"Cancer 2015": a prospective, population-based cancer cohort-phase 1: feasibility of genomics-guided precision medicine in the clinic

"Cancer 2015" is a longitudinal and prospective cohort. It is a phased study whose aim was to pilot recruiting 1000 patients during phase 1 to establish the feasibility of providing a population-based genomics cohort. Newly diagnosed adult patients with solid cancers, with residual tumour material for molecular genomics testing, were recruited into the cohort for the collection of a dataset containing clinical, molecular pathology, health resource use and outcomes data. 1685 patients have been recruited over almost 3 years from five hospitals. Thirty-two percent are aged between 61-70 years old, with a median age of 63 years. Diagnostic tumour samples were obtained for 90% of these patients for multiple parallel sequencing. Patients identified with somatic mutations of potentially "actionable" variants represented almost 10% of those tumours sequenced, while 42% of the cohort had no mutations identified. These genomic data were annotated with information such as cancer site, stage, morphology, treatment and patient outcomes and health resource use and cost. This cohort has delivered its main objective of establishing an upscalable genomics cohort within a clinical setting and in phase 2 aims to develop a protocol for how genomics testing can be used in real-time clinical decision-making, providing evidence on the value of precision medicine to clinical practice.

Retail competition and shelf space allocation

We develop a model to study shelf space allocation in retail. Retailers compete for consumers not only choosing prices but also by the space allocated to each product on shelves. Our approach depart from the existing literature on shelf allocation, as we model the problem of price setting and shelf allocation in an oligopolistic retail market. We present a simple model of retail competition in which prices are dispersed in the crosssection of stores but shelf allocation is not.

Gestão por sustentabilidade integrada - GSI: uma análise nas micro, pequenas, médias e grandes empresas - MPMGEs, a partir da literatura e da visão dos gestores industriais do Estado do Maranhão

A Tese analisou nas Micro, Pequenas e Médias Empresas, em sua primeira etapa, através da literatura, e descreveu: o seu papel na sociedade – suas definições, concepções, fases e processos; aspectos políticos, econômicos sociais, legais, de gestão, sucesso, perenidade, insucesso e mortalidade da realidade brasileira; dados comparativos das Micro, Pequenas e Médias Empresas em alguns países e a Grande Empresa. Prosseguindo, o Modelo Conceitual da Gestão por Sustentabilidade Integrada, suas Dimensões, Componentes e Variáveis, como Gestão Profissional para as empresas fundamentada no Empreendedorismo em dois ramos da literatura: a Econômica e a Gerencial; e o panorama mundial e brasileiro do Empreendedorismo. Na sequência a Gestão por Sustentabilidade Integrada em dois cenários: no Cenário I – o impacto na Gestão, Sucesso e Perenidade das Micro, Pequenas, Médias e Grandes Empresas industriais do Estado do Maranhão; e no Cenário II – o impacto da Perenidade das Micro, Pequenas, Médias e Grandes Empresas industriais no Desenvolvimento Industrial do Estado do Maranhão. Na segunda etapa, apresenta os resultados e análises de dados da Pesquisa de Campo realizada na amostra das Micro, Pequenas, Médias e Grandes Empresas industriais do Estado do Maranhão em 14 (quatorze) municípios, representando o universo dos 170 (cento e setenta) que tem indústrias formais com base no cadastro da Federação das Indústrias do Estado do Maranhão (2006). A partir da análise da literatura e da visão dos gestores da amostra industrial, a Tese analisou a problemática de “Como a Gestão por Sustentabilidade Integrada favorece a Gestão, Sucesso e Perenidade das Micro, Pequenas, Médias e Grandes Empresas industriais do Estado do Maranhão e da perenidade dessas Micro, Pequenas, Médias e Grandes Empresas no Desenvolvimento Industrial?”, em que os resultados confirmam que “A Gestão das Micro, Pequenas, Médias e Grandes Empresas industriais do Estado do Maranhão, quando aplicada na Gestão por Sustentabilidade Integrada, na visão dos gestores , favorece a Gestão, Sucesso e Perenidade das Micro, Pequenas, Médias e Grandes Empresas”; e “A perenidade das Micro, Pequenas, Médias e Grandes Empresas industriais do Estado do Maranhão, na visão dos gestores, impacta positivamente no Desenvolvimento Industrial do Estado do Maranhão”. Finalizando, apresenta as limitações, recomendações da pesquisa para futuras investigações e as conclusões.

