Quantification of gammaH2AX foci in response to ionising radiation

DNA double-strand breaks (DSBs), which are induced by either endogenous metabolic processes or by exogenous sources, are one of the most critical DNA lesions with respect to survival and preservation of genomic integrity. An early response to the induction of DSBs is phosphorylation of the H2A histone variant, H2AX, at the serine-139 residue, in the highly conserved C-terminal SQEY motif, forming gammaH2AX(1). Following induction of DSBs, H2AX is rapidly phosphorylated by the phosphatidyl-inosito 3-kinase (PIKK) family of proteins, ataxia telangiectasia mutated (ATM), DNA-protein kinase catalytic subunit and ATM and RAD3-related (ATR)(2). Typically, only a few base-pairs (bp) are implicated in a DSB, however, there is significant signal amplification, given the importance of chromatin modifications in DNA damage signalling and repair. Phosphorylation of H2AX mediated predominantly by ATM spreads to adjacent areas of chromatin, affecting approximately 0.03% of total cellular H2AX per DSB(2,3). This corresponds to phosphorylation of approximately 2000 H2AX molecules spanning approximately 2 Mbp regions of chromatin surrounding the site of the DSB and results in the formation of discrete gammaH2AX foci which can be easily visualized and quantitated by immunofluorescence microscopy(2). The loss of gammaH2AX at DSB reflects repair, however, there is some controversy as to what defines complete repair of DSBs; it has been proposed that rejoining of both strands of DNA is adequate however, it has also been suggested that re-instatement of the original chromatin state of compaction is necessary(4-8). The disappearence of gammaH2AX involves at least in part, dephosphorylation by phosphatases, phosphatase 2A and phosphatase 4C(5,6). Further, removal of gammaH2AX by redistribution involving histone exchange with H2A.Z has been implicated(7,8). Importantly, the quantitative analysis of gammaH2AX foci has led to a wide range of applications in medical and nuclear research. Here, we demonstrate the most commonly used immunofluorescence method for evaluation of initial DNA damage by detection and quantitation of gammaH2AX foci in gamma-irradiated adherent human keratinocytes(9)

Uncertainty quantification applied to the performance analysis of a conical diffuser

This paper offers an uncertainty quantification (UQ) study applied to the performance analysis of the ERCOFTAC conical diffuser. A deterministic CFD solver is coupled with a non-statistical generalised Polynomial Chaos(gPC)representation based on a pseudo-spectral projection method. Such approach has the advantage to not require any modification of the CFD code for the propagation of random disturbances in the aerodynamic field. The stochactic results highlihgt the importance of the inlet velocity uncertainties on the pressure recovery both alone and when coupled with a second uncertain variable. From a theoretical point of view, we investigate the possibility to build our gPC representation on arbitray grid, thus increasing the flexibility of the stochastic framework.

Automated fit quantification of tibial nail designs during the insertion using computer three-dimensional modelling

Intramedullary nailing is the standard fixation method for displaced diaphyseal fractures of the tibia. An optimal nail design should both facilitate insertion and anatomically fit the bone geometry at its final position in order to reduce the risk of stress fractures and malalignments. Due to the nonexistence of suitable commercial software, we developed a software tool for the automated fit assessment of nail designs. Furthermore, we demonstrated that an optimised nail, which fits better at the final position, is also easier to insert. Three-dimensional models of two nail designs and 20 tibiae were used. The fitting was quantified in terms of surface area, maximum distance, sum of surface areas and sum of maximum distances by which the nail was protruding into the cortex. The software was programmed to insert the nail into the bone model and to quantify the fit at defined increment levels. On average, the misfit during the insertion in terms of the four fitting parameters was smaller for the Expert Tibial Nail Proximal bend (476.3 mm2, 1.5 mm, 2029.8 mm2, 6.5 mm) than the Expert Tibial Nail (736.7 mm2, 2.2 mm, 2491.4 mm2, 8.0 mm). The differences were statistically significant (p ≤ 0.05). The software could be used by nail implant manufacturers for the purpose of implant design validation.

Is there a bone-nail specific entry point? automated fit quantification of tibial nail designs during the insertion for six different nail entry points

Intramedullary nailing is the standard fixation method for displaced diaphyseal fractures of tibia. Selection of the correct nail insertion point is important for axial alignment of bone fragments and to avoid iatrogenic fractures. However, the standard entry point (SEP) may not always optimise the bone-nail fit due to geometric variations of bones. This study aimed to investigate the optimal entry for a given bone-nail pair using the fit quantification software tool previously developed by the authors. The misfit was quantified for 20 bones with two nail designs (ETN and ETN-Proximal Bend) related to the SEP and 5 entry points which were 5 mm and 10 mm away from the SEP. The SEP was the optimal entry point for 50% of the bones used. For the remaining bones, the optimal entry point was located 5 mm away from the SEP, which improved the overall fit by 40% on average. However, entry points 10 mm away from the SEP doubled the misfit. The optimised bone-nail fit can be achieved through the SEP and within the range of a 5 mm radius, except posteriorly. The study results suggest that the optimal entry point should be selected by considering the fit during insertion and not only at the final position.

Fully validated LC–MS/MS method for quantification of homocysteine concentrations in samples of human serum : a new approach

Reported homocysteine (HCY) concentrations in human serum show poor concordance amongst laboratories due to endogenous HCY in the matrices used for assay calibrators and QCs. Hence, we have developed a fully validated LC–MS/MS method for measurement of HCY concentrations in human serum samples that addresses this issue by minimising matrix effects. We used small volumes (20 μL) of 2% Bovine Serum Albumin (BSA) as surrogate matrix for making calibrators and QCs with concentrations adjusted for the endogenous HCY concentration in the surrogate matrix using the method of standard additions. To aliquots (20 μL) of human serum samples, calibrators or QCs, were added HCY-d4 (internal standard) and tris-(2-carboxyethyl) phosphine hydrochloride (TCEP) as reducing agent. After protein precipitation, diluted supernatants were injected into the LC–MS/MS. Calibration curves were linear; QCs were accurate (5.6% deviation from nominal), precise (CV% ≤ 9.6%), stable for four freeze–thaw cycles, and when stored at room temperature for 5 h or at −80 °C (27 days). Recoveries from QCs in surrogate matrix or pooled human serum were 91.9 and 95.9%, respectively. There was no matrix effect using 6 different individual serum samples including one that was haemolysed. Our LC–MS/MS method has satisfied all of the validation criteria of the 2012 EMA guideline.

Characterization of the sulphate mineral coquimbite, a secondary iron sulphate from Javier Ortega mine, Lucanas Province, Peru – Using infrared, Raman spectroscopy and thermogravimetry

The mineral coquimbite has been analysed using a range of techniques including SEM with EDX, thermal analytical techniques and Raman and infrared spectroscopy. The mineral originated from the Javier Ortega mine, Lucanas Province, Peru. The chemical formula was determined as ðFe3þ 1:37; Al0:63ÞP2:00ðSO4Þ3 9H2O. Thermal analysis showed a total mass loss of 73.4% on heating to 1000 C. A mass loss of 30.43% at 641.4 C is attributed to the loss of SO3. Observed Raman and infrared bands were assigned to the stretching and bending vibrations of sulphate tetrahedra, aluminium oxide/hydroxide octahedra, water molecules and hydroxyl ions. The Raman spectrum shows well resolved bands at 2994, 3176, 3327, 3422 and 3580 cm 1 attributed to water stretching vibrations. Vibrational spectroscopy combined with thermal analysis provides insight into the structure of coquimbite.

Quantification of the total neuronal structure of the fear conditioning circuit of the lateral amygdala of the rat

During Pavlovian auditory fear conditioning a previously neutral auditory stimulus (CS) gains emotional significance through pairing with a noxious unconditioned stimulus (US). These associations are believed to be formed by way of plasticity at auditory input synapses on principal neurons in the lateral nucleus of the amygdala (LA). In order to begin to understand how fear memories are stored and processed by synaptic changes in the LA, we have quantified both the entire neural number and the sub-cellular structure of LA principal neurons.We first used stereological cell counting methods on Gimsa or GABA immunostained rat brain. We identified 60,322+/-1408 neurons in the LA unilaterally (n=7). Of these 16,917+/-471 were GABA positive. The intercalated nuclei were excluded from the counts and thus GABA cells are believed to represent GABAergic interneurons. The sub-nuclei of the LA were also independently counted. We then quantified the morphometric properties of in vitro electrophysiologically identified principal neurons of the LA, corrected for shrinkage in xyz planes. The total dendritic length was 9.97+/-2.57mm, with 21+/-4 nodes (n=6). Dendritic spine density was 0.19+/-0.03 spines/um (n=6). Intra-LA axon collaterals had a bouton density of 0.1+/-0.02 boutons/um (n=5). These data begin to reveal the finite cellular and sub-cellular processing capacity of the lateral amygdala, and should facilitate efforts to understand mechanisms of plasticity in LA.

Vibrational spectroscopic characterization of the sulphate-carbonate mineral burkeite: Implications for evaporites

Burkeite formation is important in saline evaporites and in pipe scales. Burkeite is an anhydrous sulphate-carbonate with an apparent variable anion ratio. Such a formula with two oxyanions lends itself to vibrational spectroscopy. Two symmetric sulphate stretching modes are observed, indicating at least at the molecular level the nonequivalence of the sulphate ions in the burkeite structure. The strong Raman band at 1065 cm−1 is assigned to the carbonate symmetric stretching vibration. The series of Raman bands at 622, 635, 645, and 704 cm−1 are assigned to the ν4 sulphate bending modes. The observation of multiple bands supports the concept of a reduction in symmetry of the sulphate anion from T d to C 3v or even C 2v.

Quantification of functional hand grip using electromyography and inertial sensor-derived accelerations: Clinical implications

Background Assessing hand injury is of great interest given the level of involvement of the hand with the environment. Knowing different assessment systems and their limitations generates new perspectives. The integration of digital systems (accelerometry and electromyography) as a tool to supplement functional assessment allows the clinician to know more about the motor component and its relation to movement. Therefore, the purpose of this study was the kinematic and electromyography analysis during functional hand movements. Method Ten subjects carried out six functional movements (terminal pinch, termino-lateral pinch, tripod pinch, power grip, extension grip and ball grip). Muscle activity (hand and forearm) was measured in real time using electromyograms, acquired with the Mega ME 6000, whilst acceleration was measured using the AcceleGlove. Results Electrical activity and acceleration variables were recorded simultaneously during the carrying out of the functional movements. The acceleration outcome variables were the modular vectors of each finger of the hand and the palm. In the electromyography, the main variables were normalized by the mean and by the maximum muscle activity of the thenar region, hypothenar, first interosseous dorsal, wrist flexors, carpal flexors and wrist extensors. Conclusions Knowing muscle behavior allows the clinician to take a more direct approach in the treatment. Based on the results, the tripod grip shows greater kinetic activity and the middle finger is the most relevant in this regard. Ball grip involves most muscle activity, with the thenar region playing a fundamental role in hand activity. Clinical relevance Relating muscle activation, movements, individual load and displacement offers the possibility to proceed with rehabilitation by individual component.

Cortisol and dehydroepiandrosterone-sulphate levels correlate with symptom severity in first-episode psychosis

