Consensus clustering methodology to improve molecular stratification of non-small cell lung cancer.

Recent advances in machine learning research, combined with the reduced sequencing costs enabled by modern next-generation sequencing, paved the way to the implementation of precision medicine through routine multi-omics molecular profiling of tumours. Thus, there is an emerging need of reliable models exploiting such data to retrieve clinically useful information. Here, we introduce an original consensus clustering approach, overcoming the intrinsic instability of common clustering methods based on molecular data. This approach is applied to the case of non-small cell lung cancer (NSCLC), integrating data of an ongoing clinical study (PROMOLE) with those made available by The Cancer Genome Atlas, to define a molecular-based stratification of the patients beyond, but still preserving, histological subtyping. The resulting subgroups are biologically characterized by well-defined mutational and gene-expression profiles and are significantly related to disease-free survival (DFS). Interestingly, it was observed that (1) cluster B, characterized by a short DFS, is enriched in KEAP1 and SKP2 mutations, that makes it an ideal candidate for further studies with inhibitors, and (2) over- and under-representation of inflammation and immune systems pathways in squamous-cell carcinomas subgroups could be potentially exploited to stratify patients treated with immunotherapy.

Melatonin reduces the need for sedation in ICU patients: a randomized controlled trial.

BACKGROUND: Critically ill patients suffer from physiological sleep deprivation and have reduced blood melatonin levels. This study was designed to determine whether nocturnal melatonin supplementation would reduce the need for sedation in patients with critical illness. METHODS: A single-center, double-blind randomized placebo-controlled trial was carried out from July 2007 to December 2009, in a mixed medical-surgical Intensive Care Unit of a University hospital, without any form of external funding. Of 1158 patients admitted to ICU and treated with conscious enteral sedation, 82 critically-ill with mechanical ventilation >48 hours and Simplified Acute Physiology Score II>32 points were randomized 1:1 to receive, at eight p.m. and midnight, melatonin (3+3mg) or placebo, from the third ICU day until ICU discharge. Primary outcome was total amount of enteral hydroxyzine administered. RESULTS: Melatonin treated patients received lower amount of enteral hydroxyzine. Other neurological indicators (amount of some neuroactive drugs, pain, agitation, anxiety, sleep observed by nurses, need for restraints, need for extra sedation, nurse evaluation of sedation adequacy) seemed improved, with reduced cost for neuroactive drugs. Post-traumatic stress disorder prevalence did not differ between groups, nor did ICU or hospital mortality. Study limitations include the differences between groups before intervention, the small sample size, and the single-center observation. CONCLUSION: Long-term enteral melatonin supplementation may result in a decreased need for sedation, with improved neurological indicators and cost reduction. Further multicenter evaluations are required to confirm these results with different sedation protocols.

Behavioral flexibility of a group of bearded capuchin monkeys (Cebus libidinosus) in the National Park of Brasília (Brazil): consequences of cohabitation with visitors / Flexibilidade comportamental de um grupo de macacos-prego (Cebus libidinosus) no Parque Nacional de Brasília (Brasil): conseqüências da convivência com os visitantes

Increasing urbanization and deforestation have enhanced the opportunities of contact between humans and monkeys and the impact of human activities on primate behavior is receiving growing attention. This study explores whether activity budgets and diet of a group of capuchin monkeys (Cebus libidinosus) inhabiting the area of the swimming pools of the National Park of Brasília is affected by the presence of visitors providing food to them. During one year, both in the dry and the wet seasons, we scored capuchins' behavior via scan sampling every ten minutes. Results showed that this group spent less time foraging for wild foods than other comparable groups living in similar habitats. Moreover, capuchins relied more on human food during the dry season, when pulpy fruits were less available, than in the wet season. Our findings confirm other studies on different monkey species that have shown that access to human food decreases the time spent foraging for wild food and the home range size. They also show that capuchins are able to modify their diet, to exploit alternative food sources, and to change their activity budget in response to the availability of new food opportunities and to seasonal food availability.

Recentemente, o impacto de atividades humanas sobre o comportamento de primatas tem recebido maior importância dado o crescente desmatamento e urbanização, que têm favorecido o aumento do contato entre humanos e macacos. O presente estudo descreve os padrões de atividade e a dieta de um grupo de macacos-prego (Cebus libidinosus) que vive no Parque Nacional de Brasília. O Parque é freqüentado diariamente por visitantes, de modo que os animais estão habituados à presença humana, bem como ao consumo de itens de sua dieta. Observações comportamentais do grupo foram realizadas ao longo de um ano, compreendendo a estação seca e a chuvosa, utilizando-se registro de varredura a cada 10 minutos. Resultados obtidos indicaram que o grupo despendeu menos tempo forrageando itens naturais do que outros grupos vivendo em habitats similares. Além disso, durante a estação seca, quando há menor disponibilidade dos frutos de polpa, os macacos-prego alimentaram-se mais de itens da dieta humana como uma fonte alternativa de recurso. Como demonstrado em estudos anteriores realizados com outras espécies de macacos, a alimentação baseada em itens da dieta humana pareceu diminuir a motivação dos animais para forragear no seu habitat natural, assim como promoveu a redução do tempo gasto no forrageamento e a redução de sua área de uso. Nossos resultados indicaram ainda que o consumo de comida humana reflete o caráter adaptável dos animais em explorar fontes alternativas de recurso, bem como a sua habilidade em modificar a sua dieta e padrões de comportamento face às mudanças ambientais.

Physical properties of palm fruits processed with tools by wild bearded capuchins (Cebus libidinosus).

Habitually, capuchin monkeys access encased hard foods by using their canines and premolars and/or by pounding the food on hard surfaces. Instead, the wild bearded capuchins (Cebus libidinosus) of Boa Vista (Brazil) routinely crack palm fruits with tools. We measured size, weight, structure, and peak-force-at-failure of the four palm fruit species most frequently processed with tools by wild capuchin monkeys living in Boa Vista. Moreover, for each nut species we identify whether peak-force-at-failure was consistently associated with greater weight/volume, endocarp thickness, and structural complexity. The goals of this study were (a) to investigate whether these palm fruits are difficult, or impossible, to access other than with tools and (b) to collect data on the physical properties of palm fruits that are comparable to those available for the nuts cracked open with tools by wild chimpanzees. Results showed that the four nut species differ in terms of peak-force-at-failure and that peak-force-at-failure is positively associated with greater weight (and consequently volume) and apparently with structural complexity (i.e. more kernels and thus more partitions); finally for three out of four nut species shell thickness is also positively associated with greater volume. The finding that the nuts exploited by capuchins with tools have very high resistance values support the idea that tool use is indeed mandatory to crack them open. Finally, the peak-force-at-failure of the piassava nuts is similar to that reported for the very tough panda nuts cracked open by wild chimpanzees; this highlights the ecological importance of tool use for exploiting high resistance foods in this capuchin species.

Sleep and delirium in the intensive care unit.

Intensive Care Unit (ICU) patients almost uniformly suffer from sleep disruption. Even though the role of sleep disturbances is not still adequately understood, they may be related to metabolic, immune, neurological and respiratory dysfunction and could worsen the quality of life after discharge. A harsh ICU environment, underlying disease, mechanical ventilation, pain and drugs are the main reasons that underlie sleep disruption in the critically ill. Polysomnography is the gold standard in evaluating sleep, but it is not feasible in clinical practice; therefore, other objective (bispectral index score [BIS] and actigraphy) and subjective (nurse and patient assessment) methods have been proposed, but their adequacy in ICU patients is not clear. Frequent evaluation of neurological status with validated tools is necessary to avoid excessive or prolonged sedation in order to better titrate patient-focused therapy. Hypnotic agents like benzodiazepines can increase total sleep time, but they alter the physiological progression of sleep phases, and decrease the time spent in the most restorative phases compared to the phases normally mediated by melatonin; melatonin production is decreased in critically ill patients, and as such, exogenous melatonin supplementation may improve sleep quality. Sleep disruption and the development of delirium are frequently related, both because of sleep scarcity and inappropriate dosing with sedatives. Delirium is strongly related to increased ICU morbidity and mortality, thus the resolution of sleep disruption could significantly contribute to improved ICU outcomes. An early evaluation of delirium is strongly recommended because of the potential to resolve the underlying causes or to begin an appropriate therapy. Further studies are needed on the effects of strategies to promote sleep and on the evaluation of better sleep in clinical outcomes, particularly on the development of delirium.

An experimental analysis of ingestion rates in an omnivorous species.

Food intake is difficult to estimate under natural conditions. We investigated ingestion rates of 14 different food types in 26 captive capuchin monkeys (Cebus apella). The procedure consisted in weighing a piece of food and using a two alternative choice tests to present food to the subject, alone in its cage. We recorded the food chosen and the time it took the subject to consume the food entirely. Consumption time was converted into ingestion rates (g/s) for each food type. Ingestion rates of food types significantly differed, and the difference was significantly higher among foods than among subjects. In particular, ingestion rates of the fruits were higher than those of human-processed food. Interestingly, food preferences were significantly related to energy intake rate, i.e., to the amount of energy ingested per unit of time, but not with ingestion rates or energy content alone. The energy acquired by eating different types of food cannot be calculated on the basis of the time spent eating unless a correction factor for each given food (or similar ones) is applied. Future controlled studies should provide field researchers with such corrections factors, possibly using foods collected in the wild.

Behavioral flexibility of a group of bearded capuchin monkeys (Cebus libidinosus) in the National Park of Brasília (Brazil): consequences of cohabitation with visitors.

Increasing urbanization and deforestation have enhanced the opportunities of contact between humans and monkeys and the impact of human activities on primate behavior is receiving growing attention. This study explores whether activity budgets and diet of a group of capuchin monkeys (Cebus libidinosus) inhabiting the area of the swimming pools of the National Park of Brasília is affected by the presence of visitors providing food to them. During one year, both in the dry and the wet seasons, we scored capuchins' behavior via scan sampling every ten minutes. Results showed that this group spent less time foraging for wild foods than other comparable groups living in similar habitats. Moreover, capuchins relied more on human food during the dry season, when pulpy fruits were less available, than in the wet season. Our findings confirm other studies on different monkey species that have shown that access to human food decreases the time spent foraging for wild food and the home range size. They also show that capuchins are able to modify their diet, to exploit alternative food sources, and to change their activity budget in response to the availability of new food opportunities and to seasonal food availability.

The integration of high throughput technologies for drug discovery.

Producing quality clinical candidates less prone to late stage failure is greatly facilitated by better integration of the relevant high throughput functions and the inclusion of ADME/toxicology further upstream in the discovery process. We describe the tasks and their integration in the context of the design, make and test triad.

A 46 kDa NTPase common to rat liver nuclear envelope, mitochondria, plasma membrane, and endoplasmic reticulum.

A 46 kDa ATP binding polypeptide of the nuclear envelope, virtually identical to the nuclear envelope NTPase putatively involved in mRNA efflux [6], is present in all rat liver cell membranes. Its presence in nuclear envelope is not the result of cross contamination during isolation.

Identification of nuclear envelope proteins and glycoproteins which co-isolate with the nuclear protein matrix.

Nuclear envelopes and nuclear matrices were isolated from rat liver nuclei. Although differences in polypeptide composition of the structures are evident on SDS gel electrophoresis, they have an almost identical distribution of concanavalin A-binding glycoproteins. These matrix-associated concanavalin A-binding glycoproteins derive entirely from the nuclear envelope and are recovered almost quantitatively in the matrix. They constitute easily identifiable markers for nuclear envelope association with matrix or other nuclear subfractions. Surface labelling of nuclei with 125I using solid-phase lactoperoxidase further confirmed that a large number of envelope-associated nuclear surface proteins co-isolate with the matrix. Protein kinase activity, as well as endogenous substrates for the kinase(s) are shown to be the same in both envelopes and matrix. Envelope-derived proteins and glycoproteins may comprise a substantial proportion of total matrix protein.

Carrier-free 8-azidoadenosine 5'-[gamma-32P]triphosphate.

We found 8-azidoadenosine 5'-diphosphate to be a phosphoryl acceptor in the enzymatic conversion of 1,3-diphosphoglyceric acid to 3-phosphoglycerate. This has allowed us to synthesize in a single-step procedure carrier-free 8-azidoadenosine 5'-[gamma-32P]triphosphate, requiring no further purification of the end product. The synthesized 8-azidoadenosine 5'-[gamma-32P]triphosphate has been characterized and shown to meet all the criteria for a specific photoreactive ATP analogue.

Rat liver glucocorticoid receptor isolated by affinity chromatography is not a Mg2+- or Ca2+-dependent protein kinase.

The glucocorticoid hormone receptor (92 kDa), purified 9000-fold from rat liver cytosol by steroid affinity chromatography and DEAE-Sephacel chromatography, was assayed for the presence of protein kinase activity by incubations with [gamma-32P]ATP and the photoaffinity label 8-azido-[gamma-32P]ATP. Control preparations isolated by affinity chromatography in the presence of excess steroid to prevent the receptor from binding to the affinity matrix were assayed for kinase activity in parallel. The receptor was not labeled by the photoaffinity label under photoactivation conditions in the presence of Ca2+ or Mg2+. A Mg2+-dependent protein kinase (48 kDa) that could be photoaffinity labeled with 8-azido-ATP copurified with the receptor. This kinase was also present in control preparations. The kinase could phosphorylate several minor contaminants present in the receptor preparation, including a protein (or proteins) of similar molecular weight to the receptor. The phosphorylation of 90-92-kDa proteins was independent of the state of transformation or steroid-binding activity of the receptor. These experiments provide direct evidence that neither the glucocorticoid receptor nor the 90-92-kDa non-steroid-binding protein associated with the molybdate-stabilized glucocorticoid receptor possesses intrinsic Ca2+- or Mg2+-dependent protein kinase activity.