Direct searches for dark matter: Recent results

There is abundant evidence for large amounts of unseen matter in the universe. This dark matter, by its very nature, couples feebly to ordinary matter and is correspondingly difficult to detect. Nonetheless, several experiments are now underway with the sensitivity required to detect directly galactic halo dark matter through their interactions with matter and radiation. These experiments divide into two broad classes: searches for weakly interacting massive particles (WIMPs) and searches for axions. There exists a very strong theoretical bias for supposing that supersymmetry (SUSY) is a correct description of nature. WIMPs are predicted by this SUSY theory and have the required properties to be dark matter. These WIMPs are detected from the byproducts of their occasional recoil against nucleons. There are efforts around the world to detect these rare recoils. The WIMP part of this overview focuses on the cryogenic dark matter search (CDMS) underway in California. Axions, another favored dark matter candidate, are predicted to arise from a minimal extension of the standard model that explains the absence of the expected large CP violating effects in strong interactions. Axions can, in the presence of a large magnetic field, turn into microwave photons. It is the slight excess of photons above noise that signals the axion. Axion searches are underway in California and Japan. The axion part of this overview focuses on the California effort. Brevity does not allow me to discuss other WIMP and axion searches, likewise for accelerator and satellite based searches; I apologize for their omission.

New methods of structure refinement for macromolecular structure determination by NMR

Recent advances in multidimensional NMR methodology have permitted solution structures of proteins in excess of 250 residues to be solved. In this paper, we discuss several methods of structure refinement that promise to increase the accuracy of macromolecular structures determined by NMR. These methods include the use of a conformational database potential and direct refinement against three-bond coupling constants, secondary 13C shifts, 1H shifts, T1/T2 ratios, and residual dipolar couplings. The latter two measurements provide long range restraints that are not accessible by other solution NMR parameters.

Hepatitis B virus transactivator protein, HBx, associates with the components of TFIIH and stimulates the DNA helicase activity of TFIIH.

Human hepatitis B virus genome encodes a protein, termed HBx, that is widely recognized as a transcriptional transactivator. While HBx does not directly bind cis-acting transcriptional control elements, it has been shown to associate with cellular proteins that bind DNA. Because HBx transactivated a large number of viral/cellular transcriptional control elements, we looked for its targets within the components of the basal transcriptional machinery. This search led to the identification of its interactions with TFIIH. Here, we show that HBx interacts with yeast and mammalian TFIIH complexes both in vitro and in vivo. These interactions between HBx and the components of TFIIH are supported by several lines of evidence including results from immunoprocedures and direct methods of measuring interactions. We have identified ERCC3 and ERCC2 DNA helicase subunits of holoenzyme TFIIH as targets of HBx interactions. Furthermore, the DNA helicase activity of purified TFIIH from rat liver and, individually, the ERCC2 component of TFIIH is stimulated in the presence of HBx. These observations suggest a role for HBx in transcription and DNA repair.

Mutation detection by highly sensitive methods indicates that p53 gene mutations in breast cancer can have important prognostic value.

Human cancer cells with a mutated p53 tumor-suppressor gene have a selective growth advantage and may exhibit resistance to ionizing radiation and certain chemotherapeutic agents. To examine the prognostic value of mutations in the p53 gene, a cohort of 90 Midwestern Caucasian breast cancer patients were analyzed with methodology that detects virtually 100% of all mutations. The presence of a p53 gene mutation was by far the single most predictive indicator for recurrence and death (relative risks of 4.7 and 23.2, respectively). Direct detection of p53 mutations had substantially greater prognostic value than immunohistochemical detection of p53 overexpression. Analysis of p53 gene mutations may permit identification of a subset of breast cancer patients who, despite lack of conventional indicators of poor prognosis, are at high risk of early recurrence and death.

Direct structure analysis in protein electron crystallography: crystallographic phases for halorhodopsin to 6-A resolution.

The crystal structure of halorhodopsin was determined in (centrosymmetric) projection to 6-A resolution by direct methods that use only the amplitudes of the electron diffraction pattern. A multisolution technique was used to generate initial 15-A-resolution basis sets, and after selection of the best phase set (by the closest match of magnitude of Eobs and magnitude of Ecalc), annealing of individual reflections was used to improve its accuracy. The Sayre equation was then used to expand the phase terms to 10 A, followed again by phase annealing. A final expansion with the Sayre equation enlarged this corrected phase set to 6 A. When the condition of density flatness was used to locate the best phase solution after each extension, a final structure could be observed that was quite similar to the one found earlier by analysis of electron micrographs.

