Extracting DNA from ‘jaws’: high yield and quality from archived tiger shark (Galeocerdo cuvier) skeletal material

Archived specimens are highly valuable sources of DNA for retrospective genetic/genomic analysis. However, often limited effort has been made to evaluate and optimize extraction methods, which may be crucial for downstream applications. Here, we assessed and optimized the usefulness of abundant archived skeletal material from sharks as a source of DNA for temporal genomic studies. Six different methods for DNA extraction, encompassing two different commercial kits and three different protocols, were applied to material, so-called bio-swarf, from contemporary and archived jaws and vertebrae of tiger sharks (Galeocerdo cuvier). Protocols were compared for DNA yield and quality using a qPCR approach. For jaw swarf, all methods provided relatively high DNA yield and quality, while large differences in yield between protocols were observed for vertebrae. Similar results were obtained from samples of white shark (Carcharodon carcharias). Application of the optimized methods to 38 museum and private angler trophy specimens dating back to 1912 yielded sufficient DNA for downstream genomic analysis for 68% of the samples. No clear relationships between age of samples, DNA quality and quantity were observed, likely reflecting different preparation and storage methods for the trophies. Trial sequencing of DNA capture genomic libraries using 20 000 baits revealed that a significant proportion of captured sequences were derived from tiger sharks. This study demonstrates that archived shark jaws and vertebrae are potential high-yield sources of DNA for genomic-scale analysis. It also highlights that even for similar tissue types, a careful evaluation of extraction protocols can vastly improve DNA yield.

Effect of foliar application of Cu, Zn, and Mn on yield and quality indicators of winter wheat grain

Micronutrients are part of many crucial physiological plant processes. The combined application of N and micronutrients helps in obtaining grain yield with beneficial technological and consumer properties. The main micronutrients needed by cereals include Cu, Mn, and Zn. The subject of this study was to determine yield, quality indicators (protein content and composition, gluten content, grain bulk density, Zeleny sedimentation index, and grain hardness), as well as mineral content (Cu, Zn, Mn, Fe) in winter wheat grain ( Triticum aestivum L.) fertilized by foliar micronutrient application. A field experiment was carried out at the Educational and Experimental Station in Tomaszkowo, Poland. The application of mineral fertilizers (NPK) supplemented with Cu increased Cu content (13.0%) and ω, α/β, and γ (18.7%, 4.9%, and 3.4%, respectively) gliadins in wheat grain. Foliar Zn fertilization combined with NPK increased Cu content (14.9%) as well as high (HMW) and low molecular weight (LMW) glutenins (38.8% and 6.7%, respectively). Zinc fertilization significantly reduced monomeric gliadin content and increased polymeric glutenin content in grain, which contributed in reducing the gliadin:glutenin ratio (0.77). Mineral fertilizers supplemented with Mn increased Fe content in wheat grain (14.3%). It also significantly increased protein (3.8%) and gluten (4.4%) content, Zeleny sedimentation index (12.4%), and grain hardness (18.5%). Foliar Mn fertilization increased the content of ω, α/β, and γ gliadin fractions (19.9%, 9.5%, and 2.1%, respectively), as well as HMW and LMW glutenins (18.9% and 4.5%, respectively). Mineral NPK fertilization, combined with micronutrients (Cu + Zn + Mn), increased Cu and Zn content in grain (22.6% and 17.7%, respectively). The content of ω, α/β, and γ gliadins increased (20.3%, 10.5%, and 12.1%, respectively) as well as HMW glutenins (7.9%).

High temperature and vapor pressure deficit aggravate architectural effects but ameliorate non-architectural effects of salinity on dry mass production of tomato

Tomato (Solanum lycopersicum L.) is an important vegetable crop and often cultivated in regions exposed to salinity and high temperatures (HT) which change plant architecture, decrease canopy light interception and disturb physiological functions. However, the long-term effects of salinity and HT combination (S+HT) on plant growth are still unclear. A dynamic functional-structural plant model (FSPM) of tomato was parameterized and evaluated for different levels of S+HT combinations. The evaluated model was used to quantify the contributions of morphological changes (architectural effects) and physiological disturbances (non-architectural effects) on the reduction of shoot dry mass under S+HT. The model predicted architectural variables with high accuracy (>85%), which ensured the reliability of the model analyses. HT enhanced architectural effects but reduced non-architectural effects of salinity on dry mass production. The stronger architectural effects of salinity under HT could not be counterbalanced by the smaller non-architectural effects. Therefore, long-term influences of HT on shoot dry mass under salinity were negative at the whole plant level. Our model analysis highlights the importance of plant architecture at canopy level in studying the plant responses to the environments and shows the merits of dynamic FSPMs as heuristic tools.