Dehydroepiandrosterone (DHEA) and its sulphate form (DHEA) are neuroactive steroids with antiglucocorticoid properties. An imbalance in the ratio of cortisol to DHEA(S) has been implicated in the pathophysiology of stress-related psychiatric disorders. This study prospectively investigated circulating cortisol, DHEAS and their ratio in first-episode psychosis (FEP) patients compared to healthy controls, and their relationship to perceived stress, psychotic, negative and mood symptoms. METHODS: Blood cortisol and DHEAS levels were obtained in 39 neuroleptic-naïve or minimally-treated FEP patients and 25 controls. Twenty-three patients and 15 controls received repeat assessments after 12 weeks. Perceived stress was assessed using the Perceived Stress Scale and symptoms were assessed in patients using standard rating scales. RESULTS: At baseline, no differences were observed in cortisol, DHEAS or the cortisol/DHEAS ratio between patients and controls. There were also no group differences in the change in these biological variables during the study period. Within FEP patients, decreases in cortisol and the cortisol/DHEAS ratio over time were directly related to the improvement in depression (r = 0.45; p = 0.031, r = 0.52; p = 0.01), negative (r = 0.51; p = 0.006, r = 0.55; p = 0.008) and psychotic symptoms (cortisol only, r = 0.53; p = 0.01). Perceived stress significantly correlated with DHEAS (r = 0.51; p = 0.019) and the cortisol/DHEAS ratio (r = -0.49; p = 0.024) in controls, but not patients, possibly reflecting an impaired hormonal response to stress in FEP patients. CONCLUSIONS: These findings further support the involvement of the stress system in the pathophysiology of psychotic disorders, with implications for treatment strategies that modulate these neurosteroids.

A Raman and infrared spectroscopic study of the sulphate mineral aluminite Al2(SO4)(OH)4·7H2O

The mineral aluminite has been studied using a number of techniques, including scanning electron microscopy (SEM) with energy dispersive spectroscopy (EDX) and Raman and infrared spectroscopy. Raman spectroscopy identifies multiple sulphate symmetric stretching modes in line with the three sulphate crystallographically different sites. Raman spectroscopy also identifies a low intensity band at 1069 cm−1 which may be attributed to a carbonate symmetric stretching mode, indicating the presence of thaumasite. The observation of multiple bands in this ν4 spectral region offers evidence for the reduction in symmetry of the sulphate anion from Td to C2v or even lower symmetry. The Raman band at 3588 cm−1 is assigned to the OH unit stretching vibration and the broad feature at around 3439 cm−1 to water stretching bands. Water stretching vibrations are observed at 3157, 3294, 3378 and 3439 cm−1. Vibrational spectroscopy enables an assessment of the molecular structure of aluminite to be made.

Microscopy for the detection, identification and quantification of malaria parasites on stained thick and thin blood films in research settings

Summary This manual was developed to guide a move towards common standards for undertaking and reporting research microscopy for malaria parasite detection, identification and quantification. It contains procedures based on agreed quality assurance standards for research malaria microscopy defined at a consultation of: TDR, the Special Programme for Research and Training in Tropical Diseases; the Worldwide Antimalarial Resistance Network (WWARN), United Kingdom; the Foundation for Innovative New Diagnostics (FIND), Switzerland; the Centers for Disease Control and Prevention (CDC), USA; the Kenya Medical Research Institute (KEMRI) and later expanded to include Amref Health Africa (Kenya); the Eijkman-Oxford Clinical Research Unit (EOCRU), Indonesia; Institut Pasteur du Cambodge (IPC); Institut de recherche pour le Développement (IRD), Senegal; the Global Good and Intellectual Ventures Laboratory (GG-IVL), USA; the Mahidol-Oxford Tropical Medicine Research Unit (MORU), Thailand; Queensland University of Technology (QUT), Australia, and the Shoklo Malaria Research Unit (SMRU), Thailand. These collaborating institutions commit to adhering to these standards in published research studies. It is hoped that they will form a solid basis for the wider adoption of standardized reference microscopy protocols for malaria research.

Molecular characterisation and carotenoid quantification of pro-vitamin A biofortified genetically modified bananas in Uganda

In Uganda, a significant proportion of the population depends on the micronutrient poor East African highland banana as a food staple. Consequently, micronutrient deficiencies such as vitamin A deficiency are an important health concern in the country. To reach most vulnerable rural poor populations, staple crops can be biofortified with essential micronutrients though conventional breeding or genetic engineering. This thesis provided proof of concept that genetically modified East African highland bananas with enhanced provitamin A levels can be generated and fully characterised in Uganda. In addition, provitamin A levels present in popular banana varieties was documented.