Modulation of Sarco/Endoplasmic Reticulum Ca2+-ATPase 2 (SERCA2) function by acetylation following the treatment with histone deacetylase inhibitor suberoylanilide hydroxamic acid (SAHA)

Background: Acetylation and deacetylation at specific lysine (K) residues is mediated by histone acetylases (HATs) and deacetylases (HDACs), respectively. HATs and HDACs act on both histone and non-histone proteins, regulating various processes, including cardiac impulse propagation. Aim of the present work was to establish whether the function of the Ca2+ ATPase SERCA2, one of the major players in Ca2+ reuptake during excitation-contraction coupling in cardiac myocytes (CMs), could be modulated by direct K acetylation. Materials and methods: HL-1 atrial mouse cells (donated by Prof. Claycomb), zebrafish and Streptozotocin-induced diabetic rat CMs were treated with the pan-inhibitor of class I and II HDACs suberanilohydroxamic acid (SAHA) for 1.5 hour. Evaluation of SERCA2 acetylation was analyzed by co-immunoprecipitation. SERCA2 activity was measured on microsomes by pyruvate/NADH coupled reaction assay. SERCA2 mutants were obtained after cloning wild-type and mutated sequences into the pCDNA3 vector and transfected into HEK cells. Ca2+ transients in CMs (loading with Fluo3-AM, field stimulation, 0.5 Hz) and in transfected HEK cells (loading with FLUO-4, caffeine pulse) were recorded. Results: Co-Immunoprecipitation experiments performed on HL-1 cells demonstrated a significant increase in the acetylation of SERCA2 after SAHA-treatment (2.5 µM, n=3). This was associated with an increase in SERCA2 activity in microsomes obtained from HL-1 cells, after SAHA exposure (n=5). Accordingly, SAHA-treatment significantly shortened the Ca2+ reuptake time of adult zebrafish CMs. Further, SAHA 2.5 nM restored to control values the recovery time of Ca2+ transients decay in diabetic rat CMs. HDAC inhibition also improved contraction parameters, such as fraction of shortening, and increased pump activity in microsomes isolated from diabetic CMs (n=4). Notably, the K464, identified by bioinformatic tools as the most probable acetylation site on human SERCA2a, was mutated into Glutamine (Q) or Arginine (R) mimicking acetylation and deacetylation respectively. Measurements of Ca2+ transients in HEK cells revealed that the substitution of K464 with R significantly delayed the transient recovery time, thus indicating that deacetylation has a negative impact on SERCA2 function. Conclusions: Our results indicate that SERCA2 function can be improved by pro-acetylation interventions and that this mechanism of regulation is conserved among species. Therefore, the present work provides the basis to open the search for novel pharmacological tools able to specifically improve SERCA2 activity in diseases where its expression and/or function is impaired, such as diabetic cardiomyopathy.

Taxtomina A e Piriformospora indica no controle de Phytophthora nicotianae em citros e Phytophthora plurivora em faia (Fagus sylvatica)

