Predicting structural disruption of proteins caused by crossover

We present a machine learning model that predicts a structural disruption score from a protein s primary structure. SCHEMA was introduced by Frances Arnold and colleagues as a method for determining putative recombination sites of a protein on the basis of the full (PDB) description of its structure. The present method provides an alternative to SCHEMA that is able to determine the same score from sequence data only. Circumventing the need for resolving the full structure enables the exploration of yet unresolved and even hypothetical sequences for protein design efforts. Deriving the SCHEMA score from a primary structure is achieved using a two step approach: first predicting a secondary structure from the sequence and then predicting the SCHEMA score from the predicted secondary structure. The correlation coefficient for the prediction is 0.88 and indicates the feasibility of replacing SCHEMA with little loss of precision.

Determination of urinary thymidine glycol using affinity chromatography, HPLC and post-column reaction detection : a biomarker of oxidative DNA damage upon kidney transplantation

Reactive oxygen species are generated during ischaemia-reperfusion of tissue. Oxidation of thymidine by hydroxyl radicals (HO) leads to the formation of 5,6-dihydroxy-5,6-dihydrothymidine (thymidine glycol). Thymidine glycol is excreted in urine and can be used as biomarker of oxidative DNA damage. Time dependent changes in urinary excretion rates of thymidine glycol were determined in six patients after kidney transplantation and in six healthy controls. A new analytical method was developed involving affinity chromatography and subsequent reverse-phase high-performance liquid chromatography (RP-HPLC) with a post-column chemical reaction detector and endpoint fluorescence detection. The detection limit of this fluorimetric assay was 1.6 ng thymidine glycol per ml urine, which corresponds to about half of the physiological excretion level in healthy control persons. After kidney transplantation the urinary excretion rate of thymidine glycol increased gradually reaching a maximum around 48 h. The excretion rate remained elevated until the end of the observation period of 10 days. Severe proteinuria with an excretion rate of up to 7.2 g of total protein per mmol creatinine was also observed immediately after transplantation and declined within the first 24 h of allograft function (0.35 + 0.26 g/mmol creatinine). The protein excretion pattern, based on separation of urinary proteins on sodium dodecyl sulphate-polyacrylamide gel electrophorosis (SDS-PAGE), as well as excretion of individual biomarker proteins, indicated nonselective glomerular and tubular damage. The increased excretion of thymidine glycol after kidney transplantation may be explained by ischaemia-reperfusion induced oxidative DNA damage of the transplanted kidney.

Determination of glutathione transferase (GSTT1-1) activities in different tissues based on formation of radioactive metabolites using 35S-glutathione

A new system has been developed to determine enzyme activities of glutathione transferase θ (GSTT1-1) based on radiometric product detection resulting from the enzymic reaction of methyl chloride with 35S-labelled glutathione. In principle, the method is universally applicable for determination of glutathione transferase activities towards a multiplicity of substrates. The method distinguishes between erythrocyte GSTT1-1 activities of human 'non-conjugators', 'low conjugators' and 'high conjugators'. Application to cytosol preparations of livers and kidneys of male and female Fischer 344 and B6C3F1 mice reveals differential GSTT1-1 activities in hepatic and renal tissues. These ought to be considered in species-specific modellings of organ toxicities of chlorinated hydrocarbons.

Determination of the ethylene oxide adduct S-(2-hydroxyethyl)cysteine by a fluorometric HPLC method in albumin and globin from human blood

A new method has been developed for the quantification of 2-hydroxyethylated cysteine resulting as adduct in blood proteins after human exposure to ethylene oxide, by reversed-phase HPLC with fluorometric detection. The specific adduct is analysed in albumin and in globin. After isolation of albumin and globin from blood, acid hydrolysis of the protein and precolumn derivatisation of the digest with 9-fluorenylmethoxycarbonylchloride, the levels of derivatised S-hydroxyethylcysteine are analysed by RP-HPLC and fluorescence detection, with a detection limit of 8 nmol/g protein. Background levels of S-hydroxyethylcysteine were quantified in both albumin and globin, under special consideration of the glutathione transferase GSTT1 and GSTM1 polymorphisms. GSTT1 polymorphism had a marked influence on the physiological background alkylation of cysteine. While S-hydroxyethylcysteine levels in "non-conjugators" were between 15 and 50 nmol/g albumin, "low conjugators" displayed levels between 8 and 21 nmol/g albumin, and "high conjugators" did not show levels above the detection limit. The human GSTM1 polymorphism had no apparent effect on background levels of blood protein 2-hydroxyethylation.

An enhanced procedure for the rapid digestion of high silicate archeological specimens followed by ICP-MS determination of traces of rare earth elements (REE's)

A straightforward procedure for the acid digestion of geological samples with SiO2 concentrations ranging between about 40 to 80%, is described. A powdered sample (200 mesh) of 500 mg was used and fused with 1000 mg spectroflux at about 1000 degreesC in a platinum crucible. The molten was subsequently digested in an aqueous solution of HNO3 at 100 degreesC. Several systematic digestion procedures were followed using various concentrations of HNO3. It was found that a relationship could be established between the dissolution-time and acid concentration. For an acid concentration of 15% an optimum dissolution-time of under 4 min was recorded. To verify that the dissolutions were complete, they were subjected to rigorous quality control tests. The turbidity and viscosity were examined at different intervals and the results were compared with that of deionised water. No significant change in either parameter was observed. The shelf-life of each solution lasted for several months, after which time polymeric silicic acid formed in some solutions, resulting in the presence of a gelatinous solid. The method is cost effective and is clearly well suited for routine applications on a small scale, especially in laboratories in developing countries. ICP-MS was applied to the determination of 13 Rare Earth Elements and Hf in a set of 107 archaeological samples subjected to the above digestion procedure. The distribution of these elements was examined and the possibility of using the REE's for provenance studies is discussed.

Locality-sensitive hashing for protein classification

Determination of sequence similarity is a central issue in computational biology, a problem addressed primarily through BLAST, an alignment based heuristic which has underpinned much of the analysis and annotation of the genomic era. Despite their success, alignment-based approaches scale poorly with increasing data set size, and are not robust under structural sequence rearrangements. Successive waves of innovation in sequencing technologies – so-called Next Generation Sequencing (NGS) approaches – have led to an explosion in data availability, challenging existing methods and motivating novel approaches to sequence representation and similarity scoring, including adaptation of existing methods from other domains such as information retrieval. In this work, we investigate locality-sensitive hashing of sequences through binary document signatures, applying the method to a bacterial protein classification task. Here, the goal is to predict the gene family to which a given query protein belongs. Experiments carried out on a pair of small but biologically realistic datasets (the full protein repertoires of families of Chlamydia and Staphylococcus aureus genomes respectively) show that a measure of similarity obtained by locality sensitive hashing gives highly accurate results while offering a number of avenues which will lead to substantial performance improvements over BLAST..

Exploring Australian intensive care physicians clinical judgement during donation after cardiac death : an exploratory qualitative study

BACKGROUND: Donation after Cardiac Death (DCD) is one possible solution to the world wide organ shortage. Intensive care physicians are central to DCD becoming successful since they are responsible for making the clinical judgements and decisions associated with DCD. Yet international evidence shows health care professionals have not embraced DCD and are often reluctant to consider it as an option for patients. PURPOSE: To explore intensive care physicians' clinical judgements when selecting a suitable DCD candidate. METHODS: Using interpretative exploratory methods six intensive care physicians were interviewed from three hospital sites in Australia. Following verbatim transcription, data was subjected to thematic analysis. FINDINGS: Three distinct themes emerged. Reducing harm and increasing benefit was a major focus of intensive care physicians during determination of DCD. There was an acceptance of DCD if there was clear evidence that donation was what the patient and family wanted. Characteristics of a defensible decision reflected the characteristics of sequencing, separation and isolation, timing, consensus and collaboration, trust and communication to ensure that judgements were robust and defensible. The final theme revealed the importance of minimising uncertainty and discomfort when predicting length of survival following withdrawal of life-sustaining treatment. CONCLUSION: DCD decisions are made within an environment of uncertainty due to the imprecision associated with predicting time of death. Lack of certainty contributed to the cautious and collaborative strategies used by intensive care physicians when dealing with patients, family members and colleagues around end-of-life decisions, initiation of withdrawal of life-sustaining treatment and the discussion about DCD. This study recommends that nationally consistent policies are urgently needed to increase the degree of certainty for intensive care staff concerning the DCD processes.

Collection and determination of nucleotide metabolites in neonatal and adult saliva by high performance liquid chromatography with tandem mass spectrometry

Saliva contains a number of biochemical components which may be useful for diagnosis/monitoring of metabolic disorders, and as markers of cancer or heart disease. Saliva collection is attractive as a non-invasive sampling method for infants and elderly patients. We present a method suitable for saliva collection from neonates. We have applied this technique for the determination of salivary nucleotide metabolites. Saliva was collected from 10 healthy neonates using washed cotton swabs, and directly from 10 adults. Two methods for saliva extraction from oral swabs were evaluated. The analytes were then separated using high performance liquid chromatography (HPLC) with tandem mass spectrometry (MS/MS). The limits of detection for 14 purine/pyrimidine metabolites were variable, ranging from 0.01 to 1.0 mu M. Recovery of hydrophobic purine/pyrimidine metabolites from cotton tips was consistently high using water/acetonitrile extraction (92.7-111%) compared with water extraction alone. The concentrations of these metabolites were significantly higher in neonatal saliva than in adults. Preliminary ranges for nucleotide metabolites in neonatal and adult saliva are reported. Hypoxanthine and xanthine were grossly raised in neonates (49.3 +/- 25.4; 30.9 +/- 19.5 mu M respectively) compared to adults (4.3 +/- 3.3; 4.6 +/- 4.5 mu M); nucleosides were also markedly raised in neonates. This study focuses on three essential details: contamination of oral swabs during manufacturing and how to overcome this; weighing swabs to accurately measure small saliva volumes; and methods for extracting saliva metabolites of interest from cotton swabs. A method is described for determining nucleotide metabolites using HPLC with photo-diode array or MS/MS. The advantages of utilising saliva are highlighted. Nucleotide metabolites were not simply in equilibrium with plasma, but may be actively secreted into saliva, and this process is more active in neonates than adults. (C) 2013 Elsevier B.V. All rights reserved.

Maternal concern about her toddler undereating and becoming underweight and use of feeding practices - analysis of the NOURISH and SAIDI cohorts using structural equation modeling

The chubby baby who eats well is desirable in our culture. Perceived low weight gains and feeding concerns are common reasons mothers seek advice in the early years. In contrast, childhood obesity is a global public health concern. Use of coercive feeding practices, prompted by maternal concern about weight, may disrupt a child’s innate self regulation of energy intake, promoting overeating and overweight. This study describes predictors of maternal concern about her child undereating/becoming underweight and feeding practices. Mothers in the control group of the NOURISH and South Australian Infants Dietary Intake studies (n = 332) completed a self-administered questionnaire when the child was aged 12–16 months. Weight-for-age z-score (WAZ)was derived from weight measured by study staff. Mean age (SD) was 13.8 (1.3) months, mean WAZ (SD), 0.58 (0.86) and 49% were male. WAZ and two questions describing food refusal were combined in a structural equation model with four items from the Infant feeding Questionnaire (IFQ) to form the factor ‘Concern about undereating/weight’. Structural relationships were drawn between concern and IFQ factors ‘awareness of infant’s hunger and satiety cues’, ‘use of food to calm infant’s fussiness’ and ‘feeding infant on a schedule’, resulting in a model of acceptable fit. Lower WAZ and higher frequency of food refusal predicted higher maternal concern. Higher maternal concern was associated with lower awareness of infant cues (r = −.17, p = .01) and greater use of food to calm (r = .13, p = .03). In a cohort of healthy children, maternal concern about undereating and underweight was associated with practices that have the potential to disrupt self-regulation.

Determination of l-dopa using electropolymerized 3,3′,3″,3‴-tetraaminophthalocyanatonickel(II) film on glassy carbon electrode

Electropolymerized film of 3,3′,3″,3‴-tetraaminophthalocyanatonickel(II) (p-NiIITAPc) on glassy carbon (GC) electrode was used for the selective and stable determination of 3,4-dihydroxy-l-phenylalanine (l-dopa) in acetate buffer (pH 4.0) solution. Bare GC electrode fails to determine the concentration of l-dopa accurately in acetate buffer solution due to the cyclization reaction of dopaquinone to cyclodopa in solution. On the other hand, p-NiIITAPc electrode successfully determines the concentration of l-dopa accurately because the cyclization reaction was prevented at this electrode. It was found that the electrochemical reaction of l-dopa at the modified electrode is faster than that at the bare GC electrode. This was confirmed from the higher heterogeneous electron transfer rate constant (k0) of l-dopa at p-NiIITAPc electrode (3.35 × 10−2 cm s−1) when compared to that at the bare GC electrode (5.18 × 10−3 cm s−1). Further, it was found that p-NiIITAPc electrode separates the signals of ascorbic acid (AA) and l-dopa in a mixture with a peak separation of 220 mV. Lowest detection limit of 100 nM was achieved at the modified electrode using amperometric method. Common physiological interferents like uric acid, glucose and urea does not show any interference within the potential window of l-dopa oxidation. The present electrode system was also successfully applied to estimate the concentration of l-dopa in the commercially available tablets.

An interpretative structural modeling based network reconfiguration strategy for power systems

The network reconfiguration is an important stage of restoring a power system after a complete blackout or a local outage. Reasonable planning of the network reconfiguration procedure is essential for rapidly restoring the power system concerned. An approach for evaluating the importance of a line is first proposed based on the line contraction concept. Then, the interpretative structural modeling (ISM) is employed to analyze the relationship among the factors having impacts on the network reconfiguration. The security and speediness of restoring generating units are considered with priority, and a method is next proposed to select the generating unit to be restored by maximizing the restoration benefit with both the generation capacity of the restored generating unit and the importance of the line in the restoration path considered. Both the start-up sequence of generating units and the related restoration paths are optimized together in the proposed method, and in this way the shortcomings of separately solving these two issues in the existing methods are avoided. Finally, the New England 10-unit 39-bus power system and the Guangdong power system in South China are employed to demonstrate the basic features of the proposed method.

A critical review of structural equation modeling applications in construction research

Structural equation modeling (SEM) is a versatile multivariate statistical technique, and applications have been increasing since its introduction in the 1980s. This paper provides a critical review of 84 articles involving the use of SEM to address construction related problems over the period 1998–2012 including, but not limited to, seven top construction research journals. After conducting a yearly publication trend analysis, it is found that SEM applications have been accelerating over time. However, there are inconsistencies in the various recorded applications and several recurring problems exist. The important issues that need to be considered are examined in research design, model development and model evaluation and are discussed in detail with reference to current applications. A particularly important issue concerns the construct validity. Relevant topics for efficient research design also include longitudinal or cross-sectional studies, mediation and moderation effects, sample size issues and software selection. A guideline framework is provided to help future researchers in construction SEM applications.

A new ambiguity acceptance test threshold determination method with controllable failure rate

The ambiguity acceptance test is an important quality control procedure in high precision GNSS data processing. Although the ambiguity acceptance test methods have been extensively investigated, its threshold determine method is still not well understood. Currently, the threshold is determined with the empirical approach or the fixed failure rate (FF-) approach. The empirical approach is simple but lacking in theoretical basis, while the FF-approach is theoretical rigorous but computationally demanding. Hence, the key of the threshold determination problem is how to efficiently determine the threshold in a reasonable way. In this study, a new threshold determination method named threshold function method is proposed to reduce the complexity of the FF-approach. The threshold function method simplifies the FF-approach by a modeling procedure and an approximation procedure. The modeling procedure uses a rational function model to describe the relationship between the FF-difference test threshold and the integer least-squares (ILS) success rate. The approximation procedure replaces the ILS success rate with the easy-to-calculate integer bootstrapping (IB) success rate. Corresponding modeling error and approximation error are analysed with simulation data to avoid nuisance biases and unrealistic stochastic model impact. The results indicate the proposed method can greatly simplify the FF-approach without introducing significant modeling error. The threshold function method makes the fixed failure rate threshold determination method feasible for real-time applications.

Retinal anatomy of the New Zealand kiwi: Structural traits consistent with their nocturnal behavior

Kiwi (Apteryx spp.) have a visual system unlike that of other nocturnal birds, and have specializations to their auditory, olfactory and tactile systems. Eye size, binocular visual fields and visual brain centers in kiwi are proportionally the smallest yet recorded among birds. Given the many unique features of the kiwi visual system, we examined the laminar organization of the kiwi retina to determine if they evolved increased light sensitivity with a shift to a nocturnal niche or if they retained features of their diurnal ancestor. The laminar organization of the kiwi retina was consistent with an ability to detect low light levels similar to that of other nocturnal species. In particular, the retina appeared to have a high proportion of rod photoreceptors compared to diurnal species, as evidenced by a thick outer nuclear layer, and also numerous thin photoreceptor segments intercalated among the conical shaped cone photoreceptor inner segments. Therefore, the retinal structure of kiwi was consistent with increased light sensitivity, although other features of the visual system, such as eye size, suggest a reduced reliance on vision. The unique combination of a nocturnal retina and smaller than expected eye size, binocular visual fields and brain regions make the kiwi visual system unlike that of any bird examined to date. Whether these features of their visual system are an evolutionary design that meets their specific visual needs or are a remnant of a kiwi ancestor that relied more heavily on vision is yet to be determined.

A novel ambiguity acceptance test threshold determination method with controllable failure rate

Ambiguity validation as an important procedure of integer ambiguity resolution is to test the correctness of the fixed integer ambiguity of phase measurements before being used for positioning computation. Most existing investigations on ambiguity validation focus on test statistic. How to determine the threshold more reasonably is less understood, although it is one of the most important topics in ambiguity validation. Currently, there are two threshold determination methods in the ambiguity validation procedure: the empirical approach and the fixed failure rate (FF-) approach. The empirical approach is simple but lacks of theoretical basis. The fixed failure rate approach has a rigorous probability theory basis, but it employs a more complicated procedure. This paper focuses on how to determine the threshold easily and reasonably. Both FF-ratio test and FF-difference test are investigated in this research and the extensive simulation results show that the FF-difference test can achieve comparable or even better performance than the well-known FF-ratio test. Another benefit of adopting the FF-difference test is that its threshold can be expressed as a function of integer least-squares (ILS) success rate with specified failure rate tolerance. Thus, a new threshold determination method named threshold function for the FF-difference test is proposed. The threshold function method preserves the fixed failure rate characteristic and is also easy-to-apply. The performance of the threshold function is validated with simulated data. The validation results show that with the threshold function method, the impact of the modelling error on the failure rate is less than 0.08%. Overall, the threshold function for the FF-difference test is a very promising threshold validation method and it makes the FF-approach applicable for the real-time GNSS positioning applications.