Biallelic ATM inactivation significantly reduces survival in patients treated on the United Kingdom Leukemia Research Fund Chronic Lymphocytic Leukemia 4 trial.

PURPOSE: The prognostic significance of ATM mutations in chronic lymphocytic leukemia (CLL) is unclear. We assessed their impact in the context of a prospective randomized trial. PATIENTS AND METHODS: We analyzed the ATM gene in 224 patients treated on the Leukemia Research Fund Chronic Lymphocytic Leukemia 4 (LRF-CLL4) trial with chlorambucil or fludarabine with and without cyclophosphamide. ATM status was analyzed by denaturing high-performance liquid chromatography and was related to treatment response, survival, and the impact of TP53 alterations for the same patient cohort. RESULTS: We identified 36 ATM mutations in 33 tumors, 16 with and 17 without 11q deletion. Mutations were associated with advanced disease stage and involvement of multiple lymphoid sites. Patients with both ATM mutation and 11q deletion showed significantly reduced progression-free survival (median, 7.4 months) compared with those with ATM wild type (28.6 months), 11q deletion alone (17.1 months), or ATM mutation alone (30.8 months), but survival was similar to that in patients with monoallelic (6.7 months) or biallelic (3.4 months) TP53 alterations. This effect was independent of treatment, immunoglobulin heavy chain variable gene (IGHV) status, age, sex, or disease stage. Overall survival for patients with biallelic ATM alterations was also significantly reduced compared with those with ATM wild type or ATM mutation alone (median, 42.2 v 85.5 v 77.6 months, respectively). CONCLUSION: The combination of 11q deletion and ATM mutation in CLL is associated with significantly shorter progression-free and overall survival following first-line treatment with alkylating agents and purine analogs. Assessment of ATM mutation status in patients with 11q deletion may influence the choice of subsequent therapy.

Studies on Bio-Geochemistry, Bio-Optical Properties and Satellite Validation of Coastal Waters of South Eastern Arabian Sea

In situ methods used for water quality assessment have both physical and time constraints. Just a limited number of sampling points can be performed due to this, making it difficult to capture the range and variability of coastal processes and constituents. In addition, the mixing between fresh and oceanic water creates complex physical, chemical and biological environment that are difficult to understand, causing the existing measurement methodologies to have significant logistical, technical, and economic challenges and constraints. Remote sensing of ocean colour makes it possible to acquire information on the distribution of chlorophyll and other constituents over large areas of the oceans in short periods. There are many potential applications of ocean colour data. Satellite-derived products are a key data source to study the distribution pattern of organisms and nutrients (Guillaud et al. 2008) and fishery research (Pillai and Nair 2010; Solanki et al. 2001. Also, the study of spatial and temporal variability of phytoplankton blooms, red tide identification or harmful algal blooms monitoring (Sarangi et al. 2001; Sarangi et al. 2004; Sarangi et al. 2005; Bhagirathan et al., 2014), river plume or upwelling assessments (Doxaran et al. 2002; Sravanthi et al. 2013), global productivity analyses (Platt et al. 1988; Sathyendranath et al. 1995; IOCCG2006) and oil spill detection (Maianti et al. 2014). For remote sensing to be accurate in the complex coastal waters, it has to be validated with the in situ measured values. In this thesis an attempt to study, measure and validate the complex waters with the help of satellite data has been done. Monitoring of coastal ecosystem health of Arabian Sea in a synoptic way requires an intense, extensive and continuous monitoring of the water quality indicators. Phytoplankton determined from chl-a concentration, is considered as an indicator of the state of the coastal ecosystems. Currently, satellite sensors provide the most effective means for frequent, synoptic, water-quality observations over large areas and represent a potential tool to effectively assess chl-a concentration over coastal and oceanic waters; however, algorithms designed to estimate chl-a at global scales have been shown to be less accurate in Case 2 waters, due to the presence of water constituents other than phytoplankton which do not co-vary with the phytoplankton. The constituents of Arabian Sea coastal waters are region-specific because of the inherent variability of these optically-active substances affected by factors such as riverine input (e.g. suspended matter type and grain size, CDOM) and phytoplankton composition associated with seasonal changes.