Espécies de Phytophthora tem se destacado ao longo da história devido ao seu potencial destrutivo, se iniciando com a devastadora P. infestans na Irlanda e se estende até os dias de hoje com P. nicotianae em citros e P. plurivora em faia. Uma característica importante deste grupo de patógenos é que as medidas de controle da doença se baseiam na prevenção da entrada do patógeno na área visto que, uma vez instalado, o produtor precisa conviver com o mesmo, pois não se dispõem de métodos efetivos de controle. Neste sentido, a busca por métodos de controle torna-se primordial. O endofítico radicular Piriformospora indica, tem-se destacado em vários patossistemas devido a sua habilidade de induzir resistência contra patógenos, aumentar a tolerância à estresses abióticos e promover o crescimento de plantas. Taxtomina A, produzida por Streptomyces scabies, é capaz de ativar mecanismos de defesa de plantas, os quais são efetivos contra agentes patogênicos. Objetivou-se com este trabalho avaliar o efeito de P. indica e da taxtomina A sobre P. nicotianae em citros e P. plurivora em faia. Ambos foram avaliados quanto ao seu efeito direto sobre os patógenos em questão. O indutor de defesa vegetal Bion® foi utilizado em alguns ensaios para fins de comparação. Plântulas de citros e faia foram tratadas com concentrações crescentes de taxtomina e parâmetros fisiológicos, bioquímicos e de controle da doença foram avaliados. Taxtomina A não apresenta efeito direto sobre os patógenos avaliados. Os dados de incidência da doença em plântulas de faia tratadas com taxtomina A nas concentrações de 10, 25, 50 e 100 μg se mostraram consistentes com a quantidade de DNA do patógeno no sistema radicular, demonstrando que, aparentemente, a toxina induziu suscetibilidade nas plântulas de faia. Em citros, para os parâmetros fisiológicos e bioquímicos avaliados, em linhas gerais, a taxtomina A nas concentrações de 50 e 100 μg demonstrou potencial de aplicação no patossistema citros - P. nicotianae. Quando avaliada a mortalidade de plantas inoculadas com o patógeno e tratadas com taxtomina, bem como, quando quantificado o DNA do oomiceto no sistema radicular, as referidas concentrações também apresentaram os melhores desempenhos. Plântulas das mesmas espécies foram submetidas a inoculação com P. indica, sendo avaliados os efeitos na promoção de crescimento, na atividade de enzimas e de genes relacionados ao processo de defesa, bem como, no controle da doença. Não foi observado efeito direto do endofítico radicular sobre os patógenos avaliados. Quando plântulas de citros foram inoculadas com P. indica e depois com P. nicotianae, não foi observada promoção de crescimento e controle da doença. As análises histológicas e moleculares demonstraram a presença do endofítico no sistema radicular de plântulas de citros e faia. Análises bioquímicas revelaram apenas aumentos pontuais no teor de proteínas e na atividade da β-1,3-glucanase e da peroxidase no tratamento com P. indica + P. nicotianae. Os genes PR-1.4, PR-1.8, PR-β-glucosidase e Hsp70 foram induzidos em plântulas inoculadas com P. indica e com o patógeno, bem como no tratamento com Bion® e patógeno, porém em menor magnitude. O endofítico P. indica ativa o sistema de defesa de plântulas de citros, no entanto, os mecanismos ativados não são efetivos para o controle da doença na interação citros - P. nicotianae.

A search for anisotropy in the arrival directions of ultra high energy cosmic rays recorded at the Pierre Auger Observatory

Observations of cosmic rays arrival directions made with the Pierre Auger Observatory have previously provided evidence of anisotropy at the 99% CL using the correlation of ultra high energy cosmic rays (UHECRs) with objects drawn from the Veron-Cetty Veron catalog. In this paper we report on the use of three catalog independent methods to search for anisotropy. The 2pt-L, 2pt+ and 3pt methods, each giving a different measure of self-clustering in arrival directions, were tested on mock cosmic ray data sets to study the impacts of sample size and magnetic smearing on their results, accounting for both angular and energy resolutions. If the sources of UHECRs follow the same large scale structure as ordinary galaxies in the local Universe and if UHECRs are deflected no more than a few degrees, a study of mock maps suggests that these three method can efficiently respond to the resulting anisotropy with a P-value = 1.0% or smaller with data sets as few as 100 events. using data taken from January 1, 2004 to July 31, 2010 we examined the 20, 30, ... , 110 highest energy events with a corresponding minimum energy threshold of about 49.3 EeV. The minimum P-values found were 13.5% using the 2pt-L method, 1.0% using the 2pt+ method and 1.1% using the 3pt method for the highest 100 energy events. In view of the multiple (correlated) scans performed on the data set, these catalog-independent methods do not yield strong evidence of anisotropy in the highest energy cosmic rays.

Applying logic forms and statistical methods to CL-SR performance

This paper describes a CL-SR system that employs two different techniques: the first one is based on NLP rules that consist on applying logic forms to the topic processing while the second one basically consists on applying the IR-n statistical search engine to the spoken document collection. The application of logic forms to the topics allows to increase the weight of topic terms according to a set of syntactic rules. Thus, the weights of the topic terms are used by IR-n system in the information retrieval process.

A Highly Efficient Solvent-Free Asymmetric Direct Aldol Reaction Organocatalyzed by Recoverable (s)-Binam-L-Prolinamides. ESI-MS Evidence of the Enamine-Iminium Formation

Recoverable (Sa)-binam-l-prolinamide in combination with benzoic acid is used as catalysts in the direct aldol reaction between cycloalkyl, alkyl, and α-functionalized ketones and aldehydes under solvent-free reaction conditions. Three different methods are assayed: simple conventional magnetic stirring, magnetic stirring after previous dissolution in THF and evaporation, and ball mill technique. These procedures allow one to reduce not only the amount of required ketone to 2 equiv but also the reaction time to give the aldol products with regio-, diastereo-, and enantioselectivities comparable to those in organic or aqueous solvents. Generally anti-isomers are mainly obtained with enantioselectivities up to 97%. The reaction can be carried out under these conditions also using aldehydes as nucleophiles, yielding after in situ reduction of the aldol products the corresponding chiral 1,3-diols with moderate to high enantioselectivities mainly as anti-isomers. The aldol reaction has been studied by the use of positive ESI-MS technique, providing the evidence of the formation of the corresponding enamine−iminium intermediates.