Observed Social Problem Solving and Friendship Quality in Children with a Traumatic Brain Injury

Children who have experienced a traumatic brain injury (TBI) are at risk for a variety of maladaptive cognitive, behavioral and social outcomes (Yeates et al., 2007). Research involving the social problem solving (SPS) abilities of children with TBI indicates a preference for lower level strategies when compared to children who have experienced an orthopedic injury (OI; Hanten et al., 2008, 2011). Research on SPS in non-injured populations has highlighted the significance of the identity of the social partner (Rubin et al., 2006). Within the pediatric TBI literature few studies have utilized friends as the social partner in SPS contexts, and fewer have used in-vivo SPS assessments. The current study aimed to build on existing research of SPS in children with TBI by utilizing an observational coding scheme to capture in-vivo problem solving behaviors between children with TBI and a best friend. The current study included children with TBI (n = 41), children with OI (n = 43), and a non-injured typically developing group (n = 41). All participants were observed completing a task with a friend and completed a measure of friendship quality. SPS was assessed using an observational coding scheme that captured SPS goals, strategies, and outcomes. It was expected children with TBI would produce fewer successes, fewer direct strategies, and more avoidant strategies. ANOVAs tested for group differences in SPS successes, direct strategies and avoidant strategies. Analyses were run to see if positive or negative friendship quality moderated the relation between group type and SPS behaviors. Group differences were found between the TBI and non-injured group in the SPS direct strategy of commands. No group differences were found for other SPS outcome variables of interest. Moderation analyses partially supported study hypotheses regarding the effect of friendship quality as a moderator variable. Additional analyses examined SPS goal-strategy sequencing and grouped SPS goals into high cost and low cost categories. Results showed a trend supporting the hypothesis that children with TBI had fewer SPS successes, especially with high cost goals, compared to the other two groups. Findings were discussed highlighting the moderation results involving children with severe TBI.

Voice acoustic profi le of males exposed to occupational infrasound and low-frequency noise

Background: Vibroacoustic disease (VAD) is a systematic pathology characterized by the abnormal growth of extra-cellular matrices in the absence of infl ammatory processes, namely collagen and elastin, both of which are abundant in the basement membrane zone of the vocal folds. VAD can develop due to long-term exposure to infrasound and low-frequency noise (ILFN, <500 Hz). Mendes et al. (2006, 2008 and 2012) revealed that ILFN-exposed males and females presented an increased fundamental frequency (F0), decreased jitter %, and reduced maximum phonation frequency range, when compared with normative data. Temporal measures of maximum phonation time and S/Z ratio were generally reduced. Study Aims: Herein, the same voice acoustic parameters of 48 males, 36 airline pilots and 12 cabin crewmembers (age range 25-60 years) were studied, and the effects and interaction of age and years of ILFN exposure were investigated within those parameters. ILFN-exposure time (i.e. years of professional activity) ranged from 3.5 to 36 years. Materials and Methods: Spoken and sung phonatory tasks were recorded with a DA-P1 Tascam DAT and a C420III PP AKG head-worn microphone, positioned at 3 cm from the mouth. Acoustic analyses were performed using KayPENTAX Computer Speech Lab and Multi-Dimensional Voice Program. Results: Results revealed that even though pilots and cabin crewmembers were exposed to occupational environments with distinct (ILFN-rich) acoustical frequency distributions and sound pressure levels, differences in the vocal acoustic parameters were not evident. Analyzing data from both professional groups (N = 48) revealed that F0 increased signifi cantly with the number of years of professional activity. Conclusion: These results strongly suggest that the number of years of professional activity (i.e. total ILFN exposure time) had a signifi cant effect on F0. Furthermore, they may refl ect the histological changes specifi cally observed on the vocal folds of ILFN-exposed professionals.

Applications of synchrotron x-ray powder diffraction in hydrated cements: high-resolution and high-pressure studies

The main aim of this study is to apply synchrotron radiation techniques for the study of hydrated cement pastes. In particular, the tetracalcium aluminoferrite phase, C4AF in cement nomenclature, is the major iron-containing phase in Ordinary Portland Cement (OPC) and in iron rich belite calcium sulfoaluminate cements. In a first study, the hydration mechanism of pure tetracalcium aluminoferrite phase with water-to-solid ratio of 1.0 has been investigated by HR-SXRPD (high resolution synchrotron X-ray powder diffraction). C4AF in the presence of water hydrates to form mainly an iron-containing hydrogarnet-type (katoite) phase, C3A0.84F0.16H6, as single crystalline phase. Its crystal structure and stoichiometry were determined by the Rietveld method and the final disagreement factors were RWP=8.1% and RF=4.8% [1]. As the iron content in the product is lower than that in C4AF, it is assumed that part of the iron also goes to an amorphous iron rich gel, like the hydrated alumina-type gel, as hydration proceeds. Further results from the high-resolution study will be discussed. In a second study, the behavior of pure and iron-containing katoites (C3AH6 and C3A0.84F0.16H6) under pressure have been analyzed by SXRPD using a diamond anvil cell (DAC) and then their bulk moduli were determined. The role of the pressure transmitting medium (PTM) has also been studied. In this case, silicone oil as well as methanol/ethanol mixtures have been used as PTM. Some “new peaks” were detected in the pattern for C3A0.84F0.16H6 as pressure increases, when using ethanol/methanol as PTM. These new peaks were still present at ambient pressure after releasing the applied pressure. They may correspond to crystalline nordstrandite or doyleite from the crystallization of amorphous aluminium hydroxide. The results from the high-pressure study will also be discussed.

Effects of high CO2 and light quality on the growth of the seagrass Cymodocea nodosa (Ucria) Ascherson

Dissertação de Mestrado, Biologia Marinha, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2015

Body image dissatisfaction and low self-esteem due to physical appeareance in students of the faculty of medicine at the university of los andes (mérida, venezuela)

The purpose of this investigation was to evaluate body image dissatisfaction in relation to low self-esteem due to physical appearance in students of the Faculty of Medicine at the University of Los Andes in Mérida, Venezuela.  It was a non-experimental and correlational study.  The sample included 189 students (27% male and 73% female) with an average age of 19.58 ± 1.57 (men: 19.81 years of age ± 1.74 and women: 20.24 years of age ± 1.76).  Participants were intentionally selected from first-year courses of the Medicine, Nursing and Nutrition programs.  The Body Shape Questionnaire (BSQ) (Cooper and Taylor, 1987) was the instrument used to measure body image dissatisfaction and Graffar’s modified method (Méndez and De Méndez, 1994) was applied to determine the participants’ socioeconomic status.  A descriptive analysis (frequency, percentages, mean) and an inferential analysis (one-way ANOVA) were applied to the data using SPSS (Statistical Package for Social Sciences) version 9.0.  One of the most important findings in this study was the determination of a statistically significant relationship between dissatisfaction and body image and between low self-esteem and gender χ2 (2, N= 189) = 9.686, p=0.008.  Using ANOVA also helped determine that differences in the mean for dissatisfaction and low self-esteem levels with body image and gender are statistically significant, F= 11.236; p=0.008, F=10.23; p=0.002, respectively.  Conclusions: results obtained suggest a relationship between dissatisfaction and low self-esteem due to physical appearance. Consequently, subjects reject their body image because of a distorted or undistorted perception of their physical appearance, which can possibly affect self-esteem.  Moreover, it is observed that the students’ psychological health is more related to their satisfaction with their body-image than to the way their body image is perceived. Consequently, this group of participants must be analyzed regarding their self-esteem due to body image, as an expression in the institutional environment.  It is also important to emphasize that gender may be a risk factor concerning eating disorders.  We believe the foregoing because women showed higher dissatisfaction levels because of their physical appearance being conditioned by a higher dissatisfaction with their perceived body image, which is characterized by an overestimation of the physical dimension of their body image.

The association between the activity profile and cardiovascular risk.

OBJECTIVES: This study sought to better understand the interrelationships between physical activity and sedentary behaviour and the relationship to risk of cardiovascular disease (CVDR) in adults aged 30-75 years. DESIGN: Cross-sectional. METHODS: Data from two-year waves (2003-2004 and 2005-2006) of the National Health and Nutritional Examination survey were analysed in 2014. Accelerometer-derived time and proportion of time spent sedentary and on moderate-to-vigorous physical activity (MVPA) were calculated to generate four activity profiles based on cut-points to define low and high levels for the respective behaviours. Using health outcome data, CVDR was calculated for each person. Weighted multiple linear regression models were used to evaluate the predicted effects of sedentary and physical activity behaviours on the CVDR score, adjusting for participants' sex, age group, race, annual household income, and accelerometer wear time. RESULTS: The lowest CVDR was observed among Busy Exercisers (high MVPA and low sedentary; 8.5%), whereas Couch Potatoes (low MVPA and high sedentary) had the highest (18.6%). Compared with the reference group (Busy Exercisers), the activity profile associated with the highest CVDR was Couch Potatoes (adjusted mean difference 3.6, SE 0.38, p<0.0001). A smoothed three-dimensional response surface "risk landscape" was developed to better visualise the conjoint associations of MVPA and sedentary behaviour on CVDR for each activity profile. The association between MVPA was greater than that of sedentary behaviour; however, for people with low MVPA, shifts in sedentary behaviour may have the greatest impact on CVDR. CONCLUSIONS: Activity profiles that consider the interrelationships between physical activity and sedentary behaviour differ in terms of CVDR. Future interventions may need to be tailored to specific profiles and be dynamic enough to reflect change in the profile over time.

Chronic condition management and self-management in Aboriginal communities in South Australia : outcomes of a longitudinal study

OBJECTIVES: This paper describes the longitudinal component of a larger mixed methods study into the processes and outcomes of chronic condition management and self-management strategies implemented in three Aboriginal communities in South Australia. The study was designed to document the connection between the application of structured systems of care for Aboriginal people and their longer-term health status. METHODS: The study concentrated on three diverse Aboriginal communities in South Australia; the Port Lincoln Aboriginal Health Service, the Riverland community, and Nunkuwarrin Yunti Aboriginal Health Service in the Adelaide metropolitan area. Repeated-measure clinical data were collected for individual participants using a range of clinical indicators for diabetes (type 1 and 2) and related chronic conditions. Clinical data were analysed using random effects modelling techniques with changes in key clinical indicators being modelled at both the individual and group levels. RESULTS: Where care planning has been in place longer than in other sites overall improvements were noted in BMI, cholesterol (high density and low density lipids) and HbA1c. These results indicate that for Aboriginal patients with complex chronic conditions, participation in and adherence to structured care planning and self-management strategies can contribute to improved overall health status and health outcomes. CONCLUSIONS: The outcomes reported here represent an initial and important step in quantifying the health benefits that can accrue for Aboriginal people living with complex chronic conditions such as diabetes, heart disease and respiratory disease. The study highlights the benefits of developing long-term working relationships with Aboriginal communities as a basis for conducting effective collaborative health research programs.

Inner architecture of bonded splats under combined high pressure and shear

Micron size aluminum particles (Figure 1) are deformed into “interlocked splats” at room temperature under high pressure and shear. Sample's induced inner architecture is examined (Figure 2). Tests are carried out to characterize material's heterogeneous properties (Figure 3). Presented formulation of the test data indicates an excellent shear strength; stronger than its solid counterpart.

Early Triassic disaster and opportunistic foraminifers in South China

Survival and recovery are important dynamic processes of biotic evolution during major geological transitions. Disaster and opportunistic taxa are two significant groups that dominate the ecosystem in the aftermath of mass extinction events. Disaster taxa appear immediately after such crises whilst opportunists pre-date the crisis but also bloom in the aftermath. This paper documents three disaster foraminiferal species and seven opportunistic foraminiferal species from Lower Triassic successions of South China. They are characterized by extreme high abundance and low diversity and occurred occasionally in Griesbachian, Smithian and Spathian strata. The characteristics (small size, simple morphology) and stratigraphic ranges of these groups suggest that r-selection is a commonly used strategy for survivors to cope with either harsh post-extinction conditions and/or environments lacking incumbents.

High-dimensional and large-scale anomaly detection using a linear one-class SVM with deep learning

High-dimensional problem domains pose significant challenges for anomaly detection. The presence of irrelevant features can conceal the presence of anomalies. This problem, known as the '. curse of dimensionality', is an obstacle for many anomaly detection techniques. Building a robust anomaly detection model for use in high-dimensional spaces requires the combination of an unsupervised feature extractor and an anomaly detector. While one-class support vector machines are effective at producing decision surfaces from well-behaved feature vectors, they can be inefficient at modelling the variation in large, high-dimensional datasets. Architectures such as deep belief networks (DBNs) are a promising technique for learning robust features. We present a hybrid model where an unsupervised DBN is trained to extract generic underlying features, and a one-class SVM is trained from the features learned by the DBN. Since a linear kernel can be substituted for nonlinear ones in our hybrid model without loss of accuracy, our model is scalable and computationally efficient. The experimental results show that our proposed model yields comparable anomaly detection performance with a deep autoencoder, while reducing its training and testing time by a factor of 3 and 1000, respectively.

Structural transformation of polyacrylonitrile fibers during stabilization and low temperature carbonization

The effect of oxidative stabilization and carbonization processes on the structure, mass and mechanical properties of polyacrylonitrile (PAN) precursor fibers was analyzed. A gradual densification of the fibers occurring from mass loss, decrease in fiber diameter and increase in density were observed after stabilization at a maximum temperature of 255 °C and carbonization at a maximum temperature of 800 °C. The tensile strength and modulus of the fibers were found to decrease after stabilization but then increased after low temperature carbonization. The thermal processing of the precursor fibers affected their mode of failure after tensile loading, changing from a ductile type of failure to a brittle type. The type of failure correlated well with the crystal structure changes in the fibers. Whilst the PAN precursor fiber started to exotherm above 225 °C in air, no prominent exothermic reaction was measured in the carbonized fibers in air up to 430 °C. The aromatization index of stabilized fiber was calculated to be ∼66%, and that of carbonized fiber was ∼99%. FTIR studies indicated that the variation in the chemical structure of the fibers with the stabilization of the fibers. Radial heterogeneity in the stabilized fibers was observed however it was not promoted to the carbonized fibers. Finally, a method to calculate mass retention of PAN precursor fiber after heat treatment was developed, and the calculated percentage mass retained of the precursor fiber after oxidation and carbonization were found to be 81% and 51%, respectively. . This study proposes an effective method to calculate the percentage of mass retained by precursor fibers after stabilization and low temperature carbonization to provide a model for evaluating carbon fiber yield from a given amount of fibers.

The effect of low parental warmth and low monitoring on disordered eating in mid-adolescence: findings from the Australian Temperament Project

OBJECTIVE: To investigate the interactions between low parental warmth and monitoring at age 13-14 years and disordered eating attitudes and behaviours at age 15-16 years. METHOD: Data on 1300 (667 females) adolescents and their parents were drawn from The Australian Temperament Project (ATP), a 30 year (15 wave) population based longitudinal study of social-emotional development. Parent participants completed surveys on parenting practices in late childhood, and adolescent participants reported disordered eating using the drive for thinness and bulimia subscales of the Eating Disorder Inventory (EDI) and an additional body dissatisfaction scale. Interaction was examined on the additive scale by estimating super-additive risk; i.e., risk in excess of the sum of individual risks. RESULTS: For boys, neither parental warmth or monitoring, nor their interaction, was related to disordered eating. For girls, low parental warmth (alone) was associated with bulimic behaviours. In contrast, exposure to both low monitoring and warmth was associated with ∼3½-fold, ∼4-fold and ∼5-fold increases in the odds of reporting body dissatisfaction, drive for thinness and bulimia, respectively. For body dissatisfaction and drive for thinness, risk associated with joint exposure exceeded the sum of individual risks, suggesting an additive interaction between parenting styles. CONCLUSION: Further investment in family-level interventions that focus on promoting parental monitoring behaviour and a warm parent-child relationship remain important strategies for preventing a range of disordered eating behaviours in adolescents.