Studies on Quasinormal Modes and Late-time Tails in Black Hole Spacetimes

Black hole's response to external perturbations will carry significant information about these exotic objects. Its response, shortly after the initial `kick', is known to be ruled by the damped oscillation of the perturbating eld, called quasinormal modes(QNMs), followed by the tails of decay and is the characteristic of the background black hole spacetime. In the last three decades, several shortcomings came out in the Einstein's General Theory of Relativity(GTR). Such issues come, especially, from observational cosmology and quantum eld theory. In the rst case, for example, the observed accelerated expansion of the universe and the hypothesized mysterious dark energy still lack a satisfactory explanation. Secondly, GTR is a classical theory which does not work as a fundamental theory, when one wants to achieve a full quantum description of gravity. Due to these facts modi cation to GTR or alternative theories for gravity have been considered. Two potential approaches towards these problems are the quintessence model for dark energy and Ho rava-Lifshitz(HL) gravity. Quintessence is a dynamical model of dark energy which is often realized by scalar eld mechanism. HL gravity is the recently proposed theory of gravity, which is renormalizable in power counting arguments. The two models are considered as a potential candidate in explaining these issues.

Studies on Mahshahr Creeks macrobenthos with emphasis on their importance in fish feeding

To study the macrobenthic community at Mahshahr creek four Creeks namely Bihad, Doragh, Ghazaleh and Ghanam were chosen. Sampling was conducted on bimonthly basis and carried out from August 1996 to June 1997, 216 sediment samples were collected from 12 stations using 0.1 m^2 Van Veen Grab, The stations were located at the mouth, middle and the end of each Creek. In situ measurements of temperature pH, DO and salinity were done using different sensors. The samples for the measurements of TOM, grain size were collected and analysed in vitro. The results indicate spatial and temporal heterogeneity in the structure of macro faunal assemblages of the creeks. A total of 12 macrofaunal groups were identified within the study area. Amphipods were the most dominant group (43%) followed by polychaetes (42%), copepods (3.5%), tanaids (3.1%) and other groups (8.4%). The range for the numerical abundance of macrobenthos was between 12583 to 3648 individual per m2 and the variation was done to different bottom texture the variable environment conditions governing the different parts of each creek as well as within creeks. Application of diversity indices (Shannon H and Simpson indices) on the dominant macrobenthic assemblages (crustaceans & polychaetes) was varied between 1 to 2.5 being higher in Bihad and Ghanarn and much reduced Shannon H index or a higher Simpson in Ghazaleh. Probably brought about activities in this creek. Gut content analysis of four species of fish showed that the main food items consist of Crab, Shrimps and other crustacean species, The secondary production of macrobenthic fauna and hence a fish production were assessed. To do this first the production of most dominant species Apseudes sp. was computed through Cohort analysis. The total macrobenthic production was estimated and from this fish production was computed. The macrobenthic and fish secondary productions were 24300 tons/year) and 24300 (tons/year) respectively. These values were lower than those with similar areas in the Indian Ocean.

Studies on diversity of Hara's Laft - Khamir and Sout Beaches of the Gheshm polychaetes

One of the most important marine ecologic phenomenon, is the study of animal community among the bed or benthic fauna. Macrobenthoses are the great part of the benthic fauna that are more biomass than meiofauna and microfauna. To study polychaetes diversity of mangroves, located in Khoore-Khooran, sampling was conducted on a bimonthly and carried out from December 2001 to October 2002. Bottom samples were collected by Van Veen grab (0.025 m2) at 6 station from 2 transect in situ measurement of temperature, pH, DO and salinity were done. A total of polychaetes were identified within study 32 Family and 43 Genus. Cirriphormia and Nephtys were the most dominant genus in the studies. The range numerical abundance of polychaetes was between 3006 per m2 in the station A3 to 559 individual per m2 in the station A1 and the variation was done to different bottom, texture the variable environment conditions governing the different parts of each creeks as well as within creeks. Application of diversity indices (Shannon H') on the dominant polychaetes assemblages has higher H' in the Azar and lower H' in the Mehr and the stations B3 has the highest H' and the station A2 has the lowest H' Application of diversity and Richness, Evennes were studied and showed that the station A3 has the lowest evenness and the most individual, and station A I has the middle pollution.

Five-year review of an international clinical research-training program

The exponential increase in clinical research has profoundly changed medical sciences. Evidence that has accumulated in the past three decades from clinical trials has led to the proposal that clinical care should not be based solely on clinical expertise and patient values, and should integrate robust data from systematic research. As a consequence, clinical research has become more complex and methods have become more rigorous, and evidence is usually not easily translated into clinical practice. Therefore, the instruction of clinical research methods for scientists and clinicians must adapt to this new reality. To address this challenge, a global distance-learning clinical research-training program was developed, based on collaborative learning, the pedagogical goal of which was to develop critical thinking skills in clinical research. We describe and analyze the challenges and possible solutions of this course after 5 years of experience (2008-2012) with this program. Through evaluation by students and faculty, we identified and reviewed the following challenges of our program: 1) student engagement and motivation, 2) impact of heterogeneous audience on learning, 3) learning in large groups, 4) enhancing group learning, 5) enhancing social presence, 6) dropouts, 7) quality control, and 8) course management. We discuss these issues and potential alternatives with regard to our research and background.

Studies on the synthesis of novel PP2A inhibitors and a GPCR detergent

Chapter 1 While targeting kinases in oncology research has been explored extensively, targeting protein phosphatases is currently in its infancy. However, a number of pharmaceutical companies are currently looking to expand their research efforts in this area. PP2A has been shown to down-regulate ERK5, a mitogen-activated protein kinase (MAPK) that has been shown to be important in driving the invasive phenotype of prostate cancer. Fostriecin and its related structural analogues PD 113,270 and 113,271 have been shown to inhibit a mitotic entry checkpoint in cell growth through the potent and selective inhibition of protein phosphatases PP1, PP2A, and PP4 (IC50 of 45 μM, 1.5 nM, and 3 nM respectively). Fostriecin is one of the most selective protein phosphatase inhibitors disclosed to date with a 104 fold selectivity for PP2A/PP4 versus PP1. Unfortunately, fostriecin and its analogues are very unstable, and this instability has effectively prevented them from being used as effective therapeutic leads. The microcystins and nodularins on the other hand, exhibit significant inhibitory activity against PP1 and PP2A (IC50 = 26 pM and 1.8 nM respectively), but their high toxicity has prevented any therapeutic application. Truncation of the ADDA chain from these polypeptides completely attenuates PP inhibitory activity. Simpler analogues incorporating the N-acylated ADDA chain and D-Ala retain moderate activity against PP1 and PP2A (IC50 = 1.0 μM and 0.17 μM respectively). The generation of a new series of fostriecin analogues to further expand its structure-activity relationship is envisaged with a view to creating new more stable PP2A inhibitors. It was hoped that by incorporating some of the more stable structural features of ADDA into fostriecin that stability and activity could be reconciled. With that in mind a series of PP2A inhibitors were synthesised and biologically evaluated. Chapter 2 GPCRs are an important area of research and are the targets of a quarter of the drugs on the market (2005). As a result, GPCRs continue to be at the forefront of research in both small and large drug companies. However one of the difficulties in studying this diverse class of membrane proteins is their tendency to denature in aqueous solution. As a result there is a pressing need to develop new detergents to solubilise, stabilise and crystallise GPCRs in their native form for further study. Cholesterol analogues have been shown to be important for stabilising membrane proteins and preventing their thermal inactivation. In addition the β2-adrenergic receptor, a GPCR membrane protein, has been crystallised in the active state with two cholesterol molecules bound between the I, II, III and IV helices of the protein. This appears to represent a distinct cholesterol binding pocket on the membrane protein that is speculated to be conserved across up to 44% of the rhodopsin class of GPCRs. CHOBIMALT is a cholesterol-based detergent that has been shown to exhibit promising GPCR-stabilising properties. When benchmarked against other cholesterol based detergents it was found to be superior to all others tested except for cholesteryl hemisuccinate.1 CHOBIMALT has an aggregation number of roughly 200 and forms 210 ± 30 kDa micelles, which are significantly larger than those of most detergents used for biological systems which is likely due to the packing constraints associated with CHOBMALT’s large polar headgroup.2 As a result, CHOBIMALT is used mostly as an additive to other commercially available detergents in order to decrease micelle size. A branched dimaltoside motif is common in recently synthesised detergents by Chae and co-workers. These detergents have shown promising detergent properties, for example the maltose neopentyl glycol (MNG) detergent synthesised by Chae. This branched dimaltoside detergent was shown to be able to solubilise and stabilise the very labile light harvesting complex I (LHI) from Rhodopsin capsulatus in its active form for 20 days with little loss of protein conformation.3 A cholesterol-based detergent was envisaged that combines the cholesterol framework of CHOBIMALT but replaces its linear tetrasaccharide with a branched dimaltoside. This detergent would then be investigated to assess its ability to solubilise, stabilise and crystallise GPCR proteins. This cholesterol-based detergent (shown below) was eventually synthesised in 9 linear steps from cholesterol.

Studies on bovine oocytes and ovarian tissues cryopreservation : fundamental and applied aspects

Tese de Doutoramento, Ciências Agrárias (Reprodução Animal), 26 de Junho de 2013, Universidade dos Açores.

Studies on terpenes solubility in water and deep eutectic solvents diagrams for biomedical applications

The main objectives of this work are the measurement of terpenes solubility in water at different temperatures, and the formulation of Deep Eutectic Solvents based on choline chloride and polycarboxylic acids, that can be used as hydrotropes of aqueous solutions in terpenes, replacing conventional organic solvents. In this work a new experimental methodology was implemented, using dialysis membranes, for the measurement of terpenes solubility in water. Concerning the deep eutectic diagrams formulation, the determination of the melting points of the eutectic mixtures was performed using a visual method. The method used for determining solubilities was previously validated using a well-studied model compound, toluene. The experimental results of terpenes solubilities in water resulted in a very satisfactory coefficients of variation, always below 6%. The experimental solubility data were analysed and the temperature dependence is also studied in a thermodynamic perspective. The compound with the largest solubility dependence with the temperature is geraniol, while thymol presents the smallest. The phase diagrams of DES formulated were quite satisfactory, presenting always eutectic points below to 373.15 K. For some compositions, the systems composed by choline chloride and lactic, or malonic, or myristic acid were liquid at room temperature. In the case of monocarboxylic acids, eutectic is formed at 60% mol of the acid, to dicarboxylic acid is formed at 50% mol of the acid and for tricarboxylic acid these point is formed at 30% mol of the acid. In the future, it will be important to study the effect of DES as hydrotropes in aqueous solutions of terpenes. Furthermore, it would be interesting to study more terpenes in order to assess the effect of the size of the alkyl chain and the structures of the compounds.

In-vitro evaluation of the quality of Paracetamol and Co-trimoxazole tablets used in Malawi based on pharmacopoeial standards

Objectives This study was an in-vitro evaluation of different brands of paracetamol and cotrimoxazole tablets, used or found in Malawi, based on Pharmacopoeia standards, in order to ascertain the existence and extent of substandard medicines in Malawi and to give an overview of their distribution in the public and private sectors. Methodology A cross-sectional analytical study was conducted using 11 samples each of paracetamol and cotrimoxazole tablets. Stratified random sampling was used to collect samples. Samples were analyzed using HPLC and Spectrophometric methods as outlined in the BP-2007 and USP-32 at the National Drug Quality Control Laboratory (NDQCL)-Lilongwe (under Pharmacy Medicines and Poisons Board-PMPB) and Orient Pharma Co. Ltd of Taiwan. The results were analyzed using Epi Info. Results and discussion Fifty percent of samples (n=22) were not registered in the country by the PMPB as required by the PMP Act with the majority of those coming from public health facilities. All paracetamol and cotrimoxazole samples complied with identification tests using spectrophotometric and HPLC method. Overall, 27.3% of samples failed to meet the BP-2007 standards for Active Ingredient content, while 22.7% of the samples failed the Friability test. The results from Malawi are similar in magnitude to those within surrounding countries in Africa. Conclusion This pilot study provides objective evidence to show that substandard and unregistered paracetamol and cotrimoxazole are present and being used in Malawi, and thus posing a considerable hazard to public health in Malawi. PMPB, together with the Ministry of Health, must continue to develop a quality assurance system to ensure that medicines are randomly and routinely checked.

Patterns of sedentary behavior : insights from observational and experimental studies on body composition and energy expenditure