Bénéfices de la diversité culturelle en entreprises : Études de cas dans les entreprises québécoises

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal

The EU regime on biofuels in transport: Still in search of sustainability. Egmont Paper No. 68, July 2014

Like other regions of the world, the EU is developing biofuels in the transport sector to reduce oil consumption and mitigate climate change. To promote them, it has adopted favourable legislation since the 2000s. In 2009 it even decided to oblige each Member State to ensure that by 2020 the share of energy coming from renewable sources reached at least 10% of their final consumption of energy in the transport sector. Biofuels are considered the main instrument to reach that percentage since the development of other alternatives (such as hydrogen and electricity) will take much longer than expected. Meanwhile, these various legislative initiatives have driven the production and consumption of biofuels in the EU. Biofuels accounted for 4.7% of EU transport fuel consumption in 2011. They have also led to trade and investment in biofuels on a global scale. This large-scale expansion of biofuels has, however, revealed numerous negative impacts. These stem from the fact that first-generation biofuels (i.e., those produced from food crops), of which the most important types are biodiesel and bioethanol, are used almost exclusively to meet the EU’s renewable 10% target in transport. Their negative impacts are: socioeconomic (food price rises), legal (land-grabbing), environmental (for instance, water stress and water pollution; soil erosion; reduction of biodiversity), climatic (direct and indirect land-use effects resulting in more greenhouse gas emissions) and public finance issues (subsidies and tax relief). The extent of such negative impacts depends on how biofuel feedstocks are produced and processed, the scale of production, and in particular, how they influence direct land use change (DLUC) and indirect land use change (ILUC) and the international trade. These negative impacts have thus provoked mounting debates in recent years, with a particular focus on ILUC. They have forced the EU to re-examine how it deals with biofuels and submit amendments to update its legislation. So far, the EU legislation foresees that only sustainable biofuels (produced in the EU or imported) can be used to meet the 10% target and receive public support; and to that end, mandatory sustainability criteria have been defined. Yet they have a huge flaw. Their measurement of greenhouse gas savings from biofuels does not take into account greenhouse gas emissions resulting from ILUC, which represent a major problem. The Energy Council of June 2014 agreed to set a limit on the extent to which firstgeneration biofuels can count towards the 10% target. But this limit appears to be less stringent than the ones made previously by the European Commission and the European Parliament. It also agreed to introduce incentives for the use of advanced (second- and third-generation) biofuels which would be allowed to count double towards the 10% target. But this again appears extremely modest by comparison with what was previously proposed. Finally, the approach chosen to take into account the greenhouse gas emissions due to ILUC appears more than cautious. The Energy Council agreed that the European Commission will carry out a reporting of ILUC emissions by using provisional estimated factors. A review clause will permit the later adjustment of these ILUC factors. With such legislative orientations made by the Energy Council, one cannot consider yet that there is a major shift in the EU biofuels policy. Bolder changes would have probably meant risking the collapse of the high-emission conventional biodiesel industry which currently makes up the majority of Europe’s biofuel production. The interests of EU farmers would have also been affected. There is nevertheless a tension between these legislative orientations and the new Commission’s proposals beyond 2020. In any case, many uncertainties remain on this issue. As long as solutions have not been found to minimize the important collateral damages provoked by the first generation biofuels, more scientific studies and caution are needed. Meanwhile, it would be wise to improve alternative paths towards a sustainable transport sector, i.e., stringent emission and energy standards for all vehicles, better public transport systems, automobiles that run on renewable energy other than biofuels, or other alternatives beyond the present imagination.