Gonad development and hormone titres in Loggerhead Sea Turtles (Caretta caretta) in the NE Atlantic

The study proposed to describe sexual development in pelagic stage loggerhead sea turtles Caretta caretta and compare this to hatchlings and adults. It is meant as an ontogenic approach, in order to understand reproductive development and population composition and their dynamics in the pelagic environment. The study focused on the pelagic loggerheads that are found in the waters offshore Madeira Island (Portugal) in the North-eastern Atlantic and use it as a developmental habitat. The innovating character of this work relied on the lack of any description regarding the gonad ontogenesis and reproductive development for the pelagic stage in any of the 7 existing sea turtle species, all of them in danger of extinction. Three methods were used to diagnose the sex of each juvenile individual and asses the level of reproductive development: (1) laparoscopy, (2) gonad biopsy and (3) the assessment of two sex steroids circulating levels, namely testosterone and estradiol. In order to cover all life stages and compare data obtained for the juvenile stage, hatchlings and nesting female adults were sampled at the nearest nesting rookery at Boa Vista Island in the Cape Verde Archipelago. Gonads from dead hatchlings were collected for gonad histology and blood was collected from nesting females for sex steroids assessment. Laparoscopies revealed to be a valid sexing method for the juvenile stage, since gonads are morphologically differentiated at these size classes. Moreover, laparoscopy was validated using gonad histology. Gonad histology of juveniles showed that gonads are already completely differentiated into ovaries or testes at the size classes examined, but development seems to be quiescent. Males present already developed seminiferous tubules with spermatogonia lining the interior of the seminiferous tubule. Female gonads present oocytes at different development stages, but only oocytes up to stage III were observed. The maximum oocyte diameter in each individual correlated with body size, suggesting that reproductive development is an on-going process in juvenile females. The circulating levels of both testosterone and estradiol in juveniles of both sexes were very low and consistently lower than the ones observed in the nesting females from Boa Vista Island. No bimodal distribution was found for any of the sex steroids analysed and thus circulating hormone levels were not a reliable tool for sexing juvenile individuals with a non-invasive technique. The ratio testosterone:estradiol did not show a bimodal distribution either. The levels of testosterone correlated with sea surface temperature. The fact that temperatures observed during this study were below 24ºC might have hindered a differential testosterone pattern between juvenile males and females. Sex ratios for this population were generated according to laparoscopy results and compared among years and size classes. An overall sex ratio of 2 females for each male was found, but they varied among size classes but not among years. Possible causes for the sex ratios observed are discussed. This study is a contribution to our knowledge on the pelagic stage of loggerhead turtles, namely on the population structure regarding sex ratio, which is a vital tool for implementing conservation strategies.

Effects of Hormonal Supplementation on Nuclear Maturation and Cortical Granules Distribution of Canine Oocytes During Various Reproductive Stages

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Observation of the embryonic development in Pseudoplatystoma coruscans (Siluriformes: Pimelodidae) under light and scanning electron microscopy

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Sleep complaints and polysomnographic findings: A study of nuclear power plant shift workers

The literature widely recognizes that shift workers have more health complaints than the general population. The objective of this study was to describe the prevalence of sleep complaints and verify the polysomnographic (PSG) variables of shift workers in two Brazilian nuclear power plants. We carried out a subjective evaluation with a sleep questionnaire. Based on these results, the interviewees that reported sleep-related complaints were referred for polysomnographic evaluation. of the 327 volunteers initially evaluated by the sleep questionnaire, 113 (35%) reported sleep complaints; they were significantly older, had higher body mass index (BMI), and worked more years on shifts than those without sleep complaints. of these 113, 90 met criteria for various sleep disorders: 30 (9%) showed obstructive sleep apnea (OSA), 18 (5.5%) showed limb movement, and 42 (13%) evidenced both sleep problems and had a significantly higher proportion of sleep stage 1 and arousals compared with the 23 shift workers that had no indices of sleep problems. The present study found that 90 (27.5%) of the evaluated participants met the PSG criteria of some type of clinical sleep disorder. This high proportion should be investigated for associations with other aspects of work, such as working hours, working schedule, years performing shift work, and access to health services. Due to the strong association between sleep disorders and the incidence of fatigue and sleepiness, the evaluation of the sleep patterns and complaints of shift workers is essential and should be considered to be one of the basic strategies of industry to prevent accidents.

Influence of pursed-lip breathing on heart rate variability and cardiorespiratory parameters in subjects with chronic obstructive pulmonary disease (COPD)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Caracterização tectono-estratigráfica da sequência transicional na sub-bacia de Sergipe

This thesis deals with the tectonic-stratigraphic evolution of the Transitional Sequence in the Sergipe Sub-basin (the southern segment of the Sergipe-Alagoas Basin, Northeast Brazil), deposited in the time interval of the upper Alagoas/Aptian stage. Sequence boundaries and higher order internal sequences were identified, as well as the structures that affect or control its deposition. This integrated approach aimed to characterize the geodynamic setting and processes active during deposition of the Transitional Sequence, and its relations with the evolutionary tectonic stages recognized in the East Brazilian Margin basins. This subject addresses more general questions discussed in the literature, regarding the evolution from the Rift to the Drift stages, the expression and significance of the breakup unconformity, the relationships between sedimentation and tectonics at extensional settings, as well as the control on subsidence processes during this time interval. The tectonic-stratigraphic analysis of the Transitional Sequence was based on seismic sections and well logs, distributed along the Sergipe Sub-basin (SBSE). Geoseismic sections and seismic facies analysis, stratigraphic profiles and sections, were compiled through the main structural blocks of this sub-basin. These products support the depositional and tectonic-stratigraphic evolutionary models built for this sequence. The structural analysis highlighted similarities in deformation styles and kinematics during deposition of the Rift and Transitional sequences, pointing to continuing lithospheric extensional processes along a NW trend (X strain axis) until the end of deposition of the latter sequence was finished by the end of late Aptian. The late stage of extension/rifting was marked by (i) continuous (or as pulses) fault activity along the basin, controling subsidence and creation of depositional space, thereby characterizing upper crustal thinning and (ii) sagstyle deposition of the Transitional Sequence at a larger scale, reflecting the ductile stretching and thinnning of lower and sub crustal layers combined with an increasing importance of the thermal subsidence regime. Besides the late increments of rift tectonics, the Transitional Sequence is also affected by reactivation of the border faults of SBSE, during and after deposition of the Riachuelo Formation (lower section of the Transgressive Marine Sequence, of Albian age). It is possible that this reactivation reflects (through stress propagation along the newlycreated continental margin) the rifting processes still active further north, between the Alagoas Sub-basin and the Pernambuco-Paraíba Basin. The evaporitic beds of the Transitional Sequence contributed to the development of post-rift structures related to halokinesis and the continental margin collapse, affecting strata of the overlying marine sequences during the Middle Albian to the Maastrichtian, or even the Paleogene time interval. The stratigraphic analysis evidenced 5 depositional sequences of higher order, whose vertical succession indicates an upward increase of the base level, marked by deposition of continental siliciclastic systems overlain by lagunar-evaporitic and restricted marine systems, indicating that the Transitional Sequence was deposited during relative increase of the eustatic sea level. At a 2nd order cycle, the Transitional Sequence may represent the initial deposition of a Transgressive Systems Tract, whose passage to a Marine Transgressive Sequence would also be marked by the drowning of the depositional systems. At a 3rd order cycle, the sequence boundary corresponds to a local unconformity that laterally grades to a widespread correlative conformity. This boundary surface corresponds to a breakup unconformity , being equivalent to the Pre-Albian Unconformity at the SBSE and contrasting with the outstanding Pre-upper Alagoas Unconformity at the base of the Transitional Sequence; the latter is alternatively referred, in the literature, as the breakup unconformity. This Thesis supports the Pre-Albian Unconformity as marker of a major change in the (Rift-Drift) depositional and tectonic setting at SBSE, with equivalent but also diachronous boundary surfaces in other basins of the Atlantic margin. The Pre-upper Alagoas Unconformity developed due to astenosphere uplift (heating under high lithospheric extension rates) and post-dates the last major fault pulse and subsequent extensive block erosion. Later on, the number and net slip of active faults significantly decrease. At deep to ultra deep water basin segments, seaward-dipping reflectors (SDRs) are unconformably overlain by the seismic horizons correlated to the Transitional Sequence. The SDRs volcanic rocks overly (at least in part) continental crust and are tentatively ascribed to melting by adiabatic decompression of the rising astenospheric mantle. Even though being a major feature of SBSE (and possibly of other basins), the Pre-upper Alagoas Unconformity do not correspond to the end of lithospheric extension processes and beginning of seafloor spreading, as shown by the crustal-scale extensional structures that post-date the Transitional Sequence. Based on this whole context, deposition of the Transitional Sequence is better placed at a late interval of the Rift Stage, with the advance of an epicontinental sea over a crustal segment still undergoing extension. Along this segment, sedimentation was controled by a combination of thermal and mechanical subsidence. In continuation, the creation of oceanic lithosphere led to a decline in the mechanical subsidence component, extension was transferred to the mesoceanic ridge and the newly-formed continental margin (and the corresponding Marine Sequence) began to be controlled exclusively by the thermal subsidence component. Classical concepts, multidisciplinary data and new architectural and evolutionary crustal models can be reconciled and better understood under these lines

Recalled and recorded bowel habits confirm early onset and high frequency of constipation in day-care nursery children

CONTEXTO: Mães relatam início precoce de constipação em crianças atendidas em clínicas de gastroenterologia. OBJETIVOS: Estudar o hábito intestinal em crianças de baixa idade na comunidade, para avaliar se início precoce da constipação é confirmado neste contexto e se há concordância entre o hábito intestinal relatado e o registrado prospectivamente. MÉTODOS: Obtiveram-se dados sobre evacuações de 57 crianças com idade 6.0-40.7 meses, mediante relato materno (questionário sobre características fecais predominantes) e, a seguir, foram registradas 1.934 evacuações em casa e na creche. O hábito intestinal foi classificado como adequado, constipação, diarréia funcional, outro hábito intestinal, conforme frequência evacuatória e proporção das características fecais (macias, duras e/ou que escorrem). Usaram-se dois critérios para classificar o hábito intestinal registrado, devido indefinição no ponto de corte para fezes duras na identificação de constipação em crianças: critério predominante e critério adulto, respectivamente com >50% e >25% de evacuações com consistência alterada. Usou-se estatística não-paramétrica e, para concordância entre hábito intestinal relatado e registrado, o índice Kappa. RESULTADOS: Constipação ocorreu em 17.5%, 10.5%, 19.3% das crianças, respectivamente pelo relato e pelo registro segundo critérios predominante e adulto. Constipação foi o hábito intestinal mais frequentemente relatado, versus 12.3% outro hábito intestinal. Só uma criança se classificou como tendo diarréia funcional (pelo critério adulto). Concordância entre o hábito intestinal relatado e o registrado foi razoável (fair) para constipação, pelos critérios predominante e adulto (K=0.28 e 0.24, respectivamente), mas apenas leve (slight) para os demais hábito intestinal (K <0.16). Entretanto, dados individuais indicaram melhor relação entre relato de constipação com o critério adulto do que com o critério predominante. CONCLUSÕES: Confirmou-se que constipação é frequente e de início precoce. Concordância razoável entre o hábito intestinal relatado e o registrado segundo os dois critérios indica que o relato materno é razoavelmente confiável para detectar constipação.

Performance, carcass yield, and meat quality of free-range broilers fed wet grain corn silage

This study aimed at evaluating the effect of total replacement of dry corn by wet grain corn silage (WGCS) in the feed of label broilers older than 28 days of age on performance, mortality, carcass, parts, breast meat and thighs meat yields, and meat quality. A mixed-sex flock of 448 ISA S 757-N (naked-neck ISA JA Label) day-old chicks was randomly distributed in to randomized block experimental design with four treatments (T1 - with no WGCS; T2 - WGCS between 28 and 83 days; T3 - WGCS between 42 and 83 days; and T4 - WGCS between 63 and 83 days) and four replicates of 28 birds each. Birds were raised under the same management and feeding conditions until 28 days of age, when they started to have free access to paddock with pasture (at least 3m²/bird) and to be fed the experimental diets. Feed and water were offered ad libitum throughout the rearing period, which was divided in three stages: starter (1 to 28 days), grower (29 to 63 days), and finisher (64 to 83 days) according to the feeding schedule. During the short periods of WGCS use (group T2 during grower stage and T4 during the finisher stage), performance and mortality results were similar as to those of the control group (T1). At the end of the experiment, it was observed that the extended use of WGCS (T2 and T3) determined a negative effect on feed conversion ratio. However, the best results of breast meat yield were observed with birds fed WGCS since 28 days (T2). It was concluded that WGCS can replace dry corn grain for short periods during the grower and finisher stages with no impairment of meat quality and yield in slow growth broilers.

Expression of fibroblast growth factor 10 and its receptor, fibroblast growth factor receptor 2B, in the bovine corpus luteum

There is evidence that several fibroblast growth factors (FGFs) are involved in growth and development of the corpus luteum (CL), but many FGFs have not been investigated in this tissue, including FGF10. The objective of this study was to determine if FGF10 and its receptor (FGFR2B) are expressed in the CL. Bovine CL were collected from an abattoir and classed as corpus hemorrhagica (stage 1), developing (stage 11), developed (stage 111), and regressed (stage IV) CL. Expression of FGF10 and FGFR2B mRNA was measured by reverse transcription-polymerase chain reaction (RT-PCR). Both genes were expressed in bovine CL, and FGF10 expression did not differ between stages of CL development. FGF10 protein was localized to large and small luteal cells by immunohistochemistry. FGFR2B expression was approximately threefold higher in regressed compared to developing and developed CL (P < 0.05). To determine if FGF10 and FGFR2B expression is regulated during functional luteolysis, cattle were injected with PGF2 alpha and CL collected at 0, 0.5, 2, 4, 12, 24, 48, and 64 hr thereafter (n = 5 CL/time point), and mRNA abundance was measured by real-time RT-PCR. FGF10 mRNA expression did not change during functional luteolysis, whereas FGFR2B mRNA abundance decreased significantly at 2, 4, and 12 hr after PGF2a, and returned to pretreatment levels for the period 24-64 hr post-PGF2 alpha. These data suggest a potential role for FGFR2B signaling during structural luteolysis in bovine CL.

Solution approaches for the soft drink integrated production lot sizing and scheduling problem

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Surveillance Programme for Healthcare Associated Infections in the State of São Paulo, Brazil. Implementation and the first three years' results

Governmental programmes should be developed to collect and analyse data on healthcare associated infections (HAIs). This study describes the healthcare setting and both the implementation and preliminary results of the Programme for Surveillance of Healthcare Associated Infections in the State of São Paulo (PSHAISP), Brazil, from 2004 to 2006. Characterisation of the healthcare settings was carried out using a national database. The PSHAISP was implemented using components for acute care hospitals (ACH) or long term care facilities (LTCF). The components for surveillance in ACHs were surgical unit, intensive care unit and high risk nursery. The infections included in the surveillance were surgical site infection in clean surgery, pneumonia, urinary tract infection and device-associated bloodstream infections. Regarding the LTCF component, pneumonia, scabies and gastroenteritis in all inpatients were reported. In the first year of the programme there were 457 participating healthcare settings, representing 51.1% of the hospitals registered in the national database. Data obtained in this study are the initial results and have already been used for education in both surveillance and the prevention of HAI. The results of the PSHAISP show that it is feasible to collect data from a large number of hospitals. This will assist the State of São Paulo in assessing the impact of interventions and in resource allocation. (C) 2010 The Hospital Infection Society. Published by Elsevier Ltd. All rights reserved.

Detection of HPV in mouth floor squamous cell carcinoma and its correlation with clinicopathologic variables, risk factors and survival

The human papillomavirus (HPV) has been historically associated with head and neck cancers, although its role in oral carcinogenesis remains poorly defined. The purpose of this study was to investigate the prevalence of HPV in mouth floor squamous cell carcinoma and correlate it with clinicopathologic variables, risk factors and survival. HPV presence was evaluated by nested polymerase chain reaction (nPCR) in 29 paraffin-embedded specimens of mouth floor squamous cell carcinoma. HPV DNA was detected in 17.2% (5 of 29) of the specimens; the highest prevalence was observed in non-smoking patients over the age of 60 years. All HPV DNA positive specimens were detected in men with clinical stage III and IV lesions, being most of which were moderately differentiated. Despite this correlation there were no statistically significant differences observed among the analyzed variables, including patients' survival. The relatively low incidence of HPV DNA present in these tumors suggests that this virus does not, by itself, have a significant role in the development of mouth floor squamous cell carcinoma. J Oral Pathol Med (2008) 37: 593-598