It is recognized that sedentary behavior (SB) has deleterious effects on numerous health outcomes and it appears that physiological mechanisms underlying these harms are distinct from the ones explaining moderate-to-vigorous physical activity (MVPA) benefits. Sedentary behavior represents a large portion of human’s life and is increasing with technological development. A new current of opinion supports the idea that the manner SB is accumulated plays an important role. This dissertation presents six research studies conducted under the scope of SB. In the methodological area, the first study highlighted the magnitude of potential errors in estimating SB and its patterns from common alternative methods (accelerometer and heart rate monitor) compared to ActivPAL. This study presented the accelerometer as a valid method at a group level. Two studies (2 and 5) were performed in older adults (the most sedentary group in the population) to test the associations for SB patterns with abdominal obesity using accelerometry. The findings showed positive graded associations for prolonged sedentary bouts with abdominal obesity and showed that those who interrupted SB more frequently were less likely to present abdominal obesity. Therefore, public health recommendations regarding breaking up SB more often are expected to be relevant. The associations between sedentary patterns and abdominal obesity were independent of MVPA in older adults. However, the low MVPA in this group makes it unclear whether this independent relationship still exists if highly active persons are analysed. Study 3 inovates by examining the association of SB with body fatness in highly trained athletes and found SB to predict total fat mass and trunk fat mass, independently of age and weekly training time. Study 4 also brings novelty to this research field by quantifying the metabolic and energetic cost of the transition from sitting to standing and then sitting back down (a break), informing about the modest energetic costs (0.32 kcal·min−1). Finally, from a successful multicomponent pilot intervention to reduce and break up SB (study 6), an important behavioral resistance to make more sit/stand transitions despite successfully reducing sitting time (~ 1.85 hours·day-1) was found, which may be relevant to inform future behavioral modification programs. The present work provides observational and experimental evidence on the relation for SB patterns with body composition outcomes and energy regulation that may be relevant for public health interventions.

A Systematic Review of Studies on Blood Pressure in Iranian Pediatric Population: First Report From the Middle East and North Africa

Context:Blood pressure (BP) tracks from childhood to adulthood, and has ethnic variations. Therefore, it is important to assess the situation of pediatric BP in different populations. This study aims to systematically review the studies conducted on BP in Iranian children and adolescents. Evidence Acquisition: We conducted a systematic review on published and national data about pediatric BP in Iran, our search was conducted in Pub Med, Medline, ISI, and Scopus, as well as in national databases including Scientific Information database (SID), IranMedex and Irandoc from 1990 to 2014. Results: We found 1373 records in the primary search including 840 from international and 533 from national databases. After selection and quality assessment phases, data were extracted from 36 papers and four national data sources. Mean systolic BP (SBP) varied from 90.1 ± 14 mmHg (95% CI 89.25, 90.94) to 120.2 ± 12.3 (118.98, 121.41) mmHg, and for diastolic BP (DBP) from 50.7 ± 11.4 (50.01, 51.38) to 79.2 ± 12.3 (77.95, 80.44) mmHg. The frequency of elevated BP had large variation in sub-national studies with rates as low as 0.4% (0.009, 1.98) for high SBP and as high as 24.1% (20.8, 27.67) for high DBP. At national level, three surveys reported slightly raised rates of elevated BP from 2009 to 2012. Conclusions: The findings provide practical information on BP levels in Iranian pediatric population. Although differences exist on the findings of various studies, this review underscores the necessity of tracking BP from childhood, and implementing interventions for primordial prevention of hypertension.

Clinical Studies on conformal radiotherapy combined with epidermal growth factor receptor-tyrosine kinase inhibitor in second-line treatment of non-small cell lung cancer

Purpose: To study the effect of conformal radiotherapy combined with epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI) in the second-line treatment of non-small cell lung cancer (NSCLC). Methods: A total of 316 patients attending Shanghai Pulmonary Hospital affiliated to Tongji University, were divided into two groups: 106 patients were treated with conformal radiotherapy combined with EGFR-TKI (gefitinib, 250 mg/day; or erlotinib, 150 mg/day), while 210 patients were treated with EGFRTKI alone. Some factors, including adverse reactions (AR), disease control rate (DCR), progression-free survival (PFS), overall survival (OS), and one-year and two-year survival rate, were evaluated. Results: No obvious difference was observed in AR between the two groups (p > 0.05). In the combination therapy group, complete response (CR) was 5 cases, partial response (PR) 43 cases, and stable disease (SD) 47 cases, progressive disease (PD) was 11 cases, response rate (RR) was 45.3 %, and DCR 89.6 %. Median PFS in the combination therapy group and targeted therapy group was 6.5 and 5.0 months, respectively. On the other hand, median OS in the combination therapy group and targeted group was 14.1 and 12.6 months, respectively. One-year survival rate of the combination therapy group and EGFR-TKI group was 60.3 and 50.0 %, respectively, while the two-year survival rate was 26.3 and 19.0 %, respectively. Conclusion: Conformal radiotherapy combined with EGFR-TKI can be used as an effective second-line treatment for NSCLC.