Cuidar no parto : prática de episiotomia

Enquadramento – A episiotomia é uma incisão feita no períneo para aumentar o canal vaginal com o objetivo de evitar outros traumas perineais durante o parto. No entanto, esta prática, por si só, já se considera um trauma perineal pelo corte em estruturas que podem desencadear problemas futuros. A Organização Mundial de Saúde (1996) recomenda a utilização limitada da episiotomia uma vez que não existem evidências credíveis de que a utilização generalizada ou de rotina desta prática tenha um efeito benéfico. Objetivos: Demonstrar evidência científica dos determinantes da prática de episiotomia seletiva em mulheres com parto normal/eutócico; identificar a prevalência de episiotomia; analisar os fatores (variáveis sociodemográficas, variáveis relativas ao recém-nascido, variáveis contextuais da gravidez e contextuais do parto) que influenciam na ocorrência de episiotomia. Métodos: O estudo empírico I seguiu a metodologia de revisão sistemática da literatura. Efetuou-se uma pesquisa na EBSCO, PubMed, SciELO, RCAAP de estudos publicados entre janeiro de 2008 e 23 de dezembro de 2014. Os estudos encontrados foram avaliados tendo em consideração os critérios de inclusão previamente estabelecidos. Dois revisores avaliaram a qualidade dos estudos a incluir utilizando a grelha para avaliação crítica de um estudo descrevendo um ensaio clínico prospetivo, aleatorizado e controlado de Carneiro (2008). Após avaliação crítica da qualidade, foram incluídos no corpus do estudo 4 artigos nos quais se obteve um score entre 87,5% e 95%. O estudo empírico II enquadra-se num estudo quantitativo, transversal, descritivo e retrospetivo, desenvolvido no serviço de Obstetrícia do Centro Hospitalar Cova da Beira, segundo um processo de amostragem não probabilística por conveniência (n = 382). A recolha de dados efetuou-se através da consulta dos processos clínicos das mulheres com idade ≥ 18 anos que tiveram um parto vaginal com feto vivo após as 37 semanas de gestação. Resultados: Evidência de que a episiotomia não deve ser realizada de forma rotineira, cujo uso deve restringir-se a situações clínicas específicas. A episiotomia seletiva, comparada com a episiotomia de rotina, está relacionada com um menor risco de trauma do períneo posterior, a uma menor necessidade de sutura e a menos complicações na cicatrização. Amostra constituída por 382 mulheres, na faixa etária dos 18-46 anos. Apenas, não se procedeu à episiotomia em 41,7% da amostra, apontando para a presença da episiotomia seletiva. Número significativo de mulheres com parto eutócico (80,5%), com sutura (95,0%), laceração de grau I (64,9%), dor perineal (89,1%) sujeitas a episiotomia (58,3%). A maioria dos recém-nascidos nasceram com peso normal (92,3%), com um valor expressivo de mulheres sujeitas a episiotomia (91,4%). Ainda se constatou a existência de casos, apesar de reduzidos, em que o recém-nascido nasceu macrossómico (5,4%), tendo-se recorrido igualmente a esta prática. Não há uma associação direta entre a realização de episiotomia e os scores do APGAR. Conclusão: Face a estes resultados e com base na evidência científica disponível que recomenda, desde há vários anos, que se faça um uso seletivo da episiotomia, sugere-se que os profissionais de saúde estejam mais despertos para esta realidade, de modo a que se possam anular as resistências e as barreiras de mudanças por parte dos mesmos face ao uso seletivo da episiotomia. Para promover essa mudança de comportamentos é importante não só mostrar as evidências científicas, bem como transpô-las para a prática, capacitando os profissionais de saúde, sobretudo os enfermeiros, na sua atuação. Palavras-chave: Parto Normal/eutócico; Episiotomia; Episiotomia seletiva; Episiotomia de rotina.

Bivalirudin for Alternative Anticoagulation in Extracorporeal Membrane Oxygenation: A Systematic Review.

BACKGROUND Extracorporeal membrane oxygenation (ECMO) offers therapeutic options in refractory respiratory and/or cardiac failure. Systemic anticoagulation with heparin is routinely administered. However, in patients with heparin-induced thrombocytopenia or heparin resistance, the direct thrombin inhibitor bivalirudin is a valid option and has been increasingly used for ECMO anticoagulation. We aimed at evaluating its safety and its optimal dosing for ECMO. METHODS Systematic web-based literature search of PubMed and EMBASE performed via National Health Service Library Evidence and manually, updated until January 30, 2016. RESULTS The search revealed 8 publications relevant to the topic (5 case reports). In total, 58 patients (24 pediatrics) were reported (18 received heparin as control groups). Bivalirudin was used with or without loading dose, followed by infusion at different ranges (lowest 0.1-0.2 mg/kg/h without loading dose; highest 0.5 mg/kg/h after loading dose). The strategies for monitoring anticoagulation and optimal targets were dissimilar (activated partial thromboplastin time 45-60 seconds to 42-88 seconds; activated clotting time 180-200 seconds to 200-220 seconds; thromboelastography in 1 study). CONCLUSION Bivalirudin loading dose was not always used; infusion range and anticoagulation targets were different. In this systematic review, we discuss the reasons for this variability. Larger studies are needed to establish the optimal approach with the use of bivalirudin for ECMO.

Bénéfices de la diversité culturelle en entreprises : Études de cas dans les entreprises québécoises

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal