (~1 nm thick). The fabricated FETs exhibit an impressive peak transconductance of ~1.6 mS/{\mu}m at VDS=0.5V with ON/OFF current ratio of greater than 10,000 and a subthreshold swing of 107-150 mV/decade for a channel length of ~0.5 {\mu}m

PLASTICS IN THE ANTARCTIC ENVIRONMENT: ARE WE LOOKING ONLY AT THE TIP OF THE ICEBERG?

The available literature on marine debris and its impacts in the sub-Antarctic Islands, the Antarctic Peninsula and on the coasts of Antarctica was organized and interpreted here. A total of 98 documents covering from 1982 to 2010 were found and 95% had their full contents accessed. Seventy documents were on line scientific abstracts from the Commission on the Conservation of Antarctic Marine Living Resources (CCAMLR). The occurrence of marine debris in the Antarctic environment, fur seals entanglement in marine debris, interactions between seabirds and marine debris and long range transport of benthos on floating plastics were the main issues discussed. Fishing operations in the Southern Ocean were identified as the major source of marine debris, but according to the type of debris reported, plastics from lower latitudes may also cross the Polar Front (PF). Possible links between Antarctic and South America, the closest intercontinental connection, in relation to plastic marine debris pollution are highlighted. As reported for lower latitudinal gradients, plastic pollution is an important problem to the Antarctic environment. However, specific and detailed works are necessary since our current knowledge probably expose only a small part of the real problem. Concerning this sort of pollution in the Antarctic marine and coastal environments, we may be looking solely at the tip of iceberg.PLÁSTICOS   EN   EL   ECOSISTEMA   ANTÁRTICO:   ¿SERÁ   QUE   ESTAMOS   VIENDO SOLAMENTE LA PUNTA DEL ICEBERG?  En este trabajo fue organizada y interpretada la literatura científica relacionada con la presencia y los impactos de basura marina en islas sub-antárticas, en la Península Antártica y en la costa del continente Antártico. Fueron encontrados un total de 98 documentos, publicados entre 1982 e 2010, de los cuales se tuvo acceso a la totalidad del documento en el 95% de los casos. Setenta documentos son resúmenes científicos de la Comisión para la Conservación de los Recursos Marinos en la Antártica (CCAMLR, en inglés) disponibles para consulta en internet. La ocurrencia de basura marina en el ecosistema Antártico  (principalmente  en  playas  arenosas),  el  enredamiento  de  lobos  marinos  en  diferentes ítems de basura, interacciones (ingestión, enredamiento y ocurrencia de basura en áreas de nidificación) entre aves marinas y la basura, y el transporte de organismos bentónicos en plásticos flotantes fueron los asuntos más abordados en los documentos analizados. Operaciones de pesca en el Océano Atlántico Sur fueron identificadas como  la  mayor  fuente  de  basura  para  el  ambiente,  pero  plásticos  originados  en  menores  latitudes  también fueron  identificados,  indicando  transporte  a  través  del  Frente  Polar  (PF,  en  inglés). También  se  abordan  y se  discuten  en  este  trabajo,  posibles  links  entre  la Antártica  y América  del  Sul,  la  conexión  más  próxima intercontinental, en relación a la contaminación por plásticos. Como es reportado para gradientes latitudinales menores, la contaminación por plásticos es un problema relevante para el ecosistema Antártico. Sin embargo, estudios más específicos y detallados son necesarios ya que el conocimiento actual representa, probablemente, solo una pequeña parte del verdadero problema. En relación a este tipo de contaminación en los ambientes marinos y costeros del ecosistema Antártico, posiblemente estamos viendo solo la punta del iceberg. Palabras clave: Especies exóticas; A. gazella; Procellariiformes; hilos de nylon; fragmentos plásticos.PLÁSTICOS NO ECOSSISTEMA ANTÁRTICO: SERÁ QUE ESTAMOS VENDO SOMENTE A PONTA DO ICEBERG? A literatura científica relacionada à presença e aos impactos do lixo marinho em Ilhas Sub-Antárticas, na Península Antártica e na costa do continente Antártico foi organizada e interpretada neste trabalho. Um total de 98 documentos, publicados entre 1982 e 2010, foi encontrado e 95% tiveram seu conteúdo acessado integralmente. Setenta documentos são resumos científicos da Comissão para a Conservação dos Recursos Marinhos na Antártica (CCAMLR, em inglês) disponíveis para consulta na internet.  A ocorrência de lixo marinho no ecossistema Antártico (principalmente praias arenosas), o enredamento de lobos marinhos em itens do lixo, interações (ingestão, enredamento e ocorrência de lixo em áreas de nidificação) entre aves marinhas e o lixo, e o transporte de organismos bentônicos em plásticos flutuantes foram os assuntos mais abordados  nos  documentos  analisados.  Operações  de  pesca  no  Oceano  Atlântico  Sul  foram  identificadas como a maior fonte de lixo para o ambiente, mas plásticos originados em menores latitudes também foram identificados, indicando transporte através da Frente Polar (PF, em inglês). Possíveis links entre a Antárticae a América do Sul, a mais próxima conexão intercontinental, em relação à poluição por plásticos também estão destacados e discutidos neste trabalho. Como reportado para menores gradientes latitudinais, a poluição por plásticos é um problema relevante para o ecossistema Antártico. Entretanto, estudos mais específicos e detalhados são necessários já que o conhecimento atual representa, provavelmente, só uma pequena parte do verdadeiro problema. Em relação a este tipo de poluição nos ambientes marinhos e costeiros do ecossistema Antártico, nós estamos possivelmente vendo somente a ponta do iceberg. Palavras-chave: Espécies exóticas;  A. gazella; Procellariiformes; linhas de nylon; fragmentos plásticos

Rare Copy Number Variants in \u3cem\u3eNRXN1\u3c/em\u3e and \u3cem\u3eCNTN6\u3c/em\u3e Increase Risk for Tourette Syndrome

Tourette syndrome (TS) is a model neuropsychiatric disorder thought to arise from abnormal development and/or maintenance of cortico-striato-thalamo-cortical circuits. TS is highly heritable, but its underlying genetic causes are still elusive, and no genome-wide significant loci have been discovered to date. We analyzed a European ancestry sample of 2,434 TS cases and 4,093 ancestry-matched controls for rare (\u3c 1% frequency) copy-number variants (CNVs) using SNP microarray data. We observed an enrichment of global CNV burden that was prominent for large (\u3e 1 Mb), singleton events (OR = 2.28, 95% CI [1.39–3.79], p = 1.2 × 10−3) and known, pathogenic CNVs (OR = 3.03 [1.85–5.07], p = 1.5 × 10−5). We also identified two individual, genome-wide significant loci, each conferring a substantial increase in TS risk (NRXN1 deletions, OR = 20.3, 95% CI [2.6–156.2]; CNTN6 duplications, OR = 10.1, 95% CI [2.3–45.4]). Approximately 1% of TS cases carry one of these CNVs, indicating that rare structural variation contributes significantly to the genetic architecture of TS